Title: Spatial Search Trees
Description: The QuadTree data structure is useful for fast,
neighborhood-restricted lookups. We use it to implement fast k-Nearest
Neighbor and Rectangular range lookups in 2 dimenions. The
primary target is high performance interactive graphics.
Author: Gabriel Becker
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between SearchTrees versions 0.5.2 dated 2012-08-24 and 0.5.3 dated 2022-05-11
DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- NAMESPACE | 5 +++-- R/quadtree2.R | 22 +++++++++++----------- man/createTree.Rd | 3 ++- man/knnLookup-methods.Rd | 1 - man/rectLookup-methods.Rd | 6 ++---- src/quadtree2.c | 18 ++++++++++++++++++ 8 files changed, 51 insertions(+), 33 deletions(-)
Title: Schloss Lab Tools for Reproducible Microbiome Research
Description: A collection of useful functions and example code created and
used by the Schloss Lab for reproducible microbiome research. Perform
common tasks like read files created by mothur <https://mothur.org/>,
tidy up your microbiome data, and format R Markdown documents for
publication. See the website <http://www.schlosslab.org/schtools/>
for more information, documentation, and examples.
Author: Kelly Sovacool [aut, cre] ,
Nick Lesniak [aut] ,
Patrick Schloss [aut],
Sarah Lucas [ctb] ,
Courtney Armour [ctb] ,
Jacqueline Moltzau [ctb] ,
Andrew Hannah [ctb],
Nielson Baxter [ctb],
Alyxandria Schubert [ctb],
Kathryn Iverson [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between schtools versions 0.1.1 dated 2022-03-11 and 0.2.1 dated 2022-05-11
DESCRIPTION | 14 - MD5 | 20 +- NEWS.md | 10 + R/read_tax.R | 12 + README.md | 50 ++++-- build/vignette.rds |binary inst/doc/introduction.R | 31 ++++ inst/doc/introduction.Rmd | 42 +++++ inst/doc/introduction.html | 300 +++++++++++++++++++++++++++++++++++++---- tests/testthat/test-read_tax.R | 24 +++ vignettes/introduction.Rmd | 42 +++++ 11 files changed, 484 insertions(+), 61 deletions(-)
Title: Estimating Regional Trends of a Prevalence from a DHS and
Similar Surveys
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey, see Larmarange et al. (2011)
<doi:10.4000/cybergeo.24606>.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 3.4.1 dated 2020-08-28 and 4.0.0 dated 2022-05-11
prevR-3.4.1/prevR/R/eyefit.prevR.r |only prevR-4.0.0/prevR/DESCRIPTION | 20 prevR-4.0.0/prevR/MD5 | 75 - prevR-4.0.0/prevR/NAMESPACE | 2 prevR-4.0.0/prevR/NEWS.md | 39 prevR-4.0.0/prevR/R/Noptim.r | 2 prevR-4.0.0/prevR/R/as.SpatialGrid.prevR.r | 6 prevR-4.0.0/prevR/R/as.prevR.r | 4 prevR-4.0.0/prevR/R/changeproj.prevR.r | 2 prevR-4.0.0/prevR/R/colors.prevR.r | 8 prevR-4.0.0/prevR/R/direct.label_prevR.r | 2 prevR-4.0.0/prevR/R/is.prevR.r | 4 prevR-4.0.0/prevR/R/kde.prevR.r | 50 - prevR-4.0.0/prevR/R/krige.prevR.r | 59 - prevR-4.0.0/prevR/R/prevR-package.r | 17 prevR-4.0.0/prevR/R/quick.prevR.r | 2 prevR-4.0.0/prevR/R/rings.prevR.r | 10 prevR-4.0.0/prevR/R/theme_prevR.r | 2 prevR-4.0.0/prevR/R/xyz2dataframe.prevR.r | 13 prevR-4.0.0/prevR/build/vignette.rds |binary prevR-4.0.0/prevR/data/TMWorldBorders.rda |binary prevR-4.0.0/prevR/data/fdhs.rda |binary prevR-4.0.0/prevR/inst/doc/intro_prevR.Rmd | 18 prevR-4.0.0/prevR/inst/doc/intro_prevR.html | 818 ++++++++++++++++---- prevR-4.0.0/prevR/inst/po/fr/LC_MESSAGES/R-prevR.mo |binary prevR-4.0.0/prevR/man/Noptim.Rd | 2 prevR-4.0.0/prevR/man/as.SpatialGrid.Rd | 4 prevR-4.0.0/prevR/man/direct.label_prevR.Rd | 2 prevR-4.0.0/prevR/man/kde-prevR-method.Rd | 20 prevR-4.0.0/prevR/man/krige-ANY-prevR-method.Rd | 23 prevR-4.0.0/prevR/man/prevR-package.Rd | 16 prevR-4.0.0/prevR/man/prevR.colors.Rd | 6 prevR-4.0.0/prevR/man/quick.prevR.Rd | 2 prevR-4.0.0/prevR/man/rings-prevR-method.Rd | 10 prevR-4.0.0/prevR/man/theme_prevR.Rd | 2 prevR-4.0.0/prevR/man/xyz2dataframe.Rd | 11 prevR-4.0.0/prevR/po/R-fr.po | 362 ++++---- prevR-4.0.0/prevR/po/R-prevR.pot | 51 - prevR-4.0.0/prevR/vignettes/intro_prevR.Rmd | 18 39 files changed, 1096 insertions(+), 586 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.7.0 dated 2018-08-27 and 0.8.0 dated 2022-05-11
pdp-0.7.0/pdp/R/getIcePredCls.R |only pdp-0.7.0/pdp/R/getIcePredReg.R |only pdp-0.7.0/pdp/R/getParDepCls.R |only pdp-0.7.0/pdp/R/getParDepGBM.R |only pdp-0.7.0/pdp/R/getParDepMan.R |only pdp-0.7.0/pdp/R/getParDepReg.R |only pdp-0.7.0/pdp/R/getParPredCls.R |only pdp-0.7.0/pdp/R/getParPredReg.R |only pdp-0.7.0/pdp/R/progress.R |only pdp-0.7.0/pdp/R/super_type.R |only pdp-0.7.0/pdp/man/figures/README-example-rf-1.png |only pdp-0.7.0/pdp/man/figures/README-example-rf-2-1.png |only pdp-0.7.0/pdp/man/figures/README-example-rf-3-1.png |only pdp-0.7.0/pdp/man/figures/README-example-svm-1.png |only pdp-0.7.0/pdp/man/figures/README-example-svm-2-1.png |only pdp-0.7.0/pdp/man/figures/pdp-logo.svg |only pdp-0.7.0/pdp/man/figures/pdp-logos.png |only pdp-0.7.0/pdp/man/grid.arrange.Rd |only pdp-0.7.0/pdp/man/pipe.Rd |only pdp-0.7.0/pdp/man/progress_progress.Rd |only pdp-0.7.0/pdp/tests/testthat |only pdp-0.7.0/pdp/tests/testthat.R |only pdp-0.7.0/pdp/tools |only pdp-0.8.0/pdp/DESCRIPTION | 43 ++-- pdp-0.8.0/pdp/MD5 | 176 +++++++++++-------- pdp-0.8.0/pdp/NAMESPACE | 16 + pdp-0.8.0/pdp/NEWS.md | 57 ++++++ pdp-0.8.0/pdp/R/autoplot.R | 124 ++++++------- pdp-0.8.0/pdp/R/exemplar.R |only pdp-0.8.0/pdp/R/get_predictions.R |only pdp-0.8.0/pdp/R/get_task.R |only pdp-0.8.0/pdp/R/get_training_data.R | 159 ++++++++++++++--- pdp-0.8.0/pdp/R/pardep.R |only pdp-0.8.0/pdp/R/partial.R | 140 +++++++-------- pdp-0.8.0/pdp/R/plotPartial.R | 124 +++++-------- pdp-0.8.0/pdp/R/pred_grid.R | 12 - pdp-0.8.0/pdp/R/topPredictors.R | 5 pdp-0.8.0/pdp/R/utils.R | 70 ++++--- pdp-0.8.0/pdp/README.md | 47 ++--- pdp-0.8.0/pdp/build |only pdp-0.8.0/pdp/inst/CITATION | 2 pdp-0.8.0/pdp/inst/doc |only pdp-0.8.0/pdp/inst/tinytest |only pdp-0.8.0/pdp/man/autoplot.partial.Rd | 87 ++++++--- pdp-0.8.0/pdp/man/boston.Rd | 6 pdp-0.8.0/pdp/man/exemplar.Rd |only pdp-0.8.0/pdp/man/get_training_data.Rd |only pdp-0.8.0/pdp/man/partial.Rd | 66 +++++-- pdp-0.8.0/pdp/man/pdp.Rd | 1 pdp-0.8.0/pdp/man/pima.Rd | 6 pdp-0.8.0/pdp/man/plotPartial.Rd | 79 +++++--- pdp-0.8.0/pdp/src/in_out.c |only pdp-0.8.0/pdp/src/pdp-init.c | 8 pdp-0.8.0/pdp/src/pdp.h |only pdp-0.8.0/pdp/tests/tinytest.R |only pdp-0.8.0/pdp/vignettes |only 56 files changed, 765 insertions(+), 463 deletions(-)
Title: Extra Recipes Steps for Dealing with Unbalanced Data
Description: A dataset with an uneven number of cases in each class is
said to be unbalanced. Many models produce a subpar performance on
unbalanced datasets. A dataset can be balanced by increasing the
number of minority cases using SMOTE 2011 <arXiv:1106.1813>,
BorderlineSMOTE 2005 <doi:10.1007/11538059_91> and ADASYN 2008
<https://ieeexplore.ieee.org/document/4633969>. Or by decreasing the
number of majority cases using NearMiss 2003
<https://www.site.uottawa.ca/~nat/Workshop2003/jzhang.pdf> or Tomek
link removal 1976 <https://ieeexplore.ieee.org/document/4309452>.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between themis versions 0.2.1 dated 2022-04-13 and 0.2.2 dated 2022-05-11
DESCRIPTION | 8 +-- MD5 | 64 ++++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 4 + R/step_tomek.R | 32 +++------------ R/themis-package.R | 1 R/tomek_impl.R |only man/adasyn.Rd | 3 - man/bsmote.Rd | 3 - man/nearmiss.Rd | 3 - man/smote.Rd | 3 - man/smotenc.Rd | 3 - man/step_tomek.Rd | 6 +- man/tomek.Rd |only tests/testthat/_snaps/smotenc.md | 36 +++++++++++++++++ tests/testthat/_snaps/step_adasyn.md | 5 -- tests/testthat/_snaps/step_bsmote.md | 5 -- tests/testthat/_snaps/step_downsample.md | 5 -- tests/testthat/_snaps/step_nearmiss.md | 5 -- tests/testthat/_snaps/step_rose.md | 5 -- tests/testthat/_snaps/step_smote.md | 5 -- tests/testthat/_snaps/step_tomek.md | 12 ----- tests/testthat/_snaps/step_upsample.md | 5 -- tests/testthat/_snaps/tomek_impl.md |only tests/testthat/test-S3-methods.R | 2 tests/testthat/test-smotenc.R | 4 - tests/testthat/test-step_adasyn.R | 2 tests/testthat/test-step_bsmote.R | 2 tests/testthat/test-step_downsample.R | 2 tests/testthat/test-step_nearmiss.R | 2 tests/testthat/test-step_rose.R | 2 tests/testthat/test-step_smote.R | 2 tests/testthat/test-step_tomek.R | 15 ------- tests/testthat/test-step_upsample.R | 2 tests/testthat/test-tomek_impl.R |only 35 files changed, 119 insertions(+), 131 deletions(-)
Title: Robust Data Analysis Through Monitoring and Dynamic
Visualization
Description: Provides interface to the 'MATLAB' toolbox 'Flexible Statistical Data Analysis
(FSDA)' which is comprehensive and computationally efficient
software package for robust statistics in regression, multivariate
and categorical data analysis. The current R version implements tools
for regression: (forward search, S- and MM-estimation, least trimmed
squares (LTS) and least median of squares (LMS)), for multivariate analysis
(forward search, S- and MM-estimation), for cluster analysis and cluster-wise regression.
The distinctive feature of our package is the possibility of
monitoring the statistics of interest as a function of breakdown point,
efficiency or subset size, depending on the estimator. This is
accompanied by a rich set of graphical features, such as dynamic
brushing, linking, particularly useful for exploratory data analysis.
Author: Valentin Todorov [aut, cre] ,
Emmanuele Sordini [aut],
Aldo Corbellini [ctb],
Francesca Torti [ctb],
Marco Riani [ctb],
Domenico Perrotta [ctb],
Andrea Cerioli [ctb]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between fsdaR versions 0.6-5 dated 2021-11-28 and 0.7-0 dated 2022-05-11
fsdaR-0.6-5/fsdaR/inst/work/carbike-example-3.R |only fsdaR-0.6-5/fsdaR/inst/work/mult-test.R |only fsdaR-0.7-0/fsdaR/ChangeLog | 13 fsdaR-0.7-0/fsdaR/DESCRIPTION | 17 fsdaR-0.7-0/fsdaR/MD5 | 224 +++-- fsdaR-0.7-0/fsdaR/NAMESPACE | 9 fsdaR-0.7-0/fsdaR/R/FSR_control.R | 8 fsdaR-0.7-0/fsdaR/R/corfwdplot.R | 11 fsdaR-0.7-0/fsdaR/R/covplot.R | 4 fsdaR-0.7-0/fsdaR/R/datadoc.R | 33 fsdaR-0.7-0/fsdaR/R/fanplot.R | 50 - fsdaR-0.7-0/fsdaR/R/fsmmmdrs.R | 2 fsdaR-0.7-0/fsdaR/R/fsmult.R | 3 fsdaR-0.7-0/fsdaR/R/fsreg.R | 21 fsdaR-0.7-0/fsdaR/R/fsrfan.R | 448 ++++++++--- fsdaR-0.7-0/fsdaR/R/internal.R | 2 fsdaR-0.7-0/fsdaR/R/levfwdplot.R | 2 fsdaR-0.7-0/fsdaR/R/malfwdplot.R | 4 fsdaR-0.7-0/fsdaR/R/malindexplot.R | 6 fsdaR-0.7-0/fsdaR/R/mdrplot.R | 2 fsdaR-0.7-0/fsdaR/R/mmdplot.R | 6 fsdaR-0.7-0/fsdaR/R/mmdrsplot.R | 9 fsdaR-0.7-0/fsdaR/R/mmmult.R | 3 fsdaR-0.7-0/fsdaR/R/resfwdplot.R | 2 fsdaR-0.7-0/fsdaR/R/resindexplot.R | 2 fsdaR-0.7-0/fsdaR/R/s3objectsdoc.R | 10 fsdaR-0.7-0/fsdaR/R/smult.R | 3 fsdaR-0.7-0/fsdaR/R/spmplot.R | 2 fsdaR-0.7-0/fsdaR/R/tclust.R | 21 fsdaR-0.7-0/fsdaR/R/tclustIC.R | 17 fsdaR-0.7-0/fsdaR/R/tclustICplot.R | 2 fsdaR-0.7-0/fsdaR/R/tclustICsol.R | 2 fsdaR-0.7-0/fsdaR/build/partial.rdb |binary fsdaR-0.7-0/fsdaR/build/vignette.rds |only fsdaR-0.7-0/fsdaR/data/z1.rda |only fsdaR-0.7-0/fsdaR/inst/NEWS.Rd | 16 fsdaR-0.7-0/fsdaR/inst/doc |only fsdaR-0.7-0/fsdaR/inst/java/fsda4java.jar |binary fsdaR-0.7-0/fsdaR/inst/java/r_fsda.jar |binary fsdaR-0.7-0/fsdaR/inst/tests |only fsdaR-0.7-0/fsdaR/inst/work/Bug-examples-2.R | 9 fsdaR-0.7-0/fsdaR/inst/work/Bug-examples.R | 62 - fsdaR-0.7-0/fsdaR/inst/work/Forward_Score_test.R | 91 ++ fsdaR-0.7-0/fsdaR/inst/work/error-10.R |only fsdaR-0.7-0/fsdaR/inst/work/error-3.R | 2 fsdaR-0.7-0/fsdaR/inst/work/error-4.R | 4 fsdaR-0.7-0/fsdaR/inst/work/error-5.R | 2 fsdaR-0.7-0/fsdaR/inst/work/error-6.R | 2 fsdaR-0.7-0/fsdaR/inst/work/error-8.R |only fsdaR-0.7-0/fsdaR/inst/work/error-9.R |only fsdaR-0.7-0/fsdaR/inst/work/examples-spmplot.R | 4 fsdaR-0.7-0/fsdaR/inst/work/examples.R | 2 fsdaR-0.7-0/fsdaR/inst/work/test-corfwdplot.R | 2 fsdaR-0.7-0/fsdaR/inst/work/test-fsmult.R | 26 fsdaR-0.7-0/fsdaR/inst/work/test-fsrbase.R | 1 fsdaR-0.7-0/fsdaR/inst/work/test-fsreg.R | 38 fsdaR-0.7-0/fsdaR/inst/work/test-fsrfan.r |only fsdaR-0.7-0/fsdaR/inst/work/test-lts.R | 1 fsdaR-0.7-0/fsdaR/inst/work/test-mmdrsplot.R | 3 fsdaR-0.7-0/fsdaR/inst/work/test-mult.R |only fsdaR-0.7-0/fsdaR/inst/work/test-resfwdplot.R | 1 fsdaR-0.7-0/fsdaR/inst/work/test-spmplot.R | 55 - fsdaR-0.7-0/fsdaR/inst/work/test-tclust.R | 38 fsdaR-0.7-0/fsdaR/inst/work/test-tclustIC.R | 100 +- fsdaR-0.7-0/fsdaR/inst/work/ttclust.R |only fsdaR-0.7-0/fsdaR/man/FSR_control.Rd | 8 fsdaR-0.7-0/fsdaR/man/FSReda_control.Rd | 1 fsdaR-0.7-0/fsdaR/man/LXS_control.Rd | 1 fsdaR-0.7-0/fsdaR/man/MMreg_control.Rd | 4 fsdaR-0.7-0/fsdaR/man/MMregeda_control.Rd | 1 fsdaR-0.7-0/fsdaR/man/Sreg_control.Rd | 3 fsdaR-0.7-0/fsdaR/man/Sregeda_control.Rd | 4 fsdaR-0.7-0/fsdaR/man/corfwdplot.Rd | 5 fsdaR-0.7-0/fsdaR/man/diabetes.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsdalms.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsdalts.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsmeda.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsmmmdrs.Rd | 2 fsdaR-0.7-0/fsdaR/man/fsmmmdrs.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/fsmult.Rd | 2 fsdaR-0.7-0/fsdaR/man/fsmult.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsr.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsreda.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/fsreg.Rd | 3 fsdaR-0.7-0/fsdaR/man/fsrfan.Rd | 236 +++++ fsdaR-0.7-0/fsdaR/man/fsrfan.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmdplot.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmdrsplot.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmmult.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmmult.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmmulteda.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/mmreg.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/mmregeda.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/poison.Rd | 2 fsdaR-0.7-0/fsdaR/man/resfwdplot.Rd | 2 fsdaR-0.7-0/fsdaR/man/smult.Rd | 2 fsdaR-0.7-0/fsdaR/man/smult.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/smulteda.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/sreg.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/sregeda.object.Rd | 1 fsdaR-0.7-0/fsdaR/man/summary.lms.Rd | 1 fsdaR-0.7-0/fsdaR/man/summary.lts.Rd | 1 fsdaR-0.7-0/fsdaR/man/swissbanknotes.Rd | 1 fsdaR-0.7-0/fsdaR/man/swissheads.Rd | 1 fsdaR-0.7-0/fsdaR/man/tclustIC.Rd | 17 fsdaR-0.7-0/fsdaR/man/tclusteda.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/tclustfsda.Rd | 929 +++++++++++------------ fsdaR-0.7-0/fsdaR/man/tclustfsda.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/tclustic.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/tclusticsol.object.Rd | 2 fsdaR-0.7-0/fsdaR/man/z1.Rd |only fsdaR-0.7-0/fsdaR/vignettes |only 112 files changed, 1661 insertions(+), 999 deletions(-)
Title: Calculating Linkage Disequilibrium (LD) in Human Population
Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nci.nih.gov/?tab=apiaccess>)
using the R console. This programmatic access facilitates researchers who are
interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393>
data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying
germline variants in human population groups of interest. For more details, please see
Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre] ,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>
Diff between LDlinkR versions 1.1.2 dated 2021-02-19 and 1.2.0 dated 2022-05-11
DESCRIPTION | 19 MD5 | 82 - NEWS.md | 16 R/LDexpress.R | 58 + R/LDhap.R | 251 +++-- R/LDmatrix.R | 124 +- R/LDpair.R | 78 + R/LDpop.R | 57 + R/LDproxy.R | 53 + R/LDproxy_batch.R | 43 R/LDtrait.R | 294 +++--- R/SNPchip.R | 93 +- R/SNPclip.R | 39 R/list_chips.R | 98 +- README.md | 43 build/vignette.rds |binary inst/WORDLIST | 22 inst/doc/LDlinkR.R | 71 + inst/doc/LDlinkR.Rmd | 438 ++++++--- inst/doc/LDlinkR.html | 1642 ++++++++++++++++++++++-------------- man/LDexpress.Rd | 6 man/LDhap.Rd | 18 man/LDlinkR-package.Rd | 11 man/LDmatrix.Rd | 17 man/LDpair.Rd | 14 man/LDpop.Rd | 14 man/LDproxy.Rd | 13 man/LDproxy_batch.Rd | 16 man/LDtrait.Rd | 7 man/SNPchip.Rd | 12 man/SNPclip.Rd | 7 tests/testthat/test-ldexpress.R | 14 tests/testthat/test-ldhap.R | 53 + tests/testthat/test-ldmatrix.R | 12 tests/testthat/test-ldpair.R | 14 tests/testthat/test-ldpop.R | 19 tests/testthat/test-ldproxy.R | 18 tests/testthat/test-ldproxy_batch.R | 18 tests/testthat/test-ldtrait.R | 13 tests/testthat/test-snpchip.R | 14 tests/testthat/test-snpclip.R | 16 vignettes/LDlinkR.Rmd | 438 ++++++--- 42 files changed, 2849 insertions(+), 1436 deletions(-)
Title: Measuring Agreement Using Krippendorff's Alpha Coefficient
Description: Provides tools for applying Krippendorff's Alpha methodology <DOI:10.1080/19312450709336664>. The framework supports common and user-defined distance functions, and can accommodate any number of units, any number of coders, and missingness. Bootstrap inference is permitted, and the computation can be done in parallel.
Author: John Hughes
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between krippendorffsalpha versions 1.1-1 dated 2021-11-03 and 1.1-2 dated 2022-05-11
COPYING | 2 +- DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- R/data.R |only R/krippendorff.R | 3 +-- man/cartilage.Rd | 29 ++++++++++++----------------- 6 files changed, 24 insertions(+), 29 deletions(-)
More information about krippendorffsalpha at CRAN
Permanent link
Title: Simple Key-Value Database Using SQLite
Description: Simple key-value database using SQLite as the back end.
Author: Roger D. Peng <rpeng@jhsph.edu>
Maintainer: Roger D. Peng <rpeng@jhsph.edu>
Diff between filehashSQLite versions 0.2-4 dated 2012-03-23 and 0.2-6 dated 2022-05-11
filehashSQLite-0.2-4/filehashSQLite/man/filehashSQLite-class.Rd |only filehashSQLite-0.2-4/filehashSQLite/tests/reg-tests.R |only filehashSQLite-0.2-4/filehashSQLite/tests/reg-tests.Rout.save |only filehashSQLite-0.2-6/filehashSQLite/DESCRIPTION | 22 - filehashSQLite-0.2-6/filehashSQLite/MD5 | 23 + filehashSQLite-0.2-6/filehashSQLite/NAMESPACE | 64 ++-- filehashSQLite-0.2-6/filehashSQLite/R/filehash-SQLite.R | 136 +++++++++- filehashSQLite-0.2-6/filehashSQLite/R/zzz.R | 5 filehashSQLite-0.2-6/filehashSQLite/man/dbDelete-filehashSQLite-character-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbDisconnect-filehashSQLite-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbExists-filehashSQLite-character-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbFetch-filehashSQLite-character-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbInsert-filehashSQLite-character-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbList-filehashSQLite-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbMultiFetch-filehashSQLite-character-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/dbUnlink-filehashSQLite-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/filehashSQLite.Rd |only filehashSQLite-0.2-6/filehashSQLite/man/sub-filehashSQLite-character-ANY-ANY-method.Rd |only filehashSQLite-0.2-6/filehashSQLite/tests/testthat |only filehashSQLite-0.2-6/filehashSQLite/tests/testthat.R |only 20 files changed, 191 insertions(+), 59 deletions(-)
More information about filehashSQLite at CRAN
Permanent link
Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between BGLR versions 1.0.9 dated 2021-11-13 and 1.1.0 dated 2022-05-11
CHANGELOG | 14 DESCRIPTION | 6 MD5 | 41 - R/BGLR.R | 10 R/Multitrait.R | 284 +++++++----- R/utils.R | 7 data/datalist | 2 data/mice.RData |binary inst/CITATION | 1 inst/md/GxE_usingInteractions.md | 41 + inst/md/Validation.md | 6 inst/md/heritability.md | 2 inst/md/heterogeneity_interactions.md | 2 inst/md/hyperparameters.md | 2 man/BGLR.Rd | 2 man/mice.Rd | 9 man/mice.X.Rd | 1 man/mice.map.Rd |only man/mice.pheno.Rd | 23 src/init.c | 8 src/sampler_multitrait.c | 791 +++++++++++++++++++++++++++++++++- src/util_plink.c | 2 22 files changed, 1080 insertions(+), 174 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@rstudio.com>
Diff between reticulate versions 1.24 dated 2022-01-26 and 1.25 dated 2022-05-11
DESCRIPTION | 15 MD5 | 124 +++--- NAMESPACE | 15 NEWS.md | 67 +++ R/RcppExports.R | 75 +--- R/conda.R | 70 ++- R/config.R | 24 - R/conversion.R | 50 ++ R/generator.R | 2 R/help.R | 4 R/import.R | 2 R/install-python.R | 20 - R/install.R | 9 R/pip.R | 4 R/poetry.R | 2 R/pyenv.R | 66 +++ R/python-tools.R | 18 R/python.R | 167 ++++++++- R/repl.R | 43 ++ R/thread.R | 2 R/use_python.R | 24 + R/utils.R | 17 R/virtualenv.R | 4 R/zzz.R | 9 build/vignette.rds |binary inst/doc/arrays.html | 10 inst/doc/calling_python.html | 5 inst/doc/package.html | 1 inst/doc/python_dependencies.html | 1 inst/doc/python_packages.html | 1 inst/doc/python_primer.html | 93 +---- inst/doc/r_markdown.Rmd | 2 inst/doc/r_markdown.html | 3 inst/doc/versions.html | 1 inst/python/rpytools/ipython.py |only man/conda-tools.Rd | 2 man/dict.Rd | 2 man/install_python.Rd | 17 man/ipython.Rd |only man/py_iterator.Rd | 2 man/py_last_error.Rd | 56 ++- man/py_main_thread_func.Rd | 2 man/py_str.Rd | 22 - man/py_unicode.Rd | 2 man/register_module_help_handler.Rd | 4 man/tuple.Rd | 2 man/use_python.Rd | 4 src/RcppExports.cpp | 88 ++-- src/common.h | 2 src/event_loop.cpp | 13 src/event_loop.h | 1 src/libpython.cpp | 4 src/libpython.h | 3 src/output.cpp | 2 src/python.cpp | 421 +++++++++++------------ src/readline.cpp | 1 src/reticulate_types.h | 42 ++ src/signals.cpp | 37 -- src/signals.h | 4 src/tinythread.h | 1 tests/testthat/test-python-complex.R | 2 tests/testthat/test-python-modules.R | 2 tests/testthat/test-python-scipy-sparse-matrix.R | 68 +++ vignettes/r_markdown.Rmd | 2 64 files changed, 1155 insertions(+), 603 deletions(-)
Title: Conjugate Gradient Minimization of Nonlinear Functions with Box
Constraints
Description: Conjugate gradient minimization of nonlinear functions with box constraints using Dai/Yuan update.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash <nashjc@uottawa.ca>
Diff between Rcgmin versions 2013-2.21 dated 2014-12-05 and 2022-4.30 dated 2022-05-11
DESCRIPTION | 23 +++++++------- MD5 | 18 +++++------ NAMESPACE | 4 -- NEWS | 28 +++++++++++++---- R/Rcgmin.R | 49 ++++++++++++++++++++++++++++-- R/Rcgminb.R | 45 ++++++++++++--------------- R/Rcgminu.R | 40 +++++++++++------------- man/Rcgmin.Rd | 93 ++++++++++++++++++++++++++------------------------------- man/Rcgminb.Rd | 9 ++--- man/Rcgminu.Rd | 15 ++++----- 10 files changed, 183 insertions(+), 141 deletions(-)
Title: Multispatial Convergent Cross Mapping
Description: The multispatial convergent cross mapping algorithm can be used as a test for causal associations between pairs of processes represented by time series. This is a combination of convergent cross mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh et al., 2008, American Naturalist, 171, 71–80. The algorithm allows CCM to be implemented on data that are not from a single long time series. Instead, data can come from many short time series, which are stitched together using bootstrapping.
Author: Adam Clark
Maintainer: Adam Clark <adam.tclark@gmail.com>
Diff between multispatialCCM versions 1.0 dated 2014-10-18 and 1.2 dated 2022-05-11
multispatialCCM-1.0/multispatialCCM/R/multispatialCCM-internal.R |only multispatialCCM-1.2/multispatialCCM/DESCRIPTION | 8 multispatialCCM-1.2/multispatialCCM/MD5 | 27 - multispatialCCM-1.2/multispatialCCM/NAMESPACE | 5 multispatialCCM-1.2/multispatialCCM/R/CCM_boot.R | 120 ++-- multispatialCCM-1.2/multispatialCCM/R/SSR_check_signal.R | 108 ++-- multispatialCCM-1.2/multispatialCCM/R/SSR_pred_boot.R | 74 +- multispatialCCM-1.2/multispatialCCM/R/ccmtest.R | 30 - multispatialCCM-1.2/multispatialCCM/R/make_ccm_data.R | 142 ++--- multispatialCCM-1.2/multispatialCCM/man/CCM_boot.Rd | 174 +++--- multispatialCCM-1.2/multispatialCCM/man/SSR_check_signal.Rd | 148 ++--- multispatialCCM-1.2/multispatialCCM/man/SSR_pred_boot.Rd | 188 +++---- multispatialCCM-1.2/multispatialCCM/man/ccmtest.Rd | 130 ++--- multispatialCCM-1.2/multispatialCCM/man/make_ccm_data.Rd | 134 ++--- multispatialCCM-1.2/multispatialCCM/man/multispatialCCM-package.Rd | 260 +++++----- 15 files changed, 775 insertions(+), 773 deletions(-)
More information about multispatialCCM at CRAN
Permanent link
Title: Write Reusable, Composable and Modular R Code
Description: A modern module system for R. Organise code into hierarchical,
composable, reusable modules, and use it effortlessly across projects via a
flexible, declarative dependency loading syntax.
Author: Konrad Rudolph [aut, cre] ,
Michael Schubert [ctb]
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>
Diff between box versions 1.1.1 dated 2022-04-23 and 1.1.2 dated 2022-05-11
DESCRIPTION | 6 MD5 | 52 ++--- build/vignette.rds |binary inst/doc/box.R |only inst/doc/box.html | 409 +++++++++++++++++++++++++++++++++++++++- inst/doc/box.rmd | 403 +++++++++++++++++++++++++++++++++++++++ inst/doc/compiled-code.R |only inst/doc/compiled-code.html | 222 +++++++++++++++++++++ inst/doc/compiled-code.rmd | 146 ++++++++++++++ inst/doc/faq.R |only inst/doc/faq.html | 218 ++++++++++++++++++++- inst/doc/faq.rmd | 98 +++++++++ inst/doc/migration.R |only inst/doc/migration.html | 382 ++++++++++++++++++++++++++++++++++++- inst/doc/migration.rmd | 317 +++++++++++++++++++++++++++++++ inst/doc/mod-env-hierarchy.R |only inst/doc/mod-env-hierarchy.html | 260 +++++++++++++++++++++++++ inst/doc/mod-env-hierarchy.rmd | 155 +++++++++++++++ inst/doc/related.html | 108 ++++++++++ inst/doc/related.rmd | 99 +++++++++ inst/doc/testing.R |only inst/doc/testing.html | 294 ++++++++++++++++++++++++++++ inst/doc/testing.rmd | 200 +++++++++++++++++++ vignettes/box.rmd | 403 +++++++++++++++++++++++++++++++++++++++ vignettes/compiled-code.rmd | 146 ++++++++++++++ vignettes/faq.rmd | 98 +++++++++ vignettes/migration.rmd | 317 +++++++++++++++++++++++++++++++ vignettes/mod-env-hierarchy.rmd | 155 +++++++++++++++ vignettes/related.rmd | 99 +++++++++ vignettes/testing.rmd | 200 +++++++++++++++++++ 30 files changed, 4733 insertions(+), 54 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
Author: Edgar Merkle [aut, cre] ,
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb]
,
Terrence D. Jorgensen [ctb] ,
Huub Hoofs [ctb] ,
Rens van de Schoot [ctb] ,
Andrew Johnson [ctb] ,
Matthew Emery [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.4-1 dated 2022-01-27 and 0.4-3 dated 2022-05-11
DESCRIPTION | 33 - MD5 | 71 +- NAMESPACE | 11 NEWS.md | 31 + R/blav_adapt_quad.R |only R/blav_compare.R | 12 R/blav_fit.R | 2 R/blav_fit_measures.R | 55 + R/blav_model_loglik.R | 859 ++++++++++++++-------------- R/blav_object_inspect.R | 40 - R/blav_object_methods.R | 12 R/blav_predict.R | 16 R/blav_test.R | 4 R/blav_utils.R | 35 + R/blavaan.R | 114 ++- R/ctr_bayes_fit.R | 40 - R/ctr_ppmc.R | 30 R/dpriors.R | 14 R/lav_export_stanmarg.R | 291 +++++---- R/lvgqs.R | 4 R/margloglik.R | 4 R/postpred.R | 60 + R/set_inits.R | 4 R/stanmarg_data.R | 40 - inst/testdata/sysdata.rda |binary inst/tinytest/tests.blavaan.R | 31 + inst/tinytest/tests.blavaanobject-methods.R | 35 + man/bcfa.Rd | 7 man/bgrowth.Rd | 7 man/blavInspect.Rd | 13 man/blavPredict.Rd | 11 man/blav_internal.Rd | 3 man/blavaan.Rd | 7 man/bsem.Rd | 7 man/ppmc.Rd | 5 src/stan_files/stanmarg.stan | 197 ++++-- tests/tinytest.R | 2 37 files changed, 1225 insertions(+), 882 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Zhigen Zhai, and Wen Zhou. (2021). BEAUTY Powered BEAST, <arXiv:2103.00674> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.4.2 dated 2022-01-24 and 0.5.0 dated 2022-05-11
DESCRIPTION | 6 MD5 | 26 + NAMESPACE | 2 R/RcppExports.R | 46 +-- R/plot.R | 723 +++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/BET.Rd | 2 man/BET_package.Rd | 2 man/BETs.Rd | 2 man/cellcount.Rd |only man/color.Rd |only man/star.Rd | 2 src/BET.h | 24 + src/BET3.cpp | 726 +++++++++++++++++++++++++++++++++++++++++++++------- src/RcppExports.cpp | 28 ++ 15 files changed, 1115 insertions(+), 474 deletions(-)
Title: R Interface to Stan
Description: Expansion and additions to 'rstan' to facilitate pharmacokinetics (PK)
and pharmacodynamics (PD) modeling with 'rstan'. A PKPD model often is specified
via a set of ordinary differential equations(ODEs) and requires flexible and
different routes of drug administrations. These features make PKPD modeling
with plain 'rstan' challenging and tedious to code. 'stanette' provides a powerful
Stan-compatible ODE solver ('LSODA') and mechanism/utilities that make easy
specification of flexible dosing records.
Author: Yuan Xiong [aut],
Huijuan Xu [aut],
Wenping Wang [cre, aut, cph],
rstan developers [aut],
Trustees of Columbia University [cph],
John Plevyak [ctb, cph] ,
Linda Petzold [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between stanette versions 2.21.3 dated 2022-04-29 and 2.21.4 dated 2022-05-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/zzz.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Lioness Algorithm (LA)
Description: Contains Lioness Algorithm (LA) for finding optimal designs over continuous design space, optimal Latin hypercube designs, and optimal order-of-addition designs. LA is a brand new nature-inspired meta-heuristic optimization algorithm. Detailed methodologies of LA and its implementation on numerical simulations can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <arXiv:2010.09154>.
Author: Hongzhi Wang [aut, cre],
Qian Xiao [aut],
Abhyuday Mandal [aut]
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Diff between LA versions 2.0 dated 2022-05-07 and 2.1 dated 2022-05-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/LA.cpp | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included.
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534.
c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57.
e) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>.
f) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>.
g) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>.
h) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>.
i) Tsagris M. and Stewart C. (2020). A folded model for compositional data analysis. Australian and New Zealand Journal of Statistics, 62(2):249--277. <doi:10.1111/anzs.12289>.
j) Tsagris M., Alenazi A. and Stewart C. (2021). Non-parametric regression models for compositional data. <arXiv:2002.05137>.
k) Alenazi A. (2021). Alenazi, A. (2021). A review of compositional data analysis and recent advances. Communications in Statistics-Theory and Methods (Accepted for publication). <doi:10.1080/03610926.2021.2014890>.
We further include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 5.5 dated 2022-03-25 and 5.6 dated 2022-05-11
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++-------- R/a.mle.R | 3 - R/ait.test.R |only R/alfa.reg.R | 2 R/diri.reg.R | 2 R/diri.reg2.R | 4 - R/james.R | 2 R/js.compreg.R | 3 + R/kl.compreg.R | 3 + R/kl.diri.normal.R |only R/ols.compcomp.R | 4 - R/ols.compreg.R | 3 + R/symkl.compreg.R | 3 + R/tv.compreg.R | 3 + R/zad.est.R | 10 ---- R/zadr.R | 106 ++++++++++++++++++++++++++++++++----------- man/Compositional-package.Rd | 9 ++- man/ait.Rd | 4 - man/ait.test.Rd |only man/helm.Rd | 2 man/james.Rd | 21 +++++--- man/kl.diri.normal.Rd |only man/ols.compcomp.Rd | 7 -- man/zad.est.Rd | 5 -- man/zadr.Rd | 20 +++++--- 26 files changed, 173 insertions(+), 97 deletions(-)
Title: Multibiplot Analysis in R
Description: Provides a GUI with which users can construct and interact
with Multibiplot Analysis.
Author: Ana Belen Nieto Librero <ananieto@usal.es>, Nora Baccala
<norabaccala@gmail.com>, Purificacion Vicente Galindo
<purivg@usal.es>, Purificacion Galindo Villardon
<pgalindo@usal.es>
Maintainer: Ana Belen Nieto Librero <ananieto@usal.es>
Diff between multibiplotGUI versions 1.0 dated 2015-06-19 and 1.1 dated 2022-05-11
DESCRIPTION | 20 MD5 | 10 NAMESPACE | 15 R/multibiplot.R | 2009 +++++++++++++++++++++--------------------- man/multibiplot.Rd | 97 -- man/multibiplotGUI-package.Rd | 42 6 files changed, 1062 insertions(+), 1131 deletions(-)
More information about multibiplotGUI at CRAN
Permanent link
Title: Download Data from the Wittgenstein Centre Human Capital Data
Explorer
Description: Download and plot education specific demographic data from the Wittgenstein Centre for Demography and Human Capital Data Explorer <http://dataexplorer.wittgensteincentre.org/>.
Author: Guy J. Abel [aut, cre, ctb] ,
Samir K.C. [ctb] ,
Michaela Potancokova [ctb],
Claudia Reiter [ctb] ,
Andrea Tamburini [ctb],
Dilek Yildiz [ctb]
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between wcde versions 0.0.3 dated 2021-10-30 and 0.0.4 dated 2022-05-11
DESCRIPTION | 10 MD5 | 74 +- NAMESPACE | 18 NEWS.md | 4 R/every_other.R | 48 - R/find_indicator.R | 42 - R/get_wcde.R | 90 ++ R/get_wcde_single.R | 12 R/past_epop.R | 32 R/utils-global.R | 2 R/utils-pipe.R | 22 R/wcde_location.R | 52 - R/wic_col4.R | 12 R/wic_col6.R | 12 R/wic_col8.R | 12 R/wic_indicators.R | 38 - R/wic_locations.R | 28 R/wic_scenarios.R | 24 R/zzz.R | 6 build/vignette.rds |binary inst/doc/wcde.R | 40 - inst/doc/wcde.Rmd | 63 + inst/doc/wcde.html | 1689 ++++++++++++++++++++++++++++++++++++++++++++----- man/edu_group_sum.Rd | 64 - man/every_other.Rd | 56 - man/find_indicator.Rd | 44 - man/get_wcde.Rd | 210 +++--- man/get_wcde_single.Rd | 42 - man/past_epop.Rd | 56 - man/pipe.Rd | 24 man/wcde_location.Rd | 46 - man/wic_col4.Rd | 32 man/wic_col6.Rd | 32 man/wic_col8.Rd | 32 man/wic_indicators.Rd | 62 - man/wic_locations.Rd | 52 - man/wic_scenarios.Rd | 48 - vignettes/wcde.Rmd | 63 + 38 files changed, 2344 insertions(+), 849 deletions(-)
Title: "A Practical Guide to Ecological Modelling - Using R as a
Simulation Platform"
Description: Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer.
All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11.
The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter.
Solutions to model projects are in the same subdirectories.
Author: Karline Soetaert <karline.soetaert@nioz.nl>, Peter MJ Herman <peter.herman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between ecolMod versions 1.2.6 dated 2014-12-29 and 1.2.6.2 dated 2022-05-11
ecolMod-1.2.6.2/ecolMod/DESCRIPTION | 17 +++++++---------- ecolMod-1.2.6.2/ecolMod/MD5 | 18 ++++++++---------- ecolMod-1.2.6.2/ecolMod/NAMESPACE | 7 ++++++- ecolMod-1.2.6.2/ecolMod/data/SCOC.rda |binary ecolMod-1.2.6.2/ecolMod/data/Zoogrowth.rda |binary ecolMod-1.2.6.2/ecolMod/data/deepCmin.rda |binary ecolMod-1.2.6.2/ecolMod/demo/chap6.r | 2 +- ecolMod-1.2.6.2/ecolMod/man/ecolMod.Rd | 2 +- ecolMod-1.2.6.2/ecolMod/src/ecolModMethods.c |only ecolMod-1.2.6/ecolMod/build |only ecolMod-1.2.6/ecolMod/inst/doc/ecolMod.R |only ecolMod-1.2.6/ecolMod/inst/doc/ecolMod.Rnw |only 12 files changed, 23 insertions(+), 23 deletions(-)
Title: Extract Circadian Rhythms Metrics from Actigraphy Data
Description: Circadian rhythms are rhythms that oscillate about every 24 h, which has been observed in multiple physiological processes including core body temperature, hormone secretion, heart rate, blood pressure, and many others. Measuring circadian rhythm with wearables is based on a principle that there is increased movement during wake periods and reduced movement during sleep periods, and has been shown to be reliable and valid. This package can be used to extract nonparametric circadian metrics like intradaily variability (IV), interdaily stability (IS), and relative amplitude (RA); and parametric cosinor model and extended cosinor model coefficient. Details can be found in Junrui Di et al (2019) <doi:10.1007/s12561-019-09236-4>.
Author: Junrui Di [aut, cre],
Vadim zipunnikov [aut],
Vincent van Hees [ctb]
Maintainer: Junrui Di <dijunrui@gmail.com>
Diff between ActCR versions 0.2.0 dated 2021-01-28 and 0.3.0 dated 2022-05-11
DESCRIPTION | 15 +++-- MD5 | 42 ++++++++-------- NAMESPACE | 54 ++++++++++---------- NEWS.md | 9 +++ R/ActCosinor.R | 40 ++++++++++++--- R/ActCosinor_long.R | 55 +++++++++++++++------ R/ActExtendCosinor.R | 35 +++++++++++-- R/ActExtendCosinor_long.R | 52 +++++++++++--------- R/IS.R | 60 +++++++++++------------ R/IS_long.R | 100 +++++++++++++++++++------------------- R/IV.R | 54 ++++++++++---------- R/IV_long.R | 90 +++++++++++++++++----------------- R/RA.R | 10 +++ R/RA_long.R | 17 ++++-- R/bin_data.R | 100 +++++++++++++++++++------------------- README.md | 2 man/ActCosinor.Rd | 65 +++++++++++++------------ man/ActCosinor_long.Rd | 82 ++++++++++++++++--------------- man/ActExtendCosinor.Rd | 94 ++++++++++++++++++------------------ man/ActExtendCosinor_long.Rd | 111 ++++++++++++++++++++++--------------------- man/RA.Rd | 5 + man/RA_long.Rd | 2 22 files changed, 609 insertions(+), 485 deletions(-)
Title: Sentiment Analysis for Text and Qualitative Data
Description: Implements sentiment analysis using huggingface <https://huggingface.co> transformer zero-shot classification model pipelines. The default pipeline is Cross-Encoder's DistilRoBERTa <https://huggingface.co/cross-encoder/nli-distilroberta-base> trained on the Stanford Natural Language Inference <https://nlp.stanford.edu/projects/snli/> and Multi-Genre Natural Language Inference <https://huggingface.co/datasets/multi_nli> datasets. Using similar models, zero-shot classification transformers have demonstrated superior performance relative to other natural language processing models <arXiv:1909.00161>. All other zero-shot classification model pipelines can be implemented using their model name from <https://huggingface.co/models?pipeline_tag=zero-shot-classification>}.
Author: Alexander Christensen [aut, cre]
,
Hudson Golino [aut]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between transforEmotion versions 0.1.0 dated 2022-04-04 and 0.1.1 dated 2022-05-11
transforEmotion-0.1.0/transforEmotion/R/python_setup.R |only transforEmotion-0.1.0/transforEmotion/inst/doc/Python_Setup.R |only transforEmotion-0.1.0/transforEmotion/inst/doc/Python_Setup.Rmd |only transforEmotion-0.1.0/transforEmotion/inst/doc/Python_Setup.pdf |only transforEmotion-0.1.0/transforEmotion/man/python_setup.Rd |only transforEmotion-0.1.0/transforEmotion/vignettes/Python_Setup.Rmd |only transforEmotion-0.1.1/transforEmotion/DESCRIPTION | 8 transforEmotion-0.1.1/transforEmotion/MD5 | 44 - transforEmotion-0.1.1/transforEmotion/NAMESPACE | 3 transforEmotion-0.1.1/transforEmotion/NEWS | 15 transforEmotion-0.1.1/transforEmotion/R/setup_miniconda.R |only transforEmotion-0.1.1/transforEmotion/R/setup_modules.R |only transforEmotion-0.1.1/transforEmotion/R/tinytrolls.R | 72 +- transforEmotion-0.1.1/transforEmotion/R/transformer_scores.R | 53 - transforEmotion-0.1.1/transforEmotion/build/vignette.rds |binary transforEmotion-0.1.1/transforEmotion/inst/CITATION | 6 transforEmotion-0.1.1/transforEmotion/inst/doc/Setup.R |only transforEmotion-0.1.1/transforEmotion/inst/doc/Setup.Rmd |only transforEmotion-0.1.1/transforEmotion/inst/doc/Setup.pdf |only transforEmotion-0.1.1/transforEmotion/man/emotions.Rd | 70 - transforEmotion-0.1.1/transforEmotion/man/neo_ipip_extraversion.Rd | 50 - transforEmotion-0.1.1/transforEmotion/man/nlp_scores.Rd | 356 +++++----- transforEmotion-0.1.1/transforEmotion/man/punctuate.Rd | 90 +- transforEmotion-0.1.1/transforEmotion/man/setup_miniconda.Rd |only transforEmotion-0.1.1/transforEmotion/man/setup_modules.Rd |only transforEmotion-0.1.1/transforEmotion/man/stop_words.Rd | 40 - transforEmotion-0.1.1/transforEmotion/man/tinytrolls.Rd | 66 - transforEmotion-0.1.1/transforEmotion/man/transforEmotion-package.Rd | 52 - transforEmotion-0.1.1/transforEmotion/man/transformer_scores.Rd | 324 ++++----- transforEmotion-0.1.1/transforEmotion/vignettes/Setup.Rmd |only 30 files changed, 623 insertions(+), 626 deletions(-)
More information about transforEmotion at CRAN
Permanent link
Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superbPlot(), can either return a plot
or a dataframe with the statistic and its precision interval so that other plotting package
can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109>
or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001> for specific references.
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 0.9.7.8 dated 2021-12-05 and 0.95.0 dated 2022-05-11
DESCRIPTION | 20 MD5 | 68 +- NAMESPACE | 1 NEWS.md | 9 R/functionsPlotting_ribbon.R |only R/superbPlot.R | 9 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 23 inst/doc/CustomizingSuperbPlots.R |only inst/doc/CustomizingSuperbPlots.Rmd |only inst/doc/CustomizingSuperbPlots.html |only inst/doc/TheMakingOf.html | 6 inst/doc/Vignette1.html | 2 inst/doc/Vignette2.html | 2 inst/doc/Vignette3.html | 4 inst/doc/Vignette4.html | 4 inst/doc/Vignette5.R | 16 inst/doc/Vignette5.Rmd | 8 inst/doc/Vignette5.html | 29 inst/doc/Vignette6.html | 48 - inst/doc/Vignette8.html | 2 inst/doc/Vignette9.html | 12 inst/doc/VignetteA.R | 315 +++++++++- inst/doc/VignetteA.Rmd | 299 +++++++++ inst/doc/VignetteA.html | 29 inst/doc/VignetteB.html | 4 inst/doc/VignetteD.R | 2 inst/doc/VignetteD.Rmd | 6 inst/doc/VignetteD.html | 1 inst/superbShiny/rsconnect/shinyapps.io/superbplot/superbshiny.dcf | 6 man/superbPlot.lineBand.Rd |only tests/testthat/test_GRD.R | 56 - tests/testthat/test_superbPlot.R | 20 vignettes/CustomizingSuperbPlots.Rmd |only vignettes/Vignette5.Rmd | 8 vignettes/VignetteA.Rmd | 299 +++++++++ vignettes/VignetteD.Rmd | 6 38 files changed, 1111 insertions(+), 203 deletions(-)
Title: Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut, cre],
Guangyu Tong [aut],
Fan Li [aut],
Laine Thomas [aut],
Fan Li [aut]
Maintainer: Tianhui Zhou <thuizhou@outlook.com>
Diff between PSweight versions 1.1.6 dated 2021-12-02 and 1.1.7 dated 2022-05-11
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++++------ NAMESPACE | 3 +++ R/PSweight.R | 3 +-- R/PSweight_cl.R |only R/SumStat.R | 2 +- R/SumStat_cl.R |only R/bin_est_cl.R |only R/psdata_cl.R |only data/psdata_cl.rda |only inst/doc/vignette.pdf |binary man/PSweight.Rd | 3 +-- man/PSweight_cl.Rd |only man/SumStat_cl.Rd |only man/psdata_cl.Rd |only 15 files changed, 27 insertions(+), 18 deletions(-)
Title: Estimating Network Indices, Including Trophic Structure of
Foodwebs in R
Description: Given a network (e.g. a food web), estimates several network indices. These include: Ascendency network indices, Direct and indirect dependencies, Effective measures, Environ network indices, General network indices, Pathway analysis, Network uncertainty indices and constraint efficiencies and the trophic level and omnivory indices of food webs.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Julius Kipyegon Kones <jkones@uonbi.ac.ke>,
Dick van Oevelen <dick.vanoevelen@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between NetIndices versions 1.4.4 dated 2014-12-26 and 1.4.4.1 dated 2022-05-11
NetIndices-1.4.4.1/NetIndices/DESCRIPTION | 15 ++++++--------- NetIndices-1.4.4.1/NetIndices/MD5 | 12 +++++------- NetIndices-1.4.4.1/NetIndices/NAMESPACE | 1 + NetIndices-1.4.4.1/NetIndices/data/Conesprings.rda |binary NetIndices-1.4.4.1/NetIndices/data/Takapoto.rda |binary NetIndices-1.4.4.1/NetIndices/inst/CITATION | 1 - NetIndices-1.4.4/NetIndices/build |only NetIndices-1.4.4/NetIndices/inst/doc/NetIndices.rnw |only 8 files changed, 12 insertions(+), 17 deletions(-)
Title: Multiple-Output Directional Quantile Regression
Description: Contains basic tools for performing
multiple-output quantile regression and computing
regression quantile contours by means of directional
regression quantiles. In the location case, one can thus
obtain halfspace depth contours in two to six dimensions.
Hallin, M., Paindaveine, D. and Šiman, M. (2010)
Multivariate quantiles and multiple-output regression quantiles:
from L1 optimization to halfspace depth. Annals of Statistics 38, 635-669
For more references about the method, see Help pages.
Author: Miroslav Šiman [aut],
Pavel Boček [aut, cre]
Maintainer: Pavel Boček <bocek@utia.cas.cz>
Diff between modQR versions 0.1.2 dated 2019-01-16 and 0.1.3 dated 2022-05-11
DESCRIPTION | 10 ++++---- MD5 | 6 ++--- man/getCharSTM1u.Rd | 60 ++++++++++++++++++++++------------------------------ man/getCharSTM2u.Rd | 42 ++++++++++++++---------------------- 4 files changed, 51 insertions(+), 67 deletions(-)
Title: Latent Position and Cluster Models for Statistical Networks
Description: Fit and simulate latent position and cluster models for statistical networks. See Krivitsky and Handcock (2008) <doi:10.18637/jss.v024.i05> and Krivitsky, Handcock, Raftery, and Hoff (2009) <doi:10.1016/j.socnet.2009.04.001>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Jake Fisher [ctb],
Jordan T. Bates [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between latentnet versions 2.10.5 dated 2020-03-22 and 2.10.6 dated 2022-05-11
latentnet-2.10.5/latentnet/README.md |only latentnet-2.10.6/latentnet/DESCRIPTION | 20 +- latentnet-2.10.6/latentnet/LICENSE | 2 latentnet-2.10.6/latentnet/MD5 | 164 +++++++++--------- latentnet-2.10.6/latentnet/NEWS | 5 latentnet-2.10.6/latentnet/R/InitErgmm.fixed.R | 10 - latentnet-2.10.6/latentnet/R/InitErgmm.latent.R | 10 - latentnet-2.10.6/latentnet/R/InitErgmm.random.R | 10 - latentnet-2.10.6/latentnet/R/P.alloc.R | 10 - latentnet-2.10.6/latentnet/R/bayesmbc.MCMC.C.R | 10 - latentnet-2.10.6/latentnet/R/bayesmbc.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.MCMC.C.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.R | 14 - latentnet-2.10.6/latentnet/R/ergmm.defaults.R | 12 - latentnet-2.10.6/latentnet/R/ergmm.draw.utils.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.families.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.geodesicmatrix.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.get.model.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.initvals.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.latent.effects.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.par.R | 12 - latentnet-2.10.6/latentnet/R/ergmm.permutation.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.probs.R | 12 - latentnet-2.10.6/latentnet/R/ergmm.statseval.R | 10 - latentnet-2.10.6/latentnet/R/ergmm.tuner.R | 10 - latentnet-2.10.6/latentnet/R/gof.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/label.switching.R | 10 - latentnet-2.10.6/latentnet/R/latent.R | 10 - latentnet-2.10.6/latentnet/R/latentnet-package.R | 30 +-- latentnet-2.10.6/latentnet/R/mcmc.diagnostics.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/merge.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/plot.ergmm.R | 12 - latentnet-2.10.6/latentnet/R/predict.ergmm.R | 12 - latentnet-2.10.6/latentnet/R/print.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/print.ergmm.model.R | 10 - latentnet-2.10.6/latentnet/R/procrustes.R | 10 - latentnet-2.10.6/latentnet/R/simulate.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/summary.ergmm.R | 10 - latentnet-2.10.6/latentnet/R/utilities.R | 12 - latentnet-2.10.6/latentnet/R/zzz.R | 10 - latentnet-2.10.6/latentnet/build |only latentnet-2.10.6/latentnet/data/davis.RData |binary latentnet-2.10.6/latentnet/inst/CITATION | 14 - latentnet-2.10.6/latentnet/man/ergmm-terms.Rd | 18 - latentnet-2.10.6/latentnet/man/ergmm.Rd | 2 latentnet-2.10.6/latentnet/man/latentnet-package.Rd | 2 latentnet-2.10.6/latentnet/src/Makevars | 2 latentnet-2.10.6/latentnet/src/P_alloc.c | 8 latentnet-2.10.6/latentnet/src/P_alloc.h | 8 latentnet-2.10.6/latentnet/src/ergmm_families.c | 8 latentnet-2.10.6/latentnet/src/ergmm_families.h | 8 latentnet-2.10.6/latentnet/src/ergmm_latent_effects.c | 8 latentnet-2.10.6/latentnet/src/ergmm_latent_effects.h | 8 latentnet-2.10.6/latentnet/src/ergmm_probs.c | 8 latentnet-2.10.6/latentnet/src/ergmm_probs.h | 8 latentnet-2.10.6/latentnet/src/ergmm_sampler.c | 8 latentnet-2.10.6/latentnet/src/ergmm_sampler.h | 8 latentnet-2.10.6/latentnet/src/ergmm_structs.h | 8 latentnet-2.10.6/latentnet/src/ergmm_updaters.c | 8 latentnet-2.10.6/latentnet/src/ergmm_updaters.h | 8 latentnet-2.10.6/latentnet/src/ergmm_utils.c | 8 latentnet-2.10.6/latentnet/src/ergmm_utils.h | 8 latentnet-2.10.6/latentnet/src/init.c | 8 latentnet-2.10.6/latentnet/src/kl_switch.c | 8 latentnet-2.10.6/latentnet/src/kl_switch.h | 8 latentnet-2.10.6/latentnet/src/matrix_utils.c | 12 - latentnet-2.10.6/latentnet/src/matrix_utils.h | 8 latentnet-2.10.6/latentnet/src/mbc_sampler.c | 8 latentnet-2.10.6/latentnet/src/mbc_sampler.h | 8 latentnet-2.10.6/latentnet/src/mvnorm.c | 8 latentnet-2.10.6/latentnet/src/mvnorm.h | 8 latentnet-2.10.6/latentnet/src/post_predict.c | 8 latentnet-2.10.6/latentnet/src/post_predict.h | 8 latentnet-2.10.6/latentnet/src/procrustes.c | 8 latentnet-2.10.6/latentnet/src/procrustes.h | 8 latentnet-2.10.6/latentnet/src/wishart.c | 8 latentnet-2.10.6/latentnet/src/wishart.h | 8 latentnet-2.10.6/latentnet/tests/missing.R | 10 - latentnet-2.10.6/latentnet/tests/nofixed.R | 10 - latentnet-2.10.6/latentnet/tests/nolatent.R | 10 - latentnet-2.10.6/latentnet/tests/nomcmc.R | 10 - latentnet-2.10.6/latentnet/tests/nomixing.R | 10 - latentnet-2.10.6/latentnet/tests/normal.R | 10 - latentnet-2.10.6/latentnet/tests/onlymcmc.R | 10 - 84 files changed, 470 insertions(+), 459 deletions(-)
Title: User-Friendly Interface for Geographically-Weighted Models
Description: Contains the development of a tool that provides a web-based
graphical user interface (GUI) to perform Techniques from a subset of
spatial statistics known as geographically weighted (GW) models.
Contains methods described by Brunsdon et al., 1996
<doi:10.1111/j.1538-4632.1996.tb00936.x>, Brunsdon et al., 2002
<doi:10.1016/s0198-9715(01)00009-6>, Harris et al., 2011
<doi:10.1080/13658816.2011.554838>, Brunsdon et al., 2007
<doi:10.1111/j.1538-4632.2007.00709.x>.
Author: Javier De La Hoz Maestre [cre, aut]
,
Maria Jose Fernandez Gomez [aut]
,
Susana Mendez [aut]
Maintainer: Javier De La Hoz Maestre <jdelahozmaestre@gmail.com>
Diff between GeoWeightedModel versions 0.9.1 dated 2022-01-05 and 1.0.0 dated 2022-05-11
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 1 R/zzz.R |only inst/GeoWeightedModelApp/global.R | 1 inst/GeoWeightedModelApp/server.R | 466 +++++++++++++++-- inst/GeoWeightedModelApp/ui.R | 399 ++++++++++++-- inst/GeoWeightedModelApp/www/Help_Autocorrelation.html |only inst/GeoWeightedModelApp/www/help_gwr.html | 348 +++++++++++- 9 files changed, 1106 insertions(+), 133 deletions(-)
More information about GeoWeightedModel at CRAN
Permanent link
Title: Phylogenetic Analysis with Morphological Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph]
,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.1.1 dated 2022-03-22 and 1.1.2 dated 2022-05-11
TreeSearch-1.1.1/TreeSearch/build/TreeSearch.pdf |only TreeSearch-1.1.2/TreeSearch/DESCRIPTION | 6 TreeSearch-1.1.2/TreeSearch/MD5 | 31 TreeSearch-1.1.2/TreeSearch/NEWS.md | 14 TreeSearch-1.1.2/TreeSearch/R/PlotCharacter.R | 58 - TreeSearch-1.1.2/TreeSearch/R/tree_length.R | 44 TreeSearch-1.1.2/TreeSearch/build/partial.rdb |binary TreeSearch-1.1.2/TreeSearch/build/vignette.rds |binary TreeSearch-1.1.2/TreeSearch/inst/doc/custom.html | 545 +++++++--- TreeSearch-1.1.2/TreeSearch/inst/doc/getting-started.html | 231 ++++ TreeSearch-1.1.2/TreeSearch/inst/doc/profile-scores.html | 465 +++++++- TreeSearch-1.1.2/TreeSearch/inst/doc/profile.html | 266 ++++ TreeSearch-1.1.2/TreeSearch/inst/doc/tree-search.html | 414 ++++++- TreeSearch-1.1.2/TreeSearch/man/dot-NonDuplicateRoot.Rd | 92 - TreeSearch-1.1.2/TreeSearch/src/rearrange.cpp | 24 TreeSearch-1.1.2/TreeSearch/tests/testthat/test-MaximizeParsimony.R | 53 TreeSearch-1.1.2/TreeSearch/tests/testthat/test-tree_length.R | 94 + 17 files changed, 1888 insertions(+), 449 deletions(-)
Title: Ranking Responses in a Single Response Question or a Multiple
Response Question
Description: Methods for ranking responses of a single response question or a
multiple response question are described in the two papers:
1. Wang, H. (2008). Ranking Responses in Multiple-Choice Questions. Journal of
Applied Statistics, 35, 465-474. <DOI:10.1080/02664760801924533>
2. Wang, H. and Huang, W. H. (2014). Bayesian Ranking Responses in Multiple
Response Questions. Journal of the Royal Statistical Society: Series A
(Statistics in Society), 177, 191-208. <DOI:10.1111/rssa.12009>.
Author: Hsiuying Wang, Yu-Chun Lin, Wan-Ting Huang
Maintainer: Hsiuying Wang <wang@stat.nycu.edu.tw>
Diff between RankResponse versions 3.1.1 dated 2014-09-11 and 4.0.0 dated 2022-05-11
RankResponse-3.1.1/RankResponse/R/rank.L2R.R |only RankResponse-3.1.1/RankResponse/R/rank.LN.R |only RankResponse-3.1.1/RankResponse/R/rank.btmm.R |only RankResponse-3.1.1/RankResponse/R/rank.btnr.R |only RankResponse-3.1.1/RankResponse/R/rank.btqn.R |only RankResponse-3.1.1/RankResponse/man/rank.L2R.Rd |only RankResponse-3.1.1/RankResponse/man/rank.LN.Rd |only RankResponse-3.1.1/RankResponse/man/rank.btmm.Rd |only RankResponse-3.1.1/RankResponse/man/rank.btnr.Rd |only RankResponse-3.1.1/RankResponse/man/rank.btqn.Rd |only RankResponse-4.0.0/RankResponse/DESCRIPTION | 24 +- RankResponse-4.0.0/RankResponse/MD5 | 26 +-- RankResponse-4.0.0/RankResponse/NAMESPACE | 11 + RankResponse-4.0.0/RankResponse/R/rank.gs.R | 195 ++++++++++++++--------- RankResponse-4.0.0/RankResponse/R/rank.wald.R | 188 ++++++++++++++-------- RankResponse-4.0.0/RankResponse/R/rankL2R.R |only RankResponse-4.0.0/RankResponse/R/rankLN.R |only RankResponse-4.0.0/RankResponse/man/rank.gs.Rd | 117 ++++++++----- RankResponse-4.0.0/RankResponse/man/rank.wald.Rd | 117 ++++++++----- RankResponse-4.0.0/RankResponse/man/rankL2R.Rd |only RankResponse-4.0.0/RankResponse/man/rankLN.Rd |only 21 files changed, 428 insertions(+), 250 deletions(-)
Title: Bivariate (Two-Dimensional) Confidence Region and Frequency
Distribution
Description: Generic functions to analyze the distribution of two continuous
variables: 'conf2d' to calculate a smooth empirical confidence region, and
'freq2d' to calculate a frequency distribution.
Author: Arni Magnusson [aut, cre],
Julian Burgos [aut],
Gregory R. Warnes [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between r2d2 versions 1.0-0 dated 2014-03-31 and 1.0.1 dated 2022-05-11
r2d2-1.0-0/r2d2/NEWS |only r2d2-1.0.1/r2d2/DESCRIPTION | 30 ++++++++++++++++-------------- r2d2-1.0.1/r2d2/MD5 | 19 ++++++++++--------- r2d2-1.0.1/r2d2/NAMESPACE | 2 ++ r2d2-1.0.1/r2d2/NEWS.md |only r2d2-1.0.1/r2d2/R/conf2d.R | 26 +++++++++++++++----------- r2d2-1.0.1/r2d2/R/freq2d.R | 20 ++++++++++++-------- r2d2-1.0.1/r2d2/build |only r2d2-1.0.1/r2d2/data/Ushape.rda |binary r2d2-1.0.1/r2d2/data/saithe.rda |binary r2d2-1.0.1/r2d2/man/r2d2-package.Rd | 15 +++++++++------ r2d2-1.0.1/r2d2/man/saithe.Rd | 15 ++++++++++----- 12 files changed, 74 insertions(+), 53 deletions(-)
Title: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and
Machine Learning Toolkit
Description: Extracts features from amplification curve data of quantitative
Polymerase Chain Reactions (qPCR) (Pabinger S. et al. (2014)
<doi:10.1016/j.bdq.2014.08.002>) for machine learning purposes. Helper
functions prepare the amplification curve data for processing as functional
data (e.g., Hausdorff distance) or enable the plotting of amplification
curve classes (negative, ambiguous, positive). The hookreg() and hookregNL()
functions (Burdukiewicz M. et al. (2018) <doi:10.1016/j.bdq.2018.08.001>)
can be used to predict amplification curves with an hook effect-like
curvature. The pcrfit_single() function can be used to extract features
from an amplification curve.
Author: Stefan Roediger [cre, aut] ,
Michal Burdukiewicz [aut] ,
Andrej-Nikolai Spiess [aut] ,
Konstantin A. Blagodatskikh [aut]
,
Dominik Rafacz [ctb]
Maintainer: Stefan Roediger <stefan.roediger@b-tu.de>
Diff between PCRedux versions 1.1 dated 2021-03-16 and 1.1-2 dated 2022-05-11
PCRedux-1.1-2/PCRedux/CHANGELOG | 5 ++ PCRedux-1.1-2/PCRedux/DESCRIPTION | 10 ++--- PCRedux-1.1-2/PCRedux/MD5 | 24 +++++-------- PCRedux-1.1-2/PCRedux/NAMESPACE | 1 PCRedux-1.1-2/PCRedux/NEWS | 6 +++ PCRedux-1.1-2/PCRedux/R/pcrfit_single.R | 2 - PCRedux-1.1-2/PCRedux/R/run_PCRedux.R | 5 +- PCRedux-1.1-2/PCRedux/build/vignette.rds |binary PCRedux-1.1-2/PCRedux/inst/doc/PCRedux.pdf |binary PCRedux-1.1-2/PCRedux/man/run_PCRedux.Rd | 3 + PCRedux-1.1-2/PCRedux/tests/testthat/test_decision_modus.R | 5 +- PCRedux-1.1-2/PCRedux/tests/testthat/test_earlyreg.R | 4 +- PCRedux-1.1/PCRedux/R/PCRedux_gui.R |only PCRedux-1.1/PCRedux/man/PCRedux_gui.Rd |only 14 files changed, 38 insertions(+), 27 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.4.5 dated 2022-04-06 and 1.5.1 dated 2022-05-11
GetTDData-1.4.5/GetTDData/tests/testthat/test_gtdd.R |only GetTDData-1.5.1/GetTDData/DESCRIPTION | 13 GetTDData-1.5.1/GetTDData/LICENSE |only GetTDData-1.5.1/GetTDData/MD5 | 38 - GetTDData-1.5.1/GetTDData/NEWS.md | 9 GetTDData-1.5.1/GetTDData/R/gtdd_download_TD_data.R | 2 GetTDData-1.5.1/GetTDData/R/gtdd_get_yield_curve.R | 6 GetTDData-1.5.1/GetTDData/R/gtdd_read_TD_files.R | 81 -- GetTDData-1.5.1/GetTDData/R/gtdd_utils.R |only GetTDData-1.5.1/GetTDData/README.md | 21 GetTDData-1.5.1/GetTDData/build/vignette.rds |binary GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_GetTDData.R | 88 +-- GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_GetTDData.Rmd | 92 +-- GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_GetTDData.html | 272 ++++++++-- GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_YieldCurve.R | 30 - GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_YieldCurve.Rmd | 10 GetTDData-1.5.1/GetTDData/inst/doc/gtdd-vignette_YieldCurve.html | 30 - GetTDData-1.5.1/GetTDData/man/read.TD.files.Rd | 14 GetTDData-1.5.1/GetTDData/tests/testthat/test-importing-data.R |only GetTDData-1.5.1/GetTDData/tests/testthat/test-utils.R |only GetTDData-1.5.1/GetTDData/tests/testthat/test-yc.R |only GetTDData-1.5.1/GetTDData/vignettes/gtdd-vignette_GetTDData.Rmd | 92 +-- GetTDData-1.5.1/GetTDData/vignettes/gtdd-vignette_YieldCurve.Rmd | 10 23 files changed, 457 insertions(+), 351 deletions(-)
Title: Linear Inverse Model Examples and Solution Methods
Description: Functions that read and solve linear inverse problems (food web problems, linear programming problems).
These problems find solutions to linear or quadratic functions:
min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(ai*xi)
subject to equality constraints Ex=f and inequality constraints Gx>=h.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Dick van Oevelen<dick.vanoevelen@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between LIM versions 1.4.6 dated 2014-12-26 and 1.4.7 dated 2022-05-11
LIM-1.4.6/LIM/build |only LIM-1.4.6/LIM/inst/doc/LIM.Rnw |only LIM-1.4.6/LIM/inst/doc/LIMecoli.R |only LIM-1.4.6/LIM/inst/doc/LIMecoli.Rnw |only LIM-1.4.7/LIM/DESCRIPTION | 18 - LIM-1.4.7/LIM/MD5 | 48 ++-- LIM-1.4.7/LIM/NAMESPACE | 48 ++-- LIM-1.4.7/LIM/R/read.limfile.r | 2 LIM-1.4.7/LIM/data/FILERigaAutumn.rda |binary LIM-1.4.7/LIM/data/LIMBlending.rda |binary LIM-1.4.7/LIM/data/LIMBrouageMudflat.rda |binary LIM-1.4.7/LIM/data/LIMCaliforniaSediment.rda |binary LIM-1.4.7/LIM/data/LIMCoralRockall.rda |binary LIM-1.4.7/LIM/data/LIMEcoli.rda |binary LIM-1.4.7/LIM/data/LIMEverglades.rda |binary LIM-1.4.7/LIM/data/LIMRigaAutumn.rda |binary LIM-1.4.7/LIM/data/LIMRigaSpring.rda |binary LIM-1.4.7/LIM/data/LIMRigaSummer.rda |binary LIM-1.4.7/LIM/data/LIMScheldtIntertidal.rda |binary LIM-1.4.7/LIM/data/LIMTakapoto.rda |binary LIM-1.4.7/LIM/data/LIMinputBlending.rda |binary LIM-1.4.7/LIM/inst/CITATION | 1 LIM-1.4.7/LIM/man/Flowmatrix.Rd | 79 +++---- LIM-1.4.7/LIM/man/LIM.Rd | 6 LIM-1.4.7/LIM/man/LIMCoralRockall.Rd | 167 ++++++++-------- LIM-1.4.7/LIM/man/LIMEcoli.Rd | 274 +++++++++++++-------------- LIM-1.4.7/LIM/man/Xsample.Rd | 146 +++++++------- 27 files changed, 391 insertions(+), 398 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] ,
Wil Davis [ctb] ,
Spencer Matthews [ctb] ,
JavaScript and CSS libraries authors [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.6.4 dated 2022-02-06 and 0.7.0 dated 2022-05-11
shinyWidgets-0.6.4/shinyWidgets/inst/assets/autonumeric/autoNumeric.min.js.map |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/bower.json |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/composer.json |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/bootstrap-select.min.js.map |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/i18n/defaults-am_ET.js.map |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/i18n/defaults-am_ET.min.js |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/i18n/defaults-ar_AR.js.map |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/i18n/defaults-ar_AR.min.js |only shinyWidgets-0.6.4/shinyWidgets/inst/assets/bootstrap-select-1.14.0-beta2/js/i18n/defaults-bg_BG.js.map |only 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Title: One Sample Mendelian Randomization and Instrumental Variable
Analyses
Description: Useful functions for one-sample (individual level data)
Mendelian randomization and instrumental variable analyses. The
package includes implementations of; the Sanderson and Windmeijer
(2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic,
the multiplicative structural mean model Hernán and Robins (2006)
<doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor
substitution and two-stage residual inclusion estimators explained by
Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] ,
Wes Spiller [aut] ,
Eleanor Sanderson [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between OneSampleMR versions 0.1.1 dated 2022-04-28 and 0.1.2 dated 2022-05-11
DESCRIPTION | 9 MD5 | 66 - NAMESPACE | 76 - NEWS.md | 20 R/asmm.R | 118 +- R/fsw.R | 290 ++--- R/msmm.R | 2 R/onesamplemr-package.R | 58 - R/tsps.R | 1106 +++++++++---------- R/tsri.R | 1234 +++++++++++----------- README.md | 88 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/compare-smm-fits.R | 85 - inst/doc/compare-smm-fits.Rmd | 145 +- inst/doc/compare-smm-fits.html | 1165 ++++++++++---------- inst/doc/f-statistic-comparison.R | 62 - inst/doc/f-statistic-comparison.Rmd | 12 inst/doc/f-statistic-comparison.html | 1179 ++++++++++----------- man/OneSampleMR-package.Rd | 68 - man/asmm.Rd | 126 +- man/fsw.Rd | 110 - man/msmm.Rd | 348 +++--- man/summary.msmm.Rd | 76 - man/summary.tsps.Rd | 74 - man/summary.tsri.Rd | 74 - man/tsps.Rd | 242 ++-- man/tsri.Rd | 274 ++-- tests/testthat/test-fsw.R | 1949 +++++++++++++++++------------------ tests/testthat/test-msmm.R | 30 tests/testthat/test-tsps.R | 512 ++++----- tests/testthat/test-tsri.R | 582 +++++----- vignettes/compare-smm-fits.Rmd | 145 +- vignettes/f-statistic-comparison.Rmd | 12 34 files changed, 5144 insertions(+), 5193 deletions(-)
Title: Event Data Repository
Description: Event dataset repository including both real-life and artificial event logs. They can be used in combination with functionalities provided by the 'bupaR' packages. Janssenswillen et al. (2020) <http://ceur-ws.org/Vol-2703/paperTD7.pdf>.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between eventdataR versions 0.2.0 dated 2018-03-20 and 0.3.0 dated 2022-05-11
eventdataR-0.2.0/eventdataR/data/datalist |only eventdataR-0.3.0/eventdataR/DESCRIPTION | 15 +++---- eventdataR-0.3.0/eventdataR/MD5 | 36 ++++++++--------- eventdataR-0.3.0/eventdataR/R/datasets_documentation.R | 8 +++ eventdataR-0.3.0/eventdataR/build/vignette.rds |binary eventdataR-0.3.0/eventdataR/data/hospital.rda |binary eventdataR-0.3.0/eventdataR/data/hospital_billing.rda |binary eventdataR-0.3.0/eventdataR/data/patients.rda |binary eventdataR-0.3.0/eventdataR/data/patients_act.rda |only eventdataR-0.3.0/eventdataR/data/sepsis.rda |binary eventdataR-0.3.0/eventdataR/data/traffic_fines.rda |binary eventdataR-0.3.0/eventdataR/inst/doc/eventdataR.html | 34 ++++++++++++---- eventdataR-0.3.0/eventdataR/inst/doc/eventdataR.rmd | 2 eventdataR-0.3.0/eventdataR/man/eventdataR.Rd | 1 eventdataR-0.3.0/eventdataR/man/example_log.Rd | 11 ++++- eventdataR-0.3.0/eventdataR/man/hospital.Rd | 4 + eventdataR-0.3.0/eventdataR/man/hospital_billing.Rd | 4 + eventdataR-0.3.0/eventdataR/man/sepsis.Rd | 4 + eventdataR-0.3.0/eventdataR/man/traffic_fines.Rd | 4 + eventdataR-0.3.0/eventdataR/vignettes/eventdataR.rmd | 2 20 files changed, 84 insertions(+), 41 deletions(-)
Title: Managing, Querying and Analyzing Tokenized Text
Description: Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations).
Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences),
similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages,
and the possibility to reconstruct original text from tokens to facilitate interpretation.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between corpustools versions 0.4.9 dated 2022-01-23 and 0.4.10 dated 2022-05-11
corpustools-0.4.10/corpustools/DESCRIPTION | 19 ++--- corpustools-0.4.10/corpustools/MD5 | 30 +++---- corpustools-0.4.10/corpustools/R/RcppExports.R | 8 -- corpustools-0.4.10/corpustools/R/create_tcorpus.r | 16 +++- corpustools-0.4.10/corpustools/R/data.r | 1 corpustools-0.4.10/corpustools/R/preprocessing.r | 2 corpustools-0.4.10/corpustools/R/search_dictionary.r | 37 +++++---- corpustools-0.4.10/corpustools/R/untokenize.r | 1 corpustools-0.4.10/corpustools/inst/doc/corpustools.html | 8 +- corpustools-0.4.10/corpustools/man/create_tcorpus.Rd | 4 + corpustools-0.4.10/corpustools/man/search_dictionary.Rd | 2 corpustools-0.4.10/corpustools/man/tCorpus-cash-code_dictionary.Rd | 2 corpustools-0.4.10/corpustools/src/RcppExports.cpp | 38 ---------- corpustools-0.4.10/corpustools/src/dictionary_lookup.cpp | 1 corpustools-0.4.10/corpustools/src/hit_ids_sequence.cpp | 2 corpustools-0.4.9/corpustools/R/udpipe_coref.r |only corpustools-0.4.9/corpustools/src/coref.cpp |only 17 files changed, 67 insertions(+), 104 deletions(-)
Title: 'HTMLWidget' Wrapper of 'UpSet.js' for Exploring Large Set
Intersections
Description: 'UpSet.js' is a re-implementation of 'UpSetR' to create interactive set visualizations for more than three sets.
This is a 'htmlwidget' wrapper around the 'JavaScript' library 'UpSet.js'.
Author: Samuel Gratzl [aut, cre]
Maintainer: Samuel Gratzl <sam@sgratzl.com>
Diff between upsetjs versions 1.10.11 dated 2022-01-27 and 1.11.0 dated 2022-05-11
DESCRIPTION | 8 MD5 | 26 +-- R/selection.R | 23 ++ build/vignette.rds |binary inst/dash/upsetjs.js | 2 inst/doc/colors.html | 102 ++++-------- inst/doc/combinationModes.html | 128 +++++---------- inst/doc/got.html | 85 +++------- inst/doc/kmap.html | 97 ++++------- inst/doc/upsetjs.html | 340 ++++++++++++++++++++++------------------- inst/doc/venn.html | 105 ++++-------- inst/htmlwidgets/upsetjs.js | 2 man/interactiveChart.Rd | 4 man/setSelection.Rd | 2 14 files changed, 420 insertions(+), 504 deletions(-)
Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling enables to estimate net rainfall from streamflow measurements
following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>.
Resulting net rainfall is then estimated on the ungauged catchments
by spatial interpolation in order to finally simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 0.1.1 dated 2021-12-20 and 0.1.2 dated 2022-05-11
DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 1 R/hdist.R | 4 R/mixr.R | 10 R/quick_transfr.R |only build/partial.rdb |binary build/vignette.rds |binary data/Blavet.rda |binary data/Oudon.rda |binary inst/doc/V01_get_started.html | 340 ++++++++++++++++++++++++++--- inst/doc/V02_inputs_preparation_stars.R |only inst/doc/V02_inputs_preparation_stars.Rmd |only inst/doc/V02_inputs_preparation_stars.html |only man/hdist.Rd | 2 man/mixr.Rd | 8 man/quick_transfr.Rd |only vignettes/V02_inputs_preparation_stars.Rmd |only 18 files changed, 349 insertions(+), 54 deletions(-)
Title: Sparse Method to Identify Joint Effects of Functional Predictors
Description: A set of functions allowing to implement the 'SpiceFP' approach
which is iterative. It involves transformation of functional
predictors into several candidate explanatory matrices (based on contingency
tables), to which relative edge matrices with contiguity constraints are
associated. Generalized Fused Lasso regression are performed in order to
identify the best candidate matrix, the best class intervals and related
coefficients at each iteration. The approach is stopped when the maximal number
of iterations is reached or when retained coefficients are zeros. Supplementary
functions allow to get coefficients of any candidate matrix or mean of
coefficients of many candidates.
Author: Girault Gnanguenon Guesse [aut, cre],
Patrice Loisel [aut],
Benedicte Fontez [aut],
Nadine Hilgert [aut],
Thierry Simonneau [ctr],
Isabelle Sanchez [ctr]
Maintainer: Girault Gnanguenon Guesse <girault.gnanguenon@gmail.com>
Diff between SpiceFP versions 0.1.0 dated 2021-09-15 and 0.1.1 dated 2022-05-11
DESCRIPTION | 13 ++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- R/candidates.R | 6 +++--- R/coef_spicefp.R | 34 +++++++++++++++++----------------- R/hist_2d.R | 4 ++-- R/meancoef.R | 18 +++++++++--------- R/spicefp.R | 20 ++++++++++---------- README.md | 6 +++--- build/vignette.rds |binary inst/doc/article_SpiceFP.pdf |binary man/SpiceFP-package.Rd | 11 +---------- man/coef_spicefp.Rd | 34 +++++++++++++++++----------------- man/hist_2d.Rd | 4 ++-- man/meancoef.Rd | 18 +++++++++--------- man/spicefp.Rd | 18 +++++++++--------- vignettes/R_Package_SpiceFP.pdf |binary 17 files changed, 105 insertions(+), 115 deletions(-)
Title: Statistical Estimation of Cluster Parameters
Description: Estimating parameters of site clusters on 2D & 3D square lattice with various lattice sizes, relative fractions of open sites (occupation probability), iso- & anisotropy, von Neumann & Moore (1,d)-neighborhoods, described by Moskalev P.V. et al. (2011) <arXiv:1105.2334v1>.
Author: Pavel V. Moskalev
Maintainer: Pavel V. Moskalev <moskalefff@gmail.com>
Diff between SECP versions 0.1-4 dated 2012-07-09 and 0.1.5 dated 2022-05-11
DESCRIPTION | 21 +--- MD5 | 16 +-- NAMESPACE | 13 -- man/SECP-package.Rd | 59 +++++------ man/fdc2s.Rd | 260 +++++++++++++++++++++++++------------------------- man/fdc3s.Rd | 266 +++++++++++++++++++++++++-------------------------- man/fds2s.Rd | 270 ++++++++++++++++++++++++++-------------------------- man/fds3s.Rd | 266 +++++++++++++++++++++++++-------------------------- man/isc2s.Rd | 118 +++++++++++----------- 9 files changed, 639 insertions(+), 650 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@statistik.tu-dortmund.de>
Diff between glmmLasso versions 1.6.0 dated 2022-05-05 and 1.6.1 dated 2022-05-11
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/glmmLasso_RE.R | 5 ----- R/glmmLasso_noRE.R | 5 ----- man/glmmLasso.rd | 4 ++-- tests |only 6 files changed, 11 insertions(+), 20 deletions(-)
Title: Canonical Non-Symmetrical Correspondence Analysis in R
Description: A GUI with which users can construct and interact
with Canonical Correspondence Analysis and Canonical Non-Symmetrical Correspondence Analysis and provides inferential results by using Bootstrap Methods.
Author: Ana Belen Nieto Librero <ananieto@usal.es>, Priscila Willems
<pwillems@bariloche.inta.gov.ar>, Purificacion Galindo
Villardon <pgalindo@usal.es>
Maintainer: Ana Belen Nieto Librero <ananieto@usal.es>
Diff between cncaGUI versions 1.0 dated 2015-06-21 and 1.1 dated 2022-05-11
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 4 ++++ man/cncaGUI-package.Rd | 6 +++--- 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker [aut, cre],
R Development Core Team [aut],
Iago Gine-Vazquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.24 dated 2021-08-05 and 1.0.25 dated 2022-05-11
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- R/IC.R | 4 +++- R/confint.R | 2 +- R/predict.R | 23 +++++++++++++---------- inst/NEWS.Rd | 13 +++++++++++++ inst/doc/mle2.R | 27 +++++++++++++++++++++++++++ inst/doc/mle2.pdf |binary inst/doc/quasi.R | 35 +++++++++++++++++++---------------- inst/doc/quasi.Rnw | 35 +++++++++++++++++++---------------- inst/doc/quasi.pdf |binary vignettes/quasi.Rnw | 35 +++++++++++++++++++---------------- 13 files changed, 131 insertions(+), 76 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <https://cyclestreets.net/> and
calculation of route segment attributes such as bearing.
The package implements the 'travel flow aggregration' method
described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779>.
Further information on the package's aim and scope can be found
in the vignettes and in a paper in the R Journal
(Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>.
This package Suggests the 'pct' package which at the time of writing
is unavailable on CRAN. You can install it from the repository
'itsleeds/pct' on GitHub.
Author: Robin Lovelace [aut, cre] ,
Richard Ellison [aut],
Malcolm Morgan [aut] ,
Barry Rowlingson [ctb],
Nick Bearman [ctb],
Nikolai Berkoff [ctb],
Scott Chamberlain [rev] ,
Mark Padgham [ctb],
Andrea Gilardi [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.8.7 dated 2022-02-01 and 0.9.0 dated 2022-05-11
DESCRIPTION | 6 MD5 | 83 ++-- NAMESPACE | 2 NEWS.md | 6 R/google-functions.R | 6 R/line_segment.R |only R/oneway.R | 8 R/route-transport-api.R | 4 R/route_bikecitizens.R | 26 - R/route_cyclestreets.R | 5 R/zzz.R |only README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/stplanr-od.Rmd | 2 inst/doc/stplanr-od.html | 358 +++++++++++++++--- inst/doc/stplanr-paper.html | 762 +++++++++++++++++++++++++++++++++------ inst/doc/stplanr-parallel.html | 10 inst/doc/stplanr-route-nets.html | 68 ++- inst/doc/stplanr-routing.html | 20 - inst/doc/stplanr.html | 237 ++++++++++-- man/angle_diff.Rd | 1 man/geo_toptail.Rd | 1 man/is_linepoint.Rd | 1 man/line2df.Rd | 1 man/line2points.Rd | 1 man/line_bearing.Rd | 1 man/line_breakup.Rd | 1 man/line_midpoint.Rd | 1 man/line_sample.Rd | 1 man/line_segment.Rd | 1 man/line_segment_sf.Rd |only man/line_via.Rd | 1 man/mats2line.Rd | 1 man/n_sample_length.Rd | 1 man/n_vertices.Rd | 1 man/onewaygeo.Rd | 1 man/points2line.Rd | 1 man/route_bikecitizens.Rd | 12 man/toptail_buff.Rd | 1 man/toptailgs.Rd | 1 man/update_line_geometry.Rd | 1 vignettes/references.bib | 2 vignettes/stplanr-od.Rmd | 2 44 files changed, 1314 insertions(+), 325 deletions(-)
Title: Feature Selection SVM using Penalty Functions
Description: Support Vector Machine (SVM) classification with simultaneous feature selection using penalty
functions is implemented. The smoothly clipped absolute deviation (SCAD),
'L1-norm', 'Elastic Net' ('L1-norm' and 'L2-norm') and 'Elastic
SCAD' (SCAD and 'L2-norm') penalties are available. The tuning
parameters can be found using either a fixed grid or a interval
search.
Author: Natalia Becker, Wiebke Werft, Axel Benner
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between penalizedSVM versions 1.1.2 dated 2018-07-26 and 1.1.3 dated 2022-05-11
DESCRIPTION | 12 MD5 | 17 NEWS.md |only R/EPSGO.R | 938 +++++++++++++++++++++---------------------- R/penalizedSVM-internal.R | 690 +++++++++++++++---------------- man/EPSGO.Rd | 304 ++++++------- man/findgacv.scad.Rd | 106 ++-- man/penalizedSVM-internal.Rd | 34 - man/penalizedSVM-package.Rd | 81 +-- man/svmfs.Rd | 437 ++++++++++---------- 10 files changed, 1312 insertions(+), 1307 deletions(-)
Title: Models and Equations for Human Comfort Research
Description: Calculation of various common and less common comfort indices such as predicted mean vote or the two node model. Converts physical variables such as relative to absolute humidity and evaluates the performance of comfort indices.
Author: Marcel Schweiker [aut, cre] ,
Sophia Mueller [aut],
Michael Kleber [ctr],
Boris Kingma [ctr] ,
Masanori Shukuya [ctr] ,
Shaomi Rahman [ctr],
Shoaib Sarwar [ctr]
Maintainer: Marcel Schweiker <mschweiker@ukaachen.de>
Diff between comf versions 0.1.10 dated 2021-02-12 and 0.1.11 dated 2022-05-11
DESCRIPTION | 9 - MD5 | 129 +++++++++--------- NAMESPACE | 4 NEWS | 11 + R/ComfortIndices.r | 4 R/calc2Node.r | 38 +++-- R/calcATHB2.r |only R/calcATHBpmv.r | 13 + R/calcATHBpts.R | 6 R/calcATHBset.R | 6 R/calcComfInd.R | 6 R/calcMRT.r |only R/calcPMVPPD.R | 18 +- R/calcSET.r | 2 R/fctHelp.r | 15 +- README.md |only inst/doc/R_packages-comf.ltx | 36 ++--- inst/doc/R_packages-comf.pdf |binary man/calc2Node.Rd | 204 ++++++++++++++--------------- man/calcAD.Rd | 90 ++++++------- man/calcATHBpmv.Rd | 20 +- man/calcATHBpmv2015.Rd |only man/calcATHBpts.Rd | 113 ++++++++-------- man/calcATHBset.Rd | 111 ++++++++-------- man/calcAvgAcc.Rd | 100 +++++++------- man/calcBias.Rd | 130 +++++++++--------- man/calcCE.Rd | 86 ++++++------ man/calcComfInd.Rd | 218 +++++++++++++++---------------- man/calcDisc.Rd | 188 +++++++++++++-------------- man/calcET.Rd | 188 +++++++++++++-------------- man/calcHbExSteady.Rd | 288 ++++++++++++++++++++--------------------- man/calcHbExUnsteady.Rd | 264 +++++++++++++++++++------------------- man/calcIso7933.Rd | 290 +++++++++++++++++++++--------------------- man/calcMRT.Rd |only man/calcPD.Rd | 188 +++++++++++++-------------- man/calcPMV.Rd | 96 ++++++------- man/calcPMVGagge.Rd | 188 +++++++++++++-------------- man/calcPMVPPD.Rd | 110 ++++++++------- man/calcPMVStar.Rd | 192 +++++++++++++-------------- man/calcPMVadj.Rd | 86 ++++++------ man/calcPPD.Rd | 96 ++++++------- man/calcPS.Rd | 192 +++++++++++++-------------- man/calcPTS.Rd | 190 +++++++++++++-------------- man/calcPtsa.Rd | 190 +++++++++++++-------------- man/calcPtse.Rd | 190 +++++++++++++-------------- man/calcSET.Rd | 184 +++++++++++++------------- man/calcSkinWettedness.Rd | 194 ++++++++++++++-------------- man/calcSolarGain.Rd | 104 +++++++-------- man/calcTNZPDF.Rd | 264 +++++++++++++++++++------------------- man/calcTPRTSV.Rd | 88 ++++++------ man/calcTSens.Rd | 184 +++++++++++++------------- man/calcTWC.Rd | 82 +++++------ man/calcTroin.Rd | 106 +++++++-------- man/calcVTG.Rd | 94 ++++++------- man/calcdTNZ.Rd | 182 +++++++++++++------------- man/calcepCoeff.Rd | 138 +++++++++---------- man/comf-package.Rd | 4 man/createCond.Rd | 152 +++++++++++----------- man/cutTSV.Rd | 70 +++++----- man/dfASHRAETableG11.Rd | 72 +++++----- man/dfField.Rd | 74 +++++----- man/dfISO7730AppE.Rd | 62 ++++---- man/dfISO7730TableD1.Rd | 66 ++++----- man/dfISO7933AppF.Rd | 82 +++++------ man/dfSolarGainValues.Rd | 66 ++++----- man/dfUTCIValues.Rd | 60 ++++---- man/dfVariables.Rd | 56 ++++---- vignettes/R_packages-comf.ltx | 36 ++--- 68 files changed, 3382 insertions(+), 3343 deletions(-)
Title: Case Influence in Structural Equation Models
Description: A set of tools for evaluating several measures of case influence for structural equation models.
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between influence.SEM versions 2.2 dated 2018-04-14 and 2.3 dated 2022-05-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS | 7 +++++++ R/Deltachi.R | 2 +- R/Likedist.R | 2 +- R/fitinfluence.R | 4 +--- R/genCookDist.R | 7 +++---- R/parinfluence.R | 5 ++--- man/Deltachi.Rd | 5 ++++- man/sem.fitres.Rd | 4 +--- 11 files changed, 35 insertions(+), 30 deletions(-)
Title: Various R Programming Tools for Data Manipulation
Description: Various R programming tools for data manipulation, including:
- medical unit conversions ('ConvertMedUnits', 'MedUnits'),
- combining objects ('bindData', 'cbindX', 'combine', 'interleave'),
- character vector operations ('centerText', 'startsWith', 'trim'),
- factor manipulation ('levels', 'reorder.factor', 'mapLevels'),
- obtaining information about R objects ('object.size', 'elem', 'env',
'humanReadable', 'is.what', 'll', 'keep', 'ls.funs',
'Args','nPairs', 'nobs'),
- manipulating MS-Excel formatted files ('read.xls',
'installXLSXsupport', 'sheetCount', 'xlsFormats'),
- generating fixed-width format files ('write.fwf'),
- extricating components of date & time objects ('getYear', 'getMonth',
'getDay', 'getHour', 'getMin', 'getSec'),
- operations on columns of data frames ('matchcols', 'rename.vars'),
- matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'),
- operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'),
- operations on data frames ('frameApply', 'wideByFactor'),
- value of last evaluated expression ('ans'), and
- wrapper for 'sample' that ensures consistent behavior for both
scalar and vector arguments ('resample').
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
Magnusson, Jim Rogers, and others
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gdata versions 2.18.0 dated 2017-06-06 and 2.18.0.1 dated 2022-05-11
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/env.R | 2 +- R/is.what.R | 2 +- R/ll.R | 2 +- man/ConvertMedUnits.Rd | 2 +- man/MedUnits.Rd | 2 +- man/humanReadable.Rd | 6 +++--- man/rename.vars.Rd | 2 +- 9 files changed, 20 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-10 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-24 0.9.4
2016-07-01 0.9.0
2015-09-29 0.8.0
2014-08-12 0.6.1
2014-02-26 0.6
2014-01-17 0.5
2013-07-25 0.3
2013-02-27 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-26 0.8.3
2016-08-24 0.8.1
2013-12-18 0.7
2013-10-01 0.5
2013-07-23 0.4
2013-04-15 0.3