Title: Headless Chrome Web Browser Interface
Description: An implementation of the 'Chrome DevTools Protocol', for
controlling a headless Chrome web browser.
Author: Garrick Aden-Buie [aut, cre] ,
Winston Chang [aut],
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between chromote versions 0.5.0 dated 2025-03-21 and 0.5.1 dated 2025-04-23
DESCRIPTION | 14 ++-- LICENSE |only MD5 | 89 +++++++++++++-------------- NEWS.md | 8 ++ R/browser.R | 6 - R/chromote.R | 14 ++-- R/chromote_session.R | 101 +++++++++++++++++++++++++++--- R/utils.R | 13 +++ README.md | 14 +--- build/vignette.rds |binary inst/doc/chromote.html | 13 +-- inst/doc/commands-and-events.Rmd | 3 inst/doc/commands-and-events.html | 6 - inst/doc/example-authentication.Rmd | 6 - inst/doc/example-authentication.html | 6 - inst/doc/example-custom-headers.Rmd | 4 - inst/doc/example-custom-headers.html | 4 - inst/doc/example-custom-user-agent.Rmd | 4 - inst/doc/example-custom-user-agent.html | 4 - inst/doc/example-extract-text.Rmd | 13 +-- inst/doc/example-extract-text.html | 37 +++++------ inst/doc/example-loading-page.Rmd | 20 +++++- inst/doc/example-loading-page.html | 18 +++++ inst/doc/example-remote-hosts.Rmd | 18 ----- inst/doc/example-remote-hosts.html | 22 ------ inst/doc/example-screenshot.Rmd | 20 ++---- inst/doc/example-screenshot.html | 76 ++++++++++------------- inst/doc/sync-async.Rmd | 2 inst/doc/sync-async.html | 3 inst/doc/which-chrome.Rmd | 4 - inst/doc/which-chrome.html | 4 - man/Browser.Rd | 6 - man/ChromoteSession.Rd | 105 ++++++++++++++++++++++++++++---- man/chromote-package.Rd | 2 man/default_chromote_object.Rd | 8 +- man/fragments/basic-usage.Rmd | 6 - vignettes/commands-and-events.Rmd | 3 vignettes/example-authentication.Rmd | 6 - vignettes/example-custom-headers.Rmd | 4 - vignettes/example-custom-user-agent.Rmd | 4 - vignettes/example-extract-text.Rmd | 13 +-- vignettes/example-loading-page.Rmd | 20 +++++- vignettes/example-remote-hosts.Rmd | 18 ----- vignettes/example-screenshot.Rmd | 20 ++---- vignettes/sync-async.Rmd | 2 vignettes/which-chrome.Rmd | 4 - 46 files changed, 470 insertions(+), 297 deletions(-)
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.4 dated 2025-03-20 and 0.1.5 dated 2025-04-23
DESCRIPTION | 10 MD5 | 101 +++---- NAMESPACE | 1 NEWS.md | 28 ++ R/RcppExports.R | 116 +++++++- R/ipcw.R | 141 +++++++++- R/ipe.R | 65 ++++ R/liferegr.R | 10 R/logisregr.R | 7 R/phregr.R | 8 R/rpsftm.R | 44 ++- R/tsegest.R | 120 +++++++-- R/tsesimp.R | 69 ++++- inst/doc/ipcw.Rmd | 6 inst/doc/ipcw.html | 8 inst/doc/ipe.R | 11 inst/doc/ipe.Rmd | 11 inst/doc/ipe.html | 69 ++--- inst/doc/rpsftm.html | 2 inst/doc/tsegest.R | 20 + inst/doc/tsegest.Rmd | 14 - inst/doc/tsegest.html | 56 ++-- inst/doc/tsesimp.html | 16 - man/ipcw.Rd | 27 +- man/ipe.Rd | 33 +- man/liferegr.Rd | 8 man/logisregr.Rd | 8 man/phregr.Rd | 8 man/rpsftm.Rd | 19 + man/survQuantile.Rd |only man/tsegest.Rd | 64 +++- man/tsegestsim.Rd | 32 ++ man/tsesimp.Rd | 20 + src/RcppExports.cpp | 65 +++- src/ipcw.cpp | 17 - src/ipe.cpp | 18 + src/logistic_regression.cpp | 32 +- src/logistic_regression.h | 4 src/rpsftm.cpp | 20 + src/survival_analysis.cpp | 552 ++++++++++++++++++++++++++++++++++++++---- src/survival_analysis.h | 16 + src/tsegest.cpp | 161 ++++++++---- src/tsegestsim.cpp | 166 ++++++++---- src/tsesimp.cpp | 10 tests/testthat/test-ipcw.R | 58 ++-- tests/testthat/test-ipe.R | 18 - tests/testthat/test-rpsftm.R | 14 - tests/testthat/test-tsegest.R | 15 - tests/testthat/test-tsesimp.R | 21 - vignettes/ipcw.Rmd | 6 vignettes/ipe.Rmd | 11 vignettes/tsegest.Rmd | 14 - 52 files changed, 1774 insertions(+), 596 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut],
Antonio Mello [aut],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Lucas Tavares [aut],
Rebecca Salles [aut],
Diego [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.1.707 dated 2024-12-03 and 1.1.717 dated 2025-04-23
DESCRIPTION | 18 +++--- MD5 | 81 ++++++++++++++------------- R/han_autoencoder.R | 11 +-- R/hanc_ml.R | 4 - R/hanct_dtw.R | 4 - R/hanct_kmeans.R | 4 - R/hanr_arima.R | 4 - R/hanr_emd.R | 4 - R/hanr_fbiad.R | 2 R/hanr_fft.R | 2 R/hanr_garch.R | 2 R/hanr_hist.R | 2 R/hanr_ml.R | 4 - R/hanr_red.R | 2 R/hanr_remd.R | 2 R/hanr_wavelet.R | 2 R/har_ensemble.R | 4 - R/har_eval.R | 4 - R/har_eval_soft.R | 2 R/harbinger.R | 6 +- R/hcp_amoc.R | 2 R/hcp_binseg.R | 2 R/hcp_cf_arima.R | 4 - R/hcp_cf_ets.R | 2 R/hcp_cf_lr.R | 2 R/hcp_chow.R | 2 R/hcp_garch.R | 4 - R/hcp_gft.R | 2 R/hcp_pelt.R | 2 R/hcp_red.R | 6 +- R/hcp_scp.R | 4 - R/hdis_mp.R | 2 R/hdis_sax.R | 34 +++++------ R/hmo_mp.R | 2 R/hmo_sax.R | 28 ++++----- R/hmo_xsax.R | 2 R/hmu_pca.R | 3 - R/trans_sax.R | 2 R/trans_xsax.R | 2 README.md | 113 ++++++++++++++++++++++----------------- man/figures/README-example-1.png |only man/han_autoencoder.Rd | 12 +--- 42 files changed, 204 insertions(+), 192 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.2.1 dated 2025-01-24 and 5.3.0 dated 2025-04-23
Seurat-5.2.1/Seurat/tests/testthat/test_read_mtx.R |only Seurat-5.3.0/Seurat/DESCRIPTION | 6 Seurat-5.3.0/Seurat/MD5 | 69 - Seurat-5.3.0/Seurat/NAMESPACE | 9 Seurat-5.3.0/Seurat/NEWS.md | 20 Seurat-5.3.0/Seurat/R/dimensional_reduction.R | 47 Seurat-5.3.0/Seurat/R/generics.R | 35 Seurat-5.3.0/Seurat/R/integration.R | 230 +++ Seurat-5.3.0/Seurat/R/integration5.R | 67 - Seurat-5.3.0/Seurat/R/objects.R | 65 - Seurat-5.3.0/Seurat/R/preprocessing.R | 188 +-- Seurat-5.3.0/Seurat/R/preprocessing5.R | 602 +++------- Seurat-5.3.0/Seurat/R/sketching.R | 13 Seurat-5.3.0/Seurat/R/utilities.R | 189 ++- Seurat-5.3.0/Seurat/R/visualization.R | 27 Seurat-5.3.0/Seurat/README.md | 1 Seurat-5.3.0/Seurat/build/Seurat.pdf |binary Seurat-5.3.0/Seurat/build/stage23.rdb |binary Seurat-5.3.0/Seurat/man/AddModuleScore.Rd | 57 Seurat-5.3.0/Seurat/man/CountSketch.Rd | 2 Seurat-5.3.0/Seurat/man/FetchResidualSCTModel.Rd | 15 Seurat-5.3.0/Seurat/man/FetchResiduals.Rd | 53 Seurat-5.3.0/Seurat/man/FindSpatiallyVariableFeatures.Rd | 13 Seurat-5.3.0/Seurat/man/HarmonyIntegration.Rd | 4 Seurat-5.3.0/Seurat/man/LeverageScore.Rd | 2 Seurat-5.3.0/Seurat/man/PseudobulkExpression.Rd | 6 Seurat-5.3.0/Seurat/man/RunICA.Rd | 21 Seurat-5.3.0/Seurat/man/SCTransform.Rd | 119 + Seurat-5.3.0/Seurat/man/ScaleFactors.Rd | 8 Seurat-5.3.0/Seurat/man/SingleExIPlot.Rd | 6 Seurat-5.3.0/Seurat/man/VlnPlot.Rd | 6 Seurat-5.3.0/Seurat/tests/testthat/test_dimensional_reduction.R | 202 ++- Seurat-5.3.0/Seurat/tests/testthat/test_integration.R | 103 + Seurat-5.3.0/Seurat/tests/testthat/test_preprocessing.R | 26 Seurat-5.3.0/Seurat/tests/testthat/test_sketching.R | 10 Seurat-5.3.0/Seurat/tests/testthat/test_utilities.R | 161 ++ 36 files changed, 1585 insertions(+), 797 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.24 dated 2025-04-11 and 1.25 dated 2025-04-23
ChangeLog | 7 +- DESCRIPTION | 10 +-- MD5 | 14 ++-- NAMESPACE | 3 R/cgam.R | 15 ++-- R/testpar.R | 164 +++++++++++++++++++++++++++++++++++++++++----------- man/predict.cgam.Rd | 18 ++--- man/testpar.Rd | 4 - 8 files changed, 168 insertions(+), 67 deletions(-)
Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications
and R Markdown documents. 'webshot2' uses headless Chrome or Chromium
as the browser back-end.
Author: Winston Chang [aut, cre],
Barret Schloerke [ctb] ,
Posit Software, PBC [cph, fnd]
Maintainer: Winston Chang <winston@posit.co>
Diff between webshot2 versions 0.1.1 dated 2023-08-11 and 0.1.2 dated 2025-04-23
webshot2-0.1.1/webshot2/man/figures/README-demo-4.png |only webshot2-0.1.2/webshot2/DESCRIPTION | 16 - webshot2-0.1.2/webshot2/LICENSE |only webshot2-0.1.2/webshot2/MD5 | 40 +- webshot2-0.1.2/webshot2/NEWS.md | 10 webshot2-0.1.2/webshot2/R/appshot.R | 55 ++-- webshot2-0.1.2/webshot2/R/image.R | 72 +++-- webshot2-0.1.2/webshot2/R/process.R | 2 webshot2-0.1.2/webshot2/R/rmdshot.R | 20 - webshot2-0.1.2/webshot2/R/utils.R | 24 + webshot2-0.1.2/webshot2/R/wait.R | 17 + webshot2-0.1.2/webshot2/R/webshot.R | 246 ++++++++++-------- webshot2-0.1.2/webshot2/README.md | 10 webshot2-0.1.2/webshot2/man/appshot.Rd | 30 +- webshot2-0.1.2/webshot2/man/figures/README-demo-1.png |binary webshot2-0.1.2/webshot2/man/figures/README-demo-2.png |binary webshot2-0.1.2/webshot2/man/figures/README-demo-3.png |binary webshot2-0.1.2/webshot2/man/resize.Rd | 4 webshot2-0.1.2/webshot2/man/rmdshot.Rd | 8 webshot2-0.1.2/webshot2/man/shrink.Rd | 2 webshot2-0.1.2/webshot2/man/webshot.Rd | 51 ++- webshot2-0.1.2/webshot2/man/webshot2-package.Rd | 2 22 files changed, 373 insertions(+), 236 deletions(-)
Title: Query the GTEx Portal API
Description: A convenient R interface to the Genotype-Tissue Expression (GTEx)
Portal API. The GTEx project is a comprehensive public resource for studying
tissue-specific gene expression and regulation in human tissues. Through
systematic analysis of RNA sequencing data from 54 non-diseased tissue sites
across nearly 1000 individuals, GTEx provides crucial insights into the
relationship between genetic variation and gene expression. This data is
accessible through the GTEx Portal API enabling programmatic access to human
gene expression data. For more information on the API, see
<https://gtexportal.org/api/v2/redoc>.
Author: Alasdair Warwick [aut, cre, cph]
,
Benjamin Zuckerman [aut] ,
Abraham Olvera-Barrios [aut] ,
Chuin Ying Ung [aut] ,
Robert Luben [aut] ,
Zhian N. Kamvar [rev]
Maintainer: Alasdair Warwick <alasdair.warwick.19@ucl.ac.uk>
Diff between gtexr versions 0.1.0 dated 2024-09-19 and 0.2.0 dated 2025-04-23
gtexr-0.1.0/gtexr/R/get_sample_datasets_endpoints.R |only gtexr-0.1.0/gtexr/man/get_sample_datasets_endpoints.Rd |only gtexr-0.1.0/gtexr/tests/testthat/get_significant_single_tissue_isqtls.R |only gtexr-0.1.0/gtexr/tests/testthat/test-get_sample_datasets_endpoints.R |only gtexr-0.2.0/gtexr/DESCRIPTION | 36 gtexr-0.2.0/gtexr/MD5 | 363 +++++----- gtexr-0.2.0/gtexr/NAMESPACE | 2 gtexr-0.2.0/gtexr/NEWS.md | 39 + gtexr-0.2.0/gtexr/R/calculate_expression_quantitative_trait_loci.R | 99 +- gtexr-0.2.0/gtexr/R/calculate_ieqtls.R | 41 - gtexr-0.2.0/gtexr/R/calculate_isqtls.R | 40 - gtexr-0.2.0/gtexr/R/calculate_splicing_quantitative_trait_loci.R | 22 gtexr-0.2.0/gtexr/R/download.R | 15 gtexr-0.2.0/gtexr/R/get_annotation.R | 17 gtexr-0.2.0/gtexr/R/get_clustered_median_exon_expression.R | 24 gtexr-0.2.0/gtexr/R/get_clustered_median_gene_expression.R | 24 gtexr-0.2.0/gtexr/R/get_clustered_median_junction_expression.R | 24 gtexr-0.2.0/gtexr/R/get_clustered_median_transcript_expression.R | 28 gtexr-0.2.0/gtexr/R/get_collapsed_gene_model_exon.R | 8 gtexr-0.2.0/gtexr/R/get_dataset_info.R | 20 gtexr-0.2.0/gtexr/R/get_downloads_page_data.R | 54 - gtexr-0.2.0/gtexr/R/get_eqtl_genes.R | 8 gtexr-0.2.0/gtexr/R/get_exons.R | 10 gtexr-0.2.0/gtexr/R/get_expression_pca.R | 24 gtexr-0.2.0/gtexr/R/get_file_list.R | 27 gtexr-0.2.0/gtexr/R/get_fine_mapping.R | 38 - gtexr-0.2.0/gtexr/R/get_full_get_collapsed_gene_model_exon.R | 9 gtexr-0.2.0/gtexr/R/get_functional_annotation.R | 8 gtexr-0.2.0/gtexr/R/get_gene_expression.R | 60 - gtexr-0.2.0/gtexr/R/get_gene_search.R | 6 gtexr-0.2.0/gtexr/R/get_genes.R | 6 gtexr-0.2.0/gtexr/R/get_genomic_features.R | 15 gtexr-0.2.0/gtexr/R/get_gwas_catalog_by_location.R | 6 gtexr-0.2.0/gtexr/R/get_image.R | 14 gtexr-0.2.0/gtexr/R/get_independent_eqtl.R | 36 gtexr-0.2.0/gtexr/R/get_linkage_disequilibrium_by_variant_data.R | 10 gtexr-0.2.0/gtexr/R/get_linkage_disequilibrium_data.R | 10 gtexr-0.2.0/gtexr/R/get_maintenance_message.R | 6 gtexr-0.2.0/gtexr/R/get_median_exon_expression.R | 12 gtexr-0.2.0/gtexr/R/get_median_gene_expression.R | 6 gtexr-0.2.0/gtexr/R/get_median_junction_expression.R | 6 gtexr-0.2.0/gtexr/R/get_median_transcript_expression.R | 6 gtexr-0.2.0/gtexr/R/get_multi_tissue_eqtls.R | 30 gtexr-0.2.0/gtexr/R/get_neighbor_gene.R | 8 gtexr-0.2.0/gtexr/R/get_news_item.R | 6 gtexr-0.2.0/gtexr/R/get_sample_biobank_data.R | 34 gtexr-0.2.0/gtexr/R/get_sample_datasets.R |only gtexr-0.2.0/gtexr/R/get_service_info.R | 12 gtexr-0.2.0/gtexr/R/get_significant_single_tissue_eqtls.R | 24 gtexr-0.2.0/gtexr/R/get_significant_single_tissue_eqtls_by_location.R | 21 gtexr-0.2.0/gtexr/R/get_significant_single_tissue_ieqtls.R | 12 gtexr-0.2.0/gtexr/R/get_significant_single_tissue_isqtls.R | 14 gtexr-0.2.0/gtexr/R/get_significant_single_tissue_sqtls.R | 16 gtexr-0.2.0/gtexr/R/get_single_nucleus_gex.R | 66 - 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Title: Comparative Analyses of Lineage-Pair Traits
Description: Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context. Lineage-pair traits are characters that are defined for pairs of lineages instead of individual taxa. Examples include the strength of reproductive isolation, range overlap, competition coefficient, diet niche similarity, and relative hybrid fitness. Users supply a lineage-pair dataset and a phylogeny. 'phylopairs' calculates a covariance matrix for the pairwise-defined data and provides built-in models to test for relationships among variables while taking this covariance into account. Bayesian sampling is run through built-in 'Stan' programs via the 'rstan' package. The various models and methods that this package makes available are described in Anderson et al. (In Review), Coyne and Orr (1989) <doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002) <doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007) <doi:10.1002/ece3.3093>.
Author: Sean A. S. Anderson [aut, cre]
Maintainer: Sean A. S. Anderson <sean.as.anderson@gmail.com>
Diff between phylopairs versions 0.1.0 dated 2024-06-25 and 0.1.1 dated 2025-04-23
phylopairs-0.1.0/phylopairs/R/twoterm.plmm.mats.R |only phylopairs-0.1.0/phylopairs/R/twoterm.plmm.stan.R |only phylopairs-0.1.0/phylopairs/inst/stan/twoterm_plmm.stan |only phylopairs-0.1.0/phylopairs/man/twoterm.plmm.mats.Rd |only phylopairs-0.1.0/phylopairs/man/twoterm.plmm.stan.Rd |only phylopairs-0.1.0/phylopairs/src/stanExports_twoterm_plmm.cc |only phylopairs-0.1.0/phylopairs/src/stanExports_twoterm_plmm.h |only phylopairs-0.1.1/phylopairs/DESCRIPTION | 8 phylopairs-0.1.1/phylopairs/MD5 | 46 +-- phylopairs-0.1.1/phylopairs/NAMESPACE | 4 phylopairs-0.1.1/phylopairs/R/betareg.stan.R | 26 +- phylopairs-0.1.1/phylopairs/R/linreg.stan.R | 19 - phylopairs-0.1.1/phylopairs/R/phylopairs-package.R | 2 phylopairs-0.1.1/phylopairs/R/stanmodels.R | 4 phylopairs-0.1.1/phylopairs/R/taxapair.vcv.R | 17 + phylopairs-0.1.1/phylopairs/R/twoterm.lmm.mats.R |only phylopairs-0.1.1/phylopairs/R/twoterm.lmm.stan.R |only phylopairs-0.1.1/phylopairs/inst/stan/betareg.stan | 12 phylopairs-0.1.1/phylopairs/inst/stan/linreg.stan | 6 phylopairs-0.1.1/phylopairs/inst/stan/twoterm_lmm.stan |only phylopairs-0.1.1/phylopairs/man/betareg.stan.Rd | 14 - phylopairs-0.1.1/phylopairs/man/linreg.stan.Rd | 12 phylopairs-0.1.1/phylopairs/man/phylopairs-package.Rd | 2 phylopairs-0.1.1/phylopairs/man/taxapair.vcv.Rd | 8 phylopairs-0.1.1/phylopairs/man/twoterm.lmm.mats.Rd |only phylopairs-0.1.1/phylopairs/man/twoterm.lmm.stan.Rd |only phylopairs-0.1.1/phylopairs/src/RcppExports.cpp | 4 phylopairs-0.1.1/phylopairs/src/stanExports_betareg.h | 148 ++++++------ phylopairs-0.1.1/phylopairs/src/stanExports_linreg.h | 100 ++++---- phylopairs-0.1.1/phylopairs/src/stanExports_twoterm_lmm.cc |only phylopairs-0.1.1/phylopairs/src/stanExports_twoterm_lmm.h |only 31 files changed, 227 insertions(+), 205 deletions(-)
Title: Simulation of Ecological (and Other) Dynamic Systems
Description: An object oriented framework to simulate
ecological (and other) dynamic systems. It can be used for
differential equations, individual-based (or agent-based) and other
models as well. It supports structuring of simulation scenarios (to avoid copy
and paste) and aims to improve readability and re-usability of code.
Author: Thomas Petzoldt [aut, cre]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between simecol versions 0.8-14 dated 2021-10-07 and 0.9-0 dated 2025-04-23
.Rinstignore | 6 DESCRIPTION | 14 - MD5 | 114 ++++---- R/accessors.R | 424 +++++++++++++++--------------- R/addtoenv.R | 22 - R/approxTime.R | 34 +- R/approxTime1.R | 66 ++-- R/coerce.R | 82 ++--- R/constructors.R | 232 ++++++++-------- R/fromtoby.R | 42 +-- R/iteration.R | 286 ++++++++++---------- R/mixNamedVec.R | 36 +- R/neighbours.R | 140 +++++----- R/p.constrain.R | 26 - R/pcuseries.R | 88 +++--- R/peaks.R | 48 +-- R/print.R | 68 ++-- R/sEdit.R | 178 ++++++------ R/seedfill.R | 60 ++-- R/sim.R | 82 ++--- R/ssqOdeModel.R | 114 ++++---- build/partial.rdb |binary build/vignette.rds |binary demo/00Index | 4 demo/jss.R | 502 ++++++++++++++++++------------------ inst/CITATION | 46 +-- inst/FAQ.txt | 4 inst/NEWS | 5 inst/THANKS | 48 +-- inst/doc/a-simecol-introduction.pdf |binary inst/doc/b-simecol-howtos.pdf |binary man/CA.Rd | 186 ++++++------- man/addtoenv.Rd | 112 ++++---- man/approxTime.Rd | 118 ++++---- man/as.simObj.Rd | 142 +++++----- man/chemostat.Rd | 180 ++++++------ man/conway.Rd | 186 ++++++------- man/diffusion.Rd | 292 ++++++++++---------- man/eightneighbours.Rd | 112 ++++---- man/fromtoby.Rd | 58 ++-- man/initialize-methods.Rd | 174 ++++++------ man/listOrNULL.Rd | 56 ++-- man/lv.Rd | 158 +++++------ man/lv3.Rd | 170 ++++++------ man/mixNamedVec.Rd | 122 ++++---- man/neighbours.Rd | 304 ++++++++++----------- man/odeModel.Rd | 270 +++++++++---------- man/p.constrain.Rd | 120 ++++---- man/parms.Rd | 380 +++++++++++++-------------- man/pcuseries.Rd | 116 ++++---- man/peaks.Rd | 68 ++-- man/plot-methods.Rd | 116 ++++---- man/print-methods.Rd | 56 ++-- man/sEdit.Rd | 88 +++--- man/seedfill.Rd | 86 +++--- man/sim.Rd | 134 ++++----- man/ssqOdeModel.Rd | 220 +++++++-------- man/upca.Rd | 202 +++++++------- vignettes/ibm_daphnia.R | 298 ++++++++++----------- 59 files changed, 3654 insertions(+), 3641 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions, details in Prates, Lachos and Cabral (2013) <doi: 10.18637/jss.v054.i12>, Cabral, Lachos and Prates (2012) <doi:10.1016/j.csda.2011.06.026> and Basso, Lachos, Cabral and Ghosh (2010) <doi:10.1016/j.csda.2009.09.031>.
Author: Marcos Prates [aut, cre, trl] ,
Victor Lachos [aut] ,
Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-10 dated 2021-10-06 and 1.1-11 dated 2025-04-23
ChangeLog | 4 DESCRIPTION | 19 MD5 | 28 R/dens.R | 443 +++++++------- R/mix.dens.R | 24 R/mix.hist.R | 13 R/mix.print.R | 141 ++-- R/mixsmsn.R | 31 - R/smsn.mmix.R | 32 - R/utils.R | 796 +++++++++++++------------- R/utils.multi.R | 1542 +++++++++++++++++++++++++-------------------------- data/bmi.txt.gz |binary data/faithful.txt.gz |binary inst/CITATION | 9 man/mix.hist.Rd | 4 15 files changed, 1564 insertions(+), 1522 deletions(-)
Title: Clustering of Variables
Description: Cluster analysis of a set of variables. Variables can be quantitative, qualitative or a mixture of both.
Author: Marie Chavent [aut, cre],
Vanessa Kuentz [aut],
Benoit Liquet [aut],
Jerome Saracco [aut]
Maintainer: Marie Chavent <Marie.Chavent@u-bordeaux.fr>
Diff between ClustOfVar versions 1.1 dated 2017-08-12 and 1.2 dated 2025-04-23
DESCRIPTION | 15 +++--- MD5 | 50 ++++++++++++--------- NAMESPACE | 12 +---- R/clust_diss.R | 1 R/clust_diss2.R |only R/clusterscore.R | 2 R/cutreevar.R | 2 R/descript.R | 6 +- R/hclustvar.R | 14 +++--- R/hclustvar2.R |only R/kmeansvar.R | 27 ++++++++--- R/plot.clustab.R | 1 R/plot.clustvar.R | 1 R/plot.hclustvar.R | 1 R/predict.clustvar.R | 116 ++++++++++++++++++++++++++++++++++++++------------- R/print.clustab.R | 3 - R/print.clustvar.R | 1 R/print.hclustvar.R | 1 R/selvar.R |only R/stability.R | 2 R/summary.clustab.R | 1 R/summary.clustvar.R | 1 data/protein.RData |binary man/clust_diss2.Rd |only man/cutreevar.Rd | 2 man/flower.Rd | 1 man/hclustvar2.Rd |only man/kmeansvar.Rd | 12 +++-- man/selvar.Rd |only 29 files changed, 172 insertions(+), 100 deletions(-)
Title: Multi-Criteria Method for Decision (TOPSIS)
Description: Assists in the TOPSIS analysis process, designed to return at the end of the answer of the TOPSIS multicriteria analysis, a ranking table with the best option as the analysis proposes. TOPSIS is basically a technique developed by Hwang and Yoon in 1981, starting from the point that the best alternative should be closest to the positive ideal solution and farthest from the negative one, based on several criteria to result in the best benefit. (LIU, H. et al., 2019) <doi:10.1016/j.agwat.2019.105787>.
Author: Wagner Martins dos Santos [aut, cre]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
Diff between TopSisWM versions 1.0.2 dated 2022-09-01 and 1.0.3 dated 2025-04-23
DESCRIPTION | 8 +- MD5 | 6 +- R/TopSisWM.R | 167 ++++++++++++++++++++++---------------------------------- man/TopSisWM.Rd | 28 ++++----- 4 files changed, 86 insertions(+), 123 deletions(-)
Title: Structural Breaks in Quantile Regression
Description: Methods for detecting structural breaks, determining the
number of breaks, and estimating break locations in linear quantile
regression, using one or multiple quantiles, based on Qu (2008) and
Oka and Qu (2011). Applicable to both time series and repeated
cross-sectional data. The main function is rq.break().
References for detailed theoretical and empirical explanations:
(1) Qu, Z. (2008). "Testing for Structural Change in Regression
Quantiles." Journal of Econometrics, 146(1), 170-184
<doi:10.1016/j.jeconom.2008.08.006>
(2) Oka, T., and Qu, Z. (2011). "Estimating Structural Changes in
Regression Quantiles." Journal of Econometrics, 162(2), 248-267
<doi:10.1016/j.jeconom.2011.01.005>.
Author: Zhongjun Qu [aut, cre],
Tatsushi Oka [aut],
Samuel Messer [ctb]
Maintainer: Zhongjun Qu <qu@bu.edu>
Diff between QR.break versions 1.0.1 dated 2025-04-07 and 1.0.2 dated 2025-04-23
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/rq.break.R | 11 +++++++---- README.md | 10 ++++++---- 5 files changed, 29 insertions(+), 19 deletions(-)
Title: Panomics Marketplace - Quality Control and Statistical Analysis
for Panomics Data
Description: Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.
Author: Lisa Bramer [aut, cre],
Kelly Stratton [aut],
Daniel Claborne [aut],
Evan Glasscock [ctb],
Rachel Richardson [ctb],
David Degnan [ctb],
Evan Martin [ctb]
Maintainer: Lisa Bramer <lisa.bramer@pnnl.gov>
Diff between pmartR versions 2.4.6 dated 2024-10-14 and 2.5.0 dated 2025-04-23
pmartR-2.4.6/pmartR/R/combine_lipidData.R |only pmartR-2.4.6/pmartR/man/combine_lipidData.Rd |only pmartR-2.5.0/pmartR/DESCRIPTION | 12 pmartR-2.5.0/pmartR/MD5 | 209 ++++----- pmartR-2.5.0/pmartR/NAMESPACE | 2 pmartR-2.5.0/pmartR/R/MSnSet2pepData.R | 6 pmartR-2.5.0/pmartR/R/RcppExports.R | 4 pmartR-2.5.0/pmartR/R/applyFilt.R | 26 - pmartR-2.5.0/pmartR/R/as.multiData.R | 6 pmartR-2.5.0/pmartR/R/as.omicsData.R | 6 pmartR-2.5.0/pmartR/R/as.trelliData.R | 4 pmartR-2.5.0/pmartR/R/bpquant.R | 14 pmartR-2.5.0/pmartR/R/combine_omicsData.R |only pmartR-2.5.0/pmartR/R/combine_techreps.R | 6 pmartR-2.5.0/pmartR/R/custom_sampnames.R | 2 pmartR-2.5.0/pmartR/R/dim_reduction.R | 7 pmartR-2.5.0/pmartR/R/edata_summary.R | 34 - pmartR-2.5.0/pmartR/R/filter_objects.R | 39 - pmartR-2.5.0/pmartR/R/filter_summary.R | 174 ++++--- pmartR-2.5.0/pmartR/R/get_comparisons.R | 2 pmartR-2.5.0/pmartR/R/group_designation.R | 10 pmartR-2.5.0/pmartR/R/helper_fn.R | 2 pmartR-2.5.0/pmartR/R/imd_anova.R | 95 ++-- pmartR-2.5.0/pmartR/R/missingval_result.R | 8 pmartR-2.5.0/pmartR/R/nonmissing_per_group.R | 4 pmartR-2.5.0/pmartR/R/normalize_global.R | 9 pmartR-2.5.0/pmartR/R/normalize_quantile.R | 2 pmartR-2.5.0/pmartR/R/plot_fns.R | 219 ++++++---- pmartR-2.5.0/pmartR/R/print_data_objects.R | 56 +- pmartR-2.5.0/pmartR/R/print_filter_objects.R | 16 pmartR-2.5.0/pmartR/R/protein_quant.R | 85 ++- pmartR-2.5.0/pmartR/R/report_dataRes.R | 4 pmartR-2.5.0/pmartR/R/results_summary.R | 4 pmartR-2.5.0/pmartR/R/seqData_wrappers.R | 22 - pmartR-2.5.0/pmartR/R/spans.R | 10 pmartR-2.5.0/pmartR/R/statRes_class.R | 2 pmartR-2.5.0/pmartR/R/subset_funcs.R | 4 pmartR-2.5.0/pmartR/R/summary_isobaricnormRes.R | 2 pmartR-2.5.0/pmartR/R/summary_nmrnormRes.R | 2 pmartR-2.5.0/pmartR/R/summary_pmartR.R | 6 pmartR-2.5.0/pmartR/R/survival.R | 2 pmartR-2.5.0/pmartR/R/trelliPlots.R | 4 pmartR-2.5.0/pmartR/R/trelliPlots_seqData.R | 6 pmartR-2.5.0/pmartR/README.md | 2 pmartR-2.5.0/pmartR/inst/testdata/lipidData.R | 2 pmartR-2.5.0/pmartR/inst/testdata/little_prdata.R | 2 pmartR-2.5.0/pmartR/inst/testdata/metaboliteData.R | 2 pmartR-2.5.0/pmartR/inst/testdata/nmrData.R | 2 pmartR-2.5.0/pmartR/inst/testdata/standard_imd_anova_paired.R | 68 +-- pmartR-2.5.0/pmartR/inst/testdata/standards_imd_anova.R | 196 ++++---- pmartR-2.5.0/pmartR/man/anova_filter.Rd | 2 pmartR-2.5.0/pmartR/man/anova_test.Rd | 8 pmartR-2.5.0/pmartR/man/applyFilt.Rd | 2 pmartR-2.5.0/pmartR/man/as.multiData.Rd | 4 pmartR-2.5.0/pmartR/man/combine_omicsData.Rd |only pmartR-2.5.0/pmartR/man/gtest_filter.Rd | 14 pmartR-2.5.0/pmartR/man/imd_anova.Rd | 14 pmartR-2.5.0/pmartR/man/plot-SPANSRes.Rd | 11 pmartR-2.5.0/pmartR/man/pmartR.Rd | 28 + pmartR-2.5.0/pmartR/man/pquant.Rd | 3 pmartR-2.5.0/pmartR/man/protein_quant.Rd | 3 pmartR-2.5.0/pmartR/man/summary.proteomicsFilt.Rd | 8 pmartR-2.5.0/pmartR/src/RcppExports.cpp | 9 pmartR-2.5.0/pmartR/src/imd_anova.cpp | 104 ++-- pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-corres.svg | 18 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-datares-bw-theme.svg | 31 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-datares-palette.svg | 31 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-datares.svg | 31 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-imdanovafilt.svg | 6 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-moleculefilt-cumulative.svg | 14 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-normres.svg | 29 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-proteomicsfilt.svg | 14 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-rmdfilt.svg | 2 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-spansres-bw-theme.svg | 38 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-spansres-color-high-color-low.svg | 38 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-spansres-n-biomolecule-bar.svg |only pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-spansres.svg | 38 - pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-statres-combined.svg | 2 pmartR-2.5.0/pmartR/tests/testthat/_snaps/plots/plot-totalcountfilt.svg | 183 ++++---- pmartR-2.5.0/pmartR/tests/testthat/test_as_isobaricpepData.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_as_lipidData.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_as_metabData.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_as_multiData.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_as_nmrData.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_as_pepData.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_as_proData.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_as_seqData.R | 8 pmartR-2.5.0/pmartR/tests/testthat/test_combine_omicsData.R | 157 ++++--- pmartR-2.5.0/pmartR/tests/testthat/test_diffexp_seq.R | 6 pmartR-2.5.0/pmartR/tests/testthat/test_dim_reduction.R | 8 pmartR-2.5.0/pmartR/tests/testthat/test_edata_structure.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_edata_summary.R | 54 +- pmartR-2.5.0/pmartR/tests/testthat/test_filter_custom.R | 8 pmartR-2.5.0/pmartR/tests/testthat/test_filter_imdanova.R | 52 +- pmartR-2.5.0/pmartR/tests/testthat/test_filter_proteomics.R | 16 pmartR-2.5.0/pmartR/tests/testthat/test_filter_total_count.R | 2 pmartR-2.5.0/pmartR/tests/testthat/test_group_designation.R | 18 pmartR-2.5.0/pmartR/tests/testthat/test_imd_anova.R | 181 ++++++-- pmartR-2.5.0/pmartR/tests/testthat/test_normalize_spans.R | 8 pmartR-2.5.0/pmartR/tests/testthat/test_plots.R | 46 +- pmartR-2.5.0/pmartR/tests/testthat/test_quant_bp.R | 22 - pmartR-2.5.0/pmartR/tests/testthat/test_quant_protein.R | 77 ++- pmartR-2.5.0/pmartR/tests/testthat/test_result_missingval.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_summary_filter.R | 57 +- pmartR-2.5.0/pmartR/tests/testthat/test_summary_omicsData.R | 8 pmartR-2.5.0/pmartR/tests/testthat/test_trelliPlots.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_trelliPlots_seqData.R | 4 pmartR-2.5.0/pmartR/tests/testthat/test_zero_one_scaling.R | 4 108 files changed, 1738 insertions(+), 1134 deletions(-)
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Description: 'Rcpp' bindings for 'PLANC', a highly parallel
and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library.
Wraps algorithms described in
Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and
Eswar et. al (2021) <doi:10.1145/3432185>.
Implements algorithms described in
Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>,
Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and
Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Author: Andrew Robbins [aut, cre] ,
Yichen Wang [aut],
Joshua Welch [cph] ,
Ramakrishnan Kannan [cph] ,
Conrad Sanderson [cph] ,
Blue Brain Project/EPFL [cph] ,
UT-Batelle [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between RcppPlanc versions 2.0.4 dated 2025-04-14 and 2.0.5 dated 2025-04-23
RcppPlanc-2.0.4/RcppPlanc/src/planc/cmake/FindMKL.cmake |only RcppPlanc-2.0.5/RcppPlanc/DESCRIPTION | 18 ++- RcppPlanc-2.0.5/RcppPlanc/MD5 | 30 ++--- RcppPlanc-2.0.5/RcppPlanc/NEWS.md | 8 + RcppPlanc-2.0.5/RcppPlanc/R/utils.R | 2 RcppPlanc-2.0.5/RcppPlanc/build/vignette.rds |binary RcppPlanc-2.0.5/RcppPlanc/inst/COPYRIGHTS |only RcppPlanc-2.0.5/RcppPlanc/inst/doc/RcppPlanc.html | 10 - RcppPlanc-2.0.5/RcppPlanc/man/H5SpMat.Rd | 2 RcppPlanc-2.0.5/RcppPlanc/src/planc/CMakeLists.txt | 61 +++++----- RcppPlanc-2.0.5/RcppPlanc/src/planc/cmake/FindR.cmake | 4 RcppPlanc-2.0.5/RcppPlanc/src/planc/common/inmf.hpp | 14 -- RcppPlanc-2.0.5/RcppPlanc/src/planc/license.md | 91 ++++++++++++++++ RcppPlanc-2.0.5/RcppPlanc/src/planc/nmf/bppinmf.hpp | 30 +++++ RcppPlanc-2.0.5/RcppPlanc/src/planc/nmf/onlineinmf.hpp | 28 ++++ RcppPlanc-2.0.5/RcppPlanc/src/planc/pyproject.toml | 13 -- RcppPlanc-2.0.5/RcppPlanc/src/planc/vcpkg.json | 3 17 files changed, 232 insertions(+), 82 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. 'dsims' repeatedly generates
instances of a user defined population within a given survey region. It then
generates realisations of a survey design and simulates the detection process.
The data are then analysed so that the results can be compared for accuracy
and precision across all replications. This process allows users to optimise
survey designs for their specific set of survey conditions. The effects of
uncertainty in population distribution or parameters can be investigated
under a number of simulations so that users can be confident that they have
achieved a robust survey design before deploying vessels into the field. The
distance sampling designs used in this package from 'dssd' are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13:
978-0199225873). General distance sampling methods are detailed in Introduction
to Distance Sampling: Estimating Abundance of Biological Populations, Buckland
et. al. (2004 [...truncated...]
Author: Laura Marshall [aut, cre],
Thomas Len [ctb]
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between dsims versions 1.0.5 dated 2024-12-20 and 1.0.6 dated 2025-04-23
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 10 ++++++ R/Simulation.R | 2 - tests/testthat/test-check_Constructors.R | 51 +++++++++++++++++++++++++++++++ 5 files changed, 69 insertions(+), 8 deletions(-)
Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between mMARCH.AC versions 2.9.4.0 dated 2024-08-23 and 3.2.0.0 dated 2025-04-23
DESCRIPTION | 10 MD5 | 24 - R/MakeSleepDataMatrix.R | 2 R/RA2.R | 16 R/module0_maincall.R | 2 build/vignette.rds |binary inst/doc/mMARCH.AC.R | 324 ++++++++-------- inst/doc/mMARCH.AC.html | 4 inst/template/module5_Data_process_report.Rmd | 51 +- inst/template/module6_NonWear.report.Rmd | 8 inst/template/module7a_calculate_newfeatures.Rmd | 36 - inst/template/module7b_merge_GGIRfeatures.Rmd | 46 +- inst/template/module7d_calculate_WD_WE_avg_features.Rmd | 34 - 13 files changed, 285 insertions(+), 272 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [ctb]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.7.0 dated 2025-01-20 and 0.8.0 dated 2025-04-23
DESCRIPTION | 11 +- MD5 | 65 ++++++++---- NEWS.md | 20 +++ R/as_fc.R | 22 ++-- R/fc_draw.R | 43 ++++++-- R/fc_export.R | 59 ++++++++--- R/fc_filter.R | 87 +++++++++++----- R/fc_split.R | 52 ++++++--- R/fc_stack.R | 11 +- R/fc_view.R | 2 R/utils.R | 168 +++++++++++++++++++++++++++++++- README.md | 4 inst/doc/flowchart.R | 42 ++++---- inst/doc/flowchart.Rmd | 47 +++++--- inst/doc/flowchart.html | 230 +++++++++++++++++++++++--------------------- man/as_fc.Rd | 6 + man/fc_draw.Rd | 8 + man/fc_filter.Rd | 14 ++ man/fc_split.Rd | 12 ++ man/fc_view.Rd | 66 ++++++------ man/quiet_prettyNum.Rd |only man/replace_num_in_expr.Rd |only man/update_numbers.Rd |only man/update_y_stack_unite.Rd | 38 +++---- tests |only vignettes/flowchart.Rmd | 47 +++++--- 26 files changed, 726 insertions(+), 328 deletions(-)
Title: Tools for Creating and Visualizing Fixed-Effects Event Study
Models
Description: Provides functions for creating, analyzing, and visualizing event study models using fixed-effects regression.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between fixes versions 0.1.0 dated 2025-03-18 and 0.2.0 dated 2025-04-23
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 13 + R/event_study.R | 332 +++++++++++++++++++++---------------------- README.md | 74 ++++++--- build/vignette.rds |binary inst/doc/fixes-intro.Rmd | 56 ++++--- inst/doc/fixes-intro.html | 90 ++++++----- man/plot_es.Rd | 11 - man/run_es.Rd | 131 +++++++++++----- tests/testthat/test-run_es.R | 189 +++++++++++++++++------- vignettes/fixes-intro.Rmd | 56 ++++--- 12 files changed, 583 insertions(+), 397 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.81 dated 2025-04-09 and 2.0.82 dated 2025-04-23
DESCRIPTION | 8 ++--- MD5 | 16 +++++------ NEWS | 7 ++++ R/rsu.sssep.rsfreecalc.R | 5 ++- inst/doc/epiR_descriptive.html | 16 +++++------ inst/doc/epiR_measures_of_association.html | 12 ++++---- inst/doc/epiR_sample_size.html | 4 +- inst/doc/epiR_surveillance.html | 14 ++++----- man/epi.edr.Rd | 42 ++++++++++++++--------------- 9 files changed, 67 insertions(+), 57 deletions(-)
Title: Simplex Visualization of Cell Fate Similarity in Single-Cell
Data
Description: Create simplex plots to visualize the similarity between
single-cells and selected clusters in a 1-/2-/3-simplex space.
Velocity information can be added as an additional layer.
See Liu J, Wang Y et al (2023) <doi:10.1093/bioinformatics/btaf119> for more details.
Author: Yichen Wang [aut, cre] ,
Jialin Liu [aut] ,
Joshua Welch [cph]
Maintainer: Yichen Wang <wayichen@umich.edu>
Diff between CytoSimplex versions 0.1.1 dated 2023-12-15 and 0.2.0 dated 2025-04-23
CytoSimplex-0.1.1/CytoSimplex/inst/figure |only CytoSimplex-0.1.1/CytoSimplex/man/show-plist.Rd |only CytoSimplex-0.2.0/CytoSimplex/DESCRIPTION | 18 CytoSimplex-0.2.0/CytoSimplex/MD5 | 64 CytoSimplex-0.2.0/CytoSimplex/NAMESPACE | 8 CytoSimplex-0.2.0/CytoSimplex/NEWS.md | 15 CytoSimplex-0.2.0/CytoSimplex/R/data.R | 4 CytoSimplex-0.2.0/CytoSimplex/R/hdf5Access.R |only CytoSimplex-0.2.0/CytoSimplex/R/quaternary.R | 749 ++++-- CytoSimplex-0.2.0/CytoSimplex/R/ternary.R | 560 ++++ CytoSimplex-0.2.0/CytoSimplex/R/util.R | 297 ++ CytoSimplex-0.2.0/CytoSimplex/README.md | 7 CytoSimplex-0.2.0/CytoSimplex/build/vignette.rds |binary CytoSimplex-0.2.0/CytoSimplex/inst/doc/CytoSimplex.R | 29 CytoSimplex-0.2.0/CytoSimplex/inst/doc/CytoSimplex.Rmd | 54 CytoSimplex-0.2.0/CytoSimplex/inst/doc/CytoSimplex.html | 1140 ---------- CytoSimplex-0.2.0/CytoSimplex/man/plotQuaternary.Rd | 202 - CytoSimplex-0.2.0/CytoSimplex/man/plotQuaternary.Seurat.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/plotQuaternary.SingleCellExperiment.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/plotQuaternary.simMat.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/plotTernary.Rd | 212 - CytoSimplex-0.2.0/CytoSimplex/man/plotTernary.Seurat.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/plotTernary.SingleCellExperiment.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/plotTernary.simMat.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/print-quatPlot.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/readH5ADObsNames.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/readH5ADObsVar.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/readH5ADUnsSpMat.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/readVelocytoLoom.Rd |only CytoSimplex-0.2.0/CytoSimplex/man/rnaRaw.Rd | 2 CytoSimplex-0.2.0/CytoSimplex/man/rnaVelo.Rd | 2 CytoSimplex-0.2.0/CytoSimplex/man/writeQuaternaryGIF.Rd | 31 CytoSimplex-0.2.0/CytoSimplex/src/CytoSimplex.cpp | 6 CytoSimplex-0.2.0/CytoSimplex/tests/testthat/test-binary.R | 5 CytoSimplex-0.2.0/CytoSimplex/tests/testthat/test-objectS3.R | 5 CytoSimplex-0.2.0/CytoSimplex/tests/testthat/test-preprocessing.R | 1 CytoSimplex-0.2.0/CytoSimplex/tests/testthat/test-quaternary.R | 64 CytoSimplex-0.2.0/CytoSimplex/tests/testthat/test-ternary.R | 5 CytoSimplex-0.2.0/CytoSimplex/vignettes/CytoSimplex.Rmd | 54 CytoSimplex-0.2.0/CytoSimplex/vignettes/articles |only 40 files changed, 1782 insertions(+), 1752 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.2 dated 2024-12-20 and 1.2.3 dated 2025-04-23
DESCRIPTION | 8 +- MD5 | 24 +++--- NAMESPACE | 1 NEWS.md | 11 +++ R/imgw_read.R | 11 ++- R/meteo_imgw_daily.R | 165 ++++++++++++++++++++++++++++++--------------- R/meteo_imgw_hourly.R | 52 ++++++++++---- R/utils.R |only R/zzz.R |only README.md | 1 build/vignette.rds |binary data/imgw_meteo_abbrev.rda |binary inst/doc/getstarted.R | 52 +++++++------- inst/doc/getstarted.html | 42 +++++------ 14 files changed, 241 insertions(+), 126 deletions(-)
More information about biometryassist at CRAN
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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 [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.14 dated 2025-01-23 and 0.0.15 dated 2025-04-23
ChangeLog | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ src/ql/time/calendars/china.cpp | 13 ++++++++++++- src/ql/time/calendars/hongkong.cpp | 15 +++++++++++++++ src/ql/time/calendars/thailand.cpp | 9 +++++++++ 8 files changed, 67 insertions(+), 12 deletions(-)
Title: Mediterranean Landscape Simulation
Description: Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.
Author: Miquel De Caceres [aut, cre],
Aitor Ameztegui [aut] ,
Maria Gonzalez [aut] ,
Nuria Aquilue [aut],
Daniel Caviedes-Voullieme [aut],
Mario Morales-Hernandez [aut],
Mario Beltran [ctb],
Rodrigo Balaguer-Romano [ctb] ,
Roberto Molowny-Horas [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfateland versions 2.5.1 dated 2025-01-28 and 2.6.0 dated 2025-04-23
DESCRIPTION | 10 MD5 | 42 - NAMESPACE | 3 R/RcppExports.R | 20 R/default_watershed_control.R | 6 R/extract_variables.R | 35 - R/initialize_landscape.R | 37 + R/medfateland-package.R | 1 R/model_land.R | 1207 +++++++++++++++++++++++---------------- R/optimization_rock.R |only R/overland_routing.R |only R/update_landscape.R | 1 man/default_watershed_control.Rd | 3 man/initialize_landscape.Rd | 2 man/optimization_rock.Rd |only man/overland_routing.Rd |only man/spwb_land.Rd | 79 -- man/spwb_land_day.Rd | 17 src/RcppExports.cpp | 59 + src/spwbland.cpp | 121 +++ src/spwbland.h | 31 - src/tetis.cpp | 165 ++++- src/tetis.h | 2 tests/testthat/test_land.R | 7 24 files changed, 1171 insertions(+), 677 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also
contains a number of lower level 'CLI' elements: rules, boxes, trees,
and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI
colors and text styles as well.
Author: Gabor Csardi [aut, cre],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
Salim Brueggemann [ctb] ,
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <gabor@posit.co>
Diff between cli versions 3.6.4 dated 2025-02-13 and 3.6.5 dated 2025-04-23
DESCRIPTION | 6 +- MD5 | 43 +++++++-------- NEWS.md | 5 + R/format.R | 5 + R/prettycode.R | 42 ++++++++++++++ man/builtin_theme.Rd | 14 ++-- man/cli-config.Rd | 101 +++++++++++++++++++++++++++++------- man/cli_abort.Rd | 4 - man/cli_code.Rd | 10 +-- man/cli_end.Rd | 2 man/cli_progress_styles.Rd | 6 +- man/cli_vec.Rd | 5 + man/containers.Rd | 2 man/inline-markup.Rd | 2 man/links.Rd | 4 - man/progress-variables.Rd | 22 +++---- man/simple_theme.Rd | 14 ++-- src/Makevars | 3 - src/progress-altrep.c | 4 - tests/testthat/_snaps/rlang-1.1.6 |only tests/testthat/test-cliapp-output.R | 18 +++--- tests/testthat/test-prettycode.R | 29 ++++++++++ tests/testthat/test-subprocess.R | 5 + 23 files changed, 246 insertions(+), 100 deletions(-)
Title: Create a Mini Version of CRAN Containing Only Selected Packages
Description: Makes it possible to create an internally consistent
repository consisting of selected packages from CRAN-like repositories.
The user specifies a set of desired packages, and 'miniCRAN' recursively
reads the dependency tree for these packages, then downloads only this
subset. The user can then install packages from this repository directly,
rather than from CRAN. This is useful in production settings, e.g. server
behind a firewall, or remote locations with slow (or zero) Internet access.
Author: Andrie de Vries [aut, cre, cph],
Alex Chubaty [ctb],
Microsoft Corporation [cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between miniCRAN versions 0.3.0 dated 2024-03-28 and 0.3.1 dated 2025-04-23
DESCRIPTION | 6 MD5 | 78 +++--- NEWS | 7 R/P3M.R | 22 - R/addPackages.R | 210 ++++++++++++------ R/assertions.R | 2 R/getCranDescription.R | 10 R/github-functions.R | 73 ++++-- R/internal.R | 56 +++- R/makeDepGraph.R | 61 +++-- R/makeRepo.R | 67 ++++- R/minicran-package.R | 2 R/pkgDep.R | 191 ++++++++++------ R/pkgDepTools.R | 13 - R/plot.pkgDepGraph.R | 64 +++-- R/updatePackages.R | 103 +++++---- R/utils.R | 16 - R/zzz.R | 1 build/vignette.rds |binary inst/doc/miniCRAN-dependency-graph.html | 13 - inst/doc/miniCRAN-introduction.R | 92 ++++---- inst/doc/miniCRAN-introduction.html | 9 inst/doc/miniCRAN-non-CRAN-repos.R | 12 - inst/doc/miniCRAN-non-CRAN-repos.html | 9 man/makeRepo.Rd | 3 tests/testthat/helpers.R | 113 +++++----- tests/testthat/test-1-github-functions.R | 11 tests/testthat/test-1-pkgAvail.R | 10 tests/testthat/test-1-pkgDep.R | 133 ++++++++--- tests/testthat/test-1-r-version.R | 41 ++- tests/testthat/test-2-makeDepGraph.R | 74 +++--- tests/testthat/test-3-makeRepo.R | 89 ++++--- tests/testthat/test-4-makeRepo-from-localCRAN.R | 86 +++++-- tests/testthat/test-5-ask-for-confirmation.R | 68 +++--- tests/testthat/test-5-updateRepo.R | 270 ++++++++++++++---------- tests/testthat/test-6-getCranDescription.R | 2 tests/testthat/test-7-addGithubPackage.R | 4 tests/testthat/test-8-addLocalPackage.R | 46 ++-- tests/testthat/test-9-is-online.R | 6 tests/testthat/test-r-version.R | 41 ++- 40 files changed, 1292 insertions(+), 822 deletions(-)
More information about CircNNTSRaxial at CRAN
Permanent link
More information about MarginalMaxTest at CRAN
Permanent link
Title: TVA Models in 'Stan' using 'R' and 'StanTVA'
Description: 'Stan' implementation of the Theory of Visual Attention (TVA; Bundesen, 1990; <doi:10.1037/0033-295X.97.4.523>) and numerous convenience functions for generating, compiling, fitting, and analyzing TVA models.
Author: Maximilian M. Rabe [aut, cre] ,
Soeren Kyllingsbaek [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between RStanTVA versions 0.2.1 dated 2025-04-16 and 0.2.6 dated 2025-04-23
DESCRIPTION | 6 +- MD5 | 20 ++++--- R/tva.R | 101 +++++++++++++++++++++----------------- README.md | 52 +++++++++++++------ data/tva_recovery.rda |binary data/tva_recovery_true_params.rda |binary inst/StanTVA/bernoulliK.stan | 4 - inst/StanTVA/betabinomialK.stan |only inst/StanTVA/binomialK.stan |only inst/StanTVA/freeK.stan | 6 +- inst/StanTVA/tva.stan | 6 +- man/stantva_code.Rd | 2 12 files changed, 118 insertions(+), 79 deletions(-)
Title: Identify External Packages Used in a Project
Description: Screens all '.R', '.Rmd', and '.qmd' files to extract the name of
packages used in a project. This package detects packages called with
'library(foo)', 'require(foo)', 'foo::bar()' and 'use("foo", "bar")' and
adds these dependencies in the DESCRIPTION file in the sections Depends,
Imports, and Suggests.
Author: Nicolas Casajus [aut, cre, cph]
Maintainer: Nicolas Casajus <nicolas.casajus@fondationbiodiversite.fr>
Diff between rdeps versions 0.2 dated 2024-02-02 and 0.3 dated 2025-04-23
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 6 NEWS.md | 26 R/add_deps.R | 500 ++++----- R/rdeps-package.R | 14 R/utils-deps.R | 1689 ++++++++++++++++----------------- R/utils-io.R | 99 - R/utils-msg.R | 184 +-- R/utils-proj.R | 131 +- README.md | 209 ++-- inst/CITATION | 20 inst/package-sticker/package-sticker.R | 98 - man/add_deps.Rd | 99 - man/rdeps-package.Rd | 50 15 files changed, 1598 insertions(+), 1569 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.5 dated 2025-01-11 and 1.3.6 dated 2025-04-23
mets-1.3.5/mets/data/hfaction_cpx12.rda |only mets-1.3.5/mets/man/EventSplit.Rd |only mets-1.3.5/mets/man/covarianceRecurrent.Rd |only mets-1.3.5/mets/man/hfaction_cpx12.Rd |only mets-1.3.5/mets/man/predictRisk.phreg.Rd |only mets-1.3.5/mets/tests/test-all.R |only mets-1.3.5/mets/tests/testthat |only mets-1.3.6/mets/DESCRIPTION | 18 mets-1.3.6/mets/MD5 | 262 - mets-1.3.6/mets/NAMESPACE | 64 mets-1.3.6/mets/NEWS.md | 12 mets-1.3.6/mets/R/Event.Split.R | 28 mets-1.3.6/mets/R/RcppExports.R | 12 mets-1.3.6/mets/R/WA-estimands.R | 4 mets-1.3.6/mets/R/aalenfrailty.R | 1 mets-1.3.6/mets/R/binomial.regression.R | 608 -- mets-1.3.6/mets/R/binregTSR.R | 2 mets-1.3.6/mets/R/biprobit.R | 2 mets-1.3.6/mets/R/bptwin.R | 2 mets-1.3.6/mets/R/cifreg.R | 176 mets-1.3.6/mets/R/cor.R | 2 mets-1.3.6/mets/R/daggregate.R | 9 mets-1.3.6/mets/R/dby.R | 24 mets-1.3.6/mets/R/dreg.R | 4 mets-1.3.6/mets/R/dutils.R | 7 mets-1.3.6/mets/R/fastapprox.R | 29 mets-1.3.6/mets/R/glm-utils.R | 3 mets-1.3.6/mets/R/kmplot.R | 31 mets-1.3.6/mets/R/lifetable.R | 9 mets-1.3.6/mets/R/mediator-survival.R | 4 mets-1.3.6/mets/R/mets-package.R | 37 mets-1.3.6/mets/R/mutinomialreg.R | 17 mets-1.3.6/mets/R/phreg.R | 2454 +++++----- mets-1.3.6/mets/R/phreg.par.R | 247 - mets-1.3.6/mets/R/phreg_rct.R | 729 -- mets-1.3.6/mets/R/recreg.R | 2189 +++++++- mets-1.3.6/mets/R/recurrent.marginal.R | 1936 +------ mets-1.3.6/mets/R/riskRegression.R | 43 mets-1.3.6/mets/R/sim-pc-hazard.R | 10 mets-1.3.6/mets/R/tetrachor.R | 77 mets-1.3.6/mets/README.md | 307 + mets-1.3.6/mets/build/partial.rdb |binary mets-1.3.6/mets/build/vignette.rds |binary mets-1.3.6/mets/data/calgb8923.rda |binary mets-1.3.6/mets/data/hfactioncpx12.rda |only mets-1.3.6/mets/inst/_pkgdown.yml |only mets-1.3.6/mets/inst/doc/basic-dutils.html | 78 mets-1.3.6/mets/inst/doc/binomial-family.Rmd | 2 mets-1.3.6/mets/inst/doc/binomial-family.html | 72 mets-1.3.6/mets/inst/doc/binomial-twin.html | 40 mets-1.3.6/mets/inst/doc/binreg-TRS.R | 11 mets-1.3.6/mets/inst/doc/binreg-TRS.Rmd | 36 mets-1.3.6/mets/inst/doc/binreg-TRS.html | 162 mets-1.3.6/mets/inst/doc/binreg-ate.html | 40 mets-1.3.6/mets/inst/doc/binreg.Rmd | 50 mets-1.3.6/mets/inst/doc/binreg.html | 97 mets-1.3.6/mets/inst/doc/cifreg.R | 4 mets-1.3.6/mets/inst/doc/cifreg.Rmd | 6 mets-1.3.6/mets/inst/doc/cifreg.html | 74 mets-1.3.6/mets/inst/doc/cooking-survival-data.R | 22 mets-1.3.6/mets/inst/doc/cooking-survival-data.Rmd | 22 mets-1.3.6/mets/inst/doc/cooking-survival-data.html | 228 mets-1.3.6/mets/inst/doc/glm-utility.html | 40 mets-1.3.6/mets/inst/doc/haplo-discrete-ttp.html | 40 mets-1.3.6/mets/inst/doc/interval-discrete-survival.html | 40 mets-1.3.6/mets/inst/doc/marginal-cox.R | 2 mets-1.3.6/mets/inst/doc/marginal-cox.Rmd | 2 mets-1.3.6/mets/inst/doc/marginal-cox.html | 46 mets-1.3.6/mets/inst/doc/mediation-survival.html | 106 mets-1.3.6/mets/inst/doc/phreg_rct.R | 63 mets-1.3.6/mets/inst/doc/phreg_rct.Rmd | 113 mets-1.3.6/mets/inst/doc/phreg_rct.html | 627 +- mets-1.3.6/mets/inst/doc/recurrent-events.R | 220 mets-1.3.6/mets/inst/doc/recurrent-events.Rmd | 369 - mets-1.3.6/mets/inst/doc/recurrent-events.html | 1120 ++-- mets-1.3.6/mets/inst/doc/rmst-ate.R | 12 mets-1.3.6/mets/inst/doc/rmst-ate.Rmd | 15 mets-1.3.6/mets/inst/doc/rmst-ate.html | 300 - mets-1.3.6/mets/inst/doc/survival-ate.R | 6 mets-1.3.6/mets/inst/doc/survival-ate.Rmd | 6 mets-1.3.6/mets/inst/doc/survival-ate.html | 124 mets-1.3.6/mets/inst/doc/time-to-event-family-studies-arev.R | 2 mets-1.3.6/mets/inst/doc/time-to-event-family-studies-arev.Rmd | 2 mets-1.3.6/mets/inst/doc/time-to-event-family-studies-arev.html | 62 mets-1.3.6/mets/inst/doc/twostage-survival.html | 46 mets-1.3.6/mets/inst/doc/while-alive.R | 373 - mets-1.3.6/mets/inst/doc/while-alive.Rmd | 384 - mets-1.3.6/mets/inst/doc/while-alive.html | 565 -- mets-1.3.6/mets/inst/slowtest |only mets-1.3.6/mets/inst/tinytest |only mets-1.3.6/mets/man/EventSplit2.Rd |only mets-1.3.6/mets/man/basehazplot.phreg.Rd | 19 mets-1.3.6/mets/man/binreg.Rd | 21 mets-1.3.6/mets/man/binregATE.Rd | 3 mets-1.3.6/mets/man/binregG.Rd | 2 mets-1.3.6/mets/man/calgb8923.Rd | 11 mets-1.3.6/mets/man/cif.Rd | 23 mets-1.3.6/mets/man/cifreg.Rd | 68 mets-1.3.6/mets/man/cor.cif.Rd | 2 mets-1.3.6/mets/man/dby.Rd | 8 mets-1.3.6/mets/man/dreg.Rd | 4 mets-1.3.6/mets/man/dspline.Rd | 7 mets-1.3.6/mets/man/hfactioncpx12.Rd |only mets-1.3.6/mets/man/km.Rd | 37 mets-1.3.6/mets/man/mlogit.Rd | 8 mets-1.3.6/mets/man/phreg.Rd | 22 mets-1.3.6/mets/man/phreg_IPTW.Rd | 22 mets-1.3.6/mets/man/phreg_rct.Rd | 36 mets-1.3.6/mets/man/plot.phreg.Rd |only mets-1.3.6/mets/man/predict.phreg.Rd | 2 mets-1.3.6/mets/man/predictRisk.Rd |only mets-1.3.6/mets/man/predictRisk.binreg.Rd |only mets-1.3.6/mets/man/prob.exceed.recurrent.Rd | 82 mets-1.3.6/mets/man/recreg.Rd | 51 mets-1.3.6/mets/man/recurrentMarginal.Rd | 93 mets-1.3.6/mets/man/reexports.Rd | 8 mets-1.3.6/mets/man/survivalG.Rd | 9 mets-1.3.6/mets/man/tetrachoric.Rd | 3 mets-1.3.6/mets/src/RcppExports.cpp | 60 mets-1.3.6/mets/src/fastcox.cpp | 83 mets-1.3.6/mets/tests/tinytest.R |only mets-1.3.6/mets/vignettes/binomial-family.Rmd | 2 mets-1.3.6/mets/vignettes/binreg-TRS.Rmd | 36 mets-1.3.6/mets/vignettes/binreg.Rmd | 50 mets-1.3.6/mets/vignettes/cifreg.Rmd | 6 mets-1.3.6/mets/vignettes/cooking-survival-data.Rmd | 22 mets-1.3.6/mets/vignettes/marginal-cox.Rmd | 2 mets-1.3.6/mets/vignettes/phreg_rct.Rmd | 113 mets-1.3.6/mets/vignettes/recurrent-events.Rmd | 369 - mets-1.3.6/mets/vignettes/rmst-ate.Rmd | 15 mets-1.3.6/mets/vignettes/survival-ate.Rmd | 6 mets-1.3.6/mets/vignettes/time-to-event-family-studies-arev.Rmd | 2 mets-1.3.6/mets/vignettes/while-alive.Rmd | 384 - 133 files changed, 8000 insertions(+), 8679 deletions(-)
Title: Tagging and Validating Epidemiological Data
Description: Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Author: Hugo Gruson [aut, cre] ,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev]
Maintainer: Hugo Gruson <hugo@data.org>
Diff between linelist versions 1.1.4 dated 2024-06-17 and 2.0.0 dated 2025-04-23
linelist-1.1.4/linelist/R/select.linelist.R |only linelist-1.1.4/linelist/R/select_tags.R |only linelist-1.1.4/linelist/man/select.linelist.Rd |only linelist-1.1.4/linelist/man/select_tags.Rd |only linelist-1.1.4/linelist/tests/testthat/_snaps/deprecated.md |only linelist-1.1.4/linelist/tests/testthat/test-deprecated.R |only linelist-2.0.0/linelist/DESCRIPTION | 16 linelist-2.0.0/linelist/MD5 | 102 - linelist-2.0.0/linelist/NAMESPACE | 4 linelist-2.0.0/linelist/NEWS.md | 52 linelist-2.0.0/linelist/R/custom_assertions.R | 4 linelist-2.0.0/linelist/R/has_tag.R | 4 linelist-2.0.0/linelist/R/linelist-package.R | 17 linelist-2.0.0/linelist/R/lost_tags_action.R | 11 linelist-2.0.0/linelist/R/make_linelist.R | 10 linelist-2.0.0/linelist/R/modify_defaults.R | 6 linelist-2.0.0/linelist/R/names.R | 9 linelist-2.0.0/linelist/R/print.linelist.R | 6 linelist-2.0.0/linelist/R/prune_tags.R | 2 linelist-2.0.0/linelist/R/set_tags.R | 10 linelist-2.0.0/linelist/R/square_bracket.R | 11 linelist-2.0.0/linelist/R/tags_df.R | 7 linelist-2.0.0/linelist/R/validate_linelist.R | 15 linelist-2.0.0/linelist/R/validate_tags.R | 36 linelist-2.0.0/linelist/R/validate_types.R | 5 linelist-2.0.0/linelist/build/vignette.rds |binary linelist-2.0.0/linelist/inst/doc/compat-dplyr.R | 77 linelist-2.0.0/linelist/inst/doc/compat-dplyr.Rmd | 86 - linelist-2.0.0/linelist/inst/doc/compat-dplyr.html | 849 +++++----- linelist-2.0.0/linelist/inst/doc/design-principles.Rmd | 2 linelist-2.0.0/linelist/inst/doc/design-principles.html | 2 linelist-2.0.0/linelist/inst/doc/linelist.R | 23 linelist-2.0.0/linelist/inst/doc/linelist.Rmd | 39 linelist-2.0.0/linelist/inst/doc/linelist.html | 367 ++-- linelist-2.0.0/linelist/inst/doc/software-permissions.Rmd | 4 linelist-2.0.0/linelist/inst/doc/software-permissions.html | 2 linelist-2.0.0/linelist/man/figures/README-unnamed-chunk-9-1.png |binary linelist-2.0.0/linelist/man/has_tag.Rd | 4 linelist-2.0.0/linelist/man/linelist-package.Rd | 16 linelist-2.0.0/linelist/man/lost_tags_action.Rd | 4 linelist-2.0.0/linelist/man/names-set-.linelist.Rd | 2 linelist-2.0.0/linelist/man/print.linelist.Rd | 6 linelist-2.0.0/linelist/man/sub_linelist.Rd | 11 linelist-2.0.0/linelist/man/tags_df.Rd | 7 linelist-2.0.0/linelist/man/validate_linelist.Rd | 11 linelist-2.0.0/linelist/man/validate_tags.Rd | 5 linelist-2.0.0/linelist/man/validate_types.Rd | 5 linelist-2.0.0/linelist/tests/testthat.R | 14 linelist-2.0.0/linelist/tests/testthat/test-compat-dplyr.R | 13 linelist-2.0.0/linelist/tests/testthat/test-lost_tags_action.R | 15 linelist-2.0.0/linelist/tests/testthat/test-validate_linelist.R | 24 linelist-2.0.0/linelist/vignettes/compat-dplyr.Rmd | 86 - linelist-2.0.0/linelist/vignettes/design-principles.Rmd | 2 linelist-2.0.0/linelist/vignettes/linelist.Rmd | 39 linelist-2.0.0/linelist/vignettes/software-permissions.Rmd | 4 55 files changed, 1047 insertions(+), 999 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-15 2.0.4
2025-02-28 2.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-09 1.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-28 0.3.2
2021-06-13 0.3.1
2021-05-14 0.3.0
2021-04-20 0.2.0
2021-04-04 0.1.1
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph]
,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Arsene Druel [aut] ,
Julien Ruffault [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Francois Pimont [ctb] ,
Herve Cochar [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.8.0 dated 2025-01-28 and 4.8.1 dated 2025-04-23
DESCRIPTION | 20 - MD5 | 199 ++++++++--------- R/RcppExports.R | 84 +++---- R/VerticalProfiles.R | 4 R/dataset_documentation.R | 52 ++-- R/defaultControl.R | 10 R/defaultSoilParams.R | 6 R/evaluation.R | 10 R/forest_mapWoodyTables.R | 29 +- R/hydraulics_vulnerabilityCurvePlot.R | 2 R/medfate-package.R | 29 +- R/modifySpParams.R | 6 R/moisture_pressureVolumeCurvePlot.R | 4 R/plot.spwb.R | 2 R/plot_internals.R | 1 R/plot_lowlevel.R | 3 R/regeneration.R | 2 R/tree2forest.R | 6 R/utils_ldrOptimization.R |only R/utils_rockOptimization.R |only build/partial.rdb |binary man/SFM_metric.Rd | 40 +-- man/SpParams.Rd | 8 man/biophysics.Rd | 20 - man/carbon.Rd | 22 - man/defaultControl.Rd | 328 ++++++++++++++-------------- man/defaultManagementFunction.Rd | 88 +++---- man/defaultSoilParams.Rd | 16 - man/droughtStress.Rd | 12 - man/emptyforest.Rd | 2 man/evaluation.Rd | 96 ++++---- man/examplemeteo.Rd | 16 - man/exampleobs.Rd | 24 +- man/extract.Rd | 20 - man/fireHazard.Rd | 6 man/fire_behaviour.Rd | 78 +++--- man/fire_severity.Rd | 14 - man/fordyn.Rd | 72 +++--- man/forest.Rd | 76 +++--- man/forest2aboveground.Rd | 32 +- man/forest_mapWoodyTables.Rd | 27 +- man/forest_simplification.Rd | 4 man/fuel_properties.Rd | 68 ++--- man/growth.Rd | 132 +++++------ man/herb_values.Rd | 6 man/hydraulics_conductancefunctions.Rd | 18 - man/hydraulics_defoliation.Rd | 2 man/hydraulics_scalingconductance.Rd | 8 man/hydraulics_supplyfunctions.Rd | 46 +-- man/hydrology_infiltration.Rd | 12 - man/hydrology_interception.Rd | 8 man/hydrology_soilEvaporation.Rd | 8 man/hydrology_soilWaterBalance.Rd | 74 +++--- man/hydrology_verticalInputs.Rd | 10 man/light_advanced.Rd | 16 - man/medfate-package.Rd | 42 +-- man/modelInput.Rd | 374 ++++++++++++++++---------------- man/modifyParams.Rd | 20 - man/moisture.Rd | 14 - man/mortality_dailyProbability.Rd | 4 man/optimization.Rd | 32 +- man/pheno_updateLeaves.Rd | 6 man/photo.Rd | 80 +++--- man/plant_values.Rd | 40 +-- man/plot.spwb.Rd | 202 ++++++++--------- man/plot.spwb_day.Rd | 92 +++---- man/poblet_trees.Rd | 18 - man/regeneration.Rd | 18 - man/resistances.Rd | 10 man/root.Rd | 28 +- man/soil.Rd | 30 +- man/soil_thermodynamics.Rd | 12 - man/species_values.Rd | 18 - man/spwb.Rd | 256 ++++++++++----------- man/spwb_day.Rd | 66 ++--- man/summary.forest.Rd | 2 man/summary.spwb.Rd | 2 man/sureau_ecos.Rd | 14 - man/transp_maximumTranspirationModel.Rd | 20 - man/transp_modes.Rd | 196 ++++++++-------- man/transp_stomatalregulation.Rd | 16 - man/utils_ldrOptimization.Rd |only man/utils_rockOptimization.Rd |only man/vprofile_leafAreaDensity.Rd | 10 man/waterUseEfficiency.Rd | 26 +- man/wind.Rd | 30 +- man/woodformation.Rd | 14 - src/firebehaviour.cpp | 16 - src/fireseverity.cpp | 2 src/growth.cpp | 3 src/hydraulics.cpp | 8 src/hydrology.cpp | 2 src/inner_sperry.cpp | 6 src/lightextinction_advanced.cpp | 1 src/modelInput.cpp | 20 + src/root.cpp | 6 src/spwb.cpp | 12 - src/tissuemoisture.cpp | 10 src/transpiration_advanced.cpp | 17 - src/transpiration_basic.cpp | 20 - src/windKatul.cpp | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_optimization.R |only 103 files changed, 1868 insertions(+), 1827 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-13 0.3.3
2020-07-20 0.3.2
2019-06-06 0.3.1
2019-04-03 0.3.0
2017-05-05 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-09 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-21 0.7.6
Title: Computation of the Double-Entry Intraclass Correlation
Description: The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Author: Christian Bloetner [aut, cre],
Michael Paul Grosz [aut]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between iccde versions 0.3.6 dated 2024-06-05 and 0.3.8 dated 2025-04-23
DESCRIPTION | 18 +++++--- MD5 | 14 +++--- R/iccde.R | 96 ++++++++++++++++++++++--------------------- R/iccdeboot.R | 15 ++++-- R/iccdemat.R | 6 +- man/iccde.Rd | 122 +++++++++++++++++++++++++++++-------------------------- man/iccdeboot.Rd | 7 ++- man/iccdemat.Rd | 11 +++- 8 files changed, 164 insertions(+), 125 deletions(-)
Title: Interface to 'Azure Queue Storage'
Description: An interface to 'Azure Queue Storage'. This is a cloud service for storing large numbers of messages, for example from automated sensors, that can be accessed remotely via authenticated calls using HTTP or HTTPS. Queue storage is often used to create a backlog of work to process asynchronously. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureQstor versions 1.0.1 dated 2020-10-15 and 1.0.2 dated 2025-04-23
DESCRIPTION | 12 MD5 | 24 - NEWS.md | 4 R/container.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/intro.Rmd | 2 inst/doc/intro.html | 280 ++++++++++------- man/QueueMessage.Rd | 30 - man/StorageQueue.Rd | 794 +++++++++++++++++++++++++------------------------- man/queue.Rd | 240 +++++++-------- man/queue_endpoint.Rd | 104 +++--- vignettes/intro.Rmd | 2 13 files changed, 784 insertions(+), 712 deletions(-)
Title: Functions and Utilities for Jordan
Description: Provides core functions and utilities for packages and other code
developed by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between fuj versions 0.2.1 dated 2024-05-20 and 0.2.2 dated 2025-04-23
DESCRIPTION | 10 +++---- MD5 | 51 +++++++++++++++++++------------------ NEWS.md | 10 +++++++ R/colons.R | 16 ++++++----- R/condition.R | 40 ++++++++++++++++------------- R/data-frame.R | 38 ++++++++++++++++++++------- R/flip.R | 21 ++++++++------- R/if-null.R | 10 +++++-- R/include.R | 53 +++++++++++++++++++-------------------- R/list.R | 7 ++--- R/muffle.R | 10 +++---- R/namespace.R | 25 ++++++++++-------- R/utils.R | 1 R/verbose.R | 43 ++++++++++++++++--------------- R/yes-no.R |only README.md | 2 + man/new_condition.Rd | 14 +++++----- man/yes_no.Rd |only tests/spelling.R | 9 ++++-- tests/testthat/test-arithmetic.R | 1 tests/testthat/test-data-frame.R | 5 +++ tests/testthat/test-extract.R | 1 tests/testthat/test-if-null.R | 3 ++ tests/testthat/test-match.R | 2 - tests/testthat/test-namespace.R | 14 ++++++++-- tests/testthat/test-struct.R | 2 - tests/testthat/test-verbose.R | 14 ++++++---- tests/testthat/test-yes-no.R |only 28 files changed, 238 insertions(+), 164 deletions(-)