[r-cran-spatstat.data] 01/02: New upstream version 1.1-1
Andreas Tille
tille at debian.org
Fri Oct 20 15:44:35 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-spatstat.data.
commit 6a718f6ffb8882850161d0158bc9b13fba9ff70a
Author: Andreas Tille <tille at debian.org>
Date: Fri Oct 20 17:43:16 2017 +0200
New upstream version 1.1-1
---
DESCRIPTION | 30 ++++
MD5 | 131 ++++++++++++++
NAMESPACE | 11 ++
R/copyExampleFiles.R | 43 +++++
data/Kovesi.rda | Bin 0 -> 13840 bytes
data/amacrine.rda | Bin 0 -> 3213 bytes
data/anemones.rda | Bin 0 -> 1114 bytes
data/ants.rda | Bin 0 -> 2052 bytes
data/austates.rda | Bin 0 -> 40064 bytes
data/bdspots.rda | Bin 0 -> 25859 bytes
data/bei.rda | Bin 0 -> 182520 bytes
data/betacells.rda | Bin 0 -> 1892 bytes
data/bramblecanes.rda | Bin 0 -> 3754 bytes
data/bronzefilter.rda | Bin 0 -> 3804 bytes
data/cells.rda | Bin 0 -> 576 bytes
data/chicago.rda | Bin 0 -> 526332 bytes
data/chorley.rda | Bin 0 -> 6463 bytes
data/clmfires.rda | Bin 0 -> 580928 bytes
data/copper.rda | Bin 0 -> 5010 bytes
data/datalist | 55 ++++++
data/demohyper.rda | Bin 0 -> 27356 bytes
data/demopat.rda | Bin 0 -> 1342 bytes
data/dendrite.rda | Bin 0 -> 23624 bytes
data/finpines.rda | Bin 0 -> 2757 bytes
data/flu.rda | Bin 0 -> 81412 bytes
data/ganglia.rda | Bin 0 -> 1227 bytes
data/gordon.rda | Bin 0 -> 3027 bytes
data/gorillas.rda | Bin 0 -> 104024 bytes
data/hamster.rda | Bin 0 -> 2168 bytes
data/heather.rda | Bin 0 -> 52822 bytes
data/humberside.rda | Bin 0 -> 1735 bytes
data/hyytiala.rda | Bin 0 -> 2552 bytes
data/japanesepines.rda | Bin 0 -> 620 bytes
data/lansing.rda | Bin 0 -> 7115 bytes
data/letterR.rda | Bin 0 -> 609 bytes
data/longleaf.rda | Bin 0 -> 3581 bytes
data/mucosa.rda | Bin 0 -> 13424 bytes
data/murchison.rda | Bin 0 -> 53056 bytes
data/nbfires.rda | Bin 0 -> 167260 bytes
data/nztrees.rda | Bin 0 -> 541 bytes
data/osteo.rda | Bin 0 -> 3953 bytes
data/paracou.rda | Bin 0 -> 4868 bytes
data/ponderosa.rda | Bin 0 -> 1789 bytes
data/pyramidal.rda | Bin 0 -> 6180 bytes
data/redwood.rda | Bin 0 -> 608 bytes
data/redwood3.rda | Bin 0 -> 799 bytes
data/redwoodfull.rda | Bin 0 -> 2871 bytes
data/residualspaper.rda | Bin 0 -> 527946 bytes
data/shapley.rda | Bin 0 -> 37596 bytes
data/simba.rda | Bin 0 -> 6459 bytes
data/simdat.rda | Bin 0 -> 1368 bytes
data/simplenet.rda | Bin 0 -> 1287 bytes
data/spiders.rda | Bin 0 -> 8876 bytes
data/sporophores.rda | Bin 0 -> 6331 bytes
data/spruces.rda | Bin 0 -> 1199 bytes
data/swedishpines.rda | Bin 0 -> 495 bytes
data/urkiola.rda | Bin 0 -> 4814 bytes
data/vesicles.rda | Bin 0 -> 6547 bytes
data/waka.rda | Bin 0 -> 4360 bytes
data/waterstriders.rda | Bin 0 -> 1054 bytes
inst/doc/packagesizes.txt | 2 +
inst/rawdata/amacrine/amacrine.txt | 295 +++++++++++++++++++++++++++++++
inst/rawdata/finpines/finpines.txt | 127 +++++++++++++
inst/rawdata/gorillas/vegetation.asc | 155 ++++++++++++++++
inst/rawdata/osteo/osteo36.txt | 30 ++++
inst/rawdata/sandholes/sandholes.jpg | Bin 0 -> 95101 bytes
inst/rawdata/vesicles/activezone.txt | 10 ++
inst/rawdata/vesicles/mitochondria.txt | 24 +++
inst/rawdata/vesicles/presynapse.txt | 70 ++++++++
inst/rawdata/vesicles/vesicles.csv | 38 ++++
inst/rawdata/vesicles/vesicles.txt | 38 ++++
inst/rawdata/vesicles/vesiclesimage.tif | Bin 0 -> 106299 bytes
inst/rawdata/vesicles/vesiclesmask.tif | Bin 0 -> 2136 bytes
inst/rawdata/vesicles/vesicleswindow.csv | 93 ++++++++++
inst/rawdata/vesicles/vesicleswindow.txt | 93 ++++++++++
man/Kovesi.Rd | 90 ++++++++++
man/amacrine.Rd | 43 +++++
man/anemones.Rd | 72 ++++++++
man/ants.Rd | 171 ++++++++++++++++++
man/austates.Rd | 39 ++++
man/bdspots.Rd | 89 ++++++++++
man/bei.Rd | 71 ++++++++
man/betacells.Rd | 105 +++++++++++
man/bramblecanes.Rd | 66 +++++++
man/bronzefilter.Rd | 57 ++++++
man/cells.Rd | 39 ++++
man/chicago.Rd | 68 +++++++
man/chorley.Rd | 106 +++++++++++
man/clmfires.Rd | 104 +++++++++++
man/copper.Rd | 122 +++++++++++++
man/copyExampleFiles.Rd | 48 +++++
man/demohyper.Rd | 44 +++++
man/demopat.Rd | 26 +++
man/dendrite.Rd | 48 +++++
man/finpines.Rd | 69 ++++++++
man/flu.Rd | 110 ++++++++++++
man/ganglia.Rd | 71 ++++++++
man/gordon.Rd | 37 ++++
man/gorillas.Rd | 153 ++++++++++++++++
man/hamster.Rd | 48 +++++
man/heather.Rd | 109 ++++++++++++
man/humberside.Rd | 88 +++++++++
man/hyytiala.Rd | 43 +++++
man/japanesepines.Rd | 39 ++++
man/lansing.Rd | 108 +++++++++++
man/letterR.Rd | 20 +++
man/longleaf.Rd | 56 ++++++
man/macros/defns.Rd | 19 ++
man/mucosa.Rd | 56 ++++++
man/murchison.Rd | 110 ++++++++++++
man/nbfires.Rd | 237 +++++++++++++++++++++++++
man/nztrees.Rd | 48 +++++
man/osteo.Rd | 147 +++++++++++++++
man/paracou.Rd | 56 ++++++
man/ponderosa.Rd | 63 +++++++
man/pyramidal.Rd | 47 +++++
man/redwood.Rd | 70 ++++++++
man/redwoodfull.Rd | 110 ++++++++++++
man/residualspaper.Rd | 96 ++++++++++
man/shapley.Rd | 100 +++++++++++
man/simba.Rd | 37 ++++
man/simdat.Rd | 30 ++++
man/simplenet.Rd | 18 ++
man/spatstat.data-package.Rd | 23 +++
man/spiders.Rd | 68 +++++++
man/sporophores.Rd | 47 +++++
man/spruces.Rd | 64 +++++++
man/swedishpines.Rd | 52 ++++++
man/urkiola.Rd | 35 ++++
man/vesicles.Rd | 96 ++++++++++
man/waka.Rd | 46 +++++
man/waterstriders.Rd | 59 +++++++
132 files changed, 5338 insertions(+)
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..397fb1f
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,30 @@
+Package: spatstat.data
+Version: 1.1-1
+Date: 2017-10-11
+Title: Datasets for 'spatstat'
+Authors at R: c(person("Adrian", "Baddeley",
+ role = c("aut", "cre"),
+ email = "Adrian.Baddeley at curtin.edu.au"),
+ person("Rolf", "Turner",
+ role = "aut",
+ email="r.turner at auckland.ac.nz"),
+ person("Ege", "Rubak",
+ role = "aut",
+ email = "rubak at math.aau.dk"))
+Maintainer: Adrian Baddeley <Adrian.Baddeley at curtin.edu.au>
+Depends: R (>= 3.3.0)
+Suggests: spatstat
+Imports: spatstat.utils
+Description: Contains all the datasets for the 'spatstat' package.
+License: GPL (>= 2)
+URL: http://www.spatstat.org
+LazyData: true
+NeedsCompilation: no
+ByteCompile: true
+BugReports: https://github.com/spatstat/spatstat.data/issues
+Packaged: 2017-10-11 00:43:40 UTC; adrian
+Author: Adrian Baddeley [aut, cre],
+ Rolf Turner [aut],
+ Ege Rubak [aut]
+Repository: CRAN
+Date/Publication: 2017-10-11 08:11:29 UTC
diff --git a/MD5 b/MD5
new file mode 100644
index 0000000..955a618
--- /dev/null
+++ b/MD5
@@ -0,0 +1,131 @@
+f86aaea53df914826575cfde02c28d4b *DESCRIPTION
+cd38240808be689ae97d68eeaccff2b8 *NAMESPACE
+d5cf898da60af5106d32823bc2ee5c44 *R/copyExampleFiles.R
+5cea05d224857947ff5238dd53ddc8f4 *data/Kovesi.rda
+f8f3278e07fb8da32a13f62ebd44c81d *data/amacrine.rda
+396c8ae126784dad0c56fc4591fef20c *data/anemones.rda
+2cba77d45ba8989d00d9c8ba850dbdc7 *data/ants.rda
+e400bfb3386acb148b35b10d18d6ddb1 *data/austates.rda
+512cef5d451d6f7f6703b2a5895db443 *data/bdspots.rda
+67061844296bce3cdc14eb1506582b3e *data/bei.rda
+179551d2ece444515a09971fe44415f4 *data/betacells.rda
+f8beb0f02aa1f750370c7c5fb92fd2e8 *data/bramblecanes.rda
+f29a1220c91c5dfbe061d3339a196a79 *data/bronzefilter.rda
+ac9127ade4ec06d16e7670ad7597f7ed *data/cells.rda
+aab6b9792201559b78605ddf0ffa20c4 *data/chicago.rda
+7c9f5cda2f6694a056f51b69a5337ac4 *data/chorley.rda
+516bee061424305d1adeedf51c2ce37b *data/clmfires.rda
+8a4e269c4aa42b308dab7f4cd480663d *data/copper.rda
+982a453b8f8a2f8d1015a37d931738c2 *data/datalist
+2f42d8e12be11418e60a54d1334009be *data/demohyper.rda
+38dd639fa3a943f0fa51c3c1c18edf8a *data/demopat.rda
+519cde696f0e0e5ae6fb9b4dede58711 *data/dendrite.rda
+a5cabe6d8540fc6a01f2d487af11fcfc *data/finpines.rda
+5901518b150192278ecf653eaf155c95 *data/flu.rda
+dd674eac4ce1be0a5f8dd38a7ed8087a *data/ganglia.rda
+fe276d4eaaa13905dcd492d9026aa44b *data/gordon.rda
+3c66904210822d43803529550cc612eb *data/gorillas.rda
+6e717ea3dbd63d248a7f66afaf60ac26 *data/hamster.rda
+c261c5e47234deca1758c4206964ad66 *data/heather.rda
+175efb86b7b3ed627e0431e275268fd6 *data/humberside.rda
+79feb2fd200fa72a41b6db98a1fb3a70 *data/hyytiala.rda
+4f158b59dc38590d58cb1fcc3ca20b11 *data/japanesepines.rda
+dd9072fb66808567624906d76284fc0b *data/lansing.rda
+c0516df10fc5e98f76bf3f354648a35d *data/letterR.rda
+3a5be98533c11fed29399104c54f5b73 *data/longleaf.rda
+afc1a6832736c3328e7c5ea3ece4e827 *data/mucosa.rda
+959565f6310ad6df6891a96176734587 *data/murchison.rda
+2320938d48f701f55d8be5c1988cecf2 *data/nbfires.rda
+74f3401259c3dd621b815735195703fb *data/nztrees.rda
+e2bea68edca745d1665a134314b4d16c *data/osteo.rda
+1c964c925381647b168ed054e923a2cf *data/paracou.rda
+298782e15154df61eb6eaceccc14f9b0 *data/ponderosa.rda
+fdb4cfd141c431114d71728ea7561623 *data/pyramidal.rda
+68a7b3e332671b77a31c5f86d71dfe1d *data/redwood.rda
+96fb3bff59c2d29514a3281ccc04b34c *data/redwood3.rda
+e5c3ee915b5780be672ca7b7be5a3459 *data/redwoodfull.rda
+81baac4ea430391035bb7bebbadb4c9c *data/residualspaper.rda
+5b8174b437afc5f6bb0b49ee204fe534 *data/shapley.rda
+857e0ff8c8e1f54de56ba8fb1a3be6c4 *data/simba.rda
+caf4c2f0178ab178e566d5fade956d05 *data/simdat.rda
+4560e091b6b14021bd9f728d20ab8be5 *data/simplenet.rda
+d4a26433e0efe9387938a545cb112c65 *data/spiders.rda
+124b1471cb7db30aaa501c27db4f0216 *data/sporophores.rda
+3c3a7ad37e05809961910cf3f3c43802 *data/spruces.rda
+79b8bc4e7872408cd3bebae8570b10cc *data/swedishpines.rda
+c9314c98277abb350a10e67de0e2d5ef *data/urkiola.rda
+2b4e46b138195b85ce4a3287ffe8b0c4 *data/vesicles.rda
+606f8a60ccbf42cb2b1f410d726505a0 *data/waka.rda
+26dc02b8d2a7f44ee0d8cebf846aafb4 *data/waterstriders.rda
+885794cef2ede53f788667f4a4910915 *inst/doc/packagesizes.txt
+5bd85f0a101e5b39b9d3dd591bcf657f *inst/rawdata/amacrine/amacrine.txt
+5d385fac345198c0abc886db56d60cd5 *inst/rawdata/finpines/finpines.txt
+af2c22765b01d39a1efc4e82e958ec48 *inst/rawdata/gorillas/vegetation.asc
+add7704f3f0d627c818d1d0052d95964 *inst/rawdata/osteo/osteo36.txt
+a9c56bdedef6ca09bc3abca5187dbc90 *inst/rawdata/sandholes/sandholes.jpg
+ee8726f4f1c4a43da6c1826a016844a3 *inst/rawdata/vesicles/activezone.txt
+12e1f9c6f0b061dae508af6bf030a2cd *inst/rawdata/vesicles/mitochondria.txt
+cffa360131ec346baebd9bfcf3150be6 *inst/rawdata/vesicles/presynapse.txt
+7598921535774304c799a7ddeea2dc36 *inst/rawdata/vesicles/vesicles.csv
+1d1cffe05c85380eea5a4d0402705271 *inst/rawdata/vesicles/vesicles.txt
+4ffa8d56e5dc6fbda3b3d677d7f80b50 *inst/rawdata/vesicles/vesiclesimage.tif
+1127fd6a66fd3b7653de7d51ba8b3c10 *inst/rawdata/vesicles/vesiclesmask.tif
+dffcdb453f4ff4c29ca1f12889f94b76 *inst/rawdata/vesicles/vesicleswindow.csv
+bd3c9e3c64d3407632619dbeb7705b7b *inst/rawdata/vesicles/vesicleswindow.txt
+414676db142e611cc2368be92a424b5d *man/Kovesi.Rd
+7db5a15f6f6499e03d6f13a4ca1ef3ab *man/amacrine.Rd
+b4195997d3565842819d3ca74b46aa23 *man/anemones.Rd
+1325f93e044bf295351f111b2e6dfa83 *man/ants.Rd
+301fff1d561e541c7f286640d76b5d5a *man/austates.Rd
+6721e54cfceedcfa92504f384d7b8a38 *man/bdspots.Rd
+1508939ea5fae9d53e74232ec891de82 *man/bei.Rd
+bd4d7cc6704038d150578d78856f9f45 *man/betacells.Rd
+19da35b9ed4a65bd812ca7a649724a8a *man/bramblecanes.Rd
+2003cb652ea850b88e9f56e5ff4c7a84 *man/bronzefilter.Rd
+90d69b8bd2d751e604ca1c6f323583dd *man/cells.Rd
+2c1c485b88361741db325d9c0a99b31a *man/chicago.Rd
+7df5a6886211d295a9938b31fa95a04e *man/chorley.Rd
+bba2f3274eb6bf047b22ff4dd73db28e *man/clmfires.Rd
+467e7f03dff4f153eb9ede4e628b8f16 *man/copper.Rd
+b867239312cb21a975003b2339d414e8 *man/copyExampleFiles.Rd
+f50f1381bc0bd39651c2d68f3a2b83e1 *man/demohyper.Rd
+e0eec5701cb52e5e1ac372216ec9726e *man/demopat.Rd
+f95b69a6a6e32547e0f474da0457ea70 *man/dendrite.Rd
+8b137228e24ceb5f924e6b84d09a211c *man/finpines.Rd
+a823c7e777c940794fa4d5fb9e5b15ec *man/flu.Rd
+28acbe3334ba84983ac712723b784504 *man/ganglia.Rd
+b548c0e4a5a6d1becd21c246d33e10b0 *man/gordon.Rd
+fb6845c46f277d713ddbe86e1ecc6cb1 *man/gorillas.Rd
+98eabd4c56737f2e7d2b686c9256acaf *man/hamster.Rd
+5869e489039ea04159f59545f5a3bb60 *man/heather.Rd
+0d81a854e14a339084b85694f892bc81 *man/humberside.Rd
+088f5d9848ac5c3d3691fdecf9736fc8 *man/hyytiala.Rd
+d84917070675fe46b388f7bd2586fda3 *man/japanesepines.Rd
+eb80a4a1bf5fc7617cd3b240e2004206 *man/lansing.Rd
+3b037eef79fa3afd2468e5726bd902fc *man/letterR.Rd
+017490cf01c6c4a835f75da689a65f20 *man/longleaf.Rd
+8ff61b15a83accee7cc5be6b9363b347 *man/macros/defns.Rd
+53942baade521c7dca7841a52f2c55ff *man/mucosa.Rd
+4b2b9695c12e3010bb3246bdf02630c7 *man/murchison.Rd
+7331efacf19dea7f8785152ad93f924a *man/nbfires.Rd
+c93d0dd670d889f870d05a40271ffe5c *man/nztrees.Rd
+97b16edb0bf936c275caf2a42123dfb8 *man/osteo.Rd
+3d97ee963d2830367aede105a44809fc *man/paracou.Rd
+780dbb030195135dca3ca93709d7abeb *man/ponderosa.Rd
+ebeb4b97f66ae7d365cbd2c136d1b346 *man/pyramidal.Rd
+dfc66784cd16bb14778e6c7345795e90 *man/redwood.Rd
+39e7a7bda191a3e4bc2add711b44047a *man/redwoodfull.Rd
+2547e7da9ecd583ee6449320a715e282 *man/residualspaper.Rd
+c69c0735f106979cdc71021d1ff49f0d *man/shapley.Rd
+bbf30cfafd8f9e64d508117c68f2ae69 *man/simba.Rd
+120264c8bd8d55273161a33ef030d9dd *man/simdat.Rd
+9eec44b00a8171e80e128560a7ec682d *man/simplenet.Rd
+c4e6f725cf6dc6a41324ed446f5067a1 *man/spatstat.data-package.Rd
+35bf816e76fd0267e69361f4a4abb809 *man/spiders.Rd
+b0e5646c33e9b8982b4ba677d4735c0f *man/sporophores.Rd
+df047913d1d56af6ecb21e61458c7bbb *man/spruces.Rd
+adc0bfebac32b1fafb62d01507994679 *man/swedishpines.Rd
+4e5a727ed07ae364e8629292f3d2bb2a *man/urkiola.Rd
+7f8465dd67518ce68f6fac29669dfcbe *man/vesicles.Rd
+54df351da61157e8ec284fd5258270cd *man/waka.Rd
+e24cb30fd8a41eeac41ed717e25d0479 *man/waterstriders.Rd
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..6d954b5
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,11 @@
+# spatstat.data NAMESPACE file
+
+import(spatstat.utils)
+
+# Do not edit the following.
+# It is generated automatically.
+
+# ..................................................
+# Automatically-generated list of documented objects
+# ..................................................
+export("copyExampleFiles")
diff --git a/R/copyExampleFiles.R b/R/copyExampleFiles.R
new file mode 100755
index 0000000..16c0d88
--- /dev/null
+++ b/R/copyExampleFiles.R
@@ -0,0 +1,43 @@
+## copyExampleFiles.R
+## Now belongs to spatstat.data
+## $Revision: 1.10 $ $Date: 2015/03/11 05:58:50 $
+
+copyExampleFiles <- function(which, folder=getwd()) {
+ choices <- dir(system.file("rawdata", package="spatstat.data"))
+ if(missing(which) || is.null(which)) {
+ message(paste("Choices are: which=", commasep(sQuote(choices), " or ")))
+ return(invisible(NULL))
+ }
+ if(!interactive())
+ stop("Copying files requires an interactive session (by CRAN Policies).")
+ whichdata <- match.arg(which, choices)
+ sourcefolder <- system.file("rawdata", whichdata, package="spatstat.data")
+ sourcefiles <- dir(sourcefolder)
+ if(length(sourcefiles) == 0)
+ stop("No files available")
+ # set directory
+ oldfolder <- getwd()
+ setwd(folder)
+ on.exit(setwd(oldfolder))
+ # Warn user:
+ foldername <- if(identical(folder, oldfolder)) "the current folder" else
+ paste("the folder", dQuote(folder))
+ splat("You are about to have been copying",
+ ngettext(length(sourcefiles), "file", "files"),
+ commasep(dQuote(sourcefiles)), "to",
+ paste0(foldername, "."),
+ "This may overwrite existing files.")
+ # Ask permission:
+ answer <- readline("Do you want to continue? (y/n)[y] ")
+ if(!tolower(substr(answer, 1, 1)) %in% c("", "y")) {
+ splat("Aborting...")
+ return(invisible(NULL))
+ }
+ #
+ for(fn in sourcefiles) {
+ frompath <- file.path(sourcefolder, fn)
+ file.copy(from = frompath, to = fn, overwrite=TRUE)
+ }
+ splat("Copying completed.")
+ return(invisible(NULL))
+}
diff --git a/data/Kovesi.rda b/data/Kovesi.rda
new file mode 100644
index 0000000..24e7857
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diff --git a/data/amacrine.rda b/data/amacrine.rda
new file mode 100644
index 0000000..200e5f1
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diff --git a/data/anemones.rda b/data/anemones.rda
new file mode 100644
index 0000000..b072386
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diff --git a/data/ants.rda b/data/ants.rda
new file mode 100644
index 0000000..14b96be
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diff --git a/data/austates.rda b/data/austates.rda
new file mode 100644
index 0000000..272d22b
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diff --git a/data/bdspots.rda b/data/bdspots.rda
new file mode 100644
index 0000000..fa76b04
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diff --git a/data/bei.rda b/data/bei.rda
new file mode 100644
index 0000000..5dbdc3c
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diff --git a/data/betacells.rda b/data/betacells.rda
new file mode 100644
index 0000000..511a499
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diff --git a/data/bramblecanes.rda b/data/bramblecanes.rda
new file mode 100644
index 0000000..b454804
Binary files /dev/null and b/data/bramblecanes.rda differ
diff --git a/data/bronzefilter.rda b/data/bronzefilter.rda
new file mode 100644
index 0000000..1de96da
Binary files /dev/null and b/data/bronzefilter.rda differ
diff --git a/data/cells.rda b/data/cells.rda
new file mode 100644
index 0000000..43d47a0
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diff --git a/data/chicago.rda b/data/chicago.rda
new file mode 100644
index 0000000..56edf5b
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diff --git a/data/chorley.rda b/data/chorley.rda
new file mode 100644
index 0000000..000d355
Binary files /dev/null and b/data/chorley.rda differ
diff --git a/data/clmfires.rda b/data/clmfires.rda
new file mode 100644
index 0000000..652b6bf
Binary files /dev/null and b/data/clmfires.rda differ
diff --git a/data/copper.rda b/data/copper.rda
new file mode 100644
index 0000000..538a0c1
Binary files /dev/null and b/data/copper.rda differ
diff --git a/data/datalist b/data/datalist
new file mode 100644
index 0000000..7352e81
--- /dev/null
+++ b/data/datalist
@@ -0,0 +1,55 @@
+Kovesi
+amacrine
+anemones
+ants: ants ants.extra
+austates
+bdspots
+bei: bei bei.extra
+betacells
+bramblecanes
+bronzefilter
+cells
+chicago
+chorley: chorley chorley.extra
+clmfires: clmfires clmfires.extra
+copper
+demohyper
+demopat
+dendrite
+finpines
+flu
+ganglia
+gordon
+gorillas: gorillas gorillas.extra
+hamster
+heather
+humberside: humberside humberside.convex
+hyytiala
+japanesepines
+lansing
+letterR
+longleaf
+mucosa: mucosa mucosa.subwin
+murchison
+nbfires: nbfires nbfires.extra nbw.rect nbw.seg
+nztrees
+osteo
+paracou
+ponderosa: ponderosa ponderosa.extra
+pyramidal
+redwood
+redwood3
+redwoodfull: redwoodfull redwoodfull.extra
+residualspaper
+shapley: shapley shapley.extra
+simba
+simdat
+simplenet
+spiders
+sporophores
+spruces
+swedishpines
+urkiola
+vesicles: vesicles vesicles.extra
+waka
+waterstriders
diff --git a/data/demohyper.rda b/data/demohyper.rda
new file mode 100644
index 0000000..4608113
Binary files /dev/null and b/data/demohyper.rda differ
diff --git a/data/demopat.rda b/data/demopat.rda
new file mode 100644
index 0000000..fd58b9e
Binary files /dev/null and b/data/demopat.rda differ
diff --git a/data/dendrite.rda b/data/dendrite.rda
new file mode 100644
index 0000000..0ea0162
Binary files /dev/null and b/data/dendrite.rda differ
diff --git a/data/finpines.rda b/data/finpines.rda
new file mode 100644
index 0000000..a238e30
Binary files /dev/null and b/data/finpines.rda differ
diff --git a/data/flu.rda b/data/flu.rda
new file mode 100644
index 0000000..012a010
Binary files /dev/null and b/data/flu.rda differ
diff --git a/data/ganglia.rda b/data/ganglia.rda
new file mode 100644
index 0000000..dd8bf31
Binary files /dev/null and b/data/ganglia.rda differ
diff --git a/data/gordon.rda b/data/gordon.rda
new file mode 100644
index 0000000..20a9d59
Binary files /dev/null and b/data/gordon.rda differ
diff --git a/data/gorillas.rda b/data/gorillas.rda
new file mode 100644
index 0000000..4c86fc7
Binary files /dev/null and b/data/gorillas.rda differ
diff --git a/data/hamster.rda b/data/hamster.rda
new file mode 100644
index 0000000..8a986a5
Binary files /dev/null and b/data/hamster.rda differ
diff --git a/data/heather.rda b/data/heather.rda
new file mode 100644
index 0000000..3fa81d7
Binary files /dev/null and b/data/heather.rda differ
diff --git a/data/humberside.rda b/data/humberside.rda
new file mode 100644
index 0000000..8eb30cb
Binary files /dev/null and b/data/humberside.rda differ
diff --git a/data/hyytiala.rda b/data/hyytiala.rda
new file mode 100644
index 0000000..42fa303
Binary files /dev/null and b/data/hyytiala.rda differ
diff --git a/data/japanesepines.rda b/data/japanesepines.rda
new file mode 100644
index 0000000..ecbdc6b
Binary files /dev/null and b/data/japanesepines.rda differ
diff --git a/data/lansing.rda b/data/lansing.rda
new file mode 100644
index 0000000..514ad85
Binary files /dev/null and b/data/lansing.rda differ
diff --git a/data/letterR.rda b/data/letterR.rda
new file mode 100644
index 0000000..bad5273
Binary files /dev/null and b/data/letterR.rda differ
diff --git a/data/longleaf.rda b/data/longleaf.rda
new file mode 100644
index 0000000..84927ea
Binary files /dev/null and b/data/longleaf.rda differ
diff --git a/data/mucosa.rda b/data/mucosa.rda
new file mode 100644
index 0000000..b298dbb
Binary files /dev/null and b/data/mucosa.rda differ
diff --git a/data/murchison.rda b/data/murchison.rda
new file mode 100644
index 0000000..6ed24c6
Binary files /dev/null and b/data/murchison.rda differ
diff --git a/data/nbfires.rda b/data/nbfires.rda
new file mode 100644
index 0000000..16683d3
Binary files /dev/null and b/data/nbfires.rda differ
diff --git a/data/nztrees.rda b/data/nztrees.rda
new file mode 100644
index 0000000..d1528ba
Binary files /dev/null and b/data/nztrees.rda differ
diff --git a/data/osteo.rda b/data/osteo.rda
new file mode 100644
index 0000000..18db6cd
Binary files /dev/null and b/data/osteo.rda differ
diff --git a/data/paracou.rda b/data/paracou.rda
new file mode 100644
index 0000000..b709d07
Binary files /dev/null and b/data/paracou.rda differ
diff --git a/data/ponderosa.rda b/data/ponderosa.rda
new file mode 100644
index 0000000..2ef3964
Binary files /dev/null and b/data/ponderosa.rda differ
diff --git a/data/pyramidal.rda b/data/pyramidal.rda
new file mode 100644
index 0000000..62cefc3
Binary files /dev/null and b/data/pyramidal.rda differ
diff --git a/data/redwood.rda b/data/redwood.rda
new file mode 100644
index 0000000..da8c1c7
Binary files /dev/null and b/data/redwood.rda differ
diff --git a/data/redwood3.rda b/data/redwood3.rda
new file mode 100644
index 0000000..7007a76
Binary files /dev/null and b/data/redwood3.rda differ
diff --git a/data/redwoodfull.rda b/data/redwoodfull.rda
new file mode 100644
index 0000000..37e8db8
Binary files /dev/null and b/data/redwoodfull.rda differ
diff --git a/data/residualspaper.rda b/data/residualspaper.rda
new file mode 100644
index 0000000..860ef00
Binary files /dev/null and b/data/residualspaper.rda differ
diff --git a/data/shapley.rda b/data/shapley.rda
new file mode 100644
index 0000000..2b51616
Binary files /dev/null and b/data/shapley.rda differ
diff --git a/data/simba.rda b/data/simba.rda
new file mode 100644
index 0000000..511e98b
Binary files /dev/null and b/data/simba.rda differ
diff --git a/data/simdat.rda b/data/simdat.rda
new file mode 100644
index 0000000..38cce48
Binary files /dev/null and b/data/simdat.rda differ
diff --git a/data/simplenet.rda b/data/simplenet.rda
new file mode 100644
index 0000000..d729c82
Binary files /dev/null and b/data/simplenet.rda differ
diff --git a/data/spiders.rda b/data/spiders.rda
new file mode 100644
index 0000000..79f2167
Binary files /dev/null and b/data/spiders.rda differ
diff --git a/data/sporophores.rda b/data/sporophores.rda
new file mode 100644
index 0000000..0748259
Binary files /dev/null and b/data/sporophores.rda differ
diff --git a/data/spruces.rda b/data/spruces.rda
new file mode 100644
index 0000000..24a4d3c
Binary files /dev/null and b/data/spruces.rda differ
diff --git a/data/swedishpines.rda b/data/swedishpines.rda
new file mode 100644
index 0000000..4bf3da2
Binary files /dev/null and b/data/swedishpines.rda differ
diff --git a/data/urkiola.rda b/data/urkiola.rda
new file mode 100644
index 0000000..fd84b04
Binary files /dev/null and b/data/urkiola.rda differ
diff --git a/data/vesicles.rda b/data/vesicles.rda
new file mode 100644
index 0000000..8fd6f39
Binary files /dev/null and b/data/vesicles.rda differ
diff --git a/data/waka.rda b/data/waka.rda
new file mode 100644
index 0000000..ac1f788
Binary files /dev/null and b/data/waka.rda differ
diff --git a/data/waterstriders.rda b/data/waterstriders.rda
new file mode 100644
index 0000000..5ffd0f0
Binary files /dev/null and b/data/waterstriders.rda differ
diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
new file mode 100755
index 0000000..a93772a
--- /dev/null
+++ b/inst/doc/packagesizes.txt
@@ -0,0 +1,2 @@
+date version nhelpfiles nobjects ndatasets Rlines srclines
+"2017-10-11" "1.1-1" 56 0 54 0 0
diff --git a/inst/rawdata/amacrine/amacrine.txt b/inst/rawdata/amacrine/amacrine.txt
new file mode 100755
index 0000000..36baeaf
--- /dev/null
+++ b/inst/rawdata/amacrine/amacrine.txt
@@ -0,0 +1,295 @@
+ x y on
+ .0224 .0243 1
+ .0243 .1028 1
+ .1626 .1477 1
+ .1215 .0729 1
+ .2411 .0486 1
+ .0766 .1776 1
+ .1047 .2579 1
+ .0430 .3645 1
+ .1084 .4000 1
+ .1981 .2841 1
+ .2505 .2776 1
+ .2215 .1617 1
+ .3421 .1963 1
+ .2953 .0729 1
+ .3953 .0579 1
+ .4121 .1439 1
+ .3449 .2841 1
+ .3121 .3514 1
+ .0701 .5215 1
+ .0972 .6570 1
+ .0757 .7355 1
+ .0299 .8720 1
+ .0393 .9869 1
+ .0757 .8252 1
+ .1972 .8617 1
+ .1561 .9411 1
+ .2159 .7757 1
+ .1935 .6533 1
+ .2084 .5458 1
+ .2280 .4280 1
+ .3383 .4776 1
+ .3150 .5832 1
+ .3467 .5636 1
+ .3449 .3832 1
+ .4318 .3262 1
+ .4804 .2542 1
+ .5243 .1925 1
+ .5215 .1159 1
+ .5075 .0234 1
+ .5991 .0252 1
+ .6393 .1196 1
+ .6402 .2579 1
+ .6262 .3523 1
+ .5748 .3897 1
+ .4617 .4271 1
+ .4813 .4897 1
+ .4720 .6822 1
+ .3636 .7551 1
+ .3505 .6953 1
+ .3000 .8112 1
+ .2738 .9084 1
+ .2673 .9813 1
+ .3804 .8785 1
+ .4327 .8402 1
+ .5037 .8813 1
+ .5477 .9308 1
+ .5645 .8028 1
+ .5271 .5907 1
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+ .6598 .7813 1
+ .6542 .8318 1
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+ .7084 .9626 1
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+ .7654 .0299 1
+ .9056 .1514 1
+ .9093 .2206 1
+ .9355 .2019 1
+ .9056 .3093 1
+ .9860 .3299 1
+ .9430 .4280 1
+ .7486 .4047 1
+ .7832 .4084 1
+ .7935 .3234 1
+ .7869 .4953 1
+ .9056 .5150 1
+ .8673 .5720 1
+ .8636 .6374 1
+ .8065 .7093 1
+ .8636 .7486 1
+ .8533 .8495 1
+ .8561 .9579 1
+ .9346 .9009 1
+ .9991 .9888 1
+ 1.0645 .9262 1
+ 1.0262 .7916 1
+ .9822 .6794 1
+ 1.0290 .5271 1
+ 1.0673 .4729 1
+ 1.0869 .5598 1
+ 1.0981 .6953 1
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+ 1.1617 .9224 1
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+ 1.3103 .9766 1
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+ 1.4869 .9916 1
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+ 1.5972 .9449 1
+ 1.5766 .8327 1
+ 1.5860 .7729 1
+ 1.4804 .7121 1
+ 1.4234 .7981 1
+ 1.3355 .7570 1
+ 1.2206 .7626 1
+ 1.1402 .6495 1
+ 1.2477 .6523 1
+ 1.3645 .6523 1
+ 1.3776 .5598 1
+ 1.5467 .6037 1
+ 1.5794 .6280 1
+ 1.5907 .4598 1
+ 1.4907 .4963 1
+ 1.4393 .4477 1
+ 1.3187 .4766 1
+ 1.3280 .5505 1
+ 1.2159 .5299 1
+ 1.1850 .4168 1
+ 1.1766 .3047 1
+ 1.2561 .3832 1
+ 1.2850 .2589 1
+ 1.3449 .3421 1
+ 1.3748 .3607 1
+ 1.3570 .2262 1
+ 1.4944 .3467 1
+ 1.5439 .2589 1
+ 1.5421 .1626 1
+ 1.4037 .1841 1
+ 1.4766 .1318 1
+ 1.4421 .0318 1
+ 1.5196 .0393 1
+ 1.3271 .0579 1
+ 1.3075 .1570 1
+ 1.1935 .1617 1
+ 1.1972 .0822 1
+ 1.1925 .0084 1
+ 1.2682 .0140 1
+ 1.0318 .0486 1
+ 1.0785 .2196 1
+ 1.0458 .2374 1
+ 1.0467 .2907 1
+ 1.0495 .3804 1
+ .0720 .0215 0
+ .0766 .1692 0
+ .0944 .2692 0
+ .1523 .3308 0
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diff --git a/inst/rawdata/finpines/finpines.txt b/inst/rawdata/finpines/finpines.txt
new file mode 100755
index 0000000..65b968d
--- /dev/null
+++ b/inst/rawdata/finpines/finpines.txt
@@ -0,0 +1,127 @@
+ x y diameter height
+ -1.993875 0.9297642 1 1.70
+ -1.019901 0.4120694 1 1.70
+ -4.914071 1.985425 1 1.60
+ -4.469962 1.452390 5 4.10
+ -4.303847 0.9148214 3 3.10
+ -3.814774 0.8108644 4 4.30
+ -3.423515 0.7276988 2 2.30
+ -3.130071 0.6653246 4 4.00
+ -4.431633 0.7814268 7 5.40
+-0.9000000 2.0670868E-06 2 1.80
+ -3.899406 6.8073884E-02 3 3.20
+ -1.315571 -0.4788248 1 1.30
+ -2.499282 -0.7166504 5 3.80
+ -2.704594 -0.7246863 1 1.50
+ -4.510529 -1.641685 2 2.10
+ -4.134652 -1.504878 3 3.30
+ -4.107759 -1.576808 3 3.00
+ -4.040682 -1.470676 4 3.20
+ -3.174177 -1.218442 1 1.50
+ -3.150349 -2.124924 1 1.60
+ -4.948165 -3.213357 2 2.10
+-0.5656871 -0.5656838 1 1.40
+ -3.217394 -2.699698 3 2.80
+ -2.877367 -2.778625 4 4.00
+ -4.027665 -4.973723 1 1.40
+ -4.847309 -7.464154 1 1.60
+ -4.738381 -7.296420 3 4.00
+-0.3914369 -0.5803250 1 1.90
+ -3.444492 -5.512302 7 4.80
+ -1.960709 -3.019208 1 1.60
+ -2.225672 -3.561795 3 3.00
+-0.9000050 -1.558843 3 3.10
+ -2.450014 -4.243516 6 4.40
+ -3.102800 -5.597556 1 2.10
+ -3.248244 -5.859941 2 3.00
+ -3.400019 -5.888962 1 2.40
+ -3.286322 -6.180622 1 1.90
+ -3.393688 -6.122327 2 2.30
+ -3.700021 -6.408576 6 4.80
+ -4.600026 -7.967419 1 1.80
+ -1.436497 -3.946704 1 2.00
+ -2.701983 -7.423563 3 3.50
+ -1.941167 -7.244437 3 3.30
+ -1.967049 -7.341030 2 2.80
+ -1.669284 -6.695035 1 1.65
+ -1.475744 -5.918799 2 2.40
+ -1.268229 -4.733033 3 3.50
+-0.6531979 -2.619796 0 1.00
+-0.7119707 -4.037709 3 3.00
+ -1.007178 -5.711882 1 2.40
+-0.9506087 -7.741857 3 3.40
+-0.7212717 -6.862198 0 0.80
+-2.3614140E-05 -7.100000 2 2.30
+-2.2616361E-05 -6.800000 7 5.00
+-1.9623018E-05 -5.900000 4 3.60
+ 0.3820261 -7.289998 3 3.40
+ 0.3506266 -6.690819 2 4.00
+ 0.5939180 -6.674507 1 1.50
+ 0.5839180 -6.684507 4 4.70
+ 0.5752028 -6.574887 6 5.00
+ 0.4254918 -6.085142 2 2.80
+ 0.5229116 -5.977170 1 1.40
+ 0.7839378 -7.458917 2 2.90
+ 0.7734853 -7.359465 5 4.60
+ 0.6376027 -6.066586 1 1.60
+ 0.6271502 -5.967134 1 2.30
+ 0.6166977 -5.867682 3 4.40
+ 0.5957927 -5.668777 2 3.60
+ 0.6580755 -5.359752 6 4.90
+ 0.3149265 -1.364119 1 2.10
+ 0.7741384 -3.104949 1 1.50
+ 0.8709057 -3.493068 3 3.00
+ 1.204589 -3.498423 3 3.00
+ 1.530154 -4.443943 3 3.20
+ 1.953639 -4.602531 3 3.20
+ 1.992711 -4.694582 2 3.00
+ 2.031784 -4.786633 2 3.00
+ 2.198075 -5.154835 1 1.90
+ 2.188075 -5.154835 3 3.60
+ 2.237032 -5.024508 3 3.30
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new file mode 100755
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new file mode 100755
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new file mode 100755
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new file mode 100755
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new file mode 100755
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diff --git a/man/Kovesi.Rd b/man/Kovesi.Rd
new file mode 100755
index 0000000..b9a61a0
--- /dev/null
+++ b/man/Kovesi.Rd
@@ -0,0 +1,90 @@
+\name{Kovesi}
+\alias{Kovesi}
+\docType{data}
+\title{
+ Colour Sequences with Uniform Perceptual Contrast
+}
+\description{
+ A collection of 41 different sequences of colours,
+ each sequence having a uniform perceptual contrast over its whole
+ range. These sequences make very good colour maps which avoid
+ introducing artefacts when displaying image data.
+}
+\usage{data(Kovesi)}
+\format{
+ A \code{\link[spatstat]{hyperframe}} with the following columns:
+
+ \tabular{ll}{
+ \code{linear} \tab Logical: whether the sequence is linear. \cr
+ \code{diverging} \tab Logical: whether the sequence is diverging. \cr
+ \code{rainbow} \tab Logical: whether the sequence is a rainbow. \cr
+ \code{cyclic} \tab Logical: whether the sequence is cyclic. \cr
+ \code{isoluminant} \tab Logical: whether the sequence is isoluminant. \cr
+ \code{ternary} \tab Logical: whether the sequence is ternary. \cr
+ \code{colsig} \tab Character: colour signature (see Details) \cr
+ \code{l1}, \code{l2} \tab Numeric: lightness parameters \cr
+ \code{chro} \tab Numeric: average chroma (percent) \cr
+ \code{n} \tab Numeric: length of colour sequence \cr
+ \code{cycsh} \tab Numeric: cyclic shift (percent) \cr
+ \code{values} \tab: Character: the colour values.
+ }
+}
+\details{
+ Kovesi (2014, 2015) presented a collection of colour sequences
+ that have uniform perceptual contrast over their whole range.
+
+ The dataset \code{Kovesi} provides these data. It is a
+ \code{hyperframe} with 41 rows, in which each row provides information
+ about one colour sequence.
+
+ Additional information in each row specifies whether the
+ colour sequence is \sQuote{linear}, \sQuote{diverging},
+ \sQuote{rainbow}, \sQuote{cyclic}, \sQuote{isoluminant}
+ and/or \sQuote{ternary} as defined by Kovesi (2014, 2015).
+
+ The \sQuote{colour signature} is a string composed of letters
+ representing the successive hues, using the following code:
+ \tabular{ll}{
+ r \tab red \cr
+ g \tab green\cr
+ b \tab blue \cr
+ c \tab cyan \cr
+ m \tab magenta \cr
+ y \tab yellow \cr
+ o \tab orange \cr
+ v \tab violet \cr
+ k \tab black \cr
+ w \tab white \cr
+ j \tab grey (j rhymes with grey)
+ }
+ For example \code{kryw} is the sequence from black to red to yellow to
+ white.
+
+ The column \code{values} contains the colour data themselves.
+ The \code{i}th colour sequence is \code{Kovesi$values[[i]]},
+ a character vector of length 256.
+}
+\source{
+ Dr Peter Kovesi, Centre for Exploration Targeting,
+ University of Western Australia.
+}
+\references{
+ Kovesi, P. (2014)
+ Website \emph{CET Uniform Perceptual Contrast Colour Maps}
+ \url{www.peterkovesi.com/projects/colourmaps/}
+
+ Kovesi, P. (2015)
+ Designing colour maps with uniform perceptual contrast.
+ Manuscript submitted for publication.
+}
+\examples{
+ Kovesi
+ LinearBMW <- Kovesi$values[[28]]
+ if(require(spatstat)) {
+ plot(colourmap(LinearBMW, range=c(0,1)))
+
+ ## The following would be suitable for spatstat.options(image.colfun)
+ BMWfun <- function(n) { interp.colours(LinearBMW, n) }
+ }
+}
+\keyword{datasets}
diff --git a/man/amacrine.Rd b/man/amacrine.Rd
new file mode 100755
index 0000000..ddfe44a
--- /dev/null
+++ b/man/amacrine.Rd
@@ -0,0 +1,43 @@
+\name{amacrine}
+\alias{amacrine}
+\docType{data}
+\title{Hughes' Amacrine Cell Data}
+\description{
+Austin Hughes' data: a point pattern
+of displaced amacrine cells in the retina of a rabbit.
+A marked point pattern.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of cell locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of cell \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of cell \cr
+ \code{marks} \tab factor with levels \code{off} and \code{on} \cr
+ \tab indicating ``off'' and ``on'' cells
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(amacrine)}
+\source{Peter Diggle, personal communication}
+\section{Notes}{
+Austin Hughes' data: a point pattern
+of displaced amacrine cells in the retina of a rabbit.
+152 ``on'' cells and 142 ``off'' cells in a rectangular sampling frame.
+
+The true dimensions of the rectangle are 1060 by 662 microns.
+The coordinates here are scaled to a rectangle of height 1 and width
+\eqn{1060/662 = 1.601} so the unit of measurement is approximately 662 microns.
+
+The data were analysed by Diggle (1986).
+}
+\references{
+Diggle, P. J. (1986).
+Displaced amacrine cells in the retina of a
+rabbit: analysis of a bivariate spatial point pattern.
+\emph{J. Neurosci. Meth.} \bold{18}, 115--125.
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/anemones.Rd b/man/anemones.Rd
new file mode 100755
index 0000000..ed423df
--- /dev/null
+++ b/man/anemones.Rd
@@ -0,0 +1,72 @@
+\name{anemones}
+\alias{anemones}
+\docType{data}
+\title{
+ Beadlet Anemones Data
+}
+\description{
+ These data give the spatial locations and diameters
+ of sea anemones (beadlet anemone
+ \emph{Actinia equina}) in a sample plot
+ on the north face of a boulder,
+ well above low tide level, at Quiberon (Bretagne, France) in May 1976.
+
+ The data were originally described and discussed by Kooijman (1979a).
+ Kooijman (1979b) shows a hand-drawn plot of the original data.
+ The data are discussed by Upton and Fingleton (1985)
+ as Example 1.8 on pages 64--67.
+
+ The \code{anemones} dataset is taken directly from Table 1.11
+ of Upton and Fingleton (1985). The coordinates and
+ diameters are integer multiples of an idiosyncratic unit of length.
+ The boundary is a rectangle 280 by 180 units.
+}
+\section{Units}{
+ There is some confusion about the correct physical scale for these
+ data. According to Upton and Fingleton (1985), one unit in the dataset
+ is approximately 0.475 cm. According to Kooijman (1979a, 1979b)
+ and also quoted by Upton and Fingleton (1985), the
+ physical size of the sample plot was 14.5 by 9.75 decimetres
+ (145 by 97.5 centimetres).
+ However if the data are plotted at this scale, they are too small for
+ a rectangle of this size, and the appearance of the plot
+ does not match the original hand-drawn plot in Kooijman (1979b).
+ To avoid confusion, we have not assigned a unit scale to this
+ dataset.
+}
+\format{
+ \code{anemones} is an object of class \code{"ppp"}
+ representing the point pattern of anemone locations.
+ It is a marked point pattern with numeric marks representing
+ anemone diameter.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(anemones)}
+\examples{
+ data(anemones)
+ if(require(spatstat)) {
+ # plot diameters on same scale as x, y
+ plot(anemones, markscale=1)
+ }
+}
+\source{
+ Table 1.11 on pages 62--63 of Upton and Fingleton (1985),
+ who acknowledge Kooijman (1979a) as the source.
+}
+\references{
+ Kooijman, S.A.L.M. (1979a)
+ The description of point patterns.
+ In \emph{Spatial and temporal analysis in ecology} (ed. R.M. Cormack
+ and J.K. Ord), International Cooperative Publishing House,
+ Fairland, Maryland, USA. Pages 305--332.
+
+ Kooijman, S.A.L.M. (1979b)
+ Inference about dispersal patterns.
+ \emph{Acta Biotheoretica} \bold{28}, 149--189.
+
+ Upton, G.J.G. and Fingleton, B. (1985)
+ \emph{Spatial data analysis by example}. Volume 1: Point pattern
+ and quantitative data. John Wiley and Sons, Chichester.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/ants.Rd b/man/ants.Rd
new file mode 100755
index 0000000..dcdc2ca
--- /dev/null
+++ b/man/ants.Rd
@@ -0,0 +1,171 @@
+\name{ants}
+\alias{ants}
+\alias{ants.extra}
+\docType{data}
+\title{
+ Harkness-Isham ants' nests data
+}
+\description{
+ These data give the spatial locations of nests of two species of
+ ants, \emph{Messor wasmanni} and \emph{Cataglyphis bicolor},
+ recorded by Professor R.D. Harkness at a site in northern Greece,
+ and described in Harkness \& Isham (1983).
+ The full dataset (supplied here) has an irregular polygonal boundary,
+ while most analyses have been confined to two rectangular
+ subsets of the pattern (also supplied here).
+
+ The harvester ant \emph{M. wasmanni}
+ collects seeds for food and builds a nest composed mainly of
+ seed husks. \emph{C. bicolor} is a heat-tolerant desert foraging ant which
+ eats dead insects and other arthropods. Interest focuses on whether
+ there is evidence in the data for intra-species competition
+ between \emph{Messor} nests (i.e. competition for resources) and for
+ preferential placement of \emph{Cataglyphis} nests in the vicinity of
+ \emph{Messor} nests.
+
+ The full dataset is displayed in Figure 1 of Harkness \& Isham (1983).
+ See \bold{Usage} below to produce a comparable plot.
+ It comprises 97 nests (68 Messor and 29 Cataglyphis)
+ inside an irregular convex polygonal boundary, together with
+ annotations showing a foot track through the region,
+ the boundary between field and scrub areas inside the
+ region, and indicating the two rectangular subregions
+ A and B used in their analysis.
+
+ Rectangular subsets of the data were analysed by
+ Harkness \& Isham (1983), Isham (1984), Takacs \& Fiksel
+ (1986), S\"arkk\"a (1993, section 5.3),
+ H\"ogmander and S\"arkk\"a (1999) and Baddeley \& Turner (2000).
+ The full dataset (inside its irregular boundary) was first analysed
+ by Baddeley \& Turner (2005b).
+
+ The dataset \code{ants} is the full point pattern
+ enclosed by the irregular polygonal boundary.
+ The \eqn{x} and \eqn{y} coordinates are eastings (E-W) and northings (N-S)
+ scaled so that 1 unit equals 0.5 feet.
+ This is a multitype point pattern object, each point carrying a mark
+ indicating the ant species (with levels \code{Cataglyphis}
+ and \code{Messor}).
+
+ The dataset \code{ants.extra} is a list of auxiliary
+ information:
+ \describe{
+ \item{\code{A} and \code{B}}{The subsets
+ of the pattern within the rectangles A and B
+ demarcated in Figure 1 of Harkness \& Isham (1983).
+ These are multitype point pattern objects.
+ }
+ \item{\code{trackNE} and \code{trackSW}}{
+ coordinates of two straight lines bounding the foot track.
+ }
+ \item{\code{fieldscrub}}{The endpoints of a straight line
+ separating the regions of `field' and `scrub':
+ scrub to the North and field to the South.
+ }
+ \item{\code{side}}{
+ A \code{function(x,y)} that determines whether the location
+ \code{(x,y)} is in the scrub or the field. The function can be applied
+ to numeric vectors \code{x} and \code{y}, and returns a factor
+ with levels \code{"scrub"} and \code{"field"}.
+ This function is useful as a spatial covariate.
+ }
+ \item{\code{plotit}}{A function which
+ produces a plot of the full dataset.
+ }
+ }
+}
+\format{
+ \code{ants} is an object of class \code{"ppp"}
+ representing the full point pattern of ants' nests.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+ The coordinates are scaled so that 1 unit equals 0.5 feet.
+ The points are marked by species (with levels \code{Cataglyphis}
+ and \code{Messor}).
+
+ \code{ants.extra} is a list with entries
+ \describe{
+ \item{A}{point pattern of class \code{"ppp"}}
+ \item{B}{point pattern of class \code{"ppp"}}
+ \item{trackNE}{data in format \code{list(x=numeric(2),y=numeric(2))}
+ giving the two endpoints of line markings}
+ \item{trackSW}{data in format \code{list(x=numeric(2),y=numeric(2))}
+ giving the two endpoints of line markings}
+ \item{fieldscrub}{data in format \code{list(x=numeric(2),y=numeric(2))}
+ giving the two endpoints of line markings}
+ \item{side}{Function with arguments \code{x,y}}
+ \item{plotit}{Function}
+ }
+}
+\usage{data(ants)}
+\examples{
+ if(require(spatstat)) {
+
+ # Equivalent to Figure 1 of Harkness and Isham (1983)
+
+ data(ants)
+ ants.extra$plotit()
+
+ # Data in subrectangle A, rotated
+ # Approximate data used by Sarkka (1993)
+
+ angle <- atan(diff(ants.extra$fieldscrub$y)/diff(ants.extra$fieldscrub$x))
+ plot(rotate(ants.extra$A, -angle))
+
+ # Approximate window used by Takacs and Fiksel (1986)
+
+ tfwindow <- boundingbox(Window(ants))
+ antsTF <- ppp(ants$x, ants$y, window=tfwindow)
+ plot(antsTF)
+ }
+}
+\source{Harkness and Isham (1983).
+ Nest coordinates kindly provided by Prof Valerie Isham.
+ Polygon coordinates digitised by Adrian Baddeley from
+ a reprint of Harkness \& Isham (1983).
+}
+\references{
+Baddeley, A. and Turner, R. (2000)
+Practical maximum pseudolikelihood for spatial point patterns.
+\emph{Australian and New Zealand Journal of Statistics}
+\bold{42}, 283--322.
+
+ Baddeley, A. and Turner, R. (2005a)
+ Spatstat: an R package for analyzing spatial point patterns.
+ \emph{Journal of Statistical Software} \bold{12}:6, 1--42.
+ URL: \code{www.jstatsoft.org}, ISSN: 1548-7660.
+
+ Baddeley, A. and Turner, R. (2005b)
+ Modelling spatial point patterns in R.
+ In: A. Baddeley, P. Gregori, J. Mateu, R. Stoica, and D. Stoyan,
+ editors, \emph{Case Studies in Spatial Point Pattern Modelling},
+ Lecture Notes in Statistics number 185. Pages 23--74.
+ Springer-Verlag, New York, 2006.
+ ISBN: 0-387-28311-0.
+
+Harkness, R.D. and Isham, V. (1983)
+A bivariate spatial point pattern of ants' nests.
+\emph{Applied Statistics} \bold{32}, 293--303.
+
+\ifelse{latex}{\out{H\"ogmander}}{Hogmander}, H. and
+\ifelse{latex}{\out{S\"arkk\"a}}{Sarkka}, A. (1999)
+Multitype spatial point patterns with hierarchical interactions.
+\emph{Biometrics} \bold{55}, 1051--1058.
+
+Isham, V.S. (1984)
+Multitype Markov point processes: some approximations.
+\emph{Proceedings of the Royal Society of London, Series A},
+\bold{391}, 39--53.
+
+Takacs, R. and Fiksel, T. (1986)
+Interaction pair-potentials for a system of ants' nests.
+\emph{Biometrical Journal} \bold{28}, 1007--1013.
+
+\ifelse{latex}{\out{S\"arkk\"a}}{Sarkka}, A. (1993)
+\emph{Pseudo-likelihood approach for pair potential
+ estimation of Gibbs processes}.
+Number 22 in \ifelse{latex}{\out{Jyv\"askyl\"a}}{Jyvaskyla}
+Studies in Computer Science, Economics and Statistics.
+University of \ifelse{latex}{\out{Jyv\"askyl\"a}}{Jyvaskyla}, Finland.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/austates.Rd b/man/austates.Rd
new file mode 100755
index 0000000..4051f8b
--- /dev/null
+++ b/man/austates.Rd
@@ -0,0 +1,39 @@
+\name{austates}
+\alias{austates}
+\docType{data}
+\title{
+ Australian States and Mainland Territories
+}
+\description{
+ The states and large mainland territories of Australia are
+ represented as polygonal regions forming a tessellation.
+}
+\usage{data(austates)}
+\format{
+ Object of class \code{"tess"}.
+}
+\details{
+ Western Australia, South Australia, Queensland,
+ New South Wales, Victoria and Tasmania (which are states of Australia)
+ and the Northern Territory (which is a `territory' of Australia)
+ are represented as polygonal regions.
+
+ Offshore territories, and smaller mainland territories, are not shown.
+
+ The dataset \code{austates} is a tessellation object (class \code{"tess"})
+ whose tiles are the states and territories.
+
+ The coordinates are latitude and
+ longitude in degrees, so the space is effectively a Mercator
+ projection of the earth.
+}
+\source{
+ Obtained from the \pkg{oz} package and reformatted.
+}
+\examples{
+ data(austates)
+ if(require(spatstat)) {
+ plot(austates)
+ }
+}
+\keyword{datasets}
diff --git a/man/bdspots.Rd b/man/bdspots.Rd
new file mode 100755
index 0000000..d748e2b
--- /dev/null
+++ b/man/bdspots.Rd
@@ -0,0 +1,89 @@
+\name{bdspots}
+\alias{bdspots}
+\docType{data}
+\title{
+ Breakdown Spots in Microelectronic Materials
+}
+\description{
+ A list of three point patterns, each giving the locations of
+ electrical breakdown spots on a circular electrode in
+ a microelectronic capacitor.
+}
+\usage{data(bdspots)}
+\format{
+ A list (of class \code{"listof"}) of three spatial point patterns,
+ each representing the spatial locations of breakdown spots on an
+ electrode. The three electrodes are circular discs, of radii
+ 169, 282 and 423 microns respectively. Spatial coordinates are
+ given in microns.
+}
+\details{
+ The application of successive voltage sweeps to the metal gate electrode
+ of a microelectronic capacitor generates multiple breakdown spots
+ on the electrode.
+ The spatial distribution of these breakdown spots
+ in MIM (metal-insulator-metal) and MIS (metal-insulator-semiconductor)
+ structures was observed and analysed by
+ Miranda et al (2010, 2013) and Saura et al (2013a, 2013b, 2014).
+
+ The data given here are the breakdown spot patterns for three circular
+ electrodes of different radii, 169, 282 and 423 microns respectively,
+ in MIM structures analysed in Saura et al (2013a).
+}
+\source{
+ Professor Enrique Miranda, Departament d'Enginyeria
+ \ifelse{latex}{\out{Electr{\`o}nica}}{Electronica},
+ Escola d'Enginyeria, Universitat
+ \ifelse{latex}{\out{Aut{\`o}noma}}{Autonoma}
+ de Barcelona, Barcelona, Spain.
+}
+\references{
+ Miranda, E. and O'Connor, E. and Hurley, P.K. (2010)
+ Simulation of the breakdown spots spatial
+ distribution in high-\emph{K} dielectrics and model
+ validation using the \pkg{spatstat} package for \emph{R} language.
+ \emph{ECS Transactions} \bold{33} (3) 557--562.
+
+ Miranda, E.,
+ \ifelse{latex}{\out{Jim{\'e}nez}}{Jimenez}, D.,
+ \ifelse{latex}{\out{Su{\~n}{\'e}}}{Sune}, J.,
+ O'Connor, E.,
+ Monaghan, S.,
+ Povey, I.,
+ Cherkaoui, K. and Hurley, P. K. (2013)
+ Nonhomogeneous spatial distribution of filamentary leakage current
+ paths in circular area Pt/HfO2/Pt capacitors.
+ \emph{J. Vac. Sci. Technol. B} \bold{31}, 01A107.
+
+ Saura, X.,
+ \ifelse{latex}{\out{Su{\~n}{\'e}}}{Sune}, J.,
+ Monaghan, S., Hurley, P.K. and Miranda, E. (2013a)
+ Analysis of the breakdown spot spatial distribution in Pt/HfO2/Pt
+ capacitors using nearest neighbor statistics.
+ \emph{J. Appl. Phys.} \bold{114}, 154112.
+
+ Saura, X., Moix, D.,
+ \ifelse{latex}{\out{Su{\~n}{\'e}}}{Sune}, J.,
+ Hurley, P.K. and Miranda, E. (2013b)
+ Direct observation of the generation of breakdown spots in MIM
+ structures under constant voltage stress.
+ \emph{Microelectronics Reliability} \bold{53}, 1257--1260.
+
+ Saura, X.,
+ Monaghan, S.,
+ Hurley, P.K.,
+ \ifelse{latex}{\out{Su{\~n}{\'e}}}{Sune}, J.
+ and Miranda, E. (2014)
+ Failure analysis of MIM and MIS structures using point-to-event
+ distance and angular probability distributions.
+ \emph{IEEE Transactions on Devices and Materials Reliability}
+ \bold{14} (4) 1080--1090.
+}
+\examples{
+data(bdspots)
+ if(require(spatstat)) {
+plot(bdspots, equal.scales=TRUE)
+ }
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/bei.Rd b/man/bei.Rd
new file mode 100755
index 0000000..6f73bec
--- /dev/null
+++ b/man/bei.Rd
@@ -0,0 +1,71 @@
+\name{bei}
+\alias{bei}
+\alias{bei.extra}
+\docType{data}
+\title{Tropical rain forest trees}
+\description{
+ A point pattern giving the locations of 3605
+ trees in a tropical rain forest.
+ Accompanied by covariate data giving the elevation (altitude)
+ and slope of elevation in the study region.
+}
+\format{
+ \code{bei} is an object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+
+ \code{bei.extra} is a list containing
+ two pixel images, \code{elev} (elevation in metres) and
+ \code{grad} (norm of elevation gradient). These pixel images are objects
+ of class \code{"im"}, see \code{\link[spatstat]{im.object}}.
+}
+\usage{data(bei)}
+\source{
+ Hubbell and Foster (1983), Condit, Hubbell and Foster (1996)
+ and Condit (1998).
+ Data files kindly supplied by Rasmus Waagepetersen.
+ The data were collected in the forest dynamics plot of Barro Colorado
+ Island. The study was made possible through the generous support of
+ the U.S. National Science Foundation, the John D. and Catherine
+ T. MacArthur Foundation, and the Smithsonian Tropical Research Institute.
+}
+\section{Notes}{
+ The dataset \code{bei} gives the positions of 3605 trees
+ of the species \emph{Beilschmiedia pendula} (Lauraceae)
+ in a 1000 by 500 metre rectangular sampling region
+ in the tropical rainforest of Barro Colorado Island.
+
+ The accompanying dataset \code{bei.extra} gives information
+ about the altitude (elevation) in the study region. It is a list
+ containing two pixel images, \code{elev} (elevation in metres) and
+ \code{grad} (norm of elevation gradient).
+
+ These data are part of a much larger dataset containing the positions of
+ hundreds of thousands of trees belong to thousands of species;
+ see Hubbell and Foster (1983), Condit, Hubbell and Foster (1996)
+ and Condit (1998).
+
+ The present data were analysed by \ifelse{latex}{\out{M\o ller}}{Moller} and Waagepetersen (2007).
+}
+\references{
+ Condit, R. (1998) \emph{Tropical Forest Census Plots}.
+ Springer-Verlag, Berlin and R.G. Landes Company, Georgetown, Texas.
+
+ Condit, R., Hubbell, S.P and Foster, R.B. (1996)
+ Changes in tree species abundance in a neotropical forest: impact of
+ climate change. \emph{Journal of Tropical Ecology} \bold{12},
+ 231--256.
+
+ Hubbell, S.P and Foster, R.B. (1983)
+ Diversity of canopy trees in a neotropical forest and implications for
+ conservation. In: \emph{Tropical Rain Forest: Ecology and Management}
+ (eds. S.L. Sutton, T.C. Whitmore and A.C. Chadwick),
+ Blackwell Scientific Publications, Oxford, 25--41.
+
+ \ifelse{latex}{\out{M\o ller}}{Moller}, J. and Waagepetersen, R.P. (2007)
+ Modern spatial point process modelling and inference (with discussion).
+ \emph{Scandinavian Journal of Statistics} \bold{34}, 643--711.
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/betacells.Rd b/man/betacells.Rd
new file mode 100755
index 0000000..34f9734
--- /dev/null
+++ b/man/betacells.Rd
@@ -0,0 +1,105 @@
+\name{betacells}
+\alias{betacells}
+\docType{data}
+\title{Beta Ganglion Cells in Cat Retina}
+\description{
+ Point pattern of cells in the retina, each cell classified as `on' or
+ `off' and labelled with the cell profile area.
+}
+\format{
+ \code{betacells} is an object of class \code{"ppp"}
+ representing the point pattern of cell locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of cell \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of cell \cr
+ \code{marks} \tab data frame of marks
+ }
+ Cartesian coordinates are given in microns.
+
+ The data frame of marks has two columns:
+ \tabular{ll}{
+ \code{type} \tab factor with levels \code{off} and \code{on} \cr
+ \tab indicating ``off'' and ``on'' cells\cr
+ \code{area} \tab numeric vector giving the \cr
+ \tab areas of cell profiles (in square microns)
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(betacells)}
+\source{
+ W\"assle et al (1981), Figure 6(a),
+ scanned and processed by Stephen Eglen
+ \email{S.J.Eglen at damtp.cam.ac.uk}
+}
+\section{Notes}{
+ This is a new, corrected version of the old dataset
+ \code{\link[spatstat.data]{ganglia}}. See below.
+
+ These data represent a pattern of beta-type ganglion cells
+ in the retina of a cat recorded by W\"assle et al. (1981).
+ Beta cells are associated
+ with the resolution of fine detail in the cat's visual system.
+ They can be classified anatomically as ``on'' or ``off''.
+
+ Statistical independence of the arrangement of the
+ ``on''- and ``off''-components
+ would strengthen the evidence for Hering's (1878) `opponent theory'
+ that there are two separate channels for sensing
+ ``brightness'' and ``darkness''.
+ See W\"assle et al (1981). There is considerable current interest
+ in the arrangement of cell mosaics in the retina, see
+ Rockhill et al (2000).
+
+ The dataset is a marked point pattern giving the locations,
+ types (``on'' or ``off''), and profile areas of beta cells observed
+ in a rectangle of dimensions \eqn{750 \times 990}{750 x 990} microns.
+ Coordinates are given in microns (thousandths of a millimetre)
+ and areas are given in square microns.
+
+ The original source is Figure 6 of W\"assle et al (1981),
+ which is a manual drawing of the beta mosaic observed
+ in a microscope field-of-view of a whole mount of the retina.
+ Thus, all beta cells in the retina were effectively projected onto the same
+ two-dimensional plane.
+
+ The data were scanned in 2004 by Stephen Eglen from
+ Figure 6(a) of W\"assle et al (1981).
+ Image analysis software was used to identify the soma (cell
+ body). The \eqn{x,y} location of each cell was taken to be the
+ centroid of the soma. The type of each cell (``on'' or `off'')
+ was identified by referring to Figures 6(b) and 6(d).
+ The area of each soma (in square microns) was also computed.
+
+ Note that this is a corrected version of
+ the \code{\link[spatstat.data]{ganglia}}
+ dataset provided in earlier versions of \pkg{spatstat}.
+ The earlier data \code{\link[spatstat.data]{ganglia}}
+ were not faithful to the scale
+ in the original paper and contain some scanning errors.
+}
+\examples{
+ plot(betacells)
+ if(require(spatstat)) {
+ area <- marks(betacells)$area
+ plot(betacells \%mark\% sqrt(area/pi), markscale=1)
+ }
+}
+\references{
+Hering, E. (1878) Zur Lehre von Lichtsinn. Vienna.
+
+Van Lieshout, M.N.M. and Baddeley, A.J. (1999)
+Indices of dependence between types in multivariate point patterns.
+\emph{Scandinavian Journal of Statistics} \bold{26}, 511--532.
+
+Rockhill, R.L., Euler, T. and Masland, R.H. (2000)
+Spatial order within but not between types of retinal neurons.
+\emph{Proc. Nat. Acad. Sci. USA} \bold{97}(5), 2303--2307.
+
+W\"assle, H., Boycott, B. B. & Illing, R.-B. (1981).
+Morphology and mosaic of on- and off-beta cells in the cat retina and
+some functional considerations.
+\emph{Proc. Roy. Soc. London Ser. B} \bold{212}, 177--195.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/bramblecanes.Rd b/man/bramblecanes.Rd
new file mode 100755
index 0000000..a41f953
--- /dev/null
+++ b/man/bramblecanes.Rd
@@ -0,0 +1,66 @@
+\name{bramblecanes}
+\alias{bramblecanes}
+\docType{data}
+\title{Hutchings' Bramble Canes data}
+\description{
+ Data giving the locations and ages of bramble canes in a field.
+ A marked point pattern.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of plant locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of plant \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of plant \cr
+ \code{marks} \tab factor with levels 0,1, 2 indicating age
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(bramblecanes)}
+\source{Hutchings (1979), data published in Diggle (1983)}
+\section{Notes}{
+These data record the \eqn{(x,y)} locations and ages of bramble canes in a
+field \eqn{9} metres square, rescaled to the unit square.
+The canes were classified according to age as either newly emergent,
+one or two years old. These are encoded as marks 0, 1 and 2 respectively
+in the dataset.
+
+The data were recorded and analysed by Hutchings (1979)
+and further analysed by Diggle (1981a, 1981b, 1983),
+Diggle and Milne (1983), and Van Lieshout and Baddeley (1999).
+All analyses found that the pattern of newly emergent canes
+exhibits clustering, which Hutchings attributes to ``vigorous
+vegetative reproduction''.
+}
+\references{
+ Diggle, P. J. (1981a)
+ Some graphical methods in the analysis of spatial point patterns.
+ In \emph{Interpreting multivariate data}, V. Barnett (Ed.)
+ John Wiley and Sons.
+
+ Diggle, P. J. (1981b).
+ Statistical analysis of spatial point patterns.
+ \emph{N.Z. Statist.} \bold{16}, 22--41.
+
+ Diggle, P.J. (1983)
+ \emph{Statistical analysis of spatial point patterns}.
+ Academic Press.
+
+ Diggle, P. J. and Milne, R. K. (1983)
+ Bivariate Cox processes: some models for bivariate spatial point patterns.
+ \emph{Journal of the Royal Statistical Soc. Series B}
+ \bold{45}, 11--21.
+
+ Hutchings, M. J. (1979)
+ Standing crop and pattern in pure stands of Mercurialis
+ perennis and Rubus fruticosus in mixed deciduous woodland.
+ \emph{Oikos} \bold{31}, 351--357.
+
+ Van Lieshout, M.N.M. and Baddeley, A.J. (1999)
+ Indices of dependence between types in multivariate point patterns.
+ \emph{Scandinavian Journal of Statistics} \bold{26}, 511--532.
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/bronzefilter.Rd b/man/bronzefilter.Rd
new file mode 100755
index 0000000..727c1b4
--- /dev/null
+++ b/man/bronzefilter.Rd
@@ -0,0 +1,57 @@
+\name{bronzefilter}
+\alias{bronzefilter}
+\docType{data}
+\title{Bronze gradient filter data}
+\description{
+ These data represent a spatially inhomogeneous pattern of
+ circular section profiles of particles, observed in a
+ longitudinal plane section through a gradient sinter
+ filter made from bronze powder, prepared by Ricardo Bernhardt, Dresden.
+
+ The material was produced by sedimentation of bronze powder with varying
+ grain diameter and subsequent sintering,
+ as described in Bernhardt et al. (1997).
+
+ The data are supplied as a marked point pattern of circle centres marked by
+ circle radii.
+ The coordinates of the centres and the radii are recorded in mm.
+ The field of view is an \eqn{18 \times 7}{18 * 7} mm rectangle.
+
+ The data were first analysed by Hahn et al. (1999).
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of cell locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of bronze grain profile centre\cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of bronze grain profile centre\cr
+ \code{marks} \tab radius of bronze grain profile
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+ All coordinates are recorded in mm.
+}
+\usage{data(bronzefilter)}
+\examples{
+ data(bronzefilter)
+ if(require(spatstat)) {
+ plot(bronzefilter, markscale=2)
+ }
+}
+\source{
+ R.\ Bernhardt (section image), H.\ Wendrock (coordinate measurement).
+ Adjusted, formatted and communicated by U.\ Hahn.
+}
+\references{
+ Bernhardt, R., Meyer-Olbersleben, F. and Kieback, B. (1997)
+ Fundamental investigation on the preparation of gradient structures
+ by sedimentation of different powder fractions under gravity.
+ \emph{Proc. of the 4th Int. Conf. On Composite Engineering,
+ July 6--12 1997, ICCE/4}, Hawaii, Ed. David Hui, 147--148.
+
+ Hahn U., Micheletti, A., Pohlink, R., Stoyan D. and Wendrock, H.(1999)
+ Stereological analysis and modelling of gradient structures.
+ \emph{Journal of Microscopy}, \bold{195}, 113--124.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/cells.Rd b/man/cells.Rd
new file mode 100755
index 0000000..a421c00
--- /dev/null
+++ b/man/cells.Rd
@@ -0,0 +1,39 @@
+\name{cells}
+\alias{cells}
+\docType{data}
+\title{
+ Biological Cells Point Pattern
+}
+\description{
+The data record the locations of the centres of 42 biological cells
+observed under optical microscopy in a histological section.
+The microscope field-of-view has been rescaled to the unit square.
+
+The data were recorded by F.H.C. Crick and B.D. Ripley,
+and analysed in Ripley (1977, 1981) and Diggle (1983).
+They are often used as a canonical example of an `ordered'
+point pattern.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of cell centres.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(cells)}
+\source{Crick and Ripley, see Ripley (1977)}
+\references{
+ Diggle, P.J. (1983)
+ \emph{Statistical analysis of spatial point patterns}.
+ Academic Press.
+
+ Ripley, B.D. (1977)
+ Modelling spatial patterns (with discussion).
+ \emph{Journal of the Royal Statistical Society, Series B}
+ \bold{39}, 172--212.
+
+ Ripley, B.D. (1981)
+ \emph{Spatial statistics}.
+ John Wiley and Sons.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/chicago.Rd b/man/chicago.Rd
new file mode 100755
index 0000000..e53ba3d
--- /dev/null
+++ b/man/chicago.Rd
@@ -0,0 +1,68 @@
+\name{chicago}
+\alias{chicago}
+\docType{data}
+\title{
+ Chicago Crime Data
+}
+\description{
+ This dataset is a record of spatial locations of crimes
+ reported in the period 25 April to 8 May 2002,
+ in an area of Chicago (Illinois, USA)
+ close to the University of Chicago.
+ The original crime map was published in the
+ Chicago Weekly News in 2002.
+
+ The data give the spatial location (street address) of each crime report,
+ and the type of crime. The type labels are interpreted as follows:
+ \tabular{ll}{
+ \code{assault} \tab battery/assault \cr
+ \code{burglary} \tab burglary \cr
+ \code{cartheft} \tab motor vehicle theft \cr
+ \code{damage} \tab criminal damage \cr
+ \code{robbery} \tab robbery \cr
+ \code{theft} \tab theft \cr
+ \code{trespass} \tab criminal trespass
+ }
+ All crimes occurred on or near a street. The data give the
+ coordinates of all streets in the survey area, and their connectivity.
+
+ The dataset \code{chicago} is an object of class \code{"lpp"}
+ representing a point pattern on a linear network.
+ See \code{\link[spatstat]{lpp}} for further information on the format.
+
+ These data were published and analysed in
+ Ang, Baddeley and Nair (2012).
+}
+\format{
+ Object of class \code{"lpp"}.
+ See \code{\link[spatstat]{lpp}}.
+}
+\usage{data(chicago)}
+\examples{
+data(chicago)
+ if(require(spatstat)) {
+plot(chicago)
+plot(as.linnet(chicago), main="Chicago Street Crimes",col="green")
+plot(as.ppp(chicago), add=TRUE, col="red", chars=c(16,2,22,17,24,15,6))
+ }
+}
+\source{
+ Chicago Weekly News, 2002.
+ Manually digitised by \adrian.
+}
+\references{
+ Ang, Q.W. (2010)
+ \emph{Statistical methodology for events on a network}.
+ Master's thesis, School of Mathematics and Statistics, University of
+ Western Australia.
+
+ Ang, Q.W., Baddeley, A. and Nair, G. (2012)
+ Geometrically corrected second-order analysis of
+ events on a linear network, with applications to
+ ecology and criminology.
+ \emph{Scandinavian Journal of Statistics} \bold{39}, 591--617.
+
+ Chicago Weekly News website: \url{www.chicagoweeklynews.com}
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/chorley.Rd b/man/chorley.Rd
new file mode 100755
index 0000000..9f1c246
--- /dev/null
+++ b/man/chorley.Rd
@@ -0,0 +1,106 @@
+\name{chorley}
+\alias{chorley}
+\alias{chorley.extra}
+\docType{data}
+\title{Chorley-Ribble Cancer Data}
+\description{
+ Spatial locations of cases of cancer of the larynx
+ and cancer of the lung, and the location of a disused industrial
+ incinerator. A marked point pattern.
+}
+\format{
+ The dataset \code{chorley} is
+ an object of class \code{"ppp"}
+ representing a marked point pattern.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of home address \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of home address \cr
+ \code{marks} \tab factor with levels \code{larynx} and \code{lung} \cr
+ \tab indicating whether this is a case of cancer of the larynx\cr
+ \tab or cancer of the lung.
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+
+ The dataset \code{chorley.extra} is a list with two components.
+ The first component \code{plotit} is a function which will
+ plot the data in a sensible fashion. The second
+ component \code{incin} is a list with entries \code{x} and \code{y}
+ giving the location of the industrial incinerator.
+
+ Coordinates are given in kilometres,
+ and the resolution is 100 metres (0.1 km)
+}
+\usage{data(chorley)}
+\examples{
+ chorley
+ if(require(spatstat)) {
+ summary(chorley)
+ chorley.extra$plotit()
+ }
+}
+\source{
+ Coordinates of cases were provided by the
+ Chorley and South Ribble Health Authority, and were
+ kindly supplied by Professor Peter Diggle.
+ Region boundary was digitised by \adrian, 2005, from
+ a photograph of an Ordnance Survey map.
+}
+\section{Notes}{
+ The data give the precise domicile addresses of new cases
+ of cancer of the larynx (58 cases)
+ and cancer of the lung (978 cases),
+ recorded in the Chorley and South Ribble Health Authority
+ of Lancashire (England) between 1974 and 1983.
+ The supplementary data give the location of a disused industrial
+ incinerator.
+
+ The data were first presented and analysed by Diggle (1990).
+ They have subsequently been analysed by Diggle and Rowlingson (1994)
+ and Baddeley et al. (2005).
+
+ The aim is to assess evidence for an increase in
+ the incidence of cancer of the larynx in the vicinity of the
+ now-disused industrial incinerator. The lung cancer cases serve as a
+ surrogate for the spatially-varying density of the susceptible
+ population.
+
+ The data are represented as a marked point pattern,
+ with the points giving the spatial location of each individual's home address
+ and the marks identifying whether each point is a case of
+ laryngeal cancer or lung cancer.
+
+ Coordinates are in kilometres, and the resolution is
+ 100 metres (0.1 km).
+
+ The dataset \code{chorley} has a polygonal window with 132 edges
+ which closely approximates the boundary of the Chorley and South
+ Ribble Health Authority.
+
+ Note that, due to the rounding of spatial coordinates,
+ the data contain duplicated points (two points at the
+ same location). To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+}
+\references{
+ Baddeley, A., Turner, R., \ifelse{latex}{\out{M\o ller}}{Moller}, J. and Hazelton, M. (2005)
+ Residual analysis for spatial point processes.
+ \emph{Journal of the Royal Statistical Society, Series B}
+ \bold{67}, 617--666.
+
+ Diggle, P. (1990) A point process modelling approach to
+ raised incidence of a rare phenomenon in the vicinity
+ of a prespecified point.
+ \emph{Journal of the Royal Statistical Soc. Series A}
+ \bold{153}, 349-362.
+
+ Diggle, P. and Rowlingson, B. (1994) A conditional approach
+ to point process modelling of elevated risk.
+ \emph{Journal of the Royal Statistical Soc. Series A}
+ \bold{157}, 433-440.
+
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/clmfires.Rd b/man/clmfires.Rd
new file mode 100755
index 0000000..a22f7de
--- /dev/null
+++ b/man/clmfires.Rd
@@ -0,0 +1,104 @@
+\name{clmfires}
+\alias{clmfires}
+\alias{clmfires.extra}
+\docType{data}
+\title{
+ Castilla-La Mancha Forest Fires
+}
+\description{
+ This dataset is a record of forest fires in the Castilla-La Mancha
+ region of Spain between 1998 and 2007. This region is approximately
+ 400 by 400 kilometres. The coordinates are recorded in kilometres.
+
+ The dataset \code{clmfires} is a point pattern (object of class
+ \code{"ppp"}) containing the spatial coordinates of each fire,
+ with marks containing information about each fire. There are 4
+ columns of marks:
+ \tabular{ll}{
+ \code{cause} \tab cause of fire (see below) \cr
+ \code{burnt.area} \tab total area burned, in hectares \cr
+ \code{date} \tab the date of fire, as a value of class \code{Date} \cr
+ \code{julian.date} \tab number of days elapsed since 1 January 1998 \cr
+ }
+ The \code{cause} of the fire is a factor with the levels
+ \code{lightning}, \code{accident} (for accidents or negligence),
+ \code{intentional} (for intentionally started fires) and
+ \code{other} (for other causes including unknown cause).
+
+ The format of \code{date} is \dQuote{Year-month-day}, e.g.
+ \dQuote{2005-07-14} means 14 July, 2005.
+
+ The accompanying dataset \code{clmfires.extra} is a list
+ of two items \code{clmcov100} and \code{clmcov200} containing covariate
+ information for the entire Castilla-La Mancha region. Each
+ of these two elements is a list of four images (objects of
+ class \code{"im"}) named \code{elevation}, \code{orientation},
+ \code{slope} and \code{landuse}. The \code{landuse} image is
+ factor-valued with the factor having levels \code{urban},
+ \code{farm} (for farms or orchards), \code{meadow},
+ \code{denseforest} (for dense forest), \code{conifer} (for conifer
+ forest or plantation), \code{mixedforest}, \code{grassland},
+ \code{bush}, \code{scrub} and \code{artifgreen} for artificial
+ greens such as golf courses.
+
+ These images (effectively) provide values for the four
+ covariates at every location in the study area. The images in
+ \code{clmcov100} are 100 by 100 pixels in size, while those in
+ \code{clmcov200} are 200 by 200 pixels. For easy handling,
+ \code{clmcov100} and \code{clmcov200} also belong to the
+ class \code{"listof"} so that they can be plotted and printed
+ immediately.
+}
+\format{
+ \code{clmfires} is a marked point pattern (object of class \code{"ppp"}).
+ See \code{\link[spatstat]{ppp.object}}.
+
+ \code{clmfires.extra} is a list with two components, named
+ \code{clmcov100} and \code{clmcov200}, which are lists of pixel images
+ (objects of class \code{"im"}).
+}
+\section{Remark}{
+The precision with which the coordinates of the locations of the
+fires changed between 2003 and 2004. From 1998 to 2003 many of
+the locations were recorded as the centroid of the corresponding
+\dQuote{district unit}; the rest were recorded as exact UTM
+coordinates of the centroids of the fires. In 2004 the system
+changed and the exact UTM coordinates of the centroids of the fires
+were used for \emph{all} fires. There is thus a strongly apparent
+\dQuote{gridlike} quality to the fire locations for the years 1998
+to 2003.
+
+There is however no actual duplication of points in the 1998 to 2003
+patterns due to \dQuote{jittering} having been applied in order to
+avoid such duplication. It is not clear just \emph{how} the fire
+locations were jittered. It seems unlikely that the jittering was
+done using the \code{jitter()} function from \code{R} or the
+\pkg{spatstat} function \code{\link[spatstat]{rjitter}}.
+
+Of course there are many sets of points which are \emph{virtually}
+identical, being separated by distances induced by the jittering.
+Typically these distances are of the order of 40 metres which
+is unlikely to be meaningful on the scale at which forest fires
+are observed.
+
+Caution should therefore be exercised in any analyses of the patterns
+for the years 1998 to 2003.
+}
+
+\usage{data(clmfires)}
+\examples{
+ if(require(spatstat)) {
+plot(clmfires, which.marks="cause", cols=2:5, cex=0.25)
+plot(clmfires.extra$clmcov100)
+# Split the clmfires pattern by year and plot the first and last years:
+yr <- factor(format(marks(clmfires)$date,format="\%Y"))
+X <- split(clmfires,f=yr)
+fAl <- c("1998","2007")
+plot(X[fAl],use.marks=FALSE,main.panel=fAl,main="")
+ }
+}
+\source{
+ Professor Jorge Mateu.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/copper.Rd b/man/copper.Rd
new file mode 100755
index 0000000..0e20dbb
--- /dev/null
+++ b/man/copper.Rd
@@ -0,0 +1,122 @@
+\name{copper}
+\alias{copper}
+\docType{data}
+\title{
+ Berman-Huntington points and lines data
+}
+\description{
+ These data come from an intensive geological survey of
+ a 70 x 158 km region in central Queensland, Australia.
+ They consist of 67 points representing copper ore deposits,
+ and 146 line segments representing geological `lineaments'.
+ Lineaments are linear features, visible on a satellite image,
+ that are believed to consist largely of geological faults (Berman, 1986,
+ p. 55).
+ It would be of great interest to predict the occurrence of copper deposits
+ from the lineament pattern, since the latter can easily be observed on
+ satellite images.
+
+ These data were introduced and analysed by Berman (1986).
+ They have also been studied by Berman and Diggle (1989),
+ Berman and Turner (1992),
+ Baddeley and Turner (2000, 2005), Foxall and Baddeley (2002)
+ and Baddeley et al (2005).
+
+ Many analyses have been performed on the southern half of the data only.
+ This subset is also provided.
+}
+\format{
+ \code{copper} is a list with the following entries:
+ \describe{
+ \item{Points}{a point pattern (object of class \code{"ppp"})
+ representing the full point pattern of copper deposits.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+ }
+ \item{Lines}{a line segment pattern (object of class \code{"psp"})
+ representing the lineaments in the full dataset.
+ See \code{\link[spatstat]{psp.object}} for details of the format.
+ }
+ \item{SouthWindow}{the window delineating the southern half of
+ the study region. An object of class \code{"owin"}.
+ }
+ \item{SouthPoints}{the point pattern of copper deposits in the
+ southern half of the study region. An object of class
+ \code{"ppp"}.
+ }
+ \item{SouthLines}{the line segment pattern of the lineaments in the
+ southern half of the study region. An object of class \code{"psp"}.
+ }
+ }
+}
+\usage{data(copper)}
+\examples{
+
+ data(copper)
+
+ if(require(spatstat)) {
+
+ # Plot full dataset
+
+ plot(copper$Points)
+ plot(copper$Lines, add=TRUE)
+
+ # Plot southern half of data
+ plot(copper$SouthPoints)
+ plot(copper$SouthLines, add=TRUE)
+
+ \dontrun{
+ Z <- distmap(copper$SouthLines)
+ plot(Z)
+ X <- copper$SouthPoints
+ ppm(X, ~D, covariates=list(D=Z))
+ }
+ }
+}
+\source{
+ Dr Jonathan Huntington, CSIRO Earth Science and Resource Engineering,
+ Sydney, Australia.
+ Coordinates kindly provided by Dr. Mark Berman
+ and Dr. Andy Green, CSIRO, Sydney, Australia.
+}
+\references{
+Baddeley, A. and Turner, R. (2000)
+Practical maximum pseudolikelihood for spatial point patterns.
+\emph{Australian and New Zealand Journal of Statistics}
+\bold{42}, 283--322.
+
+Baddeley, A., Turner, R., \ifelse{latex}{\out{M\o ller}}{Moller}, J. and Hazelton, M. (2005)
+Residual analysis for spatial point processes.
+\emph{Journal of the Royal Statistical Society, Series B}
+\bold{67}, 617--666.
+
+Baddeley, A. and Turner, R. (2005)
+Modelling spatial point patterns in R.
+In: A. Baddeley, P. Gregori, J. Mateu, R. Stoica, and D. Stoyan,
+editors, \emph{Case Studies in Spatial Point Pattern Modelling},
+Lecture Notes in Statistics number 185. Pages 23--74.
+Springer-Verlag, New York, 2006.
+ISBN: 0-387-28311-0.
+
+Berman, M. (1986).
+Testing for spatial association between a point process and another
+ stochastic process.
+\emph{Applied Statistics} \bold{35}, 54--62.
+
+Berman, M. and Diggle, P.J. (1989)
+Estimating Weighted Integrals of the Second-order Intensity of a
+Spatial Point Process.
+\emph{Journal of the Royal Statistical Society, series B}
+\bold{51}, 81--92.
+
+Berman, M. and Turner, T.R. (1992)
+Approximating point process likelihoods with GLIM.
+\emph{Applied Statistics} \bold{41}, 31--38.
+
+Foxall, R. and Baddeley, A. (2002)
+Nonparametric measures of association between a
+spatial point process and a random set, with
+geological applications. \emph{Applied Statistics} \bold{51}, 165--182.
+
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/copyExampleFiles.Rd b/man/copyExampleFiles.Rd
new file mode 100755
index 0000000..e569f4e
--- /dev/null
+++ b/man/copyExampleFiles.Rd
@@ -0,0 +1,48 @@
+\name{copyExampleFiles}
+\alias{copyExampleFiles}
+\title{
+ Copy Data Files for Example
+}
+\description{
+ This command copies several data files to
+ a folder (directory) chosen by the user,
+ so that they can be used for a practice example.
+}
+\usage{
+copyExampleFiles(which, folder = getwd())
+}
+\arguments{
+ \item{which}{
+ Character string name (partially matched)
+ of one of the datasets installed in \code{spatstat} for which
+ the original data files are provided.
+ If \code{which} is missing, a list of available options is printed.
+ }
+ \item{folder}{
+ Character string path name of a folder (directory) in which the
+ files will be placed. Defaults to the current working directory.
+ }
+}
+\details{
+ The original text files containing data for the selected
+ dataset are copied to the chosen folder.
+
+ This is part of an exercise described in Chapter 3 of
+ Baddeley, Rubak and Turner (2015).
+}
+\references{
+ Baddeley, A., Rubak, E. and Turner, R. (2015)
+ \emph{Spatial Point Patterns: Methodology and Applications with R}.
+ Chapman and Hall/CRC Press.
+}
+\author{
+ \spatstatAuthors.
+}
+\examples{
+ copyExampleFiles()
+}
+\seealso{
+ \code{\link[spatstat.data]{vesicles}},
+ \code{\link[spatstat.data]{finpines}}
+}
+\keyword{spatial}
diff --git a/man/demohyper.Rd b/man/demohyper.Rd
new file mode 100755
index 0000000..a51cb0d
--- /dev/null
+++ b/man/demohyper.Rd
@@ -0,0 +1,44 @@
+\name{demohyper}
+\alias{demohyper}
+\docType{data}
+\title{
+ Demonstration Example of Hyperframe of Spatial Data
+}
+\description{
+ This is an artificially constructed example of a
+ hyperframe of spatial data. The data could have been obtained
+ from an experiment in which there are two groups of
+ experimental units, the response from each unit
+ is a point pattern \code{Points}, and for each unit there is explanatory
+ data in the form of a pixel image \code{Image}.
+}
+\usage{data(demohyper)}
+\format{
+ A \code{\link[spatstat]{hyperframe}} with 3 rows and 3 columns:
+ \describe{
+ \item{Points}{
+ List of spatial point patterns
+ (objects of class \code{"ppp"})
+ serving as the responses in an experiment.
+ }
+ \item{Image}{
+ List of images (objects of class \code{"im"})
+ serving as explanatory variables.
+ }
+ \item{Group}{
+ Factor with two levels \code{a} and \code{b}
+ serving as an explanatory variable.
+ }
+ }
+}
+\source{
+ Artificially generated by \adrian.
+}
+\examples{
+ if(require(spatstat)) {
+ plot(demohyper, quote({ plot(Image, main=""); plot(Points, add=TRUE) }),
+ parargs=list(mar=rep(1,4)))
+ mppm(Points ~ Group/Image, data=demohyper)
+ }
+}
+\keyword{datasets}
diff --git a/man/demopat.Rd b/man/demopat.Rd
new file mode 100755
index 0000000..eec23c5
--- /dev/null
+++ b/man/demopat.Rd
@@ -0,0 +1,26 @@
+\name{demopat}
+\alias{demopat}
+\docType{data}
+\title{
+ Artificial Data Point Pattern
+}
+\description{
+ This is an artificial dataset, for use in testing and demonstrating the
+ capabilities of the \code{spatstat} package.
+ It is a multitype point pattern in an irregular polygonal window.
+ There are two types of points. The window contains a polygonal hole.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(demopat)}
+\source{\adrian}
+\keyword{datasets}
+\keyword{spatial}
+
+
+
diff --git a/man/dendrite.Rd b/man/dendrite.Rd
new file mode 100755
index 0000000..1452c7a
--- /dev/null
+++ b/man/dendrite.Rd
@@ -0,0 +1,48 @@
+\name{dendrite}
+\alias{dendrite}
+\docType{data}
+\title{
+ Dendritic Spines Data
+}
+\description{
+ Dendrites are branching filaments which extend from the
+ main body of a neuron (nerve cell) to propagate electrochemical
+ signals. Spines are small protrusions on the dendrites.
+
+ This dataset gives the locations of 566 spines
+ observed on one branch of the dendritic tree of a rat neuron.
+ The spines are classified according to their shape into three types:
+ mushroom, stubby or thin.
+
+ The data have been analysed in Jammalamadaka et al (2013) and
+ Baddeley et al (2014). Please cite these papers and
+ acknowledge the Kosik Lab, UC Santa Barbara, in any use of the data.
+}
+\usage{data("dendrite")}
+\format{
+ Object of class \code{"lpp"}.
+ See \code{\link[spatstat]{lpp}}.
+}
+\source{
+ Kosik Lab, UC Santa Barbara (Dr Kenneth Kosik, Dr Sourav Banerjee).
+ Formatted for \code{spatstat} by Dr Aruna Jammalamadaka.
+}
+\references{
+Baddeley, A., Jammalamadaka, A. and Nair, G. (2014)
+Multitype point process analysis of spines on the
+dendrite network of a neuron.
+\emph{Applied Statistics (Journal of the Royal Statistical
+ Society, Series C)}, In press.
+\code{doi: 10.1111/rssc.12054}
+
+Jammalamadaka, A., Banerjee, S., Manjunath, B.S. and Kosik, K. (2013)
+Statistical Analysis of Dendritic Spine Distributions in
+Rat Hippocampal Cultures.
+\emph{BMC Bioinformatics} \bold{14}, 287.
+}
+\examples{
+ if(require(spatstat)) {
+plot(dendrite,leg.side="bottom", main="", cex=0.75, cols=2:4)
+ }
+}
+\keyword{datasets}
diff --git a/man/finpines.Rd b/man/finpines.Rd
new file mode 100755
index 0000000..d431ef7
--- /dev/null
+++ b/man/finpines.Rd
@@ -0,0 +1,69 @@
+\name{finpines}
+\alias{finpines}
+\docType{data}
+\title{
+ Pine saplings in Finland.
+}
+\description{
+ The data record the locations of 126 pine saplings
+ in a Finnish forest, their heights and their diameters.
+
+ The dataset \code{finpines} is a marked point pattern
+ containing the locations of the saplings marked by their heights
+ and their diameters.
+
+ Sapling locations are given in metres (to six significant digits);
+ heights are in metres (rounded to the nearest 0.1 metre,
+ except in one case to the nearest 0.05 metres);
+ diameters are in centimetres (rounded to the nearest centimetre).
+
+ The data were recorded by Professor Seppo Kellomaki, Faculty of
+ Forestry, University of Joensuu, Finland,
+ and subsequently massaged by Professor Antti Penttinen,
+ Department of Statistics, University of Jyv\"askyl\"a, Finland.
+
+ Originally the point locations were observed in polar coordinates with
+ rather poor angular precision. Hence the coordinates are imprecise for large
+ radius because of rounding errors: indeed the alignments can be observed by
+ eye.
+
+ The data were manipulated by Prof Penttinen by making small angular
+ perturbations at random. After this transformation, the original data
+ (in a circular plot) were clipped to a square window, for convenience.
+
+ Professor Penttinen emphasises that the data were intended only
+ for initial experimentation. They have some strange features.
+ For example, if the height is less than 1.3 metres then the diameter
+ can be uncertain. Also there are some very close pairs of points.
+ Some pairs of trees (namely (58,59), (78,79), (96,97) and (102,103))
+ violate the requirement that the interpoint distance should be
+ greater than half the sum of their diameters.
+
+ These data have subsequently been analysed by Van Lieshout (2004).
+}
+\format{
+ Object of class \code{"ppp"}
+ representing the point pattern of sapling locations marked by
+ their heights and diameters.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(finpines)}
+\examples{
+ data(finpines)
+ if(require(spatstat)) {
+ plot(unmark(finpines), main="Finnish pines: locations")
+ plot(finpines, which.marks="height", main="heights")
+ plot(finpines, which.marks="diameter", main="diameters")
+ plot(finpines, which.marks="diameter",
+ main="diameters to scale", markscale=1/200)
+ }
+}
+\source{Prof Antti Penttinen}
+\references{
+ Van Lieshout, M.N.M. (2004)
+ A J-function for marked point patterns.
+ Research Report PNA-R0404, June 2004.
+ Centrum voor Wiskunde en Informatica (CWI), Amsterdam, 2004.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/flu.Rd b/man/flu.Rd
new file mode 100755
index 0000000..9792b28
--- /dev/null
+++ b/man/flu.Rd
@@ -0,0 +1,110 @@
+\name{flu}
+\alias{flu}
+\docType{data}
+\title{
+ Influenza Virus Proteins
+}
+\description{
+ Replicated spatial point patterns giving the locations of two
+ different virus proteins on the membranes of cells infected with
+ influenza virus.
+}
+\usage{data(flu)}
+\format{
+ A \code{\link[spatstat]{hyperframe}} with 41 rows and four columns:
+ \describe{
+ \item{pattern}{
+ List of spatial point patterns
+ (objects of class \code{"ppp"})
+ with points of two types, identifying the locations of
+ two different proteins on a membrane sheet.
+ }
+ \item{virustype}{
+ Factor identifying whether the infecting virus was
+ the wild type (\code{wt}) or mutant (\code{mut1}).
+ }
+ \item{stain}{
+ Factor identifying whether the membrane sheet was stained
+ for the proteins \emph{M2} and \emph{M1}
+ (\code{stain="M2-M1"})
+ or stained for the proteins \emph{M2} and \emph{HA}
+ (\code{stain="M2-HA"}).
+ }
+ \item{frameid}{
+ Integer. Serial number of the microscope frame
+ in the original experiment. Frame identifier is not unique
+ across different values of \code{virustype} and \code{stain}.
+ }
+ }
+ The row names of the hyperframe can be used as succinct labels
+ in plots.
+}
+\details{
+ The data consist of 41 spatial point patterns, each
+ giving the locations of two different virus proteins
+ on the membranes of cells infected with influenza virus.
+
+ Chen et al (2008) conducted the experiment and used spatial analysis
+ to establish evidence for an interaction between the influenza virus
+ proteins M1 and M2 that is important for the study of viral replication.
+
+ Canine kidney cells were infected with human influenza, Udorn strain,
+ either the wild type or a mutant which encodes a defective M2 protein.
+ At twelve hours post-infection, membrane sheets were prepared
+ and stained for viral proteins, using two antibodies conjugated to
+ gold particles of two sizes (6 nanometre and 12 nanometre diameter)
+ enabling localisation of two different proteins on each sheet.
+ The 6 nm particles were stained for M2 (ion channel protein),
+ while the 12 nm particles were stained either for M1 (matrix protein)
+ or for HA (hemagglutinin). Membrane sheets were visualised in
+ electron microscopy.
+
+ Experimental technique and spatial analysis of the membranes
+ stained for M2 and M1 is reported in Chen et al (2008).
+ Analysis of the membranes stained for
+ M2 and HA is reported in Rossman et al (2010).
+ The M2-HA data shows a stronger association
+ between the two proteins which has also been observed biochemically
+ and functionally (Rossman et al, 2010).
+
+ The dataset \code{flu} is a \code{\link[spatstat]{hyperframe}}
+ with one row for each membrane sheet. The column named \code{pattern}
+ contains the spatial point patterns of gold particle locations,
+ with two types of points (either \code{M1} and \code{M2} or
+ \code{HA} and \code{M2}). The column named \code{virustype}
+ is a factor identifying the virus: either wild type \code{wt}
+ or mutant \code{mut1}. The column named \code{stain} is a factor
+ identifying whether the membrane was stained for
+ M1 and M2 (\code{stain="M2-M1"}) or stained for HA and M2
+ (\code{stain="M2-HA"}).
+ The row names of the hyperframe are a succinct summary of
+ the experimental conditions and can be used as labels
+ in plots. See the Examples.
+}
+\source{
+ Data generously provided by Dr G.P. Leser and Dr R.A. Lamb.
+ Please cite Chen et al (2008) in any use of these data.
+}
+\references{
+ Chen, B.J., Leser, G.P., Jackson, D. and Lamb, R.A. (2008)
+ The influenza virus M2 protein cytoplasmic tail interacts with the M1 protein
+ and influences virus assembly at the site of virus budding.
+ \emph{Journal of Virology} \bold{82}, 10059--10070.
+
+ Rossman, J.S., Jing, X.H., Leser, G.P. and Lamb, R.A. (2010)
+ Influenza virus M2 protein mediates ESCRT-independent membrane scission
+ \emph{Cell} \bold{142}, 902--913.
+}
+\examples{
+data(flu)
+ if(require(spatstat)) {
+flu
+Y <- flu$pattern[10]
+Y <- flu[10, 1, drop=TRUE]
+wildM1 <- with(flu, virustype == "wt" & stain == "M2-M1")
+plot(flu[wildM1, 1, drop=TRUE],
+ main=c("flu data", "wild type virus, M2-M1 stain"),
+ pch=c(3,16), cex=0.4, cols=2:3)
+ }
+}
+\keyword{datasets}
diff --git a/man/ganglia.Rd b/man/ganglia.Rd
new file mode 100755
index 0000000..973f135
--- /dev/null
+++ b/man/ganglia.Rd
@@ -0,0 +1,71 @@
+\name{ganglia}
+\alias{ganglia}
+\docType{data}
+\title{Beta Ganglion Cells in Cat Retina, Old Version}
+\description{
+ Point pattern of retinal ganglion cells identified as `on' or `off'.
+ A marked point pattern.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of cell locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of cell \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of cell \cr
+ \code{marks} \tab factor with levels \code{off} and \code{on} \cr
+ \tab indicating ``off'' and ``on'' cells
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(ganglia)}
+\source{W\"assle et al (1981), data supplied by Marie-Colette van
+ Lieshout and attributed to Peter Diggle}
+\section{Notes}{
+ \bold{Important: these data are INCORRECT. See below.}
+
+ The data represent a pattern of beta-type ganglion cells in the
+ retina of a cat recorded in Figure 6(a) of W\"assle et al. (1981).
+
+ The pattern was first analysed by W\"assle et al (1981) using
+ nearest neighbour distances. The data used in their analysis
+ are not available.
+
+ The present dataset \code{\link[spatstat.data]{ganglia}} was
+ scanned from Figure 6(a) of W\"assle et al (1981)
+ in the early 1990's, but we have no further information.
+ This dataset is the one analysed by Van Lieshout and Baddeley (1999)
+ using multitype J functions, and by Stoyan (1995) using second
+ order methods (pair correlation and mark correlation).
+
+ It has now been discovered that these data are \bold{incorrect}.
+ They are not faithful to the scale in Figure 6 of W\"assle et al (1981),
+ and they contain some scanning errors.
+ Hence they should not be used to address the original scientific question.
+ They have been retained only for comparison with other analyses
+ in the statistical literature.
+
+ A new, corrected dataset, scanned from the original microscope image,
+ has been provided under the name \code{\link[spatstat.data]{betacells}}. Use that
+ dataset for any further study.
+}
+\section{Warnings}{
+ These data are incorrect.
+ Use the new corrected dataset \code{\link[spatstat.data]{betacells}}.
+}
+\references{
+ Stoyan, D. (1995) Personal communication.
+
+ Van Lieshout, M.N.M. and Baddeley, A.J. (1999) Indices of
+ dependence between types in multivariate point patterns.
+ \emph{Scandinavian Journal of Statistics} \bold{26}, 511--532.
+
+ W\"assle, H., Boycott, B. B. & Illing, R.-B. (1981). Morphology
+ and mosaic of on- and off-beta cells in the cat retina and some
+ functional considerations. \emph{Proc. Roy. Soc. London Ser. B}
+ \bold{212}, 177--195.
+}
+\keyword{datasets}
+\keyword{spatial}
+
+
diff --git a/man/gordon.Rd b/man/gordon.Rd
new file mode 100755
index 0000000..5f879b0
--- /dev/null
+++ b/man/gordon.Rd
@@ -0,0 +1,37 @@
+\name{gordon}
+\alias{gordon}
+\docType{data}
+\title{
+ People in Gordon Square
+}
+\description{
+ This dataset records the location of
+ people sitting on a grass patch in Gordon Square, London,
+ at 3pm on a sunny afternoon.
+
+ The dataset \code{gordon} is a point pattern
+ (object of class \code{"ppp"}) containing the spatial coordinates
+ of each person.
+
+ The grass patch is an irregular polygon with two holes.
+
+ Coordinates are given in metres.
+}
+\usage{data(gordon)}
+\examples{
+data(gordon)
+ if(require(spatstat)) {
+plot(gordon)
+ }
+}
+\source{
+ Andrew Bevan, University College London.
+}
+\references{
+ Baddeley, A., Turner, R., Mateu, J. and Bevan, A. (2013)
+ Hybrids of Gibbs point process models and their implementation.
+ \emph{Journal of Statistical Software} \bold{55}:11, 1--43.
+ \url{http://www.jstatsoft.org/v55/i11/}
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/gorillas.Rd b/man/gorillas.Rd
new file mode 100755
index 0000000..55a5e64
--- /dev/null
+++ b/man/gorillas.Rd
@@ -0,0 +1,153 @@
+\name{gorillas}
+\alias{gorillas}
+\alias{gorillas.extra}
+\docType{data}
+\title{
+ Gorilla Nesting Sites
+}
+\description{
+ Locations of nesting sites of gorillas, and associated covariates,
+ in a National Park in Cameroon.
+}
+\usage{data(gorillas)}
+\format{
+ \code{gorillas} is a marked point pattern (object
+ of class \code{"ppp"}) representing nest site locations.
+
+ \code{gorillas.extra} is a named list of 7 pixel images (objects of
+ class \code{"im"}) containing spatial covariates.
+ It also belongs to the class \code{"listof"}.
+
+ All spatial coordinates are in metres.
+ The coordinate reference system is \code{WGS_84_UTM_Zone_32N}.
+}
+\details{
+ These data come from a study of gorillas in the Kagwene Gorilla Sanctuary,
+ Cameroon, by the Wildlife Conservation Society
+ Takamanda-Mone Landscape Project (WCS-TMLP). A detailed description
+ and analysis of the data is reported in Funwi-Gabga and Mateu (2012).
+
+ The dataset \code{gorillas} is a marked point pattern
+ (object of class \code{"ppp"})
+ giving the spatial locations of 647 nesting sites of gorilla groups
+ observed in the sanctuary over time.
+ Locations are given as UTM (Zone 32N) coordinates in metres.
+ The observation window is the boundary of the sanctuary, represented
+ as a polygon. Marks attached to the points are:
+
+ \describe{
+ \item{group}{Identifier of the gorilla group
+ that constructed the nest site:
+ a categorical variable with values \code{major} or \code{minor}.
+ }
+ \item{season}{Season in which data were collected:
+ categorical, either \code{rainy} or \code{dry}.
+ }
+ \item{date}{
+ Day of observation. A value of class \code{"Date"}.
+ }
+ }
+ Note that the data contain duplicated points (two points at the
+ same location). To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+
+ The accompanying dataset \code{gorillas.extra} contains
+ spatial covariate information. It is a named list containing
+ seven pixel images (objects of class \code{"im"}) giving the values of
+ seven covariates over the study region. It also belongs
+ to the class \code{"listof"} so that it can be plotted.
+ The component images are:
+
+ \describe{
+ \item{aspect}{
+ Compass direction of the terrain slope.
+ Categorical, with levels
+ \code{N},
+ \code{NE},
+ \code{E},
+ \code{SE},
+ \code{S},
+ \code{SW},
+ \code{W} and
+ \code{NW}.
+ }
+ \item{elevation}{
+ Digital elevation of terrain, in metres.
+ }
+ \item{heat}{
+ Heat Load Index at each point on the surface (Beer's aspect),
+ discretised. Categorical with values \code{Warmest}
+ (Beer's aspect between 0 and 0.999),
+ \code{Moderate} (Beer's aspect between 1 and 1.999),
+ \code{Coolest} (Beer's aspect equals 2).
+ }
+ \item{slopeangle}{
+ Terrain slope, in degrees.
+ }
+ \item{slopetype}{
+ Type of slope.
+ Categorical, with values
+ \code{Valley}, \code{Toe} (toe slope), \code{Flat},
+ \code{Midslope}, \code{Upper} and \code{Ridge}.
+ }
+ \item{vegetation}{
+ Vegetation or cover type.
+ Categorical, with values
+ \code{Disturbed} (highly disturbed forest), \code{Colonising}
+ (colonising forest), \code{Grassland} (savannah),
+ \code{Primary} (primary forest), \code{Secondary} (secondary forest), and
+ \code{Transition} (transitional vegetation).
+ }
+ \item{waterdist}{
+ Euclidean distance from nearest water body, in metres.
+ }
+ }
+
+ For further information see Funwi-Gabga and Mateu (2012).
+}
+\section{Raw Data}{
+ For demonstration and training purposes,
+ the raw data file for the \code{vegetation} covariate is
+ also provided in the \pkg{spatstat} package installation,
+ as the file \code{vegetation.asc} in the folder \code{rawdata/gorillas}.
+ Use \code{\link[base]{system.file}} to obtain the file path:
+ \code{system.file("rawdata/gorillas/vegetation.asc", package="spatstat")}.
+ This is a text file in the simple ASCII file format of the geospatial
+ library \code{GDAL}. The file can be read by the function
+ \code{readGDAL} in the \pkg{rgdal} package, or alternatively
+ read directly using \code{\link[base]{scan}}.
+}
+\source{
+ Field data collector: Wildlife Conservation Society Takamanda-Mone
+ Landscape Project (WCS-TMLP).
+ \emph{Please acknowledge WCS-TMLP in any use of these data.}
+
+ Data kindly provided by
+ Funwi-Gabga Neba, Data Coordinator of A.P.E.S.
+ Database Project, Department of Primatology,
+ Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
+
+ The collaboration of Prof Jorge Mateu, Universitat Jaume I, Castellon, Spain
+ is gratefully acknowledged.
+}
+\references{
+ Funwi-Gabga, N. (2008)
+ \emph{A pastoralist survey and fire impact assessment
+ in the Kagwene Gorilla Sanctuary, Cameroon}. M.Sc. thesis,
+ Geology and Environmental Science, University of Buea, Cameroon.
+
+ Funwi-Gabga, N. and Mateu, J. (2012)
+ Understanding the nesting spatial behaviour of gorillas
+ in the Kagwene Sanctuary, Cameroon.
+ \emph{Stochastic Environmental Research and Risk Assessment}
+ \bold{26} (6), 793--811.
+}
+\examples{
+ if(require(spatstat)) {
+ summary(gorillas)
+ plot(gorillas)
+ plot(gorillas.extra)
+ }
+}
+\keyword{datasets}
diff --git a/man/hamster.Rd b/man/hamster.Rd
new file mode 100755
index 0000000..7121dd7
--- /dev/null
+++ b/man/hamster.Rd
@@ -0,0 +1,48 @@
+\name{hamster}
+\alias{hamster}
+\docType{data}
+\title{Aherne's hamster tumour data}
+\description{
+ Point pattern of cell nuclei in hamster kidney, each nucleus classified as
+ either `dividing' or `pyknotic'.
+ A multitype point pattern.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of cell locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of cell \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of cell \cr
+ \code{marks} \tab factor with levels \code{"dividing"}
+ and \code{"pyknotic"}.
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+}
+\usage{data(hamster)}
+\source{Dr W. A. Aherne, Department of Pathology, University of
+ Newcastle-upon-Tyne, UK. Data supplied by Prof. Peter Diggle}
+\section{Notes}{
+ These data were presented and analysed by Diggle (1983, section 7.3).
+
+ The data give the positions of the centres of the nuclei of certain
+ cells in a histological
+ section of tissue from a laboratory-induced metastasising lymphoma
+ in the kidney of a hamster.
+
+ The nuclei are classified as either
+ "pyknotic" (corresponding to dying cells) or "dividing" (corresponding
+ to cells arrested in metaphase, i.e. in the act of dividing). The
+ background void is occupied by unrecorded, interphase cells in
+ relatively large numbers.
+
+ The sampling window is a square, originally about 0.25 mm square
+ in real units, which has been rescaled to the unit square.
+}
+\references{
+ Diggle, P.J. (1983)
+ \emph{Statistical analysis of spatial point patterns}.
+ Academic Press.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/heather.Rd b/man/heather.Rd
new file mode 100755
index 0000000..5e8d463
--- /dev/null
+++ b/man/heather.Rd
@@ -0,0 +1,109 @@
+\name{heather}
+\alias{heather}
+\docType{data}
+\title{Diggle's Heather Data}
+\description{
+ The spatial mosaic of vegetation of the heather plant
+ (\emph{Calluna vulgaris}) recorded in a 10 by 20 metre
+ sampling plot in Sweden.
+}
+\format{
+ A list with three entries, representing the same data at
+ different spatial resolutions:
+ \tabular{ll}{
+ \code{coarse} \tab original heather data, 100 by 200 pixels \cr
+ \code{medium} \tab current heather data, 256 by 512 pixels \cr
+ \code{fine} \tab finest resolution data, 778 by 1570 pixels
+ }
+ Each of these entries is an object of class \code{"owin"}
+ containing a binary pixel mask.
+}
+\usage{data(heather)}
+\source{Peter Diggle}
+\section{Notes on data}{
+ These data record the spatial mosaic of vegetation
+ of the heather plant (\emph{Calluna vulgaris}) in a 10 by 20 metre
+ sampling plot near \ifelse{latex}{\out{J{\"a}dra{\aa}s}}{Jadraas}, Sweden.
+ They were recorded and first analysed by Diggle(1981).
+
+ The dataset \code{heather} contains three different versions of the data
+ that have been analysed by different writers over the decades.
+
+ \describe{
+ \item{coarse:}{
+ Data as originally digitised by Diggle in 1983
+ at 100 by 200 pixels resolution (i.e. 10 pixels = 1 metre).
+
+ These data were entered by hand in the form of a
+ run-length encoding (original file no longer available)
+ and translated by a program into a 100 by 200 pixel binary image.
+
+ There are known to be some errors in the image
+ which arise from errors in counting the run-length
+ so that occasionally there will be an unexpected 'spike'
+ on one single column.
+ }
+ \item{fine:}{
+ A fine scale digitisation of the original map,
+ prepared by CWI (Centre for Computer Science, Amsterdam,
+ Netherlands) in 1994.
+
+ The original hand-drawn map
+ was scanned by \adrian, and processed
+ by Chris Jonker, Henk Heijmans and \adrian
+ to yield a clean binary image of 778 by 1570 pixels resolution.
+ }
+ \item{medium:}{
+ The version of the heather data currently supplied on
+ Professor Diggle's website. This is a 256 by 512 pixel image.
+ The method used to create this image is not stated.
+ }
+ }
+}
+\section{History of analysis of data}{
+ The data were recorded, presented and analysed by Diggle (1983).
+ He proposed a Boolean model consisting of discs of random size
+ with centres generated by of a Poisson point process.
+
+ Renshaw and Ford (1983) reported that spectral analysis of the data
+ suggested the presence of strong row and column effects. However, this
+ may have been attributable to errors in the run-length encoding
+ of the original data.
+
+ Hall (1985) and Hall (1988, pp 301-318) took a bootstrap approach.
+
+ Ripley (1988, pp. 121-122, 131-135] used opening and closing functions
+ to argue that a Boolean model of discs is inappropriate.
+
+ Cressie (1991, pp. 763-770) tried a more general Boolean model.
+}
+\references{
+ Cressie, N.A.C. (1991)
+ \emph{Statistics for Spatial Data}.
+ John Wiley and Sons, New York.
+
+ Diggle, P.J. (1981)
+ Binary mosaics and the spatial pattern of heather.
+ \emph{Biometrics} \bold{37}, 531-539.
+
+ Hall, P. (1985)
+ Resampling a coverage pattern.
+ \emph{Stochastic Processes and their Applications}
+ \bold{20} 231-246.
+
+ Hall, P. (1988)
+ \emph{An introduction to the theory of coverage processes}.
+ John Wiley and Sons, New York.
+
+ Renshaw, E. and Ford, E.D. (1983)
+ The interpretation of process from pattern using
+ two-dimensional spectral analysis: Methods and
+ problems of interpretation. \emph{Applied Statistics} \bold{32} 51-63.
+
+ Ripley, B.D. (1988)
+ \emph{Statistical Inference for Spatial Processes}.
+ Cambridge University Press.
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/humberside.Rd b/man/humberside.Rd
new file mode 100755
index 0000000..8c02659
--- /dev/null
+++ b/man/humberside.Rd
@@ -0,0 +1,88 @@
+\name{humberside}
+\alias{humberside}
+\alias{humberside.convex}
+\docType{data}
+\title{Humberside Data on Childhood Leukaemia and Lymphoma}
+\description{
+ Spatial locations of cases of childhood leukaemia
+ and lymphoma, and randomly-selected controls,
+ in North Humberside.
+ A marked point pattern.
+}
+\format{
+ The dataset \code{humberside} is
+ an object of class \code{"ppp"}
+ representing a marked point pattern.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of home address \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of home address \cr
+ \code{marks} \tab factor with levels \code{case} and \code{control} \cr
+ \tab indicating whether this is a disease case\cr
+ \tab or a control.
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+
+ The dataset \code{humberside.convex} is an object of the
+ same format, representing the same point pattern data,
+ but contained in a larger, 5-sided convex polygon.
+}
+\usage{data(humberside)}
+\examples{
+ if(require(spatstat)) {
+ humberside
+ summary(humberside)
+ plot(humberside)
+ plot(Window(humberside.convex), add=TRUE, lty=2)
+ }
+}
+\source{
+ Dr Ray Cartwright and Dr Freda Alexander.
+ Published and analysed in Cuzick and Edwards (1990), see Table 1.
+ Pentagonal boundary from Diggle and Chetwynd (1991), Figure 1.
+ Point coordinates and pentagonal boundary supplied by Andrew Lawson.
+ Detailed region boundary was digitised by \adrian, 2005, from
+ a reprint of Cuzick and Edwards (1990).
+}
+\section{Notes}{
+ Cuzick and Edwards (1990) first presented and analysed these data.
+
+ The data record 62 cases of childhood leukaemia and lymphoma
+ diagnosed in the North Humberside region of England between 1974 and
+ 1986, together with 141 controls selected at random from the birth
+ register for the same period.
+
+ The data are represented as a marked point pattern,
+ with the points giving the spatial location of each individual's home address
+ (actually, the centroid for the postal code)
+ and the marks identifying cases and controls.
+
+ Coordinates are expressed in units of 100 metres, and the resolution is
+ 100 metres. At this resolution, there are some duplicated points.
+ To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+
+ Two versions of the dataset are supplied, both containing the
+ same point coordinates, but using different windows.
+ The dataset \code{humberside} has a polygonal window with 102 edges
+ which closely approximates the Humberside region,
+ while \code{humberside.convex} has a convex 5-sided polygonal window
+ originally used by Diggle and Chetwynd (1991) and shown in
+ Figure 1 of that paper. (This pentagon has been modified slightly
+ from the original data, by shifting two vertices horizontally by 1 unit,
+ so that the pentagon contains all the data points.)
+}
+\references{
+ J. Cuzick and R. Edwards (1990)
+ Spatial clustering for inhomogeneous populations.
+ \emph{Journal of the Royal Statistical Society, series B},
+ \bold{52} (1990) 73-104.
+
+ P.J. Diggle and A.G. Chetwynd (1991)
+ Second-order analysis of spatial clustering for
+ inhomogeneous populations. \emph{Biometrics} 47 (1991) 1155-1163.
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/hyytiala.Rd b/man/hyytiala.Rd
new file mode 100755
index 0000000..1beba6f
--- /dev/null
+++ b/man/hyytiala.Rd
@@ -0,0 +1,43 @@
+\name{hyytiala}
+\alias{hyytiala}
+\docType{data}
+\title{
+ Scots pines and other trees at Hyytiala
+}
+\description{
+ This dataset is a spatial point pattern of trees recorded at
+ \ifelse{latex}{\out{Hyyti\"{a}l\"{a}}}{Hyytiala}, Finland.
+ The majority of the trees are Scots pines.
+ See Kokkila et al (2002).
+
+ The dataset \code{hyytiala} is a point pattern
+ (object of class \code{"ppp"}) containing the spatial coordinates
+ of each tree, marked by species (a factor with levels \code{aspen},
+ \code{birch}, \code{pine} and \code{rowan}).
+ The survey region is a 20 by 20 metre square.
+ Coordinates are given in metres.
+}
+\usage{data(hyytiala)}
+\examples{
+data(hyytiala)
+ if(require(spatstat)) {
+plot(hyytiala, cols=2:5)
+ }
+}
+\source{
+ Nicolas Picard
+}
+\references{
+ Kokkila, T., \ifelse{latex}{\out{M{\"a}kel{\"a}}}{Makela}, A. and
+ Nikinmaa E. (2002)
+ A method for generating stand structures using Gibbs marked point
+ process.
+ \emph{Silva Fennica} \bold{36} 265--277.
+
+ Picard, N, Bar-Hen, A., Mortier, F. and Chadoeuf, J. (2009)
+ The multi-scale marked area-interaction point process: a model for
+ the spatial pattern of trees.
+ \emph{Scandinavian Journal of Statistics} \bold{36} 23--41
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/japanesepines.Rd b/man/japanesepines.Rd
new file mode 100755
index 0000000..ef17ded
--- /dev/null
+++ b/man/japanesepines.Rd
@@ -0,0 +1,39 @@
+\name{japanesepines}
+\alias{japanesepines}
+\docType{data}
+\title{
+ Japanese Pines Point Pattern
+}
+\description{
+ The data give the locations of Japanese black pine saplings
+ in a square sampling region in a natural forest.
+ The observations were originally collected by Numata (1961).
+
+ These data are used as a standard example in the textbook of
+ Diggle (2003); see pages 1, 14, 19, 22, 24, 56--57 and 61.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations
+ in a 5.7 x 5.7 metre square, rescaled to the unit square
+ and rounded to two decimal places.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(japanesepines)}
+\source{Diggle (2003), obtained from Numata (1961)}
+
+\references{
+ Diggle, P.J. (2003)
+ \emph{Statistical Analysis of Spatial Point Patterns}.
+ Arnold Publishers.
+
+ Numata, M. (1961)
+ Forest vegetation in the vicinity of Choshi. Coastal flora and
+ vegetation at Choshi, Chiba Prefecture. IV.
+ \emph{Bulletin of Choshi Marine Laboratory, Chiba University}
+ \bold{3}, 28--48 (in Japanese).
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/lansing.Rd b/man/lansing.Rd
new file mode 100755
index 0000000..2cdde6f
--- /dev/null
+++ b/man/lansing.Rd
@@ -0,0 +1,108 @@
+\name{lansing}
+\alias{lansing}
+\docType{data}
+\title{
+ Lansing Woods Point Pattern
+}
+\description{
+ Locations and botanical classification of trees in Lansing Woods.
+
+ The data come from an investigation of a 924 ft x 924 ft (19.6 acre)
+ plot in Lansing Woods, Clinton County, Michigan USA
+ by D.J. Gerrard. The data give the locations of 2251 trees and
+ their botanical classification (into hickories, maples, red oaks,
+ white oaks, black oaks and miscellaneous trees).
+ The original plot size (924 x 924 feet)
+ has been rescaled to the unit square.
+
+ Note that the data contain duplicated points (two points at the
+ same location). To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of tree \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of tree \cr
+ \code{marks} \tab factor with levels indicating species of
+ each tree
+ }
+ The levels of \code{marks} are
+ \code{blackoak},
+ \code{hickory},
+ \code{maple},
+ \code{misc},
+ \code{redoak} and
+ \code{whiteoak}.
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(lansing)}
+\examples{
+ data(lansing)
+ if(require(spatstat)) {
+ plot(lansing)
+ summary(lansing)
+ plot(split(lansing))
+ plot(split(lansing)$maple)
+ }
+}
+\references{
+Besag, J. (1978)
+Some methods of statistical analysis for spatial data.
+\emph{Bull. Internat. Statist. Inst.} \bold{44}, 77--92.
+
+Cox, T.F. (1976)
+The robust estimation of the density of a forest
+stand using a new conditioned distance method.
+\emph{Biometrika} \bold{63}, 493--500.
+
+Cox, T.F. (1979)
+A method for mapping the dense and sparse regions of
+a forest stand.
+\emph{Applied Statistics} \bold{28}, 14--19.
+
+Cox, T.F. and Lewis, T. (1976)
+A conditioned distance ratio method for analysing spatial patterns.
+\emph{Biometrika} \bold{63}, 483--492.
+
+Diggle, P.J. (1979a)
+The detection of random heterogeneity in plant populations.
+\emph{Biometrics} \bold{33}, 390--394.
+
+Diggle, P.J. (1979b)
+Statistical methods for spatial point patterns in ecology.
+\emph{Spatial and temporal analysis in ecology}.
+R.M. Cormack and J.K. Ord (eds.)
+Fairland: International Co-operative Publishing House.
+pages 95--150.
+
+Diggle, P.J. (1981)
+Some graphical methods in the analysis of spatial point patterns.
+In \emph{Interpreting Multivariate Data}.
+V. Barnett (eds.) John Wiley and Sons. Pages 55--73.
+
+Diggle, P.J. (1983)
+\emph{Statistical analysis of spatial point patterns}.
+Academic Press.
+
+Gerrard, D.J. (1969)
+Competition quotient: a new measure of the competition
+affecting individual forest trees.
+Research Bulletin 20, Agricultural Experiment Station,
+Michigan State University.
+
+Lotwick, H.W. (1981)
+\emph{Spatial stochastic point processes}.
+PhD thesis, University of Bath, UK.
+
+Ord, J.K. (1978)
+How many trees in a forest?
+\emph{Mathematical Scientist} \bold{3}, 23--33.
+
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/letterR.Rd b/man/letterR.Rd
new file mode 100755
index 0000000..8639089
--- /dev/null
+++ b/man/letterR.Rd
@@ -0,0 +1,20 @@
+\name{letterR}
+\alias{letterR}
+\docType{data}
+\title{Window in Shape of Letter R}
+\description{
+ A window in the shape of the capital letter R,
+ for use in demonstrations.
+}
+\format{
+ An object of class \code{"owin"}
+ representing the capital letter R,
+ in the same font as the R package logo.
+ See \code{\link[spatstat]{owin.object}} for details of the format.
+}
+\usage{
+ data(letterR)
+}
+\source{\adrian}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/longleaf.Rd b/man/longleaf.Rd
new file mode 100755
index 0000000..7b1772a
--- /dev/null
+++ b/man/longleaf.Rd
@@ -0,0 +1,56 @@
+\name{longleaf}
+\alias{longleaf}
+\docType{data}
+\title{
+ Longleaf Pines Point Pattern
+}
+\description{
+ Locations and sizes of Longleaf pine trees.
+ A marked point pattern.
+
+ The data record the locations and diameters of
+ 584 Longleaf pine (\emph{Pinus palustris}) trees
+ in a 200 x 200 metre region in southern Georgia (USA).
+ They were collected and analysed by Platt, Evans and Rathbun (1988).
+
+ This is a marked point pattern; the mark associated with a tree is its
+ diameter at breast height (\code{dbh}), a convenient measure of its size.
+ Several analyses have considered only the ``adult'' trees which
+ are conventionally defined as those trees with \code{dbh}
+ greater than or equal to 30 cm.
+
+ The pattern is regarded as spatially inhomogeneous.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ Entries include
+ \tabular{ll}{
+ \code{x} \tab Cartesian \eqn{x}-coordinate of tree \cr
+ \code{y} \tab Cartesian \eqn{y}-coordinate of tree \cr
+ \code{marks} \tab diameter at breast height, in centimetres.
+ }
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(longleaf)}
+\examples{
+ data(longleaf)
+ if(require(spatstat)) {
+ plot(longleaf)
+ plot(cut(longleaf, breaks=c(0,30,Inf), labels=c("Sapling","Adult")))
+ }
+}
+\source{Platt, Evans and Rathbun (1988)}
+\references{
+Platt, W. J., Evans, G. W. and Rathbun, S. L. (1988)
+The population dynamics of a long-lived Conifer (Pinus palustris).
+\emph{The American Naturalist} \bold{131}, 491--525.
+
+Rathbun, S. L. and Cressie, N. (1994)
+A space-time survival point process for a longleaf
+pine forest in southern Georgia.
+\emph{Journal of the American Statistical Association} \bold{89}, 1164--1173.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/macros/defns.Rd b/man/macros/defns.Rd
new file mode 100644
index 0000000..466babb
--- /dev/null
+++ b/man/macros/defns.Rd
@@ -0,0 +1,19 @@
+%% macro definitions for spatstat man pages
+\newcommand{\adrian}{Adrian Baddeley \email{Adrian.Baddeley at curtin.edu.au}}
+\newcommand{\rolf}{Rolf Turner \email{r.turner at auckland.ac.nz}}
+\newcommand{\ege}{Ege Rubak \email{rubak at math.aau.dk}}
+\newcommand{\spatstatAuthors}{\adrian, \rolf and \ege}
+% Names with accents
+\newcommand{\Bogsted}{\ifelse{latex}{\out{B\o gsted}}{Bogsted}}
+\newcommand{\Cramer}{\ifelse{latex}{\out{Cram\'er}}{Cramer}}
+\newcommand{\Hogmander}{\ifelse{latex}{\out{H{\"o}gmander}}{Hogmander}}
+\newcommand{\Jyvaskyla}{\ifelse{latex}{\out{Jyv\"askyl\"a}}{Jyvaskyla}}
+\newcommand{\Matern}{\ifelse{latex}{\out{Mat\'ern}}{Matern}}
+\newcommand{\Moller}{\ifelse{latex}{\out{M\o ller}}{Moller}}
+\newcommand{\Oehlschlaegel}{\ifelse{latex}{\out{Oehlschl\"{a}gel}}{Oehlschlaegel}}
+\newcommand{\Prokesova}{\ifelse{latex}{\out{Proke\u{s}ov{\'{a}}}}{Prokesova}}
+\newcommand{\Sarkka}{\ifelse{latex}{\out{S\"{a}rkk\"{a}}}{Sarkka}}
+%% List of all Gibbs interactions
+\newcommand{\GibbsInteractionsList}{\code{\link{AreaInter}}, \code{\link{BadGey}}, \code{\link{Concom}}, \code{\link{DiggleGatesStibbard}}, \code{\link{DiggleGratton}}, \code{\link{Fiksel}}, \code{\link{Geyer}}, \code{\link{Hardcore}}, \code{\link{Hybrid}}, \code{\link{LennardJones}}, \code{\link{MultiStrauss}}, \code{\link{MultiStraussHard}}, \code{\link{OrdThresh}}, \code{\link{Ord}}, \code{\link{Pairwise}}, \code{\link{PairPiece}}, \code{\link{Penttinen}}, \code{\link{Poisson}}, \code [...]
+%% List of interactions recognised by RMH code
+\newcommand{\rmhInteractionsList}{\code{\link{AreaInter}}, \code{\link{BadGey}}, \code{\link{DiggleGatesStibbard}}, \code{\link{DiggleGratton}}, \code{\link{Fiksel}}, \code{\link{Geyer}}, \code{\link{Hardcore}}, \code{\link{Hybrid}}, \code{\link{LennardJones}}, \code{\link{MultiStrauss}}, \code{\link{MultiStraussHard}}, \code{\link{PairPiece}}, \code{\link{Penttinen}}, \code{\link{Poisson}}, \code{\link{Softcore}}, \code{\link{Strauss}}, \code{\link{StraussHard}} and \code{\link{Triplets}}}
diff --git a/man/mucosa.Rd b/man/mucosa.Rd
new file mode 100755
index 0000000..9595df5
--- /dev/null
+++ b/man/mucosa.Rd
@@ -0,0 +1,56 @@
+\name{mucosa}
+\alias{mucosa}
+\alias{mucosa.subwin}
+\docType{data}
+\title{
+ Cells in Gastric Mucosa
+}
+\description{
+ A bivariate inhomogeneous point pattern, giving the locations of
+ the centres of two types of cells in a cross-section of the
+ gastric mucosa of a rat.
+}
+\usage{data(mucosa)}
+\format{
+ An object of class \code{"ppp"}, see \code{\link[spatstat]{ppp.object}}.
+ This is a multitype point pattern with two types of points,
+ \code{ECL} and \code{other}.
+}
+\details{
+ This point pattern dataset gives the locations of
+ cell centres in a cross-section of the gastric mucosa (mucous membrane of the
+ stomach) of a rat. The rectangular observation window has been scaled
+ to unit width. The lower edge of the window is closest to the outside
+ of the stomach.
+
+ The cells are classified into two types: \emph{ECL cells}
+ (enterochromaffin-like cells) and \emph{other} cells. There are 86 ECL cells
+ and 807 other cells in the dataset.
+ ECL cells are a type of neuroendocrine cell which
+ synthesize and secrete histamine.
+ One hypothesis of interest is whether the
+ spatially-varying intensities of ECL cells and other cells are
+ proportional.
+
+ The data were originally collected by Dr Thomas Berntsen.
+ The data were discussed and analysed in \ifelse{latex}{\out{M\o ller}}{Moller} and Waagepetersen (2004,
+ pp. 2, 169).
+
+ The associated object \code{mucosa.subwin} is the smaller window
+ to which the data were restricted for analysis by \ifelse{latex}{\out{M\o ller}}{Moller} and Waagepetersen.
+}
+\source{
+ Dr Thomas Berntsen and Prof Rasmus Waagepetersen.
+}
+\references{
+ \ifelse{latex}{\out{M\o ller}}{Moller}, J. and Waagepetersen, R. (2004).
+ \emph{Statistical Inference and Simulation for Spatial Point Processes}.
+ Chapman and Hall/CRC.
+}
+\examples{
+ if(require(spatstat)) {
+ plot(mucosa, chars=c(1,3), cols=c("red", "green"))
+ plot(mucosa.subwin, add=TRUE, lty=3)
+ }
+}
+\keyword{datasets}
diff --git a/man/murchison.Rd b/man/murchison.Rd
new file mode 100755
index 0000000..8f102e3
--- /dev/null
+++ b/man/murchison.Rd
@@ -0,0 +1,110 @@
+\name{murchison}
+\alias{murchison}
+\docType{data}
+\title{
+ Murchison gold deposits
+}
+\description{
+ Data recording the spatial locations of gold deposits and associated
+ geological features in the Murchison area of Western Australia.
+ Extracted from a large scale (1:500,000) study of the
+ Murchison area by the Geological Survey of Western Australia
+ (Watkins and Hickman, 1990). The features recorded are
+ \itemize{
+ \item the locations of gold deposits;
+ \item the locations of geological faults;
+ \item the region that contains greenstone bedrock.
+ }
+ The study region is contained in a \eqn{330\times 400}{330 * 400} kilometre
+ rectangle. At this scale, gold deposits are points, i.e. their spatial
+ extent is negligible.
+ Gold deposits in this region occur only in greenstone bedrock.
+ Geological faults can be observed reliably only within the same
+ region. However, some faults have been extrapolated
+ (by geological ``interpretation'') outside the greenstone boundary
+ from information observed in the greenstone region.
+
+ These data were analysed by Foxall and Baddeley (2002) and Brown et al
+ (2002); see also Groves et al (2000), Knox-Robinson and Groves (1997).
+ The main aim is to predict the intensity of the
+ point pattern of gold deposits from the more easily observable fault
+ pattern.
+}
+\format{
+ \code{murchison} is a list with the following entries:
+ \describe{
+ \item{gold}{a point pattern (object of class \code{"ppp"})
+ representing the point pattern of gold deposits.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+ }
+ \item{faults}{a line segment pattern (object of class \code{"psp"})
+ representing the geological faults.
+ See \code{\link[spatstat]{psp.object}} for details of the format.
+ }
+ \item{greenstone}{the greenstone bedrock region.
+ An object of class \code{"owin"}. Consists of multiple
+ irregular polygons with holes.
+ }
+ }
+ All coordinates are given in \bold{metres}.
+}
+\usage{
+ data(murchison)
+}
+\examples{
+ if(require(spatstat)) {
+ if(interactive()) {
+ data(murchison)
+ plot(murchison$greenstone, main="Murchison data", col="lightgreen")
+ plot(murchison$gold, add=TRUE, pch="+",col="blue")
+ plot(murchison$faults, add=TRUE, col="red")
+ }
+ }
+}
+\source{
+ Data were kindly provided by Dr Carl Knox-Robinson of the
+ Department of Geology and Geophysics, University of Western Australia.
+ Permission to use the data is granted by Dr Tim Griffin,
+ Geological Survey of Western Australia and by Dr Knox-Robinson.
+ \emph{Please make appropriate acknowledgement} to
+ Watkins and Hickman (1990) and the Geological Survey of Western Australia.
+}
+\references{
+ Brown, W.M., Gedeon, T.D., Baddeley, A.J. and Groves, D.I. (2002)
+ Bivariate J-function and other graphical
+ statistical methods help select the best predictor
+ variables as inputs for a neural network method of
+ mineral prospectivity mapping.
+ In U. Bayer, H. Burger and W. Skala (eds.)
+ \emph{IAMG 2002: 8th Annual Conference of the
+ International Association for Mathematical Geology},
+ Volume 1, 2002. International Association of Mathematical Geology.
+ Pages 257--268.
+
+ Foxall, R. and Baddeley, A. (2002)
+ Nonparametric measures of association between a
+ spatial point process and a random set, with
+ geological applications. \emph{Applied Statistics} \bold{51}, 165--182.
+
+ Groves, D.I., Goldfarb, R.J., Knox-Robinson, C.M., Ojala, J., Gardoll,
+ S, Yun, G.Y. and Holyland, P. (2000)
+ Late-kinematic timing of orogenic gold deposits and significance for
+ computer-based exploration techniques with emphasis on the Yilgarn Block,
+ Western Australia.
+ \emph{Ore Geology Reviews}, \bold{17}, 1--38.
+
+ Knox-Robinson, C.M. and Groves, D.I. (1997)
+ Gold prospectivity mapping using a geographic information system
+ (GIS), with examples from the Yilgarn Block of Western Australia.
+ \emph{Chronique de la Recherche Miniere} \bold{529}, 127--138.
+
+ Watkins, K.P. and Hickman, A.H. (1990)
+ \emph{Geological evolution and mineralization of the Murchison Province,
+ Western Australia}.
+ Bulletin 137, Geological Survey of Western Australia. 267 pages.
+ Published by Department of Mines, Western Australia, 1990.
+ Available online from Department of Industry and Resources,
+ State Government of Western Australia, \code{www.doir.wa.gov.au}
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/nbfires.Rd b/man/nbfires.Rd
new file mode 100755
index 0000000..973f45a
--- /dev/null
+++ b/man/nbfires.Rd
@@ -0,0 +1,237 @@
+\name{nbfires}
+\alias{nbfires}
+\alias{nbw.rect}
+\alias{nbw.seg}
+\alias{nbfires.extra}
+\docType{data}
+\title{Point Patterns of New Brunswick Forest Fires}
+\description{
+Point patterns created from yearly records, provided by the New
+Brunswick Department of Natural Resources, of all fires falling
+under their jurisdiction for the years 1987 to 2003 inclusive
+(with the year 1988 omitted until further notice).
+}
+\usage{data(nbfires)}
+\format{
+ Executing \code{data(nbfires)} gives access to four objects:
+ \code{nbfires}, \code{nbw.rect}, \code{nbw.seg} and \code{nbfires.extra}.
+
+ The object \code{nbfires} is a marked point pattern (an object of
+ class \code{"ppp"}) consisting of all of the fires in the years
+ 1987 to 2003 inclusive, with the omission of 1988. The marks
+ consist of a data frame of auxiliary information about the fires;
+ see \emph{Details.} Patterns for individual years can be extracted
+ using the function \code{\link[spatstat]{split.ppp}()}. (See \bold{Examples}.)
+
+ The object \code{nbw.rect} is a rectangular window which covers
+ central New Brunswick. It is provided for use in illustrative and
+ \sQuote{practice} calculations inasmuch as the use of a rectangular
+ window simplifies some computations considerably.
+
+ The object \code{nbw.seg} is a line segment pattern (object of class
+ \code{"psp"}) consisting of all the boundary segments of the polygonal window
+ of New Brunswick. The \code{marks} of this pattern are categorical
+ values which classify the segments into three types:
+ \code{"border"} (land border),
+ \code{"coast"} (coast of the mainland)
+ and \code{"island"} (coast of the 5 islands).
+
+ For conformity with other datasets, \code{nbfires.extra} is a list
+ containing all the supplementary data. It contains copies of
+ \code{nbw.rect} and \code{nbw.seg}.
+}
+\details{
+The coordinates of the fire locations were provided in terms of
+latitude and longitude, to the nearest minute of arc. These were
+converted to New Brunswick stereographic projection coordinates
+(Thomson, Mephan and Steeves, 1977) which was the coordinate
+system in which the map of New Brunswick --- which constitutes the
+observation window for the pattern --- was obtained. The conversion
+was done using a \code{C} program kindly provided by Jonathan
+Beaudoin of the Department of Geodesy and Geomatics, University of
+New Brunswick.
+
+Finally the data and window were rescaled since the use of the
+New Brunswick stereographic projection coordinate system resulted
+in having to deal with coordinates which are expressed as very
+large integers with a bewildering number of digits. Amongst other
+things, these huge numbers tended to create very untidy axis labels
+on graphs. The width of the bounding box of the window was made
+equal to 1000 units. In addition the lower left hand
+corner of this bounding box was shifted to the origin. The height
+of the bounding box was changed proportionately, resulting in a
+value of approximately 959.
+
+In the final dataset \code{nbfires}, one coordinate unit is equivalent to
+0.403716 kilometres. To convert the data to kilometres,
+use \code{rescale(nbfires)}.
+
+The window for the fire patterns comprises 6 polygonal components,
+consisting of mainland New Brunswick and the 5 largest islands.
+Some lakes which should form holes in the mainland component are
+currently missing; this problem may be remedied in future releases.
+The window was formed by \sQuote{simplifying} the map that was originally
+obtained. The simplification consisted in reducing (using
+an interactive visual technique) the number of polygon edges in
+each component. For instance the number of edges in the mainland
+component was reduced from over 138,000 to 500.
+
+For some purposes it is probably better to use a discretized
+(mask type) window. See \bold{Examples}.
+
+Because of the coarseness of the coordinates of the original
+data (1 minute of longitude is approximately 1 kilometer at the
+latitude of New Brunswick), data entry errors, and the simplification
+of the observation window, many of the original fire locations
+appeared to be outside of the window. This problem was addressed
+by shifting the location of the \sQuote{outsider} points slightly,
+or deleting them, as seemed appropriate.
+
+Note that the data contain duplicated points (two points at the
+same location). To determine which points are duplicates,
+use \code{\link[spatstat]{duplicated.ppp}}.
+To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+
+The columns of the data frame comprising the marks of
+\code{nbfires} are:
+\describe{
+ \item{year}{
+ This a \emph{factor} with levels 1987, 1989,
+ \ldots, 2002, 2003. Note that 1988 is not present in
+ the levels.
+ }
+ \item{fire.type}{
+ A factor with levels \code{forest},
+ \code{grass}, \code{dump}, and \code{other}.
+ }
+ \item{dis.date}{
+ The discovery date of the fire, which is the
+ nearest possible surrogate for the starting time
+ of the fire. This is an object of class \code{POSIXct}
+ and gives the starting discovery time of the fire to
+ the nearest minute.
+ }
+ \item{dis.julian}{
+ The discovery date and time of the fire, expressed
+ in \sQuote{Julian days}, i.e. as a decimal fraction representing the number
+ of days since the beginning of the year (midnight 31 December).
+ }
+ \item{out.date}{
+ The date on which the fire was judged to be
+ \sQuote{out}. This is an object of class \code{POSIXct} and gives the
+ \sQuote{out} time of the fire to the nearest minute.
+ }
+ \item{out.julian}{
+ The date and time at which the fire was judged
+ to be \sQuote{out}, expressed in Julian days.
+ }
+ \item{cause}{
+ General cause of the fire. This is a factor with
+ levels \code{unknown}, \code{rrds} (railroads), \code{misc}
+ (miscellaneous), \code{ltning} (lightning), \code{for.ind}
+ (forest industry), \code{incend} (incendiary), \code{rec}
+ (recreation), \code{resid} (resident), and \code{oth.ind}
+ (other industry). Causes \code{unknown}, \code{ltning}, and
+ \code{incend} are supposedly designated as \sQuote{final} by the New Brunswick
+ Department of Natural Resources, meaning (it seems) \dQuote{that's
+ all there is to it}. Other causes are apparently intended
+ to be refined by being combined with \dQuote{source of ignition}.
+ However cross-tabulating \code{cause} with \code{ign.src} ---
+ see below --- reveals that very often these three \sQuote{causes}
+ are associated with an \dQuote{ignition source} as well.
+ }
+ \item{ign.src}{
+ Source of ignition, a factor with levels
+ \code{cigs} (cigarette/match/pipe/ashes), \code{burn.no.perm}
+ (burning without a permit), \code{burn.w.perm} (burning with a
+ permit), \code{presc.burn} (prescribed burn), \code{wood.spark}
+ (wood spark), \code{mach.spark} (machine spark), \code{campfire},
+ \code{chainsaw}, \code{machinery}, \code{veh.acc} (vehicle
+ accident), \code{rail.acc} (railroad accident), \code{wheelbox}
+ (wheelbox on railcars), \code{hot.flakes} (hot flakes off
+ railcar wheels), \code{dump.fire} (fire escaping from a dump),
+ \code{ashes} (ashes, briquettes, burning garbage, etc.)
+ }
+ \item{fnl.size}{
+ The final size of the fire (area burned)
+ in hectares, to the nearest 10th hectare.
+ }
+}
+Note that due to data entry errors some of the \dQuote{out dates} and
+\dQuote{out times} in the original data sets were actually \emph{earlier}
+than the corresponding \dQuote{discovery dates} and \dQuote{discover times}.
+In such cases all corresponding entries of the marks data frame
+(i.e. \code{dis.date}, \code{dis.julian}, \code{out.date}, and
+\code{out.julian}) were set equal to \code{NA}. Also, some of the
+dates and times were missing (equal to \code{NA}) in the original
+data sets.
+
+The \sQuote{ignition source} data were given as integer codes
+in the original data sets. The code book that I obtained
+gave interpretations for codes 1, 2, \ldots, 15. However
+the actually also contained codes of 0, 16, 17, 18, and in
+one instance 44. These may simply be data entry errors.
+These uninterpretable values were assigned the level
+\code{unknown}. Many of the years had most, or sometimes
+all, of the ignition source codes equal to 0 (hence turning
+out as \code{unknown}, and many of the years had many
+missing values as well. These were also assigned the
+level \code{unknown}. Of the 7108 fires in \code{nbfires},
+4354 had an \code{unknown} ignition source. This variable
+is hence unlikely to be very useful.
+
+There are also anomalies between \code{cause} and \code{ign.src},
+e.g. \code{cause} being \code{unknown} but \code{ign.src}
+being \code{cigs}, \code{burn.no.perm}, \code{mach.spark},
+\code{hot.flakes}, \code{dump.fire} or \code{ashes}. Particularly
+worrisome is the fact that the cause \code{ltning} (!!!) is
+associate with sources of ignition \code{cigs}, \code{burn.w.perm},
+\code{presc.burn}, and \code{wood.spark}.
+}
+\source{
+ The data were kindly provided by the New Brunswick Department
+ of Natural Resources. Special thanks are due to Jefferey Betts for
+ a great deal of assistance.
+}
+\references{
+Turner, Rolf.
+Point patterns of forest fire locations.
+\emph{Environmental and Ecological Statistics}
+\bold{16} (2009) 197 -- 223, doi:10.1007/s10651-007-0085-1.
+
+Thomson, D. B., Mephan, M. P., and Steeves, R. R. (1977)
+The stereographic double projection.
+Technical Report 46, University of New Brunswick,
+Fredericton, N. B., Canada
+URL: \code{gge.unb.ca/Pubs/Pubs.html}.
+}
+
+\examples{
+\dontrun{
+ if(require(spatstat)) {
+# Get the year 2000 data.
+X <- split(nbfires,"year")
+Y.00 <- X[["2000"]]
+# Plot all of the year 2000 data, marked by fire type.
+plot(Y.00,which.marks="fire.type")
+# Cut back to forest and grass fires.
+Y.00 <- Y.00[marks(Y.00)$fire.type \%in\% c("forest","grass")]
+# Plot the year 2000 forest and grass fires marked by fire duration time.
+stt <- marks(Y.00)$dis.julian
+fin <- marks(Y.00)$out.julian
+marks(Y.00) <- cbind(marks(Y.00),dur=fin-stt)
+plot(Y.00,which.marks="dur")
+# Look at just the rectangular subwindow (superimposed on the entire window).
+nbw.mask <- as.mask(Window(nbfires), dimyx=500)
+plot(nbw.mask, col=c("green", "white"))
+plot(Window(nbfires), border="red", add=TRUE)
+plot(Y.00[nbw.rect],use.marks=FALSE,add=TRUE)
+plot(nbw.rect,add=TRUE,border="blue")
+# Look at the K function for the year 2000 forest and grass fires.
+K.00 <- Kest(Y.00)
+plot(K.00)
+ }
+}
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/nztrees.Rd b/man/nztrees.Rd
new file mode 100755
index 0000000..01df0c9
--- /dev/null
+++ b/man/nztrees.Rd
@@ -0,0 +1,48 @@
+\name{nztrees}
+\alias{nztrees}
+\docType{data}
+\title{
+ New Zealand Trees Point Pattern
+}
+\description{
+ The data give the locations of trees in a forest plot.
+
+ They were collected by Mark and Esler (1970) and
+ were extracted and analysed by Ripley (1981, pp. 169-175).
+ They represent the
+ positions of 86 trees in a forest plot approximately 140 by 85 feet.
+
+ Ripley discarded from his analysis the eight trees at the right-hand edge of
+ the plot (which appear to be part of a planted border)
+ and trimmed the window by a 5-foot margin accordingly.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ The Cartesian coordinates are in feet.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(nztrees)}
+\source{Mark and Esler (1970), Ripley (1981).}
+\section{Note}{
+ To trim a 5-foot margin off the window, type
+ \code{nzsub <- nztrees[owin(c(0,148),c(0,95)) ]}
+}
+\references{
+ Ripley, B.D. (1981)
+ \emph{Spatial statistics}.
+ John Wiley and Sons.
+
+ Mark, A.F. and Esler, A.E. (1970)
+ An assessment of the point-centred quarter method of plotless
+ sampling in some New Zealand forests.
+ \emph{Proceedings of the New Zealand Ecological Society}
+ \bold{17}, 106--110.
+}
+\keyword{datasets}
+\keyword{spatial}
+
+
+
diff --git a/man/osteo.Rd b/man/osteo.Rd
new file mode 100755
index 0000000..0b53831
--- /dev/null
+++ b/man/osteo.Rd
@@ -0,0 +1,147 @@
+\name{osteo}
+\alias{osteo}
+\docType{data}
+\title{
+ Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
+}
+\description{
+ These data give the three-dimensional locations of
+ osteocyte lacunae observed in rectangular volumes of
+ solid bone using a confocal microscope.
+
+ There were four samples of bone, and ten regions were mapped
+ in each bone, yielding 40 spatial point patterns.
+ The data can be regarded as replicated observations of a
+ three-dimensional point process, nested within bone samples.
+}
+\usage{data(osteo)}
+\format{
+ A \code{\link[spatstat]{hyperframe}} with the following columns:
+
+ \tabular{ll}{
+ \code{id} \tab character string identifier of bone sample \cr
+ \code{shortid} \tab last numeral in \code{id} \cr
+ \code{brick} \tab serial number (1 to 10) of sampling volume within
+ this bone sample \cr
+ \code{pts} \tab three dimensional point pattern (class \code{pp3}) \cr
+ \code{depth} \tab the depth of the brick in microns
+ }
+}
+\details{
+ These data are three-dimensional point patterns
+ representing the positions of \emph{osteocyte lacunae}, holes
+ in bone which were occupied by osteocytes (bone-building cells) during life.
+
+ Observations were made on four different skulls of Macaque monkeys
+ iusing a three-dimensional microscope.
+ From each skull, observations were collected in 10 separate sampling volumes.
+ In all, there are 40 three-dimensional point patterns in the dataset.
+
+ The data were collected in 1984
+ by A. Baddeley, A. Boyde, C.V. Howard and S. Reid
+ (see references) using the tandem-scanning reflected light microscope
+ (TSRLM) at University College London. This was one of the first
+ optical confocal microscopes available.
+
+ Each point pattern dataset gives the \eqn{(x,y,z)} coordinates
+ (in microns) of all points visible in a
+ three-dimensional rectangular box (``brick'') of dimensions
+ \eqn{81 \times 100 \times d}{81 * 100 * d} microns,
+ where \eqn{d} varies.
+ The \eqn{z} coordinate is depth into the bone
+ (depth of the focal plane of the confocal microscope); the \eqn{(x,y)}
+ plane is parallel to the exterior surface of the bone;
+ the relative orientation of the \eqn{x} and \eqn{y} axes is not important.
+
+ The bone samples were three intact skulls and one skull
+ cap, all originally identified as belonging to the macaque monkey
+ \emph{Macaca fascicularis}, from the collection of the
+ Department of Anatomy, University of London. Later analysis
+ (Baddeley et al, 1993) suggested that the skull cap, given here as
+ the first animal, was a different subspecies, and this was confirmed by
+ anatomical inspection.
+}
+\section{Sampling Procedure}{
+ The following extract from Baddeley et al (1987)
+ describes the sampling procedure.
+
+ The parietal bones of three fully articulated adult Macaque monkey
+ \emph{(Macaca fascicularis)} skulls from the collection of
+ University College London were used. The right parietal bone was
+ examined, in each case, approximately 1 cm lateral to the sagittal
+ suture and 2 cm posterior to the coronal suture. The skulls were
+ mounted on plasticine on a moving stage placed beneath the TSRLM.
+ Immersion oil was applied and a \eqn{\times 60}{X 60}, NA 1.0 oil immersion
+ objective lens (Lomo) was focussed at 10 microns below the cranial
+ surface. The TV image was produced by a Panasonic WB 1850/B camera
+ on a Sony PVM 90CE TV monitor.
+
+ A graduated rectangular counting frame
+ \eqn{90 \times 110}{90 * 110} mm (representing
+ \eqn{82 \times 100}{82 * 100} microns in real units)
+ was marked on a Perspex overlay
+ and fixed to the screen. The area of tissue seen within the frame defined
+ a subfield: a guard area of 10 mm width was visible on all sides of the
+ frame. Ten subfields were examined, arranged approximately in
+ a rectangular grid pattern, with at least one field width separating
+ each pair of fields. The initial field position was determined randomly
+ by applying a randomly-generated coordinate shift to the moving stage.
+ Subsequent fields were attained
+ using the coarse controls of the microscope stage, in accordance with
+ the rectangular grid pattern.
+
+ For each subfield, the focal plane was racked down from its initial
+ 10 micron depth until all visible osteocyte lacunae had been examined.
+ This depth \eqn{d} was recorded. The 3-dimensional sampling volume was
+ therefore a rectangular box of dimensions
+ \eqn{82 \times 100 \times d}{82 * 100 * d} microns,
+ called a ``brick''.
+ For each visible lacuna, the fine focus racking control was adjusted until
+ maximum brightness was obtained. The depth of the focal plane was then
+ recorded as the $z$ coordinate of the ``centre point'' of the
+ lacuna. Without moving the focal plane, the \eqn{x} and \eqn{y}
+ coordinates of
+ the centre of the lacunar image were read off the graduated counting frame.
+ This required a subjective judgement of the position of the centre of the
+ 2-dimensional image. Profiles were approximately elliptical and the centre
+ was considered to be well-defined. Accuracy of
+ the recording procedure was tested by independent repetition (by the
+ same operator and by different operators) and found to be reproducible
+ to plus or minus 2 mm on the screen.
+
+ A lacuna was counted only if its \eqn{(x, y)} coordinates lay inside
+ the \eqn{90 \times 110}{90 * 110} mm counting frame.
+}
+\source{
+ Data were collected by \adrian.
+}
+\references{
+ Baddeley, A.J., Howard, C.V, Boyde, A. and Reid, S.A. (1987)
+ Three dimensional analysis of the spatial distribution of
+ particles using the tandem-scanning reflected light microscope.
+ \emph{Acta Stereologica} \bold{6} (supplement II) 87--100.
+
+ Baddeley, A.J., Moyeed, R.A., Howard, C.V. and Boyde, A. (1993)
+ Analysis of a three-dimensional point pattern
+ with replication.
+ \emph{Applied Statistics} \bold{42} (1993) 641--668.
+
+ Howard, C.V. and Reid, S. and Baddeley, A.J. and Boyde, A. (1985)
+ Unbiased estimation of particle density
+ in the tandem-scanning reflected light microscope.
+ \emph{Journal of Microscopy} \bold{138} 203--212.
+}
+\examples{
+ data(osteo)
+ if(require(spatstat)) {
+ osteo
+ if(interactive()) {
+ plot(osteo$pts[[1]], main="animal 1, brick 1")
+ ape1 <- osteo[osteo$shortid==4, ]
+ plot(ape1, tick.marks=FALSE)
+ with(osteo, intensity(pts))
+ plot(with(ape1, K3est(pts)))
+ }
+ }
+}
+\keyword{datasets}
diff --git a/man/paracou.Rd b/man/paracou.Rd
new file mode 100755
index 0000000..8dc2bc1
--- /dev/null
+++ b/man/paracou.Rd
@@ -0,0 +1,56 @@
+\name{paracou}
+\alias{paracou}
+\docType{data}
+\title{
+ Kimboto trees at Paracou, French Guiana
+}
+\description{
+ This dataset is a point pattern of adult and juvenile Kimboto trees
+ (\emph{Pradosia cochlearia} or \emph{P. ptychandra})
+ recorded at Paracou in French Guiana.
+ See Flores (2005).
+
+ The dataset \code{paracou} is a point pattern
+ (object of class \code{"ppp"}) containing the spatial coordinates
+ of each tree, marked by age (a factor with levels \code{adult} and
+ \code{juvenile}. The survey region is a rectangle
+ approximately 400 by 525 metres. Coordinates are given in metres.
+
+ Note that the data contain duplicated points (two points at the
+ same location). To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+}
+\usage{data(paracou)}
+\examples{
+ if(require(spatstat)) {
+plot(paracou, cols=2:3, chars=c(16,3))
+ }
+}
+\source{
+ Data kindly contributed by Olivier Flores.
+ All data belong to CIRAD \url{http://www.cirad.fr}
+ and UMR EcoFoG \url{http://www.ecofog.gf} and
+ are included in \pkg{spatstat} with permission.
+ Original data sources:
+ juvenile and some adult trees collected by Flores (2005);
+ adult tree data sourced from CIRAD Paracou experimental plots dataset
+ (2003 campaign).
+}
+\references{
+ Flores, O. (2005)
+ \emph{\ifelse{latex}{\out{D{\'e}terminisme de la
+ r{\'e}g{\'e}n{\'e}ration chez quinze esp{\`e}ces d'arbres tropicaux
+ en for{\^e}t guyanaise: les effets de l'environnement et de la
+ limitation par la dispersion.}}{ Determinisme de la regeneration
+ chez quinze especes d'arbres tropicaux en foret guyanaise: les
+ effets de l'environnement et de la limitation par la dispersion.}}
+ PhD Thesis, University of Montpellier 2, Montpellier, France.
+
+ Picard, N, Bar-Hen, A., Mortier, F. and Chadoeuf, J. (2009)
+ The multi-scale marked area-interaction point process: a model for
+ the spatial pattern of trees.
+ \emph{Scandinavian Journal of Statistics} \bold{36} 23--41
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/ponderosa.Rd b/man/ponderosa.Rd
new file mode 100755
index 0000000..1ca45d9
--- /dev/null
+++ b/man/ponderosa.Rd
@@ -0,0 +1,63 @@
+\name{ponderosa}
+\alias{ponderosa}
+\alias{ponderosa.extra}
+\docType{data}
+\title{
+ Ponderosa Pine Tree Point Pattern
+}
+\description{
+ The data record the locations of 108 Ponderosa Pine
+ (\emph{Pinus ponderosa}) trees in a 120 metre square region in the Klamath
+ National Forest in northern California, published as Figure 2 of
+ Getis and Franklin (1987).
+
+ Franklin et al. (1985) determined the locations of approximately 5000
+ trees from United States Forest Service aerial photographs and
+ digitised them for analysis. Getis and Franklin (1987) selected a 120
+ metre square subregion that appeared to exhibit clustering. This subregion
+ is the \code{ponderosa} dataset.
+
+ In principle these data are equivalent to
+ Figure 2 of Getis and Franklin (1987) but they are not exactly
+ identical; some of the spatial locations appear to be slightly
+ perturbed.
+
+ The data points identified as A, B, C on Figure 2 of Getis and Franklin
+ (1987) correspond to points numbered 42, 7 and 77 in the dataset
+ respectively.
+}
+\format{
+ Typing \code{data(ponderosa)} gives access to two objects,
+ \code{ponderosa} and \code{ponderosa.extra}.
+
+ The dataset \code{ponderosa} is a spatial point pattern
+ (object of class \code{"ppp"})
+ representing the point pattern of tree positions.
+ See \code{\link[spatstat]{ppp.object}} for details of the format.
+
+ The dataset \code{ponderosa.extra} is a list containing supplementary
+ data. The entry \code{id} contains the index numbers of the
+ three special points A, B, C in the point pattern. The entry
+ \code{plotit} is a function that can be called to produce a nice plot
+ of the point pattern.
+}
+\usage{data(ponderosa)}
+\source{Prof. Janet Franklin, University of California, Santa Barbara}
+\examples{
+ data(ponderosa)
+ if(require(spatstat)) {
+ ponderosa.extra$plotit()
+ }
+}
+\references{
+ Franklin, J., Michaelsen, J. and Strahler, A.H. (1985)
+ Spatial analysis of density dependent pattern in coniferous forest
+ stands.
+ \emph{Vegetatio} \bold{64}, 29--36.
+
+ Getis, A. and Franklin, J. (1987)
+ Second-order neighbourhood analysis of mapped point patterns.
+ \emph{Ecology} \bold{68}, 473--477.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/pyramidal.Rd b/man/pyramidal.Rd
new file mode 100755
index 0000000..62b950f
--- /dev/null
+++ b/man/pyramidal.Rd
@@ -0,0 +1,47 @@
+\name{pyramidal}
+\alias{pyramidal}
+\docType{data}
+\title{
+ Pyramidal Neurons in Cingulate Cortex
+}
+\description{
+ Point patterns giving the locations of pyramidal neurons in micrographs
+ from area 24, layer 2 of the cingulate cortex in the human brain.
+ There is one point pattern from each of 31 human subjects.
+ The subjects are divided into three groups:
+ controls (12 subjects), schizoaffective (9 subjects)
+ and schizophrenic (10 subjects).
+
+ Each point pattern is recorded in a unit square region; the unit of
+ measurement is unknown.
+
+ These data were introduced and analysed by
+ Diggle, Lange and Benes (1991).
+}
+\format{
+ \code{pyramidal} is a hyperframe with 31 rows, one row for each
+ subject. It has a column named
+ \code{Neurons} containing the point patterns of neuron locations,
+ and a column named \code{group} which is a factor with levels
+ \code{"control", "schizoaffective", "schizophrenic"}
+ identifying the grouping of subjects.
+}
+\usage{data(pyramidal)}
+\source{
+ Peter Diggle's website.
+}
+\references{
+ Diggle, P.J., Lange, N. and Benes, F.M. (1991). Analysis of variance
+ for replicated spatial point patterns in clinical neuroanatomy.
+ \emph{Journal of the American Statistical Association}
+ \bold{86}, 618--625.
+}
+\examples{
+ if(require(spatstat)) {
+pyr <- pyramidal
+pyr$grp <- abbreviate(pyramidal$group, minlength=7)
+plot(pyr, quote(plot(Neurons, pch=16, main=grp)), main="Pyramidal Neurons")
+ }
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/redwood.Rd b/man/redwood.Rd
new file mode 100755
index 0000000..482f3c6
--- /dev/null
+++ b/man/redwood.Rd
@@ -0,0 +1,70 @@
+\name{redwood}
+\alias{redwood}
+\alias{redwood3}
+\docType{data}
+\title{
+ California Redwoods Point Pattern (Ripley's Subset)
+}
+\description{
+ Locations of 62 seedlings and saplings
+ of California redwood trees.
+
+ The data represent the locations of 62 seedlings and saplings
+ of California redwood trees in a square sampling region.
+ They originate from Strauss (1975);
+ the present data are a subset extracted by Ripley (1977)
+ in a subregion that has been rescaled to a unit square.
+
+ Two versions of this dataset are provided: \code{redwood}
+ and \code{redwood3}.
+
+ The dataset \code{redwood} was obtained from the \pkg{spatial} package.
+ In this version the coordinates are given to 2 decimal places
+ (multiples of 0.01 units) except for one point which has an \eqn{x} coordinate
+ of 0.999, presumably to ensure that it is properly inside the window.
+
+ The dataset \code{redwood3} was obtained from Peter Diggle's webpage.
+ In this version the coordinates are given to 3 decimal places
+ (multiples of 0.001 units). The ordering of the points is not the same
+ in the two datasets.
+
+ There are many further analyses of this dataset. It is often used as a
+ canonical example of a clustered point pattern
+ (see e.g. Diggle, 1983).
+
+ The original, full redwood dataset is supplied in the \code{spatstat}
+ library as \code{redwoodfull}.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ The window has been rescaled to the unit square.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(redwood)}
+\source{
+ Original data of Strauss (1975), subset extracted by Ripley (1977).
+ Data obtained from Ripley's package \pkg{spatial}
+ and from Peter Diggle's website.
+}
+\seealso{
+ \code{\link[spatstat.data]{redwoodfull}}
+}
+\references{
+ Diggle, P.J. (1983)
+ \emph{Statistical analysis of spatial point patterns}.
+ Academic Press.
+
+ Ripley, B.D. (1977)
+ Modelling spatial patterns (with discussion).
+ \emph{Journal of the Royal Statistical Society, Series B}
+ \bold{39}, 172--212.
+
+ Strauss, D.J. (1975)
+ A model for clustering.
+ \emph{Biometrika} \bold{62}, 467--475.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/redwoodfull.Rd b/man/redwoodfull.Rd
new file mode 100755
index 0000000..3760b21
--- /dev/null
+++ b/man/redwoodfull.Rd
@@ -0,0 +1,110 @@
+\name{redwoodfull}
+\alias{redwoodfull}
+\alias{redwoodfull.extra}
+\docType{data}
+\title{
+ California Redwoods Point Pattern (Entire Dataset)
+}
+\description{
+ These data represent the locations of 195 seedlings and saplings
+ of California redwood trees in a square sampling region.
+ They were described and analysed by Strauss (1975).
+ This is the ``\bold{full}'' dataset; most writers have
+ analysed a subset extracted by Ripley (1977)
+ which is available as \code{\link[spatstat.data]{redwood}}.
+
+ Strauss (1975) divided the sampling region into two subregions I and II
+ demarcated by a diagonal line. The spatial pattern
+ appears to be slightly regular in region I and strongly clustered in
+ region II.
+
+ Strauss (1975) writes: \dQuote{It was felt that the seedlings
+ would be scattered fairly randomly, except that a number of
+ tight clusters would form around some of the redwood tree stumps
+ present in the plot. A discontinuity in the soil, very roughly
+ demarked by the diagonal line in the figure, was expected to cause
+ a difference in clustering behaviour between regions I and II. Moreover,
+ almost all the redwood stumps were situated in region II.}
+
+ The dataset \code{redwoodfull} contains the full point pattern
+ of 195 trees.
+ The window has been rescaled to the unit square.
+ Its physical size is approximately 130 feet across.
+
+ The auxiliary information about the subregions is contained in
+ \code{redwoodfull.extra}, which is a list with entries
+ \tabular{ll}{
+ \code{rdiag}\tab The coordinates of the diagonal boundary\cr
+ \tab between regions I and II \cr
+ \code{regionI} \tab Region I as a window object \cr
+ \code{regionII} \tab Region II as a window object \cr
+ \code{regionR} \tab Ripley's subrectangle (approximate) \cr
+ \code{plotit} \tab Function to plot the full data and auxiliary markings
+ }
+
+ Ripley (1977) extracted a subset of these data, containing 62 points,
+ lying within a square subregion which overlaps regions I and II.
+ He rescaled that subset to the unit square.
+ This subset has been re-analysed many times,
+ and is the dataset usually known as
+ ``the redwood data'' in the spatial statistics literature.
+ The exact dataset used by Ripley is supplied in the \pkg{spatstat}
+ library as \code{\link[spatstat.data]{redwood}}.
+
+ The approximate position of the square chosen by Ripley
+ within the \code{redwoodfull} pattern
+ is indicated by the window \code{redwoodfull.extra$regionR}.
+ There are some minor inconsistencies with
+ \code{redwood} since it originates from a different digitisation.
+}
+\format{
+ The dataset \code{redwoodfull} is an object of class \code{"ppp"}
+ representing the point pattern of tree locations.
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+ The window has been rescaled to the unit square.
+ Its physical size is approximately 128 feet across.
+
+ The dataset \code{redwoodfull.extra} is a list with entries
+ \tabular{ll}{
+ \code{rdiag}\tab coordinates of endpoints of a line,\cr
+ \tab in format \code{list(x=numeric(2),y=numeric(2))} \cr
+ \code{regionI} \tab a window object \cr
+ \code{regionII} \tab a window object \cr
+ \code{regionR} \tab a window object \cr
+ \code{plotit} \tab Function with no arguments
+ }
+}
+\usage{data(redwoodfull)}
+\examples{
+ data(redwoodfull)
+ if(require(spatstat)) {
+ plot(redwoodfull)
+ redwoodfull.extra$plotit()
+ # extract the pattern in region II
+ redwoodII <- redwoodfull[, redwoodfull.extra$regionII]
+ }
+}
+\source{Strauss (1975). The plot of the data published by Strauss (1975)
+ was scanned and digitised by Sandra Pereira, University of
+ Western Australia, 2002.
+}
+\seealso{
+ \code{\link[spatstat.data]{redwood}}
+}
+\references{
+ Diggle, P.J. (1983)
+ \emph{Statistical analysis of spatial point patterns}.
+ Academic Press.
+
+ Ripley, B.D. (1977)
+ Modelling spatial patterns (with discussion).
+ \emph{Journal of the Royal Statistical Society, Series B}
+ \bold{39}, 172--212.
+
+ Strauss, D.J. (1975)
+ A model for clustering.
+ \emph{Biometrika} \bold{62}, 467--475.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/residualspaper.Rd b/man/residualspaper.Rd
new file mode 100755
index 0000000..77fd948
--- /dev/null
+++ b/man/residualspaper.Rd
@@ -0,0 +1,96 @@
+\name{residualspaper}
+\alias{residualspaper}
+\docType{data}
+\title{
+ Data and Code From JRSS Discussion Paper on Residuals
+}
+\description{
+ This dataset contains the point patterns
+ used as examples in the paper of Baddeley et al (2005).
+ [Figure 2 is already available in \pkg{spatstat}
+ as the \code{\link[spatstat.data]{copper}} dataset.]
+
+ R code is also provided to reproduce all
+ the Figures displayed in Baddeley et al (2005).
+ The component \code{plotfig}
+ is a function, which can be called
+ with a numeric or character argument specifying the Figure or Figures
+ that should be plotted. See the Examples.
+}
+\format{
+ \code{residualspaper} is a list with the following components:
+ \describe{
+ \item{Fig1}{
+ The locations of Japanese pine seedlings and saplings
+ from Figure 1 of the paper.
+ A point pattern (object of class \code{"ppp"}).
+ }
+ \item{Fig3}{
+ The Chorley-Ribble data from Figure 3 of the paper.
+ A list with three components, \code{lung}, \code{larynx}
+ and \code{incin}. Each is a matrix with 2 columns
+ giving the coordinates of the lung cancer cases,
+ larynx cancer cases, and the incinerator, respectively.
+ Coordinates are Eastings and Northings in km.
+ }
+ \item{Fig4a}{
+ The synthetic dataset in Figure 4 (a) of the paper.
+ }
+ \item{Fig4b}{
+ The synthetic dataset in Figure 4 (b) of the paper.
+ }
+ \item{Fig4c}{
+ The synthetic dataset in Figure 4 (c) of the paper.
+ }
+ \item{Fig11}{
+ The covariate displayed in Figure 11. A pixel image (object of
+ class \code{"im"}) whose pixel values are distances to the
+ nearest line segment in the \code{copper} data.
+ }
+ \item{plotfig}{A function which will compute and plot
+ any of the Figures from the paper. The argument of
+ \code{plotfig} is either a numeric vector or a character vector,
+ specifying the Figure or Figures to be plotted. See the Examples.
+ }
+ }
+}
+\usage{data(residualspaper)}
+\examples{
+
+\dontrun{
+ data(residualspaper)
+
+ if(require(spatstat)) {
+
+ X <- residualspaper$Fig4a
+ summary(X)
+ plot(X)
+
+ # reproduce all Figures
+ residualspaper$plotfig()
+
+ # reproduce Figures 1 to 10
+ residualspaper$plotfig(1:10)
+
+ # reproduce Figure 7 (a)
+ residualspaper$plotfig("7a")
+ }
+}
+}
+\source{
+ Figure 1: Prof M. Numata. Data kindly supplied by Professor Y. Ogata
+ with kind permission of Prof M. Tanemura.
+
+ Figure 3: Professor P.J. Diggle (rescaled by \adrian)
+
+ Figure 4 (a,b,c): \adrian
+}
+\references{
+ Baddeley, A., Turner, R., \ifelse{latex}{\out{M\o ller}}{Moller}, J. and Hazelton, M. (2005)
+ Residual analysis for spatial point processes.
+ \emph{Journal of the Royal Statistical Society, Series B}
+ \bold{67}, 617--666.
+}
+\keyword{datasets}
+\keyword{spatial}
+\keyword{models}
diff --git a/man/shapley.Rd b/man/shapley.Rd
new file mode 100755
index 0000000..be86c64
--- /dev/null
+++ b/man/shapley.Rd
@@ -0,0 +1,100 @@
+\name{shapley}
+\alias{shapley}
+\alias{shapley.extra}
+\docType{data}
+\title{Galaxies in the Shapley Supercluster}
+\description{
+ A point pattern recording the sky positions of 4215 galaxies
+ in the Shapley Supercluster.
+}
+\format{
+ \code{shapley} is an object of class \code{"ppp"}
+ representing the point pattern of galaxy locations
+ (see \code{\link[spatstat]{ppp.object}}).
+
+ \code{shapley.extra} is a list containing additional data
+ described under Notes.
+}
+\usage{data(shapley)}
+\examples{
+ data(shapley)
+ if(require(spatstat)) {
+ shapley.extra$plotit(main="Shapley Supercluster")
+ }
+}
+\source{M.J. Drinkwater, Department of Physics, University of
+ Queensland}
+\section{Notes}{
+ This dataset comes from a survey by Drinkwater et al (2004)
+ of the Shapley Supercluster, one of the most massive concentrations
+ of galaxies in the local universe. The data give the sky positions
+ of 4215 galaxies observed using the FLAIR-II spectrograph
+ on the UK Schmidt Telescope (UKST). They were kindly provided by
+ Dr Michael Drinkwater through the Centre for Astrostatistics
+ at Penn State University.
+
+ Sky positions are given using the coordinates
+ Right Ascension (degrees from 0 to 360) and
+ Declination (degrees from -90 to 90).
+
+ The point pattern has three mark variables:
+ \describe{
+ \item{Mag}{
+ Galaxy magnitude (a negative logarithmic measure of
+ visible brightness).
+ }
+ \item{V}{
+ Recession velocity (km/sec) inferred from redshift,
+ with corrections applied.
+ }
+ \item{SigV}{
+ Estimated standard error for \code{V}.
+ }
+ }
+ The region covered by the survey was approximately the
+ UKST's standard quadrilateral survey fields 382 to 384 and 443 to 446.
+ However, a few of the galaxy positions lie outside these fields.
+
+ The point pattern dataset \code{shapley} consists of all 4215 galaxy
+ locations. The observation window for this pattern is a
+ dilated copy of the convex hull of the galaxy positions,
+ constructed so that all galaxies lie within the window.
+
+ Note that the data contain duplicated points (two points at the
+ same location). To determine which points are duplicates,
+ use \code{\link[spatstat]{duplicated.ppp}}.
+ To remove the duplication, use \code{\link[spatstat]{unique.ppp}}.
+
+ The auxiliary dataset \code{shapley.extra} contains
+ the following components:
+ \describe{
+ \item{\code{UKSTfields}}{
+ a list of seven windows
+ (objects of class \code{"owin"}) giving the UKST standard survey
+ fields.
+ }
+ \item{\code{UKSTdomain}}{
+ the union of these seven fields,
+ an object of class \code{"owin"}.
+ }
+ \item{\code{plotit}}{
+ a function (called without arguments)
+ that will plot the data and the survey fields
+ in the conventional astronomical presentation,
+ in which Right Ascension is converted
+ to hours and minutes (1 hour equals 15 degrees) and
+ Right Ascension decreases as we move to the right of the plot.
+ }
+ }
+}
+\references{
+ Drinkwater, M.J., Parker, Q.A., Proust, D., Slezak, E.
+ and Quintana, H. (2004)
+ The large scale distribution of galaxies in the Shapley
+ Supercluster.
+ \emph{Publications of the Astronomical Society of Australia}
+ \bold{21}, 89-96. \code{DOI 10.1071/AS03057}
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/simba.Rd b/man/simba.Rd
new file mode 100755
index 0000000..272cf0c
--- /dev/null
+++ b/man/simba.Rd
@@ -0,0 +1,37 @@
+\name{simba}
+\alias{simba}
+\docType{data}
+\title{
+ Simulated data from a two-group experiment with replication
+ within each group.
+}
+\description{
+ The \code{simba} dataset contains simulated data from an
+ experiment with a `control' group and a `treatment' group, each
+ group containing 5 experimental units.
+
+ The responses in the experiment are point patterns.
+
+ The responses in the control group are
+ independent realisations of a Poisson point process with intensity 80.
+
+ The responses in the treatment group are independent realisations of
+ a Strauss process with activity parameter \eqn{\beta=100}{beta=100},
+ interaction parameter \eqn{\gamma=0.5}{gamma=0.5} and
+ interaction radius \eqn{R=0.07} in the unit square.
+}
+\format{
+ \code{simba} is a hyperframe with 10 rows, and columns named:
+
+ \itemize{
+ \item \code{Points} containing the point patterns
+ \item \code{group} factor identifying the experimental group,
+ with levels \code{control} and \code{treatment}).
+ }
+}
+\usage{data(simba)}
+\source{
+ Simulated data, generated by \adrian.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/simdat.Rd b/man/simdat.Rd
new file mode 100755
index 0000000..83d8cf4
--- /dev/null
+++ b/man/simdat.Rd
@@ -0,0 +1,30 @@
+\name{simdat}
+\alias{simdat}
+\docType{data}
+\title{
+ Simulated Point Pattern
+}
+\description{
+ This point pattern data set was simulated (using the
+ Metropolis-Hastings algorithm)
+ from a model fitted to the Numata
+ Japanese black pine data set referred to in
+ Baddeley and Turner (2000).
+}
+\format{
+ An object of class \code{"ppp"}
+ in a square window of size 10 by 10 units.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(simdat)}
+\source{\rolf}
+\references{
+ Baddeley, A. and Turner, R. (2000)
+ Practical maximum pseudolikelihood for spatial point patterns.
+ \emph{Australian and New Zealand Journal of Statistics}
+ \bold{42}, 283--322.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/simplenet.Rd b/man/simplenet.Rd
new file mode 100755
index 0000000..ddbc8c4
--- /dev/null
+++ b/man/simplenet.Rd
@@ -0,0 +1,18 @@
+\name{simplenet}
+\alias{simplenet}
+\docType{data}
+\title{
+ Simple Example of Linear Network
+}
+\description{
+ A simple, artificially created, example of a linear network.
+}
+\format{
+ \code{simplenet} is an object of class \code{"linnet"}.
+}
+\usage{data(simplenet)}
+\source{
+ Created by \adrian.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/spatstat.data-package.Rd b/man/spatstat.data-package.Rd
new file mode 100644
index 0000000..9cb47e6
--- /dev/null
+++ b/man/spatstat.data-package.Rd
@@ -0,0 +1,23 @@
+\name{spatstat.data-package}
+\alias{spatstat.data-package}
+\alias{spatstat.data}
+\docType{package}
+\title{The spatstat.data Package}
+\description{
+ The \pkg{spatstat.data} package contains the datasets
+ for the \pkg{spatstat} package.
+}
+\details{
+ The \pkg{spatstat.data} package contains the datasets
+ for the \pkg{spatstat} package.
+}
+\section{Licence}{
+ This library and its documentation are usable under the terms of the
+ \dQuote{GNU General Public License},
+ a copy of which is distributed with \R.
+}
+\author{
+ \spatstatAuthors.
+}
+\keyword{spatial}
+\keyword{package}
diff --git a/man/spiders.Rd b/man/spiders.Rd
new file mode 100755
index 0000000..ce559ec
--- /dev/null
+++ b/man/spiders.Rd
@@ -0,0 +1,68 @@
+\name{spiders}
+\alias{spiders}
+\docType{data}
+\title{
+ Spider Webs on Mortar Lines of a Brick Wall
+}
+\description{
+ Data recording the locations of small spider webs on
+ the network of mortar lines of a brick wall.
+}
+\usage{data("spiders")}
+\format{
+ Object of class \code{"lpp"} representing a pattern of points
+ on a linear network.
+}
+\details{
+The data give the positions of 48 webs
+of the urban wall spider \emph{Oecobius navus}
+on the mortar lines of a brick wall,
+recorded by Voss (1999) and manually digitised by Mark Handcock.
+The mortar spaces provide the only opportunity for constructing webs
+(Voss 1999; Voss et al 2007) so this is a pattern of points on a
+network of lines.
+
+The habitat preferences of this species were studied in detail
+by Voss et al (2007). Questions of interest include evidence for
+non-uniform density of webs and for interaction between nearby individuals.
+
+Observations were made inside a square quadrat of side length 1.125 metres.
+The original hand-drawn map was digitised manually by Mark
+S. Handcock, and reformatted as a \code{spatstat} object by
+Ang Qi Wei.
+
+The dataset \code{spiders} is an object of class \code{"lpp"}
+(point pattern on a linear network). Coordinates are given in millimetres.
+The linear network has 156 vertices and a total length of 20.22 metres.
+
+\emph{Please cite Voss et al (2007) with any use of these data.}
+}
+\source{
+ Dr Sasha Voss. Coordinates manually recorded by M.S. Handcock
+ and formatted by Q.W. Ang.
+
+ \emph{Please cite Voss et al (2007) with any use of these data.}
+}
+\references{
+ Ang, Q.W. (2010)
+ \emph{Statistical methodology for events on a network}.
+ Master's thesis, School of Mathematics and Statistics, University of
+ Western Australia.
+
+ Voss, S. (1999)
+ Habitat preferences and spatial dynamics of the
+ urban wall spider: \emph{Oecobius annulipes} Lucas.
+ Honours Thesis, Department of Zoology, University of Western
+ Australia.
+
+ Voss, S., Main, B.Y. and Dadour, I.R. (2007)
+ Habitat preferences of the urban wall spider
+ \emph{Oecobius navus} (Araneae, Oecobiidae).
+ \emph{Australian Journal of Entomology} \bold{46}, 261--268.
+}
+\examples{
+ if(require(spatstat)) {
+plot(spiders, show.window=FALSE, pch=16)
+ }
+}
+\keyword{datasets}
diff --git a/man/sporophores.Rd b/man/sporophores.Rd
new file mode 100755
index 0000000..8f29878
--- /dev/null
+++ b/man/sporophores.Rd
@@ -0,0 +1,47 @@
+\name{sporophores}
+\alias{sporophores}
+\docType{data}
+\title{
+ Sporophores Data
+}
+\description{
+ Spatial pattern of sporophores of three species of fungi around a tree.
+}
+\usage{data(sporophores)}
+\format{
+ A multitype spatial point pattern (an object of class \code{"ppp"}
+ with factor-valued marks indicating the species).
+ Spatial coordinates are given in centimetres.
+ Levels of the species variable are
+ \code{"L laccata"}, \code{"L pubescens"} and \code{"Hebloma spp"}.
+}
+\details{
+ Ford, Mason and Pelham (1980) studied the spatial locations
+ of sporophores of three species of mycorrhizal fungi
+ distributed around a young birch tree in agricultural soil.
+ The dataset given here is the spatial pattern
+ in the fifth year after the tree was planted.
+ The species are
+ \emph{Laccaria laccata}, \emph{Lactarius pubescens}
+ and \emph{Hebloma} spp.
+}
+\source{
+ Data generously provided by Dr E.D. Ford.
+ Please cite Ford et al (1980) in any use of these data.
+}
+\references{
+ Ford, E.D., Mason, P.A. and Pelham, J. (1980)
+ Spatial patterns of sporophore distribution around a
+ young birch tree in three successive years.
+ \emph{Transactions of the British Mycological Society}
+ \bold{75}, 287--296.
+}
+\examples{
+ if(require(spatstat)) {
+## reproduce Fig 1 in Ford et al (1980)
+plot(sporophores, chars=c(16,1,2), cex=0.6, leg.args=list(cex=1.1))
+points(0,0,pch=16, cex=2)
+text(15,8,"Tree", cex=0.75)
+ }
+}
+\keyword{datasets}
diff --git a/man/spruces.Rd b/man/spruces.Rd
new file mode 100755
index 0000000..00bd4cf
--- /dev/null
+++ b/man/spruces.Rd
@@ -0,0 +1,64 @@
+\name{spruces}
+\alias{spruces}
+\docType{data}
+\title{
+ Spruces Point Pattern
+}
+\description{
+ The data give the locations of Norwegian spruce trees
+ in a natural forest stand in Saxonia, Germany.
+ Each tree is marked with its diameter at breast height.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations
+ in a 56 x 38 metre sampling region. Each tree is marked
+ with its diameter at breast height. All values are given in metres.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object. The marks are numeric.
+
+ These data have been analysed by Fiksel (1984, 1988),
+ Stoyan et al (1987), Penttinen et al (1992) and
+ Goulard et al (1996).
+}
+\usage{data(spruces)}
+\source{Stoyan et al (1987). Original source unknown.}
+\examples{
+ if(require(spatstat)) {
+ plot(spruces)
+ # To reproduce Goulard et al. Figure 3
+ # (Goulard et al: "influence zone radius equals 5 * stem diameter")
+ # (spatstat help(plot.ppp): "size of symbol = diameter")
+ plot(spruces, maxsize=10*max(spruces$marks))
+ plot(unmark(spruces), add=TRUE)
+ }
+}
+\references{
+ Fiksel, T. (1984)
+ Estimation of parameterized pair potentials of marked and
+ nonmarked Gibbsian point processes.
+ \emph{Elektron. Informationsverarb. u. Kybernet.}
+ \bold{20}, 270--278.
+
+ Fiksel, T. (1988)
+ Estimation of interaction potentials of Gibbsian point processes.
+ \emph{Statistics}
+ \bold{19}, 77-86
+
+ Goulard, M., S\"arkk\"a, A. and Grabarnik, P. (1996)
+ Parameter estimation for marked Gibbs point
+ processes through the maximum pseudolikelihood method.
+ \emph{Scandinavian Journal of Statistics}
+ \bold{23}, 365--379.
+
+ Penttinen, A., Stoyan, D. and Henttonen, H. (1992)
+ Marked point processes in forest statistics.
+ \emph{Forest Science} \bold{38}, 806--824.
+
+ Stoyan, D., Kendall, W.S. and Mecke, J. (1987)
+ \emph{Stochastic Geometry and its Applications}.
+ Wiley.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/swedishpines.Rd b/man/swedishpines.Rd
new file mode 100755
index 0000000..d90d66b
--- /dev/null
+++ b/man/swedishpines.Rd
@@ -0,0 +1,52 @@
+\name{swedishpines}
+\alias{swedishpines}
+\docType{data}
+\title{
+ Swedish Pines Point Pattern
+}
+\description{
+ The data give the locations of pine saplings
+ in a Swedish forest.
+}
+\format{
+ An object of class \code{"ppp"}
+ representing the point pattern of tree locations
+ in a rectangular plot 9.6 by 10 metres.
+
+ Cartesian coordinates are given in decimetres (multiples of 0.1 metre)
+ rounded to the nearest decimetre.
+ Type \code{\link[spatstat]{rescale}(swedishpines)} to get an equivalent dataset
+ where the coordinates are expressed in metres.
+
+ See \code{\link[spatstat]{ppp.object}} for details of the format of a
+ point pattern object.
+}
+\usage{data(swedishpines)}
+\source{Strand (1972), Ripley (1981)}
+\section{Note}{
+ For previous analyses see Ripley (1981, pp. 172-175),
+ Venables and Ripley (1997, p. 483),
+ Baddeley and Turner (2000).
+}
+\references{
+ Baddeley, A. and Turner, R. (2000)
+ Practical maximum pseudolikelihood for spatial point patterns.
+ \emph{Australian and New Zealand Journal of Statistics}
+ \bold{42}, 283--322.
+
+ Ripley, B.D. (1981)
+ \emph{Spatial statistics}.
+ John Wiley and Sons.
+
+ Strand, L. (1972).
+ A model for stand growth.
+ \emph{IUFRO Third Conference Advisory Group of Forest Statisticians},
+ INRA, Institut National de la Recherche Agronomique, Paris.
+ Pages 207--216.
+
+ Venables, W.N. and Ripley, B.D. (1997)
+ \emph{Modern applied statistics with S-PLUS}.
+ Second edition. Springer Verlag.
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/urkiola.Rd b/man/urkiola.Rd
new file mode 100755
index 0000000..dd005a8
--- /dev/null
+++ b/man/urkiola.Rd
@@ -0,0 +1,35 @@
+\encoding{latin1}
+\name{urkiola}
+\alias{urkiola}
+\docType{data}
+\title{Urkiola Woods Point Pattern}
+\description{
+ Locations of birch (\emph{Betula celtiberica}) and
+ oak (\emph{Quercus robur}) trees in a secondary wood in
+ Urkiola Natural Park (Basque country, northern Spain).
+ They are part of a more extensive dataset collected
+ and analysed by Laskurain (2008). The coordinates of the trees
+ are given in meters.
+}
+\usage{data(urkiola)}
+\format{
+ An object of class \code{"ppp"} representing the point pattern of
+ tree locations. Entries include
+ \describe{
+ \item{x}{Cartesian x-coordinate of tree}
+ \item{y}{Cartesian y-coordinate of tree }
+ \item{marks}{factor indicating species of each tree}
+ }
+ The levels of \code{marks} are \code{birch} and \code{oak}.
+ See \code{\link[spatstat]{ppp.object}}
+ for details of the format of a ppp object.
+}
+\source{N.A. Laskurain. Kindly formatted and communicated by M. de la Cruz Rot}
+\references{
+ Laskurain, N. A. (2008)
+ \emph{\enc{Din�mica}{Dinamica} espacio-temporal de un bosque
+ secundario en el Parque Natural de Urkiola (Bizkaia).}
+ Tesis Doctoral. Universidad del \enc{Pa�s}{Pais} Vasco /Euskal Herriko
+ Unibertsitatea.
+}
+\keyword{datasets}
diff --git a/man/vesicles.Rd b/man/vesicles.Rd
new file mode 100755
index 0000000..26a1b08
--- /dev/null
+++ b/man/vesicles.Rd
@@ -0,0 +1,96 @@
+\name{vesicles}
+\alias{vesicles}
+\alias{vesicles.extra}
+\docType{data}
+\title{
+ Vesicles Data
+}
+\description{
+ Point pattern of synaptic vesicles observed in rat brain tissue.
+}
+\usage{data(vesicles)}
+\format{
+ The dataset \code{vesicles} is a point pattern
+ (object of class \code{"ppp"}) representing the location
+ of the synaptic vesicles. The window of the point pattern
+ represents the region of presynapse where synaptic vesicles were
+ observed in this study.
+ There is a hole in the window, representing the region occupied by
+ mitochondria, where synaptic vesicles do not occur.
+
+ The dataset \code{vesicles.extra} is a list with entries
+ \tabular{ll}{
+ \code{presynapse}\tab outer polygonal boundary of presynapse \cr
+ \code{mitochondria} \tab polygonal boundary of mitochondria \cr
+ \code{mask} \tab binary mask representation of vesicles window \cr
+ \code{activezone} \tab line segment pattern representing \cr
+ \tab the active zone.
+ }
+ All coordinates are in nanometres (nm).
+}
+\details{
+ As part of a study on the effects of stress on brain function,
+ Khanmohammadi et al (2014) analysed the spatial pattern of
+ synaptic vesicles in 45-nanometre-thick sections of
+ rat brain tissue visualised in transmission electron microscopy.
+
+ To investigate the influence of stress, Khanmohammadi et al (2014)
+ study the distribution of the synaptic vesicles in
+ the pre-synaptic neuron in relation to the active zone of the
+ presynaptic membrane. They hypothesize that the synaptic vesicle density
+ is a decreasing function of distance to the active zone.
+
+ The boundaries for the active zone, mitochondria, pre- and post
+ synaptic terminals, and the centre of the synaptic vesicles
+ were annotated by hand on the image.
+}
+\section{Raw Data}{
+ For demonstration and training purposes,
+ the raw data files for this dataset are also
+ provided in the \pkg{spatstat} package installation:
+ \tabular{ll}{
+ \code{vesicles.txt}\tab spatial locations of vesicles \cr
+ \code{presynapse.txt}\tab vertices of \code{presynapse} \cr
+ \code{mitochondria.txt} \tab vertices of \code{mitochondria} \cr
+ \code{vesiclesimage.tif} \tab greyscale microscope image \cr
+ \code{vesiclesmask.tif} \tab binary image of \code{mask} \cr
+ \code{activezone.txt} \tab coordinates of \code{activezone}
+ }
+ The files are in the folder \code{rawdata/vesicles} in the
+ \pkg{spatstat} installation directory. The precise location of the
+ files can be obtained using \code{\link[base]{system.file}}, as shown
+ in the examples.
+}
+\source{
+ Nicoletta Nava, Mahdieh Khanmohammadi and Jens Randel Nyengaard.
+ Experiment performed by Nicoletta Nava at the
+ Stereology and Electron Microscopy Laboratory, Aarhus University,
+ Denmark. Images were annotated by Mahdieh Khanmohammadi
+ at the Department of Computer Science, University of Copenhagen.
+ Jens Randel Nyengaard provided supervision and guidance,
+ and curated the data.
+}
+\references{
+ Khanmohammadi, M., Waagepetersen, R., Nava, N.,
+ Nyengaard, J.R. and Sporring, J. (2014)
+ Analysing the distribution of synaptic vesicles using a
+ spatial point process model.
+ \emph{5th ACM Conference on Bioinformatics, Computational Biology
+ and Health Informatics}, Newport Beach, CA, USA, September 2014.
+}
+\examples{
+ if(require(spatstat)) {
+plot(vesicles)
+with(vesicles.extra,
+ plot(activezone, add=TRUE, col="red"))
+ }
+
+## read coordinates of vesicles from raw data, for training purposes
+vf <- system.file("rawdata", "vesicles", "vesicles.txt",
+ package="spatstat.data")
+if(!any(nzchar(vf)))
+ stop("Could not find raw data file vesicles.txt")
+vdf <- read.table(vf, header=TRUE)
+}
+\keyword{spatial}
+\keyword{datasets}
diff --git a/man/waka.Rd b/man/waka.Rd
new file mode 100755
index 0000000..d5704f2
--- /dev/null
+++ b/man/waka.Rd
@@ -0,0 +1,46 @@
+\name{waka}
+\alias{waka}
+\docType{data}
+\title{
+ Trees in Waka national park
+}
+\description{
+ This dataset is a spatial point pattern of trees
+ recorded at Waka National Park, Gabon.
+ See Balinga et al (2006).
+
+ The dataset \code{waka} is a point pattern
+ (object of class \code{"ppp"}) containing the spatial coordinates
+ of each tree, marked by the tree diameter at breast height
+ \code{dbh}.
+ The survey region is a 100 by 100 metre squawre.
+ Coordinates are given in metres, while the \code{dbh} is in centimetres.
+}
+\usage{data(waka)}
+\examples{
+data(waka)
+ if(require(spatstat)) {
+plot(waka, markscale=0.01)
+title(sub="Tree diameters to scale")
+plot(waka, markscale=0.04)
+title(sub="Tree diameters 4x scale")
+ }
+}
+\source{
+ Nicolas Picard
+}
+\references{
+ Balinga, M., Sunderland, T., Walters, G., Issemb{\'e}, Y., Asaha, S.
+ and Fombod, E. (2006)
+ \emph{A vegetation assessment of the Waka national park, Gabon.}
+ Herbier National du Gabon, LBG, MBG, WCS, FRP and
+ Simthsonian Institution, Libreville, Gabon. CARPE Report, 154 pp.
+ \url{http://carpe.umd.edu/}
+
+ Picard, N., Bar-Hen, A., Mortier, F. and Chadoeuf, J. (2009)
+ The multi-scale marked area-interaction point process: a model for
+ the spatial pattern of trees.
+ \emph{Scandinavian Journal of Statistics} \bold{36} 23--41
+}
+\keyword{datasets}
+\keyword{spatial}
diff --git a/man/waterstriders.Rd b/man/waterstriders.Rd
new file mode 100755
index 0000000..f9ce303
--- /dev/null
+++ b/man/waterstriders.Rd
@@ -0,0 +1,59 @@
+\name{waterstriders}
+\alias{waterstriders}
+\docType{data}
+\title{
+ Waterstriders data.
+ Three independent replications of a point pattern
+ formed by insects.
+}
+\description{
+ The territorial behaviour of an insect group
+ called waterstriders was studied in
+ a series of laboratory experiments by Dr Matti Nummelin
+ (University of Helskini). The data were analysed in
+ the pioneering PhD thesis of Antti Penttinen (1984).
+
+ The dataset \code{waterstriders} is
+ a list of three point patterns. Each point pattern gives
+ the locations of larvae of the waterstrider
+ \emph{Limnoporus (Gerris) rufoscutellatus} (larval stage V)
+ in a homogeneous area about 48 cm square. The point
+ patterns can be assumed to be independent.
+
+ It is known that this species of waterstriders
+ exhibits territorialism at older larvae stages and at the
+ adult stage. Therefore, if any deviation from Complete Spatial
+ Randomness exists in these three point patterns, it is expected
+ to be towards inhibition.
+
+ The data were obtained from photographs which were scanned manually.
+ The waterstriders are in a pool which is larger than the picture.
+ A guard area (width about 2.5 cm) has been deleted because
+ it is a source of inhomogeneity to interactions.
+
+ Penttinen (1984, chapter 5) fitted a pairwise interaction model with
+ a Strauss/hardcore interaction (see \code{\link[spatstat]{StraussHard}})
+ with hard core radius 1.5 cm and interaction radius 4.5 cm.
+}
+\format{
+ \code{waterstriders} is a list of three point patterns
+ (objects of class \code{"ppp"}). It also has class \code{"listof"}
+ so that it can be plotted and printed directly. The point pattern
+ coordinates are in centimetres.
+}
+\usage{data(waterstriders)}
+\source{
+ Data were collected by Dr. Matti Nummelin (University of
+ Helsinki, Finland).
+ Data kindly provided by Prof. Antti Penttinen,
+ University of Jyv\"askyl\"a, Finland.
+}
+\references{
+Penttinen, A. (1984)
+Modelling interaction in spatial point patterns:
+parameter estimation by the maximum likelihood method.
+\emph{Jyv\"askyl\"a Studies in Computer Science, Economics and
+ Statistics} \bold{7}, University of {Jyv\"askyl\"a}, Finland.
+}
+\keyword{datasets}
+\keyword{spatial}
--
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