Title: A Most Informative Histogram-Like Model
Description: Using the MDL principle, it is possible to estimate
parameters for a histogram-like model. The package contains
the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen
Diff between histmdl versions 0.3-2 dated 2015-03-10 and 0.4-1 dated 2015-03-16
histmdl-0.3-2/histmdl/build |only histmdl-0.3-2/histmdl/inst |only histmdl-0.3-2/histmdl/vignettes |only histmdl-0.4-1/histmdl/DESCRIPTION | 8 ++++---- histmdl-0.4-1/histmdl/MD5 | 12 +++--------- histmdl-0.4-1/histmdl/R/histmdl.R | 9 ++++++--- histmdl-0.4-1/histmdl/man/histmdl-package.Rd | 4 ++-- 7 files changed, 15 insertions(+), 18 deletions(-)
Title: Comparing Restricted Mean Survival Time
Description: Performs two-sample comparisons using the restricted mean survival time (RMST) as a summary measure of the survival time distribution. Three kinds of between-group contrast metrics (i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It performs an ANCOVA-type covariate adjustment as well as unadjusted analyses for those measures.
Author: Hajime Uno, Lu Tian, Angel Cronin, Chakib Battioui
Maintainer: Hajime Uno
Diff between survRM2 versions 1.0 dated 2015-02-05 and 1.0-1 dated 2015-03-16
survRM2-1.0-1/survRM2/DESCRIPTION | 8 +++---- survRM2-1.0-1/survRM2/MD5 | 18 ++++++++-------- survRM2-1.0-1/survRM2/R/rmst2-ver002.R | 2 - survRM2-1.0-1/survRM2/build/vignette.rds |binary survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.R |only survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.Rnw |only survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.pdf |only survRM2-1.0-1/survRM2/man/rmst2.Rd | 2 - survRM2-1.0-1/survRM2/man/survRM2-package.Rd | 4 +-- survRM2-1.0-1/survRM2/vignettes/survRM2-vignette3-1.Rnw |only survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.R |only survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.Rnw |only survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.pdf |only survRM2-1.0/survRM2/vignettes/survRM2-vignette3.Rnw |only 14 files changed, 17 insertions(+), 17 deletions(-)
Title: Design and Analysis of Mixture Experiments
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson [aut, cre],
Cameron Willden [aut],
Greg Piepel [ctb]
Maintainer: John Lawson
Diff between mixexp versions 1.1.9 dated 2014-12-13 and 1.2.1 dated 2015-03-16
mixexp-1.1.9/mixexp/R/ModelPlot.R |only mixexp-1.2.1/mixexp/DESCRIPTION | 27 - mixexp-1.2.1/mixexp/MD5 | 62 +-- mixexp-1.2.1/mixexp/NAMESPACE | 20 - mixexp-1.2.1/mixexp/R/DesignPoints.R | 30 - mixexp-1.2.1/mixexp/R/EffPlot.R | 16 mixexp-1.2.1/mixexp/R/MixModel.R | 162 ++++++--- mixexp-1.2.1/mixexp/R/MixturePlot.R | 21 - mixexp-1.2.1/mixexp/R/ModelEff.R | 518 ++++++++++++++++++++++-------- mixexp-1.2.1/mixexp/R/ModelPLot.R |only mixexp-1.2.1/mixexp/R/SLD.R | 2 mixexp-1.2.1/mixexp/R/cubic.R | 6 mixexp-1.2.1/mixexp/data/Burn.rda |binary mixexp-1.2.1/mixexp/data/SneeMq.rda |binary mixexp-1.2.1/mixexp/data/conmx.rda |binary mixexp-1.2.1/mixexp/data/etch.rda |only mixexp-1.2.1/mixexp/data/fishp.rda |only mixexp-1.2.1/mixexp/man/Burn.Rd | 11 mixexp-1.2.1/mixexp/man/DesignPoints.Rd | 23 - mixexp-1.2.1/mixexp/man/EffPlot.Rd | 20 - mixexp-1.2.1/mixexp/man/Eflags.Rd | 2 mixexp-1.2.1/mixexp/man/Fillv.Rd | 4 mixexp-1.2.1/mixexp/man/MixModel.Rd | 35 +- mixexp-1.2.1/mixexp/man/MixturePlot.Rd | 22 - mixexp-1.2.1/mixexp/man/ModelEff.Rd | 130 +++---- mixexp-1.2.1/mixexp/man/ModelPlot.Rd | 80 ++-- mixexp-1.2.1/mixexp/man/SLD.Rd | 2 mixexp-1.2.1/mixexp/man/SneeMq.Rd | 2 mixexp-1.2.1/mixexp/man/Vertcen.Rd | 2 mixexp-1.2.1/mixexp/man/Xvert.Rd | 4 mixexp-1.2.1/mixexp/man/crvtave.Rd | 2 mixexp-1.2.1/mixexp/man/cubic.Rd | 6 mixexp-1.2.1/mixexp/man/etch.Rd |only mixexp-1.2.1/mixexp/man/fishp.Rd |only mixexp-1.2.1/mixexp/man/mixexp-package.Rd | 15 35 files changed, 768 insertions(+), 456 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake
Maintainer: Jeff Laake
Diff between marked versions 1.1.6 dated 2014-06-17 and 1.1.8 dated 2015-03-16
marked-1.1.6/marked/R/compute_matrices.r |only marked-1.1.6/marked/man/cjs_dmat.Rd |only marked-1.1.8/marked/DESCRIPTION | 25 - marked-1.1.8/marked/MD5 | 200 ++++---- marked-1.1.8/marked/NAMESPACE | 14 marked-1.1.8/marked/NEWS | 51 ++ marked-1.1.8/marked/R/HMMLikelihood.r | 307 ++----------- marked-1.1.8/marked/R/HMMutilities.r |only marked-1.1.8/marked/R/Observation_functions.r | 46 +- marked-1.1.8/marked/R/RHMMLikelihood.r |only marked-1.1.8/marked/R/Transition_functions.r | 50 ++ marked-1.1.8/marked/R/cjs.R | 29 - marked-1.1.8/marked/R/cjs.hessian.r | 2 marked-1.1.8/marked/R/cjs.lnl.r | 88 ++- marked-1.1.8/marked/R/coef.r |only marked-1.1.8/marked/R/compute.real.R | 24 - marked-1.1.8/marked/R/create.dm.R | 5 marked-1.1.8/marked/R/create.dmdf.R | 148 +++--- marked-1.1.8/marked/R/crm.R | 140 +++--- marked-1.1.8/marked/R/crm.wrapper.R | 160 ++++++- marked-1.1.8/marked/R/hmmDemo.r | 191 ++------ marked-1.1.8/marked/R/js.r | 5 marked-1.1.8/marked/R/make.design.data.R | 3 marked-1.1.8/marked/R/marked-package.R | 77 ++- marked-1.1.8/marked/R/mscjs.r | 28 + marked-1.1.8/marked/R/omega.r | 1 marked-1.1.8/marked/R/predict.crm.r | 7 marked-1.1.8/marked/R/print.crm.r | 66 -- marked-1.1.8/marked/R/probitCJS.R | 242 ++++++---- marked-1.1.8/marked/R/process.ch.R | 1 marked-1.1.8/marked/R/process.data.R | 43 + marked-1.1.8/marked/R/set.initial.r | 8 marked-1.1.8/marked/R/set_mvms.r | 100 ++++ marked-1.1.8/marked/R/setup.model.R | 21 marked-1.1.8/marked/R/setup.parameters.R | 2 marked-1.1.8/marked/build/vignette.rds |binary marked-1.1.8/marked/data/mstrata.rda |only marked-1.1.8/marked/inst/CITATION |only marked-1.1.8/marked/inst/cjs.tpl | 13 marked-1.1.8/marked/inst/cjs_reml.tpl | 15 marked-1.1.8/marked/inst/cjsre.tpl | 16 marked-1.1.8/marked/inst/doc/markedVignette.R | 2 marked-1.1.8/marked/inst/doc/markedVignette.pdf |binary marked-1.1.8/marked/inst/models.txt | 2 marked-1.1.8/marked/inst/multistate.tpl | 2 marked-1.1.8/marked/inst/parameters.txt | 89 ++- marked-1.1.8/marked/man/HMMLikelihood.Rd | 119 +---- marked-1.1.8/marked/man/Phi.mean.Rd | 25 - marked-1.1.8/marked/man/R_HMMLikelihood.Rd | 69 --- marked-1.1.8/marked/man/backward_prob.Rd |only marked-1.1.8/marked/man/cjs.Rd | 133 ++--- marked-1.1.8/marked/man/cjs.accumulate.Rd | 31 - marked-1.1.8/marked/man/cjs.hessian.Rd | 11 marked-1.1.8/marked/man/cjs.initial.Rd | 15 marked-1.1.8/marked/man/cjs.lnl.Rd | 76 +-- marked-1.1.8/marked/man/cjs_delta.Rd | 26 - marked-1.1.8/marked/man/cjs_gamma.Rd | 22 marked-1.1.8/marked/man/coef.crm.Rd |only marked-1.1.8/marked/man/compute.real.Rd | 77 +-- marked-1.1.8/marked/man/compute_matrices.Rd | 14 marked-1.1.8/marked/man/convert.link.to.real.Rd | 33 - marked-1.1.8/marked/man/create.dm.Rd | 64 +- marked-1.1.8/marked/man/create.dmdf.Rd | 429 +++++++++---------- marked-1.1.8/marked/man/create.fixed.matrix.Rd | 6 marked-1.1.8/marked/man/create.links.Rd | 17 marked-1.1.8/marked/man/crm.Rd | 469 +++++++++------------ marked-1.1.8/marked/man/crm.wrapper.Rd | 101 ++-- marked-1.1.8/marked/man/deriv_inverse.link.Rd | 32 - marked-1.1.8/marked/man/dipper.Rd | 87 +-- marked-1.1.8/marked/man/fix.parameters.Rd | 22 marked-1.1.8/marked/man/function.wrapper.Rd | 25 - marked-1.1.8/marked/man/global_decode.Rd |only marked-1.1.8/marked/man/hmmDemo.Rd | 99 +--- marked-1.1.8/marked/man/inverse.link.Rd | 53 +- marked-1.1.8/marked/man/js.Rd | 121 ++--- marked-1.1.8/marked/man/js.accumulate.Rd | 31 - marked-1.1.8/marked/man/js.hessian.Rd | 11 marked-1.1.8/marked/man/js.lnl.Rd | 63 +- marked-1.1.8/marked/man/local_decode.Rd |only marked-1.1.8/marked/man/make.design.data.Rd | 104 +--- marked-1.1.8/marked/man/merge_design.covariates.Rd | 73 +-- marked-1.1.8/marked/man/mixed.model.admb.Rd | 70 +-- marked-1.1.8/marked/man/mscjs.Rd | 118 ++--- marked-1.1.8/marked/man/mstrata.Rd |only marked-1.1.8/marked/man/mvms_design_data.Rd |only marked-1.1.8/marked/man/mvms_dmat.Rd |only marked-1.1.8/marked/man/omega.Rd | 15 marked-1.1.8/marked/man/predict.crm.Rd | 44 - marked-1.1.8/marked/man/print.crm.Rd | 24 - marked-1.1.8/marked/man/print.crmlist.Rd |only marked-1.1.8/marked/man/probitCJS.Rd | 104 +++- marked-1.1.8/marked/man/proc.form.Rd | 17 marked-1.1.8/marked/man/process.ch.Rd | 47 -- marked-1.1.8/marked/man/process.data.Rd | 331 ++++++-------- marked-1.1.8/marked/man/resight.matrix.Rd | 26 - marked-1.1.8/marked/man/set.fixed.Rd | 12 marked-1.1.8/marked/man/set.initial.Rd | 11 marked-1.1.8/marked/man/set.scale.Rd | 17 marked-1.1.8/marked/man/set_mvms.Rd | 42 - marked-1.1.8/marked/man/setup.model.Rd | 62 +- marked-1.1.8/marked/man/setup.parameters.Rd | 98 +--- marked-1.1.8/marked/man/simHMM.Rd | 67 +-- marked-1.1.8/marked/man/splitCH.Rd | 35 - marked-1.1.8/marked/man/tagloss.Rd | 75 +-- marked-1.1.8/marked/man/valid.parameters.Rd | 15 marked-1.1.8/marked/src/hmm_like.f | 8 marked-1.1.8/marked/src/msgamma.f | 7 marked-1.1.8/marked/src/mvmsdmat.f |only marked-1.1.8/marked/src/umsdmat.f | 2 109 files changed, 2936 insertions(+), 2992 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
Diff between BayesFactor versions 0.9.10-2 dated 2015-02-09 and 0.9.11 dated 2015-03-16
BayesFactor-0.9.10-2/BayesFactor/R/debug.R |only BayesFactor-0.9.10-2/BayesFactor/src/BFPCL.h |only BayesFactor-0.9.10-2/BayesFactor/src/Makevars |only BayesFactor-0.9.10-2/BayesFactor/src/common.c |only BayesFactor-0.9.10-2/BayesFactor/src/debug.c |only BayesFactor-0.9.10-2/BayesFactor/src/linearReg.c |only BayesFactor-0.9.10-2/BayesFactor/src/matSums.cpp |only BayesFactor-0.9.10-2/BayesFactor/src/matrix.c |only BayesFactor-0.9.10-2/BayesFactor/src/nWayAOV.c |only BayesFactor-0.9.10-2/BayesFactor/src/oneWayAOV.c |only BayesFactor-0.9.11/BayesFactor/DESCRIPTION | 16 BayesFactor-0.9.11/BayesFactor/MD5 | 120 ++-- BayesFactor-0.9.11/BayesFactor/NAMESPACE | 41 + BayesFactor-0.9.11/BayesFactor/NEWS | 13 BayesFactor-0.9.11/BayesFactor/R/BayesFactorPCL-package.R | 2 BayesFactor-0.9.11/BayesFactor/R/RcppExports.R | 32 + BayesFactor-0.9.11/BayesFactor/R/aaClasses.R | 49 + BayesFactor-0.9.11/BayesFactor/R/aaGenerics.R | 35 + BayesFactor-0.9.11/BayesFactor/R/anovaBF.R | 4 BayesFactor-0.9.11/BayesFactor/R/checkCallback.R |only BayesFactor-0.9.11/BayesFactor/R/checking.R | 6 BayesFactor-0.9.11/BayesFactor/R/common.R | 15 BayesFactor-0.9.11/BayesFactor/R/contingency.R | 4 BayesFactor-0.9.11/BayesFactor/R/gaussApproxAOV.R | 299 +--------- BayesFactor-0.9.11/BayesFactor/R/generalTestBF.R | 4 BayesFactor-0.9.11/BayesFactor/R/meta-ttest-utility.R | 64 +- BayesFactor-0.9.11/BayesFactor/R/methods-BFBayesFactor.R | 12 BayesFactor-0.9.11/BayesFactor/R/methods-BFlinearModel-compare.R | 5 BayesFactor-0.9.11/BayesFactor/R/methods-BFmodelSample.R | 9 BayesFactor-0.9.11/BayesFactor/R/methods-BFodds.R |only BayesFactor-0.9.11/BayesFactor/R/methods-BFprobability.R |only BayesFactor-0.9.11/BayesFactor/R/model.matrix.R | 7 BayesFactor-0.9.11/BayesFactor/R/nWayAOV-utility.R | 131 ++-- BayesFactor-0.9.11/BayesFactor/R/nWayAOV.R | 225 ++----- BayesFactor-0.9.11/BayesFactor/R/newPriorOdds.R |only BayesFactor-0.9.11/BayesFactor/R/oneWayAOV-utility.R | 43 - BayesFactor-0.9.11/BayesFactor/R/proportionBF.R | 4 BayesFactor-0.9.11/BayesFactor/R/regressionBF-utility.R | 48 - BayesFactor-0.9.11/BayesFactor/R/regressionBF.R | 6 BayesFactor-0.9.11/BayesFactor/R/ttest-utility.R | 7 BayesFactor-0.9.11/BayesFactor/R/ttestBF.R | 2 BayesFactor-0.9.11/BayesFactor/build/vignette.rds |binary BayesFactor-0.9.11/BayesFactor/inst/doc/compare_lme4.html | 74 +- BayesFactor-0.9.11/BayesFactor/inst/doc/index.Rmd | 2 BayesFactor-0.9.11/BayesFactor/inst/doc/index.html | 1 BayesFactor-0.9.11/BayesFactor/inst/doc/manual.html | 246 ++++---- BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.R |only BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.Rmd |only BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.html |only BayesFactor-0.9.11/BayesFactor/inst/doc/priors.html | 18 BayesFactor-0.9.11/BayesFactor/man/BFBayesFactor-class.Rd | 3 BayesFactor-0.9.11/BayesFactor/man/BFodds-class.Rd |only BayesFactor-0.9.11/BayesFactor/man/BFprobability-class.Rd |only BayesFactor-0.9.11/BayesFactor/man/BayesFactor-package.Rd | 2 BayesFactor-0.9.11/BayesFactor/man/as.BFprobability.Rd |only BayesFactor-0.9.11/BayesFactor/man/extractOdds-methods.Rd |only BayesFactor-0.9.11/BayesFactor/man/extractProbabilities-methods.Rd |only BayesFactor-0.9.11/BayesFactor/man/nWayAOV.Rd | 42 - BayesFactor-0.9.11/BayesFactor/man/newPriorOdds.Rd |only BayesFactor-0.9.11/BayesFactor/man/priorLogodds-method.Rd |only BayesFactor-0.9.11/BayesFactor/man/priorOdds-method.Rd |only BayesFactor-0.9.11/BayesFactor/man/recompute-methods.Rd | 6 BayesFactor-0.9.11/BayesFactor/src/RcppExports.cpp | 171 +++++ BayesFactor-0.9.11/BayesFactor/src/bfcommon.h | 21 BayesFactor-0.9.11/BayesFactor/src/dinvgamma.cpp |only BayesFactor-0.9.11/BayesFactor/src/jzs_Gauss_approx_aov.cpp |only BayesFactor-0.9.11/BayesFactor/src/jzs_Gibbs.cpp |only BayesFactor-0.9.11/BayesFactor/src/jzs_bf_samplers.cpp |only BayesFactor-0.9.11/BayesFactor/src/jzs_marg_like.cpp |only BayesFactor-0.9.11/BayesFactor/src/linearRegGibbsRcpp.cpp |only BayesFactor-0.9.11/BayesFactor/src/logDeterminant.cpp |only BayesFactor-0.9.11/BayesFactor/src/metattest.cpp | 2 BayesFactor-0.9.11/BayesFactor/src/proportion.cpp | 2 BayesFactor-0.9.11/BayesFactor/src/rmvnorm.cpp |only BayesFactor-0.9.11/BayesFactor/src/ttestIndepRcpp.cpp | 18 BayesFactor-0.9.11/BayesFactor/src/ttestRcpp.cpp | 19 BayesFactor-0.9.11/BayesFactor/vignettes/index.Rmd | 2 BayesFactor-0.9.11/BayesFactor/vignettes/odds_probs.Rmd |only 78 files changed, 990 insertions(+), 842 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre],
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Felix Andrews [ctb]
Maintainer: Achim Zeileis
Diff between zoo versions 1.7-11 dated 2014-02-27 and 1.7-12 dated 2015-03-16
zoo-1.7-11/zoo/src/zoo.h |only zoo-1.7-12/zoo/DESCRIPTION | 10 - zoo-1.7-12/zoo/MD5 | 91 +++++++-------- zoo-1.7-12/zoo/NAMESPACE | 13 ++ zoo-1.7-12/zoo/NEWS | 22 +++ zoo-1.7-12/zoo/R/MATCH.R | 4 zoo-1.7-12/zoo/R/ORDER.R | 1 zoo-1.7-12/zoo/R/as.zoo.R | 27 +--- zoo-1.7-12/zoo/R/as.zoo.tis.R | 27 +--- zoo-1.7-12/zoo/R/coredata.R | 2 zoo-1.7-12/zoo/R/ggplot2.zoo.R | 22 +-- zoo-1.7-12/zoo/R/index.R | 4 zoo-1.7-12/zoo/R/na.StructTS.R | 2 zoo-1.7-12/zoo/R/na.fill.R | 6 - zoo-1.7-12/zoo/R/plot.zoo.R | 14 +- zoo-1.7-12/zoo/R/read.zoo.R | 38 ++++-- zoo-1.7-12/zoo/R/xyplot.zoo.R | 2 zoo-1.7-12/zoo/R/yearmon.R | 10 - zoo-1.7-12/zoo/R/yearqtr.R | 10 - zoo-1.7-12/zoo/R/zoo.R | 19 ++- zoo-1.7-12/zoo/R/zooreg.R | 4 zoo-1.7-12/zoo/build/vignette.rds |binary zoo-1.7-12/zoo/inst/doc/zoo-design.pdf |binary zoo-1.7-12/zoo/inst/doc/zoo-faq.pdf |binary zoo-1.7-12/zoo/inst/doc/zoo-quickref.R | 1 zoo-1.7-12/zoo/inst/doc/zoo-quickref.Rnw | 6 - zoo-1.7-12/zoo/inst/doc/zoo-quickref.pdf |binary zoo-1.7-12/zoo/inst/doc/zoo-read.Rnw | 2 zoo-1.7-12/zoo/inst/doc/zoo-read.pdf |binary zoo-1.7-12/zoo/inst/doc/zoo.R |only zoo-1.7-12/zoo/inst/doc/zoo.Rnw | 35 +++-- zoo-1.7-12/zoo/inst/doc/zoo.pdf |binary zoo-1.7-12/zoo/inst/include |only zoo-1.7-12/zoo/man/na.StructTS.Rd | 4 zoo-1.7-12/zoo/man/plot.zoo.Rd | 31 +++++ zoo-1.7-12/zoo/man/read.zoo.Rd | 75 ++++++++---- zoo-1.7-12/zoo/man/rollapply.Rd | 23 +++ zoo-1.7-12/zoo/man/zoo.Rd | 4 zoo-1.7-12/zoo/src/Makevars |only zoo-1.7-12/zoo/src/Makevars.win |only zoo-1.7-12/zoo/src/init.c | 2 zoo-1.7-12/zoo/src/lag.c | 9 + zoo-1.7-12/zoo/tests/Examples/zoo-Ex.Rout.save | 148 +++++++++++++++++++------ zoo-1.7-12/zoo/tests/bugfixes.R | 4 zoo-1.7-12/zoo/tests/bugfixes.Rout.save | 12 +- zoo-1.7-12/zoo/vignettes/zoo-quickref.Rnw | 6 - zoo-1.7-12/zoo/vignettes/zoo-read.Rnw | 2 zoo-1.7-12/zoo/vignettes/zoo.Rnw | 35 +++-- zoo-1.7-12/zoo/vignettes/zoo.bib | 2 49 files changed, 492 insertions(+), 237 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) and all of its variants in generalized linear models and the Cox proportional hazards model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana
Diff between SIS versions 0.7-4 dated 2014-08-01 and 0.7-5 dated 2015-03-16
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/partialfits.R | 2 +- data/leukemia.RData |binary data/leukemia.test.RData |binary data/leukemia.train.RData |binary data/prostate.test.RData |binary data/prostate.train.RData |binary 8 files changed, 14 insertions(+), 14 deletions(-)
Title: Regularized Categorical Effects/Categorical Effect
Modifiers/Continuous/Smooth Effects in GLMs
Description: Generalized structured regression models with regularized categorical effects, categorical effect modifiers, continuous effects and smooth effects.
Author: Margret Oelker
Maintainer: Margret Oelker
Diff between gvcm.cat versions 1.8 dated 2015-03-04 and 1.9 dated 2015-03-16
DESCRIPTION | 10 +++++----- MD5 | 13 ++++++++----- NAMESPACE | 6 ++---- R/a.R |only R/gvcm.cat.flex.R |only R/optimierung.R | 2 +- inst/CITATION | 27 ++++++++++----------------- man/gvcm.cat-internal.Rd | 1 + man/gvcm.cat.flex.Rd |only 9 files changed, 27 insertions(+), 32 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs
Diff between plotROC versions 1.3 dated 2015-01-27 and 1.3.3 dated 2015-03-16
DESCRIPTION | 10 - MD5 | 34 ++-- NEWS | 21 ++ R/ggroc.R | 122 ++++++++++---- R/interactive_roc.R | 92 ++++++----- R/plot_journal_roc.R | 83 ++++++++-- inst/doc/examples.R | 147 ++++++++++++----- inst/doc/examples.Rmd | 202 ++++++++++++++++-------- inst/doc/examples.html | 231 ++++++++++++++++------------ inst/shinyApp/server.R | 20 -- inst/shinyApp/shinyapps/sachsmc/plotROC.dcf | 2 inst/shinyApp/ui.R | 1 man/export_interactive_roc.Rd | 15 + man/ggroc.Rd | 14 + man/multi_ggroc.Rd | 21 +- man/plot_interactive_roc.Rd | 6 man/plot_journal_roc.Rd | 14 + vignettes/examples.Rmd | 202 ++++++++++++++++-------- 18 files changed, 819 insertions(+), 418 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for plotting spectra (NMR, IR, Raman) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA, model-based clustering and STOCSY analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette illustrating typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
Diff between ChemoSpec versions 4.0-0 dated 2015-03-10 and 4.0.1 dated 2015-03-16
DESCRIPTION | 19 ++-- MD5 | 74 +++++++++--------- NAMESPACE | 18 ---- NEWS | 5 + R/baselineSpectra.R | 20 ++++ R/clupaSpectra.R | 14 ++- R/coordProjCS.R | 18 ++-- R/corSpectra.R | 18 +++- R/cv_pcaSpectra.R | 8 + R/evalClusters.R | 12 +- R/files2SpectraObject.R | 10 +- R/groupNcolor.R | 15 ++- R/hmapSpectra.R | 17 +++- R/makeEllipsoid.R | 5 - R/mclust3D.R | 16 ++- R/mclustSpectra.R | 6 + R/plotLoadings.R | 12 +- R/plotScores3D.R | 14 ++- R/plotScoresCor.R | 6 + R/plotSpectraJS.R | 189 +++++++++++++++++++++++++---------------------- R/r_pcaSpectra.R | 6 + R/readJDX.R | 12 +- R/rowDist.R | 7 + R/sampleDistSpectra.R | 6 - R/surveySpectra.R | 24 +++-- inst/doc/ChemoSpec.R | 1 inst/doc/ChemoSpec.Rnw | 1 inst/doc/ChemoSpec.pdf |binary man/ChemoSpec-package.Rd | 4 man/clupaSpectra.Rd | 2 man/coordProjCS.Rd | 40 ++++----- man/evalClusters.Rd | 6 - man/hmapSpectra.Rd | 4 man/mclust3D.Rd | 1 man/mclust3dSpectra.Rd | 2 man/mclustSpectra.Rd | 5 - man/rowDist.Rd | 4 vignettes/ChemoSpec.Rnw | 1 38 files changed, 371 insertions(+), 251 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
Diff between spdep versions 0.5-86 dated 2015-03-15 and 0.5-87 dated 2015-03-16
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/lextrB.R | 17 +++++++++++++++-- R/lextrW.R | 18 ++++++++++++++++-- inst/ChangeLog | 10 ++++++++++ inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/sids.pdf |binary 10 files changed, 64 insertions(+), 17 deletions(-)
Title: Protocol Inspection and State Machine Analysis
Description: The PRISMA package is capable of loading and processing huge text
corpora processed with the sally toolbox (http://www.mlsec.org/sally/).
sally acts as a very fast preprocessor which splits the text files into
tokens or n-grams. These output files can then be read with the PRISMA
package which applies testing-based token selection and has some
replicate-aware, highly tuned non-negative matrix factorization and
principal component analysis implementation which allows the processing of
very big data sets even on desktop machines.
Author: Tammo Krueger, Nicole Kraemer
Maintainer: Tammo Krueger
Diff between PRISMA versions 0.2-3 dated 2015-03-03 and 0.2-5 dated 2015-03-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/prisma.R | 4 ++-- inst/doc/PRISMA.pdf |binary man/corpusToPrisma.Rd | 10 ++++++---- 5 files changed, 16 insertions(+), 14 deletions(-)
Title: R Based Genetic Algorithm
Description: R based genetic algorithm for binary and floating point
chromosomes.
Author: Egon Willighagen and Michel Ballings
Maintainer: Michel Ballings
Diff between genalg versions 0.1.1.1 dated 2014-01-10 and 0.2.0 dated 2015-03-16
genalg-0.1.1.1/genalg/COPYING |only genalg-0.1.1.1/genalg/TODO |only genalg-0.2.0/genalg/ChangeLog | 5 +++++ genalg-0.2.0/genalg/DESCRIPTION | 12 ++++++------ genalg-0.2.0/genalg/MD5 | 14 ++++++-------- genalg-0.2.0/genalg/NAMESPACE | 9 ++++----- genalg-0.2.0/genalg/R/rbga.R | 4 +++- genalg-0.2.0/genalg/man/rbga.Rd | 3 ++- genalg-0.2.0/genalg/man/rbga.bin.Rd | 5 +++-- 9 files changed, 29 insertions(+), 23 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. choroplethr simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein
Maintainer: Ari Lamstein
Diff between choroplethr versions 2.1.1 dated 2014-12-11 and 3.0.0 dated 2015-03-16
choroplethr-2.1.1/choroplethr/R/admin1_data.R |only choroplethr-2.1.1/choroplethr/R/choroplethr.R |only choroplethr-2.1.1/choroplethr/R/choroplethr_acs.R |only choroplethr-2.1.1/choroplethr/R/country_data.R |only choroplethr-2.1.1/choroplethr/R/county_data.R |only choroplethr-2.1.1/choroplethr/R/state_data.R |only choroplethr-2.1.1/choroplethr/R/zip.R |only choroplethr-2.1.1/choroplethr/R/zip_data.R |only choroplethr-2.1.1/choroplethr/data/df_pop_zip.rdata |only choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.R |only choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.html |only choroplethr-2.1.1/choroplethr/inst/doc/e-country-choropleth.R |only choroplethr-2.1.1/choroplethr/inst/doc/e-country-choropleth.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/e-country-choropleth.html |only choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.R |only choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.html |only choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.R |only choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.html |only choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.R |only choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.html |only choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.R |only choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.html |only choroplethr-2.1.1/choroplethr/inst/doc/j-creating-admin1-maps.R |only choroplethr-2.1.1/choroplethr/inst/doc/j-creating-admin1-maps.Rmd |only choroplethr-2.1.1/choroplethr/inst/doc/j-creating-admin1-maps.html |only choroplethr-2.1.1/choroplethr/inst/tests/test-num_buckets.R |only choroplethr-2.1.1/choroplethr/inst/tests/test-zip.R |only choroplethr-2.1.1/choroplethr/man/ZipMap.Rd |only choroplethr-2.1.1/choroplethr/man/df_pop_zip.Rd |only choroplethr-2.1.1/choroplethr/vignettes/d-zip-map.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/e-country-choropleth.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/f-mapping-us-census-data.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/g-world-bank-data.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/h-animated-choropleths.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/i-creating-your-own-maps.Rmd |only choroplethr-2.1.1/choroplethr/vignettes/j-creating-admin1-maps.Rmd |only choroplethr-3.0.0/choroplethr/DESCRIPTION | 19 - choroplethr-3.0.0/choroplethr/MD5 | 178 ++++------ choroplethr-3.0.0/choroplethr/NAMESPACE | 9 choroplethr-3.0.0/choroplethr/NEWS | 11 choroplethr-3.0.0/choroplethr/R/acs.R |only choroplethr-3.0.0/choroplethr/R/admin1.R | 10 choroplethr-3.0.0/choroplethr/R/choropleth.R | 28 - choroplethr-3.0.0/choroplethr/R/choroplethr_animate.R | 8 choroplethr-3.0.0/choroplethr/R/choroplethr_wdi.R | 16 choroplethr-3.0.0/choroplethr/R/country.R | 16 choroplethr-3.0.0/choroplethr/R/county.R | 81 ++-- choroplethr-3.0.0/choroplethr/R/county_zoom.R | 74 ---- choroplethr-3.0.0/choroplethr/R/data.R |only choroplethr-3.0.0/choroplethr/R/deprecated.R |only choroplethr-3.0.0/choroplethr/R/state.R | 25 - choroplethr-3.0.0/choroplethr/R/usa.R | 8 choroplethr-3.0.0/choroplethr/README.md | 7 choroplethr-3.0.0/choroplethr/build/vignette.rds |binary choroplethr-3.0.0/choroplethr/data/df_pop_country.rdata |binary choroplethr-3.0.0/choroplethr/data/df_president.rdata |binary choroplethr-3.0.0/choroplethr/inst/doc/a-introduction.html | 2 choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.R | 8 choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.Rmd | 14 choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.html | 20 - choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.R | 18 - choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.Rmd | 27 + choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.html | 34 + choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.R |only choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.html |only choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.R |only choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.html |only choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.R |only choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.html |only choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.R |only choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.html |only choroplethr-3.0.0/choroplethr/inst/doc/h-creating-your-own-maps.R |only choroplethr-3.0.0/choroplethr/inst/doc/h-creating-your-own-maps.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/h-creating-your-own-maps.html |only choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.R |only choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.Rmd |only choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.html |only choroplethr-3.0.0/choroplethr/inst/tests/test-acs.R |only choroplethr-3.0.0/choroplethr/inst/tests/test-country.R | 11 choroplethr-3.0.0/choroplethr/inst/tests/test-county.R | 12 choroplethr-3.0.0/choroplethr/inst/tests/test-num_colors.R |only choroplethr-3.0.0/choroplethr/inst/tests/test-state.R | 4 choroplethr-3.0.0/choroplethr/man/Admin1Choropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/Choropleth.Rd |only choroplethr-3.0.0/choroplethr/man/CountryChoropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/CountyChoropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/CountyZoomChoropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/StateChoropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/USAChoropleth.Rd | 5 choroplethr-3.0.0/choroplethr/man/admin1_choropleth.Rd | 11 choroplethr-3.0.0/choroplethr/man/choroplethr.Rd | 7 choroplethr-3.0.0/choroplethr/man/choroplethr_acs.Rd | 53 -- choroplethr-3.0.0/choroplethr/man/choroplethr_animate.Rd | 11 choroplethr-3.0.0/choroplethr/man/choroplethr_wdi.Rd | 15 choroplethr-3.0.0/choroplethr/man/country_choropleth.Rd | 13 choroplethr-3.0.0/choroplethr/man/county_choropleth.Rd | 54 +-- choroplethr-3.0.0/choroplethr/man/county_choropleth_acs.Rd |only choroplethr-3.0.0/choroplethr/man/county_zoom_choropleth.Rd | 65 --- choroplethr-3.0.0/choroplethr/man/df_japan_census.Rd | 3 choroplethr-3.0.0/choroplethr/man/df_pop_country.Rd | 3 choroplethr-3.0.0/choroplethr/man/df_pop_county.Rd | 3 choroplethr-3.0.0/choroplethr/man/df_pop_state.Rd | 3 choroplethr-3.0.0/choroplethr/man/df_president.Rd | 3 choroplethr-3.0.0/choroplethr/man/df_president_ts.Rd | 3 choroplethr-3.0.0/choroplethr/man/get_acs_data.Rd |only choroplethr-3.0.0/choroplethr/man/get_acs_df.Rd | 48 -- choroplethr-3.0.0/choroplethr/man/state_choropleth.Rd | 22 - choroplethr-3.0.0/choroplethr/man/state_choropleth_acs.Rd |only choroplethr-3.0.0/choroplethr/man/zip_map.Rd | 42 -- choroplethr-3.0.0/choroplethr/tests/test-all.R | 6 choroplethr-3.0.0/choroplethr/vignettes/b-state-choropleth.Rmd | 14 choroplethr-3.0.0/choroplethr/vignettes/c-county-choropleth.Rmd | 27 + choroplethr-3.0.0/choroplethr/vignettes/d-country-choropleth.Rmd |only choroplethr-3.0.0/choroplethr/vignettes/e-mapping-us-census-data.Rmd |only choroplethr-3.0.0/choroplethr/vignettes/f-world-bank-data.Rmd |only choroplethr-3.0.0/choroplethr/vignettes/g-animated-choropleths.Rmd |only choroplethr-3.0.0/choroplethr/vignettes/h-creating-your-own-maps.Rmd |only choroplethr-3.0.0/choroplethr/vignettes/i-creating-admin1-maps.Rmd |only 127 files changed, 494 insertions(+), 582 deletions(-)