Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling
algorithm and related algorithms. The algorithm implementations aim for
computational efficiency using matrix algebra and covariance data. The
package is designed toward Monte Carlo simulations and includes functions
to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@jyu.fi>
Diff between matrixpls versions 1.0.4 dated 2016-12-13 and 1.0.5 dated 2017-05-03
matrixpls-1.0.4/matrixpls/man/matrixpls.boot.Rd |only matrixpls-1.0.5/matrixpls/DESCRIPTION | 14 - matrixpls-1.0.5/matrixpls/MD5 | 84 ++++---- matrixpls-1.0.5/matrixpls/NAMESPACE | 1 matrixpls-1.0.5/matrixpls/R/estimator.R | 42 ++++ matrixpls-1.0.5/matrixpls/R/matrixpls.R | 9 matrixpls-1.0.5/matrixpls/R/matrixpls.boot.R | 143 ++++++++------- matrixpls-1.0.5/matrixpls/R/matrixpls.crossvalidate.R | 5 matrixpls-1.0.5/matrixpls/R/matrixpls.postestimation.R | 41 ++-- matrixpls-1.0.5/matrixpls/R/matrixpls.predict.R | 2 matrixpls-1.0.5/matrixpls/R/weightFun.R | 2 matrixpls-1.0.5/matrixpls/build/vignette.rds |binary matrixpls-1.0.5/matrixpls/man/GSCA.Rd | 7 matrixpls-1.0.5/matrixpls/man/ave.Rd | 1 matrixpls-1.0.5/matrixpls/man/convCheck.Rd | 2 matrixpls-1.0.5/matrixpls/man/cr.Rd | 1 matrixpls-1.0.5/matrixpls/man/effects.matrixpls.Rd | 1 matrixpls-1.0.5/matrixpls/man/estimator.Rd | 19 + matrixpls-1.0.5/matrixpls/man/fitSummary.Rd | 1 matrixpls-1.0.5/matrixpls/man/fitted.matrixpls.Rd | 1 matrixpls-1.0.5/matrixpls/man/gof.Rd | 1 matrixpls-1.0.5/matrixpls/man/htmt.Rd | 1 matrixpls-1.0.5/matrixpls/man/innerEstim.Rd | 6 matrixpls-1.0.5/matrixpls/man/loadings.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls-common.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls-functions.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls-package.Rd | 13 + matrixpls-1.0.5/matrixpls/man/matrixpls.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls.crossvalidate.Rd | 7 matrixpls-1.0.5/matrixpls/man/matrixpls.plspm.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls.sempls.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixpls.sim.Rd | 1 matrixpls-1.0.5/matrixpls/man/matrixplsboot.Rd |only matrixpls-1.0.5/matrixpls/man/optimCrit.Rd | 8 matrixpls-1.0.5/matrixpls/man/outerEstim.Rd | 6 matrixpls-1.0.5/matrixpls/man/parameterEstim.Rd | 2 matrixpls-1.0.5/matrixpls/man/predict.matrixpls.Rd | 1 matrixpls-1.0.5/matrixpls/man/q2.Rd | 1 matrixpls-1.0.5/matrixpls/man/r2.Rd | 1 matrixpls-1.0.5/matrixpls/man/reliabilityEstim.Rd | 2 matrixpls-1.0.5/matrixpls/man/residuals.matrixpls.Rd | 1 matrixpls-1.0.5/matrixpls/man/signChange.Rd | 4 matrixpls-1.0.5/matrixpls/man/weightFun.Rd | 8 matrixpls-1.0.5/matrixpls/man/weightSign.Rd | 2 44 files changed, 252 insertions(+), 195 deletions(-)
Title: Time-Course Gene Set Analysis
Description: Implementation of Time-course Gene Set Analysis(TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre],
Damien Chimits [aut]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between TcGSA versions 0.10.1 dated 2015-12-22 and 0.10.5 dated 2017-05-03
DESCRIPTION | 19 ++++++------- MD5 | 67 +++++++++++++++++++++++------------------------ NEWS |only R/MYheatmap.2.R | 2 - R/TcGSA-package.R | 15 +++++----- R/TcGSA.LR.R | 7 +--- R/TcGSA.LR.parallel.R | 22 +++++++-------- R/clustTrend.R | 2 + R/multtest.TcGSA.R | 3 +- R/plot.TcGSA.R | 16 ++++++----- R/plot1GS.R | 13 ++++----- R/plotFit.GS.R | 4 ++ R/plotPat.1GS.R | 10 ++----- R/plotPat.TcGSA.R | 3 +- R/plotSelect.GS.R | 45 +++++++++++++++++++++---------- R/signifLRT.TcGSA.R | 4 +- R/summary.TcGSA.R | 2 - README | 38 +++++++++++++------------- inst/CITATION | 34 +++++++++++------------ man/TcGSA-internal.Rd | 7 ++-- man/TcGSA-package.Rd | 23 +++++++--------- man/TcGSA.LR.Rd | 16 ++++------- man/TcGSA.LR.parallel.Rd | 25 ++++++++--------- man/clustTrend.Rd | 13 +++++---- man/multtest.TcGSA.Rd | 10 +++---- man/plot.TcGSA.Rd | 15 ++++------ man/plot1GS.Rd | 14 ++++----- man/plotFit.GS.Rd | 11 ++++--- man/plotPat.1GS.Rd | 17 ++++------- man/plotPat.TcGSA.Rd | 10 +++---- man/plotSelect.GS.Rd | 31 ++++++++++++++++----- man/pval_simu.Rd | 7 ++-- man/rmixchisq.Rd | 7 ++-- man/signifLRT.TcGSA.Rd | 11 +++---- man/summary.TcGSA.Rd | 16 +++++------ 35 files changed, 278 insertions(+), 261 deletions(-)
Title: Tools for the Bayesian Discount Prior Function
Description: Functions for data augmentation using the
Bayesian discount prior function for 1 arm and 2 arm clinical trials.
Author: Shawn Balcome [cre],
Donnie Musgrove [aut],
Tarek Haddad [aut],
Christopher Jackson [ctb] (For the ppexp R code that was ported to
C++.)
Maintainer: Shawn Balcome <sbalcome@mdic.org>
Diff between bayesDP versions 1.0.2 dated 2017-04-14 and 1.1.0 dated 2017-05-03
bayesDP-1.0.2/bayesDP/man/final_binomial.Rd |only bayesDP-1.0.2/bayesDP/man/final_normal.Rd |only bayesDP-1.1.0/bayesDP/DESCRIPTION | 13 bayesDP-1.1.0/bayesDP/MD5 | 67 bayesDP-1.1.0/bayesDP/NAMESPACE | 92 - bayesDP-1.1.0/bayesDP/NEWS.md | 39 bayesDP-1.1.0/bayesDP/R/RcppExports.R | 22 bayesDP-1.1.0/bayesDP/R/bdpbinomial.R | 997 +++++------- bayesDP-1.1.0/bayesDP/R/bdpnormal.R | 1085 ++++++------- bayesDP-1.1.0/bayesDP/R/bdpsurvival.R | 1246 +++++++--------- bayesDP-1.1.0/bayesDP/R/plot.R | 1167 ++++++++------ bayesDP-1.1.0/bayesDP/R/ppexp.R | 88 - bayesDP-1.1.0/bayesDP/R/print.R | 193 +- bayesDP-1.1.0/bayesDP/R/summary.R | 781 +++++----- bayesDP-1.1.0/bayesDP/README.md | 109 - bayesDP-1.1.0/bayesDP/build |only bayesDP-1.1.0/bayesDP/inst |only bayesDP-1.1.0/bayesDP/man/bdpbinomial.Rd | 377 ++-- bayesDP-1.1.0/bayesDP/man/bdpnormal.Rd | 406 ++--- bayesDP-1.1.0/bayesDP/man/bdpsurvival.Rd | 404 ++--- bayesDP-1.1.0/bayesDP/man/plot-bdpbinomial-method.Rd | 47 bayesDP-1.1.0/bayesDP/man/plot-bdpnormal-method.Rd | 47 bayesDP-1.1.0/bayesDP/man/plot-bdpsurvival-method.Rd | 45 bayesDP-1.1.0/bayesDP/man/ppexp.Rd | 85 - bayesDP-1.1.0/bayesDP/man/print-bdpbinomial-method.Rd | 36 bayesDP-1.1.0/bayesDP/man/print-bdpnormal-method.Rd | 35 bayesDP-1.1.0/bayesDP/man/print-bdpsurvival-method.Rd | 44 bayesDP-1.1.0/bayesDP/man/summary-bdpbinomial-method.Rd | 52 bayesDP-1.1.0/bayesDP/man/summary-bdpnormal-method.Rd | 52 bayesDP-1.1.0/bayesDP/man/summary-bdpsurvival-method.Rd | 52 bayesDP-1.1.0/bayesDP/src/RcppExports.cpp | 18 bayesDP-1.1.0/bayesDP/vignettes |only 32 files changed, 3960 insertions(+), 3639 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-26 1.0
Title: Interface to 'typeform' Results
Description: An R interface to the 'typeform' <https://typeform.com> application program interface.
Also provides functions for downloading your results.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between rtypeform versions 0.2.0 dated 2016-12-02 and 0.3.0 dated 2017-05-03
rtypeform-0.2.0/rtypeform/man/get_results.Rd |only rtypeform-0.3.0/rtypeform/DESCRIPTION | 10 - rtypeform-0.3.0/rtypeform/MD5 | 23 +- rtypeform-0.3.0/rtypeform/NAMESPACE | 6 rtypeform-0.3.0/rtypeform/NEWS.md | 8 rtypeform-0.3.0/rtypeform/R/get_all_typeforms.R | 16 + rtypeform-0.3.0/rtypeform/R/get_results.R | 92 ++++++++-- rtypeform-0.3.0/rtypeform/R/print.R |only rtypeform-0.3.0/rtypeform/README.md | 16 - rtypeform-0.3.0/rtypeform/man/get_all_typeforms.Rd | 12 - rtypeform-0.3.0/rtypeform/man/get_api.Rd | 5 rtypeform-0.3.0/rtypeform/man/get_questionnaire.Rd |only rtypeform-0.3.0/rtypeform/tests/testthat/test_get_all_typeforms.R | 2 rtypeform-0.3.0/rtypeform/tests/testthat/test_get_results.R | 37 +++- 14 files changed, 177 insertions(+), 50 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.5 dated 2016-04-22 and 1.6 dated 2017-05-03
DESCRIPTION | 9 ++++--- MD5 | 11 +++++---- R/plot.R | 64 +++++++++++++++++++++++++++++++++++++++++--------------- R/provenance.R | 15 +++++++------ inst/CITATION |only man/MDS.Rd | 8 ++++--- man/plot.MDS.Rd | 20 +++++++++++------ 7 files changed, 84 insertions(+), 43 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove <sabanesd@roche.com>,
Wai Yin Yeung <winnie.yeung@roche.com>,
Giuseppe Palermo <giuseppe.palermo@roche.com>,
Thomas Jaki <jaki.thomas@gmail.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between crmPack versions 0.2.0 dated 2016-07-16 and 0.2.1 dated 2017-05-03
crmPack |only 1 file changed
Title: Text Processing for Small or Big Data Files
Description: Processes big text data files in batches efficiently. For this purpose, it offers functions for splitting, parsing, tokenizing and creating a vocabulary. Moreover, it includes functions for building either a document-term matrix or a term-document matrix and extracting information from those (term-associations, most frequent terms). Lastly, it embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between textTinyR versions 1.0.5 dated 2017-04-01 and 1.0.6 dated 2017-05-03
textTinyR-1.0.5/textTinyR/R/zzz.R |only textTinyR-1.0.6/textTinyR/DESCRIPTION | 8 textTinyR-1.0.6/textTinyR/MD5 | 35 textTinyR-1.0.6/textTinyR/NEWS.md | 6 textTinyR-1.0.6/textTinyR/R/RcppExports.R | 4 textTinyR-1.0.6/textTinyR/R/utils.R | 26 textTinyR-1.0.6/textTinyR/README.md | 1 textTinyR-1.0.6/textTinyR/build/vignette.rds |binary textTinyR-1.0.6/textTinyR/configure | 14 textTinyR-1.0.6/textTinyR/inst/doc/functionality_of_textTinyR_package.html | 10 textTinyR-1.0.6/textTinyR/man/vocabulary_parser.Rd | 16 textTinyR-1.0.6/textTinyR/src/RcppExports.cpp | 10 textTinyR-1.0.6/textTinyR/src/export_all_funcs.cpp | 6 textTinyR-1.0.6/textTinyR/src/init.c | 4 textTinyR-1.0.6/textTinyR/src/token_big_files.h | 8 textTinyR-1.0.6/textTinyR/src/token_stats.h | 6 textTinyR-1.0.6/textTinyR/src/tokenization.h | 24 textTinyR-1.0.6/textTinyR/tests/testthat/test-tokenization_transformation.R | 870 +++++----- textTinyR-1.0.6/textTinyR/tests/testthat/test-vocab_file_parser_bytes_converter_dice_levenstein_cosine.R | 778 +++----- 19 files changed, 851 insertions(+), 975 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.10.4 dated 2016-12-04 and 3.0.1 dated 2017-05-03
secr-2.10.4/secr/vignettes/detectionfn.png |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.RData |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.rdb |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.rdx |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.RData |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.rdb |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.rdx |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.RData |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.rdb |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.rdx |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.RData |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.rdb |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.rdx |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.RData |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.rdb |only secr-2.10.4/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.rdx |only secr-3.0.1/secr/DESCRIPTION | 8 secr-3.0.1/secr/MD5 | 285 - secr-3.0.1/secr/NAMESPACE | 50 secr-3.0.1/secr/NEWS | 71 secr-3.0.1/secr/R/D.designdata.R | 4 secr-3.0.1/secr/R/DA.R | 2 secr-3.0.1/secr/R/DENSITY.R | 65 secr-3.0.1/secr/R/Dsurface.R | 6 secr-3.0.1/secr/R/PG.R | 2 secr-3.0.1/secr/R/addCovariates.R | 234 secr-3.0.1/secr/R/addSightings.R | 33 secr-3.0.1/secr/R/addTelemetry.R |only secr-3.0.1/secr/R/autoini.R | 27 secr-3.0.1/secr/R/clone.R | 2 secr-3.0.1/secr/R/derivedMS.R | 40 secr-3.0.1/secr/R/discretize.R | 29 secr-3.0.1/secr/R/esa.R | 33 secr-3.0.1/secr/R/fxi.R | 68 secr-3.0.1/secr/R/homerange.R | 160 secr-3.0.1/secr/R/ip.secr.R | 56 secr-3.0.1/secr/R/join.R | 147 secr-3.0.1/secr/R/logmultinom.R | 3 secr-3.0.1/secr/R/make.capthist.R | 130 secr-3.0.1/secr/R/make.grid.R | 25 secr-3.0.1/secr/R/make.mask.R | 3 secr-3.0.1/secr/R/mask.check.R | 3 secr-3.0.1/secr/R/methods.R | 934 +-- secr-3.0.1/secr/R/model.average.R | 8 secr-3.0.1/secr/R/onAttach.R | 4 secr-3.0.1/secr/R/par.secr.fit.R | 17 secr-3.0.1/secr/R/pdot.R | 278 - secr-3.0.1/secr/R/plot.capthist.r | 349 - secr-3.0.1/secr/R/plot.secr.R | 39 secr-3.0.1/secr/R/plot.traps.R |only secr-3.0.1/secr/R/plotMaskEdge.R | 37 secr-3.0.1/secr/R/predict.secr.R | 39 secr-3.0.1/secr/R/raster.R | 1 secr-3.0.1/secr/R/rbind.capthist.R | 322 + secr-3.0.1/secr/R/rbind.traps.R |only secr-3.0.1/secr/R/read.traps.R | 20 secr-3.0.1/secr/R/reduce.R | 383 - secr-3.0.1/secr/R/regionN.R | 43 secr-3.0.1/secr/R/secr.design.MS.R | 35 secr-3.0.1/secr/R/secr.fit.R | 324 - secr-3.0.1/secr/R/secr.test.R | 2 secr-3.0.1/secr/R/secrloglik.R | 894 +-- secr-3.0.1/secr/R/sim.capthist.R | 623 +- secr-3.0.1/secr/R/sim.popn.R | 1 secr-3.0.1/secr/R/sim.secr.R | 100 secr-3.0.1/secr/R/snip.R | 13 secr-3.0.1/secr/R/split.traps.R | 6 secr-3.0.1/secr/R/suggest.buffer.R | 20 secr-3.0.1/secr/R/telemetry.R | 133 secr-3.0.1/secr/R/usagePlot.R | 99 secr-3.0.1/secr/R/utility.R | 411 + secr-3.0.1/secr/R/verify.R | 417 - secr-3.0.1/secr/R/write.captures.R | 12 secr-3.0.1/secr/R/write.traps.R | 5 secr-3.0.1/secr/data/OVpossum.RData |binary secr-3.0.1/secr/data/deermouse.RData |binary secr-3.0.1/secr/data/hornedlizard.RData |binary secr-3.0.1/secr/data/housemouse.RData |binary secr-3.0.1/secr/data/ovenbird.RData |binary secr-3.0.1/secr/data/ovensong.RData |binary secr-3.0.1/secr/data/possum.RData |binary secr-3.0.1/secr/data/secrdemo.RData |binary secr-3.0.1/secr/data/skink.RData |binary secr-3.0.1/secr/data/stoatDNA.RData |binary secr-3.0.1/secr/inst/doc/secr-datainput.Rmd | 57 secr-3.0.1/secr/inst/doc/secr-datainput.pdf |binary secr-3.0.1/secr/inst/doc/secr-manual.pdf |binary secr-3.0.1/secr/inst/doc/secr-overview.R | 28 secr-3.0.1/secr/inst/doc/secr-overview.Rmd | 254 secr-3.0.1/secr/inst/doc/secr-overview.pdf |binary secr-3.0.1/secr/man/CV.Rd | 2 secr-3.0.1/secr/man/DA.Rd | 4 secr-3.0.1/secr/man/DENSITY.Rd | 8 secr-3.0.1/secr/man/OVpossum.Rd | 15 secr-3.0.1/secr/man/PG.Rd | 2 secr-3.0.1/secr/man/addCovariates.Rd | 3 secr-3.0.1/secr/man/addSightings.Rd | 14 secr-3.0.1/secr/man/addTelemetry.Rd | 62 secr-3.0.1/secr/man/as.mask.Rd |only secr-3.0.1/secr/man/capthist.Rd | 1 secr-3.0.1/secr/man/capthistfn.Rd | 4 secr-3.0.1/secr/man/deletemaskpoints.Rd | 4 secr-3.0.1/secr/man/details.Rd | 28 secr-3.0.1/secr/man/discretize.Rd | 13 secr-3.0.1/secr/man/fxi.Rd | 13 secr-3.0.1/secr/man/homerange.Rd | 11 secr-3.0.1/secr/man/make.mask.Rd | 14 secr-3.0.1/secr/man/make.systematic.Rd | 10 secr-3.0.1/secr/man/make.traps.Rd | 12 secr-3.0.1/secr/man/mask.check.Rd | 2 secr-3.0.1/secr/man/ms.Rd | 2 secr-3.0.1/secr/man/occasionKey.Rd |only secr-3.0.1/secr/man/ovenbird.Rd | 37 secr-3.0.1/secr/man/par.secr.fit.Rd | 7 secr-3.0.1/secr/man/plot.capthist.Rd | 55 secr-3.0.1/secr/man/plotmaskedge.Rd | 5 secr-3.0.1/secr/man/predict.secr.Rd | 15 secr-3.0.1/secr/man/rbind.traps.Rd | 3 secr-3.0.1/secr/man/read.telemetry.Rd | 27 secr-3.0.1/secr/man/reduce.capthist.Rd | 10 secr-3.0.1/secr/man/secr-package.Rd | 15 secr-3.0.1/secr/man/secr.fit.Rd | 5 secr-3.0.1/secr/man/secr.model.detection.Rd | 4 secr-3.0.1/secr/man/secrdemo.Rd | 2 secr-3.0.1/secr/man/sharefactorlevels.Rd |only secr-3.0.1/secr/man/sighting.Rd | 18 secr-3.0.1/secr/man/sim.capthist.Rd | 35 secr-3.0.1/secr/man/sim.popn.Rd | 2 secr-3.0.1/secr/man/smooths.Rd | 4 secr-3.0.1/secr/man/snip.Rd | 4 secr-3.0.1/secr/man/speed.Rd | 2 secr-3.0.1/secr/man/subset.popn.Rd | 2 secr-3.0.1/secr/man/traps.Rd | 9 secr-3.0.1/secr/man/troubleshooting.Rd | 18 secr-3.0.1/secr/man/updateCH.Rd |only secr-3.0.1/secr/man/usage.Rd | 2 secr-3.0.1/secr/man/usagePlot.Rd | 46 secr-3.0.1/secr/man/userdist.Rd | 6 secr-3.0.1/secr/man/verify.Rd | 4 secr-3.0.1/secr/man/writeGPS.Rd | 12 secr-3.0.1/secr/src/detectfn.c | 786 ++- secr-3.0.1/secr/src/init.c |only secr-3.0.1/secr/src/polygon.c | 20 secr-3.0.1/secr/src/secr.c | 2604 +++++----- secr-3.0.1/secr/src/secr.h | 381 - secr-3.0.1/secr/src/sighting.c | 864 ++- secr-3.0.1/secr/src/simsecr.c | 17 secr-3.0.1/secr/src/trapping.c | 29 secr-3.0.1/secr/src/unmarked.c | 130 secr-3.0.1/secr/src/utils.c | 49 secr-3.0.1/secr/vignettes/secr-datainput.Rmd | 57 secr-3.0.1/secr/vignettes/secr-overview.Rmd | 254 secr-3.0.1/secr/vignettes/secr-overview_cache/latex/__packages | 6 secr-3.0.1/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.RData |only secr-3.0.1/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.rdb |only secr-3.0.1/secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.rdx |only secr-3.0.1/secr/vignettes/secr-overview_files/figure-latex/unnamed-chunk-3-1.pdf |binary 157 files changed, 7787 insertions(+), 5377 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 5.1-0 dated 2017-01-01 and 5.1-1 dated 2017-05-03
DESCRIPTION | 8 +++---- MD5 | 57 +++++++++++++++++++++++++------------------------- NAMESPACE | 3 +- NEWS | 11 +++++++++ R/Function.rms.s | 3 +- R/Predict.s | 7 +++++- R/anova.rms.s | 12 +++++++--- R/calibrate.cph.s | 5 ++-- R/calibrate.psm.s | 7 +++--- R/hazard.ratio.plot.s | 38 ++++++++++++++++----------------- R/lrm.fit.s | 18 +++++++-------- R/matinv.s | 4 +-- R/orm.fit.s | 8 +++---- R/plot.Predict.s | 4 ++- R/predab.resample.s | 3 +- R/print.psm.s | 18 +++++++-------- R/psm.s | 3 +- R/rms.s | 2 - R/rms.trans.s | 3 +- R/rmsMisc.s | 6 ++--- R/robcov.s | 5 +--- R/summary.rms.s | 7 +++--- R/which.influence.s | 3 +- README.md | 1 inst/tests/lrm.s | 18 +++++++++++++++ man/anova.rms.Rd | 4 ++- man/summary.rms.Rd | 2 - man/validate.Rd | 2 - man/validate.cph.Rd | 2 - src/init.c |only 30 files changed, 157 insertions(+), 107 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.5 dated 2017-01-24 and 2.6 dated 2017-05-03
DESCRIPTION | 8 +- MD5 | 106 +++++++++++++++++------------------ R/as.semigroup.R | 14 +--- R/as.signed.R | 14 +--- R/as.strings.R | 6 - R/bundle.census.R | 28 ++++----- R/bundles.R | 137 ++++++++++++++++++++++----------------------- R/cngr.R | 13 ++-- R/convert.R | 21 ++++-- R/cph.R | 47 +++++++-------- R/decomp.R | 26 ++++---- R/diagram.R | 11 ++- R/iinc.R | 48 ++++++++------- R/is.mc.R | 6 - R/pacnet.R | 90 ++++++++++++++--------------- R/partial.order.R | 52 ++++++++++------- R/pi.rels.R | 26 ++++---- R/rbox.R | 135 ++++++++++++++++++++++---------------------- R/read.gml.R | 142 +++++++++++++++++++++++------------------------ R/reduc.R | 26 ++++---- R/reducs.R | 43 ++++++-------- R/rel.sys.R | 77 +++++++++++++------------ R/relabel.R | 12 +-- R/semigroup.R | 8 +- R/semiring.R | 7 +- R/signed.R | 9 +- R/summaryBundles.R | 96 ++++++++++++++++--------------- R/transf.R | 142 +++++++++++++++++++++++++++++++++-------------- R/trnf.R |only R/write.gml.R | 20 +++--- R/write.srt.R | 17 ++--- R/zbind.R | 18 +++-- inst/CHANGELOG | 24 ++++++- man/as.semigroup.Rd | 6 - man/as.signed.Rd | 4 - man/as.strings.Rd | 4 - man/bundle.census.Rd | 2 man/bundles.Rd | 2 man/convert.Rd | 6 - man/cph.Rd | 4 - man/diagram.levels.Rd | 4 - man/expos.Rd | 2 man/iinc.Rd | 4 - man/multiplex-package.Rd | 6 - man/partial.order.Rd | 7 +- man/rbox.Rd | 11 +-- man/reduc.Rd | 4 - man/rel.sys.Rd | 6 - man/relabel.Rd | 8 +- man/semigroup.Rd | 6 - man/semiring.Rd | 8 +- man/signed.Rd | 4 - man/summaryBundles.Rd | 4 - man/transf.Rd | 15 ++-- man/trnf.Rd |only 55 files changed, 824 insertions(+), 722 deletions(-)
Title: Generalized Linear Models with Clustering
Description: Binomial and Poisson regression for clustered data, fixed
and random effects with bootstrapping.
Author: Göran Broström
Maintainer: Göran Broström <goran.brostrom@umu.se>
Diff between glmmML versions 1.0.1 dated 2017-02-10 and 1.0.2 dated 2017-05-03
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 5 +++-- src/init.c |only 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Threshold Regression for Interval-Censored Data with a Cure Rate
Option
Description: Fit a threshold regression model for Interval Censored Data based on the first-hitting-time of a boundary by the sample path of a Wiener diffusion process. The threshold regression methodology is well suited to applications involving survival and time-to-event data.
Author: Man-Hua Chen
Maintainer: Man-Hua Chen <mchen@mail.tku.edu.tw>
Diff between thregI versions 1.0.2 dated 2017-01-18 and 1.0.3 dated 2017-05-03
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/plot.thregI.R | 13 ++++++++----- R/plot.thregIcure.R | 13 +++++++------ R/thregI.R | 12 +++++++----- R/thregIcure.R | 14 +++++++------- man/thregIcure.Rd | 3 ++- 7 files changed, 43 insertions(+), 36 deletions(-)
Title: Evaluation of Failure Time Surrogate Endpoints in Individual
Patient Data Meta-Analyses
Description: Provides functions for the evaluation of
surrogate endpoints when both the surrogate and the true endpoint are failure
time variables. The approaches implemented are: (1) the two-step approach
(Burzykowski et al, 2001) <DOI:10.1111/1467-9876.00244> with a copula model (Clayton, Plackett, Hougaard) at
the first step and either a linear regression of log-hazard ratios at the second
step (either adjusted or not for measurement error); (2) mixed proportional
hazard models estimated via mixed Poisson GLM.
Author: Federico Rotolo [aut, cre],
Xavier Paoletti [ctr], Marc Buyse [ctr], Tomasz Burzykowski [ctr], Stefan Michiels [ctr]
Maintainer: Federico Rotolo <federico.rotolo@gustaveroussy.fr>
Diff between surrosurv versions 1.1.10 dated 2017-02-27 and 1.1.15 dated 2017-05-03
surrosurv-1.1.10/surrosurv/inst/doc/surrosurv.Rnw |only surrosurv-1.1.10/surrosurv/inst/doc/surrosurv.pdf |only surrosurv-1.1.10/surrosurv/vignettes/loocv-1.pdf |only surrosurv-1.1.10/surrosurv/vignettes/poissonize-1.pdf |only surrosurv-1.1.10/surrosurv/vignettes/predictions-1.pdf |only surrosurv-1.1.10/surrosurv/vignettes/surrosurv.Rnw |only surrosurv-1.1.10/surrosurv/vignettes/survCurves-1.pdf |only surrosurv-1.1.15/surrosurv/DESCRIPTION | 16 surrosurv-1.1.15/surrosurv/MD5 | 49 surrosurv-1.1.15/surrosurv/NAMESPACE | 6 surrosurv-1.1.15/surrosurv/NEWS | 13 surrosurv-1.1.15/surrosurv/R/convergence.R | 91 + surrosurv-1.1.15/surrosurv/R/copulas_functions.R | 834 +++++++++-------- surrosurv-1.1.15/surrosurv/R/loocv.R | 272 +++-- surrosurv-1.1.15/surrosurv/R/poisson_functions.R | 316 ++++-- surrosurv-1.1.15/surrosurv/R/poissonize.R | 134 +- surrosurv-1.1.15/surrosurv/R/predict.R | 443 +++++---- surrosurv-1.1.15/surrosurv/R/simData.R | 137 +- surrosurv-1.1.15/surrosurv/R/surrosurv.R | 324 ++++-- surrosurv-1.1.15/surrosurv/build/partial.rdb |binary surrosurv-1.1.15/surrosurv/build/vignette.rds |binary surrosurv-1.1.15/surrosurv/inst/doc/copulas.Rnw | 4 surrosurv-1.1.15/surrosurv/inst/doc/copulas.pdf |binary surrosurv-1.1.15/surrosurv/man/loocv.Rd | 2 surrosurv-1.1.15/surrosurv/man/surrosurv.Rd | 19 surrosurv-1.1.15/surrosurv/vignettes/copulas.Rnw | 4 surrosurv-1.1.15/surrosurv/vignettes/figs |only surrosurv-1.1.15/surrosurv/vignettes/refs.bib | 22 surrosurv-1.1.15/surrosurv/vignettes/surrosurv.pdf |only surrosurv-1.1.15/surrosurv/vignettes/surrosurv.tex |only 30 files changed, 1711 insertions(+), 975 deletions(-)
Title: Collection of Rudimentary Bioinformatics Tools
Description: Provides a bundle of basic and fundamental bioinformatics tools,
such as network querying and alignment, subnetwork extraction and search,
network biomarker identification.
Author: Ling-Yun Wu [aut, cre],
Qiang Huang [aut],
Duanchen Sun [aut]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>
Diff between Corbi versions 0.4-1 dated 2016-09-20 and 0.4-2 dated 2017-05-03
Corbi-0.4-1/Corbi/tests/markrank |only Corbi-0.4-1/Corbi/tests/test_markrank.R |only Corbi-0.4-2/Corbi/DESCRIPTION | 15 ++-- Corbi-0.4-2/Corbi/MD5 | 52 +++++++------- Corbi-0.4-2/Corbi/R/markrank.R | 86 ++++++++++++++++------- Corbi-0.4-2/Corbi/README.md | 4 - Corbi-0.4-2/Corbi/build |only Corbi-0.4-2/Corbi/inst |only Corbi-0.4-2/Corbi/man/Corbi-package.Rd | 3 Corbi-0.4-2/Corbi/man/best_subnets.Rd | 1 Corbi-0.4-2/Corbi/man/column.Rd | 1 Corbi-0.4-2/Corbi/man/extend_subnets.Rd | 1 Corbi-0.4-2/Corbi/man/get_shortest_distances.Rd | 1 Corbi-0.4-2/Corbi/man/get_subnets.Rd | 1 Corbi-0.4-2/Corbi/man/kappa_score.Rd | 1 Corbi-0.4-2/Corbi/man/markrank.Rd | 88 +++++++++++++++++------- Corbi-0.4-2/Corbi/man/net_align.Rd | 1 Corbi-0.4-2/Corbi/man/net_query.Rd | 2 Corbi-0.4-2/Corbi/man/nnzero.Rd | 1 Corbi-0.4-2/Corbi/man/read_net.Rd | 1 Corbi-0.4-2/Corbi/man/rmultihyper.Rd | 1 Corbi-0.4-2/Corbi/man/submatrix.Rd | 1 Corbi-0.4-2/Corbi/man/write_net.Rd | 1 Corbi-0.4-2/Corbi/src/Corbi.cpp | 1 Corbi-0.4-2/Corbi/vignettes |only 25 files changed, 165 insertions(+), 98 deletions(-)
Title: Categorical Regression Splines
Description: Regression splines that handle a mix of continuous and categorical (discrete) data often encountered in applied settings. I would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <http://www.nserc-crsng.gc.ca>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <http://www.sshrc-crsh.gc.ca>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://www.sharcnet.ca>).
Author: Jeffrey S. Racine [aut, cre],
Zhenghua Nie [aut],
Brian D. Ripley [ctb] (stepCV.R)
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between crs versions 0.15-24 dated 2014-12-18 and 0.15-26 dated 2017-05-03
crs-0.15-24/crs/src/Makevars.win |only crs-0.15-24/crs/src/nomad_src/Mesh.cpp |only crs-0.15-24/crs/src/nomad_src/Mesh.hpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model.cpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model.hpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model_Evaluator.cpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model_Evaluator.hpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model_Search.cpp |only crs-0.15-24/crs/src/nomad_src/TGP_Model_Search.hpp |only crs-0.15-24/crs/src/nomad_src/TGP_Output_Model.cpp |only crs-0.15-24/crs/src/nomad_src/TGP_Output_Model.hpp |only crs-0.15-26/crs/CHANGELOG | 12 crs-0.15-26/crs/DESCRIPTION | 19 crs-0.15-26/crs/MD5 | 327 crs-0.15-26/crs/NAMESPACE | 104 crs-0.15-26/crs/R/crs.R | 8 crs-0.15-26/crs/R/crsiv.R | 2 crs-0.15-26/crs/R/frscvNOMAD.R | 4 crs-0.15-26/crs/R/krscvNOMAD.R | 4 crs-0.15-26/crs/R/np.regression.glp.R | 8 crs-0.15-26/crs/R/spline.R | 2 crs-0.15-26/crs/R/util.R | 4 crs-0.15-26/crs/R/zzz.R | 2 crs-0.15-26/crs/README.md | 8 crs-0.15-26/crs/build/vignette.rds |binary crs-0.15-26/crs/demo/spline.R | 2 crs-0.15-26/crs/inst/doc/crs.Rnw | 4 crs-0.15-26/crs/inst/doc/crs.pdf |binary crs-0.15-26/crs/inst/doc/crs_faq.Rnw | 43 crs-0.15-26/crs/inst/doc/crs_faq.pdf |binary crs-0.15-26/crs/inst/doc/spline_primer.R | 6 crs-0.15-26/crs/inst/doc/spline_primer.Rnw | 13 crs-0.15-26/crs/inst/doc/spline_primer.pdf |binary crs-0.15-26/crs/man/crs-package.Rd | 8 crs-0.15-26/crs/man/crs.Rd | 10 crs-0.15-26/crs/man/frscv.Rd | 4 crs-0.15-26/crs/man/frscvNOMAD.Rd | 8 crs-0.15-26/crs/man/gsl-bs.Rd | 11 crs-0.15-26/crs/man/krscv.Rd | 4 crs-0.15-26/crs/man/krscvNOMAD.Rd | 8 crs-0.15-26/crs/man/npglpreg.Rd | 4 crs-0.15-26/crs/man/snomadr.Rd | 8 crs-0.15-26/crs/src/Makevars | 35 crs-0.15-26/crs/src/crs_init.c |only crs-0.15-26/crs/src/nomad_src/Barrier.cpp | 923 crs-0.15-26/crs/src/nomad_src/Barrier.hpp | 524 crs-0.15-26/crs/src/nomad_src/Cache.cpp | 1109 crs-0.15-26/crs/src/nomad_src/Cache.hpp | 711 crs-0.15-26/crs/src/nomad_src/Cache_File_Point.cpp | 463 crs-0.15-26/crs/src/nomad_src/Cache_File_Point.hpp | 314 crs-0.15-26/crs/src/nomad_src/Cache_Point.cpp | 43 crs-0.15-26/crs/src/nomad_src/Cache_Point.hpp | 128 crs-0.15-26/crs/src/nomad_src/Cache_Search.cpp | 250 crs-0.15-26/crs/src/nomad_src/Cache_Search.hpp | 124 crs-0.15-26/crs/src/nomad_src/Clock.cpp | 44 crs-0.15-26/crs/src/nomad_src/Clock.hpp | 161 crs-0.15-26/crs/src/nomad_src/Direction.cpp | 157 crs-0.15-26/crs/src/nomad_src/Direction.hpp | 385 crs-0.15-26/crs/src/nomad_src/Directions.cpp | 1698 crs-0.15-26/crs/src/nomad_src/Directions.hpp | 578 crs-0.15-26/crs/src/nomad_src/Display.cpp | 1290 crs-0.15-26/crs/src/nomad_src/Display.hpp | 959 crs-0.15-26/crs/src/nomad_src/Double.cpp | 622 crs-0.15-26/crs/src/nomad_src/Double.hpp | 912 crs-0.15-26/crs/src/nomad_src/Eval_Point.cpp | 515 crs-0.15-26/crs/src/nomad_src/Eval_Point.hpp | 1215 crs-0.15-26/crs/src/nomad_src/Evaluator.cpp | 1520 crs-0.15-26/crs/src/nomad_src/Evaluator.hpp | 52 crs-0.15-26/crs/src/nomad_src/Evaluator_Control.cpp | 6986 ++- crs-0.15-26/crs/src/nomad_src/Evaluator_Control.hpp | 1436 crs-0.15-26/crs/src/nomad_src/Exception.cpp | 50 crs-0.15-26/crs/src/nomad_src/Exception.hpp | 110 crs-0.15-26/crs/src/nomad_src/Extended_Poll.cpp | 2264 - crs-0.15-26/crs/src/nomad_src/Extended_Poll.hpp | 395 crs-0.15-26/crs/src/nomad_src/Filter_Point.hpp | 24 crs-0.15-26/crs/src/nomad_src/GMesh.cpp |only crs-0.15-26/crs/src/nomad_src/GMesh.hpp |only crs-0.15-26/crs/src/nomad_src/LH_Search.cpp | 469 crs-0.15-26/crs/src/nomad_src/LH_Search.hpp | 196 crs-0.15-26/crs/src/nomad_src/L_Curve.cpp | 111 crs-0.15-26/crs/src/nomad_src/L_Curve.hpp | 110 crs-0.15-26/crs/src/nomad_src/Mads.cpp | 4023 +- crs-0.15-26/crs/src/nomad_src/Mads.hpp | 1128 crs-0.15-26/crs/src/nomad_src/Model_Sorted_Point.cpp | 94 crs-0.15-26/crs/src/nomad_src/Model_Sorted_Point.hpp | 160 crs-0.15-26/crs/src/nomad_src/Model_Stats.cpp | 343 crs-0.15-26/crs/src/nomad_src/Model_Stats.hpp | 642 crs-0.15-26/crs/src/nomad_src/Multi_Obj_Evaluator.cpp | 251 crs-0.15-26/crs/src/nomad_src/Multi_Obj_Evaluator.hpp | 214 crs-0.15-26/crs/src/nomad_src/Multi_Obj_Quad_Model_Evaluator.hpp | 26 crs-0.15-26/crs/src/nomad_src/OrthogonalMesh.cpp |only crs-0.15-26/crs/src/nomad_src/OrthogonalMesh.hpp |only crs-0.15-26/crs/src/nomad_src/Parameter_Entries.cpp | 88 crs-0.15-26/crs/src/nomad_src/Parameter_Entries.hpp | 149 crs-0.15-26/crs/src/nomad_src/Parameter_Entry.cpp | 314 crs-0.15-26/crs/src/nomad_src/Parameter_Entry.hpp | 24 crs-0.15-26/crs/src/nomad_src/Parameters.cpp |17771 +++++----- crs-0.15-26/crs/src/nomad_src/Parameters.hpp | 5393 +-- crs-0.15-26/crs/src/nomad_src/Pareto_Front.cpp | 676 crs-0.15-26/crs/src/nomad_src/Pareto_Front.hpp | 245 crs-0.15-26/crs/src/nomad_src/Pareto_Point.cpp | 107 crs-0.15-26/crs/src/nomad_src/Pareto_Point.hpp | 234 crs-0.15-26/crs/src/nomad_src/Phase_One_Evaluator.cpp | 77 crs-0.15-26/crs/src/nomad_src/Phase_One_Evaluator.hpp | 246 crs-0.15-26/crs/src/nomad_src/Phase_One_Search.cpp | 594 crs-0.15-26/crs/src/nomad_src/Phase_One_Search.hpp | 24 crs-0.15-26/crs/src/nomad_src/Point.cpp | 730 crs-0.15-26/crs/src/nomad_src/Point.hpp | 859 crs-0.15-26/crs/src/nomad_src/Priority_Eval_Point.cpp | 408 crs-0.15-26/crs/src/nomad_src/Priority_Eval_Point.hpp | 30 crs-0.15-26/crs/src/nomad_src/Quad_Model.cpp | 3554 + crs-0.15-26/crs/src/nomad_src/Quad_Model.hpp | 830 crs-0.15-26/crs/src/nomad_src/Quad_Model_Evaluator.cpp | 330 crs-0.15-26/crs/src/nomad_src/Quad_Model_Evaluator.hpp | 166 crs-0.15-26/crs/src/nomad_src/Quad_Model_Search.cpp | 1790 - crs-0.15-26/crs/src/nomad_src/Quad_Model_Search.hpp | 231 crs-0.15-26/crs/src/nomad_src/RNG.cpp | 121 crs-0.15-26/crs/src/nomad_src/RNG.hpp | 103 crs-0.15-26/crs/src/nomad_src/Random_Pickup.cpp | 80 crs-0.15-26/crs/src/nomad_src/Random_Pickup.hpp | 24 crs-0.15-26/crs/src/nomad_src/SMesh.cpp |only crs-0.15-26/crs/src/nomad_src/SMesh.hpp |only crs-0.15-26/crs/src/nomad_src/Search.hpp | 177 crs-0.15-26/crs/src/nomad_src/Set_Element.hpp | 24 crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Evaluator.cpp |only crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Evaluator.hpp |only crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Manager.cpp |only crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Manager.hpp |only crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Search.cpp |only crs-0.15-26/crs/src/nomad_src/Sgtelib_Model_Search.hpp |only crs-0.15-26/crs/src/nomad_src/Signature.cpp | 1991 - crs-0.15-26/crs/src/nomad_src/Signature.hpp | 1002 crs-0.15-26/crs/src/nomad_src/Signature_Element.hpp | 24 crs-0.15-26/crs/src/nomad_src/Single_Obj_Quad_Model_Evaluator.hpp | 26 crs-0.15-26/crs/src/nomad_src/Slave.cpp | 885 crs-0.15-26/crs/src/nomad_src/Slave.hpp | 428 crs-0.15-26/crs/src/nomad_src/Speculative_Search.cpp | 326 crs-0.15-26/crs/src/nomad_src/Speculative_Search.hpp | 24 crs-0.15-26/crs/src/nomad_src/Stats.cpp | 505 crs-0.15-26/crs/src/nomad_src/Stats.hpp | 1011 crs-0.15-26/crs/src/nomad_src/Uncopyable.hpp | 24 crs-0.15-26/crs/src/nomad_src/VNS_Search.cpp | 1273 crs-0.15-26/crs/src/nomad_src/VNS_Search.hpp | 153 crs-0.15-26/crs/src/nomad_src/Variable_Group.cpp | 336 crs-0.15-26/crs/src/nomad_src/Variable_Group.hpp | 363 crs-0.15-26/crs/src/nomad_src/XMesh.cpp |only crs-0.15-26/crs/src/nomad_src/XMesh.hpp |only crs-0.15-26/crs/src/nomad_src/defines.hpp | 164 crs-0.15-26/crs/src/nomad_src/lgpl.txt | 330 crs-0.15-26/crs/src/nomad_src/nomad.cpp | 525 crs-0.15-26/crs/src/nomad_src/nomad.hpp | 25 crs-0.15-26/crs/src/nomad_src/utils.cpp | 1988 - crs-0.15-26/crs/src/nomad_src/utils.hpp | 500 crs-0.15-26/crs/src/sgtelib_src |only crs-0.15-26/crs/src/snomadr.cpp | 2 crs-0.15-26/crs/vignettes/crs.Rnw | 4 crs-0.15-26/crs/vignettes/crs_faq.Rnw | 43 crs-0.15-26/crs/vignettes/spline_primer.Rnw | 13 158 files changed, 43217 insertions(+), 38548 deletions(-)
Title: Minimax and Minimax Projection Designs
Description: Provides two main functions: mMcPSO() and
miniMaxPro(), which generates minimax designs and minimax projection designs using
a hybrid clustering - particle swarm optimization (PSO) algorithm. These designs can be used
in a variety of settings, e.g., as space-filling designs for computer experiments or
sensor allocation designs. A detailed description of the two designs and the employed
algorithms can be found in Mak and Joseph (2017) <DOI:10.1080/10618600.2017.1302881>.
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Diff between minimaxdesign versions 0.1.1 dated 2016-11-22 and 0.1.2 dated 2017-05-03
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NAMESPACE | 2 +- R/minimax.R | 10 +++++----- man/mMcPSO.Rd | 16 ++++++++-------- man/miniMaxPro.Rd | 9 ++++----- man/minimaxdesign-package.Rd | 4 ++-- src/init.c |only 8 files changed, 32 insertions(+), 32 deletions(-)
Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression models
to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. The
package provides functions for model estimation, dispersion testing, and
diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016)
<doi:10.1016/j.csda.2016.01.007> is also supported.
Author: Kimberly Sellers <kfs7@georgetown.edu>
Thomas Lotze <thomas.lotze@thomaslotze.com>
Andrew Raim <andrew.raim@gmail.com>
Maintainer: Andrew Raim <andrew.raim@gmail.com>
Diff between COMPoissonReg versions 0.4.0 dated 2017-04-19 and 0.4.1 dated 2017-05-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.6 dated 2017-03-30 and 3.98-1.7 dated 2017-05-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/examples/bondsTables.R | 2 +- man/getNodeSet.Rd | 5 +++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include Sql Server, Oracle,
PostgreSql, Amazon RedShift, and Microsoft PDW.
Author: Martijn J. Schuemie [aut, cre],
Marc A. Suchard [aut],
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.3.0 dated 2017-03-24 and 1.3.7 dated 2017-05-03
DESCRIPTION | 8 MD5 | 32 - NEWS | 17 README.md | 2 build/vignette.rds |binary inst/csv/replacementPatterns.csv | 61 +- inst/doc/UsingSqlRender.R | 2 inst/doc/UsingSqlRender.Rmd | 13 inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/org/ohdsi/sql/SqlSplit.java | 6 java/org/ohdsi/sql/SqlTranslate.java | 69 ++- java/org/ohdsi/sql/StringUtils.java | 2 java/org/ohdsi/sql/TestSqlRender.java | 7 tests/testthat/test-splitSql.R | 13 tests/testthat/test-translateSql.R | 701 +++++++++++++++++++--------------- vignettes/UsingSqlRender.Rmd | 13 17 files changed, 566 insertions(+), 380 deletions(-)
Title: Business Days Calculations and Utilities
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Diff between bizdays versions 1.0.2 dated 2017-04-11 and 1.0.3 dated 2017-05-03
DESCRIPTION | 6 - MD5 | 10 - NEWS | 4 inst/doc/Creating_Calendars.html | 4 inst/doc/Setting_default_calendar_in_Rprofile.html | 4 tests/testthat/test-calendar.R | 107 ++++++++++----------- 6 files changed, 72 insertions(+), 63 deletions(-)
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and
in forecasting. Currently the package includes exponential smoothing models and
SARIMA in state-space form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.9.0 dated 2017-03-16 and 1.9.9 dated 2017-05-03
DESCRIPTION | 8 MD5 | 86 +++++---- NAMESPACE | 1 NEWS | 31 +++ R/RcppExports.R | 4 R/autoces.R | 33 ++- R/autossarima.R | 71 +++++--- R/ces.R | 36 +++- R/error-measures.R | 201 +++++++++++++++++++++-- R/es.R | 128 ++++++++++---- R/ges.R | 52 ++++- R/graphmaker.R | 38 ++-- R/methods.R | 18 +- R/sma.R | 31 ++- R/sowhat.R | 5 R/ssarima.R | 189 ++++++++++++--------- R/ssfunctions.R | 408 ++++++++++++++++++++++++++++------------------- R/ves.R |only R/vssFunctions.R |only README.md | 7 build/vignette.rds |binary inst/doc/ces.html | 94 +++++----- inst/doc/es.html | 101 +++++------ inst/doc/ges.html | 42 ++-- inst/doc/simulate.html | 76 ++++---- inst/doc/sma.html | 12 - inst/doc/smooth.html | 8 inst/doc/ssarima.R | 3 inst/doc/ssarima.Rmd | 6 inst/doc/ssarima.html | 59 ++++-- man/auto.ces.Rd | 34 ++- man/auto.ssarima.Rd | 28 +-- man/ces.Rd | 33 ++- man/error-measures.Rd | 12 - man/es.Rd | 55 +++--- man/ges.Rd | 47 +++-- man/graphmaker.Rd | 5 man/hm.Rd | 16 - man/pls.Rd |only man/sma.Rd | 11 - man/ssarima.Rd | 74 +++++--- man/ves.Rd |only src/RcppExports.cpp | 49 +++++ src/ssgeneralfun.cpp | 373 +++++++++++++++++++++--------------------- tests/testthat/test_es.R | 2 vignettes/ssarima.Rmd | 6 46 files changed, 1562 insertions(+), 931 deletions(-)
Title: Spatially Explicit Capture-Recapture for Linear Habitats
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrlinear versions 1.0.5 dated 2015-01-11 and 1.1.0 dated 2017-05-03
DESCRIPTION | 14 +- MD5 | 40 +++--- NAMESPACE | 11 + NEWS | 6 R/checkmoves.R | 11 + R/methods.R | 13 +- R/read.linearmask.R | 15 +- build/vignette.rds |binary data/arvicola.RData |binary data/glymemask.RData |binary inst/CITATION | 2 inst/doc/secrlinear-manual.pdf |binary inst/doc/secrlinear-vignette.R | 193 +++++++++++++++---------------- inst/doc/secrlinear-vignette.Rmd | 236 +++++++++++++++++++------------------- inst/doc/secrlinear-vignette.pdf |binary man/arvicola.Rd | 3 man/clipmask.Rd | 2 man/plotmethods.Rd | 8 - man/read.linearmask.Rd | 2 man/secrlinear-package.Rd | 10 - vignettes/secrlinear-vignette.Rmd | 236 +++++++++++++++++++------------------- 21 files changed, 423 insertions(+), 379 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <http://personality-project.org/r> web page.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 1.7.3.21 dated 2017-03-22 and 1.7.5 dated 2017-05-03
DESCRIPTION | 8 MD5 | 118 +++++++------- NAMESPACE | 11 - R/VSS.R | 2 R/cor.ci.R | 3 R/cor.plot.R | 95 ++++++++--- R/corr.test.R | 9 - R/cortest.R | 2 R/describe.R | 2 R/describe.by.R | 2 R/fa.R | 192 +++++++++++++++++++---- R/fa.parallel.R | 20 +- R/factor.stats.R | 92 ++++++----- R/fisherz.R | 6 R/headtail.R | 33 ++- R/mediate.r | 10 - R/misc.R | 8 R/mixed.cor.R | 57 ++++++ R/multi.hist.R | 10 - R/multilevel.reliability.R | 93 ++++++++++- R/pairs.panels.R | 8 R/plot.irt.R | 76 +++++++-- R/polychoric.R | 28 ++- R/principal.R | 2 R/print.psych.fa.R | 2 R/read.clipboard.R | 20 +- R/score.items.R | 33 +++ R/scoreOverlap.r | 10 - R/set.cor.R | 8 R/statsBy.r | 30 +++ R/tetrachor.R | 4 inst/CITATION | 4 inst/NEWS.Rd | 48 +++++ inst/doc/intro.R | 67 ++++---- inst/doc/intro.Rnw | 36 +++- inst/doc/intro.pdf |binary inst/doc/overview.R | 288 +++++++--------------------------- inst/doc/overview.Rnw | 373 --------------------------------------------- inst/doc/overview.pdf |binary inst/doc/psych_for_sem.pdf |binary man/Harman.Rd | 2 man/bifactor.Rd | 2 man/blot.Rd | 2 man/cluster.cor.Rd | 3 man/cor.plot.Rd | 48 ++++- man/fa.Rd | 31 ++- man/fa.parallel.Rd | 4 man/factor.stats.Rd | 4 man/fisherz.Rd | 37 ++-- man/headtail.Rd | 33 ++- man/mixed.cor.Rd | 26 ++- man/multi.hist.Rd | 2 man/pairs.panels.Rd | 9 - man/read.clipboard.Rd | 21 +- man/score.irt.Rd | 6 man/score.items.Rd | 13 + man/set.cor.Rd | 4 man/statsBy.Rd | 7 vignettes/intro.Rnw | 36 +++- vignettes/overview.Rnw | 373 --------------------------------------------- 60 files changed, 1117 insertions(+), 1356 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.9 dated 2016-04-15 and 0.10 dated 2017-05-03
DESCRIPTION | 9 MD5 | 50 ++--- NAMESPACE | 26 +- NEWS | 66 ++++++ R/MMD.R | 8 R/VCFloci.R | 11 - R/conversion.R | 27 ++ R/haplotype.R | 433 ++++++++++++++++++++++++++++++++++++++------- R/mjn.R |only R/plotNetMDS.R |only build/vignette.rds |binary inst/doc/ReadingFiles.Rnw | 6 inst/doc/ReadingFiles.pdf |binary man/LD.Rd | 6 man/MMD.Rd | 4 man/all.equal.haploNet.Rd |only man/conversion.Rd | 11 + man/dist.hamming.Rd |only man/haploNet.Rd | 24 +- man/haplotype.Rd | 5 man/haplotype.loci.Rd | 10 - man/mjn.Rd |only man/mst.Rd | 25 +- man/na.omit.loci.Rd | 2 man/plotNetMDS.Rd |only man/theta.h.Rd | 3 man/theta.k.Rd | 2 src/pegas.c | 24 ++ vignettes/ReadingFiles.Rnw | 6 29 files changed, 607 insertions(+), 151 deletions(-)
Title: Package Management Tool
Description: Tools to more conveniently perform tasks associated with
add-on packages. pacman conveniently wraps library and package
related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level
functions which can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut, ctb],
Keith Hughitt [ctb], Albert Wang [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between pacman versions 0.4.1 dated 2016-03-30 and 0.4.5 dated 2017-05-03
DESCRIPTION | 13 +-- MD5 | 124 +++++++++++++++++------------------ NEWS | 25 ++++++- R/p_depends.R | 6 - R/p_exists.R | 12 ++- R/p_install.R | 49 +++++++++---- R/p_install_gh.R | 6 + R/p_install_version_gh.R | 6 + R/p_install_version_single_gh.R | 4 - R/p_load_current_gh.R | 9 +- R/p_load_current_single_gh.R | 4 - R/p_load_gh.R | 6 + R/p_load_single_gh.R | 4 - R/p_search_any.R | 4 - README.md | 8 +- build/vignette.rds |binary inst/CITATION | 8 +- inst/doc/Introduction_to_pacman.R | 2 inst/doc/Introduction_to_pacman.Rmd | 8 +- inst/doc/Introduction_to_pacman.html | 71 ++++++++++---------- inst/pacman_logo |only man/p_author.Rd | 1 man/p_base.Rd | 1 man/p_boot.Rd | 1 man/p_citation.Rd | 1 man/p_cran.Rd | 1 man/p_data.Rd | 1 man/p_delete.Rd | 4 - man/p_depends.Rd | 7 - man/p_detectOS.Rd | 1 man/p_exists.Rd | 3 man/p_extract.Rd | 1 man/p_functions.Rd | 1 man/p_help.Rd | 2 man/p_information.Rd | 7 - man/p_install.Rd | 3 man/p_install_gh.Rd | 6 + man/p_install_version.Rd | 1 man/p_install_version_gh.Rd | 6 + man/p_interactive.Rd | 3 man/p_isinstalled.Rd | 1 man/p_library.Rd | 3 man/p_load.Rd | 1 man/p_load_current_gh.Rd | 10 +- man/p_load_gh.Rd | 7 + man/p_loaded.Rd | 3 man/p_news.Rd | 1 man/p_old.Rd | 1 man/p_opendir.Rd | 2 man/p_path.Rd | 1 man/p_search_any.Rd | 11 +-- man/p_search_library.Rd | 1 man/p_set_cranrepo.Rd | 1 man/p_temp.Rd | 7 - man/p_unload.Rd | 5 - man/p_unlock.Rd | 1 man/p_update.Rd | 3 man/p_version.Rd | 7 - man/p_vignette.Rd | 3 man/print.p_version_diff.Rd | 1 man/print.search_any.Rd | 1 man/print.wide_table.Rd | 1 tools |only vignettes/Introduction_to_pacman.Rmd | 8 +- 64 files changed, 269 insertions(+), 231 deletions(-)
Title: Imaging Engine, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 1.1.1 dated 2017-03-23 and 1.2.1 dated 2017-05-03
imagine-1.1.1/imagine/src/registerDynamicSymbols.c |only imagine-1.2.1/imagine/DESCRIPTION | 8 +-- imagine-1.2.1/imagine/MD5 | 24 +++++----- imagine-1.2.1/imagine/NAMESPACE | 1 imagine-1.2.1/imagine/R/imagine-main.R | 32 ++------------ imagine-1.2.1/imagine/build/vignette.rds |binary imagine-1.2.1/imagine/inst/doc/vignette.R | 47 ++++++++++++--------- imagine-1.2.1/imagine/inst/doc/vignette.Rmd | 47 ++++++++++++--------- imagine-1.2.1/imagine/inst/doc/vignette.html | 28 ++++++------ imagine-1.2.1/imagine/man/basic2DFilter.Rd | 2 imagine-1.2.1/imagine/man/convolutions.Rd | 13 +---- imagine-1.2.1/imagine/src/engines.cpp | 4 + imagine-1.2.1/imagine/src/imagine_init.c |only imagine-1.2.1/imagine/vignettes/vignette.Rmd | 47 ++++++++++++--------- 14 files changed, 123 insertions(+), 130 deletions(-)
Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in
the Lexis diagram, bootstrapping. Parametric proportional
hazards fitting with left truncation and right censoring for
common families of distributions, piecewise constant hazards,
and discrete models. AFT regression for left truncated and
right censored data. Binary and Poisson regression for
clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström [aut, cre]
Maintainer: Göran Broström <goran.brostrom@umu.se>
Diff between eha versions 2.4-4 dated 2016-09-21 and 2.4-5 dated 2017-05-03
ChangeLog | 6 ++ DESCRIPTION | 8 +-- MD5 | 25 ++++++------ R/age.window.R | 13 +++--- R/cal.window.R | 19 ++++----- R/coxreg.R | 55 +++++++++++++-------------- R/geome.fit.R | 97 ++++++++++++++++++++++++------------------------ R/phfunc.R | 32 +++++++-------- build/vignette.rds |binary inst/doc/glmmML.pdf |binary inst/doc/parametric.pdf |binary man/geome.fit.Rd | 3 - src/init.c |only src/wfunc.null.f | 2 14 files changed, 135 insertions(+), 125 deletions(-)
Title: Interface with Google BigQuery with Shiny Compatibility
Description: Interface with 'Google BigQuery',
see <https://cloud.google.com/bigquery/> for more information.
This package uses 'googleAuthR' so is compatible with similar packages,
including 'Google Cloud Storage' (<https://cloud.google.com/storage/>) for result extracts.
Author: Mark Edmondson [aut, cre],
Hadley Wickham [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between bigQueryR versions 0.2.0 dated 2016-08-11 and 0.3.0 dated 2017-05-03
bigQueryR-0.2.0/bigQueryR/R/cloudStorage.R |only bigQueryR-0.2.0/bigQueryR/README.md |only bigQueryR-0.2.0/bigQueryR/man/gcs_update_acl.Rd |only bigQueryR-0.3.0/bigQueryR/DESCRIPTION | 14 bigQueryR-0.3.0/bigQueryR/LICENSE | 4 bigQueryR-0.3.0/bigQueryR/MD5 | 102 +++--- bigQueryR-0.3.0/bigQueryR/NAMESPACE | 9 bigQueryR-0.3.0/bigQueryR/NEWS.md | 24 + bigQueryR-0.3.0/bigQueryR/R/auth.R |only bigQueryR-0.3.0/bigQueryR/R/bigQueryR.R | 36 -- bigQueryR-0.3.0/bigQueryR/R/dataParseFunctions.R | 25 - bigQueryR-0.3.0/bigQueryR/R/downloadData.R | 42 +- bigQueryR-0.3.0/bigQueryR/R/globals.R |only bigQueryR-0.3.0/bigQueryR/R/jobs.R | 47 ++ bigQueryR-0.3.0/bigQueryR/R/listBigQuery.R | 6 bigQueryR-0.3.0/bigQueryR/R/options.R | 59 +++ bigQueryR-0.3.0/bigQueryR/R/partition.R |only bigQueryR-0.3.0/bigQueryR/R/print_methods.R |only bigQueryR-0.3.0/bigQueryR/R/query.R | 26 + bigQueryR-0.3.0/bigQueryR/R/tables.R | 154 ++++++--- bigQueryR-0.3.0/bigQueryR/R/uploadData.R | 231 ++++++++++++-- bigQueryR-0.3.0/bigQueryR/R/utilities.R | 53 +++ bigQueryR-0.3.0/bigQueryR/build/vignette.rds |binary bigQueryR-0.3.0/bigQueryR/inst/doc/bigQueryR.html | 4 bigQueryR-0.3.0/bigQueryR/man/bigQueryR.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/bq_get_global_dataset.Rd |only bigQueryR-0.3.0/bigQueryR/man/bq_get_global_project.Rd |only bigQueryR-0.3.0/bigQueryR/man/bq_global_dataset.Rd |only bigQueryR-0.3.0/bigQueryR/man/bq_global_project.Rd |only bigQueryR-0.3.0/bigQueryR/man/bqr_auth.Rd | 56 +-- bigQueryR-0.3.0/bigQueryR/man/bqr_create_table.Rd | 17 - bigQueryR-0.3.0/bigQueryR/man/bqr_delete_table.Rd | 9 bigQueryR-0.3.0/bigQueryR/man/bqr_download_extract.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/bqr_extract_data.Rd | 10 bigQueryR-0.3.0/bigQueryR/man/bqr_get_job.Rd | 3 bigQueryR-0.3.0/bigQueryR/man/bqr_grant_extract_access.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/bqr_list_datasets.Rd | 6 bigQueryR-0.3.0/bigQueryR/man/bqr_list_jobs.Rd | 6 bigQueryR-0.3.0/bigQueryR/man/bqr_list_projects.Rd | 4 bigQueryR-0.3.0/bigQueryR/man/bqr_list_tables.Rd | 9 bigQueryR-0.3.0/bigQueryR/man/bqr_partition.Rd |only bigQueryR-0.3.0/bigQueryR/man/bqr_query.Rd | 12 bigQueryR-0.3.0/bigQueryR/man/bqr_query_asynch.Rd | 9 bigQueryR-0.3.0/bigQueryR/man/bqr_table_data.Rd | 7 bigQueryR-0.3.0/bigQueryR/man/bqr_table_meta.Rd | 7 bigQueryR-0.3.0/bigQueryR/man/bqr_upload_data.Rd | 63 +++ bigQueryR-0.3.0/bigQueryR/man/bqr_wait_for_job.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/cat0.Rd |only bigQueryR-0.3.0/bigQueryR/man/error.message.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/format_object_size.Rd |only bigQueryR-0.3.0/bigQueryR/man/idempotency.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/is.NullOb.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/is.error.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/js_to_posix.Rd |only bigQueryR-0.3.0/bigQueryR/man/myMessage.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/parse_bqr_query.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/rmNullObs.Rd | 1 bigQueryR-0.3.0/bigQueryR/man/schema_fields.Rd |only bigQueryR-0.3.0/bigQueryR/man/timestamp_to_r.Rd |only bigQueryR-0.3.0/bigQueryR/tests |only 60 files changed, 750 insertions(+), 315 deletions(-)
Title: Taxonomic Standardization of Plant Species Names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using 'The Plant List' website (www.theplantlist.org).
Author: Luis Cayuela, Anke Stein, Jari Oksanen
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between Taxonstand versions 1.8 dated 2016-02-11 and 2.0 dated 2017-05-03
DESCRIPTION | 11 MD5 | 15 NAMESPACE | 6 R/TPL.R | 153 ++++-- R/TPLck.R | 1153 +++++++++++++++++++++++++++++++--------------------- data/bryophytes.rda |binary inst |only man/TPL.Rd | 339 ++++++++------- man/TPLck.Rd | 378 ++++++++++++----- 9 files changed, 1300 insertions(+), 755 deletions(-)
Title: Stubbing Framework for R
Description: Create stubs of functions for use while testing.
Author: Sainath Adapa [aut, cre],
Nitin Madasu [aut]
Maintainer: Sainath Adapa <adapasainath@gmail.com>
Diff between stubthat versions 1.1.0 dated 2016-08-13 and 1.2.0 dated 2017-05-03
DESCRIPTION | 10 - MD5 | 20 +-- NEWS.md | 7 + build/vignette.rds |binary inst/doc/stubthat.R | 56 +++++++--- inst/doc/stubthat.Rmd | 79 ++++++++++---- inst/doc/stubthat.html | 214 ++++++++++++++-------------------------- man/stub.Rd | 1 man/stubtthat.Rd | 1 tests/testthat/test-with-mock.r | 113 ++++++++++----------- vignettes/stubthat.Rmd | 79 ++++++++++---- 11 files changed, 310 insertions(+), 270 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé <mx.herve@gmail.com>
Diff between RVAideMemoire versions 0.9-64 dated 2017-03-25 and 0.9-65 dated 2017-05-03
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++++------------------- NAMESPACE | 4 +++- NEWS | 6 ++++++ R/DIABLO.cv.R |only R/DIABLO.test.R |only R/MVA.cor.R | 21 +++++++++++++++++---- R/MVA.ident.R | 3 +++ R/MVA.load.R | 11 +++++++++-- R/MVA.scores.R | 5 +++-- R/MVA.synt.R | 32 ++++++++++++++++++++++++++++++++ R/to.dudi.R | 2 +- R/zzz.R | 2 +- man/CDA.test.Rd | 2 +- man/DIABLO.cv.Rd |only man/DIABLO.test.Rd |only man/MVA.cor.Rd | 2 ++ man/MVA.corplot.Rd | 3 ++- man/MVA.load.Rd | 2 ++ man/MVA.loadplot.Rd | 2 ++ man/MVA.scoreplot.Rd | 2 ++ man/MVA.scores.Rd | 2 ++ man/MVA.synt.Rd | 2 ++ man/RVAideMemoire-package.Rd | 4 ++-- 24 files changed, 119 insertions(+), 38 deletions(-)
Title: Easy to Use Tools for Common Forms of Random Assignment and
Sampling
Description: Generates random assignments for common experimental designs and
random samples for common sampling designs.
Author: Alexander Coppock [aut, cre],
Jasper Cooper [ctb]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 0.4.1 dated 2016-07-21 and 0.6.0 dated 2017-05-03
randomizr-0.4.1/randomizr/tests/testthat/test_design_declarations.R |only randomizr-0.6.0/randomizr/DESCRIPTION | 22 randomizr-0.6.0/randomizr/MD5 | 111 ++-- randomizr-0.6.0/randomizr/NAMESPACE | 15 randomizr-0.6.0/randomizr/R/block_and_cluster_ra.R | 80 +-- randomizr-0.6.0/randomizr/R/block_and_cluster_ra_probabilities.R | 50 + randomizr-0.6.0/randomizr/R/block_ra.R | 257 ++++------ randomizr-0.6.0/randomizr/R/block_ra_probabilities.R | 231 ++++---- randomizr-0.6.0/randomizr/R/cluster_ra.R | 46 + randomizr-0.6.0/randomizr/R/cluster_ra_probabilities.R | 50 + randomizr-0.6.0/randomizr/R/cluster_rs.R |only randomizr-0.6.0/randomizr/R/cluster_rs_probabilities.R |only randomizr-0.6.0/randomizr/R/complete_ra.R | 112 ++-- randomizr-0.6.0/randomizr/R/complete_ra_probabilities.R | 60 +- randomizr-0.6.0/randomizr/R/complete_rs.R |only randomizr-0.6.0/randomizr/R/complete_rs_probabilities.R |only randomizr-0.6.0/randomizr/R/declare_ra.R | 177 +++++- randomizr-0.6.0/randomizr/R/declare_rs.R |only randomizr-0.6.0/randomizr/R/helper_functions.R | 201 +++++++ randomizr-0.6.0/randomizr/R/simple_ra.R | 32 - randomizr-0.6.0/randomizr/R/simple_ra_probabilities.R | 27 - randomizr-0.6.0/randomizr/R/simple_rs.R |only randomizr-0.6.0/randomizr/R/simple_rs_probabilities.R |only randomizr-0.6.0/randomizr/R/strata_and_cluster_rs.R |only randomizr-0.6.0/randomizr/R/strata_and_cluster_rs_probabilities.R |only randomizr-0.6.0/randomizr/R/strata_rs.R |only randomizr-0.6.0/randomizr/R/strata_rs_probabilities.R |only randomizr-0.6.0/randomizr/build/vignette.rds |binary randomizr-0.6.0/randomizr/inst/doc/randomizr_vignette.html | 50 - randomizr-0.6.0/randomizr/man/block_and_cluster_ra.Rd | 28 - randomizr-0.6.0/randomizr/man/block_and_cluster_ra_probabilities.Rd | 9 randomizr-0.6.0/randomizr/man/block_ra.Rd | 27 - randomizr-0.6.0/randomizr/man/block_ra_probabilities.Rd | 12 randomizr-0.6.0/randomizr/man/cluster_ra.Rd | 5 randomizr-0.6.0/randomizr/man/cluster_ra_probabilities.Rd | 15 randomizr-0.6.0/randomizr/man/cluster_rs.Rd |only randomizr-0.6.0/randomizr/man/cluster_rs_probabilities.Rd |only randomizr-0.6.0/randomizr/man/complete_ra.Rd | 5 randomizr-0.6.0/randomizr/man/complete_ra_probabilities.Rd | 10 randomizr-0.6.0/randomizr/man/complete_rs.Rd |only randomizr-0.6.0/randomizr/man/complete_rs_probabilities.Rd |only randomizr-0.6.0/randomizr/man/conduct_ra.Rd | 48 + randomizr-0.6.0/randomizr/man/declare_ra.Rd | 10 randomizr-0.6.0/randomizr/man/declare_rs.Rd |only randomizr-0.6.0/randomizr/man/draw_rs.Rd |only randomizr-0.6.0/randomizr/man/obtain_condition_probabilities.Rd | 47 + randomizr-0.6.0/randomizr/man/obtain_inclusion_probabilities.Rd |only randomizr-0.6.0/randomizr/man/randomizr.Rd | 1 randomizr-0.6.0/randomizr/man/simple_ra.Rd | 5 randomizr-0.6.0/randomizr/man/simple_ra_probabilities.Rd | 5 randomizr-0.6.0/randomizr/man/simple_rs.Rd |only randomizr-0.6.0/randomizr/man/simple_rs_probabilities.Rd |only randomizr-0.6.0/randomizr/man/strata_and_cluster_rs.Rd |only randomizr-0.6.0/randomizr/man/strata_and_cluster_rs_probabilities.Rd |only randomizr-0.6.0/randomizr/man/strata_rs.Rd |only randomizr-0.6.0/randomizr/man/strata_rs_probabilities.Rd |only randomizr-0.6.0/randomizr/tests/testthat/test-assignment_probabilities.R | 166 +++--- randomizr-0.6.0/randomizr/tests/testthat/test-block_and_cluster_ra.R | 4 randomizr-0.6.0/randomizr/tests/testthat/test-block_ra.R | 33 - randomizr-0.6.0/randomizr/tests/testthat/test-cleaner-function.R | 8 randomizr-0.6.0/randomizr/tests/testthat/test-cluster_ra.R | 2 randomizr-0.6.0/randomizr/tests/testthat/test-cluster_rs.R |only randomizr-0.6.0/randomizr/tests/testthat/test-complete_ra.R | 85 ++- randomizr-0.6.0/randomizr/tests/testthat/test-complete_rs.R |only randomizr-0.6.0/randomizr/tests/testthat/test-condition-names.R |only randomizr-0.6.0/randomizr/tests/testthat/test-empirical-probabilities.R | 15 randomizr-0.6.0/randomizr/tests/testthat/test-simple_ra.R | 2 randomizr-0.6.0/randomizr/tests/testthat/test-simple_rs.R |only randomizr-0.6.0/randomizr/tests/testthat/test-strata_and_cluster_rs.R |only randomizr-0.6.0/randomizr/tests/testthat/test-strata_rs.R |only randomizr-0.6.0/randomizr/tests/testthat/test-tricky-examples.R | 7 randomizr-0.6.0/randomizr/tests/testthat/test_assignment_declarations.R |only randomizr-0.6.0/randomizr/tests/testthat/test_sampling_declarations.R |only 73 files changed, 1287 insertions(+), 783 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics and Polymorphic Information Content are also available. polysat can
assist the user in estimating the ploidy of samples, and it can estimate allele
frequencies in populations, calculate pairwise or global differentiation statistics
based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'.
Functions are also included for assigning alleles to isoloci in cases where one pair
of microsatellite primers amplifies alleles from two or more independently
segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.6-0 dated 2016-11-05 and 1.7-0 dated 2017-05-03
DESCRIPTION | 22 +-- MD5 | 46 ++++--- NAMESPACE | 6 - NEWS | 19 +++ R/classes_generics_methods.R | 61 ++++++++++ R/individual_distance.R | 216 ++++++++++++++++++------------------ R/population_stats.R | 246 +++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/CITATION | 12 +- inst/doc/allopolyVignette.Rnw | 6 - inst/doc/allopolyVignette.pdf |binary inst/doc/polysattutorial.R | 160 +++++++++++++++----------- inst/doc/polysattutorial.Rnw | 66 ++++++++--- inst/doc/polysattutorial.pdf |binary man/Bruvo.distance.Rd | 2 man/PIC.Rd |only man/alleleCorrelations.Rd | 5 man/calcFst.Rd | 42 ++++++- man/genIndex.Rd |only man/plotSSAllo.Rd | 5 man/read.GeneMapper.Rd | 3 man/recodeAllopoly.Rd | 5 man/simAllopoly.Rd | 5 vignettes/allopolyVignette.Rnw | 6 - vignettes/polysattutorial.Rnw | 66 ++++++++--- 25 files changed, 667 insertions(+), 332 deletions(-)
Title: Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre],
Paola Rondon-Villarreal [aut, ths],
Rodrigo Torres [aut, ths],
J. Sebastian Paez [ctb]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between Peptides versions 2.0.0 dated 2017-03-12 and 2.1 dated 2017-05-03
DESCRIPTION | 12 +++++---- MD5 | 25 ++++++++++++------ NAMESPACE | 3 ++ NEWS.md | 5 +++ R/RcppExports.R |only R/charge.R | 72 +++++++++++++++++++++++------------------------------- R/cppFunctions.R |only R/pI.R | 20 ++++++--------- R/sysdata.rda |binary README.md | 2 - data/AAdata.RData |binary inst/include |only man/charge.Rd | 6 ++-- src |only 14 files changed, 74 insertions(+), 71 deletions(-)
Title: Query HaploReg and RegulomeDB
Description: A set of utilities for querying
HaploReg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>
and RegulomeDB <http://www.regulomedb.org> web-based tools. The package connects to
HaploReg or RegulomeDB, searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.
Author: Ilya Y. Zhbannikov [aut, cre],
Konstantin Arbeev [ctb] (Konstantin supervised the technical/software
development.),
Anatoliy Yashin [ctb] (Anatoliy supervised the technical/software
development and is a Principal Invesigator of this project)
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between haploR versions 1.4.2 dated 2017-02-09 and 1.4.4 dated 2017-05-03
DESCRIPTION | 29 +- MD5 | 36 +- NAMESPACE | 13 R/general.R | 8 R/haploreg.R | 39 ++ R/haploregStudy.R | 28 +- R/regulome.R | 30 +- README.md | 402 +++++++++++++++++++++++++++++- build/vignette.rds |binary inst/NEWS | 5 inst/doc/haplor-vignette.R | 34 +- inst/doc/haplor-vignette.Rmd | 231 +++++++++++++++-- inst/doc/haplor-vignette.html | 547 ++++++++++++++++++++++-------------------- inst/unitTests |only man/haploR-getStudyList.Rd | 1 man/haploR-queryHaploreg.Rd | 11 man/haploR-queryRegulome.Rd | 10 tests |only vignettes/Workflow.png |only vignettes/haplor-vignette.Rmd | 231 +++++++++++++++-- 20 files changed, 1251 insertions(+), 404 deletions(-)
More information about EMMIXcontrasts2 at CRAN
Permanent link
Title: Linear Regression Based on Linear Structure Between Variables
Description: Linear regression based on a recursive structural equation model
(explicit multiples correlations) found by a M.C.M.C. algorithm. It permits to face
highly correlated variables. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>
Diff between CorReg versions 1.1.9 dated 2016-10-24 and 1.2.1 dated 2017-05-03
CorReg-1.1.9/CorReg/R/rechercheZ_rejet.R |only CorReg-1.1.9/CorReg/R/rechercheZ_relax.R |only CorReg-1.2.1/CorReg/DESCRIPTION | 21 +- CorReg-1.2.1/CorReg/MD5 | 80 +++++----- CorReg-1.2.1/CorReg/NAMESPACE | 2 CorReg-1.2.1/CorReg/NEWS | 1 CorReg-1.2.1/CorReg/R/BicLoc.R | 2 CorReg-1.2.1/CorReg/R/BoxPlot.R | 2 CorReg-1.2.1/CorReg/R/CVMSE.R | 21 +- CorReg-1.2.1/CorReg/R/Hist.R | 9 + CorReg-1.2.1/CorReg/R/ProbaZ.R | 12 - CorReg-1.2.1/CorReg/R/Rsquare.R |only CorReg-1.2.1/CorReg/R/readZ.R | 4 CorReg-1.2.1/CorReg/build |only CorReg-1.2.1/CorReg/inst |only CorReg-1.2.1/CorReg/man/BicZ.Rd | 1 CorReg-1.2.1/CorReg/man/BoxPlot.Rd | 3 CorReg-1.2.1/CorReg/man/CVMSE.Rd |only CorReg-1.2.1/CorReg/man/Conan.Rd | 1 CorReg-1.2.1/CorReg/man/CorReg-package.Rd | 7 CorReg-1.2.1/CorReg/man/Hist.Rd | 9 + CorReg-1.2.1/CorReg/man/MSE_loc.Rd | 1 CorReg-1.2.1/CorReg/man/ProbaZ.Rd |only CorReg-1.2.1/CorReg/man/Terminator.Rd | 1 CorReg-1.2.1/CorReg/man/cleanZ.Rd | 1 CorReg-1.2.1/CorReg/man/cleanZtest.Rd | 1 CorReg-1.2.1/CorReg/man/compare_struct.Rd | 1 CorReg-1.2.1/CorReg/man/correg.Rd | 1 CorReg-1.2.1/CorReg/man/density_estimation.Rd | 1 CorReg-1.2.1/CorReg/man/matplot_zone.Rd | 1 CorReg-1.2.1/CorReg/man/mixture_generator.Rd | 1 CorReg-1.2.1/CorReg/man/readZ.Rd | 5 CorReg-1.2.1/CorReg/man/recursive_tree.Rd | 1 CorReg-1.2.1/CorReg/man/showdata.Rd | 1 CorReg-1.2.1/CorReg/man/structureFinder.Rd | 1 CorReg-1.2.1/CorReg/src/CorReg_init.c |only CorReg-1.2.1/CorReg/src/cleanZ.cpp | 2 CorReg-1.2.1/CorReg/src/rechercheZ.cpp | 6 CorReg-1.2.1/CorReg/src/rechercheZ_rejet.cpp | 6 CorReg-1.2.1/CorReg/src/rechercheZ_relax.cpp | 6 CorReg-1.2.1/CorReg/src/rechercheZ_sparse_rejet.h | 7 CorReg-1.2.1/CorReg/src/rechercheZ_sparse_relax.cpp | 154 ++++++++++---------- CorReg-1.2.1/CorReg/src/rechercheZ_sparse_relax.h | 14 - CorReg-1.2.1/CorReg/vignettes |only 44 files changed, 200 insertions(+), 187 deletions(-)
Title: Miscellaneous Tools for Chinese Text Mining and More
Description: Efforts are made to make Chinese text mining easier, faster, and robust to errors.
Document term matrix can be generated by only one line of code; detecting encoding,
segmenting and removing stop words are done automatically.
Some convenient tools are also supplied.
Author: Jiang Wu [aut, cre] (from Tsinghua University)
Maintainer: Jiang Wu <textidea@sina.com>
Diff between chinese.misc versions 0.1.5 dated 2017-04-07 and 0.1.6 dated 2017-05-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/UsEstrIngI.R | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ R/second_dtm.R | 2 ++ R/tryscAn.R | 2 +- 6 files changed, 77 insertions(+), 10 deletions(-)