Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.3.2 dated 2021-01-10 and 1.3.3 dated 2023-04-14
DESCRIPTION | 16 - MD5 | 54 +-- NAMESPACE | 1 NEWS.md | 4 R/BinaryYScatterPlot.R | 6 R/ClevelandDotPlot.R | 10 R/ConditionalSmoothedScatterPlot.R | 12 R/DiscreteDistribution.R | 2 R/DistributionPlot.R | 14 R/DoubleDensity.R | 8 R/DoubleHistogram.R | 10 R/FitHistoryPlot.R | 14 R/GainCurve.R | 2 R/HexBinPlot.R | 4 R/PRPlot.R | 11 R/PairPlot.R | 4 R/ROC.R | 70 ++-- R/ScatterBoxPlot.R | 4 R/ScatterHist.R | 6 R/ScatterHistC.R | 12 R/SimulateAESString.R |only R/ThresholdPlot.R | 6 build/vignette.rds |binary inst/doc/WVPlots_concept.html | 386 +++++++++++++------------ inst/doc/WVPlots_examples.html | 555 ++++++++++++++++++------------------- man/ClevelandDotPlot.Rd | 6 man/GainCurvePlot.Rd | 2 man/plotlyROC.Rd | 3 man/simulate_aes_string.Rd |only 29 files changed, 638 insertions(+), 584 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] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between themis versions 1.0.0 dated 2022-07-02 and 1.0.1 dated 2023-04-14
themis-1.0.0/themis/R/tuneable.R |only themis-1.0.0/themis/man/tunable.step_adasyn.Rd |only themis-1.0.1/themis/DESCRIPTION | 32 +- themis-1.0.1/themis/LICENSE | 4 themis-1.0.1/themis/MD5 | 114 +++++----- themis-1.0.1/themis/NAMESPACE | 1 themis-1.0.1/themis/NEWS.md | 8 themis-1.0.1/themis/R/adasyn_impl.R | 7 themis-1.0.1/themis/R/bsmote_impl.R | 2 themis-1.0.1/themis/R/misc.R | 19 - themis-1.0.1/themis/R/nearmiss_impl.R | 2 themis-1.0.1/themis/R/smote_impl.R | 10 themis-1.0.1/themis/R/smotenc_impl.R | 6 themis-1.0.1/themis/R/step_adasyn.R | 25 ++ themis-1.0.1/themis/R/step_bsmote.R | 26 ++ themis-1.0.1/themis/R/step_downsample.R | 21 + themis-1.0.1/themis/R/step_nearmiss.R | 29 ++ themis-1.0.1/themis/R/step_rose.R | 22 + themis-1.0.1/themis/R/step_smote.R | 25 ++ themis-1.0.1/themis/R/step_smotenc.R | 23 +- themis-1.0.1/themis/R/step_tomek.R | 5 themis-1.0.1/themis/R/step_upsample.R | 22 + themis-1.0.1/themis/R/themis-package.R | 1 themis-1.0.1/themis/R/tomek_impl.R | 2 themis-1.0.1/themis/R/tunable.R |only themis-1.0.1/themis/README.md | 46 ++-- themis-1.0.1/themis/man/figures/logo.png |only themis-1.0.1/themis/man/rmd |only themis-1.0.1/themis/man/step_adasyn.Rd | 8 themis-1.0.1/themis/man/step_bsmote.Rd | 9 themis-1.0.1/themis/man/step_downsample.Rd | 7 themis-1.0.1/themis/man/step_nearmiss.Rd | 12 - themis-1.0.1/themis/man/step_rose.Rd | 7 themis-1.0.1/themis/man/step_smote.Rd | 8 themis-1.0.1/themis/man/step_smotenc.Rd | 8 themis-1.0.1/themis/man/step_upsample.Rd | 7 themis-1.0.1/themis/man/themis-package.Rd | 10 themis-1.0.1/themis/man/tunable_themis.Rd |only themis-1.0.1/themis/tests/testthat/_snaps/adasyn_impl.md | 2 themis-1.0.1/themis/tests/testthat/_snaps/bsmote_impl.md | 2 themis-1.0.1/themis/tests/testthat/_snaps/extension_check.md |only themis-1.0.1/themis/tests/testthat/_snaps/smote_impl.md | 2 themis-1.0.1/themis/tests/testthat/_snaps/smotenc.md | 74 +++--- themis-1.0.1/themis/tests/testthat/_snaps/step_adasyn.md | 104 ++++----- themis-1.0.1/themis/tests/testthat/_snaps/step_bsmote.md | 98 ++++---- themis-1.0.1/themis/tests/testthat/_snaps/step_downsample.md | 124 +++++------ themis-1.0.1/themis/tests/testthat/_snaps/step_nearmiss.md | 98 ++++---- themis-1.0.1/themis/tests/testthat/_snaps/step_rose.md | 98 ++++---- themis-1.0.1/themis/tests/testthat/_snaps/step_smote.md | 104 ++++----- themis-1.0.1/themis/tests/testthat/_snaps/step_tomek.md | 98 ++++---- themis-1.0.1/themis/tests/testthat/_snaps/step_upsample.md | 124 +++++------ themis-1.0.1/themis/tests/testthat/_snaps/tomek_impl.md | 2 themis-1.0.1/themis/tests/testthat/test-extension_check.R |only themis-1.0.1/themis/tests/testthat/test-smote_impl.R | 10 themis-1.0.1/themis/tests/testthat/test-smotenc.R | 54 +++- themis-1.0.1/themis/tests/testthat/test-step_adasyn.R | 42 ++- themis-1.0.1/themis/tests/testthat/test-step_bsmote.R | 44 ++- themis-1.0.1/themis/tests/testthat/test-step_downsample.R | 41 ++- themis-1.0.1/themis/tests/testthat/test-step_nearmiss.R | 43 ++- themis-1.0.1/themis/tests/testthat/test-step_rose.R | 42 ++- themis-1.0.1/themis/tests/testthat/test-step_smote.R | 43 ++- themis-1.0.1/themis/tests/testthat/test-step_upsample.R | 42 ++- 62 files changed, 1121 insertions(+), 698 deletions(-)
Title: Extra 'Recipes' for Text Processing
Description: Converting text to numerical features requires specifically
created procedures, which are implemented as steps according to the
'recipes' package. These steps allows for tokenization, filtering,
counting (tf and tfidf) and feature hashing.
Author: Emil Hvitfeldt [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between textrecipes versions 1.0.2 dated 2022-12-21 and 1.0.3 dated 2023-04-14
textrecipes-1.0.2/textrecipes/man/tunable.step.Rd |only textrecipes-1.0.3/textrecipes/DESCRIPTION | 31 textrecipes-1.0.3/textrecipes/LICENSE | 4 textrecipes-1.0.3/textrecipes/MD5 | 210 ++-- textrecipes-1.0.3/textrecipes/NAMESPACE | 8 textrecipes-1.0.3/textrecipes/NEWS.md | 12 textrecipes-1.0.3/textrecipes/R/0_imports.R | 3 textrecipes-1.0.3/textrecipes/R/aaa.R | 18 textrecipes-1.0.3/textrecipes/R/clean_levels.R | 9 textrecipes-1.0.3/textrecipes/R/clean_names.R | 9 textrecipes-1.0.3/textrecipes/R/embeddings.R | 18 textrecipes-1.0.3/textrecipes/R/hashing.R | 36 textrecipes-1.0.3/textrecipes/R/hashing_dummy.R | 29 textrecipes-1.0.3/textrecipes/R/lda.R | 10 textrecipes-1.0.3/textrecipes/R/lemma.R | 6 textrecipes-1.0.3/textrecipes/R/ngram.R | 12 textrecipes-1.0.3/textrecipes/R/pos_filter.R | 12 textrecipes-1.0.3/textrecipes/R/selections.R | 2 textrecipes-1.0.3/textrecipes/R/sequence_onehot.R | 16 textrecipes-1.0.3/textrecipes/R/stem.R | 6 textrecipes-1.0.3/textrecipes/R/stopwords.R | 6 textrecipes-1.0.3/textrecipes/R/text_normalization.R | 5 textrecipes-1.0.3/textrecipes/R/textfeature.R | 11 textrecipes-1.0.3/textrecipes/R/textrecipes-package.R | 8 textrecipes-1.0.3/textrecipes/R/tf.R | 32 textrecipes-1.0.3/textrecipes/R/tfidf.R | 25 textrecipes-1.0.3/textrecipes/R/tidy.R | 2 textrecipes-1.0.3/textrecipes/R/tokenfilter.R | 21 textrecipes-1.0.3/textrecipes/R/tokenize.R | 28 textrecipes-1.0.3/textrecipes/R/tokenize_bpe.R | 14 textrecipes-1.0.3/textrecipes/R/tokenize_sentencepiece.R | 14 textrecipes-1.0.3/textrecipes/R/tokenize_wordpiece.R | 18 textrecipes-1.0.3/textrecipes/R/tokenlist.R | 8 textrecipes-1.0.3/textrecipes/R/tokenmerge.R | 12 textrecipes-1.0.3/textrecipes/R/tunable.R |only textrecipes-1.0.3/textrecipes/R/untokenize.R | 6 textrecipes-1.0.3/textrecipes/README.md | 18 textrecipes-1.0.3/textrecipes/inst/doc/Working-with-n-grams.R | 22 textrecipes-1.0.3/textrecipes/inst/doc/Working-with-n-grams.Rmd | 22 textrecipes-1.0.3/textrecipes/inst/doc/Working-with-n-grams.html | 468 ++++------ textrecipes-1.0.3/textrecipes/inst/doc/cookbook---using-more-complex-recipes-involving-text.R | 30 textrecipes-1.0.3/textrecipes/inst/doc/cookbook---using-more-complex-recipes-involving-text.Rmd | 30 textrecipes-1.0.3/textrecipes/inst/doc/cookbook---using-more-complex-recipes-involving-text.html | 266 ++--- textrecipes-1.0.3/textrecipes/inst/doc/tokenlist.html | 2 textrecipes-1.0.3/textrecipes/man/figures/logo.png |binary textrecipes-1.0.3/textrecipes/man/rmd |only textrecipes-1.0.3/textrecipes/man/step_dummy_hash.Rd | 8 textrecipes-1.0.3/textrecipes/man/step_ngram.Rd | 7 textrecipes-1.0.3/textrecipes/man/step_texthash.Rd | 14 textrecipes-1.0.3/textrecipes/man/step_tf.Rd | 8 textrecipes-1.0.3/textrecipes/man/step_tokenfilter.Rd | 9 textrecipes-1.0.3/textrecipes/man/step_tokenize.Rd | 7 textrecipes-1.0.3/textrecipes/man/textrecipes-package.Rd | 8 textrecipes-1.0.3/textrecipes/man/tunable_textrecipes.Rd |only textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/bpe_tokenize.md | 76 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/clean_levels.md | 70 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/clean_names.md | 70 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/embeddings.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/extension_check.md |only textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/hashing.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/hashing_dummy.md | 79 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/lda.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/lemma.md | 80 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/ngram.md | 74 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/pos_filter.md | 80 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/sentencepiece_tokenize.md | 76 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/sequence_onehot.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/stem.md | 74 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/stopwords.md | 74 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/text_normalization.md | 70 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/textfeature.md | 91 + textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tf.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tfidf.md | 83 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tokenfilter.md | 94 -- textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tokenize.md | 82 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tokenizer-tokenizersbpe.md | 6 textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/tokenmerge.md | 89 + textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/untokenize.md | 74 - textrecipes-1.0.3/textrecipes/tests/testthat/_snaps/wordpiece_tokenize.md | 70 - textrecipes-1.0.3/textrecipes/tests/testthat/test-bpe_tokenize.R | 14 textrecipes-1.0.3/textrecipes/tests/testthat/test-clean_levels.R | 10 textrecipes-1.0.3/textrecipes/tests/testthat/test-clean_names.R | 1 textrecipes-1.0.3/textrecipes/tests/testthat/test-embeddings.R | 51 - textrecipes-1.0.3/textrecipes/tests/testthat/test-extension_check.R |only textrecipes-1.0.3/textrecipes/tests/testthat/test-hashing.R | 66 + textrecipes-1.0.3/textrecipes/tests/testthat/test-hashing_dummy.R | 66 + textrecipes-1.0.3/textrecipes/tests/testthat/test-lda.R | 41 textrecipes-1.0.3/textrecipes/tests/testthat/test-lemma.R | 3 textrecipes-1.0.3/textrecipes/tests/testthat/test-ngram.R | 50 - textrecipes-1.0.3/textrecipes/tests/testthat/test-pos_filter.R | 3 textrecipes-1.0.3/textrecipes/tests/testthat/test-s3-methods.R | 32 textrecipes-1.0.3/textrecipes/tests/testthat/test-sentencepiece_tokenize.R | 13 textrecipes-1.0.3/textrecipes/tests/testthat/test-sequence_onehot.R | 52 - textrecipes-1.0.3/textrecipes/tests/testthat/test-stem.R | 12 textrecipes-1.0.3/textrecipes/tests/testthat/test-stopwords.R | 12 textrecipes-1.0.3/textrecipes/tests/testthat/test-text_normalization.R | 10 textrecipes-1.0.3/textrecipes/tests/testthat/test-textfeature.R | 45 textrecipes-1.0.3/textrecipes/tests/testthat/test-tf.R | 74 + textrecipes-1.0.3/textrecipes/tests/testthat/test-tfidf.R | 66 - textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenfilter.R | 40 textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenize.R | 44 textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenizer-spacyr.R | 1 textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenizer-tokenizersbpe.R | 9 textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenlist.R | 56 - textrecipes-1.0.3/textrecipes/tests/testthat/test-tokenmerge.R | 28 textrecipes-1.0.3/textrecipes/tests/testthat/test-untokenize.R | 9 textrecipes-1.0.3/textrecipes/tests/testthat/test-wordpiece_tokenize.R | 13 textrecipes-1.0.3/textrecipes/vignettes/Working-with-n-grams.Rmd | 22 textrecipes-1.0.3/textrecipes/vignettes/cookbook---using-more-complex-recipes-involving-text.Rmd | 30 109 files changed, 2395 insertions(+), 1885 deletions(-)
Title: A Lightweight Wrapper for 'Slurm'
Description: 'Slurm', Simple Linux Utility for Resource Management
<https://slurm.schedmd.com/>, is a popular 'Linux' based software used to
schedule jobs in 'HPC' (High Performance Computing) clusters. This R package
provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to
that found in the 'parallel' R package. The package also includes a method for
creating socket cluster objects spanning multiple nodes that can be used with
the 'parallel' package.
Author: George Vega Yon [aut, cre] ,
Paul Marjoram [ctb, ths] ,
National Cancer Institute [fnd] ,
Michael Schubert [rev] ,
Michel Lang [rev]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between slurmR versions 0.5-2 dated 2022-06-22 and 0.5-3 dated 2023-04-14
DESCRIPTION | 9 MD5 | 22 - NEWS.md | 5 R/sourceSlurm.R | 3 README.md | 97 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 - inst/NEWS | 45 --- inst/doc/debugging-re-submission.html | 318 +++++++++++++++----------- inst/doc/getting-started.html | 414 +++++++++++++++++++++------------- inst/doc/working-with-slurm.html | 317 +++++++++++++++++--------- 12 files changed, 752 insertions(+), 502 deletions(-)
Title: Creates Simultaneous Testing Bands for QQ-Plots
Description: Provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous
testing bands to asses significance of sample deviation from a reference distribution <doi:10.18637/jss.v106.i10>.
Author: Eric Weine [aut, cre],
Mary Sara McPeek [aut],
Abney Mark [aut]
Maintainer: Eric Weine <ericweine15@gmail.com>
Diff between qqconf versions 1.3.1 dated 2023-01-09 and 1.3.2 dated 2023-04-14
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- R/ppplot.R | 8 +++++++- R/qqplot.R | 9 ++++++++- R/two_sided.R | 4 +++- inst/CITATION |only inst/doc/qqconf_introduction.html | 20 +++++++++----------- man/pp_conf_plot.Rd | 7 +++++++ man/qq_conf_plot.Rd | 7 +++++++ 9 files changed, 54 insertions(+), 26 deletions(-)
Title: Phylogenetic Monte Carlo
Description: Monte Carlo based model choice for applied phylogenetics of
continuous traits. Method described in Carl Boettiger, Graham Coop,
Peter Ralph (2012) Is your phylogeny informative? Measuring
the power of comparative methods, Evolution 66 (7)
2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between pmc versions 1.0.4 dated 2021-01-07 and 1.0.5 dated 2023-04-14
pmc-1.0.4/pmc/NEWS |only pmc-1.0.5/pmc/DESCRIPTION | 12 pmc-1.0.5/pmc/MD5 | 26 - pmc-1.0.5/pmc/NAMESPACE | 8 pmc-1.0.5/pmc/NEWS.md |only pmc-1.0.5/pmc/R/geiger.R | 12 pmc-1.0.5/pmc/R/pmc.R | 27 - pmc-1.0.5/pmc/README.md | 24 - pmc-1.0.5/pmc/build/vignette.rds |binary pmc-1.0.5/pmc/inst/CITATION | 4 pmc-1.0.5/pmc/inst/doc/pmc_tutorial.Rmd | 2 pmc-1.0.5/pmc/inst/doc/pmc_tutorial.html | 341 +++++++++-------- pmc-1.0.5/pmc/man/figures/README-unnamed-chunk-3-1.png |binary pmc-1.0.5/pmc/tests/testthat/test_pmc.R | 3 pmc-1.0.5/pmc/vignettes/pmc_tutorial.Rmd | 2 15 files changed, 262 insertions(+), 199 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library providing high-performance scalability protocols, a
cross-platform standard for messaging and communications. Serves as a
concurrency framework for building distributed applications, utilising 'aio'
objects which resolve automatically upon completion of asynchronous
operations. Implements synchronisation primitives, allowing R to wait upon
events being signalled by concurrent messaging threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 0.8.1 dated 2023-03-27 and 0.8.2 dated 2023-04-14
nanonext-0.8.1/nanonext/man/msg_pipe.Rd |only nanonext-0.8.1/nanonext/man/weakref-set.Rd |only nanonext-0.8.2/nanonext/DESCRIPTION | 6 nanonext-0.8.2/nanonext/MD5 | 55 +- nanonext-0.8.2/nanonext/NAMESPACE | 8 nanonext-0.8.2/nanonext/NEWS.md | 14 nanonext-0.8.2/nanonext/R/context.R | 27 + nanonext-0.8.2/nanonext/R/nano.R | 33 - nanonext-0.8.2/nanonext/R/ncurl.R | 2 nanonext-0.8.2/nanonext/R/socket.R | 12 nanonext-0.8.2/nanonext/R/stats.R | 2 nanonext-0.8.2/nanonext/R/sync.R | 49 +- nanonext-0.8.2/nanonext/R/tls.R | 1 nanonext-0.8.2/nanonext/R/utils.R | 21 - nanonext-0.8.2/nanonext/README.md | 44 +- nanonext-0.8.2/nanonext/man/close.Rd | 17 nanonext-0.8.2/nanonext/man/context.Rd | 8 nanonext-0.8.2/nanonext/man/cv.Rd | 2 nanonext-0.8.2/nanonext/man/is_aio.Rd | 2 nanonext-0.8.2/nanonext/man/lock.Rd |only nanonext-0.8.2/nanonext/man/ncurl_session.Rd | 2 nanonext-0.8.2/nanonext/man/request.Rd | 20 - nanonext-0.8.2/nanonext/man/stat.Rd | 2 nanonext-0.8.2/nanonext/src/aio.c | 508 +++++++++++---------------- nanonext-0.8.2/nanonext/src/core.c | 99 +++-- nanonext-0.8.2/nanonext/src/init.c | 10 nanonext-0.8.2/nanonext/src/nanonext.h | 11 nanonext-0.8.2/nanonext/src/tls.c | 45 -- nanonext-0.8.2/nanonext/src/utils.c | 2 nanonext-0.8.2/nanonext/tests/tests.R | 58 ++- 30 files changed, 506 insertions(+), 554 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: Barbosa A.M., Brown J.A., Jimenez-Valverde A., Real R.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.9 dated 2023-01-13 and 3.9.3 dated 2023-04-14
DESCRIPTION | 14 ++++---- MD5 | 32 +++++++++--------- NEWS | 56 ++++++++++++++++++++++++++++++++- R/AUC.R | 79 ++++++++++++++++++++++++---------------------- R/Boyce.R | 49 +++++++++++++++------------- R/confusionLabel.R | 16 ++++----- R/confusionMatrix.R | 12 +++---- R/optiThresh.R | 83 +++++++++++++++++++++++-------------------------- R/threshMeasures.R | 37 ++++++++++----------- R/varImp.R | 5 ++ data/rotif.mods.rda |binary inst/CITATION | 26 ++++++--------- man/AUC.Rd | 10 ++--- man/confusionLabel.Rd | 4 +- man/confusionMatrix.Rd | 4 +- man/modEvA-package.Rd | 4 +- man/varImp.Rd | 10 ++++- 17 files changed, 250 insertions(+), 191 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoğlu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.5.0 dated 2023-01-16 and 1.6.0 dated 2023-04-14
DESCRIPTION | 15 - MD5 | 129 +++++++++++---- NAMESPACE | 3 NEWS.md | 15 + R/checks.R | 82 +++++++-- R/compare_models.R | 11 - R/corr_feats.R | 20 +- R/cross_val.R | 15 + R/feature_importance.R | 47 +++++ R/hyperparameters.R | 22 +- R/partition.R | 8 R/performance.R | 178 +++++++++++++++++++++ R/plot.R | 5 R/preprocess.R | 28 ++- R/run_ml.R | 39 +++- R/utils.R | 24 ++ README.md | 6 build/partial.rdb |binary build/vignette.rds |binary data/otu_mini_bin_results_rf.rda |binary data/otu_mini_cont_results_glmnet.rda |binary data/otu_mini_multi_results_glmnet.rda |binary inst/CITATION | 35 +--- inst/doc/introduction.Rmd | 10 - inst/doc/introduction.html | 106 ++++++------ man/abort_packages_not_installed.Rd |only man/bootstrap_performance.Rd |only man/bounds.Rd |only man/calc_balanced_precision.Rd |only man/calc_baseline_precision.Rd | 7 man/calc_mean_perf.Rd | 3 man/calc_perf_bootstrap_split.Rd |only man/calc_pvalue.Rd |only man/change_to_num.Rd |only man/check_all.Rd |only man/check_cat_feats.Rd |only man/check_corr_thresh.Rd |only man/check_dataset.Rd |only man/check_features.Rd |only man/check_group_partitions.Rd |only man/check_groups.Rd |only man/check_kfold.Rd |only man/check_method.Rd |only man/check_ntree.Rd |only man/check_outcome_column.Rd |only man/check_outcome_value.Rd |only man/check_packages_installed.Rd |only man/check_perf_metric_function.Rd |only man/check_perf_metric_name.Rd |only man/check_permute.Rd |only man/check_remove_var.Rd |only man/check_seed.Rd |only man/check_training_frac.Rd |only man/check_training_indices.Rd |only man/cluster_corr_mat.Rd |only man/collapse_correlated_features.Rd |only man/create_grouped_data_partition.Rd |only man/create_grouped_k_multifolds.Rd |only man/find_permuted_perf_metric.Rd |only man/flatten_corr_mat.Rd |only man/get_binary_corr_mat.Rd |only man/get_caret_dummyvars_df.Rd |only man/get_corr_feats.Rd |only man/get_difference.Rd |only man/get_feature_importance.Rd | 2 man/get_groups_from_clusters.Rd |only man/get_hyperparams_from_df.Rd |only man/get_hyperparams_list.Rd | 2 man/get_seeds_trainControl.Rd |only man/is_whole_number.Rd |only man/keep_groups_in_cv_partitions.Rd |only man/mutate_all_types.Rd |only man/pbtick.Rd |only man/plot_curves.Rd | 3 man/preprocess_data.Rd | 2 man/process_cat_feats.Rd |only man/process_cont_feats.Rd |only man/process_novar_feats.Rd |only man/radix_sort.Rd |only man/randomize_feature_order.Rd | 2 man/rm_missing_outcome.Rd |only man/run_ml.Rd | 32 +++ man/select_apply.Rd |only man/sensspec.Rd | 13 + man/set_hparams_glmnet.Rd |only man/set_hparams_rf.Rd |only man/set_hparams_rpart2.Rd |only man/set_hparams_svmRadial.Rd |only man/set_hparams_xgbTree.Rd |only man/shuffle_group.Rd |only man/split_outcome_features.Rd |only tests/testthat/test-feature_importance.R | 255 ++++++++++++++++++++++--------- tests/testthat/test-performance.R | 112 +++++++++++++ vignettes/introduction.Rmd | 10 - 94 files changed, 947 insertions(+), 294 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
Davide Garolini [ctb],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between formatters versions 0.4.0 dated 2023-03-02 and 0.4.1 dated 2023-04-14
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NEWS.md | 28 ++++++++++++++++------------ R/page_size.R | 6 +++--- README.md | 2 +- inst/WORDLIST | 1 + inst/doc/formatters.html | 4 ++-- man/figures |only man/page_lcpp.Rd | 8 ++++---- tests/testthat/test-txt_wrap.R | 4 ++-- 10 files changed, 43 insertions(+), 36 deletions(-)
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <arXiv:1611.09477> or nonlinear
models <arXiv:1604.06737> can be used. There are also functions for
dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between embed versions 1.0.0 dated 2022-07-02 and 1.1.0 dated 2023-04-14
embed-1.0.0/embed/R/0_imports.R |only embed-1.0.0/embed/R/bayes.R |only embed-1.0.0/embed/R/glm.R |only embed-1.0.0/embed/R/hash.R |only embed-1.0.0/embed/R/lme.R |only embed-1.0.0/embed/R/solubility.R |only embed-1.0.0/embed/R/tf.R |only embed-1.0.0/embed/tests/testthat/_snaps/hash.md |only embed-1.0.0/embed/tests/testthat/_snaps/mixed.md |only embed-1.0.0/embed/tests/testthat/_snaps/no_pooling.md |only embed-1.0.0/embed/tests/testthat/_snaps/pooling.md |only embed-1.0.0/embed/tests/testthat/_snaps/sparse_pca.md |only embed-1.0.0/embed/tests/testthat/_snaps/tf.md |only embed-1.0.0/embed/tests/testthat/test_collapse_cart.R |only embed-1.0.0/embed/tests/testthat/test_collapse_stringdist.R |only embed-1.0.0/embed/tests/testthat/test_discretize_cart.R |only embed-1.0.0/embed/tests/testthat/test_discretize_xgb.R |only embed-1.0.0/embed/tests/testthat/test_hash.R |only embed-1.0.0/embed/tests/testthat/test_helpers.R |only embed-1.0.0/embed/tests/testthat/test_mixed.R |only embed-1.0.0/embed/tests/testthat/test_no_pooling.R |only embed-1.0.0/embed/tests/testthat/test_pooling.R |only embed-1.0.0/embed/tests/testthat/test_sparse_pca.R |only embed-1.0.0/embed/tests/testthat/test_tf.R |only embed-1.0.0/embed/tests/testthat/test_umap.R |only embed-1.0.0/embed/tests/testthat/test_woe.R |only embed-1.1.0/embed/DESCRIPTION | 32 embed-1.1.0/embed/LICENSE | 2 embed-1.1.0/embed/MD5 | 159 ++-- embed-1.1.0/embed/NAMESPACE | 12 embed-1.1.0/embed/NEWS.md | 19 embed-1.1.0/embed/R/aaa.R |only embed-1.1.0/embed/R/collapse_cart.R | 234 +++---- embed-1.1.0/embed/R/collapse_stringdist.R | 125 ++- embed-1.1.0/embed/R/data.R |only embed-1.1.0/embed/R/discretize_cart.R | 131 ++-- embed-1.1.0/embed/R/discretize_xgb.R | 225 ++++-- embed-1.1.0/embed/R/embed-package.R | 43 + embed-1.1.0/embed/R/embed.R |only embed-1.1.0/embed/R/feature_hash.R |only embed-1.1.0/embed/R/lencode_bayes.R |only embed-1.1.0/embed/R/lencode_glm.R |only embed-1.1.0/embed/R/lencode_mixed.R |only embed-1.1.0/embed/R/pca_sparse.R | 119 ++- embed-1.1.0/embed/R/pca_sparse_bayes.R | 144 ++-- embed-1.1.0/embed/R/pca_truncated.R |only embed-1.1.0/embed/R/reexports.R | 8 embed-1.1.0/embed/R/tidy.R | 7 embed-1.1.0/embed/R/tunable.R | 116 --- embed-1.1.0/embed/R/umap.R | 146 ++-- embed-1.1.0/embed/R/woe.R | 324 +++++----- embed-1.1.0/embed/man/add_woe.Rd | 27 embed-1.1.0/embed/man/dictionary.Rd | 33 - embed-1.1.0/embed/man/embed-package.Rd | 6 embed-1.1.0/embed/man/figures/logo.png |binary embed-1.1.0/embed/man/is_tf_available.Rd | 2 embed-1.1.0/embed/man/reexports.Rd | 4 embed-1.1.0/embed/man/required_pkgs.embed.Rd | 35 - embed-1.1.0/embed/man/rmd |only embed-1.1.0/embed/man/solubility.Rd | 20 embed-1.1.0/embed/man/step_collapse_cart.Rd | 65 -- embed-1.1.0/embed/man/step_collapse_stringdist.Rd | 41 - embed-1.1.0/embed/man/step_discretize_cart.Rd | 61 + embed-1.1.0/embed/man/step_discretize_xgb.Rd | 107 +-- embed-1.1.0/embed/man/step_embed.Rd | 199 ++---- embed-1.1.0/embed/man/step_feature_hash.Rd | 66 +- embed-1.1.0/embed/man/step_lencode_bayes.Rd | 121 +-- embed-1.1.0/embed/man/step_lencode_glm.Rd | 102 +-- embed-1.1.0/embed/man/step_lencode_mixed.Rd | 116 +-- embed-1.1.0/embed/man/step_pca_sparse.Rd | 80 +- embed-1.1.0/embed/man/step_pca_sparse_bayes.Rd | 105 +-- embed-1.1.0/embed/man/step_pca_truncated.Rd |only embed-1.1.0/embed/man/step_umap.Rd | 69 +- embed-1.1.0/embed/man/step_woe.Rd | 148 ++-- embed-1.1.0/embed/man/tidy.recipe.Rd | 38 - embed-1.1.0/embed/man/tunable_embed.Rd | 32 embed-1.1.0/embed/man/woe_table.Rd | 24 embed-1.1.0/embed/tests/testthat/_snaps/collapse_cart.md | 74 +- embed-1.1.0/embed/tests/testthat/_snaps/collapse_stringdist.md | 74 +- embed-1.1.0/embed/tests/testthat/_snaps/discretize_cart.md | 64 - embed-1.1.0/embed/tests/testthat/_snaps/discretize_xgb.md | 130 ++-- embed-1.1.0/embed/tests/testthat/_snaps/embed.md |only embed-1.1.0/embed/tests/testthat/_snaps/extension_check.md |only embed-1.1.0/embed/tests/testthat/_snaps/feature_hash.md |only embed-1.1.0/embed/tests/testthat/_snaps/lencode_bayes.md |only embed-1.1.0/embed/tests/testthat/_snaps/lencode_glm.md |only embed-1.1.0/embed/tests/testthat/_snaps/lencode_mixed.md |only embed-1.1.0/embed/tests/testthat/_snaps/pca_sparse.md |only embed-1.1.0/embed/tests/testthat/_snaps/pca_sparse_bayes.md |only embed-1.1.0/embed/tests/testthat/_snaps/pca_truncated.md |only embed-1.1.0/embed/tests/testthat/_snaps/umap.md | 42 - embed-1.1.0/embed/tests/testthat/_snaps/woe.md | 66 +- embed-1.1.0/embed/tests/testthat/make_binned_data.R | 1 embed-1.1.0/embed/tests/testthat/make_example_data.R | 1 embed-1.1.0/embed/tests/testthat/test-collapse_cart.R |only embed-1.1.0/embed/tests/testthat/test-collapse_stringdist.R |only embed-1.1.0/embed/tests/testthat/test-discretize_cart.R |only embed-1.1.0/embed/tests/testthat/test-discretize_xgb.R |only embed-1.1.0/embed/tests/testthat/test-embed.R |only embed-1.1.0/embed/tests/testthat/test-extension_check.R |only embed-1.1.0/embed/tests/testthat/test-feature_hash.R |only embed-1.1.0/embed/tests/testthat/test-helpers.R |only embed-1.1.0/embed/tests/testthat/test-lencode_bayes.R |only embed-1.1.0/embed/tests/testthat/test-lencode_glm.R |only embed-1.1.0/embed/tests/testthat/test-lencode_mixed.R |only embed-1.1.0/embed/tests/testthat/test-pca_sparse.R |only embed-1.1.0/embed/tests/testthat/test-pca_sparse_bayes.R |only embed-1.1.0/embed/tests/testthat/test-pca_truncated.R |only embed-1.1.0/embed/tests/testthat/test-s3-methods.R | 31 embed-1.1.0/embed/tests/testthat/test-umap.R |only embed-1.1.0/embed/tests/testthat/test-woe.R |only 111 files changed, 2045 insertions(+), 1785 deletions(-)
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a 'Google Map' from 'R' and overlay
it with shapes and markers. Also provides access to 'Google Maps' APIs,
including places, directions, roads, distances, geocoding, elevation and
timezone.
Author: David Cooley [aut, cre],
Paulo Barcelos [ctb] ,
Rstudio [ctb]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between googleway versions 2.7.6 dated 2022-01-24 and 2.7.7 dated 2023-04-14
DESCRIPTION | 10 MD5 | 27 NAMESPACE | 1 R/google_map.R | 37 + R/parameter_checks.R | 10 R/results_access.R | 4 R/scratch.R | 36 + build/vignette.rds |binary inst/doc/googleway-vignette.html | 932 +++++++++++++++++++++++--------- inst/htmlwidgets/google_map.js | 60 +- inst/htmlwidgets/lib/map/map_events.js | 27 inst/htmlwidgets/lib/markers/markers.js | 1 man/google_map.Rd | 11 man/google_map_view.Rd |only tests/testthat/test-google_map.R | 9 15 files changed, 886 insertions(+), 279 deletions(-)
Title: Argentina's Permanent Household Survey Data and Manipulation
Utilities
Description: Tools to download and manipulate the Permanent Household Survey from Argentina
(EPH is the Spanish acronym for Permanent Household Survey).
e.g: get_microdata() for downloading the datasets, get_poverty_lines() for downloading the official poverty baskets,
calculate_poverty() for the calculation of stating if a household is in poverty or not, following the official methodology.
organize_panels() is used to concatenate observations from different periods, and organize_labels()
adds the official labels to the data. The implemented methods are based on INDEC (2016) <http://www.estadistica.ec.gba.gov.ar/dpe/images/SOCIEDAD/EPH_metodologia_22_pobreza.pdf>.
As this package works with the argentinian Permanent Household Survey and its main audience is from this country,
the documentation was written in Spanish.
Author: Diego Kozlowski [aut] ,
Pablo Tiscornia [aut],
Guido Weksler [aut],
Natsumi Shokida [aut],
German Rosati [aut] ,
Juan Gabriel Juara [ctb],
Carolina Pradier [aut, cre]
Maintainer: Carolina Pradier <carolinapradier@gmail.com>
Diff between eph versions 0.5.1 dated 2022-08-29 and 0.6.0 dated 2023-04-14
DESCRIPTION | 15 +- MD5 | 26 ++-- NEWS.md | 4 R/calculate_tabulates.R | 32 ++++- R/get_microdata.R | 7 - R/get_poverty_lines.R | 4 build/vignette.rds |binary inst/CITATION | 4 inst/doc/eph.html | 211 ++++++++++++++++++++------------------- inst/doc/estimacion_pobreza.R | 183 +++++++++++++++++++++++++++++++++ inst/doc/estimacion_pobreza.Rmd | 23 ++-- inst/doc/estimacion_pobreza.html | 155 ++++++++++++++++------------ man/get_microdata.Rd | 6 - vignettes/estimacion_pobreza.Rmd | 23 ++-- 14 files changed, 463 insertions(+), 230 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.3 dated 2023-04-05 and 4.3-1 dated 2023-04-14
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NEWS | 8 ++++ configure | 113 ++++++++++++++++++++++++++++++++--------------------------- configure.ac | 35 ++++++++++++------ 5 files changed, 102 insertions(+), 70 deletions(-)
Title: A Phylogenetic Simulator for Reticulate Evolution
Description: A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
Author: Joshua Justison [aut, cre, cph],
Claudia Solis-Lemus [aut, cph],
Tracy A. Heath [aut, cph],
Klaus Schliep [cph] ,
Emmanuel Paradis [cph] ,
Daniel Lawson [cph]
Maintainer: Joshua Justison <justisnojo@gmail.com>
Diff between SiPhyNetwork versions 1.0.1 dated 2022-09-29 and 1.1.0 dated 2023-04-14
DESCRIPTION | 10 MD5 | 38 +-- NAMESPACE | 1 NEWS.md | 9 R/make.functions.R | 44 +++ R/network.gsa.R | 10 R/sim.bdh.age.R | 18 + R/sim.bdh.age.help.R | 2 R/sim.bdh.taxa.R | 36 ++- R/utils.R | 2 build/vignette.rds |binary inst/doc/introduction.R | 121 ++++++++++ inst/doc/introduction.Rmd | 139 ++++++++++++ inst/doc/introduction.html | 496 +++++++++++++++++++-------------------------- man/make.trait.model.Rd | 45 +++- man/network.gsa.Rd | 11 man/sim.bdh.age.Rd | 12 - man/sim.bdh.taxa.gsa.Rd | 12 - man/sim.bdh.taxa.ssa.Rd | 12 - vignettes/introduction.Rmd | 139 ++++++++++++ 20 files changed, 804 insertions(+), 353 deletions(-)
Title: Nonparametric Bootstrap and Permutation Tests
Description: Robust nonparametric bootstrap and permutation tests for location, correlation, and regression problems, as described in Helwig (2019a) <doi:10.1002/wics.1457> and Helwig (2019b) <doi:10.1016/j.neuroimage.2019.116030>. Univariate and multivariate tests are supported. For each problem, exact tests and Monte Carlo approximations are available. Five different nonparametric bootstrap confidence intervals are implemented. Parallel computing is implemented via the 'parallel' package.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between nptest versions 1.0-3 dated 2021-03-01 and 1.1 dated 2023-04-14
ChangeLog | 25 ++++++++++++++++- DESCRIPTION | 9 ++---- MD5 | 36 +++++++++++++------------ NAMESPACE | 5 ++- R/np.boot.R | 24 ++++++++--------- R/np.cor.test.R | 11 ++++++- R/np.loc.test.R | 6 ++-- R/np.reg.test.R | 11 ++++++- R/rand.test.cor.R | 35 +++++++++---------------- R/rand.test.lm1.R | 70 +++++++++++++++++++++++++------------------------- R/rand.test.lm2.R | 58 ++++++++++++++++++++--------------------- R/rand.test.one.R | 50 +++++++++++++++++------------------ R/rand.test.two.R | 58 ++++++++++++++++++++--------------------- R/zzz.R |only build/partial.rdb |binary man/StartupMessage.Rd |only man/np.boot.Rd | 2 - man/np.cor.test.Rd | 7 +++-- man/np.loc.test.Rd | 7 +++-- man/np.reg.test.Rd | 7 +++-- 20 files changed, 230 insertions(+), 191 deletions(-)
Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including
likelihood ratios for relationship testing, general relatedness
inference, marker simulation, and power analysis. General computation
of exclusion powers is based on Egeland et al. (2014)
<doi:10.1016/j.fsigen.2013.05.001>. Several functions deal
specifically with family reunion cases, implementing and developing
ideas from Kling et al. (2017) <doi:10.1016/j.fsigen.2017.08.006>. A
novelty of 'forrel' is the ability to model background inbreeding in
forensic pedigree computations. This can have significant impact in
applications, as exemplified in Vigeland and Egeland (2019)
<doi:10.1016/j.fsigss.2019.10.175>. 'forrel' is part of the ped suite,
a collection of packages for pedigree analysis. In particular,
'forrel' imports 'pedtools' for creating and manipulating pedigrees
and markers, 'pedprobr' for likelihood computations, and 'pedmut' for
mutation modelling. Pedigree data may be created from scratch, or
loaded [...truncated...]
Author: Magnus Dehli Vigeland [aut, cre]
,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between forrel versions 1.5.0 dated 2023-02-28 and 1.5.1 dated 2023-04-14
forrel-1.5.0/forrel/man/forrel.Rd |only forrel-1.5.1/forrel/DESCRIPTION | 8 - forrel-1.5.1/forrel/MD5 | 42 +++---- forrel-1.5.1/forrel/NAMESPACE | 1 forrel-1.5.1/forrel/NEWS.md | 23 +++ forrel-1.5.1/forrel/R/familias2ped.R | 18 +-- forrel-1.5.1/forrel/R/forrel-package.R | 27 ---- forrel-1.5.1/forrel/R/kinshipLR.R | 25 +++- forrel-1.5.1/forrel/R/missingPersonIP.R | 15 +- forrel-1.5.1/forrel/R/missingPersonLR.R | 69 +++++++++-- forrel-1.5.1/forrel/R/powerPlot.R | 7 - forrel-1.5.1/forrel/R/readFam.R | 83 ++++++++------ forrel-1.5.1/forrel/README.md | 105 +++++++++++------- forrel-1.5.1/forrel/build/partial.rdb |binary forrel-1.5.1/forrel/man/Familias2ped.Rd | 10 + forrel-1.5.1/forrel/man/figures/README-sibs-1.png |binary forrel-1.5.1/forrel/man/figures/README-triangle-1.png |binary forrel-1.5.1/forrel/man/forrel-package.Rd |only forrel-1.5.1/forrel/man/kinshipLR.Rd | 4 forrel-1.5.1/forrel/man/missingPersonIP.Rd | 15 +- forrel-1.5.1/forrel/man/missingPersonLR.Rd | 59 ++++++++-- forrel-1.5.1/forrel/man/powerPlot.Rd | 7 - forrel-1.5.1/forrel/man/readFam.Rd | 10 + 23 files changed, 358 insertions(+), 170 deletions(-)
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.2.0 dated 2020-10-09 and 1.3.0 dated 2023-04-14
toxEval-1.2.0/toxEval/inst/doc/basicWorkflow.R |only toxEval-1.2.0/toxEval/inst/doc/basicWorkflow.Rmd |only toxEval-1.2.0/toxEval/inst/doc/basicWorkflow.html |only toxEval-1.2.0/toxEval/inst/doc/shinyApp.R |only toxEval-1.2.0/toxEval/inst/doc/shinyApp.Rmd |only toxEval-1.2.0/toxEval/inst/doc/shinyApp.html |only toxEval-1.2.0/toxEval/man/figures/README-unnamed-chunk-4-1.png |only toxEval-1.2.0/toxEval/man/figures/README-unnamed-chunk-4-2.png |only toxEval-1.2.0/toxEval/man/figures/README-unnamed-chunk-4-3.png |only toxEval-1.2.0/toxEval/vignettes/annotations.png |only toxEval-1.2.0/toxEval/vignettes/assays.png |only toxEval-1.2.0/toxEval/vignettes/basicWorkflow.Rmd |only toxEval-1.2.0/toxEval/vignettes/flags.png |only toxEval-1.2.0/toxEval/vignettes/group.png |only toxEval-1.2.0/toxEval/vignettes/shinyApp.Rmd |only toxEval-1.2.0/toxEval/vignettes/sidebar.png |only toxEval-1.2.0/toxEval/vignettes/sites.png |only toxEval-1.2.0/toxEval/vignettes/thres.png |only toxEval-1.2.0/toxEval/vignettes/update.png |only toxEval-1.3.0/toxEval/DESCRIPTION | 13 toxEval-1.3.0/toxEval/MD5 | 159 +- toxEval-1.3.0/toxEval/NAMESPACE | 1 toxEval-1.3.0/toxEval/NEWS | 4 toxEval-1.3.0/toxEval/R/clean_endPoint_info.R | 141 +- toxEval-1.3.0/toxEval/R/create_toxEval.R | 459 +++---- toxEval-1.3.0/toxEval/R/endpoint_hits.R | 230 +-- toxEval-1.3.0/toxEval/R/explore_endpoints.R | 17 toxEval-1.3.0/toxEval/R/filter_endPoint_info.R | 87 - toxEval-1.3.0/toxEval/R/get_ACC.R | 68 - toxEval-1.3.0/toxEval/R/get_chemical_summary.R | 326 ++--- toxEval-1.3.0/toxEval/R/hits_by_groupings.R | 186 +- toxEval-1.3.0/toxEval/R/hits_summary.R | 171 +- toxEval-1.3.0/toxEval/R/makeMap.R | 245 +-- toxEval-1.3.0/toxEval/R/plot_chemical_boxplots.R | 366 +++-- toxEval-1.3.0/toxEval/R/plot_group_boxplots.R | 650 +++++----- toxEval-1.3.0/toxEval/R/plot_heat_chemical.R | 464 +++---- toxEval-1.3.0/toxEval/R/plot_tox_endpoints.R | 401 +++--- toxEval-1.3.0/toxEval/R/plot_tox_endpoints2.R |only toxEval-1.3.0/toxEval/R/plot_tox_stacks.R | 335 ++--- toxEval-1.3.0/toxEval/R/rank_sites.R | 293 ++-- toxEval-1.3.0/toxEval/R/side_by_side.R | 268 ++-- toxEval-1.3.0/toxEval/R/sysdata.rda |binary toxEval-1.3.0/toxEval/R/toxEval.R | 236 +-- toxEval-1.3.0/toxEval/README.md | 160 -- toxEval-1.3.0/toxEval/build/partial.rdb |only toxEval-1.3.0/toxEval/build/vignette.rds |binary toxEval-1.3.0/toxEval/inst/doc/Introduction.R | 9 toxEval-1.3.0/toxEval/inst/doc/Introduction.Rmd | 38 toxEval-1.3.0/toxEval/inst/doc/Introduction.html | 452 +++--- toxEval-1.3.0/toxEval/inst/doc/PrepareData.Rmd | 4 toxEval-1.3.0/toxEval/inst/doc/PrepareData.html | 292 +++- toxEval-1.3.0/toxEval/inst/shiny/benchmarks.R | 24 toxEval-1.3.0/toxEval/inst/shiny/boxPlot.R | 107 - toxEval-1.3.0/toxEval/inst/shiny/hitTable.R | 2 toxEval-1.3.0/toxEval/inst/shiny/hitsTableEP.R | 2 toxEval-1.3.0/toxEval/inst/shiny/manifest.json |only toxEval-1.3.0/toxEval/inst/shiny/tableGroupSumm.R | 2 toxEval-1.3.0/toxEval/inst/shiny/tableSum.R | 2 toxEval-1.3.0/toxEval/inst/shiny/ui.R | 151 +- toxEval-1.3.0/toxEval/inst/shiny/www |only toxEval-1.3.0/toxEval/man/ToxCast_ACC.Rd | 17 toxEval-1.3.0/toxEval/man/clean_endPoint_info.Rd | 14 toxEval-1.3.0/toxEval/man/create_toxEval.Rd | 74 - toxEval-1.3.0/toxEval/man/end_point_info.Rd | 20 toxEval-1.3.0/toxEval/man/endpoint_hits_DT.Rd | 26 toxEval-1.3.0/toxEval/man/explore_endpoints.Rd | 7 toxEval-1.3.0/toxEval/man/figures/logo.png |binary toxEval-1.3.0/toxEval/man/filter_groups.Rd | 38 toxEval-1.3.0/toxEval/man/get_ACC.Rd | 12 toxEval-1.3.0/toxEval/man/get_chemical_summary.Rd | 34 toxEval-1.3.0/toxEval/man/get_concentration_summary.Rd | 23 toxEval-1.3.0/toxEval/man/graph_data_prep.Rd | 18 toxEval-1.3.0/toxEval/man/helperToxEval.Rd | 12 toxEval-1.3.0/toxEval/man/hits_by_groupings_DT.Rd | 18 toxEval-1.3.0/toxEval/man/hits_summary_DT.Rd | 28 toxEval-1.3.0/toxEval/man/make_tox_map.Rd | 18 toxEval-1.3.0/toxEval/man/plot_tox_boxplots.Rd | 72 - toxEval-1.3.0/toxEval/man/plot_tox_endpoints.Rd | 45 toxEval-1.3.0/toxEval/man/plot_tox_endpoints2.Rd |only toxEval-1.3.0/toxEval/man/plot_tox_heatmap.Rd | 102 - toxEval-1.3.0/toxEval/man/plot_tox_stacks.Rd | 45 toxEval-1.3.0/toxEval/man/rank_sites_DT.Rd | 14 toxEval-1.3.0/toxEval/man/remove_flags.Rd | 18 toxEval-1.3.0/toxEval/man/summary.toxEval.Rd | 54 toxEval-1.3.0/toxEval/man/toxEval-package.Rd | 70 - toxEval-1.3.0/toxEval/man/tox_chemicals.Rd | 29 toxEval-1.3.0/toxEval/tests/testthat/test_data.R |only toxEval-1.3.0/toxEval/tests/testthat/test_utils.R | 48 toxEval-1.3.0/toxEval/tests/testthat/tests_endpoint.R | 139 +- toxEval-1.3.0/toxEval/tests/testthat/tests_summary.R | 555 ++++---- toxEval-1.3.0/toxEval/vignettes/Introduction.Rmd | 38 toxEval-1.3.0/toxEval/vignettes/PrepareData.Rmd | 4 toxEval-1.3.0/toxEval/vignettes/logo.png |only 93 files changed, 4196 insertions(+), 3761 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting absences under specified criteria, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.1237 [...truncated...]
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.9.8 dated 2023-03-06 and 4.9.9 dated 2023-04-14
DESCRIPTION | 12 +-- MD5 | 14 ++-- NEWS | 27 +++++++- R/cleanCoords.R | 145 ++++++++++++++++++++++++++++-------------------- R/gridRecords.R | 21 +++++- man/cleanCoords.Rd | 49 ++++++++-------- man/fuzzySim-package.Rd | 4 - man/gridRecords.Rd | 4 - 8 files changed, 169 insertions(+), 107 deletions(-)
Title: Spatial and Spatio-Temporal Semiparametric Regression Models
with Spatial Lags
Description: Estimation and inference of spatial and spatio-temporal
semiparametric models including spatial or spatio-temporal non-parametric
trends, parametric and non-parametric covariates and, possibly, a spatial
lag for the dependent variable and temporal correlation in the noise.
The spatio-temporal trend can be decomposed in ANOVA way including main and
interaction functional terms. Use of SAP algorithm to estimate the spatial
or spatio-temporal trend and non-parametric covariates. The methodology of
these models can be found in next references
Basile, R. et al. (2014), <doi:10.1016/j.jedc.2014.06.011>;
Rodriguez-Alvarez, M.X. et al. (2015) <doi:10.1007/s11222-014-9464-2> and,
particularly referred to the focus of the package, Minguez, R.,
Basile, R. and Durban, M. (2020) <doi:10.1007/s10260-019-00492-8>.
Author: Roman Minguez [aut, cre] ,
Roberto Basile [aut] ,
Maria Durban [aut] ,
Gonzalo Espana-Heredia [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between pspatreg versions 1.0.7 dated 2023-02-27 and 1.0.9 dated 2023-04-14
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- R/build_Omega_ar1.R | 12 ++++++------ inst/doc/A_pspatregPackage.html | 4 ++-- 4 files changed, 18 insertions(+), 18 deletions(-)
Title: Download Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut], Marcia Barbosa [ctb], Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geodata versions 0.5-3 dated 2022-12-01 and 0.5-8 dated 2023-04-14
DESCRIPTION | 16 ++--- MD5 | 85 ++++++++++++++++-------------- R/biooracle.R |only R/countries.R | 12 +++- R/crop_sacks.R | 52 +++++++++++++++--- R/crop_spam.R | 20 ++++--- R/crops_monfreda.R | 2 R/elevation.R | 42 +++++++++++++-- R/gadm.R | 85 +++++++++++++++++++----------- R/helper-functions.R | 124 +++++++++++++++++++++++++++++++-------------- R/landuse.R | 36 +++++++++---- R/occurrence.R | 70 ++++++++++++++++++++++++- R/osm.R | 5 + R/pop.R | 6 +- R/soil_afsis.R | 56 ++++++++++++++++++-- R/soil_grids.R | 26 +++++++-- R/soil_isda.R | 27 +++++++-- R/travel_time.R | 6 +- R/uri_helpers.R |only R/worldclim.R | 41 +++++++++----- build/partial.rdb |binary inst/ex/bior.rds |only man/biooracle.Rd |only man/cmip6.Rd | 2 man/countries.Rd | 10 +++ man/crop_calendar_Sacks.Rd | 2 man/crop_calendar_rice.Rd |only man/crop_monfreda.Rd | 2 man/crop_spam.Rd | 4 - man/cropland.Rd | 2 man/elevation.Rd | 2 man/footprint.Rd | 4 - man/gadm.Rd | 2 man/geodata-package.Rd | 4 + man/geodata_path.Rd |only man/landcover.Rd | 2 man/osm.Rd | 2 man/population.Rd | 2 man/soil_af.Rd | 2 man/soil_af_elements.Rd | 2 man/soil_af_isda.Rd | 5 + man/soil_af_water.Rd |only man/soil_grids.Rd | 2 man/sp_occurrence.Rd | 24 ++++++-- man/travel_time.Rd | 2 man/world.Rd | 2 man/worldclim.Rd | 2 47 files changed, 570 insertions(+), 222 deletions(-)
Title: Pattern-Based Zoneless Method for Analysis and Visualization of
Racial Topography
Description: Implements a computational framework for a pattern-based,
zoneless analysis, and visualization of (ethno)racial topography
(Dmowska, Stepinski, and Nowosad (2020) <doi:10.1016/j.apgeog.2020.102239>).
It is a reimagined
approach for analyzing residential segregation and racial diversity based on
the concept of 'landscape’ used in the domain of landscape ecology.
Author: Jakub Nowosad [aut, cre] ,
Anna Dmowska [aut],
Tomasz Stepinski [aut]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between raceland versions 1.1.2 dated 2022-02-11 and 1.2.1 dated 2023-04-14
raceland-1.1.2/raceland/data/race_raster.rda |only raceland-1.1.2/raceland/man/race_raster.Rd |only raceland-1.2.1/raceland/DESCRIPTION | 16 raceland-1.2.1/raceland/MD5 | 93 - raceland-1.2.1/raceland/R/calculate_densities.R | 25 raceland-1.2.1/raceland/R/calculate_metrics.R | 44 raceland-1.2.1/raceland/R/create_densities.R | 31 raceland-1.2.1/raceland/R/create_grid.R | 21 raceland-1.2.1/raceland/R/create_realizations.R | 28 raceland-1.2.1/raceland/R/data.R | 10 raceland-1.2.1/raceland/R/plot_realization.R | 32 raceland-1.2.1/raceland/R/quantify_raceland.R | 5 raceland-1.2.1/raceland/R/utils.R |only raceland-1.2.1/raceland/R/zones_to_raster.R | 24 raceland-1.2.1/raceland/README.md | 32 raceland-1.2.1/raceland/build/partial.rdb |only raceland-1.2.1/raceland/build/vignette.rds |binary raceland-1.2.1/raceland/data/pop_vector.rda |binary raceland-1.2.1/raceland/inst/CITATION | 2 raceland-1.2.1/raceland/inst/doc/raceland-intro1.R | 12 raceland-1.2.1/raceland/inst/doc/raceland-intro1.Rmd | 38 raceland-1.2.1/raceland/inst/doc/raceland-intro1.html | 131 +- raceland-1.2.1/raceland/inst/doc/raceland-intro2.R | 28 raceland-1.2.1/raceland/inst/doc/raceland-intro2.Rmd | 30 raceland-1.2.1/raceland/inst/doc/raceland-intro2.html | 115 + raceland-1.2.1/raceland/inst/doc/raceland-intro3.R | 24 raceland-1.2.1/raceland/inst/doc/raceland-intro3.Rmd | 30 raceland-1.2.1/raceland/inst/doc/raceland-intro3.html | 577 +++++----- raceland-1.2.1/raceland/inst/extdata |only raceland-1.2.1/raceland/man/calculate_densities.Rd | 7 raceland-1.2.1/raceland/man/calculate_metrics.Rd | 9 raceland-1.2.1/raceland/man/create_densities.Rd | 9 raceland-1.2.1/raceland/man/create_grid.Rd | 4 raceland-1.2.1/raceland/man/create_realizations.Rd | 7 raceland-1.2.1/raceland/man/figures/README-unnamed-chunk-3-1.png |binary raceland-1.2.1/raceland/man/figures/README-unnamed-chunk-4-1.png |binary raceland-1.2.1/raceland/man/figures/README-unnamed-chunk-5-1.png |binary raceland-1.2.1/raceland/man/figures/README-unnamed-chunk-6-1.png |binary raceland-1.2.1/raceland/man/plot_realization.Rd | 9 raceland-1.2.1/raceland/man/quantify_raceland.Rd | 5 raceland-1.2.1/raceland/man/race_raster.tif.Rd |only raceland-1.2.1/raceland/man/raceland-package.Rd | 2 raceland-1.2.1/raceland/man/zones_to_raster.Rd | 6 raceland-1.2.1/raceland/tests/testthat.R | 3 raceland-1.2.1/raceland/tests/testthat/test-metrics.R | 1 raceland-1.2.1/raceland/tests/testthat/test-realizations.R | 4 raceland-1.2.1/raceland/tests/testthat/test-results-legacy.R |only raceland-1.2.1/raceland/tests/testthat/test-results.R | 9 raceland-1.2.1/raceland/vignettes/raceland-intro1.Rmd | 38 raceland-1.2.1/raceland/vignettes/raceland-intro2.Rmd | 30 raceland-1.2.1/raceland/vignettes/raceland-intro3.Rmd | 30 51 files changed, 767 insertions(+), 754 deletions(-)
Title: Rank and Factor Loadings Estimation in Time Series Tensor Factor
Models
Description: A set of functions to estimate rank and factor loadings of time series tensor factor models. A tensor is a multidimensional array. To analyze high-dimensional tensor time series, factor model is a major dimension reduction tool. 'TensorPreAve' provides functions to estimate the rank of core tensors and factor loading spaces of tensor time series. More specifically, a pre-averaging method that accumulates information from tensor fibres is used to estimate the factor loading spaces. The estimated directions corresponding to the strongest factors are then used for projecting the data for a potentially improved re-estimation of the factor loading spaces themselves. A new rank estimation method is also implemented to utilizes correlation information from the projected data.
See Chen and Lam (2023) <arXiv:2208.04012> for more details.
Author: Weilin Chen [aut, cre]
Maintainer: Weilin Chen <w.chen56@lse.ac.uk>
Diff between TensorPreAve versions 0.1.1 dated 2022-11-08 and 1.1.0 dated 2023-04-14
DESCRIPTION | 8 MD5 | 42 ++- NAMESPACE | 1 R/bs_cor_rank.R | 43 ++- R/data.R | 8 R/iter_proj.R | 16 - R/pre_eigenplot.R |only R/pre_est.R | 45 ++-- R/rank_factors_est.R | 24 +- R/tensor_data_gen.R | 216 ++++++++++++++------ inst/doc/my-vignette.R | 20 + inst/doc/my-vignette.Rmd | 56 ++++- inst/doc/my-vignette.html | 485 +++++++++++++++++++++++++-------------------- man/bs_cor_rank.Rd | 18 - man/equal_weight_tensor.Rd | 4 man/iter_proj.Rd | 10 man/pre_eigenplot.Rd |only man/pre_est.Rd | 10 man/rank_factors_est.Rd | 15 - man/tensor_data_gen.Rd | 16 - man/value_weight_tensor.Rd | 4 vignettes/my-vignette.Rmd | 56 ++++- vignettes/ref.bib | 2 23 files changed, 682 insertions(+), 417 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.0-6 dated 2023-02-21 and 3.1-0 dated 2023-04-14
DESCRIPTION | 11 ++--- MD5 | 56 ++++++++++++++--------------- NEWS | 48 +++++++++++++++++++++++++ R/density.lpp.R | 26 ++++++++++++- R/linearK.R | 30 ++++++++++++--- R/linearKeuclid.R | 36 +++++++++++++----- R/linearKmulti.R | 26 +++++++------ R/linearpcf.R | 32 +++++++++++----- R/linearpcfmulti.R | 39 ++++++++++++++------ R/quickndirty.R | 30 +++++++++------ inst/doc/packagesizes.txt | 1 man/density.lpp.Rd | 12 ++++++ man/densityEqualSplit.Rd | 16 +++++++- man/densityHeat.lpp.Rd | 18 +++++++-- man/densityQuick.lpp.Rd | 17 ++++++-- man/linearKEuclidInhom.Rd | 53 +++++++++++++++++++++------ man/linearKcross.Rd | 2 - man/linearKcross.inhom.Rd | 19 +++++++--- man/linearKdot.Rd | 2 - man/linearKdot.inhom.Rd | 18 ++++++--- man/linearKinhom.Rd | 49 ++++++++++++++++++------- man/linearpcfEuclidInhom.Rd | 76 ++++++++++++++++++++++++++++++---------- man/linearpcfcross.Rd | 2 - man/linearpcfcross.inhom.Rd | 31 +++++++++++++--- man/linearpcfdot.Rd | 2 - man/linearpcfdot.inhom.Rd | 35 ++++++++++++++---- man/linearpcfinhom.Rd | 60 ++++++++++++++++++++++++------- man/macros/defns.Rd | 4 +- man/spatstat.linnet-internal.Rd | 9 ++-- 29 files changed, 563 insertions(+), 197 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations, for models that are often used in statistical genetics.
Important applications are the use of splines to model spatial or temporal
trends. Another application area is mixed model QTL analysis for
multiparental populations, allowing for heterogeneous residual variance and
random design matrices with Identity-By-Descent (IBD) probabilities.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.4 dated 2022-12-15 and 1.0.5 dated 2023-04-14
LMMsolver-1.0.4/LMMsolver/man/calcNomEffDim.Rd |only LMMsolver-1.0.4/LMMsolver/man/checkFormVars.Rd |only LMMsolver-1.0.4/LMMsolver/man/checkGroup.Rd |only LMMsolver-1.0.4/LMMsolver/man/constructCCt.Rd |only LMMsolver-1.0.4/LMMsolver/man/constructGinvSplines.Rd |only LMMsolver-1.0.4/LMMsolver/man/constructPenalty.Rd |only LMMsolver-1.0.4/LMMsolver/man/constructX.Rd |only LMMsolver-1.0.4/LMMsolver/man/expandGinv.Rd |only LMMsolver-1.0.4/LMMsolver/man/nameCoefs.Rd |only LMMsolver-1.0.4/LMMsolver/man/normVec.Rd |only LMMsolver-1.0.4/LMMsolver/man/removeIntercept.Rd |only LMMsolver-1.0.5/LMMsolver/DESCRIPTION | 8 LMMsolver-1.0.5/LMMsolver/MD5 | 99 +-- LMMsolver-1.0.5/LMMsolver/NAMESPACE | 1 LMMsolver-1.0.5/LMMsolver/NEWS.md | 10 LMMsolver-1.0.5/LMMsolver/R/ConditionalFactor.R |only LMMsolver-1.0.5/LMMsolver/R/DifferentiationCholesky.R | 4 LMMsolver-1.0.5/LMMsolver/R/LMMsolve-class.R | 67 ++ LMMsolver-1.0.5/LMMsolver/R/LMMsolve.R | 166 ++++- LMMsolver-1.0.5/LMMsolver/R/RcppExports.R | 12 LMMsolver-1.0.5/LMMsolver/R/obtainSmoothTrend.R | 243 ++++---- LMMsolver-1.0.5/LMMsolver/R/predictFunctions.R | 6 LMMsolver-1.0.5/LMMsolver/R/sparseMixedModels.R | 42 - LMMsolver-1.0.5/LMMsolver/R/spl1D.R | 39 + LMMsolver-1.0.5/LMMsolver/R/spl2D.R | 37 + LMMsolver-1.0.5/LMMsolver/R/spl3D.R | 9 LMMsolver-1.0.5/LMMsolver/R/splinesFunctions.R | 15 LMMsolver-1.0.5/LMMsolver/R/utils.R | 285 +++++++--- LMMsolver-1.0.5/LMMsolver/build/partial.rdb |binary LMMsolver-1.0.5/LMMsolver/build/vignette.rds |binary LMMsolver-1.0.5/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.html | 9 LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve0 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve1 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve2 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve3 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve4 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/LMMsolve5 |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/cfFull |only LMMsolver-1.0.5/LMMsolver/inst/tinytest/gam1DFull |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/modCoefsSe |only LMMsolver-1.0.5/LMMsolver/inst/tinytest/spl1DFull |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/spl2DFull |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/spl3DFull |binary LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_LMMsolve-class.R | 8 LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_LMMsolve.R | 45 + LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_conditionalFactor.R |only LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_gam.R | 6 LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_spl1D.R | 24 LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_spl2D.R | 23 LMMsolver-1.0.5/LMMsolver/inst/tinytest/test_spl3D.R | 190 +++--- LMMsolver-1.0.5/LMMsolver/man/LMMsolve.Rd | 268 ++++----- LMMsolver-1.0.5/LMMsolver/man/LMMsolveObject.Rd | 9 LMMsolver-1.0.5/LMMsolver/man/coef.LMMsolve.Rd | 7 LMMsolver-1.0.5/LMMsolver/man/spl1D.Rd | 24 LMMsolver-1.0.5/LMMsolver/src/ADcholesky.cpp | 170 +++++ LMMsolver-1.0.5/LMMsolver/src/Makevars.in | 1 LMMsolver-1.0.5/LMMsolver/src/Makevars.win | 14 LMMsolver-1.0.5/LMMsolver/src/RcppExports.cpp | 35 + 58 files changed, 1259 insertions(+), 617 deletions(-)
Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions.
Provides access to 'RStudio' public repositories at
<https://packagemanager.rstudio.com>, and transparent management of
system requirements without administrative privileges. Currently supported
distributions are 'CentOS' / 'RHEL' 7-9, and several 'RHEL' derivatives
('Rocky Linux', 'AlmaLinux', 'Oracle Linux', and 'Amazon Linux' 2),
'openSUSE' / 'SLES' 15.3-4, and 'Ubuntu' 18.04, 20.04 and 22.04.
Author: Inaki Ucar [aut, cph, cre] ,
R Core Team [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between rspm versions 0.3.1 dated 2023-03-26 and 0.4.0 dated 2023-04-14
DESCRIPTION | 6 ++-- LICENSE | 2 - MD5 | 28 ++++++++++---------- NEWS.md | 6 ++++ R/integration.R | 34 +----------------------- R/manager.R | 8 ++--- R/os.R |only R/utils.R | 37 ++++++++++++++++++++------ R/zzz_centos_base.R | 54 +++++++++++---------------------------- R/zzz_centos_like.R | 33 +++++++++++++---------- R/zzz_opensuse_base.R | 18 ++++++++----- R/zzz_opensuse_like.R | 9 ++++-- R/zzz_rpm.R |only R/zzz_ubuntu_base.R | 42 ++++++++++++++++++++---------- README.md | 10 +++++++ inst/tinytest/test_integration.R | 3 -- 16 files changed, 152 insertions(+), 138 deletions(-)
Title: Analyse Biological Invasion Costs with the 'InvaCost' Database
Description: Provides an up-to-date version of the 'InvaCost' database
(<doi:10.6084/m9.figshare.12668570>) in R, and
several functions to analyse the costs of invasive alien species
(<doi:10.1111/2041-210X.13929>).
Author: Boris Leroy [cre, aut], Andrew Kramer [aut], Anne-Charlotte Vaissiere [ctb], Christophe Diagne [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between invacost versions 1.1-4 dated 2022-02-05 and 1.1-5 dated 2023-04-14
DESCRIPTION | 12 - MD5 | 44 ++-- R/expandYearlyCosts.R | 6 R/genericfunctions.R | 14 - R/getInvaCostVersion.R | 6 R/invacost.R | 6 R/modelcosts.R | 6 R/prettySummary.R | 6 R/summarizeCosts.R | 12 - build/partial.rdb |binary inst/CITATION | 33 +-- man/calculateRawAvgCosts-deprecated.Rd | 150 ++++++++-------- man/computeAvgTotCost.Rd | 196 ++++++++++----------- man/expandYearlyCosts.Rd | 150 ++++++++-------- man/getInvaCostVersion.Rd | 96 +++++----- man/invacost-deprecated.Rd | 136 +++++++------- man/invacost.Rd | 212 +++++++++++----------- man/modelCosts.Rd | 306 ++++++++++++++++----------------- man/plot.invacost.costmodel.Rd | 202 ++++++++++----------- man/plot.invacost.costsummary.Rd | 166 +++++++++-------- man/prettySummary.Rd | 98 +++++----- man/rawAvgCost-deprecated.Rd | 264 ++++++++++++++-------------- man/summarizeCosts.Rd | 244 +++++++++++++------------- 23 files changed, 1196 insertions(+), 1169 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features.
All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] ,
Edzer Pebesma [ctb] ,
Roger Bivand [ctb],
Jeroen Ooms [ctb] ,
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>
Diff between gdalcubes versions 0.6.3 dated 2023-01-19 and 0.6.4 dated 2023-04-14
DESCRIPTION | 17 - MD5 | 51 +-- NEWS.md | 9 R/apply_pixel.R | 5 R/apply_time.R | 5 R/extract.R | 17 - R/image_collection.R | 2 R/reduce.R | 13 R/zzz.R | 2 build/vignette.rds |binary configure | 18 - configure.ac | 2 inst/doc/gc01_MODIS.html | 542 +++++++++++++-------------------- inst/formats/MAXAR.json |only man/add_collection_format.Rd | 2 man/extract_geom.Rd | 17 - man/reduce_time.cube.Rd | 3 src/Makevars.in | 1 src/Makevars.ucrt | 20 - src/Makevars.win | 2 src/gdalcubes/src/datetime.cpp | 106 +++--- src/gdalcubes/src/datetime.h | 1 src/gdalcubes/src/image_collection.cpp | 30 - src/gdalcubes/src/reduce_time.cpp | 155 ++++----- src/gdalcubes/src/reduce_time.h | 4 src/gdalcubes/src/simple_cube.cpp | 138 ++++---- src/multiprocess.cpp | 11 27 files changed, 549 insertions(+), 624 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.4-5 dated 2023-03-09 and 1.4-6 dated 2023-04-14
DESCRIPTION | 10 ++++---- MD5 | 14 +++++------ NAMESPACE | 2 + R/mlt.R | 12 +++++---- R/mltoptim.R | 66 ++++++++++++++++++++++++++---------------------------- build/partial.rdb |binary inst/NEWS.Rd | 14 +++++++++++ man/mltoptim.Rd | 6 ++++ 8 files changed, 72 insertions(+), 52 deletions(-)
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Description: Smoothed bootstrap and functions for random generation from
univariate and multivariate kernel densities. It does not
estimate kernel densities.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Diff between kernelboot versions 0.1.9 dated 2022-09-04 and 0.1.10 dated 2023-04-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- README.md | 1 - man/kernelboot.Rd | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.2 dated 2023-01-25 and 1.3.3 dated 2023-04-14
DESCRIPTION | 8 - MD5 | 90 ++++++----- NAMESPACE | 1 R/MAplotW.R | 72 ++++----- R/VolcanoPlotW.R | 205 +++++++++++++++++--------- R/addBagPlot.R | 18 +- R/checkForLegLoc.R | 59 +++++-- R/convertPlotCoordPix.R | 109 +++++++++---- R/cumFrqPlot.R | 30 ++- R/foldChangeArrow.R | 38 ++-- R/histW.R | 38 ++-- R/imageW.R | 35 ++-- R/legendHist.R | 105 ++++++------- R/mouseOverHtmlFile.R | 47 ++++- R/partitionPlot.R | 3 R/plotBy2Groups.R | 48 +++--- R/plotLinReg.R | 44 +++-- R/plotPCAw.R | 83 ++++++---- R/plotW2Leg.R | 17 +- R/profileAsClu.R | 23 +- R/staggerdCountsPlot.R | 44 +++-- R/vioplotW.R | 323 +++++++---------------------------------- build/vignette.rds |binary inst/doc/wrGraphVignette1.Rmd | 5 inst/doc/wrGraphVignette1.html | 172 ++++++++++----------- man/VolcanoPlotW.Rd | 6 man/addBagPlot.Rd | 2 man/checkForLegLoc.Rd | 5 man/convertPlotCoordPix.Rd | 15 + man/dot-addTextToPoints.Rd |only man/dot-bestLegendLoc.Rd |only man/dot-colorByPvalue.Rd |only man/dot-determFigMargPix.Rd |only man/dot-levIndex.Rd |only man/dot-predPointsPix.Rd |only man/dot-sampNoDeMArrayLM.Rd |only man/dot-serachColName.Rd |only man/foldChangeArrow.Rd | 11 - man/histW.Rd | 6 man/imageW.Rd | 8 - man/legendHist.Rd | 13 + man/mouseOverHtmlFile.Rd | 7 man/plotBy2Groups.Rd | 7 man/plotLinReg.Rd | 7 man/plotPCAw.Rd | 12 - man/plotW2Leg.Rd | 5 man/profileAsClu.Rd | 12 - man/staggerdCountsPlot.Rd | 5 man/vioplotW.Rd | 3 vignettes/wrGraphVignette1.Rmd | 5 50 files changed, 902 insertions(+), 844 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and it's 'API' borrows heavily from
'PyTorch' vision package.
Author: Daniel Falbel [aut, cre],
Christophe Regouby [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvision versions 0.5.0 dated 2023-03-15 and 0.5.1 dated 2023-04-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/transforms-defaults.R | 1 + R/transforms-tensor.R | 3 +-- 6 files changed, 16 insertions(+), 11 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-13 dated 2022-09-09 and 1.2-14 dated 2023-04-14
ChangeLog | 15 + DESCRIPTION | 8 MD5 | 33 +-- R/bfgs.r | 28 +- R/estimate.scam.R | 501 ++++++++++++++++++++++++++++++++++++++++++------- R/scam.check.R | 2 R/scam.fit1.r |only R/scam.r | 216 ++++++++++++++------- R/summary.scam.R | 7 build/partial.rdb |binary man/bfgs_gcv.ubre.Rd | 4 man/derivative.scam.Rd | 2 man/gcv.ubre_grad.Rd | 4 man/plot.scam.Rd | 4 man/predict.scam.Rd | 12 - man/scam.Rd | 37 ++- man/scam.fit.Rd | 5 man/summary.scam.Rd | 1 18 files changed, 683 insertions(+), 196 deletions(-)
Title: Interface for the 'QuickJS' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript' engine.
The engine is bundled entirely within the package, requiring no external system
dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
Fabrice Bellard [ctb, cph] ,
Charlie Gordon [ctb, cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.0.2 dated 2023-04-13 and 1.0.3 dated 2023-04-14
QuickJSR-1.0.2/QuickJSR/tests/spelling.R |only QuickJSR-1.0.3/QuickJSR/DESCRIPTION | 10 - QuickJSR-1.0.3/QuickJSR/MD5 | 7 QuickJSR-1.0.3/QuickJSR/src/quickjs/quickjs-libc.c | 210 ++++++++++----------- QuickJSR-1.0.3/QuickJSR/src/quickjs/quickjs.c | 7 5 files changed, 122 insertions(+), 112 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-19 dated 2023-03-19 and 1.2-20 dated 2023-04-14
partykit-1.2-19/partykit/tests/Examples |only partykit-1.2-20/partykit/DESCRIPTION | 8 - partykit-1.2-20/partykit/MD5 | 23 ++--- partykit-1.2-20/partykit/R/party.R | 6 + partykit-1.2-20/partykit/inst/NEWS.Rd | 9 + partykit-1.2-20/partykit/inst/doc/constparty.pdf |binary partykit-1.2-20/partykit/inst/doc/ctree.pdf |binary partykit-1.2-20/partykit/inst/doc/mob.pdf |binary partykit-1.2-20/partykit/inst/doc/partykit.pdf |binary partykit-1.2-20/partykit/man/cforest.Rd | 14 --- partykit-1.2-20/partykit/tests/bugfixes.R | 7 + partykit-1.2-20/partykit/tests/bugfixes.Rout.save | 17 ++- partykit-1.2-20/partykit/vignettes/ctree.Rout.save | 96 ++++++++++----------- 13 files changed, 92 insertions(+), 88 deletions(-)
Title: Intergovernmental Organizations Database
Description: Tools to extract information from the Intergovernmental
Organizations ('IGO') Database , version 3, provided by the Correlates
of War Project <https://correlatesofwar.org/>. See also Pevehouse, J.
C. et al. (2020). Version 3 includes information from 1815 to 2014.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between igoR versions 0.1.4 dated 2022-08-13 and 0.1.5 dated 2023-04-14
DESCRIPTION | 8 MD5 | 66 ++--- NEWS.md | 4 R/data.R | 35 ++ R/igo_dyadic.R | 22 - R/igo_members.R | 4 R/igo_search.R | 2 R/igo_state_membership.R | 3 R/sysdata.rda |binary README.md | 22 - build/vignette.rds |binary data/igo_year_format3.rda |binary data/state_year_format3.rda |binary data/states2016.rda |binary inst/REFERENCES.bib | 4 inst/WORDLIST | 11 inst/doc/igoR.R | 20 - inst/doc/igoR.Rmd | 37 -- inst/doc/igoR.html | 563 +++++++++++++++++++++----------------------- inst/doc/mapping.Rmd | 10 inst/doc/mapping.html | 472 ++++++++++++++++++------------------ man/figures/logo.png |binary man/igo_dyadic.Rd | 17 - man/igo_search.Rd | 2 man/igo_year_format3.Rd | 12 man/state_year_format3.Rd | 13 - man/states2016.Rd | 11 tests/testthat.R | 16 - vignettes/AustShared-1.png |binary vignettes/NAShared-1.png |binary vignettes/UNMaps-1.png |binary vignettes/igoR.Rmd | 37 -- vignettes/mapping.Rmd | 10 vignettes/refs_igo.bib | 4 34 files changed, 706 insertions(+), 699 deletions(-)
Title: Provides an R Interface to 'Enrichr'
Description: Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@alumni.cam.ac.uk>
Diff between enrichR versions 3.1 dated 2022-08-10 and 3.2 dated 2023-04-14
DESCRIPTION | 10 +- MD5 | 33 +++---- NAMESPACE | 4 NEWS.md | 5 + R/enrichR-package.r | 19 ++-- R/functions.R | 132 +++++++++++++++++++--------- README.md | 138 +++++++++++++++++------------ build/vignette.rds |binary inst/doc/enrichR.R | 27 +++-- inst/doc/enrichR.Rmd | 29 +++--- inst/doc/enrichR.html | 230 ++++++++++++++++++++++++++++--------------------- man/enrichR-package.Rd |only man/enrichr.Rd | 2 man/genes790.Rd | 9 + man/getEnrichr.Rd | 2 man/plotEnrich.Rd | 6 - man/printEnrich.Rd | 30 ++++-- vignettes/enrichR.Rmd | 29 +++--- 18 files changed, 437 insertions(+), 268 deletions(-)
Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions for probability
distributions in R.
Primary focus is on (central and non-central) beta, gamma and related
distributions such as the chi-squared, F, and t.
--
This is for the use of researchers in these numerical approximation
implementations, notably for my own use in order to improve standard
R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] ,
Morten Welinder [ctb] ),
Wolfgang Viechtbauer [ctb] , 2002),
Ross Ihaka [ctb] ,
Marius Hofert [ctb] , lssum),
R-core [ctb] ,
R Foundation [cph]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQ versions 0.5-3 dated 2022-12-01 and 0.5-4 dated 2023-04-14
DESCRIPTION | 9 MD5 | 76 ++++---- NAMESPACE | 10 - R/AAA_consts.R |only R/beta-fns.R | 126 ++++++++++++- R/dgamma.R | 1 R/dpq-h.R | 28 +-- R/nmath-h.R | 1 R/norm_f.R | 135 +++++++++++++- R/t-dist.R | 9 TODO | 1 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 33 +++ inst/doc/Noncentral-Chisq.pdf |binary inst/doc/comp-beta.pdf |binary inst/doc/log1pmx-etc.pdf |binary inst/doc/qnorm-asymp.R | 118 +++++++++--- inst/doc/qnorm-asymp.Rnw | 364 +++++++++++++++++++++++----------------- inst/doc/qnorm-asymp.pdf |binary inst/extraR/qnorm-asymp-utils.R | 5 inst/test-tools.R | 2 man/dbinom_raw.Rd | 2 man/dgamma-utils.Rd | 8 man/dot_D_utils.Rd |only man/log1pmx.Rd | 47 ++++- man/pnchisqAppr.Rd | 3 man/pnormAsymp.Rd | 13 - man/pnt.Rd | 2 man/qnormAsymp.Rd | 13 - man/qnormR.Rd | 58 ++++-- man/qnormUappr.Rd | 90 +++++++-- man/rexpm1.Rd |only tests/chisq-nonc-ex.R | 8 tests/dnbinom-tst.R | 27 +- tests/log4p1p-exp.R |only tests/pqnorm_extreme.R | 72 +++++-- tests/stirlerr-tst.R | 9 vignettes/R-numerics.bib | 2 vignettes/qnorm-asymp.Rnw | 364 +++++++++++++++++++++++----------------- vignettes/qnorm-litt.bib | 53 +++++ 41 files changed, 1149 insertions(+), 540 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) &l [...truncated...]
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.51-1 dated 2023-04-03 and 0.51-2 dated 2023-04-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 5 +++-- R/dist.GDM.r | 4 ++-- R/dist.SM.r | 2 +- R/index.G2.r | 2 +- man/index.G2.rd | 9 ++++----- src/clusterSim.cpp | 4 ++-- src/clusterSim.h | 3 +++ 9 files changed, 28 insertions(+), 25 deletions(-)
Title: Save Output of Statistical Tests
Description: Save the output of statistical tests in an organized file that can
be shared with others or used to report statistics in scientific papers.
Author: Willem Sleegers
Maintainer: Willem Sleegers <w.sleegers@me.com>
Diff between tidystats versions 0.5.1 dated 2022-01-04 and 0.5.2 dated 2023-04-14
tidystats-0.5.1/tidystats/tests/testthat/test_anova_glm.R |only tidystats-0.5.2/tidystats/DESCRIPTION | 8 tidystats-0.5.2/tidystats/MD5 | 55 - tidystats-0.5.2/tidystats/NAMESPACE | 1 tidystats-0.5.2/tidystats/R/add_stats.R | 119 +- tidystats-0.5.2/tidystats/R/count_data.r | 27 tidystats-0.5.2/tidystats/R/describe_data.r | 100 +- tidystats-0.5.2/tidystats/R/info.R | 9 tidystats-0.5.2/tidystats/R/tidy_stats_to_data_frame.R | 87 +- tidystats-0.5.2/tidystats/R/write_stats.R | 30 tidystats-0.5.2/tidystats/README.md | 162 +-- tidystats-0.5.2/tidystats/build/partial.rdb |binary tidystats-0.5.2/tidystats/build/vignette.rds |binary tidystats-0.5.2/tidystats/inst/doc/introduction-to-tidystats.html | 422 ++++++++-- tidystats-0.5.2/tidystats/inst/doc/read-and-use-a-tidystats-file.Rmd | 2 tidystats-0.5.2/tidystats/inst/doc/read-and-use-a-tidystats-file.html | 367 +++++++- tidystats-0.5.2/tidystats/inst/doc/tidystats-taxonomy.html | 265 +++++- tidystats-0.5.2/tidystats/man/add_stats.Rd | 22 tidystats-0.5.2/tidystats/man/count_data.Rd | 10 tidystats-0.5.2/tidystats/man/describe_data.Rd | 19 tidystats-0.5.2/tidystats/man/tidy_matrix.Rd | 4 tidystats-0.5.2/tidystats/man/tidy_stats.Rd | 30 tidystats-0.5.2/tidystats/man/tidy_stats_to_data_frame.Rd | 18 tidystats-0.5.2/tidystats/man/write_stats.Rd | 11 tidystats-0.5.2/tidystats/tests/testthat/test_counts.R | 43 - tidystats-0.5.2/tidystats/tests/testthat/test_descriptives.R | 43 - tidystats-0.5.2/tidystats/tests/testthat/test_glm.R | 122 +- tidystats-0.5.2/tidystats/tests/testthat/test_tidy_stats_to_data_frame.R | 34 tidystats-0.5.2/tidystats/vignettes/read-and-use-a-tidystats-file.Rmd | 2 29 files changed, 1355 insertions(+), 657 deletions(-)
More information about TensorComplete at CRAN
Permanent link
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut]
,
Diana Marcela Perez Valencia [aut]
,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.6 dated 2022-12-13 and 1.0.6.1 dated 2023-04-14
DESCRIPTION | 11 ++-- MD5 | 36 +++++++------- NAMESPACE | 1 NEWS.md | 4 + R/createFitMod.R | 45 +++++++++-------- R/createTimePoints.R | 64 +++++++++++++++---------- R/detectSerieOut.R | 25 +++++---- R/detectSingleOut.R | 15 +++-- R/estimateSplineParameters.R | 6 +- R/fitSpline.R | 5 + R/plot.psHDM.R | 91 +++++++++++++++++++----------------- R/statgenHTP.R | 1 R/utils.R | 20 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.html | 6 +- inst/tinytest/test_TPPlots.R | 7 +- inst/tinytest/test_detectSerieOut.R | 2 inst/tinytest/test_fitSpline.R | 2 19 files changed, 189 insertions(+), 152 deletions(-)
Title: Non-Crossing Additive Regression Quantiles and Non-Parametric
Growth Charts
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms, including varying coefficients, via B-splines with L1-norm difference penalties.
Random intercepts and variable selection are allowed via the lasso penalties.
The smoothing parameters are estimated as part of the model fitting, see Muggeo and others (2021) <doi:10.1177/1471082X20929802>. Monotonicity and concavity
constraints on the fitted curves are allowed, see Muggeo and others (2013) <doi:10.1007/s10651-012-0232-1>,
and also <doi:10.13140/RG.2.2.12924.85122> or <doi:10.13140/RG.2.2.29306.21445> some code examples.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 1.6-0 dated 2023-04-04 and 1.6-1 dated 2023-04-14
DESCRIPTION | 10 MD5 | 26 NEWS | 375 +++++---- R/charts.R | 30 R/plot.gcrq.R | 964 +++++++++++++------------ build/vignette.rds |binary inst/doc/quantregGrowth.R | 279 +++---- inst/doc/quantregGrowth.Rmd | 29 inst/doc/quantregGrowth.html | 1588 ++++++++++++++++++++++-------------------- man/charts.Rd | 160 ++-- man/plot.gcrq.Rd | 8 man/ps.Rd | 2 man/quantregGrowth-package.Rd | 150 +-- vignettes/quantregGrowth.Rmd | 29 14 files changed, 1913 insertions(+), 1737 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: Geographic Networks
Description: Provides classes and methods for handling networks or
graphs whose nodes are geographical (i.e. locations in the globe).
The functionality includes the creation of objects of class geonetwork
as a graph with node coordinates, the computation of network measures,
the support of spatial operations (projection to different Coordinate
Reference Systems, handling of bounding boxes, etc.) and the plotting of
the geonetwork object combined with supplementary cartography for spatial
representation.
Author: Facundo Munoz [aut, cre]
Maintainer: Facundo Munoz <facundo.munoz@cirad.fr>
Diff between geonetwork versions 0.4.1 dated 2021-09-03 and 0.5.0 dated 2023-04-14
DESCRIPTION | 16 ++++++++-------- MD5 | 20 ++++++++++---------- NAMESPACE | 3 --- NEWS.md | 8 ++++++++ R/data.R | 2 +- R/geonetwork.R | 13 ++++++------- README.md | 22 +++++++++++----------- data/eurodist.rda |binary man/eurodist.Rd | 2 +- man/figures/README-plotting-1.png |binary man/geonetwork.Rd | 8 +++++--- 11 files changed, 50 insertions(+), 44 deletions(-)
Title: Generating Bootstrap Estimation Distributions of HR Data
Description: Creates plots showing scored HR experiments and plots of distribution of
means of ranks of HR score from bootstrapping. Authors (2019) <doi:10.5281/zenodo.3374507>.
Author: Dan MacLean [aut, cre]
Maintainer: Dan MacLean <dan.maclean@tsl.ac.uk>
Diff between besthr versions 0.3.1 dated 2022-10-06 and 0.3.2 dated 2023-04-14
DESCRIPTION | 6 - MD5 | 10 +- NAMESPACE | 2 R/functions.R | 4 - build/vignette.rds |binary inst/doc/basic-use.html | 188 ++++++++++++++++++++++++------------------------ 6 files changed, 108 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-08 1.1-6
2014-01-26 1.1-5
2013-08-12 1.1-4
2012-10-24 1.1-3
2011-12-27 1.1-2
2011-09-28 1.1-1
2011-04-27 0.1-9
2011-03-15 0.1-8
2008-09-11 0.1-6
2007-12-19 0.1-5
2007-10-18 0.1-4
2007-09-23 0.1-3
2007-02-11 0.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-26 2.0.31
2021-01-12 2.0.17
2019-04-10 2.0.13
2018-05-16 1.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-03 4.1
2018-02-19 3.7
2017-08-16 3.4
2017-05-19 3.3
2015-01-15 3.0
2014-02-10 1.8
2014-01-28 1.7
2013-09-04 1.6
2013-08-06 1.5
2013-07-19 1.4
2013-05-14 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-09 1.0.5
2020-04-12 1.0.4
2018-02-07 1.0.3
2012-12-06 1.0.2
2009-02-24 1.0.1
2006-02-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-09 0.3.2.1
2022-06-01 0.3.2
2020-08-26 0.3.1
2019-12-12 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-27 0.1.0
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
,
Chuck Powell [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.11.0 dated 2023-02-15 and 0.11.1 dated 2023-04-14
ggstatsplot-0.11.0/ggstatsplot/tests/testthat/_snaps/ggbetweenstats/outlier-tagging-works.svg |only ggstatsplot-0.11.0/ggstatsplot/tests/testthat/_snaps/ggwithinstats/default-plots.svg |only ggstatsplot-0.11.0/ggstatsplot/tests/testthat/_snaps/ggwithinstats/outlier-tagging-and-themes-work.svg |only ggstatsplot-0.11.1/ggstatsplot/DESCRIPTION | 19 ggstatsplot-0.11.1/ggstatsplot/MD5 | 122 ggstatsplot-0.11.1/ggstatsplot/NAMESPACE | 8 ggstatsplot-0.11.1/ggstatsplot/NEWS.md | 216 - ggstatsplot-0.11.1/ggstatsplot/R/attach.R | 2 ggstatsplot-0.11.1/ggstatsplot/R/ggbetweenstats.R | 111 ggstatsplot-0.11.1/ggstatsplot/R/ggbetweenstats_helpers.R | 34 ggstatsplot-0.11.1/ggstatsplot/R/ggcorrmat.R | 4 ggstatsplot-0.11.1/ggstatsplot/R/ggpiestats.R | 22 ggstatsplot-0.11.1/ggstatsplot/R/ggpiestats_ggbarstats_helpers.R | 4 ggstatsplot-0.11.1/ggstatsplot/R/ggscatterstats.R | 2 ggstatsplot-0.11.1/ggstatsplot/R/ggstatsplot-package.R | 4 ggstatsplot-0.11.1/ggstatsplot/R/ggwithinstats.R | 44 ggstatsplot-0.11.1/ggstatsplot/R/global_vars.R | 1 ggstatsplot-0.11.1/ggstatsplot/README.md | 17 ggstatsplot-0.11.1/ggstatsplot/inst/WORDLIST | 3 ggstatsplot-0.11.1/ggstatsplot/inst/doc/additional.html | 4 ggstatsplot-0.11.1/ggstatsplot/inst/doc/ggstatsplot.html | 6 ggstatsplot-0.11.1/ggstatsplot/man/figures/README-ggbetweenstats1-1.png |binary ggstatsplot-0.11.1/ggstatsplot/man/figures/README-ggbetweenstats2-1.png |binary ggstatsplot-0.11.1/ggstatsplot/man/ggbetweenstats.Rd | 33 ggstatsplot-0.11.1/ggstatsplot/man/ggwithinstats.Rd | 24 ggstatsplot-0.11.1/ggstatsplot/man/grouped_ggbetweenstats.Rd | 15 ggstatsplot-0.11.1/ggstatsplot/man/grouped_ggwithinstats.Rd | 10 ggstatsplot-0.11.1/ggstatsplot/man/rmd-fragments/ggbetweenstats_graphics.Rmd | 2 ggstatsplot-0.11.1/ggstatsplot/man/rmd-fragments/ggwithinstats_graphics.Rmd | 2 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggbetweenstats/default-plot-as-expected.svg | 6 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggbetweenstats/modification-with-ggplot2-works-as-expected.svg | 39 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggwithinstats.md | 6 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggwithinstats/defaults-plots-more-than-two-groups.svg | 24 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggwithinstats/defaults-plots-two-groups.svg | 16 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/ggwithinstats/grouped-plots-default.svg |only ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-bayes.svg | 85 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-non-parametric-all.svg | 1983 +++++----- ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-non-parametric-only-non-significant.svg | 1983 +++++----- ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-non-parametric-only-significant.svg | 1983 +++++----- ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-parametric-all.svg | 81 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-parametric-only-non-significant.svg | 81 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-parametric-only-significant.svg | 81 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-robust-all.svg | 82 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-robust-only-non-significant.svg | 82 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/_snaps/pairwise_ggsignif/between-robust-only-significant.svg | 82 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggbarstats.R | 4 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 28 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggcoefstats.R | 4 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggcorrmat.R | 2 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggdotplotstats.R | 4 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggpiestats.R | 2 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggscatterstats.R | 4 ggstatsplot-0.11.1/ggstatsplot/tests/testthat/test-ggwithinstats.R | 41 ggstatsplot-0.11.1/ggstatsplot/vignettes/setup.R | 3 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/faq.Rmd | 19 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 11 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 4 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 4 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 4 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 4 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 11 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/pairwise.Rmd | 11 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/principles.Rmd | 8 ggstatsplot-0.11.1/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 23 64 files changed, 3620 insertions(+), 3894 deletions(-)
Title: Manipulate and Analyze Growth Curve Data
Description: Easy import, manipulation, and model-free analysis of
microbial growth curve data, as commonly output by plate readers.
Tools for reshaping common plate reader outputs into 'tidy' formats and
merging them with design information, making data easy to work with using
'gcplyr' and other packages. Also streamlines common growth curve
processing steps, like smoothing and calculating derivatives, and
facilitates model-free characterization and analysis of growth data.
See methods at <https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Diff between gcplyr versions 1.1.0 dated 2023-02-03 and 1.5.1 dated 2023-04-14
gcplyr-1.1.0/gcplyr/man/find_local_extrema.Rd |only gcplyr-1.1.0/gcplyr/man/find_threshold_crosses.Rd |only gcplyr-1.1.0/gcplyr/man/first_below.Rd |only gcplyr-1.1.0/gcplyr/vignettes/analyze.docx |only gcplyr-1.1.0/gcplyr/vignettes/conclusion.docx |only gcplyr-1.1.0/gcplyr/vignettes/gcplyr.docx |only gcplyr-1.1.0/gcplyr/vignettes/import_transform.docx |only gcplyr-1.1.0/gcplyr/vignettes/incorporate_designs.docx |only gcplyr-1.1.0/gcplyr/vignettes/noise.docx |only gcplyr-1.1.0/gcplyr/vignettes/pkg-workflow.png |only gcplyr-1.1.0/gcplyr/vignettes/preprocess_plot.docx |only gcplyr-1.1.0/gcplyr/vignettes/process.docx |only gcplyr-1.5.1/gcplyr/DESCRIPTION | 10 gcplyr-1.5.1/gcplyr/MD5 | 171 - gcplyr-1.5.1/gcplyr/NAMESPACE | 12 gcplyr-1.5.1/gcplyr/NEWS.md | 74 gcplyr-1.5.1/gcplyr/R/functions.R | 1464 ++++------ gcplyr-1.5.1/gcplyr/R/utility_functions.R |only gcplyr-1.5.1/gcplyr/README.md | 67 gcplyr-1.5.1/gcplyr/inst/doc/analyze.R | 294 +- gcplyr-1.5.1/gcplyr/inst/doc/analyze.Rmd | 489 +-- gcplyr-1.5.1/gcplyr/inst/doc/analyze.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/conclusion.R | 47 gcplyr-1.5.1/gcplyr/inst/doc/conclusion.Rmd | 76 gcplyr-1.5.1/gcplyr/inst/doc/conclusion.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/gcplyr.R | 52 gcplyr-1.5.1/gcplyr/inst/doc/gcplyr.Rmd | 70 gcplyr-1.5.1/gcplyr/inst/doc/gcplyr.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/import_transform.R | 36 gcplyr-1.5.1/gcplyr/inst/doc/import_transform.Rmd | 73 gcplyr-1.5.1/gcplyr/inst/doc/import_transform.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/incorporate_designs.R | 65 gcplyr-1.5.1/gcplyr/inst/doc/incorporate_designs.Rmd | 174 - gcplyr-1.5.1/gcplyr/inst/doc/incorporate_designs.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/noise.R | 481 +-- gcplyr-1.5.1/gcplyr/inst/doc/noise.Rmd | 561 +-- gcplyr-1.5.1/gcplyr/inst/doc/noise.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/preprocess_plot.R | 27 gcplyr-1.5.1/gcplyr/inst/doc/preprocess_plot.Rmd | 42 gcplyr-1.5.1/gcplyr/inst/doc/preprocess_plot.pdf |binary gcplyr-1.5.1/gcplyr/inst/doc/process.R | 79 gcplyr-1.5.1/gcplyr/inst/doc/process.Rmd | 153 - gcplyr-1.5.1/gcplyr/inst/doc/process.pdf |binary gcplyr-1.5.1/gcplyr/man/ExtremaFunctions.Rd |only gcplyr-1.5.1/gcplyr/man/MinMaxGC.Rd |only gcplyr-1.5.1/gcplyr/man/ThresholdFunctions.Rd |only gcplyr-1.5.1/gcplyr/man/WhichMinMaxGC.Rd |only gcplyr-1.5.1/gcplyr/man/auc.Rd | 72 gcplyr-1.5.1/gcplyr/man/block_tidydesign.Rd | 74 gcplyr-1.5.1/gcplyr/man/calc_deriv.Rd | 4 gcplyr-1.5.1/gcplyr/man/doubling_time.Rd |only gcplyr-1.5.1/gcplyr/man/extr_val.Rd |only gcplyr-1.5.1/gcplyr/man/first_peak.Rd | 19 gcplyr-1.5.1/gcplyr/man/from_excel.Rd | 35 gcplyr-1.5.1/gcplyr/man/import_blockdesigns.Rd | 12 gcplyr-1.5.1/gcplyr/man/import_blockmeasures.Rd | 12 gcplyr-1.5.1/gcplyr/man/lag_time.Rd |only gcplyr-1.5.1/gcplyr/man/make_design.Rd | 8 gcplyr-1.5.1/gcplyr/man/make_designpattern.Rd | 34 gcplyr-1.5.1/gcplyr/man/make_tidydesign.Rd | 2 gcplyr-1.5.1/gcplyr/man/merge_dfs.Rd | 2 gcplyr-1.5.1/gcplyr/man/moving_average.Rd | 2 gcplyr-1.5.1/gcplyr/man/moving_median.Rd | 2 gcplyr-1.5.1/gcplyr/man/paste_blocks.Rd | 70 gcplyr-1.5.1/gcplyr/man/read_blocks.Rd | 15 gcplyr-1.5.1/gcplyr/man/read_tidys.Rd | 15 gcplyr-1.5.1/gcplyr/man/read_wides.Rd | 18 gcplyr-1.5.1/gcplyr/man/separate_tidy.Rd | 5 gcplyr-1.5.1/gcplyr/man/smooth_data.Rd | 12 gcplyr-1.5.1/gcplyr/man/solve_linear.Rd |only gcplyr-1.5.1/gcplyr/man/to_excel.Rd | 34 gcplyr-1.5.1/gcplyr/man/trans_block_to_wide.Rd | 2 gcplyr-1.5.1/gcplyr/man/trans_wide_to_tidy.Rd | 2 gcplyr-1.5.1/gcplyr/man/uninterleave.Rd | 48 gcplyr-1.5.1/gcplyr/tests/testthat/allfunctions_argumentsmatching_files/full_matches_ref.csv | 5 gcplyr-1.5.1/gcplyr/tests/testthat/allfunctions_argumentsmatching_files/gcplyr_function_subfunction_calls.csv | 12 gcplyr-1.5.1/gcplyr/tests/testthat/allfunctions_argumentsmatching_files/part_matches_ref.csv | 5 gcplyr-1.5.1/gcplyr/tests/testthat/test_analysisfunctions.R | 151 + gcplyr-1.5.1/gcplyr/tests/testthat/test_derivativefunctions.R | 340 +- gcplyr-1.5.1/gcplyr/tests/testthat/test_smoothingfunctions.R | 116 gcplyr-1.5.1/gcplyr/tests/testthat/test_utilityfunctions.R | 46 gcplyr-1.5.1/gcplyr/vignettes/analyze.Rmd | 489 +-- gcplyr-1.5.1/gcplyr/vignettes/analyze.html | 1414 +++++---- gcplyr-1.5.1/gcplyr/vignettes/conclusion.Rmd | 76 gcplyr-1.5.1/gcplyr/vignettes/conclusion.html | 376 +- gcplyr-1.5.1/gcplyr/vignettes/gcplyr.Rmd | 70 gcplyr-1.5.1/gcplyr/vignettes/gcplyr.html | 187 - gcplyr-1.5.1/gcplyr/vignettes/import_transform.Rmd | 73 gcplyr-1.5.1/gcplyr/vignettes/import_transform.html | 670 ++-- gcplyr-1.5.1/gcplyr/vignettes/incorporate_designs.Rmd | 174 - gcplyr-1.5.1/gcplyr/vignettes/incorporate_designs.html | 1200 +++----- gcplyr-1.5.1/gcplyr/vignettes/noise.Rmd | 561 +-- gcplyr-1.5.1/gcplyr/vignettes/noise.html | 1089 +++---- gcplyr-1.5.1/gcplyr/vignettes/preprocess_plot.Rmd | 42 gcplyr-1.5.1/gcplyr/vignettes/preprocess_plot.html | 200 - gcplyr-1.5.1/gcplyr/vignettes/process.Rmd | 153 - gcplyr-1.5.1/gcplyr/vignettes/process.html | 426 +- 97 files changed, 6292 insertions(+), 6599 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.15.0 dated 2023-03-27 and 0.16.0 dated 2023-04-14
DESCRIPTION | 6 MD5 | 42 +- R/help.R |only R/microtable.R | 57 +-- R/trans_abund.R | 34 +- R/trans_alpha.R | 37 +- R/trans_beta.R | 81 +++-- R/trans_diff.R | 727 +++++++++++++++---------------------------------- R/trans_env.R | 18 - R/trans_network.R | 88 +++++ R/trans_nullmodel.R | 52 ++- R/trans_venn.R | 70 ++-- R/utility.R | 468 +++++++++++++++++++++++++++++++ data/dataset.RData |binary man/microeco.Rd |only man/microtable.Rd | 53 +-- man/trans_abund.Rd | 33 +- man/trans_alpha.Rd | 37 +- man/trans_beta.Rd | 44 +- man/trans_diff.Rd | 21 - man/trans_network.Rd | 66 +++- man/trans_nullmodel.Rd | 49 +-- man/trans_venn.Rd | 52 +-- 23 files changed, 1191 insertions(+), 844 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.4.0 dated 2023-03-10 and 1.4.1 dated 2023-04-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/jsBasicGadget.R | 4 ++-- README.md | 2 -- build/vignette.rds |binary inst/doc/jsmodule.html | 4 ++-- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Prediction Performance Metrics
Description: A compilation of more than 80 functions designed to quantitatively and visually evaluate prediction performance of regression (continuous variables) and classification (categorical variables) of point-forecast models (e.g. APSIM, DSSAT, DNDC, supervised Machine Learning). For regression, it includes functions to generate plots (scatter, tiles, density, & Bland-Altman plot), and to estimate error metrics (e.g. MBE, MAE, RMSE), error decomposition (e.g. lack of accuracy-precision), model efficiency (e.g. NSE, E1, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), adjusted correlation coefficients (e.g. CCC, dcorr), symmetric regression coefficients (intercept, slope), and mean absolute scaled error (MASE) for time series predictions. For classification (binomial and multinomial), it offers functions to generate and plot confusion matrices, and to estimate performance metrics such as accuracy, precision, recall, specificity, F-score, Cohen's Kappa, G-mean, and man [...truncated...]
Author: Adrian A. Correndo [cre, cph] ,
Adrian A. Correndo [aut] ,
Luiz H. Moro Rosso [aut] ,
Rai Schwalbert [aut] ,
Carlos Hernandez [aut] ,
Leonardo M. Bastos [aut] ,
Luciana Nieto [aut] ,
Dean Holzworth [aut],
Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <correndo@ksu.edu>
Diff between metrica versions 2.0.2 dated 2023-04-02 and 2.0.3 dated 2023-04-14
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS.md | 21 +++++ R/import_apsim_db.R | 4 - README.md | 54 ++++++++------- inst/doc/Cheatsheet.html | 4 - inst/doc/Shinyapp.html | 4 - inst/doc/apsim_open.R | 42 +++++------ inst/doc/apsim_open.Rmd | 8 +- inst/doc/apsim_open.html | 90 ++----------------------- inst/doc/available_metrics_classification.html | 4 - inst/doc/available_metrics_regression.html | 4 - inst/doc/classification_case.html | 4 - inst/doc/regression_case.html | 4 - vignettes/apsim_open.Rmd | 8 +- 15 files changed, 121 insertions(+), 166 deletions(-)
Title: Event Prediction
Description: Predicts enrollment and events at the design stage using assumed enrollment and treatment-specific time-to-event models, or at the analysis stage using blinded data and specified enrollment and time-to-event models through simulations.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between eventPred versions 0.0.1 dated 2023-03-10 and 0.1.0 dated 2023-04-14
eventPred-0.0.1/eventPred/R/utilities.R |only eventPred-0.0.1/eventPred/data/observedData.rda |only eventPred-0.0.1/eventPred/man/observedData.Rd |only eventPred-0.1.0/eventPred/DESCRIPTION | 17 eventPred-0.1.0/eventPred/MD5 | 48 eventPred-0.1.0/eventPred/NAMESPACE | 40 eventPred-0.1.0/eventPred/NEWS.md |only eventPred-0.1.0/eventPred/R/data.R | 38 eventPred-0.1.0/eventPred/R/eventPred-package.R | 38 eventPred-0.1.0/eventPred/R/fitDropout.R | 187 ++- eventPred-0.1.0/eventPred/R/fitEnrollment.R | 233 ++-- eventPred-0.1.0/eventPred/R/fitEvent.R | 288 ++--- eventPred-0.1.0/eventPred/R/getPrediction.R | 1107 ++++++++++++++------- eventPred-0.1.0/eventPred/R/predictEnrollment.R | 310 +++-- eventPred-0.1.0/eventPred/R/predictEvent.R | 786 +++++++++++--- eventPred-0.1.0/eventPred/R/summarizeObserved.R | 258 ++-- eventPred-0.1.0/eventPred/data/finalData.rda |only eventPred-0.1.0/eventPred/data/interimData1.rda |only eventPred-0.1.0/eventPred/data/interimData2.rda |only eventPred-0.1.0/eventPred/man/eventPred-package.Rd | 16 eventPred-0.1.0/eventPred/man/finalData.Rd |only eventPred-0.1.0/eventPred/man/fitDropout.Rd | 29 eventPred-0.1.0/eventPred/man/fitEnrollment.Rd | 33 eventPred-0.1.0/eventPred/man/fitEvent.Rd | 39 eventPred-0.1.0/eventPred/man/getPrediction.Rd | 146 +- eventPred-0.1.0/eventPred/man/interimData1.Rd |only eventPred-0.1.0/eventPred/man/interimData2.Rd |only eventPred-0.1.0/eventPred/man/predictEnrollment.Rd | 48 eventPred-0.1.0/eventPred/man/predictEvent.Rd | 72 - eventPred-0.1.0/eventPred/man/summarizeObserved.Rd | 24 30 files changed, 2427 insertions(+), 1330 deletions(-)