Title: Bayesian Generalized Linear Models with Time-Varying
Coefficients
Description: Bayesian generalized linear models with time-varying coefficients
as in Helske (2020, <arXiv:2009.07063>). Gaussian, Poisson, and binomial
observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, the package uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 1.0.1 dated 2021-01-25 and 1.0.1-1 dated 2021-01-30
DESCRIPTION | 8 +-- MD5 | 18 +++--- R/walker_rw1.R | 27 ++++++---- README.md | 4 + inst/doc/walker.R | 39 +++++++++----- inst/doc/walker.Rmd | 49 ++++++++++++------ inst/doc/walker.html | 109 ++++++++++++++++++++++++++--------------- man/walker_rw1.Rd | 3 - vignettes/vignette_results.rds |binary vignettes/walker.Rmd | 49 ++++++++++++------ 10 files changed, 197 insertions(+), 109 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.2.1 dated 2021-01-08 and 1.2.4 dated 2021-01-30
sigminer-1.2.1/sigminer/inst/extdata/human_hg19_gene_info.rds |only sigminer-1.2.1/sigminer/inst/extdata/human_hg38_gene_info.rds |only sigminer-1.2.1/sigminer/inst/extdata/mouse_mm10_gene_info.rds |only sigminer-1.2.4/sigminer/DESCRIPTION | 14 sigminer-1.2.4/sigminer/MD5 | 104 +++-- sigminer-1.2.4/sigminer/NAMESPACE | 2 sigminer-1.2.4/sigminer/NEWS.md | 44 ++ sigminer-1.2.4/sigminer/R/CN-mutex-classification-methed.R | 58 +++ sigminer-1.2.4/sigminer/R/best_practice.R | 129 ++++++- sigminer-1.2.4/sigminer/R/best_practice_helper.R | 79 +--- sigminer-1.2.4/sigminer/R/get_reconstructed_similarity.R | 3 sigminer-1.2.4/sigminer/R/get_shannon_diversity_index.R |only sigminer-1.2.4/sigminer/R/get_sig_db.R |only sigminer-1.2.4/sigminer/R/get_sig_exposure.R | 39 -- sigminer-1.2.4/sigminer/R/get_sig_similarity.R | 111 ------ sigminer-1.2.4/sigminer/R/read_copynumber.R | 9 sigminer-1.2.4/sigminer/R/read_vcf.R | 26 - sigminer-1.2.4/sigminer/R/show_cn_group_profile.R | 35 + sigminer-1.2.4/sigminer/R/show_group_enrichment.R | 10 sigminer-1.2.4/sigminer/R/show_sig_profile.R | 176 +++++++--- sigminer-1.2.4/sigminer/R/show_sig_profile_loop.R | 6 sigminer-1.2.4/sigminer/R/sig_auto_extract.R | 8 sigminer-1.2.4/sigminer/R/sig_estimate.R | 5 sigminer-1.2.4/sigminer/R/sig_extract.R | 1 sigminer-1.2.4/sigminer/R/sig_fit.R | 11 sigminer-1.2.4/sigminer/R/sig_fit_bootstrap.R | 3 sigminer-1.2.4/sigminer/R/sig_tally.R | 24 + sigminer-1.2.4/sigminer/R/sigflow.R |only sigminer-1.2.4/sigminer/R/sigprofiler.R | 2 sigminer-1.2.4/sigminer/R/utils.R | 16 sigminer-1.2.4/sigminer/README.md | 17 sigminer-1.2.4/sigminer/build/partial.rdb |binary sigminer-1.2.4/sigminer/inst/doc/sigminer.html | 8 sigminer-1.2.4/sigminer/inst/extdata/CN40-Map.txt |only sigminer-1.2.4/sigminer/inst/extdata/CN48-Map.txt |only sigminer-1.2.4/sigminer/inst/extdata/CNS_signatures_USARC.rds |only sigminer-1.2.4/sigminer/inst/extdata/RS_signatures_BRCA560.rds |only sigminer-1.2.4/sigminer/inst/extdata/RS_signatures_Nik_lab.rds |binary sigminer-1.2.4/sigminer/inst/extdata/RS_signatures_Nik_lab_Organ.rds |binary sigminer-1.2.4/sigminer/inst/extdata/RS_signatures_USARC.rds |only sigminer-1.2.4/sigminer/man/bp.Rd | 36 +- sigminer-1.2.4/sigminer/man/figures/README-unnamed-chunk-8-1.png |binary sigminer-1.2.4/sigminer/man/get_shannon_diversity_index.Rd |only sigminer-1.2.4/sigminer/man/get_sig_db.Rd | 36 +- sigminer-1.2.4/sigminer/man/get_sig_similarity.Rd | 12 sigminer-1.2.4/sigminer/man/read_copynumber.Rd | 2 sigminer-1.2.4/sigminer/man/read_vcf.Rd | 4 sigminer-1.2.4/sigminer/man/show_cn_components.Rd | 2 sigminer-1.2.4/sigminer/man/show_cn_features.Rd | 2 sigminer-1.2.4/sigminer/man/show_cn_group_profile.Rd | 4 sigminer-1.2.4/sigminer/man/show_cosmic_sig_profile.Rd | 3 sigminer-1.2.4/sigminer/man/show_sig_profile.Rd | 7 sigminer-1.2.4/sigminer/man/show_sig_profile_heatmap.Rd | 2 sigminer-1.2.4/sigminer/man/show_sig_profile_loop.Rd | 2 sigminer-1.2.4/sigminer/man/sig_fit.Rd | 8 sigminer-1.2.4/sigminer/man/sig_fit_bootstrap.Rd | 3 sigminer-1.2.4/sigminer/man/sig_tally.Rd | 7 sigminer-1.2.4/sigminer/man/sigprofiler.Rd | 2 sigminer-1.2.4/sigminer/vignettes/e1.rds |binary 59 files changed, 711 insertions(+), 361 deletions(-)
Title: Advanced and Parallel Random Number Generation via 'TRNG'
Description: Embeds sources and headers from Tina's Random
Number Generator ('TRNG') C++ library. Exposes some functionality for
easier access, testing and benchmarking into R. Provides examples of
how to use parallel RNG with 'RcppParallel'. The methods and
techniques behind 'TRNG' are illustrated in the package vignettes and
examples. Full documentation is available in Bauke (2021)
<https://github.com/rabauke/trng4/blob/v4.23.1/doc/trng.pdf>.
Author: Riccardo Porreca [aut, cre],
Roland Schmid [aut],
Mirai Solutions GmbH [cph],
Heiko Bauke [ctb, cph] (TRNG sources and headers)
Maintainer: Riccardo Porreca <riccardo.porreca@mirai-solutions.com>
Diff between rTRNG versions 4.20-1 dated 2019-05-03 and 4.23.1-1 dated 2021-01-30
rTRNG-4.20-1/rTRNG/inst/include/trng/config.hpp |only rTRNG-4.20-1/rTRNG/inst/include/trng/static_assertion.hpp |only rTRNG-4.23.1-1/rTRNG/DESCRIPTION | 12 rTRNG-4.23.1-1/rTRNG/MD5 | 241 - rTRNG-4.23.1-1/rTRNG/NAMESPACE | 1 rTRNG-4.23.1-1/rTRNG/NEWS.md | 17 rTRNG-4.23.1-1/rTRNG/R/LdFlags.R | 31 rTRNG-4.23.1-1/rTRNG/R/TRNG.Version.R | 2 rTRNG-4.23.1-1/rTRNG/R/rTRNG-package.R | 24 rTRNG-4.23.1-1/rTRNG/README.md | 75 rTRNG-4.23.1-1/rTRNG/build/vignette.rds |binary rTRNG-4.23.1-1/rTRNG/inst/COPYRIGHTS | 2 rTRNG-4.23.1-1/rTRNG/inst/WORDLIST | 4 rTRNG-4.23.1-1/rTRNG/inst/demos/rTRNGinPkg.R | 3 rTRNG-4.23.1-1/rTRNG/inst/demos/skeletonFiles/Makevars | 1 rTRNG-4.23.1-1/rTRNG/inst/demos/skeletonFiles/Makevars.win | 1 rTRNG-4.23.1-1/rTRNG/inst/doc/mcMat.R | 31 rTRNG-4.23.1-1/rTRNG/inst/doc/mcMat.Rmd | 23 rTRNG-4.23.1-1/rTRNG/inst/doc/mcMat.html | 381 +- rTRNG-4.23.1-1/rTRNG/inst/doc/rTRNG.R | 18 rTRNG-4.23.1-1/rTRNG/inst/doc/rTRNG.Rmd | 25 rTRNG-4.23.1-1/rTRNG/inst/doc/rTRNG.html | 181 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/bernoulli_dist.hpp | 234 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/beta_dist.hpp | 236 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/binomial_dist.hpp | 205 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/cauchy_dist.hpp | 221 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/chi_square_dist.hpp | 252 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/constants.hpp | 51 rTRNG-4.23.1-1/rTRNG/inst/include/trng/correlated_normal_dist.hpp | 240 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/cuda.hpp | 16 rTRNG-4.23.1-1/rTRNG/inst/include/trng/discrete_dist.hpp | 280 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/exponential_dist.hpp | 183 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/extreme_value_dist.hpp | 202 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/fast_discrete_dist.hpp | 259 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/gamma_dist.hpp | 250 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/generate_canonical.hpp | 74 rTRNG-4.23.1-1/rTRNG/inst/include/trng/geometric_dist.hpp | 153 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/hypergeometric_dist.hpp | 213 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/int_math.hpp | 456 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/int_types.hpp | 115 rTRNG-4.23.1-1/rTRNG/inst/include/trng/lagfib2plus.hpp | 334 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/lagfib2xor.hpp | 357 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/lagfib4plus.hpp | 343 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/lagfib4xor.hpp | 364 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/lcg64.hpp | 322 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/lcg64_shift.hpp | 335 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/limits.hpp | 327 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/linear_algebra.hpp |only rTRNG-4.23.1-1/rTRNG/inst/include/trng/logistic_dist.hpp | 195 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/lognormal_dist.hpp | 198 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/math.hpp | 406 -- rTRNG-4.23.1-1/rTRNG/inst/include/trng/maxwell_dist.hpp | 224 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/minstd.hpp | 181 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg2.hpp | 339 -- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg3.hpp | 394 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg3s.hpp | 397 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg4.hpp | 456 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg5.hpp | 544 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg5s.hpp | 548 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg_parameter.hpp |only rTRNG-4.23.1-1/rTRNG/inst/include/trng/mrg_status.hpp |only rTRNG-4.23.1-1/rTRNG/inst/include/trng/mt19937.hpp | 262 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/mt19937_64.hpp | 268 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/negative_binomial_dist.hpp | 216 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/normal_dist.hpp | 201 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/pareto_dist.hpp | 220 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/poisson_dist.hpp | 184 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/powerlaw_dist.hpp | 204 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/rayleigh_dist.hpp | 200 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/snedecor_f_dist.hpp | 241 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/special_functions.hpp | 1438 ++-------- rTRNG-4.23.1-1/rTRNG/inst/include/trng/student_t_dist.hpp | 198 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/tent_dist.hpp | 219 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/truncated_normal_dist.hpp | 273 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/twosided_exponential_dist.hpp | 178 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/uniform01_dist.hpp | 174 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/uniform_dist.hpp | 224 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/uniform_int_dist.hpp | 191 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/uniformxx.hpp | 246 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/utility.hpp | 265 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/weibull_dist.hpp | 220 - rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn2.hpp | 349 -- rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn3.hpp | 408 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn3s.hpp | 410 +- rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn4.hpp | 474 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn5.hpp | 557 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/yarn5s.hpp | 556 +-- rTRNG-4.23.1-1/rTRNG/inst/include/trng/zero_truncated_poisson_dist.hpp | 190 - rTRNG-4.23.1-1/rTRNG/inst/tools/fix_uninitialized-memory_read_access-backport-v4.23.patch |only rTRNG-4.23.1-1/rTRNG/inst/tools/upgradeTRNG.R | 104 rTRNG-4.23.1-1/rTRNG/inst/tools/valgrind-check.sh |only rTRNG-4.23.1-1/rTRNG/man/TRNG.Engine.Rd | 2 rTRNG-4.23.1-1/rTRNG/man/TRNG.Random.Rd | 2 rTRNG-4.23.1-1/rTRNG/man/check_rTRNG_linking.Rd |only rTRNG-4.23.1-1/rTRNG/man/rTRNG-package.Rd | 26 rTRNG-4.23.1-1/rTRNG/man/rbinom_trng.Rd | 8 rTRNG-4.23.1-1/rTRNG/man/rlnorm_trng.Rd | 11 rTRNG-4.23.1-1/rTRNG/man/rnorm_trng.Rd | 8 rTRNG-4.23.1-1/rTRNG/man/rpois_trng.Rd | 8 rTRNG-4.23.1-1/rTRNG/man/runif_trng.Rd | 8 rTRNG-4.23.1-1/rTRNG/src/Makevars | 2 rTRNG-4.23.1-1/rTRNG/src/Makevars.win | 2 rTRNG-4.23.1-1/rTRNG/src/trng/lcg64.cc | 108 rTRNG-4.23.1-1/rTRNG/src/trng/lcg64_shift.cc | 113 rTRNG-4.23.1-1/rTRNG/src/trng/minstd.cc | 60 rTRNG-4.23.1-1/rTRNG/src/trng/mrg2.cc | 113 rTRNG-4.23.1-1/rTRNG/src/trng/mrg3.cc | 124 rTRNG-4.23.1-1/rTRNG/src/trng/mrg3s.cc | 122 rTRNG-4.23.1-1/rTRNG/src/trng/mrg4.cc | 126 rTRNG-4.23.1-1/rTRNG/src/trng/mrg5.cc | 131 rTRNG-4.23.1-1/rTRNG/src/trng/mrg5s.cc | 138 rTRNG-4.23.1-1/rTRNG/src/trng/mt19937.cc | 74 rTRNG-4.23.1-1/rTRNG/src/trng/mt19937_64.cc | 86 rTRNG-4.23.1-1/rTRNG/src/trng/yarn2.cc | 103 rTRNG-4.23.1-1/rTRNG/src/trng/yarn3.cc | 122 rTRNG-4.23.1-1/rTRNG/src/trng/yarn3s.cc | 119 rTRNG-4.23.1-1/rTRNG/src/trng/yarn4.cc | 128 rTRNG-4.23.1-1/rTRNG/src/trng/yarn5.cc | 133 rTRNG-4.23.1-1/rTRNG/src/trng/yarn5s.cc | 140 rTRNG-4.23.1-1/rTRNG/tests/testthat/helper-invalid_argument.R |only rTRNG-4.23.1-1/rTRNG/tests/testthat/test-TRNG.Engine.R | 4 rTRNG-4.23.1-1/rTRNG/tests/testthat/test-TRNG.Random.R | 4 rTRNG-4.23.1-1/rTRNG/vignettes/code/mcMat.cpp | 2 rTRNG-4.23.1-1/rTRNG/vignettes/code/mcMatParallel.cpp | 2 rTRNG-4.23.1-1/rTRNG/vignettes/mcMat.Rmd | 23 rTRNG-4.23.1-1/rTRNG/vignettes/rTRNG.Rmd | 25 126 files changed, 9581 insertions(+), 12143 deletions(-)
More information about RandomForestsGLS at CRAN
Permanent link
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/index.htm>.
Author: Christopher J. Endres
Maintainer: Christopher J. Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.5.2 dated 2021-01-24 and 0.6.5.3 dated 2021-01-30
DESCRIPTION | 8 +- MD5 | 12 +-- R/nhanes.R | 24 +++++-- inst/doc/Introducing_nhanesA.R | 9 +- inst/doc/Introducing_nhanesA.Rmd | 15 ++-- inst/doc/Introducing_nhanesA.html | 128 +++++++++++++++++++------------------- vignettes/Introducing_nhanesA.Rmd | 15 ++-- 7 files changed, 116 insertions(+), 95 deletions(-)
Title: Interface to the Fish Tree of Life API
Description: An interface to the Fish Tree of Life API to download taxonomies,
phylogenies, fossil calibrations, and diversification rate information for
ray-finned fishes.
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>),
Michael E Alfaro [ctb],
Daniel L Rabosky [ctb],
Stephen A Smith [ctb]
Maintainer: Jonathan Chang <me@jonathanchang.org>
Diff between fishtree versions 0.3.3 dated 2020-10-31 and 0.3.4 dated 2021-01-30
DESCRIPTION | 18 - MD5 | 34 +- NEWS.md | 6 R/functions.R | 10 README.md | 66 ++-- inst/WORDLIST | 42 +- inst/doc/community-analysis.html | 365 ++++------------------ inst/doc/comparative-analysis.R | 2 inst/doc/comparative-analysis.Rmd | 2 inst/doc/comparative-analysis.html | 575 ++++++++++------------------------- man/fishtree_alignment.Rd | 2 man/fishtree_phylogeny.Rd | 2 man/fishtree_rogues.Rd | 2 man/fishtree_taxonomy.Rd | 2 man/fishtree_tip_rates.Rd | 2 vignettes/comparative-analysis.Rmd | 2 vignettes/comparative-analysis_cache |only 17 files changed, 357 insertions(+), 775 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph] (Original author of included code for priority
heaps)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.2.7 dated 2020-05-05 and 0.2.8 dated 2021-01-30
dodgr-0.2.7/dodgr/R/dodgr-package.r |only dodgr-0.2.7/dodgr/inst/doc/iso.R |only dodgr-0.2.7/dodgr/inst/doc/iso.Rmd |only dodgr-0.2.7/dodgr/inst/doc/iso.html |only dodgr-0.2.7/dodgr/vignettes/iso.Rmd |only dodgr-0.2.8/dodgr/DESCRIPTION | 64 dodgr-0.2.8/dodgr/MD5 | 122 - dodgr-0.2.8/dodgr/NEWS.md | 14 dodgr-0.2.8/dodgr/R/RcppExports.R | 13 dodgr-0.2.8/dodgr/R/centrality.R | 82 dodgr-0.2.8/dodgr/R/compare-heaps.R | 8 dodgr-0.2.8/dodgr/R/dists.R | 276 +- dodgr-0.2.8/dodgr/R/dodgr-package.R |only dodgr-0.2.8/dodgr/R/dodgr-streetnet.R | 40 dodgr-0.2.8/dodgr/R/flowmap.R | 4 dodgr-0.2.8/dodgr/R/flows.R | 116 - dodgr-0.2.8/dodgr/R/fund-cycles.R | 96 dodgr-0.2.8/dodgr/R/graph-contraction.R | 61 dodgr-0.2.8/dodgr/R/graph-conversion.R | 28 dodgr-0.2.8/dodgr/R/graph-functions-misc.R | 119 - dodgr-0.2.8/dodgr/R/graph-functions.R | 98 - dodgr-0.2.8/dodgr/R/graph-merge.R | 11 dodgr-0.2.8/dodgr/R/iso.R | 53 dodgr-0.2.8/dodgr/R/paths.R | 90 dodgr-0.2.8/dodgr/R/times.R | 12 dodgr-0.2.8/dodgr/R/utils.R | 40 dodgr-0.2.8/dodgr/R/weight-streetnet-times.R | 134 - dodgr-0.2.8/dodgr/R/weight-streetnet.R | 187 - dodgr-0.2.8/dodgr/R/weighting_profiles.R | 30 dodgr-0.2.8/dodgr/R/zzz.R | 5 dodgr-0.2.8/dodgr/README.md | 305 ++- dodgr-0.2.8/dodgr/build/vignette.rds |binary dodgr-0.2.8/dodgr/inst/doc/dodgr.html | 1458 +-------------- dodgr-0.2.8/dodgr/inst/doc/flows.html | 1332 ------------- dodgr-0.2.8/dodgr/inst/doc/times.Rmd | 3 dodgr-0.2.8/dodgr/inst/doc/times.html | 1340 ------------- dodgr-0.2.8/dodgr/man/compare_heaps.Rd | 2 dodgr-0.2.8/dodgr/man/dodgr.Rd | 2 dodgr-0.2.8/dodgr/man/dodgr_centrality.Rd | 18 dodgr-0.2.8/dodgr/man/dodgr_flows_aggregate.Rd | 12 dodgr-0.2.8/dodgr/man/hampi.Rd | 2 dodgr-0.2.8/dodgr/man/os_roads_bristol.Rd | 14 dodgr-0.2.8/dodgr/man/pipe.Rd | 2 dodgr-0.2.8/dodgr/man/weighting_profiles.Rd | 2 dodgr-0.2.8/dodgr/src/RcppExports.cpp | 14 dodgr-0.2.8/dodgr/src/centrality.cpp | 4 dodgr-0.2.8/dodgr/src/flows.cpp | 8 dodgr-0.2.8/dodgr/src/graph-contract.cpp | 3 dodgr-0.2.8/dodgr/src/graph.cpp | 63 dodgr-0.2.8/dodgr/src/graph.h | 3 dodgr-0.2.8/dodgr/tests/sc-conversion-fns.R | 7 dodgr-0.2.8/dodgr/tests/testthat/test-cache.R | 17 dodgr-0.2.8/dodgr/tests/testthat/test-centrality.R | 6 dodgr-0.2.8/dodgr/tests/testthat/test-cycles.R | 6 dodgr-0.2.8/dodgr/tests/testthat/test-dists.R | 579 +++-- dodgr-0.2.8/dodgr/tests/testthat/test-flows.R | 40 dodgr-0.2.8/dodgr/tests/testthat/test-graph-conversion.R | 5 dodgr-0.2.8/dodgr/tests/testthat/test-graph-fns.R | 8 dodgr-0.2.8/dodgr/tests/testthat/test-iso.R | 19 dodgr-0.2.8/dodgr/tests/testthat/test-paths.R | 8 dodgr-0.2.8/dodgr/tests/testthat/test-sc.R | 40 dodgr-0.2.8/dodgr/tests/testthat/test-streetnet.R | 15 dodgr-0.2.8/dodgr/tests/testthat/test-wt-profiles.R | 2 dodgr-0.2.8/dodgr/vignettes/dodgr.bib | 3 dodgr-0.2.8/dodgr/vignettes/times.Rmd | 3 65 files changed, 1852 insertions(+), 5196 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble
clustering framework, Chiu & Talhouk (2018)
<doi:10.1186/s12859-017-1996-y>. Results from a diverse set of
algorithms are pooled together using methods such as majority voting,
K-Modes, LinkCluE, and CSPA. There are options to compare cluster
assignments across algorithms using internal and external indices,
visualizations such as heatmaps, and significance testing for the
existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 1.0.0 dated 2020-07-07 and 1.0.1 dated 2021-01-30
DESCRIPTION | 6 MD5 | 12 NEWS.md | 6 R/consensus_evaluate.R | 2 R/graphs.R | 2 build/vignette.rds |binary inst/doc/overview.html | 667 ++++++++++++++++++------------------------------- 7 files changed, 270 insertions(+), 425 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>) and generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample. An online demonstration is available via <https://cnorm.shinyapps.io/cNORM/>.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [aut]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 2.0.1 dated 2021-01-05 and 2.0.2 dated 2021-01-30
DESCRIPTION | 11 - MD5 | 37 ++--- NAMESPACE | 1 NEWS.md | 13 + R/cNORM.R | 17 +- R/data.R | 2 R/modelling.R | 8 - R/plot.R | 82 +++++------ R/predict.R | 13 + R/preparation.R | 7 - R/s3methods.R | 3 R/utilities.R | 328 ++++++++++++++++++++++++++--------------------- inst/doc/cNORM-Demo.html | 10 - man/cNORM.Rd | 10 + man/getGroups.Rd |only man/mortality.Rd | 2 man/plot.cnorm.Rd | 3 man/plotCnorm.Rd | 3 man/prepareData.Rd | 2 tests |only 20 files changed, 314 insertions(+), 238 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'
color support is automatically detected. Colors and highlighting can
be combined and nested. New styles can also be created easily.
This package was inspired by the 'chalk' 'JavaScript' project.
Author: Gábor Csárdi [aut, cre],
Brodie Gaslam [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between crayon versions 1.3.4 dated 2017-09-16 and 1.4.0 dated 2021-01-30
crayon-1.3.4/crayon/inst |only crayon-1.3.4/crayon/tests/testthat/test-has-color.r |only crayon-1.4.0/crayon/DESCRIPTION | 15 - crayon-1.4.0/crayon/MD5 | 75 ++++---- crayon-1.4.0/crayon/NAMESPACE | 3 crayon-1.4.0/crayon/NEWS.md |only crayon-1.4.0/crayon/R/aaa-rstudio-detect.R |only crayon-1.4.0/crayon/R/aab-num-ansi-colors.R |only crayon-1.4.0/crayon/R/combine.r | 2 crayon-1.4.0/crayon/R/crayon-package.r | 2 crayon-1.4.0/crayon/R/has_color.r | 167 +------------------ crayon-1.4.0/crayon/R/link.R |only crayon-1.4.0/crayon/R/machinery.r | 12 - crayon-1.4.0/crayon/R/rematch2.R |only crayon-1.4.0/crayon/R/styles.r | 63 +++---- crayon-1.4.0/crayon/R/utils.r | 7 crayon-1.4.0/crayon/README.md |only crayon-1.4.0/crayon/man/col_align.Rd | 17 + crayon-1.4.0/crayon/man/col_nchar.Rd | 11 - crayon-1.4.0/crayon/man/col_strsplit.Rd | 15 + crayon-1.4.0/crayon/man/col_substr.Rd | 21 +- crayon-1.4.0/crayon/man/col_substring.Rd | 23 +- crayon-1.4.0/crayon/man/combine_styles.Rd | 10 - crayon-1.4.0/crayon/man/crayon.Rd | 12 - crayon-1.4.0/crayon/man/drop_style.Rd | 6 crayon-1.4.0/crayon/man/has_color.Rd | 37 ---- crayon-1.4.0/crayon/man/hyperlink.Rd |only crayon-1.4.0/crayon/man/make_style.Rd | 16 + crayon-1.4.0/crayon/man/num_ansi_colors.Rd |only crayon-1.4.0/crayon/man/num_colors.Rd | 31 --- crayon-1.4.0/crayon/tests/testthat/helper.R |only crayon-1.4.0/crayon/tests/testthat/test-ansi256.R | 2 crayon-1.4.0/crayon/tests/testthat/test-color.r | 29 +-- crayon-1.4.0/crayon/tests/testthat/test-combine.R | 2 crayon-1.4.0/crayon/tests/testthat/test-has-style.r | 8 crayon-1.4.0/crayon/tests/testthat/test-hyperlink.R |only crayon-1.4.0/crayon/tests/testthat/test-make-style.r | 2 crayon-1.4.0/crayon/tests/testthat/test-operations.R | 2 crayon-1.4.0/crayon/tests/testthat/test-style-var.r | 5 crayon-1.4.0/crayon/tests/testthat/test-styles.r | 2 crayon-1.4.0/crayon/tests/testthat/test-utils.R | 1 crayon-1.4.0/crayon/tests/testthat/test-vectors.r | 23 +- 42 files changed, 214 insertions(+), 407 deletions(-)
Title: Using 'Mathjax' in Rd Files
Description: Provides 'MathJax' and macros to enable its use within Rd files for rendering equations in the HTML help files.
Author: Wolfgang Viechtbauer [aut, cre]
(<https://orcid.org/0000-0003-3463-4063>)
Maintainer: Wolfgang Viechtbauer <wvb@wvbauer.com>
Diff between mathjaxr versions 1.0-1 dated 2020-06-25 and 1.2-0 dated 2021-01-30
mathjaxr-1.0-1/mathjaxr/inst/doc/mathjax |only mathjaxr-1.2-0/mathjaxr/DESCRIPTION | 11 + mathjaxr-1.2-0/mathjaxr/MD5 | 141 +++++++++++------------- mathjaxr-1.2-0/mathjaxr/NEWS.md | 10 + mathjaxr-1.2-0/mathjaxr/R/preview_rd.r | 31 ++++- mathjaxr-1.2-0/mathjaxr/README.md | 13 +- mathjaxr-1.2-0/mathjaxr/build/mathjaxr.pdf |binary mathjaxr-1.2-0/mathjaxr/inst/doc/R_dark.css |only mathjaxr-1.2-0/mathjaxr/man/mathjaxr-package.Rd | 6 - mathjaxr-1.2-0/mathjaxr/man/preview_rd.Rd | 12 +- mathjaxr-1.2-0/mathjaxr/src |only 11 files changed, 130 insertions(+), 94 deletions(-)
Title: R Scripts in the Google Cloud via Cloud Run, Cloud Build and
Cloud Scheduler
Description: Tools to easily enable R scripts in the Google Cloud Platform.
Utilise cloud services such as Cloud Run <https://cloud.google.com/run/> for R over HTTP,
Cloud Build <https://cloud.google.com/cloud-build/> for Continuous Delivery
and Integration services and
Cloud Scheduler <https://cloud.google.com/scheduler/> for scheduled scripts.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>),
Sunholo Ltd [cph]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between googleCloudRunner versions 0.4.0 dated 2021-01-13 and 0.4.1 dated 2021-01-30
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- NEWS.md | 6 ++++ R/buildsteps_templates.R | 3 ++ R/setup.R | 6 +++- R/setup_tests.R | 9 +++---- inst/docker/packages/cloud_build.R | 8 +++--- inst/docker/packages/cloudbuild.yml | 46 +++++++++++++++++++++++++++++++++--- 8 files changed, 79 insertions(+), 21 deletions(-)
More information about googleCloudRunner at CRAN
Permanent link
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre],
Jarrett Byrnes [aut] (<https://orcid.org/0000-0002-9791-9472>)
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between coronavirus versions 0.3.2 dated 2021-01-23 and 0.3.21 dated 2021-01-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/refresh_coronvirus.R | 6 ++++++ data/coronavirus.rda |binary 5 files changed, 17 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-01 0.17.0
2018-11-23 0.16.1
2018-01-10 0.16.0
2017-12-15 0.15.0
2017-11-05 0.14.0
2017-07-12 0.13.0
2017-06-02 0.12.0
2017-05-15 0.11.0
2016-08-18 0.10.0
2016-02-18 0.9.0
2016-02-12 0.8.0
Title: R Functions to Download and Clean Brazilian Electoral Data
Description: Offers a set of functions to easily download and clean
Brazilian electoral data from the Superior Electoral Court website.
Among others, the package retrieves data on local and
federal elections for all positions (city councilor, mayor, state deputy,
federal deputy, governor, and president) aggregated by
state, city, and electoral zones.
Author: Denisson Silva [aut, cre],
Fernando Meireles [aut],
Beatriz Costa [ctb]
Maintainer: Denisson Silva <denissoncsol@gmail.com>
Diff between electionsBR versions 0.3.1 dated 2019-07-09 and 0.3.2 dated 2021-01-30
DESCRIPTION | 10 - MD5 | 98 +++++++++---------- NAMESPACE | 2 NEWS.md | 11 ++ R/candidate_fed.R | 41 +++----- R/candidate_local.R | 47 +++------ R/details_mun_zone_fed.R | 26 +++-- R/details_mun_zone_local.R | 27 +++-- R/electionsBR.R | 4 R/legend_fed.R | 32 ++++-- R/legend_local.R | 26 +++-- R/party_mun_zone_fed.R | 35 +++--- R/party_mun_zone_local.R | 30 +++-- R/personal_finances_fed.R | 26 +++-- R/personal_finances_local.R | 24 +++- R/pipe.R |only R/seats_fed.R | 28 +++-- R/seats_local.R | 26 +++-- R/utils.R | 40 ++++++- R/vote_mun_zone_fed.R | 48 +++++---- R/vote_mun_zone_local.R | 29 +++-- R/vote_section_fed.R | 24 +++- R/vote_section_local.R | 63 ++++++++---- R/voter_profile.R | 39 +++++-- R/voter_profile_by_section.R |only README.md | 2 build/vignette.rds |binary inst/doc/introduction.R | 36 +++---- inst/doc/introduction.Rmd | 6 - inst/doc/introduction.html | 205 ++++++++++++++++++++++------------------ man/candidate_fed.Rd | 13 ++ man/candidate_local.Rd | 14 ++ man/details_mun_zone_fed.Rd | 13 ++ man/details_mun_zone_local.Rd | 14 ++ man/electionsBR-package.Rd | 4 man/legend_fed.Rd | 13 ++ man/legend_local.Rd | 12 +- man/party_mun_zone_fed.Rd | 13 ++ man/party_mun_zone_local.Rd | 14 ++ man/personal_finances_fed.Rd | 13 ++ man/personal_finances_local.Rd | 14 ++ man/pipe.Rd |only man/seats_fed.Rd | 15 ++ man/seats_local.Rd | 14 ++ man/vote_mun_zone_fed.Rd | 15 ++ man/vote_mun_zone_local.Rd | 14 ++ man/vote_section_fed.Rd | 12 +- man/vote_section_local.Rd | 14 ++ man/voter_affiliation.Rd | 9 + man/voter_profile.Rd | 13 +- man/voter_profile_by_section.Rd |only vignettes/introduction.Rmd | 6 - 52 files changed, 788 insertions(+), 446 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-27 1.4
2016-09-09 1.3
2016-01-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-19 2.3
2016-10-27 2.2
2016-09-09 2.1
2016-08-05 2.0
2016-01-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-10 0.0.9
2020-05-15 0.0.6
2020-05-14 0.0.5
2020-03-19 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-28 2.0
2018-05-09 1.6
2017-03-02 1.5
2016-06-20 1.3
2016-05-20 1.1
2016-03-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-15 3.0
2016-08-16 2.1
2016-03-06 1.4
2016-01-13 1.3
2015-09-15 1.2
2015-08-27 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-01 2.0.2
2018-05-10 2.0.1
2017-10-09 2.0
2017-03-13 1.1
2017-03-08 1.0
2016-11-10 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-27 1.0.2
2020-11-29 1.0.1
2020-11-18 1.0.0
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>),
Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>),
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e9>s Bov<e9> [ctb],
Ma<eb>lle Salmon [ctb],
Dirk Schumacher [ctb],
Stefan Steiner [ctb],
Mikko Virtanen [ctb],
Wei Wei [ctb],
Valentin Wimmer [ctb],
R Core Team [ctb] (A few code segments are modified versions of code
from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.18.0 dated 2020-03-19 and 1.19.0 dated 2021-01-30
surveillance-1.18.0/surveillance/tests/testthat.R |only surveillance-1.18.0/surveillance/tests/testthat/test-earsc.R |only surveillance-1.19.0/surveillance/DESCRIPTION | 26 surveillance-1.19.0/surveillance/MD5 | 230 +++---- surveillance-1.19.0/surveillance/NAMESPACE | 17 surveillance-1.19.0/surveillance/R/AllGeneric.R | 13 surveillance-1.19.0/surveillance/R/boda.R | 4 surveillance-1.19.0/surveillance/R/bodaDelay.R | 2 surveillance-1.19.0/surveillance/R/epidataCS.R | 30 surveillance-1.19.0/surveillance/R/farringtonFlexible.R | 14 surveillance-1.19.0/surveillance/R/hcl.colors.R | 10 surveillance-1.19.0/surveillance/R/hhh4.R | 26 surveillance-1.19.0/surveillance/R/hhh4_W.R | 30 surveillance-1.19.0/surveillance/R/hhh4_simulate_plot.R | 15 surveillance-1.19.0/surveillance/R/nowcast.R | 214 ++++--- surveillance-1.19.0/surveillance/R/spatial_tools.R | 15 surveillance-1.19.0/surveillance/R/stsNC.R | 60 + surveillance-1.19.0/surveillance/R/stsNClist_animate.R | 7 surveillance-1.19.0/surveillance/R/sts_animate.R | 50 - surveillance-1.19.0/surveillance/R/sts_coerce.R | 7 surveillance-1.19.0/surveillance/R/stsplot_space.R | 41 - surveillance-1.19.0/surveillance/R/twinstim_siaf.R | 8 surveillance-1.19.0/surveillance/R/twinstim_simulation.R | 41 - surveillance-1.19.0/surveillance/build/partial.rdb |binary surveillance-1.19.0/surveillance/build/vignette.rds |binary surveillance-1.19.0/surveillance/inst/NEWS.Rd | 95 +++ surveillance-1.19.0/surveillance/inst/doc/glrnb.R | 1 surveillance-1.19.0/surveillance/inst/doc/glrnb.Rnw | 2 surveillance-1.19.0/surveillance/inst/doc/glrnb.pdf |binary surveillance-1.19.0/surveillance/inst/doc/hhh4.R | 1 surveillance-1.19.0/surveillance/inst/doc/hhh4.pdf |binary surveillance-1.19.0/surveillance/inst/doc/hhh4_spacetime.R | 7 surveillance-1.19.0/surveillance/inst/doc/hhh4_spacetime.Rnw | 37 - surveillance-1.19.0/surveillance/inst/doc/hhh4_spacetime.pdf |binary surveillance-1.19.0/surveillance/inst/doc/monitoringCounts.R | 155 +---- surveillance-1.19.0/surveillance/inst/doc/monitoringCounts.Rnw | 75 -- surveillance-1.19.0/surveillance/inst/doc/monitoringCounts.pdf |binary surveillance-1.19.0/surveillance/inst/doc/surveillance.R | 3 surveillance-1.19.0/surveillance/inst/doc/surveillance.Rnw | 8 surveillance-1.19.0/surveillance/inst/doc/surveillance.pdf |binary surveillance-1.19.0/surveillance/inst/doc/twinSIR.Rnw | 4 surveillance-1.19.0/surveillance/inst/doc/twinSIR.pdf |binary surveillance-1.19.0/surveillance/inst/doc/twinstim.R | 2 surveillance-1.19.0/surveillance/inst/doc/twinstim.Rnw | 27 surveillance-1.19.0/surveillance/inst/doc/twinstim.pdf |binary surveillance-1.19.0/surveillance/inst/jags/bhpm.bugs | 210 +++--- surveillance-1.19.0/surveillance/man/LRCUSUM.runlength.Rd | 17 surveillance-1.19.0/surveillance/man/algo.outbreakP.Rd | 5 surveillance-1.19.0/surveillance/man/campyDE.Rd | 2 surveillance-1.19.0/surveillance/man/discpoly.Rd | 10 surveillance-1.19.0/surveillance/man/epidataCS.Rd | 14 surveillance-1.19.0/surveillance/man/epidata_plot.Rd | 3 surveillance-1.19.0/surveillance/man/farringtonFlexible.Rd | 2 surveillance-1.19.0/surveillance/man/hagelloch.Rd | 2 surveillance-1.19.0/surveillance/man/hcl.colors.Rd | 3 surveillance-1.19.0/surveillance/man/hhh4.Rd | 9 surveillance-1.19.0/surveillance/man/hhh4_W.Rd | 7 surveillance-1.19.0/surveillance/man/hhh4_plot.Rd | 7 surveillance-1.19.0/surveillance/man/hhh4_simulate_scores.Rd | 3 surveillance-1.19.0/surveillance/man/hhh4_validation.Rd | 15 surveillance-1.19.0/surveillance/man/imdepi.Rd | 10 surveillance-1.19.0/surveillance/man/inside.gpc.poly.Rd | 2 surveillance-1.19.0/surveillance/man/intersectPolyCircle.Rd | 2 surveillance-1.19.0/surveillance/man/knox.Rd | 2 surveillance-1.19.0/surveillance/man/ks.plot.unif.Rd | 18 surveillance-1.19.0/surveillance/man/marks.Rd | 6 surveillance-1.19.0/surveillance/man/momo.Rd | 7 surveillance-1.19.0/surveillance/man/multiplicity.Rd | 8 surveillance-1.19.0/surveillance/man/multiplicity.Spatial.Rd | 6 surveillance-1.19.0/surveillance/man/nowcast.Rd | 108 ++- surveillance-1.19.0/surveillance/man/permutationTest.Rd | 19 surveillance-1.19.0/surveillance/man/runifdisc.Rd | 5 surveillance-1.19.0/surveillance/man/stK.Rd | 2 surveillance-1.19.0/surveillance/man/sts-class.Rd | 8 surveillance-1.19.0/surveillance/man/sts_animate.Rd | 37 - surveillance-1.19.0/surveillance/man/sts_tidy.Rd | 4 surveillance-1.19.0/surveillance/man/stsplot_space.Rd | 27 surveillance-1.19.0/surveillance/man/stsplot_time.Rd | 4 surveillance-1.19.0/surveillance/man/surveillance.options.Rd | 6 surveillance-1.19.0/surveillance/man/twinstim.Rd | 2 surveillance-1.19.0/surveillance/man/twinstim_epitest.Rd | 2 surveillance-1.19.0/surveillance/man/twinstim_iaf.Rd | 2 surveillance-1.19.0/surveillance/man/twinstim_simulation.Rd | 33 - surveillance-1.19.0/surveillance/tests/testthat/test-algo.glrnb.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-bodaDelay.R | 62 +- surveillance-1.19.0/surveillance/tests/testthat/test-calibration.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-createLambda.R | 8 surveillance-1.19.0/surveillance/tests/testthat/test-determineSources.R | 14 surveillance-1.19.0/surveillance/tests/testthat/test-earsC.R |only surveillance-1.19.0/surveillance/tests/testthat/test-farringtonFlexible.R | 302 ++++------ surveillance-1.19.0/surveillance/tests/testthat/test-formatDate.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-hhh4+derivatives.R | 12 surveillance-1.19.0/surveillance/tests/testthat/test-hhh4_ARasNE.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-hhh4_NegBinGrouped.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-hhh4_offsets.R | 9 surveillance-1.19.0/surveillance/tests/testthat/test-hhh4_weights.R |only surveillance-1.19.0/surveillance/tests/testthat/test-nbOrder.R | 5 surveillance-1.19.0/surveillance/tests/testthat/test-plapply.R | 2 surveillance-1.19.0/surveillance/tests/testthat/test-siafs.R | 29 surveillance-1.19.0/surveillance/tests/testthat/test-sts.R | 14 surveillance-1.19.0/surveillance/tests/testthat/test-tiafs.R | 4 surveillance-1.19.0/surveillance/tests/testthat/test-toLatex.sts.R | 8 surveillance-1.19.0/surveillance/tests/testthat/test-twinstim_score.R | 2 surveillance-1.19.0/surveillance/tests/tinytest.R |only surveillance-1.19.0/surveillance/vignettes/glrnb.Rnw | 2 surveillance-1.19.0/surveillance/vignettes/hhh4_spacetime.Rnw | 37 - surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/boda.RData |binary surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/boda.covars.RData |binary surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/fPlot.R |only surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/fPlot1.pdf |only surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/fPlot2.pdf |only surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/pMC.RData |binary surveillance-1.19.0/surveillance/vignettes/monitoringCounts-cache/pMarkovChain.RData |binary surveillance-1.19.0/surveillance/vignettes/monitoringCounts.Rnw | 75 -- surveillance-1.19.0/surveillance/vignettes/monitoringCounts.bib | 8 surveillance-1.19.0/surveillance/vignettes/references.bib | 43 + surveillance-1.19.0/surveillance/vignettes/surveillance-hmm.pdf |binary surveillance-1.19.0/surveillance/vignettes/surveillance.Rnw | 8 surveillance-1.19.0/surveillance/vignettes/twinSIR.Rnw | 4 surveillance-1.19.0/surveillance/vignettes/twinstim.Rnw | 27 120 files changed, 1343 insertions(+), 1248 deletions(-)
Title: Supplemental S-PLUS Functionality in R
Description: Currently there are many functions in S-PLUS that are
missing in R. To facilitate the conversion of S-PLUS packages to R packages,
this package provides some missing S-PLUS functionality in R.
Author: William Constantine [aut],
Tim Hesterberg [aut],
Knut Wittkowski [ctb],
Tingting Song [ctb],
Bill Dunlap [ctb],
Stephen Kaluzny [ctb, cre]
Maintainer: Stephen Kaluzny <spkaluzny@gmail.com>
Diff between splus2R versions 1.2-2 dated 2016-09-02 and 1.3-3 dated 2021-01-30
splus2R-1.2-2/splus2R/src/peaks.f |only splus2R-1.3-3/splus2R/DESCRIPTION | 31 ++++++++++++++++++++++--------- splus2R-1.3-3/splus2R/MD5 | 13 +++++++------ splus2R-1.3-3/splus2R/NAMESPACE | 1 + splus2R-1.3-3/splus2R/NEWS | 12 +++++++++--- splus2R-1.3-3/splus2R/R/peaks.R | 16 ++++++---------- splus2R-1.3-3/splus2R/man/peaks.Rd | 24 +++++++++++++++++++++--- splus2R-1.3-3/splus2R/src/cpeaks.c |only splus2R-1.3-3/splus2R/src/init.c |only 9 files changed, 66 insertions(+), 31 deletions(-)
Title: Fit Text Inside a Box in 'ggplot2'
Description: Provides 'ggplot2' geoms to fit text into a box by growing, shrinking
or wrapping the text.
Author: David Wilkins [aut, cre]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.9.0 dated 2020-06-14 and 0.9.1 dated 2021-01-30
ggfittext-0.9.0/ggfittext/data/coffees.rda |only ggfittext-0.9.0/ggfittext/man/coffees.Rd |only ggfittext-0.9.1/ggfittext/DESCRIPTION | 14 ggfittext-0.9.1/ggfittext/MD5 | 118 +- ggfittext-0.9.1/ggfittext/NEWS.md | 17 ggfittext-0.9.1/ggfittext/R/data.R | 14 ggfittext-0.9.1/ggfittext/R/expect_doppelganger.R |only ggfittext-0.9.1/ggfittext/R/geom_fit_text.R | 40 ggfittext-0.9.1/ggfittext/README.md | 84 - ggfittext-0.9.1/ggfittext/build/vignette.rds |binary ggfittext-0.9.1/ggfittext/data/animals.rda |binary ggfittext-0.9.1/ggfittext/data/beverages.rda |only ggfittext-0.9.1/ggfittext/data/gold.rda |binary ggfittext-0.9.1/ggfittext/inst/WORDLIST | 14 ggfittext-0.9.1/ggfittext/inst/doc/introduction-to-ggfittext.R | 14 ggfittext-0.9.1/ggfittext/inst/doc/introduction-to-ggfittext.Rmd | 57 - ggfittext-0.9.1/ggfittext/inst/doc/introduction-to-ggfittext.html | 178 ++- ggfittext-0.9.1/ggfittext/man/animals.Rd | 4 ggfittext-0.9.1/ggfittext/man/beverages.Rd |only ggfittext-0.9.1/ggfittext/man/figures/README-hero-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-hero-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-10-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-10-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-11-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-11-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-12-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-12-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-13-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-13-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-14-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-14-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-15-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-15-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-4-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-4-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-5-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-5-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-6-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-6-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-7-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-7-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-8-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-8-1.png |binary ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-9-1.pdf |only ggfittext-0.9.1/ggfittext/man/figures/README-unnamed-chunk-9-1.png |binary ggfittext-0.9.1/ggfittext/man/gold.Rd | 8 ggfittext-0.9.1/ggfittext/tests/figs/deps.txt | 2 ggfittext-0.9.1/ggfittext/tests/figs/geom-bar-text/coord-flip-with-dodge-and-grow-and-reflow.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/geom-bar-text/coord-flip-with-dodge.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/geom-bar-text/implied-doesn-t-misfire-with-integer-y.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/geom-bar-text/implied-flip-with-dodge-and-grow-and-reflow.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/geom-bar-text/implied-flip-with-dodge.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/basic-placement.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/basic-reflowing.svg | 4 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/contrasting-text.svg | 6 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/contrasting-works-with-non-black-text.svg | 6 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/dodged-and-flipped-bar-plot.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/height-of-20-mm.svg | 476 +++++----- ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/height-of-5-mm.svg | 476 +++++----- ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/placing.svg | 4 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/reflowing-and-growing.svg | 4 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/stacked-and-flipped-bar-plot.svg |only ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/stacked-bar-plot-with-0-value.svg |only ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/stacked-bar-plot.svg | 2 ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/width-of-100-mm.svg | 476 +++++----- ggfittext-0.9.1/ggfittext/tests/figs/visual-tests-of-plots/width-of-40-mm.svg | 476 +++++----- ggfittext-0.9.1/ggfittext/tests/testthat/test-geom_bar_text.R | 22 ggfittext-0.9.1/ggfittext/tests/testthat/test-polar.R | 22 ggfittext-0.9.1/ggfittext/tests/testthat/test_plots.R | 85 + ggfittext-0.9.1/ggfittext/vignettes/introduction-to-ggfittext.Rmd | 57 - 70 files changed, 1406 insertions(+), 1288 deletions(-)
Title: Transform Models into 'LaTeX' Equations
Description: The goal of 'equatiomatic' is to reduce the pain associated with
writing 'LaTeX' formulas from fitted models. The primary function of
the package, extract_eq(), takes a fitted model object as its input
and returns the corresponding 'LaTeX' code for the model.
Author: Daniel Anderson [aut, cre] (<https://orcid.org/0000-0003-4699-4680>),
Andrew Heiss [aut] (<https://orcid.org/0000-0002-3948-3914>),
Jay Sumners [aut],
Joshua Rosenberg [ctb] (<https://orcid.org/0000-0003-2170-0447>),
Jonathan Sidi [ctb] (<https://orcid.org/0000-0002-4222-1819>),
Ellis Hughes [ctb] (<https://orcid.org/0000-0003-0637-4436>),
Thomas Fung [ctb] (<https://orcid.org/0000-0003-2601-0728>),
Reza Norouzian [ctb] (<https://orcid.org/0000-0002-0531-6886>)
Maintainer: Daniel Anderson <daniela@uoregon.edu>
Diff between equatiomatic versions 0.1.0 dated 2020-08-27 and 0.2.0 dated 2021-01-30
equatiomatic-0.1.0/equatiomatic/tests/testthat/helper.R |only equatiomatic-0.1.0/equatiomatic/vignettes/results-asis.png |only equatiomatic-0.2.0/equatiomatic/DESCRIPTION | 41 - equatiomatic-0.2.0/equatiomatic/MD5 | 134 ++- equatiomatic-0.2.0/equatiomatic/NAMESPACE | 16 equatiomatic-0.2.0/equatiomatic/NEWS.md | 10 equatiomatic-0.2.0/equatiomatic/R/create_eq.R | 347 ++++++++- equatiomatic-0.2.0/equatiomatic/R/equatiomatic-package.R | 4 equatiomatic-0.2.0/equatiomatic/R/extract_eq.R | 161 ++++ equatiomatic-0.2.0/equatiomatic/R/extract_lhs.R | 241 ++++-- equatiomatic-0.2.0/equatiomatic/R/extract_rhs.R | 377 +++++++++- equatiomatic-0.2.0/equatiomatic/R/helpers_forecast.R |only equatiomatic-0.2.0/equatiomatic/R/hsb.R |only equatiomatic-0.2.0/equatiomatic/R/merMod.R |only equatiomatic-0.2.0/equatiomatic/R/penguins.R | 9 equatiomatic-0.2.0/equatiomatic/R/print.R | 55 + equatiomatic-0.2.0/equatiomatic/R/sim_longitudinal.R |only equatiomatic-0.2.0/equatiomatic/R/simple_ts.R |only equatiomatic-0.2.0/equatiomatic/R/ts_reg_list.R |only equatiomatic-0.2.0/equatiomatic/README.md | 223 +++-- equatiomatic-0.2.0/equatiomatic/build/partial.rdb |only equatiomatic-0.2.0/equatiomatic/build/vignette.rds |binary equatiomatic-0.2.0/equatiomatic/data/hsb.rda |only equatiomatic-0.2.0/equatiomatic/data/sim_longitudinal.rda |only equatiomatic-0.2.0/equatiomatic/data/simple_ts.rda |only equatiomatic-0.2.0/equatiomatic/data/ts_reg_list.rda |only equatiomatic-0.2.0/equatiomatic/inst/doc/forecast-arima.R |only equatiomatic-0.2.0/equatiomatic/inst/doc/forecast-arima.Rmd |only equatiomatic-0.2.0/equatiomatic/inst/doc/forecast-arima.html |only equatiomatic-0.2.0/equatiomatic/inst/doc/intro-equatiomatic.R | 17 equatiomatic-0.2.0/equatiomatic/inst/doc/intro-equatiomatic.Rmd | 21 equatiomatic-0.2.0/equatiomatic/inst/doc/intro-equatiomatic.html | 144 ++- equatiomatic-0.2.0/equatiomatic/inst/doc/lme4-lmer.R |only equatiomatic-0.2.0/equatiomatic/inst/doc/lme4-lmer.Rmd |only equatiomatic-0.2.0/equatiomatic/inst/doc/lme4-lmer.html |only equatiomatic-0.2.0/equatiomatic/inst/doc/plotting-integration.R |only equatiomatic-0.2.0/equatiomatic/inst/doc/plotting-integration.Rmd |only equatiomatic-0.2.0/equatiomatic/inst/doc/plotting-integration.html |only equatiomatic-0.2.0/equatiomatic/inst/doc/tests_and_coverage.R | 2 equatiomatic-0.2.0/equatiomatic/inst/doc/tests_and_coverage.Rmd | 2 equatiomatic-0.2.0/equatiomatic/inst/doc/tests_and_coverage.html | 25 equatiomatic-0.2.0/equatiomatic/man/equatiomatic-package.Rd | 4 equatiomatic-0.2.0/equatiomatic/man/extract_eq.Rd | 14 equatiomatic-0.2.0/equatiomatic/man/figures/README-example-basic-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-categorical-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-clm-ologit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-clm-oprobit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-italics-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-logit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-ologit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-polr-probit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-preserve-order-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-probit-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-shortcut-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-wrap-longer-location-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-wrap-longer-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-example-wrap-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-fix-signs-long-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-fix-signs-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/figures/README-use-coefs-preview-1.png |binary equatiomatic-0.2.0/equatiomatic/man/hsb.Rd |only equatiomatic-0.2.0/equatiomatic/man/penguins.Rd | 9 equatiomatic-0.2.0/equatiomatic/man/sim_longitudinal.Rd |only equatiomatic-0.2.0/equatiomatic/man/simple_ts.Rd |only equatiomatic-0.2.0/equatiomatic/man/ts_reg_list.Rd |only equatiomatic-0.2.0/equatiomatic/tests/README.md | 126 ++- equatiomatic-0.2.0/equatiomatic/tests/testthat/_snaps |only equatiomatic-0.2.0/equatiomatic/tests/testthat/test-clm.R | 57 - 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Title: Multiple Imputation with Denoising Autoencoders
Description: A tool for multiply imputing missing data using 'MIDAS', a deep learning method based on denoising autoencoder neural networks. This algorithm offers significant accuracy and efficiency advantages over other multiple imputation strategies, particularly when applied to large datasets with complex features. Alongside interfacing with 'Python' to run the core algorithm, this package contains functions for processing data before and after model training, running imputation model diagnostics, generating multiple completed datasets, and estimating regression models on these datasets.
Author: Thomas Robinson [aut, cre, cph]
(<https://orcid.org/0000-0001-7097-1599>),
Ranjit Lall [aut, cph] (<https://orcid.org/0000-0003-1455-3506>),
Alex Stenlake [ctb, cph]
Maintainer: Thomas Robinson <ts.robinson1994@gmail.com>
Diff between rMIDAS versions 0.2.0 dated 2020-11-02 and 0.3.0 dated 2021-01-30
DESCRIPTION | 6 +- MD5 | 24 ++++---- NEWS.md | 20 +++--- R/midas_functions.R | 18 ++++-- R/pre_processing.R | 25 +++++++- README.md | 47 ++++++++-------- inst/doc/custom_python_versions.html | 102 +++++++++++++---------------------- inst/doc/imputation_demo.html | 102 +++++++++++++---------------------- inst/python/midas_base.py | 71 +++++++++++++++++------- man/complete.Rd | 2 man/convert.Rd | 2 man/overimpute.Rd | 6 ++ man/train.Rd | 3 + 13 files changed, 226 insertions(+), 202 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
Hua Zhou [aut, ctb] (<https://orcid.org/0000-0003-1822-1306>),
Nicole Doudican [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>),
John Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>),
Adriana Heguy [aut, ctb],
Boris Reizis [aut, ctb] (<https://orcid.org/0000-0003-1140-7853>),
Aristotelis Tsirigos [aut, ctb]
(<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.5.9 dated 2021-01-21 and 1.6.0 dated 2021-01-30
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++++------- NAMESPACE | 6 ++++++ R/F00100.R | 10 +++++++--- R/F0030.R | 46 ++++++---------------------------------------- R/F0031.R | 2 +- R/F0044.R | 1 + R/F0068.R |only R/F0069.R |only R/F0070.R |only man/add.10x.image.Rd |only man/capture.image.10x.Rd |only man/gene.plot.Rd | 2 +- man/spatial.plot.Rd |only 14 files changed, 39 insertions(+), 56 deletions(-)