Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.7.2 dated 2015-08-13 and 2.8.0 dated 2016-03-25
rebmix-2.7.2/rebmix/R/extractTheta.R |only rebmix-2.7.2/rebmix/R/print.REBMIX.R |only rebmix-2.7.2/rebmix/R/print.RNGMIX.R |only rebmix-2.7.2/rebmix/R/print.boot.REBMIX.R |only rebmix-2.7.2/rebmix/R/summary.REBMIX.R |only rebmix-2.7.2/rebmix/R/summary.boot.REBMIX.R |only rebmix-2.7.2/rebmix/man/print.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/print.RNGMIX.Rd |only rebmix-2.7.2/rebmix/man/print.boot.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/summary.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/summary.boot.REBMIX.Rd |only rebmix-2.7.2/rebmix/src/Makevars |only rebmix-2.8.0/rebmix/DESCRIPTION | 13 rebmix-2.8.0/rebmix/MD5 | 164 rebmix-2.8.0/rebmix/NAMESPACE | 79 rebmix-2.8.0/rebmix/R/AllClasses.R |only rebmix-2.8.0/rebmix/R/AllGenerics.R |only rebmix-2.8.0/rebmix/R/IC.R | 238 - rebmix-2.8.0/rebmix/R/RCLRMIX.R |only rebmix-2.8.0/rebmix/R/RCLSMIX.R | 267 - rebmix-2.8.0/rebmix/R/REBMIX.R | 740 +-- rebmix-2.8.0/rebmix/R/RNGMIX.R | 277 - rebmix-2.8.0/rebmix/R/boot.REBMIX.R | 389 + rebmix-2.8.0/rebmix/R/coef.REBMIX.R | 97 rebmix-2.8.0/rebmix/R/demix.R | 34 rebmix-2.8.0/rebmix/R/dfmix.R | 87 rebmix-2.8.0/rebmix/R/dfmvnorm.x.R |only rebmix-2.8.0/rebmix/R/dfmvnorm.xy.R |only rebmix-2.8.0/rebmix/R/extractThetaA.R |only rebmix-2.8.0/rebmix/R/extractThetaB.R |only rebmix-2.8.0/rebmix/R/is.error.R |only rebmix-2.8.0/rebmix/R/is.number.R |only rebmix-2.8.0/rebmix/R/pemix.R | 6 rebmix-2.8.0/rebmix/R/pfmix.R | 87 rebmix-2.8.0/rebmix/R/pfmvnorm.x.R |only rebmix-2.8.0/rebmix/R/pfmvnorm.xy.R |only rebmix-2.8.0/rebmix/R/plot.RCLRMIX.R |only rebmix-2.8.0/rebmix/R/plot.RCLSMIX.R |only rebmix-2.8.0/rebmix/R/plot.REBMIX.R | 1233 +++++ rebmix-2.8.0/rebmix/R/summary.R |only rebmix-2.8.0/rebmix/data/iris.rda |only rebmix-2.8.0/rebmix/demo/rebmix.galaxy.R | 7 rebmix-2.8.0/rebmix/demo/rebmix.mixed.continuous.discrete.R | 39 rebmix-2.8.0/rebmix/demo/rebmix.multivariate.normal.R | 37 rebmix-2.8.0/rebmix/demo/rebmix.truck.R | 38 rebmix-2.8.0/rebmix/demo/rebmix.univariate.normal.R | 56 rebmix-2.8.0/rebmix/demo/rebmix.weibullnormal.R | 38 rebmix-2.8.0/rebmix/inst/NEWS.Rd | 16 rebmix-2.8.0/rebmix/inst/doc/rebmix.R | 406 + rebmix-2.8.0/rebmix/inst/doc/rebmix.Rnw | 423 +- rebmix-2.8.0/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.8.0/rebmix/man/AIC.Rd | 46 rebmix-2.8.0/rebmix/man/AWE.Rd | 20 rebmix-2.8.0/rebmix/man/BIC.Rd | 19 rebmix-2.8.0/rebmix/man/CLC.Rd | 19 rebmix-2.8.0/rebmix/man/HQC.Rd | 19 rebmix-2.8.0/rebmix/man/ICL.Rd | 19 rebmix-2.8.0/rebmix/man/ICLBIC.Rd | 19 rebmix-2.8.0/rebmix/man/MDL.Rd | 24 rebmix-2.8.0/rebmix/man/PC.Rd | 19 rebmix-2.8.0/rebmix/man/PRD.Rd | 23 rebmix-2.8.0/rebmix/man/RCLRMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RCLRMIX.Rd |only rebmix-2.8.0/rebmix/man/RCLSMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RCLSMIX.Rd | 188 rebmix-2.8.0/rebmix/man/REBMIX-class.Rd |only rebmix-2.8.0/rebmix/man/REBMIX.Rd | 161 rebmix-2.8.0/rebmix/man/REBMIX.boot-class.Rd |only rebmix-2.8.0/rebmix/man/RNGMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RNGMIX.Rd | 164 rebmix-2.8.0/rebmix/man/SSE.Rd | 19 rebmix-2.8.0/rebmix/man/adult.Rd | 50 rebmix-2.8.0/rebmix/man/boot.REBMIX.Rd | 106 rebmix-2.8.0/rebmix/man/coef.REBMIX.Rd | 47 rebmix-2.8.0/rebmix/man/demix.Rd | 29 rebmix-2.8.0/rebmix/man/dfmix.Rd | 79 rebmix-2.8.0/rebmix/man/galaxy.Rd | 6 rebmix-2.8.0/rebmix/man/iris.Rd |only rebmix-2.8.0/rebmix/man/kseq.Rd | 9 rebmix-2.8.0/rebmix/man/logL.Rd | 18 rebmix-2.8.0/rebmix/man/pemix.Rd | 22 rebmix-2.8.0/rebmix/man/pfmix.Rd | 77 rebmix-2.8.0/rebmix/man/plot.REBMIX.Rd | 72 rebmix-2.8.0/rebmix/man/rebmix-internal.Rd |only rebmix-2.8.0/rebmix/man/truck.Rd | 3 rebmix-2.8.0/rebmix/man/weibull.Rd | 2 rebmix-2.8.0/rebmix/man/weibullnormal.Rd | 3 rebmix-2.8.0/rebmix/man/wine.Rd | 98 rebmix-2.8.0/rebmix/src/Rrebmix.cpp | 1338 +++--- rebmix-2.8.0/rebmix/src/Rrebmvnorm.cpp |only rebmix-2.8.0/rebmix/src/base.cpp | 281 + rebmix-2.8.0/rebmix/src/base.h | 36 rebmix-2.8.0/rebmix/src/rebmix.cpp | 14 rebmix-2.8.0/rebmix/src/rebmixf.cpp | 2528 +++++------- rebmix-2.8.0/rebmix/src/rebmixf.h | 58 rebmix-2.8.0/rebmix/src/rebmvnormf.cpp |only rebmix-2.8.0/rebmix/src/rebmvnormf.h |only rebmix-2.8.0/rebmix/src/rngmixf.cpp | 376 - rebmix-2.8.0/rebmix/src/rngmixf.h | 30 rebmix-2.8.0/rebmix/src/rngmvnormf.cpp |only rebmix-2.8.0/rebmix/src/rngmvnormf.h |only rebmix-2.8.0/rebmix/vignettes/rebmix.Rnw | 423 +- rebmix-2.8.0/rebmix/vignettes/rebmix.bib | 46 103 files changed, 6806 insertions(+), 4475 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between missMDA versions 1.9 dated 2015-12-15 and 1.10 dated 2016-03-25
DESCRIPTION | 13 +++++++------ MD5 | 27 ++++++++++++++------------- R/estim_ncpFAMD.R | 3 ++- inst |only man/gene.Rd | 2 ++ man/geno.Rd | 3 ++- man/imputeFAMD.Rd | 2 ++ man/imputeMCA.Rd | 2 ++ man/imputeMFA.Rd | 3 ++- man/imputePCA.Rd | 2 ++ man/missMDA-package.Rd | 2 ++ man/orange.Rd | 3 ++- man/ozone.Rd | 3 +++ man/snorena.Rd | 3 +++ man/vnf.Rd | 3 +++ 15 files changed, 48 insertions(+), 23 deletions(-)
Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard
errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE
computation for expectation and quantile estimators is
supported as well as multivariate estimations. The package also provides
functions for computing effective sample size and for plotting
Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes
<hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>
Diff between mcmcse versions 1.1-2 dated 2015-08-24 and 1.2-1 dated 2016-03-25
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + R/mcse_multi.R | 11 +++++++---- R/minESS.R |only build/vignette.rds |binary inst/doc/mcmcse_vignette.R | 12 ++++++++++++ inst/doc/mcmcse_vignette.Rnw | 35 +++++++++++++++++++++++++++++++++-- inst/doc/mcmcse_vignette.pdf |binary man/ess.Rd | 5 +++++ man/mcmcse-package.Rd | 4 ++++ man/mcse.Rd | 4 ++++ man/minESS.Rd |only man/multiESS.Rd | 9 +++++++-- vignettes/mcmcse_vignette.Rnw | 35 +++++++++++++++++++++++++++++++++-- vignettes/mcse.bib | 12 +++++++++--- 16 files changed, 135 insertions(+), 31 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.1 dated 2015-12-04 and 0.1.2 dated 2016-03-25
GetoptLong-0.1.1/GetoptLong/man/source.rd |only GetoptLong-0.1.2/GetoptLong/DESCRIPTION | 10 GetoptLong-0.1.2/GetoptLong/MD5 | 47 ++-- GetoptLong-0.1.2/GetoptLong/NAMESPACE | 1 GetoptLong-0.1.2/GetoptLong/NEWS | 6 GetoptLong-0.1.2/GetoptLong/R/0_global.R | 39 ++- GetoptLong-0.1.2/GetoptLong/R/GetoptLong.R | 106 ++++++---- GetoptLong-0.1.2/GetoptLong/R/qq.R | 43 +++- GetoptLong-0.1.2/GetoptLong/build/vignette.rds |binary GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.R | 26 -- GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.Rnw | 78 +++---- GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.pdf |binary GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.R | 14 + GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.Rnw | 57 ++++- GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.pdf |binary GetoptLong-0.1.2/GetoptLong/inst/tests/test_GetoptLong.R | 4 GetoptLong-0.1.2/GetoptLong/man/GetOptions.rd | 10 GetoptLong-0.1.2/GetoptLong/man/GetoptLong.options.rd | 19 + GetoptLong-0.1.2/GetoptLong/man/GetoptLong.rd | 20 + GetoptLong-0.1.2/GetoptLong/man/get_scriptname.rd | 16 + GetoptLong-0.1.2/GetoptLong/man/qq.options.rd | 20 + GetoptLong-0.1.2/GetoptLong/man/qq.rd | 23 +- GetoptLong-0.1.2/GetoptLong/man/qqcat.rd | 25 +- GetoptLong-0.1.2/GetoptLong/vignettes/GetoptLong.Rnw | 78 +++---- GetoptLong-0.1.2/GetoptLong/vignettes/variable_interpolation.Rnw | 57 ++++- 25 files changed, 448 insertions(+), 251 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.0.0 dated 2016-01-21 and 3.0.1 dated 2016-03-25
geomorph-3.0.0/geomorph/R/geomorph.utils.R |only geomorph-3.0.0/geomorph/R/gridPar.R |only geomorph-3.0.0/geomorph/R/integration.test.R |only geomorph-3.0.0/geomorph/R/modularity.test.R |only geomorph-3.0.0/geomorph/R/nested.update.R |only geomorph-3.0.0/geomorph/R/phylo.integration.R |only geomorph-3.0.0/geomorph/R/phylo.modularity.R |only geomorph-3.0.0/geomorph/R/procD.allometry.R |only geomorph-3.0.0/geomorph/R/trajectory.analysis.R |only geomorph-3.0.1/geomorph/DESCRIPTION | 11 geomorph-3.0.1/geomorph/MD5 | 146 ++-- geomorph-3.0.1/geomorph/NAMESPACE | 1 geomorph-3.0.1/geomorph/NEWS | 52 - geomorph-3.0.1/geomorph/R/advanced.procD.lm.r | 16 geomorph-3.0.1/geomorph/R/digitize2d.r | 29 geomorph-3.0.1/geomorph/R/digitsurface.r | 2 geomorph-3.0.1/geomorph/R/geomorph.support.code.r | 473 +++++++------ geomorph-3.0.1/geomorph/R/geomorph.utils.r |only geomorph-3.0.1/geomorph/R/gpagen.r | 8 geomorph-3.0.1/geomorph/R/gridPar.r |only geomorph-3.0.1/geomorph/R/integration.test.r |only geomorph-3.0.1/geomorph/R/modularity.test.r |only geomorph-3.0.1/geomorph/R/morphol.disparity.r | 4 geomorph-3.0.1/geomorph/R/nested.update.r |only geomorph-3.0.1/geomorph/R/phylo.integration.r |only geomorph-3.0.1/geomorph/R/phylo.modularity.r |only geomorph-3.0.1/geomorph/R/plotGMPhyloMorphoSpace.r | 34 geomorph-3.0.1/geomorph/R/plotOutliers.r | 4 geomorph-3.0.1/geomorph/R/procD.allometry.r |only geomorph-3.0.1/geomorph/R/procD.lm.r | 2 geomorph-3.0.1/geomorph/R/procD.pgls.r | 13 geomorph-3.0.1/geomorph/R/trajectory.analysis.r |only geomorph-3.0.1/geomorph/README.md | 17 geomorph-3.0.1/geomorph/man/digitsurface.Rd | 2 geomorph-3.0.1/geomorph/man/gpagen.Rd | 3 geomorph-3.0.1/geomorph/man/gridPar.Rd | 2 geomorph-3.0.1/geomorph/man/integration.test.Rd | 2 geomorph-3.0.1/geomorph/man/modularity.test.Rd | 2 geomorph-3.0.1/geomorph/man/morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/nested.update.Rd | 35 geomorph-3.0.1/geomorph/man/phylo.integration.Rd | 12 geomorph-3.0.1/geomorph/man/phylo.modularity.Rd | 2 geomorph-3.0.1/geomorph/man/plot.CR.Rd | 2 geomorph-3.0.1/geomorph/man/plot.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/plot.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/plot.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/plot.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/plot.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/plot.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/plot.pls.Rd | 2 geomorph-3.0.1/geomorph/man/plot.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/plot.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/plot.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/plotGMPhyloMorphoSpace.Rd | 2 geomorph-3.0.1/geomorph/man/print.CR.Rd | 2 geomorph-3.0.1/geomorph/man/print.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/print.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/print.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/print.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/print.evolrate1.Rd | 2 geomorph-3.0.1/geomorph/man/print.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/print.morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/print.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/print.pls.Rd | 2 geomorph-3.0.1/geomorph/man/print.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/print.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/print.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/procD.allometry.Rd | 11 geomorph-3.0.1/geomorph/man/procD.pgls.Rd | 2 geomorph-3.0.1/geomorph/man/summary.CR.Rd | 2 geomorph-3.0.1/geomorph/man/summary.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/summary.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/summary.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/summary.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/summary.evolrate1.Rd | 2 geomorph-3.0.1/geomorph/man/summary.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/summary.morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/summary.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/summary.pls.Rd | 2 geomorph-3.0.1/geomorph/man/summary.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/summary.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/summary.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/trajectory.analysis.Rd | 2 83 files changed, 540 insertions(+), 425 deletions(-)
Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between CALF versions 0.1.1 dated 2016-01-04 and 0.1.2 dated 2016-03-25
CALF-0.1.1/CALF/R/CALF.R |only CALF-0.1.2/CALF/DESCRIPTION | 9 +++++---- CALF-0.1.2/CALF/MD5 | 18 +++++++++++------- CALF-0.1.2/CALF/NAMESPACE | 8 +++++++- CALF-0.1.2/CALF/R/CALF-package.R | 11 ++++++----- CALF-0.1.2/CALF/R/calf_internal.R |only CALF-0.1.2/CALF/R/calf_wrappers.R |only CALF-0.1.2/CALF/R/print.calf.R |only CALF-0.1.2/CALF/man/CALF-package.Rd | 12 ++++++------ CALF-0.1.2/CALF/man/CaseControl.Rd | 2 +- CALF-0.1.2/CALF/man/calf.Rd | 8 ++++++-- CALF-0.1.2/CALF/man/calf_randomize.Rd |only CALF-0.1.2/CALF/man/calf_subset.Rd |only 13 files changed, 42 insertions(+), 26 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.6-1 dated 2016-01-24 and 2.7-0 dated 2016-03-25
DESCRIPTION | 8 MD5 | 36 NAMESPACE | 2 R/ensemble.analogue.R | 1 R/ensemble.batch.R | 39 - R/ensemble.mean.R | 14 R/ensemble.novel.R | 1 R/ensemble.plot.R |only R/ensemble.raster.R | 3 R/ensemble.test.R | 9 R/ensemble.zones.R | 1 R/evaluation.strip.data.R | 19 R/evaluation.strip.plot.R | 31 inst/ChangeLog | 24 inst/doc |only inst/etc/BiodiversityGUI.R | 1488 ++++++++++++++++++++++++++++++++++++++- inst/etc/BiodiversityR-menus.txt | 37 inst/etc/Rcmdr-menus.txt | 40 - man/ensemble.batch.Rd | 41 - man/evaluation.strip.Rd | 14 20 files changed, 1746 insertions(+), 62 deletions(-)
Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre],
Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
Diff between archivist.github versions 0.1 dated 2016-02-17 and 0.1.1 dated 2016-03-25
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/archive.R | 4 ++-- README.md | 9 ++++++--- man/archive.Rd | 2 +- 6 files changed, 26 insertions(+), 19 deletions(-)
More information about archivist.github at CRAN
Permanent link
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.6 dated 2016-01-30 and 1.7.0 dated 2016-03-25
TMB-1.6.6/TMB/man/mcmc.Rd |only TMB-1.6.6/TMB/man/mcmc.hmc.Rd |only TMB-1.6.6/TMB/man/mcmc.nuts.Rd |only TMB-1.6.6/TMB/man/mcmc.rwm.Rd |only TMB-1.7.0/TMB/DESCRIPTION | 27 +++++----- TMB-1.7.0/TMB/MD5 | 69 +++++++++++++------------- TMB-1.7.0/TMB/NAMESPACE | 3 - TMB-1.7.0/TMB/NEWS | 13 ++++ TMB-1.7.0/TMB/R/examples.R | 6 +- TMB-1.7.0/TMB/R/mcmc.R | 23 ++++---- TMB-1.7.0/TMB/R/sdreport.R | 74 +++++++++++++++++++++++++++- TMB-1.7.0/TMB/inst/CITATION | 39 +++++++++----- TMB-1.7.0/TMB/inst/examples/mcmc_examples.R | 6 +- TMB-1.7.0/TMB/inst/include/tmb_core.hpp | 63 ++++++++++++++++------- TMB-1.7.0/TMB/man/MakeADFun.Rd | 2 TMB-1.7.0/TMB/man/Rinterface.Rd | 2 TMB-1.7.0/TMB/man/as.list.sdreport.Rd |only TMB-1.7.0/TMB/man/benchmark.Rd | 2 TMB-1.7.0/TMB/man/compile.Rd | 2 TMB-1.7.0/TMB/man/config.Rd | 2 TMB-1.7.0/TMB/man/confint.tmbprofile.Rd | 2 TMB-1.7.0/TMB/man/dynlib.Rd | 2 TMB-1.7.0/TMB/man/gdbsource.Rd | 2 TMB-1.7.0/TMB/man/newton.Rd | 2 TMB-1.7.0/TMB/man/newtonOption.Rd | 2 TMB-1.7.0/TMB/man/oneStepPredict.Rd | 2 TMB-1.7.0/TMB/man/openmp.Rd | 2 TMB-1.7.0/TMB/man/plot.tmbprofile.Rd | 2 TMB-1.7.0/TMB/man/precompile.Rd | 2 TMB-1.7.0/TMB/man/print.sdreport.Rd | 2 TMB-1.7.0/TMB/man/runExample.Rd | 6 +- TMB-1.7.0/TMB/man/runSymbolicAnalysis.Rd | 2 TMB-1.7.0/TMB/man/run_mcmc.Rd |only TMB-1.7.0/TMB/man/run_mcmc.hmc.Rd |only TMB-1.7.0/TMB/man/run_mcmc.nuts.Rd |only TMB-1.7.0/TMB/man/run_mcmc.rwm.Rd |only TMB-1.7.0/TMB/man/sdreport.Rd | 6 +- TMB-1.7.0/TMB/man/summary.sdreport.Rd | 2 TMB-1.7.0/TMB/man/template.Rd | 2 TMB-1.7.0/TMB/man/tmbprofile.Rd | 2 40 files changed, 249 insertions(+), 124 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.7-8 dated 2015-11-09 and 0.7-9 dated 2016-03-25
DESCRIPTION | 8 ++--- MD5 | 31 +++++++++++----------- R/aucJM.JMbayes.R | 43 +++++++++++++++++++++++-------- R/check_td.R | 3 -- R/dns.R | 3 -- R/dwish.R | 3 -- R/fastSumID.R | 3 -- R/fastSumID2.R | 3 -- R/find_positions.R | 3 -- R/makepredictcall.dns.R | 3 -- R/prederrJM.JMbayes.R | 66 +++++++++++++++++++++++++++++++++++++----------- R/rocJM.JMbayes.R | 42 +++++++++++++++++++++++------- R/survfitJM.JMbayes.R | 2 - README.md |only inst/NEWS | 6 ++++ man/JMbayes.Rd | 4 +- man/pbc.Rd | 4 -- 17 files changed, 152 insertions(+), 75 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JM versions 1.4-2 dated 2015-11-09 and 1.4-4 dated 2016-03-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/cumHaz.R | 7 ++++++- R/log.posterior.b2.R | 4 ++-- R/phGH.fit.R | 2 +- inst/NEWS | 16 ++++++++++++++-- man/JM.Rd | 4 ++-- man/pbc.Rd | 4 ---- 8 files changed, 36 insertions(+), 23 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.0-7 dated 2016-02-20 and 3.1-0 dated 2016-03-25
DESCRIPTION | 12 MD5 | 33 - NEWS | 4 R/Effect.R | 783 +++++++++++++--------------- R/plot-methods.R | 1300 +++++++++++++++++++++++------------------------ R/utilities.R | 874 +++++++++++++------------------ data/Arrests.rda |binary data/BEPS.rda |binary data/Cowles.rda |binary data/Hartnagel.rda |binary data/Prestige.rda |binary data/TitanicSurvival.rda |binary data/WVS.rda |binary data/Wells.rda |binary man/effect.Rd | 1204 +++++++++++++++++++++---------------------- man/effects-package.Rd | 4 man/summary.effect.Rd | 29 - tests/effect-tests-2.R |only 18 files changed, 2052 insertions(+), 2191 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.5.0 dated 2016-02-28 and 3.5.1 dated 2016-03-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/choropleth.R | 14 ++++++++++++-- R/startup_messages.R | 9 ++++----- build/vignette.rds |binary inst/doc/h-creating-your-own-maps.html | 2 +- 7 files changed, 32 insertions(+), 17 deletions(-)
Title: Estimate Parameter of Bivariate Copula
Description: Implement an interval censor method
to break ties when using data with ties to fitting a
bivariate copula.
Author: Yan Li, Yang Li, Yichen Qin, and Jun yan
Maintainer: Yan Li <YanLi_stats@hotmail.com>
Diff between censorcopula versions 1.0 dated 2016-03-13 and 2.0 dated 2016-03-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary man/censorcopula-package.Rd | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Companion to Applied Regression
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 2.1-1 dated 2015-12-14 and 2.1-2 dated 2016-03-25
DESCRIPTION | 12 - MD5 | 114 ++++++------ NEWS | 454 ++++++++++++++++++++++++------------------------ R/scatter3d.R | 3 build/vignette.rds |binary data/AMSsurvey.rda |binary data/Adler.rda |binary data/Angell.rda |binary data/Anscombe.rda |binary data/Baumann.rda |binary data/Bfox.rda |binary data/Blackmore.rda |binary data/Burt.rda |binary data/CanPop.rda |binary data/Chile.rda |binary data/Chirot.rda |binary data/Cowles.rda |binary data/Davis.rda |binary data/DavisThin.rda |binary data/Depredations.rda |binary data/Duncan.rda |binary data/Ericksen.rda |binary data/Florida.rda |binary data/Freedman.rda |binary data/Friendly.rda |binary data/Ginzberg.rda |binary data/Greene.rda |binary data/Guyer.rda |binary data/Hartnagel.rda |binary data/Highway1.rda |binary data/KosteckiDillon.rda |binary data/Leinhardt.rda |binary data/LoBD.rda |binary data/Mandel.rda |binary data/Migration.rda |binary data/Moore.rda |binary data/Mroz.rda |binary data/OBrienKaiser.rda |binary data/Ornstein.rda |binary data/Pottery.rda |binary data/Prestige.rda |binary data/Quartet.rda |binary data/Robey.rda |binary data/SLID.rda |binary data/Sahlins.rda |binary data/Salaries.rda |binary data/Soils.rda |binary data/States.rda |binary data/Transact.rda |binary data/UN.rda |binary data/USPop.rda |binary data/Vocab.rda |binary data/WeightLoss.rda |binary data/Womenlf.rda |binary data/Wong.rda |binary data/Wool.rda |binary inst/doc/embedding.pdf |binary man/car-package.Rd | 72 +++---- 58 files changed, 328 insertions(+), 327 deletions(-)
Title: Tools for Temporal Social Network Analysis
Description: Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.
Author: Skye Bender-deMoll [aut, cre],
Martina Morris [aut],
James Moody [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between tsna versions 0.1.3 dated 2015-10-01 and 0.2.0 dated 2016-03-25
ChangeLog |only DESCRIPTION | 13 +- MD5 | 24 ++-- NAMESPACE | 14 ++ R/durations.R | 7 - R/randomwalk.R |only R/summaryStats.R | 27 ++++- build/vignette.rds |binary inst/doc/tsna_vignette.Rmd | 7 - inst/doc/tsna_vignette.html | 231 ++++++++++++++++++++++---------------------- man/tErgmStats.Rd | 10 + man/tSnaStats.Rd | 8 + tests/statsWrapper_tests.R | 14 ++ vignettes/tsna_vignette.Rmd | 7 - 14 files changed, 216 insertions(+), 146 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.5.1 dated 2015-10-24 and 3.6.0 dated 2016-03-25
ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.R |only ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.Rmd |only ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.html |only ergm-3.5.1/ergm/man/robust.inverse.Rd |only ergm-3.5.1/ergm/tests/off |only ergm-3.6.0/ergm/BUGS | 5 ergm-3.6.0/ergm/DESCRIPTION | 15 - ergm-3.6.0/ergm/LICENSE | 2 ergm-3.6.0/ergm/MD5 | 109 +++++----- ergm-3.6.0/ergm/NAMESPACE | 33 +-- ergm-3.6.0/ergm/R/InitErgmTerm.R | 66 ++++-- ergm-3.6.0/ergm/R/InitErgmTerm.dgw_sp.R |only ergm-3.6.0/ergm/R/InitWtErgmTerm.R | 179 +++++++++++++++- ergm-3.6.0/ergm/R/MHproposal.R | 28 +- ergm-3.6.0/ergm/R/approx.hotelling.diff.test.R | 13 - ergm-3.6.0/ergm/R/build_term_index.R | 4 ergm-3.6.0/ergm/R/coef.ergm.R | 5 ergm-3.6.0/ergm/R/control.ergm.R | 6 ergm-3.6.0/ergm/R/ergm.CD.fixed.R | 22 +- ergm-3.6.0/ergm/R/ergm.MCMLE.R | 14 - ergm-3.6.0/ergm/R/ergm.R | 3 ergm-3.6.0/ergm/R/ergm.bridge.R | 4 ergm-3.6.0/ergm/R/ergm.estimate.R | 6 ergm-3.6.0/ergm/R/ergm.getCDsample.R | 2 ergm-3.6.0/ergm/R/ergm.getMCMCsample.R | 4 ergm-3.6.0/ergm/R/ergm.getmodel.R | 100 +++------ ergm-3.6.0/ergm/R/ergm.logitreg.R | 5 ergm-3.6.0/ergm/R/ergm.pen.glm.R | 8 ergm-3.6.0/ergm/R/ergm.robmon.R | 2 ergm-3.6.0/ergm/R/ergm.stepping.R | 97 ++++++--- ergm-3.6.0/ergm/R/ergm.stocapprox.R | 2 ergm-3.6.0/ergm/R/ergm.utility.R | 23 ++ ergm-3.6.0/ergm/R/gof.ergm.R | 28 +- ergm-3.6.0/ergm/R/is.inCH.R | 68 +++--- ergm-3.6.0/ergm/R/mcmc.diagnostics.ergm.R | 10 ergm-3.6.0/ergm/R/parallel.utils.R | 5 ergm-3.6.0/ergm/R/robust.inverse.R | 1 ergm-3.6.0/ergm/R/simulate.ergm.R | 28 ++ ergm-3.6.0/ergm/R/summary.ergm.R | 6 ergm-3.6.0/ergm/R/zzz.R | 5 ergm-3.6.0/ergm/build/vignette.rds |binary ergm-3.6.0/ergm/inst/NEWS.Rd | 115 ++++++++-- ergm-3.6.0/ergm/inst/doc/ergm.pdf |binary ergm-3.6.0/ergm/man/control.ergm.Rd | 24 +- ergm-3.6.0/ergm/man/ergm-terms.Rd | 234 ++++++++-------------- ergm-3.6.0/ergm/man/ergm_deprecated.Rd | 2 ergm-3.6.0/ergm/man/gof.ergm.Rd | 5 ergm-3.6.0/ergm/man/is.inCH.Rd | 12 - ergm-3.6.0/ergm/man/samplk.Rd | 27 +- ergm-3.6.0/ergm/man/sampson.Rd | 6 ergm-3.6.0/ergm/man/summary.ergm.Rd | 4 ergm-3.6.0/ergm/src/changestats.c | 22 ++ ergm-3.6.0/ergm/src/changestats.dgw_sp.c |only ergm-3.6.0/ergm/src/changestats.dgw_sp.h |only ergm-3.6.0/ergm/src/wtchangestats.c | 78 +++++++ ergm-3.6.0/ergm/tests/Rplots.pdf |only ergm-3.6.0/ergm/tests/gw_sp_tests.R |only ergm-3.6.0/ergm/tests/requireNamespaceTest.R |only ergm-3.6.0/ergm/tests/termTests.bipartite.R | 27 ++ ergm-3.6.0/ergm/tests/termTests.valued.R |only ergm-3.6.0/ergm/vignettes/ergm-term-crossRef.html |only 61 files changed, 965 insertions(+), 499 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral sciences and related fields. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial(Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of means, which are easily interpretable for behavioral researchers. BANOVA uses JAGS as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 0.2 dated 2014-06-29 and 0.4 dated 2016-03-25
DESCRIPTION | 15 +- MD5 | 122 +++++++++---------- NAMESPACE | 67 +++++----- R/BANOVA.Bern.R | 4 R/BANOVA.BernNormal.R | 123 ++++++++++--------- R/BANOVA.Bin.R | 4 R/BANOVA.BinNormal.R | 133 +++++++++++---------- R/BANOVA.MultiNormal.R | 157 +++++++++++++----------- R/BANOVA.Multinomial.R | 4 R/BANOVA.Normal.R | 4 R/BANOVA.NormalNormal.R | 114 +++++++++--------- R/BANOVA.PNormal.R | 123 ++++++++++--------- R/BANOVA.Poisson.R | 4 R/BANOVA.T.R | 4 R/BANOVA.TNormal.R | 114 +++++++++--------- R/BANOVA.ordMultiNormal.R | 153 +++++++++++++----------- R/BANOVA.ordMultinomial.R | 4 R/JAGSgen.PNormal.R | 175 ++++++++++++++++----------- R/JAGSgen.TNormal.R | 173 ++++++++++++++++----------- R/JAGSgen.bernNormal.R | 164 +++++++++++++++---------- R/JAGSgen.binNormal.R | 165 +++++++++++++++----------- R/JAGSgen.multiNormal.R | 171 ++++++++++++++++----------- R/JAGSgen.normalNormal.R | 169 +++++++++++++++----------- R/JAGSgen.ordmultiNormal.R | 202 ++++++++++++++++++-------------- R/conv.geweke.heidel.R | 55 ++++---- R/print.conv.diag.R | 23 ++- R/print.summary.BANOVA.Bern.R | 33 ++--- R/print.summary.BANOVA.Bin.R | 33 ++--- R/print.summary.BANOVA.Multinomial.R | 33 ++--- R/print.summary.BANOVA.Normal.R | 33 ++--- R/print.summary.BANOVA.Poisson.R | 33 ++--- R/print.summary.BANOVA.T.R | 33 ++--- R/print.summary.BANOVA.ordMultinomial.R | 33 ++--- R/ssquares.R | 68 +++++----- R/summary.BANOVA.Bern.R | 16 +- R/summary.BANOVA.Bin.R | 16 +- R/summary.BANOVA.Multinomial.R | 16 +- R/summary.BANOVA.Normal.R | 16 +- R/summary.BANOVA.Poisson.R | 16 +- R/summary.BANOVA.T.R | 16 +- R/summary.BANOVA.ordMultinomial.R | 16 +- R/table.ANCOVA.R | 66 +++++----- man/BANOVA-package.Rd | 12 + man/BANOVA.Bern.Rd | 164 +++++++++++++------------ man/BANOVA.Bin.Rd | 175 ++++++++++++++------------- man/BANOVA.Multinomial.Rd | 194 +++++++++++++++--------------- man/BANOVA.Normal.Rd | 169 ++++++++++++++------------ man/BANOVA.Poisson.Rd | 174 ++++++++++++++------------- man/BANOVA.T.Rd | 157 +++++++++++++----------- man/BANOVA.ordMultinomial.Rd | 176 ++++++++++++++------------- man/BAnova.Rd | 96 +++++++-------- man/bernlogtime.Rd | 86 ++++++------- man/bpndata.Rd | 104 ++++++++-------- man/choicedata.Rd | 2 man/colorad.Rd | 84 ++++++------- man/colorad2.Rd | 90 +++++++------- man/conv.diag.Rd | 108 ++++++++--------- man/goalstudy.Rd | 102 ++++++++-------- man/ipadstudy.Rd | 98 +++++++-------- man/table.means.Rd | 48 +++---- man/table.pvalues.Rd | 86 ++++++------- man/trace.plot.Rd | 50 +++---- 62 files changed, 2746 insertions(+), 2352 deletions(-)