Title: Multi-Objective Optimization in R
Description: The 'rmoo' package is a framework for multi- and many-objective
optimization, which allows researchers and users versatility
in parameter configuration, as well as tools for analysis, replication
and visualization of results. The 'rmoo' package was built as a fork of
the 'GA' package by Luca Scrucca(2017) <DOI:10.32614/RJ-2017-008> and
implementing the Non-Dominated Sorting Genetic Algorithms proposed
by K. Deb's.
Author: Francisco Benitez [aut, cre],
Diego Pinto Roa [aut]
Maintainer: Francisco Benitez <benitezfj94@gmail.com>
Diff between rmoo versions 0.1.8 dated 2022-08-11 and 0.2.0 dated 2022-09-23
rmoo-0.1.8/rmoo/R/nsga-class.R |only rmoo-0.1.8/rmoo/R/nsga2-class.R |only rmoo-0.1.8/rmoo/R/nsga3-class.R |only rmoo-0.1.8/rmoo/R/numberOrNAOrMatrix-class.R |only rmoo-0.1.8/rmoo/R/plotting.R |only rmoo-0.1.8/rmoo/man/heat_map.Rd |only rmoo-0.1.8/rmoo/man/pcp.Rd |only rmoo-0.1.8/rmoo/man/polar.Rd |only rmoo-0.1.8/rmoo/man/scatter.Rd |only rmoo-0.1.8/rmoo/man/summary.Rd |only rmoo-0.2.0/rmoo/DESCRIPTION | 38 - rmoo-0.2.0/rmoo/MD5 | 63 +- rmoo-0.2.0/rmoo/NAMESPACE | 18 rmoo-0.2.0/rmoo/R/AllClasses.R |only rmoo-0.2.0/rmoo/R/AllGenerics.R |only rmoo-0.2.0/rmoo/R/geneticoperator.R | 2 rmoo-0.2.0/rmoo/R/miscfun.R | 579 +++++++++++++++++++-- rmoo-0.2.0/rmoo/R/nsga.R | 129 ++++ rmoo-0.2.0/rmoo/R/nsga2.R | 86 ++- rmoo-0.2.0/rmoo/R/nsga3.R | 120 ++++ rmoo-0.2.0/rmoo/R/rmoo.R | 2 rmoo-0.2.0/rmoo/R/rmoo_func.R |only rmoo-0.2.0/rmoo/R/zzz.R | 22 rmoo-0.2.0/rmoo/README.md | 56 +- rmoo-0.2.0/rmoo/man/algorithm-class.Rd |only rmoo-0.2.0/rmoo/man/getCrowdingDistance-methods.Rd |only rmoo-0.2.0/rmoo/man/getDummyFitness-methods.Rd |only rmoo-0.2.0/rmoo/man/getFitness-methods.Rd |only rmoo-0.2.0/rmoo/man/getMetrics-methods.Rd |only rmoo-0.2.0/rmoo/man/getPopulation-methods.Rd |only rmoo-0.2.0/rmoo/man/nsga-class.Rd | 17 rmoo-0.2.0/rmoo/man/nsga.Rd | 2 rmoo-0.2.0/rmoo/man/nsga1-class.Rd |only rmoo-0.2.0/rmoo/man/nsga2-class.Rd | 64 -- rmoo-0.2.0/rmoo/man/nsga3-class.Rd | 65 -- rmoo-0.2.0/rmoo/man/numberOrNAOrMatrix-class.Rd | 4 rmoo-0.2.0/rmoo/man/plot-methods.Rd |only rmoo-0.2.0/rmoo/man/print-methods.Rd |only rmoo-0.2.0/rmoo/man/progress-methods.Rd |only rmoo-0.2.0/rmoo/man/rmoo-package.Rd | 4 rmoo-0.2.0/rmoo/man/rmoo_func.Rd |only rmoo-0.2.0/rmoo/man/summary-methods.Rd |only rmoo-0.2.0/rmoo/tests/testthat/test-nsga3.r | 2 rmoo-0.2.0/rmoo/tests/testthat/test-pcp.r | 8 rmoo-0.2.0/rmoo/tests/testthat/test-scatter.r | 12 45 files changed, 1001 insertions(+), 292 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric
objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and
calculate deviance residuals as well as 'R' translations of some
'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs
Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between extras versions 0.3.0 dated 2022-06-08 and 0.4.0 dated 2022-09-23
DESCRIPTION | 6 +-- MD5 | 35 ++++++++++--------- NAMESPACE | 3 + NEWS.md | 6 +++ R/bern.R |only R/odds.R | 35 +++++++++++++++++++ R/params.R | 4 ++ README.md | 4 +- build/partial.rdb |binary inst/WORDLIST | 1 man/bern.Rd |only man/inv_odds.Rd | 2 + man/log_odds-set.Rd |only man/log_odds.Rd |only man/log_odds_ratio.Rd | 2 + man/odds-set.Rd | 2 + man/odds.Rd | 2 + man/odds_ratio.Rd | 2 + man/params.Rd | 8 ++++ tests/testthat/test-bern.R |only tests/testthat/test-odds.R | 82 +++++++++++++++++++++++++++++++++++++++++++++ 21 files changed, 174 insertions(+), 20 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.0.4 dated 2021-04-19 and 2.0.5 dated 2022-09-23
ChangeLog | 4 DESCRIPTION | 20 - MD5 | 63 ++-- NAMESPACE | 1 R/RcppExports.R | 8 R/gh_mixture.R | 111 ++++++-- R/mixture.R | 69 ++++- R/pcm.R | 11 R/st_mixture.R | 82 +++++- R/t_mixture.R | 70 ++++- R/vg_mixture.R | 74 +++++ man/ghpcm.Rd | 1 man/gpcm.Rd | 1 man/main_loop_st.Rd | 7 man/main_loop_vg.Rd | 7 man/mixture.Rd | 4 man/pcm.Rd | 1 man/stpcm.Rd | 8 man/tpcm.Rd | 1 man/vgpcm.Rd | 7 src/Cluster_Error.hpp | 7 src/GH_Model/GH_Mixture_Model.h | 530 +++++++++++++++++++++++----------------- src/Random_GIG.hpp |only src/RcppExports.cpp | 23 + src/ST_Model/ST_Mixture_Model.h | 354 ++++++++++++++++++++++---- src/T_Model/General_Methods.hpp | 8 src/VG_Model/VG_Mixture_Model.h | 391 ++++++++++++++++++++++++----- src/ghpcm_arma.hpp | 267 ++++++++------------ src/gpcm_arma.hpp | 11 src/pcm.cpp | 3 src/stpcm_arma.hpp | 276 +++++++++----------- src/tpcm_arma.hpp | 11 src/vgpcm_arma.hpp | 261 ++++++++----------- 33 files changed, 1794 insertions(+), 898 deletions(-)
Title: Fast, Consistent Tokenization of Natural Language Text
Description: Convert natural language text into tokens. Includes tokenizers for
shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs,
characters, shingled characters, lines, tweets, Penn Treebank, regular
expressions, as well as functions for counting characters, words, and sentences,
and a function for splitting longer texts into separate documents, each with
the same number of words. The tokenizers have a consistent interface, and
the package is built on the 'stringi' and 'Rcpp' packages for fast
yet correct tokenization in 'UTF-8'.
Author: Lincoln Mullen [aut, cre] ,
Os Keyes [ctb] ,
Dmitriy Selivanov [ctb],
Jeffrey Arnold [ctb] ,
Kenneth Benoit [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between tokenizers versions 0.2.1 dated 2018-03-29 and 0.2.3 dated 2022-09-23
DESCRIPTION | 14 MD5 | 56 +-- NEWS.md | 5 R/basic-tokenizers.R | 9 R/chunk-text.R | 4 R/ngram-tokenizers.R | 6 R/ptb-tokenizer.R | 2 R/stem-tokenizers.R | 9 R/tokenize_tweets.R | 170 +++++---- R/utils.R | 2 README.md | 65 +-- build/vignette.rds |binary inst/doc/introduction-to-tokenizers.R | 28 - inst/doc/introduction-to-tokenizers.html | 544 +++++++++++++++++-------------- inst/doc/tif-and-tokenizers.R | 10 inst/doc/tif-and-tokenizers.Rmd | 2 inst/doc/tif-and-tokenizers.html | 334 +++++++++++-------- man/basic-tokenizers.Rd | 60 ++- man/mobydick.Rd | 4 man/ngram-tokenizers.Rd | 46 +- man/ptb-tokenizer.Rd | 14 man/shingle-tokenizers.Rd | 10 man/stem-tokenizers.Rd | 35 + man/tokenizers.Rd | 1 src/RcppExports.cpp | 5 src/shingle_ngrams.cpp | 2 tests/testthat/test-ptb.R | 2 tests/testthat/test-tokenize_tweets.R | 29 + vignettes/tif-and-tokenizers.Rmd | 2 29 files changed, 854 insertions(+), 616 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.9.1 dated 2022-08-22 and 0.9.2 dated 2022-09-23
DESCRIPTION | 12 MD5 | 96 ++--- NAMESPACE | 34 - R/ARMA.R | 154 ++++---- R/ARMA_optim.R | 97 ++--- R/Boost.R | 55 +-- R/Internal_Functions.R | 61 --- R/Mode.R |only R/Multivariate_Regression.R | 273 +++++++-------- R/NNS_Distance.R | 22 - R/NNS_VAR.R | 134 +++---- R/NNS_meboot.R | 15 R/Nowcast.R | 45 -- R/Partition_Map.R | 10 R/Regression.R | 223 ++++++------ R/Stack.R | 340 +++++++++---------- R/dy_d_wrt.R | 9 R/dy_dx.R | 8 R/gvload.R | 41 -- README.md | 4 build/partial.rdb |binary inst/doc/NNSvignette_Classification.R | 1 inst/doc/NNSvignette_Classification.Rmd | 1 inst/doc/NNSvignette_Classification.html | 62 --- inst/doc/NNSvignette_Clustering_and_Regression.R | 2 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 2 inst/doc/NNSvignette_Clustering_and_Regression.html | 54 +-- inst/doc/NNSvignette_Correlation_and_Dependence.R | 1 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 1 inst/doc/NNSvignette_Correlation_and_Dependence.html | 19 - inst/doc/NNSvignette_Forecasting.R | 1 inst/doc/NNSvignette_Forecasting.Rmd | 1 inst/doc/NNSvignette_Forecasting.html | 3 inst/doc/NNSvignette_Partial_Moments.Rmd | 3 inst/doc/NNSvignette_Partial_Moments.html | 6 man/NNS.ARMA.optim.Rd | 2 man/NNS.VAR.Rd | 13 man/NNS.boost.Rd | 7 man/NNS.distance.Rd | 2 man/NNS.mode.Rd |only man/NNS.nowcast.Rd | 14 man/NNS.reg.Rd | 5 man/NNS.stack.Rd | 7 tests/testthat/Rplots.pdf |binary tests/testthat/test_Partition_Map.R | 26 - vignettes/NNSvignette_Classification.Rmd | 1 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 2 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 1 vignettes/NNSvignette_Forecasting.Rmd | 1 vignettes/NNSvignette_Partial_Moments.Rmd | 3 50 files changed, 845 insertions(+), 1029 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.8.0 dated 2022-07-05 and 1.9.0 dated 2022-09-23
DESCRIPTION | 8 MD5 | 72 ++-- NAMESPACE | 1 NEWS.md | 15 R/assert_package.R | 94 ++++-- R/model_get_model_matrix.R | 4 R/model_get_terms.R | 4 R/model_identify_variables.R | 9 R/model_list_variables.R | 4 R/select_utilities.R | 2 R/tidiers.R | 2 R/tidy_add_contrasts.R | 4 R/tidy_add_estimate_to_reference_rows.R | 4 R/tidy_add_header_rows.R | 10 R/tidy_add_reference_rows.R | 16 - R/tidy_add_term_labels.R | 2 R/tidy_add_variable_labels.R | 2 R/tidy_disambiguate_terms.R | 2 R/tidy_plus_plus.R | 2 build/vignette.rds |binary data/supported_models.rda |binary inst/doc/tidy.R | 5 inst/doc/tidy.Rmd | 5 inst/doc/tidy.html | 453 ++++++++++++++--------------- man/assert_package.Rd | 37 +- man/model_get_model_matrix.Rd | 4 man/model_get_terms.Rd | 4 man/model_list_variables.Rd | 2 man/tidy_add_estimate_to_reference_rows.Rd | 4 man/tidy_add_header_rows.Rd | 2 man/tidy_add_reference_rows.Rd | 2 man/tidy_disambiguate_terms.Rd | 2 man/tidy_parameters.Rd | 2 man/tidy_plus_plus.Rd | 2 tests/testthat/test-assert_package.R | 37 +- tests/testthat/test-tidy_plus_plus.R | 2 vignettes/tidy.Rmd | 5 37 files changed, 465 insertions(+), 360 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Claire Kelley [aut],
Trang Nguyen [aut],
Huade Huo [aut],
Eric Buehler [ctb],
Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.2.1 dated 2021-12-07 and 3.2.2 dated 2022-09-23
DESCRIPTION | 8 MD5 | 18 R/adaptiveQuad.R | 7 R/analyticSolve.R | 71 ++ R/helpers.R | 42 + build/vignette.rds |binary inst/NEWS.Rd | 17 inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary tests/testthat/test-1-main.R | 286 ++++++++++- 10 files changed, 397 insertions(+), 52 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table',
giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Robert On [ctb],
Alexander Sevostianov [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.8.1 dated 2022-08-17 and 0.9.0 dated 2022-09-23
tidytable-0.8.1/tidytable/tests/testthat/test-lead..R |only tidytable-0.9.0/tidytable/DESCRIPTION | 43 tidytable-0.9.0/tidytable/MD5 | 522 ++++++---- tidytable-0.9.0/tidytable/NAMESPACE | 171 +++ tidytable-0.9.0/tidytable/NEWS.md | 32 tidytable-0.9.0/tidytable/R/across.R | 20 tidytable-0.9.0/tidytable/R/add_count.R | 45 tidytable-0.9.0/tidytable/R/arrange.R | 21 tidytable-0.9.0/tidytable/R/as_tidytable.R | 37 tidytable-0.9.0/tidytable/R/between.R | 19 tidytable-0.9.0/tidytable/R/bind.R | 25 tidytable-0.9.0/tidytable/R/c_across.R | 13 tidytable-0.9.0/tidytable/R/case.R | 9 tidytable-0.9.0/tidytable/R/case_match.R |only tidytable-0.9.0/tidytable/R/case_when.R | 25 tidytable-0.9.0/tidytable/R/coalesce.R | 13 tidytable-0.9.0/tidytable/R/complete.R | 32 tidytable-0.9.0/tidytable/R/consecutive_id.R | 9 tidytable-0.9.0/tidytable/R/count.R | 98 + tidytable-0.9.0/tidytable/R/crossing.R | 17 tidytable-0.9.0/tidytable/R/cur-context.R | 62 - tidytable-0.9.0/tidytable/R/desc.R | 12 tidytable-0.9.0/tidytable/R/distinct.R | 40 tidytable-0.9.0/tidytable/R/drop_na.R | 16 tidytable-0.9.0/tidytable/R/dt.R | 29 tidytable-0.9.0/tidytable/R/enframe.R | 9 tidytable-0.9.0/tidytable/R/expand.R | 53 - tidytable-0.9.0/tidytable/R/expand_grid.R | 28 tidytable-0.9.0/tidytable/R/extract.R | 20 tidytable-0.9.0/tidytable/R/fill.R | 25 tidytable-0.9.0/tidytable/R/filter.R | 32 tidytable-0.9.0/tidytable/R/first-last-nth.R | 39 tidytable-0.9.0/tidytable/R/fread-fwrite.R | 21 tidytable-0.9.0/tidytable/R/get_dummies.R | 29 tidytable-0.9.0/tidytable/R/group_by.R |only tidytable-0.9.0/tidytable/R/group_split.R | 27 tidytable-0.9.0/tidytable/R/if_all-if_any.R | 24 tidytable-0.9.0/tidytable/R/if_else.R | 22 tidytable-0.9.0/tidytable/R/in-notin.R | 7 tidytable-0.9.0/tidytable/R/inv_gc.R | 4 tidytable-0.9.0/tidytable/R/join.R | 187 +-- tidytable-0.9.0/tidytable/R/lag-lead.R | 24 tidytable-0.9.0/tidytable/R/mutate.R | 102 + tidytable-0.9.0/tidytable/R/mutate_rowwise.R | 66 + tidytable-0.9.0/tidytable/R/n.R | 17 tidytable-0.9.0/tidytable/R/n_distinct.R | 9 tidytable-0.9.0/tidytable/R/na_if.R | 13 tidytable-0.9.0/tidytable/R/nest.R | 28 tidytable-0.9.0/tidytable/R/nest_by.R | 39 tidytable-0.9.0/tidytable/R/pivot_longer.R | 105 +- tidytable-0.9.0/tidytable/R/pivot_wider.R | 104 + tidytable-0.9.0/tidytable/R/print.R | 43 tidytable-0.9.0/tidytable/R/pull.R | 25 tidytable-0.9.0/tidytable/R/purrr-map.R | 104 + tidytable-0.9.0/tidytable/R/purrr-map2.R | 88 + tidytable-0.9.0/tidytable/R/purrr-pmap.R | 92 + tidytable-0.9.0/tidytable/R/relocate.R | 16 tidytable-0.9.0/tidytable/R/rename.R | 42 tidytable-0.9.0/tidytable/R/rename_with.R | 17 tidytable-0.9.0/tidytable/R/replace_na.R | 44 tidytable-0.9.0/tidytable/R/row_number.R | 18 tidytable-0.9.0/tidytable/R/rowwise.R |only tidytable-0.9.0/tidytable/R/select.R | 30 tidytable-0.9.0/tidytable/R/separate.R | 21 tidytable-0.9.0/tidytable/R/separate_rows.R | 17 tidytable-0.9.0/tidytable/R/slice-head-tail.R |only tidytable-0.9.0/tidytable/R/slice-min-max.R |only tidytable-0.9.0/tidytable/R/slice.R | 186 --- tidytable-0.9.0/tidytable/R/slice_sample.R |only tidytable-0.9.0/tidytable/R/summarize.R | 108 +- tidytable-0.9.0/tidytable/R/tidytable-package.R | 13 tidytable-0.9.0/tidytable/R/tidytable.R | 4 tidytable-0.9.0/tidytable/R/top_n.R | 18 tidytable-0.9.0/tidytable/R/transmute.R | 18 tidytable-0.9.0/tidytable/R/uncount.R | 16 tidytable-0.9.0/tidytable/R/unite.R | 32 tidytable-0.9.0/tidytable/R/unnest.R | 61 - 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Title: Simple Geographical Operations (with OSGB36)
Description: Methods focused in performing the OSGB36/ETRS89 transformation
(Great Britain and the Isle of Man only) by using the Ordnance Survey's
OSTN15/OSGM15 transformation model. Calculation of distances and areas from
sets of points defined in any of the supported Coordinated Systems is also
available.
Author: Carlos Lozano Ruiz [aut, cre]
Maintainer: Carlos Lozano Ruiz <carloslozanoruiz@outlook.com>
Diff between sgo versions 0.9.1 dated 2021-12-11 and 0.9.2 dated 2022-09-23
sgo-0.9.1/sgo/man/sgo.Rd |only sgo-0.9.1/sgo/tests/testthat |only sgo-0.9.1/sgo/tests/testthat.R |only sgo-0.9.2/sgo/DESCRIPTION | 13 +-- sgo-0.9.2/sgo/MD5 | 86 +++++++++++++------------- sgo-0.9.2/sgo/NEWS.md | 9 ++ sgo-0.9.2/sgo/R/sgo.R | 8 +- sgo-0.9.2/sgo/R/sgo_area.R | 14 ++-- sgo-0.9.2/sgo/R/sgo_bng.R | 30 ++++----- sgo-0.9.2/sgo/R/sgo_distance.R | 31 ++++----- sgo-0.9.2/sgo/R/sgo_laea.R | 14 ++-- sgo-0.9.2/sgo/R/sgo_ngr.R | 28 ++------ sgo-0.9.2/sgo/R/sgo_points.R | 115 +++++++++++++++++++++++++++++++---- sgo-0.9.2/sgo/R/sgo_set_gcs.R | 28 +++----- sgo-0.9.2/sgo/R/sgo_transform.R | 6 - sgo-0.9.2/sgo/R/sgo_wgs84.R | 8 +- sgo-0.9.2/sgo/R/sysdata.rda |binary sgo-0.9.2/sgo/README.md | 41 +++++++++--- sgo-0.9.2/sgo/inst |only sgo-0.9.2/sgo/man/sgo-package.Rd |only sgo-0.9.2/sgo/man/sgo_area.Rd | 2 sgo-0.9.2/sgo/man/sgo_bng_lonlat.Rd | 12 +-- sgo-0.9.2/sgo/man/sgo_bng_ngr.Rd | 4 - sgo-0.9.2/sgo/man/sgo_cart_lonlat.Rd | 3 sgo-0.9.2/sgo/man/sgo_coordinates.Rd | 16 ++++ sgo-0.9.2/sgo/man/sgo_distance.Rd | 21 +++--- sgo-0.9.2/sgo/man/sgo_lonlat_bng.Rd | 4 - sgo-0.9.2/sgo/man/sgo_lonlat_cart.Rd | 3 sgo-0.9.2/sgo/man/sgo_ngr_bng.Rd | 4 - sgo-0.9.2/sgo/man/sgo_points.Rd | 2 sgo-0.9.2/sgo/man/sgo_set_gcs.Rd | 6 - sgo-0.9.2/sgo/man/sgo_transform.Rd | 2 sgo-0.9.2/sgo/man/sgo_wgs84_en.Rd | 2 sgo-0.9.2/sgo/tests/tinytest.R |only 34 files changed, 319 insertions(+), 193 deletions(-)
Title: Tools for Data Analysis in Experimental Agriculture
Description: Toolkit for a workflow to analyse experimental agriculture data,
from data synthesis to model selection and visualisation.
The package is named after W.S. Gosset aka ‘Student’, a pioneer
of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
David Brown [aut] ,
Jonathan Steinke [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between gosset versions 0.4 dated 2022-06-28 and 0.5 dated 2022-09-23
DESCRIPTION | 16 ++++++------- MD5 | 23 +++++++++---------- NEWS.md | 7 +++++ R/kendallW.R | 17 -------------- R/reliability.R | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.html | 2 - inst/paper/paper.Rmd | 59 ++++++++++++++++++++++++------------------------- inst/paper/paper.docx |only man/gosset.Rd | 2 - man/kendallW.Rd | 17 -------------- man/reliability.Rd | 4 ++- 13 files changed, 64 insertions(+), 87 deletions(-)
Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between EnrichIntersect versions 0.3 dated 2022-09-14 and 0.4 dated 2022-09-23
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/intersectSankey.R | 6 +++++- inst/doc/EnrichIntersect.Rmd | 2 +- inst/doc/EnrichIntersect.html | 2 +- vignettes/EnrichIntersect.Rmd | 2 +- 7 files changed, 24 insertions(+), 16 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education S [...truncated...]
Author: Paul Bailey [aut, cre],
Ahmad Emad [aut],
Huade Huo [aut],
Michael Lee [aut],
Yuqi Liao [aut],
Alex Lishinski [aut],
Trang Nguyen [aut],
Qingshu Xie [aut],
Jiao Yu [aut],
Ting Zhang [aut],
Eric Buehler [aut],
person,
person),
Jeppe Bundsgaard [ctb],
[...truncated...]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.7.1 dated 2021-10-05 and 3.0.0 dated 2022-09-23
DESCRIPTION | 15 MD5 | 195 +++--- NAMESPACE | 18 R/achievementLevels.R | 9 R/all.R | 9 R/cor.sdf.R | 49 - R/descriptionOfFile.R | 173 ++--- R/dim.edsurvey.data.frame.R | 2 R/downloadPIAAC.R | 2 R/downloadTIMSS.R | 6 R/drawPVs.sdf.R |only R/edsurvey.data.frame.R | 88 -- R/edsurveyTable.R | 11 R/gap.R | 20 R/getAttributes.R | 7 R/getData.R | 290 ++++----- R/getItems.R |only R/glm.sdf.R | 16 R/levelsSDF.R | 6 R/lm.sdf.R | 11 R/mergev.R |only R/mml.paramtabs.R | 194 ++++-- R/mml.scoreNAEP.R | 65 +- R/mml.scoreTIMSS.R | 54 + R/mml.sdf.R | 858 +++++++++++++-------------- R/mml.sdf.helpers.R | 48 + R/mvrlm.sdf.R | 8 R/percentile.R | 24 R/readELS.R | 2 R/readICCS.R | 305 ++++----- R/readNAEP.r | 880 +++++++++++++++++++--------- R/readPIAAC.R | 3 R/readPISA_YAFS.R | 2 R/readTIMSS.R | 867 ++++++++++++++++++++------- R/readUTILS.R | 47 + R/readUTILS_PRINT.R |only R/read_ePIRLS.R | 78 +- R/rebindAttributes.R | 2 R/rq.sdf.R | 10 R/sameSurvey.R | 9 R/setAttributes.R | 2 R/showPlausibleValues.R | 2 R/subset.edsurvey.data.frame.list.R | 37 - R/subset.light.edsurvey.data.frame.R | 38 - R/suggestWeights.R |only R/summary2.R | 4 R/utilities.R | 180 +++++ R/waldTest.R | 2 R/zzz.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 21 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 13 inst/suggestWeights |only man/UnclassCols.Rd |only man/checkIdVar.Rd |only man/checkPsuStrata.Rd |only man/cor.sdf.Rd | 6 man/drawPVs.sdf.Rd |only man/edsurvey-class.Rd | 8 man/examples/getAllItems.R |only man/examples/readPIAAC.R | 18 man/examples/suggestWeights.R |only man/getAllItems.Rd |only man/mergev.Rd |only man/mml.sdf.Rd | 40 - man/readNAEP.Rd | 42 - man/readPIAAC.Rd | 18 man/scoreDefault.Rd |only man/scoreTIMSS.Rd | 5 man/setNAEPScoreCard.Rd |only man/suggestWeights.Rd |only man/summary2.Rd | 2 tests/testthat/NHESlm1.rds |only tests/testthat/PISAedTable1.rds |only tests/testthat/PISAgd0.rds |only tests/testthat/PISAgd1.rds |only tests/testthat/PISAgd2.rds |only tests/testthat/PISAgd3.rds |only tests/testthat/PISAgd4.rds |only tests/testthat/REF-0-main.R | 698 ++++++++++------------ tests/testthat/REF-11-NHES.R |only tests/testthat/REF-12-SSOCS.R | 2 tests/testthat/REF-2-esdfl.R | 12 tests/testthat/REF-3-TIMSS.R | 35 - tests/testthat/REF-6-ECLS_K.R | 2 tests/testthat/REF-7-ELS.R | 10 tests/testthat/TIMSSes1Fin.rds |only tests/testthat/TIMSSes1Fin4.rds |only tests/testthat/TIMSSes1USA.rds |only tests/testthat/TIMSSes1USA4.rds |only tests/testthat/TIMSSgap3d_varest.rds |only tests/testthat/TIMSSgap_AL1.rds |only tests/testthat/TIMSSgap_main_percentile.rds |only tests/testthat/TIMSSgap_percentage1.rds |only tests/testthat/TIMSSgd1.rds |only tests/testthat/TIMSSgd2.rds |only tests/testthat/TIMSSgd3.rds |only tests/testthat/TIMSSlm1.rds |only tests/testthat/TIMSSlm1_sum.rds |only tests/testthat/TIMSSlm1t.rds |only tests/testthat/TIMSSlm1t_sum.rds |only tests/testthat/TIMSSpct1.rds |only tests/testthat/gddat.rds |binary tests/testthat/lm1t.rds |binary tests/testthat/pisa_1re_REF.rds |only tests/testthat/test-05-mergev.R |only tests/testthat/test-10-main.R | 134 +++- tests/testthat/test-15-lesdf.R | 3 tests/testthat/test-20-esdfl.R | 5 tests/testthat/test-25-NHES.R |only tests/testthat/test-27-SSOCS.R | 4 tests/testthat/test-30-TIMSS.R | 92 ++ tests/testthat/test-40-ELS.R | 16 tests/testthat/test-45-HSLS.R | 22 tests/testthat/test-50-pisa.R | 12 tests/testthat/test-51-YAFS.R | 2 tests/testthat/test-60-ECLS_K.R | 4 tests/testthat/test-75-iccs.R | 4 vignettes/introduction.Rmd | 2 120 files changed, 3593 insertions(+), 2292 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenie [aut, cre] ,
Pierre Denelle [aut] ,
Caroline Tucker [aut] ,
Francois Munoz [ths] ,
Cyrille Violle [ths]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>
Diff between funrar versions 1.4.1 dated 2020-04-20 and 1.5.0 dated 2022-09-23
funrar-1.4.1/funrar/inst/doc/rarity_indices.R |only funrar-1.4.1/funrar/inst/doc/rarity_indices.Rmd |only funrar-1.4.1/funrar/inst/doc/rarity_indices.html |only funrar-1.4.1/funrar/vignettes/rarity_indices.Rmd |only funrar-1.5.0/funrar/DESCRIPTION | 16 funrar-1.5.0/funrar/MD5 | 140 - funrar-1.5.0/funrar/NAMESPACE | 61 funrar-1.5.0/funrar/NEWS.md | 186 + funrar-1.5.0/funrar/R/check_functions.R | 498 ++--- funrar-1.5.0/funrar/R/compute_dist_matrix.R | 198 +- funrar-1.5.0/funrar/R/distinctiveness.R | 662 +++--- funrar-1.5.0/funrar/R/distinctiveness_alt.R | 217 +- funrar-1.5.0/funrar/R/distinctiveness_global.R | 127 - funrar-1.5.0/funrar/R/distinctiveness_range.R | 342 +-- funrar-1.5.0/funrar/R/funrar.R | 226 +- funrar-1.5.0/funrar/R/make_relative.R | 186 - funrar-1.5.0/funrar/R/rarity_dimensions.R | 271 +- funrar-1.5.0/funrar/R/restrictedness.R | 359 +-- funrar-1.5.0/funrar/R/scarcity.R | 368 +-- funrar-1.5.0/funrar/R/stack_matrix.R | 372 +-- funrar-1.5.0/funrar/R/uniqueness.R | 300 +-- funrar-1.5.0/funrar/README.md | 112 - funrar-1.5.0/funrar/build/vignette.rds |binary funrar-1.5.0/funrar/inst/CITATION | 46 funrar-1.5.0/funrar/inst/doc/funrar.R |only funrar-1.5.0/funrar/inst/doc/funrar.Rmd |only funrar-1.5.0/funrar/inst/doc/funrar.html |only funrar-1.5.0/funrar/inst/doc/new_distinctiveness.R | 366 +-- funrar-1.5.0/funrar/inst/doc/new_distinctiveness.Rmd | 854 ++++---- funrar-1.5.0/funrar/inst/doc/new_distinctiveness.pdf |binary funrar-1.5.0/funrar/inst/doc/other_functions.R |only funrar-1.5.0/funrar/inst/doc/other_functions.Rmd |only funrar-1.5.0/funrar/inst/doc/other_functions.html |only funrar-1.5.0/funrar/inst/doc/sparse_matrices.R | 186 - funrar-1.5.0/funrar/inst/doc/sparse_matrices.Rmd | 320 +-- funrar-1.5.0/funrar/inst/doc/sparse_matrices.html | 990 +++++----- funrar-1.5.0/funrar/man/combination_trait_dist.Rd | 44 funrar-1.5.0/funrar/man/compute_dist_matrix.Rd | 156 - funrar-1.5.0/funrar/man/distinctiveness.Rd | 170 - funrar-1.5.0/funrar/man/distinctiveness_alt.Rd | 141 - funrar-1.5.0/funrar/man/distinctiveness_com.Rd | 114 - funrar-1.5.0/funrar/man/distinctiveness_dimensions.Rd | 94 funrar-1.5.0/funrar/man/distinctiveness_global.Rd | 64 funrar-1.5.0/funrar/man/distinctiveness_range.Rd | 226 +- funrar-1.5.0/funrar/man/distinctiveness_stack.Rd | 174 - funrar-1.5.0/funrar/man/funrar.Rd | 90 funrar-1.5.0/funrar/man/funrar_stack.Rd | 98 funrar-1.5.0/funrar/man/is_relative.Rd | 79 funrar-1.5.0/funrar/man/make_relative.Rd | 59 funrar-1.5.0/funrar/man/matrix_to_stack.Rd | 98 funrar-1.5.0/funrar/man/restrictedness.Rd | 152 - funrar-1.5.0/funrar/man/restrictedness_stack.Rd | 104 - funrar-1.5.0/funrar/man/scarcity.Rd | 102 - funrar-1.5.0/funrar/man/scarcity_com.Rd | 96 funrar-1.5.0/funrar/man/scarcity_stack.Rd | 110 - funrar-1.5.0/funrar/man/stack_to_matrix.Rd | 108 - funrar-1.5.0/funrar/man/uniqueness.Rd | 128 - funrar-1.5.0/funrar/man/uniqueness_dimensions.Rd | 90 funrar-1.5.0/funrar/man/uniqueness_stack.Rd | 108 - funrar-1.5.0/funrar/tests/testthat.R | 8 funrar-1.5.0/funrar/tests/testthat/test-check_functions.R | 348 +-- funrar-1.5.0/funrar/tests/testthat/test-dist_matrix.R | 308 +-- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness.R | 669 +++--- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_alt.R | 309 +-- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_global.R | 180 + funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_range.R | 458 ++-- funrar-1.5.0/funrar/tests/testthat/test-funrar.R | 295 +- funrar-1.5.0/funrar/tests/testthat/test-rarity_dimensions.R | 322 +-- funrar-1.5.0/funrar/tests/testthat/test-rel_abund.R | 164 - funrar-1.5.0/funrar/tests/testthat/test-restrictedness.R | 106 - funrar-1.5.0/funrar/tests/testthat/test-scarcity.R | 313 +-- funrar-1.5.0/funrar/tests/testthat/test-tidy_matrix.R | 344 +-- funrar-1.5.0/funrar/tests/testthat/test-uniqueness.R | 159 - funrar-1.5.0/funrar/vignettes/funrar.Rmd |only funrar-1.5.0/funrar/vignettes/new_distinctiveness.Rmd | 854 ++++---- funrar-1.5.0/funrar/vignettes/other_functions.Rmd |only funrar-1.5.0/funrar/vignettes/sparse_matrices.Rmd | 320 +-- 77 files changed, 7646 insertions(+), 7519 deletions(-)
Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@hpi.de>
Diff between DrDimont versions 0.1.3 dated 2022-05-17 and 0.1.4 dated 2022-09-23
DrDimont-0.1.3/DrDimont/vignettes/pipeline_bpmn.png |only DrDimont-0.1.3/DrDimont/vignettes/pipeline_overview.png |only DrDimont-0.1.4/DrDimont/DESCRIPTION | 43 DrDimont-0.1.4/DrDimont/MD5 | 138 DrDimont-0.1.4/DrDimont/R/checks.R | 725 +-- DrDimont-0.1.4/DrDimont/R/drug_targets.R | 2 DrDimont-0.1.4/DrDimont/R/graph_combination.R | 3 DrDimont-0.1.4/DrDimont/R/interaction_score.R | 72 DrDimont-0.1.4/DrDimont/R/network_generation.R | 3 DrDimont-0.1.4/DrDimont/R/network_reduction.R | 5 DrDimont-0.1.4/DrDimont/R/pipeline_functions.R | 2144 +++++----- DrDimont-0.1.4/DrDimont/R/settings.R | 129 DrDimont-0.1.4/DrDimont/R/utilities.R | 196 DrDimont-0.1.4/DrDimont/build/vignette.rds |binary DrDimont-0.1.4/DrDimont/data/combined_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/correlation_matrices_example.rda |binary DrDimont-0.1.4/DrDimont/data/differential_graph_example.rda |binary DrDimont-0.1.4/DrDimont/data/drug_response_scores_example.rda |binary DrDimont-0.1.4/DrDimont/data/drug_target_edges_example.rda |binary DrDimont-0.1.4/DrDimont/data/individual_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/interaction_score_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/layers_example.rda |binary DrDimont-0.1.4/DrDimont/data/metabolite_data.rda |binary DrDimont-0.1.4/DrDimont/data/metabolite_protein_interactions.rda |binary DrDimont-0.1.4/DrDimont/inst/CITATION |only DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.R | 377 - DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.Rmd | 854 ++- DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.html | 2110 +++++---- DrDimont-0.1.4/DrDimont/inst/requirements_pip.txt | 2 DrDimont-0.1.4/DrDimont/man/calculate_interaction_score.Rd | 8 DrDimont-0.1.4/DrDimont/man/check_connection.Rd | 8 DrDimont-0.1.4/DrDimont/man/check_drug_target.Rd | 10 DrDimont-0.1.4/DrDimont/man/check_drug_targets_in_layers.Rd | 11 DrDimont-0.1.4/DrDimont/man/check_input.Rd | 24 DrDimont-0.1.4/DrDimont/man/check_layer.Rd | 14 DrDimont-0.1.4/DrDimont/man/check_sensible_connections.Rd | 29 DrDimont-0.1.4/DrDimont/man/chunk.Rd | 1 DrDimont-0.1.4/DrDimont/man/chunk_2gether.Rd | 1 DrDimont-0.1.4/DrDimont/man/combine_graphs.Rd | 1 DrDimont-0.1.4/DrDimont/man/compute_correlation_matrices.Rd | 23 DrDimont-0.1.4/DrDimont/man/compute_drug_response_scores.Rd | 12 DrDimont-0.1.4/DrDimont/man/corPvalueStudentParallel.Rd | 1 DrDimont-0.1.4/DrDimont/man/create_unique_layer_node_ids.Rd | 1 DrDimont-0.1.4/DrDimont/man/determine_drug_targets.Rd | 18 DrDimont-0.1.4/DrDimont/man/drdimont_settings.Rd | 112 DrDimont-0.1.4/DrDimont/man/find_targets.Rd | 1 DrDimont-0.1.4/DrDimont/man/generate_combined_graphs.Rd | 26 DrDimont-0.1.4/DrDimont/man/generate_differential_score_graph.Rd | 10 DrDimont-0.1.4/DrDimont/man/generate_individual_graphs.Rd | 26 DrDimont-0.1.4/DrDimont/man/generate_interaction_score_graphs.Rd | 38 DrDimont-0.1.4/DrDimont/man/generate_reduced_graph.Rd | 1 DrDimont-0.1.4/DrDimont/man/get_layer.Rd | 1 DrDimont-0.1.4/DrDimont/man/get_layer_setting.Rd | 1 DrDimont-0.1.4/DrDimont/man/graph_metrics.Rd | 12 DrDimont-0.1.4/DrDimont/man/install_python_dependencies.Rd | 16 DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_id.Rd | 1 DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_table.Rd | 1 DrDimont-0.1.4/DrDimont/man/load_interaction_score_output.Rd | 1 DrDimont-0.1.4/DrDimont/man/make_connection.Rd | 23 DrDimont-0.1.4/DrDimont/man/make_drug_target.Rd | 7 DrDimont-0.1.4/DrDimont/man/make_layer.Rd | 18 DrDimont-0.1.4/DrDimont/man/network_reduction_by_p_value.Rd | 1 DrDimont-0.1.4/DrDimont/man/network_reduction_by_pickHardThreshold.Rd | 1 DrDimont-0.1.4/DrDimont/man/return_errors.Rd | 26 DrDimont-0.1.4/DrDimont/man/run_pipeline.Rd | 44 DrDimont-0.1.4/DrDimont/man/sample_size.Rd | 1 DrDimont-0.1.4/DrDimont/man/set_cluster.Rd | 1 DrDimont-0.1.4/DrDimont/man/shutdown_cluster.Rd | 1 DrDimont-0.1.4/DrDimont/man/target_edge_list.Rd | 1 DrDimont-0.1.4/DrDimont/man/write_interaction_score_input.Rd | 1 DrDimont-0.1.4/DrDimont/vignettes/220401_overview.png |only DrDimont-0.1.4/DrDimont/vignettes/DrDimont_Vignette.Rmd | 854 ++- 72 files changed, 4189 insertions(+), 4002 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.3 dated 2022-03-17 and 0.1.4 dated 2022-09-23
DESCRIPTION | 8 - MD5 | 14 - R/wdnr.gis-package.R | 3 inst/doc/wdnr.gis-intro.Rmd | 2 inst/doc/wdnr.gis-intro.html | 273 +++++++++++++++++++++++++++++++++--- man/wdnr.gis-package.Rd | 3 tests/testthat/test-get-functions.R | 37 ++-- vignettes/wdnr.gis-intro.Rmd | 2 8 files changed, 291 insertions(+), 51 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.2-1 dated 2022-08-14 and 1.2-2 dated 2022-09-23
DESCRIPTION | 12 ++-- MD5 | 10 ++-- NEWS.md | 7 ++ R/memoiR.R | 14 +++++ inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 12 ++-- inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 25 +++++----- 6 files changed, 51 insertions(+), 29 deletions(-)
Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <arXiv:2209.03218>.
Author: Robert Adamek [cre, aut],
Stephan Smeekes [aut],
Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>
Diff between desla versions 0.1.0 dated 2021-11-11 and 0.2.0 dated 2022-09-23
DESCRIPTION | 15 MD5 | 33 NAMESPACE | 7 NEWS.md | 19 R/R_functions.R | 800 +++++++++++++++++------ R/RcppExports.R | 12 README.md | 184 +++++ build/partial.rdb |binary inst/REFERENCES.bib | 10 man/HDLP.Rd | 49 - man/coef.desla.Rd |only man/confint.desla.Rd |only man/create_state_dummies.Rd |only man/create_state_dummies_from_datamatrix.Rd |only man/create_state_dummies_from_vector.Rd |only man/desla.Rd | 116 --- man/plot.hdlp.Rd |only man/print.desla.Rd |only man/print.summary.desla.Rd |only man/summary.desla.Rd |only src/RcppExports.cpp | 46 + src/rcpp_functions.cpp | 954 ++++++++++++++++++++++------ 22 files changed, 1699 insertions(+), 546 deletions(-)
Title: 3D Volcano Plots and Polar Plots for Three-Class Data
Description: Generates interactive plots for analysing and visualising
three-class high dimensional data. It is particularly suited to visualising
differences in continuous attributes such as gene/protein/biomarker
expression levels between three groups. Differential gene/biomarker
expression analysis between two classes is typically shown as a volcano
plot. However, with three groups this type of visualisation is particularly
difficult to interpret. This package generates 3D volcano plots and 3-way
polar plots for easier interpretation of three-class data.
Author: Katriona Goldmann [aut, cre] ,
Myles Lewis [aut]
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>
Diff between volcano3D versions 2.0.0 dated 2022-07-05 and 2.0.8 dated 2022-09-23
DESCRIPTION | 12 +-- MD5 | 92 +++++++++++++++++------------ NAMESPACE | 30 +++++++++ NEWS.md | 19 ++++++ R/add_animation.R | 7 +- R/boxplot_trio.R | 67 +++++++++++---------- R/boxplot_trio_old.R | 1 R/deseq_2x3.R |only R/deseq_2x3_polar.R |only R/deseq_polar.R | 62 +++++++++++++------- R/forest_plot.R |only R/polar_coords.R | 133 ++++++++++++++++++++++++++++++++----------- R/polar_coords_2x3.R |only R/polar_grid.R | 7 +- R/radial_ggplot.R | 25 +++----- R/radial_ggplot_old.R | 1 R/radial_plotly.R | 52 +++++++++------- R/radial_plotly_old.R | 1 R/show_grid.R | 2 R/significance_subset.R | 8 +- R/volcano3D.R | 25 +++++--- R/volcano3D_old.R | 2 R/voom_polar.R | 46 ++++++++++---- build/vignette.rds |binary inst/WORDLIST | 42 ++++++------- inst/doc/Vignette.R | 5 + inst/doc/Vignette.html | 52 ++++++++++++---- inst/doc/Vignette.rmd | 47 ++++++++++++--- inst/doc/Vignette_2x3.R |only inst/doc/Vignette_2x3.Rmd |only inst/doc/Vignette_2x3.html |only man/add_animation.Rd | 17 +++-- man/boxplot_trio.Rd | 28 ++++----- man/calc_pvals.Rd | 6 - man/calc_stats_2x3.Rd |only man/deseq_2x3.Rd |only man/deseq_2x3_polar.Rd |only man/deseq_polar.Rd | 36 +++++++---- man/forest_plot.Rd |only man/polar_coords.Rd | 63 ++++++++++++-------- man/polar_coords_2x3.Rd |only man/polar_grid.Rd | 18 ++--- man/radial_ggplot.Rd | 21 +++--- man/radial_plotly.Rd | 42 ++++++++----- man/significance_subset.Rd | 6 - man/syn_example_meta.Rd | 4 - man/syn_example_rld.Rd | 4 - man/volc3d-class.Rd |only man/volcano3D.Rd | 24 ++++--- man/voom_polar.Rd | 32 +++++++--- vignettes/Vignette.rmd | 47 ++++++++++++--- vignettes/Vignette_2x3.Rmd |only vignettes/forest.png |only vignettes/radial_2x3_neg.png |only vignettes/radial_2x3_pos.png |only vignettes/volc3d_2x3.png |only 56 files changed, 715 insertions(+), 371 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph]
,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 0.2.3 dated 2022-08-15 and 0.3.0 dated 2022-09-23
cffr-0.2.3/cffr/R/cff.R |only cffr-0.2.3/cffr/man/cff.Rd |only cffr-0.2.3/cffr/tests/testthat/_snaps/cff.md |only cffr-0.2.3/cffr/tests/testthat/test-cff.R |only cffr-0.3.0/cffr/DESCRIPTION | 6 cffr-0.3.0/cffr/MD5 | 87 cffr-0.3.0/cffr/NAMESPACE | 1 cffr-0.3.0/cffr/NEWS.md | 8 cffr-0.3.0/cffr/R/cff_create.R | 57 cffr-0.3.0/cffr/R/cff_gha_update.R | 146 - cffr-0.3.0/cffr/R/cff_parse_citation.R | 863 ++++---- cffr-0.3.0/cffr/R/cff_parse_person.R | 468 ++-- cffr-0.3.0/cffr/R/cff_read.R |only cffr-0.3.0/cffr/R/cff_to_bibtex.R | 19 cffr-0.3.0/cffr/R/parse_citation.R | 602 +++--- cffr-0.3.0/cffr/R/write_bib.R | 206 +- cffr-0.3.0/cffr/README.md | 12 cffr-0.3.0/cffr/inst/doc/bibtex_cff.html | 13 cffr-0.3.0/cffr/inst/doc/cffr.html | 288 +- cffr-0.3.0/cffr/inst/doc/crosswalk.R | 4 cffr-0.3.0/cffr/inst/doc/crosswalk.Rmd | 4 cffr-0.3.0/cffr/inst/doc/crosswalk.html | 339 +-- cffr-0.3.0/cffr/inst/doc/paper.html | 13 cffr-0.3.0/cffr/inst/examples/DESCRIPTION_two_emails |only cffr-0.3.0/cffr/man/cff_create.Rd | 4 cffr-0.3.0/cffr/man/cff_parse_citation.Rd | 2 cffr-0.3.0/cffr/man/cff_parse_person.Rd | 4 cffr-0.3.0/cffr/man/cff_read.Rd |only cffr-0.3.0/cffr/man/cff_to_bibtex.Rd | 5 cffr-0.3.0/cffr/man/cff_validate.Rd | 4 cffr-0.3.0/cffr/man/cff_write.Rd | 4 cffr-0.3.0/cffr/man/write_bib.Rd | 7 cffr-0.3.0/cffr/tests/testthat/_snaps/bibtex2cff.md | 14 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_create.md | 70 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_description.md | 304 --- cffr-0.3.0/cffr/tests/testthat/_snaps/cff_parse_citation.md | 71 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_read.md |only cffr-0.3.0/cffr/tests/testthat/_snaps/cff_to_bibtex.md | 8 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_write.md | 51 cffr-0.3.0/cffr/tests/testthat/_snaps/encoding.md | 51 cffr-0.3.0/cffr/tests/testthat/_snaps/merge_desc_cit.md | 64 cffr-0.3.0/cffr/tests/testthat/test-bibtex2cff.R | 1162 ++++++------ cffr-0.3.0/cffr/tests/testthat/test-cff_create.R | 168 - cffr-0.3.0/cffr/tests/testthat/test-cff_description.R | 1 cffr-0.3.0/cffr/tests/testthat/test-cff_parse_citation.R | 5 cffr-0.3.0/cffr/tests/testthat/test-cff_parse_person.R | 220 +- cffr-0.3.0/cffr/tests/testthat/test-cff_read.R |only cffr-0.3.0/cffr/tests/testthat/test-cff_to_bibtex.R | 11 cffr-0.3.0/cffr/vignettes/crosswalk.Rmd | 4 49 files changed, 2478 insertions(+), 2892 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph]
,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.2.0 dated 2022-06-21 and 0.2.1 dated 2022-09-23
tidyterra-0.2.0/tidyterra/inst/doc/tidyterra.R |only tidyterra-0.2.1/tidyterra/DESCRIPTION | 15 tidyterra-0.2.1/tidyterra/MD5 | 58 tidyterra-0.2.1/tidyterra/NEWS.md | 118 + tidyterra-0.2.1/tidyterra/R/geom_spat_contour.R | 199 +-- tidyterra-0.2.1/tidyterra/R/geom_spat_contour_fill.R | 158 -- tidyterra-0.2.1/tidyterra/R/geom_spatraster.R | 20 tidyterra-0.2.1/tidyterra/R/geom_spatraster_rgb.R | 600 +++++----- tidyterra-0.2.1/tidyterra/R/sysdata.rda |binary tidyterra-0.2.1/tidyterra/README.md | 2 tidyterra-0.2.1/tidyterra/build/partial.rdb |binary tidyterra-0.2.1/tidyterra/build/vignette.rds |binary tidyterra-0.2.1/tidyterra/data/cross_blended_hypsometric_tints_db.rda |binary tidyterra-0.2.1/tidyterra/data/hypsometric_tints_db.rda |binary tidyterra-0.2.1/tidyterra/data/volcano2.rda |binary tidyterra-0.2.1/tidyterra/inst/WORDLIST | 1 tidyterra-0.2.1/tidyterra/inst/doc/tidyterra.Rmd | 145 ++ tidyterra-0.2.1/tidyterra/inst/doc/tidyterra.html | 70 - tidyterra-0.2.1/tidyterra/man/as_tibble.Rd | 2 tidyterra-0.2.1/tidyterra/man/tidyterra-package.Rd | 1 tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spat_contour.R | 68 - tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spat_contour_fill.R | 68 - tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spatraster_1lyr.R | 48 tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spatraster_rgb.R | 64 - tidyterra-0.2.1/tidyterra/vignettes/full_spatvector-1.png |only tidyterra-0.2.1/tidyterra/vignettes/hypso-1.png |only tidyterra-0.2.1/tidyterra/vignettes/rgb-1.png |only tidyterra-0.2.1/tidyterra/vignettes/rgb-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terra_sf-1.png |only tidyterra-0.2.1/tidyterra/vignettes/terra_sf-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-1.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-3.png |only tidyterra-0.2.1/tidyterra/vignettes/tidyterra.Rmd | 145 ++ tidyterra-0.2.1/tidyterra/vignettes/unnamed-chunk-3-1.png |only tidyterra-0.2.1/tidyterra/vignettes/unnamed-chunk-8-1.png |only 36 files changed, 1052 insertions(+), 730 deletions(-)
Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode',
'Rscript' (Shells Including Windows Command-Line / / Unix
Terminal), and 'source'
Description: Determine the full path of the executing script. Works when
running a line or selection from a script in 'RStudio', 'Rgui', and
'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio',
and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>
Diff between this.path versions 1.0.0 dated 2022-09-21 and 1.0.1 dated 2022-09-23
DESCRIPTION | 6 - MD5 | 8 - build/partial.rdb |binary src/basename2.c | 308 +++++++++++++++++++++++++++++++++++++++++++++++++----- src/pathjoin.c | 4 5 files changed, 292 insertions(+), 34 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant
versions of 'install.packages' and `require` for CRAN packages, packages
no longer on CRAN (i.e., archived), specific versions of packages,
and GitHub packages. This approach is developed to create reproducible
workflows that are flexible and fast enough to use while in development stages,
while able to build snapshots once a stable package collection is found.
As with other functions in a reproducible workflow, this package
emphasizes functions that return the same result whether it is
the first or subsequent times running the function, with subsequent times being
sufficiently fast that they can be run every time without undue waiting burden on
the user or developer.
Author: Eliot J B McIntire [aut, cre] ,
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.0.13 dated 2021-05-31 and 0.1.2 dated 2022-09-23
Require-0.0.13/Require/R/pkgDepAlt.R |only Require-0.0.13/Require/man/messageDF.Rd |only Require-0.0.13/Require/tests/testit/test-extract.R |only Require-0.0.13/Require/tests/testit/test-helpers.R |only Require-0.0.13/Require/tests/testit/test-other.R |only Require-0.0.13/Require/tests/testit/test-packagesLong.R |only Require-0.0.13/Require/tests/testit/test-pkgDep.R |only Require-0.1.2/Require/DESCRIPTION | 33 Require-0.1.2/Require/MD5 | 107 Require-0.1.2/Require/NAMESPACE | 139 Require-0.1.2/Require/NEWS.md | 299 - Require-0.1.2/Require/R/CRAN.R | 102 Require-0.1.2/Require/R/Require-helpers.R | 3953 +++++++++------- Require-0.1.2/Require/R/Require-package.R | 6 Require-0.1.2/Require/R/Require.R | 1106 ++-- Require-0.1.2/Require/R/RequireOptions.R | 199 Require-0.1.2/Require/R/extract.R | 210 Require-0.1.2/Require/R/helpers.R | 618 +- Require-0.1.2/Require/R/pkgDep.R | 1771 +++---- Require-0.1.2/Require/R/pkgSnapshot.R | 222 Require-0.1.2/Require/R/setLibPaths.R | 396 - Require-0.1.2/Require/R/setup.R | 438 + Require-0.1.2/Require/R/zzz.R | 83 Require-0.1.2/Require/README.md | 419 - Require-0.1.2/Require/inst/WORDLIST | 50 Require-0.1.2/Require/inst/cache-README |only Require-0.1.2/Require/inst/dotR |only Require-0.1.2/Require/inst/dotccache |only Require-0.1.2/Require/inst/examples/example_checkPath.R | 45 Require-0.1.2/Require/man/DESCRIPTION-helpers.Rd | 89 Require-0.1.2/Require/man/GitHubTools.Rd | 100 Require-0.1.2/Require/man/Require-internals.Rd | 197 Require-0.1.2/Require/man/Require.Rd | 579 +- Require-0.1.2/Require/man/RequireCacheDir.Rd |only Require-0.1.2/Require/man/RequireOptions.Rd | 163 Require-0.1.2/Require/man/checkPath.Rd | 131 Require-0.1.2/Require/man/chooseCRANmirror2.Rd | 30 Require-0.1.2/Require/man/detachAll.Rd | 75 Require-0.1.2/Require/man/extractPkgName.Rd | 70 Require-0.1.2/Require/man/getOptionRPackageCache.Rd |only Require-0.1.2/Require/man/installGithubPackage.Rd |only Require-0.1.2/Require/man/invertList.Rd | 44 Require-0.1.2/Require/man/linkOrCopy.Rd |only Require-0.1.2/Require/man/messageVerbose.Rd |only Require-0.1.2/Require/man/modifyList2.Rd | 54 Require-0.1.2/Require/man/normPath.Rd | 118 Require-0.1.2/Require/man/paddedFloatToChar.Rd |only Require-0.1.2/Require/man/pkgDep.Rd | 411 - Require-0.1.2/Require/man/pkgDepIfDepRemoved.Rd | 69 Require-0.1.2/Require/man/pkgSnapshot.Rd | 216 Require-0.1.2/Require/man/rCurrentVersion.Rd |only Require-0.1.2/Require/man/rversions.Rd |only Require-0.1.2/Require/man/setLibPaths.Rd | 161 Require-0.1.2/Require/man/setLinuxBinaryRepo.Rd |only Require-0.1.2/Require/man/setup.Rd | 117 Require-0.1.2/Require/man/tempdir2.Rd | 46 Require-0.1.2/Require/man/tempfile2.Rd | 56 Require-0.1.2/Require/man/trimVersionNumber.Rd | 40 Require-0.1.2/Require/man/useLinuxSourceCache.Rd |only Require-0.1.2/Require/tests/test-all.R | 7 Require-0.1.2/Require/tests/testit/test-0pkgSnapshot.R | 240 Require-0.1.2/Require/tests/testit/test-1packages.R | 400 - Require-0.1.2/Require/tests/testit/test-2extract.R |only Require-0.1.2/Require/tests/testit/test-3helpers.R |only Require-0.1.2/Require/tests/testit/test-4other.R |only Require-0.1.2/Require/tests/testit/test-5packagesLong.R |only Require-0.1.2/Require/tests/testit/test-6pkgDep.R |only 67 files changed, 7579 insertions(+), 6030 deletions(-)
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes,
Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection,
Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric [...truncated...]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.36.1.2 dated 2022-05-27 and 3.38.0.1 dated 2022-09-23
h2o-3.36.1.2/h2o/man/with_no_h2o_progress.Rd |only h2o-3.38.0.1/h2o/DESCRIPTION | 27 h2o-3.38.0.1/h2o/MD5 | 103 +-- h2o-3.38.0.1/h2o/NAMESPACE | 9 h2o-3.38.0.1/h2o/R/communication.R | 41 + h2o-3.38.0.1/h2o/R/deeplearning.R | 2 h2o-3.38.0.1/h2o/R/explain.R | 376 +++++++++--- h2o-3.38.0.1/h2o/R/export.R | 10 h2o-3.38.0.1/h2o/R/extendedisolationforest.R | 2 h2o-3.38.0.1/h2o/R/frame.R | 12 h2o-3.38.0.1/h2o/R/gbm.R | 29 h2o-3.38.0.1/h2o/R/glm.R | 86 ++ h2o-3.38.0.1/h2o/R/import.R | 2 h2o-3.38.0.1/h2o/R/infogram.R | 1 h2o-3.38.0.1/h2o/R/isolationforest.R | 2 h2o-3.38.0.1/h2o/R/isotonicregression.R |only h2o-3.38.0.1/h2o/R/models.R | 131 +++- h2o-3.38.0.1/h2o/R/modelselection.R | 54 + h2o-3.38.0.1/h2o/R/naivebayes.R | 2 h2o-3.38.0.1/h2o/R/randomforest.R | 15 h2o-3.38.0.1/h2o/R/rulefit.R | 38 + h2o-3.38.0.1/h2o/R/segment.R | 2 h2o-3.38.0.1/h2o/R/stackedensemble.R | 2 h2o-3.38.0.1/h2o/R/upliftrandomforest.R | 2 h2o-3.38.0.1/h2o/R/xgboost.R | 13 h2o-3.38.0.1/h2o/inst/branch.txt | 2 h2o-3.38.0.1/h2o/inst/buildnum.txt | 2 h2o-3.38.0.1/h2o/man/case_insensitive_match_arg.Rd |only h2o-3.38.0.1/h2o/man/dot-has_model_coefficients.Rd |only h2o-3.38.0.1/h2o/man/dot-process_models_or_automl.Rd | 5 h2o-3.38.0.1/h2o/man/h2o-package.Rd | 6 h2o-3.38.0.1/h2o/man/h2o.anomaly.Rd | 2 h2o-3.38.0.1/h2o/man/h2o.as_date.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.confusionMatrix.Rd | 4 h2o-3.38.0.1/h2o/man/h2o.day.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.dayOfWeek.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.exportFile.Rd | 7 h2o-3.38.0.1/h2o/man/h2o.gbm.Rd | 17 h2o-3.38.0.1/h2o/man/h2o.get_predictors_added_per_step.Rd |only h2o-3.38.0.1/h2o/man/h2o.get_predictors_removed_per_step.Rd |only h2o-3.38.0.1/h2o/man/h2o.get_variable_inflation_factors.Rd |only h2o-3.38.0.1/h2o/man/h2o.glm.Rd | 46 + h2o-3.38.0.1/h2o/man/h2o.hour.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.isotonicregression.Rd |only h2o-3.38.0.1/h2o/man/h2o.make_leaderboard.Rd |only h2o-3.38.0.1/h2o/man/h2o.modelSelection.Rd | 20 h2o-3.38.0.1/h2o/man/h2o.month.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.no_progress.Rd | 11 h2o-3.38.0.1/h2o/man/h2o.pareto_front.Rd |only h2o-3.38.0.1/h2o/man/h2o.r2.Rd | 2 h2o-3.38.0.1/h2o/man/h2o.randomForest.Rd | 9 h2o-3.38.0.1/h2o/man/h2o.rule_importance.Rd |only h2o-3.38.0.1/h2o/man/h2o.rulefit.Rd | 6 h2o-3.38.0.1/h2o/man/h2o.show_progress.Rd | 11 h2o-3.38.0.1/h2o/man/h2o.upload_model.Rd | 12 h2o-3.38.0.1/h2o/man/h2o.xgboost.Rd | 9 h2o-3.38.0.1/h2o/man/is.factor.Rd | 11 h2o-3.38.0.1/h2o/man/plot-methods.Rd |only h2o-3.38.0.1/h2o/man/show-H2OParetoFront-method.Rd |only 59 files changed, 973 insertions(+), 220 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for
fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] ,
PostgreSQL Global Development Group [cph] ,
Oracle Inc. [cph] ,
Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 5.0.4 dated 2022-06-28 and 5.1.0 dated 2022-09-23
DatabaseConnector-5.0.4/DatabaseConnector/build/DatabaseConnector.pdf |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbAppendTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbClearResult-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbColumnInfo-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbCreateTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbDisconnect-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbExecute-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbFetch-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetRowCount-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetRowsAffected-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetStatement-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbHasCompleted-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbListFields-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbListTables-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbQuoteIdentifier-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbQuoteString-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbReadTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbRemoveTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbWriteTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/show-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.1.0/DatabaseConnector/DESCRIPTION | 14 DatabaseConnector-5.1.0/DatabaseConnector/MD5 | 95 +--- DatabaseConnector-5.1.0/DatabaseConnector/NAMESPACE | 1 DatabaseConnector-5.1.0/DatabaseConnector/NEWS.md | 23 + DatabaseConnector-5.1.0/DatabaseConnector/R/Andromeda.R | 77 ++- DatabaseConnector-5.1.0/DatabaseConnector/R/BulkLoad.R | 8 DatabaseConnector-5.1.0/DatabaseConnector/R/Connect.R | 100 +++- DatabaseConnector-5.1.0/DatabaseConnector/R/CtasHack.R | 17 DatabaseConnector-5.1.0/DatabaseConnector/R/DBI.R | 207 ++++------ DatabaseConnector-5.1.0/DatabaseConnector/R/DatabaseConnector.R | 2 DatabaseConnector-5.1.0/DatabaseConnector/R/Drivers.R | 27 - DatabaseConnector-5.1.0/DatabaseConnector/R/InsertTable.R | 62 +- DatabaseConnector-5.1.0/DatabaseConnector/R/ListTables.R | 8 DatabaseConnector-5.1.0/DatabaseConnector/R/RStudio.R | 20 DatabaseConnector-5.1.0/DatabaseConnector/R/Sql.R | 26 - DatabaseConnector-5.1.0/DatabaseConnector/build/vignette.rds |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/COPYRIGHTS | 9 DatabaseConnector-5.1.0/DatabaseConnector/inst/doc/Connecting.pdf |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/doc/Querying.pdf |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/java/DatabaseConnector.jar |binary DatabaseConnector-5.1.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedInsert.java | 18 DatabaseConnector-5.1.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedQuery.java | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnector-package.Rd | 2 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorConnection-class.Rd | 107 +++++ DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorDbiConnection-class.Rd | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorJdbcConnection-class.Rd | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorResult-class.Rd | 22 + DatabaseConnector-5.1.0/DatabaseConnector/man/connect.Rd | 12 DatabaseConnector-5.1.0/DatabaseConnector/man/createConnectionDetails.Rd | 12 DatabaseConnector-5.1.0/DatabaseConnector/man/dbms.Rd |only DatabaseConnector-5.1.0/DatabaseConnector/man/downloadJdbcDrivers.Rd | 6 DatabaseConnector-5.1.0/DatabaseConnector/man/jdbcDrivers.Rd | 2 DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/setup.R | 1 DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-connection.R | 108 ++++- DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-fetchResults.R | 161 ++++--- DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-sqlite.R |only 63 files changed, 754 insertions(+), 414 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also
contains a number of lower level 'CLI' elements: rules, boxes, trees,
and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI
colors and text styles as well.
Author: Gabor Csardi [aut, cre],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cli versions 3.4.0 dated 2022-09-08 and 3.4.1 dated 2022-09-23
cli-3.4.0/cli/R/rstudio-detect.R |only cli-3.4.1/cli/DESCRIPTION | 6 - cli-3.4.1/cli/MD5 | 99 ++++++++++-------- cli-3.4.1/cli/NEWS.md | 7 + cli-3.4.1/cli/R/aaa-utils.R | 10 + cli-3.4.1/cli/R/aab-rstudio-detect.R |only cli-3.4.1/cli/R/ansi-hyperlink.R | 2 cli-3.4.1/cli/R/ansi-palette.R | 4 cli-3.4.1/cli/R/ansi.R | 25 +++- cli-3.4.1/cli/R/ansiex.R | 36 ++++-- cli-3.4.1/cli/R/app.R | 7 + cli-3.4.1/cli/R/cli-errors.R |only cli-3.4.1/cli/R/cli.R | 99 ++++++++++++------ cli-3.4.1/cli/R/cliapp-docs.R | 2 cli-3.4.1/cli/R/cliapp.R | 4 cli-3.4.1/cli/R/defer.R | 6 - cli-3.4.1/cli/R/diff.R | 14 +- cli-3.4.1/cli/R/errors.R |only cli-3.4.1/cli/R/format-conditions.R | 10 + cli-3.4.1/cli/R/inline.R | 71 ++++++++---- cli-3.4.1/cli/R/onload.R | 2 cli-3.4.1/cli/R/rlang.R | 8 - cli-3.4.1/cli/R/themes.R | 3 cli-3.4.1/cli/R/tty.R | 9 + cli-3.4.1/cli/R/utf8.R | 28 +++-- cli-3.4.1/cli/R/width.R | 42 +++++-- cli-3.4.1/cli/man/format_inline.Rd | 5 cli-3.4.1/cli/man/links.Rd | 2 cli-3.4.1/cli/src/cli.h | 2 cli-3.4.1/cli/tests/testthat/_snaps/ansi-hyperlink.md |only cli-3.4.1/cli/tests/testthat/_snaps/ansi-make.md |only cli-3.4.1/cli/tests/testthat/_snaps/ansiex.md | 46 ++++++++ cli-3.4.1/cli/tests/testthat/_snaps/app.md |only cli-3.4.1/cli/tests/testthat/_snaps/console-width.md |only cli-3.4.1/cli/tests/testthat/_snaps/defer.md |only cli-3.4.1/cli/tests/testthat/_snaps/diff.md | 10 + cli-3.4.1/cli/tests/testthat/_snaps/inline-2.md | 24 ++++ cli-3.4.1/cli/tests/testthat/_snaps/lists.md | 9 + cli-3.4.1/cli/tests/testthat/_snaps/new-r |only cli-3.4.1/cli/tests/testthat/_snaps/old-r |only cli-3.4.1/cli/tests/testthat/_snaps/progress-along.md | 4 cli-3.4.1/cli/tests/testthat/_snaps/rlang-errors.md | 80 -------------- cli-3.4.1/cli/tests/testthat/_snaps/utf8.md |only cli-3.4.1/cli/tests/testthat/helper.R | 8 + cli-3.4.1/cli/tests/testthat/test-ansi-hyperlink.R | 7 + cli-3.4.1/cli/tests/testthat/test-ansi-make.R | 7 + cli-3.4.1/cli/tests/testthat/test-ansiex.R | 30 +++-- cli-3.4.1/cli/tests/testthat/test-app.R |only cli-3.4.1/cli/tests/testthat/test-console-width.R |only cli-3.4.1/cli/tests/testthat/test-defer.R |only cli-3.4.1/cli/tests/testthat/test-diff.R | 15 +- cli-3.4.1/cli/tests/testthat/test-format-conditions.R | 10 + cli-3.4.1/cli/tests/testthat/test-inline-2.R | 20 +++ cli-3.4.1/cli/tests/testthat/test-lists.R | 3 cli-3.4.1/cli/tests/testthat/test-progress-along.R | 5 cli-3.4.1/cli/tests/testthat/test-rlang-errors.R | 29 ----- cli-3.4.1/cli/tests/testthat/test-utf8.R | 6 + cli-3.4.1/cli/tests/testthat/test-utils.R | 2 58 files changed, 517 insertions(+), 301 deletions(-)
Title: Variational Inference for Hierarchical Generalized Linear Models
Description: Estimates hierarchical models using mean-field variational Bayes.
At present, it can estimate logistic, linear, and negative binomial models.
It can accommodate models with an arbitrary number of random effects and
requires no integration to estimate. It also provides the ability to improve
the quality of the approximation using marginal augmentation.
Goplerud (2022) <doi:10.1214/21-BA1266> provides details on the variational
algorithms.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@pitt.edu>
Diff between vglmer versions 1.0.1 dated 2022-09-17 and 1.0.2 dated 2022-09-23
DESCRIPTION | 6 - MD5 | 24 ++-- NAMESPACE | 1 NEWS.md | 5 R/aux_functions.R | 19 ++- R/predict_functions.R | 9 + R/print_functions.R | 13 ++ R/spline_functions.R | 29 +++-- R/vglmer_regression.R | 67 +++++++---- man/v_s.Rd | 14 ++ man/vglmer-class.Rd | 6 + tests/testthat/test-predict.R | 20 +-- tests/testthat/test-splines.R | 240 ++++++++++++++++++++++++++++++++++++++---- 13 files changed, 370 insertions(+), 83 deletions(-)
Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut]
,
Juan Carlos Oliveros [aut, ctb]
,
Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>
Diff between Rgff versions 0.1.4 dated 2022-09-19 and 0.1.5 dated 2022-09-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/Rgff.R | 4 +++- inst/doc/Using_Rgff.html | 10 +++++----- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test
and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between fbst versions 1.7 dated 2022-03-08 and 1.9 dated 2022-09-23
DESCRIPTION | 11 MD5 | 40 +- NAMESPACE | 5 R/fbst.R | 359 ++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/fbet.R | 11 inst/doc/fbet.Rmd | 19 inst/doc/fbet.html | 873 +++++++++++++++++++++------------------------ inst/doc/fbst.R | 12 inst/doc/fbst.Rmd | 15 inst/doc/fbst.html | 729 ++++++++++++++++--------------------- inst/doc/twodimfbst.R |only inst/doc/twodimfbst.Rmd |only inst/doc/twodimfbst.html |only man/bdm.Rd |only man/fbst.Rd | 26 - man/plot.fbet.Rd | 12 man/plot.fbst.Rd | 8 vignettes/fbet.Rmd | 19 vignettes/fbst.Rmd | 15 vignettes/normalModel.stan |only vignettes/twodimfbst.Rmd |only vignettes/twodimfbst_files |only 24 files changed, 1092 insertions(+), 1062 deletions(-)
Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of loss-based estimator selection to
identify the optimal estimator of the covariance matrix from among a
prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
,
Nima Hejazi [aut] ,
Brian Collica [aut] ,
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] ,
Sandrine Dudoit [ctb, ths]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 1.1.0 dated 2022-05-04 and 1.1.1 dated 2022-09-23
DESCRIPTION | 6 MD5 | 10 NEWS.md | 5 R/summary_functions.R | 6 build/partial.rdb |binary inst/doc/using_cvCovEst.html | 731 +++++++++++++++++++++++++++++++++---------- 6 files changed, 585 insertions(+), 173 deletions(-)
Title: Network-Based Communities and Kernel Machine Methods
Description: Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).
Author: Alexandria Jensen [aut, cre] ,
Peter DeWitt [ctb] ,
Debashis Ghosh [ths]
Maintainer: Alexandria Jensen <alexandria.jensen@cuanschutz.edu>
Diff between CommKern versions 1.0.0 dated 2022-09-20 and 1.0.1 dated 2022-09-23
CommKern-1.0.0/CommKern/data/simasd_covars.RData |only CommKern-1.0.1/CommKern/DESCRIPTION | 6 ++--- CommKern-1.0.1/CommKern/MD5 | 25 ++++++++++------------ CommKern-1.0.1/CommKern/NEWS.md | 7 ++++++ CommKern-1.0.1/CommKern/R/community_plot.R | 4 +-- CommKern-1.0.1/CommKern/R/hier_mult_spin.R | 15 +++++++------ CommKern-1.0.1/CommKern/README.md | 5 ++++ CommKern-1.0.1/CommKern/inst/doc/CommKern.R | 2 - CommKern-1.0.1/CommKern/inst/doc/CommKern.Rmd | 4 +-- CommKern-1.0.1/CommKern/inst/doc/CommKern.html | 16 ++++++-------- CommKern-1.0.1/CommKern/man/community_plot.Rd | 4 +-- CommKern-1.0.1/CommKern/man/hms.Rd | 11 +++++---- CommKern-1.0.1/CommKern/tests/test-matrix_to_df.R | 8 ++++++- CommKern-1.0.1/CommKern/vignettes/CommKern.Rmd | 4 +-- 14 files changed, 64 insertions(+), 47 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 3.0.2 dated 2022-09-02 and 3.0.3 dated 2022-09-23
autostsm-3.0.2/autostsm/R/RcppExports.R |only autostsm-3.0.2/autostsm/man/Rginv.Rd |only autostsm-3.0.2/autostsm/man/gen_inv.Rd |only autostsm-3.0.2/autostsm/man/kalman_filter.Rd |only autostsm-3.0.2/autostsm/src |only autostsm-3.0.3/autostsm/DESCRIPTION | 15 - autostsm-3.0.3/autostsm/MD5 | 34 +--- autostsm-3.0.3/autostsm/NAMESPACE | 3 autostsm-3.0.3/autostsm/NEWS.md | 7 autostsm-3.0.3/autostsm/R/stsm_detect_anomalies.R | 6 autostsm-3.0.3/autostsm/R/stsm_detect_breaks.R | 6 autostsm-3.0.3/autostsm/R/stsm_estimate.R | 14 - autostsm-3.0.3/autostsm/R/stsm_forecast.R | 11 - autostsm-3.0.3/autostsm/inst/doc/autostsm_vignette.Rmd | 17 -- autostsm-3.0.3/autostsm/inst/doc/autostsm_vignette.html | 57 ++++-- autostsm-3.0.3/autostsm/man/DGS5.Rd | 38 ++-- autostsm-3.0.3/autostsm/man/stsm_detect_anomalies.Rd | 108 ++++++------- autostsm-3.0.3/autostsm/man/stsm_detect_breaks.Rd | 132 ++++++++-------- autostsm-3.0.3/autostsm/vignettes/autostsm_vignette.Rmd | 17 -- 19 files changed, 226 insertions(+), 239 deletions(-)
Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.3.0 dated 2020-07-10 and 2.4.0 dated 2022-09-23
strvalidator-2.3.0/strvalidator/R/tableBalance.r |only strvalidator-2.3.0/strvalidator/R/tableBalance_gui.r |only strvalidator-2.3.0/strvalidator/R/tableCapillary.r |only strvalidator-2.3.0/strvalidator/R/tableCapillary_gui.r |only strvalidator-2.3.0/strvalidator/R/tablePrecision.r |only strvalidator-2.3.0/strvalidator/R/tablePrecision_gui.r |only strvalidator-2.3.0/strvalidator/R/tableStutter.r |only strvalidator-2.3.0/strvalidator/R/tableStutter_gui.r |only strvalidator-2.3.0/strvalidator/man/tableBalance.Rd |only strvalidator-2.3.0/strvalidator/man/tableBalance_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tableCapillary.Rd |only strvalidator-2.3.0/strvalidator/man/tableCapillary_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tablePrecision.Rd |only strvalidator-2.3.0/strvalidator/man/tablePrecision_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tableStutter.Rd |only strvalidator-2.3.0/strvalidator/man/tableStutter_gui.Rd |only strvalidator-2.4.0/strvalidator/DESCRIPTION | 17 strvalidator-2.4.0/strvalidator/MD5 | 213 ++--- strvalidator-2.4.0/strvalidator/NAMESPACE | 30 strvalidator-2.4.0/strvalidator/NEWS | 50 + strvalidator-2.4.0/strvalidator/R/addData.r | 2 strvalidator-2.4.0/strvalidator/R/addData_gui.r | 89 +- strvalidator-2.4.0/strvalidator/R/addDye_gui.r | 58 - strvalidator-2.4.0/strvalidator/R/addMarker_gui.r | 62 - strvalidator-2.4.0/strvalidator/R/addSize_gui.r | 66 - strvalidator-2.4.0/strvalidator/R/calculateAT.r | 7 strvalidator-2.4.0/strvalidator/R/calculateAT6.r | 3 strvalidator-2.4.0/strvalidator/R/calculateAT6_gui.r | 164 ++-- strvalidator-2.4.0/strvalidator/R/calculateAT_gui.r | 135 +-- strvalidator-2.4.0/strvalidator/R/calculateAllT_gui.r | 60 - strvalidator-2.4.0/strvalidator/R/calculateAllele_gui.r | 138 +-- strvalidator-2.4.0/strvalidator/R/calculateCapillary_gui.r | 110 +- strvalidator-2.4.0/strvalidator/R/calculateConcordance_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/calculateCopies_gui.r | 51 - strvalidator-2.4.0/strvalidator/R/calculateDropout.r | 5 strvalidator-2.4.0/strvalidator/R/calculateDropout_gui.r | 115 +-- strvalidator-2.4.0/strvalidator/R/calculateHb_gui.r | 74 - strvalidator-2.4.0/strvalidator/R/calculateHeight.r | 49 - strvalidator-2.4.0/strvalidator/R/calculateHeight_gui.r | 111 +- strvalidator-2.4.0/strvalidator/R/calculateLb.r | 3 strvalidator-2.4.0/strvalidator/R/calculateLb_gui.r | 124 +-- strvalidator-2.4.0/strvalidator/R/calculateMixture.r | 3 strvalidator-2.4.0/strvalidator/R/calculateMixture_gui.r | 135 +-- strvalidator-2.4.0/strvalidator/R/calculateOL_gui.r | 29 strvalidator-2.4.0/strvalidator/R/calculateOverlap_gui.r | 33 strvalidator-2.4.0/strvalidator/R/calculatePeaks_gui.r | 58 - strvalidator-2.4.0/strvalidator/R/calculatePullup_gui.r | 91 +- strvalidator-2.4.0/strvalidator/R/calculateRatio_gui.r | 97 +- strvalidator-2.4.0/strvalidator/R/calculateResultType_gui.r | 77 -- strvalidator-2.4.0/strvalidator/R/calculateSlope.r | 4 strvalidator-2.4.0/strvalidator/R/calculateSlope_gui.r | 100 +- strvalidator-2.4.0/strvalidator/R/calculateSpike_gui.R | 72 - strvalidator-2.4.0/strvalidator/R/calculateStatistics.r | 20 strvalidator-2.4.0/strvalidator/R/calculateStatistics_gui.r | 129 ++- strvalidator-2.4.0/strvalidator/R/calculateStutter.r | 2 strvalidator-2.4.0/strvalidator/R/calculateStutter_gui.r | 125 +-- strvalidator-2.4.0/strvalidator/R/checkSubset_gui.r | 78 +- strvalidator-2.4.0/strvalidator/R/columns.r | 7 strvalidator-2.4.0/strvalidator/R/columns_gui.r | 109 +- strvalidator-2.4.0/strvalidator/R/combine_gui.r | 86 +- strvalidator-2.4.0/strvalidator/R/cropData_gui.r | 68 - strvalidator-2.4.0/strvalidator/R/editData_gui.r | 81 +- strvalidator-2.4.0/strvalidator/R/export.r | 2 strvalidator-2.4.0/strvalidator/R/export_gui.r | 32 strvalidator-2.4.0/strvalidator/R/filterProfile.r | 4 strvalidator-2.4.0/strvalidator/R/filterProfile_gui.r | 158 ++-- strvalidator-2.4.0/strvalidator/R/generateEPG_gui.r | 94 +- strvalidator-2.4.0/strvalidator/R/getStrings.r | 7 strvalidator-2.4.0/strvalidator/R/ggsave_gui.r | 277 ++----- strvalidator-2.4.0/strvalidator/R/guessProfile_gui.r | 60 - strvalidator-2.4.0/strvalidator/R/import_gui.r | 28 strvalidator-2.4.0/strvalidator/R/makeKit_gui.r | 45 - strvalidator-2.4.0/strvalidator/R/modelDropout_gui.r | 93 +- strvalidator-2.4.0/strvalidator/R/plotAT_gui.r | 46 - strvalidator-2.4.0/strvalidator/R/plotBalance_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/plotCapillary_gui.r | 50 - strvalidator-2.4.0/strvalidator/R/plotContamination_gui.r | 51 - strvalidator-2.4.0/strvalidator/R/plotDistribution_gui.r | 146 +-- strvalidator-2.4.0/strvalidator/R/plotDropout_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/plotEPG2.R |only strvalidator-2.4.0/strvalidator/R/plotEPG2_gui.r |only strvalidator-2.4.0/strvalidator/R/plotGroups_gui.r | 133 +-- strvalidator-2.4.0/strvalidator/R/plotKit_gui.r | 31 strvalidator-2.4.0/strvalidator/R/plotPeaks_gui.r | 47 - strvalidator-2.4.0/strvalidator/R/plotPrecision_gui.r | 56 - strvalidator-2.4.0/strvalidator/R/plotPullup_gui.r | 72 - strvalidator-2.4.0/strvalidator/R/plotRatio_gui.r | 48 - strvalidator-2.4.0/strvalidator/R/plotResultType_gui.r | 48 - strvalidator-2.4.0/strvalidator/R/plotSlope_gui.r | 85 -- strvalidator-2.4.0/strvalidator/R/plotStutter_gui.r | 73 - strvalidator-2.4.0/strvalidator/R/readBinsFile.r | 2 strvalidator-2.4.0/strvalidator/R/readPanelsFile.r | 2 strvalidator-2.4.0/strvalidator/R/removeArtefact_gui.r | 107 +- strvalidator-2.4.0/strvalidator/R/removeSpike_gui.r | 102 +- strvalidator-2.4.0/strvalidator/R/sample_tableToList.R |only strvalidator-2.4.0/strvalidator/R/slim_gui.r | 84 -- strvalidator-2.4.0/strvalidator/R/strvalidator.r | 195 +++-- strvalidator-2.4.0/strvalidator/R/trim_gui.r | 62 - strvalidator-2.4.0/strvalidator/build |only strvalidator-2.4.0/strvalidator/inst/extdata/kit.txt | 378 ++++++++++ strvalidator-2.4.0/strvalidator/inst/extdata/languages/en_GB.txt | 329 +++----- strvalidator-2.4.0/strvalidator/inst/extdata/languages/es_ES.txt | 327 +++----- strvalidator-2.4.0/strvalidator/inst/extdata/languages/it_IT.txt | 327 +++----- strvalidator-2.4.0/strvalidator/man/calculateAT.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateAT6.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateDropout.Rd | 4 strvalidator-2.4.0/strvalidator/man/calculateHeight.Rd | 35 strvalidator-2.4.0/strvalidator/man/calculateHeight_gui.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateLb.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateMixture.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateStatistics.Rd | 3 strvalidator-2.4.0/strvalidator/man/calculateStatistics_gui.Rd | 3 strvalidator-2.4.0/strvalidator/man/modelDropout_gui.Rd | 22 strvalidator-2.4.0/strvalidator/man/plotContamination_gui.Rd | 2 strvalidator-2.4.0/strvalidator/man/plotDropout_gui.Rd | 8 strvalidator-2.4.0/strvalidator/man/plotEPG2.Rd |only strvalidator-2.4.0/strvalidator/man/plotEPG2_gui.Rd |only strvalidator-2.4.0/strvalidator/man/sample_tableToList.Rd |only strvalidator-2.4.0/strvalidator/tests/testthat/test-calculateHeight.r | 159 +++- 119 files changed, 3626 insertions(+), 3550 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 1.2.0 dated 2022-09-10 and 1.2.1 dated 2022-09-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/hBayesDM.R | 2 ++ R/plot.hBayesDM.R | 2 ++ man/hBayesDM-package.Rd | 1 + man/plot.hBayesDM.Rd | 1 + 7 files changed, 20 insertions(+), 10 deletions(-)
Title: Integration for the UM-Bridge Protocol
Description: A convenient wrapper for the UM-Bridge protocol. UM-Bridge is a protocol designed for coupling uncertainty quantification (or statistical / optimization) software to numerical models. A model is represented as a mathematical function with optional support for derivatives via Jacobian actions etc.
Author: Linus Seelinger [aut, cre]
Maintainer: Linus Seelinger <mail@linusseelinger.de>
Diff between umbridge versions 0.9 dated 2022-09-12 and 1.0 dated 2022-09-23
DESCRIPTION | 6 +- MD5 | 29 ++++++----- NAMESPACE | 1 R/umbridge.R | 100 +++++++++++++++++++++++++++++++---------- man/apply_hessian.Rd | 3 + man/apply_jacobian.Rd | 3 + man/evaluate.Rd | 4 + man/get_models.Rd |only man/gradient.Rd | 3 + man/model_input_sizes.Rd | 6 ++ man/model_output_sizes.Rd | 6 ++ man/supports_apply_hessian.Rd | 4 + man/supports_apply_jacobian.Rd | 4 + man/supports_evaluate.Rd | 4 + man/supports_gradient.Rd | 4 + tests/testthat/test-umbridge.R | 31 ++++++------ 16 files changed, 147 insertions(+), 61 deletions(-)
Title: 'anndata' for R
Description: A 'reticulate' wrapper for the Python package 'anndata'.
Provides a scalable way of keeping track of data and learned
annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [ccp] ,
Alex Wolf [ccp] ,
Isaac Virshup [ccp] ,
Sergei Rybakov [ccp] ,
Robrecht Cannoodt [aut, cre, cph]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between anndata versions 0.7.5.4 dated 2022-08-23 and 0.7.5.5 dated 2022-09-23
DESCRIPTION | 6 +-- MD5 | 23 +++++++------- NAMESPACE | 2 + NEWS.md | 4 ++ R/class_anndata.R | 56 +++++++++++++++++++++++++++++++----- R/package.R | 2 - README.md | 20 ------------ inst/doc/getting_started.html | 21 +++++++++---- inst/doc/scanpy_demo.html | 13 ++++++-- man/AnnDataHelpers.Rd | 6 +++ tests/testthat/test-anndata.R | 4 +- tests/testthat/test-backed_sparse.R |only tests/testthat/test-base.R | 2 - 13 files changed, 105 insertions(+), 54 deletions(-)
Title: Partition/Decomposition of Breeding Values by Paths of
Information
Description: A software that implements a method for partitioning genetic trends to
quantify the sources of genetic gain in breeding programmes.
The partitioning method is described in Garcia-Cortes et al.
(2008) <doi:10.1017/S175173110800205X>. The package includes the
main function AlphaPart for partitioning breeding values and auxiliary
functions for manipulating data and summarizing, visualizing, and saving
results.
Author: Gregor Gorjanc [aut, cre] ,
Jana Obsteter [aut] ,
Thiago de Paula Oliveira [aut]
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>
Diff between AlphaPart versions 0.9.5 dated 2022-07-07 and 0.9.7 dated 2022-09-23
DESCRIPTION | 13 +++++++------ MD5 | 25 +++++++++++++++---------- R/AlphaPartSubset.R | 4 ++-- R/AlphaPartSum.R | 4 ++-- R/methods.R | 6 +++--- R/write.csv.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alphapart-variance.R |only inst/doc/alphapart-variance.Rmd |only inst/doc/alphapart-variance.html |only inst/doc/alphapart-vignette.Rmd | 4 +++- inst/doc/alphapart-vignette.html | 8 ++++---- inst/extdata |only vignettes/alphapart-variance.Rmd |only vignettes/alphapart-vignette.Rmd | 4 +++- 16 files changed, 43 insertions(+), 33 deletions(-)
Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for
simulating large systems with Gillespie's Stochastic Simulation
Algorithm ('SSA'). This package is the spiritual successor to the
'GillespieSSA' package originally written by Mario Pineda-Krch.
Benefits of this package include major speed improvements (>100x),
easier to understand documentation, and many unit tests that try to
ensure the package works as intended. Cannoodt and Saelens et al. (2020)
<doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between GillespieSSA2 versions 0.2.8 dated 2021-05-18 and 0.2.10 dated 2022-09-23
DESCRIPTION | 8 +++--- MD5 | 38 ++++++++++++++--------------- NEWS.md | 8 ++++++ R/zzz.R | 2 - README.md | 25 ++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/an_introduction.html | 18 +++++++++---- inst/doc/converting_from_GillespieSSA.html | 22 +++++++++++----- inst/doc/decaying_dimer.html | 20 ++++++++++----- inst/doc/epi_chain.html | 20 ++++++++++----- inst/doc/linear_chain.html | 20 ++++++++++----- inst/doc/logistic_growth.html | 20 ++++++++++----- inst/doc/lotka_predator_prey.html | 20 ++++++++++----- inst/doc/radioactive_decay.html | 20 ++++++++++----- inst/doc/rm_predator_prey.html | 20 ++++++++++----- inst/doc/sir.html | 20 ++++++++++----- src/RcppExports.cpp | 5 +++ src/ssa_simulation.cpp | 16 ++++-------- src/test_helper_funs.cpp | 2 + 20 files changed, 188 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-08 2.2.0
2022-03-25 2.1.0
2021-05-10 2.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 3.2.0
2020-09-10 3.1.2
2020-07-05 3.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-08 2.0.2
Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Si Gao [aut, cre, dtc] ,
Peter Kochunov [aut, dtc, cph, fnd] ,
Kathryn Hatch [ctb, dtc] ,
Yizhou Ma [ctb, dtc] ,
Fatima Talib [ctb]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Diff between RVIpkg versions 0.3.0 dated 2022-03-10 and 0.3.1 dated 2022-09-23
DESCRIPTION | 50 ++++++----- MD5 | 28 +++--- R/EP.GM.R | 6 - R/EP.Subcortical.R | 6 - R/EP.WM.R | 6 - R/RVI_func.R | 208 ++++++++++++++++++++++++------------------------ R/sysdata.rda |binary build/partial.rdb |binary data/EP.GM.rda |binary data/EP.Subcortical.rda |binary data/EP.WM.rda |binary man/EP.GM.Rd | 6 - man/EP.Subcortical.Rd | 6 - man/EP.WM.Rd | 6 - man/RVI_func.Rd | 9 +- 15 files changed, 175 insertions(+), 156 deletions(-)
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.9 dated 2021-10-08 and 1.0.10 dated 2022-09-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/calculate_distance.R | 14 +++++++------- README.md | 34 ++-------------------------------- build/vignette.rds |binary inst/doc/functionality.html | 30 +++++++++++++++++++----------- man/calculate_distance.Rd | 24 ++++++++++++++++++------ tests/testthat/test-h5.R | 2 +- 9 files changed, 63 insertions(+), 69 deletions(-)