[r-cran-erm] 09/33: Import Debian patch 0.12-2.3-1
Andreas Tille
tille at debian.org
Mon Dec 12 11:19:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-erm.
commit 118cec7cf440adfb8770fe77c750999498d69309
Merge: c6f5406 a922e3f
Author: Julian Gilbey <jdg at debian.org>
Date: Thu Jun 3 11:24:17 2010 +0100
Import Debian patch 0.12-2.3-1
DESCRIPTION | 54 ++--
NAMESPACE | 1 +
NEWS | 34 +++
R/LRtest.Rm.R | 15 +-
R/MLoef.R | 15 +-
R/cmlprep.R | 50 ++--
R/datcheck.R | 4 +-
R/fitcml.R | 100 ++++----
R/invalid.R | 13 +
R/itemfit.ppar.r | 14 +-
R/likLR.R | 2 +-
R/personfit.ppar.R | 13 +-
R/pifit.internal.r | 7 +-
R/plotPImap.R | 40 ++-
R/plotPWmap.R | 228 +++++++++++++++++
R/print.ifit.R | 4 +-
R/print.pfit.R | 4 +-
debian/README.Debian | 11 -
debian/changelog | 8 +
debian/control | 4 +-
debian/patches/01_plotPImap-bugfixes | 41 ---
debian/patches/01_plotPWmap_patches | 193 ++++++++++++++
debian/patches/02_plotPImap-pp-reuse | 53 ----
debian/patches/03_plotPImap-prettify | 76 ------
debian/patches/04_PathwayMap | 469 -----------------------------------
debian/patches/series | 5 +-
inst/doc/Rplots.pdf | 119 ++++-----
inst/doc/{eRmvig.R => eRm.R} | 0
inst/doc/{eRmvig.Rnw => eRm.Rnw} | 0
inst/doc/{eRmvig.pdf => eRm.pdf} | Bin 433168 -> 433229 bytes
man/LRtest.Rd | 1 +
man/MLoef.Rd | 5 +-
man/eRm-package.Rd | 17 +-
man/plotPImap.Rd | 13 +-
man/plotPWmap.Rd | 106 ++++++++
src/eRm.dll | Bin 0 -> 5632 bytes
36 files changed, 847 insertions(+), 872 deletions(-)
diff --cc debian/changelog
index 7cf3dd3,0000000..86baa38
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,51 -1,0 +1,59 @@@
++erm (0.12-2.3-1) unstable; urgency=low
++
++ * New upstream release
++ * Upstream now incorporates all of the patches in version 0.12-0-6, so
++ these have been removed from the package (thanks!)
++
++ -- Julian Gilbey <jdg at debian.org> Thu, 03 Jun 2010 11:24:17 +0100
++
+erm (0.12-0-6) unstable; urgency=low
+
+ * Fix showstopping-bug in plotPathwayMap which broke the code if there
+ were any NA values in the data
+ * Rename plotPathwayMap to plotPWMap, following upstream's request
+ * plotPWMap enhancements requested by upstream: Offer options for colour
+ and size of confidence intervals allow plotting both persons and items
+ on same plot; allow not plotting confidence intervals;
+
+ -- Julian Gilbey <jdg at debian.org> Tue, 01 Jun 2010 11:35:33 +0100
+
+erm (0.12-0-5) unstable; urgency=low
+
+ * Fixed incorrect Build-Depends; hopefully this will work, but can't be
+ sure as pbuilder isn't working (bug in util-linux) (Closes: #583770)
+
+ -- Julian Gilbey <jdg at debian.org> Sun, 30 May 2010 19:47:44 +0100
+
+erm (0.12-0-4) unstable; urgency=low
+
+ * Fixed incorrect variable name in plotPathwayMap (thanks to Reinhold
+ Hatzinger again)
+
+ -- Julian Gilbey <jdg at debian.org> Sun, 23 May 2010 23:49:55 +0100
+
+erm (0.12-0-3) unstable; urgency=low
+
+ * Fix bug with plotPathwayMap - failed if pp was not given as a
+ parameter
+ * Allow more colour possibilities for nonordinal warnings in plotPImap
+ (with thanks to Reinhold Hatzinger for suggesting this)
+
+ -- Julian Gilbey <jdg at debian.org> Mon, 17 May 2010 21:54:21 +0100
+
+erm (0.12-0-2) unstable; urgency=low
+
+ * Fixed dRM -> dRm bug in plotPImap
+ * Fixed missing warning labels in plotPImap
+
+ -- Julian Gilbey <jdg at debian.org> Sun, 16 May 2010 21:53:16 +0100
+
+erm (0.12-0-1) unstable; urgency=low
+
+ * Initial Debian release (Closes: #544402)
+ * Fixed subsetting bugs in plotPImap code, and allowed reuse of
+ person.parameter calculations
+ * Added Infit and Outfit t statistics, as per Rating Scale Analysis by
+ Wright and Masters
+ * Added ability to plot (slightly modified) Bond-and-Fox Pathway Maps
+
+ -- Julian Gilbey <jdg at debian.org> Sun, 16 May 2010 17:13:21 +0100
diff --cc debian/control
index b62d62d,0000000..1d33dd3
mode 100644,000000..100644
--- a/debian/control
+++ b/debian/control
@@@ -1,24 -1,0 +1,24 @@@
+Source: erm
+Section: gnu-r
+Priority: optional
+Maintainer: Julian Gilbey <jdg at debian.org>
+Build-Depends: debhelper (>> 7), r-base-dev (>= 2.9.0-4), cdbs, r-cran-mass,
- r-cran-raschsampler, r-cran-gtools
++ r-cran-raschsampler
+Standards-Version: 3.8.4
+Homepage: http://cran.r-project.org/web/packages/eRm/index.html
+
+Package: r-cran-erm
+Architecture: any
- Depends: r-base-core (>= 2.8.1), r-cran-gtools, r-cran-mass,
++Depends: r-base-core (>= 2.8.1), r-cran-mass,
+ r-cran-raschsampler, ${shlibs:Depends}, ${misc:Depends}
+Description: GNU R package for 'extended Rasch modelling'
+ eRm fits Rasch models (RM), linear logistic test models (LLTM),
+ rating scale model (RSM), linear rating scale models (LRSM), partial
+ credit models (PCM), and linear partial credit models (LPCM). Missing
+ values are allowed in the data matrix. Additional features are the ML
+ estimation of the person parameters, Andersen's LR-test,
+ item-specific Wald test, itemfit and personfit statistics including
+ infit and outfit measures, various ICC and related plots, automated
+ stepwise item elimination, simulation module for various binary data
+ matrices. An eRm platform is provided at R-forge (see URL).
+
diff --cc debian/patches/01_plotPWmap_patches
index 0000000,0000000..6ca3b46
new file mode 100644
--- /dev/null
+++ b/debian/patches/01_plotPWmap_patches
@@@ -1,0 -1,0 +1,193 @@@
++--- a/R/plotPWmap.R
+++++ b/R/plotPWmap.R
++@@ -50,18 +50,46 @@
++ tl<-tlevels
++ }
++
++- ## Item subsetting is pretty ugly as there are multiple cases.
+++ if (is.null(pp))
+++ suppressWarnings(pp<-person.parameter(object))
+++ else if (class(pp) != "ppar" || !identical(pp$X,object$X))
+++ stop("pp is not a person.parameter object which matches the main Rasch data object!")
+++
+++
+++ ## We will be plotting the infit data versus the parameters for
+++ ## both items and persons
+++ iloc<-tt[,1]
+++ ise<-tt[,2]
+++ ifit <- itemfit(pp)
+++ ifitZ <- ifit$i.infitZ
+++
+++ ploc <- as.matrix(pp$theta.table['Person Parameter'])[,1]
+++ pse <- unlist(pp$se.theta, recursive=FALSE)
+++ names(pse) <- sub("^NAgroup[0-9]*\\.","",names(pse))
+++ pfit <- personfit(pp)
+++ pfitZ <- pfit$p.infitZ
+++
+++ ## We can now do item and person subsetting; the item subsetting is
+++ ## pretty ugly as there are multiple cases. (We dare not do it earlier
+++ ## as we have to take items from all of iloc, ise and ifitZ.)
++ if (imap && is.character(item.subset)) {
++ ## Case 1: item subsetting by item names
++ if (dRm) {
++- if (length(item.subset)>1 && all(item.subset %in% rownames(tt)))
++- tt<-tt[item.subset,]
+++ if (length(item.subset)>1 && all(item.subset %in% rownames(tt))) {
+++ iloc <- iloc[item.subset]
+++ ise <- ise[item.subset]
+++ ifitZ <- ifitZ[item.subset]
+++ tt <- tt[item.subset,]
+++ }
++ else if(length(item.subset)!=1 || !(item.subset=="all"))
++ stop("item.subset misspecified. Use 'all' or vector of at least two valid item indices/names.")
++ } else {
++ if (length(item.subset)>1 && all(item.subset %in% rownames(as.matrix(tl)))) {
++- keep.subset<-NULL
++- tl<-tl[item.subset]
+++ iloc <- iloc[item.subset]
+++ ise <- ise[item.subset]
+++ ifitZ <- ifitZ[item.subset]
+++ tl <- tl[item.subset]
+++
++ for (i in rownames(as.matrix(tl)))
++ if (tl[i]==1)
++ keep.subset<-c(keep.subset,i)
++@@ -75,14 +103,22 @@
++ } else if (imap) {
++ ## Case 2: item subsetting by item numbers
++ if (dRm) {
++- if (length(item.subset)>1 && all(item.subset %in% 1:nrow(tt)))
++- tt<-tt[item.subset,]
+++ if (length(item.subset)>1 && all(item.subset %in% 1:nrow(tt))) {
+++ iloc <- iloc[item.subset]
+++ ise <- ise[item.subset]
+++ ifitZ <- ifitZ[item.subset]
+++ tt <- tt[item.subset,]
+++ }
++ else
++ stop("item.subset misspecified. Use 'all' or vector of at least two valid item indices/names.")
++ }
++ else {
++ if (length(item.subset)>1 && all(item.subset %in% 1:length(tl))) {
++- tl<-tl[item.subset]
+++ iloc <- iloc[item.subset]
+++ ise <- ise[item.subset]
+++ ifitZ <- ifitZ[item.subset]
+++ tl <- tl[item.subset]
+++
++ for (i in rownames(as.matrix(tl)))
++ if (tl[i]==1)
++ keep.subset<-c(keep.subset,i)
++@@ -95,44 +131,23 @@
++ }
++ }
++
++- ## We have to postpone the person subsetting code until after we have
++- ## done the person plot calculations
++-
++- if (is.null(pp))
++- suppressWarnings(pp<-person.parameter(object))
++- else if (class(pp) != "ppar" || !identical(pp$X,object$X))
++- stop("pp is not a person.parameter object which matches the main Rasch data object!")
++-
++- ## We plot the infit data versus the parameters for both items and persons
++- iloc<-tt[,1]
++- ise<-tt[,2]
++- ifit <- itemfit(pp)
++- ifitZ <- ifit$i.infitZ
++-
++- ploc <- as.matrix(pp$theta.table['Person Parameter'])
++- pse <- unlist(pp$se.theta, recursive=FALSE)
++- names(pse) <- sub("^NAgroup[0-9]*\\.","",names(pse))
++- pse <- as.matrix(pse)
++- pfit <- personfit(pp)
++- pfitZ <- pfit$p.infitZ
++-
++ ## We can now do person subsetting; this is significantly easier than
++ ## item subsetting, as there is no dRM/eRm distinction.
++ if (pmap && is.character(person.subset)) {
++ ## Case 1: person subsetting by person names
++- if (length(person.subset)>1 && all(person.subset %in% rownames(ploc))) {
++- ploc<-ploc[person.subset,]
++- pse<-pse[person.subset,]
++- pfitZ<-pfitZ[person.subset]
+++ if (length(person.subset)>1 && all(person.subset %in% names(ploc))) {
+++ ploc <- ploc[person.subset]
+++ pse <- pse[person.subset]
+++ pfitZ <- pfitZ[person.subset]
++ }
++ else if(length(person.subset)!=1 || !(person.subset=="all"))
++ stop("person.subset misspecified. Use 'all' or vector of at least two valid person indices/names.")
++ } else if (pmap) {
++ ## Case 2: person subsetting by person numbers
++- if (length(person.subset)>1 && all(person.subset %in% 1:nrow(ploc))) {
++- ploc<-ploc[person.subset,]
++- pse<-pse[person.subset,]
++- pfitZ<-pfitZ[person.subset]
+++ if (length(person.subset)>1 && all(person.subset %in% 1:length(ploc))) {
+++ ploc <- ploc[person.subset]
+++ pse <- pse[person.subset]
+++ pfitZ <- pfitZ[person.subset]
++ }
++ else
++ stop("person.subset misspecified. Use 'all' or vector of at least two valid person indices/names.")
++@@ -183,19 +198,21 @@
++ }
++
++ if (pmap && !imap) {
++- xrange = xrange.pmap
++- yrange = yrange.pmap
++- maintitle = mainperson
+++ xrange <- xrange.pmap
+++ yrange <- yrange.pmap
+++ maintitle <- mainperson
++ } else if (!pmap && imap) {
++- xrange = xrange.imap
++- yrange = yrange.imap
++- maintitle = mainitem
+++ xrange <- xrange.imap
+++ yrange <- yrange.imap
+++ maintitle <- mainitem
++ } else {
+++ xrange <- numeric(2)
+++ yrange <- numeric(2)
++ xrange[1] <- min(xrange.pmap[1], xrange.imap[1])
++ xrange[2] <- max(xrange.pmap[2], xrange.imap[2])
++ yrange[1] <- min(yrange.pmap[1], yrange.imap[1])
++ yrange[2] <- max(yrange.pmap[2], yrange.imap[2])
++- maintitle = mainboth
+++ maintitle <- mainboth
++ }
++
++ par(mar=c(5,4,4,2))
++@@ -209,7 +226,7 @@
++ arrows(zt,ploc+pci*pse, zt,ploc-pci*pse, angle=90, code=3, length=0.04,
++ col=personCI$col, lty=personCI$lty)
++ points(zt,ploc,pch=person.pch,cex=0.6)
++- text(zt,ploc,rownames(ploc),cex=cex.gen,pos=4)
+++ text(zt,ploc,names(ploc),cex=cex.gen,pos=4)
++ }
++ if (imap) { ## item map
++ if (dRm)
++--- a/R/itemfit.ppar.r
+++++ b/R/itemfit.ppar.r
++@@ -22,7 +22,7 @@
++
++ i.outfitMSQ <- ifit/idf
++
++- qsq.outfitMSQ <- (colSums(sq.res/Vmat^2, na.rm=TRUE)/idf^2) - 1/idf
+++ qsq.outfitMSQ <- (colSums(Cmat/Vmat^2, na.rm=TRUE)/idf^2) - 1/idf
++ q.outfitMSQ <- sqrt(qsq.outfitMSQ)
++
++ isumVmat<-colSums(Vmat)
++--- a/R/personfit.ppar.R
+++++ b/R/personfit.ppar.R
++@@ -32,7 +32,7 @@
++
++ p.outfitMSQ <- pfit/pdf
++
++- qsq.outfitMSQ <- (rowSums(sq.res/Vmat^2, na.rm=TRUE)/pdf^2) - 1/pdf
+++ qsq.outfitMSQ <- (rowSums(Cmat/Vmat^2, na.rm=TRUE)/pdf^2) - 1/pdf
++ q.outfitMSQ <- sqrt(qsq.outfitMSQ)
++
++ psumVmat<-rowSums(Vmat)
diff --cc debian/patches/series
index 48bf41b,0000000..729c849
mode 100644,000000..100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,4 -1,0 +1,1 @@@
- 01_plotPImap-bugfixes
- 02_plotPImap-pp-reuse
- 03_plotPImap-prettify
- 04_PathwayMap
++01_plotPWmap_patches
--
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