[r-cran-msm] 31/31: Merge tag 'upstream/1.6.4'
Sébastien Villemot
sebastien at debian.org
Thu Nov 16 16:17:11 UTC 2017
This is an automated email from the git hooks/post-receive script.
sebastien pushed a commit to branch master
in repository r-cran-msm.
commit c440dbe1271b86de3b50a90fb6ffe10c94622eda
Merge: 9ec99ed 379ae86
Author: Sébastien Villemot <sebastien at debian.org>
Date: Thu Nov 16 17:16:44 2017 +0100
Merge tag 'upstream/1.6.4'
Upstream version 1.6.4
ChangeLog | 2177 +++++++++++++++++++
DESCRIPTION | 21 +
MD5 | 185 ++
NAMESPACE | 133 ++
R/boot.R | 362 ++++
R/constants.R | 150 ++
R/draic.R | 263 +++
R/hmm-dists.R | 196 ++
R/hmm.R | 463 ++++
R/msm.R | 1990 ++++++++++++++++++
R/mstate.R | 57 +
R/olddata.R | 70 +
R/optim.R | 245 +++
R/outputs.R | 1993 ++++++++++++++++++
R/pearson.R | 673 ++++++
R/phase.R | 215 ++
R/simul.R | 368 ++++
R/utils.R | 467 ++++
build/vignette.rds | Bin 0 -> 225 bytes
data/bos3.rda | Bin 0 -> 3106 bytes
data/bos4.rda | Bin 0 -> 3564 bytes
data/msmdata.rda | Bin 0 -> 88345 bytes
inst/CITATION | 19 +
inst/NEWS | 1189 +++++++++++
inst/doc/msm-manual.R | 295 +++
inst/doc/msm-manual.pdf | Bin 0 -> 387496 bytes
man/2phase.Rd | 138 ++
man/MatrixExp.Rd | 89 +
man/aneur.Rd | 54 +
man/boot.msm.Rd | 145 ++
man/bos.Rd | 46 +
man/cav.Rd | 41 +
man/cmodel.object.Rd | 20 +
man/coef.msm.Rd | 35 +
man/crudeinits.msm.Rd | 76 +
man/deltamethod.Rd | 90 +
man/draic.msm.Rd | 130 ++
man/ecmodel.object.Rd | 29 +
man/efpt.msm.Rd | 139 ++
man/ematrix.msm.Rd | 97 +
man/emodel.object.Rd | 37 +
man/fev.Rd | 47 +
man/hazard.msm.Rd | 37 +
man/hmm-dists.Rd | 201 ++
man/hmmMV.Rd | 115 +
man/hmodel.object.Rd | 76 +
man/logLik.msm.Rd | 29 +
man/lrtest.msm.Rd | 32 +
man/medists.Rd | 137 ++
man/model.frame.msm.Rd | 65 +
man/msm.Rd | 987 +++++++++
man/msm.form.qoutput.Rd | 40 +
man/msm.object.Rd | 121 ++
man/msm2Surv.Rd | 137 ++
man/odds.msm.Rd | 38 +
man/paramdata.object.Rd | 70 +
man/pearson.msm.Rd | 262 +++
man/pexp.Rd | 78 +
man/phasemeans.msm.Rd | 37 +
man/plot.msm.Rd | 61 +
man/plot.prevalence.msm.Rd | 80 +
man/plot.survfit.msm.Rd | 110 +
man/plotprog.msm.Rd | 48 +
man/pmatrix.msm.Rd | 127 ++
man/pmatrix.piecewise.msm.Rd | 125 ++
man/pnext.msm.Rd | 90 +
man/ppass.msm.Rd | 126 ++
man/prevalence.msm.Rd | 190 ++
man/print.msm.Rd | 58 +
man/printold.msm.Rd | 23 +
man/psor.Rd | 48 +
man/qcmodel.object.Rd | 40 +
man/qgeneric.Rd | 60 +
man/qmatrix.msm.Rd | 115 +
man/qmodel.object.Rd | 52 +
man/qratio.msm.Rd | 94 +
man/recreate.olddata.Rd | 27 +
man/scoreresid.msm.Rd | 39 +
man/sim.msm.Rd | 74 +
man/simfitted.msm.Rd | 51 +
man/simmulti.msm.Rd | 142 ++
man/sojourn.msm.Rd | 85 +
man/statetable.msm.Rd | 47 +
man/summary.msm.Rd | 37 +
man/surface.msm.Rd | 72 +
man/tnorm.Rd | 95 +
man/totlos.msm.Rd | 194 ++
man/transient.msm.Rd | 22 +
man/viterbi.msm.Rd | 47 +
src/Makevars | 1 +
src/analyticp.c | 1337 ++++++++++++
src/hmm.c | 132 ++
src/hmm.h | 37 +
src/hmmderiv.c | 114 +
src/lik.c | 1604 ++++++++++++++
src/msm.h | 108 +
src/pijt.c | 609 ++++++
tests/test_base.R | 2 +
tests/testthat/helper.r | 27 +
tests/testthat/test_analyticp.r | 262 +++
tests/testthat/test_datasumm.r | 40 +
tests/testthat/test_deriv.r | 184 ++
tests/testthat/test_models.r | 689 ++++++
tests/testthat/test_models_hmm.r | 153 ++
tests/testthat/test_models_hmmmulti.r | 99 +
tests/testthat/test_models_misc.r | 114 +
tests/testthat/test_utils.r | 114 +
vignettes/Sweave-local.sty | 17 +
vignettes/figures/dags/p2q1.odg | Bin 0 -> 7665 bytes
vignettes/figures/dags/p2q1.pdf | 82 +
vignettes/figures/dags/p2q1.ps | 83 +
vignettes/figures/dags/p2q12.odg | Bin 0 -> 7643 bytes
vignettes/figures/dags/p2q12.pdf | 82 +
vignettes/figures/dags/p2q12.ps | 85 +
vignettes/figures/dags/p3q12.odg | Bin 0 -> 7767 bytes
vignettes/figures/dags/p3q12.pdf | Bin 0 -> 1389 bytes
vignettes/figures/dags/p3q12.ps | 87 +
vignettes/figures/dags/p3q124.odg | Bin 0 -> 7809 bytes
vignettes/figures/dags/p3q124.pdf | Bin 0 -> 1409 bytes
vignettes/figures/dags/p3q124.ps | 89 +
vignettes/figures/dags/p3q1246.odg | Bin 0 -> 7828 bytes
vignettes/figures/dags/p3q1246.pdf | 82 +
vignettes/figures/dags/p3q1246.ps | 91 +
vignettes/figures/dags/p3q135.odg | Bin 0 -> 7787 bytes
vignettes/figures/dags/p3q135.pdf | 80 +
vignettes/figures/dags/p3q135.ps | 89 +
vignettes/figures/dags/p3q14.odg | Bin 0 -> 7701 bytes
vignettes/figures/dags/p3q14.pdf | Bin 0 -> 1387 bytes
vignettes/figures/dags/p3q14.ps | 88 +
vignettes/figures/dags/p3q16.odg | Bin 0 -> 7764 bytes
vignettes/figures/dags/p3q16.pdf | 82 +
vignettes/figures/dags/p3q16.ps | 87 +
vignettes/figures/dags/p4q13569.odg | Bin 0 -> 8023 bytes
vignettes/figures/dags/p4q13569.pdf | Bin 0 -> 1573 bytes
vignettes/figures/dags/p4q13569.ps | 105 +
vignettes/figures/dags/p4q159.odg | Bin 0 -> 7726 bytes
vignettes/figures/dags/p4q159.pdf | 80 +
vignettes/figures/dags/p4q159.ps | 93 +
vignettes/figures/dags/p5q1_4_6_8_11_12_16.odg | Bin 0 -> 8023 bytes
vignettes/figures/dags/p5q1_4_6_8_11_12_16.pdf | Bin 0 -> 1648 bytes
vignettes/figures/dags/p5q1_4_6_8_11_12_16.ps | 113 +
vignettes/figures/dags/p5q1_6_11_16.odg | Bin 0 -> 7732 bytes
vignettes/figures/dags/p5q1_6_11_16.pdf | Bin 0 -> 1484 bytes
vignettes/figures/dags/p5q1_6_11_16.ps | 99 +
vignettes/figures/dags/p5q1_6_7_11_12.odg | Bin 0 -> 7823 bytes
vignettes/figures/dags/p5q1_6_7_11_12.pdf | 80 +
vignettes/figures/dags/p5q1_6_7_11_12.ps | 101 +
vignettes/figures/fev_viterbi.pdf | Bin 0 -> 4985 bytes
vignettes/figures/general.eps | 316 +++
vignettes/figures/general.pdf | Bin 0 -> 2456 bytes
vignettes/figures/hidden.pdf | Bin 0 -> 2579 bytes
vignettes/figures/hidden.ps | 267 +++
vignettes/figures/illdeath.eps | 158 ++
vignettes/figures/illdeath.pdf | Bin 0 -> 1727 bytes
vignettes/figures/multistate.eps | 251 +++
vignettes/figures/multistate.pdf | Bin 0 -> 2154 bytes
vignettes/figures/p2q1.eps | 80 +
vignettes/figures/p2q1.pdf | 61 +
vignettes/figures/p2q12.eps | 82 +
vignettes/figures/p2q12.pdf | Bin 0 -> 1051 bytes
vignettes/figures/p3q12.eps | 84 +
vignettes/figures/p3q12.pdf | Bin 0 -> 1076 bytes
vignettes/figures/p3q124.eps | 86 +
vignettes/figures/p3q124.pdf | 59 +
vignettes/figures/p3q1246.eps | 88 +
vignettes/figures/p3q1246.pdf | 60 +
vignettes/figures/p3q135.eps | 86 +
vignettes/figures/p3q135.pdf | Bin 0 -> 1097 bytes
vignettes/figures/p3q14.eps | 85 +
vignettes/figures/p3q14.pdf | 61 +
vignettes/figures/p3q16.eps | 84 +
vignettes/figures/p3q16.pdf | 63 +
vignettes/figures/p4q13569.eps | 102 +
vignettes/figures/p4q13569.pdf | Bin 0 -> 1228 bytes
vignettes/figures/p4q159.eps | 90 +
vignettes/figures/p4q159.pdf | Bin 0 -> 1108 bytes
vignettes/figures/p5q1_4_6_8_11_12_16.eps | 110 +
vignettes/figures/p5q1_4_6_8_11_12_16.pdf | Bin 0 -> 1284 bytes
vignettes/figures/p5q1_6_11_16.eps | 96 +
vignettes/figures/p5q1_6_11_16.pdf | Bin 0 -> 1147 bytes
vignettes/figures/p5q1_6_7_11_12.eps | 98 +
vignettes/figures/p5q1_6_7_11_12.pdf | 61 +
vignettes/figures/sampling.pdf | Bin 0 -> 2304 bytes
vignettes/figures/sampling.ps | 261 +++
vignettes/msm-manual.Rnw | 2688 ++++++++++++++++++++++++
vignettes/msm.bib | 790 +++++++
186 files changed, 31273 insertions(+)
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