Title: Download 'nflverse' Data
Description: A minimal package for downloading data from 'GitHub'
repositories of the 'nflverse' project.
Author: Tan Ho [aut, cre, cph] (<https://orcid.org/0000-0001-8388-5155>),
Sebastian Carl [aut],
John Edwards [ctb],
Ben Baldwin [ctb],
Thomas Mock [ctb],
Lee Sharpe [ctb]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between nflreadr versions 1.1.2 dated 2021-12-08 and 1.1.3 dated 2022-01-27
DESCRIPTION | 6 - MD5 | 152 ++++++++++++++++++++------------ NAMESPACE | 2 NEWS.md | 23 ++++ R/data.R | 48 ++++++++++ R/from_url.R | 4 R/load_ffverse.R | 68 ++++++++++++-- R/load_nflverse.R | 101 +++++++++++++++------ R/name_cleaning.R | 4 R/sitrep.R | 4 R/utils.R | 17 ++- R/zzz.R | 2 README.md | 17 ++- build/vignette.rds |binary data/dictionary_combine.rda |only data/dictionary_depth_charts.rda |only data/dictionary_draft_picks.rda |binary data/dictionary_espn_qbr.rda |only data/dictionary_ff_opportunity.rda |only data/dictionary_ff_playerids.rda |binary data/dictionary_ff_rankings.rda |binary data/dictionary_injuries.rda |only data/dictionary_pbp.rda |binary data/dictionary_pfr_passing.rda |binary data/dictionary_player_stats.rda |binary data/dictionary_rosters.rda |binary data/dictionary_schedules.rda |binary data/dictionary_snap_counts.rda |binary data/dictionary_trades.rda |only inst/doc/dictionary_combine.R |only inst/doc/dictionary_combine.Rmd |only inst/doc/dictionary_combine.html |only inst/doc/dictionary_depth_charts.R |only inst/doc/dictionary_depth_charts.Rmd |only inst/doc/dictionary_depth_charts.html |only inst/doc/dictionary_espn_qbr.R |only inst/doc/dictionary_espn_qbr.Rmd |only inst/doc/dictionary_espn_qbr.html |only inst/doc/dictionary_ff_opportunity.R |only inst/doc/dictionary_ff_opportunity.Rmd |only inst/doc/dictionary_ff_opportunity.html |only inst/doc/dictionary_injuries.R |only inst/doc/dictionary_injuries.Rmd |only inst/doc/dictionary_injuries.html |only inst/doc/dictionary_pbp.html | 4 inst/doc/dictionary_player_stats.Rmd | 1 inst/doc/dictionary_player_stats.html | 4 inst/doc/dictionary_rosters.Rmd | 3 inst/doc/dictionary_rosters.html | 4 inst/doc/dictionary_schedules.R | 2 inst/doc/dictionary_schedules.Rmd | 4 inst/doc/dictionary_schedules.html | 4 inst/doc/dictionary_snap_counts.html | 2 inst/doc/dictionary_trades.R |only inst/doc/dictionary_trades.Rmd |only inst/doc/dictionary_trades.html |only man/dictionary_combine.Rd |only man/dictionary_depth_charts.Rd |only man/dictionary_espn_qbr.Rd |only man/dictionary_ff_opportunity.Rd |only man/dictionary_injuries.Rd |only man/dictionary_nextgen_stats.Rd | 2 man/dictionary_trades.Rd |only man/load_combine.Rd | 9 + man/load_depth_charts.Rd | 6 + man/load_draft_picks.Rd | 6 - man/load_espn_qbr.Rd | 6 + man/load_ff_opportunity.Rd |only man/load_ff_playerids.Rd | 4 man/load_ff_rankings.Rd | 10 +- man/load_injuries.Rd | 8 + man/load_nextgen_stats.Rd | 9 + man/load_pbp.Rd | 6 - man/load_pfr_advstats.Rd | 11 +- man/load_pfr_passing.Rd | 6 - man/load_player_stats.Rd | 6 - man/load_rosters.Rd | 6 - man/load_schedules.Rd | 4 man/load_snap_counts.Rd | 8 + man/load_teams.Rd | 2 man/load_trades.Rd | 6 + man/most_recent_season.Rd |only man/nflreadr-package.Rd | 2 man/sitrep.Rd | 7 + tests/testthat/test-ffverse.R | 16 +++ tests/testthat/test-name_cleaning.R | 3 tests/testthat/test-nflverse.R | 7 - vignettes/dictionary_combine.Rmd |only vignettes/dictionary_depth_charts.Rmd |only vignettes/dictionary_espn_qbr.Rmd |only vignettes/dictionary_ff_opportunity.Rmd |only vignettes/dictionary_injuries.Rmd |only vignettes/dictionary_player_stats.Rmd | 1 vignettes/dictionary_rosters.Rmd | 3 vignettes/dictionary_schedules.Rmd | 4 vignettes/dictionary_trades.Rmd |only 96 files changed, 454 insertions(+), 180 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.1.2 dated 2021-11-25 and 0.1.3 dated 2022-01-27
DESCRIPTION | 8 +- MD5 | 31 +++++----- NAMESPACE | 1 NEWS.md | 16 +++++ R/aaa.R | 38 ++++++++++++- R/bind.R | 119 +++++++++++++++++++++++++++++++++++++---- R/class_filearray.R | 101 ++++++++++++++++++++++++++++++---- R/filearray-package.R | 43 ++++++++++++++ R/header.R | 11 +++ R/load.R | 54 ++++++++++++++++++ R/write.R | 4 - man/FileArray-class.Rd | 2 man/filearray.Rd | 34 +++++++++++ man/filearray_bind.Rd | 49 ++++++++++++++-- src/core.cpp | 48 ++++++++++++++++ tests/testthat/test-bind.R |only tests/testthat/test-dimnames.R | 2 17 files changed, 504 insertions(+), 57 deletions(-)
Title: The Extreme Learning Machine Algorithm
Description: Training and predict functions for Single Hidden-layer Feedforward Neural Networks (SLFN) using the Extreme Learning Machine (ELM) algorithm. The ELM algorithm differs from the traditional gradient-based algorithms for very short training times (it doesn't need any iterative tuning, this makes learning time very fast) and there is no need to set any other parameters like learning rate, momentum, epochs, etc. This is a reimplementation of the 'elmNN' package using 'RcppArmadillo' after the 'elmNN' package was archived. For more information, see "Extreme learning machine: Theory and applications" by Guang-Bin Huang, Qin-Yu Zhu, Chee-Kheong Siew (2006), Elsevier B.V, <doi:10.1016/j.neucom.2005.12.126>.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Alberto Gosso [aut],
Edwin de Jonge [ctb] (<https://orcid.org/0000-0002-6580-4718>, Github
Contributor)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between elmNNRcpp versions 1.0.3 dated 2021-05-04 and 1.0.4 dated 2022-01-27
DESCRIPTION | 16 MD5 | 18 NAMESPACE | 5 NEWS.md | 5 R/elm.R |only README.md | 22 + build/vignette.rds |binary inst/doc/extreme_learning_machine.html | 660 +++++++++++---------------------- man/elm.Rd |only man/predict.elm.Rd |only src/RcppExports.cpp | 5 tests/testthat/test-elm.R |only 12 files changed, 292 insertions(+), 439 deletions(-)
Title: Tufte's Styles for R Markdown Documents
Description: Provides R Markdown output formats to use Tufte styles for
PDF and HTML output.
Author: Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>),
Christophe Dervieux [ctb, cre]
(<https://orcid.org/0000-0003-4474-2498>),
JJ Allaire [aut],
Andrzej Oles [ctb],
Dave Liepmann [ctb] (Tufte CSS in
inst/rmarkdown/templates/tufte_html/resources),
RStudio, PBC [cph]
Maintainer: Christophe Dervieux <cderv@rstudio.com>
Diff between tufte versions 0.11 dated 2021-12-18 and 0.12 dated 2022-01-27
tufte-0.11/tufte/inst/NEWS.Rd |only tufte-0.12/tufte/DESCRIPTION | 28 ++++++++++++++++------------ tufte-0.12/tufte/MD5 | 12 ++++++------ tufte-0.12/tufte/NEWS.md |only tufte-0.12/tufte/R/html.R | 4 ++-- tufte-0.12/tufte/man/tufte_handout.Rd | 10 ++++++---- tufte-0.12/tufte/tests/testthat/helpers.R | 27 +++++++++++++++++++++++++++ tufte-0.12/tufte/tests/testthat/test-html.R | 18 +++++++++++++++--- 8 files changed, 72 insertions(+), 27 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre] (<https://orcid.org/0000-0003-1855-0046>)
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 2.0.0 dated 2022-01-25 and 2.0.1 dated 2022-01-27
DESCRIPTION | 6 MD5 | 13 +- NEWS.md | 9 + R/inline.R |only build/partial.rdb |binary inst/include/RcppThread/ThreadPool.hpp | 35 ++--- inst/include/RcppThread/quickpool.hpp | 214 ++++++++++++++++++++++----------- tests/tests.cpp | 24 +-- 8 files changed, 186 insertions(+), 115 deletions(-)
Title: Easy-to-Use Tools for Common Forms of Random Assignment and
Sampling
Description: Generates random assignments for common experimental designs and
random samples for common sampling designs.
Author: Alexander Coppock [aut, cre] (<https://orcid.org/0000-0002-5733-2386>),
Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>),
Neal Fultz [ctb] (C version of restricted partitions),
Graeme Blair [ctb] (<https://orcid.org/0000-0001-9164-2102>)
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 0.20.0 dated 2019-09-06 and 0.22.0 dated 2022-01-27
DESCRIPTION | 25 MD5 | 91 +- NEWS.md |only R/cluster_ra.R | 2 R/complete_ra.R | 5 R/declare_ra.R | 4 R/declare_rs.R | 6 R/helper_functions.R | 6 R/obtain_num_permutations.R | 152 ++++ R/obtain_permutation_matrix.R | 167 +++++ R/randomizr-package.r | 2 build/vignette.rds |binary inst/doc/randomizr_vignette.R | 173 ++--- inst/doc/randomizr_vignette.Rmd | 9 inst/doc/randomizr_vignette.html | 936 +++++++++++------------------ man/block_and_cluster_ra.Rd | 21 man/block_and_cluster_ra_probabilities.Rd | 21 man/block_ra.Rd | 19 man/block_ra_probabilities.Rd | 19 man/cluster_ra.Rd | 18 man/cluster_ra_probabilities.Rd | 19 man/cluster_rs.Rd | 11 man/cluster_rs_probabilities.Rd | 12 man/complete_ra.Rd | 15 man/complete_ra_probabilities.Rd | 15 man/complete_rs.Rd | 10 man/complete_rs_probabilities.Rd | 10 man/conduct_ra.Rd | 27 man/declare_ra.Rd | 26 man/declare_rs.Rd | 16 man/draw_rs.Rd | 18 man/obtain_condition_probabilities.Rd | 29 man/obtain_inclusion_probabilities.Rd | 18 man/obtain_num_permutations.Rd | 42 + man/randomizr.Rd | 3 man/simple_ra.Rd | 13 man/simple_ra_probabilities.Rd | 13 man/simple_rs.Rd | 3 man/simple_rs_probabilities.Rd | 9 man/strata_and_cluster_rs.Rd | 14 man/strata_and_cluster_rs_probabilities.Rd | 14 man/strata_rs.Rd | 13 man/strata_rs_probabilities.Rd | 13 tests/testthat/test-block_and_cluster_ra.R | 2 tests/testthat/test-block_ra.R | 30 tests/testthat/test-complete_ra.R | 13 vignettes/randomizr_vignette.Rmd | 9 47 files changed, 1245 insertions(+), 848 deletions(-)
Title: Single-Cell Immune Repertoire and Gene Expression Analysis
Description: We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology (Yermanos A, et al (2021) <doi:10.1093/nargab/lqab023>).
Author: Alexander Yermanos [aut, cre],
Andreas Agrafiotis [ctb],
Raphael Kuhn [ctb],
Victor Kreiner [ctb],
Damiano Robbiani [ctb],
Josephine Yates [ctb],
Jiami Han [ctb],
Chrysa Papadopoulou [ctb],
Cédric Weber [ctb],
Danielle Shlesinger [ctb],
Raphael Dizerens [ctb]
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Diff between Platypus versions 3.2.3 dated 2021-10-19 and 3.3.2 dated 2022-01-27
Platypus-3.2.3/Platypus/data/ABForests_sysdata.rda |only Platypus-3.2.3/Platypus/man/new.Rd |only Platypus-3.2.3/Platypus/man/select.top.Rd |only Platypus-3.2.3/Platypus/man/simulate_repertoire.Rd |only Platypus-3.3.2/Platypus/DESCRIPTION | 27 Platypus-3.3.2/Platypus/MD5 | 436 Platypus-3.3.2/Platypus/NAMESPACE | 203 Platypus-3.3.2/Platypus/R/AbForests_AntibodyForest.R | 528 Platypus-3.3.2/Platypus/R/AbForests_CompareForests.R | 168 Platypus-3.3.2/Platypus/R/AbForests_ConvertStructure.R | 74 Platypus-3.3.2/Platypus/R/AbForests_CsvToDf.R | 76 Platypus-3.3.2/Platypus/R/AbForests_ForestMetrics.R | 256 Platypus-3.3.2/Platypus/R/AbForests_PlotGraphs.R | 190 Platypus-3.3.2/Platypus/R/AbForests_PlyloToMatrix.R | 32 Platypus-3.3.2/Platypus/R/AbForests_RemoveNets.R | 132 Platypus-3.3.2/Platypus/R/AbForests_SubRepertoiresByCells.R | 102 Platypus-3.3.2/Platypus/R/AbForests_SubRepertoiresByUniqueSeq.R | 114 Platypus-3.3.2/Platypus/R/AbForests_UniqueAntibodyVariants.R | 80 Platypus-3.3.2/Platypus/R/AbForests_data.R | 29 Platypus-3.3.2/Platypus/R/AbForests_internal.R | 3144 ++--- Platypus-3.3.2/Platypus/R/Echidna_Internal_functions.R | 950 - Platypus-3.3.2/Platypus/R/Echidna_data.R | 622 - Platypus-3.3.2/Platypus/R/Echidna_other_functions.R | 1522 +- Platypus-3.3.2/Platypus/R/Echidna_simulate_repertoire.R | 2395 ++-- Platypus-3.3.2/Platypus/R/Echidna_vae_generate.R | 320 Platypus-3.3.2/Platypus/R/Echidna_vae_internal_functions.R | 124 Platypus-3.3.2/Platypus/R/GEX_DEgenes.R | 344 Platypus-3.3.2/Platypus/R/GEX_DEgenes_persample.R | 124 Platypus-3.3.2/Platypus/R/GEX_GOterm.R | 512 Platypus-3.3.2/Platypus/R/GEX_GSEA.R | 292 Platypus-3.3.2/Platypus/R/GEX_automate.R | 326 Platypus-3.3.2/Platypus/R/GEX_clonotype.R | 68 Platypus-3.3.2/Platypus/R/GEX_cluster_genes.R | 92 Platypus-3.3.2/Platypus/R/GEX_cluster_genes_heatmap.R | 138 Platypus-3.3.2/Platypus/R/GEX_cluster_membership.R | 256 Platypus-3.3.2/Platypus/R/GEX_coexpression_coefficient.R | 174 Platypus-3.3.2/Platypus/R/GEX_dottile_plot.R | 154 Platypus-3.3.2/Platypus/R/GEX_heatmap.R | 76 Platypus-3.3.2/Platypus/R/GEX_pairwise_degs.R | 178 Platypus-3.3.2/Platypus/R/GEX_phenotype.R | 172 Platypus-3.3.2/Platypus/R/GEX_phenotype_per_clone.R | 266 Platypus-3.3.2/Platypus/R/GEX_proportions_barplot.R | 168 Platypus-3.3.2/Platypus/R/GEX_scatter_coexpression.R | 82 Platypus-3.3.2/Platypus/R/GEX_topN_DE_genes_per_cluster.R | 112 Platypus-3.3.2/Platypus/R/GEX_visualize_clones.R | 208 Platypus-3.3.2/Platypus/R/GEX_volcano.R | 568 Platypus-3.3.2/Platypus/R/PlatypusDB_AIRR_to_VGM.R | 1133 - Platypus-3.3.2/Platypus/R/PlatypusDB_VGM_to_AIRR.R | 390 Platypus-3.3.2/Platypus/R/PlatypusDB_fetch.R | 716 - Platypus-3.3.2/Platypus/R/PlatypusDB_find_CDR3s.R | 158 Platypus-3.3.2/Platypus/R/PlatypusDB_list_projects.R | 128 Platypus-3.3.2/Platypus/R/PlatypusDB_load_from_disk.R | 686 - Platypus-3.3.2/Platypus/R/Platypus_data.R | 10 Platypus-3.3.2/Platypus/R/VDJ_GEX_clonal_lineage_clusters.R | 58 Platypus-3.3.2/Platypus/R/VDJ_GEX_clonotype_clusters_circos.R | 328 Platypus-3.3.2/Platypus/R/VDJ_GEX_expansion.R | 102 Platypus-3.3.2/Platypus/R/VDJ_GEX_integrate.R | 114 Platypus-3.3.2/Platypus/R/VDJ_GEX_matrix.R | 4717 +++---- Platypus-3.3.2/Platypus/R/VDJ_GEX_overlay_clones.R | 569 Platypus-3.3.2/Platypus/R/VDJ_GEX_stats.R | 576 Platypus-3.3.2/Platypus/R/VDJ_VJ_usage_circos.R | 631 - Platypus-3.3.2/Platypus/R/VDJ_Vgene_usage.R | 238 Platypus-3.3.2/Platypus/R/VDJ_Vgene_usage_barplot.R | 305 Platypus-3.3.2/Platypus/R/VDJ_Vgene_usage_stacked_barplot.R | 732 - Platypus-3.3.2/Platypus/R/VDJ_abundances.R |only Platypus-3.3.2/Platypus/R/VDJ_alpha_beta_Vgene_circos.R | 1015 - Platypus-3.3.2/Platypus/R/VDJ_analyze.R | 190 Platypus-3.3.2/Platypus/R/VDJ_antigen_integrate.R |only Platypus-3.3.2/Platypus/R/VDJ_assemble_for_PnP.R | 464 Platypus-3.3.2/Platypus/R/VDJ_call_MIXCR.R | 1124 - Platypus-3.3.2/Platypus/R/VDJ_call_recon.R |only Platypus-3.3.2/Platypus/R/VDJ_circos.R | 192 Platypus-3.3.2/Platypus/R/VDJ_clonal_donut.R | 200 Platypus-3.3.2/Platypus/R/VDJ_clonal_expansion.R | 1012 - Platypus-3.3.2/Platypus/R/VDJ_clonal_expansion_abundances.R |only Platypus-3.3.2/Platypus/R/VDJ_clonal_lineages.R | 130 Platypus-3.3.2/Platypus/R/VDJ_clonotype.R | 5976 +++++----- Platypus-3.3.2/Platypus/R/VDJ_clonotype_v3.R |only Platypus-3.3.2/Platypus/R/VDJ_contigs_to_vgm.R | 194 Platypus-3.3.2/Platypus/R/VDJ_db_annotate.R |only Platypus-3.3.2/Platypus/R/VDJ_db_load.R |only Platypus-3.3.2/Platypus/R/VDJ_diversity.R | 360 Platypus-3.3.2/Platypus/R/VDJ_dublets.R | 54 Platypus-3.3.2/Platypus/R/VDJ_dynamics.R |only Platypus-3.3.2/Platypus/R/VDJ_expand_aberrants.R |only Platypus-3.3.2/Platypus/R/VDJ_extract_germline.R | 178 Platypus-3.3.2/Platypus/R/VDJ_get_public.R |only Platypus-3.3.2/Platypus/R/VDJ_isotypes_per_clone.R | 748 - Platypus-3.3.2/Platypus/R/VDJ_logoplot_vector.R | 74 Platypus-3.3.2/Platypus/R/VDJ_network.R | 570 Platypus-3.3.2/Platypus/R/VDJ_overlap_heatmap.R | 366 Platypus-3.3.2/Platypus/R/VDJ_per_clone.R | 248 Platypus-3.3.2/Platypus/R/VDJ_phylogenetic_trees.R |only Platypus-3.3.2/Platypus/R/VDJ_phylogenetic_trees_plot.R |only Platypus-3.3.2/Platypus/R/VDJ_plot_SHM.R | 266 Platypus-3.3.2/Platypus/R/VDJ_reclonotype_list_arrange.R | 58 Platypus-3.3.2/Platypus/R/VDJ_tree.R | 128 Platypus-3.3.2/Platypus/R/VDJ_variants_per_clone.R | 234 Platypus-3.3.2/Platypus/R/VGM_expand_featurebarcodes.R |only Platypus-3.3.2/Platypus/R/automate_GEX.R | 310 Platypus-3.3.2/Platypus/R/call_MIXCR.R | 328 Platypus-3.3.2/Platypus/README.md | 266 Platypus-3.3.2/Platypus/build/vignette.rds |binary Platypus-3.3.2/Platypus/data/small_vgm.rda |binary Platypus-3.3.2/Platypus/inst/doc/PlatypusV3_agedCNS.R | 1050 - Platypus-3.3.2/Platypus/inst/doc/PlatypusV3_agedCNS.Rmd | 1550 +- Platypus-3.3.2/Platypus/inst/doc/PlatypusV3_agedCNS.html | 1332 +- Platypus-3.3.2/Platypus/man/AbForests_AntibodyForest.Rd | 182 Platypus-3.3.2/Platypus/man/AbForests_CompareForests.Rd | 180 Platypus-3.3.2/Platypus/man/AbForests_ConvertStructure.Rd | 60 Platypus-3.3.2/Platypus/man/AbForests_CsvToDf.Rd | 50 Platypus-3.3.2/Platypus/man/AbForests_ForestMetrics.Rd | 176 Platypus-3.3.2/Platypus/man/AbForests_PlotGraphs.Rd | 66 Platypus-3.3.2/Platypus/man/AbForests_PlyloToMatrix.Rd | 50 Platypus-3.3.2/Platypus/man/AbForests_RemoveNets.Rd | 108 Platypus-3.3.2/Platypus/man/AbForests_SubRepertoiresByCells.Rd | 50 Platypus-3.3.2/Platypus/man/AbForests_SubRepertoiresByUniqueSeq.Rd | 102 Platypus-3.3.2/Platypus/man/AbForests_UniqueAntibodyVariants.Rd | 96 Platypus-3.3.2/Platypus/man/Bcell_sequences_example_tree.Rd | 38 Platypus-3.3.2/Platypus/man/Bcell_tree_2.Rd | 38 Platypus-3.3.2/Platypus/man/Echidna_simulate_repertoire.Rd |only Platypus-3.3.2/Platypus/man/Echidna_vae_generate.Rd | 86 Platypus-3.3.2/Platypus/man/GEX_DEgenes.Rd | 182 Platypus-3.3.2/Platypus/man/GEX_DEgenes_persample.Rd | 110 Platypus-3.3.2/Platypus/man/GEX_GOterm.Rd | 124 Platypus-3.3.2/Platypus/man/GEX_GSEA.Rd | 144 Platypus-3.3.2/Platypus/man/GEX_automate.Rd | 138 Platypus-3.3.2/Platypus/man/GEX_clonotype.Rd | 50 Platypus-3.3.2/Platypus/man/GEX_cluster_genes.Rd | 70 Platypus-3.3.2/Platypus/man/GEX_cluster_genes_heatmap.Rd | 108 Platypus-3.3.2/Platypus/man/GEX_cluster_membership.Rd | 54 Platypus-3.3.2/Platypus/man/GEX_coexpression_coefficient.Rd | 64 Platypus-3.3.2/Platypus/man/GEX_dottile_plot.Rd | 62 Platypus-3.3.2/Platypus/man/GEX_heatmap.Rd | 92 Platypus-3.3.2/Platypus/man/GEX_pairwise_DEGs.Rd | 86 Platypus-3.3.2/Platypus/man/GEX_phenotype.Rd | 54 Platypus-3.3.2/Platypus/man/GEX_phenotype_per_clone.Rd | 88 Platypus-3.3.2/Platypus/man/GEX_proportions_barplot.Rd | 76 Platypus-3.3.2/Platypus/man/GEX_scatter_coexpression.Rd | 58 Platypus-3.3.2/Platypus/man/GEX_topN_DE_genes_per_cluster.Rd | 58 Platypus-3.3.2/Platypus/man/GEX_visualize_clones.Rd | 80 Platypus-3.3.2/Platypus/man/GEX_volcano.Rd | 154 Platypus-3.3.2/Platypus/man/PlatypusDB_AIRR_to_VGM.Rd | 93 Platypus-3.3.2/Platypus/man/PlatypusDB_VGM_to_AIRR.Rd | 158 Platypus-3.3.2/Platypus/man/PlatypusDB_fetch.Rd | 166 Platypus-3.3.2/Platypus/man/PlatypusDB_find_CDR3s.Rd | 56 Platypus-3.3.2/Platypus/man/PlatypusDB_list_projects.Rd | 66 Platypus-3.3.2/Platypus/man/PlatypusDB_load_from_disk.Rd | 78 Platypus-3.3.2/Platypus/man/VDJ_GEX_clonal_lineage_clusters.Rd | 60 Platypus-3.3.2/Platypus/man/VDJ_GEX_expansion.Rd | 70 Platypus-3.3.2/Platypus/man/VDJ_GEX_integrate.Rd | 60 Platypus-3.3.2/Platypus/man/VDJ_GEX_matrix.Rd | 414 Platypus-3.3.2/Platypus/man/VDJ_GEX_overlay_clones.Rd | 169 Platypus-3.3.2/Platypus/man/VDJ_GEX_stats.Rd | 82 Platypus-3.3.2/Platypus/man/VDJ_VJ_usage_circos.Rd | 97 Platypus-3.3.2/Platypus/man/VDJ_Vgene_usage.Rd | 48 Platypus-3.3.2/Platypus/man/VDJ_Vgene_usage_barplot.Rd | 73 Platypus-3.3.2/Platypus/man/VDJ_Vgene_usage_stacked_barplot.Rd | 88 Platypus-3.3.2/Platypus/man/VDJ_abundances.Rd |only Platypus-3.3.2/Platypus/man/VDJ_alpha_beta_Vgene_circos.Rd | 103 Platypus-3.3.2/Platypus/man/VDJ_analyze.Rd | 76 Platypus-3.3.2/Platypus/man/VDJ_antigen_integrate.Rd |only Platypus-3.3.2/Platypus/man/VDJ_assemble_for_PnP.Rd | 124 Platypus-3.3.2/Platypus/man/VDJ_call_MIXCR.Rd | 98 Platypus-3.3.2/Platypus/man/VDJ_call_recon.Rd |only Platypus-3.3.2/Platypus/man/VDJ_circos.Rd | 64 Platypus-3.3.2/Platypus/man/VDJ_clonal_donut.Rd | 94 Platypus-3.3.2/Platypus/man/VDJ_clonal_expansion.Rd | 166 Platypus-3.3.2/Platypus/man/VDJ_clonal_expansion_abundances.Rd |only Platypus-3.3.2/Platypus/man/VDJ_clonal_lineages.Rd | 76 Platypus-3.3.2/Platypus/man/VDJ_clonotype.Rd | 94 Platypus-3.3.2/Platypus/man/VDJ_clonotype_clusters_circos.Rd | 94 Platypus-3.3.2/Platypus/man/VDJ_clonotype_v3.Rd |only Platypus-3.3.2/Platypus/man/VDJ_contigs_to_vgm.Rd | 58 Platypus-3.3.2/Platypus/man/VDJ_db_annotate.Rd |only Platypus-3.3.2/Platypus/man/VDJ_db_load.Rd |only Platypus-3.3.2/Platypus/man/VDJ_diversity.Rd | 120 Platypus-3.3.2/Platypus/man/VDJ_dublets.Rd | 50 Platypus-3.3.2/Platypus/man/VDJ_dynamics.Rd |only Platypus-3.3.2/Platypus/man/VDJ_expand_aberrants.Rd |only Platypus-3.3.2/Platypus/man/VDJ_extract_germline.Rd | 72 Platypus-3.3.2/Platypus/man/VDJ_get_public.Rd |only Platypus-3.3.2/Platypus/man/VDJ_isotypes_per_clone.Rd | 108 Platypus-3.3.2/Platypus/man/VDJ_logoplot_vector.Rd | 54 Platypus-3.3.2/Platypus/man/VDJ_network.Rd | 82 Platypus-3.3.2/Platypus/man/VDJ_overlap_heatmap.Rd | 93 Platypus-3.3.2/Platypus/man/VDJ_per_clone.Rd | 92 Platypus-3.3.2/Platypus/man/VDJ_phylogenetic_trees.Rd |only Platypus-3.3.2/Platypus/man/VDJ_phylogenetic_trees_plot.Rd |only Platypus-3.3.2/Platypus/man/VDJ_plot_SHM.Rd | 104 Platypus-3.3.2/Platypus/man/VDJ_reclonotype_list_arrange.Rd | 66 Platypus-3.3.2/Platypus/man/VDJ_tree.Rd | 82 Platypus-3.3.2/Platypus/man/VDJ_variants_per_clone.Rd | 80 Platypus-3.3.2/Platypus/man/VGM_expand_featurebarcodes.Rd |only Platypus-3.3.2/Platypus/man/automate_GEX.Rd | 138 Platypus-3.3.2/Platypus/man/call_MIXCR.Rd | 60 Platypus-3.3.2/Platypus/man/class_switch_prob_hum.Rd | 38 Platypus-3.3.2/Platypus/man/class_switch_prob_mus.Rd | 38 Platypus-3.3.2/Platypus/man/clonofreq.Rd | 42 Platypus-3.3.2/Platypus/man/clonofreq.isotype.data.Rd | 38 Platypus-3.3.2/Platypus/man/clonofreq.isotype.plot.Rd | 46 Platypus-3.3.2/Platypus/man/clonofreq.trans.data.Rd | 46 Platypus-3.3.2/Platypus/man/clonofreq.trans.plot.Rd | 68 Platypus-3.3.2/Platypus/man/cluster.id.igraph.Rd | 46 Platypus-3.3.2/Platypus/man/colors.Rd | 36 Platypus-3.3.2/Platypus/man/get.avr.mut.data.Rd | 46 Platypus-3.3.2/Platypus/man/get.avr.mut.plot.Rd | 50 Platypus-3.3.2/Platypus/man/get.barplot.errorbar.Rd | 42 Platypus-3.3.2/Platypus/man/get.elbow.Rd | 34 Platypus-3.3.2/Platypus/man/get.n.node.data.Rd | 38 Platypus-3.3.2/Platypus/man/get.n.node.plot.Rd | 42 Platypus-3.3.2/Platypus/man/get.seq.distance.Rd | 38 Platypus-3.3.2/Platypus/man/get.umap.Rd | 42 Platypus-3.3.2/Platypus/man/get.vgu.matrix.Rd | 38 Platypus-3.3.2/Platypus/man/hotspot_df.Rd | 70 Platypus-3.3.2/Platypus/man/hum_b_h.Rd | 68 Platypus-3.3.2/Platypus/man/hum_b_l.Rd | 62 Platypus-3.3.2/Platypus/man/hum_t_h.Rd | 68 Platypus-3.3.2/Platypus/man/hum_t_l.Rd | 62 Platypus-3.3.2/Platypus/man/iso_SHM_prob.Rd | 36 Platypus-3.3.2/Platypus/man/mus_b_h.Rd | 68 Platypus-3.3.2/Platypus/man/mus_b_l.Rd | 62 Platypus-3.3.2/Platypus/man/mus_b_trans.Rd | 76 Platypus-3.3.2/Platypus/man/mus_t_h.Rd | 68 Platypus-3.3.2/Platypus/man/mus_t_l.Rd | 62 Platypus-3.3.2/Platypus/man/no.empty.node.Rd | 42 Platypus-3.3.2/Platypus/man/one_spot_df.Rd | 64 Platypus-3.3.2/Platypus/man/pheno_SHM_prob.Rd | 36 Platypus-3.3.2/Platypus/man/select.top.clone.Rd |only Platypus-3.3.2/Platypus/man/special_v.Rd | 36 Platypus-3.3.2/Platypus/man/trans_switch_prob_b.Rd | 38 Platypus-3.3.2/Platypus/man/trans_switch_prob_t.Rd | 36 Platypus-3.3.2/Platypus/man/umap.top.highlight.Rd | 42 Platypus-3.3.2/Platypus/man/vdj_length_prob.Rd | 68 Platypus-3.3.2/Platypus/vignettes/PlatypusV3_agedCNS.Rmd | 1550 +- 235 files changed, 28410 insertions(+), 28174 deletions(-)
Title: For Implementation of Feed Reduction, Learning Examples, NLP and
Code Management
Description: This is for code management functions, NLP tools, a Monty Hall simulator, and for implementing my own variable reduction technique called Feed Reduction. The Feed Reduction technique is not yet published, but is merely a tool for implementing a series of binary neural networks meant for reducing data into N dimensions, where N is the number of possible values of the response variable.
Author: Travis Barton (2018)
Maintainer: Travis Barton <tbarton@csumb.edu>
Diff between LilRhino versions 1.2.0 dated 2019-10-31 and 1.2.1 dated 2022-01-27
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- man/Binary_Network.Rd | 2 +- man/Feed_Reduction.Rd | 2 +- man/Load_Glove_Embeddings.Rd | 2 +- 5 files changed, 11 insertions(+), 12 deletions(-)
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between jti versions 0.8.0 dated 2021-07-05 and 0.8.2 dated 2022-01-27
jti-0.8.0/jti/man/pot_list.Rd |only jti-0.8.2/jti/DESCRIPTION | 10 jti-0.8.2/jti/MD5 | 73 +- jti-0.8.2/jti/NAMESPACE | 9 jti-0.8.2/jti/NEWS.md | 11 jti-0.8.2/jti/R/RcppExports.R | 4 jti-0.8.2/jti/R/api_compile.R | 381 +++++++----- jti-0.8.2/jti/R/api_jt.R | 152 ----- jti-0.8.2/jti/R/api_query.R |only jti-0.8.2/jti/R/asserters.R | 101 +++ jti-0.8.2/jti/R/helper_binary_ops.R | 108 ++- jti-0.8.2/jti/R/helper_charge.R | 129 ++-- jti-0.8.2/jti/R/helper_compile.R | 51 - jti-0.8.2/jti/R/helper_elimination_game.R | 89 +++ jti-0.8.2/jti/R/helper_jt.R | 108 --- jti-0.8.2/jti/R/helper_misc.R | 1 jti-0.8.2/jti/R/helper_mpd.R | 1 jti-0.8.2/jti/R/helper_set_evidence.R |only jti-0.8.2/jti/R/helper_triang.R | 1 jti-0.8.2/jti/R/sandbox.R | 473 ++++++---------- jti-0.8.2/jti/README.md |only jti-0.8.2/jti/inst/extdata/derma.rds |only jti-0.8.2/jti/inst/extdata/derma_igraph.rds |only jti-0.8.2/jti/inst/tinytest/test_evidence.R |only jti-0.8.2/jti/man/compile.Rd | 25 jti-0.8.2/jti/man/cpt_list.Rd | 2 jti-0.8.2/jti/man/figures/README-unnamed-chunk-18-1.png |binary jti-0.8.2/jti/man/figures/README-unnamed-chunk-20-1.png |binary jti-0.8.2/jti/man/figures/README-unnamed-chunk-22-1.png |binary jti-0.8.2/jti/man/figures/README-unnamed-chunk-23-1.png |binary jti-0.8.2/jti/man/figures/README-unnamed-chunk-5-1.png |binary jti-0.8.2/jti/man/figures/README-unnamed-chunk-8-1.png |binary jti-0.8.2/jti/man/get-graph.Rd | 2 jti-0.8.2/jti/man/get-triang-graph.Rd |only jti-0.8.2/jti/man/initialize.Rd |only jti-0.8.2/jti/man/jt_nbinary_ops.Rd | 11 jti-0.8.2/jti/man/plot.charge.Rd |only jti-0.8.2/jti/man/query_belief.Rd | 2 jti-0.8.2/jti/man/set_evidence.Rd | 12 jti-0.8.2/jti/man/triangulate.Rd | 1 jti-0.8.2/jti/src/RcppExports.cpp | 15 jti-0.8.2/jti/src/binary_ops.cpp |only jti-0.8.2/jti/src/set_ops.cpp | 2 43 files changed, 914 insertions(+), 860 deletions(-)
Title: R Interface to 'IGN' Web Services
Description: Interface to easily access the National Institute of
Geographic and Forestry Information open-source data for any area of
interest in France via WFS (shapefile) and WMS (raster) web services
<https://geoservices.ign.fr/services-web-experts>.
Author: Paul Carteron [aut, cre] (<https://orcid.org/0000-0002-6942-6662>)
Maintainer: Paul Carteron <carteronpaul@gmail.com>
Diff between happign versions 0.1.0 dated 2022-01-20 and 0.1.1 dated 2022-01-27
DESCRIPTION | 14 +- MD5 | 50 +++++---- NAMESPACE | 6 + NEWS.md | 6 + R/get_layers_metadata.R | 2 R/get_wfs.R | 13 +- R/get_wms_raster.R | 54 ++++++--- R/init.R |only README.md | 84 ++++++++++++--- build/vignette.rds |binary inst/doc/Getting_started.Rmd | 26 ---- inst/doc/Getting_started.html | 165 ++++++++++++++---------------- inst/doc/Non_functional_APIs.R |only inst/doc/Non_functional_APIs.Rmd |only inst/doc/Non_functional_APIs.html |only man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/logo.png |only man/get_layers_metadata.Rd | 2 man/get_wms_raster.Rd | 20 ++- tests/fixtures/get_wfs.yml | 9 - tests/testthat.R | 8 - tests/testthat/test-get_layers_metadata.R | 40 ++++--- tests/testthat/test-get_wfs.R | 57 ++++------ tests/testthat/test-get_wms_raster.R | 13 -- vignettes/Getting_started.Rmd | 26 ---- vignettes/Non_functional_APIs.Rmd |only 33 files changed, 329 insertions(+), 266 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Conrad Sanderson [cph] (Author of the C++ Armadillo library),
Ryan Curtin [cph] (Author of the C++ Armadillo library),
Siddharth Agrawal [cph] (Author of the C code of the Mini-Batch-Kmeans
algorithm
(https://github.com/siddharth-agrawal/Mini-Batch-K-Means)),
Brendan Frey [cph] (Author of the matlab code of the Affinity
propagation algorithm (for commercial use please contact the author
of the matlab code)),
Delbert Dueck [cph] (Author of the matlab code of the Affinity
propagation algorithm),
Vitalie Spinu [ctb] (Github Contributor)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.2.5 dated 2021-05-21 and 1.2.6 dated 2022-01-27
DESCRIPTION | 15 MD5 | 39 - NAMESPACE | 6 NEWS.md | 7 R/clustering_functions.R | 234 +++++--- README.md | 4 build/vignette.rds |binary inst/doc/the_clusterR_package.R | 26 inst/doc/the_clusterR_package.Rmd | 28 inst/doc/the_clusterR_package.html | 287 ++++------ inst/include/ClusterRHeader.h | 179 ++++-- man/predict_GMM.Rd | 5 man/predict_KMeans.Rd | 5 man/predict_Medoids.Rd | 5 src/RcppExports.cpp | 35 - src/init.c |only tests/testthat/test-gmm.R | 146 +---- tests/testthat/test-kmeans.R | 166 ++--- tests/testthat/test-medoids.R | 99 +-- tests/testthat/test-plot2d_silhouette_plot_ext_validation_center_scale_dist_mat.R | 8 vignettes/the_clusterR_package.Rmd | 28 21 files changed, 686 insertions(+), 636 deletions(-)
Title: Idealisation of Patch Clamp Recordings
Description: Implements the model-free multiscale idealisation approaches: Jump-Segmentation by MUltiResolution Filter (JSMURF) <doi:10.1109/TNB.2013.2284063>, JUmp Local dEconvolution Segmentation filter (JULES) <doi:10.1109/TNB.2018.2845126> and Heterogeneous Idealization by Local testing and DEconvolution (HILDE) <arXiv:2008.02658>. Further details on how to use them are given in the accompanying vignette.
Author: Pein Florian [aut, cre],
Timo Aspelmeier [ctb]
Maintainer: Pein Florian <f.pein@lancaster.ac.uk>
Diff between clampSeg versions 1.1-0 dated 2020-08-25 and 1.1-1 dated 2022-01-27
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/Vignette.pdf |binary 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Piecewise Smooth Regression by Bootstrapped Binary Segmentation
Description: Provides methods for piecewise smooth regression. A piecewise smooth signal is estimated by applying a bootstrapped test recursively (binary segmentation approach). Each bootstrapped test decides whether the underlying signal is smooth on the currently considered subsegment or contains at least one further change-point.
Author: McDaid Kate [aut],
Pein Florian [aut, cre]
Maintainer: Pein Florian <f.pein@lancaster.ac.uk>
Diff between BinSegBstrap versions 1.0 dated 2019-11-06 and 1.0-1 dated 2022-01-27
BinSegBstrap-1.0-1/BinSegBstrap/ChangeLog |only BinSegBstrap-1.0-1/BinSegBstrap/DESCRIPTION | 10 ++++---- BinSegBstrap-1.0-1/BinSegBstrap/MD5 | 12 +++++----- BinSegBstrap-1.0-1/BinSegBstrap/build/vignette.rds |binary BinSegBstrap-1.0-1/BinSegBstrap/inst/doc/BinSegBstrap.R | 4 +-- BinSegBstrap-1.0-1/BinSegBstrap/inst/doc/BinSegBstrap.pdf |binary BinSegBstrap-1.0-1/BinSegBstrap/src/RcppExports.cpp | 5 ++++ BinSegBstrap-1.0/BinSegBstrap/vignettes/BinSegBstrap-concordance.tex |only 8 files changed, 18 insertions(+), 13 deletions(-)
Title: Boltzmann Bayes Learner
Description: Supervised learning using Boltzmann Bayes model inference,
which extends naive Bayes model to include interactions. Enables
classification of data into multiple response groups based on a large
number of discrete predictors that can take factor values of
heterogeneous levels. Either pseudo-likelihood or mean field
inference can be used with L2 regularization, cross-validation, and
prediction on new data.
<doi:10.18637/jss.v101.i05>.
Author: Jun Woo [aut, cre] (<https://orcid.org/0000-0003-3220-2064>)
Maintainer: Jun Woo <junwoo035@gmail.com>
Diff between bbl versions 0.4.1 dated 2021-11-18 and 1.0.0 dated 2022-01-27
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/bbl_s3.R | 2 ++ build/partial.rdb |only inst/CITATION |only inst/doc/article.pdf |binary man/bbl.Rd | 6 ++++++ vignettes/ref.bib | 4 ++-- 8 files changed, 21 insertions(+), 11 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Sight Machine [cph] (findHOGFeatures function of the SimpleCV computer
vision platform),
Johannes Buchner [cph] (average_hash, dhash and phash functions of the
ImageHash python library),
Mohammad Haghighat [cph] (Gabor Feature Extraction),
Radhakrishna Achanta [cph] (Author of the C++ code of the SLIC and
SLICO algorithms (for commercial use please contact the author))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.2.0 dated 2021-09-10 and 1.2.1 dated 2022-01-27
DESCRIPTION | 10 +- MD5 | 33 ++++---- NEWS.md | 5 + R/open_image_rscript.R | 7 + README.md | 6 - build/vignette.rds |binary inst/doc/Gabor_Feature_Extraction.Rmd | 2 inst/doc/Gabor_Feature_Extraction.html | 6 - inst/doc/Image_segmentation_superpixels_clustering.html | 4 - inst/doc/The_OpenImageR_package.R | 6 - inst/doc/The_OpenImageR_package.Rmd | 6 - inst/doc/The_OpenImageR_package.html | 24 +++--- inst/include/OpenImageRheader.h | 2 man/resizeImage.Rd | 4 - src/RcppExports.cpp | 63 ---------------- src/init.c |only vignettes/Gabor_Feature_Extraction.Rmd | 2 vignettes/The_OpenImageR_package.Rmd | 6 - 18 files changed, 67 insertions(+), 119 deletions(-)
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change). References: Mestre, F., Canovas, F., Pita, R.,
Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F.,
Risk, B., Mira, A., Beja, P., Pita, R. (2017)
<doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja,
P. (2020) <doi:10.1186/s12898-019-0273-5>.
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita,
Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 1.0.8 dated 2021-02-16 and 1.0.9 dated 2022-01-27
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NAMESPACE | 8 ++++---- R/vmm.R |only build/vignette.rds |binary inst/doc/landscape_simulation-knitr.pdf |binary inst/doc/parameter_estimation-knitr.pdf |binary inst/doc/range_expansion-knitr.pdf |binary 8 files changed, 16 insertions(+), 15 deletions(-)
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.1.0 dated 2021-12-10 and 2.1.1 dated 2022-01-27
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Title: Crunch.io Data Tools
Description: The Crunch.io service <https://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Mike Malecki [aut],
Neal Richardson [aut],
Gordon Shotwell [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunch versions 1.28.2 dated 2021-11-10 and 1.29.0 dated 2022-01-27
DESCRIPTION | 6 MD5 | 135 - NAMESPACE | 3 R/AllGenerics.R | 2 R/api.R | 50 R/auth.R | 196 + R/consent.R | 4 R/context-manager.R | 21 R/crunch.R | 2 R/dataset-extract.R | 12 R/dataset-reference.R | 4 R/dataset.R | 8 R/github.R | 2 R/hide-variables.R | 2 R/json.R | 2 R/make-array.R | 2 R/misc.R | 125 + R/progress.R | 8 R/share.R | 2 R/shoji-folder.R | 2 R/show.R | 13 R/subtotals-and-headings.R | 2 R/tab-book.R | 4 R/user.R | 3 inst/crunch-test.R | 22 inst/doc/crunch.R | 24 inst/doc/crunch.Rmd | 43 inst/doc/crunch.html | 94 inst/doc/fork-and-merge.html | 54 man/crunch-api-key.Rd |only man/crunch_sitrep.Rd |only man/describe-catalog.Rd | 2 man/envOrOption.Rd | 54 man/hide.Rd | 2 man/login.Rd | 9 man/retry.Rd | 2 man/setupCrunchAuth.Rd |only man/temp.options.Rd | 9 man/tokenAuth.Rd | 2 tests/testthat.R | 2 tests/testthat/helper.R | 11 tests/testthat/print-folders.R | 2 tests/testthat/test-api.R | 57 tests/testthat/test-appending.R | 6 tests/testthat/test-auth.R | 90 tests/testthat/test-context-manager.R | 8 tests/testthat/test-cube-bases.R | 118 - tests/testthat/test-cube-residuals-zed-scores.R | 796 +++---- tests/testthat/test-cube-subset.R | 864 ++++---- tests/testthat/test-cube-transforms.R | 2563 ++++++++++++------------ tests/testthat/test-dataset-entity.R | 1323 ++++++------ tests/testthat/test-dimension-transforms.R | 2 tests/testthat/test-expressions.R | 1867 ++++++++--------- tests/testthat/test-folders.R | 719 +++--- tests/testthat/test-github.R | 4 tests/testthat/test-hide-variables.R | 4 tests/testthat/test-misc.R | 79 tests/testthat/test-multitables.R | 1251 +++++------ tests/testthat/test-private-variables.R | 4 tests/testthat/test-progress.R | 14 tests/testthat/test-share.R | 4 tests/testthat/test-slides.R | 1497 +++++++------- tests/testthat/test-subtotals-and-headings.R | 1029 ++++----- tests/testthat/test-subvariables.R | 2 tests/testthat/test-summary-insertions.R | 1005 ++++----- tests/testthat/test-user.R | 2 tests/testthat/test-variable-order.R | 6 tests/testthat/test-webApp.R | 2 tests/testthat/test-weighting.R | 2 vignettes/crunch.Rmd | 43 70 files changed, 7499 insertions(+), 6804 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
Author: Edgar Merkle [aut, cre] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb]
(<https://orcid.org/0000-0002-2951-6647>, R/blav_compare.R,
R/ctr_bayes_fit.R),
Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>,
R/ctr_bayes_fit.R, R/ctr_ppmc.R),
Huub Hoofs [ctb] (R/ctr_bayes_fit.R),
Rens van de Schoot [ctb] (R/ctr_bayes_fit.R)
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.3-18 dated 2021-11-27 and 0.4-1 dated 2022-01-27
DESCRIPTION | 14 - MD5 | 65 ++++----- NAMESPACE | 5 NEWS.md | 7 R/blav_cond_utils.R | 5 R/blav_fit.R | 2 R/blav_fit_measures.R | 16 +- R/blav_model_loglik.R |only R/blav_object_methods.R | 27 ++- R/blav_predict.R | 2 R/blav_test.R | 14 + R/blav_utils.R | 274 -------------------------------------- R/blavaan.R | 92 +++++++++--- R/ctr_bayes_fit.R | 7 R/ctr_ppmc.R | 17 ++ R/dpriors.R | 9 - R/lav_export_stanmarg.R | 28 +++ R/lvgqs.R | 33 +++- R/postpred.R | 90 ++++++++++-- R/set_priors.R | 3 R/stanmarg_data.R | 14 + R/zzz.R | 2 README.md | 2 inst/testdata/sysdata.rda |binary inst/tinytest/tests.blavaan.R | 8 - man/bcfa.Rd | 15 +- man/bgrowth.Rd | 15 +- man/blavFitIndices.Rd | 10 - man/blavaan.Rd | 15 +- man/bsem.Rd | 15 +- man/ppmc.Rd | 9 - src/Makevars | 8 - src/Makevars.win | 4 src/stan_files/stanmarg.stan | 300 +++++++++++++++++++++++++++++++++--------- 34 files changed, 637 insertions(+), 490 deletions(-)
Title: Bayesian Inference on Univariate Normal Mixtures
Description: A program for Bayesian analysis of univariate normal mixtures with an unknown number
of components, following the approach of Richardson and Green (1997) <doi:10.1111/1467-9868.00095>.
This makes use of reversible jump Markov chain Monte Carlo methods that are capable of jumping
between the parameter sub-spaces corresponding to different numbers of components in the mixture.
A sample from the full joint distribution of all unknown variables is thereby generated,
and this can be used as a basis for a thorough presentation of many aspects of the posterior
distribution.
Author: Peter Green [aut, cre] (<https://orcid.org/0000-0002-4367-4756>)
Maintainer: Peter Green <P.J.Green@bristol.ac.uk>
Diff between Nmix versions 1.1.2 dated 2022-01-12 and 1.2.0 dated 2022-01-27
Nmix-1.1.2/Nmix/R/pltraces.R |only Nmix-1.1.2/Nmix/src/rgamma.f |only Nmix-1.2.0/Nmix/DESCRIPTION | 29 ++++++++------- Nmix-1.2.0/Nmix/MD5 | 23 ++++++------ Nmix-1.2.0/Nmix/NAMESPACE | 5 +- Nmix-1.2.0/Nmix/R/Nmix.R | 9 ++++ Nmix-1.2.0/Nmix/R/plot.nmix.R | 66 ++++++++++++++++++++++++++++++++---- Nmix-1.2.0/Nmix/build/partial.rdb |binary Nmix-1.2.0/Nmix/man/Nmix-package.Rd | 6 +-- Nmix-1.2.0/Nmix/man/Nmix.Rd | 9 +++- Nmix-1.2.0/Nmix/man/plot.nmix.Rd | 13 ++++++- Nmix-1.2.0/Nmix/man/sdrni.Rd |only Nmix-1.2.0/Nmix/src/Nmix-sub3z.f | 18 ++++++++- Nmix-1.2.0/Nmix/src/Nmix_init.c | 4 +- 14 files changed, 138 insertions(+), 44 deletions(-)
Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Description: Produces ANOVA tables in the format used by Judd, McClelland, and Ryan
(2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes
proportional reduction in error and formatting to improve ease the transition between the book
and R.
Author: Adam Blake [cre, aut] (<https://orcid.org/0000-0001-7881-8652>),
Jeff Chrabaszcz [aut],
Ji Son [aut] (<https://orcid.org/0000-0002-4258-4791>),
Jim Stigler [aut] (<https://orcid.org/0000-0001-6107-7827>)
Maintainer: Adam Blake <adamblake@g.ucla.edu>
Diff between supernova versions 2.5.0 dated 2022-01-04 and 2.5.1 dated 2022-01-27
DESCRIPTION | 8 - MD5 | 18 +- NEWS.md | 5 R/generate_models.R | 9 - R/listwise_delete.R | 8 - inst/WORDLIST | 1 tests/testthat/_snaps/generate_models.md | 192 +++++++++++++------------------ tests/testthat/_snaps/pairwise.md | 2 tests/testthat/test-listwise_delete.R | 12 + tests/testthat/test-supernova.r | 4 10 files changed, 131 insertions(+), 128 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre],
John Magnotti [ctb] (Contributed to `rutabaga.R`),
Xiang Zhang [ctb] (Contributed to `rutabaga.R`)
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.1.9 dated 2021-10-13 and 0.2.0 dated 2022-01-27
DESCRIPTION | 26 ++++++++++++++++---------- MD5 | 36 +++++++++++++++++++++--------------- NAMESPACE | 7 +++++++ NEWS.md | 16 ++++++++++++++++ R/fastmap2.R | 14 ++++++++++++-- R/parallels-apply-script.R | 4 ++-- R/parallels-future.R | 2 +- R/reexports.R |only R/rutabaga.R |only R/shiny-flex-div.R | 38 ++++++++++++++++++++++++++++++++++++++ R/shiny-progress.R | 14 +++++++++++++- R/systems.R | 12 ++++++------ R/utils-rstudio.R | 8 +++++++- build/vignette.rds |binary inst/doc/r_expr_addons.html | 6 +++--- inst/doc/utility_functions.html | 2 +- man/fastmap2.Rd | 4 +++- man/handler_dipsaus_progress.Rd | 3 +++ man/html_class.Rd |only man/mean_se.Rd |only man/reexports.Rd |only man/ste_mean.Rd |only 22 files changed, 149 insertions(+), 43 deletions(-)
Title: 'HTMLWidget' Wrapper of 'UpSet.js' for Exploring Large Set
Intersections
Description: 'UpSet.js' is a re-implementation of 'UpSetR' to create interactive set visualizations for more than three sets.
This is a 'htmlwidget' wrapper around the 'JavaScript' library 'UpSet.js'.
Author: Samuel Gratzl [aut, cre]
Maintainer: Samuel Gratzl <sam@sgratzl.com>
Diff between upsetjs versions 1.10.10 dated 2022-01-04 and 1.10.11 dated 2022-01-27
DESCRIPTION | 8 ++-- MD5 | 16 +++++---- inst/dash/upsetjs.js |only inst/doc/colors.html | 16 ++++----- inst/doc/combinationModes.html | 16 ++++----- inst/doc/got.html | 16 ++++----- inst/doc/kmap.html | 12 +++---- inst/doc/upsetjs.html | 68 ++++++++++++++++++++--------------------- inst/doc/venn.html | 16 ++++----- inst/htmlwidgets/upsetjs.js |only 10 files changed, 85 insertions(+), 83 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.4.3 dated 2021-12-06 and 0.4.4 dated 2022-01-27
DESCRIPTION | 7 +- MD5 | 96 ++++++++++++++++------------ NAMESPACE | 2 NEWS.md | 5 + R/build.R | 2 R/count.R | 13 ++- R/count_bindings.R | 13 +++ R/denom.R | 22 ++++-- R/nested.R | 4 - R/shift.R | 2 R/sort.R | 32 +++++++-- R/stats.R | 2 R/zzz.R | 4 - inst/doc/Tplyr.html | 12 +-- inst/doc/denom.html | 110 ++++++++++++++++----------------- inst/doc/options.html | 2 man/ordering.Rd | 8 ++ man/process_formatting.Rd | 1 man/process_statistic_data.Rd | 1 man/process_statistic_formatting.Rd | 1 man/process_summaries.Rd | 1 tests/testthat/_snaps |only tests/testthat/test-assertions.R | 8 +- tests/testthat/test-column_headers.R | 25 +++---- tests/testthat/test-count.R | 99 ++++++++++++++--------------- tests/testthat/test-desc.R | 10 +-- tests/testthat/test-format.R | 7 -- tests/testthat/test-functional.R | 2 tests/testthat/test-get_numeric.R | 31 ++++----- tests/testthat/test-layer.R | 65 ++++++++----------- tests/testthat/test-layering.R | 14 +--- tests/testthat/test-opts.R | 1 tests/testthat/test-pop_data.R | 6 - tests/testthat/test-precision.R | 1 tests/testthat/test-print.R | 16 ++-- tests/testthat/test-properties_layer.R | 20 ++---- tests/testthat/test-riskdiff.R | 29 ++++---- tests/testthat/test-shift.R | 2 tests/testthat/test-sort.R | 110 ++++++++++++++++++--------------- tests/testthat/test-table.R | 6 - tests/testthat/test-table_bindings.R | 26 +++---- tests/testthat/test-utils.R | 17 ++--- 42 files changed, 458 insertions(+), 377 deletions(-)
Title: A Solver for 'ompr' that Uses the R Optimization Infrastructure
('ROI')
Description: A solver for 'ompr' based on the R Optimization Infrastructure ('ROI').
The package makes all solvers in 'ROI' available to solve 'ompr' models. Please see the
'ompr' website <https://dirkschumacher.github.io/ompr/> and package docs for more information
and examples on how to use it.
Author: Dirk Schumacher [aut, cre]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Diff between ompr.roi versions 0.8.0 dated 2018-06-11 and 1.0.0 dated 2022-01-27
DESCRIPTION | 16 ++++++++-------- LICENSE |only MD5 | 13 +++++++------ NEWS.md | 17 ++++++++++++++++- R/with-roi.R | 30 +++++++++++++++++++++--------- man/ompr.roi.Rd | 1 - man/with_ROI.Rd | 8 ++++++-- tests/testthat/test-solver-roi.R | 22 ++++++++++++++++------ 8 files changed, 74 insertions(+), 33 deletions(-)
Title: MLOps Metadata Store - Experiment Tracking and Model Registry
for Production Teams
Description: An interface to Neptune. A metadata store for MLOps, built for teams that run a lot of experiments.
It gives you a single place to log, store, display, organize, compare, and query all your model-building metadata.
Neptune is used for:
• Experiment tracking: Log, display, organize, and compare ML experiments in a single place.
• Model registry: Version, store, manage, and query trained models, and model building metadata.
• Monitoring ML runs live: Record and monitor model training, evaluation, or production runs live
For more information see <https://neptune.ai/>.
Author: Mateusz Dominiak [aut],
Rafal Jankowski [aut, cre]
Maintainer: Rafal Jankowski <rafal.jankowski@neptune.ai>
Diff between neptune versions 0.2.0 dated 2022-01-13 and 0.2.1 dated 2022-01-27
DESCRIPTION | 18 ++-- MD5 | 12 +- NAMESPACE | 1 R/neptune_init.R | 12 +- R/neptune_install.R | 37 ++++---- R/parse_neptune_version.R | 2 README.md | 198 +++++++++++++++++++++++++++------------------- 7 files changed, 165 insertions(+), 115 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [aut]
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.0.1 dated 2021-11-18 and 1.0.2 dated 2022-01-27
DESCRIPTION | 14 ++++++++------ MD5 | 16 ++++++++-------- R/MAGEE.R | 39 ++++++++++++++++++++++++++------------- README.md | 8 ++++---- inst/COPYRIGHTS | 2 +- inst/doc/MAGEE.Rnw | 12 +++++++++--- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- vignettes/MAGEE.Rnw | 12 +++++++++--- 9 files changed, 67 insertions(+), 40 deletions(-)
Title: Lemna Ecotox Effect Model
Description: An implementation of model equations and default parameters for the
toxicokinetic-toxicodynamic (TKTD) model of the Lemna (duckweed) aquatic
plant. Lemna is a standard test macrophyte used in ecotox effect studies.
The model was described and published by the SETAC Europe Interest Group
Effect Modeling. It is a refined description of the Lemna TKTD model
published by Schmitt et al. (2013) <doi:10.1016/j.ecolmodel.2013.01.017>.
Author: Nils Kehrein [aut, cre],
SETAC Europe IG Effect Modeling [ccp]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between lemna versions 0.9.0 dated 2021-12-21 and 0.9.1 dated 2022-01-27
DESCRIPTION | 6 +- MD5 | 46 ++++++++++--------- NAMESPACE | 2 NEWS.md |only R/data.R | 44 ++++++++----------- R/lemna.R | 90 +++++++++++++++++++++++++++++++-------- R/param.R | 65 ++++++++++++++++------------ README.md | 27 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/lemna-introduction.Rmd | 8 +-- inst/doc/lemna-introduction.html | 26 +++++------ inst/doc/lemna-verification.Rmd | 18 ++++--- inst/doc/lemna-verification.html | 10 ++-- man/focusd1.Rd | 16 ++---- man/focusd2.Rd | 16 ++---- man/focusr3.Rd | 16 ++---- man/hommen212.Rd | 12 +---- man/lemna.Rd | 85 ++++++++++++++++++++++++++++-------- man/lemna_desolve.Rd |only man/metsulfuron.Rd | 13 ++--- man/param_defaults.Rd | 58 ++++++++++++++----------- man/schmitt77.Rd | 7 --- vignettes/lemna-introduction.Rmd | 8 +-- vignettes/lemna-verification.Rmd | 18 ++++--- 25 files changed, 345 insertions(+), 246 deletions(-)
Title: Fast Kernel Sums
Description: Implements the method of Hofmeyr, D.P. (2021) <DOI:10.1109/TPAMI.2019.2930501> for fast evaluation of univariate kernel smoothers based on recursive computations.
Applications to the basic problems of density and regression function estimation are provided, as well as some projection pursuit methods
for which the objective is based on non-parametric functionals of the projected density, or conditional density of a response given projected
covariates.
The package is accompanied by an instructive paper in the Journal of Statistical Software <doi:10.18637/jss.v101.i03>.
Author: David P. Hofmeyr
Maintainer: David P. Hofmeyr <dhofmeyr@sun.ac.za>
Diff between FKSUM versions 0.1.4 dated 2020-04-29 and 1.0.0 dated 2022-01-27
DESCRIPTION | 12 ++++++------ MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 1 + R/PPR_WORKS.R | 8 ++++---- R/fk_density.R | 17 ++++++++++++----- R/fk_regression.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 38 +++++++++++++++++++++++++------------- man/FKSUM-package.Rd | 9 +++++++-- man/fk_ICA.Rd | 2 +- man/fk_density.Rd | 4 ++-- man/fk_mdh.Rd | 2 +- man/fk_ppr.Rd | 2 +- man/fk_regression.Rd | 4 ++-- man/fk_sum.Rd | 4 ++-- man/h_Gauss_to_K.Rd | 2 +- man/h_K_to_Gauss.Rd | 2 +- man/norm_K.Rd | 2 +- man/norm_const_K.Rd | 2 +- man/plot_kernel.Rd | 2 +- man/roughness_K.Rd | 2 +- src/RcppExports.cpp | 5 +++++ 22 files changed, 98 insertions(+), 68 deletions(-)
Title: Discrete Laplace Exponential Family
Description: The discrete Laplace exponential family for use in fitting generalized linear models.
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between disclap versions 1.5 dated 2014-04-07 and 1.5.1 dated 2022-01-27
DESCRIPTION | 9 ++++----- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS | 3 +++ R/DiscreteLaplace.R | 2 +- README.md |only 6 files changed, 14 insertions(+), 10 deletions(-)
Title: Bayesian Synthetic Likelihood
Description: Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>)
is an alternative to standard, non-parametric approximate Bayesian
computation (ABC). BSL assumes a multivariate normal distribution
for the summary statistic likelihood and it is suitable when the
distribution of the model summary statistics is sufficiently regular.
This package provides a Metropolis Hastings Markov chain Monte Carlo
implementation of four methods (BSL, uBSL, semiBSL and BSLmisspec) and two
shrinkage estimators (graphical lasso and Warton's estimator).
uBSL (Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) uses
an unbiased estimator to the normal density. A semi-parametric version
of BSL (semiBSL, An et al. (2018) <arXiv:1809.05800>) is more robust
to non-normal summary statistics. BSLmisspec (Frazier et al. 2019
<arXiv:1904.04551>) estimates the Gaussian synthetic likelihood whilst
acknowledging that there may be incompatibility between the model and the
observed summary statistic. Shrinkage estimation can help to decrease the
number of model simulations when the dimension of the summary statistic is
high (e.g., BSLasso, An et al. (2019) <doi:10.1080/10618600.2018.1537928>).
Extensions to this package are planned. For a journal article describing how
to use this package, see An et al. (2022) <doi:10.18637/jss.v101.i11>.
Author: Ziwen An [aut] (<https://orcid.org/0000-0002-9947-5182>),
Leah F. South [aut, cre] (<https://orcid.org/0000-0002-5646-2963>),
Christopher C. Drovandi [aut] (<https://orcid.org/0000-0001-9222-8763>)
Maintainer: Leah F. South <l1.south@qut.edu.au>
Diff between BSL versions 3.2.2 dated 2021-10-26 and 3.2.3 dated 2022-01-27
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- R/BSL-package.R | 4 +++- R/ma2.R | 2 ++ R/toad.R | 2 ++ build/partial.rdb |binary inst/CITATION |only inst/REFERENCES.bib | 11 +++++++++++ man/BSL-package.Rd | 4 +++- man/ma2.Rd | 2 ++ man/toad.Rd | 2 ++ 11 files changed, 41 insertions(+), 16 deletions(-)
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), ANOVA of aligned ranks (Wobbrock, J.O., Findlater, L., Gergle, D., Higgins, JJ (2011), <doi:10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre]
(<https://orcid.org/0000-0001-8524-508X>),
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
(<https://orcid.org/0000-0003-2778-8654>),
Leandro Simoes Azeredo Goncalves [aut, ctb]
(<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Diff between AgroR versions 1.2.5 dated 2021-12-03 and 1.2.6 dated 2022-01-27
DESCRIPTION | 10 MD5 | 52 + NAMESPACE | 7 NEWS.md | 6 R/FAT2DBC_function.R | 2 R/FAT2DBCad_function.R | 52 - R/FAT2DIC_function.R | 2 R/FAT2DICad_function.R | 47 - R/FAT3DBC_function.R | 257 ++------ R/FAT3DBCad_function.R |only R/FAT3DIC_function.R | 89 +-- R/FAT3DICad_function.R |only R/PSUBSUB_function.R | 23 R/barfacets_function.R |only R/bargraph_onefactor.R |only R/bargraph_twofactor.R |only R/confinterval_function.R |only R/croqui_function.R | 1329 +++++++++++++++++++++++++++++++++++----------- R/dbc_function.R | 2 R/dic_function.R | 2 R/dql_function.R | 2 R/seggraph_function.R | 4 R/test_two_function.R | 61 +- README.md | 9 man/FAT3DBC.ad.Rd |only man/FAT3DIC.ad.Rd |only man/PSUBFAT2DBC.Rd | 4 man/barfacet.Rd |only man/bargraph_onefactor.Rd |only man/bargraph_twofactor.Rd |only man/confinterval.Rd |only man/sketch.Rd | 76 ++ man/test_two.Rd | 9 33 files changed, 1328 insertions(+), 717 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 10. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood estimation" , Hammond (2021, <doi:10.2166/nh.2021.059>). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>).
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.2.0 dated 2021-10-14 and 0.2.2 dated 2022-01-27
DESCRIPTION | 10 MD5 | 53 +- R/All.R | 1061 ++++++++++++++++++++++++++++++++++++++------------- man/AMextract.Rd | 2 man/DesHydro.Rd | 8 man/ERPlot.Rd | 9 man/EVPlot.Rd | 17 man/EVPlotAdd.Rd |only man/GEVEst.Rd | 7 man/GEVGF.Rd | 4 man/GEVPars.Rd | 4 man/GenLogEst.Rd | 7 man/GenLogGF.Rd | 2 man/GenLogPars.Rd | 4 man/GenParetoEst.Rd | 7 man/GenParetoPars.Rd | 4 man/GoTF.Rd | 8 man/GoTFPool.Rd | 6 man/GumbelAM.Rd |only man/GumbelEst.Rd |only man/GumbelGF.Rd |only man/GumbelPars.Rd |only man/HydroPlot.Rd | 3 man/OptimPars.Rd | 8 man/PoolEst.Rd | 11 man/QuickResults.Rd | 4 man/ReFH.Rd | 12 man/SimData.Rd | 22 - man/Uncertainty.Rd | 6 man/Zdists.Rd | 2 30 files changed, 924 insertions(+), 357 deletions(-)
Title: Functions for Generating Restricted Permutations of Data
Description: A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
Author: Gavin L. Simpson [aut, cph, cre]
(<https://orcid.org/0000-0002-9084-8413>),
R Core Team [cph],
Douglas M. Bates [ctb],
Jari Oksanen [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between permute versions 0.9-5 dated 2019-03-12 and 0.9-7 dated 2022-01-27
permute-0.9-5/permute/inst/doc/permutations.Rnw |only permute-0.9-5/permute/inst/doc/permutations.pdf |only permute-0.9-5/permute/vignettes/permutations.Rnw |only permute-0.9-7/permute/DESCRIPTION | 14 permute-0.9-7/permute/MD5 | 26 - permute-0.9-7/permute/R/allPerms.R | 8 permute-0.9-7/permute/R/shuffle-utils.R | 12 permute-0.9-7/permute/README.md | 9 permute-0.9-7/permute/build/vignette.rds |binary permute-0.9-7/permute/inst/NEWS | 31 + permute-0.9-7/permute/inst/doc/permutations.R | 221 ++------------ permute-0.9-7/permute/inst/doc/permutations.Rmd |only permute-0.9-7/permute/inst/doc/permutations.html |only permute-0.9-7/permute/tests/Examples/permute-Ex.Rout.save | 10 permute-0.9-7/permute/tests/testthat/test-allPerms.R | 12 permute-0.9-7/permute/tests/testthat/test-shuffle-utils.R | 7 permute-0.9-7/permute/vignettes/permutations.Rmd |only 17 files changed, 134 insertions(+), 216 deletions(-)
Title: Data Management of Large Hierarchical Data
Description: Import 'SPSS' data, handle and change 'SPSS' meta data, store and access large hierarchical data in 'SQLite' data bases.
Author: Benjamin Becker [aut, cre],
Karoline Sachse [ctb],
Johanna Busse [ctb]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatGADS versions 0.18.1 dated 2021-10-06 and 0.19.1 dated 2022-01-27
eatGADS-0.18.1/eatGADS/R/checkLEStructure.R |only eatGADS-0.18.1/eatGADS/man/checkLEStructure.Rd |only eatGADS-0.18.1/eatGADS/tests/testthat/test_checkLEStructure.R |only eatGADS-0.19.1/eatGADS/DESCRIPTION | 6 eatGADS-0.19.1/eatGADS/MD5 | 103 ++++--- eatGADS-0.19.1/eatGADS/NAMESPACE | 14 eatGADS-0.19.1/eatGADS/NEWS.md | 27 + eatGADS-0.19.1/eatGADS/R/assimilateValLabels.R |only eatGADS-0.19.1/eatGADS/R/calculateScale.R |only eatGADS-0.19.1/eatGADS/R/cbind.R |only eatGADS-0.19.1/eatGADS/R/char_valLabels2numeric.R |only eatGADS-0.19.1/eatGADS/R/checkUniqueness.R |only eatGADS-0.19.1/eatGADS/R/extractData.R | 57 ++-- eatGADS-0.19.1/eatGADS/R/extractDataOld.R |only eatGADS-0.19.1/eatGADS/R/extract_labels.R | 38 +- eatGADS-0.19.1/eatGADS/R/getTrendGADS.R | 142 ++++------ eatGADS-0.19.1/eatGADS/R/getTrendGADSOld.R |only eatGADS-0.19.1/eatGADS/R/import_spss.R | 5 eatGADS-0.19.1/eatGADS/R/mergeLabels.R | 3 eatGADS-0.19.1/eatGADS/R/prepare_labels.R | 11 eatGADS-0.19.1/eatGADS/R/updateMeta.R | 5 eatGADS-0.19.1/eatGADS/README.md | 2 eatGADS-0.19.1/eatGADS/build/partial.rdb |binary eatGADS-0.19.1/eatGADS/inst/doc/createGADS.html | 4 eatGADS-0.19.1/eatGADS/inst/doc/getGADS.R | 18 - eatGADS-0.19.1/eatGADS/inst/doc/getGADS.Rmd | 21 - eatGADS-0.19.1/eatGADS/inst/doc/getGADS.html | 34 +- eatGADS-0.19.1/eatGADS/inst/doc/import_raw.html | 4 eatGADS-0.19.1/eatGADS/inst/doc/import_spss.html | 4 eatGADS-0.19.1/eatGADS/inst/doc/meta_data.Rmd | 2 eatGADS-0.19.1/eatGADS/inst/doc/meta_data.html | 8 eatGADS-0.19.1/eatGADS/inst/doc/recoding_forcedChoice.html | 4 eatGADS-0.19.1/eatGADS/inst/doc/recoding_multipleChoice.html | 4 eatGADS-0.19.1/eatGADS/inst/extdata/gads_LEs.db |only eatGADS-0.19.1/eatGADS/inst/extdata/trend_gads_2010.db |only eatGADS-0.19.1/eatGADS/inst/extdata/trend_gads_2015.db |only eatGADS-0.19.1/eatGADS/inst/extdata/trend_gads_2015_pkList.db |only eatGADS-0.19.1/eatGADS/inst/extdata/trend_gads_2020.db |only eatGADS-0.19.1/eatGADS/man/assimilateValLabels.Rd |only eatGADS-0.19.1/eatGADS/man/calculateScale.Rd |only eatGADS-0.19.1/eatGADS/man/cbind.GADSdat.Rd |only eatGADS-0.19.1/eatGADS/man/checkUniqueness.Rd |only eatGADS-0.19.1/eatGADS/man/extractData.Rd | 9 eatGADS-0.19.1/eatGADS/man/extractDataOld.Rd |only eatGADS-0.19.1/eatGADS/man/getTrendGADS.Rd | 30 -- eatGADS-0.19.1/eatGADS/man/getTrendGADSOld.Rd |only eatGADS-0.19.1/eatGADS/man/import_spss.Rd | 4 eatGADS-0.19.1/eatGADS/tests/testthat/helper_comp3.db |only eatGADS-0.19.1/eatGADS/tests/testthat/test_assimilateValLabels.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_calculateScale.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_cbind.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_char_valLabels2numeric.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_checkUniqueness.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_extractData.R | 65 +--- eatGADS-0.19.1/eatGADS/tests/testthat/test_extractDataOld.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_extractGADSdat.R | 4 eatGADS-0.19.1/eatGADS/tests/testthat/test_extractMeta.R | 4 eatGADS-0.19.1/eatGADS/tests/testthat/test_extract_labels.R | 21 - eatGADS-0.19.1/eatGADS/tests/testthat/test_getTrendGADS.R | 122 +++----- eatGADS-0.19.1/eatGADS/tests/testthat/test_getTrendGADSOld.R |only eatGADS-0.19.1/eatGADS/tests/testthat/test_import_spss.R | 2 eatGADS-0.19.1/eatGADS/tests/testthat/test_merge.R | 2 eatGADS-0.19.1/eatGADS/tests/testthat/test_mergeLabels.R | 4 eatGADS-0.19.1/eatGADS/tests/testthat/test_times2character.R | 5 eatGADS-0.19.1/eatGADS/tests/testthat/test_updateMeta.R | 8 eatGADS-0.19.1/eatGADS/vignettes/getGADS.Rmd | 21 - eatGADS-0.19.1/eatGADS/vignettes/meta_data.Rmd | 2 67 files changed, 418 insertions(+), 401 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.15.0 dated 2022-01-12 and 1.15.2 dated 2022-01-27
DESCRIPTION | 6 +-- MD5 | 20 ++++++------ NEWS | 90 ++++++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/cce.Rd | 3 + man/cce.factor.Rd | 2 + man/hyavar.Rd | 3 + man/ntv.Rd | 2 + man/phi.test.Rd | 3 + man/rng.Rd | 2 - src/euler.c | 26 ++++++++++----- 11 files changed, 92 insertions(+), 65 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-43 dated 2020-11-28 and 3.1-47 dated 2022-01-27
DESCRIPTION | 8 +-- MD5 | 100 +++++++++++++++++++++------------------- NAMESPACE | 10 +++- NEWS | 48 +++++++++++++++++++ R/as.matrix.listOfMatrices.R | 4 - R/latex.array.R |only R/latex.ftable.R |only R/likert.formula.R | 3 + R/likertWeighted.R |only R/rowPcts.R |only build/partial.rdb |binary inst/CITATION | 11 ++-- man/HH-internal.Rd |only man/HH.package.Rd | 4 - man/HHscriptnames.Rd | 2 man/NormalAndT.Rd | 2 man/NormalAndTplot.Rd | 2 man/X.residuals.Rd | 2 man/ancova-class.Rd | 2 man/ancova.Rd | 2 man/ancovaplot.Rd | 2 man/arma.loop.Rd | 2 man/as.likert.Rd | 3 - man/as.matrix.listOfMatrices.Rd | 38 ++++++++++----- man/as.multicomp.Rd | 2 man/cp.Rd | 2 man/datasets.Rd | 2 man/hov.Rd | 2 man/interaction2wt.Rd | 2 man/ladder.Rd | 2 man/latex.array.Rd |only man/likert.Rd | 10 ++-- man/likertMosaic.Rd | 3 - man/likertWeighted.Rd |only man/lm.case.Rd | 2 man/mmc.Rd | 2 man/mmc.mean.Rd | 2 man/multicomp.order.Rd | 2 man/multicomp.reverse.Rd | 2 man/odds.ratio.Rd | 2 man/orthog.complete.Rd | 2 man/panel.cartesian.Rd | 2 man/panel.interaction2wt.Rd | 2 man/plot.hov.Rd | 2 man/plot.mmc.multicomp.Rd | 2 man/plot.multicomp.Rd | 2 man/positioned-class.Rd | 2 man/regr1.plot.Rd | 2 man/regr2.plot.Rd | 2 man/resid.squares.Rd | 2 man/residual.plots.Rd | 2 man/rowPcts.Rd |only man/tsdiagplot.Rd | 2 man/vif.Rd | 2 man/xysplom.Rd | 2 55 files changed, 197 insertions(+), 113 deletions(-)
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Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>),
John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between popkin versions 1.3.13 dated 2021-07-27 and 1.3.17 dated 2022-01-27
popkin-1.3.13/popkin/tests/testthat/Xs.grm.N.bin |only popkin-1.3.13/popkin/tests/testthat/Xs.grm.bin |only popkin-1.3.13/popkin/tests/testthat/Xs.grm.id |only popkin-1.3.17/popkin/DESCRIPTION | 8 popkin-1.3.17/popkin/MD5 | 38 - popkin-1.3.17/popkin/NAMESPACE | 2 popkin-1.3.17/popkin/NEWS.md | 34 + popkin-1.3.17/popkin/R/avg_kinship_subpops.R |only popkin-1.3.17/popkin/R/get_mem_lim.R | 103 ++- popkin-1.3.17/popkin/R/plot_admix.R | 267 +++++++- popkin-1.3.17/popkin/R/plot_popkin.R | 37 - popkin-1.3.17/popkin/R/popkin_A_min_subpops.R | 48 - popkin-1.3.17/popkin/README.md | 2 popkin-1.3.17/popkin/build/vignette.rds |binary popkin-1.3.17/popkin/inst/doc/popkin.R | 46 + popkin-1.3.17/popkin/inst/doc/popkin.Rmd | 57 + popkin-1.3.17/popkin/inst/doc/popkin.html | 708 ++++++++-------------- popkin-1.3.17/popkin/man/avg_kinship_subpops.Rd |only popkin-1.3.17/popkin/man/plot_admix.Rd |only popkin-1.3.17/popkin/man/plot_popkin.Rd | 6 popkin-1.3.17/popkin/man/popkin_A_min_subpops.Rd | 12 popkin-1.3.17/popkin/tests/testthat/test_popkin.R | 167 ++++- popkin-1.3.17/popkin/vignettes/popkin.Rmd | 57 + 23 files changed, 1026 insertions(+), 566 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1>.
Author: Eric Gilleland [aut, cre],
Kim Elmore [ctb],
Caren Marzban [ctb],
Matt Pocernich [ctb],
Gregor Skok [ctb]
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.8 dated 2021-03-27 and 0.9 dated 2022-01-27
SpatialVx-0.8/SpatialVx/R/Geom.R |only SpatialVx-0.8/SpatialVx/R/SpatialVx_dFSS_FSSwind_R_code_v07.R |only SpatialVx-0.8/SpatialVx/R/SpatialVx_dNSS_R_code_v03.R |only SpatialVx-0.9/SpatialVx/DESCRIPTION | 27 SpatialVx-0.9/SpatialVx/MD5 | 49 SpatialVx-0.9/SpatialVx/R/Aindex.R |only SpatialVx-0.9/SpatialVx/R/Cindex.R |only SpatialVx-0.9/SpatialVx/R/CircleHistogram.R | 395 +- SpatialVx-0.9/SpatialVx/R/Sindex.R |only SpatialVx-0.9/SpatialVx/R/Vgrams.R | 1538 +++++----- SpatialVx-0.9/SpatialVx/R/calculate_FSS_from_enlarged_summed_fields.R |only SpatialVx-0.9/SpatialVx/R/calculate_FSSvector_from_binary_fields.R |only SpatialVx-0.9/SpatialVx/R/calculate_FSSvector_from_enlarged_summed_fields.R |only SpatialVx-0.9/SpatialVx/R/calculate_FSSwind.R |only SpatialVx-0.9/SpatialVx/R/calculate_dFSS.R |only SpatialVx-0.9/SpatialVx/R/calculate_fractions_from_enlarged_summed_field.R |only SpatialVx-0.9/SpatialVx/R/calculate_n05_using_bisection_from_the_summed_fields.R |only SpatialVx-0.9/SpatialVx/R/calculate_summed_field.R |only SpatialVx-0.9/SpatialVx/R/enlarge_matrix.R |only SpatialVx-0.9/SpatialVx/R/iwarper.R | 312 +- SpatialVx-0.9/SpatialVx/R/plot.warped.R | 154 - SpatialVx-0.9/SpatialVx/R/warper.R | 448 +- SpatialVx-0.9/SpatialVx/data/datalist | 6 SpatialVx-0.9/SpatialVx/man/Aindex.Rd | 11 SpatialVx-0.9/SpatialVx/man/Cindex.Rd | 11 SpatialVx-0.9/SpatialVx/man/CircleHistogram.Rd | 4 SpatialVx-0.9/SpatialVx/man/SpatialVx-internal.Rd | 5 SpatialVx-0.9/SpatialVx/man/SpatialVx-package.Rd | 2 SpatialVx-0.9/SpatialVx/man/datasets.Rd | 6 SpatialVx-0.9/SpatialVx/man/imomenter.Rd | 2 SpatialVx-0.9/SpatialVx/man/iwarper.Rd |only SpatialVx-0.9/SpatialVx/man/surrogater2d.Rd | 2 SpatialVx-0.9/SpatialVx/man/vxstats.Rd | 2 SpatialVx-0.9/SpatialVx/man/warper.Rd |only 34 files changed, 1495 insertions(+), 1479 deletions(-)
Title: Plot Hidden Markov Models
Description: Hidden Markov Models are useful for modeling
sequential data. This package provides several functions
implemented in C++ for explaining the algorithms used for
Hidden Markov Models (forward, backward, decoding,
learning).
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between plotHMM versions 2022.1.18 dated 2022-01-19 and 2022.1.25 dated 2022-01-27
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ inst/doc/compare_depmixS4.html | 8 ++++---- src/backward.cpp | 2 +- src/forward.cpp | 4 ++-- src/multiply.cpp | 4 ++-- src/pairwise.cpp | 4 ++-- src/transition.cpp | 4 ++-- src/viterbi.cpp | 4 ++-- 10 files changed, 35 insertions(+), 27 deletions(-)