Title: Rapid and Accurate Genetic Prediction Modeling for Genome-Wide
Association or Whole-Genome Sequencing Study Data
Description: Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
Author: Masao Ueki [aut, cre]
Maintainer: Masao Ueki <uekimrsd@nifty.com>
Diff between stmgp versions 1.0.4 dated 2021-07-18 and 1.0.4.1 dated 2025-02-11
stmgp-1.0.4.1/stmgp/DESCRIPTION | 11 ++++++----- stmgp-1.0.4.1/stmgp/MD5 | 17 +++++++++-------- stmgp-1.0.4.1/stmgp/NEWS.md | 3 +++ stmgp-1.0.4.1/stmgp/R/stplink1.0.4.1.R |only stmgp-1.0.4.1/stmgp/build/partial.rdb |binary stmgp-1.0.4.1/stmgp/man/lapprox.Rd |only stmgp-1.0.4.1/stmgp/man/stmgeplink.Rd | 6 ++++-- stmgp-1.0.4.1/stmgp/man/stmgp-package.Rd | 10 ++++++++-- stmgp-1.0.4.1/stmgp/man/stmgp.Rd | 4 ++-- stmgp-1.0.4.1/stmgp/man/stmgplink.Rd | 4 ++-- stmgp-1.0.4/stmgp/R/stplink1.0.4.R |only 11 files changed, 34 insertions(+), 21 deletions(-)
Title: Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit
Description: Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.
Author: Wei Cui [aut, cre, cph]
Maintainer: Wei Cui <m2c.w@outlook.com>
Diff between easybio versions 1.1.0 dated 2024-09-16 and 1.1.1 dated 2025-02-11
DESCRIPTION | 14 +-- MD5 | 56 ++++++------ NAMESPACE | 3 NEWS.md | 52 ++++++----- R/limma.R | 14 ++- R/misc.R | 94 ++++++++++++-------- R/ora.R | 3 R/prepare.R | 4 R/sc.R | 121 +++++++++++++++++++++------ R/uniprot.R | 2 README.md | 42 ++------- inst/CITATION | 22 ++-- inst/doc/example-bulk-rna-seq-workflow.html | 2 inst/doc/example-single-cell-annotation.html | 8 - inst/example-single-cell.R | 10 +- man/available_tissue_class.Rd |only man/available_tissue_type.Rd |only man/check_marker.Rd | 20 +++- man/get_marker.Rd | 13 ++ man/groupStat.Rd | 10 +- man/groupStatI.Rd | 14 ++- man/list2dt.Rd | 4 man/list2graph.Rd | 2 man/matchCellMarker2.Rd | 19 +++- man/plotMarkerDistribution.Rd | 2 man/plotSeuratDot.Rd | 2 man/setcolnames.Rd | 2 man/setrownames.Rd | 2 man/split_matrix.Rd | 17 ++- man/uniprot_id_map.Rd | 2 30 files changed, 355 insertions(+), 201 deletions(-)
Title: The LIC for T Distribution Regression Analysis
Description: This comprehensive toolkit for T-distributed regression is designated as "TLIC" (The LIC for T Distribution Regression Analysis) analysis. It is predicated on the assumption that the error term adheres to a T-distribution. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02664763.2022.2053949>.
Author: Guangbao Guo [aut, cre] ,
Guofu Jing [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between TLIC versions 0.3 dated 2024-10-29 and 0.4 dated 2025-02-11
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++++-- NAMESPACE | 3 +++ R/LICnew.R |only R/beta_AD.R |only R/beta_cor.R |only build |only man/LICnew.Rd |only man/beta_AD.Rd |only man/beta_cor.Rd |only 10 files changed, 16 insertions(+), 6 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox
regression models using lasso or nonconvex penalties, in particular the
minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD)
penalty, with options for additional L2 penalties (the "elastic net" idea).
Utilities for carrying out cross-validation as well as post-fitting
visualization, summarization, inference, and prediction are also provided.
For more information, see Breheny and Huang (2011) <doi:10.1214/10-AOAS388>
or visit the ncvreg homepage <https://pbreheny.github.io/ncvreg/>.
Author: Patrick Breheny [aut, cre] ,
Ryan Miller [aut] ,
Logan Harris [aut]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.14.3 dated 2024-09-02 and 3.15.0 dated 2025-02-11
DESCRIPTION | 19 +++++++---- MD5 | 23 ++++++++------ NAMESPACE | 2 + NEWS.md | 70 +++++++++++++++++++++++--------------------- R/assign_fold.R |only R/boot-ncvreg.R |only R/cv-ncvreg.R | 29 ++---------------- R/cv-ncvsurv.R | 24 ++------------- README.md | 8 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/tinytest/boot-ncvreg.R |only man/assign_fold.Rd |only man/boot_ncvreg.Rd |only man/cv.ncvreg.Rd | 4 -- 15 files changed, 78 insertions(+), 101 deletions(-)
Title: Bayesian Generalized Additive Model Selection
Description: Generalized additive model selection via approximate Bayesian inference is provided. Bayesian mixed model-based penalized splines with spike-and-slab-type coefficient prior distributions are used to facilitate fitting and selection. The approximate Bayesian inference engine options are: (1) Markov chain Monte Carlo and (2) mean field variational Bayes. Markov chain Monte Carlo has better Bayesian inferential accuracy, but requires a longer run-time. Mean field variational Bayes is faster, but less accurate. The methodology is described in He and Wand (2024) <doi:10.1007/s10182-023-00490-y>.
Author: Virginia X. He [aut] ,
Matt P. Wand [aut, cre]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between gamselBayes versions 2.0-1 dated 2023-09-03 and 2.0-2 dated 2025-02-11
gamselBayes-2.0-1/gamselBayes/R/logUnnDensGamsel.r |only gamselBayes-2.0-2/gamselBayes/DESCRIPTION | 10 +++++----- gamselBayes-2.0-2/gamselBayes/MD5 | 13 ++++++------- gamselBayes-2.0-2/gamselBayes/R/displayAllGAMfits.r | 5 ++--- gamselBayes-2.0-2/gamselBayes/R/gamselBayesMCMC.r | 2 +- gamselBayes-2.0-2/gamselBayes/R/gamselBayesUpdate.r | 6 +++--- gamselBayes-2.0-2/gamselBayes/build/vignette.rds |binary gamselBayes-2.0-2/gamselBayes/inst/doc/manual.pdf |binary 8 files changed, 17 insertions(+), 19 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.0 dated 2024-12-05 and 7.1 dated 2025-02-11
DESCRIPTION | 14 +++++++------- MD5 | 34 ++++++++++++++++++---------------- NAMESPACE | 4 ++-- R/dwrapnormal.R |only R/esag.reg.R | 3 ++- R/iag.reg.R | 16 +++++++--------- R/pkbd.reg.R | 3 ++- R/pkbd.reg2.R | 3 ++- R/sespc.reg.R | 3 ++- R/sipc.reg.R | 3 ++- R/spcauchy.reg.R | 3 ++- R/vm.kde.R | 6 +++--- R/vmf.kde.R | 11 ++++++----- R/vmf.reg.R | 3 ++- R/vmfreg.R | 1 + R/wrapnormal.mle.R |only man/Directional-package.Rd | 6 +++--- man/dvm.Rd | 10 +++++++--- man/spml.mle.Rd | 11 +++++------ 19 files changed, 73 insertions(+), 61 deletions(-)
Title: Chat-Based Interactive Artificial Intelligence for R
Description: The Large Language Model (LLM) represents a groundbreaking advancement
in data science and programming, and also allows us to extend the world of R.
A seamless interface for integrating the 'OpenAI' Web APIs into R is provided in this package.
This package leverages LLM-based AI techniques, enabling efficient knowledge discovery and data analysis
(see 'OpenAI' Web APIs details <https://openai.com/blog/openai-api>).
The previous functions such as seamless translation and image generation have been moved
to other packages 'deepRstudio' and 'stableDiffusion4R'.
Author: Satoshi Kume [aut, cre]
Maintainer: Satoshi Kume <satoshi.kume.1984@gmail.com>
Diff between chatAI4R versions 0.2.10 dated 2023-09-12 and 0.3.6 dated 2025-02-11
DESCRIPTION | 12 +-- MD5 | 132 ++++++++++++++++++++----------------- NAMESPACE | 16 ++++ R/OptimizeRcode.R | 10 +- R/RcodeImprovements.R | 10 +- R/RevisedText.R | 8 +- R/TextSummaryAsBullet.R | 23 ++++-- R/addCommentCode.R | 14 ++- R/addRoxygenDescription.R | 14 ++- R/chat4R.R | 17 ++-- R/chat4R_history.R | 7 + R/chat4R_streaming.R |only R/chat4Rv2.R |only R/checkErrorDet.R | 10 +- R/checkErrorDet_JP.R | 10 +- R/completions4R.R | 7 + R/conversation4R.R | 46 ++++++------ R/convertBullet2Sentence.R | 16 ++-- R/convertRscript2Function.R | 12 ++- R/convertScientificLiterature.R | 10 +- R/createImagePrompt_v1.R | 2 R/createImagePrompt_v2.R | 4 - R/createRcode.R | 6 - R/createRfunction.R | 6 - R/createSpecifications4R.R | 10 +- R/create_eBay_Description.R |only R/designPackage.R | 11 +-- R/discussion_flow_v1.R | 8 +- R/discussion_flow_v2.R |only R/enrichTextContent.R | 19 ++--- R/extractKeywords.R | 14 ++- R/proofreadEnglishText.R | 14 +-- R/proofreadText.R | 8 +- R/replicateAPI4R.R |only R/searchFunction.R | 8 +- R/supportIdeaGeneration.R | 12 ++- R/textEmbedding.R | 4 - R/textFileInput4ai.R |only R/vision4R.R |only inst/rstudio/addins.dcf | 8 +- man/OptimizeRcode.Rd | 4 - man/RcodeImprovements.Rd | 6 - man/TextSummaryAsBullet.Rd | 10 +- man/addCommentCode.Rd | 14 +++ man/addRoxygenDescription.Rd | 10 +- man/chat4R.Rd | 15 ++-- man/chat4R_history.Rd | 4 - man/chat4R_streaming.Rd |only man/chat4Rv2.Rd |only man/checkErrorDet.Rd | 6 - man/checkErrorDet_JP.Rd | 6 - man/completions4R.Rd | 5 - man/conversation4R.Rd | 8 +- man/convertBullet2Sentence.Rd | 10 +- man/convertRscript2Function.Rd | 10 +- man/convertScientificLiterature.Rd | 8 +- man/createEBAYdes.Rd |only man/createImagePrompt_v1.Rd | 2 man/createImagePrompt_v2.Rd | 4 - man/createRcode.Rd | 4 - man/createRfunction.Rd | 4 - man/createSpecifications4R.Rd | 8 +- man/designPackage.Rd | 7 + man/discussion_flow_v1.Rd | 4 - man/discussion_flow_v2.Rd |only man/enrichTextContent.Rd | 12 ++- man/extractKeywords.Rd | 10 +- man/proofreadEnglishText.Rd | 14 ++- man/proofreadText.Rd | 4 - man/replicatellmAPI4R.Rd |only man/searchFunction.Rd | 4 - man/supportIdeaGeneration.Rd | 8 +- man/textFileInput4ai.Rd |only man/vision4R.Rd |only 74 files changed, 424 insertions(+), 285 deletions(-)
Title: Model Wrappers for Tree-Based Models
Description: Bindings for additional tree-based model engines for use with
the 'parsnip' package. Models include gradient boosted decision trees
with 'LightGBM' (Ke et al, 2017.), conditional inference trees and
conditional random forests with 'partykit' (Hothorn and Zeileis, 2015.
and Hothorn et al, 2006. <doi:10.1198/106186006X133933>), and
accelerated oblique random forests with 'aorsf' (Jaeger et al, 2022
<doi:10.5281/zenodo.7116854>).
Author: Daniel Falbel [aut],
Athos Damiani [aut],
Roel M. Hogervorst [aut] ,
Max Kuhn [aut] ,
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between bonsai versions 0.3.1 dated 2024-07-23 and 0.3.2 dated 2025-02-11
bonsai-0.3.1/bonsai/tests/testthat/helper-tests.R |only bonsai-0.3.2/bonsai/DESCRIPTION | 30 +-- bonsai-0.3.2/bonsai/MD5 | 29 +-- bonsai-0.3.2/bonsai/NAMESPACE | 2 bonsai-0.3.2/bonsai/NEWS.md | 6 bonsai-0.3.2/bonsai/R/bonsai_package.R | 4 bonsai-0.3.2/bonsai/R/import-standalone-obj-type.R |only bonsai-0.3.2/bonsai/R/import-standalone-types-check.R |only bonsai-0.3.2/bonsai/R/lightgbm.R | 63 ++++---- bonsai-0.3.2/bonsai/R/lightgbm_data.R | 4 bonsai-0.3.2/bonsai/inst/doc/bonsai.R | 2 bonsai-0.3.2/bonsai/inst/doc/bonsai.Rmd | 2 bonsai-0.3.2/bonsai/tests/testthat/_snaps/lightgbm.md | 60 ++++--- bonsai-0.3.2/bonsai/tests/testthat/test-aorsf.R | 2 bonsai-0.3.2/bonsai/tests/testthat/test-lightgbm.R | 140 +++++++++++------- bonsai-0.3.2/bonsai/tests/testthat/test-partykit.R | 38 ++-- bonsai-0.3.2/bonsai/vignettes/bonsai.Rmd | 2 17 files changed, 228 insertions(+), 156 deletions(-)
Title: A Collection of ML Tools for Conservation Research
Description: Functions required to classify subjects within camera trap field data. The package can handle both images and videos. The authors recommend a two-step approach using Microsoft's 'MegaDector' model and then a second model trained on the classes of interest.
Author: Kyra Swanson [aut, cre] ,
Mathias Tobler [aut]
Maintainer: Kyra Swanson <tswanson@sdzwa.org>
Diff between animl versions 1.1.0 dated 2023-05-13 and 2.0.0 dated 2025-02-11
animl-1.1.0/animl/R/applyPredictions.R |only animl-1.1.0/animl/R/bestGuess.R |only animl-1.1.0/animl/R/convertCoordinates.R |only animl-1.1.0/animl/R/dataManagement.R |only animl-1.1.0/animl/R/detectMD.R |only animl-1.1.0/animl/R/extractBoxes.R |only animl-1.1.0/animl/R/fileManagement.R |only animl-1.1.0/animl/R/generators.R |only animl-1.1.0/animl/R/imagesFromVideos.R |only animl-1.1.0/animl/R/loadMDModel.R |only animl-1.1.0/animl/R/parseMD.R |only animl-1.1.0/animl/R/parseMDjson.R |only animl-1.1.0/animl/R/pipeline.R |only animl-1.1.0/animl/R/plotBoxes.R |only animl-1.1.0/animl/R/predictSpecies.R |only animl-1.1.0/animl/R/sequenceClassification.R |only animl-1.1.0/animl/R/setupDirectory.R |only animl-1.1.0/animl/R/splitData.R |only animl-1.1.0/animl/R/symlink.R |only animl-1.1.0/animl/R/testMD.R |only animl-1.1.0/animl/R/updateResults.R |only animl-1.1.0/animl/R/utils-pipe.R |only animl-1.1.0/animl/man/ImageGenerator.Rd |only animl-1.1.0/animl/man/ImageGeneratorSize.Rd |only animl-1.1.0/animl/man/animl.Rd |only animl-1.1.0/animl/man/applyPredictions.Rd |only animl-1.1.0/animl/man/bestGuess.Rd |only animl-1.1.0/animl/man/buildFileManifest.Rd |only animl-1.1.0/animl/man/checkFile.Rd |only animl-1.1.0/animl/man/convertCoordinates.Rd |only animl-1.1.0/animl/man/cropImageGenerator.Rd |only animl-1.1.0/animl/man/cropImageTrainGenerator.Rd |only animl-1.1.0/animl/man/detectObject.Rd |only animl-1.1.0/animl/man/detectObjectBatch.Rd |only animl-1.1.0/animl/man/extractBoxes.Rd |only animl-1.1.0/animl/man/extractBoxesFromFlat.Rd |only animl-1.1.0/animl/man/extractBoxesFromMD.Rd |only animl-1.1.0/animl/man/getAnimals.Rd |only animl-1.1.0/animl/man/getEmpty.Rd |only animl-1.1.0/animl/man/imageAugmentationColor.Rd |only animl-1.1.0/animl/man/imageAugmentationGeometry.Rd |only animl-1.1.0/animl/man/imageLabel.Rd |only animl-1.1.0/animl/man/imageLabelCrop.Rd |only animl-1.1.0/animl/man/imagesFromVideos.Rd |only animl-1.1.0/animl/man/loadData.Rd |only animl-1.1.0/animl/man/loadImage.Rd |only animl-1.1.0/animl/man/loadImageResize.Rd |only animl-1.1.0/animl/man/loadImageResizeCrop.Rd |only animl-1.1.0/animl/man/loadImageResizeSize.Rd |only animl-1.1.0/animl/man/loadMDModel.Rd |only animl-1.1.0/animl/man/parseMD.Rd |only animl-1.1.0/animl/man/parseMDjson.Rd |only animl-1.1.0/animl/man/pipe.Rd |only animl-1.1.0/animl/man/plotBoxes.Rd |only animl-1.1.0/animl/man/predictSpecies.Rd |only animl-1.1.0/animl/man/processYOLO5.Rd |only animl-1.1.0/animl/man/resizePad.Rd |only animl-1.1.0/animl/man/saveData.Rd |only animl-1.1.0/animl/man/sequenceClassification.Rd |only animl-1.1.0/animl/man/setupDirectory.Rd |only animl-1.1.0/animl/man/symUnlink.Rd |only animl-1.1.0/animl/man/symlinkMD.Rd |only animl-1.1.0/animl/man/symlinkSpecies.Rd |only animl-1.1.0/animl/man/testMD.Rd |only animl-1.1.0/animl/man/updateResults.Rd |only animl-2.0.0/animl/DESCRIPTION | 19 - animl-2.0.0/animl/LICENSE | 4 animl-2.0.0/animl/MD5 | 105 +++------ animl-2.0.0/animl/NAMESPACE | 68 ++--- animl-2.0.0/animl/R/classification.R |only animl-2.0.0/animl/R/data_management.R |only animl-2.0.0/animl/R/detect.R |only animl-2.0.0/animl/R/file_management.R |only animl-2.0.0/animl/R/link.R |only animl-2.0.0/animl/R/plot_boxes.R |only animl-2.0.0/animl/R/sequence_classification.R |only animl-2.0.0/animl/R/split.R |only animl-2.0.0/animl/R/video_processing.R |only animl-2.0.0/animl/README.md | 241 ++++++++++----------- animl-2.0.0/animl/inst |only animl-2.0.0/animl/man/WorkingDirectory.Rd |only animl-2.0.0/animl/man/build_file_manifest.Rd |only animl-2.0.0/animl/man/check_file.Rd |only animl-2.0.0/animl/man/crop_images.Rd |only animl-2.0.0/animl/man/detect_MD_batch.Rd |only animl-2.0.0/animl/man/extract_frame_single.Rd |only animl-2.0.0/animl/man/extract_frames.Rd |only animl-2.0.0/animl/man/extract_frames_old.Rd |only animl-2.0.0/animl/man/get_animals.Rd |only animl-2.0.0/animl/man/get_empty.Rd |only animl-2.0.0/animl/man/load_data.Rd |only animl-2.0.0/animl/man/load_model.Rd |only animl-2.0.0/animl/man/megadetector.Rd |only animl-2.0.0/animl/man/parse_MD.Rd |only animl-2.0.0/animl/man/plot_boxes.Rd |only animl-2.0.0/animl/man/predict_species.Rd |only animl-2.0.0/animl/man/remove_link.Rd |only animl-2.0.0/animl/man/save_data.Rd |only animl-2.0.0/animl/man/sequence_classification.Rd |only animl-2.0.0/animl/man/sort_MD.Rd |only animl-2.0.0/animl/man/sort_species.Rd |only animl-2.0.0/animl/man/update_labels.Rd |only 102 files changed, 200 insertions(+), 237 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: In longitudinal studies, the same subjects are measured repeatedly over time, leading to correlations among the repeated measurements. Properly accounting for the intra-cluster correlations in the presence of data heterogeneity and long tailed distributions of the disease phenotype is challenging, especially in the context of high dimensional regressions. In this package, we developed a Bayesian quantile mixed effects model with spike- and -slab priors to dissect important gene - environment interactions under longitudinal genomics studies. An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.4.1 dated 2025-01-29 and 0.1.5 dated 2025-02-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/mixedBayes-package.R | 2 +- R/mixedBayes.R | 10 +++++----- README.md | 4 ++++ man/mixedBayes-package.Rd | 2 +- man/mixedBayes.Rd | 10 +++++----- 7 files changed, 26 insertions(+), 22 deletions(-)
Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests.
Includes tools for stubbing 'HTTP' requests, including expected
request conditions and response conditions. Match on
'HTTP' method, query parameters, request body, headers and
more. Can be used for unit tests or outside of a testing
context.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [ctb] ,
rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between webmockr versions 1.0.0 dated 2024-07-23 and 2.0.0 dated 2025-02-11
DESCRIPTION | 15 LICENSE | 2 MD5 | 175 ++++---- NAMESPACE | 27 + NEWS.md | 27 + R/HttpLibAdapterRegistry.R | 16 R/RequestPattern.R | 512 ++++++++++++++++++-------- R/RequestRegistry.R | 31 - R/RequestSignature.R | 61 +-- R/Response.R | 52 +- R/StubRegistry.R | 105 +++-- R/StubbedRequest.R | 199 ++++++---- R/adapter-crul.R | 30 - R/adapter-httr.R | 27 - R/adapter-httr2.R | 26 - R/adapter.R | 200 +++++----- R/error-handling.R |only R/flipswitch.R | 20 - R/headers.R | 50 +- R/last.R |only R/mock_file.R | 14 R/mocking-disk-writing.R | 18 R/partial.R |only R/pluck_body.R | 36 - R/request_registry.R | 6 R/stub_body_diff.R |only R/stub_registry.R | 1 R/stub_request.R | 139 +++++-- R/to_raise.R | 43 +- R/to_return.R | 69 +-- R/to_timeout.R | 7 R/webmockr-opts.R | 80 ++-- R/webmockr-package.R | 6 R/wi_th.R | 100 +++-- R/zzz.R | 219 ++++++----- man/Adapter.Rd | 58 +- man/BodyPattern.Rd | 42 +- man/HeadersPattern.Rd | 7 man/RequestPattern.Rd | 64 ++- man/RequestRegistry.Rd | 2 man/Response.Rd | 4 man/StubRegistry.Rd | 27 + man/StubbedRequest.Rd | 36 + man/UriPattern.Rd | 24 + man/handle_stub_removal.Rd |only man/including.Rd |only man/last_request.Rd |only man/last_stub.Rd |only man/mocking-disk-writing.Rd | 18 man/stub_body_diff.Rd |only man/stub_request.Rd | 111 ++++- man/to_raise.Rd | 16 man/to_return.Rd | 24 - man/webmockr-package.Rd | 2 man/webmockr_configure.Rd | 14 man/wi_th.Rd | 37 + tests/testthat/helper-webmockr.R | 15 tests/testthat/httr2_obj.rda |binary tests/testthat/httr2_obj_auth.rda |binary tests/testthat/httr_obj.rda |binary tests/testthat/httr_obj_auth.rda |binary tests/testthat/test-Adapter.R | 12 tests/testthat/test-CrulAdapter.R | 50 +- tests/testthat/test-HttpLibAdapaterRegistry.R | 6 tests/testthat/test-Httr2Adapter.R | 48 +- tests/testthat/test-HttrAdapter.R | 74 ++- tests/testthat/test-RequestPattern.R | 220 ++++++++++- tests/testthat/test-RequestRegistry.R | 2 tests/testthat/test-RequestSignature.R | 32 + tests/testthat/test-Response.R | 4 tests/testthat/test-StubRegistry.R | 11 tests/testthat/test-StubbedRequest.R | 152 ++++--- tests/testthat/test-auth_handling.R | 6 tests/testthat/test-flipswitch.R | 22 - tests/testthat/test-last_request.R |only tests/testthat/test-last_stub.R |only tests/testthat/test-onload.R | 24 - tests/testthat/test-partial_matching.R |only tests/testthat/test-pluck_body.R | 16 tests/testthat/test-remove_request_stub.R | 4 tests/testthat/test-request_registry.R | 2 tests/testthat/test-stub_body_diff.R |only tests/testthat/test-stub_registry.R | 32 + tests/testthat/test-stub_request.R | 7 tests/testthat/test-stub_requests_crul.R | 63 +-- tests/testthat/test-to_raise.R | 16 tests/testthat/test-to_return.R | 47 +- tests/testthat/test-to_return_body.R | 4 tests/testthat/test-to_return_then.R | 24 - tests/testthat/test-to_timeout.R | 3 tests/testthat/test-uri_regex.R | 46 +- tests/testthat/test-wi_th.R | 110 +++-- tests/testthat/test-within_test_that_blocks.R | 8 tests/testthat/test-writing-to-disk.R | 42 +- tests/testthat/test-zutils.R | 79 ++-- 95 files changed, 2623 insertions(+), 1357 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.5.0 dated 2024-12-18 and 0.6.0 dated 2025-02-11
DESCRIPTION | 12 MD5 | 124 +++++----- NAMESPACE | 3 NEWS.md | 75 ++++-- R/connect.R | 51 +++- R/content.R | 117 ++++++++- R/deploy.R | 99 +++++-- R/get.R | 12 R/parse.R | 4 R/ptype.R | 8 R/utils.R | 29 +- README.md | 10 inst/doc/customize-http.html | 9 inst/doc/getting-started.html | 9 inst/scratch/2025-01-10-swap-vanity-scratch.R |only inst/scratch/job-scratch-2024-12-11.R | 64 +++++ inst/scratch/r6-scratch-2025-01-02.R |only man/connect.Rd | 36 ++ man/connectapi-package.Rd | 12 man/content_delete.Rd | 2 man/content_item.Rd | 2 man/content_title.Rd | 2 man/content_update.Rd | 2 man/create_random_name.Rd | 2 man/dashboard_url.Rd | 2 man/dashboard_url_chr.Rd | 2 man/delete_thumbnail.Rd | 2 man/delete_vanity_url.Rd | 4 man/deploy_repo.Rd | 2 man/environment.Rd | 2 man/get_bundles.Rd | 4 man/get_image.Rd | 2 man/get_job.Rd | 3 man/get_jobs.Rd | 40 ++- man/get_log.Rd |only man/get_oauth_credentials.Rd | 13 - man/get_thumbnail.Rd | 2 man/get_vanity_url.Rd | 4 man/git.Rd | 2 man/has_thumbnail.Rd | 2 man/permissions.Rd | 2 man/set_image.Rd | 2 man/set_run_as.Rd | 2 man/set_thumbnail.Rd | 2 man/set_vanity_url.Rd | 4 man/swap_vanity_url.Rd | 16 - man/swap_vanity_urls.Rd |only man/terminate_jobs.Rd | 13 - man/verify_content_name.Rd | 2 tests/integrated/test-deploy.R | 53 ++-- tests/integrated/test-git.R | 16 - tests/testthat/2024.08.0/__api__/v1/content/8f37d6e0/jobs/mxPGVOMVk6f8dso2 |only tests/testthat/2024.08.0/__api__/v1/content/951bf3ad |only tests/testthat/2024.08.0/__api__/v1/content/c3426b0b |only tests/testthat/2024.08.0/__api__/v1/content/c3426b0b.json |only tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-a1e6cf-POST.json |only tests/testthat/2025.01.0 |only tests/testthat/Rplots.pdf |binary tests/testthat/test-connect.R | 75 ++++++ tests/testthat/test-content.R | 72 +++++ tests/testthat/test-deploy.R | 26 ++ tests/testthat/test-git.R | 10 tests/testthat/test-parse.R | 14 + tests/testthat/test-utils.R | 25 +- 64 files changed, 871 insertions(+), 233 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-26 1.1.6
2024-01-22 1.1.5
2023-12-04 1.1.4
2023-05-23 1.1.3
2023-05-17 1.1.2
2023-05-05 1.1.1
2023-03-22 1.1.0
2022-10-20 1.0.13
2022-09-19 1.0.10
2022-08-09 1.0.9
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.3.4 dated 2024-12-06 and 2.3.5 dated 2025-02-11
fdasrvf-2.3.4/fdasrvf/R/bayesian_functions.R |only fdasrvf-2.3.4/fdasrvf/src/fdasrsf/bayesian.cpp |only fdasrvf-2.3.4/fdasrvf/src/fdasrsf/pair_align_functions_expomap.cpp |only fdasrvf-2.3.4/fdasrvf/src/registerDynamicSymbol.cpp |only fdasrvf-2.3.4/fdasrvf/src/wrapper.cpp |only fdasrvf-2.3.4/fdasrvf/src/wrapper_rbfgs.cpp |only fdasrvf-2.3.5/fdasrvf/DESCRIPTION | 8 fdasrvf-2.3.5/fdasrvf/MD5 | 82 ++-- fdasrvf-2.3.5/fdasrvf/NAMESPACE | 4 fdasrvf-2.3.5/fdasrvf/NEWS.md | 3 fdasrvf-2.3.5/fdasrvf/R/RcppExports.R |only fdasrvf-2.3.5/fdasrvf/R/curve_functions.R | 12 fdasrvf-2.3.5/fdasrvf/R/fdasrvf-package.R | 2 fdasrvf-2.3.5/fdasrvf/R/image_funcs.R | 6 fdasrvf-2.3.5/fdasrvf/R/jointfPCA.R | 121 ++++-- fdasrvf-2.3.5/fdasrvf/R/multivariate_karcher_mean.R | 10 fdasrvf-2.3.5/fdasrvf/R/optimum.reparam.R | 16 fdasrvf-2.3.5/fdasrvf/R/predict.jfpca.R | 9 fdasrvf-2.3.5/fdasrvf/R/predict.jfpcah.R | 14 fdasrvf-2.3.5/fdasrvf/R/refactoring.R | 194 ++++++---- fdasrvf-2.3.5/fdasrvf/R/regression_functions.R | 9 fdasrvf-2.3.5/fdasrvf/R/reparam_curve.R | 9 fdasrvf-2.3.5/fdasrvf/README.md | 2 fdasrvf-2.3.5/fdasrvf/man/get_curve_centroid.Rd |only fdasrvf-2.3.5/fdasrvf/man/get_l2_norm.Rd |only fdasrvf-2.3.5/fdasrvf/man/get_shape_distance.Rd | 17 fdasrvf-2.3.5/fdasrvf/man/jointFPCA.Rd | 5 fdasrvf-2.3.5/fdasrvf/man/multivariate_karcher_mean.Rd | 2 fdasrvf-2.3.5/fdasrvf/man/to_hilbert_sphere.Rd | 2 fdasrvf-2.3.5/fdasrvf/src/Makevars | 6 fdasrvf-2.3.5/fdasrvf/src/Makevars.win | 6 fdasrvf-2.3.5/fdasrvf/src/RcppExports.cpp |only fdasrvf-2.3.5/fdasrvf/src/bayesian.cpp |only fdasrvf-2.3.5/fdasrvf/src/bayesian.h |only fdasrvf-2.3.5/fdasrvf/src/fdaqmap/incl/ImageRegister.h | 6 fdasrvf-2.3.5/fdasrvf/src/fdaqmap/incl/UnitSquareImage.h | 31 - fdasrvf-2.3.5/fdasrvf/src/fdaqmap/incl/myVector.h | 2 fdasrvf-2.3.5/fdasrvf/src/fdaqmap/src/UnitSquareImage.cpp | 51 -- fdasrvf-2.3.5/fdasrvf/src/fdasrsf/DP.h | 8 fdasrvf-2.3.5/fdasrvf/src/fdasrsf/DynamicProgrammingQ2.h | 11 fdasrvf-2.3.5/fdasrvf/src/fdasrsf/dp_grid.h | 2 fdasrvf-2.3.5/fdasrvf/src/fdasrsf/dp_nbhd.h | 4 fdasrvf-2.3.5/fdasrvf/src/fdasrsf/misc_funcs.h | 20 - fdasrvf-2.3.5/fdasrvf/src/fdasrsf/mlogit_warp_grad.h | 10 fdasrvf-2.3.5/fdasrvf/src/fdasrsf/rbfgs.h | 5 fdasrvf-2.3.5/fdasrvf/src/pair_align_functions_expomap.cpp |only fdasrvf-2.3.5/fdasrvf/src/pair_align_functions_expomap.h |only fdasrvf-2.3.5/fdasrvf/src/wrapperQMAP.cpp |only fdasrvf-2.3.5/fdasrvf/src/wrapperSRSF.cpp |only fdasrvf-2.3.5/fdasrvf/tests/testthat/test-refactoring.R | 14 50 files changed, 421 insertions(+), 282 deletions(-)
More information about gaussratiovegind at CRAN
Permanent link
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.9.1 dated 2024-01-30 and 1.10.0 dated 2025-02-11
DESCRIPTION | 8 +-- MD5 | 8 +-- R/growthcurve.R | 94 +++++++++++++++++++++++++++--------------- man/enve.GrowthCurve-class.Rd | 6 +- man/plot.enve.GrowthCurve.Rd | 3 + 5 files changed, 76 insertions(+), 43 deletions(-)
Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable
functions f(x,y) over simple closed polygonal domains.
The following cubature methods are implemented:
product Gauss cubature (Sommariva and Vianello, 2007,
<doi:10.1007/s10543-007-0131-2>),
the simple two-dimensional midpoint rule
(wrapping 'spatstat.geom' functions), and
adaptive cubature for radially symmetric functions via line
integrate() along the polygon boundary (Meyer and Held, 2014,
<doi:10.1214/14-AOAS743>, Supplement B).
For simple integration along the axes, the 'cubature' package
is more appropriate.
Author: Sebastian Meyer [aut, cre, trl]
,
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between polyCub versions 0.9.1 dated 2024-05-21 and 0.9.2 dated 2025-02-11
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 6 ++++++ R/coerce-sp-methods.R | 6 ++++-- R/plotpolyf.R | 5 +++-- R/polyCub.midpoint.R | 4 ++-- R/xylist.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/polyCub.html | 18 +++++++++--------- man/coerce-sp-methods.Rd | 6 ++++-- man/plot_polyregion.Rd | 5 +++-- man/plotpolyf.Rd | 5 +++-- man/polyCub.Rd | 5 +++-- man/polyCub.SV.Rd | 5 +++-- man/polyCub.iso.Rd | 5 +++-- man/polyCub.midpoint.Rd | 4 ++-- man/xylist.Rd | 6 +++--- 18 files changed, 73 insertions(+), 57 deletions(-)
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves or epigantt charts in 'ggplot2'. Prepare
data for visualisation or other reporting for infectious disease
surveillance and outbreak investigation. Includes tidy functions to solve
date based transformations for common reporting tasks, like
(A) seasonal date alignment for respiratory disease surveillance,
(B) date-based case binning based on specified time intervals like
isoweek, epiweek, month and more, (C) automated detection and marking
of the new year based on the date/datetime axis of the 'ggplot2'.
An introduction on how to use epicurves can be found on the US CDC website
(2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.1.1 dated 2025-01-31 and 0.1.2 dated 2025-02-11
DESCRIPTION | 11 +++---- MD5 | 42 ++++++++++++++-------------- NEWS.md | 5 +++ R/align_dates_seasonal.R | 6 ++-- R/geom_epicurve.R | 28 +++++++++--------- README.md | 11 ++++--- inst/WORDLIST | 2 - inst/doc/Epicurves_with_ggsurveillance.R | 4 ++ inst/doc/Epicurves_with_ggsurveillance.Rmd | 18 ++++++++---- inst/doc/Epicurves_with_ggsurveillance.html | 12 ++++---- inst/doc/Epigantt_with_ggsurveillance.R | 4 ++ inst/doc/Epigantt_with_ggsurveillance.Rmd | 4 ++ inst/doc/Epigantt_with_ggsurveillance.html | 4 +- inst/doc/align_dates_seasonal.R | 4 ++ inst/doc/align_dates_seasonal.Rmd | 4 ++ inst/doc/align_dates_seasonal.html | 8 ++--- man/geom_epicurve.Rd | 6 ++-- tests/testthat/test-align_dates_seasonal.R | 4 +- tests/testthat/test-geom_epicurve.R | 20 +++++++++++++ vignettes/Epicurves_with_ggsurveillance.Rmd | 18 ++++++++---- vignettes/Epigantt_with_ggsurveillance.Rmd | 4 ++ vignettes/align_dates_seasonal.Rmd | 4 ++ 22 files changed, 140 insertions(+), 83 deletions(-)
More information about ggsurveillance at CRAN
Permanent link
Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including
likelihood ratios for relationship testing, general relatedness
inference, marker simulation, and power analysis. 'forrel' is part of
the 'pedsuite', a collection of packages for pedigree analysis,
further described in the book 'Pedigree Analysis in R' (Vigeland,
2021, ISBN:9780128244302). Several functions deal specifically with
power analysis in missing person cases, implementing methods described
in Vigeland et al. (2020) <doi:10.1016/j.fsigen.2020.102376>. Data
import from the 'Familias' software (Egeland et al. (2000)
<doi:10.1016/S0379-0738(00)00147-X>) is supported through the
'pedFamilias' package.
Author: Magnus Dehli Vigeland [aut, cre]
,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between forrel versions 1.7.0 dated 2024-09-04 and 1.7.1 dated 2025-02-11
DESCRIPTION | 10 +- MD5 | 28 +++---- NAMESPACE | 1 NEWS.md | 13 +++ R/checkPairwise.R | 59 ++++++++++------ R/familias-deprecated.R | 3 R/ibdBootstrap.R | 27 ++++--- R/ibdEstimTools.R | 139 -------------------------------------- R/ibdEstimate.R | 20 ++++- README.md | 19 ++++- build/partial.rdb |binary man/checkPairwise.Rd | 19 +++-- man/figures/README-triangle-1.png |binary man/ibdBootstrap.Rd | 29 ++++--- man/ibdEstimate.Rd | 6 + 15 files changed, 152 insertions(+), 221 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 2.7.2 dated 2024-09-12 and 2.9.0 dated 2025-02-11
DESCRIPTION | 6 MD5 | 46 - NAMESPACE | 1 NEWS.md | 29 + R/API-methods.R | 2 R/giveSize.R | 39 + R/importOutput.R | 66 +- R/readAntares.R | 4 R/readClusterDesc.R | 138 +++-- R/setSimulationPath.R | 38 + R/setSimulationPathAPI.R | 5 R/zzz.R | 15 inst/doc/antaresRead.html | 4 inst/format_output/simulation_variables_names_by_support.csv | 5 inst/referential_properties/properties_input_renewable.csv | 8 inst/referential_properties/properties_input_storage.csv | 16 inst/test_files |only man/dot-transform_antares_version.Rd |only man/readAntares.Rd | 2 man/readClusterDesc.Rd | 31 + man/setSimulationPath.Rd | 1 tests/testthat/test-giveSize.R |only tests/testthat/test-importOutputForClusters.R | 16 tests/testthat/test-readClusterDesc.R | 301 +++++++++-- tests/testthat/test-setSimulationPath.R | 60 ++ 25 files changed, 674 insertions(+), 159 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <thartl@diw.de>
Diff between opendataformat versions 2.1.2 dated 2025-01-15 and 2.1.3 dated 2025-02-11
DESCRIPTION | 6 MD5 | 17 +- R/opendataformat-package.R | 4 R/read_odf.R | 151 ++++++++++++------------ R/write_odf.R | 91 +++++++------- inst/doc/opendataformat.html | 2 man/opendataformat-package.Rd | 6 tests/testthat/test-as_odf_tbl.R | 23 +++ tests/testthat/test-read-and-write-odf.R | 61 +++++++++ tests/testthat/testdata/data_special_values.zip |only 10 files changed, 236 insertions(+), 125 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Plots for Visualizing the Data Produced by the 'irace' Package
Description: Graphical visualization tools for analyzing the data produced by 'irace'. The 'iraceplot' package enables users to analyze the performance and the parameter space data sampled by the configuration during the search process. It provides a set of functions that generate different plots to visualize the configurations sampled during the execution of 'irace' and their performance. The functions just require the log file generated by 'irace' and, in some cases, they can be used with user-provided data.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Pablo Onate Marin [aut],
Leslie Perez Caceres [aut]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between iraceplot versions 2.0.0 dated 2024-11-27 and 2.1.0 dated 2025-02-11
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------- NEWS.md | 8 +++++++ R/ablation_plot.R | 35 +++++++++++++++++++++++--------- R/sampling_distance.R | 3 -- build/partial.rdb |binary inst/doc/iraceplot_package.R | 46 +++++++++++++++++++++---------------------- man/ablation_plot.Rd | 12 +++++++---- 8 files changed, 75 insertions(+), 49 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.17 dated 2024-11-22 and 1.0.18 dated 2025-02-11
DESCRIPTION | 8 MD5 | 114 +-- NEWS.md | 4 R/data.R | 1034 +++++++++++++++-------------- R/get_municipalities.R | 4 R/get_zipcodes.R | 4 README.md | 2 data/grid_ahvenanmaa.rda |binary data/grid_etela_karjala.rda |binary data/grid_etela_pohjanmaa.rda |binary data/grid_etela_savo.rda |binary data/grid_hyvinvointialue.rda |binary data/grid_kainuu.rda |binary data/grid_kanta_hame.rda |binary data/grid_keski_pohjanmaa.rda |binary data/grid_keski_suomi.rda |binary data/grid_kymenlaakso.rda |binary data/grid_lappi.rda |binary data/grid_maakunta.rda |binary data/grid_paijat_hame.rda |binary data/grid_pirkanmaa.rda |binary data/grid_pohjanmaa.rda |binary data/grid_pohjois_karjala.rda |binary data/grid_pohjois_pohjanmaa.rda |binary data/grid_pohjois_savo.rda |binary data/grid_sairaanhoitop.rda |binary data/grid_satakunta.rda |binary data/grid_uusimaa.rda |binary data/grid_varsinais_suomi.rda |binary data/municipality_key.rda |binary data/municipality_key_2013.rda |binary data/municipality_key_2014.rda |binary data/municipality_key_2015.rda |binary data/municipality_key_2016.rda |binary data/municipality_key_2017.rda |binary data/municipality_key_2018.rda |binary data/municipality_key_2019.rda |binary data/municipality_key_2020.rda |binary data/municipality_key_2021.rda |binary data/municipality_key_2022.rda |binary data/municipality_key_2023.rda |binary data/municipality_key_2024.rda |binary data/municipality_key_2025.rda |only inst/doc/geofi_datasets.html | 45 - inst/doc/geofi_joining_attribute_data.html | 10 inst/doc/geofi_making_maps.html | 48 - inst/doc/geofi_spatial_analysis.html | 38 - man/figures/readme_map-1.png |binary man/get_municipalities.Rd | 4 man/get_zipcodes.Rd | 4 man/grid_etela_savo.Rd | 2 man/municipality_key.Rd | 164 ++-- man/municipality_key_2018.Rd | 122 +-- man/municipality_key_2019.Rd | 130 +-- man/municipality_key_2020.Rd | 130 +-- man/municipality_key_2021.Rd | 130 +-- man/municipality_key_2022.Rd | 134 +-- man/municipality_key_2024.Rd | 130 +-- man/municipality_key_2025.Rd |only 59 files changed, 1145 insertions(+), 1116 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: A unified interface to interact with various Large Language Model (LLM) APIs such as 'OpenAI' (see <https://platform.openai.com/docs/quickstart> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), 'Gemini' (see <https://aistudio.google.com> for details), and 'Voyage AI' (see <https://docs.voyageai.com/docs/introduction> for details). Allows users to configure API parameters, send messages, and retrieve responses seamlessly within R.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.1.2 dated 2025-01-17 and 0.2.1 dated 2025-02-11
DESCRIPTION | 13 ++++-- LICENSE | 2 - MD5 | 17 +++++--- NAMESPACE | 6 +++ R/LLMR.R | 96 ++++++++++++++++++++++++++++++++++++++++++++++--- R/Zagent.R |only README.md |only man/Agent.Rd |only man/AgentAction.Rd |only man/LLMConversation.Rd |only man/call_llm.Rd | 30 +++++++++++++++ man/llm_config.Rd | 3 + 12 files changed, 150 insertions(+), 17 deletions(-)
Title: Automated Tuning and Evaluations of Ecological Niche Models
Description: Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.
Author: Jamie M. Kass [aut, cre],
Robert Muscarella [aut],
Peter J. Galante [aut],
Corentin Bohl [aut],
Gonzalo E. Buitrago-Pinilla [aut],
Robert A. Boria [aut],
Mariano Soley-Guardia [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jamie.m.kass@gmail.com>
Diff between ENMeval versions 2.0.4 dated 2023-01-09 and 2.0.5 dated 2025-02-11
ENMeval-2.0.4/ENMeval/R/rmaxent_similarity.R |only ENMeval-2.0.4/ENMeval/man/pipe.Rd |only ENMeval-2.0.4/ENMeval/man/rasStackNAs.Rd |only ENMeval-2.0.4/ENMeval/man/similarity.Rd |only ENMeval-2.0.4/ENMeval/tests/testthat/test_mods.R |only ENMeval-2.0.5/ENMeval/DESCRIPTION | 24 ENMeval-2.0.5/ENMeval/MD5 | 94 +-- ENMeval-2.0.5/ENMeval/NAMESPACE | 18 ENMeval-2.0.5/ENMeval/NEWS | 21 ENMeval-2.0.5/ENMeval/R/ENMeval-package.R | 1 ENMeval-2.0.5/ENMeval/R/ENMevaluate.R | 449 ++++++++++-------- ENMeval-2.0.5/ENMeval/R/ENMnulls.R | 250 ++++++---- ENMeval-2.0.5/ENMeval/R/classes.R | 12 ENMeval-2.0.5/ENMeval/R/enm.bioclim.R | 10 ENMeval-2.0.5/ENMeval/R/enm.maxent.jar.R | 32 - ENMeval-2.0.5/ENMeval/R/enm.maxnet.R | 22 ENMeval-2.0.5/ENMeval/R/enmeval_results.R | 6 ENMeval-2.0.5/ENMeval/R/partitions.R | 269 ++++++---- ENMeval-2.0.5/ENMeval/R/plotting.R | 411 ++++++++++------ ENMeval-2.0.5/ENMeval/R/rmaxnet_parse_lambdas.r |only ENMeval-2.0.5/ENMeval/R/rmm.R | 21 ENMeval-2.0.5/ENMeval/R/tune.enm.R | 209 ++++---- ENMeval-2.0.5/ENMeval/R/utilities.R | 202 +++++--- ENMeval-2.0.5/ENMeval/R/zzz.R | 5 ENMeval-2.0.5/ENMeval/README.md | 27 - ENMeval-2.0.5/ENMeval/build/partial.rdb |binary ENMeval-2.0.5/ENMeval/data/enmeval_results.rda |binary ENMeval-2.0.5/ENMeval/inst/CITATION | 39 - ENMeval-2.0.5/ENMeval/man/ENMeval-package.Rd | 2 ENMeval-2.0.5/ENMeval/man/ENMevaluate.Rd | 152 +++--- ENMeval-2.0.5/ENMeval/man/ENMevaluation.Rd | 4 ENMeval-2.0.5/ENMeval/man/ENMevaluation_convert.Rd | 2 ENMeval-2.0.5/ENMeval/man/ENMnulls.Rd | 187 +++++-- ENMeval-2.0.5/ENMeval/man/aic.maxent.Rd | 4 ENMeval-2.0.5/ENMeval/man/buildRMM.Rd | 2 ENMeval-2.0.5/ENMeval/man/calc.niche.overlap.Rd | 6 ENMeval-2.0.5/ENMeval/man/clamp.vars.Rd | 8 ENMeval-2.0.5/ENMeval/man/enm.bioclim.Rd | 2 ENMeval-2.0.5/ENMeval/man/enmeval_results.Rd | 6 ENMeval-2.0.5/ENMeval/man/evalplot.envSim.hist.Rd | 44 + ENMeval-2.0.5/ENMeval/man/evalplot.envSim.map.Rd | 49 + ENMeval-2.0.5/ENMeval/man/evalplot.grps.Rd | 32 + ENMeval-2.0.5/ENMeval/man/evalplot.nulls.Rd | 33 + ENMeval-2.0.5/ENMeval/man/evalplot.stats.Rd | 21 ENMeval-2.0.5/ENMeval/man/loadENMevaluation.Rd |only ENMeval-2.0.5/ENMeval/man/maxnet.predictRaster.Rd |only ENMeval-2.0.5/ENMeval/man/parse_lambdas.Rd |only ENMeval-2.0.5/ENMeval/man/partitions.Rd | 65 +- ENMeval-2.0.5/ENMeval/man/plot.sim.dataPrep.Rd |only ENMeval-2.0.5/ENMeval/man/saveENMevaluation.Rd |only ENMeval-2.0.5/ENMeval/man/tune.enm.Rd | 30 - ENMeval-2.0.5/ENMeval/tests/testthat/helper_funcs.R | 225 ++++----- ENMeval-2.0.5/ENMeval/tests/testthat/test_bioclim.R |only ENMeval-2.0.5/ENMeval/tests/testthat/test_maxentJar.R |only ENMeval-2.0.5/ENMeval/tests/testthat/test_maxnet.R |only 55 files changed, 1844 insertions(+), 1152 deletions(-)
Title: Extract Drugs from Differential Expression Data from LINCS
Database
Description: Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide gene expression signature (GES) from tens of thousands of drug and genetic perturbations (Subramanian et al. (2017) <DOI:10.1016/j.cell.2017.10.049>).
Author: Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between DFD versions 0.2.0 dated 2024-08-28 and 0.3.0 dated 2025-02-11
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Resolving Plant Taxon Names Using the Australian Plant Census
Description: The process of resolving taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the established status of plant taxa across different states/territories.
Author: Daniel Falster [aut, cre, cph]
,
Elizabeth Wenk [aut, ctb] ,
Will Cornwell [aut, ctb] ,
Fonti Kar [aut, ctb] ,
Carl Boettiger [ctb]
Maintainer: Daniel Falster <daniel.falster@unsw.edu.au>
Diff between APCalign versions 1.1.2 dated 2025-01-28 and 1.1.3 dated 2025-02-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-versions.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: QTL Mapping for Multi Parent Populations
Description: For Multi Parent Populations (MPP) Identity By Descend (IBD)
probabilities are computed using Hidden Markov Models. These probabilities
are then used in a mixed model approach for QTL Mapping as described in
Li et al. (<doi:10.1007/s00122-021-03919-7>).
Author: Martin Boer [aut] ,
Wenhao Li [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenMPP versions 1.0.3 dated 2024-10-29 and 1.0.4 dated 2025-02-11
DESCRIPTION | 13 MD5 | 67 +-- NEWS.md | 5 R/calcIBDMPP.R | 20 R/createGDataMPP.R | 6 R/createGDataMPPInternal.R | 30 - R/createQTLMPP.R | 40 + R/data.R | 56 +- R/kinshipIBD.R | 2 R/parCIsPlot.R |only R/readRabbitMPP.R | 402 ++++---------------- R/selQTLMPP.R | 2 README.md | 10 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 44 +- inst/doc/QTLMapping_in_MultiParentPopulations.R | 68 +-- inst/doc/QTLMapping_in_MultiParentPopulations.Rmd | 30 + inst/doc/QTLMapping_in_MultiParentPopulations.html | 422 ++++++++++----------- inst/tinytest/test_calcIBDmpp.R | 228 +++++------ inst/tinytest/test_createQTLmpp.R | 99 ++-- inst/tinytest/test_readRABBIT.R | 6 man/barleyMQM.Rd | 32 - man/barleyPheno.Rd | 54 +- man/calcDistance.Rd | 24 - man/effectPlot.Rd | 48 +- man/figures/README-plotCIACMQM-1.png |only man/maizeMQM.Rd | 32 - man/maizeSQM.Rd | 32 - man/parCIsPlot.Rd |only man/plot.QTLMPP.Rd | 17 man/print.summary.QTLMPP.Rd | 32 - man/readRABBITMPP.Rd | 2 man/statgenMPP-package.Rd | 9 tests/tinytest.R | 10 vignettes/QTLMapping_in_MultiParentPopulations.Rmd | 30 + 36 files changed, 876 insertions(+), 996 deletions(-)
Title: The Symmetric Group: Permutations of a Finite Set
Description: Manipulates invertible functions from a finite set to
itself. Can transform from word form to cycle form and
back. To cite the package in publications please use
Hankin (2020) "Introducing the permutations R package",
SoftwareX, volume 11 <doi:10.1016/j.softx.2020.100453>.
Author: Robin K. S. Hankin [aut, cre] ,
Paul Egeler [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between permutations versions 1.1-5 dated 2024-07-17 and 1.1-6 dated 2025-02-11
DESCRIPTION | 12 +- MD5 | 80 ++++++++++------- NEWS.md | 46 +++++----- R/perm_ops.R | 2 R/permfuns.R | 46 ++++++++-- build/partial.rdb |binary build/vignette.rds |binary data/dot.rda |binary data/megaminx.rda |binary inst/doc/cyclist.Rmd | 1 inst/doc/cyclist.html | 13 +- inst/doc/groupaction.R |only inst/doc/groupaction.Rmd |only inst/doc/groupaction.html |only inst/doc/order_of_ops.R | 19 +++- inst/doc/order_of_ops.Rmd | 121 ++++++++++++++++----------- inst/doc/order_of_ops.html | 165 ++++++++++++++++++++----------------- inst/doc/permutations.pdf |binary inst/doc/print.R | 3 inst/doc/print.Rmd | 17 ++- inst/doc/print.html | 23 ++--- inst/doc/representation.Rmd | 1 inst/doc/representation.html | 7 - inst/dodecahedron_group.py | 3 inst/outer_automorphisms_of_S6.Rmd |only man/Ops.permutation.Rd | 35 +++++-- man/allperms.Rd | 4 man/as.function.permutation.Rd | 65 +++++++++++++- man/capply.Rd | 4 man/conjugate.Rd | 5 - man/cyclist.Rd | 2 man/faro.Rd | 21 +++- man/keepcyc.Rd |only man/stabilizer.Rd |only man/valid.Rd | 15 ++- tests/testthat/test_aaf.R |only tests/testthat/test_aag.R |only tests/testthat/test_aah.R |only tests/testthat/test_aai.R |only tests/testthat/test_aaj.R |only tests/testthat/test_aak.R |only tests/testthat/test_aal.R |only vignettes/cyclist.Rmd | 1 vignettes/groupaction.Rmd |only vignettes/order_of_ops.Rmd | 121 ++++++++++++++++----------- vignettes/permutations.bib | 11 ++ vignettes/print.Rmd | 17 ++- vignettes/representation.Rmd | 1 48 files changed, 557 insertions(+), 304 deletions(-)
Title: Utilities for Nephrology
Description: Set of functions to estimate kidney function and other traits of interest in nephrology.
Author: Cristian Pattaro [aut, cre],
Ryosuke Fujii [aut],
Janina Herold [aut]
Maintainer: Cristian Pattaro <cristian.pattaro@eurac.edu>
Diff between nephro versions 1.4 dated 2023-10-16 and 1.5 dated 2025-02-11
nephro-1.4/nephro/ChangeLog |only nephro-1.4/nephro/man/CKDEpi_RF.creat.Rd |only nephro-1.4/nephro/man/CKDEpi_RF.creat.cys.Rd |only nephro-1.5/nephro/DESCRIPTION | 17 nephro-1.5/nephro/MD5 | 23 nephro-1.5/nephro/NEWS.md |only nephro-1.5/nephro/R/nephro.R | 1659 +++++++++++++------------- nephro-1.5/nephro/README.md |only nephro-1.5/nephro/man/BCR.Rd |only nephro-1.5/nephro/man/CKDEpi.creat.Rd | 2 nephro-1.5/nephro/man/CKDEpi.creat.cys.Rd | 2 nephro-1.5/nephro/man/CKDEpi2021.creat.Rd |only nephro-1.5/nephro/man/CKDEpi2021.creat.cys.Rd |only nephro-1.5/nephro/man/Convert.mgdL.mmolL.Rd |only nephro-1.5/nephro/man/Convert.mgdL.umolL.Rd |only nephro-1.5/nephro/man/UACR.Rd |only nephro-1.5/nephro/man/UCR.Rd |only nephro-1.5/nephro/man/UPCR.Rd |only nephro-1.5/nephro/man/nephro-package.Rd | 29 19 files changed, 935 insertions(+), 797 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.2.1 dated 2025-01-21 and 2.2.2 dated 2025-02-11
DESCRIPTION | 7 ++- MD5 | 14 +++---- NEWS.md | 4 ++ R/GitHost.R | 55 ++++++++++++++++++++-------- R/get_repos.R | 8 ++-- inst/roche/roche_get_repos_workflow.R | 18 +++++++++ man/get_repos_urls.Rd | 8 ++-- tests/testthat/test-get_urls_repos-GitHub.R | 43 +++++++++++++++++++++ 8 files changed, 123 insertions(+), 34 deletions(-)
Title: Combination Matrix Axis for 'ggplot2' to Create 'UpSet' Plots
Description: Replace the standard x-axis in 'ggplots' with a combination matrix
to visualize complex set overlaps. 'UpSet' has introduced a new way to visualize
the overlap of sets as an alternative to Venn diagrams.
This package provides a simple way to produce such plots using 'ggplot2'.
In addition it can convert any categorical axis into a combination
matrix axis.
Author: Constantin Ahlmann-Eltze [aut, cre]
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between ggupset versions 0.4.0 dated 2024-06-24 and 0.4.1 dated 2025-02-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 ++++++- R/axis_combmatrix.R | 9 +++++---- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: Calculating Optimal and D-Augmented Designs
Description: Calculates D-, Ds-, A-, I- and L-optimal designs for non-linear models, via an implementation of the cocktail algorithm (Yu, 2011, <doi:10.1007/s11222-010-9183-2>). Compares designs via their efficiency, and augments any design with a controlled efficiency. An efficient rounding function has been provided to transform approximate designs to exact designs.
Author: Carlos de la Calle-Arroyo [aut, cre]
,
Jesus Lopez-Fidalgo [aut] ,
Licesio J. Rodriguez-Aragon [aut]
Maintainer: Carlos de la Calle-Arroyo <carlos.calle.arroyo@gmail.com>
Diff between optedr versions 2.0.0 dated 2022-11-18 and 2.2.0 dated 2025-02-11
DESCRIPTION | 21 MD5 | 82 NAMESPACE | 25 NEWS.md | 5 R/augment.R | 38 R/crit_eff.R | 54 R/efficient_round.R | 92 R/inf_mat_sens.R | 5 R/input_checks.R | 327 +- R/shiny_examples.R | 110 R/utils.R | 18 R/wf_mult.R | 74 README.md | 73 inst/CITATION |only inst/shiny-examples/AddPoints/app.R | 4342 +++++++++++++++---------------- man/DsWFMult.Rd | 2 man/IWFMult.Rd | 17 man/WFMult.Rd | 12 man/augment_design.Rd | 6 man/check_inputs.Rd | 10 man/combinatorial_round.Rd |only man/crit.Rd | 9 man/daugment_design.Rd | 112 man/design_efficiency.Rd | 8 man/dsaugment_design.Rd | 120 man/eff.Rd | 5 man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/get_augment_region.Rd | 150 - man/get_daugment_region.Rd | 100 man/get_dsaugment_region.Rd | 114 man/get_laugment_region.Rd | 115 man/gradient22.Rd | 56 man/icrit.Rd | 2 man/isens.Rd | 2 man/laugment_design.Rd | 121 man/opt_des.Rd | 14 man/plot.optdes.Rd | 2 man/print.optdes.Rd | 2 man/sens.Rd | 3 man/summary.optdes.Rd | 2 man/weight_function.Rd | 59 tests/testthat/test-effiency.R | 63 43 files changed, 3255 insertions(+), 3117 deletions(-)
More information about PatientLevelPrediction at CRAN
Permanent link
Title: Fast AUC Computation
Description: Fast calculation of Area Under Curve (AUC) metric of a
Receiver Operating Characteristic (ROC) curve, using the algorithm
of Fawcett (2006) <doi:10.1016/j.patrec.2005.10.010>. Therefore it
is appropriate for large-scale AUC metric calculations.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between lightAUC versions 0.1.1 dated 2025-02-03 and 0.1.2 dated 2025-02-11
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 6 + README.md | 22 ++++--- src/lightauc.cpp | 125 ++++++++++++++++++++++++++++++++--------- tests/testthat/test-lightAUC.r | 14 ++++ 6 files changed, 140 insertions(+), 43 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] ,
Laurent Coron [aut] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.3.3 dated 2024-07-23 and 0.3.4 dated 2025-02-11
airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_brigode_pierre.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_coron_laurent.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_delaigue_olivier.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_michel_claude.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_perrin_charles.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/photo_thirel_guillaume.jpg |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/fig/sheet_W1110010_thumbnail.png |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/tab_authors.md |only airGRteaching-0.3.3/airGRteaching/inst/ShinyGR/www/tab_authors.rmd |only airGRteaching-0.3.4/airGRteaching/DESCRIPTION | 8 - airGRteaching-0.3.4/airGRteaching/MD5 | 46 ++----- airGRteaching-0.3.4/airGRteaching/NEWS.md | 13 +- airGRteaching-0.3.4/airGRteaching/build/partial.rdb |binary airGRteaching-0.3.4/airGRteaching/inst/ShinyGR/server.R | 22 +-- airGRteaching-0.3.4/airGRteaching/inst/ShinyGR/ui.R | 5 airGRteaching-0.3.4/airGRteaching/inst/ShinyGR/www/fig/airGRteaching_GUI_Description.png |binary airGRteaching-0.3.4/airGRteaching/inst/ShinyGR/www/fig/sheet_W111001001_thumbnail.png |only airGRteaching-0.3.4/airGRteaching/inst/doc/get_started.R | 8 - airGRteaching-0.3.4/airGRteaching/inst/doc/get_started.html | 28 ++-- airGRteaching-0.3.4/airGRteaching/inst/doc/v00_teaching_hydrology.R | 36 ++--- airGRteaching-0.3.4/airGRteaching/inst/doc/v00_teaching_hydrology.html | 64 +++++----- airGRteaching-0.3.4/airGRteaching/inst/doc/v00_teaching_hydrology.rmd | 40 +++--- airGRteaching-0.3.4/airGRteaching/inst/doc/v01_EN_flow_reconstruction.html | 18 +- airGRteaching-0.3.4/airGRteaching/inst/doc/v01_FR_flow_reconstruction.html | 18 +- airGRteaching-0.3.4/airGRteaching/inst/doc/v02_EN_flow_forecasting.html | 22 +-- airGRteaching-0.3.4/airGRteaching/inst/doc/v02_FR_flow_forecasting.html | 22 +-- airGRteaching-0.3.4/airGRteaching/inst/doc/v03_EN_impact_CC_flow.html | 18 +- airGRteaching-0.3.4/airGRteaching/inst/doc/v03_FR_impact_CC_flow.html | 18 +- airGRteaching-0.3.4/airGRteaching/vignettes/v00_teaching_hydrology.rmd | 40 +++--- 29 files changed, 213 insertions(+), 213 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024>
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>).
Since version 3.0, it provides dedicated functions to estimate Poisson models.
Author: Simen Gaure [aut] ,
Grant McDermott [ctb],
Mauricio Vargas Sepulveda [ctb, cre]
,
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between lfe versions 3.1.0 dated 2024-11-06 and 3.1.1 dated 2025-02-11
lfe-3.1.0/lfe/LICENSE |only lfe-3.1.1/lfe/DESCRIPTION | 8 ++++---- lfe-3.1.1/lfe/MD5 | 24 ++++++++++++------------ lfe-3.1.1/lfe/NEWS.md | 4 ++++ lfe-3.1.1/lfe/R/nlexpect.R | 4 ++-- lfe-3.1.1/lfe/build/partial.rdb |binary lfe-3.1.1/lfe/build/vignette.rds |binary lfe-3.1.1/lfe/inst/doc/biascorrection.pdf |binary lfe-3.1.1/lfe/inst/doc/identification.pdf |binary lfe-3.1.1/lfe/inst/doc/lfehow.pdf |binary lfe-3.1.1/lfe/inst/doc/speed.pdf |binary lfe-3.1.1/lfe/man/nlexpect.Rd | 4 ++-- lfe-3.1.1/lfe/src/Makevars.win | 6 ++++++ lfe-3.1.1/lfe/src/config.h.win |only 14 files changed, 30 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-27 2.3.3
2024-12-12 2.3.2
2024-01-29 2.3.1
2024-01-25 2.3
2022-08-31 2.2
2022-02-02 2.1
2021-09-11 2.0
2020-01-28 1.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-12 0.0.112
2022-03-16 0.0.111
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-12 0.0.2