Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), geeglm() (from package 'geepack'), ivreg() (from package 'AER'), ivreg() (from package 'ivreg' when
estimated by ordinary least squares), [...truncated...]
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.9 dated 2023-07-12 and 0.5.10 dated 2023-07-19
DESCRIPTION | 6 - MD5 | 16 +-- NEWS.md | 5 R/conf_int.R | 3 inst/doc/Wald-tests-in-clubSandwich.html | 162 +++++++++++++++---------------- inst/doc/meta-analysis-with-CRVE.html | 64 ++++++------ inst/doc/panel-data-CRVE.html | 102 +++++++++---------- tests/testthat/test_linear_contrast.R | 41 +++++++ tests/testthat/test_rma-mv.R | 2 9 files changed, 224 insertions(+), 177 deletions(-)
Title: Text to Speech Conversion
Description: Converts text into speech using various text-to-speech (TTS) engines and provides an unified interface for accessing their functionality.
With this package, users can easily generate audio files of spoken words, phrases, or sentences from plain text data. The package supports multiple TTS engines,
including Google's 'Cloud Text-to-Speech API', 'Amazon Polly', Microsoft's 'Cognitive Services Text to Speech REST API', and a free TTS engine called 'Coqui TTS'.
Author: Howard Baek [cre] ,
John Muschelli [aut, ctb]
Maintainer: Howard Baek <howardbaek.fh@gmail.com>
Diff between text2speech versions 0.2.13 dated 2020-06-30 and 1.0.0 dated 2023-07-19
text2speech-0.2.13/text2speech/R/tts_amazon_auth.R |only text2speech-0.2.13/text2speech/R/tts_backend.R |only text2speech-0.2.13/text2speech/R/tts_google_auth.R |only text2speech-0.2.13/text2speech/R/tts_microsoft_auth.R |only text2speech-0.2.13/text2speech/R/tts_synthesize.R |only text2speech-0.2.13/text2speech/inst/doc/listing_voices.R |only text2speech-0.2.13/text2speech/inst/doc/listing_voices.Rmd |only text2speech-0.2.13/text2speech/inst/doc/listing_voices.html |only text2speech-0.2.13/text2speech/man/figures |only text2speech-0.2.13/text2speech/tests/testthat/test-translate.R |only text2speech-0.2.13/text2speech/tests/testthat/test-voices.R |only text2speech-0.2.13/text2speech/vignettes/listing_voices.Rmd |only text2speech-1.0.0/text2speech/DESCRIPTION | 46 +- text2speech-1.0.0/text2speech/MD5 | 62 +-- text2speech-1.0.0/text2speech/NAMESPACE | 12 text2speech-1.0.0/text2speech/NEWS.md | 8 text2speech-1.0.0/text2speech/R/aaa_utils.R | 161 +++++++- text2speech-1.0.0/text2speech/R/pcm_to_wav.R | 19 - text2speech-1.0.0/text2speech/R/text2speech-package.R |only text2speech-1.0.0/text2speech/R/tts.R |only text2speech-1.0.0/text2speech/R/tts_auth.R | 147 +++++-- text2speech-1.0.0/text2speech/R/tts_bind_wav.R |only text2speech-1.0.0/text2speech/R/tts_speak_engine.R | 15 text2speech-1.0.0/text2speech/R/tts_voices.R | 188 ++++++--- text2speech-1.0.0/text2speech/README.md | 190 ++++++---- text2speech-1.0.0/text2speech/build/vignette.rds |binary text2speech-1.0.0/text2speech/inst/doc/coqui-tts.R |only text2speech-1.0.0/text2speech/inst/doc/coqui-tts.Rmd |only text2speech-1.0.0/text2speech/inst/doc/coqui-tts.html |only text2speech-1.0.0/text2speech/man/pcm_to_wav.Rd | 7 text2speech-1.0.0/text2speech/man/play_audio.Rd |only text2speech-1.0.0/text2speech/man/set_coqui_path.Rd |only text2speech-1.0.0/text2speech/man/text2speech-package.Rd |only text2speech-1.0.0/text2speech/man/tts.Rd | 140 ++++--- text2speech-1.0.0/text2speech/man/tts_auth.Rd | 62 +-- text2speech-1.0.0/text2speech/man/tts_bind_wav.Rd | 30 - text2speech-1.0.0/text2speech/man/tts_default_voice.Rd |only text2speech-1.0.0/text2speech/man/tts_speak_engine.Rd | 15 text2speech-1.0.0/text2speech/man/tts_voices.Rd | 63 ++- text2speech-1.0.0/text2speech/tests/testthat.R | 8 text2speech-1.0.0/text2speech/tests/testthat/test-tts.R |only text2speech-1.0.0/text2speech/tests/testthat/test-tts_voices.R |only text2speech-1.0.0/text2speech/vignettes/audio |only text2speech-1.0.0/text2speech/vignettes/coqui-tts.Rmd |only 44 files changed, 805 insertions(+), 368 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph] ,
David Barnett [ctb],
Michael Brusco [ctb, cph],
Michael Friendly [ctb],
Hans-Friedrich Koehn [ctb, cph],
Fionn Murtagh [ctb, cph],
Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.4.2 dated 2023-03-08 and 1.5.0 dated 2023-07-19
seriation-1.4.2/seriation/R/seriate_SA.R |only seriation-1.4.2/seriation/man/registry_criterion.Rd |only seriation-1.4.2/seriation/man/registry_seriate.Rd |only seriation-1.4.2/seriation/tests/testthat/test-DendSer_GA.R |only seriation-1.5.0/seriation/DESCRIPTION | 47 seriation-1.5.0/seriation/MD5 | 195 +-- seriation-1.5.0/seriation/NAMESPACE | 16 seriation-1.5.0/seriation/NEWS.md | 44 seriation-1.5.0/seriation/R/AAA_defaults.R |only seriation-1.5.0/seriation/R/AAA_parameters.R | 25 seriation-1.5.0/seriation/R/AAA_registry_criterion.R | 100 + seriation-1.5.0/seriation/R/AAA_registry_seriate.R | 181 ++- seriation-1.5.0/seriation/R/SupremeCourt.R | 17 seriation-1.5.0/seriation/R/criterion.R | 77 - seriation-1.5.0/seriation/R/criterion.dist.R | 44 seriation-1.5.0/seriation/R/criterion.matrix.R | 10 seriation-1.5.0/seriation/R/dissplot.R | 4 seriation-1.5.0/seriation/R/get_order.R | 67 - seriation-1.5.0/seriation/R/ggdissplot.R | 94 - seriation-1.5.0/seriation/R/ggpimage.R | 27 seriation-1.5.0/seriation/R/hmap.R | 50 seriation-1.5.0/seriation/R/lle.R |only seriation-1.5.0/seriation/R/pimage.R | 50 seriation-1.5.0/seriation/R/register_DendSer.R | 107 + seriation-1.5.0/seriation/R/register_GA.R | 91 - seriation-1.5.0/seriation/R/register_optics.R | 13 seriation-1.5.0/seriation/R/register_smacof.R |only seriation-1.5.0/seriation/R/register_tsne.R | 198 +++ seriation-1.5.0/seriation/R/register_umap.R | 105 + seriation-1.5.0/seriation/R/ser_dist.R | 11 seriation-1.5.0/seriation/R/ser_permutation.R | 2 seriation-1.5.0/seriation/R/ser_permutation_vector.R | 34 seriation-1.5.0/seriation/R/ser_permutation_vector2matrix.R | 4 seriation-1.5.0/seriation/R/seriate.R | 556 ++++++--- seriation-1.5.0/seriation/R/seriate.array.R | 24 seriation-1.5.0/seriation/R/seriate.data.frame.R | 2 seriation-1.5.0/seriation/R/seriate.dist.R | 33 seriation-1.5.0/seriation/R/seriate.matrix.R | 56 seriation-1.5.0/seriation/R/seriate.table.R | 4 seriation-1.5.0/seriation/R/seriate_ARSA_Branch-Bound.R | 43 seriation-1.5.0/seriation/R/seriate_BEA.R | 68 - seriation-1.5.0/seriation/R/seriate_CA.R | 8 seriation-1.5.0/seriation/R/seriate_GSA.R |only seriation-1.5.0/seriation/R/seriate_HC.R | 116 +- seriation-1.5.0/seriation/R/seriate_LLE.R |only seriation-1.5.0/seriation/R/seriate_MDS.R | 144 +- seriation-1.5.0/seriation/R/seriate_Mean.R |only seriation-1.5.0/seriation/R/seriate_PCA.R | 126 +- seriation-1.5.0/seriation/R/seriate_QAP.R | 32 seriation-1.5.0/seriation/R/seriate_R2E.R | 2 seriation-1.5.0/seriation/R/seriate_SGD.R |only seriation-1.5.0/seriation/R/seriate_SPIN.R | 46 seriation-1.5.0/seriation/R/seriate_TSP.R | 22 seriation-1.5.0/seriation/R/seriate_best.R |only seriation-1.5.0/seriation/R/seriate_enumerate.R |only seriation-1.5.0/seriation/R/seriate_heatmap.R | 114 +- seriation-1.5.0/seriation/R/seriate_identity.R |only seriation-1.5.0/seriation/R/seriate_random.R |only seriation-1.5.0/seriation/R/seriate_reverse.R |only seriation-1.5.0/seriation/R/seriate_spectral.R | 13 seriation-1.5.0/seriation/R/seriate_vegan.R |only seriation-1.5.0/seriation/R/uniscale.R | 283 +++-- seriation-1.5.0/seriation/README.md | 366 ++++-- seriation-1.5.0/seriation/build/partial.rdb |binary seriation-1.5.0/seriation/build/vignette.rds |binary seriation-1.5.0/seriation/data/Chameleon.rda |binary seriation-1.5.0/seriation/data/Irish.rda |binary seriation-1.5.0/seriation/data/Munsingen.rda |binary seriation-1.5.0/seriation/data/Psych24.rda |binary seriation-1.5.0/seriation/data/SupremeCourt.rda |binary seriation-1.5.0/seriation/data/Townships.rda |binary seriation-1.5.0/seriation/data/Wood.rda |binary seriation-1.5.0/seriation/data/Zoo.rda |binary seriation-1.5.0/seriation/inst/README_files/configuration-1.png |only seriation-1.5.0/seriation/inst/README_files/seriation-1.png |binary seriation-1.5.0/seriation/inst/README_files/seriation-2.png |binary seriation-1.5.0/seriation/inst/doc/seriation.R | 53 seriation-1.5.0/seriation/inst/doc/seriation.Rnw | 12 seriation-1.5.0/seriation/inst/doc/seriation.pdf |binary seriation-1.5.0/seriation/man/LS.Rd | 2 seriation-1.5.0/seriation/man/SupremeCourt.Rd | 17 seriation-1.5.0/seriation/man/criterion.Rd | 84 - seriation-1.5.0/seriation/man/dissplot.Rd | 4 seriation-1.5.0/seriation/man/get_order.Rd | 55 seriation-1.5.0/seriation/man/hmap.Rd | 5 seriation-1.5.0/seriation/man/lle.Rd |only seriation-1.5.0/seriation/man/permutation_vector2matrix.Rd | 2 seriation-1.5.0/seriation/man/pimage.Rd | 83 - seriation-1.5.0/seriation/man/register_DendSer.Rd | 32 seriation-1.5.0/seriation/man/register_GA.Rd | 44 seriation-1.5.0/seriation/man/register_optics.Rd | 4 seriation-1.5.0/seriation/man/register_smacof.Rd |only seriation-1.5.0/seriation/man/register_tsne.Rd | 51 seriation-1.5.0/seriation/man/register_umap.Rd | 37 seriation-1.5.0/seriation/man/registry_for_criterion_methods.Rd |only seriation-1.5.0/seriation/man/registry_for_seriaiton_methods.Rd |only seriation-1.5.0/seriation/man/ser_permutation_vector.Rd | 22 seriation-1.5.0/seriation/man/seriate.Rd | 562 ++++++---- seriation-1.5.0/seriation/man/seriate_best.Rd |only seriation-1.5.0/seriation/man/uniscale.Rd | 106 + seriation-1.5.0/seriation/src/arsa.f | 12 seriation-1.5.0/seriation/src/bburcg.f | 17 seriation-1.5.0/seriation/src/bbwrcg.f | 9 seriation-1.5.0/seriation/src/init.c | 12 seriation-1.5.0/seriation/src/nextperm.c |only seriation-1.5.0/seriation/tests/testthat/test-criterion.R | 5 seriation-1.5.0/seriation/tests/testthat/test-dissimilarity.R | 1 seriation-1.5.0/seriation/tests/testthat/test-permuation_vector.R | 4 seriation-1.5.0/seriation/tests/testthat/test-seriate.R | 96 + seriation-1.5.0/seriation/tests/testthat/test-zzz_seriate_extra.R |only seriation-1.5.0/seriation/vignettes/seriation.Rnw | 12 111 files changed, 3291 insertions(+), 1723 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.6.2 dated 2023-03-28 and 3.7.0 dated 2023-07-19
DESCRIPTION | 6 MD5 | 66 +-- NAMESPACE | 1 NEWS.md | 15 R/B_Low_functions.R | 2 R/Class_definitions.R | 35 + R/Data_Functions.R | 3 R/Data_fit_index.R | 132 ++++++- R/Data_make_update.R | 914 ++++++++++++++++++++++++++++++++++++++++++++++++- R/MMSE_Object.r | 4 R/Misc_Exported.R | 4 R/OM_init_doc.R | 6 R/RcppExports.R | 20 - R/SS2Data.R | 24 - R/SS2OM.R | 65 ++- R/SSinternal.R | 2 R/SampleOM.R | 46 +- R/VPA2OM.R | 50 ++ R/applyMMP.R | 6 R/multiMSE.R | 285 ++++++--------- R/popdyn.R | 21 - R/runMSE.R | 15 R/sysdata.rda |binary build/partial.rdb |binary inst/Rmd/Hist/Hist.Rmd | 1 man/Assess2OM.Rd | 1 man/CheckOM.Rd | 48 +- man/Lag_Data.Rd | 114 +++--- man/MSYCalcs.Rd |only man/getnIVs.Rd | 38 +- man/plot.MOM.Rd | 44 +- man/plotRel.Rd | 54 +- man/show-MSEtool.Rd |only man/summary-MMSE.Rd | 40 +- src/MSYcalcs.cpp | 354 +++++++++--------- 35 files changed, 1767 insertions(+), 649 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Nicholas Rockwood [aut] ,
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini K [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-15 dated 2023-03-14 and 0.6-16 dated 2023-07-19
DESCRIPTION | 6 MD5 | 115 ++-- NAMESPACE | 2 R/00generic.R | 4 R/ctr_mplus2lavaan.R | 37 + R/lav_bootstrap.R | 9 R/lav_cfa_bentler1982.R | 61 +- R/lav_cfa_guttman1952.R | 48 + R/lav_data.R | 41 + R/lav_data_update.R | 107 ++++ R/lav_fit.R | 13 R/lav_fit_aic.R | 8 R/lav_fit_cfi.R | 30 - R/lav_fit_measures.R | 16 R/lav_fit_rmsea.R | 11 R/lav_matrix.R | 21 R/lav_model_compute.R | 2 R/lav_model_estimate.R | 7 R/lav_model_gradient.R | 38 - R/lav_model_h1_information.R | 60 ++ R/lav_model_h1_omega.R | 12 R/lav_model_vcov.R | 6 R/lav_mvnorm_missing_h1.R | 1 R/lav_object_generate.R | 6 R/lav_object_inspect.R | 163 ++---- R/lav_object_methods.R | 3 R/lav_object_summary.R | 5 R/lav_options.R | 54 +- R/lav_partable.R | 43 + R/lav_partable_flat.R | 11 R/lav_partable_full.R | 5 R/lav_partable_subset.R | 16 R/lav_partable_unrestricted.R | 12 R/lav_predict.R | 27 + R/lav_print.R | 31 + R/lav_sam_step0.R |only R/lav_sam_step1.R |only R/lav_sam_step2.R |only R/lav_sam_step2_se.R |only R/lav_sam_utils.R |only R/lav_samplestats.R | 19 R/lav_simulate_old.R | 2 R/lav_start.R | 22 R/lav_syntax.R | 24 R/lav_test.R | 2 R/lav_test_satorra_bentler.R | 4 R/lav_test_yuan_bentler.R | 7 R/lav_utils.R | 22 R/xxx_lavaan.R | 70 +- R/xxx_sam.R | 1078 ++++-------------------------------------- README.md | 4 build/partial.rdb |binary man/fitMeasures.Rd | 6 man/lavOptions.Rd | 4 man/lavPredict.Rd | 9 man/lavTestLRT.Rd | 4 man/lav_matrix.Rd | 15 man/model.syntax.Rd | 12 man/modificationIndices.Rd | 2 man/sam.Rd | 31 - man/simulateData.Rd | 10 61 files changed, 1038 insertions(+), 1340 deletions(-)
Title: Cluster-Based Permutation Analysis for Densely Sampled Time Data
Description: An implementation of fast cluster-based permutation analysis
(CPA) for densely-sampled time data developed in Maris & Oostenveld,
2007 <doi:10.1016/j.jneumeth.2007.03.024>. Supports (generalized,
mixed-effects) regression models for the calculation of timewise
statistics. Provides both a wholesale and a piecemeal interface to the
CPA procedure with an emphasis on interpretability and diagnostics.
Integrates 'Julia' libraries 'MixedModels.jl' and 'GLM.jl' for
performance improvements, with additional functionalities for
interfacing with 'Julia' from 'R' powered by the 'JuliaConnectoR'
package.
Author: June Choe [aut, cre, cph]
Maintainer: June Choe <jchoe001@gmail.com>
Diff between jlmerclusterperm versions 1.0.2 dated 2023-07-15 and 1.0.3 dated 2023-07-19
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 8 ++++ R/aaa.R | 2 - R/interop-utils-unexported.R | 82 +++++++++++++++++++++---------------------- README.md | 13 +++--- 6 files changed, 64 insertions(+), 57 deletions(-)
More information about jlmerclusterperm at CRAN
Permanent link
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.4.0 dated 2022-10-12 and 3.5.0 dated 2023-07-19
DESCRIPTION | 16 MD5 | 121 +- NAMESPACE | 16 NEWS.md | 28 R/as_gt.R |only R/as_table.R |only R/globals.R |only R/gsBinomialExact.R | 10 R/gsCP.R | 10 R/gsDesign.R | 20 R/gsMethods.R | 5 R/gsNormalGrid.R | 5 R/gsSpending.R | 56 - R/gsSurv.R | 84 + R/gsWTPT.R | 5 R/gsqplot.R | 46 - R/package.R | 5 R/ssrCP.R | 23 R/toBinomialExact.R |only R/toInteger.R |only R/utils-pipe.R |only README.md | 2 build/vignette.rds |binary inst/doc/GentleIntroductionToGSD.R |only inst/doc/GentleIntroductionToGSD.Rmd |only inst/doc/GentleIntroductionToGSD.html |only inst/doc/PoissonMixtureModel.R | 22 inst/doc/PoissonMixtureModel.html | 377 ++++---- inst/doc/VaccineEfficacy.R | 189 ++-- inst/doc/VaccineEfficacy.Rmd | 271 +++--- inst/doc/VaccineEfficacy.html | 1483 +++++++++++++++++++++++----------- inst/doc/binomialSPRTExample.R |only inst/doc/binomialSPRTExample.Rmd |only inst/doc/binomialSPRTExample.html |only inst/doc/gsSurvBasicExamples.html | 763 +++++++++-------- inst/doc/nNormal.html | 2 inst/doc/toInteger.R |only inst/doc/toInteger.Rmd |only inst/doc/toInteger.html |only man/Spending_Function_Overview.Rd | 5 man/as_gt.Rd |only man/as_table.Rd |only man/eEvents.Rd | 2 man/figures |only man/gsBinomialExact.Rd | 7 man/gsBound.Rd | 5 man/gsBoundCP.Rd | 5 man/gsBoundSummary.Rd | 5 man/gsCP.Rd | 5 man/gsDensity.Rd | 5 man/gsDesign.Rd | 5 man/gsProbability.Rd | 5 man/nSurv.Rd | 20 man/normalGrid.Rd | 5 man/pipe.Rd |only man/plot.gsDesign.Rd | 5 man/sfDistribution.Rd | 5 man/sfExponential.Rd | 8 man/sfHSD.Rd | 5 man/sfLDOF.Rd | 5 man/sfLinear.Rd | 5 man/sfPoints.Rd | 5 man/sfPower.Rd | 7 man/sfSpecial.Rd | 5 man/sfTDist.Rd | 5 man/ssrCP.Rd | 21 man/toBinomialExact.Rd |only man/toInteger.Rd |only vignettes/GentleIntroductionToGSD.Rmd |only vignettes/VaccineEfficacy.Rmd | 271 +++--- vignettes/binomialSPRTExample.Rmd |only vignettes/gsDesign.bib | 54 + vignettes/toInteger.Rmd |only 73 files changed, 2470 insertions(+), 1564 deletions(-)
Title: Estimate Streamflow Depletion Due to Groundwater Pumping
Description: Implementation of analytical models for estimating streamflow
depletion due to groundwater pumping, and other related tools. Functions
are broadly split into two groups: (1) analytical streamflow depletion
models, which estimate streamflow depletion for a single stream reach
resulting from groundwater pumping; and (2) depletion apportionment
equations, which distribute estimated streamflow depletion among multiple
stream reaches within a stream network. See Zipper et al. (2018) <doi:10.1029/2018WR022707>
for more information on depletion apportionment equations and Zipper et
al. (2019) <doi:10.1029/2018WR024403> for more information on analytical
depletion functions, which combine analytical models and depletion apportionment
equations.
Author: Sam Zipper [aut, cre] ,
Ben Kerr [ctb],
Tom Gleeson [ctb] ,
Qiang Li [rev] ,
Foundry Spatial Ltd. [cph]
Maintainer: Sam Zipper <samzipper@ku.edu>
Diff between streamDepletr versions 0.1.1 dated 2020-03-25 and 0.2.0 dated 2023-07-19
DESCRIPTION | 19 MD5 | 69 +- NAMESPACE | 3 NEWS.md | 5 R/apportion_inverse.R | 11 R/apportion_polygon.R | 102 +-- R/apportion_web.R | 10 R/data.R | 2 R/depletion_max_distance.R | 7 R/globals.R | 3 R/hantush.R | 17 R/hunt.R | 15 R/intermittent_pumping.R | 10 R/prep_reach_dist.R | 42 - build/vignette.rds |binary data/stream_lines.rda |binary inst/CITATION |only inst/doc/intro-to-streamDepletr.R | 343 ++++++------ inst/doc/intro-to-streamDepletr.Rmd | 345 +++++++----- inst/doc/intro-to-streamDepletr.html | 947 +++++++++++++++++++++-------------- man/apportion_inverse.Rd | 126 ++-- man/apportion_polygon.Rd | 146 ++--- man/apportion_web.Rd | 130 ++-- man/apportion_wedge.Rd | 66 +- man/depletion_max_distance.Rd | 116 ++-- man/discharge_df.Rd | 56 +- man/glover.Rd | 104 +-- man/hantush.Rd | 110 ++-- man/hunt.Rd | 116 ++-- man/induce_infiltration_rate.Rd | 96 +-- man/induce_infiltration_time.Rd | 110 ++-- man/intermittent_pumping.Rd | 102 +-- man/prep_reach_dist.Rd | 105 +-- man/stream_lines.Rd | 46 - man/streambed_conductance.Rd | 76 +- vignettes/intro-to-streamDepletr.Rmd | 345 +++++++----- 36 files changed, 2062 insertions(+), 1738 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 1.1.2 dated 2023-07-18 and 1.1.3 dated 2023-07-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 14 ++++++++++++++ R/Utilities.R | 6 +++--- build/partial.rdb |binary man/Merge_Seurat_List.Rd | 4 ++-- 6 files changed, 28 insertions(+), 14 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.6 dated 2023-05-25 and 0.0.7 dated 2023-07-19
ChangeLog | 14 +++ DESCRIPTION | 8 - MD5 | 122 +++++++++++++++--------------- R/calendars.R | 1 build/partial.rdb |binary inst/NEWS.Rd | 9 ++ src/calendars.cpp | 3 src/ql/time/calendars/argentina.hpp | 2 src/ql/time/calendars/australia.hpp | 4 src/ql/time/calendars/austria.hpp | 4 src/ql/time/calendars/bespokecalendar.cpp | 4 src/ql/time/calendars/bespokecalendar.hpp | 4 src/ql/time/calendars/botswana.hpp | 2 src/ql/time/calendars/brazil.hpp | 4 src/ql/time/calendars/canada.hpp | 4 src/ql/time/calendars/chile.hpp | 2 src/ql/time/calendars/china.hpp | 4 src/ql/time/calendars/czechrepublic.hpp | 2 src/ql/time/calendars/denmark.cpp | 2 src/ql/time/calendars/denmark.hpp | 4 src/ql/time/calendars/finland.cpp | 4 src/ql/time/calendars/finland.hpp | 4 src/ql/time/calendars/france.hpp | 4 src/ql/time/calendars/germany.hpp | 10 +- src/ql/time/calendars/hongkong.cpp | 17 ++++ src/ql/time/calendars/hongkong.hpp | 2 src/ql/time/calendars/hungary.hpp | 2 src/ql/time/calendars/iceland.hpp | 2 src/ql/time/calendars/india.cpp | 5 - src/ql/time/calendars/india.hpp | 4 src/ql/time/calendars/indonesia.hpp | 2 src/ql/time/calendars/israel.hpp | 2 src/ql/time/calendars/italy.hpp | 4 src/ql/time/calendars/japan.hpp | 2 src/ql/time/calendars/jointcalendar.hpp | 2 src/ql/time/calendars/mexico.hpp | 2 src/ql/time/calendars/newzealand.hpp | 2 src/ql/time/calendars/norway.hpp | 2 src/ql/time/calendars/nullcalendar.hpp | 2 src/ql/time/calendars/poland.hpp | 2 src/ql/time/calendars/romania.hpp | 2 src/ql/time/calendars/russia.hpp | 4 src/ql/time/calendars/saudiarabia.hpp | 2 src/ql/time/calendars/singapore.cpp | 6 - src/ql/time/calendars/singapore.hpp | 4 src/ql/time/calendars/slovakia.hpp | 2 src/ql/time/calendars/southafrica.cpp | 1 src/ql/time/calendars/southafrica.hpp | 2 src/ql/time/calendars/southkorea.cpp | 109 +++++++++++++++++++++----- src/ql/time/calendars/southkorea.hpp | 7 - src/ql/time/calendars/sweden.hpp | 2 src/ql/time/calendars/switzerland.hpp | 2 src/ql/time/calendars/taiwan.cpp | 99 ++++++++++++++++++++++++ src/ql/time/calendars/taiwan.hpp | 6 - src/ql/time/calendars/target.hpp | 2 src/ql/time/calendars/thailand.hpp | 2 src/ql/time/calendars/turkey.hpp | 2 src/ql/time/calendars/ukraine.hpp | 2 src/ql/time/calendars/unitedkingdom.hpp | 6 - src/ql/time/calendars/unitedstates.cpp | 36 +++++--- src/ql/time/calendars/unitedstates.hpp | 16 ++- src/ql/time/calendars/weekendsonly.hpp | 2 62 files changed, 407 insertions(+), 184 deletions(-)
Title: Dataset and Tools to Research the Riddle of Literary Quality
Description: Dataset and functions to explore quality of literary novels. The package is a part of the Riddle of Literary Quality project, and it contains the data of a reader survey about fiction in Dutch, a description of the novels the readers rated, and the results of stylistic measurements of the novels. The package also contains functions to combine, analyze, and visualize these data. For more details, see: Eder M, van Zundert J, Lensink S, van Dalen-Oskam K (2022). Replicating The Riddle of Literary Quality: The litRiddle package for R. In _Digital Humanities 2022: Conference Abstracts_, 636-637.
Author: Maciej Eder [aut, cre],
Joris van Zundert [aut],
Karina van Dalen-Oskam [aut],
Saskia Lensink [aut]
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between litRiddle versions 0.4.1 dated 2021-12-03 and 1.0.0 dated 2023-07-19
DESCRIPTION | 15 MD5 | 60 +- NAMESPACE | 4 NEWS.md |only R/columnNames.R | 6 R/explain.R | 169 ++++--- R/motivations.R |only R/zzz.R | 19 README.md | 17 build/partial.rdb |binary build/vignette.rds |binary data/books.rda |binary data/datalist | 1 data/motivations.rda |only data/respondents.rda |binary data/reviews.rda |binary inst/CITATION | 49 +- inst/doc/litRiddle.R | 90 +++ inst/doc/litRiddle.Rmd | 230 ++++++++- inst/doc/litRiddle.html | 1020 +++++++++++++++++++++++++++++++++---------- man/books.Rd | 2 man/combine.all.Rd | 2 man/explain.Rd | 2 man/find.dataset.Rd | 2 man/frequencies.Rd | 2 man/get.columns.Rd | 2 man/litRiddle-package.Rd | 7 man/motivations.Rd |only man/motivations.sentences.Rd |only man/motivations.text.Rd |only man/order.responses.Rd | 2 man/respondents.Rd | 2 man/reviews.Rd | 2 vignettes/litRiddle.Rmd | 230 ++++++++- 34 files changed, 1531 insertions(+), 404 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see <doi:10.1016/j.csda.2023.107796>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 2.0.1 dated 2023-05-09 and 2.0.2 dated 2023-07-19
DESCRIPTION | 8 - MD5 | 117 ++++++++++++++------------ NAMESPACE | 1 NEWS.md | 18 ++++ R/BurkinaFarms.R |only R/BurkinaFarms_polys.R |only R/RcppExports.R | 10 +- R/cdf2quantile.R | 2 R/dcomper.R | 6 - R/dcomper_mv.R | 14 +-- R/dcop.R | 70 +++++++-------- R/delta_bounds.R | 20 ++-- R/dnormexp.R | 6 - R/dnormhnorm.R | 2 R/dsfa-package.R | 64 +++++++------- R/dsfa.R |only R/efficiency.R | 22 +++-- R/elasticity.R | 30 ++++-- R/mgcv_comper.R | 113 ++++++++++++++++--------- R/mgcv_comper_mv.R | 184 +++++++++++++++++++++++++++++++----------- R/mgcv_cop.R | 53 ++++++++---- R/mom2par.R | 2 R/par2mom.R | 5 - build/partial.rdb |binary data/BurkinaFarms.RData |only data/BurkinaFarms_polys.RData |only data/manuf.RData |binary inst/REFERENCES.bib | 33 ++++--- man/BurkinaFarms.Rd |only man/BurkinaFarms_polys.Rd |only man/cdf2quantile.Rd | 2 man/chainrule.Rd | 6 - man/comper.Rd | 37 +++++--- man/comper_mv.Rd | 77 +++++++++++++---- man/cop.Rd | 30 +++--- man/dcomper.Rd | 10 +- man/dcomper_mv.Rd | 30 +++--- man/dcop.Rd | 36 ++++---- man/delta_bounds.Rd | 38 ++++---- man/derivs_transform.Rd | 28 +++--- man/differencerule.Rd | 6 - man/dnormexp.Rd | 9 +- man/dnormhnorm.Rd | 4 man/dsfa.Rd | 103 +++++++++++++++-------- man/efficiency.Rd | 9 +- man/elasticity.Rd | 9 +- man/ind2joint.Rd | 4 man/list2derivs.Rd | 2 man/manuf.Rd | 16 +-- man/mom2par.Rd | 6 - man/par2mom.Rd | 6 - man/productrule.Rd | 6 - man/quotientrule.Rd | 6 - man/sumrule.Rd | 6 - man/transform.Rd | 24 ++--- man/trind.Rd | 22 ++--- man/trind_generator.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 16 +-- src/copulas.cpp | 22 ++--- src/copulas.h | 4 src/trind.cpp | 2 63 files changed, 815 insertions(+), 549 deletions(-)
Title: Continuous-Time Multivariate Analysis
Description: Implements a basis function or functional data analysis framework
for several techniques of multivariate analysis in continuous-time
setting. Specifically, we introduced continuous-time analogues of
several classical techniques of multivariate analysis, such as
principal component analysis, canonical correlation analysis,
Fisher linear discriminant analysis, K-means clustering, and so
on. Details are in Biplab Paul, Philip T. Reiss and Erjia Cui (2023)
"Continuous-time multivariate analysis" <doi:10.48550/arXiv.2307.09404>.
Author: Biplab Paul [aut, cre],
Philip Tzvi Reiss [aut]
Maintainer: Biplab Paul <paul.biplab497@gmail.com>
Diff between ctmva versions 1.2.0 dated 2023-07-04 and 1.3.0 dated 2023-07-19
DESCRIPTION | 14 ++++++-------- MD5 | 6 +++--- R/ctmva-package.R | 5 ++--- man/ctmva-package.Rd | 7 ++----- 4 files changed, 13 insertions(+), 19 deletions(-)
Title: Small N Sequential Multiple Assignment Randomized Trial Methods
Description: Consolidated data simulation, sample size calculation and
analysis functions for several snSMART (small sample sequential,
multiple assignment, randomized trial) designs under one library. See
Wei, B., Braun, T.M., Tamura, R.N. and Kidwell, K.M. "A Bayesian
analysis of small n sequential multiple assignment randomized trials
(snSMARTs)." (2018) Statistics in medicine, 37(26), pp.3723-3732
<doi:10.1002/sim.7900>.
Author: Sidi Wang [aut],
Kelley Kidwell [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between snSMART versions 0.2.2 dated 2022-11-16 and 0.2.3 dated 2023-07-19
DESCRIPTION | 15 +++++++-------- MD5 | 22 +++++++++++----------- R/BJSM_binary.R | 2 +- R/BJSM_c.R | 12 ++++++------ R/bug_files.R | 3 +++ R/group_seq.R | 4 +--- R/sample_size.R | 5 +---- build/partial.rdb |binary man/BJSM_binary.Rd | 2 +- man/BJSM_c.Rd | 8 ++++---- man/group_seq.Rd | 4 +--- man/sample_size.Rd | 3 --- 12 files changed, 36 insertions(+), 44 deletions(-)
Title: Bayesian Inference on Univariate Normal Mixtures
Description: A program for Bayesian analysis of univariate normal mixtures with an unknown number
of components, following the approach of Richardson and Green (1997) <doi:10.1111/1467-9868.00095>.
This makes use of reversible jump Markov chain Monte Carlo methods that are capable of jumping
between the parameter sub-spaces corresponding to different numbers of components in the mixture.
A sample from the full joint distribution of all unknown variables is thereby generated,
and this can be used as a basis for a thorough presentation of many aspects of the posterior
distribution.
Author: Peter Green [aut, cre]
Maintainer: Peter Green <P.J.Green@bristol.ac.uk>
Diff between Nmix versions 2.0.3 dated 2022-04-06 and 2.0.4 dated 2023-07-19
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ build/partial.rdb |binary data/enz.rda |binary data/galx.rda |binary data/lnacid.rda |binary man/Nmix-package.Rd | 2 -- man/Nmix.Rd | 6 +++--- man/plot.nmix.Rd | 2 +- man/print.nmix.Rd | 21 +++++---------------- src/Makevars | 2 +- src/Nmix-sub3z.f | 4 ++-- src/wrapper.c | 2 +- 13 files changed, 29 insertions(+), 42 deletions(-)
Title: Accessing the Flipside Crypto ShroomDK API
Description: Programmatic access to Flipside Crypto data via the Compass RPC API: <https://api-docs.flipsidecrypto.xyz/>. As simple as auto_paginate_query() but with core functions as needed for troubleshooting. Note, 0.1.1 support deprecated 2023-05-31.
Author: Carlos Mercado
Maintainer: Carlos Mercado <carlos.mercado@flipsidecrypto.com>
Diff between shroomDK versions 0.2.1 dated 2023-05-30 and 0.2.2 dated 2023-07-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/auto_paginate_query.R | 7 +++++-- README.md | 9 +++++++++ 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.5.3 dated 2023-05-23 and 1.6.0 dated 2023-07-19
SAMtool-1.5.3/SAMtool/src/Makevars |only SAMtool-1.6.0/SAMtool/DESCRIPTION | 17 SAMtool-1.6.0/SAMtool/MD5 | 41 +- SAMtool-1.6.0/SAMtool/NAMESPACE | 3 SAMtool-1.6.0/SAMtool/NEWS.md | 16 SAMtool-1.6.0/SAMtool/R/RCM2MOM.R | 18 SAMtool-1.6.0/SAMtool/R/RCM_assess.R | 54 +- SAMtool-1.6.0/SAMtool/R/RCM_data.R | 210 +++++++---- SAMtool-1.6.0/SAMtool/R/RCM_est.R | 283 ++++++++------ SAMtool-1.6.0/SAMtool/R/RCM_int.R | 342 +++++++++--------- SAMtool-1.6.0/SAMtool/R/RCM_rmd.R | 53 +- SAMtool-1.6.0/SAMtool/R/define_S4_class_RCModel.R | 95 +++-- SAMtool-1.6.0/SAMtool/R/define_S4_generic_RCM.R | 19 - SAMtool-1.6.0/SAMtool/R/define_S4_generic_posterior.R | 99 +---- SAMtool-1.6.0/SAMtool/R/report_auxiliary.R | 142 +++++-- SAMtool-1.6.0/SAMtool/R/rmd_report.R | 15 SAMtool-1.6.0/SAMtool/inst/include/RCM.hpp | 233 +++++++----- SAMtool-1.6.0/SAMtool/inst/include/ns/ns_RCM.hpp | 225 +++++++---- SAMtool-1.6.0/SAMtool/man/RCM.Rd | 24 - SAMtool-1.6.0/SAMtool/man/plot.RCModel.Rd | 4 SAMtool-1.6.0/SAMtool/man/plot_composition.Rd | 44 +- SAMtool-1.6.0/SAMtool/man/posterior.Rd | 4 22 files changed, 1167 insertions(+), 774 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230224.1731 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.2-0 dated 2023-02-02 and 1.3-0 dated 2023-07-19
DESCRIPTION | 10 - MD5 | 62 ++++++--- NAMESPACE | 5 NEWS.md | 25 +++ R/deleteParticipant.R |only R/expressionFromAttributeValue.R |only R/expressionFromAttributeValues.R |only R/expressionFromIds.R |only R/expressionFromTranscriptTypes.R |only R/formatTranscript.R | 2 R/getAllUtterances.R | 12 + R/getMatches.R | 126 +++++++++++++++----- R/getParticipant.R |only R/getParticipantAttributes.R | 2 R/labbcatVersionInfo.R |only R/nzilbb.labbcat.R | 4 R/processWithPraat.R | 9 + R/removeDictionaryEntry.R | 1 R/renameParticipants.R |only R/saveLayer.R | 60 ++++----- R/saveParticipant.R |only build/partial.rdb |binary man/deleteParticipant.Rd |only man/expressionFromAttributeValue.Rd |only man/expressionFromAttributeValues.Rd |only man/expressionFromIds.Rd |only man/expressionFromTranscriptTypes.Rd |only man/formatTranscript.Rd | 2 man/getMatches.Rd | 41 ++++-- man/getParticipant.Rd |only man/labbcatVersionInfo.Rd |only man/nzilbb.labbcat.Rd | 2 man/processWithPraat.Rd | 9 + man/renameParticipants.Rd |only man/saveLayer.Rd | 32 ++--- man/saveParticipant.Rd |only tests/testthat/test-expressionFromAttribute.R |only tests/testthat/test-expressionFromIds.R |only tests/testthat/test-expressionFromTranscriptTypes.R |only tests/testthat/test-getAnchors.R | 3 tests/testthat/test-getMatches.R | 14 +- tests/testthat/test-participantManagement.R |only tests/testthat/test-processWithPraat.R | 3 43 files changed, 298 insertions(+), 126 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment
policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment,
and traditional longitudinal effects. Continuous, binary, and categorical treatments are allowed as well are
censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure
irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects
can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Author: Nicholas Williams [aut, cre, cph]
,
Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between lmtp versions 1.3.1 dated 2022-09-07 and 1.3.2 dated 2023-07-19
DESCRIPTION | 6 ++--- MD5 | 16 ++++++------- NEWS.md | 12 ++++++++++ R/sdr.R | 69 ++++++++++++++++++++-------------------------------------- R/theta.R | 11 ++++----- R/tmle.R | 8 ++---- R/utils.R | 6 +++++ README.md | 51 +++++++++++++++--------------------------- inst/CITATION | 13 +++++----- 9 files changed, 86 insertions(+), 106 deletions(-)
Title: A 'Linter' for R Code
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with
'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual
Studio Code'.
Author: Jim Hester [aut, cre],
Florent Angly [aut] ,
Russ Hyde [aut],
Michael Chirico [aut],
Kun Ren [aut],
Alexander Rosenstock [aut] ,
Indrajeet Patil [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 3.0.2 dated 2022-10-19 and 3.1.0 dated 2023-07-19
lintr-3.0.2/lintr/R/closed_curly_linter.R |only lintr-3.0.2/lintr/R/consecutive_stopifnot_linter.R |only lintr-3.0.2/lintr/R/no_tab_linter.R |only lintr-3.0.2/lintr/R/object_name_linters.R |only lintr-3.0.2/lintr/R/open_curly_linter.R |only lintr-3.0.2/lintr/R/paren_brace_linter.R |only lintr-3.0.2/lintr/R/path_linters.R |only lintr-3.0.2/lintr/R/single_quotes_linter.R |only lintr-3.0.2/lintr/R/tree-utils.R |only lintr-3.0.2/lintr/R/unneeded_concatenation_linter.R |only lintr-3.0.2/lintr/man/closed_curly_linter.Rd |only lintr-3.0.2/lintr/man/consecutive_stopifnot_linter.Rd |only lintr-3.0.2/lintr/man/no_tab_linter.Rd |only lintr-3.0.2/lintr/man/open_curly_linter.Rd |only lintr-3.0.2/lintr/man/paren_brace_linter.Rd |only lintr-3.0.2/lintr/man/single_quotes_linter.Rd |only lintr-3.0.2/lintr/man/unneeded_concatenation_linter.Rd |only lintr-3.0.2/lintr/tests/testthat/test-consecutive_stopifnot_linter.R |only lintr-3.0.2/lintr/tests/testthat/test-namespace.R |only lintr-3.0.2/lintr/tests/testthat/test-no_tab_linter.R |only lintr-3.0.2/lintr/tests/testthat/test-single_quotes_linter.R |only lintr-3.1.0/lintr/DESCRIPTION | 108 - lintr-3.1.0/lintr/MD5 | 706 +++++----- lintr-3.1.0/lintr/NAMESPACE | 29 lintr-3.1.0/lintr/NEWS.md | 256 +++ lintr-3.1.0/lintr/R/T_and_F_symbol_linter.R | 57 lintr-3.1.0/lintr/R/aaa.R | 16 lintr-3.1.0/lintr/R/absolute_path_linter.R |only lintr-3.1.0/lintr/R/addins.R | 4 lintr-3.1.0/lintr/R/any_duplicated_linter.R | 105 - lintr-3.1.0/lintr/R/any_is_na_linter.R | 49 lintr-3.1.0/lintr/R/assignment_linter.R | 53 lintr-3.1.0/lintr/R/backport_linter.R | 41 lintr-3.1.0/lintr/R/boolean_arithmetic_linter.R |only lintr-3.1.0/lintr/R/brace_linter.R | 169 +- lintr-3.1.0/lintr/R/cache.R | 1 lintr-3.1.0/lintr/R/class_equals_linter.R | 41 lintr-3.1.0/lintr/R/commas_linter.R | 43 lintr-3.1.0/lintr/R/comment_linters.R | 66 lintr-3.1.0/lintr/R/comments.R | 7 lintr-3.1.0/lintr/R/condition_message_linter.R | 50 lintr-3.1.0/lintr/R/conjunct_test_linter.R | 63 lintr-3.1.0/lintr/R/consecutive_assertion_linter.R |only lintr-3.1.0/lintr/R/cyclocomp_linter.R | 19 lintr-3.1.0/lintr/R/declared_functions.R | 11 lintr-3.1.0/lintr/R/deprecated.R | 4 lintr-3.1.0/lintr/R/duplicate_argument_linter.R | 45 lintr-3.1.0/lintr/R/empty_assignment_linter.R |only lintr-3.1.0/lintr/R/equals_na_linter.R | 36 lintr-3.1.0/lintr/R/exclude.R | 26 lintr-3.1.0/lintr/R/expect_comparison_linter.R | 51 lintr-3.1.0/lintr/R/expect_identical_linter.R | 89 - lintr-3.1.0/lintr/R/expect_length_linter.R | 28 lintr-3.1.0/lintr/R/expect_lint.R | 84 - lintr-3.1.0/lintr/R/expect_named_linter.R | 37 lintr-3.1.0/lintr/R/expect_not_linter.R | 25 lintr-3.1.0/lintr/R/expect_null_linter.R | 50 lintr-3.1.0/lintr/R/expect_s3_class_linter.R | 107 - lintr-3.1.0/lintr/R/expect_s4_class_linter.R |only lintr-3.1.0/lintr/R/expect_true_false_linter.R | 35 lintr-3.1.0/lintr/R/expect_type_linter.R | 51 lintr-3.1.0/lintr/R/extract.R | 66 lintr-3.1.0/lintr/R/extraction_operator_linter.R | 59 lintr-3.1.0/lintr/R/fixed_regex_linter.R | 94 + lintr-3.1.0/lintr/R/for_loop_index_linter.R |only lintr-3.1.0/lintr/R/function_argument_linter.R | 46 lintr-3.1.0/lintr/R/function_left_parentheses_linter.R | 93 + lintr-3.1.0/lintr/R/function_return_linter.R |only lintr-3.1.0/lintr/R/get_source_expressions.R | 190 +- lintr-3.1.0/lintr/R/ids_with_token.R | 9 lintr-3.1.0/lintr/R/ifelse_censor_linter.R | 35 lintr-3.1.0/lintr/R/implicit_assignment_linter.R |only lintr-3.1.0/lintr/R/implicit_integer_linter.R | 54 lintr-3.1.0/lintr/R/indentation_linter.R |only lintr-3.1.0/lintr/R/infix_spaces_linter.R | 125 + lintr-3.1.0/lintr/R/inner_combine_linter.R | 39 lintr-3.1.0/lintr/R/is_lint_level.R | 8 lintr-3.1.0/lintr/R/is_numeric_linter.R |only lintr-3.1.0/lintr/R/lengths_linter.R |only lintr-3.1.0/lintr/R/line_length_linter.R | 21 lintr-3.1.0/lintr/R/lint.R | 346 ++-- lintr-3.1.0/lintr/R/linter_tag_docs.R | 4 lintr-3.1.0/lintr/R/linter_tags.R | 35 lintr-3.1.0/lintr/R/lintr-deprecated.R |only lintr-3.1.0/lintr/R/lintr-package.R |only lintr-3.1.0/lintr/R/literal_coercion_linter.R | 99 + lintr-3.1.0/lintr/R/make_linter_from_regex.R | 8 lintr-3.1.0/lintr/R/matrix_apply_linter.R |only lintr-3.1.0/lintr/R/methods.R | 122 + lintr-3.1.0/lintr/R/missing_argument_linter.R | 30 lintr-3.1.0/lintr/R/missing_package_linter.R | 52 lintr-3.1.0/lintr/R/namespace.R | 49 lintr-3.1.0/lintr/R/namespace_linter.R | 59 lintr-3.1.0/lintr/R/nested_ifelse_linter.R | 34 lintr-3.1.0/lintr/R/nonportable_path_linter.R |only lintr-3.1.0/lintr/R/numeric_leading_zero_linter.R | 23 lintr-3.1.0/lintr/R/object_length_linter.R |only lintr-3.1.0/lintr/R/object_name_linter.R |only lintr-3.1.0/lintr/R/object_usage_linter.R | 241 ++- lintr-3.1.0/lintr/R/outer_negation_linter.R | 45 lintr-3.1.0/lintr/R/package_hooks_linter.R | 90 - lintr-3.1.0/lintr/R/paren_body_linter.R | 27 lintr-3.1.0/lintr/R/paste_linter.R | 135 + lintr-3.1.0/lintr/R/path_utils.R |only lintr-3.1.0/lintr/R/pipe_call_linter.R | 19 lintr-3.1.0/lintr/R/pipe_continuation_linter.R | 115 - lintr-3.1.0/lintr/R/quotes_linter.R |only lintr-3.1.0/lintr/R/redundant_equals_linter.R |only lintr-3.1.0/lintr/R/redundant_ifelse_linter.R | 65 lintr-3.1.0/lintr/R/regex_subset_linter.R | 62 lintr-3.1.0/lintr/R/routine_registration_linter.R |only lintr-3.1.0/lintr/R/semicolon_linter.R | 72 - lintr-3.1.0/lintr/R/seq_linter.R | 71 - lintr-3.1.0/lintr/R/settings.R | 76 - lintr-3.1.0/lintr/R/settings_utils.R |only lintr-3.1.0/lintr/R/sort_linter.R |only lintr-3.1.0/lintr/R/spaces_inside_linter.R | 38 lintr-3.1.0/lintr/R/spaces_left_parentheses_linter.R | 19 lintr-3.1.0/lintr/R/sprintf_linter.R | 43 lintr-3.1.0/lintr/R/string_boundary_linter.R | 107 + lintr-3.1.0/lintr/R/strings_as_factors_linter.R | 60 lintr-3.1.0/lintr/R/system_file_linter.R | 37 lintr-3.1.0/lintr/R/trailing_blank_lines_linter.R | 25 lintr-3.1.0/lintr/R/trailing_whitespace_linter.R | 36 lintr-3.1.0/lintr/R/tree_utils.R |only lintr-3.1.0/lintr/R/undesirable_function_linter.R | 53 lintr-3.1.0/lintr/R/undesirable_operator_linter.R | 34 lintr-3.1.0/lintr/R/unnecessary_concatenation_linter.R |only lintr-3.1.0/lintr/R/unnecessary_lambda_linter.R |only lintr-3.1.0/lintr/R/unnecessary_nested_if_linter.R |only lintr-3.1.0/lintr/R/unnecessary_placeholder_linter.R |only lintr-3.1.0/lintr/R/unreachable_code_linter.R | 33 lintr-3.1.0/lintr/R/unused_import_linter.R | 71 - lintr-3.1.0/lintr/R/use_lintr.R | 16 lintr-3.1.0/lintr/R/utils.R | 81 - lintr-3.1.0/lintr/R/vector_logic_linter.R | 40 lintr-3.1.0/lintr/R/whitespace_linter.R |only lintr-3.1.0/lintr/R/with.R | 100 - lintr-3.1.0/lintr/R/xml_nodes_to_lints.R | 12 lintr-3.1.0/lintr/R/yoda_test_linter.R | 34 lintr-3.1.0/lintr/R/zzz.R | 117 + lintr-3.1.0/lintr/README.md | 46 lintr-3.1.0/lintr/build/lintr.pdf |binary lintr-3.1.0/lintr/inst/WORDLIST |only lintr-3.1.0/lintr/inst/doc/continuous-integration.Rmd | 33 lintr-3.1.0/lintr/inst/doc/continuous-integration.html | 32 lintr-3.1.0/lintr/inst/doc/creating_linters.Rmd | 14 lintr-3.1.0/lintr/inst/doc/creating_linters.html | 13 lintr-3.1.0/lintr/inst/doc/editors.R | 6 lintr-3.1.0/lintr/inst/doc/editors.Rmd | 6 lintr-3.1.0/lintr/inst/doc/lintr.R | 26 lintr-3.1.0/lintr/inst/doc/lintr.Rmd | 78 - lintr-3.1.0/lintr/inst/doc/lintr.html | 293 ++-- lintr-3.1.0/lintr/inst/lintr/linters.csv | 45 lintr-3.1.0/lintr/man/T_and_F_symbol_linter.Rd | 32 lintr-3.1.0/lintr/man/absolute_path_linter.Rd | 24 lintr-3.1.0/lintr/man/all_linters.Rd |only lintr-3.1.0/lintr/man/any_duplicated_linter.Rd | 33 lintr-3.1.0/lintr/man/any_is_na_linter.Rd | 37 lintr-3.1.0/lintr/man/assignment_linter.Rd | 55 lintr-3.1.0/lintr/man/available_linters.Rd | 11 lintr-3.1.0/lintr/man/backport_linter.Rd | 24 lintr-3.1.0/lintr/man/best_practices_linters.Rd | 13 lintr-3.1.0/lintr/man/boolean_arithmetic_linter.Rd |only lintr-3.1.0/lintr/man/brace_linter.Rd | 41 lintr-3.1.0/lintr/man/class_equals_linter.Rd | 28 lintr-3.1.0/lintr/man/commas_linter.Rd | 45 lintr-3.1.0/lintr/man/commented_code_linter.Rd | 29 lintr-3.1.0/lintr/man/common_mistakes_linters.Rd | 1 lintr-3.1.0/lintr/man/condition_message_linter.Rd | 44 lintr-3.1.0/lintr/man/configurable_linters.Rd | 17 lintr-3.1.0/lintr/man/conjunct_test_linter.Rd | 33 lintr-3.1.0/lintr/man/consecutive_assertion_linter.Rd |only lintr-3.1.0/lintr/man/consistency_linters.Rd | 7 lintr-3.1.0/lintr/man/cyclocomp_linter.Rd | 18 lintr-3.1.0/lintr/man/default_linters.Rd | 9 lintr-3.1.0/lintr/man/default_settings.Rd | 34 lintr-3.1.0/lintr/man/default_undesirable_functions.Rd | 2 lintr-3.1.0/lintr/man/deprecated_linters.Rd | 6 lintr-3.1.0/lintr/man/duplicate_argument_linter.Rd | 36 lintr-3.1.0/lintr/man/efficiency_linters.Rd | 9 lintr-3.1.0/lintr/man/empty_assignment_linter.Rd |only lintr-3.1.0/lintr/man/equals_na_linter.Rd | 27 lintr-3.1.0/lintr/man/expect_comparison_linter.Rd | 41 lintr-3.1.0/lintr/man/expect_identical_linter.Rd | 37 lintr-3.1.0/lintr/man/expect_length_linter.Rd | 16 lintr-3.1.0/lintr/man/expect_lint.Rd | 15 lintr-3.1.0/lintr/man/expect_named_linter.Rd | 26 lintr-3.1.0/lintr/man/expect_not_linter.Rd | 16 lintr-3.1.0/lintr/man/expect_null_linter.Rd | 27 lintr-3.1.0/lintr/man/expect_s3_class_linter.Rd | 31 lintr-3.1.0/lintr/man/expect_s4_class_linter.Rd | 23 lintr-3.1.0/lintr/man/expect_true_false_linter.Rd | 26 lintr-3.1.0/lintr/man/expect_type_linter.Rd | 21 lintr-3.1.0/lintr/man/extraction_operator_linter.Rd | 48 lintr-3.1.0/lintr/man/fixed_regex_linter.Rd | 52 lintr-3.1.0/lintr/man/for_loop_index_linter.Rd |only lintr-3.1.0/lintr/man/function_argument_linter.Rd | 46 lintr-3.1.0/lintr/man/function_left_parentheses_linter.Rd | 43 lintr-3.1.0/lintr/man/function_return_linter.Rd |only lintr-3.1.0/lintr/man/get_r_string.Rd |only lintr-3.1.0/lintr/man/get_source_expressions.Rd | 14 lintr-3.1.0/lintr/man/ids_with_token.Rd | 9 lintr-3.1.0/lintr/man/ifelse_censor_linter.Rd | 26 lintr-3.1.0/lintr/man/implicit_assignment_linter.Rd |only lintr-3.1.0/lintr/man/implicit_integer_linter.Rd | 47 lintr-3.1.0/lintr/man/indentation_linter.Rd |only lintr-3.1.0/lintr/man/infix_spaces_linter.Rd | 49 lintr-3.1.0/lintr/man/inner_combine_linter.Rd | 25 lintr-3.1.0/lintr/man/is_lint_level.Rd | 10 lintr-3.1.0/lintr/man/is_numeric_linter.Rd |only lintr-3.1.0/lintr/man/lengths_linter.Rd |only lintr-3.1.0/lintr/man/line_length_linter.Rd | 22 lintr-3.1.0/lintr/man/lint-s3.Rd | 2 lintr-3.1.0/lintr/man/lint.Rd | 35 lintr-3.1.0/lintr/man/linters.Rd | 67 lintr-3.1.0/lintr/man/linters_with_defaults.Rd | 20 lintr-3.1.0/lintr/man/linters_with_tags.Rd | 25 lintr-3.1.0/lintr/man/lintr-deprecated.Rd |only lintr-3.1.0/lintr/man/lintr-package.Rd | 6 lintr-3.1.0/lintr/man/literal_coercion_linter.Rd | 34 lintr-3.1.0/lintr/man/matrix_apply_linter.Rd |only lintr-3.1.0/lintr/man/missing_argument_linter.Rd | 31 lintr-3.1.0/lintr/man/missing_package_linter.Rd | 16 lintr-3.1.0/lintr/man/modify_defaults.Rd | 25 lintr-3.1.0/lintr/man/namespace_linter.Rd | 29 lintr-3.1.0/lintr/man/nested_ifelse_linter.Rd | 29 lintr-3.1.0/lintr/man/nonportable_path_linter.Rd | 7 lintr-3.1.0/lintr/man/numeric_leading_zero_linter.Rd | 24 lintr-3.1.0/lintr/man/object_length_linter.Rd | 21 lintr-3.1.0/lintr/man/object_name_linter.Rd | 62 lintr-3.1.0/lintr/man/object_usage_linter.Rd | 48 lintr-3.1.0/lintr/man/outer_negation_linter.Rd | 26 lintr-3.1.0/lintr/man/package_hooks_linter.Rd | 34 lintr-3.1.0/lintr/man/paren_body_linter.Rd | 20 lintr-3.1.0/lintr/man/parse_exclusions.Rd | 2 lintr-3.1.0/lintr/man/paste_linter.Rd | 67 lintr-3.1.0/lintr/man/pipe_call_linter.Rd | 18 lintr-3.1.0/lintr/man/pipe_continuation_linter.Rd | 48 lintr-3.1.0/lintr/man/quotes_linter.Rd |only lintr-3.1.0/lintr/man/read_settings.Rd | 3 lintr-3.1.0/lintr/man/readability_linters.Rd | 24 lintr-3.1.0/lintr/man/redundant_equals_linter.Rd |only lintr-3.1.0/lintr/man/redundant_ifelse_linter.Rd | 38 lintr-3.1.0/lintr/man/regex_subset_linter.Rd | 26 lintr-3.1.0/lintr/man/robustness_linters.Rd | 4 lintr-3.1.0/lintr/man/routine_registration_linter.Rd |only lintr-3.1.0/lintr/man/semicolon_linter.Rd | 63 lintr-3.1.0/lintr/man/seq_linter.Rd | 34 lintr-3.1.0/lintr/man/sort_linter.Rd |only lintr-3.1.0/lintr/man/spaces_inside_linter.Rd | 30 lintr-3.1.0/lintr/man/spaces_left_parentheses_linter.Rd | 21 lintr-3.1.0/lintr/man/sprintf_linter.Rd | 26 lintr-3.1.0/lintr/man/string_boundary_linter.Rd | 41 lintr-3.1.0/lintr/man/strings_as_factors_linter.Rd | 28 lintr-3.1.0/lintr/man/style_linters.Rd | 14 lintr-3.1.0/lintr/man/system_file_linter.Rd | 21 lintr-3.1.0/lintr/man/todo_comment_linter.Rd | 34 lintr-3.1.0/lintr/man/trailing_blank_lines_linter.Rd | 19 lintr-3.1.0/lintr/man/trailing_whitespace_linter.Rd | 35 lintr-3.1.0/lintr/man/undesirable_function_linter.Rd | 50 lintr-3.1.0/lintr/man/undesirable_operator_linter.Rd | 31 lintr-3.1.0/lintr/man/unnecessary_concatenation_linter.Rd |only lintr-3.1.0/lintr/man/unnecessary_lambda_linter.Rd |only lintr-3.1.0/lintr/man/unnecessary_nested_if_linter.Rd |only lintr-3.1.0/lintr/man/unnecessary_placeholder_linter.Rd |only lintr-3.1.0/lintr/man/unreachable_code_linter.Rd | 18 lintr-3.1.0/lintr/man/unused_import_linter.Rd | 35 lintr-3.1.0/lintr/man/use_lintr.Rd | 14 lintr-3.1.0/lintr/man/vector_logic_linter.Rd | 32 lintr-3.1.0/lintr/man/whitespace_linter.Rd |only lintr-3.1.0/lintr/man/yoda_test_linter.Rd | 24 lintr-3.1.0/lintr/tests/testthat.R | 6 lintr-3.1.0/lintr/tests/testthat/default_linter_testcode.R | 4 lintr-3.1.0/lintr/tests/testthat/dummy_packages/assignmentLinter/DESCRIPTION | 3 lintr-3.1.0/lintr/tests/testthat/dummy_packages/assignmentLinter/exec |only lintr-3.1.0/lintr/tests/testthat/dummy_packages/assignmentLinter/tests |only lintr-3.1.0/lintr/tests/testthat/dummy_packages/clean/DESCRIPTION | 1 lintr-3.1.0/lintr/tests/testthat/dummy_packages/clean/NAMESPACE | 10 lintr-3.1.0/lintr/tests/testthat/dummy_packages/clean/R/clean_generics.R | 8 lintr-3.1.0/lintr/tests/testthat/dummy_packages/clean/R/eat_me.R |only lintr-3.1.0/lintr/tests/testthat/dummy_packages/github_lintr_file |only lintr-3.1.0/lintr/tests/testthat/dummy_packages/package/exec |only lintr-3.1.0/lintr/tests/testthat/helper.R | 7 lintr-3.1.0/lintr/tests/testthat/knitr_extended_formats |only lintr-3.1.0/lintr/tests/testthat/knitr_formats/test.qmd |only lintr-3.1.0/lintr/tests/testthat/knitr_malformed/incomplete_r_block.qmd |only lintr-3.1.0/lintr/tests/testthat/test-T_and_F_symbol_linter.R | 13 lintr-3.1.0/lintr/tests/testthat/test-absolute_path_linter.R | 59 lintr-3.1.0/lintr/tests/testthat/test-any_duplicated_linter.R | 9 lintr-3.1.0/lintr/tests/testthat/test-any_is_na_linter.R | 14 lintr-3.1.0/lintr/tests/testthat/test-assignment_linter.R | 69 lintr-3.1.0/lintr/tests/testthat/test-backport_linter.R | 28 lintr-3.1.0/lintr/tests/testthat/test-boolean_arithmetic_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-brace_linter.R | 216 ++- lintr-3.1.0/lintr/tests/testthat/test-cache.R | 304 ++-- lintr-3.1.0/lintr/tests/testthat/test-checkstyle_output.R | 27 lintr-3.1.0/lintr/tests/testthat/test-ci.R | 8 lintr-3.1.0/lintr/tests/testthat/test-class_equals_linter.R | 15 lintr-3.1.0/lintr/tests/testthat/test-closed_curly_linter.R | 114 - lintr-3.1.0/lintr/tests/testthat/test-commas_linter.R | 4 lintr-3.1.0/lintr/tests/testthat/test-commented_code_linter.R | 95 - lintr-3.1.0/lintr/tests/testthat/test-comments.R | 22 lintr-3.1.0/lintr/tests/testthat/test-condition_message_linter.R | 45 lintr-3.1.0/lintr/tests/testthat/test-consecutive_assertion_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-cyclocomp_linter.R | 8 lintr-3.1.0/lintr/tests/testthat/test-defaults.R | 7 lintr-3.1.0/lintr/tests/testthat/test-dir_linters.R | 10 lintr-3.1.0/lintr/tests/testthat/test-duplicate_argument_linter.R | 125 - lintr-3.1.0/lintr/tests/testthat/test-empty_assignment_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-equals_na_linter.R | 77 - lintr-3.1.0/lintr/tests/testthat/test-error.R | 26 lintr-3.1.0/lintr/tests/testthat/test-exclusions.R | 41 lintr-3.1.0/lintr/tests/testthat/test-expect_comparison_linter.R | 10 lintr-3.1.0/lintr/tests/testthat/test-expect_identical_linter.R | 14 lintr-3.1.0/lintr/tests/testthat/test-expect_lint.R | 42 lintr-3.1.0/lintr/tests/testthat/test-expect_named_linter.R | 20 lintr-3.1.0/lintr/tests/testthat/test-expect_not_linter.R | 28 lintr-3.1.0/lintr/tests/testthat/test-expect_null_linter.R | 10 lintr-3.1.0/lintr/tests/testthat/test-expect_s3_class_linter.R | 45 lintr-3.1.0/lintr/tests/testthat/test-expect_s4_class.R |only lintr-3.1.0/lintr/tests/testthat/test-expect_type_linter.R | 1 lintr-3.1.0/lintr/tests/testthat/test-extraction_operator_linter.R | 11 lintr-3.1.0/lintr/tests/testthat/test-fixed_regex_linter.R | 234 +-- lintr-3.1.0/lintr/tests/testthat/test-for_loop_index_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-function_argument_linter.R | 26 lintr-3.1.0/lintr/tests/testthat/test-function_left_parentheses_linter.R | 161 ++ lintr-3.1.0/lintr/tests/testthat/test-function_return_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-get_source_expressions.R | 154 +- lintr-3.1.0/lintr/tests/testthat/test-ids_with_token.R | 10 lintr-3.1.0/lintr/tests/testthat/test-ifelse_censor_linter.R | 3 lintr-3.1.0/lintr/tests/testthat/test-implicit_assignment_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-implicit_integer_linter.R | 141 + lintr-3.1.0/lintr/tests/testthat/test-indentation_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-infix_spaces_linter.R | 47 lintr-3.1.0/lintr/tests/testthat/test-inner_combine_linter.R | 1 lintr-3.1.0/lintr/tests/testthat/test-is_numeric_linter.R |only lintr-3.1.0/lintr/tests/testthat/test-knitr_extended_formats.R |only lintr-3.1.0/lintr/tests/testthat/test-knitr_formats.R | 82 - 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lintr-3.1.0/lintr/tests/testthat/test-xml_nodes_to_lints.R | 84 + lintr-3.1.0/lintr/vignettes/continuous-integration.Rmd | 33 lintr-3.1.0/lintr/vignettes/creating_linters.Rmd | 14 lintr-3.1.0/lintr/vignettes/editors.Rmd | 6 lintr-3.1.0/lintr/vignettes/lintr.Rmd | 78 - 403 files changed, 11214 insertions(+), 4463 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Infrastructure for Person [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.0.0 dated 2023-03-01 and 2.0.1 dated 2023-07-19
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377 files changed, 5786 insertions(+), 3053 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models for conditional quantile functions:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press,
<doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression,
CRC Press, <doi:10.1201/9781315120256>.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] ,
Pin Tian Ng [ctb] ,
Blaise Melly [ctb] ,
Achim Zeileis [ctb] ,
Philip Grosjean [ctb] ,
Cleve Moler [ctb] ,
Yousef Saad [ctb] ,
Victor Chernozhukov [ctb] ,
Ivan Fernandez-Val [ctb] ,
Brian D Ripley [tr [...truncated...]
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.95 dated 2023-04-08 and 5.96 dated 2023-07-19
quantreg-5.95/quantreg/src/etime.f |only quantreg-5.96/quantreg/DESCRIPTION | 6 +++--- quantreg-5.96/quantreg/MD5 | 7 +++---- quantreg-5.96/quantreg/inst/ChangeLog | 4 ++++ quantreg-5.96/quantreg/src/cholesky.f | 8 +++++--- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Lightweight parallel code execution and distributed computing.
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously,
on local or network resources, resolving automatically upon completion.
Features efficient task scheduling, fast inter-process communications, and
Transport Layer Security over TCP/IP for remote connections, courtesy of
'nanonext' and 'NNG' (Nanomsg Next Gen).
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.9.0 dated 2023-06-24 and 0.9.1 dated 2023-07-19
mirai-0.9.0/mirai/man/dot-server.Rd |only mirai-0.9.0/mirai/man/launch_server.Rd |only mirai-0.9.0/mirai/man/server.Rd |only mirai-0.9.1/mirai/DESCRIPTION | 16 mirai-0.9.1/mirai/MD5 | 31 - mirai-0.9.1/mirai/NAMESPACE | 12 mirai-0.9.1/mirai/NEWS.md | 17 mirai-0.9.1/mirai/R/mirai-package.R | 32 - mirai-0.9.1/mirai/R/mirai.R | 780 ++++++++++++++++++++------------- mirai-0.9.1/mirai/README.md | 374 +++++++++------ mirai-0.9.1/mirai/man/daemon.Rd |only mirai-0.9.1/mirai/man/daemons.Rd | 207 ++++---- mirai-0.9.1/mirai/man/dispatcher.Rd | 55 +- mirai-0.9.1/mirai/man/dot-daemon.Rd |only mirai-0.9.1/mirai/man/launch_local.Rd |only mirai-0.9.1/mirai/man/mirai-package.Rd | 15 mirai-0.9.1/mirai/man/mirai.Rd | 11 mirai-0.9.1/mirai/man/saisei.Rd | 19 mirai-0.9.1/mirai/man/status.Rd |only mirai-0.9.1/mirai/tests/tests.R | 46 + 20 files changed, 968 insertions(+), 647 deletions(-)
Title: Multivariable Fractional Polynomials
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: Georg Heinze [cre],
Gareth Ambler [aut],
Axel Benner [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between mfp versions 1.5.2.2 dated 2022-01-20 and 1.5.4 dated 2023-07-19
mfp-1.5.2.2/mfp/NEWS |only mfp-1.5.2.2/mfp/inst/doc/mfp_vignette.Rnw |only mfp-1.5.2.2/mfp/inst/doc/mfp_vignette.pdf |only mfp-1.5.2.2/mfp/vignettes/mfp_vignette.Rnw |only mfp-1.5.4/mfp/DESCRIPTION | 11 mfp-1.5.4/mfp/MD5 | 55 +- mfp-1.5.4/mfp/NAMESPACE | 2 mfp-1.5.4/mfp/NEWS.md |only mfp-1.5.4/mfp/R/cox.R | 12 mfp-1.5.4/mfp/R/fp.R | 24 - mfp-1.5.4/mfp/R/fp.fit.R | 218 ++++----- mfp-1.5.4/mfp/R/fp.order.R | 104 ++-- mfp-1.5.4/mfp/R/fp.out.R | 62 +- mfp-1.5.4/mfp/R/fp.sel.R | 122 ++--- mfp-1.5.4/mfp/R/mfp.R | 663 ++++++++++++++--------------- mfp-1.5.4/mfp/R/mfp.fit.R | 342 +++++++------- mfp-1.5.4/mfp/R/mx.com.R | 40 - mfp-1.5.4/mfp/R/plot.mfp.R | 176 +++---- mfp-1.5.4/mfp/R/predict.mfp.R | 149 +++++- mfp-1.5.4/mfp/R/summary.mfp.R | 12 mfp-1.5.4/mfp/build/vignette.rds |binary mfp-1.5.4/mfp/inst/doc/mfp_vignette.R | 65 +- mfp-1.5.4/mfp/inst/doc/mfp_vignette.Rmd |only mfp-1.5.4/mfp/inst/doc/mfp_vignette.html |only mfp-1.5.4/mfp/man/GBSG.Rd | 88 +-- mfp-1.5.4/mfp/man/bodyfat.Rd | 142 +++--- mfp-1.5.4/mfp/man/cox.Rd | 24 - mfp-1.5.4/mfp/man/fp.Rd | 64 +- mfp-1.5.4/mfp/man/mfp.Rd | 7 mfp-1.5.4/mfp/man/mfp.object.Rd | 114 ++-- mfp-1.5.4/mfp/man/predict.mfp.Rd |only mfp-1.5.4/mfp/vignettes/mfp_vignette.Rmd |only mfp-1.5.4/mfp/vignettes/mfp_vignette.bib | 138 ++---- 33 files changed, 1362 insertions(+), 1272 deletions(-)
Title: 1d Water Level Interpolation along the Rivers Elbe and Rhine
Description: An S4 class and several functions which utilize internally stored
datasets and gauging data enable 1d water level interpolation. The S4 class
(WaterLevelDataFrame) structures the computation and visualisation
of 1d water level information along the German federal waterways Elbe and
Rhine. 'hyd1d' delivers 1d water level data - extracted from the 'FLYS'
database - and validated gauging data - extracted from the hydrological
database 'HyDaBa' - package-internally. For computations near real time
gauging data are queried externally from the 'PEGELONLINE REST API'
<https://pegelonline.wsv.de/webservice/dokuRestapi>.
Author: Arnd Weber [aut, cre] ,
Marcus Hatz [aut],
Wolfgang Stuermer [ctb],
Wilfried Wiechmann [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hyd1d versions 0.4.4 dated 2023-03-06 and 0.4.5 dated 2023-07-19
DESCRIPTION | 8 +++--- MD5 | 36 +++++++++++++++--------------- NEWS.md | 7 +++++ R/data.R | 2 - R/getPegelonlineW.R | 54 +++++++++++++++++++++++++++++++++++++--------- R/updateGaugingData.R | 8 +++--- R/waterLevelFlys3Seq.R | 3 +- R/waterLevelPegelonline.R | 50 ++++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 3 +- inst/REFERENCES.bib | 6 ++--- inst/doc/hyd1d.html | 36 +++++++++++++++--------------- inst/doc/vignette_DE.R | 29 +++++++++++------------- inst/doc/vignette_DE.Rmd | 29 +++++++++++------------- inst/doc/vignette_DE.html | 36 +++++++++++++++--------------- man/df.flys.Rd | 2 - man/getPegelonlineW.Rd | 8 +++++- vignettes/vignette_DE.Rmd | 29 +++++++++++------------- 19 files changed, 221 insertions(+), 125 deletions(-)
Title: User-Friendly GUI Plotting Tools
Description: Create a user-friendly plotting GUI for 'R'.
In addition, one purpose of creating the 'R' package is to facilitate third-party software to call 'R' for drawing, for example, 'Phoenix WinNonlin' software calls 'R' to draw the drug concentration versus time curve.
Author: Fu Yongchao [aut, cre, cph]
Maintainer: Fu Yongchao <3212418315@qq.com>
Diff between guiplot versions 0.4.0 dated 2023-03-27 and 0.4.1 dated 2023-07-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/guiplotServer.R | 48 ++++++++++++++++++++++++++++++++++++++---------- 3 files changed, 43 insertions(+), 15 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.13.0 dated 2023-06-26 and 2.14.0 dated 2023-07-19
DESCRIPTION | 8 - MD5 | 56 +++++---- NAMESPACE | 8 + NEWS.md | 4 R/mrs_data_display.R | 21 ++- R/mrs_data_proc.R | 198 +++++++++++++++++++++++++++++++--- R/mrs_read_dicom.R | 9 - R/mrs_read_ima.R | 2 R/mrs_read_nifti.R | 1 R/mrs_read_pfile.R | 13 +- R/mrs_read_rda.R | 3 R/mrs_read_spar_sdat.R | 9 - R/mrs_read_twix.R | 4 R/mrs_write_nifti.R | 5 inst/doc/spant-intro.html | 129 +++++++++++----------- inst/doc/spant-preprocessing.html | 4 man/Ntrans.Rd |only man/bc_gauss.Rd |only man/bc_spline.Rd |only man/deconv_mrs.Rd |only man/fd_gauss_smo.Rd |only man/ppm.Rd | 4 man/set_Ntrans.Rd |only man/set_tr.Rd |only man/stackplot.mrs_data.Rd | 3 man/tr.Rd |only tests/testthat/abfit_res_coarse.rds |binary tests/testthat/abfit_res_default.rds |binary tests/testthat/abfit_res_fine.rds |binary tests/testthat/abfit_res_no_optim.rds |binary tests/testthat/abfit_sim_mrs_data.rds |binary tests/testthat/abfit_sim_res.rds |binary tests/testthat/def_basis.rds |binary 33 files changed, 347 insertions(+), 134 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability
of linear structural equation models as described in Drton, Foygel, and
Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012)
<doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical
representation of structural equation models.
Author: Rina Foygel Barber [aut],
Mathias Drton [aut],
Luca Weihs [aut],
Nils Sturma [cre, aut]
Maintainer: Nils Sturma <nils.sturma@tum.de>
Diff between SEMID versions 0.4.0 dated 2022-01-13 and 0.4.1 dated 2023-07-19
SEMID-0.4.0/SEMID/man/graphID.globalID.Rd |only SEMID-0.4.0/SEMID/tests/testthat/test_graphID.globalID.R |only SEMID-0.4.1/SEMID/DESCRIPTION | 10 SEMID-0.4.1/SEMID/MD5 | 238 - SEMID-0.4.1/SEMID/NAMESPACE | 253 - SEMID-0.4.1/SEMID/NEWS.md | 10 SEMID-0.4.1/SEMID/R/FlowGraph.R | 280 - SEMID-0.4.1/SEMID/R/LatentDigraph.R | 1954 ++++++------ SEMID-0.4.1/SEMID/R/MixedGraph.R | 914 ++--- SEMID-0.4.1/SEMID/R/SEMID.R | 231 - SEMID-0.4.1/SEMID/R/ancestralID.R | 1024 +++--- SEMID-0.4.1/SEMID/R/edgewiseID.R | 348 +- SEMID-0.4.1/SEMID/R/globalID.R |only SEMID-0.4.1/SEMID/R/graphID.R | 956 ++--- SEMID-0.4.1/SEMID/R/htcID.R | 638 +-- SEMID-0.4.1/SEMID/R/lfhtcID.R | 909 ++--- SEMID-0.4.1/SEMID/R/plotting.R | 152 SEMID-0.4.1/SEMID/R/trekSepId.R | 282 - SEMID-0.4.1/SEMID/R/utils.R | 1183 +++---- SEMID-0.4.1/SEMID/README.md | 656 ++-- SEMID-0.4.1/SEMID/demo/00Index | 2 SEMID-0.4.1/SEMID/demo/SEMID.R | 564 +-- SEMID-0.4.1/SEMID/man/FlowGraph.Rd | 52 SEMID-0.4.1/SEMID/man/L.Rd | 50 SEMID-0.4.1/SEMID/man/LatentDigraph.Rd | 100 SEMID-0.4.1/SEMID/man/LatentDigraphFixedOrder.Rd | 46 SEMID-0.4.1/SEMID/man/MixedGraph.Rd | 94 SEMID-0.4.1/SEMID/man/O.Rd | 38 SEMID-0.4.1/SEMID/man/SEMID-package.Rd | 225 - SEMID-0.4.1/SEMID/man/ancestors.Rd | 70 SEMID-0.4.1/SEMID/man/ancestralID.Rd | 52 SEMID-0.4.1/SEMID/man/ancestralIdentifyStep.Rd | 124 SEMID-0.4.1/SEMID/man/bidirectedComponents.Rd |only SEMID-0.4.1/SEMID/man/children.Rd | 70 SEMID-0.4.1/SEMID/man/createAncestralIdentifier.Rd | 98 SEMID-0.4.1/SEMID/man/createEdgewiseIdentifier.Rd | 86 SEMID-0.4.1/SEMID/man/createHtcIdentifier.Rd | 80 SEMID-0.4.1/SEMID/man/createIdentifierBaseCase.Rd | 75 SEMID-0.4.1/SEMID/man/createLFHtcIdentifier.Rd | 84 SEMID-0.4.1/SEMID/man/createLFIdentifierBaseCase.Rd | 69 SEMID-0.4.1/SEMID/man/createSimpleBiDirIdentifier.Rd | 38 SEMID-0.4.1/SEMID/man/createTrGraph.Rd | 38 SEMID-0.4.1/SEMID/man/createTrekFlowGraph.Rd | 38 SEMID-0.4.1/SEMID/man/createTrekSeparationIdentifier.Rd | 86 SEMID-0.4.1/SEMID/man/descendants.Rd | 64 SEMID-0.4.1/SEMID/man/edgewiseID.Rd | 68 SEMID-0.4.1/SEMID/man/edgewiseIdentifyStep.Rd | 128 SEMID-0.4.1/SEMID/man/edgewiseTSID.Rd | 94 SEMID-0.4.1/SEMID/man/flowBetween.Rd | 54 SEMID-0.4.1/SEMID/man/generalGenericID.Rd | 116 SEMID-0.4.1/SEMID/man/getAncestors.Rd | 40 SEMID-0.4.1/SEMID/man/getDescendants.Rd | 42 SEMID-0.4.1/SEMID/man/getHalfTrekSystem.Rd | 126 SEMID-0.4.1/SEMID/man/getMaxFlow.Rd | 98 SEMID-0.4.1/SEMID/man/getMixedCompForNode.Rd | 62 SEMID-0.4.1/SEMID/man/getMixedGraph.Rd | 38 SEMID-0.4.1/SEMID/man/getParents.Rd | 40 SEMID-0.4.1/SEMID/man/getSiblings.Rd | 40 SEMID-0.4.1/SEMID/man/getTrekSystem.Rd | 130 SEMID-0.4.1/SEMID/man/globalID.Rd |only SEMID-0.4.1/SEMID/man/graphID.Rd | 216 - SEMID-0.4.1/SEMID/man/graphID.ancestralID.Rd | 68 SEMID-0.4.1/SEMID/man/graphID.decompose.Rd | 106 SEMID-0.4.1/SEMID/man/graphID.genericID.Rd | 76 SEMID-0.4.1/SEMID/man/graphID.htcID.Rd | 64 SEMID-0.4.1/SEMID/man/graphID.main.Rd | 84 SEMID-0.4.1/SEMID/man/graphID.nonHtcID.Rd | 66 SEMID-0.4.1/SEMID/man/htcID.Rd | 72 SEMID-0.4.1/SEMID/man/htcIdentifyStep.Rd | 132 SEMID-0.4.1/SEMID/man/htr.Rd | 52 SEMID-0.4.1/SEMID/man/htrFrom.Rd | 68 SEMID-0.4.1/SEMID/man/inducedSubgraph.Rd | 48 SEMID-0.4.1/SEMID/man/isSibling.Rd | 52 SEMID-0.4.1/SEMID/man/latentDigraphHasSimpleNumbering.Rd | 38 SEMID-0.4.1/SEMID/man/latentNodes.Rd | 38 SEMID-0.4.1/SEMID/man/lfhtcID.Rd | 88 SEMID-0.4.1/SEMID/man/lfhtcIdentifyStep.Rd | 156 SEMID-0.4.1/SEMID/man/mixedGraphHasSimpleNumbering.Rd | 30 SEMID-0.4.1/SEMID/man/nodes.Rd | 38 SEMID-0.4.1/SEMID/man/numLatents.Rd | 44 SEMID-0.4.1/SEMID/man/numNodes.Rd | 50 SEMID-0.4.1/SEMID/man/numObserved.Rd | 44 SEMID-0.4.1/SEMID/man/observedNodes.Rd | 38 SEMID-0.4.1/SEMID/man/observedParents.Rd | 42 SEMID-0.4.1/SEMID/man/parents.Rd | 70 SEMID-0.4.1/SEMID/man/plot.Rd | 42 SEMID-0.4.1/SEMID/man/plotLatentDigraph.Rd | 66 SEMID-0.4.1/SEMID/man/plotMixedGraph.Rd | 56 SEMID-0.4.1/SEMID/man/print.GenericIDResult.Rd | 36 SEMID-0.4.1/SEMID/man/print.LfhtcIDResult.Rd | 36 SEMID-0.4.1/SEMID/man/print.SEMIDResult.Rd | 36 SEMID-0.4.1/SEMID/man/semID.Rd | 172 - SEMID-0.4.1/SEMID/man/siblings.Rd | 48 SEMID-0.4.1/SEMID/man/stronglyConnectedComponent.Rd | 54 SEMID-0.4.1/SEMID/man/subsetsOfSize.Rd | 40 SEMID-0.4.1/SEMID/man/tianComponent.Rd | 38 SEMID-0.4.1/SEMID/man/tianDecompose.Rd | 50 SEMID-0.4.1/SEMID/man/tianIdentifier.Rd | 44 SEMID-0.4.1/SEMID/man/tianSigmaForComponent.Rd | 68 SEMID-0.4.1/SEMID/man/toEx.Rd | 48 SEMID-0.4.1/SEMID/man/toIn.Rd | 48 SEMID-0.4.1/SEMID/man/trFrom.Rd | 114 SEMID-0.4.1/SEMID/man/trekSeparationIdentifyStep.Rd | 122 SEMID-0.4.1/SEMID/man/updateEdgeCapacities.Rd | 44 SEMID-0.4.1/SEMID/man/updateVertexCapacities.Rd | 42 SEMID-0.4.1/SEMID/man/validateLatentNodesAreSources.Rd | 28 SEMID-0.4.1/SEMID/man/validateMatrices.Rd | 44 SEMID-0.4.1/SEMID/man/validateMatrix.Rd | 42 SEMID-0.4.1/SEMID/man/validateNodes.Rd | 34 SEMID-0.4.1/SEMID/man/validateVarArgsEmpty.Rd | 28 SEMID-0.4.1/SEMID/tests/testthat.R | 26 SEMID-0.4.1/SEMID/tests/testthat/graphExamples.R | 718 ++-- SEMID-0.4.1/SEMID/tests/testthat/helperFunctions.R | 124 SEMID-0.4.1/SEMID/tests/testthat/test_LatentDigraph.R | 652 ++-- SEMID-0.4.1/SEMID/tests/testthat/test_ancestral.R | 398 +- SEMID-0.4.1/SEMID/tests/testthat/test_edgewiseID.R | 100 SEMID-0.4.1/SEMID/tests/testthat/test_globalID.R |only SEMID-0.4.1/SEMID/tests/testthat/test_graphID.ancestralID.R | 74 SEMID-0.4.1/SEMID/tests/testthat/test_graphID.htcID.R | 44 SEMID-0.4.1/SEMID/tests/testthat/test_graphID.nonID.R | 42 SEMID-0.4.1/SEMID/tests/testthat/test_lfhtcID.R | 24 SEMID-0.4.1/SEMID/tests/testthat/test_tianDecompose.R | 88 SEMID-0.4.1/SEMID/tests/testthat/test_trekSepID.R | 62 123 files changed, 9453 insertions(+), 9416 deletions(-)
Title: Discrete Event Simulation in R and C++, with Tools for
Cost-Effectiveness Analysis
Description: Discrete event simulation using both R and C++ (Karlsson et al 2016; <doi:10.1109/eScience.2016.7870915>). The C++ code is adapted from the SSIM library <https://www.inf.usi.ch/carzaniga/ssim/>, allowing for event-oriented simulation. The code includes a SummaryReport class for reporting events and costs by age and other covariates. The C++ code is available as a static library for linking to other packages. A priority queue implementation is given in C++ together with an S3 closure and a reference class implementation. Finally, some tools are provided for cost-effectiveness analysis.
Author: Mark Clements [aut, cre, cph],
Alexandra Jauhiainen [aut],
Andreas Karlsson [aut],
Antonio Carzaniga [cph],
University of Colorado [cph],
Pierre L'Ecuyer [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between microsimulation versions 1.4.2 dated 2023-03-08 and 1.4.3 dated 2023-07-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/examples.org | 2 +- inst/include/microsimulation.h | 32 ++++++++++++++++++-------------- inst/include/siena/ssim.h | 7 +++++-- src/gsm.cpp | 2 +- src/ssim.cc | 2 +- 7 files changed, 36 insertions(+), 29 deletions(-)
More information about microsimulation at CRAN
Permanent link
Title: Gene Registration from Expression and Time-Courses in R
Description: A tool for registering (aligning) gene expression profiles
between two species (reference data and data to transform).
Author: Ruth Kristianingsih [aut, cre]
,
Alex Calderwood [aut]
Maintainer: Ruth Kristianingsih <ruth.kristianingsih30@gmail.com>
Diff between greatR versions 0.2.0 dated 2022-06-08 and 1.0.0 dated 2023-07-19
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More information about signatureSurvival at CRAN
Permanent link
More information about randomForestVIP at CRAN
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Title: Flood Extents and Durations along the Rivers Elbe and Rhine
Description: Raster based flood modelling internally using 'hyd1d', an R package
to interpolate 1d water level and gauging data. The package computes flood
extent and durations through strategies originally developed for 'INFORM',
an 'ArcGIS'-based hydro-ecological modelling framework. It does not provide
a full, physical hydraulic modelling algorithm, but a simplified, near real
time 'GIS' approach for flood extent and duration modelling. Computationally
demanding annual flood durations have been computed already and data
products were published by Weber (2022) <doi:10.1594/PANGAEA.948042>.
Author: Arnd Weber [aut, cre] ,
Stephan Rosenzweig [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hydflood versions 0.5.3 dated 2023-03-08 and 0.5.4 dated 2023-07-19
DESCRIPTION | 8 +-- MD5 | 49 +++++++++++----------- NEWS.md | 8 +++ R/data.R | 1 R/flood3Points.R | 5 +- R/getDEM.R | 79 +++++++++++++++++++++++++++++------- R/hydSpatRaster.R | 18 +++++--- R/w80ToSpatial.R | 8 +-- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/df.pnv.rda |binary inst/CITATION | 5 +- inst/REFERENCES.bib | 3 - inst/doc/hydflood.R | 18 ++++---- inst/doc/hydflood.Rmd | 18 ++++---- inst/doc/hydflood.html | 4 - man/df.pnv.Rd | 1 man/getDEM.Rd | 7 ++- man/hydSpatRaster.Rd | 7 ++- man/w80ToSFL.Rd | 2 man/w80ToSFP.Rd | 2 tests/testthat/test_getDEM.R | 4 - tests/testthat/test_hydSpatRaster.R | 2 vignettes/flood3daily_Dessau.R |only vignettes/hydflood.Rmd | 18 ++++---- 26 files changed, 172 insertions(+), 97 deletions(-)
Title: Analysis of Cardiac Magnetic Resonance Images
Description: Computes maximum response from Cardiac Magnetic Resonance Images using spatial and voxel wise spline based Bayesian model. This is an implementation of the methods described in Schmid (2011) <doi:10.1109/TMI.2011.2109733> "Voxel-Based Adaptive Spatio-Temporal Modelling of Perfusion Cardiovascular MRI". IEEE TMI 30(7) p. 1305 - 1313.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <volker.schmid@lmu.de>
Diff between cmR versions 1.0.3 dated 2021-06-14 and 1.1 dated 2023-07-19
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 28 +++++++++++++++++++++++----- R/bullseye.R | 22 +++++++++++++--------- README.md | 1 - build/vignette.rds |binary man/bullseye.Rd | 2 +- 8 files changed, 51 insertions(+), 29 deletions(-)
More information about pseudohouseholds at CRAN
Permanent link
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>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
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 0.1.23 dated 2023-07-16 and 0.1.25 dated 2023-07-19
leidenbase-0.1.23/leidenbase/src/dummy.c |only leidenbase-0.1.25/leidenbase/DESCRIPTION | 6 +++--- leidenbase-0.1.25/leidenbase/MD5 | 6 +++--- leidenbase-0.1.25/leidenbase/NEWS.md | 2 +- leidenbase-0.1.25/leidenbase/src/dummy.cpp |only 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Practical Tools for Scientific Computations and Visualizations
Description: Collection of routines for efficient scientific computations in physics and astrophysics. These routines include utility functions, numerical computation tools, as well as visualisation tools. They can be used, for example, for generating random numbers from spherical and custom distributions, information and entropy analysis, special Fourier transforms, two-point correlation estimation (e.g. as in Landy & Szalay (1993) <doi:10.1086/172900>), binning & gridding of point sets, 2D interpolation, Monte Carlo integration, vector arithmetic and coordinate transformations. Also included is a non-exhaustive list of important constants and cosmological conversion functions. The graphics routines can be used to produce and export publication-ready scientific plots and movies, e.g. as used in Obreschkow et al. (2020, MNRAS Vol 493, Issue 3, Pages 4551–4569). These routines include special color scales, projection functions, and bitmap handling routines.
Author: Danail Obreschkow
Maintainer: Danail Obreschkow <danail.obreschkow@gmail.com>
Diff between cooltools versions 2.0 dated 2022-10-05 and 2.1.27 dated 2023-07-19
DESCRIPTION | 10 - MD5 | 78 +++++++------ NAMESPACE | 9 + R/approxfun2.R | 4 R/bindata.R | 67 +++++++---- R/car2pol.R | 4 R/car2sph.R | 4 R/colorbar.R | 30 +++-- R/contourlevel.R | 4 R/equal.R |only R/gradient.R |only R/grf.R |only R/griddata.R | 51 ++++---- R/inertia.R |only R/kde2.R | 311 +++++++++++++++++++++++++++++++++++++--------------- R/lim.R | 6 - R/makeframe.R | 11 + R/makemovie.R | 10 + R/mcintegral.R | 17 +- R/moments.R |only R/quadrupole.R | 15 +- R/rng.R | 34 ++++- R/smartround.R |only R/stretch.R |only R/tock.R | 19 ++- man/approxfun2.Rd | 2 man/bindata.Rd | 6 - man/car2pol.Rd | 4 man/car2sph.Rd | 4 man/colorbar.Rd | 14 +- man/contourlevel.Rd | 4 man/gradient.Rd |only man/grf.Rd |only man/griddata.Rd | 21 +-- man/inertia.Rd |only man/is.equal.Rd |only man/kde2.Rd | 99 +++++++++++----- man/lim.Rd | 7 - man/makeframe.Rd | 9 + man/makemovie.Rd | 9 + man/mcintegral.Rd | 4 man/moments.Rd |only man/quadrupole.Rd | 7 - man/rng.Rd | 21 ++- man/smartround.Rd |only man/stretch.Rd |only man/tock.Rd | 8 - 47 files changed, 607 insertions(+), 296 deletions(-)
Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <arXiv:1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon M. Greenwell [aut, cre]
,
Brad Boehmke [aut]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.3.2 dated 2020-12-17 and 0.4.0 dated 2023-07-19
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Title: Tools for Handling Extraction of Features from Time Series
Description: Consolidates and calculates different sets of time-series features from multiple
'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>,
'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>,
'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020)
<https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J.,
and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020)
<doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021)
<https://facebookresearch.github.io/Kats/>. Provides a standardised workflow from feature calculation to
feature processing, machine learning classification procedures, and the production of statistical graphics.
Author: Trent Henderson [cre, aut],
Annie Bryant [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theft versions 0.4.2.4 dated 2023-03-27 and 0.5.1 dated 2023-07-19
theft-0.4.2.4/theft/R/compute_top_features.R |only theft-0.4.2.4/theft/R/fit_multi_feature_classifier.R |only theft-0.4.2.4/theft/R/fit_single_feature_classifier.R |only theft-0.4.2.4/theft/man/compute_top_features.Rd |only theft-0.4.2.4/theft/man/fit_multi_feature_classifier.Rd |only theft-0.4.2.4/theft/man/fit_single_feature_classifier.Rd |only theft-0.4.2.4/theft/tests/testthat/test-compute_top_features.R |only theft-0.4.2.4/theft/tests/testthat/test-fit_multi_feature_classifier.R |only theft-0.4.2.4/theft/tests/testthat/test-process_hctsa_file.R |only theft-0.4.2.4/theft/vignettes/FeatureFeatureCorrelationPlot.png |only theft-0.4.2.4/theft/vignettes/FeatureSetResultsPlot.png |only theft-0.4.2.4/theft/vignettes/ViolinPlots.png |only theft-0.4.2.4/theft/vignettes/workflow-graphic2.png |only theft-0.5.1/theft/DESCRIPTION | 10 theft-0.5.1/theft/LICENSE | 2 theft-0.5.1/theft/MD5 | 121 theft-0.5.1/theft/NAMESPACE | 31 theft-0.5.1/theft/R/calculate_features.R | 950 ++--- theft-0.5.1/theft/R/check_vector_quality.R | 20 theft-0.5.1/theft/R/compare_features.R |only theft-0.5.1/theft/R/data.R | 52 theft-0.5.1/theft/R/filter_duplicates.R |only theft-0.5.1/theft/R/find_good_features.R |only theft-0.5.1/theft/R/fit_models.R |only theft-0.5.1/theft/R/get_rescale_vals.R |only theft-0.5.1/theft/R/init_theft.R | 30 theft-0.5.1/theft/R/install_python_pkgs.R |only theft-0.5.1/theft/R/mywhere.R |only theft-0.5.1/theft/R/normalise.R | 132 theft-0.5.1/theft/R/plots.R | 878 ++-- theft-0.5.1/theft/R/process_hctsa_file.R | 136 theft-0.5.1/theft/R/reduce_dims.R | 199 - theft-0.5.1/theft/R/resample_data.R |only theft-0.5.1/theft/R/resampled_ttest.R |only theft-0.5.1/theft/R/rescalers.R | 178 theft-0.5.1/theft/R/select_stat_cols.R |only theft-0.5.1/theft/R/stat_test.R |only theft-0.5.1/theft/R/theft.R | 52 theft-0.5.1/theft/R/tsfeature_classifier.R |only theft-0.5.1/theft/README.md | 230 - theft-0.5.1/theft/build/vignette.rds |binary theft-0.5.1/theft/inst/doc/theft.R | 269 - theft-0.5.1/theft/inst/doc/theft.Rmd | 666 +-- theft-0.5.1/theft/inst/doc/theft.html | 1833 +++++----- theft-0.5.1/theft/inst/python/kats_calculator.py | 64 theft-0.5.1/theft/inst/python/tsfel_calculator.py | 46 theft-0.5.1/theft/inst/python/tsfresh_calculator.py | 46 theft-0.5.1/theft/man/calculate_features.Rd | 112 theft-0.5.1/theft/man/check_vector_quality.Rd | 40 theft-0.5.1/theft/man/compare_features.Rd |only theft-0.5.1/theft/man/feature_list.Rd | 40 theft-0.5.1/theft/man/filter_duplicates.Rd |only theft-0.5.1/theft/man/filter_good_features.Rd |only theft-0.5.1/theft/man/find_good_features.Rd |only theft-0.5.1/theft/man/fit_models.Rd |only theft-0.5.1/theft/man/get_rescale_vals.Rd |only theft-0.5.1/theft/man/init_theft.Rd | 44 theft-0.5.1/theft/man/install_python_pkgs.Rd |only theft-0.5.1/theft/man/minmax_scaler.Rd | 40 theft-0.5.1/theft/man/normalise.Rd | 44 theft-0.5.1/theft/man/plot.feature_calculations.Rd | 76 theft-0.5.1/theft/man/plot.low_dimension.Rd | 48 theft-0.5.1/theft/man/process_hctsa_file.Rd | 48 theft-0.5.1/theft/man/reduce_dims.Rd | 71 theft-0.5.1/theft/man/resample_data.Rd |only theft-0.5.1/theft/man/resampled_ttest.Rd |only theft-0.5.1/theft/man/rescale_zscore.Rd |only theft-0.5.1/theft/man/robustsigmoid_scaler.Rd | 50 theft-0.5.1/theft/man/select_stat_cols.Rd |only theft-0.5.1/theft/man/sigmoid_scaler.Rd | 44 theft-0.5.1/theft/man/simData.Rd | 44 theft-0.5.1/theft/man/stat_test.Rd |only theft-0.5.1/theft/man/theft.Rd | 18 theft-0.5.1/theft/man/tsfeature_classifier.Rd |only theft-0.5.1/theft/man/zscore_scaler.Rd | 44 theft-0.5.1/theft/tests/testthat.R | 8 theft-0.5.1/theft/tests/testthat/helper-core_data.R | 22 theft-0.5.1/theft/tests/testthat/test-calculate_features.R | 66 theft-0.5.1/theft/tests/testthat/test-compare_features.R |only theft-0.5.1/theft/tests/testthat/test-tsfeature_classifier.R |only theft-0.5.1/theft/vignettes/theft.Rmd | 666 +-- theft-0.5.1/theft/vignettes/workflow-graphic_v05.png |only 82 files changed, 3863 insertions(+), 3607 deletions(-)
Title: Fuzzily Search a Dataframe to Find Relevant Columns
Description: Analysts who change projects frequently know that it can be hard
to find the right column in an unfamiliar dataframe, especially when the
dataframe spans hundreds of columns and millions of rows. 'siftr' is an
interactive tool that finds relevant columns by fuzzily searching through
a dataframe's column names, labels, factor levels, and unique values.
Author: Desi Quintans [cre, aut, cph]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between siftr versions 1.0.1 dated 2023-05-30 and 1.1.0 dated 2023-07-19
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 21 +++++++++++++++++++++ R/exp_save_dictionary.R | 18 ++++++++++++------ R/exp_sift.R | 4 ++-- R/prv_msg_sift.R | 2 +- R/prv_private_funs.R | 24 ++++++++++++++++++++++++ R/prv_should_approx.R | 8 ++++---- R/siftr-package.R | 1 - README.md | 44 ++++++++++++++++++++++++++++++++++++++++---- man/save_dictionary.Rd | 2 +- man/siftr-package.Rd | 3 ++- 12 files changed, 121 insertions(+), 34 deletions(-)
Title: An R Autograding Extension for Otter-Grader
Description: An R autograding extension for Otter-Grader (<https://otter-grader.readthedocs.io>). It supports
grading R scripts, R Markdown documents, and R Jupyter Notebooks.
Author: Christopher Pyles [aut, cre] ,
UC Berkeley Data Science Education Program [cph]
Maintainer: Christopher Pyles <cpyles@berkeley.edu>
Diff between ottr versions 1.3.1 dated 2023-01-26 and 1.4.0 dated 2023-07-19
ottr-1.3.1/ottr/man/make_secret.Rd |only ottr-1.3.1/ottr/man/valid_expr_chars.Rd |only ottr-1.3.1/ottr/tests/testthat/test_make_secret.R |only ottr-1.4.0/ottr/DESCRIPTION | 8 +- ottr-1.4.0/ottr/MD5 | 18 +++--- ottr-1.4.0/ottr/R/export.R | 28 ++++++++- ottr-1.4.0/ottr/R/save_notebook.R |only ottr-1.4.0/ottr/R/utils.R | 42 +++++--------- ottr-1.4.0/ottr/man/export.Rd | 10 +++ ottr-1.4.0/ottr/man/running_on_jupyter.Rd |only ottr-1.4.0/ottr/man/save_notebook.Rd |only ottr-1.4.0/ottr/tests/testthat/test_export.R | 43 +++++++++++++++ ottr-1.4.0/ottr/tests/testthat/test_running_on_jupyter.R |only ottr-1.4.0/ottr/tests/testthat/test_save_notebook.R |only 14 files changed, 106 insertions(+), 43 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut] ,
Julien Papaix [aut],
Jean-Francois Rey [aut, cre] ,
Marta Zaffaroni [ctb] ,
Jean-Loup Gaussen [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.2.5 dated 2023-02-27 and 1.3.0 dated 2023-07-19
landsepi-1.2.5/landsepi/man/CroptypeBDD2Params.Rd |only landsepi-1.2.5/landsepi/man/CultivarBDD2Params.Rd |only landsepi-1.2.5/landsepi/man/CultivarGeneBDD2Params.Rd |only landsepi-1.2.5/landsepi/man/GPKGAddInputData.Rd |only landsepi-1.2.5/landsepi/man/GPKGAddTables.Rd |only landsepi-1.2.5/landsepi/man/GeneBDD2Params.Rd |only landsepi-1.2.5/landsepi/man/createLandscapeGPKG.Rd |only landsepi-1.2.5/landsepi/man/figures |only landsepi-1.2.5/landsepi/man/getGPKGArea.Rd |only landsepi-1.2.5/landsepi/man/getGPKGCroptypes.Rd |only landsepi-1.2.5/landsepi/man/getGPKGCroptypesRaw.Rd |only landsepi-1.2.5/landsepi/man/getGPKGCultivars.Rd |only landsepi-1.2.5/landsepi/man/getGPKGCultivarsGenes.Rd |only landsepi-1.2.5/landsepi/man/getGPKGGeneIDForCultivar.Rd |only landsepi-1.2.5/landsepi/man/getGPKGGenes.Rd |only landsepi-1.2.5/landsepi/man/getGPKGRotation.Rd |only landsepi-1.2.5/landsepi/man/params2CroptypeBDD.Rd |only landsepi-1.2.5/landsepi/man/params2CultivarBDD.Rd |only landsepi-1.2.5/landsepi/man/params2GeneBDD.Rd |only landsepi-1.2.5/landsepi/man/params2GeneListBDD.Rd |only landsepi-1.3.0/landsepi/DESCRIPTION | 8 landsepi-1.3.0/landsepi/MD5 | 146 +-- landsepi-1.3.0/landsepi/NAMESPACE | 2 landsepi-1.3.0/landsepi/R/AgriLand.R | 5 landsepi-1.3.0/landsepi/R/Cultivars_List.R | 21 landsepi-1.3.0/landsepi/R/GPKGTools.R | 19 landsepi-1.3.0/landsepi/R/Math-Functions.R | 16 landsepi-1.3.0/landsepi/R/Methods-LandsepiParams.R | 149 ++- landsepi-1.3.0/landsepi/R/RcppExports.R | 20 landsepi-1.3.0/landsepi/R/demo_landsepi.R | 11 landsepi-1.3.0/landsepi/R/landsepi.R | 23 landsepi-1.3.0/landsepi/R/output.R | 63 + landsepi-1.3.0/landsepi/R/simul_landsepi.R | 25 landsepi-1.3.0/landsepi/build/vignette.rds |binary landsepi-1.3.0/landsepi/configure | 20 landsepi-1.3.0/landsepi/configure.ac | 4 landsepi-1.3.0/landsepi/data/dispP_a40_b7.rda |binary landsepi-1.3.0/landsepi/data/landscapesTEST.rda |binary landsepi-1.3.0/landsepi/inst/doc/O1-run_simple_simul.R | 14 landsepi-1.3.0/landsepi/inst/doc/O1-run_simple_simul.Rmd | 97 +- landsepi-1.3.0/landsepi/inst/doc/O1-run_simple_simul.html | 397 +++++++--- landsepi-1.3.0/landsepi/inst/doc/O3-landscape_dispersal.R | 23 landsepi-1.3.0/landsepi/inst/doc/O3-landscape_dispersal.Rmd | 30 landsepi-1.3.0/landsepi/inst/doc/O3-landscape_dispersal.html | 112 +- landsepi-1.3.0/landsepi/inst/doc/landsepi_poster.pdf |binary landsepi-1.3.0/landsepi/inst/doc/list_of_parameters.pdf |binary landsepi-1.3.0/landsepi/inst/shiny-landsepi/global.R | 15 landsepi-1.3.0/landsepi/inst/shiny-landsepi/server.R | 3 landsepi-1.3.0/landsepi/inst/shiny-landsepi/ui.R | 1 landsepi-1.3.0/landsepi/inst/shiny-landsepi/www/CSIRO_Logo.png |binary landsepi-1.3.0/landsepi/inst/shiny-landsepi/www/LogoINRAE_Fr_rvb_web.png |binary landsepi-1.3.0/landsepi/inst/shiny-landsepi/www/PATHO_inra_logo.png |binary landsepi-1.3.0/landsepi/inst/shiny-landsepi/www/Republique_Francaise_RVB.jpg |binary landsepi-1.3.0/landsepi/inst/shiny-landsepi/www/logoBIOSP.jpeg |binary landsepi-1.3.0/landsepi/man/antideriv_verhulst.Rd | 2 landsepi-1.3.0/landsepi/man/compute_audpc100S.Rd | 14 landsepi-1.3.0/landsepi/man/epid_output.Rd | 2 landsepi-1.3.0/landsepi/man/evol_output.Rd | 15 landsepi-1.3.0/landsepi/man/initialize-methods.Rd | 3 landsepi-1.3.0/landsepi/man/landsepi-package.Rd | 23 landsepi-1.3.0/landsepi/man/loadCultivar.Rd | 3 landsepi-1.3.0/landsepi/man/loadPathogen.Rd | 3 landsepi-1.3.0/landsepi/man/loadTreatment.Rd | 4 landsepi-1.3.0/landsepi/man/model_landsepi.Rd | 20 landsepi-1.3.0/landsepi/man/price_reduction.Rd | 20 landsepi-1.3.0/landsepi/man/runSimul.Rd | 4 landsepi-1.3.0/landsepi/man/setDispersalPathogen.Rd | 13 landsepi-1.3.0/landsepi/man/setGenes.Rd | 8 landsepi-1.3.0/landsepi/man/setPathogen.Rd | 2 landsepi-1.3.0/landsepi/man/setTreatment.Rd | 4 landsepi-1.3.0/landsepi/man/simul_landsepi.Rd | 16 landsepi-1.3.0/landsepi/man/video.Rd | 2 landsepi-1.3.0/landsepi/src/Gene.cpp | 22 landsepi-1.3.0/landsepi/src/Gene.hpp | 10 landsepi-1.3.0/landsepi/src/Model.cpp | 119 ++ landsepi-1.3.0/landsepi/src/Model.hpp | 38 landsepi-1.3.0/landsepi/src/Treatment.cpp | 12 landsepi-1.3.0/landsepi/src/Treatment.hpp | 3 landsepi-1.3.0/landsepi/src/initialisation.cpp | 34 landsepi-1.3.0/landsepi/src/printReadWrite.cpp | 13 landsepi-1.3.0/landsepi/vignettes/O1-run_simple_simul.Rmd | 97 +- landsepi-1.3.0/landsepi/vignettes/O3-landscape_dispersal.Rmd | 30 landsepi-1.3.0/landsepi/vignettes/landsepiposter.pdf |binary landsepi-1.3.0/landsepi/vignettes/listofparameters.pdf |binary 84 files changed, 1183 insertions(+), 577 deletions(-)
Title: Genesys PGR Client
Description: Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>).
Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.
Author: Global Crop Diversity Trust [cph],
Matija Obreza [aut, cre],
Nora Castaneda [ctb]
Maintainer: Matija Obreza <matija.obreza@croptrust.org>
Diff between genesysr versions 1.1.0 dated 2023-02-15 and 2.0.0 dated 2023-07-19
DESCRIPTION | 8 +-- MD5 | 15 +++--- NAMESPACE | 2 NEWS.md | 4 + R/api-client.R | 105 ++++++++++++++++++++++++++++++++++++----------- README.md | 12 ++--- inst/doc/tutorial.html | 4 - inst/doc/validation.html | 4 - man/dot-LISTENER.Rd |only 9 files changed, 110 insertions(+), 44 deletions(-)
Title: Functions to Assist Design and Analysis of Agronomic Experiments
Description: Provides functions to aid in the design and analysis of
agronomic and agricultural experiments through easy access to
documentation and helper functions, especially for users who are
learning these concepts. While not required for most functionality,
this package enhances the `asreml` package which provides a
computationally efficient algorithm for fitting mixed models
using Residual Maximum Likelihood. It is a commercial package
that can be purchased as 'asreml-R' from 'VSNi'
<https://vsni.co.uk/>, who will supply a zip file for local
installation/updating (see <https://asreml.kb.vsni.co.uk/>).
Author: Sharon Nielsen [aut],
Sam Rogers [aut, cre],
Annie Conway [aut],
University of Adelaide [cph, fnd] ,
Grains Research and Development Corporation [cph, fnd]
Maintainer: Sam Rogers <biometrytraining@adelaide.edu.au>
Diff between biometryassist versions 1.1.2 dated 2022-11-25 and 1.1.3 dated 2023-07-19
DESCRIPTION | 17 MD5 | 145 NAMESPACE | 3 NEWS.md | 12 R/autoplot.R | 38 R/biometryassist-package.R | 2 R/install_asreml.R | 93 R/mct.R | 110 R/resplot.R | 2 R/utility_functions.R | 104 R/variogram.r | 340 README.md | 4 build |only inst |only man/autoplot.Rd | 1 man/install_asreml.Rd | 2 man/print.mct.Rd | 2 man/variogram.Rd | 2 tests/testthat/_snaps/all-w2.md | 458 - tests/testthat/_snaps/all-w2/example6variogram.svg | 4563 +++------- tests/testthat/_snaps/all-w2/example7variogram.svg | 4563 +++------- tests/testthat/_snaps/all-w2/exercise13variogram.svg | 4563 +++------- tests/testthat/_snaps/all-w2/exercise14variogram.svg | 4563 +++------- tests/testthat/_snaps/all-w2/exercise15variogram.svg | 4563 +++------- tests/testthat/_snaps/all-w2/exercise1autoplot.svg | 14 tests/testthat/_snaps/des/crd-without-trt.svg | 58 tests/testthat/_snaps/des/rcbd-without-trt.svg | 138 tests/testthat/_snaps/design/3-way-factorial-with-names.svg | 64 tests/testthat/_snaps/design/3-way-factorial.svg | 64 tests/testthat/_snaps/design/3-way-rcbd-factorial-with-names.svg | 70 tests/testthat/_snaps/design/autoplot-with-margin.svg | 58 tests/testthat/_snaps/design/autoplot-with-rotation.svg | 58 tests/testthat/_snaps/design/autoplot-with-size.svg | 58 tests/testthat/_snaps/design/crd-paired-palatte.svg | 146 tests/testthat/_snaps/design/crd-plot-produced.svg | 58 tests/testthat/_snaps/design/crd-rdbu-palatte.svg | 144 tests/testthat/_snaps/design/crd-set3-palatte.svg | 144 tests/testthat/_snaps/design/factorial-crd-plot-no-space-sep.svg | 46 tests/testthat/_snaps/design/factorial-crd-with-names.svg | 54 tests/testthat/_snaps/design/factorial-lsd-plot-names-and-sep.svg | 108 tests/testthat/_snaps/design/factorial-lsd-plot-with-sep.svg | 116 tests/testthat/_snaps/design/factorial-lsd-with-names.svg | 108 tests/testthat/_snaps/design/factorial-rcbd-plot-double-row-blocks.svg | 50 tests/testthat/_snaps/design/factorial-rcbd-plot-produced.svg | 50 tests/testthat/_snaps/design/factorial-rcbd-plot-square-blocks.svg | 70 tests/testthat/_snaps/design/factorial-rcbd-plot-with-row-blocks.svg | 50 tests/testthat/_snaps/design/lsd-plot-produced.svg | 48 tests/testthat/_snaps/design/nested-lsd.svg | 156 tests/testthat/_snaps/design/plot-produced-with-plot-false.svg | 58 tests/testthat/_snaps/design/rcbd-paired-palatte.svg | 138 tests/testthat/_snaps/design/rcbd-plot-produced.svg | 138 tests/testthat/_snaps/design/rcbd-rdbu-palatte.svg | 140 tests/testthat/_snaps/design/rcbd-set3-palatte.svg | 136 tests/testthat/_snaps/design/rcbd-with-row-blocks.svg | 70 tests/testthat/_snaps/design/rcbd-with-square-blocks.svg | 70 tests/testthat/_snaps/design/split-plot-byrow-f.svg | 98 tests/testthat/_snaps/design/split-plot-double-row-blocks.svg | 98 tests/testthat/_snaps/design/split-plot-ntrt-bcol.svg | 98 tests/testthat/_snaps/design/split-plot-produced.svg | 98 tests/testthat/_snaps/design/split-plot-with-names.svg | 96 tests/testthat/_snaps/design/split-plot-with-vector-names.svg | 98 tests/testthat/_snaps/mct.md | 2 tests/testthat/_snaps/mct/lme4-output.svg | 68 tests/testthat/_snaps/mct/mct-power-output.svg | 2 tests/testthat/_snaps/utility_functions.md | 2 tests/testthat/_snaps/variogram/variogram-dsum-2.svg |only tests/testthat/_snaps/variogram/variogram-dsum.svg |only tests/testthat/_snaps/variogram/variogram-produced.svg | 4563 +++------- tests/testthat/data/asreml_model.Rdata |binary tests/testthat/test-all-w2.r | 5 tests/testthat/test-design.R | 1434 +-- tests/testthat/test-mct.R | 43 tests/testthat/test-resplot.R | 2 tests/testthat/test-variogram.r | 39 vignettes |only 75 files changed, 12492 insertions(+), 21084 deletions(-)
More information about biometryassist at CRAN
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Title: Confidentiality of Spatial Point Data
Description: Provides an automatic aggregation tool to manage point data privacy,
intended to be helpful for the production of official spatial data and for researchers.
The package pursues the data accuracy at the smallest possible areas preventing
individual information disclosure. The methodology, based on hierarchical geographic
data structures performs aggregation and local suppression of point data to ensure privacy
as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>.
The data structures are created following the guidelines for grid datasets from the
European Forum for Geography and Statistics.
Author: Raymond Lagonigro [aut, cre] ,
Ramon Oller [aut] ,
Joan Carles Martori [aut]
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>
Diff between AQuadtree versions 1.0.3 dated 2023-04-20 and 1.0.4 dated 2023-07-19
AQuadtree-1.0.3/AQuadtree/man/writeOGR.QT.Rd |only AQuadtree-1.0.4/AQuadtree/DESCRIPTION | 12 +++---- AQuadtree-1.0.4/AQuadtree/MD5 | 23 ++++++-------- AQuadtree-1.0.4/AQuadtree/NAMESPACE | 2 - AQuadtree-1.0.4/AQuadtree/NEWS | 6 +++ AQuadtree-1.0.4/AQuadtree/R/AQuadtree-class.R | 30 ------------------- AQuadtree-1.0.4/AQuadtree/R/AQuadtree.R | 2 - AQuadtree-1.0.4/AQuadtree/build/vignette.rds |binary AQuadtree-1.0.4/AQuadtree/inst/doc/AQuadtreeUse.Rmd | 2 - AQuadtree-1.0.4/AQuadtree/inst/doc/AQuadtreeUse.pdf |binary AQuadtree-1.0.4/AQuadtree/man/AQuadtree-package.Rd | 2 - AQuadtree-1.0.4/AQuadtree/vignettes/AQuadtreeUse.Rmd | 2 - AQuadtree-1.0.4/AQuadtree/vignettes/References.bib | 6 --- 13 files changed, 27 insertions(+), 60 deletions(-)
Title: Analyze Group Patterns using Graph Theory in Educational
Settings
Description: Analyzes group patterns using discourse analysis data with
graph theory mathematics. Takes the order of which individuals talk
and converts it to a network edge and weight list. Returns the
density, centrality, centralization, and subgroup information for each
group. Based on the analytical framework laid out in Chai et al.
(2019) <doi:10.1187/cbe.18-11-0222>.
Author: Albert Chai [aut],
Andrew Lee [aut],
Joshua Le [aut],
Katherine Ly [ctb],
Kevin Banh [ctb],
Priya Pahal [ctb],
Jitarth Sheth [aut],
Qi Cui [aut, cre],
Stanley Lo [aut]
Maintainer: Qi Cui <q1cui@ucsd.edu>
Diff between discourseGT versions 1.1.8 dated 2022-10-27 and 1.2.0 dated 2023-07-19
discourseGT-1.1.8/discourseGT/R/discourseGT.R |only discourseGT-1.1.8/discourseGT/man/discourseGT.Rd |only discourseGT-1.1.8/discourseGT/vignettes/discourseGT.Rmd.old |only discourseGT-1.1.8/discourseGT/vignettes/discourseGT_files |only discourseGT-1.2.0/discourseGT/DESCRIPTION | 56 +- discourseGT-1.2.0/discourseGT/LICENSE | 4 discourseGT-1.2.0/discourseGT/MD5 | 91 +-- discourseGT-1.2.0/discourseGT/NAMESPACE | 37 + discourseGT-1.2.0/discourseGT/R/basicPlot.R | 5 discourseGT-1.2.0/discourseGT/R/coreNetAnalysis.R | 3 discourseGT-1.2.0/discourseGT/R/discourseGT-package.R |only discourseGT-1.2.0/discourseGT/R/edgelist_raw.R | 29 - discourseGT-1.2.0/discourseGT/R/plot1Att.R | 265 +++++----- discourseGT-1.2.0/discourseGT/R/plot2Att.R | 200 +++---- discourseGT-1.2.0/discourseGT/R/plotNGTData.R | 126 ++-- discourseGT-1.2.0/discourseGT/R/prepareGraphs.R | 3 discourseGT-1.2.0/discourseGT/R/subgroupsNetAnalysis.R | 6 discourseGT-1.2.0/discourseGT/R/summaryNet.R | 35 - discourseGT-1.2.0/discourseGT/R/tabulate_edges.R | 41 + discourseGT-1.2.0/discourseGT/R/writeData.R | 3 discourseGT-1.2.0/discourseGT/README.md | 65 ++ discourseGT-1.2.0/discourseGT/build/vignette.rds |binary discourseGT-1.2.0/discourseGT/data/attributeData.rda |binary discourseGT-1.2.0/discourseGT/data/sampleData1.rda |binary discourseGT-1.2.0/discourseGT/inst/doc/discourseGT.pdf |binary discourseGT-1.2.0/discourseGT/inst/doc/discourseGT.pdf.asis | 4 discourseGT-1.2.0/discourseGT/man/attributeData.Rd | 32 - discourseGT-1.2.0/discourseGT/man/basicPlot.Rd | 4 discourseGT-1.2.0/discourseGT/man/coreNetAnalysis.Rd | 2 discourseGT-1.2.0/discourseGT/man/discourseGT-package.Rd |only discourseGT-1.2.0/discourseGT/man/edgelist_raw.Rd | 6 discourseGT-1.2.0/discourseGT/man/plot1Att.Rd | 6 discourseGT-1.2.0/discourseGT/man/plot2Att.Rd | 6 discourseGT-1.2.0/discourseGT/man/plotNGTData.Rd | 6 discourseGT-1.2.0/discourseGT/man/prepareGraphs.Rd | 2 discourseGT-1.2.0/discourseGT/man/sampleData1.Rd | 12 discourseGT-1.2.0/discourseGT/man/subgroupsNetAnalysis.Rd | 2 discourseGT-1.2.0/discourseGT/man/summaryNet.Rd | 8 discourseGT-1.2.0/discourseGT/man/tabulate_edges.Rd | 6 discourseGT-1.2.0/discourseGT/man/writeData.Rd | 6 discourseGT-1.2.0/discourseGT/tests |only discourseGT-1.2.0/discourseGT/vignettes/discourseGT.pdf.asis | 4 discourseGT-1.2.0/discourseGT/vignettes/discourseGT_rmd.Rmd_backup |only discourseGT-1.2.0/discourseGT/vignettes/references.bib | 14 44 files changed, 607 insertions(+), 482 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-05 1.5.2
2023-05-04 1.4.2
2022-08-27 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-17 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-11 1.1.0
2022-10-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-07 1.0.1
2023-06-23 1.0.0