Title: Simulate Genetic Sequence Data for Pedigrees
Description: Methods to simulate genetic sequence data for pedigrees, with
functionality to simulate genetic heterogeneity among pedigrees.
Christina Nieuwoudt, Angela Brooks-Wilson,
and Jinko Graham (2019) <doi:10.1101/534552>.
Author: Christina Nieuwoudt [aut, cre],
Jinko Graham [aut]
Maintainer: Christina Nieuwoudt <cnieuwou@sfu.ca>
Diff between SimRVSequences versions 0.2.0 dated 2019-11-03 and 0.2.2 dated 2019-12-07
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/utility_Functions.R | 5 +++-- inst/doc/SimRVSequences.Rmd | 4 ++-- inst/doc/SimRVSequences.html | 4 ++-- vignettes/SimRVSequences.Rmd | 4 ++-- 7 files changed, 21 insertions(+), 18 deletions(-)
More information about SimRVSequences at CRAN
Permanent link
Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, SCORPIUS
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [ctb] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.4.1 dated 2019-08-07 and 1.0.5 dated 2019-12-07
SCORPIUS-1.0.4.1/SCORPIUS/R/distance_functions.R |only SCORPIUS-1.0.4.1/SCORPIUS/R/evaluation.R |only SCORPIUS-1.0.4.1/SCORPIUS/R/knn.R |only SCORPIUS-1.0.4.1/SCORPIUS/inst/NEWS |only SCORPIUS-1.0.4.1/SCORPIUS/man/deprecated.Rd |only SCORPIUS-1.0.4.1/SCORPIUS/man/distance.Rd |only SCORPIUS-1.0.4.1/SCORPIUS/man/knn.Rd |only SCORPIUS-1.0.4.1/SCORPIUS/man/knn_distances.Rd |only SCORPIUS-1.0.4.1/SCORPIUS/tests/testthat/test-knn.R |only SCORPIUS-1.0.5/SCORPIUS/DESCRIPTION | 16 +- SCORPIUS-1.0.5/SCORPIUS/MD5 | 70 ++++----- SCORPIUS-1.0.5/SCORPIUS/NAMESPACE | 22 +-- SCORPIUS-1.0.5/SCORPIUS/NEWS.md |only SCORPIUS-1.0.5/SCORPIUS/R/dimensionality_reduction.R | 13 - SCORPIUS-1.0.5/SCORPIUS/R/dynwrap_integration.R |only SCORPIUS-1.0.5/SCORPIUS/R/extract_modules.R | 2 SCORPIUS-1.0.5/SCORPIUS/R/gene_importances.R | 2 SCORPIUS-1.0.5/SCORPIUS/R/package.R | 2 SCORPIUS-1.0.5/SCORPIUS/R/trajectory_inference.R | 51 ++----- SCORPIUS-1.0.5/SCORPIUS/README.md | 72 ++-------- SCORPIUS-1.0.5/SCORPIUS/build/vignette.rds |binary SCORPIUS-1.0.5/SCORPIUS/inst/doc/ginhoux.R | 24 +-- SCORPIUS-1.0.5/SCORPIUS/inst/doc/ginhoux.html | 13 + SCORPIUS-1.0.5/SCORPIUS/inst/doc/simulated-data.R | 22 +-- SCORPIUS-1.0.5/SCORPIUS/inst/doc/simulated-data.html | 9 - SCORPIUS-1.0.5/SCORPIUS/inst/dynwrap |only SCORPIUS-1.0.5/SCORPIUS/man/draw_trajectory_heatmap.Rd | 14 + SCORPIUS-1.0.5/SCORPIUS/man/draw_trajectory_plot.Rd | 16 +- SCORPIUS-1.0.5/SCORPIUS/man/extract_modules.Rd | 9 - SCORPIUS-1.0.5/SCORPIUS/man/figures/README_infer_trajectory-1.png |binary SCORPIUS-1.0.5/SCORPIUS/man/figures/README_moduled_tafs-1.png |binary SCORPIUS-1.0.5/SCORPIUS/man/figures/README_reduce_dimensionality-1.png |binary SCORPIUS-1.0.5/SCORPIUS/man/figures/README_visualise_tafs-1.png |binary SCORPIUS-1.0.5/SCORPIUS/man/gene_importances.Rd | 12 + SCORPIUS-1.0.5/SCORPIUS/man/infer_initial_trajectory.Rd | 14 - SCORPIUS-1.0.5/SCORPIUS/man/infer_trajectory.Rd | 11 + SCORPIUS-1.0.5/SCORPIUS/man/reduce_dimensionality.Rd | 11 - SCORPIUS-1.0.5/SCORPIUS/man/reexports.Rd | 2 SCORPIUS-1.0.5/SCORPIUS/man/run_fun.Rd |only SCORPIUS-1.0.5/SCORPIUS/man/ti_scorpius.Rd |only SCORPIUS-1.0.5/SCORPIUS/tests/testthat/test-dimensionality_reduction.R | 34 ++-- SCORPIUS-1.0.5/SCORPIUS/tests/testthat/test-sparse.R | 2 42 files changed, 210 insertions(+), 233 deletions(-)
Title: Bivariate Zero-Inflated Negative Binomial Model Estimator
Description: Provides a maximum likelihood estimation of Bivariate Zero-Inflated Negative Binomial (BZINB) model or the nested model parameters. Also estimates the underlying correlation of the a pair of count data. See Cho, H., Liu, C., Preisser, J., and Wu, D. (In preparation) for details.
Author: Hunyong Cho, Chuwen Liu, Jinyoung Park, Di Wu
Maintainer: Hunyong Cho <hunycho@live.unc.edu>
Diff between bzinb versions 1.0.3 dated 2019-07-08 and 1.0.4 dated 2019-12-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/bnb.R | 4 ++-- R/bzinb.R | 10 +++++----- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Biological Image Analysis
Description: Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.
Author: Zachary Colburn
Maintainer: Zachary Colburn <zcolburn@gmail.com>
Diff between Bioi versions 0.2.9 dated 2018-01-22 and 0.2.10 dated 2019-12-07
DESCRIPTION | 8 - MD5 | 44 ++++--- NAMESPACE | 2 NEWS.md | 10 - R/RcppExports.R | 8 - R/euclidean_linker.R | 4 R/find_blobs.R | 8 - R/find_min_dists.R | 4 R/perform_grouping.R | 2 R/perform_partitioning.R | 5 README.md | 6 - build/vignette.rds |binary inst/doc/Bioi.R | 10 - inst/doc/Bioi.html | 200 ++++++++++++++++++++---------------- man/Bioi.Rd | 17 +-- man/dot-euclidean_linker_cpp.Rd |only man/dot-find_min_dists_cpp.Rd |only man/dot-perform_grouping.Rd |only man/dot-perform_partitioning.Rd |only man/euclidean_linker.Rd | 118 +++++++++++---------- man/find_blobs.Rd | 116 ++++++++++---------- man/find_min_dists.Rd | 92 ++++++++-------- man/identify_thresholded_objects.Rd | 80 +++++++------- src/euclidean_linker_cpp.cpp | 2 src/find_min_dists_cpp.cpp | 6 - 25 files changed, 392 insertions(+), 350 deletions(-)
Title: Weighting by Inverse Distance with Adaptive Least Squares
Description: Computationally easy modeling, interpolation, forecasting of massive temporal-spacial data.
Author: Dave Zes
Maintainer: Dave Zes <zesdave@gmail.com>
Diff between widals versions 0.5.4 dated 2014-03-03 and 0.6.1 dated 2019-12-07
widals-0.5.4/widals/.Rinstignore |only widals-0.5.4/widals/vignettes/jes.bst |only widals-0.6.1/widals/DESCRIPTION | 21 +- widals-0.6.1/widals/MD5 | 138 +++++++------- widals-0.6.1/widals/NAMESPACE | 6 widals-0.6.1/widals/R/H.Earth.solar.R | 30 +-- widals-0.6.1/widals/R/H.als.b.R | 71 +++---- widals-0.6.1/widals/R/Hals.fastcv.snow.R | 14 - widals-0.6.1/widals/R/Hals.ses.R | 2 widals-0.6.1/widals/R/Hals.snow.R | 8 widals-0.6.1/widals/R/Hst.sumup.R | 17 - widals-0.6.1/widals/R/MSS.snow.R | 32 ++- widals-0.6.1/widals/R/Z.clean.up.R | 6 widals-0.6.1/widals/R/applystnd.Hs.R | 10 - widals-0.6.1/widals/R/applystnd.Hst.ls.R | 11 - widals-0.6.1/widals/R/crispify.R | 54 ++--- widals-0.6.1/widals/R/distance.R | 26 +- widals-0.6.1/widals/R/dlog.norm.R | 2 widals-0.6.1/widals/R/fun.load.hals.a.R | 66 ++++-- widals-0.6.1/widals/R/fun.load.hals.fill.R | 67 +++++- widals-0.6.1/widals/R/fun.load.widals.a.R | 76 ++++++- widals-0.6.1/widals/R/fun.load.widals.fill.R | 83 ++++++-- widals-0.6.1/widals/R/load.Hst.ls.2Zs.R | 24 +- widals-0.6.1/widals/R/load.Hst.ls.Z.R | 8 widals-0.6.1/widals/R/stnd.Hs.R | 30 +-- widals-0.6.1/widals/R/stnd.Hst.ls.R | 50 ++--- widals-0.6.1/widals/R/stnd.Ht.R | 10 - widals-0.6.1/widals/R/subsetsites.Hst.ls.R | 8 widals-0.6.1/widals/R/unif.mh.R | 11 - widals-0.6.1/widals/R/unload.Hst.ls.R | 14 - widals-0.6.1/widals/R/widals.predict.R | 92 ++++----- widals-0.6.1/widals/R/widals.snow.R | 156 +++++++--------- widals-0.6.1/widals/build/vignette.rds |binary widals-0.6.1/widals/inst/doc/funwithfunload.R | 38 ++- widals-0.6.1/widals/inst/doc/funwithfunload.Snw | 22 +- widals-0.6.1/widals/inst/doc/funwithfunload.pdf |binary widals-0.6.1/widals/inst/doc/widals.R | 4 widals-0.6.1/widals/inst/doc/widals.Snw | 12 - widals-0.6.1/widals/inst/doc/widals.pdf |binary widals-0.6.1/widals/man/H.Earth.solar.Rd | 4 widals-0.6.1/widals/man/H.als.b.Rd | 95 --------- widals-0.6.1/widals/man/Hals.fastcv.snow.Rd | 43 ---- widals-0.6.1/widals/man/Hals.ses.Rd | 5 widals-0.6.1/widals/man/Hals.snow.Rd | 16 - widals-0.6.1/widals/man/Hst.sumup.Rd | 4 widals-0.6.1/widals/man/MSS.snow.Rd | 93 +-------- widals-0.6.1/widals/man/O3.Rd | 2 widals-0.6.1/widals/man/Z.clean.up.Rd | 4 widals-0.6.1/widals/man/applystnd.Hs.Rd | 4 widals-0.6.1/widals/man/applystnd.Hst.ls.Rd | 5 widals-0.6.1/widals/man/create.rm.ndx.ls.Rd | 4 widals-0.6.1/widals/man/crispify.Rd | 52 ----- widals-0.6.1/widals/man/distance.Rd | 4 widals-0.6.1/widals/man/dlog.norm.Rd | 4 widals-0.6.1/widals/man/fun.load.Rd | 55 +++-- widals-0.6.1/widals/man/fuse.Hst.ls.Rd | 4 widals-0.6.1/widals/man/load.Hst.ls.2Zs.Rd | 23 -- widals-0.6.1/widals/man/load.Hst.ls.Z.Rd | 20 -- widals-0.6.1/widals/man/rm.cols.Hst.ls.Rd | 4 widals-0.6.1/widals/man/stnd.Hs.Rd | 4 widals-0.6.1/widals/man/stnd.Hst.ls.Rd | 4 widals-0.6.1/widals/man/stnd.Ht.Rd | 4 widals-0.6.1/widals/man/subsetsites.Hst.ls.Rd | 4 widals-0.6.1/widals/man/unif.mh.Rd | 4 widals-0.6.1/widals/man/unload.Hst.ls.Rd | 4 widals-0.6.1/widals/man/widals-package.Rd | 4 widals-0.6.1/widals/man/widals.predict.Rd | 41 ---- widals-0.6.1/widals/man/widals.snow.Rd | 84 -------- widals-0.6.1/widals/src/registerDynamicSymbol.c |only widals-0.6.1/widals/src/widals.c | 222 +++++++++++++++++++++-- widals-0.6.1/widals/vignettes/funwithfunload.Snw | 22 +- widals-0.6.1/widals/vignettes/widals.Snw | 12 - 72 files changed, 1055 insertions(+), 1018 deletions(-)
Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more
accessible to students and professionals from Epidemiology and
Public Health related disciplines. Includes a function to report
coefficients and confidence intervals from models using robust
standard errors (when available), functions that expand 'ggplot2'
plots and functions relevant for introductory papers in Epidemiology
or Public Health. Please note that use of the
provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre],
Frank Harell [ctb],
John Fox [ctb],
R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>
Diff between pubh versions 0.4.3 dated 2018-11-02 and 1.1.2 dated 2019-12-07
pubh-0.4.3/pubh/man/coef_plot.Rd |only pubh-0.4.3/pubh/man/panel.errbars.Rd |only pubh-0.4.3/pubh/man/panel.errbars1.Rd |only pubh-0.4.3/pubh/man/rvf_plot.Rd |only pubh-0.4.3/pubh/man/xymultiple.Rd |only pubh-1.1.2/pubh/DESCRIPTION | 37 pubh-1.1.2/pubh/MD5 | 165 pubh-1.1.2/pubh/NAMESPACE | 25 pubh-1.1.2/pubh/R/data.R | 135 pubh-1.1.2/pubh/R/descriptive_functions.R | 219 pubh-1.1.2/pubh/R/display_functions.R | 65 pubh-1.1.2/pubh/R/epi_functions.R | 166 pubh-1.1.2/pubh/R/misc_functions.R | 34 pubh-1.1.2/pubh/R/plot_functions.R | 899 ++- pubh-1.1.2/pubh/build/vignette.rds |binary pubh-1.1.2/pubh/data/Bernard.rda |binary pubh-1.1.2/pubh/data/Brenner.rda |binary pubh-1.1.2/pubh/data/Fentress.rda |binary pubh-1.1.2/pubh/data/Hodgkin.rda |binary pubh-1.1.2/pubh/data/Kirkwood.rda |binary pubh-1.1.2/pubh/data/Macmahon.rda |binary pubh-1.1.2/pubh/data/Oncho.rda |binary pubh-1.1.2/pubh/data/Roberts.rda |binary pubh-1.1.2/pubh/data/Rothman.rda |binary pubh-1.1.2/pubh/data/Sandler.rda |binary pubh-1.1.2/pubh/data/Tuzson.rda |binary pubh-1.1.2/pubh/data/Vanderpump.rda |binary pubh-1.1.2/pubh/inst/doc/introduction.R | 293 - pubh-1.1.2/pubh/inst/doc/introduction.Rmd | 271 - pubh-1.1.2/pubh/inst/doc/introduction.html | 2417 +++++++--- pubh-1.1.2/pubh/inst/doc/regression.R | 552 +- pubh-1.1.2/pubh/inst/doc/regression.Rmd | 531 +- pubh-1.1.2/pubh/inst/doc/regression.html | 2156 ++++++-- pubh-1.1.2/pubh/inst/rmarkdown/templates/report/skeleton/skeleton.Rmd | 34 pubh-1.1.2/pubh/man/Bernard.Rd | 7 pubh-1.1.2/pubh/man/Brenner.Rd | 5 pubh-1.1.2/pubh/man/Fentress.Rd | 8 pubh-1.1.2/pubh/man/Hodgkin.Rd | 22 pubh-1.1.2/pubh/man/Kirkwood.Rd | 10 pubh-1.1.2/pubh/man/Macmahon.Rd | 10 pubh-1.1.2/pubh/man/Oncho.Rd | 7 pubh-1.1.2/pubh/man/Roberts.Rd | 13 pubh-1.1.2/pubh/man/Rothman.Rd | 16 pubh-1.1.2/pubh/man/Sandler.Rd | 10 pubh-1.1.2/pubh/man/Sharples.Rd | 6 pubh-1.1.2/pubh/man/Thall.Rd | 2 pubh-1.1.2/pubh/man/Tuzson.Rd | 8 pubh-1.1.2/pubh/man/Vanderpump.Rd | 12 pubh-1.1.2/pubh/man/axis_labs.Rd |only pubh-1.1.2/pubh/man/bar_error.Rd | 68 pubh-1.1.2/pubh/man/bland_altman.Rd | 47 pubh-1.1.2/pubh/man/box_plot.Rd | 54 pubh-1.1.2/pubh/man/bst.Rd | 7 pubh-1.1.2/pubh/man/coef_det.Rd | 8 pubh-1.1.2/pubh/man/contingency.Rd | 35 pubh-1.1.2/pubh/man/contingency2.Rd | 14 pubh-1.1.2/pubh/man/cross_tab.Rd |only pubh-1.1.2/pubh/man/diag_test.Rd | 16 pubh-1.1.2/pubh/man/diag_test2.Rd | 6 pubh-1.1.2/pubh/man/estat.Rd | 32 pubh-1.1.2/pubh/man/freq_cont.Rd | 3 pubh-1.1.2/pubh/man/gen_bst_df.Rd | 42 pubh-1.1.2/pubh/man/geo_mean.Rd | 3 pubh-1.1.2/pubh/man/gf_star.Rd |only pubh-1.1.2/pubh/man/glm_coef.Rd | 54 pubh-1.1.2/pubh/man/harm_mean.Rd | 3 pubh-1.1.2/pubh/man/hist_norm.Rd | 50 pubh-1.1.2/pubh/man/inv_logit.Rd | 3 pubh-1.1.2/pubh/man/jack_knife.Rd | 3 pubh-1.1.2/pubh/man/knife_mean.Rd | 3 pubh-1.1.2/pubh/man/leverage.Rd | 3 pubh-1.1.2/pubh/man/mhor.Rd | 32 pubh-1.1.2/pubh/man/multiple.Rd |only pubh-1.1.2/pubh/man/odds_trend.Rd | 27 pubh-1.1.2/pubh/man/predict_inv.Rd | 16 pubh-1.1.2/pubh/man/prop_or.Rd | 3 pubh-1.1.2/pubh/man/pseudo_r2.Rd | 4 pubh-1.1.2/pubh/man/qq_plot.Rd | 44 pubh-1.1.2/pubh/man/rank_influence.Rd | 6 pubh-1.1.2/pubh/man/rank_leverage.Rd | 3 pubh-1.1.2/pubh/man/reference_range.Rd | 3 pubh-1.1.2/pubh/man/rel_dis.Rd | 3 pubh-1.1.2/pubh/man/round_pval.Rd | 3 pubh-1.1.2/pubh/man/ss_jk.Rd | 3 pubh-1.1.2/pubh/man/stats_quotes.Rd | 3 pubh-1.1.2/pubh/man/strip_error.Rd | 83 pubh-1.1.2/pubh/vignettes/introduction.Rmd | 271 - pubh-1.1.2/pubh/vignettes/regression.Rmd | 531 +- 88 files changed, 6367 insertions(+), 3257 deletions(-)
Title: Post-Selection Inference for Nonlinear Variable Selection
Description: Different post-selection inference strategies for kernel
selection, as described in "kernelPSI: a Post-Selection Inference Framework
for Nonlinear Variable Selection", Slim et al., Proceedings of Machine
Learning Research, 2019, <http://proceedings.mlr.press/v97/slim19a/slim19a.pdf>. The strategies rest upon quadratic kernel
association scores to measure the association between a given kernel and an
outcome of interest. The inference step tests for the joint effect of the
selected kernels on the outcome. A fast constrained sampling algorithm is
proposed to derive empirical p-values for the test statistics.
Author: Lotfi Slim [aut, cre],
Clément Chatelain [ctb],
Chloé-Agathe Azencott [ctb],
Jean-Philippe Vert [ctb]
Maintainer: Lotfi Slim <lotfi.slim@mines-paristech.fr>
Diff between kernelPSI versions 1.1.0 dated 2019-09-08 and 1.1.1 dated 2019-12-07
DESCRIPTION | 10 +- MD5 | 24 +++--- NEWS.md | 3 R/statistic.R | 2 build/vignette.rds |binary inst/doc/kernelPSI.R | 16 ++-- inst/doc/kernelPSI.html | 168 ++++++++++++++++++++++++------------------------ man/anovaLR.Rd | 3 man/kernelPSI.Rd | 13 +++ man/maxLR.Rd | 3 man/pcaLR.Rd | 3 man/ridgeLR.Rd | 6 - man/sampleH.Rd | 11 ++- 13 files changed, 142 insertions(+), 120 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories
(also known as a Sankey diagram), flow charts by extending the grid package,
a method for variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.9.0 dated 2019-07-07 and 1.9.1 dated 2019-12-07
DESCRIPTION | 10 MD5 | 96 ++++---- R/bezierArrowSmpl.R | 4 R/bezier_private_functions.R | 12 - R/descriptionStats.R | 2 R/fastDoCall.R | 6 R/getDescriptionStatsBy.R | 4 R/mergeDesc.R | 2 build/vignette.rds |binary inst/doc/Descriptives.R | 18 - inst/doc/Descriptives.html | 307 +++++++++++++-------------- inst/doc/Grid-based_flowcharts.R | 20 - inst/doc/Grid-based_flowcharts.html | 323 ++++++++++++++--------------- inst/doc/Transition-class.R | 14 - inst/doc/Transition-class.html | 161 +++++++------- inst/doc/transitionPlot.R | 24 +- inst/doc/transitionPlot.html | 185 ++++++++-------- man/Gmisc-deprecated.Rd | 1 man/assert.Rd | 8 man/bezierArrowGradient.Rd | 24 +- man/bezierArrowSmpl.Rd | 18 + man/box.Rd | 19 + man/boxPropGrob.Rd | 36 ++- man/calculateLinesAndArrow.Rd | 11 man/connect.Rd | 19 + man/descGetMissing.Rd | 11 man/describeFactors.Rd | 27 +- man/describeMean.Rd | 27 +- man/describeMedian.Rd | 27 +- man/describeProp.Rd | 27 +- man/docx_document.Rd | 16 + man/figCapNo.Rd | 12 - man/figCapNoLast.Rd | 5 man/figCapNoNext.Rd | 5 man/getDescriptionStatsBy.Rd | 48 +++- man/getPval.Rd | 10 man/getSvdMostInfluential.Rd | 10 man/has.Rd | 3 man/prGetStatistics.Rd | 20 + man/prGridPlotTitle.Rd | 9 man/prTcPlotArrows.Rd | 19 + man/prTpGetBoxPositions.Rd | 11 man/prTpPlotArrows.Rd | 22 + man/prTpPlotBoxes.Rd | 37 ++- man/retrieve.Rd | 3 man/transitionPlot.Rd | 45 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-getDescriptionStats.R | 26 +- tests/testthat/test-insertRowAndKeepAttr.R | 2 49 files changed, 995 insertions(+), 751 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies, e.g. conservative or liberal.
The objective of this package is to make it as simple as possible to
identify global objects for the purpose of exporting them in distributed
compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.12.4 dated 2018-10-11 and 0.12.5 dated 2019-12-07
DESCRIPTION | 8 - MD5 | 34 +++--- NEWS | 8 + R/findGlobals.R | 24 +++- man/cleanup.Globals.Rd | 3 man/globalsOf.Rd | 28 +++-- man/walkAST.Rd | 10 + tests/Globals.R | 4 tests/conservative.R | 37 +++--- tests/dotdotdot.R | 63 +++++------ tests/findGlobals.R |only tests/formulas.R | 12 -- tests/globalsByName.R |only tests/globalsOf.R | 273 +++++-------------------------------------------- tests/incl |only tests/liberal.R | 36 +++--- tests/utils.R | 18 --- tests/walkAST.R | 46 ++++---- 18 files changed, 215 insertions(+), 389 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT, CRI, and SSI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 1.0-1 dated 2019-06-24 and 1.1-1 dated 2019-12-07
colorSpec-1.0-1/colorSpec/vignettes/framed.sty |only colorSpec-1.1-1/colorSpec/DESCRIPTION | 8 +-- colorSpec-1.1-1/colorSpec/MD5 | 35 ++++++-------- colorSpec-1.1-1/colorSpec/NEWS.md | 3 + colorSpec-1.1-1/colorSpec/build/vignette.rds |binary colorSpec-1.1-1/colorSpec/inst/doc/blueflame.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/colorSpec-guide.R | 36 +++++++------- colorSpec-1.1-1/colorSpec/inst/doc/colorSpec-guide.html | 35 +++++++------- colorSpec-1.1-1/colorSpec/inst/doc/convexity.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/emulation.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/gallery.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/inversion.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/lens-aging.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/optimals.pdf |binary colorSpec-1.1-1/colorSpec/inst/doc/phenolred.R | 14 ++--- colorSpec-1.1-1/colorSpec/inst/doc/phenolred.html | 39 ++++++++-------- colorSpec-1.1-1/colorSpec/inst/doc/photoncounting.R | 10 ++-- colorSpec-1.1-1/colorSpec/inst/doc/photoncounting.html | 37 ++++++++------- colorSpec-1.1-1/colorSpec/tests/test-organization.R | 33 +++++++------ 19 files changed, 133 insertions(+), 117 deletions(-)
Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference,
including distance correlation, one-sample, two-sample, and multi-sample tests for
comparing multivariate distributions, are implemented. Measuring and testing
multivariate independence based on distance correlation, partial distance correlation,
multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy
distance, testing for multivariate normality, distance components (disco) for non-parametric
analysis of structured data, and other energy statistics/methods are implemented.
Author: Maria Rizzo [aut, cre],
Gabor Szekely [aut]
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>
Diff between energy versions 1.7-6 dated 2019-07-06 and 1.7-7 dated 2019-12-07
energy-1.7-6/energy/R/dcovU.R |only energy-1.7-6/energy/man/dcor.ttest.Rd |only energy-1.7-7/energy/DESCRIPTION | 8 energy-1.7-7/energy/MD5 | 39 +- energy-1.7-7/energy/NAMESPACE | 108 +++---- energy-1.7-7/energy/NEWS.md | 314 +++++++++++---------- energy-1.7-7/energy/R/Ecluster.R | 36 +- energy-1.7-7/energy/R/Eindep.R | 17 - energy-1.7-7/energy/R/Emvnorm.R | 252 ++++++++--------- energy-1.7-7/energy/R/centering.R | 62 ++-- energy-1.7-7/energy/R/dcorT.R | 163 +++++------ energy-1.7-7/energy/R/dcov.R | 387 +++++++++++++-------------- energy-1.7-7/energy/R/dcovu.R |only energy-1.7-7/energy/R/disco.R | 376 +++++++++++++------------- energy-1.7-7/energy/R/edist.R | 152 +++++----- energy-1.7-7/energy/R/energy-defunct.R |only energy-1.7-7/energy/R/energy-deprecated.R |only energy-1.7-7/energy/R/kgroups.R | 138 ++++----- energy-1.7-7/energy/R/pdcor.R | 48 +-- energy-1.7-7/energy/R/pdcov-test.R | 184 ++++++------ energy-1.7-7/energy/man/dcorT.Rd |only energy-1.7-7/energy/man/edist.Rd | 242 +++++++--------- energy-1.7-7/energy/man/energy-deprecated.Rd |only energy-1.7-7/energy/man/mvnorm-etest.Rd | 184 ++++++------ 24 files changed, 1355 insertions(+), 1355 deletions(-)
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
R package for matching 'HTTP' requests by various rules ('HTTP' method,
'URL', query parameters, headers, body, etc.), and then caching
real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
matching any previous requests in the same 'cassette' use a cached
'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between vcr versions 0.3.0 dated 2019-08-20 and 0.4.0 dated 2019-12-07
vcr-0.3.0/vcr/man/NullList.Rd |only vcr-0.4.0/vcr/DESCRIPTION | 16 vcr-0.4.0/vcr/MD5 | 171 +- vcr-0.4.0/vcr/NEWS.md | 25 vcr-0.4.0/vcr/R/cassette_class.R | 290 +++- vcr-0.4.0/vcr/R/configuration.R | 43 vcr-0.4.0/vcr/R/error_suggestions.R | 18 vcr-0.4.0/vcr/R/errors.R | 55 vcr-0.4.0/vcr/R/hooks.R | 43 vcr-0.4.0/vcr/R/http_interaction.R | 22 vcr-0.4.0/vcr/R/http_interaction_list.R | 83 - vcr-0.4.0/vcr/R/insert_cassette.R | 10 vcr-0.4.0/vcr/R/lightswitch.R | 73 + vcr-0.4.0/vcr/R/match_helpers.R | 8 vcr-0.4.0/vcr/R/onLoad.R | 2 vcr-0.4.0/vcr/R/persisters-file.R | 52 vcr-0.4.0/vcr/R/persisters.R | 56 vcr-0.4.0/vcr/R/request_class.R | 212 ++- vcr-0.4.0/vcr/R/request_handler-crul.R | 31 vcr-0.4.0/vcr/R/request_handler-httr.R | 38 vcr-0.4.0/vcr/R/request_handler.R | 43 vcr-0.4.0/vcr/R/request_ignorer.R | 66 - vcr-0.4.0/vcr/R/request_matcher_registry.R | 39 vcr-0.4.0/vcr/R/request_response.R | 23 vcr-0.4.0/vcr/R/response_class.R | 112 + vcr-0.4.0/vcr/R/serialize_to_crul.R | 6 vcr-0.4.0/vcr/R/serialize_to_httr.R | 17 vcr-0.4.0/vcr/R/serializers-yaml.R | 67 - vcr-0.4.0/vcr/R/serializers.R | 15 vcr-0.4.0/vcr/R/use_cassette.R | 32 vcr-0.4.0/vcr/R/vcr-package.R | 2 vcr-0.4.0/vcr/R/vcr_setup.R | 2 vcr-0.4.0/vcr/R/write.R | 33 vcr-0.4.0/vcr/R/zzz.R | 13 vcr-0.4.0/vcr/README.md | 17 vcr-0.4.0/vcr/inst/doc/configuration.R | 44 vcr-0.4.0/vcr/inst/doc/configuration.Rmd | 28 vcr-0.4.0/vcr/inst/doc/configuration.html | 46 vcr-0.4.0/vcr/inst/doc/request_matching.R | 16 vcr-0.4.0/vcr/inst/doc/request_matching.Rmd | 2 vcr-0.4.0/vcr/inst/doc/request_matching.html | 23 vcr-0.4.0/vcr/inst/doc/vcr.R | 16 vcr-0.4.0/vcr/inst/doc/vcr.Rmd | 2 vcr-0.4.0/vcr/inst/doc/vcr.html | 23 vcr-0.4.0/vcr/man/Cassette.Rd | 599 ++++++++-- vcr-0.4.0/vcr/man/FileSystem.Rd | 155 ++ vcr-0.4.0/vcr/man/HTTPInteraction.Rd | 102 + vcr-0.4.0/vcr/man/HTTPInteractionList.Rd | 198 ++- vcr-0.4.0/vcr/man/Hooks.Rd | 123 +- vcr-0.4.0/vcr/man/Persisters.Rd | 64 - vcr-0.4.0/vcr/man/Request.Rd | 144 +- vcr-0.4.0/vcr/man/RequestHandler.Rd | 86 + vcr-0.4.0/vcr/man/RequestHandlerCrul.Rd | 88 - vcr-0.4.0/vcr/man/RequestHandlerHttr.Rd | 107 - vcr-0.4.0/vcr/man/RequestIgnorer.Rd | 167 ++ vcr-0.4.0/vcr/man/RequestMatcherRegistry.Rd | 133 +- vcr-0.4.0/vcr/man/Serializers.Rd | 62 - vcr-0.4.0/vcr/man/UnhandledHTTPRequestError.Rd | 330 +++++ vcr-0.4.0/vcr/man/VcrResponse.Rd | 276 +++- vcr-0.4.0/vcr/man/YAML.Rd | 138 +- vcr-0.4.0/vcr/man/eject_cassette.Rd | 7 vcr-0.4.0/vcr/man/insert_cassette.Rd | 23 vcr-0.4.0/vcr/man/lightswitch.Rd | 34 vcr-0.4.0/vcr/man/request_response.Rd | 13 vcr-0.4.0/vcr/man/testing.Rd | 6 vcr-0.4.0/vcr/man/use_cassette.Rd | 19 vcr-0.4.0/vcr/man/vcr.Rd | 2 vcr-0.4.0/vcr/man/vcr_configure.Rd | 48 vcr-0.4.0/vcr/tests/testthat/crul_resp1.rda |only vcr-0.4.0/vcr/tests/testthat/crul_resp2.rda |only vcr-0.4.0/vcr/tests/testthat/google_response.rda |only vcr-0.4.0/vcr/tests/testthat/helper-vcr.R | 9 vcr-0.4.0/vcr/tests/testthat/httr_resp1.rda |only vcr-0.4.0/vcr/tests/testthat/httr_resp2.rda |only vcr-0.4.0/vcr/tests/testthat/png_eg.rda |only vcr-0.4.0/vcr/tests/testthat/test-Cassette.R | 40 vcr-0.4.0/vcr/tests/testthat/test-Request.R |only vcr-0.4.0/vcr/tests/testthat/test-RequestIgnorer.R |only vcr-0.4.0/vcr/tests/testthat/test-ause_cassette.R | 13 vcr-0.4.0/vcr/tests/testthat/test-ause_cassette_write_to_disk.R |only vcr-0.4.0/vcr/tests/testthat/test-ause_cassette_write_to_disk_binary_files.R |only vcr-0.4.0/vcr/tests/testthat/test-cassettes.R | 3 vcr-0.4.0/vcr/tests/testthat/test-httr.R | 95 + vcr-0.4.0/vcr/tests/testthat/test-insert_cassette.R | 12 vcr-0.4.0/vcr/tests/testthat/test-lightswitch.R | 102 + vcr-0.4.0/vcr/tests/testthat/test-logger.R | 2 vcr-0.4.0/vcr/tests/testthat/test-request_summary.R | 27 vcr-0.4.0/vcr/tests/testthat/test-response_summary.R |only vcr-0.4.0/vcr/tests/testthat/test-serializers_yaml.R |only vcr-0.4.0/vcr/tests/testthat/test-utils.R |only vcr-0.4.0/vcr/tests/testthat/test-write_utils.R |only vcr-0.4.0/vcr/vignettes/configuration.Rmd | 28 vcr-0.4.0/vcr/vignettes/request_matching.Rmd | 2 vcr-0.4.0/vcr/vignettes/vcr.Rmd | 2 94 files changed, 3847 insertions(+), 1347 deletions(-)
Title: 'Rcpp' Interface to 'PostgreSQL'
Description: Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>,
an open-source relational database.
Author: Hadley Wickham [aut],
Jeroen Ooms [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph],
R Consortium [fnd],
Tomoaki Nishiyama [ctb] (Code for encoding vectors into strings derived
from RPostgreSQL)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RPostgres versions 1.1.2 dated 2019-12-03 and 1.1.3 dated 2019-12-07
DESCRIPTION | 8 +-- MD5 | 9 ++-- NEWS.md | 10 ++++ configure | 113 ---------------------------------------------------- src/DbDataFrame.cpp | 2 src/configure.bash |only 6 files changed, 22 insertions(+), 120 deletions(-)
Title: Fast Kernel Sums
Description: Implements the method of Hofmeyr, D.P. (2019) <10.1109/TPAMI.2019.2930501> for fast evaluation of univariate kernel smoothers based on recursive computations.
Applications to the basic problems of density and regression function estimation are provided, as well as some projection pursuit methods
for which the objective is based on non-parametric functionals of the projected density, or conditional density of a response given projected
covariates.
Author: David P. Hofmeyr
Maintainer: David P. Hofmeyr <dhofmeyr@sun.ac.za>
Diff between FKSUM versions 0.1.0 dated 2019-12-02 and 0.1.1 dated 2019-12-07
DESCRIPTION | 6 MD5 | 22 - R/RcppExports.R | 2 R/fk_ICA.R | 191 +++++++++--- R/fk_density.R | 66 ++-- R/fk_mdh.R | 113 ++++++- R/fk_regression.R | 201 +++++++++---- R/fk_sum.R | 18 + build/partial.rdb |binary man/FKSUM-package.Rd | 2 src/FKSUM_CPP_FUNCTIONS.cpp | 391 +++++++++++++++---------- src/mdh.cpp | 670 +++++++++++++++++++++++++------------------- 12 files changed, 1088 insertions(+), 594 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 2.9.2 dated 2019-12-05 and 2.9.4 dated 2019-12-07
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 8 +++++++- 3 files changed, 14 insertions(+), 8 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 0.2.3.1 dated 2019-08-21 and 0.2.4.0 dated 2019-12-07
DESCRIPTION | 8 MD5 | 50 ++-- R/coo.R | 19 - R/embedding.R | 9 R/knn.R | 224 ++++++++++----------- R/umap.R | 298 ++++++++++++++--------------- R/umap_checks.R | 9 R/umap_learn.R | 75 +++---- R/umap_naive.R | 12 - R/umap_print.R | 74 +++---- R/umap_small.R | 20 - R/umap_universal.R | 1 inst/doc/umap.R | 2 inst/doc/umap.Rmd | 2 inst/doc/umap.html | 348 +++++++++++++++++++++++++++------- inst/doc/umap_learn.html | 316 +++++++++++++++++++++++++----- man/column.seeds.Rd | 1 man/find.ab.params.Rd | 9 man/knn.from.data.Rd | 9 man/naive.simplicial.set.embedding.Rd | 3 man/smooth.knn.dist.Rd | 12 - tests/testthat/test_checks.R | 6 tests/testthat/test_coo.R | 4 tests/testthat/test_naive.R | 15 + tests/testthat/test_python.R | 4 vignettes/umap.Rmd | 2 26 files changed, 967 insertions(+), 565 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David W. Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.8.9 dated 2019-08-25 and 3.9.0 dated 2019-12-07
DESCRIPTION | 8 +- MD5 | 94 ++++++++++++++++---------------- NEWS | 48 ++++++++++++++++ R/ANOVA.R | 6 +- R/BarChart.R | 88 ++++++++++++++++-------------- R/Density.R | 6 +- R/Help.R | 144 +++++++++++++++++++++++++------------------------- R/Histogram.R | 8 +- R/LineChart.R | 6 +- R/Logit.R | 10 +-- R/PieChart.R | 6 +- R/Plot.R | 72 ++++++++++++------------- R/Read.R | 4 - R/Regression.R | 6 +- R/Sort.R | 7 +- R/Subset.R | 18 +++--- R/bc.zmain.R | 19 +++--- R/corCFA.R | 2 R/corEFA.R | 2 R/corProp.R | 2 R/corReflect.R | 2 R/corReorder.R | 2 R/corScree.R | 2 R/dn.zmain.R | 3 - R/logit.z4Pred.R | 21 ++++++- R/param.zold.R | 13 ++++ R/plt.zMD.R | 6 +- R/plt.zadd.R | 20 +++--- R/plt.zbad.R | 6 +- R/plt.zmain.R | 8 +- R/plt.zmat.R | 4 - R/rec.zmain.R | 8 +- R/reg.z3txtResidual.R | 3 - R/ttest.R | 8 +- R/zzz.R | 2 man/ANOVA.Rd | 8 +- man/BarChart.Rd | 44 +++++---------- man/Density.Rd | 6 +- man/Histogram.Rd | 14 ++-- man/LineChart.Rd | 6 +- man/Logit.Rd | 33 +++++++---- man/Merge.Rd | 2 man/PieChart.Rd | 8 +- man/Plot.Rd | 44 ++++++--------- man/Read.Rd | 4 - man/Regression.Rd | 25 ++++---- man/Subset.Rd | 12 ++-- man/ttest.Rd | 6 +- 48 files changed, 477 insertions(+), 399 deletions(-)
Title: Simple yet Flexible Letters via the 'KOMA-Script LaTeX Bundle'
Description: An R Markdown template for writing beautiful yet versatile letters,
using the 'KOMA-Script' letter class 'scrlttr2' and an adaptation of the
'pandoc-letter' template. 'scrlttr2' provides layouts for many different
window envelope types and the possibility to define your own.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>),
Dirk Eddelbuettel [aut],
Aaron Wolen [aut]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between komaletter versions 0.3.1 dated 2019-08-23 and 0.3.2 dated 2019-12-07
DESCRIPTION | 8 MD5 | 16 NEWS.md | 3 inst/doc/intro.html | 207 +++++++++ inst/doc/letter_example1.pdf |binary inst/doc/letter_example2.pdf |binary inst/doc/letter_example3.pdf |binary inst/doc/parameterized_letter.html | 422 ++++++++++++++------ inst/rmarkdown/templates/pdf/resources/template.tex | 21 9 files changed, 538 insertions(+), 139 deletions(-)
Title: Dimension Reduction for Outlier Detection
Description: A dimension reduction technique for outlier detection. DOBIN: a Distance
based Outlier BasIs using Neighbours, constructs a set of basis vectors for outlier
detection. This is not an outlier detection method; rather it is a pre-processing
method for outlier detection. It brings outliers to the fore-front using fewer basis
vectors (Kandanaarachchi, Hyndman 2019) <doi:10.13140/RG.2.2.15437.18403>.
Author: Sevvandi Kandanaarachchi [aut, cre]
(<https://orcid.org/0000-0002-0337-0395>)
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between dobin versions 1.0.0 dated 2019-09-20 and 1.0.1 dated 2019-12-07
DESCRIPTION | 9 +- MD5 | 11 +- inst/doc/dobin.R | 179 ++++++++++++++++++++++++++++++++++++++++++-- inst/doc/dobin.Rmd | 206 ++++++++++++++++++++++++++++++++++++++++++++++++--- inst/doc/dobin.html | 56 +++++++++++-- man/figures/logo.png |only vignettes/dobin.Rmd | 206 ++++++++++++++++++++++++++++++++++++++++++++++++--- 7 files changed, 614 insertions(+), 53 deletions(-)
Title: Computing General Equilibrium
Description: Developing general equilibrium models, computing general equilibrium and simulating economic dynamics with structural dynamic models in LI (2019, ISBN: 9787521804225) "General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press".
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between CGE versions 0.1.9 dated 2019-06-16 and 0.2.5 dated 2019-12-07
CGE-0.1.9/CGE/man/Example6.13.Rd |only CGE-0.2.5/CGE/DESCRIPTION | 6 - CGE-0.2.5/CGE/MD5 | 39 ++++----- CGE-0.2.5/CGE/NAMESPACE | 1 CGE-0.2.5/CGE/R/F_Z.R | 2 CGE-0.2.5/CGE/R/sdm.R | 22 ++--- CGE-0.2.5/CGE/R/sdm_examples.R | 15 +-- CGE-0.2.5/CGE/man/CES_A.Rd | 2 CGE-0.2.5/CGE/man/ChinaCGE2012.Rd | 2 CGE-0.2.5/CGE/man/Example.MWG.15.B.2.Rd | 2 CGE-0.2.5/CGE/man/Example4.2.Rd | 2 CGE-0.2.5/CGE/man/Example9.10.Rd | 2 CGE-0.2.5/CGE/man/Example9.10.policy.deficit.fiscal.Rd | 4 CGE-0.2.5/CGE/man/Example9.10.policy.deflation.Rd | 4 CGE-0.2.5/CGE/man/Example9.10.policy.interest.rate.Rd | 4 CGE-0.2.5/CGE/man/Example9.10.policy.money.supply.Rd | 4 CGE-0.2.5/CGE/man/Example9.10.policy.quantitative.easing.Rd | 4 CGE-0.2.5/CGE/man/Example9.10.policy.tax.Rd | 4 CGE-0.2.5/CGE/man/Example9.6.Rd | 4 CGE-0.2.5/CGE/man/Example9.7.Rd | 4 CGE-0.2.5/CGE/man/sdm.Rd | 51 ++++++++++-- 21 files changed, 108 insertions(+), 70 deletions(-)
Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Diff between solitude versions 0.2.0 dated 2019-08-24 and 0.2.1 dated 2019-12-07
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 5 + R/isolationForest_r6.R | 141 ++++++++++++++++++++++++++------------- R/terminal_nodes.R | 49 +++++-------- man/isolationForest.Rd | 25 ++++-- man/terminalNodesDepthPerTree.Rd | 4 - 7 files changed, 148 insertions(+), 94 deletions(-)
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library is included, but if a version is already installed
it will be used instead.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.0 dated 2018-12-21 and 0.2.1 dated 2019-12-07
ChangeLog | 48 +++++ DESCRIPTION | 10 - MD5 | 62 +++---- build/vignette.rds |binary configure | 149 ++---------------- configure.ac | 182 +++++++++++----------- inst/doc/RDieHarder.pdf |binary inst/doc/r_generators_result.rds |only src/dieharder.h | 55 +++--- src/globals.c |only src/libdieharder/Makefile | 8 src/libdieharder/Makefile.in | 8 src/libdieharder/Makefile.win |only src/libdieharder/bits.c | 4 src/libdieharder/chisq.c | 3 src/libdieharder/dab_dct.c | 5 src/libdieharder/dab_filltree2.c | 59 +++---- src/libdieharder/diehard_runs.c | 5 src/libdieharder/dieharder/dab_opso2.h | 3 src/libdieharder/dieharder/dieharder_rng_types.h | 21 +- src/libdieharder/dieharder/dieharder_test_types.h | 15 - src/libdieharder/dieharder/libdieharder.h | 115 ++++++------- src/libdieharder/dieharder/parse.h | 2 src/libdieharder/dieharder/rgb_operm.h | 2 src/libdieharder/dieharder/rgb_persist.h | 2 src/libdieharder/parse.c | 3 src/libdieharder/random_seed.c | 2 src/libdieharder/rank.c | 5 src/libdieharder/rng_ca.c | 77 ++++----- src/libdieharder/rng_dev_arandom.c | 1 src/libdieharder/rng_dev_random.c | 1 src/libdieharder/rng_dev_urandom.c | 1 vignettes/.install_extras |only vignettes/r_generators_result.rds |only vignettes/r_rngs.r | 4 35 files changed, 390 insertions(+), 462 deletions(-)
Title: Create Cartograms with R
Description: Construct continuous and non-contiguous area cartograms.
Author: Sebastian Jeworutzki [aut, cre]
(<https://orcid.org/0000-0002-2671-5253>),
Timothee Giraud [ctb],
Nicolas Lambert [ctb],
Roger Bivand [cph],
Edzer Pebesma [cph],
Jakub Nowosad [ctb] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Sebastian Jeworutzki <sebastian.jeworutzki@ruhr-uni-bochum.de>
Diff between cartogram versions 0.1.1 dated 2018-12-01 and 0.2.0 dated 2019-12-07
cartogram-0.1.1/cartogram/man/checkPolygonsGEOS.Rd |only cartogram-0.2.0/cartogram/DESCRIPTION | 12 cartogram-0.2.0/cartogram/MD5 | 33 - cartogram-0.2.0/cartogram/NAMESPACE | 8 cartogram-0.2.0/cartogram/NEWS | 1 cartogram-0.2.0/cartogram/R/cartogram_cont.R | 268 +---------- cartogram-0.2.0/cartogram/R/cartogram_dorling.R | 6 cartogram-0.2.0/cartogram/R/cartogram_ncont.R | 94 +-- cartogram-0.2.0/cartogram/README.md | 27 - cartogram-0.2.0/cartogram/man/cartogram.Rd | 17 cartogram-0.2.0/cartogram/man/cartogram_cont.Rd | 31 - cartogram-0.2.0/cartogram/man/cartogram_dorling.Rd | 6 cartogram-0.2.0/cartogram/man/cartogram_ncont.Rd | 3 cartogram-0.2.0/cartogram/man/figures/README-cont-1.png |binary cartogram-0.2.0/cartogram/man/figures/README-dorling-1.png |binary cartogram-0.2.0/cartogram/man/figures/README-ncont-1.png |binary cartogram-0.2.0/cartogram/man/figures/README-sfsupport-1.png |binary cartogram-0.2.0/cartogram/man/nc_cartogram.Rd | 13 18 files changed, 163 insertions(+), 356 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.800.1.0 dated 2019-10-09 and 0.9.800.3.0 dated 2019-12-07
ChangeLog | 17 +++++ DESCRIPTION | 8 +- MD5 | 46 ++++++------- R/RcppArmadillo.package.skeleton.R | 7 +- README.md | 9 ++ inst/NEWS.Rd | 8 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.R | 2 inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadilloExtensions/sample.h | 26 ++++--- inst/include/armadillo_bits/Mat_bones.hpp | 6 - inst/include/armadillo_bits/Mat_meat.hpp | 71 ++++++--------------- inst/include/armadillo_bits/arma_ostream_bones.hpp | 2 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/auxlib_meat.hpp | 6 + inst/include/armadillo_bits/compiler_setup.hpp | 6 - inst/include/armadillo_bits/config.hpp | 2 inst/include/armadillo_bits/config.hpp.cmake | 2 inst/include/armadillo_bits/def_lapack.hpp | 32 ++++----- inst/include/armadillo_bits/diskio_bones.hpp | 4 - inst/include/armadillo_bits/diskio_meat.hpp | 18 ++++- inst/include/armadillo_bits/sp_auxlib_meat.hpp | 6 + inst/include/armadillo_bits/subview_bones.hpp | 2 inst/include/armadillo_bits/subview_meat.hpp | 39 ++--------- 24 files changed, 165 insertions(+), 156 deletions(-)
Title: Logic Regression
Description: Routines for fitting Logic Regression models. Logic Regression is described
in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte
Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005)
<DOI:10.1002/gepi.20042>.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between LogicReg versions 1.6.1 dated 2019-11-07 and 1.6.2 dated 2019-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/LogicReg.R | 22 +++++++++++----------- src/clogic.c | 6 +++--- src/external.f | 6 +++--- src/slogic.f | 6 ++---- 6 files changed, 28 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-13 1.1.2
2013-11-05 1.1.1
2013-10-25 1.1
2013-03-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-12 1.2.1
2018-11-22 1.2.0
2018-08-07 1.1.0
2018-04-13 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-05 0.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-21 2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-02 1.3
2016-10-07 1.2
2015-06-26 1.1
2015-04-08 1.0
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),
Christian Che-Castaldo [aut] (<https://orcid.org/0000-0002-7670-2178>),
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.13.3 dated 2019-10-23 and 0.13.5 dated 2019-12-07
DESCRIPTION | 8 - MD5 | 16 +- NEWS.md | 10 + R/MCMCchains.R | 169 +++++++++++++------------- R/MCMCpstr.R | 26 ++-- R/MCMCsummary.R | 316 ++++++++++++++++++++++++++++++++------------------ R/MCMCtrace.R | 56 ++++---- build/vignette.rds |binary inst/doc/MCMCvis.html | 14 +- 9 files changed, 356 insertions(+), 259 deletions(-)
Title: Biclustering with Missing Data
Description: Biclustering is a statistical learning technique that simultaneously
partitions and clusters rows and columns of a data matrix. Since the solution
space of biclustering is in infeasible to completely search with current
computational mechanisms, this package uses a greedy heuristic. The algorithm
featured in this package is, to the best our knowledge, the first biclustering
algorithm to work on data with missing values. Li, J., Reisner, J., Pham, H.,
Olafsson, S., and Vardeman, S. (2020) Biclustering with Missing Data. Information
Sciences, 510, 304–316.
Author: John Reisner [cre, aut, cph],
Hieu Pham [ctb, cph],
Jing Li [ctb, cph]
Maintainer: John Reisner <johntreisner@gmail.com>
Diff between biclustermd versions 0.1.0 dated 2019-09-30 and 0.2.0 dated 2019-12-07
DESCRIPTION | 10 +- MD5 | 54 +++++------ NAMESPACE | 1 R/autoplot.biclustermd.R | 97 +++++++++++++-------- R/autoplot.biclustermd_sim.R | 41 ++++++-- R/biclustermd.R | 14 ++- R/compare_biclusters.R | 46 +++++----- R/gather.biclustermd.R | 11 +- R/tune_biclustermd.R | 2 README.md | 2 inst/doc/Airports.html | 133 ++++++++++++++--------------- man/autoplot.biclustermd.Rd | 28 +++--- man/autoplot.biclustermd_sim.Rd | 16 ++- man/biclustermd.Rd | 34 ++++--- man/cell_mse.Rd | 4 man/col_cluster_names.Rd | 2 man/compare_biclusters.Rd | 10 +- man/gather.biclustermd.Rd | 2 man/part_matrix_to_vector.Rd | 2 man/rep_biclustermd.Rd | 8 - man/results_heatmap.Rd | 6 - man/row_cluster_names.Rd | 2 man/runtimes.Rd | 30 +++--- man/synthetic.Rd | 2 man/tune_biclustermd.Rd | 10 +- tests/testthat/test-autoplot_biclustermd.R | 22 ++-- tests/testthat/test-biclustermd.R | 64 ++++++++----- tests/testthat/test-synthetic.R | 4 28 files changed, 371 insertions(+), 286 deletions(-)