Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.29.0 dated 2022-11-06 and 1.30.0 dated 2022-12-15
DESCRIPTION | 8 MD5 | 62 +-- NAMESPACE | 2 NEWS.md | 22 + R/999.DEPRECATED.R | 2 R/ClusterFuture-class.R | 2 R/backtrace.R | 2 R/futureOf.R | 6 R/options.R | 5 R/remote.R | 3 R/utils.R | 32 + R/zzz.plan.R | 10 inst/doc/future-1-overview.html | 215 ++----------- inst/doc/future-2-output.html | 215 ++----------- inst/doc/future-3-topologies.html | 215 ++----------- inst/doc/future-4-issues.html | 215 ++----------- inst/doc/future-4-non-exportable-objects.html | 215 ++----------- inst/doc/future-5-startup.html | 215 ++----------- inst/doc/future-6-future-api-backend-specification.html | 180 +++------- inst/doc/future-6-future-api-backend-specification.md.rsp | 8 inst/doc/future-7-for-package-developers.html | 215 ++----------- inst/doc/future-8-how-future-is-validated.html | 174 ++-------- man/future.options.Rd | 3 man/plan.Rd | 6 man/remote.Rd | 18 - man/sequential.Rd | 7 tests/early-signaling.R | 16 tests/nbrOfWorkers.R | 11 tests/relaying.R | 13 tests/remote.R | 48 -- tests/rng.R | 21 - vignettes/future-6-future-api-backend-specification.md.rsp | 8 32 files changed, 591 insertions(+), 1583 deletions(-)
Title: Optimal Two-Period Multiarm Platform Design with New
Experimental Arms Added During the Trial
Description: Design parameters of the optimal two-period multiarm platform design
(controlling for either family-wise error rate or pair-wise error rate) can be calculated
using this package, allowing pre-planned deferred arms to be added during the trial. More
details about the design method can be found in the paper: Pan, H., Yuan, X. and Ye, J.
(2022) "An optimal two-period multiarm platform design with new experimental arms added
during the trial". Manuscript submitted for publication. For additional references: Dunnett,
C. W. (1955) <doi:10.2307/2281208>.
Author: Xiaomeng Yuan [aut, cre],
Haitao Pan [aut]
Maintainer: Xiaomeng Yuan <xiaomeng.yuan@stjude.org>
Diff between PlatformDesign versions 2.1.3 dated 2022-10-24 and 2.1.4 dated 2022-12-15
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md | 10 ++++------ R/one_design2.R | 2 +- R/platform_design.R | 13 +++++++++---- R/platform_design2.R |only inst/doc/PlatformDesign.R | 22 ++++++++++++++++++++++ inst/doc/PlatformDesign.Rmd | 34 ++++++++++++++++++++++++++++++++-- inst/doc/PlatformDesign.html | 38 ++++++++++++++++++++++++++++++++++---- man/platform_design.Rd | 13 +++++++++---- man/platform_design2.Rd |only vignettes/PlatformDesign.Rmd | 34 ++++++++++++++++++++++++++++++++-- 13 files changed, 159 insertions(+), 36 deletions(-)
More information about PlatformDesign at CRAN
Permanent link
Title: Power and Sample Size Calculations for Clinical Trials
Description: Efficient simulation-based power and sample size calculations are supported for a
broad class of late-stage clinical trials. The following modules are included in
the package:
Adaptive designs with data-driven sample size or event count re-estimation,
Adaptive designs with data-driven treatment selection,
Adaptive designs with data-driven population selection,
Optimal selection of a futility stopping rule,
Event prediction in event-driven trials,
Adaptive trials with response-adaptive randomization (experimental module),
Traditional trials with multiple objectives (experimental module).
Traditional trials with cluster-randomized designs (experimental module).
Author: Alex Dmitrienko [aut, cre]
Maintainer: Alex Dmitrienko <admitrienko@mediana.us>
Diff between MedianaDesigner versions 0.10 dated 2022-11-01 and 0.11 dated 2022-12-15
CHANGELOG | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/EventPredData.RData |binary tests/testthat/test-ADRand.r | 4 ++-- 5 files changed, 14 insertions(+), 11 deletions(-)
More information about MedianaDesigner at CRAN
Permanent link
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut, cre],
Andrea Paz [aut],
Bethany A. Johnson [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [aut],
Robert P. Anderson [...truncated...]
Maintainer: Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@gradcenter.cuny.edu>
Diff between wallace versions 2.0.0 dated 2022-12-08 and 2.0.1 dated 2022-12-15
DESCRIPTION | 8 +- MD5 | 26 ++++---- NEWS.md | 59 ++++++++++++------ R/envs_ecoClimate.R | 2 R/occs_queryDb.R | 34 +++++----- README.md | 4 - inst/shiny/Rmd/text_about.Rmd | 2 inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/occs_queryDb.R | 6 - inst/shiny/modules/occs_queryDb.md | 2 inst/shiny/modules/rep_rmms.md | 2 man/occs_queryDb.Rd | 2 tests/testthat/test_occs_queryDb.R | 114 ++++++++++++++++++------------------ 14 files changed, 144 insertions(+), 121 deletions(-)
Title: Functions and Data for "Epidemics: Models and Data in R (2nd
Edition)"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <https://link.springer.com/book/10.1007/978-3-319-97487-3>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the 'Coursera' Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between epimdr2 versions 1.0-8 dated 2022-11-21 and 1.0-9 dated 2022-12-15
CHANGES | 4 +++- DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 1 + R/shiny2.r | 16 ++++++---------- 5 files changed, 21 insertions(+), 22 deletions(-)
Title: Scientific Data on Time of Lineage Divergence for Your Taxa
Description: Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths
proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence.
This package constitutes the main underlying code of the DateLife web service
at <https:www.datelife.org>. To obtain a single summary chronogram from a group of
relevant chronograms, we implement the Super Distance Matrix (SDM) method
described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>.
To find the grove of chronograms with a sufficiently overlapping set of taxa
for summarizing, we implement theorem 1.1. from Ané et al. (2009)
<doi:10.1007/s00026-009-0017-x>.
A given phylogenetic tree can be dated using time of lineage divergence data
as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>).
To obtain and apply secondary calibrations, the package implements the congruification method described
in Eastman et al. [...truncated...]
Author: Brian O'Meara [aut],
Jonathan Eastman [aut],
Tracy Heath [aut],
April Wright [aut],
Klaus Schliep [aut],
Scott Chamberlain [aut],
Peter Midford [aut],
Luke Harmon [aut],
Joseph Brown [aut],
Matt Pennell [aut],
Mike Alfaro [aut],
Luna L. Sanchez Reyes [...truncated...]
Maintainer: Luna L. Sanchez Reyes <sanchez.reyes.luna@gmail.com>
Diff between datelife versions 0.6.5 dated 2022-06-21 and 0.6.6 dated 2022-12-15
DESCRIPTION | 10 +- MD5 | 66 +++++++++------- NAMESPACE | 2 NEWS.md | 31 +++++-- R/calibrations_congruify.R | 27 +++++- R/calibrations_extract.R | 23 +++-- R/calibrations_get.R | 2 R/datelife_internal.R | 48 +++++++++--- R/datelife_query.R | 73 ++++++++++++------ R/datelife_query2.R |only R/datelife_query_tnrs.R |only R/datelife_result.R | 2 R/datelife_summary.R | 2 R/datelife_use.R | 2 R/get_species_from_ott.R | 123 ++++++++++++++++++++++++------- R/opentree_taxonomy.R | 94 ++++++++++++++++++----- R/opentree_taxonomy_general.R | 33 ++++---- R/use_calibrations_bladj_matched.R | 27 +++--- README.md | 92 +++++++++++++++++------ build/vignette.rds |binary inst/doc/make_datelife_query.R |only inst/doc/make_datelife_query.Rmd |only inst/doc/make_datelife_query.html |only inst/pkgdown.yml | 5 - man/check_ott_input.Rd | 4 - man/congruify_and_mrca_multiPhylo.Rd | 2 man/datelife_use.Rd | 2 man/extract_ott_ids.Rd | 10 +- man/get_datelife_result.Rd | 2 man/get_datelife_result_datelifequery.Rd | 2 man/get_opentree_species.Rd | 12 +-- man/get_ott_children.Rd | 2 man/get_tnrs_names.Rd |only man/get_valid_children.Rd | 4 - man/make_datelife_query.Rd | 4 - man/make_datelife_query2.Rd |only man/tnrs_match.Rd | 7 + vignettes/make_datelife_query.Rmd |only 38 files changed, 498 insertions(+), 215 deletions(-)
Title: Non-Trivial Balance of Centrifuge Rotors
Description: Find the numbers of test tubes that can be balanced in centrifuge
rotors and show various ways to load them. Refer to Pham (2020)
<doi:10.31224/osf.io/4xs38> for more information on package functionality.
Author: Duy Nghia Pham [aut, cre]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between centrifugeR versions 0.1.6 dated 2022-06-23 and 0.1.7 dated 2022-12-15
DESCRIPTION | 13 ++++++++----- MD5 | 17 ++++++++++------- NAMESPACE | 3 +++ R/centrifugeR-package.R | 4 +++- R/launch.R |only R/rotor.R | 1 + build/partial.rdb |binary inst/shiny |only man/centrifugeR-package.Rd | 3 ++- man/figures/logo.png |binary man/launch.Rd |only 11 files changed, 27 insertions(+), 14 deletions(-)
Title: Fast Raster Summary and Manipulation
Description: Fast alternatives to several relatively slow 'raster' package
functions. For large rasters, the functions run from 5 to
approximately 100 times faster than the 'raster' package functions
they replace. The 'fasterize' package, on which one function in this
package depends, includes an implementation of the scan line
algorithm attributed to Wylie et al. (1967)
<doi:10.1145/1465611.1465619>.
Author: Joshua O'Brien
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between rasterDT versions 0.3.1 dated 2020-03-04 and 0.3.2 dated 2022-12-15
DESCRIPTION | 15 +++++++-------- MD5 | 13 +++++++------ NAMESPACE | 28 ++++++++++++++-------------- NEWS.md |only R/fasterizeDT.R | 6 +++++- R/zzz.R | 4 ++-- build/partial.rdb |binary man/fasterizeDT.Rd | 6 +++++- 8 files changed, 40 insertions(+), 32 deletions(-)
Title: Word Embedding Research Framework for Psychological Science
Description: An integrated toolbox of word embedding research that provides:
(1) a collection of 'pre-trained' static word vectors in the '.RData'
compressed format <https://psychbruce.github.io/WordVector_RData.pdf>;
(2) a series of functions to process, analyze, and visualize word vectors;
(3) a range of tests to examine conceptual associations, including
the Word Embedding Association Test <doi:10.1126/science.aal4230>
and the Relative Norm Distance <doi:10.1073/pnas.1720347115>,
with permutation test of significance;
(4) a set of training methods to locally train (static) word vectors
from text corpora, including 'Word2Vec' <arXiv:1301.3781>,
'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <arXiv:1607.04606>;
(5) a group of functions to download 'pre-trained' language models
(e.g., 'GPT', 'BERT'), extract contextualized (dynamic) word vectors
(based on the R package 'text'), and perform language analysis tasks
(e.g., fill in the blank masks).
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between PsychWordVec versions 0.2.0 dated 2022-11-30 and 0.3.0 dated 2022-12-15
PsychWordVec-0.2.0/PsychWordVec/R/PWV1_static.R |only PsychWordVec-0.2.0/PsychWordVec/R/PWV2_dynamic.R |only PsychWordVec-0.2.0/PsychWordVec/R/utils.R |only PsychWordVec-0.2.0/PsychWordVec/man/as_wordvec.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/data_wordvec_normalize.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/get_wordvecs.Rd |only PsychWordVec-0.3.0/PsychWordVec/DESCRIPTION | 10 - PsychWordVec-0.3.0/PsychWordVec/MD5 | 75 ++++---- PsychWordVec-0.3.0/PsychWordVec/NAMESPACE | 19 +- PsychWordVec-0.3.0/PsychWordVec/NEWS.md | 45 +++- PsychWordVec-0.3.0/PsychWordVec/R/00-utils.R |only PsychWordVec-0.3.0/PsychWordVec/R/01-basic.R |only PsychWordVec-0.3.0/PsychWordVec/R/02-static.R |only PsychWordVec-0.3.0/PsychWordVec/R/03-dynamic.R |only PsychWordVec-0.3.0/PsychWordVec/README.md | 39 ++-- PsychWordVec-0.3.0/PsychWordVec/man/as_embed.Rd |only PsychWordVec-0.3.0/PsychWordVec/man/cosine_similarity.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/data_transform.Rd | 6 PsychWordVec-0.3.0/PsychWordVec/man/data_wordvec_load.Rd | 36 ++- PsychWordVec-0.3.0/PsychWordVec/man/data_wordvec_subset.Rd | 33 +-- PsychWordVec-0.3.0/PsychWordVec/man/demodata.Rd | 6 PsychWordVec-0.3.0/PsychWordVec/man/dict_expand.Rd | 6 PsychWordVec-0.3.0/PsychWordVec/man/dict_reliability.Rd | 28 ++- PsychWordVec-0.3.0/PsychWordVec/man/figures/logo.png |binary PsychWordVec-0.3.0/PsychWordVec/man/get_wordvec.Rd | 93 ++++++++-- PsychWordVec-0.3.0/PsychWordVec/man/most_similar.Rd | 14 - PsychWordVec-0.3.0/PsychWordVec/man/normalize.Rd |only PsychWordVec-0.3.0/PsychWordVec/man/orth_procrustes.Rd | 21 +- PsychWordVec-0.3.0/PsychWordVec/man/pair_similarity.Rd | 34 ++- PsychWordVec-0.3.0/PsychWordVec/man/plot_network.Rd |only PsychWordVec-0.3.0/PsychWordVec/man/plot_similarity.Rd | 30 ++- PsychWordVec-0.3.0/PsychWordVec/man/plot_wordvec.Rd | 17 + PsychWordVec-0.3.0/PsychWordVec/man/plot_wordvec_tSNE.Rd | 10 - PsychWordVec-0.3.0/PsychWordVec/man/reexports.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/sum_wordvec.Rd | 6 PsychWordVec-0.3.0/PsychWordVec/man/tab_similarity.Rd | 36 +-- PsychWordVec-0.3.0/PsychWordVec/man/test_RND.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/test_WEAT.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/text_init.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/text_model_download.Rd | 7 PsychWordVec-0.3.0/PsychWordVec/man/text_model_remove.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/text_to_vec.Rd | 42 ++-- PsychWordVec-0.3.0/PsychWordVec/man/text_unmask.Rd | 32 ++- PsychWordVec-0.3.0/PsychWordVec/man/tokenize.Rd | 2 PsychWordVec-0.3.0/PsychWordVec/man/train_wordvec.Rd | 4 45 files changed, 435 insertions(+), 228 deletions(-)
Title: Wrappers for 'GDAL' Utilities Executables
Description: R's 'sf' package ships with self-contained 'GDAL'
executables, including a bare bones interface to several
'GDAL'-related utility programs collectively known as the 'GDAL
utilities'. For each of those utilities, this package provides an
R wrapper whose formal arguments closely mirror those of the
'GDAL' command line interface. The utilities operate on data
stored in files and typically write their output to other
files. Therefore, to process data stored in any of R's more common
spatial formats (i.e. those supported by the 'sp', 'sf', and
'raster' packages), first write them to disk, then process them
with the package's wrapper functions before reading the outputted
results back into R. GDAL function arguments introduced in GDAL
version 3.5.2 or earlier are supported.
Author: Joshua O'Brien
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between gdalUtilities versions 1.2.2 dated 2022-11-28 and 1.2.3 dated 2022-12-15
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/gdal_grid.R | 3 +-- R/gdalmdiminfo.R | 2 ++ build/partial.rdb |binary man/gdal_grid.Rd | 3 +-- man/gdalmdiminfo.Rd | 2 ++ 8 files changed, 27 insertions(+), 17 deletions(-)
Title: Automated Analysis of Multiplex Digital PCR Data
Description: The automated clustering and quantification of the digital PCR
data is based on the combination of 'DBSCAN' (Hahsler et al. (2019)
<doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et al. (1981)
<doi:10.1007/978-1-4757-0450-1>) algorithms.
The analysis is independent of multiplexing geometry, dPCR system,
and input amount.
The details about input data and parameters are available in the
vignette.
Author: Alfonso De Falco [aut, cre] ,
Michel Mittelbronn [ctb],
Christophe Olinger [ctb],
Daniel Stieber [ctb],
Laboratoire national de sante [cph]
Maintainer: Alfonso De Falco <alfonsodefalco90@gmail.com>
Diff between dPCP versions 1.0.4 dated 2021-07-29 and 2.0.0 dated 2022-12-15
DESCRIPTION | 14 MD5 | 38 R/1.input_data.R | 1456 ++++++++++++------------- R/2.clustering_part1.R | 1118 +++++++++---------- R/3.clustering_part2.R | 2284 ++++++++++++++++++++-------------------- R/4.quantification_and_export.R | 1395 ++++++++++++------------ R/dPCPclustering.R | 469 +++++--- build/vignette.rds |binary inst/doc/dPCP_vignette.R | 134 +- inst/doc/dPCP_vignette.Rmd | 549 ++++----- inst/doc/dPCP_vignette.html | 1121 +++++++++++++------ man/dbscan_combination.Rd | 2 man/manual_correction.Rd | 12 man/plot.cmeans_clus.Rd | 5 man/plot.dPCP.Rd | 31 man/plot.rain_reclus.Rd | 5 man/plot.reference_dbscan.Rd | 6 man/read_sample.Rd | 7 man/report_dPCP.Rd | 5 vignettes/dPCP_vignette.Rmd | 549 ++++----- 20 files changed, 4969 insertions(+), 4231 deletions(-)
Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques.
Intrinsic dimension estimation methods for exploratory analysis are also provided.
For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.
Author: Kisung You [aut, cre] ,
Changhee Suh [ctb],
Dennis Shung [ctb]
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between Rdimtools versions 1.1.1 dated 2022-11-24 and 1.1.2 dated 2022-12-15
Rdimtools-1.1.1/Rdimtools/R/nonlinear_LAPEIG.R |only Rdimtools-1.1.1/Rdimtools/R/v_feature_CSCOREG.R |only Rdimtools-1.1.1/Rdimtools/R/v_feature_ENET.R |only Rdimtools-1.1.1/Rdimtools/R/v_feature_LASSO.R |only Rdimtools-1.1.1/Rdimtools/R/v_feature_PROCRUSTES.R |only Rdimtools-1.1.1/Rdimtools/R/v_feature_RSR.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_ASI.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_BPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_FA.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_LDA.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_LMDS.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_MMC.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_MVP.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_NPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_OLPP.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_PPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_linear_SPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_BMDS.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_DPPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_HYDRA.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_LAMP.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_MMDS.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_PHATE.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_PLP.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_RPCA.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_SNE.R |only Rdimtools-1.1.1/Rdimtools/R/v_nonlinear_TSNE.R |only Rdimtools-1.1.2/Rdimtools/DESCRIPTION | 6 Rdimtools-1.1.2/Rdimtools/MD5 | 116 +++++++++---------- Rdimtools-1.1.2/Rdimtools/NEWS.md | 4 Rdimtools-1.1.2/Rdimtools/R/feature_CSCOREG.R |only Rdimtools-1.1.2/Rdimtools/R/feature_ENET.R |only Rdimtools-1.1.2/Rdimtools/R/feature_LASSO.R |only Rdimtools-1.1.2/Rdimtools/R/feature_PROCRUSTES.R |only Rdimtools-1.1.2/Rdimtools/R/feature_RSR.R |only Rdimtools-1.1.2/Rdimtools/R/linear_ASI.R |only Rdimtools-1.1.2/Rdimtools/R/linear_BPCA.R |only Rdimtools-1.1.2/Rdimtools/R/linear_FA.R |only Rdimtools-1.1.2/Rdimtools/R/linear_LDA.R |only Rdimtools-1.1.2/Rdimtools/R/linear_LMDS.R |only Rdimtools-1.1.2/Rdimtools/R/linear_MMC.R |only Rdimtools-1.1.2/Rdimtools/R/linear_MVP.R |only Rdimtools-1.1.2/Rdimtools/R/linear_NPCA.R |only Rdimtools-1.1.2/Rdimtools/R/linear_OLPP.R |only Rdimtools-1.1.2/Rdimtools/R/linear_PPCA.R |only Rdimtools-1.1.2/Rdimtools/R/linear_SPCA.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_BMDS.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_DPPCA.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_HYDRA.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_LAMP.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_MMDS.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_PHATE.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_PLP.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_RPCA.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_SNE.R |only Rdimtools-1.1.2/Rdimtools/R/nonlinear_TSNE.R |only Rdimtools-1.1.2/Rdimtools/R/v1_nonlinear_LAPEIG.R |only Rdimtools-1.1.2/Rdimtools/build/partial.rdb |binary Rdimtools-1.1.2/Rdimtools/man/feature_CSCOREG.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/feature_ENET.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/feature_LASSO.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/feature_PROCRUSTES.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/feature_RSR.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_ASI.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_BPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_FA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_LDA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_LMDS.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_MMC.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_MVP.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_NPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_OLPP.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_PPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/linear_SPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_BMDS.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_DPPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_HYDRA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_LAMP.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_LAPEIG.Rd | 41 ++---- Rdimtools-1.1.2/Rdimtools/man/nonlinear_MMDS.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_PHATE.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_PLP.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_RPCA.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_SNE.Rd | 2 Rdimtools-1.1.2/Rdimtools/man/nonlinear_TSNE.Rd | 2 Rdimtools-1.1.2/Rdimtools/vignettes/quick-start.html | 115 +++++++++--------- 86 files changed, 164 insertions(+), 170 deletions(-)
Title: Variable Selection Using a Smooth Information Criterion
Description: Implementation of the SIC epsilon-telescope method, either
using single or multi-parameter regression. Includes classical regression
with normally distributed errors and robust regression, where the errors are from
the Laplace distribution. The "smooth generalized normal distribution" is used,
where the estimation of an additional shape parameter allows the user to move
smoothly between both types of regression. See O'Neill and Burke (2022)
"Robust Distributional Regression with Automatic Variable Selection" for more details.
<arXiv:2212.07317>. This package also contains the data analyses from O'Neill and
Burke (2021). "Variable Selection Using a Smooth Information Criterion for
Multi-Parameter Regression Models". <arXiv:2110.02643>.
Author: Meadhbh O'Neill [aut, cre],
Kevin Burke [aut]
Maintainer: Meadhbh O'Neill <meadhbh.oneill@ul.ie>
Diff between smoothic versions 0.1.0 dated 2021-10-27 and 1.0.0 dated 2022-12-15
DESCRIPTION | 27 MD5 | 32 NAMESPACE | 5 NEWS.md |only R/data.R | 69 R/smoothic_functions.R | 3601 ++++++++++++++++++++++++++++++++++++------- README.md |only build |only data/bostonhouseprice2.RData |only data/diabetes.RData |only inst |only man/bostonhouseprice.Rd | 9 man/bostonhouseprice2.Rd |only man/diabetes.Rd |only man/figures |only man/smoothic.Rd | 59 man/summary.smoothic.Rd | 2 vignettes |only 18 files changed, 3256 insertions(+), 548 deletions(-)
Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a
statistical method that allows to predict survival from
high-dimensional longitudinal predictors. PRC is described in
Signorelli et al. (2021) <doi:10.1002/sim.9178>.
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 1.3.1 dated 2022-12-09 and 1.3.2 dated 2022-12-15
DESCRIPTION | 8 +-- MD5 | 26 ++++----- R/fit_lmms.R | 6 +- R/fit_prclmm.R | 6 +- R/summarize_lmms.R | 22 ++++---- R/summarize_mlpmms.R | 16 +++--- inst/NEWS.md | 6 ++ inst/doc/pencal-vignette.R | 16 +++++- inst/doc/pencal-vignette.Rmd | 27 ++++++++-- inst/doc/pencal-vignette.html | 111 ++++++++++++++++++++++++++++-------------- man/fit_lmms.Rd | 6 +- man/fit_prclmm.Rd | 6 +- man/summarize_lmms.Rd | 6 +- vignettes/pencal-vignette.Rmd | 27 ++++++++-- 14 files changed, 193 insertions(+), 96 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] ,
Florian De Boissieu [ctb] ,
Andrew Sanchez Meador [ctb] for
segment_snags),
Bourdon Jean-Francois [ctb] for
track_sensor),
Gatziolis Demetrios [ctb] for
track_sensor),
Leon Steinmeier [c [...truncated...]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 4.0.1 dated 2022-05-04 and 4.0.2 dated 2022-12-15
lidR-4.0.1/lidR/tests/testthat/Rplots.pdf |only lidR-4.0.2/lidR/DESCRIPTION | 10 lidR-4.0.2/lidR/MD5 | 75 lidR-4.0.2/lidR/NAMESPACE | 2 lidR-4.0.2/lidR/NEWS.md | 16 lidR-4.0.2/lidR/R/add_attribute.R | 2 lidR-4.0.2/lidR/R/algorithm-dsm.R | 25 lidR-4.0.2/lidR/R/algorithm-itd.R | 12 lidR-4.0.2/lidR/R/algorithm-its.R | 24 lidR-4.0.2/lidR/R/algorithm-noi.R | 9 lidR-4.0.2/lidR/R/backward_compatibility.R | 9 lidR-4.0.2/lidR/R/metrics_crowns.R | 25 lidR-4.0.2/lidR/R/metrics_stdmetrics.R | 1 lidR-4.0.2/lidR/R/metrics_template.R | 117 - lidR-4.0.2/lidR/R/normalize.R | 4 lidR-4.0.2/lidR/R/normalize_height.R | 7 lidR-4.0.2/lidR/R/print.R | 2 lidR-4.0.2/lidR/R/st_area.R | 2 lidR-4.0.2/lidR/R/track_sensor.R | 9 lidR-4.0.2/lidR/R/utils_raster.R | 16 lidR-4.0.2/lidR/build/vignette.rds |binary lidR-4.0.2/lidR/inst/doc/lidR-LAS-class.html | 558 +++++- lidR-4.0.2/lidR/inst/doc/lidR-LAScatalog-class.html | 440 ++++- lidR-4.0.2/lidR/inst/doc/lidR-LAScatalog-engine.R | 1 lidR-4.0.2/lidR/inst/doc/lidR-LAScatalog-engine.Rmd | 1 lidR-4.0.2/lidR/inst/doc/lidR-LAScatalog-engine.html | 869 ++++++++-- lidR-4.0.2/lidR/inst/doc/lidR-catalog-apply-examples.html | 360 +++- lidR-4.0.2/lidR/inst/doc/lidR-computation-speed-LAScatalog.html | 427 +++- lidR-4.0.2/lidR/man/aggregate.Rd | 113 - lidR-4.0.2/lidR/man/catalog_apply.Rd | 18 lidR-4.0.2/lidR/man/dsm_pitfree.Rd | 10 lidR-4.0.2/lidR/man/dsm_tin.Rd | 5 lidR-4.0.2/lidR/man/its_dalponte2016.Rd | 5 lidR-4.0.2/lidR/man/normalize.Rd | 4 lidR-4.0.2/lidR/src/LAS.cpp | 118 - lidR-4.0.2/lidR/src/LAS.h | 2 lidR-4.0.2/lidR/tests/testthat/test-delaunay.R | 6 lidR-4.0.2/lidR/tests/testthat/test-roughness.R | 2 lidR-4.0.2/lidR/vignettes/lidR-LAScatalog-engine.Rmd | 1 39 files changed, 2583 insertions(+), 724 deletions(-)
Title: Calculating Linkage Disequilibrium (LD) in Human Population
Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nci.nih.gov/?tab=apiaccess>)
using the R console. This programmatic access facilitates researchers who are
interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393>
data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying
germline variants in human population groups of interest. For more details, please see
Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre] ,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>
Diff between LDlinkR versions 1.2.2 dated 2022-08-08 and 1.2.3 dated 2022-12-15
DESCRIPTION | 8 +- MD5 | 58 ++++++++-------- NEWS.md | 5 + R/LDexpress.R | 7 + R/LDhap.R | 8 +- R/LDmatrix.R | 7 + R/LDpair.R | 6 + R/LDpop.R | 6 + R/LDproxy.R | 7 + R/LDproxy_batch.R | 12 ++- R/LDtrait.R | 6 + R/SNPchip.R | 6 + R/SNPclip.R | 6 + README.md | 1 build/partial.rdb |binary inst/WORDLIST | 1 inst/doc/LDlinkR.Rmd | 22 +++--- inst/doc/LDlinkR.html | 159 +++++++++++++++++++++++--------------------- man/LDexpress.Rd | 7 + man/LDhap.Rd | 5 + man/LDmatrix.Rd | 5 + man/LDpair.Rd | 5 + man/LDpop.Rd | 5 + man/LDproxy.Rd | 5 + man/LDproxy_batch.Rd | 5 + man/LDtrait.Rd | 5 + man/SNPchip.Rd | 5 + man/SNPclip.Rd | 5 + tests/testthat/test-ldhap.R | 4 - vignettes/LDlinkR.Rmd | 22 +++--- 30 files changed, 243 insertions(+), 160 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp],
A [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-9 dated 2022-12-02 and 0.7-10 dated 2022-12-15
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/aggSEM.R | 1 + R/indSEM.R | 1 + build/vignette.rds |binary data/HRFsim.rda |binary data/ms.fit.rda |binary data/simData.rda |binary data/simDataLV.rda |binary data/ts.rda |binary inst/doc/gimme_vignette.html | 5 +++-- 11 files changed, 19 insertions(+), 16 deletions(-)
Title: Boltzmann Entropy of a Landscape Gradient
Description: Calculates the Boltzmann entropy of a landscape gradient.
This package uses the analytical method created by Gao, P., Zhang, H.
and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019
(<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by
allowing calculations on data with missing values.
Author: Jakub Nowosad [aut, cre] ,
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between belg versions 1.5.2 dated 2022-05-01 and 1.5.3 dated 2022-12-15
DESCRIPTION | 10 - MD5 | 11 - build/partial.rdb |only build/vignette.rds |binary inst/doc/belg1.html | 496 +++++++++++++++++++++++++++++++++++++++------------- inst/doc/belg2.html | 251 ++++++++++++++++++++++++-- man/belg-package.Rd | 2 7 files changed, 627 insertions(+), 143 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 0.5.0 dated 2021-05-17 and 0.5.1 dated 2022-12-15
DESCRIPTION | 6 MD5 | 12 NEWS.md | 6 R/paths_OCN.R | 29 + build/vignette.rds |binary inst/doc/OCNet.html | 853 ++++++++++++++++++++++++---------------------------- man/paths_OCN.Rd | 8 7 files changed, 448 insertions(+), 466 deletions(-)
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 1.0.3 dated 2022-08-19 and 1.0.4 dated 2022-12-15
DESCRIPTION | 10 +- MD5 | 30 +++--- NEWS.md | 5 + R/RcppExports.R | 8 + R/predictFunctions.R | 13 -- R/sparseMixedModels.R | 11 ++ R/splinesFunctions.R | 136 +++++++++++++++-------------- R/utils.R | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Solving_Linear_Mixed_Models.html | 137 +++++++++++++++--------------- inst/tinytest/test_LMMsolve.R | 26 +++++ src/ADcholesky.cpp | 112 ++++++++++++++++++++++++ src/AuxFun.cpp | 2 src/RcppExports.cpp | 26 +++++ src/SparseMatrix.cpp |only src/SparseMatrix.h |only 17 files changed, 359 insertions(+), 163 deletions(-)
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods,
such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
databases and clonotype tracking in vaccination and cancer studies. A successor to our
previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Author: Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [aut],
Eugene Rumynskiy [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut],
Maria Samokhina [aut],
Anna Lorenc [ctb],
Daniel J. Moore [ctb],
Victor Greiff [ctb],
ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <support@immunomind.io>
Diff between immunarch versions 0.8.0 dated 2022-10-17 and 0.9.0 dated 2022-12-15
DESCRIPTION | 8 +- MD5 | 28 ++++----- NAMESPACE | 4 + R/RcppExports.R | 5 + R/align_lineage.R | 3 - R/diversity.R | 13 +--- R/io-parsers.R | 110 +++++++++++++++++++++++++++++-------- R/io-utility.R | 6 +- R/io.R | 12 ++-- R/phylip.R | 63 +++++++++++++++++---- R/tools.R | 9 +++ inst/doc/v2_data.html | 4 - man/repClonalFamily.Rd | 10 +++ man/repLoad.Rd | 4 + vignettes/web_only/BCRpipeline.Rmd | 34 ++++++++--- 15 files changed, 228 insertions(+), 85 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] ,
Laurent Coron [aut] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.2.13 dated 2022-03-03 and 0.3.1 dated 2022-12-15
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Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015)
<https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@u-bordeaux.fr>
Diff between VSURF versions 1.1.0 dated 2019-07-18 and 1.2.0 dated 2022-12-15
DESCRIPTION | 17 ++++----- MD5 | 41 +++++++++++------------ NAMESPACE | 2 - NEWS | 13 ++++++- R/VSURF.R | 36 +++++++++++--------- R/VSURF_interp.R | 32 ++++++++---------- R/VSURF_pred.R | 51 +++++++++++++++------------- R/VSURF_thres.R | 19 ++++++---- man/PM10.Rd | 18 +++++++++- man/VSURF.Rd | 55 +++++++++++++++++++++---------- man/VSURF_interp.Rd | 33 ++++++++++++------ man/VSURF_pred.Rd | 35 +++++++++++++------ man/VSURF_thres.Rd | 31 ++++++++++++----- man/plot.VSURF.Rd | 34 ++++++++++++------- man/predict.VSURF.Rd | 2 - man/summary.VSURF.Rd | 2 - man/toys.Rd | 10 +++-- tests/testthat/case_win32_test_iris.R | 5 +- tests/testthat/case_win32b_test_orange.R | 4 +- tests/testthat/test_iris.R | 5 +- tests/testthat/test_orange.R | 5 +- tests/testthat/testthat-problems.rds |only 22 files changed, 280 insertions(+), 170 deletions(-)
Title: Custom Components for Shiny Applications
Description: Provides useful UI components and input widgets for 'Shiny'
applications. The offered components allow to apply non-standard
operations and view to your 'Shiny' application, but also help to
overcome common performance issues.
Author: Krystian Igras [cre, aut],
Adam Forys [ctb],
Stephane Laurent [ctb],
Craig Dennis [cph] ,
Daniel Eden [cph]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyGizmo versions 0.2 dated 2022-06-13 and 0.3 dated 2022-12-15
DESCRIPTION | 42 +++-- MD5 | 34 +++- NAMESPACE | 9 + NEWS.md | 9 + R/commonInput.R |only R/conditionalJS.R | 314 ++++++++++++++++++++++++++++++++++++++++++- R/imports.R |only R/shinyGizmo-package.R | 6 README.md | 18 +- inst/www/commoninput.js |only inst/www/conditionaljs.css | 4 inst/www/conditionaljs.js | 53 ++++++- inst/www/libs |only man/animation.Rd |only man/commonInput.Rd |only man/conditionalJS.Rd | 33 +++- man/custom-callbacks.Rd |only man/dot-cssEffects.Rd |only man/figures/commoninputs.gif |only man/figures/condjsanim.gif |only man/jsCalls.Rd | 52 ++++++- man/js_calls.Rd | 23 +++ man/shinyGizmo-imports.Rd |only 23 files changed, 541 insertions(+), 56 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut] ,
Barret Schloerke [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
RStudio [cph],
jQuery Foundation [cph] [...truncated...]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.7.3 dated 2022-10-25 and 1.7.4 dated 2022-12-15
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Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dunning [ctb] ,
Atsushi Yasumot [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.18 dated 2022-11-09 and 2.19 dated 2022-12-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/html_document.R | 6 +++--- man/html_document.Rd | 2 +- man/html_document_base.Rd | 2 +- man/html_notebook.Rd | 2 +- man/html_vignette.Rd | 2 +- man/ioslides_presentation.Rd | 2 +- 9 files changed, 26 insertions(+), 20 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut],
Joe Cheng [aut],
Carson Sievert [aut, cre] ,
Kenton Russell [aut, cph],
Ellis Hughes [ctb],
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between htmlwidgets versions 1.5.4 dated 2021-09-08 and 1.6.0 dated 2022-12-15
htmlwidgets-1.5.4/htmlwidgets/R/shim.R |only htmlwidgets-1.6.0/htmlwidgets/DESCRIPTION | 14 htmlwidgets-1.6.0/htmlwidgets/MD5 | 41 htmlwidgets-1.6.0/htmlwidgets/NEWS.md | 19 htmlwidgets-1.6.0/htmlwidgets/R/htmlwidgets.R | 177 +- htmlwidgets-1.6.0/htmlwidgets/R/knitr-methods.R | 40 htmlwidgets-1.6.0/htmlwidgets/R/pandoc.R | 258 --- htmlwidgets-1.6.0/htmlwidgets/R/savewidget.R | 13 htmlwidgets-1.6.0/htmlwidgets/R/scaffold.R | 4 htmlwidgets-1.6.0/htmlwidgets/R/sizing.R | 77 - htmlwidgets-1.6.0/htmlwidgets/R/staticimports.R |only htmlwidgets-1.6.0/htmlwidgets/R/utils.R | 33 htmlwidgets-1.6.0/htmlwidgets/build/vignette.rds |binary htmlwidgets-1.6.0/htmlwidgets/inst/doc/develop_advanced.R | 2 htmlwidgets-1.6.0/htmlwidgets/inst/doc/develop_advanced.html | 595 ++++++--- htmlwidgets-1.6.0/htmlwidgets/inst/doc/develop_intro.Rmd | 2 htmlwidgets-1.6.0/htmlwidgets/inst/doc/develop_intro.html | 719 ++++++++--- htmlwidgets-1.6.0/htmlwidgets/inst/doc/develop_sizing.html | 598 ++++++--- htmlwidgets-1.6.0/htmlwidgets/inst/www/htmlwidgets.js | 60 htmlwidgets-1.6.0/htmlwidgets/man/htmlwidgets-shiny.Rd | 17 htmlwidgets-1.6.0/htmlwidgets/man/sizingPolicy.Rd | 14 htmlwidgets-1.6.0/htmlwidgets/tests/testthat/test-pandoc.R |only htmlwidgets-1.6.0/htmlwidgets/vignettes/develop_intro.Rmd | 2 23 files changed, 1677 insertions(+), 1008 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut] ,
Simon Couch [aut, cre] ,
RStudio [cph, fnd],
Indrajeet Patil [ctb] ,
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ct [...truncated...]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between broom versions 1.0.1 dated 2022-08-29 and 1.0.2 dated 2022-12-15
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broom-1.0.2/broom/R/psych-tidiers.R | 2 broom-1.0.2/broom/R/stats-anova-tidiers.R | 4 broom-1.0.2/broom/R/stats-decompose-tidiers.R | 2 broom-1.0.2/broom/R/stats-htest-tidiers.R | 2 broom-1.0.2/broom/R/stats-lm-tidiers.R | 2 broom-1.0.2/broom/R/stats-nls-tidiers.R | 2 broom-1.0.2/broom/R/stats-prcomp-tidiers.R | 2 broom-1.0.2/broom/R/stats-smooth.spline-tidiers.R | 2 broom-1.0.2/broom/R/stats-time-series-tidiers.R | 2 broom-1.0.2/broom/R/survival-cch-tidiers.R | 2 broom-1.0.2/broom/R/survival-coxph-tidiers.R | 8 broom-1.0.2/broom/R/survival-survfit-tidiers.R | 2 broom-1.0.2/broom/R/survival-survreg-tidiers.R | 8 broom-1.0.2/broom/R/utilities.R | 46 + broom-1.0.2/broom/R/zoo-tidiers.R | 2 broom-1.0.2/broom/build/vignette.rds |binary broom-1.0.2/broom/inst/doc/adding-tidiers.html | 18 broom-1.0.2/broom/inst/doc/available-methods.html | 18 broom-1.0.2/broom/inst/doc/bootstrapping.html | 18 broom-1.0.2/broom/inst/doc/broom.html | 115 +-- broom-1.0.2/broom/inst/doc/broom_and_dplyr.R | 10 broom-1.0.2/broom/inst/doc/broom_and_dplyr.Rmd | 10 broom-1.0.2/broom/inst/doc/broom_and_dplyr.html | 115 +-- broom-1.0.2/broom/inst/doc/kmeans.html | 14 broom-1.0.2/broom/man/augment.Mclust.Rd | 13 broom-1.0.2/broom/man/augment.betamfx.Rd | 13 broom-1.0.2/broom/man/augment.betareg.Rd | 13 broom-1.0.2/broom/man/augment.clm.Rd | 13 broom-1.0.2/broom/man/augment.coxph.Rd | 17 broom-1.0.2/broom/man/augment.decomposed.ts.Rd | 15 broom-1.0.2/broom/man/augment.drc.Rd | 13 broom-1.0.2/broom/man/augment.factanal.Rd | 13 broom-1.0.2/broom/man/augment.felm.Rd | 13 broom-1.0.2/broom/man/augment.fixest.Rd | 13 broom-1.0.2/broom/man/augment.gam.Rd | 13 broom-1.0.2/broom/man/augment.glm.Rd | 13 broom-1.0.2/broom/man/augment.glmRob.Rd | 13 broom-1.0.2/broom/man/augment.htest.Rd | 13 broom-1.0.2/broom/man/augment.ivreg.Rd | 13 broom-1.0.2/broom/man/augment.kmeans.Rd | 13 broom-1.0.2/broom/man/augment.lm.Rd | 16 broom-1.0.2/broom/man/augment.lmRob.Rd | 13 broom-1.0.2/broom/man/augment.mfx.Rd | 13 broom-1.0.2/broom/man/augment.mjoint.Rd | 13 broom-1.0.2/broom/man/augment.mlogit.Rd | 13 broom-1.0.2/broom/man/augment.nlrq.Rd | 3 broom-1.0.2/broom/man/augment.nls.Rd | 16 broom-1.0.2/broom/man/augment.pam.Rd | 15 broom-1.0.2/broom/man/augment.plm.Rd | 13 broom-1.0.2/broom/man/augment.poLCA.Rd | 15 broom-1.0.2/broom/man/augment.polr.Rd | 13 broom-1.0.2/broom/man/augment.prcomp.Rd | 13 broom-1.0.2/broom/man/augment.rlm.Rd | 13 broom-1.0.2/broom/man/augment.rma.Rd | 13 broom-1.0.2/broom/man/augment.robustbase.glmrob.Rd | 13 broom-1.0.2/broom/man/augment.robustbase.lmrob.Rd | 13 broom-1.0.2/broom/man/augment.rq.Rd | 13 broom-1.0.2/broom/man/augment.rqs.Rd | 13 broom-1.0.2/broom/man/augment.sarlm.Rd | 13 broom-1.0.2/broom/man/augment.smooth.spline.Rd | 2 broom-1.0.2/broom/man/augment.speedlm.Rd | 13 broom-1.0.2/broom/man/augment.stl.Rd | 13 broom-1.0.2/broom/man/augment.survreg.Rd | 17 broom-1.0.2/broom/man/broom.Rd | 1 broom-1.0.2/broom/man/data.frame_tidiers.Rd | 3 broom-1.0.2/broom/man/glance.binDesign.Rd | 2 broom-1.0.2/broom/man/glance.cch.Rd | 2 broom-1.0.2/broom/man/glance.coxph.Rd | 2 broom-1.0.2/broom/man/glance.cv.glmnet.Rd | 2 broom-1.0.2/broom/man/glance.glmnet.Rd | 2 broom-1.0.2/broom/man/glance.gmm.Rd | 2 broom-1.0.2/broom/man/glance.lm.Rd | 3 broom-1.0.2/broom/man/glance.lmodel2.Rd | 2 broom-1.0.2/broom/man/glance.nls.Rd | 3 broom-1.0.2/broom/man/glance.pam.Rd | 2 broom-1.0.2/broom/man/glance.poLCA.Rd | 2 broom-1.0.2/broom/man/glance.ridgelm.Rd | 2 broom-1.0.2/broom/man/glance.smooth.spline.Rd | 2 broom-1.0.2/broom/man/glance.summary.lm.Rd | 3 broom-1.0.2/broom/man/glance.survfit.Rd | 2 broom-1.0.2/broom/man/glance.survreg.Rd | 2 broom-1.0.2/broom/man/tidy.binDesign.Rd | 6 broom-1.0.2/broom/man/tidy.cch.Rd | 2 broom-1.0.2/broom/man/tidy.cld.Rd | 2 broom-1.0.2/broom/man/tidy.confint.glht.Rd | 2 broom-1.0.2/broom/man/tidy.coxph.Rd | 2 broom-1.0.2/broom/man/tidy.cv.glmnet.Rd | 2 broom-1.0.2/broom/man/tidy.emmGrid.Rd | 2 broom-1.0.2/broom/man/tidy.glht.Rd | 2 broom-1.0.2/broom/man/tidy.glmnet.Rd | 2 broom-1.0.2/broom/man/tidy.gmm.Rd | 2 broom-1.0.2/broom/man/tidy.kappa.Rd | 2 broom-1.0.2/broom/man/tidy.kde.Rd | 2 broom-1.0.2/broom/man/tidy.lm.Rd | 3 broom-1.0.2/broom/man/tidy.lmodel2.Rd | 2 broom-1.0.2/broom/man/tidy.lsmobj.Rd | 2 broom-1.0.2/broom/man/tidy.map.Rd | 2 broom-1.0.2/broom/man/tidy.nls.Rd | 3 broom-1.0.2/broom/man/tidy.pam.Rd | 2 broom-1.0.2/broom/man/tidy.poLCA.Rd | 2 broom-1.0.2/broom/man/tidy.power.htest.Rd | 2 broom-1.0.2/broom/man/tidy.prcomp.Rd | 2 broom-1.0.2/broom/man/tidy.rcorr.Rd | 2 broom-1.0.2/broom/man/tidy.ref.grid.Rd | 2 broom-1.0.2/broom/man/tidy.ridgelm.Rd | 2 broom-1.0.2/broom/man/tidy.roc.Rd | 2 broom-1.0.2/broom/man/tidy.spec.Rd | 2 broom-1.0.2/broom/man/tidy.summary.glht.Rd | 2 broom-1.0.2/broom/man/tidy.summary_emm.Rd | 2 broom-1.0.2/broom/man/tidy.survfit.Rd | 2 broom-1.0.2/broom/man/tidy.survreg.Rd | 2 broom-1.0.2/broom/man/tidy.zoo.Rd | 2 broom-1.0.2/broom/man/tidy_irlba.Rd | 2 broom-1.0.2/broom/man/tidy_svd.Rd | 2 broom-1.0.2/broom/tests/testthat/test-cluster.R | 12 broom-1.0.2/broom/tests/testthat/test-lfe.R | 31 - broom-1.0.2/broom/tests/testthat/test-mclust.R | 24 broom-1.0.2/broom/tests/testthat/test-mfx.R | 4 broom-1.0.2/broom/tests/testthat/test-mgcv.R | 12 broom-1.0.2/broom/tests/testthat/test-muhaz.R | 4 broom-1.0.2/broom/tests/testthat/test-robustbase.R | 5 broom-1.0.2/broom/tests/testthat/test-stats-glm.R | 9 broom-1.0.2/broom/tests/testthat/test-survival-coxph.R | 5 broom-1.0.2/broom/tests/testthat/test-survival-survreg.R | 5 broom-1.0.2/broom/tests/testthat/test-utilities.R | 152 ++--- broom-1.0.2/broom/vignettes/broom_and_dplyr.Rmd | 10 149 files changed, 820 insertions(+), 855 deletions(-)
Title: Interactive Shiny App for Bulk Sequencing Data
Description: Given an expression matrix from a bulk sequencing experiment,
pre-processes it and creates a shiny app for interactive data
analysis and visualisation. The app contains quality checks,
differential expression analysis, volcano and cross plots,
enrichment analysis and gene regulatory network inference,
and can be customised to contain more panels by the user.
Author: Ilias Moutsopoulos [aut, cre],
Eleanor Williams [aut, ctb],
Irina Mohorianu [aut, ctb]
Maintainer: Ilias Moutsopoulos <im383@cam.ac.uk>
Diff between bulkAnalyseR versions 1.0.0 dated 2022-04-07 and 1.1.0 dated 2022-12-15
DESCRIPTION | 10 MD5 | 70 +-- NAMESPACE | 4 R/DEfuns.R | 6 R/DEpanel.R | 4 R/DEsummaryPanel.R | 6 R/GRNpanel.R | 29 + R/QCpanel.R | 158 +++++++ R/QCplotFuns.R | 201 +++++++++ R/crossPanel.R | 43 +- R/cross_plot.R | 86 ++-- R/enrichmentPanel.R | 42 +- R/generateShinyApp.R | 1 R/preprocessExpressionMatrix.R | 23 - R/sampleSelectPanel.R | 18 README.md | 2 build/vignette.rds |binary inst/doc/GEO_App.R |only inst/doc/GEO_App.Rmd |only inst/doc/GEO_App.html |only inst/doc/IntegratingMultiomics.html | 461 +++++++++++++++++----- inst/doc/bulkAnalyseR.R | 45 -- inst/doc/bulkAnalyseR.Rmd | 49 -- inst/doc/bulkAnalyseR.html | 749 +++++++++++++++++++++++++++--------- man/cross_plot.Rd | 13 man/determine_uds.Rd | 44 +- man/generateShinyApp.Rd | 14 man/genes_barplot.Rd |only man/ma_plot.Rd | 12 man/make_heatmap_matrix.Rd | 68 +-- man/make_pattern_matrix.Rd | 68 +-- man/noisyr_counts_with_plot.Rd | 9 man/plot_line_pattern.Rd | 86 ++-- man/preprocessExpressionMatrix.Rd | 14 man/qc_density_plot.Rd |only man/qc_violin_plot.Rd |only man/rescale_matrix.Rd | 66 +-- man/scatter_plot.Rd |only vignettes/GEO_App.Rmd |only vignettes/bulkAnalyseR.Rmd | 49 -- 40 files changed, 1740 insertions(+), 710 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.3.0 dated 2022-07-22 and 0.4.0 dated 2022-12-15
audubon-0.3.0/audubon/R/strj-segment.R |only audubon-0.3.0/audubon/tests/testthat/test_pack.R |only audubon-0.3.0/audubon/tests/testthat/test_strj-fill.R |only audubon-0.3.0/audubon/tests/testthat/test_strj-japanese.R |only audubon-0.3.0/audubon/tests/testthat/test_strj-normalize.R |only audubon-0.3.0/audubon/tests/testthat/test_strj-rewrite.R |only audubon-0.3.0/audubon/tests/testthat/test_strj-tokenize-and-segment.R |only audubon-0.4.0/audubon/DESCRIPTION | 12 audubon-0.4.0/audubon/MD5 | 60 + audubon-0.4.0/audubon/NAMESPACE | 6 audubon-0.4.0/audubon/NEWS.md | 8 audubon-0.4.0/audubon/R/audubon-package.R | 11 audubon-0.4.0/audubon/R/bind_tf_idf2.R |only audubon-0.4.0/audubon/R/collapse_tokens.R |only audubon-0.4.0/audubon/R/lexical_density.R |only audubon-0.4.0/audubon/R/mute_tokens.R |only audubon-0.4.0/audubon/R/pack.R | 2 audubon-0.4.0/audubon/R/prettify.R | 30 audubon-0.4.0/audubon/R/strj-tokenize.R | 325 ++++------ audubon-0.4.0/audubon/R/tokenize-impl.R |only audubon-0.4.0/audubon/README.md | 37 - audubon-0.4.0/audubon/data/hiroba.rda |only audubon-0.4.0/audubon/inst/WORDLIST | 6 audubon-0.4.0/audubon/inst/testdata |only audubon-0.4.0/audubon/man/bind_tf_idf2.Rd |only audubon-0.4.0/audubon/man/collapse_tokens.Rd |only audubon-0.4.0/audubon/man/hiroba.Rd |only audubon-0.4.0/audubon/man/lex_density.Rd |only audubon-0.4.0/audubon/man/mute_tokens.Rd |only audubon-0.4.0/audubon/man/pack.Rd | 2 audubon-0.4.0/audubon/man/prettify.Rd | 25 audubon-0.4.0/audubon/man/strj_segment.Rd | 16 audubon-0.4.0/audubon/man/strj_tinyseg.Rd | 4 audubon-0.4.0/audubon/man/strj_tokenize.Rd | 5 audubon-0.4.0/audubon/tests/testthat/_snaps |only audubon-0.4.0/audubon/tests/testthat/test-bind_tf_idf2.R |only audubon-0.4.0/audubon/tests/testthat/test-collapse_tokens.R |only audubon-0.4.0/audubon/tests/testthat/test-lex_density.R |only audubon-0.4.0/audubon/tests/testthat/test-mute_tokens.R |only audubon-0.4.0/audubon/tests/testthat/test-other-utils.R |only audubon-0.4.0/audubon/tests/testthat/test-strj-fill.R |only audubon-0.4.0/audubon/tests/testthat/test-strj-japanese.R |only audubon-0.4.0/audubon/tests/testthat/test-strj-rewrite-and-normalize.R |only audubon-0.4.0/audubon/tests/testthat/test-strj-tokenize_1.R |only audubon-0.4.0/audubon/tests/testthat/test-strj-tokenize_2.R |only 45 files changed, 288 insertions(+), 261 deletions(-)
Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models. See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between deaR versions 1.3.2 dated 2022-12-01 and 1.3.3 dated 2022-12-15
DESCRIPTION | 10 - MD5 | 46 +++--- R/data_sets.R | 2 R/efficiencies.R | 14 - R/efficiencies.dea.R | 15 + R/efficiencies.dea_fuzzy.R | 36 ++-- R/make_malmquist.R | 4 R/model_supereff.R | 10 - R/plot.dea.R | 8 - R/plot.dea_fuzzy.R | 6 R/read_data.R | 251 +------------------------------- R/read_data_fuzzy.R | 320 ++---------------------------------------- R/read_malmquist.R | 91 +---------- man/PFT1981.Rd | 2 man/efficiencies.Rd | 8 - man/efficiencies.dea.Rd | 15 + man/efficiencies.dea_fuzzy.Rd | 36 ++-- man/make_malmquist.Rd | 4 man/model_supereff.Rd | 4 man/plot.dea.Rd | 4 man/plot.dea_fuzzy.Rd | 6 man/read_data.Rd | 59 ------- man/read_data_fuzzy.Rd | 27 --- man/read_malmquist.Rd | 45 ----- 24 files changed, 178 insertions(+), 845 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro [aut] ,
Douglas Bates [aut] ,
Saikat DebRoy [ctb] ,
Deepayan Sarkar [ctb] ,
EISPACK authors [ctb] ,
Siem Heisterkamp [ctb] ,
Bert Van Willigen [ctb] ,
Johannes Ranke [ctb] ),
R Core Team [aut, cre]
Maintainer: R Core Team <R-core@R-project.org>
Diff between nlme versions 3.1-160 dated 2022-10-10 and 3.1-161 dated 2022-12-15
ChangeLog | 7 +++++ DESCRIPTION | 8 +++--- MD5 | 22 ++++++++-------- NAMESPACE | 4 ++- R/pdMat.R | 13 +++++++++- build/partial.rdb |binary man/lme.Rd | 70 +++++++++++++++++++++++++++++------------------------- man/lmeObject.Rd | 2 + man/nlme.Rd | 43 +++++++-------------------------- man/pdMat.Rd | 19 +++++++------- man/pdMatrix.Rd | 4 +-- man/reStruct.Rd | 3 +- 12 files changed, 101 insertions(+), 94 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 0.1-5 dated 2022-12-11 and 0.1-6 dated 2022-12-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/HiGHS/src/qpsolver/factor.hpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers
Description: The classical (i.e. Efron's, see Efron and Tibshirani (1994, ISBN:978-0412042317) "An Introduction to the Bootstrap") bootstrap is widely used for both the real (i.e. "crisp") and fuzzy data.
The main aim of the algorithms implemented in this package is to overcome a problem with repetition of a few distinct values and to create fuzzy numbers, which are "similar" (but not the same) to values from the initial sample.
To do this, different characteristics of triangular/trapezoidal numbers are kept (like the value, the ambiguity, etc., see Grzegorzewski et al. <doi:10.2991/eusflat-19.2019.68>, Grzegorzewski et al. (2020) <doi:10.2991/ijcis.d.201012.003>, Grzegorzewski et al. (2020) <doi:10.34768/amcs-2020-0022>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-030-95929-6_3>, Romaniuk and Hryniewicz (2019) <doi:10.1007/s00500-018-3251-5>).
Some additional procedures related to these resampling methods are also provided,
like calculation of the Bertoluz [...truncated...]
Author: Maciej Romaniuk [cre],
Przemyslaw Grzegorzewski [aut],
Olgierd Hryniewicz [aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyResampling versions 0.5.0 dated 2022-12-02 and 0.6.0 dated 2022-12-15
DESCRIPTION | 10 +++--- MD5 | 63 +++++++++++++++++++++++++++++++++-------- R/ComparePowerOneSampleCTest.R | 5 +-- R/ComparisonOneSampleCTest.R | 6 ++- R/GeneratorFuzzyNumbers.R | 2 - R/GeneratorNExpUU.R | 2 - R/GeneratorNU.R | 4 +- R/OneSampleCTest.R | 17 +++++++---- R/SEResamplingMean.R | 14 +++++---- R/resamplingMethods.R | 2 - man/FuzzyResampling-package.Rd | 2 - man/resamplingMethods.Rd | 2 - tests |only 13 files changed, 92 insertions(+), 37 deletions(-)
More information about FuzzyResampling at CRAN
Permanent link
Title: Ensemble Learning Algorithms Based on Support Vector Machines
Description: Three ensemble learning algorithms based on support vector machines.
They all train support vector machines on subset of data and combine the result.
Author: Tong He <hetong007@gmail.com>, Aydin Demircioglu <aydin.demircioglu@ini.ruhr-uni-bochum.de>
Maintainer: Tong He <hetong007@gmail.com>
Diff between SwarmSVM versions 0.1-6 dated 2020-01-31 and 0.1-7 dated 2022-12-15
DESCRIPTION | 11 MD5 | 22 R/alphasvm.R | 6 build/vignette.rds |binary inst/doc/SwarmSVM.Rmd | 2 inst/doc/SwarmSVM.html | 1194 ++++++++++++++++++----------------------- man/alphasvm.Rd | 6 man/svmguide1.Rd | 6 src/Rsvm.c | 2 src/svm.cpp | 210 ------- tests/testthat/test_alphasvm.R | 4 vignettes/SwarmSVM.Rmd | 2 12 files changed, 582 insertions(+), 883 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.9 dated 2022-11-08 and 1.6.10 dated 2022-12-15
DESCRIPTION | 14 - MD5 | 36 +-- NEWS.md | 5 R/inputs-webprocess.R | 248 +++++++++++++------------- R/result.R | 4 build/vignette.rds |binary inst/CITATION | 28 +- inst/doc/custom_data_sources.Rmd | 164 ++++++++--------- inst/doc/custom_data_sources.html | 5 inst/doc/geoknife.R | 2 inst/doc/geoknife.Rmd | 2 inst/doc/geoknife.html | 8 inst/doc/plot_geotiff.html | 4 inst/unnamed-chunk-6-1.png |binary man/inputs-webprocess.Rd | 112 +++++------ tests/testthat/data/test_webprocess_knife.rds |binary tests/testthat/test-webprocess_object.R | 1 vignettes/custom_data_sources.Rmd | 164 ++++++++--------- vignettes/geoknife.Rmd | 2 19 files changed, 402 insertions(+), 397 deletions(-)
Title: Evolutionary Trait Divergence Between Sister Species and Other
Paired Lineages
Description: Compares the fit of alternative models of continuous trait differentiation between sister species and other paired lineages. Differences in trait means between two lineages arise as they diverge from a common ancestor, and alternative processes of evolutionary divergence are expected to leave unique signatures in the distribution of trait differentiation in datasets comprised of many lineage pairs. Models include approximations of divergent selection, drift, and stabilizing selection. A variety of model extensions facilitate the testing of process-to-pattern hypotheses. Users supply trait data and divergence times for each lineage pair. The fit of alternative models is compared in a likelihood framework.
Author: Sean A. S. Anderson and Jason T. Weir
Maintainer: Sean A. S. Anderson <sean.as.anderson@gmail.com>
Diff between diverge versions 2.0.4 dated 2022-01-19 and 2.0.6 dated 2022-12-15
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/expected_val.R | 33 +++++++++++++++++++++++---------- R/find_mle.R | 26 +++++++++++++------------- R/likelihood_func.R | 4 +++- R/model_select.R | 2 +- R/re_estimator.R | 4 ++-- R/simulate_div.R | 7 ++++--- man/diverge-package.Rd | 7 ++++--- man/expected_val.Rd | 6 ++++++ man/model_select.Rd | 6 ++++-- man/simulate_div.Rd | 2 +- 12 files changed, 77 insertions(+), 52 deletions(-)
Title: Deep Gaussian Processes using MCMC
Description: Performs posterior inference for deep Gaussian processes following
Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>. Models are trained through
MCMC including elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Vecchia-approximation for faster computation is implemented
following Sauer, Cooper, and Gramacy (2022) <arXiv:2204.02904>. Downstream tasks include
sequential design through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer,
Gramacy, and Higdon, 2020) and optimization through expected improvement (EI;
Gramacy, Sauer, and Wycoff, 2021 <arXiv:2112.07457>). Models
extend up to three layers deep; a one layer model is equivalent to typical Gaussian
process regression. Covariance kernel options are matern (default) and squared
exponential. Incorporates OpenMP and SNOW parallelization and utilizes C/C++ under the hood.
Author: Annie Sauer <anniees@vt.edu>
Maintainer: Annie Sauer <anniees@vt.edu>
Diff between deepgp versions 1.0.1 dated 2022-06-20 and 1.1.0 dated 2022-12-15
DESCRIPTION | 12 +- MD5 | 49 ++++++----- NAMESPACE | 1 R/RcppExports.R | 28 ++++-- R/fit.R | 39 +++++--- R/general.R | 81 ++++++++++++++++-- R/gibbs.R | 47 ++++++++++ R/gibbs_vecchia.R | 52 +++++++++++ R/mcmc.R | 92 +++++++++++++++++++- R/mcmc_vecchia.R | 45 ++++++++-- R/plot.R | 23 +++-- R/predict.R | 40 +++++---- R/predict_vecchia.R | 15 ++- R/seq_design.R | 34 ++++--- R/trim.R | 4 R/vecchia.R | 20 ++-- README.md | 12 ++ build |only inst |only man/crps.Rd |only man/fit_one_layer.Rd | 4 man/predict.Rd | 19 +--- src/RcppExports.cpp | 123 +++++++++++++++++++++++---- src/cov.cpp | 226 +++++++++++++++++++++++---------------------------- src/cov.h |only src/vecchia.cpp |only vignettes |only 27 files changed, 691 insertions(+), 275 deletions(-)
Title: Calibrated Correlation and Two-Sample Tests
Description: Implementation of corrected two-sample tests. A corrected version of the Pearson and Kendall correlation tests,
the Mann-Whitney (Wilcoxon) rank sum test, the Wilcoxon signed rank test and a variance test are implemented.
The package also proposes a test for the median and an independence test between two continuous variables of Kolmogorov-Smirnov's type.
All these corrected tests are asymptotically calibrated in the sense that the probability of rejection under the null hypothesis is
asymptotically equal to the level of the test. See <arXiv:2211.08784> for more details on the statistical tests.
Author: Olivier Bouaziz [aut, cre],
Jerome Dedecker [aut],
Anatole Dedecker [aut]
Maintainer: Olivier Bouaziz <olivier.bouaziz@parisdescartes.fr>
Diff between robusTest versions 1.0.0 dated 2022-11-16 and 1.0.1 dated 2022-12-15
DESCRIPTION | 32 +++++++++++++++++++++----------- MD5 | 4 ++-- README.md | 10 ++++------ 3 files changed, 27 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-29 0.2.0
2022-07-16 0.1.0
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.0.2.5 dated 2022-10-31 and 2.1.0.0 dated 2022-12-15
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bayesnec-2.1.0.0/bayesnec/R/pred_equations.R | 260 - bayesnec-2.1.0.0/bayesnec/R/predict.R |only bayesnec-2.1.0.0/bayesnec/R/print.R |only bayesnec-2.1.0.0/bayesnec/R/pull_brmsfit.R |only bayesnec-2.1.0.0/bayesnec/R/pull_out.R | 204 - bayesnec-2.1.0.0/bayesnec/R/pull_prior.R | 60 bayesnec-2.1.0.0/bayesnec/R/rhat.R |only bayesnec-2.1.0.0/bayesnec/R/sample_priors.R | 165 - bayesnec-2.1.0.0/bayesnec/R/set_distribution.R | 102 bayesnec-2.1.0.0/bayesnec/R/show_params.R | 76 bayesnec-2.1.0.0/bayesnec/R/summary.R |only bayesnec-2.1.0.0/bayesnec/R/sysdata.rda |binary bayesnec-2.1.0.0/bayesnec/R/validate_family.R | 64 bayesnec-2.1.0.0/bayesnec/R/validate_loo_controls.R | 80 bayesnec-2.1.0.0/bayesnec/R/validate_priors.R | 64 bayesnec-2.1.0.0/bayesnec/README.md | 135 - bayesnec-2.1.0.0/bayesnec/build/vignette.rds |binary bayesnec-2.1.0.0/bayesnec/data/beta_binomial2.rda |binary bayesnec-2.1.0.0/bayesnec/data/herbicide.rda |binary bayesnec-2.1.0.0/bayesnec/data/manec_example.rda |binary bayesnec-2.1.0.0/bayesnec/data/nec_data.rda |binary bayesnec-2.1.0.0/bayesnec/inst/doc/example1.Rmd | 122 bayesnec-2.1.0.0/bayesnec/inst/doc/example1.html | 319 +- bayesnec-2.1.0.0/bayesnec/inst/doc/example2.Rmd | 118 bayesnec-2.1.0.0/bayesnec/inst/doc/example2.html | 181 - 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bayesnec-2.1.0.0/bayesnec/tests/testthat/test-wrangle_model_formula.R | 28 bayesnec-2.1.0.0/bayesnec/vignettes/bayesnec.bib | 358 +- bayesnec-2.1.0.0/bayesnec/vignettes/example1.Rmd | 122 bayesnec-2.1.0.0/bayesnec/vignettes/example1.Rmd.orig | 561 ++-- bayesnec-2.1.0.0/bayesnec/vignettes/example2.Rmd | 118 bayesnec-2.1.0.0/bayesnec/vignettes/example2.Rmd.orig | 422 +-- bayesnec-2.1.0.0/bayesnec/vignettes/example2b.Rmd | 42 bayesnec-2.1.0.0/bayesnec/vignettes/example2b.Rmd.orig | 730 ++--- bayesnec-2.1.0.0/bayesnec/vignettes/example3.Rmd | 94 bayesnec-2.1.0.0/bayesnec/vignettes/example3.Rmd.orig | 331 +- bayesnec-2.1.0.0/bayesnec/vignettes/example4.Rmd | 65 bayesnec-2.1.0.0/bayesnec/vignettes/example4.Rmd.orig | 343 +- bayesnec-2.1.0.0/bayesnec/vignettes/exmp2b_theoretical_curves.R | 142 - bayesnec-2.1.0.0/bayesnec/vignettes/precompile.R | 66 bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-bbinom-1.png |only bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-beta-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-binom-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-gammabase-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-negbinbase-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp1-poisson-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-allmods-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-checkpriors-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-decline-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-ecx4param-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-goodmod-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp2-pretty-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp3-checkpriors-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp4-differences-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp4-fitted-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp4-fitteddiff-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp4-posterior-1.png |binary bayesnec-2.1.0.0/bayesnec/vignettes/vignette-fig-exmp4-probplot-1.png |binary 195 files changed, 10907 insertions(+), 10645 deletions(-)
Title: RNA-Seq Profile Classifier
Description: We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, International Journal of Molecular Sciences 23:4574, <doi:10.3390/ijms23094574>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.
Author: Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Allspice versions 1.0.5 dated 2022-06-11 and 1.0.6 dated 2022-12-15
DESCRIPTION | 8 MD5 | 39 R/Asset.assemble.R | 35 R/Asset.classify.R | 4 R/Asset.normalize.R | 2 R/Classifier.profiles.R | 17 R/Classifier.report.R | 4 build/vignette.rds |binary inst/doc/intro.html | 1424 +++++ inst/doc/intro.rmd | 6 inst/subtypes/coefficients.txt | 72 inst/tissues/categories.txt | 99 inst/tissues/centroids.txt | 92 inst/tissues/coefficients.txt | 204 inst/tissues/covariates.txt |only inst/tissues/nomenclature.txt | 1398 ----- inst/tissues/reference.txt |10134 +++++++++++++++++------------------------ man/Asset.assemble.Rd | 8 man/Asset.classify.Rd | 12 man/Classifier.profiles.Rd | 3 vignettes/intro.rmd | 6 21 files changed, 6046 insertions(+), 7521 deletions(-)