Title: Flexible and Robust Agreement and Reliability Analyses
Description: Reliability and agreement analyses often have limited software support. Therefore, this package was created to make agreement and reliability analyses easier for the average researcher. The functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability. In addition, this package contains a set of functions to help when planning studies looking to assess measurement agreement. For robust analyses of agreement, limits of agreement through a bootstrap method can also be calculated.
Author: Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between SimplyAgree versions 0.1.0 dated 2022-08-24 and 0.1.2 dated 2022-12-14
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SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-agree_np.R | 256 - SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-agree_reps.R | 250 - SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-blandPowerCurve.R | 198 SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-dem_reg.R | 150 SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-loa_lme.R | 140 SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-loa_mixed.R | 168 SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test-reli_stats.R | 494 +- SimplyAgree-0.1.2/SimplyAgree/tests/testthat/test_agree_test.R | 258 - SimplyAgree-0.1.2/SimplyAgree/vignettes/Deming.Rmd | 414 - SimplyAgree-0.1.2/SimplyAgree/vignettes/agreement_analysis.Rmd | 1062 ++-- SimplyAgree-0.1.2/SimplyAgree/vignettes/reanalysis.Rmd | 524 +- SimplyAgree-0.1.2/SimplyAgree/vignettes/ref.bib | 174 SimplyAgree-0.1.2/SimplyAgree/vignettes/refs.bib | 440 - SimplyAgree-0.1.2/SimplyAgree/vignettes/reliability_analysis.Rmd | 891 ++- 97 files changed, 17481 insertions(+), 16944 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.3.3 dated 2022-10-18 and 1.3.4 dated 2022-12-14
DESCRIPTION | 10 +- MD5 | 8 - NEWS.md | 9 ++ R/roc.R | 116 ++++++++++++++++------------ inst/doc/jsmodule.html | 200 ++++++++++++++++++++++++++++++++++++++++++++++++- 5 files changed, 280 insertions(+), 63 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] ,
Arnaud Barras [aut] ,
Veronika Braunisch [aut] ,
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@unibe.ch>
Diff between SDMtune versions 1.1.6 dated 2022-08-25 and 1.2.0 dated 2022-12-14
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SDMtune-1.2.0/SDMtune/tests/testthat/test-trainMaxnet.R | 5 SDMtune-1.2.0/SDMtune/tests/testthat/test-trainRF.R | 5 SDMtune-1.2.0/SDMtune/tests/testthat/test-trainValTest.R | 61 + SDMtune-1.2.0/SDMtune/tests/testthat/test-tss.R | 6 SDMtune-1.2.0/SDMtune/tests/testthat/test-utils.R | 62 - SDMtune-1.2.0/SDMtune/tests/testthat/test-varImp.R | 16 SDMtune-1.2.0/SDMtune/tests/testthat/test-varSel.R | 74 + SDMtune-1.2.0/SDMtune/vignettes/articles/evaluate-model.Rmd | 11 SDMtune-1.2.0/SDMtune/vignettes/articles/evaluation-strategies.Rmd | 100 +- SDMtune-1.2.0/SDMtune/vignettes/articles/make-predictions.Rmd | 69 + SDMtune-1.2.0/SDMtune/vignettes/articles/prepare-data.Rmd | 51 - SDMtune-1.2.0/SDMtune/vignettes/articles/train-model.Rmd | 31 SDMtune-1.2.0/SDMtune/vignettes/articles/train-tune-presence-absence-models.Rmd | 81 + SDMtune-1.2.0/SDMtune/vignettes/articles/tune-hyperparameters.Rmd | 190 +++- SDMtune-1.2.0/SDMtune/vignettes/articles/variable-importance.Rmd | 113 ++ SDMtune-1.2.0/SDMtune/vignettes/articles/variable-selection.Rmd | 126 ++ SDMtune-1.2.0/SDMtune/vignettes/basic-use.Rmd | 151 ++- SDMtune-1.2.0/SDMtune/vignettes/hyper-tuning.Rmd | 129 ++- SDMtune-1.2.0/SDMtune/vignettes/presence-absence.Rmd | 46 - SDMtune-1.2.0/SDMtune/vignettes/var-selection.Rmd | 152 ++- 179 files changed, 7988 insertions(+), 3454 deletions(-)
Title: Calculate Phenotype Risk Scores
Description: Use phenotype risk scores based on linked clinical and genetic data
to study Mendelian disease and rare genetic variants. See Bastarache et al.
2018 <doi:10.1126/science.aal4043>.
Author: Jake Hughey [aut, cre],
Layla Aref [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between phers versions 0.0.3 dated 2022-05-31 and 1.0.0 dated 2022-12-14
phers-0.0.3/phers/man/phers.Rd |only phers-1.0.0/phers/DESCRIPTION | 13 phers-1.0.0/phers/MD5 | 65 ++-- phers-1.0.0/phers/NAMESPACE | 5 phers-1.0.0/phers/NEWS.md | 6 phers-1.0.0/phers/R/examples.R | 93 ++++-- phers-1.0.0/phers/R/genetic_association.R | 41 +- phers-1.0.0/phers/R/genetic_diagnosis.R | 26 - phers-1.0.0/phers/R/map.R | 7 phers-1.0.0/phers/R/phers.R | 148 ---------- phers-1.0.0/phers/R/utils.R | 78 ++++- phers-1.0.0/phers/R/weights.R |only phers-1.0.0/phers/data/demoSample.rda |binary phers-1.0.0/phers/data/icdSample.rda |binary phers-1.0.0/phers/data/preCalcWeights.rda |binary phers-1.0.0/phers/man/getDxStatus.Rd | 20 - phers-1.0.0/phers/man/getGeneticAssociations.Rd | 5 phers-1.0.0/phers/man/getPhecodeOccurrences.Rd | 7 phers-1.0.0/phers/man/getResidualScores.Rd | 7 phers-1.0.0/phers/man/getScores.Rd | 17 - phers-1.0.0/phers/man/getWeights.Rd | 114 ++++++- phers-1.0.0/phers/man/hpoPhecodeMap.Rd | 2 phers-1.0.0/phers/man/mapDiseaseToPhecode.Rd | 53 ++- phers-1.0.0/phers/man/preCalcWeights.Rd | 3 phers-1.0.0/phers/tests/testthat/data/get_genetic_associations_additive_output.qs |binary phers-1.0.0/phers/tests/testthat/data/get_weights_cox_negative_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_cox_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_logistic_negative_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_logistic_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_loglinear_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_prevalence_negative_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_prevalence_output.qs |only phers-1.0.0/phers/tests/testthat/data/get_weights_prevalence_precalc_output.qs |only phers-1.0.0/phers/tests/testthat/data/run_linear_additive_output.qs |binary phers-1.0.0/phers/tests/testthat/data/run_linear_dominant_output.qs |binary phers-1.0.0/phers/tests/testthat/data/run_linear_recessive_output.qs |binary phers-1.0.0/phers/tests/testthat/setup.R | 29 + phers-1.0.0/phers/tests/testthat/test_phers.R | 116 +------ phers-1.0.0/phers/tests/testthat/test_weights.R |only 39 files changed, 432 insertions(+), 423 deletions(-)
Title: Tools for Handling Spatial Objects
Description: Please note that 'maptools' will be retired during 2023, plan transition at your earliest convenience; some functionality will be moved to 'sp'. Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat.geom', 'maps', and others.
Author: Roger Bivand [cre, aut] ,
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Joerg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stephane Dray [ctb],
Dav [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 1.1-5 dated 2022-10-21 and 1.1-6 dated 2022-12-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 27 ++++++++++++++------------- NEWS.md | 6 +++++- build/vignette.rds |binary data/SplashDams.rda |binary data/wrld_simpl.rda |binary inst/doc/combine_maptools.pdf |binary src/Rgshhs.c | 6 +++--- src/shpopen.c | 25 ++++++++++++++----------- 10 files changed, 49 insertions(+), 41 deletions(-)
Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference.
GRF provides non-parametric methods for heterogeneous treatment effects estimation
(optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables),
as well as least-squares regression, quantile regression, and survival regression,
all with support for missing covariates.
Author: Julie Tibshirani [aut, cre],
Susan Athey [aut],
Rina Friedberg [ctb],
Vitor Hadad [ctb],
David Hirshberg [ctb],
Luke Miner [ctb],
Erik Sverdrup [aut],
Stefan Wager [aut],
Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>
Diff between grf versions 2.2.0 dated 2022-08-06 and 2.2.1 dated 2022-12-14
DESCRIPTION | 6 - MD5 | 43 +++---- NAMESPACE | 1 R/average_treatment_effect.R | 4 R/causal_forest.R | 10 + R/causal_survival_forest.R | 54 +++++++-- R/dgps.R | 4 R/forest_summary.R | 8 - R/get_scores.R | 2 R/grf-package.R | 11 + R/rank_average_treatment.R | 173 ++++++++++++++++++++++++++++++- R/survival_forest.R | 40 +------ man/average_treatment_effect.Rd | 4 man/best_linear_projection.Rd | 4 man/causal_forest.Rd | 10 + man/causal_survival_forest.Rd | 27 +++- man/get_scores.instrumental_forest.Rd | 2 man/grf-package.Rd | 11 + man/predict.causal_survival_forest.Rd | 27 +++- man/predict.survival_forest.Rd | 19 --- man/rank_average_treatment_effect.Rd | 6 - man/rank_average_treatment_effect.fit.Rd |only man/survival_forest.Rd | 21 +-- 23 files changed, 354 insertions(+), 133 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <Sylvain.Jasson@inrae.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.6-8 dated 2022-11-09 and 0.6-9 dated 2022-12-14
DESCRIPTION | 8 +- MD5 | 34 ++++----- man/add.biginteger.Rd | 2 man/comp.biginteger.Rd | 2 man/operators_bigq.Rd | 2 src/bigintegerR.cc | 17 ---- src/bigintegerR.h | 7 - src/bigrationalR.cc | 18 ---- src/bigrationalR.h | 5 - src/bigvec.cc | 4 - src/bigvec_q.cc | 13 +-- src/matrix.cc | 86 +++++++++++++++++++---- src/matrix.h | 6 + src/matrixq.cc | 70 +++++++++++++++---- src/matrixq.h | 4 - src/templateMatrix.h | 2 tests/gmp-test.R | 4 - tests/gmp-test.Rout.save | 172 ++++++++++++++++++++++++++++++++++++++++++++--- 18 files changed, 332 insertions(+), 124 deletions(-)
Title: Differential Expression Enrichment Tool
Description: Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share sim [...truncated...]
Author: Dustin Sokolowski [aut, cre],
Jedid Ahn [aut],
Lauren Erdman [aut],
Kai Ellis [aut],
Huayun Hou [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between DEET versions 1.0.6 dated 2022-10-09 and 1.0.7 dated 2022-12-14
DESCRIPTION | 8 +++--- MD5 | 28 ++++++++++++++---------- NAMESPACE | 3 ++ R/DEET_Input_as_Reference.R |only R/DEET_enrich.R | 18 +++++++++------ R/DEET_enrich_genesonly.R |only R/DEET_feature_extract.R | 31 ++++++++++++++++++++++++++- R/DEET_feature_extract_example_matrix.R | 3 +- R/adjust_DE_cutoffs.R |only README.md | 6 ++--- data/DEET_example_data.rda |binary data/DEET_feature_extract_example_matrix.rda |binary inst/doc/DEET_vignette.html | 4 +-- man/DEET_Input_as_Reference.Rd |only man/DEET_enrich_genesonly.Rd |only man/DEET_feature_extract.Rd | 5 +++- man/DEET_feature_extract_example_matrix.Rd | 3 +- man/adjust_DE_cutoffs.Rd |only 18 files changed, 78 insertions(+), 31 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Thomas J. Faulkenberry [rev],
Robert Garrett [rev]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 0.6.4 dated 2022-11-19 and 0.6.5 dated 2022-12-14
datawizard-0.6.4/datawizard/tests/testthat/test-skewness.R |only datawizard-0.6.4/datawizard/tests/testthat/test-skewness_kurtosis.R |only datawizard-0.6.5/datawizard/DESCRIPTION | 22 datawizard-0.6.5/datawizard/MD5 | 75 - datawizard-0.6.5/datawizard/NAMESPACE | 2 datawizard-0.6.5/datawizard/NEWS.md | 23 datawizard-0.6.5/datawizard/R/adjust.R | 18 datawizard-0.6.5/datawizard/R/center.R | 11 datawizard-0.6.5/datawizard/R/convert_na_to.R | 70 - datawizard-0.6.5/datawizard/R/data_arrange.R | 4 datawizard-0.6.5/datawizard/R/data_codebook.R | 81 + datawizard-0.6.5/datawizard/R/data_rename.R | 10 datawizard-0.6.5/datawizard/R/data_rescale.R | 50 - datawizard-0.6.5/datawizard/R/makepredictcall.R |only datawizard-0.6.5/datawizard/R/normalize.R | 51 - datawizard-0.6.5/datawizard/R/remove_empty.R | 2 datawizard-0.6.5/datawizard/R/skewness_kurtosis.R | 6 datawizard-0.6.5/datawizard/R/standardize.R | 8 datawizard-0.6.5/datawizard/R/standardize.models.R | 10 datawizard-0.6.5/datawizard/R/utils_standardize_center.R | 24 datawizard-0.6.5/datawizard/inst/doc/standardize_data.R | 2 datawizard-0.6.5/datawizard/inst/doc/standardize_data.Rmd | 2 datawizard-0.6.5/datawizard/man/center.Rd | 3 datawizard-0.6.5/datawizard/man/data_arrange.Rd | 4 datawizard-0.6.5/datawizard/man/data_rename.Rd | 2 datawizard-0.6.5/datawizard/man/datawizard-package.Rd | 4 datawizard-0.6.5/datawizard/man/figures/logo.png |binary datawizard-0.6.5/datawizard/man/makepredictcall.dw_transformer.Rd |only datawizard-0.6.5/datawizard/man/normalize.Rd | 2 datawizard-0.6.5/datawizard/man/rescale.Rd | 2 datawizard-0.6.5/datawizard/man/skewness.Rd | 6 datawizard-0.6.5/datawizard/man/standardize.Rd | 3 datawizard-0.6.5/datawizard/tests/testthat/_snaps/skewness-kurtosis.md |only datawizard-0.6.5/datawizard/tests/testthat/test-center.R | 11 datawizard-0.6.5/datawizard/tests/testthat/test-data_codebook.R | 454 ++++++---- datawizard-0.6.5/datawizard/tests/testthat/test-data_rename.R | 5 datawizard-0.6.5/datawizard/tests/testthat/test-data_to_numeric.R | 3 datawizard-0.6.5/datawizard/tests/testthat/test-makepredictcall.R |only datawizard-0.6.5/datawizard/tests/testthat/test-skewness-kurtosis.R |only datawizard-0.6.5/datawizard/tests/testthat/test-standardize-data.R | 4 datawizard-0.6.5/datawizard/tests/testthat/test-standardize_models.R | 9 datawizard-0.6.5/datawizard/vignettes/standardize_data.Rmd | 2 42 files changed, 635 insertions(+), 350 deletions(-)
Title: Create Data Frames that are Easier to Exchange and Reuse
Description: The aim of the 'dataset' package is to make tidy datasets easier to release,
exchange and reuse. It organizes and formats data frame 'R' objects into well-referenced,
well-described, interoperable datasets into release and reuse ready form. A subjective
interpretation of the W3C DataSet recommendation and the datacube model <https://www.w3.org/TR/vocab-data-cube/>,
which is also used in the global Statistical Data and Metadata eXchange standards,
the application of the connected Dublin Core <https://www.dublincore.org/specifications/dublin-core/dcmi-terms/>
and DataCite <https://support.datacite.org/docs/datacite-metadata-schema-44/> standards
preferred by European open science repositories to improve the findability, accessibility,
interoperability and reusability of the datasets.
Author: Daniel Antal [aut, cre] ,
Marcelo Perlin [rev]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Diff between dataset versions 0.1.9 dated 2022-12-02 and 0.2.0 dated 2022-12-14
DESCRIPTION | 19 +- MD5 | 79 ++++---- NAMESPACE | 7 NEWS.md | 5 R/dataset.R | 220 ++++++++++++++++++++++- R/dataset_download.R | 17 - R/dataset_export.R | 15 + R/dataset_title.R | 17 - R/dublincore.R | 209 +++++++++++++++------- R/iris_dataset.R |only R/resource_type.R | 6 R/source.R | 6 README.md | 176 ++++++++++++------ build/vignette.rds |binary data |only inst/WORDLIST | 10 - inst/doc/RDF.html | 16 - inst/doc/dataset.R | 19 +- inst/doc/dataset.Rmd | 27 ++ inst/doc/dataset.html | 230 +++++++++++++----------- inst/doc/dataspice.R |only inst/doc/dataspice.Rmd |only inst/doc/dataspice.html |only inst/doc/metadata.R | 14 - inst/doc/metadata.Rmd | 18 + inst/doc/metadata.html | 307 ++++++++++++--------------------- inst/doc/motivation.html | 97 +++++----- inst/doc/survey.R | 27 +- inst/doc/survey.Rmd | 18 - inst/doc/survey.html | 210 +++++----------------- man/dataset.Rd | 36 +++ man/dataset_download.Rd | 17 - man/dataset_source.Rd | 6 man/dataset_title.Rd | 1 man/iris_dataset.Rd |only man/resource_type.Rd | 2 tests/testthat/test-dataset.R | 31 ++- tests/testthat/test-dataset_download.R | 24 +- tests/testthat/test-dataset_title.R | 13 - tests/testthat/test-resource_type.R | 4 vignettes/dataset.Rmd | 27 ++ vignettes/dataspice.Rmd |only vignettes/metadata.Rmd | 18 + vignettes/survey.Rmd | 18 - 44 files changed, 1143 insertions(+), 823 deletions(-)
Title: Wrapper for 'RcppSpdlog' Functions
Description: Logging functions in 'RcppSpdlog' provide access to the logging
functionality from the 'spdlog' 'C++' library. This package offers shorter convenience
wrappers for the 'R' functions which match the 'C++' functions, namely via, say,
'spdl::debug()' at the debug level. The actual formatting is done by the
'fmt::format()' function from the 'fmtlib' library (that is also 'std::format()'
in 'C++20' or later).
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between spdl versions 0.0.2 dated 2022-12-01 and 0.0.3 dated 2022-12-14
ChangeLog | 16 +++++++++++++++- DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/wrap.R | 5 ++++- inst/NEWS.Rd | 6 ++++++ man/setup.Rd | 5 ++++- 6 files changed, 39 insertions(+), 13 deletions(-)
Title: Interactive Graphics for Monitoring Clinical Trial Safety
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Author: Jeremy Wildfire [cre, aut],
Becca Krouse [aut],
Preston Burns [aut],
Xiao Ni [aut],
James Buchanan [aut],
Susan Duke [aut]
Maintainer: Jeremy Wildfire <jwildfire@gmail.com>
Diff between safetyGraphics versions 2.1.0 dated 2022-04-08 and 2.1.1 dated 2022-12-14
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ R/evaluateStandard.R | 2 +- R/mod_filterTab.R | 18 ++++++++++++++---- R/mod_safetyGraphicsUI.R | 14 ++++++++++---- inst/doc/ChartConfiguration.html | 4 ++-- inst/doc/Cookbook.html | 4 ++-- inst/doc/Intro.html | 4 ++-- inst/doc/TechnicalFAQ.Rmd | 6 +++--- inst/doc/TechnicalFAQ.html | 10 +++++----- inst/report/safetyGraphicsReport.Rmd | 2 +- inst/www/index.css | 4 ++++ tests/testthat/test_evaluateStandard.R | 6 ++++++ vignettes/TechnicalFAQ.Rmd | 6 +++--- 16 files changed, 77 insertions(+), 47 deletions(-)
More information about safetyGraphics at CRAN
Permanent link
Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages
exist to process MS data, many of these make it difficult to
access the underlying mass-to-charge ratio (m/z), intensity, and
retention time of the files
themselves. This package is designed to format MS data in a tidy fashion and
allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph],
Ricardo Cunha [ctb],
Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>
Diff between RaMS versions 1.3.0 dated 2022-11-28 and 1.3.1 dated 2022-12-14
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++-------- NAMESPACE | 1 NEWS.md | 7 +++++ R/grabMSdataCode.R | 2 - inst/doc/Intro-to-RaMS.html | 44 ++++++++++++++++---------------- inst/doc/Intro-to-tmzML.html | 4 +- inst/doc/Minifying-files-with-RaMS.html | 2 - inst/doc/RaMS-and-friends.html | 32 +++++++++++------------ tests/testthat/test_errors_n_messes.R | 6 ---- tests/testthat/test_minify.R | 15 ++++++---- tests/testthat/test_tmzML_things.R | 37 +++++++++++++------------- 12 files changed, 92 insertions(+), 86 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.10.0 dated 2021-01-04 and 0.11.0 dated 2022-12-14
future.batchtools-0.10.0/future.batchtools/NEWS |only future.batchtools-0.11.0/future.batchtools/DESCRIPTION | 13 future.batchtools-0.11.0/future.batchtools/MD5 | 77 +- future.batchtools-0.11.0/future.batchtools/NAMESPACE | 31 + future.batchtools-0.11.0/future.batchtools/NEWS.md |only future.batchtools-0.11.0/future.batchtools/R/BatchtoolsCustomFuture-class.R |only future.batchtools-0.11.0/future.batchtools/R/BatchtoolsFuture-class.R | 117 +++ future.batchtools-0.11.0/future.batchtools/R/BatchtoolsMultiprocessFuture-class.R |only future.batchtools-0.11.0/future.batchtools/R/BatchtoolsSSHFuture-class.R |only future.batchtools-0.11.0/future.batchtools/R/BatchtoolsSSHRegistry.R |only future.batchtools-0.11.0/future.batchtools/R/BatchtoolsUniprocessFuture-class.R |only future.batchtools-0.11.0/future.batchtools/R/batchtools_bash.R |only future.batchtools-0.11.0/future.batchtools/R/batchtools_custom.R | 29 future.batchtools-0.11.0/future.batchtools/R/batchtools_interactive.R | 30 - future.batchtools-0.11.0/future.batchtools/R/batchtools_local.R | 38 - future.batchtools-0.11.0/future.batchtools/R/batchtools_multicore.R | 30 - future.batchtools-0.11.0/future.batchtools/R/batchtools_ssh.R |only future.batchtools-0.11.0/future.batchtools/R/batchtools_template.R | 131 ++-- future.batchtools-0.11.0/future.batchtools/R/find_template_file.R |only future.batchtools-0.11.0/future.batchtools/R/future_cache_path.R | 2 future.batchtools-0.11.0/future.batchtools/R/nbrOfWorkers.R | 101 ++- future.batchtools-0.11.0/future.batchtools/R/options.R | 118 +++- future.batchtools-0.11.0/future.batchtools/R/temp_registry.R | 29 future.batchtools-0.11.0/future.batchtools/R/utils,conditions.R |only future.batchtools-0.11.0/future.batchtools/R/utils.R | 39 + future.batchtools-0.11.0/future.batchtools/R/waitForWorker.R |only future.batchtools-0.11.0/future.batchtools/R/with_stealth_rng.R |only future.batchtools-0.11.0/future.batchtools/R/zzz.R | 21 future.batchtools-0.11.0/future.batchtools/build/vignette.rds |binary future.batchtools-0.11.0/future.batchtools/inst/CITATION | 54 - future.batchtools-0.11.0/future.batchtools/inst/doc/future.batchtools.html | 293 ++-------- future.batchtools-0.11.0/future.batchtools/inst/doc/future.batchtools.md.rsp | 2 future.batchtools-0.11.0/future.batchtools/inst/templates/bash.tmpl |only future.batchtools-0.11.0/future.batchtools/inst/templates/sge.tmpl |only future.batchtools-0.11.0/future.batchtools/inst/templates/slurm.tmpl |only future.batchtools-0.11.0/future.batchtools/inst/templates/torque.tmpl | 2 future.batchtools-0.11.0/future.batchtools/man/BatchtoolsFuture.Rd | 130 ++++ future.batchtools-0.11.0/future.batchtools/man/batchtools_custom.Rd | 5 future.batchtools-0.11.0/future.batchtools/man/batchtools_local.Rd | 47 - future.batchtools-0.11.0/future.batchtools/man/batchtools_multicore.Rd | 2 future.batchtools-0.11.0/future.batchtools/man/batchtools_ssh.Rd |only future.batchtools-0.11.0/future.batchtools/man/batchtools_template.Rd | 5 future.batchtools-0.11.0/future.batchtools/man/future.batchtools.options.Rd | 30 - future.batchtools-0.11.0/future.batchtools/man/nbrOfWorkers.batchtools.Rd | 2 future.batchtools-0.11.0/future.batchtools/tests/batchtools_ssh.R |only future.batchtools-0.11.0/future.batchtools/tests/incl/end.R | 36 - future.batchtools-0.11.0/future.batchtools/tests/nbrOfWorkers.R | 55 + future.batchtools-0.11.0/future.batchtools/tests/rng.R |only future.batchtools-0.11.0/future.batchtools/vignettes/future.batchtools.md.rsp | 2 49 files changed, 903 insertions(+), 568 deletions(-)
More information about future.batchtools at CRAN
Permanent link
Title: Blinding Assessment Indexes for Randomized, Controlled, Clinical
Trials
Description: Generate the James Blinding Index, as described in James et al (1996)
<https://pubmed.ncbi.nlm.nih.gov/8841652/> and the Bang Blinding Index,
as described in Bang et al (2004) <https://pubmed.ncbi.nlm.nih.gov/15020033/>.
These are measures to assess whether or not satisfactory blinding has been
maintained in a randomized, controlled, clinical trial. These can be generated
for trial subjects, research coordinators and principal investigators, based
upon standardized questionnaires that have been administered, to assess whether
or not they can correctly guess to which treatment arm (e.g. placebo or treatment)
subjects were assigned at randomization.
Author: Marc Schwartz [aut, cre],
Nate Mercaldo [aut]
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between BI versions 1.1.0 dated 2022-09-30 and 1.2.0 dated 2022-12-14
DESCRIPTION | 8 +++--- MD5 | 6 ++--- R/BI.r | 69 ++++++++++++++++++++++++++++++++++++------------------------ man/BI.Rd | 16 ++++++++----- 4 files changed, 59 insertions(+), 40 deletions(-)
Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome
association studies are implemented. These analyses include descriptive
statistics and exploratory analysis of missing values, calculation of
Hardy-Weinberg equilibrium, analysis of association based on generalized
linear models (either for quantitative or binary traits), and analysis
of multiple SNPs (haplotype and epistasis analysis). Permutation test
and related tests (sum statistic and truncated product) are also
implemented. Max-statistic and genetic risk-allele score exact
distributions are also possible to be estimated. The methods are
described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Author: Victor Moreno [aut],
Juan R Gonzalez [aut] ,
Dolors Pelegri [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri@isglobal.org>
Diff between SNPassoc versions 2.0-18 dated 2022-11-15 and 2.1-0 dated 2022-12-14
SNPassoc-2.0-18/SNPassoc/R/dscore.R |only SNPassoc-2.0-18/SNPassoc/R/dscore.character.R |only SNPassoc-2.0-18/SNPassoc/R/dscore.default.R |only SNPassoc-2.0-18/SNPassoc/R/dscore.setupSNP.R |only SNPassoc-2.0-18/SNPassoc/man/dscore.Rd |only SNPassoc-2.1-0/SNPassoc/DESCRIPTION | 27 SNPassoc-2.1-0/SNPassoc/MD5 | 221 SNPassoc-2.1-0/SNPassoc/NAMESPACE | 11 SNPassoc-2.1-0/SNPassoc/R/GenotypeRate.R | 16 SNPassoc-2.1-0/SNPassoc/R/Table.N.Per.R | 38 SNPassoc-2.1-0/SNPassoc/R/Table.mean.se.R | 24 SNPassoc-2.1-0/SNPassoc/R/WGassociation.R | 186 SNPassoc-2.1-0/SNPassoc/R/WGstats.R | 32 SNPassoc-2.1-0/SNPassoc/R/additive.R | 6 SNPassoc-2.1-0/SNPassoc/R/additive.WGassociation.R | 12 SNPassoc-2.1-0/SNPassoc/R/additive.default.R | 14 SNPassoc-2.1-0/SNPassoc/R/additive.snp.R | 42 SNPassoc-2.1-0/SNPassoc/R/as.snp.R | 12 SNPassoc-2.1-0/SNPassoc/R/assoc.R | 98 SNPassoc-2.1-0/SNPassoc/R/association.R | 364 - SNPassoc-2.1-0/SNPassoc/R/association.fit.R | 630 - SNPassoc-2.1-0/SNPassoc/R/c.WGassociation.r | 68 SNPassoc-2.1-0/SNPassoc/R/codominant.R | 6 SNPassoc-2.1-0/SNPassoc/R/codominant.WGassociation.R | 12 SNPassoc-2.1-0/SNPassoc/R/codominant.default.R | 16 SNPassoc-2.1-0/SNPassoc/R/codominant.snp.R | 16 SNPassoc-2.1-0/SNPassoc/R/crea.lab.R | 32 SNPassoc-2.1-0/SNPassoc/R/dominant.R | 6 SNPassoc-2.1-0/SNPassoc/R/dominant.WGassociation.R | 12 SNPassoc-2.1-0/SNPassoc/R/dominant.default.R | 24 SNPassoc-2.1-0/SNPassoc/R/dominant.snp.R | 12 SNPassoc-2.1-0/SNPassoc/R/extractPval.R | 44 SNPassoc-2.1-0/SNPassoc/R/extractPval.i.R | 74 SNPassoc-2.1-0/SNPassoc/R/getNiceTable.R | 92 SNPassoc-2.1-0/SNPassoc/R/getSignificantSNPs.R | 80 SNPassoc-2.1-0/SNPassoc/R/int.R | 12 SNPassoc-2.1-0/SNPassoc/R/interactionPval.R | 330 - SNPassoc-2.1-0/SNPassoc/R/interleave.R | 74 SNPassoc-2.1-0/SNPassoc/R/intervals.R | 8 SNPassoc-2.1-0/SNPassoc/R/intervals.dif.R | 110 SNPassoc-2.1-0/SNPassoc/R/intervals.haplo.glm.R | 136 SNPassoc-2.1-0/SNPassoc/R/intervals.or.R | 84 SNPassoc-2.1-0/SNPassoc/R/is.Monomorphic.R | 28 SNPassoc-2.1-0/SNPassoc/R/is.quantitative.R | 24 SNPassoc-2.1-0/SNPassoc/R/is.snp.R | 12 SNPassoc-2.1-0/SNPassoc/R/labels.WGassociation.R | 6 SNPassoc-2.1-0/SNPassoc/R/labels.setupSNP.R | 6 SNPassoc-2.1-0/SNPassoc/R/maxstat.R | 4 SNPassoc-2.1-0/SNPassoc/R/maxstat.default.R | 32 SNPassoc-2.1-0/SNPassoc/R/maxstat.matrix.R | 438 - SNPassoc-2.1-0/SNPassoc/R/maxstat.setupSNP.R | 28 SNPassoc-2.1-0/SNPassoc/R/maxstat.table.R | 12 SNPassoc-2.1-0/SNPassoc/R/modelTest.R | 80 SNPassoc-2.1-0/SNPassoc/R/odds.r | 102 SNPassoc-2.1-0/SNPassoc/R/orderChromosome.R | 30 SNPassoc-2.1-0/SNPassoc/R/overdominant.R | 6 SNPassoc-2.1-0/SNPassoc/R/overdominant.WGassociation.R | 12 SNPassoc-2.1-0/SNPassoc/R/overdominant.default.R | 26 SNPassoc-2.1-0/SNPassoc/R/overdominant.snp.R | 46 SNPassoc-2.1-0/SNPassoc/R/plot.permTest.R | 42 SNPassoc-2.1-0/SNPassoc/R/plot.setupSNP.R | 6 SNPassoc-2.1-0/SNPassoc/R/plotWGassociation.R | 60 SNPassoc-2.1-0/SNPassoc/R/print.SNPinteraction.R | 12 SNPassoc-2.1-0/SNPassoc/R/print.WGassociation.R | 48 SNPassoc-2.1-0/SNPassoc/R/print.haploOut.R | 68 SNPassoc-2.1-0/SNPassoc/R/print.intervals.R | 94 SNPassoc-2.1-0/SNPassoc/R/print.maxstat.R | 6 SNPassoc-2.1-0/SNPassoc/R/print.permTest.R | 62 SNPassoc-2.1-0/SNPassoc/R/print.snp.r | 92 SNPassoc-2.1-0/SNPassoc/R/print.snpOut.R | 128 SNPassoc-2.1-0/SNPassoc/R/print.summary.snp.R | 20 SNPassoc-2.1-0/SNPassoc/R/print.tableHWE.R | 26 SNPassoc-2.1-0/SNPassoc/R/pvalTest.R | 18 SNPassoc-2.1-0/SNPassoc/R/pvalues.R | 6 SNPassoc-2.1-0/SNPassoc/R/pvalues.WGassociation.R | 6 SNPassoc-2.1-0/SNPassoc/R/qqpval.r | 14 SNPassoc-2.1-0/SNPassoc/R/recessive.R | 6 SNPassoc-2.1-0/SNPassoc/R/recessive.WGassociation.R | 12 SNPassoc-2.1-0/SNPassoc/R/recessive.default.R | 44 SNPassoc-2.1-0/SNPassoc/R/recessive.snp.R | 16 SNPassoc-2.1-0/SNPassoc/R/scanWGassociation.R | 22 SNPassoc-2.1-0/SNPassoc/R/summary.snp.R | 108 SNPassoc-2.1-0/SNPassoc/R/table.corner.R | 344 - SNPassoc-2.1-0/SNPassoc/R/table.interaction.R | 370 - SNPassoc-2.1-0/SNPassoc/R/togeno.R | 22 SNPassoc-2.1-0/SNPassoc/R/trim.R | 10 SNPassoc-2.1-0/SNPassoc/R/z$.setupSNP.R | 8 SNPassoc-2.1-0/SNPassoc/R/z[.WGassociation.R | 72 SNPassoc-2.1-0/SNPassoc/R/z[.setupSNP.R | 40 SNPassoc-2.1-0/SNPassoc/R/z[.snp.r | 24 SNPassoc-2.1-0/SNPassoc/R/z[[_-.setupSNP.R | 64 SNPassoc-2.1-0/SNPassoc/R/z[_-.setupSNP.R | 10 SNPassoc-2.1-0/SNPassoc/README.md | 6 SNPassoc-2.1-0/SNPassoc/build/vignette.rds |binary SNPassoc-2.1-0/SNPassoc/inst/doc/SNPassoc.R | 418 - SNPassoc-2.1-0/SNPassoc/inst/doc/SNPassoc.Rmd | 864 +- SNPassoc-2.1-0/SNPassoc/inst/doc/SNPassoc.html | 5426 ++++++++--------- SNPassoc-2.1-0/SNPassoc/inst/docs/changelog.txt | 416 - SNPassoc-2.1-0/SNPassoc/man/BonferroniSig.Rd | 92 SNPassoc-2.1-0/SNPassoc/man/GenomicControl.Rd | 98 SNPassoc-2.1-0/SNPassoc/man/LD.Rd | 144 SNPassoc-2.1-0/SNPassoc/man/association.Rd | 266 SNPassoc-2.1-0/SNPassoc/man/asthma.Rd | 40 SNPassoc-2.1-0/SNPassoc/man/interactionPval.Rd | 168 SNPassoc-2.1-0/SNPassoc/man/makegeno.Rd | 78 SNPassoc-2.1-0/SNPassoc/man/maxstat.Rd | 128 SNPassoc-2.1-0/SNPassoc/man/odds.Rd | 80 SNPassoc-2.1-0/SNPassoc/man/related.Rd | 44 SNPassoc-2.1-0/SNPassoc/man/setupSNP.Rd | 134 SNPassoc-2.1-0/SNPassoc/man/snp.Rd | 288 SNPassoc-2.1-0/SNPassoc/man/sortSNPs.Rd | 88 SNPassoc-2.1-0/SNPassoc/man/tableHWE.Rd | 114 SNPassoc-2.1-0/SNPassoc/vignettes/SNPassoc.Rmd | 864 +- SNPassoc-2.1-0/SNPassoc/vignettes/multiomic.bib | 4232 ++++++------- 114 files changed, 9853 insertions(+), 9888 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.32.1 dated 2022-07-21 and 1.33.0 dated 2022-12-14
DESCRIPTION | 8 MD5 | 58 +- NAMESPACE | 4 NEWS.md | 1067 ++++++++++++++++++++++++-------------------- R/autoStopCluster.R | 5 R/availableConnections.R | 2 R/availableCores.R | 86 ++- R/availableWorkers.R | 6 R/cgroups.R | 173 ++++++- R/getOptionOrEnvVar.R | 22 R/isNodeAlive.R | 4 R/killNode.R |only R/makeClusterPSOCK.R | 32 - R/makeNodePSOCK.R | 34 + R/makeZZZ.R |only R/ports.R | 4 R/utils,cluster.R | 15 R/utils,pid.R | 70 +- R/utils.R | 50 ++ README.md | 6 inst/WORDLIST | 11 man/autoStopCluster.Rd | 11 man/availableConnections.Rd | 2 man/availableCores.Rd | 54 +- man/availableWorkers.Rd | 6 man/freePort.Rd | 4 man/isNodeAlive.Rd | 4 man/killNode.Rd |only man/makeClusterPSOCK.Rd | 64 ++ man/pid_exists.Rd | 8 tests/cgroups.R | 11 tests/killNode.R |only 32 files changed, 1227 insertions(+), 594 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] ,
Kurt Hornik [aut] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-9 dated 2022-10-19 and 0.7-10 dated 2022-12-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/source.R | 34 +++++++++++++++++++--------------- build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary 9 files changed, 39 insertions(+), 27 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore [aut,cre],
Pierfrancesco Alaimo Di Loro [ctb],
Marco Mingione [ctb],
Antonio Calcagni' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 2.0 dated 2022-10-20 and 2.1 dated 2022-12-14
DESCRIPTION | 8 +-- MD5 | 10 ++-- NEWS.md | 108 +++++++++++++++++++++++++++++++++++----------------- R/boot.overlap.R | 7 ++- build/partial.rdb |binary man/boot.overlap.Rd | 4 - 6 files changed, 89 insertions(+), 48 deletions(-)
Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for
mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means
Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining
and Knowledge Discovery 2, 283-304.
Author: Gero Szepannek [aut, cre], Rabea Aschenbruck [aut]
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between clustMixType versions 0.2-15 dated 2021-08-18 and 0.3-9 dated 2022-12-14
DESCRIPTION | 12 MD5 | 27 - NAMESPACE | 3 NEWS | 63 ++ R/clustervalidation.R | 11 R/kprototypes.R | 749 ++++++++++++++++++++------------ R/kprototypes_gower.R |only README.md | 17 build/partial.rdb |binary man/figures/logo.png |binary man/kproto.Rd | 276 ++++++----- man/kproto_gower.Rd |only man/plot.kproto.Rd |only man/validation_kproto.Rd | 308 ++++++------- tests/testthat/test_basics.R | 91 +++ tests/testthat/test_clustervalidation.R | 88 +-- 16 files changed, 1008 insertions(+), 637 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.7.5 dated 2022-11-10 and 1.7.6 dated 2022-12-14
DESCRIPTION | 8 - MD5 | 20 +++- NAMESPACE | 4 R/RcppExports.R | 12 ++ R/auxiliary_routines.R | 8 - R/extract_tip_neighborhood.R |only R/extract_tip_radius.R |only R/get_all_distances_to_tip.R |only R/get_ancestral_nodes.R |only man/extract_tip_neighborhood.Rd |only man/extract_tip_radius.Rd |only man/get_all_distances_to_tip.Rd |only man/get_ancestral_nodes.Rd |only src/RcppExports.cpp | 52 +++++++++++ src/phylogenetics_cpp_routines.cpp | 162 +++++++++++++++++++++++++++++++++++-- 15 files changed, 247 insertions(+), 19 deletions(-)
Title: Efficient Computations of Standard Clustering Comparison
Measures
Description: Implements an efficient O(n) algorithm based on bucket-sorting for
fast computation of standard clustering comparison measures. Available measures
include adjusted Rand index (ARI), normalized information distance (NID),
normalized mutual information (NMI), adjusted mutual information (AMI),
normalized variation information (NVI) and entropy, as described in Vinh et al (2009)
<doi:10.1145/1553374.1553511>. Include AMI (Adjusted Mutual Information) since version 0.1.2,
a modified version of ARI (MARI), as described in Sundqvist et al. <doi:10.1007/s00180-022-01230-7>
and simple Chi-square distance since version 1.0.0.
Author: Julien Chiquet [aut, cre] ,
Guillem Rigaill [aut],
Martina Sundqvist [aut],
Valentin Dervieux [ctb],
Florent Bersani [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between aricode versions 1.0.1 dated 2022-09-05 and 1.0.2 dated 2022-12-14
DESCRIPTION | 14 ++++++++------ MD5 | 6 +++--- NEWS.md | 4 ++++ R/aricode.R | 6 ++---- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <htt [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodrìguez [aut] ,
Duncan Temple Lang [aut] ,
Sally Paganin [aut [...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.13.0 dated 2022-11-15 and 0.13.1 dated 2022-12-14
DESCRIPTION | 8 +- MD5 | 8 +- R/MCMC_build.R | 47 ++++++++------ inst/NEWS.md | 8 ++ tests/testthat/test-mcmc.R | 148 +++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 192 insertions(+), 27 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.12 dated 2022-09-29 and 0.1.14 dated 2022-12-14
DESCRIPTION | 6 MD5 | 44 +++---- NEWS.md | 10 + build/vignette.rds |binary configure | 18 +- configure.ac | 2 configure.win | 18 +- inst/doc/leidenbase.html | 237 +++++++++++++++++++-------------------- src/Makevars.in | 2 src/Makevars.win.in | 2 src/rigraph/src/NetRoutines.cpp | 4 src/rigraph/src/attributes.c | 2 src/rigraph/src/bliss/defs.cc | 4 src/rigraph/src/glpk_support.c | 4 src/rigraph/src/init.c | 4 src/rigraph/src/plfit/gss.c | 2 src/rigraph/src/plfit/gss.h | 2 src/rigraph/src/plfit/mt.c | 2 src/rigraph/src/plfit/platform.c | 2 src/rigraph/src/random.c | 2 src/rigraph/src/rinterface.c | 6 src/rigraph/src/uuid/unparse.c | 2 tests/testthat/test-leidenbase.R | 18 +- 23 files changed, 201 insertions(+), 192 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng [aut],
Winston Chang [aut, cre],
RStudio, PBC [cph],
Hector Corrada Bravo [ctb],
Jeroen Ooms [ctb],
Andrzej Krzemienski [cph]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between httpuv versions 1.6.6 dated 2022-09-08 and 1.6.7 dated 2022-12-14
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 118 +++++++++++++++++++++------------------------------------ src/timegm.cpp | 69 ++++++++++++--------------------- src/timegm.h | 2 5 files changed, 79 insertions(+), 126 deletions(-)
Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.callr versions 0.8.0 dated 2022-04-01 and 0.8.1 dated 2022-12-14
future.callr-0.8.0/future.callr/NEWS |only future.callr-0.8.1/future.callr/DESCRIPTION | 10 future.callr-0.8.1/future.callr/MD5 | 16 future.callr-0.8.1/future.callr/NEWS.md |only future.callr-0.8.1/future.callr/R/CallrFuture-class.R | 5 future.callr-0.8.1/future.callr/R/with_stealth_rng.R |only future.callr-0.8.1/future.callr/build/vignette.rds |binary future.callr-0.8.1/future.callr/inst/doc/future.callr.html | 326 +++------- future.callr-0.8.1/future.callr/inst/doc/future.callr.md.rsp | 84 +- future.callr-0.8.1/future.callr/tests/rng.R |only future.callr-0.8.1/future.callr/vignettes/future.callr.md.rsp | 84 +- 11 files changed, 254 insertions(+), 271 deletions(-)
Title: Diagnostic Analysis Using Forward Search Procedure for Various
Models
Description: Identifies potential data outliers and their impact on estimates and analyses. Uses the forward search approach of Atkinson and Riani, "Robust Diagnostic Regression Analysis", 2000,<ISBN: o-387-95017-6>) to prepare descriptive statistics of a dataset that is to be analyzed by stats::lm(), stats::glm(), or nlme::lme(). Includes graphics functions to display the descriptive statistics.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between forsearch versions 2.3.0 dated 2022-04-24 and 3.0.0 dated 2022-12-14
forsearch-2.3.0/forsearch/inst/doc/qc_dataset.R |only forsearch-2.3.0/forsearch/inst/doc/qc_dataset.Rmd |only forsearch-2.3.0/forsearch/inst/doc/qc_dataset.html |only forsearch-2.3.0/forsearch/man/identifyFixedCoeffs.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.Cook.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.deviances.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.leverage.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.params.fixed.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.params.random.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.residuals.Rd |only forsearch-2.3.0/forsearch/man/plotdiag.s2.Rd |only forsearch-2.3.0/forsearch/man/search.history.Rd |only forsearch-2.3.0/forsearch/man/showme.Rd |only forsearch-2.3.0/forsearch/man/showmegl.Rd |only forsearch-2.3.0/forsearch/man/showmelme.Rd |only forsearch-2.3.0/forsearch/vignettes/qc_dataset.Rmd |only forsearch-3.0.0/forsearch/DESCRIPTION | 20 forsearch-3.0.0/forsearch/MD5 | 111 - forsearch-3.0.0/forsearch/NAMESPACE | 7 forsearch-3.0.0/forsearch/NEWS.md | 26 forsearch-3.0.0/forsearch/R/aStep1.R |only forsearch-3.0.0/forsearch/R/aStep2.R |only forsearch-3.0.0/forsearch/R/bStep1.R |only forsearch-3.0.0/forsearch/R/bStep2.R |only forsearch-3.0.0/forsearch/R/forsearch_glm.R | 172 +- forsearch-3.0.0/forsearch/R/forsearch_lm.R | 315 ++-- forsearch-3.0.0/forsearch/R/forsearch_lme.R | 707 ++++------ forsearch-3.0.0/forsearch/R/picksome.R |only forsearch-3.0.0/forsearch/R/plotdiag.AICX.R | 21 forsearch-3.0.0/forsearch/R/plotdiag.Cook.R | 21 forsearch-3.0.0/forsearch/R/plotdiag.allgraphs.R |only forsearch-3.0.0/forsearch/R/plotdiag.deviance.residuals.R | 22 forsearch-3.0.0/forsearch/R/plotdiag.deviances.R | 25 forsearch-3.0.0/forsearch/R/plotdiag.fit3.R | 18 forsearch-3.0.0/forsearch/R/plotdiag.leverage.R | 16 forsearch-3.0.0/forsearch/R/plotdiag.params.fixed.R | 20 forsearch-3.0.0/forsearch/R/plotdiag.params.random.R | 21 forsearch-3.0.0/forsearch/R/plotdiag.phihatx.R | 23 forsearch-3.0.0/forsearch/R/plotdiag.residuals.R | 18 forsearch-3.0.0/forsearch/R/plotdiag.s2.R | 21 forsearch-3.0.0/forsearch/R/plotdiag.tstats.R | 22 forsearch-3.0.0/forsearch/R/search.history.R | 11 forsearch-3.0.0/forsearch/R/showme.R | 13 forsearch-3.0.0/forsearch/R/showmegl.R | 8 forsearch-3.0.0/forsearch/R/showmelme.R | 5 forsearch-3.0.0/forsearch/R/variablelist.R |only forsearch-3.0.0/forsearch/README.md | 1 forsearch-3.0.0/forsearch/build/partial.rdb |binary forsearch-3.0.0/forsearch/build/vignette.rds |binary forsearch-3.0.0/forsearch/inst/doc/quality-control-of-the-dataset-using-the-forward-search.R |only forsearch-3.0.0/forsearch/inst/doc/quality-control-of-the-dataset-using-the-forward-search.Rmd |only forsearch-3.0.0/forsearch/inst/doc/quality-control-of-the-dataset-using-the-forward-search.html |only forsearch-3.0.0/forsearch/inst/extdata/train.for3.R |only forsearch-3.0.0/forsearch/man/aStep1.rd |only forsearch-3.0.0/forsearch/man/aStep2.rd |only forsearch-3.0.0/forsearch/man/bStep1.Rd |only forsearch-3.0.0/forsearch/man/bStep2.rd |only forsearch-3.0.0/forsearch/man/forsearch_glm.Rd | 77 - forsearch-3.0.0/forsearch/man/forsearch_lm.Rd | 88 - forsearch-3.0.0/forsearch/man/forsearch_lme.Rd | 133 + forsearch-3.0.0/forsearch/man/identifyCoeffs.Rd | 16 forsearch-3.0.0/forsearch/man/identifyFixedCoeffs.rd |only forsearch-3.0.0/forsearch/man/picksome.Rd |only forsearch-3.0.0/forsearch/man/plotdiag.AICX.rd | 61 forsearch-3.0.0/forsearch/man/plotdiag.Cook.rd |only forsearch-3.0.0/forsearch/man/plotdiag.allgraphs.rd |only forsearch-3.0.0/forsearch/man/plotdiag.deviances.rd |only forsearch-3.0.0/forsearch/man/plotdiag.fit3.rd | 6 forsearch-3.0.0/forsearch/man/plotdiag.leverage.rd |only forsearch-3.0.0/forsearch/man/plotdiag.params.fixed.rd |only forsearch-3.0.0/forsearch/man/plotdiag.params.random.rd |only forsearch-3.0.0/forsearch/man/plotdiag.phihatx.rd | 9 forsearch-3.0.0/forsearch/man/plotdiag.residuals.rd |only forsearch-3.0.0/forsearch/man/plotdiag.s2.rd |only forsearch-3.0.0/forsearch/man/search.history.rd |only forsearch-3.0.0/forsearch/man/showme.rd |only forsearch-3.0.0/forsearch/man/showmegl.rd |only forsearch-3.0.0/forsearch/man/showmelme.rd |only forsearch-3.0.0/forsearch/man/variablelist.Rd |only forsearch-3.0.0/forsearch/vignettes/quality-control-of-the-dataset-using-the-forward-search.Rmd |only 80 files changed, 971 insertions(+), 1063 deletions(-)
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut],
Julia Silge [cre, aut] ,
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between butcher versions 0.3.0 dated 2022-08-25 and 0.3.1 dated 2022-12-14
DESCRIPTION | 22 ++--- MD5 | 142 +++++++++++++++++---------------- NAMESPACE | 4 NEWS.md | 6 + R/KMeansCluster.R |only R/c5.R | 8 - R/classbagg.R | 8 - R/earth.R | 4 R/elnet.R | 11 -- R/flexsurvreg.R | 4 R/function.R | 6 - R/gausspr.R | 4 R/glmnet.R | 9 -- R/kknn.R | 10 +- R/kproto.R |only R/ksvm.R | 8 - R/lm.R | 6 - R/mda.R | 4 R/model_fit.R | 6 - R/multnet.R | 9 -- R/nnet.R | 6 - R/randomForest.R | 10 +- R/ranger.R | 8 - R/recipe.R | 8 - R/rpart.R | 9 -- R/sclass.R | 8 - R/spark.R | 9 -- R/survreg.R | 6 - R/survreg.penal.R | 7 - R/terms.R | 6 - R/train.R | 4 R/train.recipe.R | 10 -- R/xgb.R | 6 - README.md | 47 +++++----- build/butcher.pdf |binary inst/doc/adding-models-to-butcher.html | 111 ++++++++++++------------- inst/doc/available-axe-methods.R | 3 inst/doc/available-axe-methods.Rmd | 3 inst/doc/available-axe-methods.html | 80 +++++++++++------- inst/doc/butcher.R | 3 inst/doc/butcher.Rmd | 3 inst/doc/butcher.html | 113 +++++++++++++------------- man/axe-C5.0.Rd | 9 +- man/axe-KMeansCluster.Rd |only man/axe-classbagg.Rd | 9 +- man/axe-earth.Rd | 5 - man/axe-elnet.Rd | 12 -- man/axe-flexsurvreg.Rd | 4 man/axe-function.Rd | 6 - man/axe-gausspr.Rd | 5 - man/axe-glmnet.Rd | 10 -- man/axe-kknn.Rd | 10 +- man/axe-kproto.Rd |only man/axe-ksvm.Rd | 8 - man/axe-lm.Rd | 7 - man/axe-mda.Rd | 5 - man/axe-model_fit.Rd | 7 - man/axe-multnet.Rd | 10 -- man/axe-nnet.Rd | 7 - man/axe-randomForest.Rd | 10 +- man/axe-ranger.Rd | 9 +- man/axe-recipe.Rd | 9 -- man/axe-rpart.Rd | 10 +- man/axe-sclass.Rd | 9 +- man/axe-spark.Rd | 10 -- man/axe-survreg.Rd | 7 - man/axe-survreg.penal.Rd | 8 - man/axe-terms.Rd | 6 - man/axe-train.Rd | 5 - man/axe-train.recipe.Rd | 10 +- man/axe-xgb.Booster.Rd | 7 - tests/testthat/test-KMeansCluster.R |only tests/testthat/test-kproto.R |only vignettes/available-axe-methods.Rmd | 3 vignettes/butcher.Rmd | 3 75 files changed, 477 insertions(+), 474 deletions(-)
Title: Tidy Model Stacking
Description: Model stacking is an ensemble technique
that involves training a model to combine the outputs of many
diverse statistical models, and has been shown to improve
predictive performance in a variety of settings. 'stacks'
implements a grammar for 'tidymodels'-aligned model stacking.
Author: Simon Couch [aut, cre],
Max Kuhn [aut],
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between stacks versions 1.0.0 dated 2022-07-06 and 1.0.1 dated 2022-12-14
DESCRIPTION | 10 - MD5 | 101 ++++++----- NAMESPACE | 4 NEWS.md | 25 ++ R/add_candidates.R | 186 ++++++++++++--------- R/blend_predictions.R | 55 +++--- R/butcher.R | 6 R/collect_parameters.R | 18 +- R/fit_members.R | 79 +++++---- R/predict.R | 21 +- R/utils.R | 89 ++++------ build/partial.rdb |binary build/vignette.rds |binary data/class_folds.rda |binary data/class_res_nn.rda |binary data/class_res_rf.rda |binary data/log_res_nn.rda |binary data/log_res_rf.rda |binary data/reg_folds.rda |binary data/reg_res_lr.rda |binary data/reg_res_sp.rda |binary data/reg_res_svm.rda |binary data/tree_frogs.rda |binary data/tree_frogs_class_test.rda |binary data/tree_frogs_reg_test.rda |binary inst/doc/basics.R | 41 ++-- inst/doc/basics.Rmd | 42 ++-- inst/doc/basics.html | 237 ++++++++++++++-------------- inst/doc/classification.R | 15 - inst/doc/classification.Rmd | 15 - inst/doc/classification.html | 180 ++++++++++----------- man/add_candidates.Rd | 23 +- man/axe_model_stack.Rd | 6 man/blend_predictions.Rd | 4 man/collect_parameters.Rd | 4 man/fit_members.Rd | 6 man/predict.model_stack.Rd | 5 tests/testthat/_snaps/add_candidates.md |only tests/testthat/_snaps/blend_predictions.md |only tests/testthat/_snaps/collect_parameters.md |only tests/testthat/_snaps/fit_members.md | 32 +++ tests/testthat/_snaps/predict.md |only tests/testthat/_snaps/print.md | 12 - tests/testthat/_snaps/utils.md |only tests/testthat/helper_functions.R | 15 - tests/testthat/test_add_candidates.R | 159 ++++++++++++++---- tests/testthat/test_blend_predictions.R | 128 ++++++--------- tests/testthat/test_butcher.R | 23 -- tests/testthat/test_collect_parameters.R | 32 +-- tests/testthat/test_fit_members.R | 17 -- tests/testthat/test_predict.R | 29 +-- tests/testthat/test_utils.R | 17 -- vignettes/basics.Rmd | 42 ++-- vignettes/classification.Rmd | 15 - 54 files changed, 904 insertions(+), 789 deletions(-)
Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided
by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Thimo Kasper <thimo.kasper@plus.ac.at>,
Florian Griessenberger <florian.griessenberger@plus.ac.at>,
Robert R. Junker <>,
Valentin Petzel <valetin.petzel@sbg.ac.at>,
Wolfgang Trutschnig <wolfgang.trutschnig@plus.ac.at>
Maintainer: Nicolas Dietrich <nicolaspascal.dietrich@plus.ac.at>
Diff between qad versions 1.0.3 dated 2022-07-05 and 1.0.4 dated 2022-12-14
DESCRIPTION | 35 - MD5 | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/qad-vignette.html | 786 +++++++++++++++++------- vignettes/man/figures/README-plotforecast-2.png |binary 6 files changed, 603 insertions(+), 228 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 2.6 dated 2022-09-09 and 2.7 dated 2022-12-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/LinearModel.R | 10 +++++++++- R/plot.MFA.R | 12 +++++++++++- R/print.LinearModel.R | 6 ++++-- man/LinearModel.Rd | 12 +++++++----- man/textual.Rd | 24 ++++++++++++++---------- man/write.infile.Rd | 15 ++++++++------- 9 files changed, 65 insertions(+), 38 deletions(-)
Title: Tool-Box of Chain Ladder Plus Models
Description: Implementation of the chain ladder model under the reverse time framework
introduced in Hiabu (2017) <doi:10.1080/03461238.2016.1240709>.
It also implements extensions that add flexibility to the individual development factors modeling
by allowing practitioners to set their own hazard rate model.
Author: Gabriele Pittarello [aut, cre, cph]
,
Munir Hiabu [aut, cph] ,
Andres Villegas [aut, cph]
Maintainer: Gabriele Pittarello <gabriele.pittarello@uniroma1.it>
Diff between clmplus versions 0.0.1 dated 2022-09-01 and 0.1.0 dated 2022-12-14
clmplus-0.0.1/clmplus/vignettes/chunk10.png |only clmplus-0.0.1/clmplus/vignettes/chunk11.png |only clmplus-0.0.1/clmplus/vignettes/chunk15.png |only clmplus-0.0.1/clmplus/vignettes/chunk18.png |only clmplus-0.0.1/clmplus/vignettes/chunk5.png |only clmplus-0.1.0/clmplus/DESCRIPTION | 12 clmplus-0.1.0/clmplus/MD5 | 61 clmplus-0.1.0/clmplus/R/RtTriangle.R | 21 clmplus-0.1.0/clmplus/R/clmplusRtTriangle.R | 171 + clmplus-0.1.0/clmplus/R/data.R | 13 clmplus-0.1.0/clmplus/R/globalVariables.R | 154 + clmplus-0.1.0/clmplus/R/plotclmplus.R | 446 +-- clmplus-0.1.0/clmplus/R/plotresidualsclmplusmodel.R | 2 clmplus-0.1.0/clmplus/R/properties.R | 2 clmplus-0.1.0/clmplus/README.md | 3 clmplus-0.1.0/clmplus/inst/doc/casestudy1.R | 34 clmplus-0.1.0/clmplus/inst/doc/casestudy1.Rmd | 57 clmplus-0.1.0/clmplus/inst/doc/casestudy1.html | 284 +- clmplus-0.1.0/clmplus/inst/doc/modelscomparison.R | 1597 +++++------ clmplus-0.1.0/clmplus/inst/doc/modelscomparison.Rmd | 531 +-- clmplus-0.1.0/clmplus/inst/doc/modelscomparison.html | 2563 ++++++++++++++----- clmplus-0.1.0/clmplus/man/RtTriangle.Rd | 4 clmplus-0.1.0/clmplus/man/amases.gtpl.Rd | 2 clmplus-0.1.0/clmplus/man/amases.mod.Rd | 2 clmplus-0.1.0/clmplus/man/amases.mtpl.Rd | 2 clmplus-0.1.0/clmplus/man/clmplus.Rd | 68 clmplus-0.1.0/clmplus/man/clmplus.RtTriangle.Rd | 15 clmplus-0.1.0/clmplus/man/clmplus.default.Rd | 66 clmplus-0.1.0/clmplus/man/plot.clmplusmodel.Rd | 4 clmplus-0.1.0/clmplus/man/sifa.gtpl.Rd | 2 clmplus-0.1.0/clmplus/man/sifa.mod.Rd | 2 clmplus-0.1.0/clmplus/man/sifa.mtpl.Rd | 2 clmplus-0.1.0/clmplus/vignettes/casestudy1.Rmd | 57 clmplus-0.1.0/clmplus/vignettes/modelscomparison.Rmd | 531 +-- 34 files changed, 4234 insertions(+), 2474 deletions(-)
Title: Species Distribution Modelling Predictor Datasets
Description: Terrestrial and marine predictors for species distribution modelling
from multiple sources, including WorldClim <https://www.worldclim.org/>,,
ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/>
and MARSPEC <http://www.marspec.org/>.
Author: Samuel Bosch [aut],
Lennert Tyberghein [ctb],
Olivier De Clerck [ctb],
Salvador Fernandez [aut, cre],
Lennert Schepers [ctb],
LifeWatch Belgium [fnd]
Maintainer: Salvador Fernandez <salvador.fernandez@vliz.be>
Diff between sdmpredictors versions 0.2.13 dated 2022-09-13 and 0.2.14 dated 2022-12-14
DESCRIPTION | 11 LICENSE | 2 MD5 | 108 +-- NAMESPACE | 52 - NEWS.md | 123 +-- R/citations.R | 202 +++--- R/compression.R | 156 ++-- R/get_sysdata.R | 6 R/list.R | 804 ++++++++++++------------- R/load.R | 364 +++++------ R/sdmpredictors.R | 72 +- R/stats.R | 822 ++++++++++++------------- R/sysdata.rda |binary R/translator.R | 262 ++++---- README.md | 262 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/quickstart.R | 186 ++--- inst/doc/quickstart.Rmd | 324 +++++----- inst/doc/quickstart.html | 1214 +++++++++++++++++++------------------- man/calculate_statistics.Rd | 72 +- man/compress_file.Rd | 68 +- man/correlation_groups.Rd | 98 +-- man/dataset_citations.Rd | 78 +- man/decompress_file.Rd | 60 - man/equalarea_project.Rd | 42 - man/equalareaproj.Rd | 36 - man/get_datadir.Rd | 52 - man/get_future_layers.Rd | 82 +- man/get_layers_info.Rd | 70 +- man/get_paleo_layers.Rd | 90 +- man/layer_citations.Rd | 82 +- man/layer_stats.Rd | 62 - man/layers_correlation.Rd | 70 +- man/list_datasets.Rd | 78 +- man/list_layers.Rd | 126 +-- man/list_layers_future.Rd | 114 +-- man/list_layers_paleo.Rd | 120 +-- man/load_layers.Rd | 88 +- man/lonlatproj.Rd | 36 - man/pearson_correlation.Rd | 30 man/pearson_correlation_matrix.Rd | 86 +- man/plot_correlation.Rd | 86 +- man/sdm_to_bo.Rd | 42 - man/sdmpredictors.Rd | 74 +- tests/testthat.R | 10 tests/testthat/test-http_status.R | 58 - tests/testthat/test_citations.R | 124 +-- tests/testthat/test_compression.R | 158 ++-- tests/testthat/test_get_sysdata.R | 184 ++--- tests/testthat/test_list.R | 62 - tests/testthat/test_load.R | 360 +++++------ tests/testthat/test_stats.R | 242 +++---- tests/testthat/test_zzzfinal.R | 36 - vignettes/quickstart.Rmd | 324 +++++----- 55 files changed, 4215 insertions(+), 4155 deletions(-)
Title: Fast and Easy Eurostat Data Import and Search
Description: Interface to Eurostat’s Bulk Download Facility with fast data.table-based import of
data, labels, and metadata. On top of the core functionality, data search and data
description/comparison functions are also provided.
Author: Aleksander Rutkowski [aut, cre]
Maintainer: Aleksander Rutkowski <alek.rutkowski@gmail.com>
Diff between eurodata versions 1.5.0 dated 2022-08-31 and 1.6.0 dated 2022-12-14
DESCRIPTION | 10 +++--- MD5 | 6 +-- R/core_import.R | 82 ++++++++++++++++++++++++++++++++++++++++++------------ man/importData.Rd | 13 +++++++- 4 files changed, 85 insertions(+), 26 deletions(-)
Title: Download Data from the CSO 'PxStat' API
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide
format. The Central Statistics Office (CSO) is the national statistical institute of Ireland
and 'PxStat' is the CSOs online database of Official Statistics. This database contains current
and historical data series compiled from CSO statistical releases and is accessed at
<http://data.cso.ie>.
The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides
access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>.
This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Author: Eoin Horgan [aut] ,
Conor Crowley [aut, cre],
Vytas Vaiciulis [aut],
Mervyn O'Luing [aut],
James O'Rourke [aut]
Maintainer: Conor Crowley <conor.crowley@cso.ie>
Diff between csodata versions 1.3.0 dated 2022-10-21 and 1.4.0 dated 2022-12-14
DESCRIPTION | 12 +++--- MD5 | 26 ++++++------- NEWS.md | 14 ++++++- R/cso_get_data.R | 78 +++++++++++++++++++++++++++++++--------- R/cso_get_geo.R | 1 R/cso_get_meta.R | 25 +++++++++--- R/cso_get_toc.R | 20 ++++++---- build/vignette.rds |binary inst/doc/quick_start_guide.Rmd | 2 - inst/doc/quick_start_guide.html | 48 +++++++----------------- man/cso_get_data.Rd | 20 ++++++---- man/cso_get_toc.Rd | 9 +++- man/cso_get_vars.Rd | 2 - vignettes/quick_start_guide.Rmd | 2 - 14 files changed, 162 insertions(+), 97 deletions(-)
Title: GUI for the Generalised Blockmodeling of Valued Networks
Description: This app provides some useful tools for Offering an accessible GUI for generalised blockmodeling of single-relation, one-mode networks. The user can execute blockmodeling without having to write a line code by using the app's visual helps. Moreover, there are several ways to visualisations networks and their partitions. Finally, the results can be exported as if they were produced by writing code. The development of this package is financially supported by the Slovenian Research Agency (www.arrs.gov.si) within the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Fabio Ashtar Telarico [aut, cre]
,
Ales Ziberna [aut]
Maintainer: Fabio Ashtar Telarico <telaricof@fdv.uni-lj.si>
Diff between BlockmodelingGUI versions 1.8.3 dated 2022-05-31 and 1.8.4 dated 2022-12-14
DESCRIPTION | 13 +-- MD5 | 12 +-- NAMESPACE | 28 +++++++ R/BlockmodelingGUI-package.R |only R/app.R | 9 ++ inst/apps/BlockmodelingGUI.R | 66 ++++++++++++----- inst/apps/style.css | 149 ++++++++++++++++++++++------------------ man/BlockmodelingGUI-package.Rd |only 8 files changed, 179 insertions(+), 98 deletions(-)
More information about BlockmodelingGUI at CRAN
Permanent link
Title: Get Data from the Swiss Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.4.3 dated 2022-09-07 and 0.4.4 dated 2022-12-14
BFS-0.4.3/BFS/R/bfs_get_dataset.R |only BFS-0.4.3/BFS/R/bfs_get_metadata.R |only BFS-0.4.3/BFS/man/bfs_get_dataset.Rd |only BFS-0.4.3/BFS/man/bfs_get_metadata.Rd |only BFS-0.4.4/BFS/DESCRIPTION | 10 - BFS-0.4.4/BFS/MD5 | 14 -- BFS-0.4.4/BFS/NAMESPACE | 2 BFS-0.4.4/BFS/NEWS.md | 4 BFS-0.4.4/BFS/R/bfs_get_data.R | 4 BFS-0.4.4/BFS/README.md | 204 ++++++++++++++++++++++++---------- 10 files changed, 161 insertions(+), 77 deletions(-)
Title: Variational Techniques in Epidemiology
Description: Using variational techniques we address some epidemiological
problems as the incidence curve decomposition by inverting the renewal
equation as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118>
and Alvarez et al. (2022) <doi:10.3390/biology11040540> or the estimation of
the functional relationship between epidemiological indicators. We also
propose a learning method for the short time forecast of the trend
incidence curve as described in
Morel et al. (2022) <doi:10.1101/2022.11.05.22281904>.
Author: Luis Alvarez [aut, cre] ,
Jean-David Morel [ctb] ,
Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>
Diff between EpiInvert versions 0.3.0 dated 2022-12-08 and 0.3.1 dated 2022-12-14
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/EpiIndicators.R | 2 +- R/EpiInvert.R | 2 +- R/data.R | 8 ++++---- README.md | 2 +- man/EpiInvertForecast.Rd | 2 +- man/apply_delay.Rd | 2 +- man/owid.Rd | 8 ++++---- tests/testthat/test-EpiInvert.R | 4 ++-- 11 files changed, 35 insertions(+), 29 deletions(-)
Title: Accelerated Oblique Random Survival Forests
Description: Fit, interpret, and make predictions with oblique random survival forests. Oblique decision trees are notoriously slow compared to their axis based counterparts, but 'aorsf' runs as fast or faster than axis-based decision tree algorithms for right-censored time-to-event outcomes. Methods to accelerate and interpret the oblique random survival forest are described in Jaeger et al., (2022) <arXiv:2208.01129>.
Author: Byron Jaeger [aut, cre] ,
Nicholas Pajewski [ctb],
Sawyer Welden [ctb],
Christopher Jackson [rev],
Marvin Wright [rev],
Lukas Burk [rev]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Diff between aorsf versions 0.0.4 dated 2022-11-07 and 0.0.5 dated 2022-12-14
DESCRIPTION | 8 MD5 | 54 ++-- NAMESPACE | 1 NEWS.md | 103 +++++---- R/check.R | 14 - R/orsf.R | 52 +++- R/orsf_attr.R | 21 + R/orsf_pd.R | 21 + R/orsf_vi.R | 11 - R/orsf_vs.R |only R/penalized_cph.R | 108 ++++----- R/roxy.R | 4 README.md | 171 ++++++++------- inst/CITATION | 22 ++ inst/doc/aorsf.html | 161 +++++++------- inst/doc/oobag.html | 137 ++++++------ inst/doc/pd.html | 401 ++++++++++++++++++------------------- man/orsf.Rd | 16 + man/orsf_control_custom.Rd | 7 man/orsf_ice_oob.Rd | 26 +- man/orsf_pd_oob.Rd | 52 ++-- man/orsf_vi.Rd | 111 +++++----- man/orsf_vs.Rd |only man/predict.orsf_fit.Rd | 44 ++-- src/orsf.cpp | 5 tests/testthat/test-orsf.R | 10 tests/testthat/test-orsf_pd.R | 14 + tests/testthat/test-orsf_predict.R | 34 +++ tests/testthat/test-orsf_vi.R | 107 +++++++++ 29 files changed, 1003 insertions(+), 712 deletions(-)
Title: Using Network Evolution Models to Generate Networks with
Selected Blockmodel Type
Description: To study network evolution models and different blockmodeling approaches. Various functions enable generating (temporal) networks with a selected blockmodel type, taking into account selected local network mechanisms. The development of this package is financially supported the Slovenian Research Agency (www.arrs.gov.si) within the research program P5<96>0168 and the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Marjan Cugmas [aut, cre],
Ales Ziberna [aut]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>
Diff between nemBM versions 1.00.00 dated 2022-12-13 and 1.00.01 dated 2022-12-14
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Bivariate Correlated Frailty Models with Varied Variances
Description: Fit and simulate bivariate correlated frailty models with
proportional hazard structure. Frailty distributions, such as gamma and
lognormal models are supported for semiparametric procedures. Frailty variances of the two subjects
can be varied or equal. Details on the models are available in book of
Wienke (2011,ISBN:978-1-4200-7388-1). Bivariate gamma fit is obtained using the approach given
in Iachine (1995) with modifications. Lognormal fit is based on the approach
by Ripatti and Palmgren (2000) <doi:10.1111/j.0006-341X.2000.01016.x>. Frailty distributions,
such as gamma, inverse gaussian and power variance frailty models are supported for parametric approach.
Author: Mesfin Tsegaye [aut, cre],
Yehenew Kifle [aut, ctb]
Maintainer: Mesfin Tsegaye <mesfin.tsegaye@ddu.edu.et>
Diff between bcfrailphdv versions 0.1.0 dated 2020-11-30 and 0.1.1 dated 2022-12-14
bcfrailphdv-0.1.0/bcfrailphdv/R/bcgfrailev.R |only bcfrailphdv-0.1.0/bcfrailphdv/R/coxphgmfr.R |only bcfrailphdv-0.1.0/bcfrailphdv/R/print.bcgfrailev.R |only bcfrailphdv-0.1.0/bcfrailphdv/R/print.coxphgmfr.R |only bcfrailphdv-0.1.0/bcfrailphdv/R/summary.bcgfrailev.R |only bcfrailphdv-0.1.0/bcfrailphdv/R/summary.coxphgmfr.R |only bcfrailphdv-0.1.0/bcfrailphdv/man/bcgfrailev.Rd |only bcfrailphdv-0.1.0/bcfrailphdv/man/coxphgmfr.Rd |only bcfrailphdv-0.1.0/bcfrailphdv/man/print.bcgfrailev.Rd |only bcfrailphdv-0.1.0/bcfrailphdv/man/print.coxphgmfr.Rd |only bcfrailphdv-0.1.0/bcfrailphdv/man/summary.bcgfrailev.Rd |only bcfrailphdv-0.1.0/bcfrailphdv/man/summary.coxphgmfr.Rd |only bcfrailphdv-0.1.1/bcfrailphdv/DESCRIPTION | 19 bcfrailphdv-0.1.1/bcfrailphdv/MD5 | 44 bcfrailphdv-0.1.1/bcfrailphdv/NAMESPACE | 14 bcfrailphdv-0.1.1/bcfrailphdv/R/bcfraildv.R | 265 bcfrailphdv-0.1.1/bcfrailphdv/R/bcfraildv.control.R | 57 bcfrailphdv-0.1.1/bcfrailphdv/R/bcfrailpar.R |only bcfrailphdv-0.1.1/bcfrailphdv/R/print.bcfraildv.R | 39 bcfrailphdv-0.1.1/bcfrailphdv/R/print.bcfrailpar.R |only bcfrailphdv-0.1.1/bcfrailphdv/R/simbcfraildv.R | 330 - bcfrailphdv-0.1.1/bcfrailphdv/R/summary.bcfraildv.R | 40 bcfrailphdv-0.1.1/bcfrailphdv/R/summary.bcfrailpar.R |only bcfrailphdv-0.1.1/bcfrailphdv/R/utilities.R | 4715 ++++++++++------ bcfrailphdv-0.1.1/bcfrailphdv/man/bcfraildv.Rd | 176 bcfrailphdv-0.1.1/bcfrailphdv/man/bcfraildv.control.Rd | 61 bcfrailphdv-0.1.1/bcfrailphdv/man/bcfrailpar.Rd |only bcfrailphdv-0.1.1/bcfrailphdv/man/print.bcfraildv.Rd | 15 bcfrailphdv-0.1.1/bcfrailphdv/man/print.bcfrailpar.Rd |only bcfrailphdv-0.1.1/bcfrailphdv/man/simbcfraildv.Rd | 235 bcfrailphdv-0.1.1/bcfrailphdv/man/summary.bcfraildv.Rd | 18 bcfrailphdv-0.1.1/bcfrailphdv/man/summary.bcfrailpar.Rd |only 32 files changed, 3800 insertions(+), 2228 deletions(-)
Title: Additive Isotonic Proportional Hazards Model
Description: Nonparametric estimation of additive isotonic covariate effects for proportional hazards model.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between aisoph versions 0.2 dated 2022-11-19 and 0.3 dated 2022-12-14
aisoph-0.2/aisoph/R/RcppExports.R |only aisoph-0.2/aisoph/R/newton.raphson.R |only aisoph-0.2/aisoph/R/picm.R |only aisoph-0.2/aisoph/R/print.aisoph.R |only aisoph-0.2/aisoph/src |only aisoph-0.3/aisoph/DESCRIPTION | 14 - aisoph-0.3/aisoph/MD5 | 25 -- aisoph-0.3/aisoph/NAMESPACE | 23 -- aisoph-0.3/aisoph/R/BTF.r |only aisoph-0.3/aisoph/R/NR.R |only aisoph-0.3/aisoph/R/aisoph.R | 53 ++-- aisoph-0.3/aisoph/R/aisoph.ti.R | 360 ++++++++++++++------------------ aisoph-0.3/aisoph/R/cpicm.R |only aisoph-0.3/aisoph/R/initial.R |only aisoph-0.3/aisoph/R/plot.aisoph.R | 60 ++--- aisoph-0.3/aisoph/man/aisoph-package.Rd | 44 +-- aisoph-0.3/aisoph/man/aisoph.Rd | 173 +++++++-------- 17 files changed, 349 insertions(+), 403 deletions(-)
More information about tRophicPosition at CRAN
Permanent link
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.3.5 dated 2021-08-05 and 1.3.6 dated 2022-12-14
DESCRIPTION | 8 MD5 | 22 NEWS.md | 18 R/optim.R | 2 R/sar_average.R | 4 README.md | 6 build/vignette.rds |binary inst/doc/sars-r-package.Rmd | 161 ++++- inst/doc/sars-r-package.html | 838 ++++++++++++++++++++++++++++--- man/figures/README-unnamed-chunk-5-1.png |binary vignettes/REFERENCES.bib | 62 ++ vignettes/sars-r-package.Rmd | 161 ++++- 12 files changed, 1093 insertions(+), 189 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source
package. 'pkgdown' converts your documentation, vignettes, 'README',
and more to 'HTML' making it easy to share information about your
package online.
Author: Hadley Wickham [aut, cre] ,
Jay Hesselberth [aut] ,
Maelle Salmon [aut] ,
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 2.0.6 dated 2022-07-16 and 2.0.7 dated 2022-12-14
pkgdown-2.0.6/pkgdown/tools |only pkgdown-2.0.7/pkgdown/DESCRIPTION | 10 pkgdown-2.0.7/pkgdown/MD5 | 105 +++---- pkgdown-2.0.7/pkgdown/NEWS.md | 12 pkgdown-2.0.7/pkgdown/R/build-reference-index.R | 2 pkgdown-2.0.7/pkgdown/R/build.R | 5 pkgdown-2.0.7/pkgdown/R/pkgdown.R | 2 pkgdown-2.0.7/pkgdown/R/rd-example.R | 7 pkgdown-2.0.7/pkgdown/R/rd-html.R | 2 pkgdown-2.0.7/pkgdown/R/topics.R | 10 pkgdown-2.0.7/pkgdown/R/tweak-homepage.R | 12 pkgdown-2.0.7/pkgdown/R/tweak-reference.R | 4 pkgdown-2.0.7/pkgdown/README.md | 26 - pkgdown-2.0.7/pkgdown/build/pkgdown.pdf |binary pkgdown-2.0.7/pkgdown/build/vignette.rds |binary pkgdown-2.0.7/pkgdown/inst/BS5/templates/head.html | 2 pkgdown-2.0.7/pkgdown/inst/doc/customise.html | 130 +++++---- pkgdown-2.0.7/pkgdown/inst/doc/how-to-update-released-site.html | 124 ++++---- pkgdown-2.0.7/pkgdown/inst/doc/linking.html | 124 ++++---- pkgdown-2.0.7/pkgdown/inst/doc/metadata.Rmd | 6 pkgdown-2.0.7/pkgdown/inst/doc/metadata.html | 130 ++++----- pkgdown-2.0.7/pkgdown/inst/doc/pkgdown.html | 124 ++++---- pkgdown-2.0.7/pkgdown/inst/doc/search.Rmd | 4 pkgdown-2.0.7/pkgdown/inst/doc/search.html | 138 +++++----- pkgdown-2.0.7/pkgdown/inst/po/de/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/inst/po/es/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/inst/po/ko/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/inst/po/pt/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/inst/po/tr/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/inst/po/zh_CN/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.7/pkgdown/man/build_home.Rd | 5 pkgdown-2.0.7/pkgdown/man/build_site.Rd | 5 pkgdown-2.0.7/pkgdown/man/rmd-fragments/home-configuration.Rmd | 3 pkgdown-2.0.7/pkgdown/man/rmd-fragments/sidebar-configuration.Rmd | 2 pkgdown-2.0.7/pkgdown/man/test-links.Rd | 4 pkgdown-2.0.7/pkgdown/po/R-de.po | 122 ++++---- pkgdown-2.0.7/pkgdown/po/R-dk.po | 106 +++---- pkgdown-2.0.7/pkgdown/po/R-es.po | 108 ++++--- pkgdown-2.0.7/pkgdown/po/R-fr.po | 106 +++---- pkgdown-2.0.7/pkgdown/po/R-ko.po | 106 +++---- pkgdown-2.0.7/pkgdown/po/R-pkgdown.pot | 108 ++++--- pkgdown-2.0.7/pkgdown/po/R-pt.po | 106 +++---- pkgdown-2.0.7/pkgdown/po/R-tr.po | 106 +++---- pkgdown-2.0.7/pkgdown/po/R-zh_CN.po | 106 +++---- pkgdown-2.0.7/pkgdown/tests/testthat/_snaps/build-reference-index.md | 2 pkgdown-2.0.7/pkgdown/tests/testthat/_snaps/check.md | 2 pkgdown-2.0.7/pkgdown/tests/testthat/_snaps/rmarkdown.md | 3 pkgdown-2.0.7/pkgdown/tests/testthat/_snaps/tweak-homepage.md | 9 pkgdown-2.0.7/pkgdown/tests/testthat/test-highlight.R | 18 + pkgdown-2.0.7/pkgdown/tests/testthat/test-rd-example.R | 15 + pkgdown-2.0.7/pkgdown/tests/testthat/test-topics.R | 20 + pkgdown-2.0.7/pkgdown/tests/testthat/test-tweak-homepage.R | 20 + pkgdown-2.0.7/pkgdown/vignettes/metadata.Rmd | 6 pkgdown-2.0.7/pkgdown/vignettes/search.Rmd | 4 54 files changed, 1125 insertions(+), 946 deletions(-)
Title: Quantifying Evolution and Selection on Complex Traits
Description: Functions are provided for quantifying evolution and selection on complex traits.
The package implements effective handling and analysis algorithms scaled for
genome-wide data and calculates a composite statistic, denoted Ghat, which is used
to test for selection on a trait. The package provides a number of simple examples
for handling and analysing the genome data and visualising the output and results.
Beissinger et al., (2018) <doi:10.1534/genetics.118.300857>.
Author: Medhat Mahmoud [aut],
Ngoc-Thuy Ha [aut],
Tim Beissinger [aut, cre]
Maintainer: Tim Beissinger <timbeissinger@gmail.com>
Diff between Ghat versions 0.1.0 dated 2019-08-02 and 0.2.0 dated 2022-12-14
DESCRIPTION | 18 +- LICENSE | 4 MD5 | 19 +- NAMESPACE | 46 +++--- R/Ghat.R | 400 +++++++++++++++++++++++++++---------------------------- R/Maiz_wqs.R | 40 ++--- R/ld_decay.R | 218 ++++++++++++++--------------- README.md |only man/Ghat.Rd | 200 +++++++++++++-------------- man/Maize_wqs.Rd | 66 ++++----- man/ld_decay.Rd | 84 +++++------ 11 files changed, 548 insertions(+), 547 deletions(-)
More information about ExNRuleEnsemble at CRAN
Permanent link
Title: Cell Ranger Output Filtering and Metrics Visualization
Description: Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'D [...truncated...]
Author: Rasmus Rydbirk [aut, cre],
Fabienne Kick [aut],
Henrietta Holze [aut],
Xian Xin [ctb]
Maintainer: Rasmus Rydbirk <rasmus.rydbirk@bric.ku.dk>
Diff between CRMetrics versions 0.2.2 dated 2022-11-30 and 0.2.3 dated 2022-12-14
DESCRIPTION | 8 - MD5 | 14 - NEWS.md | 4 R/CRMetrics.R | 109 +++++++++++++-- R/inner_functions.R | 3 man/CRMetrics.Rd | 316 +++++++++++++++++++++------------------------ man/addPlotStatsSamples.Rd | 2 tests/testthat/tests.R | 14 + 8 files changed, 273 insertions(+), 197 deletions(-)
Title: Derivative-Free Optimization in R using C++
Description: Perform derivative-free optimization algorithms in R using C++.
A wrapper interface is provided to call C function of the 'bobyqa' implementation
(See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).
Author: Sam Watson [aut],
Yi Pan [aut, cre],
Éric Thiebaut [aut],
Mike Powell [aut]
Maintainer: Yi Pan <ypan1988@gmail.com>
Diff between rminqa versions 0.1.1 dated 2022-05-10 and 0.2.1 dated 2022-12-14
rminqa-0.1.1/rminqa/src/bobyqa.h |only rminqa-0.1.1/rminqa/src/bobyqa_impl.h |only rminqa-0.1.1/rminqa/src/functor.h |only rminqa-0.1.1/rminqa/src/rbobyqa.h |only rminqa-0.2.1/rminqa/DESCRIPTION | 10 - rminqa-0.2.1/rminqa/MD5 | 28 +-- rminqa-0.2.1/rminqa/NAMESPACE | 14 - rminqa-0.2.1/rminqa/R/zzz.R | 22 +- rminqa-0.2.1/rminqa/inst/include/bobyqa.h | 4 rminqa-0.2.1/rminqa/inst/include/bobyqa_impl.h | 178 ++++++++++----------- rminqa-0.2.1/rminqa/inst/include/functor.h | 211 +++++++++++++------------ rminqa-0.2.1/rminqa/inst/include/rbobyqa.h | 84 ++++----- rminqa-0.2.1/rminqa/man/bobyqa_rosen_x1.Rd | 56 +++--- rminqa-0.2.1/rminqa/man/bobyqa_rosen_x1e.Rd | 58 +++--- rminqa-0.2.1/rminqa/man/rminqa.Rd | 26 +-- rminqa-0.2.1/rminqa/src/RcppExports.cpp | 1 rminqa-0.2.1/rminqa/src/rbobyqa_example.cpp | 30 ++- 17 files changed, 365 insertions(+), 357 deletions(-)
Title: Download and Parse Public Data Released by B3 Exchange
Description: Download and parse public files released by B3 and convert them
into useful formats and data structures common to data analysis
practitioners.
Author: Wilson Freitas [aut, cre],
Marcelo Perlin [aut]
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Diff between rb3 versions 0.0.6 dated 2022-08-19 and 0.0.7 dated 2022-12-14
DESCRIPTION | 12 MD5 | 114 +++-- NAMESPACE | 15 NEWS.md | 29 + R/addin-display-template.R | 4 R/download-data.R | 7 R/downloaders.R | 26 + R/fields.R | 2 R/file.R | 13 R/handlers.R | 2 R/marketdata.R | 26 - R/rb3-package.R | 44 ++ R/readers.R | 21 - R/scraper-cdi.R | 2 R/scraper-cotahist.R | 18 R/scraper-futures.R | 43 +- R/scraper-indexes.R | 133 ++++++ R/scraper-yc.R | 69 +-- R/util.R | 75 +++ R/zzz.R | 8 README.md | 229 ++++++------ build/vignette.rds |binary inst/doc/B3-Indexes.R |only inst/doc/B3-Indexes.Rmd |only inst/doc/B3-Indexes.html |only inst/doc/Fetching-historical-future-rates.R | 3 inst/doc/Fetching-historical-future-rates.Rmd | 5 inst/doc/Fetching-historical-future-rates.html | 60 +-- inst/doc/Fetching-historical-yield-curve.html | 25 - inst/extdata/IBOV.rds |only inst/extdata/templates/GetPortfolioDay.yaml | 62 +-- inst/extdata/templates/GetPortfolioDay_IndexStatistics.yaml |only inst/extdata/templates/GetTheoricalPortfolio.yaml | 36 - man/cotahist_get.Rd | 6 man/download_marketdata.Rd | 2 man/figures/README-setup-1.png |binary man/index_get.Rd |only man/index_weights_get.Rd | 2 man/indexreport_get.Rd | 2 man/maturity2date.Rd | 7 man/rb3-package.Rd | 35 + tests/fixtures |only tests/testthat.R | 2 tests/testthat/helper-help.R | 2 tests/testthat/helper-vcr.R |only tests/testthat/setup.R | 7 tests/testthat/test-bd_arbit.R | 2 tests/testthat/test-cache.R | 2 tests/testthat/test-contrcad.R | 2 tests/testthat/test-downloaders.R | 111 ++++- tests/testthat/test-fields.R | 2 tests/testthat/test-file.R | 2 tests/testthat/test-indexes.R | 22 + tests/testthat/test-indic.R | 2 tests/testthat/test-transmute.R | 22 - vignettes/B3-Indexes.Rmd |only vignettes/Fetching-historical-future-rates.Rmd | 5 57 files changed, 880 insertions(+), 440 deletions(-)
Title: Spatial Structural Diversity Quantification in Raster Data
Description: Spatial structural diversity refers to the spatial, i.e.
horizontal arrangement of landscape elements and can reveal itself as
landscape features, such as patches and linear features. The 'R' package
'StrucDiv' provides methods to quantify spatial structural diversity
in continuous remote sensing data, or in other data in raster format.
Structure is based on the spatial arrangement of value pairs. The 'R' package 'StrucDiv'
includes methods to combine information from different spatial scales, which allows to quantify
multi-scale spatial structural diversity.
Author: Leila Schuh [aut, cre] ,
Reinhard Furrer [aut] ,
Kalina Cherneva [ctb, ctr],
Kirill Mueller [ctr],
Patrick Schratz [ctr],
University Research Priority Progam Global Change and Biodiversity of
the University of Zurich [fnd]
Maintainer: Leila Schuh <l.schuh@posteo.net>
Diff between StrucDiv versions 0.2.0 dated 2022-12-13 and 0.2.1 dated 2022-12-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 5 +++++ inst/doc/StrucDiv.Rmd | 6 +++++- inst/doc/StrucDiv.html | 6 +++++- vignettes/StrucDiv.Rmd | 6 +++++- 6 files changed, 28 insertions(+), 11 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired during 2023, plan transition to sf functions using 'GEOS' at your earliest convenience. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if i [...truncated...]
Author: Roger Bivand [cre, aut] ,
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.5-9 dated 2021-12-14 and 0.6-1 dated 2022-12-14
rgeos-0.5-9/rgeos/man/misc-gBuffer.Rd |only rgeos-0.5-9/rgeos/man/topo-bin-gDifference.Rd |only rgeos-0.5-9/rgeos/man/topo-bin-gIntersection.Rd |only rgeos-0.5-9/rgeos/man/topo-bin-gSymdifference.Rd |only rgeos-0.6-1/rgeos/ChangeLog | 9 rgeos-0.6-1/rgeos/DESCRIPTION | 10 rgeos-0.6-1/rgeos/MD5 | 43 rgeos-0.6-1/rgeos/NAMESPACE | 194 +++- rgeos-0.6-1/rgeos/NEWS.md | 10 rgeos-0.6-1/rgeos/R/AAA.R | 2 rgeos-0.6-1/rgeos/R/rgeos_buffer.R | 1 rgeos-0.6-1/rgeos/R/rgeos_topology_binary.R | 1 rgeos-0.6-1/rgeos/R/rgeos_util.R | 2 rgeos-0.6-1/rgeos/configure | 880 ++++++++++---------- rgeos-0.6-1/rgeos/inst/ChangeLog | 9 rgeos-0.6-1/rgeos/inst/SVN_VERSION | 2 rgeos-0.6-1/rgeos/man/experimental-functions.Rd | 4 rgeos-0.6-1/rgeos/man/rgeos-deprecated.Rd |only rgeos-0.6-1/rgeos/man/topo-bin-gUnion.Rd | 10 rgeos-0.6-1/rgeos/src/Makevars.win | 6 rgeos-0.6-1/rgeos/src/rgeos.c | 2 rgeos-0.6-1/rgeos/src/rgeos_buffer.c | 2 rgeos-0.6-1/rgeos/src/rgeos_geos2R.c | 2 rgeos-0.6-1/rgeos/src/rgeos_topology.c | 4 rgeos-0.6-1/rgeos/tests/leak_by_exception.Rout.save | 10 25 files changed, 690 insertions(+), 513 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.6-2 dated 2022-11-08 and 1.6-3 dated 2022-12-14
DESCRIPTION | 8 +-- MD5 | 34 ++++++------- NAMESPACE | 63 ++++++++++++------------ NEWS.md | 10 +++ configure | 26 +++++----- inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.html | 66 +++++++++++++------------- inst/doc/OGR_shape_encoding.R | 8 +-- inst/doc/OGR_shape_encoding.Rnw | 8 +-- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.R | 5 + inst/doc/PROJ6_GDAL3.Rmd | 6 ++ inst/doc/PROJ6_GDAL3.html | 20 +++---- tests/test_proj.Rout.save | 24 +++------ tests/tests.Rout.save | 56 ++++++++++++++++++---- tests/tripup.Rout.save | 9 ++- vignettes/OGR_shape_encoding.Rnw | 8 +-- vignettes/PROJ6_GDAL3.Rmd | 6 ++ 18 files changed, 210 insertions(+), 149 deletions(-)
Title: Power and Sample Size Calculation Tools
Description: Statistical power and minimum required sample size calculations for (1) testing a proportion (one-sample) against a constant, (2) testing a mean (one-sample) against a constant, (3) testing difference between two proportions (independent samples), (4) testing difference between two means (independent and paired samples), (5) testing a correlation (one-sample) against a constant, (6) testing difference between two correlations (independent samples), (7) testing a coefficient against a constant in multiple linear regression, (8) testing an indirect effect in the mediation analysis (Sobel, Joint, and Monte Carlo), (9) testing an R-squared against zero in linear regression, (10) testing an R-squared difference against zero in hierarchical regression, (11) testing an eta-squared or f-squared (for main and interaction effects) against zero in analysis of variance (could be one-way, two-way, and three-way), (12) testing an eta-squared or f-squared (for main and interaction effects) ag [...truncated...]
Author: Metin Bulus [aut, cre]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between pwrss versions 0.1.0 dated 2022-11-09 and 0.2.0 dated 2022-12-14
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 5 R/pwrss.R | 322 ++++++++++++++++++++++++++++++++++++++++++++++++- README.md | 19 +- inst/CITATION | 2 inst/doc/examples.R | 54 ++++++++ inst/doc/examples.Rmd | 78 ++++++++++- inst/doc/examples.html | 215 ++++++++++++++++++++++++++++++-- man/pwrss.f.reg.Rd | 2 man/pwrss.t.reg.Rd |only man/pwrss.z.med.Rd |only vignettes/examples.Rmd | 78 ++++++++++- 13 files changed, 743 insertions(+), 64 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.12 dated 2022-11-22 and 2.6.13 dated 2022-12-14
DESCRIPTION | 8 MD5 | 24 NEWS.md | 5 build/vignette.rds |binary inst/doc/advanced.html | 1024 ++++++++++----------------------------- inst/testdb.tar.gz |binary src/EMRTrack.h | 8 src/EMRTrackDense.h | 12 src/EMRTrackSparse.h | 4 src/NRExtract.cpp | 2 src/NRPoint.cpp | 14 src/NRTrackExpressionScanner.cpp | 6 src/NRTrackExpressionScanner.h | 6 13 files changed, 324 insertions(+), 789 deletions(-)
Title: Gene and Region Counting of Mutations ("GARCOM")
Description: Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.
Author: Sanjeev Sariya [aut, cre, cph],
Giuseppe Tosto [aut, cph]
Maintainer: Sanjeev Sariya <sanjeevsariya@gmail.com>
Diff between GARCOM versions 1.2.0 dated 2020-10-16 and 1.2.1 dated 2022-12-14
DESCRIPTION | 10 ++++----- MD5 | 9 ++++---- NEWS.md | 59 +++++++++++++++++++++++++++++++++------------------------- README.md | 4 --- inst/CITATION | 5 ++-- inst/extdata |only 6 files changed, 48 insertions(+), 39 deletions(-)
Title: The Free Group
Description: The free group in R; juxtaposition is represented by a
plus. Includes inversion, multiplication by a scalar,
group-theoretic power operation, and Tietze forms. To cite the
package in publications please use Hankin (2022)
<doi:10.48550/ARXIV.2212.05883>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between freegroup versions 1.1-3 dated 2021-11-20 and 1.1-6 dated 2022-12-14
freegroup-1.1-3/freegroup/man/abc.Rd |only freegroup-1.1-6/freegroup/DESCRIPTION | 18 - freegroup-1.1-6/freegroup/MD5 | 75 +++-- freegroup-1.1-6/freegroup/NAMESPACE | 3 freegroup-1.1-6/freegroup/NEWS.md |only freegroup-1.1-6/freegroup/R/freegroup.R | 25 + freegroup-1.1-6/freegroup/R/freeops.R | 10 freegroup-1.1-6/freegroup/build/partial.rdb |binary freegroup-1.1-6/freegroup/build/vignette.rds |binary freegroup-1.1-6/freegroup/data |only freegroup-1.1-6/freegroup/inst/CITATION |only freegroup-1.1-6/freegroup/inst/doc/freegroup.R | 38 +- freegroup-1.1-6/freegroup/inst/doc/freegroup.Rnw | 101 ++++--- freegroup-1.1-6/freegroup/inst/doc/freegroup.pdf |binary freegroup-1.1-6/freegroup/inst/doc/freevig.html | 260 ++------------------ freegroup-1.1-6/freegroup/man/Extract.Rd | 4 freegroup-1.1-6/freegroup/man/Ops.free.Rd | 22 - freegroup-1.1-6/freegroup/man/abelianize.Rd | 23 + freegroup-1.1-6/freegroup/man/alpha.Rd | 30 +- freegroup-1.1-6/freegroup/man/backwards.Rd | 2 freegroup-1.1-6/freegroup/man/c.Rd | 7 freegroup-1.1-6/freegroup/man/char_to_free.Rd | 20 - freegroup-1.1-6/freegroup/man/cumsum.Rd | 1 freegroup-1.1-6/freegroup/man/cycred.Rd | 3 freegroup-1.1-6/freegroup/man/donames.Rd | 2 freegroup-1.1-6/freegroup/man/dot.Rd |only freegroup-1.1-6/freegroup/man/free.Rd | 10 freegroup-1.1-6/freegroup/man/getlet.Rd | 4 freegroup-1.1-6/freegroup/man/keep.Rd | 6 freegroup-1.1-6/freegroup/man/outer.Rd | 32 +- freegroup-1.1-6/freegroup/man/print.Rd | 1 freegroup-1.1-6/freegroup/man/reduce.Rd | 2 freegroup-1.1-6/freegroup/man/rfree.Rd | 8 freegroup-1.1-6/freegroup/man/size.Rd | 5 freegroup-1.1-6/freegroup/man/subs.Rd | 7 freegroup-1.1-6/freegroup/man/sum.Rd | 11 freegroup-1.1-6/freegroup/man/tietze.Rd | 10 freegroup-1.1-6/freegroup/tests/testthat/test_aaa.R | 3 freegroup-1.1-6/freegroup/tests/testthat/test_aab.R | 9 freegroup-1.1-6/freegroup/vignettes/freegroup.Rnw | 101 ++++--- freegroup-1.1-6/freegroup/vignettes/freegroup.bib | 10 41 files changed, 408 insertions(+), 455 deletions(-)
Title: Print a Daily Bible Proverb to Console
Description: A simple package to grab a Bible proverb corresponding to the
day of the month.
Author: Brad Lindblad [aut, cre, cph]
Maintainer: Brad Lindblad <me@bradlindblad.com>
Diff between proverbs versions 0.2.0 dated 2022-11-16 and 0.3.0 dated 2022-12-14
DESCRIPTION | 8 ++-- MD5 | 19 +++++++-- NEWS.md | 5 ++ R/get_proverbs.R | 89 ++++++++++++++++++++++++++++++++++++++++++---- README.md | 3 + build/vignette.rds |binary inst/doc/esv_api_key.R |only inst/doc/esv_api_key.Rmd |only inst/doc/esv_api_key.html |only vignettes/esv_api_key.Rmd |only vignettes/images |only 11 files changed, 109 insertions(+), 15 deletions(-)
Title: Estimating Personalized Diagnostics Rules
Description: Recommend the optimal biomarker for disease screening or diagnosis based on patients' individual characteristics.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between persDx versions 0.1.0 dated 2022-05-30 and 0.2.0 dated 2022-12-14
persDx-0.1.0/persDx/R/lin.persDx.r |only persDx-0.1.0/persDx/man/lin.persDx.Rd |only persDx-0.2.0/persDx/DESCRIPTION | 23 +++++++++------ persDx-0.2.0/persDx/MD5 | 10 +++--- persDx-0.2.0/persDx/NAMESPACE | 8 ++--- persDx-0.2.0/persDx/R/np.lin.persDx.r |only persDx-0.2.0/persDx/man/np.lin.persDx.Rd |only persDx-0.2.0/persDx/man/persDx-package.Rd | 46 +++++++++++++++--------------- 8 files changed, 47 insertions(+), 40 deletions(-)
Title: Draw Histograms and Restricted Cubic Splines (RCS)
Description: You can use this function to easily draw a combined histogram and restricted cubic spline.
The function draws the graph through 'ggplot2'. RCS fitting requires the use of the rcs() function of the 'rms' package.
Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between ggrcs versions 0.2.6 dated 2022-11-28 and 0.2.7 dated 2022-12-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ggrcs.R | 12 +++++++----- R/predata.ols.R | 2 +- man/predata.ols.Rd | 2 +- 5 files changed, 16 insertions(+), 14 deletions(-)
Title: Consensus Clustering for Different Sample Coverage Data
Description: Consensus clustering, also called meta-clustering or cluster ensembles, has been increasingly
used in clinical data. Current consensus clustering methods tend to ensemble a number of different
clusters from mathematical replicates with similar sample coverage. As the fact of common variety
of sample coverage in the real-world data, a new consensus clustering strategy dealing with
such biological replicates is required. This is a two-step consensus clustering package, which
is used to input multiple predictive labels with different sample coverage (missing labels).
Author: Chuanxing Li [aut, cre],
Meng Zhou [aut]
Maintainer: Chuanxing Li <chuan-xing.li@ki.se>
Diff between ccml versions 1.1.0 dated 2022-08-29 and 1.2.0 dated 2022-12-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 39 ++++++++++++++++++++++++--------------- R/callNCW.R | 10 ++++++++-- R/ccml.R | 4 ++-- R/plotCompareCW.R | 6 +++--- R/spectralClusteringAffinity.R | 2 +- man/callNCW.Rd | 2 +- 8 files changed, 49 insertions(+), 34 deletions(-)
Title: Bayesian Multivariate Receptor Modeling
Description: Bayesian analysis of multivariate receptor modeling. The package consists of implementations of the methods of Park and Oh (2015) <doi:10.1016/j.chemolab.2015.08.021>.The package uses 'JAGS'(Just Another Gibbs Sampler) to generate Markov chain Monte Carlo samples of parameters.
Author: Man-Suk Oh [aut, cre],
Eun-Kyung Lee [aut],
Eun Sug Park [aut]
Maintainer: Man-Suk Oh <msoh@ewha.ac.kr>
Diff between bayesMRM versions 2.3.0 dated 2022-11-29 and 2.4.0 dated 2022-12-14
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: R Interface to the CSDP Semidefinite Programming Library
Description: R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.
Author: Hector Corrada Bravo [aut, cre],
Florian Schwendinger [ctb],
Brian Borchers [aut],
Don van den Bergh [ctb]
Maintainer: Hector Corrada Bravo <hcorrada@gmail.com>
Diff between Rcsdp versions 0.1.57.2 dated 2021-11-02 and 0.1.57.4 dated 2022-12-14
Rcsdp-0.1.57.2/Rcsdp/src/Csdp/lib/Csdp.ts |only Rcsdp-0.1.57.4/Rcsdp/DESCRIPTION | 10 + Rcsdp-0.1.57.4/Rcsdp/MD5 | 87 ++++++++--------- Rcsdp-0.1.57.4/Rcsdp/R/Rcsdp.R | 2 Rcsdp-0.1.57.4/Rcsdp/README.md | 2 Rcsdp-0.1.57.4/Rcsdp/man/csdp.Rd | 2 Rcsdp-0.1.57.4/Rcsdp/man/csdp.control.Rd | 4 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/include/declarations.h | 96 +++++++------------ Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/Fnorm.c | 16 --- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/add_mat.c | 5 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/addscaledmat.c | 10 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/allocmat.c | 9 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/calc_dobj.c | 10 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/calc_pobj.c | 8 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/chol.c | 23 ---- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/copy_mat.c | 4 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/easysdp.c | 46 +++------ Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/freeprob.c | 12 -- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/initparams.c | 5 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/initsoln.c | 18 +-- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/linesearch.c | 23 ++-- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/make_i.c | 4 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/makefill.c | 14 +- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/mat_mult.c | 37 +++---- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/mat_multsp.c | 33 +++--- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/matvec.c | 6 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/norms.c | 15 -- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_a.c | 10 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_at.c | 10 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_o.c | 18 +-- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/packed.c | 21 ---- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/psd_feas.c | 40 +++---- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/qreig.c | 6 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/readprob.c | 56 ++--------- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/readsol.c | 18 +-- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sdp.c | 85 +++++++--------- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/solvesys.c | 7 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sortentries.c | 6 - Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sym_mat.c | 4 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/trace_prod.c | 5 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/tweakgap.c | 20 +-- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/user_exit.c | 56 ++++------- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/writeprob.c | 14 +- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/writesol.c | 14 +- Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/zero_mat.c | 4 45 files changed, 355 insertions(+), 540 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-11 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-17 0.1.0