Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
David Robinson [aut],
Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.1.1 dated 2016-06-25 and 0.1.2 dated 2016-10-27
DESCRIPTION | 14 +-- MD5 | 72 ++++++++------- NAMESPACE | 1 NEWS.md | 9 + R/globals.R | 2 R/pair_count.R | 6 - R/sentiments.R | 44 +++++++++ R/sparse_casters.R | 4 R/tidytext.R |only R/unnest_tokens.R | 41 +++++++- README.md | 73 +++++++-------- build/vignette.rds |binary inst/CITATION |only inst/doc/tf_idf.R | 2 inst/doc/tf_idf.Rmd | 4 inst/doc/tf_idf.html | 26 ++--- inst/doc/tidying_casting.R | 11 -- inst/doc/tidying_casting.Rmd | 11 -- inst/doc/tidying_casting.html | 162 +++++++++++++---------------------- inst/doc/tidytext.R | 25 +++-- inst/doc/tidytext.Rmd | 29 +++--- inst/doc/tidytext.html | 131 +++++++++++++--------------- inst/doc/topic_modeling.R | 23 +++- inst/doc/topic_modeling.Rmd | 18 +++ inst/doc/topic_modeling.html | 99 +++++++++------------ inst/extdata |only man/cast_sparse.Rd | 3 man/document_term_casters.Rd | 1 man/get_sentiments.Rd |only man/pair_count.Rd | 2 man/tidytext.Rd |only man/unnest_tokens.Rd | 17 +++ tests/testthat/test-pair-count.R | 69 -------------- tests/testthat/test-sentiments.R |only tests/testthat/test-sparse-casters.R | 7 + tests/testthat/test-unnest-tokens.R | 78 ++++++++++++++++ vignettes/tf_idf.Rmd | 4 vignettes/tidying_casting.Rmd | 11 -- vignettes/tidytext.Rmd | 29 +++--- vignettes/topic_modeling.Rmd | 18 +++ 40 files changed, 580 insertions(+), 466 deletions(-)
Title: Functions for Calculating Ontological Similarities
Description: Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologySimilarity versions 2.1 dated 2016-09-09 and 2.2 dated 2016-10-27
ontologySimilarity-2.1/ontologySimilarity/src/Makevars |only ontologySimilarity-2.2/ontologySimilarity/DESCRIPTION | 10 - ontologySimilarity-2.2/ontologySimilarity/MD5 | 27 +-- ontologySimilarity-2.2/ontologySimilarity/R/data.R | 4 ontologySimilarity-2.2/ontologySimilarity/data/GO_IC.RData |binary ontologySimilarity-2.2/ontologySimilarity/data/gene_GO_terms.RData |binary ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.R | 7 ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.Rmd | 11 - ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-GO-example.html | 29 +-- ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-examples.html | 84 +++++----- ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-introduction.Rmd | 2 ontologySimilarity-2.2/ontologySimilarity/inst/doc/ontologySimilarity-introduction.html | 40 ++-- ontologySimilarity-2.2/ontologySimilarity/man/gene_GO_terms.Rd | 4 ontologySimilarity-2.2/ontologySimilarity/vignettes/ontologySimilarity-GO-example.Rmd | 11 - ontologySimilarity-2.2/ontologySimilarity/vignettes/ontologySimilarity-introduction.Rmd | 2 15 files changed, 121 insertions(+), 110 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: Multiple Hypotheses Testing for Discrete Data
Description: A Comprehensive tool for almost all existing multiple testing
methods for discrete data. The package also provides some novel multiple testing
procedures controlling FWER/FDR for discrete data. Given discrete p-values
and their domains, the [method].p.adjust function returns adjusted p-values,
which can be used to compare with the nominal significant level alpha and make
decisions.
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>
Diff between MHTdiscrete versions 0.1.0 dated 2016-10-20 and 0.1.1 dated 2016-10-27
DESCRIPTION | 16 +++-- MD5 | 43 ++++++++------- NAMESPACE | 4 + R/FDRSD.R |only R/FDRSU.R | 140 ++++++++++++++++++++++++++++++++++++++++--------- R/FWERSD.R | 19 +++++- R/FWERSS.R | 30 +++++++++- R/FWERSU.R | 20 +++++-- R/MHTdiscrete.R | 15 ++++- R/Pval.R | 1 man/GTBH.p.adjust.Rd |only man/GTBY.p.adjust.Rd |only man/MBH.p.adjust.Rd | 8 ++ man/MBL.p.adjust.Rd |only man/MBY.p.adjust.Rd | 8 ++ man/MBonf.p.adjust.Rd | 3 + man/MHTdiscrete.Rd | 23 +++++++- man/MHoch.p.adjust.Rd | 8 ++ man/MHolm.p.adjust.Rd | 8 ++ man/Roth.p.adjust.Rd | 3 + man/Roth.rej.Rd | 7 ++ man/Sidak.p.adjust.Rd |only man/TH.p.adjust.Rd | 7 ++ man/Tarone.p.adjust.Rd | 5 + man/getPval.Rd | 3 + 25 files changed, 305 insertions(+), 66 deletions(-)
Title: Detecting Differentially Expressed Genes in Time Course RNA-Seq
Data
Description: Uses a negative binomial mixed-effects (NBME) model to detect
nonparallel differential expression(NPDE) genes and parallel differential
expression(PDE) genes in the time course RNA-seq data.
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao <fangaohz@gmail.com>
Diff between timeSeq versions 1.0.1 dated 2015-09-25 and 1.0.2 dated 2016-10-27
timeSeq-1.0.1/timeSeq/R/timeSeq.geneset.R |only timeSeq-1.0.1/timeSeq/R/timeSeq.genesetscreeplot.R |only timeSeq-1.0.1/timeSeq/R/timeSeq.plot.R |only timeSeq-1.0.1/timeSeq/data/Idgf2.RData |only timeSeq-1.0.1/timeSeq/data/object_by_timeSeq.RData |only timeSeq-1.0.1/timeSeq/data/object_by_timeSeq.geneset.RData |only timeSeq-1.0.1/timeSeq/man/Idgf2.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.geneset.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.geneset.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.genesetscreeplot.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq.plot.Rd |only timeSeq-1.0.1/timeSeq/man/timeSeq_1.0.1-package.Rd |only timeSeq-1.0.1/timeSeq/vignettes/Idgf2.png |only timeSeq-1.0.2/timeSeq/DESCRIPTION | 17 timeSeq-1.0.2/timeSeq/MD5 | 57 +-- timeSeq-1.0.2/timeSeq/NAMESPACE | 7 timeSeq-1.0.2/timeSeq/R/timeSeq.R | 226 +++++------- timeSeq-1.0.2/timeSeq/R/timeSeq.heatmap.R | 4 timeSeq-1.0.2/timeSeq/R/timeSeq.permutate.R | 229 ++++--------- timeSeq-1.0.2/timeSeq/R/timeSeq.screeplot.R | 6 timeSeq-1.0.2/timeSeq/R/timeSeq.sort.R | 4 timeSeq-1.0.2/timeSeq/build/vignette.rds |binary timeSeq-1.0.2/timeSeq/data/pAbp.RData |only timeSeq-1.0.2/timeSeq/data/simulate.dt.RData |only timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.R | 23 - timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.Rmd | 209 +++++------ timeSeq-1.0.2/timeSeq/inst/doc/my-vignette.html | 122 ++++-- timeSeq-1.0.2/timeSeq/man/pAbp.Rd |only timeSeq-1.0.2/timeSeq/man/simulate.dt.Rd |only timeSeq-1.0.2/timeSeq/man/timeSeq.Rd | 202 ++++------- timeSeq-1.0.2/timeSeq/man/timeSeq.heatmap.Rd | 117 ++---- timeSeq-1.0.2/timeSeq/man/timeSeq.permutate.Rd | 89 ++--- timeSeq-1.0.2/timeSeq/man/timeSeq.screeplot.Rd | 119 ++---- timeSeq-1.0.2/timeSeq/man/timeSeq.sort.Rd | 72 ++-- timeSeq-1.0.2/timeSeq/man/timeSeq_1.0.2-package.Rd |only timeSeq-1.0.2/timeSeq/vignettes/heatmap.png |binary timeSeq-1.0.2/timeSeq/vignettes/my-vignette.Rmd | 209 +++++------ timeSeq-1.0.2/timeSeq/vignettes/scree.png |binary 39 files changed, 742 insertions(+), 970 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-77 dated 2016-10-01 and 0.1-79 dated 2016-10-27
DESCRIPTION | 8 MD5 | 37 NAMESPACE | 9 NEWS | 5 R/CausalDiagramContCont.R | 1 R/ICA.BinBin.Grid.Sample.Uncert.R | 1524 +++++++++++++++++++------------------- R/MaxEntContCont.R |only R/MaxEntICABinBin.R | 695 ++++++++--------- R/Pred.TrialT.ContCont.R | 248 +++--- R/plot.MaxEntContCont.R |only R/plot.MetaAnalyticMTS.R | 16 R/plot.SurvSurv.R | 80 - R/plot.TrialLevelMA.R | 38 R/summary_MaxEntContCont.R |only man/ARMD.Rd | 40 man/ICA.BinBin.Grid.Sample.Rd | 2 man/ICAContCont.Rd | 178 ++-- man/MICAContCont.Rd | 208 ++--- man/MaxEntICAContCont.Rd |only man/Pred.TrialT.ContCont.Rd | 198 ++-- man/plot.MaxEntContCont.Rd |only man/summary.gen.Rd | 2 22 files changed, 1653 insertions(+), 1636 deletions(-)
Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between snplist versions 0.15 dated 2015-11-20 and 0.16 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/makeGeneSet.R | 4 ++-- build/vignette.rds |binary inst/doc/snplist.R | 18 +++++++----------- inst/doc/snplist.Rnw | 20 ++++++++------------ inst/doc/snplist.pdf |binary man/snplist-package.Rd | 4 ++-- vignettes/snplist.Rnw | 20 ++++++++------------ 10 files changed, 45 insertions(+), 52 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals and other
information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.2.0 dated 2016-09-07 and 3.2.1 dated 2016-10-27
DESCRIPTION | 8 MD5 | 61 + NEWS | 8 R/as.char.R | 4 R/call.dots.R | 2 R/dotlib.R | 14 R/gbm.R | 43 - R/gbm.backcompat.R |only R/lib.R | 83 +- R/plot_gbm.R | 81 +- R/plotmo.R | 7 R/plotres.R | 2 R/printcall.R | 6 R/w1.R | 6 R/xgboost.R |only R/xy.R | 21 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf | 982 +++++++++++++++---------------- inst/doc/plotres-notes.pdf |binary inst/slowtests/linmod.R | 139 ++-- inst/slowtests/linmod.milbo.tutorial.R | 1 inst/slowtests/make.bat | 2 inst/slowtests/test.gbm.R | 206 +++++- inst/slowtests/test.gbm.Rout.save | 218 +++++- inst/slowtests/test.linmod.R |only inst/slowtests/test.linmod.Rout.save |only inst/slowtests/test.linmod.bat |only inst/slowtests/test.ltut.R | 475 +-------------- inst/slowtests/test.ltut.Rout.save | 1009 +------------------------------- inst/slowtests/test.non.earth.Rout.save | 6 inst/slowtests/test.plotmo.Rout.save | 4 inst/slowtests/test.plotmo3.R | 5 inst/slowtests/test.plotmo3.Rout.save | 5 inst/slowtests/test.plotres.Rout.save | 2 34 files changed, 1248 insertions(+), 2152 deletions(-)
Title: Functions for Visualising Sets of Ontological Terms
Description: Functions for visualising sets of ontological terms using the 'graphviz' layout system.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyPlot versions 1.3 dated 2016-09-09 and 1.4 dated 2016-10-27
ontologyPlot-1.3/ontologyPlot/man/only_phenotype_abnormalities.Rd |only ontologyPlot-1.4/ontologyPlot/DESCRIPTION | 10 - ontologyPlot-1.4/ontologyPlot/MD5 | 29 ++--- ontologyPlot-1.4/ontologyPlot/NAMESPACE | 2 ontologyPlot-1.4/ontologyPlot/R/attributes.R | 2 ontologyPlot-1.4/ontologyPlot/R/graphs.R | 30 +---- ontologyPlot-1.4/ontologyPlot/R/sets.R | 8 - ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.R | 3 ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.Rmd | 42 ++++++-- ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-ontological-terms.html | 52 +++++++--- ontologyPlot-1.4/ontologyPlot/inst/doc/plotting-term-grids.html | 6 - ontologyPlot-1.4/ontologyPlot/man/n_most_frequent_terms.Rd | 2 ontologyPlot-1.4/ontologyPlot/man/ontologyPlot-package.Rd | 2 ontologyPlot-1.4/ontologyPlot/man/remove_links.Rd | 8 - ontologyPlot-1.4/ontologyPlot/man/remove_uninformative_terms.Rd | 6 - ontologyPlot-1.4/ontologyPlot/vignettes/plotting-ontological-terms.Rmd | 42 ++++++-- 16 files changed, 144 insertions(+), 100 deletions(-)
Title: Odds Ratio Calculation for GAM(M)s & GLM(M)s
Description: Simplified odds ratio calculation of GAM(M)s & GLM(M)s.
Provides structured output (data frame) of all predictors and their corresponding odds ratios and confident intervals
for further analyses. It helps to avoid false references of predictors and increments by
specifying these parameters in a list instead of using 'exp(coef(model))'
(standard approach of odds ratio calculation for GLMs) which just returns a plain numeric output.
For GAM(M)s, odds ratio calculation is highly simplified with this package since it takes care of
the multiple 'predict()' calls of the chosen predictor while holding other predictors constant.
Also, this package allows odds ratio calculation of percentage steps across the whole
predictor distribution range for GAM(M)s. In both cases, confident intervals are returned additionally.
Calculated odds ratio of GAM(M)s can be inserted into the smooth function plot.
Author: Patrick Schratz
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between oddsratio versions 0.2 dated 2016-10-11 and 0.3.0 dated 2016-10-27
oddsratio-0.2/oddsratio/R/odds.ratio.gam.R |only oddsratio-0.2/oddsratio/R/odds.ratio.glm.R |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.R |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.Rmd |only oddsratio-0.2/oddsratio/inst/doc/exemplary-function-usage.html |only oddsratio-0.2/oddsratio/vignettes/exemplary-function-usage.Rmd |only oddsratio-0.3.0/oddsratio/DESCRIPTION | 20 ++-- oddsratio-0.3.0/oddsratio/MD5 | 41 ++++++---- oddsratio-0.3.0/oddsratio/NAMESPACE | 12 ++ oddsratio-0.3.0/oddsratio/NEWS | 12 ++ oddsratio-0.3.0/oddsratio/NEWS.md | 15 +++ oddsratio-0.3.0/oddsratio/R/add.oddsratio.into.plot.R |only oddsratio-0.3.0/oddsratio/R/calc.oddsratio.gam.R |only oddsratio-0.3.0/oddsratio/R/calc.oddsratio.glm.R |only oddsratio-0.3.0/oddsratio/R/helper.funs.R |only oddsratio-0.3.0/oddsratio/R/pl.smooth.gam.R |only oddsratio-0.3.0/oddsratio/build/vignette.rds |binary oddsratio-0.3.0/oddsratio/inst/Plots |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.R |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.Rmd |only oddsratio-0.3.0/oddsratio/inst/doc/function.tutorial.html |only oddsratio-0.3.0/oddsratio/inst/wordpress.Rmd |only oddsratio-0.3.0/oddsratio/inst/wordpress.md |only oddsratio-0.3.0/oddsratio/inst/wordpress_files |only oddsratio-0.3.0/oddsratio/man/add.oddsratio.into.plot.Rd |only oddsratio-0.3.0/oddsratio/man/calc.oddsratio.gam.Rd | 31 +++++-- oddsratio-0.3.0/oddsratio/man/calc.oddsratio.glm.Rd | 24 ++++- oddsratio-0.3.0/oddsratio/man/gam.to.df.Rd |only oddsratio-0.3.0/oddsratio/man/no.plot.Rd |only oddsratio-0.3.0/oddsratio/man/pl.smooth.gam.Rd |only oddsratio-0.3.0/oddsratio/vignettes/function.tutorial.Rmd |only 31 files changed, 119 insertions(+), 36 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.9.4 dated 2016-08-16 and 1.9.5 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/CA.R | 8 ++++---- man/MVar.pt-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Calibrates and Reweights Units in Samples
Description: Provides user-friendly tools for calibration in survey sampling.
The package is production-oriented, and its interface is inspired by the famous
popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to
'icarus'. In addition to calibration (with linear, raking and logit methods),
'icarus' features functions for calibration on tight bounds and penalized
calibration.
Author: Antoine Rebecq [aut, cre]
Maintainer: Antoine Rebecq <antoine.rebecq@m4x.org>
Diff between icarus versions 0.2.1 dated 2016-04-18 and 0.2.2 dated 2016-10-27
DESCRIPTION | 14 ++++-- MD5 | 50 ++++++++++++------------ NAMESPACE | 2 R/calib.R | 7 +-- R/calibration.R | 4 + README.md | 4 - man/HTmean.Rd | 4 - man/HTtotal.Rd | 2 man/addMargin.Rd | 2 man/calWeights_ex2.Rd | 2 man/calibration.Rd | 15 +++---- man/calibrationMarginStats.Rd | 4 - man/colToDummies.Rd | 2 man/dataPop.Rd | 8 +-- man/data_ex2.Rd | 4 - man/marginStats.Rd | 6 +- man/poptest_calmar.Rd | 8 +-- man/poptest_calmar_nr.Rd | 8 +-- man/regroupCalibrationModalities.Rd | 15 +++---- man/regroupModalities.Rd | 2 man/table_margins_1.Rd | 2 man/table_margins_2.Rd | 2 man/weightedMean.Rd | 4 - man/weightedTotal.Rd | 2 tests/testthat/test_calibration.R | 37 ++++++++++++++++- tests/testthat/test_calibration_small_dataset.R | 36 +++++++++++++---- 26 files changed, 156 insertions(+), 90 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.3.0 dated 2016-04-06 and 1.4.0 dated 2016-10-27
DESCRIPTION | 15 +++++---- MD5 | 54 +++++++++++++++++----------------- R/01-webdata-obj.R | 12 ++----- R/02-webgeom-obj.R | 34 +++++++++++++++++++-- R/04-webprocess-obj.R | 2 - R/06-simplegeom-obj.R | 3 + R/geoknife-generic.R | 4 ++ R/parseTimeseries.R | 1 R/query-webdata.R | 2 - R/query-webgeom.R | 4 +- R/result.R | 2 - R/values-webgeom.R | 35 +++++++++++++++++----- README.md | 6 +-- build/vignette.rds |binary inst/doc/geoknife.R | 2 - inst/doc/geoknife.Rmd | 13 +++----- inst/doc/geoknife.html | 39 +++++++++++------------- inst/doc/plot_geotiff.html | 20 +++++------- inst/extdata/get_attribute_values.xml | 2 - inst/extdata/multi_poly_post.xml | 2 - man/geoknife-methods.Rd | 5 +++ man/query.Rd | 2 - man/simplegeom-methods.Rd | 1 man/webgeom-methods.Rd | 28 +++++++++++++++++ man/webprocess-methods.Rd | 4 +- tests/testthat/test-query_webgeom.R | 8 +++++ tests/testthat/test-webdata_object.R | 2 - vignettes/geoknife.Rmd | 13 +++----- 28 files changed, 201 insertions(+), 114 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
package. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot package.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.6.3 dated 2016-09-30 and 0.7.0 dated 2016-10-27
cowplot-0.6.3/cowplot/man/plot_theme.Rd |only cowplot-0.6.3/cowplot/man/switch_axis_position.Rd |only cowplot-0.7.0/cowplot/DESCRIPTION | 8 - cowplot-0.7.0/cowplot/MD5 | 42 ++++----- cowplot-0.7.0/cowplot/NAMESPACE | 2 cowplot-0.7.0/cowplot/NEWS | 5 + cowplot-0.7.0/cowplot/R/draw.R | 2 cowplot-0.7.0/cowplot/R/switch_axis.R | 36 ++++---- cowplot-0.7.0/cowplot/R/themes.R | 38 ++------ cowplot-0.7.0/cowplot/inst/doc/axis_position.R | 50 +++++------ cowplot-0.7.0/cowplot/inst/doc/axis_position.Rmd | 57 +++++-------- cowplot-0.7.0/cowplot/inst/doc/axis_position.html | 82 ++++++++----------- cowplot-0.7.0/cowplot/inst/doc/introduction.html | 52 ++++++------ cowplot-0.7.0/cowplot/inst/doc/plot_annotations.Rmd | 2 cowplot-0.7.0/cowplot/inst/doc/plot_annotations.html | 38 ++++---- cowplot-0.7.0/cowplot/inst/doc/plot_grid.R | 8 - cowplot-0.7.0/cowplot/inst/doc/plot_grid.Rmd | 8 - cowplot-0.7.0/cowplot/inst/doc/plot_grid.html | 52 ++++-------- cowplot-0.7.0/cowplot/inst/doc/shared_legends.html | 28 +++--- cowplot-0.7.0/cowplot/man/theme_nothing.Rd | 11 -- cowplot-0.7.0/cowplot/vignettes/axis_position.Rmd | 57 +++++-------- cowplot-0.7.0/cowplot/vignettes/plot_annotations.Rmd | 2 cowplot-0.7.0/cowplot/vignettes/plot_grid.Rmd | 8 - 23 files changed, 251 insertions(+), 337 deletions(-)
Title: A Bit of Glue Between R and Stata
Description: A simple R -> Stata interface allowing the user to
execute Stata commands (both inline and from a .do file)
from R.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between RStata versions 1.1.0 dated 2016-09-15 and 1.1.1 dated 2016-10-27
RStata-1.1.0/RStata/NEWS |only RStata-1.1.1/RStata/DESCRIPTION | 6 +++--- RStata-1.1.1/RStata/MD5 | 7 +++---- RStata-1.1.1/RStata/R/stata.R | 22 +++++++++++++--------- RStata-1.1.1/RStata/README.md | 19 +++++++++++++------ 5 files changed, 32 insertions(+), 22 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 2.2-0 dated 2016-07-25 and 2.3-0 dated 2016-10-27
DESCRIPTION | 8 +-- MD5 | 86 +++++++++++++++++++++-------------------- NAMESPACE | 2 R/jomo.MCMCchain.R | 6 +- R/jomo.R | 6 +- R/jomo.lm.MCMCchain.R |only R/jomo.lm.R |only R/jomo1ran.MCMCchain.R | 8 +-- R/jomo1ran.R | 8 +-- R/jomo1rancathr.MCMCchain.R | 9 ++-- R/jomo1rancathr.R | 9 ++-- R/jomo1ranconhr.MCMCchain.R | 5 +- R/jomo1ranconhr.R | 7 +-- R/jomo1ranmixhr.MCMCchain.R | 7 +-- R/jomo1ranmixhr.R | 9 ++-- R/jomo2.MCMCchain.R | 4 - R/jomo2.R | 4 - R/jomo2hr.MCMCchain.R | 7 +-- R/jomo2hr.R | 9 ++-- inst/CITATION | 2 man/cldata.Rd | 2 man/jomo.MCMCchain.Rd | 13 +++--- man/jomo.Rd | 15 ++++--- man/jomo.lm.MCMCchain.Rd |only man/jomo.lm.Rd |only man/jomo1.MCMCchain.Rd | 2 man/jomo1.Rd | 2 man/jomo1ran.MCMCchain.Rd | 12 +++-- man/jomo1ran.Rd | 11 +++-- man/jomo1rancathr.MCMCchain.Rd | 10 ++-- man/jomo1rancathr.Rd | 9 ++-- man/jomo1ranconhr.MCMCchain.Rd | 13 +++--- man/jomo1ranconhr.Rd | 11 +++-- man/jomo1ranmixhr.MCMCchain.Rd | 9 ++-- man/jomo1ranmixhr.Rd | 9 ++-- man/jomo2.MCMCchain.Rd | 13 +++--- man/jomo2.Rd | 13 +++--- man/jomo2hr.MCMCchain.Rd | 9 ++-- man/jomo2hr.Rd | 9 ++-- src/MCMCjomo1ranconhr.c | 7 +-- src/MCMCjomo1ranmixhr.c | 7 +-- src/MCMCjomo2hr.c | 7 +-- src/MCMCjomolm.c |only src/Makevars | 2 src/jomo1ranconhr.c | 7 +-- src/jomo1ranmixhr.c | 7 +-- src/jomolm.c |only 47 files changed, 229 insertions(+), 166 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.2-0 dated 2016-10-26 and 0.2-1 dated 2016-10-27
DESCRIPTION | 6 ++--- MD5 | 41 ++++++++++++++++++++---------------- R/geom.R | 11 +++++++-- R/read.R | 3 +- inst/doc/sfr.R | 10 ++++---- inst/doc/sfr.Rmd | 42 ++++++++++++++++++------------------- inst/doc/sfr.html | 52 +++++++++++++++++++++++----------------------- inst/shape |only src/gdal_geom.cpp | 17 ++++++++------- src/gdal_read.cpp | 4 +-- src/gdal_write.cpp | 2 - tests/gdal_geom.R | 5 ++-- tests/gdal_geom.Rout.save | 10 +++++--- tests/geos.R | 3 +- tests/geos.Rout.save | 8 ++++--- tests/grid.R | 5 ++-- tests/grid.Rout.save | 29 ++++++------------------- tests/roundtrip.R | 3 +- tests/roundtrip.Rout.save | 8 ++++--- vignettes/nc.gpkg |only vignettes/sfr.Rmd | 42 ++++++++++++++++++------------------- 21 files changed, 156 insertions(+), 145 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.3-7 dated 2016-08-21 and 1.3-8 dated 2016-10-27
DESCRIPTION | 8 +++---- MD5 | 52 +++++++++++++++++++++++------------------------ man/MCMCSVDreg.Rd | 2 - man/MCMCdynamicEI.Rd | 2 - man/MCMCfactanal.Rd | 2 - man/MCMChierEI.Rd | 2 - man/MCMChlogit.Rd | 2 - man/MCMChpoisson.Rd | 2 - man/MCMChregress.Rd | 2 - man/MCMCirt1d.Rd | 2 - man/MCMCirtHier1d.Rd | 2 - man/MCMCirtKd.Rd | 2 - man/MCMCirtKdRob.Rd | 2 - man/MCMClogit.Rd | 2 - man/MCMCmetrop1R.Rd | 2 - man/MCMCmixfactanal.Rd | 2 - man/MCMCmnl.Rd | 2 - man/MCMCoprobit.Rd | 2 - man/MCMCordfactanal.Rd | 2 - man/MCMCpoisson.Rd | 2 - man/MCMCprobit.Rd | 2 - man/MCMCquantreg.Rd | 2 - man/MCMCregress.Rd | 2 - man/MCMCregressChange.Rd | 6 +++-- man/MCMCtobit.Rd | 2 - man/SSVSquantreg.Rd | 2 - src/MCMCpoissonChange.cc | 2 - 27 files changed, 58 insertions(+), 56 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee, Catherine Lee, and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.4 dated 2016-03-09 and 2.5 dated 2016-10-27
SemiCompRisks-2.4/SemiCompRisks/R/BayesID.R |only SemiCompRisks-2.4/SemiCompRisks/R/BayesSurv.R |only SemiCompRisks-2.4/SemiCompRisks/R/FreqID.R |only SemiCompRisks-2.4/SemiCompRisks/R/FreqSurv.R |only SemiCompRisks-2.4/SemiCompRisks/R/initiate.startValues.R |only SemiCompRisks-2.4/SemiCompRisks/man/BayesID.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/BayesSurv.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/FreqID.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/FreqSurv.Rd |only SemiCompRisks-2.4/SemiCompRisks/man/initiate.startValues.Rd |only SemiCompRisks-2.5/SemiCompRisks/DESCRIPTION | 14 SemiCompRisks-2.5/SemiCompRisks/MD5 | 64 SemiCompRisks-2.5/SemiCompRisks/NAMESPACE | 39 SemiCompRisks-2.5/SemiCompRisks/R/BayesID_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesID_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesSurv_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/BayesSurv_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/FreqID_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/FreqSurv_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/initiate.startValues_AFT.R |only SemiCompRisks-2.5/SemiCompRisks/R/initiate.startValues_HReg.R |only SemiCompRisks-2.5/SemiCompRisks/R/internalFunc.R | 358 - SemiCompRisks-2.5/SemiCompRisks/R/methods.R | 3393 +++++++--- SemiCompRisks-2.5/SemiCompRisks/R/old.functions.R |only SemiCompRisks-2.5/SemiCompRisks/R/simID.R | 5 SemiCompRisks-2.5/SemiCompRisks/R/simSurv.R | 2 SemiCompRisks-2.5/SemiCompRisks/build |only SemiCompRisks-2.5/SemiCompRisks/inst |only SemiCompRisks-2.5/SemiCompRisks/man/BayesID_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesID_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesSurv_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/BayesSurv_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/FreqID_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/FreqSurv_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/SemiCompRisks-package.Rd | 25 SemiCompRisks-2.5/SemiCompRisks/man/initiate.startValues_AFT.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/initiate.startValues_HReg.Rd |only SemiCompRisks-2.5/SemiCompRisks/man/methods.Rd | 58 SemiCompRisks-2.5/SemiCompRisks/man/old.functions.Rd |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPscr_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_DPsurv_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNscr_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv.c |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv.h |only SemiCompRisks-2.5/SemiCompRisks/src/BAFT_LNsurv_Updates.c |only SemiCompRisks-2.5/SemiCompRisks/src/BpeDpCorScrSM.h | 8 SemiCompRisks-2.5/SemiCompRisks/src/Utilities.c | 1192 +++ SemiCompRisks-2.5/SemiCompRisks/vignettes |only 54 files changed, 4068 insertions(+), 1090 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen, Kathleen Gates, and Mikko Rönkkö.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.7 dated 2016-03-22 and 0.4.8 dated 2016-10-27
DESCRIPTION | 9 MD5 | 10 R/miive.R | 612 ++++++++++++++++++++----------------------- R/miivs.R | 806 ++++++++++++++++++++++++++++++--------------------------- R/miivvarcov.R |only R/optimMIIV.R |only man/miive.Rd | 22 + 7 files changed, 751 insertions(+), 708 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 1.1.1 dated 2016-05-03 and 1.2.0 dated 2016-10-27
lamW-1.1.1/lamW/inst/NEWS.Rd |only lamW-1.2.0/lamW/DESCRIPTION | 13 +- lamW-1.2.0/lamW/MD5 | 24 ++- lamW-1.2.0/lamW/NAMESPACE | 3 lamW-1.2.0/lamW/R/RcppExports.R | 2 lamW-1.2.0/lamW/build/partial.rdb |binary lamW-1.2.0/lamW/inst/News.Rd |only lamW-1.2.0/lamW/inst/include/lamW.h | 8 - lamW-1.2.0/lamW/inst/include/lamW_RcppExports.h | 36 ++--- lamW-1.2.0/lamW/man/lamW-package.Rd | 4 lamW-1.2.0/lamW/man/lamW.Rd | 2 lamW-1.2.0/lamW/src/Makevars |only lamW-1.2.0/lamW/src/Makevars.win |only lamW-1.2.0/lamW/src/RcppExports.cpp | 54 ++++---- lamW-1.2.0/lamW/src/lambertW.cpp | 155 ++++++++++++++++-------- 15 files changed, 179 insertions(+), 122 deletions(-)
Title: Decrypt Passwords from Gnome Keyring and Windows Data Protection
API
Description: Currently this package decrypts passwords stored in the Gnome
Keyring using secret tool, and strings encrypted with the Windows Data
Protection API. OSX Keychain coming soon.
Author: Josh Gilfillan
Maintainer: Josh Gilfillan <joshua.i.gilfillan+keyringr@gmail.com>
Diff between keyringr versions 0.1.0 dated 2016-10-23 and 0.2.0 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/decrypt_dpapi_pw.R | 22 +++++++++++++++++++++- R/decrypt_gk_pw.R | 17 +++++++++++++---- man/decrypt_dpapi_pw.Rd | 20 ++++++++++++++++++++ man/decrypt_gk_pw.Rd | 12 ++++++++++-- 6 files changed, 73 insertions(+), 16 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.1 dated 2016-10-12 and 2.3.2 dated 2016-10-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/NED_FUNCTIONS.R | 4 ++-- R/NHD_FUNCTIONS.R | 2 +- README.md | 2 +- inst/CITATION | 4 ++-- man/FedData-package.Rd | 4 ++-- tests/testthat/test.NED.R | 6 +++--- tests/testthat/test.NHD.R | 4 ++-- 9 files changed, 25 insertions(+), 25 deletions(-)