More information about RTransferEntropy at CRAN
Permanent link
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Duong (2017) <doi:10.18637/jss.v021.i07>.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.11.2 dated 2018-06-09 and 1.11.3 dated 2018-07-25
CHANGELOG | 8 ++++- DESCRIPTION | 11 +++---- MD5 | 22 +++++++-------- R/binning.R | 4 +- R/kda.R | 30 +++++++++++++++----- R/kde.R | 40 ++++++++++++++++++--------- R/kms.R | 2 - R/normal.R | 76 +++++++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/kde.pdf |binary man/kde.Rd | 19 ++++++++----- man/mixt.Rd | 2 - 12 files changed, 130 insertions(+), 84 deletions(-)
Title: Rapid Deployment of Machine Learning Algorithms
Description: Supervised machine learning has an increasingly important role in data
analysis. This package introduces a framework for rapidly building and deploying
supervised machine learning in a high-throughput manner. This package provides a
user-friendly interface that empowers investigators to execute state-of-the-art
binary and multi-class classification, as well as regression, with minimal
programming experience necessary.
Author: Thomas Quinn [aut, cre],
Daniel Tylee [ctb],
Samuel Lee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between exprso versions 0.3.6 dated 2018-05-08 and 0.4.0 dated 2018-07-25
DESCRIPTION | 10 MD5 | 39 - NAMESPACE | 1 NEWS.md | 27 R/1.3-exprso.R | 6 R/2-mod.R | 69 +- R/5.1-fs.R | 6 inst/doc/a_introduction-vignette.R | 4 inst/doc/a_introduction-vignette.Rmd | 6 inst/doc/a_introduction-vignette.html | 1156 ---------------------------------- inst/doc/b_advanced-vignette.R | 4 inst/doc/b_advanced-vignette.Rmd | 4 inst/doc/b_advanced-vignette.html | 46 - inst/doc/c_readme.html | 4 man/fs.Rd | 2 man/mod.Rd | 2 man/modScale.Rd | 18 man/modSkew.Rd |only tests/testthat/test-pl-multi.R | 143 ++-- vignettes/a_introduction-vignette.Rmd | 6 vignettes/b_advanced-vignette.Rmd | 4 21 files changed, 225 insertions(+), 1332 deletions(-)
Title: Simulate Models Based on the Generalized Linear Model
Description: Easily simulates regression models,
including both simple regression and generalized linear mixed
models with up to three level of nesting. Power simulations that are
flexible allowing the specification of missing data, unbalanced designs,
and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
Diff between simglm versions 0.7.0 dated 2018-06-01 and 0.7.1 dated 2018-07-25
DESCRIPTION | 6 MD5 | 38 NEWS.md | 4 R/data_reg.r | 2 R/pow_sim.r | 87 build/vignette.rds |binary inst/doc/GeneralizedModels_legacy.html | 528 -- inst/doc/Intro_legacy.html | 964 +-- inst/doc/Power_legacy.html | 814 +-- inst/doc/simulation_arguments.R | 103 inst/doc/simulation_arguments.Rmd | 121 inst/doc/simulation_arguments.html | 8466 ++++++++++++++++++++++----------- inst/doc/tidy_simulation.R | 3 inst/doc/tidy_simulation.Rmd | 3 inst/doc/tidy_simulation.html | 2095 ++------ inst/doc/unbalanced_legacy.html | 118 man/model_fit.Rd | 3 man/replicate_simulation.Rd | 6 vignettes/simulation_arguments.Rmd | 121 vignettes/tidy_simulation.Rmd | 3 20 files changed, 7531 insertions(+), 5954 deletions(-)
Title: Graphing for Markov, Hidden Markov, and Mixture Transition
Distribution Models
Description: Produces parallel coordinate plots of probability transition matrices from Markov, hidden Markov, and mixture transition distribution models.
Author: Pauline Adamopoulou [aut, cre, cph],
Gilbert Ritschard [ths],
Andre Berchtold [ths],
Reto Buergin [ctb],
Ogier Maitre [ctb]
Maintainer: Pauline Adamopoulou <padamopo@gmail.com>
Diff between MmgraphR versions 0.2 dated 2018-06-24 and 0.3 dated 2018-07-25
DESCRIPTION | 18 ++++--- MD5 | 21 +++++--- NAMESPACE | 13 ++++- NEWS | 106 ++++++++++---------------------------------- R/trmatplot.depmix.fitted.R | 5 ++ R/trmatplot.dthmm.R |only R/trmatplot.msm.R |only README |only ToDo |only inst |only man/MmgraphR-package.Rd | 44 ++++++++++-------- man/trmat.Rd | 2 man/trmatplot.Rd | 40 +++++++++------- man/trmatplot.march.Dcmm.Rd | 4 - 14 files changed, 116 insertions(+), 137 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison, Tom Drake, Riinu Ots
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.8.2 dated 2018-07-24 and 0.8.3 dated 2018-07-25
finalfit-0.8.2/finalfit/R/finalfit_coxph.R |only finalfit-0.8.2/finalfit/R/finalfit_glm.R |only finalfit-0.8.2/finalfit/R/finalfit_lm.R |only finalfit-0.8.2/finalfit/R/fit2df_coxph.R |only finalfit-0.8.2/finalfit/R/fit2df_coxphlist.R |only finalfit-0.8.2/finalfit/R/fit2df_glm.R |only finalfit-0.8.2/finalfit/R/fit2df_glmboot.R |only finalfit-0.8.2/finalfit/R/fit2df_glmerMod.R |only finalfit-0.8.2/finalfit/R/fit2df_glmlist.R |only finalfit-0.8.2/finalfit/R/fit2df_lm.R |only finalfit-0.8.2/finalfit/R/fit2df_lmerMod.R |only finalfit-0.8.2/finalfit/R/fit2df_lmlist.R |only finalfit-0.8.2/finalfit/R/fit2df_stanfit.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist0.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist1.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist2.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist3.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist4.R |only finalfit-0.8.2/finalfit/R/summaryfactorlist5.R |only finalfit-0.8.2/finalfit/man/finalfit.coxph.Rd |only finalfit-0.8.2/finalfit/man/finalfit.glm.Rd |only finalfit-0.8.2/finalfit/man/finalfit.lm.Rd |only finalfit-0.8.3/finalfit/DESCRIPTION | 6 finalfit-0.8.3/finalfit/MD5 | 52 - finalfit-0.8.3/finalfit/NAMESPACE | 5 finalfit-0.8.3/finalfit/R/finalfit.R | 280 +++++++ finalfit-0.8.3/finalfit/R/fit2df.R | 537 ++++++++++++++ finalfit-0.8.3/finalfit/R/missing_plot.R | 8 finalfit-0.8.3/finalfit/R/summaryfactorlist.R | 689 ++++++++++++++++++ finalfit-0.8.3/finalfit/inst/doc/finalfit_basics.html | 4 finalfit-0.8.3/finalfit/man/finalfit.Rd | 25 finalfit-0.8.3/finalfit/man/fit2df.Rd | 67 - finalfit-0.8.3/finalfit/man/summary_factorlist0.Rd | 38 finalfit-0.8.3/finalfit/man/summary_factorlist1.Rd | 42 - finalfit-0.8.3/finalfit/man/summary_factorlist2.Rd | 42 - finalfit-0.8.3/finalfit/man/summary_factorlist3.Rd | 42 - finalfit-0.8.3/finalfit/man/summary_factorlist4.Rd | 42 - finalfit-0.8.3/finalfit/man/summary_factorlist5.Rd | 42 - 38 files changed, 1589 insertions(+), 332 deletions(-)
Title: Directly Extracts Complete CANSIM Data Tables / Extrait Des
Tableaux CANSIM Directement
Description: Extract CANSIM (Statistics Canada) tables and transform them into readily usable data in panel (wide) format. It can also extract more than one table at a time and produce the resulting merge by time period and geographical region.
Author: Marco Lugo <marco.lugo.rodriguez@umontreal.ca>
Maintainer: Marco Lugo <marco.lugo.rodriguez@umontreal.ca>
Diff between CANSIM2R versions 1.13.0 dated 2018-07-22 and 1.13.1 dated 2018-07-25
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/downloadCANSIM.r | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between umap versions 0.1.0.3 dated 2018-06-24 and 0.2.0.0 dated 2018-07-25
umap-0.1.0.3/umap/R/umap_python.R |only umap-0.1.0.3/umap/man/lanczos.coo.Rd |only umap-0.1.0.3/umap/man/multiplicationprep.coo.Rd |only umap-0.1.0.3/umap/man/spectral.coo.Rd |only umap-0.1.0.3/umap/man/umap.python.Rd |only umap-0.1.0.3/umap/man/vector.norm.Rd |only umap-0.1.0.3/umap/man/vectormultiplication.coo.Rd |only umap-0.1.0.3/umap/src/clip4.cpp |only umap-0.2.0.0/umap/DESCRIPTION | 11 umap-0.2.0.0/umap/MD5 | 120 +-- umap-0.2.0.0/umap/NAMESPACE | 1 umap-0.2.0.0/umap/R/RcppExports.R | 69 + umap-0.2.0.0/umap/R/coo.R | 52 - umap-0.2.0.0/umap/R/coo_spectral.R | 230 ------ umap-0.2.0.0/umap/R/embedding.R |only umap-0.2.0.0/umap/R/knn.R | 171 +++- umap-0.2.0.0/umap/R/umap.R | 146 ++-- umap-0.2.0.0/umap/R/umap_checks.R | 54 + umap-0.2.0.0/umap/R/umap_learn.R |only umap-0.2.0.0/umap/R/umap_naive.R | 176 ++-- umap-0.2.0.0/umap/R/umap_small.R | 6 umap-0.2.0.0/umap/R/umap_universal.R | 182 ----- umap-0.2.0.0/umap/R/utils.R | 27 umap-0.2.0.0/umap/build/vignette.rds |binary umap-0.2.0.0/umap/inst/doc/umap.R | 51 + umap-0.2.0.0/umap/inst/doc/umap.Rmd | 106 ++ umap-0.2.0.0/umap/inst/doc/umap.html | 502 +++++--------- umap-0.2.0.0/umap/inst/doc/umap_learn.R |only umap-0.2.0.0/umap/inst/doc/umap_learn.Rmd |only umap-0.2.0.0/umap/inst/doc/umap_learn.html |only umap-0.2.0.0/umap/man/check.learn.available.Rd |only umap-0.2.0.0/umap/man/clip.Rd | 4 umap-0.2.0.0/umap/man/detect.umap.learn.Rd |only umap-0.2.0.0/umap/man/get.global.seed.Rd |only umap-0.2.0.0/umap/man/knn.from.data.Rd | 9 umap-0.2.0.0/umap/man/knn.from.data.reps.Rd | 2 umap-0.2.0.0/umap/man/knn.info.Rd | 6 umap-0.2.0.0/umap/man/make.initial.embedding.Rd | 2 umap-0.2.0.0/umap/man/make.initial.spectator.embedding.Rd |only umap-0.2.0.0/umap/man/make.random.embedding.Rd | 2 umap-0.2.0.0/umap/man/make.spectral.embedding.Rd | 2 umap-0.2.0.0/umap/man/mdCenteredPearson.Rd | 8 umap-0.2.0.0/umap/man/mdCosine.Rd | 8 umap-0.2.0.0/umap/man/mdEuclidean.Rd | 8 umap-0.2.0.0/umap/man/mdManhattan.Rd | 6 umap-0.2.0.0/umap/man/naive.simplicial.set.embedding.Rd | 4 umap-0.2.0.0/umap/man/optimize_epoch.Rd |only umap-0.2.0.0/umap/man/predict.umap.Rd |only umap-0.2.0.0/umap/man/set.global.seed.Rd |only umap-0.2.0.0/umap/man/spectator.knn.info.Rd |only umap-0.2.0.0/umap/man/spectral.eigenvectors.Rd |only umap-0.2.0.0/umap/man/umap.Rd | 11 umap-0.2.0.0/umap/man/umap.check.config.class.Rd |only umap-0.2.0.0/umap/man/umap.defaults.Rd | 32 umap-0.2.0.0/umap/man/umap.learn.Rd |only umap-0.2.0.0/umap/man/umap.learn.predict.Rd |only umap-0.2.0.0/umap/man/umap.naive.predict.Rd |only umap-0.2.0.0/umap/src/RcppExports.cpp | 117 +-- umap-0.2.0.0/umap/src/distances.cpp | 70 + umap-0.2.0.0/umap/src/optimize.cpp |only umap-0.2.0.0/umap/tests/testthat/synthetic.R | 17 umap-0.2.0.0/umap/tests/testthat/test_checks.R | 91 +- umap-0.2.0.0/umap/tests/testthat/test_coo.R | 21 umap-0.2.0.0/umap/tests/testthat/test_embedding.R | 35 umap-0.2.0.0/umap/tests/testthat/test_knn.R | 108 ++- umap-0.2.0.0/umap/tests/testthat/test_methods.R | 48 - umap-0.2.0.0/umap/tests/testthat/test_naive.R | 104 ++ umap-0.2.0.0/umap/tests/testthat/test_predict.R |only umap-0.2.0.0/umap/tests/testthat/test_print.R | 2 umap-0.2.0.0/umap/tests/testthat/test_python.R | 78 +- umap-0.2.0.0/umap/tests/testthat/test_rcpp.R | 24 umap-0.2.0.0/umap/tests/testthat/test_spectral.R | 59 - umap-0.2.0.0/umap/tests/testthat/test_universal.R | 31 umap-0.2.0.0/umap/tests/testthat/train_test.R |only umap-0.2.0.0/umap/vignettes/umap.Rmd | 106 ++ umap-0.2.0.0/umap/vignettes/umap_learn.Rmd |only 76 files changed, 1502 insertions(+), 1417 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 0.9 dated 2018-04-25 and 1.0 dated 2018-07-25
DESCRIPTION | 13 - MD5 | 48 ++-- NAMESPACE | 10 NEWS | 6 R/allmetap.R | 9 R/invchisq.R |only R/invt.R |only R/meanz.R |only build/partial.rdb |only build/vignette.rds |binary inst/REFERENCES.bib |only inst/doc/metap.R | 95 ++------- inst/doc/metap.Rnw | 529 ++++++++++++++++++++++----------------------------- inst/doc/metap.pdf |binary man/invchisq.Rd |only man/invt.Rd |only man/logitp.Rd | 7 man/meanp.Rd | 16 - man/meanz.Rd |only man/metap-package.Rd | 50 +--- man/package-data.Rd | 47 +--- man/schweder.Rd | 29 -- man/sumlog.Rd | 25 -- man/sump.Rd | 17 - man/sumz.Rd | 29 -- man/votep.Rd | 9 man/wilkinsonp.Rd | 26 -- vignettes/metap.Rnw | 529 ++++++++++++++++++++++----------------------------- vignettes/metap.bib | 24 ++ 29 files changed, 647 insertions(+), 871 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<http://pyyaml.org/wiki/LibYAML>) for R.
Author: Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb],
Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb],
Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb]
Maintainer: Jeremy Stephens <jeremy.f.stephens@vumc.org>
Diff between yaml versions 2.1.19 dated 2018-05-01 and 2.2.0 dated 2018-07-25
yaml-2.1.19/yaml/tests/testthat |only yaml-2.1.19/yaml/tests/testthat.R |only yaml-2.2.0/yaml/DESCRIPTION | 10 yaml-2.2.0/yaml/MD5 | 40 +-- yaml-2.2.0/yaml/R/as.yaml.R | 9 yaml-2.2.0/yaml/inst/CHANGELOG | 14 + yaml-2.2.0/yaml/inst/implicit.re | 2 yaml-2.2.0/yaml/inst/tests |only yaml-2.2.0/yaml/man/as.yaml.Rd | 66 +++++ yaml-2.2.0/yaml/man/read_yaml.Rd | 9 yaml-2.2.0/yaml/man/write_yaml.Rd | 8 yaml-2.2.0/yaml/man/yaml.load.Rd | 8 yaml-2.2.0/yaml/src/implicit.c | 2 yaml-2.2.0/yaml/src/r_emit.c | 484 ++++++++++++++++++++++++-------------- yaml-2.2.0/yaml/src/r_ext.c | 202 ++++++++++++--- yaml-2.2.0/yaml/src/r_ext.h | 22 + yaml-2.2.0/yaml/src/r_parse.c | 236 +++++------------- yaml-2.2.0/yaml/tests/RUnit.R |only 18 files changed, 692 insertions(+), 420 deletions(-)
Title: Methods and Measures for Brain, Cognitive, and Psychometric
Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between NetworkToolbox versions 1.1.2 dated 2018-04-29 and 1.2.0 dated 2018-07-25
NetworkToolbox-1.1.2/NetworkToolbox/R/NetworkToolbox--master.R |only NetworkToolbox-1.1.2/NetworkToolbox/data/animals.RData |only NetworkToolbox-1.1.2/NetworkToolbox/man/animals.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/bootgenPlot.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/commboot.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/neuralcorrtest.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/neuralgrouptest.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/neuralstat.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/semnetboot.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/semnetmeas.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/splitsamp.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/splitsampNet.Rd |only NetworkToolbox-1.1.2/NetworkToolbox/man/splitsampStats.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/DESCRIPTION | 12 NetworkToolbox-1.2.0/NetworkToolbox/MD5 | 194 ++++++---- NetworkToolbox-1.2.0/NetworkToolbox/NAMESPACE | 20 - NetworkToolbox-1.2.0/NetworkToolbox/NEWS | 48 ++ NetworkToolbox-1.2.0/NetworkToolbox/R/ECO.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/ECOplusMaST.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/LoGo.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/MaST.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/NetworkToolbox.R | 8 NetworkToolbox-1.2.0/NetworkToolbox/R/TMFG.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/adapt.a.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/behavOpen.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/betweenness.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/binarize.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/bootgen.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/bootgen.plot.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/centlist.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/closeness.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/clustcoeff.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/comcat.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/comm.close.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/comm.eigen.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/comm.str.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/conn.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/convert2igraph.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/convertConnBrainMat.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/cor2cov.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/core.items.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/cpmEV.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/cpmFP.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/cpmFPperm.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/cpmIV.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/degree.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/depend.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/depna.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/distance.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/diversity.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/edgerep.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/eigenvector.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/flow.frac.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/gateway.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/hybrid.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/impact.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/is.graphical.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/kld.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/lattnet.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/leverage.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/louvain.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/nams.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/neoOpen.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/net.coverage.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/neuralnetfilter.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/participation.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/pathlengths.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/randnet.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/reg.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/rmse.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/rspbc.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/sim.swn.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/smallworldness.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/stable.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/strength.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/threshold.R |only NetworkToolbox-1.2.0/NetworkToolbox/R/transitivity.R |only NetworkToolbox-1.2.0/NetworkToolbox/inst/CITATION | 24 - NetworkToolbox-1.2.0/NetworkToolbox/man/ECO.Rd | 20 - NetworkToolbox-1.2.0/NetworkToolbox/man/ECOplusMaST.Rd | 17 NetworkToolbox-1.2.0/NetworkToolbox/man/LoGo.Rd | 29 - NetworkToolbox-1.2.0/NetworkToolbox/man/MaST.Rd | 23 - NetworkToolbox-1.2.0/NetworkToolbox/man/NetworkToolbox-package.Rd | 5 NetworkToolbox-1.2.0/NetworkToolbox/man/TMFG.Rd | 41 +- NetworkToolbox-1.2.0/NetworkToolbox/man/adapt.a.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/behavOpen.Rd | 4 NetworkToolbox-1.2.0/NetworkToolbox/man/betweenness.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/binarize.Rd | 7 NetworkToolbox-1.2.0/NetworkToolbox/man/bootgen.Rd | 36 - NetworkToolbox-1.2.0/NetworkToolbox/man/bootgen.plot.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/centlist.Rd | 35 + NetworkToolbox-1.2.0/NetworkToolbox/man/closeness.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/clustcoeff.Rd | 20 - NetworkToolbox-1.2.0/NetworkToolbox/man/comcat.Rd | 18 NetworkToolbox-1.2.0/NetworkToolbox/man/comm.close.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/comm.eigen.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/comm.str.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/conn.Rd | 20 - NetworkToolbox-1.2.0/NetworkToolbox/man/convert2igraph.Rd | 8 NetworkToolbox-1.2.0/NetworkToolbox/man/convertConnBrainMat.Rd | 9 NetworkToolbox-1.2.0/NetworkToolbox/man/cor2cov.Rd | 3 NetworkToolbox-1.2.0/NetworkToolbox/man/core.items.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/cpmEV.Rd | 23 - NetworkToolbox-1.2.0/NetworkToolbox/man/cpmFP.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/cpmFPperm.Rd | 17 NetworkToolbox-1.2.0/NetworkToolbox/man/cpmIV.Rd | 23 - NetworkToolbox-1.2.0/NetworkToolbox/man/degree.Rd | 29 + NetworkToolbox-1.2.0/NetworkToolbox/man/depend.Rd | 13 NetworkToolbox-1.2.0/NetworkToolbox/man/depna.Rd | 9 NetworkToolbox-1.2.0/NetworkToolbox/man/distance.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/diversity.Rd | 37 + NetworkToolbox-1.2.0/NetworkToolbox/man/edgerep.Rd | 42 +- NetworkToolbox-1.2.0/NetworkToolbox/man/eigenvector.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/flow.frac.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/gateway.Rd | 34 + NetworkToolbox-1.2.0/NetworkToolbox/man/hybrid.Rd | 15 NetworkToolbox-1.2.0/NetworkToolbox/man/impact.Rd | 27 - NetworkToolbox-1.2.0/NetworkToolbox/man/is.graphical.Rd | 5 NetworkToolbox-1.2.0/NetworkToolbox/man/kld.Rd | 6 NetworkToolbox-1.2.0/NetworkToolbox/man/lattnet.Rd | 8 NetworkToolbox-1.2.0/NetworkToolbox/man/leverage.Rd | 18 NetworkToolbox-1.2.0/NetworkToolbox/man/louvain.Rd | 18 NetworkToolbox-1.2.0/NetworkToolbox/man/nams.Rd | 60 +-- NetworkToolbox-1.2.0/NetworkToolbox/man/neoOpen.Rd | 15 NetworkToolbox-1.2.0/NetworkToolbox/man/net.coverage.Rd |only NetworkToolbox-1.2.0/NetworkToolbox/man/neuralnetfilter.Rd | 12 NetworkToolbox-1.2.0/NetworkToolbox/man/participation.Rd | 36 + NetworkToolbox-1.2.0/NetworkToolbox/man/pathlengths.Rd | 31 + NetworkToolbox-1.2.0/NetworkToolbox/man/randnet.Rd | 8 NetworkToolbox-1.2.0/NetworkToolbox/man/reg.Rd | 3 NetworkToolbox-1.2.0/NetworkToolbox/man/rmse.Rd | 4 NetworkToolbox-1.2.0/NetworkToolbox/man/rspbc.Rd | 22 - NetworkToolbox-1.2.0/NetworkToolbox/man/sim.swn.Rd | 26 - NetworkToolbox-1.2.0/NetworkToolbox/man/smallworldness.Rd | 27 + NetworkToolbox-1.2.0/NetworkToolbox/man/stable.Rd | 14 NetworkToolbox-1.2.0/NetworkToolbox/man/strength.Rd | 29 + NetworkToolbox-1.2.0/NetworkToolbox/man/threshold.Rd | 23 - NetworkToolbox-1.2.0/NetworkToolbox/man/transitivity.Rd | 9 138 files changed, 828 insertions(+), 486 deletions(-)
More information about NetworkToolbox at CRAN
Permanent link
Title: Performance Measures for Statistical Learning
Description: Provides the biggest amount of statistical measures in the whole R world. Includes measures of regression, (multiclass) classification and multilabel classification. The measures come mainly from the 'mlr' package and were programed by several 'mlr' developers.
Author: Philipp Probst [aut, cre]
Maintainer: Philipp Probst <philipp_probst@gmx.de>
Diff between measures versions 0.1 dated 2018-07-05 and 0.2 dated 2018-07-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/listAllMeasures.R | 23 ++++++++++++++++------- R/sysdata.rda |binary 4 files changed, 22 insertions(+), 13 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5-1 dated 2017-11-15 and 1.5-2 dated 2018-07-25
ChangeLog | 12 ++++++ DESCRIPTION | 10 ++--- MD5 | 62 +++++++++++++++---------------- R/gp.R | 11 ++++- R/gp_sep.R | 11 ++++- R/laGP.R | 4 +- R/laGP_sep.R | 4 +- build/vignette.rds |binary inst/doc/laGP.pdf |binary man/aGP.Rd | 58 ++++++++++++++--------------- man/alcGP.Rd | 103 ++++++++++++++++++++++++++++------------------------ man/blhs.Rd | 25 ++++++------ man/darg.Rd | 4 +- man/deleteGP.Rd | 4 +- man/discrep.est.Rd | 24 +++++------- man/distance.Rd | 4 +- man/fcalib.Rd | 26 ++++++------- man/laGP.Rd | 19 ++++----- man/llikGP.Rd | 4 +- man/mleGP.Rd | 12 +++--- man/optim.auglag.Rd | 35 ++++++++--------- man/predGP.Rd | 21 ++++++---- src/covar.c | 10 ++--- src/covar_sep.c | 6 +-- src/gp.c | 79 ++++++++++++++++++--------------------- src/gp.h | 12 +++--- src/gp_sep.c | 65 ++++++++++++++++++-------------- src/gp_sep.h | 10 ++--- src/init.c | 16 ++++---- src/laGP.c | 7 +-- src/laGP_sep.c | 4 +- src/matrix.c | 4 +- 32 files changed, 346 insertions(+), 320 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with
remote database tables as if they are in-memory data frames. Basic features
works with any database that has a 'DBI' back end; more advanced features
require 'SQL' translation to be provided by the package author.
Author: Hadley Wickham [aut, cre],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 1.2.1 dated 2018-02-19 and 1.2.2 dated 2018-07-25
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/dbplyr.R | 1 + R/sql-expr.R | 2 +- inst/doc/dbplyr.html | 46 +++++++++++++++++++++++----------------------- inst/doc/new-backend.html | 10 +++++----- man/dbplyr-package.Rd | 2 ++ man/join.tbl_sql.Rd | 3 ++- man/sql_expr.Rd | 2 +- 11 files changed, 56 insertions(+), 46 deletions(-)
Title: 'jQuery UI' Interactions and Effects for Shiny
Description: An extension to shiny that brings interactions and animation effects from
'jQuery UI' library.
Author: Yang Tang [aut, cre]
Maintainer: Yang Tang <tang_yang@outlook.com>
Diff between shinyjqui versions 0.3.1 dated 2018-07-08 and 0.3.2 dated 2018-07-25
shinyjqui-0.3.1/shinyjqui/inst/shinydemos/sort.R |only shinyjqui-0.3.2/shinyjqui/DESCRIPTION | 6 +-- shinyjqui-0.3.2/shinyjqui/MD5 | 17 ++++------ shinyjqui-0.3.2/shinyjqui/NEWS.md | 7 ++++ shinyjqui-0.3.2/shinyjqui/R/effects.R | 14 ++++++++ shinyjqui-0.3.2/shinyjqui/R/utils.R | 14 +++++--- shinyjqui-0.3.2/shinyjqui/inst/doc/introduction.html | 4 +- shinyjqui-0.3.2/shinyjqui/inst/doc/orderInput.html | 4 +- shinyjqui-0.3.2/shinyjqui/inst/doc/save-and-restore.html | 4 +- shinyjqui-0.3.2/shinyjqui/inst/shinydemos/resizable_combine_with_other_interactions.R | 1 10 files changed, 48 insertions(+), 23 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 [aut, cre] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between oddsratio versions 1.0.2 dated 2017-12-07 and 1.0.3 dated 2018-07-25
DESCRIPTION | 25 +- MD5 | 29 +- NEWS | 39 ++- NEWS.md | 6 R/helper_funs.R | 4 R/insert_or.R | 8 R/or_gam.R | 6 R/or_glm.R | 13 - R/plot_gam.R | 4 build/vignette.rds |binary inst/convert_to_ascii_news.sh |only inst/doc/function_tutorial.html | 412 ++++++++++++++++++++++++++++++---------- man/or_glm.Rd | 2 tests/testthat/test-insert-or.R | 29 +- tests/testthat/test-or-gam.R | 8 tests/testthat/test-or-glm.R | 4 16 files changed, 409 insertions(+), 180 deletions(-)
Title: Easily Download and Visualise Climate Data from CliFlo
Description: CliFlo is a web portal to the New Zealand National Climate
Database and provides public access (via subscription) to around 6,500
various climate stations (see <https://cliflo.niwa.co.nz/> for more
information). Collating and manipulating data from CliFlo
(hence clifro) and importing into R for further analysis, exploration and
visualisation is now straightforward and coherent. The user is required to
have an internet connection, and a current CliFlo subscription (free) if
data from stations, other than the public Reefton electronic weather
station, is sought.
Author: Blake Seers [aut, cre] (<https://orcid.org/0000-0001-6841-4312>)
Maintainer: Blake Seers <blake.seers@gmail.com>
Diff between clifro versions 3.1-5 dated 2017-10-05 and 3.2-0 dated 2018-07-25
DESCRIPTION | 19 MD5 | 76 - NAMESPACE | 23 NEWS.md | 14 R/cfData-plotMethods.R | 20 R/cfDatatype.R | 67 - R/cfQuery.R | 9 R/cfStation.R | 19 R/cfUser.R | 27 R/findStations.R | 342 +++---- README.md | 8 build/vignette.rds |binary inst/doc/cfStation.Rmd | 35 inst/doc/cfStation.html | 57 - inst/doc/choose-datatype.html | 46 inst/doc/choose-station.R | 140 ++- inst/doc/choose-station.Rmd | 198 ++-- inst/doc/choose-station.html | 225 ++-- inst/doc/clifro.Rmd | 8 inst/doc/clifro.html | 22 inst/extdata/auckStations | 1586 ++++++++++++++++++++-------------- inst/extdata/queenStations | 612 +++++++------ man/cfDatatype-class.Rd | 2 man/cf_last_query.Rd | 2 man/cf_query.Rd | 2 man/cf_save_kml.Rd | 4 man/plot-cfTemp-missing-method.Rd | 2 man/plot-cfWind-missing-method.Rd | 4 man/windrose.Rd | 4 tests/testthat/test-cf_find_station.R | 5 tests/testthat/test-cf_last_query.R | 7 tests/testthat/test-cf_query.R | 5 tests/testthat/test-cf_station.R | 5 tools/README-rain-wind-example-1.png |binary tools/README-rain-wind-example-2.png |binary vignettes/cfStation.Rmd | 35 vignettes/choose-station.Rmd | 198 ++-- vignettes/clifro.Rmd | 8 vignettes/figures/ggmap.png |binary 39 files changed, 2205 insertions(+), 1631 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.67-4 dated 2017-12-08 and 0.68-2 dated 2018-07-25
DESCRIPTION | 10 ++-- MD5 | 25 +++++----- NAMESPACE | 1 NEWS | 10 +++- R/holmans_triangle.R | 122 +++++++++++++++++++++++++++++++++++++++++-------- R/openfile.R | 18 +++++-- data/numbers-cap.RData |binary data/numbers.RData |binary man/openfile.Rd | 11 ++-- man/triarrow.Rd | 20 ++++---- man/trilines.Rd | 20 ++++---- man/triplot.Rd | 24 ++++----- man/tripoints.Rd | 20 ++++---- man/tritext.Rd |only 14 files changed, 195 insertions(+), 86 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>,
David Barrios <metal@usal.es>,
Carlos Prieto <cprietos@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 0.2.9 dated 2018-07-23 and 0.3.0 dated 2018-07-25
netCoin-0.2.9/netCoin/man/plot.Rd |only netCoin-0.2.9/netCoin/man/print.Rd |only netCoin-0.2.9/netCoin/man/summary.Rd |only netCoin-0.3.0/netCoin/DESCRIPTION | 12 ++++++------ netCoin-0.3.0/netCoin/MD5 | 11 ++++------- netCoin-0.3.0/netCoin/NAMESPACE | 14 +------------- netCoin-0.3.0/netCoin/R/netcoin.R | 6 ------ netCoin-0.3.0/netCoin/inst/doc/netCoin.html | 4 ++-- 8 files changed, 13 insertions(+), 34 deletions(-)
Title: GEO RNA-Seq Experiments Processing Pipeline
Description: An R based pipeline to download and process Gene Expression Omnibus (GEO) RNA-seq data.
For a given GEO series accession ID, this pipeline generates metadata,
both gene and transcript level counts, and quality control (QC) report.
This package is mainly developed to process the GEO RNA-seq datasets
for the web platform GREIN. More details about GREP2 and GREIN can be
found here <doi:10.1101/326223>.
Author: Naim Al Mahi [cre, aut],
Mario Medvedovic [aut, ctb]
Maintainer: Naim Al Mahi <mahina@mail.uc.edu>
Diff between GREP2 versions 1.0.0 dated 2018-06-06 and 1.0.1 dated 2018-07-25
DESCRIPTION | 6 +- MD5 | 16 +++---- R/get_fastq.R | 15 ++++-- R/run_tximport.R | 2 README.md | 42 ++++++++++++------- inst/doc/vignette.R | 41 +++++++++++------- inst/doc/vignette.Rmd | 41 +++++++++++------- inst/doc/vignette.html | 106 ++++++++++++++++++++++++++----------------------- vignettes/vignette.Rmd | 41 +++++++++++------- 9 files changed, 177 insertions(+), 133 deletions(-)
Title: 'Rcpp' Interface to 'sparsepp'
Description: Provides interface to 'sparsepp' - fast, memory efficient hash map.
It is derived from Google's excellent 'sparsehash' implementation.
We believe 'sparsepp' provides an unparalleled combination of performance and memory usage,
and will outperform your compiler's unordered_map on both counts.
Only Google's 'dense_hash_map' is consistently faster, at the cost of much greater
memory usage (especially when the final size of the map is not known in advance).
Author: Gregory Popovitch [aut, cph],
Google Inc [aut, cph],
Dmitriy Selivanov [cre]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between sparsepp versions 0.2.0 dated 2017-08-07 and 1.21 dated 2018-07-25
DESCRIPTION | 8 +- MD5 | 30 ++++----- NEWS.md |only R/package-sparsepp.R | 4 - inst/include/README.md | 12 ++- inst/include/examples/makefile | 10 ++- inst/include/sparsepp/spp.h | 59 +++++++++-------- inst/include/sparsepp/spp_dlalloc.h | 50 ++++++++++----- inst/include/sparsepp/spp_memory.h | 79 ++++++++++++++++++++++-- inst/include/sparsepp/spp_smartptr.h | 2 inst/include/sparsepp/spp_stdint.h | 2 inst/include/sparsepp/spp_traits.h | 7 +- inst/include/sparsepp/spp_utils.h | 64 +++++++++++++------ inst/include/tests/makefile | 16 ++++ inst/include/tests/spp_relative_include_test.cc |only inst/include/tests/spp_test.cc | 35 +++++++++- man/sparsepp-package.Rd | 4 - 17 files changed, 277 insertions(+), 105 deletions(-)
Title: Text Processing for Small or Big Data Files
Description: It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. 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 1.1.1 dated 2018-05-17 and 1.1.2 dated 2018-07-25
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NEWS.md | 7 ++ README.md | 1 inst/doc/functionality_of_textTinyR_package.html | 4 - inst/doc/word_vectors_doc2vec.html | 4 - src/ngram_stemmer.h | 4 + src/porter2_stemmer.cpp | 45 ++++++++++++------- src/term_matrix.h | 5 ++ src/token_stats.h | 4 + src/tokenization.h | 3 + tests/testthat/test-tokenization_transformation.R | 52 +++++++++++----------- 12 files changed, 98 insertions(+), 61 deletions(-)
Title: Summarize and Explore the Data
Description: Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.
Author: Dayanand Ubrangala; Kiran R; Ravi Prasad Kondapalli
Maintainer: Dayanand Ubrangala<daya6489@gmail.com>
Diff between SmartEDA versions 0.2.0 dated 2018-05-21 and 0.3.0 dated 2018-07-25
SmartEDA-0.2.0/SmartEDA/inst/doc/Report_r1.R |only SmartEDA-0.2.0/SmartEDA/inst/doc/Report_r1.Rmd |only SmartEDA-0.2.0/SmartEDA/inst/doc/Report_r1.html |only SmartEDA-0.2.0/SmartEDA/vignettes/Report_r1.Rmd |only SmartEDA-0.3.0/SmartEDA/DESCRIPTION | 8 SmartEDA-0.3.0/SmartEDA/MD5 | 64 - SmartEDA-0.3.0/SmartEDA/NAMESPACE | 9 SmartEDA-0.3.0/SmartEDA/NEWS.md | 18 SmartEDA-0.3.0/SmartEDA/R/fn_Overview_data.R | 11 SmartEDA-0.3.0/SmartEDA/R/fn_custom_tab.R | 319 ++++--- SmartEDA-0.3.0/SmartEDA/R/fn_exp_ParCoordPlot.R |only SmartEDA-0.3.0/SmartEDA/R/fn_exp_QQPlot.R |only SmartEDA-0.3.0/SmartEDA/R/fn_exp_categorical.R | 49 - SmartEDA-0.3.0/SmartEDA/R/fn_exp_categorical_viz.R | 219 +++-- SmartEDA-0.3.0/SmartEDA/R/fn_exp_numeric.R | 46 - SmartEDA-0.3.0/SmartEDA/R/fn_exp_numeric_viz.R | 24 SmartEDA-0.3.0/SmartEDA/R/fn_exp_report.R | 29 SmartEDA-0.3.0/SmartEDA/README.md | 2 SmartEDA-0.3.0/SmartEDA/build/vignette.rds |binary SmartEDA-0.3.0/SmartEDA/inst/doc/CustomTable.R | 4 SmartEDA-0.3.0/SmartEDA/inst/doc/CustomTable.Rmd | 10 SmartEDA-0.3.0/SmartEDA/inst/doc/CustomTable.html | 520 +++++++++---- SmartEDA-0.3.0/SmartEDA/inst/doc/SmartEDA.R |only SmartEDA-0.3.0/SmartEDA/inst/doc/SmartEDA.Rmd |only SmartEDA-0.3.0/SmartEDA/inst/doc/SmartEDA.html |only SmartEDA-0.3.0/SmartEDA/inst/rmd_template/report_tmp.Rmd | 23 SmartEDA-0.3.0/SmartEDA/inst/rmd_template/report_tmp_1.Rmd | 6 SmartEDA-0.3.0/SmartEDA/inst/rmd_template/report_tmp_2.Rmd | 10 SmartEDA-0.3.0/SmartEDA/man/ExpCTable.Rd | 2 SmartEDA-0.3.0/SmartEDA/man/ExpCatStat.Rd | 2 SmartEDA-0.3.0/SmartEDA/man/ExpCatViz.Rd | 15 SmartEDA-0.3.0/SmartEDA/man/ExpCustomStat.Rd | 13 SmartEDA-0.3.0/SmartEDA/man/ExpData.Rd | 2 SmartEDA-0.3.0/SmartEDA/man/ExpNumStat.Rd | 30 SmartEDA-0.3.0/SmartEDA/man/ExpOutQQ.Rd |only SmartEDA-0.3.0/SmartEDA/man/ExpParcoord.Rd |only SmartEDA-0.3.0/SmartEDA/man/ExpReport.Rd | 13 SmartEDA-0.3.0/SmartEDA/vignettes/CustomTable.Rmd | 10 SmartEDA-0.3.0/SmartEDA/vignettes/SmartEDA.Rmd |only 39 files changed, 976 insertions(+), 482 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 3.5.1 dated 2018-05-08 and 4.0.0 dated 2018-07-25
propr-3.5.1/propr/R/aldex2propr.R |only propr-3.5.1/propr/R/deprecated.R |only propr-3.5.1/propr/R/deprecated2.R |only propr-3.5.1/propr/R/global.R |only propr-3.5.1/propr/R/methods.R |only propr-3.5.1/propr/R/prop2prob.R |only propr-3.5.1/propr/R/propd.R |only propr-3.5.1/propr/R/propdViz.R |only propr-3.5.1/propr/R/propr.R |only propr-3.5.1/propr/R/proprViz.R |only propr-3.5.1/propr/R/theta.R |only propr-3.5.1/propr/inst/doc/c_indexing.R |only propr-3.5.1/propr/inst/doc/c_indexing.Rmd |only propr-3.5.1/propr/inst/doc/c_indexing.html |only propr-3.5.1/propr/man/abstract.Rd |only propr-3.5.1/propr/man/differentialCheck.Rd |only propr-3.5.1/propr/man/prop2prob.Rd |only propr-3.5.1/propr/man/proportionality.Rd |only propr-3.5.1/propr/src/theta.cpp |only propr-3.5.1/propr/tests/testthat/test-prop2prob.R |only propr-3.5.1/propr/vignettes/c_indexing.Rmd |only propr-4.0.0/propr/DESCRIPTION | 20 - propr-4.0.0/propr/MD5 | 218 ++++++++--------- propr-4.0.0/propr/NAMESPACE | 15 - propr-4.0.0/propr/NEWS.md | 40 +++ propr-4.0.0/propr/R/0-params.R |only propr-4.0.0/propr/R/1-propr.R |only propr-4.0.0/propr/R/2-proprCall.R |only propr-4.0.0/propr/R/3-proprViz.R |only propr-4.0.0/propr/R/4-propd.R |only propr-4.0.0/propr/R/5-propdCall.R |only propr-4.0.0/propr/R/6-propdViz.R |only propr-4.0.0/propr/R/7-aldex2propr.R |only propr-4.0.0/propr/R/8-qtheta.R |only propr-4.0.0/propr/R/9-deprecated.R |only propr-4.0.0/propr/R/9-deprecated2.R |only propr-4.0.0/propr/R/9-global.R |only propr-4.0.0/propr/R/RcppExports.R | 24 - propr-4.0.0/propr/build/vignette.rds |binary propr-4.0.0/propr/data/pd.d.rda |binary propr-4.0.0/propr/data/pd.e.rda |binary propr-4.0.0/propr/inst/doc/a_introduction.R | 17 - propr-4.0.0/propr/inst/doc/a_introduction.Rmd | 32 +- propr-4.0.0/propr/inst/doc/a_introduction.html | 46 ++- propr-4.0.0/propr/inst/doc/b_visualization.R | 6 propr-4.0.0/propr/inst/doc/b_visualization.Rmd | 12 propr-4.0.0/propr/inst/doc/b_visualization.html | 32 +- propr-4.0.0/propr/inst/doc/d_advanced.R | 16 - propr-4.0.0/propr/inst/doc/d_advanced.Rmd | 20 - propr-4.0.0/propr/inst/doc/d_advanced.html | 112 ++++----- propr-4.0.0/propr/inst/doc/e_differential.R | 2 propr-4.0.0/propr/inst/doc/e_differential.Rmd | 12 propr-4.0.0/propr/inst/doc/e_differential.html | 23 - propr-4.0.0/propr/inst/doc/f_moderation.R | 2 propr-4.0.0/propr/inst/doc/f_moderation.Rmd | 10 propr-4.0.0/propr/inst/doc/f_moderation.html | 11 propr-4.0.0/propr/inst/doc/g_questions.R | 2 propr-4.0.0/propr/inst/doc/g_questions.Rmd | 12 propr-4.0.0/propr/inst/doc/g_questions.html | 16 - propr-4.0.0/propr/man/aldex.cor.Rd | 11 propr-4.0.0/propr/man/aldex.glm.Rd |only propr-4.0.0/propr/man/aldex2propr.Rd | 14 - propr-4.0.0/propr/man/all.Rd |only propr-4.0.0/propr/man/alphaThetaW_old.Rd | 2 propr-4.0.0/propr/man/alphaTheta_old.Rd | 2 propr-4.0.0/propr/man/calculateFDR.Rd | 4 propr-4.0.0/propr/man/calculateFDR_old.Rd | 4 propr-4.0.0/propr/man/calculateTheta.Rd | 7 propr-4.0.0/propr/man/calculateThetaW_old.Rd | 2 propr-4.0.0/propr/man/calculateTheta_old.Rd | 2 propr-4.0.0/propr/man/caneToad.counts.Rd | 2 propr-4.0.0/propr/man/caneToad.groups.Rd | 2 propr-4.0.0/propr/man/dendroCheck.Rd | 2 propr-4.0.0/propr/man/ggdend.Rd | 2 propr-4.0.0/propr/man/ivar2index.Rd | 5 propr-4.0.0/propr/man/lr2cor.Rd | 12 propr-4.0.0/propr/man/lr2glm.Rd |only propr-4.0.0/propr/man/mail.Rd | 2 propr-4.0.0/propr/man/marg.abs.Rd | 2 propr-4.0.0/propr/man/migraph.Rd | 2 propr-4.0.0/propr/man/multiplot.Rd | 2 propr-4.0.0/propr/man/packageCheck.Rd | 2 propr-4.0.0/propr/man/pals.Rd | 11 propr-4.0.0/propr/man/pd.d.Rd | 4 propr-4.0.0/propr/man/pd.e.Rd | 4 propr-4.0.0/propr/man/permuteTheta.Rd | 2 propr-4.0.0/propr/man/permuteTheta_false.Rd | 2 propr-4.0.0/propr/man/permuteTheta_naive.Rd | 2 propr-4.0.0/propr/man/permuteTheta_old.Rd | 2 propr-4.0.0/propr/man/permuteTheta_prime.Rd | 2 propr-4.0.0/propr/man/plotCheck.Rd | 6 propr-4.0.0/propr/man/progress.Rd | 2 propr-4.0.0/propr/man/promptCheck.Rd | 2 propr-4.0.0/propr/man/propd.Rd | 233 ++++-------------- propr-4.0.0/propr/man/propr.Rd | 166 ++++++++++--- propr-4.0.0/propr/man/proprALR.Rd | 2 propr-4.0.0/propr/man/proprCLR.Rd | 2 propr-4.0.0/propr/man/proprPairs.Rd | 2 propr-4.0.0/propr/man/proprPerb.Rd | 2 propr-4.0.0/propr/man/proprPhit.Rd | 2 propr-4.0.0/propr/man/proprSym.Rd | 2 propr-4.0.0/propr/man/proprTri.Rd | 2 propr-4.0.0/propr/man/proprVLR.Rd | 2 propr-4.0.0/propr/man/qtheta.Rd |only propr-4.0.0/propr/man/ratios.Rd | 2 propr-4.0.0/propr/man/top.counts.Rd | 2 propr-4.0.0/propr/man/top.lr.Rd | 2 propr-4.0.0/propr/man/updateCutoffs.Rd |only propr-4.0.0/propr/man/visualize.Rd | 247 ++++++++++++++++---- propr-4.0.0/propr/src/RcppExports.cpp | 76 +++--- propr-4.0.0/propr/src/backend.cpp | 18 + propr-4.0.0/propr/src/backend.h | 2 propr-4.0.0/propr/src/ctzRcpp.cpp |only propr-4.0.0/propr/src/deprecated.cpp | 1 propr-4.0.0/propr/src/lr2propr.cpp | 1 propr-4.0.0/propr/src/lrm.cpp |only propr-4.0.0/propr/src/lrv.cpp |only propr-4.0.0/propr/src/omega.cpp |only propr-4.0.0/propr/tests/testthat/test-Fstat.R | 24 - propr-4.0.0/propr/tests/testthat/test-aldex2propr.R | 206 ++++++++-------- propr-4.0.0/propr/tests/testthat/test-backend.R | 6 propr-4.0.0/propr/tests/testthat/test-linRcpp.R | 2 propr-4.0.0/propr/tests/testthat/test-lr2propr.R | 17 + propr-4.0.0/propr/tests/testthat/test-perb.R | 4 propr-4.0.0/propr/tests/testthat/test-propd.R | 24 - propr-4.0.0/propr/vignettes/a_introduction.Rmd | 32 +- propr-4.0.0/propr/vignettes/b_visualization.Rmd | 12 propr-4.0.0/propr/vignettes/d_advanced.Rmd | 20 - propr-4.0.0/propr/vignettes/e_differential.Rmd | 12 propr-4.0.0/propr/vignettes/f_moderation.Rmd | 10 propr-4.0.0/propr/vignettes/g_questions.Rmd | 12 131 files changed, 1109 insertions(+), 860 deletions(-)
Title: Color Science Methods and Data
Description: Methods and data for color science - color conversions by observer,
illuminant and gamma. Color matching functions and chromaticity diagrams.
Color indices, color differences and spectral data conversion/analysis.
Author: Jose Gama [aut],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorscience versions 1.0.4 dated 2016-10-01 and 1.0.5 dated 2018-07-25
DESCRIPTION | 20 ++++++++++---------- MD5 | 18 ++++++++++-------- NAMESPACE | 2 +- NEWS.md |only R/munsellinterpol.R |only man/RGB2YUV.Rd | 13 +++---------- man/XYZ2Lab.Rd | 2 +- man/XYZ2Luv.Rd | 2 +- man/YUV2RGB.Rd | 12 ++---------- man/Yuv2Luv.Rd | 12 ++---------- man/colorscience-internal.Rd | 2 ++ 11 files changed, 32 insertions(+), 51 deletions(-)
Title: Add Trendline of Basic Regression Models to Plot
Description: Plot, draw regression line and confidence interval, and show regression equation, R-square and P-value, as simple as possible, by using different models ("line2P", "line3P", "log2P", "exp2P", "exp3P", "power2P", "power3P") built in the 'trendline()' function.
Author: Weiping Mei [aut, cre, cph] (<https://orcid.org/0000-0001-6400-9862>),
Guangchuang Yu [aut] (<https://orcid.org/0000-0002-6485-8781>),
Jiangshan Lai [ctb],
Qiang Rao [ctb],
Yu Umezawa [ctb]
Maintainer: Weiping Mei <meiweipingg@163.com>
Diff between basicTrendline versions 1.2.0 dated 2018-07-13 and 2.0.2 dated 2018-07-25
DESCRIPTION | 26 +++- MD5 | 14 +- NAMESPACE | 2 NEWS | 11 ++ R/trendline.R | 255 +++++++++++++++++++++++------------------------ R/trendline_summary.R | 15 ++ man/trendline.Rd | 110 +++++++++++++------- man/trendline_summary.Rd | 2 8 files changed, 254 insertions(+), 181 deletions(-)
More information about basicTrendline at CRAN
Permanent link
Title: Regression of Network Responses
Description: Regress network responses (both directed and undirected) onto covariates of interest that may be actor-, relation-, or network-valued. In addition, compute principled variance estimates of the coefficients assuming that the errors are jointly exchangeable. Missing data is accommodated. Additionally implements building and inversion of covariance matrices under joint exchangeability, and generates random covariance matrices of this class. For more detail on methods, see Marrs, Fosdick, and McCormick (2017) <arXiv:1701.05530>.
Author: Frank W. Marrs [aut, cre],
Bailey K. Fosdick [aut],
Tyler H. McCormick [aut]
Maintainer: Frank W. Marrs <frank.marrs@colostate.edu>
Diff between netregR versions 0.3.1 dated 2018-05-06 and 1.0.0 dated 2018-07-25
netregR-0.3.1/netregR/inst/doc/netregR_vignette_single.R |only netregR-0.3.1/netregR/inst/doc/netregR_vignette_single.Rmd |only netregR-0.3.1/netregR/inst/doc/netregR_vignette_single.html |only netregR-0.3.1/netregR/vignettes/netregR_vignette_single.Rmd |only netregR-1.0.0/netregR/DESCRIPTION | 8 netregR-1.0.0/netregR/MD5 | 52 +++--- netregR-1.0.0/netregR/NAMESPACE | 1 netregR-1.0.0/netregR/R/data_description.R | 32 +++ netregR-1.0.0/netregR/R/helpers.R | 32 ++- netregR-1.0.0/netregR/R/helpers_time.R |only netregR-1.0.0/netregR/R/imports.R | 1 netregR-1.0.0/netregR/R/inputs_lmnet.R | 101 +++++++++--- netregR-1.0.0/netregR/R/lmnet.R | 39 +++- netregR-1.0.0/netregR/R/vnet.R | 9 - netregR-1.0.0/netregR/build/vignette.rds |binary netregR-1.0.0/netregR/data/interactions.rda |only netregR-1.0.0/netregR/data/wolf.rda |binary netregR-1.0.0/netregR/inst/doc/netregR_vignette.R |only netregR-1.0.0/netregR/inst/doc/netregR_vignette.Rmd |only netregR-1.0.0/netregR/inst/doc/netregR_vignette.html |only netregR-1.0.0/netregR/man/GEE.est.Rd | 5 netregR-1.0.0/netregR/man/GEE_est_time.Rd |only netregR-1.0.0/netregR/man/build_blocklist.Rd |only netregR-1.0.0/netregR/man/calculate_matrix_params.Rd |only netregR-1.0.0/netregR/man/calculate_parameter_inverse.Rd |only netregR-1.0.0/netregR/man/eigen_exch_time.Rd |only netregR-1.0.0/netregR/man/inputs_lmnet.Rd | 26 ++- netregR-1.0.0/netregR/man/interactions.Rd |only netregR-1.0.0/netregR/man/lmnet.Rd | 13 + netregR-1.0.0/netregR/man/model.matrix.lmnet.Rd | 2 netregR-1.0.0/netregR/man/node_gen_time.Rd |only netregR-1.0.0/netregR/man/node_preprocess.Rd | 4 netregR-1.0.0/netregR/man/node_preprocess_time.Rd |only netregR-1.0.0/netregR/man/param_est_single_ilist.Rd |only netregR-1.0.0/netregR/man/row_list_time.Rd |only netregR-1.0.0/netregR/man/vnet.Rd | 7 netregR-1.0.0/netregR/vignettes/netregR_vignette.Rmd |only 37 files changed, 248 insertions(+), 84 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (submitted). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>
Diff between MapGAM versions 1.1 dated 2018-04-09 and 1.2 dated 2018-07-25
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/MapGAM.version.R | 6 +++--- R/colormap.R | 8 ++++---- man/MapGAM-package.Rd | 4 ++-- man/colormap.Rd | 11 +++++++---- 7 files changed, 34 insertions(+), 23 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <http://canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.19.0 dated 2018-04-17 and 1.20.1 dated 2018-07-25
DESCRIPTION | 6 MD5 | 18 NEWS.md | 3 README.md | 2 build/vignette.rds |binary inst/doc/additional_examples.html | 4 inst/doc/getting_started.html | 4 inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 700 +++++++++++------- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 27 10 files changed, 499 insertions(+), 267 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-16 1.1.2
2018-07-10 1.1.1
2017-10-08 1.0