Title: Genotype by Environment (GxE) Analysis
Description: Analysis of multi environment data of plant breeding experiments
following the analyses described in Malosetti, Ribaut,
and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>.
One of a series of statistical genetic packages for streamlining the analysis of
typical plant breeding experiments developed by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb],
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGxE versions 1.0.6 dated 2023-12-12 and 1.0.7 dated 2024-03-19
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenGxE.html | 33 +++++++++++++++++---------------- tests/testthat/Rplots.pdf |binary tests/testthat/test-plots.R | 6 ++---- 8 files changed, 35 insertions(+), 32 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between PRECAST versions 1.6.4 dated 2024-01-25 and 1.6.5 dated 2024-03-19
DESCRIPTION | 12 +- MD5 | 18 +-- R/main.R | 2 README.md | 4 build/vignette.rds |binary inst/doc/PRECAST.BreastCancer.html | 41 ++++--- inst/doc/PRECAST.DLPFC.html | 41 ++++--- inst/doc/PRECAST.DLPFC4.html | 41 ++++--- inst/doc/PRECAST.Simu.html | 191 +++++++++++++++++++------------------ inst/doc/PRECAST.html | 29 ++++- 10 files changed, 215 insertions(+), 164 deletions(-)
Title: Model Species Distributions by Estimating the Probability of
Occurrence Using Presence-Only Data
Description: Provides a likelihood-based approach to modeling species distributions using presence-only data. In contrast to the popular software program MAXENT, this approach yields estimates of the probability of occurrence, which is a natural descriptor of a species' distribution.
Author: Richard Chandler, Andy Royle and Roeland Kindt
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between maxlike versions 0.1-10 dated 2023-09-17 and 0.1-11 dated 2024-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/maxlike.R | 10 +++++++--- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between DR.SC versions 3.3 dated 2023-08-09 and 3.4 dated 2024-03-19
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- R/main.R | 6 ++---- README.md | 3 +++ build/vignette.rds |binary inst/doc/DR-SC.html | 40 ++++++++++++++++++++++++++++------------ inst/doc/DR.SC.DLPFC.R | 5 +++-- inst/doc/DR.SC.DLPFC.Rmd | 5 +++-- inst/doc/DR.SC.DLPFC.html | 25 +++++++++++++++++-------- inst/doc/DR.SC.Simu.R | 8 ++++---- inst/doc/DR.SC.Simu.Rmd | 8 ++++---- inst/doc/DR.SC.Simu.html | 26 +++++++++++++++++--------- vignettes/DR.SC.DLPFC.Rmd | 5 +++-- vignettes/DR.SC.Simu.Rmd | 8 ++++---- 14 files changed, 107 insertions(+), 70 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.0-6 dated 2024-02-22 and 3.0-9 dated 2024-03-19
DESCRIPTION | 23 +-- MD5 | 84 ++++++------ NEWS.md | 37 +++++ R/GGIR.R | 29 ---- R/HASPT.R | 119 ++++++++++------- R/applyExtFunction.R | 1 R/check_params.R | 8 - R/convertEpochData.R | 35 ++--- R/create_test_sleeplog_csv.R | 12 + R/extract_params.R | 3 R/g.conv.actlog.R | 2 R/g.convert.part2.long.R | 92 ++++++------- R/g.loadlog.R | 6 R/g.part1.R | 2 R/g.part3.R | 3 R/g.part4.R | 31 +++- R/g.part5.R | 22 ++- R/g.part5.classifyNaps.R | 1 R/g.part5.definedays.R | 102 +++++---------- R/g.part5_analyseSegment.R | 39 +++-- R/g.part5_initialise_ts.R | 27 ++-- R/g.report.part2.R | 1 R/g.report.part4.R | 6 R/g.sib.det.R | 24 +-- R/load_params.R | 5 R/read.myacc.csv.R | 50 ++++--- inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.Rmd | 9 - inst/doc/GGIR.html | 22 ++- inst/doc/GGIRParameters.Rmd | 4 inst/doc/GGIRParameters.html | 44 ++++-- man/GGIR-package.Rd | 4 man/GGIR.Rd | 21 ++- man/HASPT.Rd | 28 +--- man/g.part5.definedays.Rd | 6 man/g.part5.savetimeseries.Rd | 6 tests/testthat/test_chainof5parts.R | 7 - tests/testthat/test_convertExtEpochData.R | 14 +- tests/testthat/test_gloadlog.R | 70 +++++++--- tests/testthat/test_greadaccfile.R | 201 +++++++++++++++--------------- tests/testthat/test_load_check_params.R | 7 - vignettes/GGIR.Rmd | 9 - vignettes/GGIRParameters.Rmd | 4 43 files changed, 689 insertions(+), 531 deletions(-)
Title: Frequently Used Functions for Easy R Programming
Description: Some utility functions for validation, data manipulation or color palettes. These functions can be helpful to reduce internal codes everywhere in package development.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <ycli1995@outlook.com>
Diff between easy.utils versions 0.0.3 dated 2023-10-17 and 0.0.4 dated 2024-03-19
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/color_palettes.R | 24 +++++++++--------------- R/verbose.R |only R/zzz.R | 1 + man/verboseMsg.Rd |only 8 files changed, 27 insertions(+), 23 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-12 0.2.3
2021-11-10 0.2.2
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] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
Longda Jiang [ctb] ,
Ma [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.0.2 dated 2024-02-28 and 5.0.3 dated 2024-03-18
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++-------- NEWS.md | 7 ++++ R/convenience.R | 2 - R/preprocessing5.R | 16 ++++++---- R/utilities.R | 2 - R/visualization.R | 7 +++- build/Seurat.pdf |binary build/stage23.rdb |binary man/FeatureScatter.Rd | 5 ++- man/ReadAkoya.Rd | 6 --- tests/testthat/test_integration5.R | 56 +++++++++++++++-------------------- tests/testthat/test_preprocessing.R | 57 ++++++++++++++++++++++-------------- tests/testthat/test_utilities.R | 5 +++ 14 files changed, 112 insertions(+), 85 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the fu [...truncated...]
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.4.1 dated 2024-01-18 and 2.4.3 dated 2024-03-18
DESCRIPTION | 8 +-- MD5 | 62 +++++++++++++++--------------- NAMESPACE | 2 R/VSS.R | 17 ++++++++ R/bigCor.R | 18 +++++--- R/describe.R | 94 ++++++++++++++++++++++++++++++++++++++++------ R/fa.R | 3 + R/fa.parallel.R | 16 +++++++ R/factor.stats.R | 12 +++++ R/kappa.R | 12 ++--- R/misc.R | 10 ++-- R/pairs.panels.R | 10 +++- R/print.psych.R | 16 +++++++ R/print.psych.vss.R | 14 +++--- R/reliability.R | 44 ++++++++++++--------- R/score.multiple.choice.R | 24 +++++++++-- R/sim.structural.R | 5 +- R/statsBy.r | 25 +++++++++++- R/unidim.r | 57 ++++++++++++++++++++------- inst/CITATION | 2 inst/NEWS.Rd | 27 +++++++++---- inst/doc/scoring.pdf |binary man/VSS.Rd | 15 +++++-- man/bigCor.Rd | 30 +++++++++----- man/describe.Rd | 10 ++-- man/fa.parallel.Rd | 6 ++ man/kappa.Rd | 9 ++-- man/pairs.panels.Rd | 3 - man/reliability.Rd | 14 +++++- man/sim.Rd | 3 - man/statsBy.Rd | 4 + man/unidim.Rd | 15 +++++-- 32 files changed, 431 insertions(+), 156 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.2.0 dated 2023-10-09 and 1.2.1 dated 2024-03-18
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 14 ++++++++++++++ R/internal.R | 31 +++++++++++++++++++++++++++---- R/phylopath.R | 14 ++++++++++++-- build/vignette.rds |binary inst/doc/binary_models.html | 6 +++--- inst/doc/intro_to_phylopath.html | 4 ++-- man/phylo_path.Rd | 2 +- 9 files changed, 70 insertions(+), 23 deletions(-)
Title: Automated Tool for Vertical Fuel Continuity Analysis using
Airborne Laser Scanning Data
Description: Set of tools for analyzing vertical fuel continuity at the tree level using Airborne Laser Scanning data. The workflow consisted of: 1) calculating the vertical height profiles of each segmented tree; 2) identifying gaps and fuel layers; 3) estimating the distance between fuel layers; and 4) retrieving the fuel layers base height and depth. Additionally, other functions recalculate previous metrics after considering distances greater than 1 m and calculate the canopy base height as the fuel base height located at the largest- and at the last-distance. Moreover, the package calculates: i) the percentage of Leaf Area Density comprised in each fuel layer, ii) remove fuel layers with Leaf Area Density percentage less than 25, iii) recalculate the distances among the reminder ones, and iv) identify the canopy base height as the fuel base height with the highest Leaf Area Density percentage. On the other hand, when there is only one fuel layer, it identifies the canopy base height performing [...truncated...]
Author: Olga Viedma [aut, cph, cre],
Carlos Alberto Silva [aut, cph],
Jose Manuel Moreno [aut, cph]
Maintainer: Olga Viedma <olga.viedma@uclm.es>
Diff between LadderFuelsR versions 0.0.3 dated 2024-01-26 and 0.0.4 dated 2024-03-18
DESCRIPTION | 6 +-- MD5 | 8 ++-- R/depths_calculation.R | 73 +++++++++++++++++++-------------------- R/distances_calculation.R | 85 +++++++++++++++++++++++++++------------------- README.md | 2 - 5 files changed, 94 insertions(+), 80 deletions(-)
Title: OD-Means: k-Means for Origin-Destination
Description: OD-means is a hierarchical adaptive k-means algorithm based on origin-destination pairs.
In the first layer of the hierarchy, the clusters are separated automatically based on the variation
of the within-cluster distance of each cluster until convergence. The second layer of the hierarchy
corresponds to the sub clustering process of small clusters based on the distance between the origin
and destination of each cluster.
Author: Sebastian Moreno [aut, cre],
Cristobal Heredia [aut],
Wilfredo Yushimito [ths],
Gonzalo Huerta [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Diff between ODMeans versions 0.2.0 dated 2024-01-10 and 0.2.1 dated 2024-03-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/first_hierarchy.R | 30 +++++++++++++++++++++++++++++- R/odmeans.R | 5 +++-- man/first_hierarchy.Rd | 4 +++- man/odmeans.Rd | 5 ++++- 6 files changed, 48 insertions(+), 14 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Damir Pulatov [cre, aut],
Michel Lang [aut]
Maintainer: Damir Pulatov <damirpolat@protonmail.com>
Diff between mlr3cluster versions 0.1.8 dated 2023-03-12 and 0.1.9 dated 2024-03-18
mlr3cluster-0.1.8/mlr3cluster/tests/testthat/setup.R |only mlr3cluster-0.1.9/mlr3cluster/DESCRIPTION | 24 mlr3cluster-0.1.9/mlr3cluster/MD5 | 159 ++-- mlr3cluster-0.1.9/mlr3cluster/NAMESPACE | 3 mlr3cluster-0.1.9/mlr3cluster/NEWS.md | 9 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClust.R | 11 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustAffinityPropagation.R | 48 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustAgnes.R | 47 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustCMeans.R | 57 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustCobweb.R | 20 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustDBSCAN.R | 52 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustDBSCANfpc.R |only mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustDiana.R | 22 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustEM.R | 34 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustFanny.R | 26 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustFarthestFirst.R | 24 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustFeatureless.R | 18 mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustHDBSCAN.R |only mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustHclust.R | 40 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustKKMeans.R | 67 -- mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustKMeans.R | 45 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustMclust.R | 62 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustMeanShift.R | 42 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustMiniBatchKMeans.R | 57 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustOPTICS.R |only mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustPAM.R | 53 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustSimpleKMeans.R | 36 - mlr3cluster-0.1.9/mlr3cluster/R/LearnerClustXMeans.R | 32 mlr3cluster-0.1.9/mlr3cluster/R/MeasureClustInternal.R | 2 mlr3cluster-0.1.9/mlr3cluster/R/PredictionDataClust.R | 2 mlr3cluster-0.1.9/mlr3cluster/R/bibentries.R | 331 +++++++++- mlr3cluster-0.1.9/mlr3cluster/R/helper.R | 14 mlr3cluster-0.1.9/mlr3cluster/R/zzz.R | 5 mlr3cluster-0.1.9/mlr3cluster/README.md | 15 mlr3cluster-0.1.9/mlr3cluster/build/partial.rdb |binary mlr3cluster-0.1.9/mlr3cluster/man/LearnerClust.Rd | 4 mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.MBatchKMeans.Rd | 46 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.SimpleKMeans.Rd | 60 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.agnes.Rd | 46 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.ap.Rd | 54 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.cmeans.Rd | 52 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.cobweb.Rd | 54 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.dbscan.Rd | 58 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.dbscan_fpc.Rd |only mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.diana.Rd | 46 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.em.Rd | 50 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.fanny.Rd | 48 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.featureless.Rd | 43 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.ff.Rd | 52 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.hclust.Rd | 85 ++ mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.hdbscan.Rd |only mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.kkmeans.Rd | 52 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.kmeans.Rd | 61 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.mclust.Rd | 52 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.meanshift.Rd | 46 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.optics.Rd |only mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.pam.Rd | 53 + mlr3cluster-0.1.9/mlr3cluster/man/mlr_learners_clust.xmeans.Rd | 50 + mlr3cluster-0.1.9/mlr3cluster/tests/testthat/Rplots.pdf |only mlr3cluster-0.1.9/mlr3cluster/tests/testthat/helper_mlr3.R | 7 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_LearnerClust.R | 23 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_MeasureClust.R | 8 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_PredictionClust.R | 12 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_TaskClust.R | 11 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_agnes.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_ap.R | 8 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_cmeans.R | 8 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_cobweb.R | 5 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan.R | 12 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan_fpc.R |only mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_diana.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_em.R | 5 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_fanny.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_featureless.R | 7 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_ff.R | 5 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_hclust.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_hdbscan.R |only mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_kkmeans.R | 7 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmeans.R | 7 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_mbatchkmeans.R | 7 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_mclust.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_meanshift.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_optics.R |only mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_pam.R | 6 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_simplekmeans.R | 5 mlr3cluster-0.1.9/mlr3cluster/tests/testthat/test_mlr_learners_clust_xmeans.R | 5 86 files changed, 1868 insertions(+), 685 deletions(-)
Title: Gene Set Networking Analysis Package
Description: Create networks of gene sets, infer clusters of functionally-related gene sets based
on similarity statistics, and visualize the results. This package simplifies and accelerates
interpretation of pathways analysis data sets. It is designed to work in tandem with standard
pathways analysis methods, such as the 'GSEA' program (Gene Set Enrichment Analysis), CERNO
(Coincident Extreme Ranks in Numerical Observations, implemented in the 'tmod' package) and others.
Inputs to 'GSNA' are the outputs of pathways analysis methods: a list of gene sets (or "modules"),
pathways or GO-terms with associated p-values. Since pathways analysis methods may be used to
analyze many different types of data including transcriptomic, epigenetic, and high-throughput
screen data sets, the 'GSNA' pipeline is applicable to these data as well. The use of 'GSNA' has
been described in the following papers:
Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, et al. (2021) <doi:10.1016/j.immuni.2021.0 [...truncated...]
Author: Jonathan M Urbach [aut, cre]
Maintainer: Jonathan M Urbach <jurbach@mgh.harvard.edu>
Diff between GSNA versions 0.1.4.1 dated 2024-02-14 and 0.1.4.2 dated 2024-03-18
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- NAMESPACE | 1 NEWS.md | 3 ++ R/gsnAddPathwaysData.R | 15 +++++----- README.md | 4 +- inst/doc/using_the_gsna_package.html | 48 +++++++++++++++++------------------ man/gsnAddPathwaysData.Rd | 29 ++++++++++----------- 8 files changed, 61 insertions(+), 59 deletions(-)
Title: Building and Training Neural Networks
Description: The 'cito' package provides a user-friendly interface for training and interpreting deep neural networks (DNN). 'cito' simplifies the fitting of DNNs by supporting the familiar formula syntax, hyperparameter tuning under cross-validation, and helps to detect and handle convergence problems. DNNs can be trained on CPU, GPU and MacOS GPUs. In addition, 'cito' has many downstream functionalities such as various explainable AI (xAI) metrics (e.g. variable importance, partial dependence plots, accumulated local effect plots, and effect estimates) to interpret trained DNNs. 'cito' optionally provides confidence intervals (and p-values) for all xAI metrics and predictions. At the same time, 'cito' is computationally efficient because it is based on the deep learning framework 'torch'. The 'torch' package is native to R, so no Python installation or other API is required for this package.
Author: Christian Amesoeder [aut],
Maximilian Pichler [aut, cre] ,
Florian Hartig [ctb] ,
Armin Schenk [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between cito versions 1.0.2 dated 2023-10-06 and 1.1 dated 2024-03-18
cito-1.0.2/cito/R/ALE.R |only cito-1.0.2/cito/R/PDP.R |only cito-1.0.2/cito/R/conditionalEffects.R |only cito-1.0.2/cito/R/lr_scheduler.R |only cito-1.0.2/cito/R/plot.R |only cito-1.0.2/cito/R/variable_importance.R |only cito-1.1/cito/DESCRIPTION | 15 cito-1.1/cito/MD5 | 230 +- cito-1.1/cito/NAMESPACE | 10 cito-1.1/cito/NEWS.md | 21 cito-1.1/cito/R/cito.R | 2 cito-1.1/cito/R/cnn.R |only cito-1.1/cito/R/continue_training.R | 152 - cito-1.1/cito/R/data_simulation.R |only cito-1.1/cito/R/dnn.R | 370 ++- cito-1.1/cito/R/mmn.R |only cito-1.1/cito/R/model.R | 300 +- cito-1.1/cito/R/reformulate_glmmTMB.R |only cito-1.1/cito/R/structures.R |only cito-1.1/cito/R/training.R | 435 +++- cito-1.1/cito/R/tuner.R |only cito-1.1/cito/R/utils.R | 548 +++++ cito-1.1/cito/R/xAI.R |only cito-1.1/cito/README.md | 128 - cito-1.1/cito/inst/WORDLIST |only cito-1.1/cito/inst/doc/A-Introduction_to_cito.Rmd | 395 ++- cito-1.1/cito/inst/doc/A-Introduction_to_cito.html | 477 +++- cito-1.1/cito/inst/doc/B-Training_neural_networks.Rmd | 284 +- cito-1.1/cito/inst/doc/B-Training_neural_networks.html | 307 +- cito-1.1/cito/inst/doc/C-Example_Species_distribution_modeling.Rmd | 917 ++++---- cito-1.1/cito/inst/doc/C-Example_Species_distribution_modeling.html | 1033 ++++------ cito-1.1/cito/inst/doc/D-Advanced_custom_loss_functions.Rmd | 372 +-- cito-1.1/cito/inst/doc/D-Advanced_custom_loss_functions.html | 387 +-- cito-1.1/cito/inst/examples/dnn-example.R | 32 cito-1.1/cito/inst/examples/predict.citocnn-example.R |only cito-1.1/cito/inst/examples/print.citodnn-example.R | 2 cito-1.1/cito/man/ALE.Rd | 2 cito-1.1/cito/man/PDP.Rd | 2 cito-1.1/cito/man/analyze_training.Rd | 4 cito-1.1/cito/man/avgPool.Rd |only cito-1.1/cito/man/cito.Rd | 34 cito-1.1/cito/man/cnn.Rd |only cito-1.1/cito/man/coef.citocnn.Rd |only cito-1.1/cito/man/conditionalEffects.Rd | 4 cito-1.1/cito/man/config_lr_scheduler.Rd | 2 cito-1.1/cito/man/config_tuning.Rd |only cito-1.1/cito/man/continue_training.Rd | 41 cito-1.1/cito/man/conv.Rd |only cito-1.1/cito/man/create_architecture.Rd |only cito-1.1/cito/man/dnn.Rd | 110 - cito-1.1/cito/man/e.Rd |only cito-1.1/cito/man/figures/README-unnamed-chunk-7-1.png |only cito-1.1/cito/man/findReTrmClasses.Rd |only cito-1.1/cito/man/linear.Rd |only cito-1.1/cito/man/maxPool.Rd |only cito-1.1/cito/man/plot.citoarchitecture.Rd |only cito-1.1/cito/man/plot.citocnn.Rd |only cito-1.1/cito/man/predict.citocnn.Rd |only cito-1.1/cito/man/predict.citodnn.Rd | 6 cito-1.1/cito/man/print.avgPool.Rd |only cito-1.1/cito/man/print.citoarchitecture.Rd |only cito-1.1/cito/man/print.citocnn.Rd |only cito-1.1/cito/man/print.citodnn.Rd | 4 cito-1.1/cito/man/print.conditionalEffects.Rd | 2 cito-1.1/cito/man/print.conv.Rd |only cito-1.1/cito/man/print.linear.Rd |only cito-1.1/cito/man/print.maxPool.Rd |only cito-1.1/cito/man/print.transfer.Rd |only cito-1.1/cito/man/simulate_shapes.Rd |only cito-1.1/cito/man/sumTerms.Rd |only cito-1.1/cito/man/summary.citocnn.Rd |only cito-1.1/cito/man/summary.citodnn.Rd | 4 cito-1.1/cito/man/transfer.Rd |only cito-1.1/cito/man/tune.Rd |only cito-1.1/cito/tests/spelling.R |only cito-1.1/cito/tests/testthat/test-dnn.R | 146 + cito-1.1/cito/tests/testthat/test-xAI.R | 5 cito-1.1/cito/vignettes/A-Introduction_to_cito.Rmd | 395 ++- cito-1.1/cito/vignettes/A-Introduction_to_cito.Rmd.orig | 157 + cito-1.1/cito/vignettes/A/A-activation-1.png |binary cito-1.1/cito/vignettes/A/A-activation-2.png |binary cito-1.1/cito/vignettes/A/A-alpha-1.png |binary cito-1.1/cito/vignettes/A/A-continue_training-1.png |binary cito-1.1/cito/vignettes/A/A-continue_training2-1.png |binary cito-1.1/cito/vignettes/A/A-dropout-1.png |binary cito-1.1/cito/vignettes/A/A-early_stopping-1.png |binary cito-1.1/cito/vignettes/A/A-lr_scheduler-1.png |binary cito-1.1/cito/vignettes/A/A-optim-1.png |binary cito-1.1/cito/vignettes/A/A-plotnn-1.png |binary cito-1.1/cito/vignettes/A/A-simp_models-1.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-10-1.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-11-1.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-11-2.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-14-1.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-15-1.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-15-2.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-16-1.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-17-1.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-17-2.png |only cito-1.1/cito/vignettes/A/A-unnamed-chunk-2-1.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-3-1.png |binary cito-1.1/cito/vignettes/A/A-unnamed-chunk-9-1.png |binary cito-1.1/cito/vignettes/A/A-validation-1.png |binary cito-1.1/cito/vignettes/B-Training_neural_networks.Rmd | 284 +- cito-1.1/cito/vignettes/B-Training_neural_networks.Rmd.orig | 19 cito-1.1/cito/vignettes/B/B-unnamed-chunk-10-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-11-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-2-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-3-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-4-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-5-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-6-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-7-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-8-1.png |binary cito-1.1/cito/vignettes/B/B-unnamed-chunk-9-1.png |binary cito-1.1/cito/vignettes/C-Example_Species_distribution_modeling.Rmd | 917 ++++---- cito-1.1/cito/vignettes/C-Example_Species_distribution_modeling.Rmd.orig | 43 cito-1.1/cito/vignettes/C/C-unnamed-chunk-11-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-12-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-13-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-15-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-15-2.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-15-3.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-15-4.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-18-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-19-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-24-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-25-1.png |only cito-1.1/cito/vignettes/C/C-unnamed-chunk-26-1.png |only cito-1.1/cito/vignettes/C/C-unnamed-chunk-4-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-5-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-6-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-7-1.png |binary cito-1.1/cito/vignettes/C/C-unnamed-chunk-8-1.png |binary cito-1.1/cito/vignettes/D-Advanced_custom_loss_functions.Rmd | 372 +-- cito-1.1/cito/vignettes/D-Advanced_custom_loss_functions.Rmd.orig | 5 cito-1.1/cito/vignettes/D/D-unnamed-chunk-2-1.png |binary cito-1.1/cito/vignettes/D/D-unnamed-chunk-4-1.png |binary cito-1.1/cito/vignettes/D/D-unnamed-chunk-5-1.png |binary cito-1.1/cito/vignettes/D/D-unnamed-chunk-6-1.png |binary cito-1.1/cito/vignettes/build.R | 39 141 files changed, 5262 insertions(+), 3752 deletions(-)
Title: Construct Nomograms for Competing Risks Regression Models
Description: Nomograms are constructed to predict the cumulative incidence
rate which is calculated after adjusting for competing causes to the event of interest.
K-fold cross-validation is implemented to validate predictive accuracy using a competing-risk version of the concordance index.
Methods are as described in: Kattan MW, Heller G,
Brennan MF (2003).
Author: Michael Kattan [aut],
Changhong Yu [aut],
Xinge Ji [aut],
Zajichek Alex [cre]
Maintainer: Zajichek Alex <zajicha2@ccf.org>
Diff between QHScrnomo versions 3.0.0 dated 2023-04-18 and 3.0.1 dated 2024-03-18
DESCRIPTION | 8 MD5 | 10 - NEWS.md | 4 R/crr.R | 2 README.md | 8 inst/doc/QHScrnomo.html | 408 ++++++++++++++++++++++++------------------------ 6 files changed, 221 insertions(+), 219 deletions(-)
Title: Studio Ghibli Colour Palettes
Description: Colour palettes inspired by Studio Ghibli <https://en.wikipedia.org/wiki/Studio_Ghibli>
films, ported to R for your enjoyment.
Author: Ewen Henderson [aut, cre] ,
Danielle Desrosiers [ctb],
Michael Chirico [ctb]
Maintainer: Ewen Henderson <ewenhenderson@gmail.com>
Diff between ghibli versions 0.3.3 dated 2022-08-26 and 0.3.4 dated 2024-03-18
DESCRIPTION | 7 +- MD5 | 8 +- NEWS.md | 5 + inst/doc/ghibli.html | 141 +++++++++++++++++++++---------------------- tests/testthat/test-scales.R | 21 +----- 5 files changed, 89 insertions(+), 93 deletions(-)
Title: Data Set and Helper Functions for Wind Farm Layout Optimization
Problems
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for
economically (profit) driven wind farm layout optimization. This enables researchers in the field
of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization
to focus on their optimization methodology contribution and also provides a realistic benchmark
setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020)
<doi:10.1016/j.energy.2020.119244>.
Author: Carsten Croonenbroeck [aut, cre],
David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between wflo versions 1.8 dated 2023-01-15 and 1.9 dated 2024-03-18
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NEWS | 17 ++++++++++++++++- inst/CITATION | 22 ++++++++-------------- inst/doc/wflo.R | 38 ++++++++++++++++---------------------- inst/doc/wflo.Rnw | 10 ++++------ inst/doc/wflo.pdf |binary man/wflo.Rd | 1 + vignettes/Fig4.pdf |only vignettes/wflo-PlotResult.pdf |only vignettes/wflo.Rnw | 10 ++++------ 11 files changed, 63 insertions(+), 61 deletions(-)
Title: Selection Bias Approach to Sensitivity Analysis for Causal
Effects
Description: The causalsens package provides functions to perform sensitivity analyses and to study how various assumptions about selection bias affects estimates of causal effects.
Author: Matthew Blackwell <mblackwell@gov.harvard.edu.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>
Diff between causalsens versions 0.1.2 dated 2018-06-18 and 0.1.3 dated 2024-03-18
causalsens-0.1.2/causalsens/README.md |only causalsens-0.1.2/causalsens/inst/doc/causalsens.Rnw |only causalsens-0.1.2/causalsens/inst/doc/causalsens.pdf |only causalsens-0.1.2/causalsens/vignettes/causalsens.Rnw |only causalsens-0.1.3/causalsens/DESCRIPTION | 14 causalsens-0.1.3/causalsens/MD5 | 29 - causalsens-0.1.3/causalsens/NAMESPACE | 42 - causalsens-0.1.3/causalsens/R/causalsens.R | 405 ++++++++++--------- causalsens-0.1.3/causalsens/build/vignette.rds |binary causalsens-0.1.3/causalsens/inst/doc/causalsens.R | 19 causalsens-0.1.3/causalsens/inst/doc/causalsens.Rmd |only causalsens-0.1.3/causalsens/inst/doc/causalsens.html |only causalsens-0.1.3/causalsens/man/causalsens.Rd | 93 ++-- causalsens-0.1.3/causalsens/man/lalonde.exp.Rd | 43 +- causalsens-0.1.3/causalsens/man/lalonde.psid.Rd | 43 +- causalsens-0.1.3/causalsens/man/one.sided.Rd | 28 - causalsens-0.1.3/causalsens/man/plot.causalsens.Rd | 23 - causalsens-0.1.3/causalsens/vignettes/causalsens.Rmd |only causalsens-0.1.3/causalsens/vignettes/causalsens.bib | 4 19 files changed, 412 insertions(+), 331 deletions(-)
Title: Time Series Methods
Description: Generic methods for use in a time series probabilistic framework, allowing for a common calling convention across packages. Additional methods for time series prediction ensembles and probabilistic plotting of predictions is included. A more detailed description is available at <https://www.nopredict.com/packages/tsmethods> which shows the currently implemented methods in the 'tsmodels' framework.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsmethods versions 1.0.0 dated 2024-03-09 and 1.0.1 dated 2024-03-18
tsmethods-1.0.0/tsmethods/Changelog |only tsmethods-1.0.1/tsmethods/DESCRIPTION | 8 ++++---- tsmethods-1.0.1/tsmethods/MD5 | 6 +++--- tsmethods-1.0.1/tsmethods/NEWS.md |only tsmethods-1.0.1/tsmethods/tests/testthat/test-ensemble.R | 6 +++--- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: ShangMi(SM) Cryptographic Algorithms(SM2/SM3/SM4)
Description: Bindings to 'smcrypto' <https://github.com/zhuobie/smcrypto>: a 'Rust'
implementation of China's Standards of Encryption Algorithms, which is usually
called 'ShangMi(SM)' algorithms. It contains 'SM3' message digest algorithm,
'SM2' asymmetric encryption algorithm and 'SM4' symmetric encryption algorithm.
Users can do message hash, encrypt/decrypt, sign/verify, key exchange and more.
Author: Meng Yu [aut, cre]
Maintainer: Meng Yu <610074@gmail.com>
Diff between smcryptoR versions 0.1.1 dated 2024-02-26 and 0.1.2 dated 2024-03-18
DESCRIPTION | 6 +- MD5 | 23 ++++---- NEWS |only build/vignette.rds |binary inst/AUTHORS | 8 -- inst/doc/intro.html | 26 ++++----- src/sm2.c | 20 +++---- src/sm4.c | 16 ++--- src/smcrypto/Cargo.lock | 52 ------------------- src/smcrypto/Cargo.toml | 10 +-- src/smcrypto/src/ffi.rs | 15 ++--- src/smcrypto/src/sm2.rs | 130 +++++++++++++++++++++--------------------------- src/smcrypto/src/sm3.rs | 2 13 files changed, 119 insertions(+), 189 deletions(-)
Title: Power and Sample Size for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used in bioequivalence studies. Use known.designs() to
see the designs supported. Power and sample size can be obtained based on
different methods, amongst them prominently the TOST procedure (two one-sided
t-tests). See README and NEWS for further information.
Author: Detlew Labes [aut, cre] ,
Helmut Schuetz [aut] ,
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.5-4 dated 2022-02-21 and 1.5-6 dated 2024-03-18
DESCRIPTION | 10 MD5 | 92 - NAMESPACE | 16 NEWS.md | 38 R/BE_CI.R | 18 R/pa.NTID.R | 6 R/power_RSABE_NTID.R | 6 R/power_TOST_sds.R | 14 R/pwrA_S3methods.R | 35 R/samplesize_RSABE_NTID.R | 4 R/scABEL.R | 5 README.md | 303 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ABE.R | 2 inst/doc/ABE.Rmd | 2 inst/doc/ABE.html | 1685 +++++++++++++++++++++-------------- inst/doc/DP.R | 2 inst/doc/DP.html | 519 ++++++---- inst/doc/Expected_Power_for_TOST.pdf |binary inst/doc/NI.R | 2 inst/doc/NI.Rmd | 2 inst/doc/NI.html | 458 +++++---- inst/doc/PA.R | 2 inst/doc/PA.html | 576 +++++++---- inst/doc/RSABE.Rmd | 18 inst/doc/RSABE.html | 1453 +++++++++++++++++------------- inst/doc/vignette.R | 2 inst/doc/vignette.html | 474 +++++++-- man/CI.RatioF.Rd | 2 man/CVpooled.Rd | 2 man/defunct.Rd | 21 man/deprecated.Rd | 4 man/pa.NTID.Rd | 2 man/power.2TOST.Rd | 2 man/power.NTID.Rd | 2 man/power.RatioF.Rd | 2 man/power.TOST.sds.Rd | 14 man/power.noninf.Rd | 2 man/sampleN.2TOST.Rd | 4 man/sampleN.NTID.Rd | 2 man/sampleN.RatioF.Rd | 2 man/scABEL.ad.Rd | 5 vignettes/ABE.Rmd | 2 vignettes/NI.Rmd | 2 vignettes/RSABE.Rmd | 18 vignettes/RSABE.Rmd.orig | 14 47 files changed, 3509 insertions(+), 2337 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.7.12 dated 2024-02-06 and 0.8.0 dated 2024-03-18
DESCRIPTION | 10 - MD5 | 202 +++++++++++++++++------------------ NAMESPACE | 2 NEWS.md | 11 + R/tar_age.R | 6 - R/tar_change.R | 17 +- R/tar_combine.R | 6 - R/tar_combine_raw.R | 12 +- R/tar_download.R | 9 + R/tar_file_read.R | 9 + R/tar_files.R | 6 - R/tar_files_input.R | 6 - R/tar_files_input_raw.R | 9 + R/tar_files_raw.R | 9 + R/tar_force.R | 6 - R/tar_formats.R | 6 - R/tar_group_by.R | 6 - R/tar_group_count.R | 6 - R/tar_group_select.R | 6 - R/tar_group_size.R | 6 - R/tar_knit.R | 47 ++++++-- R/tar_knit_raw.R | 23 +++ R/tar_map.R | 46 ++++++- R/tar_map2.R | 8 + R/tar_map2_count.R | 8 + R/tar_map2_count_raw.R | 8 + R/tar_map2_raw.R | 17 ++ R/tar_map2_size.R | 8 + R/tar_map2_size_raw.R | 8 + R/tar_map_rep.R | 8 + R/tar_map_rep_raw.R | 24 +++- R/tar_package.R | 4 R/tar_quarto.R | 10 + R/tar_quarto_raw.R | 27 +++- R/tar_quarto_rep.R | 10 + R/tar_quarto_rep_raw.R | 30 +++-- R/tar_render.R | 35 +++++- R/tar_render_raw.R | 30 +++-- R/tar_render_rep.R | 4 R/tar_render_rep_raw.R | 36 ++++-- R/tar_rep.R | 6 - R/tar_rep2.R | 6 - R/tar_rep2_raw.R | 6 - R/tar_rep_map.R | 3 R/tar_rep_map_raw.R | 3 R/tar_rep_raw.R | 21 ++- R/tar_skip.R | 6 - R/utils_targets.R | 3 inst/WORDLIST | 1 man/tar_age.Rd | 12 +- man/tar_change.Rd | 12 +- man/tar_combine.Rd | 12 +- man/tar_combine_raw.Rd | 12 +- man/tar_download.Rd | 12 +- man/tar_file_read.Rd | 12 +- man/tar_files.Rd | 12 +- man/tar_files_input.Rd | 12 +- man/tar_files_input_raw.Rd | 12 +- man/tar_files_raw.Rd | 12 +- man/tar_force.Rd | 12 +- man/tar_formats.Rd | 75 +++++++++--- man/tar_group_by.Rd | 12 +- man/tar_group_count.Rd | 12 +- man/tar_group_select.Rd | 12 +- man/tar_group_size.Rd | 12 +- man/tar_knit.Rd | 25 ++++ man/tar_knit_raw.Rd | 25 ++++ man/tar_knit_run.Rd | 16 ++ man/tar_map.Rd | 17 ++ man/tar_map2.Rd | 18 ++- man/tar_map2_count.Rd | 18 ++- man/tar_map2_count_raw.Rd | 18 ++- man/tar_map2_raw.Rd | 18 ++- man/tar_map2_size.Rd | 18 ++- man/tar_map2_size_raw.Rd | 18 ++- man/tar_map_rep.Rd | 18 ++- man/tar_map_rep_raw.Rd | 18 ++- man/tar_quarto.Rd | 29 ++++- man/tar_quarto_raw.Rd | 29 ++++- man/tar_quarto_rep.Rd | 29 ++++- man/tar_quarto_rep_raw.Rd | 29 ++++- man/tar_render.Rd | 25 ++++ man/tar_render_raw.Rd | 25 ++++ man/tar_render_rep.Rd | 22 +++ man/tar_render_rep_raw.Rd | 22 +++ man/tar_rep.Rd | 12 +- man/tar_rep2.Rd | 12 +- man/tar_rep2_raw.Rd | 12 +- man/tar_rep_map.Rd | 12 +- man/tar_rep_map_raw.Rd | 12 +- man/tar_rep_raw.Rd | 12 +- man/tar_skip.Rd | 12 +- tests/testthat/test-tar_knit.R | 43 +++++++ tests/testthat/test-tar_knit_raw.R | 43 +++++++ tests/testthat/test-tar_map.R | 90 +++++++++++++++ tests/testthat/test-tar_map_rep.R | 13 ++ tests/testthat/test-tar_quarto.R | 42 +++++++ tests/testthat/test-tar_quarto_rep.R | 45 +++++++ tests/testthat/test-tar_render.R | 43 +++++++ tests/testthat/test-tar_render_raw.R | 43 +++++++ tests/testthat/test-tar_render_rep.R | 45 +++++++ tests/testthat/test-tar_rep.R | 17 ++ 102 files changed, 1680 insertions(+), 316 deletions(-)
Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] ,
Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>
Diff between hyperbolicDEA versions 0.1.1 dated 2024-02-22 and 1.0.0 dated 2024-03-18
DESCRIPTION | 6 MD5 | 26 +-- NAMESPACE | 1 R/check_arguments.R |only R/costDEA.R | 27 +-- R/hyperbolicDEA.R | 273 +++++++++++++----------------------- R/lprofitDEA.R | 37 ++-- R/nlprofitDEA.R | 41 +++-- R/slack.R |only R/wrDEA.R |only man/costDEA.Rd | 24 +-- man/hyperbolicDEA.Rd | 52 +++++- man/lprofitDEA.Rd | 27 +-- man/nlprofitDEA.Rd | 31 ++-- man/wrDEA.Rd |only tests/testthat/test-hyperbolicDEA.R | 165 +++++++++++++++++++-- 16 files changed, 411 insertions(+), 299 deletions(-)
Title: Multivariate Profile Analysis
Description: R functions for criterion profile analysis, Davison and Davenport (2002) <doi:10.1037/1082-989X.7.4.468> and meta-analytic criterion profile analysis, Wiernik, Wilmot, Davison, and Ones (2020) <doi:10.1037/met0000305>. Sensitivity analyses to aid in interpreting criterion profile analysis results are also included.
Author: Brenton M. Wiernik [aut, cre]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between configural versions 0.1.4 dated 2021-01-18 and 0.1.5 dated 2024-03-18
configural-0.1.4/configural/NEWS |only configural-0.1.4/configural/man/configural_news.Rd |only configural-0.1.5/configural/DESCRIPTION | 10 configural-0.1.5/configural/MD5 | 80 configural-0.1.5/configural/NAMESPACE | 79 configural-0.1.5/configural/NEWS.md |only configural-0.1.5/configural/R/configural.R | 18 configural-0.1.5/configural/R/cpa_mat.R | 767 ++++----- configural-0.1.5/configural/R/data_doc.R | 487 +++-- configural-0.1.5/configural/R/fungible.R | 800 ++++----- configural-0.1.5/configural/R/utility.R | 1324 ++++++++-------- configural-0.1.5/configural/R/var_error_cpa.R | 623 +++---- configural-0.1.5/configural/R/zzz.R | 80 configural-0.1.5/configural/README.md | 4 configural-0.1.5/configural/build/partial.rdb |binary configural-0.1.5/configural/inst/CITATION | 56 configural-0.1.5/configural/man/adjust_Rsq.Rd | 64 configural-0.1.5/configural/man/complete_matrix.Rd |only configural-0.1.5/configural/man/configural-package.Rd | 50 configural-0.1.5/configural/man/cor_covariance.Rd | 62 configural-0.1.5/configural/man/cor_covariance_meta.Rd | 112 - configural-0.1.5/configural/man/cor_labels.Rd | 42 configural-0.1.5/configural/man/cpa_mat.Rd | 126 - configural-0.1.5/configural/man/disorders.Rd | 70 configural-0.1.5/configural/man/dot-fungible_extrema.Rd | 78 configural-0.1.5/configural/man/fungible.Rd | 116 - configural-0.1.5/configural/man/fungible.cpa.Rd | 102 - configural-0.1.5/configural/man/fungible.lm.Rd | 90 - configural-0.1.5/configural/man/grapes-and-grapes.Rd | 46 configural-0.1.5/configural/man/gre.Rd | 78 configural-0.1.5/configural/man/harmonic_mean.Rd | 56 configural-0.1.5/configural/man/hrm.Rd | 70 configural-0.1.5/configural/man/jobchar.Rd | 81 configural-0.1.5/configural/man/mindfulness.Rd | 78 configural-0.1.5/configural/man/n_effective_R2.Rd | 80 configural-0.1.5/configural/man/prejudice.Rd | 60 configural-0.1.5/configural/man/team.Rd | 74 configural-0.1.5/configural/man/transition.Rd | 54 configural-0.1.5/configural/man/var_error_cpa.Rd | 70 configural-0.1.5/configural/man/vech.Rd | 88 - configural-0.1.5/configural/man/vech2full.Rd | 80 configural-0.1.5/configural/man/wt_cov.Rd | 108 - configural-0.1.5/configural/man/wt_dist.Rd | 116 - 43 files changed, 3219 insertions(+), 3160 deletions(-)
Title: Estimate Migratory Connectivity for Migratory Animals
Description: Allows the user to estimate transition probabilities for
migratory animals between any two phases of the annual cycle, using a
variety of different data types. Also quantifies the strength of
migratory connectivity (MC), a standardized metric to quantify the
extent to which populations co-occur between two phases of the annual
cycle. Includes functions to estimate MC and the more traditional
metric of migratory connectivity strength (Mantel correlation)
incorporating uncertainty from multiple sources of sampling error. For
cross-species comparisons, methods are provided to estimate
differences in migratory connectivity strength, incorporating
uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>,
Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al.
(2023) <doi:10.1002/eap.2788> for details on some of these methods.
Author: Jeffrey A. Hostetler [cre, aut],
Michael T. Hallworth [aut],
Clark S. Rushing [ctb],
Emily B. Cohen [ctb],
Valentine Herrmann [ctb]
Maintainer: Jeffrey A. Hostetler <jhostetler@usgs.gov>
Diff between MigConnectivity versions 0.4.5 dated 2024-01-16 and 0.4.6 dated 2024-03-18
DESCRIPTION | 25 ++++++++------- MD5 | 18 +++++------ R/estConnectivity.R | 61 ++++++++++++++++++++++++++++++++++++--- R/simConnectivity.R | 6 +-- README.md | 16 ++-------- inst/NEWS.md | 6 +++ inst/doc/MigConnectivity.html | 4 +- inst/doc/olderFunctionality.html | 46 ++++++++++++++--------------- inst/doc/simulateIsoMC.html | 4 +- man/simTelemetryData.Rd | 6 +-- 10 files changed, 122 insertions(+), 70 deletions(-)
More information about MigConnectivity at CRAN
Permanent link
Title: Estimating Public and Private Sector Contraceptive Market Supply
Shares
Description: Family Planning programs and initiatives typically use nationally representative surveys to estimate key indicators of a country’s family planning progress. However, in recent years, routinely collected family planning services data (Service Statistics) have been used as a supplementary data source to bridge gaps in the surveys. The use of service statistics comes with the caveat that adjustments need to be made for missing private sector contributions to the contraceptive method supply chain. Evaluating the supply source of modern contraceptives often relies on Demographic Health Surveys (DHS), where many countries do not have recent data beyond 2015/16. Fortunately, in the absence of recent surveys we can rely on statistical model-based estimates and projections to fill the knowledge gap. We present a Bayesian, hierarchical, penalized-spline model with multivariate-normal spline coefficients, to account for across method correlations, to produce country-specific,annual estimates for [...truncated...]
Author: Hannah Comiskey [aut, cre],
Niamh Cahill [aut],
Leontine Alkema [aut]
Maintainer: Hannah Comiskey <hannah.comiskey.2015@mumail.ie>
Diff between mcmsupply versions 1.0.1 dated 2024-03-12 and 1.1.1 dated 2024-03-18
mcmsupply-1.0.1/mcmsupply/inst/data-raw/my_custom_data_bad.xlsx |only mcmsupply-1.0.1/mcmsupply/inst/data-raw/my_custom_data_good.xlsx |only mcmsupply-1.1.1/mcmsupply/DESCRIPTION | 6 mcmsupply-1.1.1/mcmsupply/MD5 | 103 +++--- mcmsupply-1.1.1/mcmsupply/NEWS.md | 11 mcmsupply-1.1.1/mcmsupply/R/get_data.R | 3 mcmsupply-1.1.1/mcmsupply/R/get_modelinputs.R | 5 mcmsupply-1.1.1/mcmsupply/R/internal_functions.R | 158 +++++----- mcmsupply-1.1.1/mcmsupply/R/national_FPsource_VARCOV_bivarlogitnormal.R | 2 mcmsupply-1.1.1/mcmsupply/R/national_FPsource_data.R | 2 mcmsupply-1.1.1/mcmsupply/R/national_theta_rms_hat_bivarlogitnormal.R | 2 mcmsupply-1.1.1/mcmsupply/R/national_varcov_order_bivarlogitnormal.R | 2 mcmsupply-1.1.1/mcmsupply/data/national_FPsource_VARCOV_bivarlogitnormal.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_FPsource_data.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_FPsource_format.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_inv_sigma_delta_hat_bivarlogitnorm.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_tau_alpha_cms_hat_bivarlogitnorm.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_theta_rms_hat_bivarlogitnorm.rda |binary mcmsupply-1.1.1/mcmsupply/data/national_varcov_order_bivarlogitnormal.rda |binary mcmsupply-1.1.1/mcmsupply/inst/data-raw/my_custom_national_data_good.xlsx |binary mcmsupply-1.1.1/mcmsupply/inst/data-raw/my_custom_subnational_data_bad.xlsx |only mcmsupply-1.1.1/mcmsupply/inst/data-raw/my_custom_subnational_data_good.xlsx |only mcmsupply-1.1.1/mcmsupply/inst/data-raw/mycovvar_array.RDS |only mcmsupply-1.1.1/mcmsupply/inst/data-raw/national_FPsource_format_check.R | 71 +++- mcmsupply-1.1.1/mcmsupply/inst/doc/national_multicountry_mod.R | 5 mcmsupply-1.1.1/mcmsupply/inst/doc/national_multicountry_mod.Rmd | 11 mcmsupply-1.1.1/mcmsupply/inst/doc/national_multicountry_mod.html | 15 mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_customdata_models.R | 14 mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_customdata_models.Rmd | 24 + mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_customdata_models.html | 43 ++ mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_mod.R | 7 mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_mod.Rmd | 13 mcmsupply-1.1.1/mcmsupply/inst/doc/national_singlecountry_mod.html | 23 + mcmsupply-1.1.1/mcmsupply/inst/doc/package_data.html | 60 ++- mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_multicountry_models.R | 3 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_multicountry_models.Rmd | 5 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_multicountry_models.html | 9 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_customdata_models.R | 4 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_customdata_models.Rmd | 4 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_customdata_models.html | 4 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_models.R | 8 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_models.Rmd | 8 mcmsupply-1.1.1/mcmsupply/inst/doc/subnational_singlecountry_models.html | 11 mcmsupply-1.1.1/mcmsupply/man/get_data.Rd | 3 mcmsupply-1.1.1/mcmsupply/man/get_subnational_modelinputs.Rd | 10 mcmsupply-1.1.1/mcmsupply/man/national_FPsource_VARCOV_bivarlogitnormal.Rd | 2 mcmsupply-1.1.1/mcmsupply/man/national_FPsource_data.Rd | 2 mcmsupply-1.1.1/mcmsupply/man/national_theta_rms_hat_bivarlogitnorm.Rd | 2 mcmsupply-1.1.1/mcmsupply/man/national_varcov_order_bivarlogitnormal.Rd | 2 mcmsupply-1.1.1/mcmsupply/vignettes/national_multicountry_mod.Rmd | 11 mcmsupply-1.1.1/mcmsupply/vignettes/national_singlecountry_customdata_models.Rmd | 24 + mcmsupply-1.1.1/mcmsupply/vignettes/national_singlecountry_mod.Rmd | 13 mcmsupply-1.1.1/mcmsupply/vignettes/subnational_multicountry_models.Rmd | 5 mcmsupply-1.1.1/mcmsupply/vignettes/subnational_singlecountry_customdata_models.Rmd | 4 mcmsupply-1.1.1/mcmsupply/vignettes/subnational_singlecountry_models.Rmd | 8 55 files changed, 466 insertions(+), 256 deletions(-)
Title: Quantify the Robustness of Causal Inferences
Description: Statistical methods that quantify the conditions necessary to
alter inferences, also known as sensitivity analysis, are becoming
increasingly important to a variety of quantitative sciences. A series
of recent works, including Frank (2000)
<doi:10.1177/0049124100029002001> and Frank et al. (2013)
<doi:10.3102/0162373713493129> extend previous sensitivity analyses by
considering the characteristics of omitted variables or unobserved
cases that would change an inference if such variables or cases were
observed. These analyses generate statements such as "an omitted
variable would have to be correlated at xx with the predictor of
interest (e.g., treatment) and outcome to invalidate an inference of a
treatment effect". Or "one would have to replace pp percent of the
observed data with null hypothesis cases to invalidate the inference".
We implement these recent developments of sensitivity analysis and
provide modules to calculate these two robustness indices and generate
such [...truncated...]
Author: Joshua M Rosenberg [aut, cre],
Ran Xu [ctb],
Qinyun Lin [ctb],
Spiro Maroulis [ctb],
Sarah Narvaiz [ctb],
Kenneth A Frank [ctb],
Wei Wang [ctb]
Maintainer: Joshua M Rosenberg <jmrosen48@gmail.com>
Diff between konfound versions 0.4.0 dated 2021-06-01 and 0.5.0 dated 2024-03-18
konfound-0.4.0/konfound/man/launch_shiny.Rd |only konfound-0.4.0/konfound/man/summary.konfound.Rd |only konfound-0.5.0/konfound/DESCRIPTION | 78 konfound-0.5.0/konfound/LICENSE | 4 konfound-0.5.0/konfound/MD5 | 102 - konfound-0.5.0/konfound/NAMESPACE | 62 konfound-0.5.0/konfound/NEWS.md | 7 konfound-0.5.0/konfound/R/concord1.R | 6 konfound-0.5.0/konfound/R/cop_pse_auxiliary.R |only konfound-0.5.0/konfound/R/core-sensitivity-mkonfound.R |only konfound-0.5.0/konfound/R/helper_output_dataframe.R | 26 konfound-0.5.0/konfound/R/helper_output_print.R | 228 +- konfound-0.5.0/konfound/R/helper_output_table.R | 36 konfound-0.5.0/konfound/R/helper_plot_correlation.R | 139 + konfound-0.5.0/konfound/R/helper_plot_threshold.R | 32 konfound-0.5.0/konfound/R/konfound-glm-dichotomous.R | 26 konfound-0.5.0/konfound/R/konfound-glm.R | 85 konfound-0.5.0/konfound/R/konfound-lm.R | 79 konfound-0.5.0/konfound/R/konfound-lmer.R | 89 konfound-0.5.0/konfound/R/konfound.R | 94 konfound-0.5.0/konfound/R/mkonfound-data.R | 5 konfound-0.5.0/konfound/R/mkonfound.R | 91 konfound-0.5.0/konfound/R/nonlinear_auxiliary.R | 77 konfound-0.5.0/konfound/R/pkonfound.R | 96 konfound-0.5.0/konfound/R/test_cop.R |only konfound-0.5.0/konfound/R/test_pse.R |only konfound-0.5.0/konfound/R/test_sensitivity.R | 201 -- konfound-0.5.0/konfound/R/test_sensitivity_ln.R | 596 +++-- konfound-0.5.0/konfound/R/tkonfound.R | 511 ++--- konfound-0.5.0/konfound/R/tkonfound_fig.R |only konfound-0.5.0/konfound/R/zzz.R | 30 konfound-0.5.0/konfound/README.md | 124 - konfound-0.5.0/konfound/build/vignette.rds |binary konfound-0.5.0/konfound/inst/doc/introduction-to-konfound.R | 53 konfound-0.5.0/konfound/inst/doc/introduction-to-konfound.Rmd | 76 konfound-0.5.0/konfound/inst/doc/introduction-to-konfound.html | 995 ++++++---- konfound-0.5.0/konfound/man/cal_delta_star.Rd |only konfound-0.5.0/konfound/man/cal_rxy.Rd |only konfound-0.5.0/konfound/man/cal_rxz.Rd |only konfound-0.5.0/konfound/man/cal_ryz.Rd |only konfound-0.5.0/konfound/man/chisq_p.Rd |only konfound-0.5.0/konfound/man/concord1.Rd | 4 konfound-0.5.0/konfound/man/get_kr_df.Rd |only konfound-0.5.0/konfound/man/konfound.Rd | 38 konfound-0.5.0/konfound/man/konfound_glm.Rd |only konfound-0.5.0/konfound/man/konfound_glm_dichotomous.Rd |only konfound-0.5.0/konfound/man/konfound_lm.Rd |only konfound-0.5.0/konfound/man/konfound_lmer.Rd |only konfound-0.5.0/konfound/man/mkonfound.Rd | 24 konfound-0.5.0/konfound/man/mkonfound_ex.Rd | 3 konfound-0.5.0/konfound/man/output_df.Rd |only konfound-0.5.0/konfound/man/output_print.Rd |only konfound-0.5.0/konfound/man/output_table.Rd |only konfound-0.5.0/konfound/man/pkonfound.Rd | 35 konfound-0.5.0/konfound/man/plot_correlation.Rd |only konfound-0.5.0/konfound/man/plot_threshold.Rd |only konfound-0.5.0/konfound/man/tkonfound.Rd |only konfound-0.5.0/konfound/man/tkonfound_fig.Rd |only konfound-0.5.0/konfound/man/verify_reg_Gzcv.Rd |only konfound-0.5.0/konfound/man/verify_reg_uncond.Rd |only konfound-0.5.0/konfound/man/zzz.Rd |only konfound-0.5.0/konfound/tests/testthat/test-konfound.R | 61 konfound-0.5.0/konfound/tests/testthat/test-mkonfound.r | 21 konfound-0.5.0/konfound/tests/testthat/test-pkonfound.R | 196 + konfound-0.5.0/konfound/tests/testthat/test-tkonfound.R |only konfound-0.5.0/konfound/vignettes/introduction-to-konfound.Rmd | 76 66 files changed, 2611 insertions(+), 1795 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-28 1.1
2022-09-19 1.0
2022-06-14 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-17 0.2.7
Title: Coordinated Networks Detection on Social Media
Description: Detects a variety of coordinated actions on social media and outputs the network of coordinated users along with related information.
Author: Nicola Righetti [aut, cre] ,
Paul Balluff [aut]
Maintainer: Nicola Righetti <nicola.righetti@univie.ac.at>
Diff between CooRTweet versions 2.0.0 dated 2024-01-15 and 2.0.1 dated 2024-03-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- R/generate_coordinated_network.R | 5 +++++ inst/doc/vignette.html | 2 +- 5 files changed, 19 insertions(+), 10 deletions(-)
Title: The Maraca Plot: Visualization of Hierarchical Composite
Endpoints in Clinical Trials
Description: Library that supports visual interpretation of hierarchical composite
endpoints (HCEs). HCEs are complex constructs used as primary endpoints in
clinical trials, combining outcomes of different types into ordinal endpoints,
in which each patient contributes the most clinically important event (one and
only one) to the analysis. See Karpefors M et al. (2022)
<doi:10.1177/17407745221134949>.
Author: Martin Karpefors [aut] ,
Samvel B. Gasparyan [aut] ,
Stefano Borini [ctb],
Monika Huhn [aut, cre]
Maintainer: Monika Huhn <monika.huhn@astrazeneca.com>
Diff between maraca versions 0.6 dated 2023-10-24 and 0.7 dated 2024-03-18
DESCRIPTION | 31 + MD5 | 83 ++--- NAMESPACE | 5 NEWS.md | 32 + R/aaa.R | 13 R/general.R | 1 R/internal.R | 542 ++++++++++++++++++++------------ R/internal_validation.R |only R/internal_winOdds.R |only R/maraca.R | 695 ++++++++++++++++++++++++++++++------------ R/themes.R | 6 R/winOddsPlots.R | 224 ++++++++++++- build/vignette.rds |binary inst/doc/faq.R | 97 +++++ inst/doc/faq.Rmd | 129 +++++++ inst/doc/faq.html | 113 ++++++ inst/doc/maraca.R | 15 inst/doc/maraca.Rmd | 30 + inst/doc/maraca.html | 31 + inst/doc/otherEndpoints.R |only inst/doc/otherEndpoints.Rmd |only inst/doc/otherEndpoints.html |only inst/doc/themes.R | 4 inst/doc/themes.Rmd | 4 inst/doc/themes.html | 26 - inst/doc/validation.R | 4 inst/doc/validation.Rmd | 23 - inst/doc/validation.html | 92 ++--- inst/doc/winOdds.R | 43 ++ inst/doc/winOdds.Rmd | 278 ++++++++++------ inst/doc/winOdds.html | 68 +++- man/component_plot.hce.Rd | 24 + man/component_plot.maraca.Rd | 4 man/cumulative_plot.Rd |only man/cumulative_plot.hce.Rd |only man/cumulative_plot.maraca.Rd |only man/maraca.Rd | 58 ++- man/plot.hce.Rd | 75 +++- man/plot.maraca.Rd | 23 - man/plot_maraca.Rd | 25 - man/validate_maraca_plot.Rd | 4 vignettes/faq.Rmd | 129 +++++++ vignettes/maraca.Rmd | 30 + vignettes/otherEndpoints.Rmd |only vignettes/themes.Rmd | 4 vignettes/validation.Rmd | 23 - vignettes/winOdds.Rmd | 278 ++++++++++------ 47 files changed, 2420 insertions(+), 846 deletions(-)
Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Description: An interface to 'DifferentialEquations.jl' <https://diffeq.sciml.ai/dev/> from the R programming language.
It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE),
delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality,
including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods.
Supports GPUs, with support for CUDA (NVIDIA), AMD GPUs, Intel oneAPI GPUs, and Apple's Metal (M-series chip GPUs).
'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users. For more information,
see Rackauckas and Nie (2017) <doi:10.5334/jors.151>.
Author: Christopher Rackauckas [aut, cre, cph]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>
Diff between diffeqr versions 2.0.0 dated 2023-10-20 and 2.0.1 dated 2024-03-18
DESCRIPTION | 6 MD5 | 34 - NEWS.md | 74 +- R/diffeqr.R | 391 +++++++------- README.md | 1405 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary inst/doc/dae.R | 12 inst/doc/dae.html | 830 +++++++++++++++---------------- inst/doc/dde.R | 12 inst/doc/dde.html | 804 +++++++++++++++--------------- inst/doc/gpu.R | 12 inst/doc/gpu.Rmd | 500 +++++++++--------- inst/doc/gpu.html | 1064 ++++++++++++++++++++-------------------- inst/doc/ode.R | 12 inst/doc/ode.html | 1036 +++++++++++++++++++-------------------- inst/doc/sde.R | 12 inst/doc/sde.html | 950 +++++++++++++++++------------------ vignettes/gpu.Rmd | 500 +++++++++--------- 18 files changed, 3834 insertions(+), 3820 deletions(-)
Title: Simulation of Populations by Sampling Waiting-Time Distributions
Description: Constructs a virtual population from fertility and mortality rates for any country,
calendar year and birth cohort in the Human Mortality Database <https://www.mortality.org> and the Human Fertility Database <https://www.humanfertility.org>. Fertility histories are simulated for every individual and their offspring, producing a multi-generation virtual population.
Author: Frans Willekens [aut, cre] ,
Tim Riffe [ctb]
Maintainer: Frans Willekens <willekens@nidi.nl>
Diff between VirtualPop versions 1.0.2 dated 2022-06-23 and 2.0.2 dated 2024-03-18
VirtualPop-1.0.2/VirtualPop/R/Partnership.R |only VirtualPop-1.0.2/VirtualPop/data/dataLH.rda |only VirtualPop-1.0.2/VirtualPop/data/dpopus.rda |only VirtualPop-1.0.2/VirtualPop/inst/doc/Validation.R |only VirtualPop-1.0.2/VirtualPop/inst/doc/Validation.Rmd |only VirtualPop-1.0.2/VirtualPop/inst/doc/Validation.html |only VirtualPop-1.0.2/VirtualPop/man/Partnership.Rd |only VirtualPop-1.0.2/VirtualPop/man/dataLH.Rd |only VirtualPop-1.0.2/VirtualPop/man/dpopus.Rd |only VirtualPop-1.0.2/VirtualPop/vignettes/Validation.Rmd |only VirtualPop-1.0.2/VirtualPop/vignettes/demography.csl |only VirtualPop-1.0.2/VirtualPop/vignettes/table1.png |only VirtualPop-2.0.2/VirtualPop/DESCRIPTION | 20 VirtualPop-2.0.2/VirtualPop/MD5 | 101 VirtualPop-2.0.2/VirtualPop/NAMESPACE | 24 VirtualPop-2.0.2/VirtualPop/NEWS.md | 38 VirtualPop-2.0.2/VirtualPop/R/BuildViP.R |only VirtualPop-2.0.2/VirtualPop/R/Children.R | 162 VirtualPop-2.0.2/VirtualPop/R/GetData.R | 52 VirtualPop-2.0.2/VirtualPop/R/GetGenerations.R | 189 VirtualPop-2.0.2/VirtualPop/R/GetRates.R | 88 VirtualPop-2.0.2/VirtualPop/R/GetRatesC.R |only VirtualPop-2.0.2/VirtualPop/R/H_pw.R | 23 VirtualPop-2.0.2/VirtualPop/R/Lifespan.R | 66 VirtualPop-2.0.2/VirtualPop/R/PartnerSearch.R |only VirtualPop-2.0.2/VirtualPop/R/Sim_bio.R | 24 VirtualPop-2.0.2/VirtualPop/R/VirtualPop-package.R | 132 VirtualPop-2.0.2/VirtualPop/R/e0.R |only VirtualPop-2.0.2/VirtualPop/R/pw_root.R | 20 VirtualPop-2.0.2/VirtualPop/R/r.pw_exp.R | 23 VirtualPop-2.0.2/VirtualPop/build/vignette.rds |binary VirtualPop-2.0.2/VirtualPop/data/dLH.rda |only VirtualPop-2.0.2/VirtualPop/data/rates.rda |binary VirtualPop-2.0.2/VirtualPop/data/ratesC.rda |only VirtualPop-2.0.2/VirtualPop/inst/doc/MultistateLH.R | 97 VirtualPop-2.0.2/VirtualPop/inst/doc/MultistateLH.Rmd | 348 - VirtualPop-2.0.2/VirtualPop/inst/doc/MultistateLH.html | 2880 +--------- VirtualPop-2.0.2/VirtualPop/inst/doc/Piecewise_exponential.R | 200 VirtualPop-2.0.2/VirtualPop/inst/doc/Piecewise_exponential.Rmd | 368 - VirtualPop-2.0.2/VirtualPop/inst/doc/Piecewise_exponential.html | 2521 +------- VirtualPop-2.0.2/VirtualPop/inst/doc/Tutorial.R | 396 + VirtualPop-2.0.2/VirtualPop/inst/doc/Tutorial.Rmd | 839 ++ VirtualPop-2.0.2/VirtualPop/inst/doc/Tutorial.html | 2844 ++------- VirtualPop-2.0.2/VirtualPop/inst/doc/Validation.pdf |only VirtualPop-2.0.2/VirtualPop/man/BuildViP.Rd |only VirtualPop-2.0.2/VirtualPop/man/Children.Rd | 32 VirtualPop-2.0.2/VirtualPop/man/GetData.Rd | 25 VirtualPop-2.0.2/VirtualPop/man/GetGenerations.Rd | 58 VirtualPop-2.0.2/VirtualPop/man/GetRates.Rd | 41 VirtualPop-2.0.2/VirtualPop/man/GetRatesC.Rd |only VirtualPop-2.0.2/VirtualPop/man/H_pw.Rd | 24 VirtualPop-2.0.2/VirtualPop/man/Lifespan.Rd | 26 VirtualPop-2.0.2/VirtualPop/man/PartnerSearch.Rd |only VirtualPop-2.0.2/VirtualPop/man/Sim_bio.Rd | 22 VirtualPop-2.0.2/VirtualPop/man/dLH.Rd |only VirtualPop-2.0.2/VirtualPop/man/e0.Rd |only VirtualPop-2.0.2/VirtualPop/man/pw_root.Rd | 21 VirtualPop-2.0.2/VirtualPop/man/r.pw_exp.Rd | 16 VirtualPop-2.0.2/VirtualPop/man/rates.Rd | 16 VirtualPop-2.0.2/VirtualPop/man/ratesC.Rd |only VirtualPop-2.0.2/VirtualPop/vignettes/MultistateLH.Rmd | 348 - VirtualPop-2.0.2/VirtualPop/vignettes/Piecewise_exponential.Rmd | 368 - VirtualPop-2.0.2/VirtualPop/vignettes/References.bib | 176 VirtualPop-2.0.2/VirtualPop/vignettes/Tutorial.Rmd | 839 ++ 64 files changed, 5118 insertions(+), 8349 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.2.0 dated 2024-03-06 and 0.3.0 dated 2024-03-18
DESCRIPTION | 6 MD5 | 36 +++-- NAMESPACE | 13 ++ NEWS.md | 11 + R/cpp11.R | 20 ++- R/extras.R | 19 ++ R/gcd.R | 2 R/nas.R | 45 ++++-- R/overview.R |only R/utils.R | 66 +++++++--- README.md | 191 +++++++++++++++++++++-------- man/cheapr-package.Rd | 48 +++---- man/extras.Rd | 5 man/gcd.Rd | 2 man/is_na.Rd | 46 +++++-- man/overview.Rd |only src/cpp11.cpp | 40 ++++-- src/nas.cpp | 266 ++++++++++++++++++++++------------------- src/utils.cpp | 80 ++++++++++-- tests/testthat/_snaps |only tests/testthat/test-overview.R |only 21 files changed, 601 insertions(+), 295 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Theresa Burkard [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.0.3 dated 2024-01-31 and 1.0.4 dated 2024-03-18
DESCRIPTION | 6 - MD5 | 50 ++++++------ NEWS.md | 4 R/checkDaysSupply.R | 2 R/checkDrugDose.R | 4 R/checkDrugSig.R | 2 R/checkVerbatimEndDate.R | 2 R/drugRecordChecks.R | 4 R/executeChecks.R | 34 ++++++-- R/getDrugRecords.R | 4 R/getDrugStrength.R | 4 R/histogram.R | 2 R/ingredientDescendantsInDb.R | 4 R/mockDrugExposure.R | 4 R/obscureCounts.R | 4 R/summariseChecks.R | 2 R/summariseQuantity.R | 2 R/utils.R | 4 inst/doc/IntroductionToDrugExposureDiagnostics.R | 27 ++---- inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 45 +++++------ inst/doc/IntroductionToDrugExposureDiagnostics.html | 81 ++++++++++++-------- inst/doc/SummaryOfChecks.html | 12 +- man/executeChecks.Rd | 8 + man/executeChecksSingleIngredient.Rd | 4 tests/testthat/test-Eunomia.R | 19 ++++ vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 45 +++++------ 26 files changed, 217 insertions(+), 162 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Bayesian Additive Models for Location, Scale, and Shape (and
Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework.
The distribution parameters may capture location, scale, shape, etc. and every parameter may depend
on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model.
The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019)
<doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021)
<doi:10.18637/jss.v100.i04>.
Author: Nikolaus Umlauf [aut, cre] ,
Nadja Klein [aut] ,
Achim Zeileis [aut] ,
Meike Koehler [ctb],
Thorsten Simon [aut] ,
Stanislaus Stadlmann [ctb],
Alexander Volkmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between bamlss versions 1.2-2 dated 2023-10-29 and 1.2-3 dated 2024-03-18
bamlss-1.2-2/bamlss/data/Austria.rda |only bamlss-1.2-2/bamlss/data/GEFCom2014.rda |only bamlss-1.2-2/bamlss/data/datalist |only bamlss-1.2-2/bamlss/man/Austria.Rd |only bamlss-1.2-2/bamlss/man/GEFCom2014.Rd |only bamlss-1.2-3/bamlss/DESCRIPTION | 8 bamlss-1.2-3/bamlss/MD5 | 81 bamlss-1.2-3/bamlss/NAMESPACE | 11 bamlss-1.2-3/bamlss/NEWS.md | 6 bamlss-1.2-3/bamlss/R/BAMLSS.R |19341 +++++++++++++----------------- bamlss-1.2-3/bamlss/R/BayesX.R | 2938 ++-- bamlss-1.2-3/bamlss/R/GAMart.R | 323 bamlss-1.2-3/bamlss/R/JAGS.R | 736 - bamlss-1.2-3/bamlss/R/JM.R | 8982 +++++-------- bamlss-1.2-3/bamlss/R/bnd.R | 9 bamlss-1.2-3/bamlss/R/data.R | 110 bamlss-1.2-3/bamlss/R/families.R | 9073 +++++--------- bamlss-1.2-3/bamlss/R/homstart.R | 465 bamlss-1.2-3/bamlss/R/imports.R | 444 bamlss-1.2-3/bamlss/R/maps.R | 833 - bamlss-1.2-3/bamlss/R/mvnchol.R |only bamlss-1.2-3/bamlss/R/optimizers.R |10790 +++++++--------- bamlss-1.2-3/bamlss/R/samplers.R | 2751 +--- bamlss-1.2-3/bamlss/R/sigmoid.R | 369 bamlss-1.2-3/bamlss/R/stabsel.R | 473 bamlss-1.2-3/bamlss/R/survival.R | 2417 +-- bamlss-1.2-3/bamlss/R/topmodels.R | 432 bamlss-1.2-3/bamlss/R/vis.R | 3561 ++--- bamlss-1.2-3/bamlss/build/partial.rdb |binary bamlss-1.2-3/bamlss/build/vignette.rds |binary bamlss-1.2-3/bamlss/data/Golf.rda |binary bamlss-1.2-3/bamlss/data/LondonFire.rda |binary bamlss-1.2-3/bamlss/data/TempIbk.rda |only bamlss-1.2-3/bamlss/data/fatalities.rda |binary bamlss-1.2-3/bamlss/data/simdata.rda |only bamlss-1.2-3/bamlss/inst/CITATION | 19 bamlss-1.2-3/bamlss/inst/doc/bamlss.R | 34 bamlss-1.2-3/bamlss/inst/doc/bamlss.html | 521 bamlss-1.2-3/bamlss/man/TempIbk.Rd |only bamlss-1.2-3/bamlss/man/bamlss.Rd | 4 bamlss-1.2-3/bamlss/man/dist_mvnchol.Rd |only bamlss-1.2-3/bamlss/man/make_formula.Rd |only bamlss-1.2-3/bamlss/man/mvn_chol.Rd |only bamlss-1.2-3/bamlss/man/mvn_modchol.Rd |only bamlss-1.2-3/bamlss/man/mvnchol_bamlss.Rd |only bamlss-1.2-3/bamlss/man/simdata.Rd |only bamlss-1.2-3/bamlss/src/bamlss_init.c | 18 bamlss-1.2-3/bamlss/src/mvnchol.c |only bamlss-1.2-3/bamlss/src/mvnmodchol.c |only bamlss-1.2-3/bamlss/vignettes/bamlss.bib | 9 50 files changed, 27841 insertions(+), 36917 deletions(-)
Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rolog versions 0.9.14 dated 2023-06-29 and 0.9.15 dated 2024-03-18
rolog-0.9.14/rolog/src/rolog.cpp |only rolog-0.9.15/rolog/.aspell |only rolog-0.9.15/rolog/DESCRIPTION | 14 +-- rolog-0.9.15/rolog/MD5 | 25 +++-- rolog-0.9.15/rolog/NAMESPACE | 3 rolog-0.9.15/rolog/NEWS.md | 4 rolog-0.9.15/rolog/R/plbase.R |only rolog-0.9.15/rolog/R/rolog.R | 140 ++++++++++++++++----------------- rolog-0.9.15/rolog/build/vignette.rds |binary rolog-0.9.15/rolog/inst/doc/rolog.R | 34 ++++---- rolog-0.9.15/rolog/inst/doc/rolog.Rmd | 24 ++--- rolog-0.9.15/rolog/inst/doc/rolog.html | 84 ++++++++----------- rolog-0.9.15/rolog/src/Makevars | 54 +----------- rolog-0.9.15/rolog/src/Makevars.win | 72 +--------------- rolog-0.9.15/rolog/src/crolog.cpp |only rolog-0.9.15/rolog/vignettes/rolog.Rmd | 24 ++--- 16 files changed, 186 insertions(+), 292 deletions(-)
Title: Flexible Identification of Phenotype-Specific Subpathways
Description: A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data
with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed
Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes
include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification
of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA,
and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific
abnormal subpathways in the cancer dataset with multi-phenotype samples.
Author: Xudong Han,
Junwei Han,
Qing Fei
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between psSubpathway versions 0.1.2 dated 2023-08-09 and 0.1.3 dated 2024-03-18
DESCRIPTION | 10 +- MD5 | 44 ++++----- NAMESPACE | 82 +++++++++--------- R/DCSAcs.R | 13 ++ R/SubSEA.R | 10 +- build/vignette.rds |binary inst/doc/vignette.html | 163 ++++++++++++++++++------------------ man/DCSA.Rd | 206 +++++++++++++++++++++++----------------------- man/FastSEAscore.Rd | 42 ++++----- man/ReadClsFile.Rd | 42 ++++----- man/SEAscore.Rd | 38 ++++---- man/SubSEA.Rd | 200 ++++++++++++++++++++++---------------------- man/compute_rank_score.Rd | 42 ++++----- man/getgenedensity.Rd | 42 ++++----- man/isPackageLoaded.Rd | 42 ++++----- man/ks_test_m.Rd | 42 ++++----- man/plotSpwACmap.Rd | 84 +++++++++--------- man/plotSpwNetmap.Rd | 186 ++++++++++++++++++++--------------------- man/plotSpwPSheatmap.Rd | 86 +++++++++---------- man/plotSubSEScurve.Rd | 90 ++++++++++---------- man/plotheatmap.Rd | 128 ++++++++++++++-------------- man/rndWalk.Rd | 42 ++++----- man/ssgsea.Rd | 46 +++++----- 23 files changed, 844 insertions(+), 836 deletions(-)
Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.3 dated 2024-01-11 and 1.4 dated 2024-03-18
DESCRIPTION | 24 ++--- MD5 | 60 +++++++++--- NAMESPACE | 39 +++++++- R/CoFAST.R |only R/RcppExports.R | 8 + R/main.R | 200 ++++++++++++++++++++++++++++++++++++++++--- README.md | 23 ++++ build/vignette.rds |binary data |only inst/doc/CosMx.R |only inst/doc/CosMx.Rmd |only inst/doc/CosMx.html |only inst/doc/FASTdlpfc.R |only inst/doc/FASTdlpfc.Rmd |only inst/doc/FASTdlpfc.html |only inst/doc/FASTdlpfc2.Rmd | 4 inst/doc/FASTdlpfc2.html | 45 +++++---- inst/doc/FASTsimu.html | 41 +++++--- inst/doc/pbmc3k.R |only inst/doc/pbmc3k.Rmd |only inst/doc/pbmc3k.html |only man/AddAdj.Rd |only man/CosMx_subset.Rd |only man/FAST_single.Rd |only man/NCFM.Rd |only man/NCFM_fast.Rd |only man/RunHarmonyLouvain.Rd | 4 man/RuniSCMEB.Rd | 4 man/coembed_plot.Rd |only man/coembedding_umap.Rd |only man/diagnostic.cor.eigs.Rd |only man/find.signature.genes.Rd |only man/get.top.signature.dat.Rd |only man/iscmeb_run.Rd | 4 man/model_set_FAST.Rd | 2 man/pbmc3k_subset.Rd |only man/pdistance.Rd |only man/top5_signatures.Rd |only src/RcppExports.cpp | 27 +++++ src/cofast_util.cpp |only vignettes/CosMx.Rmd |only vignettes/FASTdlpfc.Rmd |only vignettes/FASTdlpfc2.Rmd | 4 vignettes/pbmc3k.Rmd |only 44 files changed, 400 insertions(+), 89 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.21.5 dated 2024-02-07 and 0.21.6 dated 2024-03-18
DESCRIPTION | 19 - MD5 | 85 ++-- NAMESPACE | 1 NEWS.md | 30 + R/compare_parameters.R | 4 R/display.R | 8 R/equivalence_test.R | 4 R/format.R | 3 R/format_parameters.R | 14 R/methods_epi2x2.R | 1 R/methods_serp.R |only R/p_function.R | 34 + R/print.compare_parameters.R | 3 R/print.parameters_model.R | 26 - R/print_html.R | 27 + R/print_md.R | 161 ++++++++- R/print_table.R | 14 R/utils.R | 37 +- R/utils_format.R | 36 +- R/utils_model_parameters.R | 13 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 5 man/compare_parameters.Rd | 20 + man/display.parameters_model.Rd | 3 man/equivalence_test.lm.Rd | 2 man/model_parameters.Rd | 3 man/p_function.Rd | 29 + man/print.parameters_model.Rd | 3 tests/testthat/_snaps/compare_parameters.md | 124 +++++++ tests/testthat/_snaps/include_reference.md |only tests/testthat/_snaps/serp.md |only tests/testthat/test-compare_parameters.R | 326 ++++++++++++------- tests/testthat/test-format_parameters.R | 15 tests/testthat/test-helper.R |only tests/testthat/test-include_reference.R |only tests/testthat/test-marginaleffects.R | 8 tests/testthat/test-model_parameters.BFBayesFactor.R | 2 tests/testthat/test-model_parameters.aov.R | 38 +- tests/testthat/test-model_parameters.epi2x2.R |only tests/testthat/test-model_parameters_df.R | 12 tests/testthat/test-model_parameters_ordinal.R | 11 tests/testthat/test-p_calibrate.R | 14 tests/testthat/test-pipe.R | 4 tests/testthat/test-printing_reference_level.R | 23 + tests/testthat/test-random_effects_ci.R | 51 ++ tests/testthat/test-serp.R |only 47 files changed, 917 insertions(+), 296 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 0.10.2 dated 2023-08-09 and 1.0.0 dated 2024-03-18
DESCRIPTION | 16 MD5 | 72 NAMESPACE | 6 NEWS.md | 66 R/clintrials_gov_convert.R | 148 - R/clintrials_gov_upload.R | 5 R/dot_plot.R | 470 ++-- R/eudract_convert.R | 72 R/incidence_table.R | 100 R/relative_risk.R | 350 +-- README.md | 152 - build/vignette.rds |binary inst/doc/eudract.R | 116 - inst/doc/eudract.html | 1374 +++++------ inst/doc/standard_reporting.R |only inst/doc/standard_reporting.Rmd |only inst/doc/standard_reporting.html |only inst/extdata/ProtocolRecordSchema.xsd | 1452 ++++++------ man/clintrials_gov_convert.Rd | 134 - man/clintrials_gov_upload.Rd | 170 - man/dot_plot.Rd | 19 man/figures |only man/incidence_table.Rd | 66 man/plot.dot_plot.Rd |only man/print.dot_plot.Rd |only man/relative_risk.Rd | 14 tests/testthat/GROUP.csv | 8 tests/testthat/NONSERIOUS.csv | 164 - tests/testthat/SERIOUS.csv | 164 - tests/testthat/_snaps |only tests/testthat/bak_study_file.xml | 1806 +++++++++------ tests/testthat/events.csv | 3328 ++++++++++++++--------------- tests/testthat/simple.xml | 1886 ++++++++-------- tests/testthat/study_file.xml | 3680 +++++++++++++++++--------------- tests/testthat/table_ct.xml | 3666 +++++++++++++++++--------------- tests/testthat/table_eudract.xml | 3894 +++++++++++++++++----------------- tests/testthat/test_basic.R | 758 +++--- tests/testthat/test_dotplot.R |only tests/testthat/test_errors.R | 50 tests/testthat/test_relative_risk.R |only vignettes/standard_reporting.Rmd |only 41 files changed, 12797 insertions(+), 11409 deletions(-)
Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference
using a spectral analysis of Gaussian process priors.
Gaussian processes are represented with a Fourier series
based on cosine basis functions. Currently the package
includes parametric linear models, partial linear additive
models with/without shape restrictions, generalized linear
additive models with/without shape restrictions, and
density estimation model. To maximize computational
efficiency, the actual Markov chain Monte Carlo sampling
for each model is done using codes written in FORTRAN 90.
This software has been developed using funding supported by
Basic Science Research Program through the National Research
Foundation of Korea (NRF) funded by the Ministry of Education
(no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut, cre],
Taeryon Choi [aut],
Beomjo Park [aut, cre],
Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjop@gmail.com>
Diff between bsamGP versions 1.2.4 dated 2022-03-17 and 1.2.5 dated 2024-03-18
DESCRIPTION | 12 - MD5 | 8 - man/bsaqdpm.Rd | 442 ++++++++++++++++++++++++++++----------------------------- man/bsardpm.Rd | 424 +++++++++++++++++++++++++++--------------------------- man/plasma.Rd | 94 ++++++------ 5 files changed, 490 insertions(+), 490 deletions(-)
Title: Functions for Timing R Scripts, as Well as Implementations of
"Stack" and "StackList" Structures
Description: Code execution timing functions 'tic' and 'toc' that
can be nested. One can record all timings while a complex script is
running, and examine the values later. It is also possible to instrument
the timing calls with custom callbacks. In addition, this package provides
class 'Stack', implemented as a vector, and class 'StackList', which is a
stack implemented as a
list, both of which support operations 'push', 'pop', 'first_element',
'last_element' and 'clear'.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev <sizrailev@jabiruventures.com>
Diff between tictoc versions 1.2 dated 2023-04-23 and 1.2.1 dated 2024-03-18
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 2 ++ inst/tictoc_1.2.1.pdf |only tests/testthat/test-tictoc.R | 18 +++++++++++------- 5 files changed, 21 insertions(+), 14 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.7 dated 2024-01-21 and 0.1.8 dated 2024-03-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/getDrugSpw.R | 3 ++- inst/doc/vignette.html | 8 ++++---- man/getDrugSpw.Rd | 3 ++- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Nearest Neighbor Descent Method for Approximate Nearest
Neighbors
Description: The Nearest Neighbor Descent method for finding approximate
nearest neighbors by Dong and co-workers (2010)
<doi:10.1145/1963405.1963487>. Based on the 'Python' package
'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Author: James Melville [aut, cre, cph],
Vitalie Spinu [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between rnndescent versions 0.1.3 dated 2023-12-07 and 0.1.4 dated 2024-03-18
DESCRIPTION | 8 MD5 | 178 - NAMESPACE | 44 NEWS.md | 787 ++-- R/RcppExports.R | 374 +- R/corrections.R | 395 +- R/hubness.R | 164 R/internals.R | 942 ++--- R/rnndescent-package.R | 158 R/rnndescent.R | 5414 ++++++++++++++++---------------- R/rptree.R | 1460 ++++---- R/sparse.R | 164 R/util.R | 108 build/partial.rdb |binary build/vignette.rds |binary inst/doc/brute-force.R | 56 inst/doc/brute-force.Rmd | 108 inst/doc/brute-force.html | 824 ++-- inst/doc/hubness.R | 615 +-- inst/doc/hubness.Rmd | 1749 +++++----- inst/doc/hubness.html | 2319 ++++++------- inst/doc/metrics.R | 54 inst/doc/metrics.Rmd | 269 - inst/doc/metrics.html | 1052 +++--- inst/doc/nearest-neighbor-descent.R | 36 inst/doc/nearest-neighbor-descent.Rmd | 480 +- inst/doc/nearest-neighbor-descent.html | 1250 +++---- inst/doc/querying-data.R | 200 - inst/doc/querying-data.Rmd | 710 ++-- inst/doc/querying-data.html | 1472 ++++---- inst/doc/random-partition-forests.R | 124 inst/doc/random-partition-forests.Rmd | 616 +-- inst/doc/random-partition-forests.html | 1336 +++---- inst/doc/rnndescent.R | 118 inst/doc/rnndescent.Rmd | 372 +- inst/doc/rnndescent.html | 1160 +++--- inst/include/tdoann/distance.h | 2 inst/include/tdoann/nndcommon.h | 17 inst/include/tdoann/nndescent.h | 32 inst/include/tdoann/nndparallel.h | 31 inst/include/tdoann/prepare.h | 34 inst/include/tdoann/sparse.h | 2 man/brute_force_knn.Rd | 266 - man/brute_force_knn_query.Rd | 304 - man/graph_knn_query.Rd | 464 +- man/k_occur.Rd | 152 man/merge_knn.Rd | 130 man/neighbor_overlap.Rd | 106 man/nnd_knn.Rd | 532 +-- man/prepare_search_graph.Rd | 430 +- man/random_knn.Rd | 278 - man/random_knn_query.Rd | 302 - man/rnnd_build.Rd | 612 +-- man/rnnd_knn.Rd | 512 +-- man/rnnd_query.Rd | 214 - man/rnndescent-package.Rd | 208 - man/rpf_build.Rd | 360 +- man/rpf_filter.Rd | 134 man/rpf_knn.Rd | 412 +- man/rpf_knn_query.Rd | 200 - src/RcppExports.cpp | 27 src/rnn_nnd.cpp | 33 src/rnn_search.cpp | 2 tests/testthat/helper_data.R | 846 ++--- tests/testthat/helper_nncheck.R | 240 - tests/testthat/test_brute_force.R | 486 +- tests/testthat/test_correlation.R | 216 - tests/testthat/test_descent_bhamming.R | 140 tests/testthat/test_descent_cosine.R | 286 - tests/testthat/test_descent_euclidean.R | 763 ++-- tests/testthat/test_descent_hamming.R | 200 - tests/testthat/test_descent_manhattan.R | 94 tests/testthat/test_distance.R | 718 ++-- tests/testthat/test_idx_to_graph.R | 164 tests/testthat/test_koccurrences.R | 76 tests/testthat/test_merge.R | 430 +- tests/testthat/test_overlap.R | 54 tests/testthat/test_random_nbrs.R | 324 - tests/testthat/test_rnnd.R | 257 + tests/testthat/test_rptree.R | 1160 +++--- tests/testthat/test_search_prep.R | 686 ++-- tests/testthat/test_unload.R | 18 vignettes/bibliography.bibtex | 450 +- vignettes/brute-force.Rmd | 108 vignettes/hubness.Rmd | 1749 +++++----- vignettes/metrics.Rmd | 269 - vignettes/nearest-neighbor-descent.Rmd | 480 +- vignettes/querying-data.Rmd | 710 ++-- vignettes/random-partition-forests.Rmd | 616 +-- vignettes/rnndescent.Rmd | 372 +- 90 files changed, 21745 insertions(+), 21079 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre] ,
Joshua Cook [ctb],
Clara Jegousse [ctb],
Miaozhu Li [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 3.0.1 dated 2024-03-02 and 3.0.2 dated 2024-03-17
DESCRIPTION | 8 ++-- MD5 | 92 +++++++++++++++++++++++----------------------- NEWS.md | 7 +++ R/continuous-gsea.R | 5 +- R/continuous-material.R | 45 +++++++++++----------- R/discrete-aaas.R | 12 +++--- R/discrete-cosmic.R | 24 ++++++------ R/discrete-d3.R | 6 +-- R/discrete-flatui.R | 6 +-- R/discrete-frontiers.R | 12 +++--- R/discrete-futurama.R | 12 +++--- R/discrete-igv.R | 6 +-- R/discrete-jama.R | 16 ++++---- R/discrete-jco.R | 16 ++++---- R/discrete-lancet.R | 16 ++++---- R/discrete-locuszoom.R | 16 ++++---- R/discrete-nejm.R | 16 ++++---- R/discrete-npg.R | 16 ++++---- R/discrete-rickandmorty.R | 16 ++++---- R/discrete-simpsons.R | 16 ++++---- R/discrete-startrek.R | 16 ++++---- R/discrete-tron.R | 16 ++++---- R/discrete-uchicago.R | 6 +-- R/discrete-ucscgb.R | 16 ++++---- README.md | 4 +- build/vignette.rds |binary inst/doc/ggsci-faq.html | 2 - inst/doc/ggsci.Rmd | 12 +++--- inst/doc/ggsci.html | 69 +++++++++++++++++----------------- man/scale_aaas.Rd | 6 ++- man/scale_cosmic.Rd | 6 ++- man/scale_frontiers.Rd | 6 ++- man/scale_futurama.Rd | 6 ++- man/scale_gsea.Rd | 3 + man/scale_jama.Rd | 6 ++- man/scale_jco.Rd | 6 ++- man/scale_lancet.Rd | 6 ++- man/scale_locuszoom.Rd | 6 ++- man/scale_material.Rd | 3 + man/scale_nejm.Rd | 6 ++- man/scale_npg.Rd | 6 ++- man/scale_rickandmorty.Rd | 6 ++- man/scale_simpsons.Rd | 6 ++- man/scale_startrek.Rd | 6 ++- man/scale_tron.Rd | 6 ++- man/scale_ucscgb.Rd | 6 ++- vignettes/ggsci.Rmd | 12 +++--- 47 files changed, 341 insertions(+), 271 deletions(-)
Title: Regression with Multiple Change Points
Description: Flexible and informed regression with Multiple Change Points. 'mcp' can infer change points in means, variances, autocorrelation structure, and any combination of these, as well as the parameters of the segments in between. All parameters are estimated with uncertainty and prediction intervals are supported - also near the change points. 'mcp' supports hypothesis testing via Savage-Dickey density ratio, posterior contrasts, and cross-validation. 'mcp' is described in Lindeløv (submitted) <doi:10.31219/osf.io/fzqxv> and generalizes the approach described in Carlin, Gelfand, & Smith (1992) <doi:10.2307/2347570> and Stephens (1994) <doi:10.2307/2986119>.
Author: Jonas Kristoffer Lindeloev [aut, cre]
Maintainer: Jonas Kristoffer Lindeloev <jonas@lindeloev.dk>
Diff between mcp versions 0.3.3 dated 2023-03-22 and 0.3.4 dated 2024-03-17
DESCRIPTION | 12 ++++++------ MD5 | 31 ++++++++++++++++--------------- NEWS.md | 13 ++++++++++++- R/get_formula.R | 5 +---- R/mcp-package.R | 28 ++-------------------------- R/mcpfit_methods.R | 13 +++++++------ R/misc.R | 13 ++++++++----- R/plot.R | 3 --- R/run_jags.R | 2 +- build |only man/fitted.mcpfit.Rd | 2 +- man/geom_cp_density.Rd | 4 ---- man/get_simulate.Rd | 9 ++------- man/mcp-package.Rd | 29 +++++++++++++---------------- man/pp_eval.Rd | 5 +++-- man/predict.mcpfit.Rd | 2 +- man/residuals.mcpfit.Rd | 2 +- 17 files changed, 74 insertions(+), 99 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance.
Also defines a set of generics that provide a low-level
implementer's interface for the high-level user interface of 'dplyr'.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 0.3.1 dated 2024-03-10 and 0.3.2 dated 2024-03-17
duckplyr-0.3.1/duckplyr/R/csv.R |only duckplyr-0.3.2/duckplyr/DESCRIPTION | 7 - duckplyr-0.3.2/duckplyr/MD5 | 18 +-- duckplyr-0.3.2/duckplyr/NAMESPACE | 5 duckplyr-0.3.2/duckplyr/NEWS.md | 11 + duckplyr-0.3.2/duckplyr/R/fallback.R | 8 + duckplyr-0.3.2/duckplyr/R/io-csv.R |only duckplyr-0.3.2/duckplyr/R/io-parquet.R |only duckplyr-0.3.2/duckplyr/R/io.R |only duckplyr-0.3.2/duckplyr/man/df_from_file.Rd | 83 ++++++++++++--- duckplyr-0.3.2/duckplyr/tests/testthat/_snaps/select.md | 2 duckplyr-0.3.2/duckplyr/tests/testthat/test-io-csv.R |only duckplyr-0.3.2/duckplyr/tests/testthat/test-io-parquet.R |only 13 files changed, 107 insertions(+), 27 deletions(-)
Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies. Implements stopping rule methods described in Goldman (1987) <doi:10.1016/0197-2456(87)90153-X>; Geller et al. (2003, ISBN:9781135524388); Ivanova, Qaqish, and Schell (2005) <doi:10.1111/j.1541-0420.2005.00311.x>; Chen and Chaloner (2006) <doi:10.1002/sim.2429>; and Kulldorff et al. (2011) <doi:10.1080/07474946.2011.539924>.
Author: Michael J. Martens [aut,cre], Qinghua Lian [aut], Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>
Diff between stoppingrule versions 0.3.0 dated 2023-09-01 and 0.4.0 dated 2024-03-17
DESCRIPTION | 10 +-- MD5 | 96 +++++++++++++++++-------------- NAMESPACE | 5 + R/OC.rule.R |only R/OC.rule.bin.R | 44 ++++++++++---- R/OC.rule.surv.R | 67 +++++++++++++++++---- R/bdryfcn.R |only R/bdryfcn.bin.R | 4 - R/bdryfcn.surv.R | 14 ++-- R/calc.bnd.bin.R | 4 - R/calc.bnd.surv.R | 15 ++-- R/calc.rule.R |only R/calc.rule.bin.R | 20 +++++- R/calc.rule.surv.R | 33 ++++++++-- R/findconst.bin.R | 2 R/findconst.surv.R | 14 ++-- R/lines.rule.bin.R | 7 +- R/lines.rule.surv.R | 10 +-- R/opchars.bin.R | 130 ++++++++++++++++++++++++++++++++---------- R/opchars.surv.R | 25 ++++++-- R/plot.rule.bin.R | 7 +- R/plot.rule.surv.R | 8 +- R/simdata_weibull.R |only R/simtrials.surv.R |only R/stopping.prob.surv.R | 2 R/stoppingrule.R | 1 R/table.rule.bin.R | 2 R/table.rule.surv.R | 11 +-- README.md | 60 ++++++++++--------- man/OC.rule.Rd |only man/OC.rule.bin.Rd | 22 +++++-- man/OC.rule.surv.Rd | 46 ++++++++++++-- man/bdryfcn.Rd |only man/bdryfcn.bin.Rd | 4 - man/bdryfcn.surv.Rd | 12 +-- man/calc.bnd.bin.Rd | 4 - man/calc.bnd.surv.Rd | 6 - man/calc.rule.Rd |only man/calc.rule.bin.Rd | 20 +++++- man/calc.rule.surv.Rd | 33 ++++++++-- man/figures/README-plot-1.png |binary man/findconst.bin.Rd | 2 man/findconst.surv.Rd | 10 +-- man/lines.rule.bin.Rd | 7 +- man/lines.rule.surv.Rd | 10 +-- man/opchars.bin.Rd | 10 ++- man/opchars.surv.Rd | 14 +++- man/plot.rule.bin.Rd | 7 +- man/plot.rule.surv.Rd | 8 +- man/simdata_weibull.Rd |only man/simtrials.surv.Rd |only man/stopping.prob.surv.Rd | 2 man/table.rule.bin.Rd | 2 man/table.rule.surv.Rd | 6 - 54 files changed, 563 insertions(+), 253 deletions(-)
Title: Monte Carlo Confidence Intervals in Structural Equation Modeling
Description: Monte Carlo confidence intervals for free and defined parameters
in models fitted in the structural equation modeling package 'lavaan'
can be generated using the 'semmcci' package.
'semmcci' has three main functions, namely, MC(), MCMI(), and MCStd().
The output of 'lavaan' is passed as the first argument
to the MC() function or the MCMI() function to generate Monte Carlo confidence intervals.
Monte Carlo confidence intervals for the standardized estimates
can also be generated by passing the output of the MC() function or the MCMI() function
to the MCStd() function.
A description of the package and code examples
are presented in Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
,
Shu Fai Cheung [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between semmcci versions 1.1.3 dated 2023-10-14 and 1.1.4 dated 2024-03-17
DESCRIPTION | 10 +- MD5 | 48 ++++++----- NAMESPACE | 2 NEWS.md | 4 R/semmcci-func.R |only R/semmcci-mc-ci-dot.R | 5 - R/semmcci-mc-func.R |only R/semmcci-mc-generic.R | 4 R/semmcci-mc-mi.R | 8 + R/semmcci-mc-std.R | 4 R/semmcci-mc.R | 2 R/semmcci-methods.R | 37 ++++---- build/partial.rdb |binary inst/CITATION | 2 man/Func.Rd |only man/MC.Rd | 4 man/MCFunc.Rd |only man/MCGeneric.Rd | 10 +- man/MCMI.Rd | 8 + man/MCStd.Rd | 10 +- man/coef.semmcci.Rd | 6 - man/confint.semmcci.Rd | 6 - man/print.semmcci.Rd | 6 - man/semmcci-package.Rd | 2 man/summary.semmcci.Rd | 6 - man/vcov.semmcci.Rd | 6 - tests/testthat/test-semmcci-mc-func-simple-med.R |only tests/testthat/test-semmcci-mc-simple-med-defined-equality.R |only 28 files changed, 110 insertions(+), 80 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph] [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.7.1 dated 2023-12-10 and 0.7.2 dated 2024-03-17
pak-0.7.1/pak/src/library/filelock.patch |only pak-0.7.1/pak/src/library/ps.patch |only pak-0.7.2/pak/DESCRIPTION | 20 - pak-0.7.2/pak/MD5 | 188 +++++----- pak-0.7.2/pak/NEWS.md | 7 pak-0.7.2/pak/R/embed.R | 1 pak-0.7.2/pak/R/pak-sitrep.R | 4 pak-0.7.2/pak/inst/COPYRIGHTS |only pak-0.7.2/pak/man/chunks/sysreqs.Rmd | 2 pak-0.7.2/pak/man/chunks/tldr.Rmd | 2 pak-0.7.2/pak/man/pak-package.Rd | 2 pak-0.7.2/pak/src/dummy |only pak-0.7.2/pak/src/install-embedded.R | 76 +++- pak-0.7.2/pak/src/library/callr/DESCRIPTION | 28 - pak-0.7.2/pak/src/library/callr/LICENSE | 4 pak-0.7.2/pak/src/library/callr/NEWS.md | 13 pak-0.7.2/pak/src/library/callr/R/aaa-rstudio-detect.R | 2 pak-0.7.2/pak/src/library/callr/R/errors.R | 63 ++- pak-0.7.2/pak/src/library/callr/R/eval-bg.R | 2 pak-0.7.2/pak/src/library/callr/R/load-client.R | 19 - pak-0.7.2/pak/src/library/callr/R/package.R | 20 - pak-0.7.2/pak/src/library/callr/R/r-session.R | 8 pak-0.7.2/pak/src/library/callr/R/result.R | 4 pak-0.7.2/pak/src/library/callr/R/rscript.R | 2 pak-0.7.2/pak/src/library/callr/R/script.R | 84 ++-- pak-0.7.2/pak/src/library/callr/inst/WORDLIST | 1 pak-0.7.2/pak/src/library/cli/DESCRIPTION | 6 pak-0.7.2/pak/src/library/cli/NEWS.md | 2 pak-0.7.2/pak/src/library/curl/DESCRIPTION | 10 pak-0.7.2/pak/src/library/curl/NAMESPACE | 1 pak-0.7.2/pak/src/library/curl/NEWS | 10 pak-0.7.2/pak/src/library/curl/R/email.R | 11 pak-0.7.2/pak/src/library/curl/R/handle.R | 21 - pak-0.7.2/pak/src/library/curl/src/Makevars.in | 2 pak-0.7.2/pak/src/library/curl/src/Makevars.win | 2 pak-0.7.2/pak/src/library/curl/src/callbacks.c | 18 pak-0.7.2/pak/src/library/curl/src/curl.c | 24 - pak-0.7.2/pak/src/library/curl/src/download.c | 28 - pak-0.7.2/pak/src/library/curl/src/escape.c | 8 pak-0.7.2/pak/src/library/curl/src/fetch.c | 22 - pak-0.7.2/pak/src/library/curl/src/findport.c | 2 pak-0.7.2/pak/src/library/curl/src/form.c | 30 - pak-0.7.2/pak/src/library/curl/src/getdate.c | 8 pak-0.7.2/pak/src/library/curl/src/handle.c | 138 +++---- pak-0.7.2/pak/src/library/curl/src/ieproxy.c | 68 +-- pak-0.7.2/pak/src/library/curl/src/init.c | 1 pak-0.7.2/pak/src/library/curl/src/multi.c | 74 +-- pak-0.7.2/pak/src/library/curl/src/nslookup.c | 6 pak-0.7.2/pak/src/library/curl/src/reflist.c | 8 pak-0.7.2/pak/src/library/curl/src/split.c | 6 pak-0.7.2/pak/src/library/curl/src/utils.c | 18 pak-0.7.2/pak/src/library/curl/src/version.c | 44 +- pak-0.7.2/pak/src/library/curl/src/writer.c | 6 pak-0.7.2/pak/src/library/curl/vignettes/intro.Rmd | 15 pak-0.7.2/pak/src/library/filelock/DESCRIPTION | 30 + pak-0.7.2/pak/src/library/filelock/LICENSE | 4 pak-0.7.2/pak/src/library/filelock/NEWS.md | 7 pak-0.7.2/pak/src/library/filelock/R/filelock-package.R |only pak-0.7.2/pak/src/library/filelock/R/package.R | 9 pak-0.7.2/pak/src/library/pkgbuild/DESCRIPTION | 6 pak-0.7.2/pak/src/library/pkgbuild/NEWS.md | 4 pak-0.7.2/pak/src/library/pkgbuild/R/rtools.R | 40 ++ pak-0.7.2/pak/src/library/pkgdepends/DESCRIPTION | 6 pak-0.7.2/pak/src/library/pkgdepends/R/install-plan.R | 23 - pak-0.7.2/pak/src/library/pkgdepends/R/parse-remotes.R | 6 pak-0.7.2/pak/src/library/pkgdepends/R/resolution.R | 4 pak-0.7.2/pak/src/library/pkgdepends/inst/docs/download-result.rds |binary pak-0.7.2/pak/src/library/pkgdepends/inst/docs/resolution-result.rds |binary pak-0.7.2/pak/src/library/processx.patch |only pak-0.7.2/pak/src/library/processx/DESCRIPTION | 12 pak-0.7.2/pak/src/library/processx/LICENSE | 4 pak-0.7.2/pak/src/library/processx/NEWS.md | 4 pak-0.7.2/pak/src/library/processx/R/client-lib.R | 4 pak-0.7.2/pak/src/library/processx/R/on-load.R | 3 pak-0.7.2/pak/src/library/processx/src/init.c | 19 + pak-0.7.2/pak/src/library/ps/DESCRIPTION | 18 pak-0.7.2/pak/src/library/ps/LICENSE | 4 pak-0.7.2/pak/src/library/ps/NEWS.md | 8 pak-0.7.2/pak/src/library/ps/R/linux.R | 6 pak-0.7.2/pak/src/library/ps/R/low-level.R | 4 pak-0.7.2/pak/src/library/ps/configure | 4 pak-0.7.2/pak/src/library/ps/src/api-linux.c | 2 pak-0.7.2/pak/src/library/ps/src/arch/windows/process_handles.c | 1 pak-0.7.2/pak/src/library/zip/DESCRIPTION | 32 + pak-0.7.2/pak/src/library/zip/LICENSE | 2 pak-0.7.2/pak/src/library/zip/NEWS.md | 5 pak-0.7.2/pak/src/library/zip/R/zip-package.R |only pak-0.7.2/pak/src/library/zip/src/Makevars | 2 pak-0.7.2/pak/src/library/zip/src/init.c | 4 89 files changed, 868 insertions(+), 550 deletions(-)
Title: Package Dependency Resolution and Downloads
Description: Find recursive dependencies of 'R' packages from various
sources. Solve the dependencies to obtain a consistent set of packages
to install. Download packages, and install them. It supports packages
on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories,
'GitHub', package 'URLs', and local package trees and files. It caches
metadata and package files via the 'pkgcache' package, and performs
all 'HTTP' requests, downloads, builds and installations in parallel.
'pkgdepends' is the workhorse of the 'pak' package.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgdepends versions 0.7.1 dated 2023-12-10 and 0.7.2 dated 2024-03-17
DESCRIPTION | 6 ++--- MD5 | 24 +++++++++++++-------- R/install-plan.R | 23 ++++++++++++++++---- R/parse-remotes.R | 6 ++--- R/resolution.R | 4 +-- tests/testthat/_snaps/install-plan.md | 32 +++++++++++++++++++++++++++++ tests/testthat/fixtures/packages/badbuild |only tests/testthat/fixtures/packages/goodbuild |only tests/testthat/setup.R | 8 +++++++ tests/testthat/test-assertions.R | 13 +++++++++++ tests/testthat/test-assertthat.R | 1 tests/testthat/test-install-plan.R | 28 +++++++++++++++++++++++++ 12 files changed, 123 insertions(+), 22 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates
compilers needed to build R packages on various platforms and ensures
the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgbuild versions 1.4.3 dated 2023-12-10 and 1.4.4 dated 2024-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/rtools.R | 40 +++++++++++++++++++++++++++++++++++++++- tests/testthat/test-build.R | 3 +++ 5 files changed, 53 insertions(+), 8 deletions(-)
Title: R Package Installation from Remote Repositories, Including
'GitHub'
Description: Download and install R packages stored in 'GitHub', 'GitLab',
'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git'
repositories. This package provides the 'install_*' functions in
'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Posit Software, PBC [cph, fnd],
Ascent Digital Services [cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between remotes versions 2.4.2.1 dated 2023-07-18 and 2.5.0 dated 2024-03-17
remotes-2.4.2.1/remotes/tests/testthat/github-error-local.txt |only remotes-2.4.2.1/remotes/tests/testthat/github-error-travis.txt |only remotes-2.5.0/remotes/DESCRIPTION | 42 remotes-2.5.0/remotes/LICENSE | 4 remotes-2.5.0/remotes/MD5 | 119 - remotes-2.5.0/remotes/NAMESPACE | 3 remotes-2.5.0/remotes/NEWS.md | 15 remotes-2.5.0/remotes/R/bioc-standalone.R | 26 remotes-2.5.0/remotes/R/deps.R | 4 remotes-2.5.0/remotes/R/git-auth.R |only remotes-2.5.0/remotes/R/github.R | 29 remotes-2.5.0/remotes/R/install-bioc.R | 1 remotes-2.5.0/remotes/R/install-dev.R | 2 remotes-2.5.0/remotes/R/install-gitlab.R | 2 remotes-2.5.0/remotes/R/install-remote.R | 5 remotes-2.5.0/remotes/R/package.R | 2 remotes-2.5.0/remotes/R/remotes-package.R |only remotes-2.5.0/remotes/R/system_requirements.R | 6 remotes-2.5.0/remotes/README.md | 227 +- remotes-2.5.0/remotes/build/vignette.rds |binary remotes-2.5.0/remotes/inst/COPYRIGHTS |only remotes-2.5.0/remotes/inst/doc/dependencies.Rmd | 4 remotes-2.5.0/remotes/inst/doc/dependencies.html | 421 +++- remotes-2.5.0/remotes/inst/install-github.R | 906 +++++++++- remotes-2.5.0/remotes/man/install_gitlab.Rd | 4 remotes-2.5.0/remotes/man/remotes-package.Rd |only remotes-2.5.0/remotes/tests/testthat.R | 12 remotes-2.5.0/remotes/tests/testthat/_snaps |only remotes-2.5.0/remotes/tests/testthat/archives/foo/DESCRIPTION | 2 remotes-2.5.0/remotes/tests/testthat/helper.R | 18 remotes-2.5.0/remotes/tests/testthat/submodule/DESCRIPTION | 2 remotes-2.5.0/remotes/tests/testthat/test-bioc.R | 5 remotes-2.5.0/remotes/tests/testthat/test-cran.R | 3 remotes-2.5.0/remotes/tests/testthat/test-dcf.R | 3 remotes-2.5.0/remotes/tests/testthat/test-decompress.R | 3 remotes-2.5.0/remotes/tests/testthat/test-deps.R | 21 remotes-2.5.0/remotes/tests/testthat/test-devel.R | 2 remotes-2.5.0/remotes/tests/testthat/test-download.R | 3 remotes-2.5.0/remotes/tests/testthat/test-git.R | 3 remotes-2.5.0/remotes/tests/testthat/test-github.R | 21 remotes-2.5.0/remotes/tests/testthat/test-install-bioc.R | 2 remotes-2.5.0/remotes/tests/testthat/test-install-bitbucket.R | 3 remotes-2.5.0/remotes/tests/testthat/test-install-cran.R | 8 remotes-2.5.0/remotes/tests/testthat/test-install-deps.R | 3 remotes-2.5.0/remotes/tests/testthat/test-install-dev.R | 11 remotes-2.5.0/remotes/tests/testthat/test-install-git.R | 95 - remotes-2.5.0/remotes/tests/testthat/test-install-github.R | 10 remotes-2.5.0/remotes/tests/testthat/test-install-gitlab.R | 14 remotes-2.5.0/remotes/tests/testthat/test-install-local.R | 3 remotes-2.5.0/remotes/tests/testthat/test-install-remote.R | 2 remotes-2.5.0/remotes/tests/testthat/test-install-svn.R | 88 remotes-2.5.0/remotes/tests/testthat/test-install-url.R | 5 remotes-2.5.0/remotes/tests/testthat/test-install-version.R | 7 remotes-2.5.0/remotes/tests/testthat/test-install.R | 2 remotes-2.5.0/remotes/tests/testthat/test-json.R | 3 remotes-2.5.0/remotes/tests/testthat/test-package-deps.R | 3 remotes-2.5.0/remotes/tests/testthat/test-package.R | 2 remotes-2.5.0/remotes/tests/testthat/test-parse-git.R | 2 remotes-2.5.0/remotes/tests/testthat/test-script.R | 7 remotes-2.5.0/remotes/tests/testthat/test-submodule.R | 2 remotes-2.5.0/remotes/tests/testthat/test-system.R | 3 remotes-2.5.0/remotes/tests/testthat/test-system_requirements.R | 17 remotes-2.5.0/remotes/tests/testthat/test-utils.R | 3 remotes-2.5.0/remotes/vignettes/dependencies.Rmd | 4 64 files changed, 1567 insertions(+), 652 deletions(-)
Title: Interface Between 'GRASS' Geographical Information System and
'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [cre, aut] ,
Rainer Krug [ctb] ,
Robin Lovelace [ctb] ,
Markus Neteler [ctb] ,
Sebastian Jeworutzki [ctb] ,
Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass versions 0.4-1 dated 2024-01-08 and 0.4-2 dated 2024-03-17
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------ NEWS.md | 6 +++- R/rast_link.R | 52 +++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/coerce.html | 6 ++-- man/readRAST.Rd | 23 +++++++++++++++++- tests/test_XML_xml2.Rout.save | 8 +++--- tests/test_terra_ptr.Rout.save | 8 +++--- 9 files changed, 92 insertions(+), 35 deletions(-)
Title: Creates an 'igraph' Object that Duplicates Nodes with Self-Loops
Description: Creates a new graph from an existing one, duplicating nodes
with self-loops. This can be used for a computation of betweenness
centrality that does not drop this essential information. Implements
Merelo & Molinari (2024) <doi:10.1007/s42001-023-00245-4>.
Author: Juan Julian Merelo-Guervos
Maintainer: Juan Julian Merelo-Guervos <jjmerelo@gmail.com>
Diff between dupNodes versions 0.1.0 dated 2024-02-05 and 0.2.0 dated 2024-03-17
DESCRIPTION | 15 ++++++++------- MD5 | 27 +++++++++++++++++++-------- NAMESPACE | 4 ++-- NEWS.md | 7 +++++++ R/dup.nodes.from.graph.R |only R/florentine.sn.R |only README.md | 19 +++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary data |only inst/auto/florentine-families.el |only inst/doc/doges-social-network.html | 21 +++++++++++++-------- inst/doc/florentine-social-network.R |only inst/doc/florentine-social-network.Rmd |only inst/doc/florentine-social-network.html |only inst/florentine-families.bib |only man/dup.nodes.from.graph.Rd |only man/florentine.sn.Rd |only tests/testthat/test-dup.nodes.from.R | 28 ++++++++++++++++++++++++++++ vignettes/florentine-social-network.Rmd |only 20 files changed, 90 insertions(+), 31 deletions(-)
More information about tsdistributions at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-26 0.1.7
Title: Flexible Estimation of Conditional Survival Functions Using
Machine Learning
Description: Tools for flexible estimation of conditional survival
functions using off-the-shelf machine learning tools. Implements both
global and local survival stacking. See Wolock CJ, Gilbert PB,
Simon N, and Carone M (2024) <doi:10.1080/10618600.2024.2304070>.
Author: Charles Wolock [aut, cre, cph]
Maintainer: Charles Wolock <cwolock@gmail.com>
Diff between survML versions 1.0.0 dated 2023-07-08 and 1.1.0 dated 2024-03-17
DESCRIPTION | 11 MD5 | 57 - NAMESPACE | 14 NEWS.md | 6 R/compute_exponential.R | 70 - R/compute_prodint.R | 51 - R/f_w_algorithms.R | 31 R/f_w_stack.R | 2 R/f_y_algorithms.R | 29 R/f_y_stack.R | 2 R/stackG.R | 45 R/stackL.R | 4 R/stack_utils.R | 100 - R/survML-package.R | 14 README.md | 482 ++++----- build/partial.rdb |only build/vignette.rds |binary inst/doc/basic-usage.R | 205 ++-- inst/doc/basic-usage.Rmd | 5 inst/doc/basic-usage.html | 1105 +++++++++++----------- man/figures/README-plot_stackG_example-1.png |binary man/figures/README-plot_stackG_example_cens-1.png |binary man/figures/README-plot_stackL_example-1.png |binary man/stackG.Rd | 364 +++---- man/stackL.Rd | 292 ++--- man/survML-package.Rd | 46 tests/testthat.R | 24 tests/testthat/test-test-stackG.R | 371 +++++-- tests/testthat/test-test-stackL.R | 139 +- vignettes/basic-usage.Rmd | 5 30 files changed, 1808 insertions(+), 1666 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.3.3 dated 2023-11-13 and 4.3.4 dated 2024-03-17
DESCRIPTION | 8 MD5 | 50 +- NAMESPACE | 4 R/FUN_markers.R | 29 + R/FUN_special.R | 91 ++--- R/FUN_stats.R | 4 R/FUN_utils.R | 3 R/FUN_vsc.R | 6 R/mmec.R | 2 R/mmer.R | 2 R/predict_mmer.R | 541 ------------------------------ README.md | 2 man/DT_mohring.Rd | 34 + man/atc.Rd | 32 + man/atcg1234BackTransform.Rd |only man/csc.Rd | 20 - man/dsc.Rd | 31 + man/propMissing.Rd |only man/rrc.Rd | 6 man/usc.Rd | 33 + man/vsc.Rd | 4 vignettes/v1.sommer.quick.start.html | 4 vignettes/v2.sommer.changes.and.faqs.html | 4 vignettes/v3.sommer.qg.html | 4 vignettes/v4.sommer.gxe.html | 4 vignettes/v5.sommer.vs.lme4.html | 4 vignettes/v6.sommer.spatial.html | 4 27 files changed, 272 insertions(+), 654 deletions(-)
Title: Creates Bivariate Maps
Description: Contains functions to plot bivariate maps. For more info, see: Hidasi-Neto, J (2015) <https://rfunctions.blogspot.com/2015/03/bivariate-maps-bivariatemap-function.html>.
Author: Jose Hidasi-Neto [aut, cre]
Maintainer: Jose Hidasi-Neto <hidasineto@gmail.com>
Diff between bivariatemaps versions 1.2 dated 2023-11-21 and 1.3 dated 2024-03-17
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders,
truncated normal and mixture of inverse Gaussian as the distribution for the frailty terms.
For the basal model, it is considered a parametric approach based on the exponential,
Weibull and the piecewise exponential distributions as well as a semiparametric approach.
For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between extrafrail versions 1.8 dated 2023-09-26 and 1.9 dated 2024-03-16
DESCRIPTION | 12 MD5 | 12 NAMESPACE | 3 NEWS.md | 4 R/frailty.fit.R | 1586 +++++++++++++++++++++++++++++++++++-------------- R/summary.extrafrail.R | 34 + man/frailty.fit.Rd | 5 7 files changed, 1207 insertions(+), 449 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available
from several federated data sources (mainly sources maintained by the
US Federal government). Currently, the package enables extraction from
nine datasets: The National Elevation Dataset digital elevation
models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset
(USGS); The Soil Survey Geographic (SSURGO) database from the National
Cooperative Soil Survey (NCSS), which is led by the Natural Resources
Conservation Service (NRCS) under the USDA; the Global Historical
Climatology Network (GHCN), coordinated by National Climatic Data
Center at NOAA; the Daymet gridded estimates of daily weather
parameters for North America, version 4, available from the Oak Ridge
National Laboratory's Distributed Active Archive Center (DAAC); the
International Tree Ring Data Bank; the National Land Cover
Database (NLCD); the Cropland Data Layer from the National Agricultural
Statistics Service; and the PAD-US dataset of protected area [...truncated...]
Author: R. Kyle Bocinsky [aut, cre, cph]
,
Dylan Beaudette [ctb],
Scott Chamberlain [ctb, rev],
Jeffrey Hollister [ctb],
Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 4.0.0 dated 2023-10-03 and 4.0.1 dated 2024-03-16
FedData-4.0.0/FedData/R/esri.R |only FedData-4.0.1/FedData/DESCRIPTION | 30 ++++--- FedData-4.0.1/FedData/MD5 | 19 ++-- FedData-4.0.1/FedData/NEWS.md | 5 + FedData-4.0.1/FedData/R/NHD_FUNCTIONS.R | 116 ++++++++++++++++++---------- FedData-4.0.1/FedData/R/NLCD_FUNCTIONS.R | 6 - FedData-4.0.1/FedData/R/PADUS_FUNCTIONS.R | 29 ++++--- FedData-4.0.1/FedData/R/UTILITY_FUNCTIONS.R | 3 FedData-4.0.1/FedData/README.md | 8 - FedData-4.0.1/FedData/man/get_nlcd.Rd | 6 - FedData-4.0.1/FedData/man/get_wbd.Rd | 2 11 files changed, 140 insertions(+), 84 deletions(-)
Title: Elegant Tools for Processing and Visualization of Lipidomics
Data
Description: An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
Author: Mingshi Li [aut],
Hengyu Zhu [aut, cre]
Maintainer: Hengyu Zhu <hengyu.21@intl.zju.edu.cn>
Diff between LipidomicsR versions 0.1.0 dated 2024-03-14 and 0.1.6 dated 2024-03-16
DESCRIPTION | 6 MD5 | 6 R/data_cleaner.R | 912 ++++++++++++++++++++++++++--------------------------- R/volcano_master.R | 4 4 files changed, 464 insertions(+), 464 deletions(-)
Title: Retrieving and Analyzing Air Quality and Weather Data from ARPA
Lombardia
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>).
Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network.
See the webpage <https://www.arpalombardia.it/> for further information on ARPA Lombardia's activities and history.
Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control.
The package makes available observations since 1989 (for weather) and 1968 (for air quality) and are updated with daily frequency by the regional agency.
Full description of the package can be retrieved in the companion paper Maranzano \& Algieri (2024), "ARPALData: an R package for retrieving and analyzing air quality
and weather data from ARPA Lombardia (Italy)", Environmental and Ecological Statistics, <doi:1 [...truncated...]
Author: Paolo Maranzano [aut, cre, cph]
,
Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Diff between ARPALData versions 1.5.1 dated 2024-02-24 and 1.5.2 dated 2024-03-16
DESCRIPTION | 12 +++++----- MD5 | 37 +++++++++++++++---------------- NAMESPACE | 5 ++-- R/AQ_metadata_reshape.R | 18 ++++++++++----- R/AQ_municipal_metadata_reshape.R | 14 +++++++++-- R/ARPALdf_Summary_map.R | 7 ++++- R/Time_aggregate.R | 6 ++--- R/W_metadata_reshape.R | 6 ++--- R/get_ARPA_Lombardia_AQ_data.R | 25 +++++++++++++++----- R/get_ARPA_Lombardia_AQ_municipal_data.R | 24 ++++++++++++++------ R/get_ARPA_Lombardia_W_data.R | 26 ++++++++++++++------- R/get_ARPA_Lombardia_zoning.R | 30 ++++++++++++++++++------- R/get_Lombardia_geospatial.R | 16 +++++++++---- R/map_Lombardia_stations.R | 30 ++++++++++++++++++++----- R/registry_KNN_dist.R | 11 +++++---- inst |only man/Time_aggregate.Rd | 6 ++--- man/get_ARPA_Lombardia_zoning.Rd | 10 ++++---- man/map_Lombardia_stations.Rd | 18 ++++++++++----- man/registry_KNN_dist.Rd | 11 +++++---- 20 files changed, 206 insertions(+), 106 deletions(-)
Title: Date/Time Classes Based on Jalali Calendar
Description: Implements S3 classes for storing dates and date-times based on the Jalali calendar.
The main design goal of 'shide' is consistency with base R's 'Date' and 'POSIXct'.
It provide features such as: date-time parsing, formatting and arithmetic.
Author: Mohsen Mollayi [aut, cre, cph]
Maintainer: Mohsen Mollayi <mmollayi@gmail.com>
Diff between shide versions 0.1.3 dated 2024-02-04 and 0.2.0 dated 2024-03-16
shide-0.1.3/shide/R/accessors.R |only shide-0.1.3/shide/tests/testthat/test-test-jdatetime.R |only shide-0.2.0/shide/DESCRIPTION | 8 - shide-0.2.0/shide/MD5 | 64 +++++++++---- shide-0.2.0/shide/NAMESPACE | 58 +++++++++++- shide-0.2.0/shide/NEWS.md | 27 +++++ shide-0.2.0/shide/R/cpp11.R | 40 ++++++++ shide-0.2.0/shide/R/date.R | 2 shide-0.2.0/shide/R/datetime.R | 28 ----- shide-0.2.0/shide/R/getters.R |only shide-0.2.0/shide/R/jdate.R | 18 ++- shide-0.2.0/shide/R/jdatetime.R | 20 +++- shide-0.2.0/shide/R/leap_years.R |only shide-0.2.0/shide/R/round.R | 75 +++++++++++++++ shide-0.2.0/shide/R/seq.R |only shide-0.2.0/shide/R/setters.R |only shide-0.2.0/shide/R/sysdata.rda |only shide-0.2.0/shide/R/update.R |only shide-0.2.0/shide/R/utils.R | 4 shide-0.2.0/shide/README.md | 13 +- shide-0.2.0/shide/man/jdate.Rd | 2 shide-0.2.0/shide/man/seq.jdate.Rd |only shide-0.2.0/shide/man/sh_day.Rd |only shide-0.2.0/shide/man/sh_hour.Rd |only shide-0.2.0/shide/man/sh_month.Rd |only shide-0.2.0/shide/man/sh_quarter.Rd |only shide-0.2.0/shide/man/sh_round.Rd |only shide-0.2.0/shide/man/sh_tzone.Rd |only shide-0.2.0/shide/man/sh_year.Rd |only shide-0.2.0/shide/man/sh_year_is_leap.Rd |only shide-0.2.0/shide/src/accessors.cpp |only shide-0.2.0/shide/src/cpp11.cpp | 80 +++++++++++++++++ shide-0.2.0/shide/src/jalali.cpp | 8 + shide-0.2.0/shide/src/leap_years.cpp |only shide-0.2.0/shide/src/make.cpp | 21 ++-- shide-0.2.0/shide/src/round.cpp |only shide-0.2.0/shide/src/seq.cpp |only shide-0.2.0/shide/src/sh_year_month_day.h |only shide-0.2.0/shide/src/shide.h | 1 shide-0.2.0/shide/src/utils.cpp | 23 ++-- shide-0.2.0/shide/tests/testthat/test-getters.R |only shide-0.2.0/shide/tests/testthat/test-jdate.R | 20 +++- shide-0.2.0/shide/tests/testthat/test-jdatetime.R |only shide-0.2.0/shide/tests/testthat/test-leap_years.R |only shide-0.2.0/shide/tests/testthat/test-round.R |only shide-0.2.0/shide/tests/testthat/test-seq.R |only shide-0.2.0/shide/tests/testthat/test-setters.R |only 47 files changed, 417 insertions(+), 95 deletions(-)
Title: Recursive Non-Additive Emulator for Multi-Fidelity Data
Description: Performs RNA emulation and active learning proposed by Heo and Sung (2023+) <arXiv:2309.11772> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.
Author: Junoh Heo [aut, cre],
Chih-Li Sung [aut]
Maintainer: Junoh Heo <heojunoh@msu.edu>
Diff between RNAmf versions 0.1.0 dated 2023-12-06 and 0.1.1 dated 2024-03-16
DESCRIPTION | 8 MD5 | 18 - R/ALC.R | 552 ++++++++++++++++++++++++++++++++++++------------------ R/ALM.R | 136 ------------- R/ALMC.R | 158 +-------------- R/GP.R | 10 R/matGP.R | 10 man/ALC_RNAmf.Rd | 2 man/ALMC_RNAmf.Rd | 2 man/ALM_RNAmf.Rd | 2 10 files changed, 401 insertions(+), 497 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.3 dated 2023-09-24 and 0.9.5 dated 2024-03-16
DESCRIPTION | 16 - MD5 | 45 ++-- NAMESPACE | 10 NEWS.md | 10 R/basefunctions.R | 426 +++++++++++++++++++++-------------------- R/clin_estimates.R |only R/descriptives.R | 24 ++ R/pkgstart.R | 14 + R/plots.R | 104 ++++++++++ R/tests.R | 21 +- README.md | 53 +++-- build/vignette.rds |binary inst/doc/wrappedtools.html | 6 man/ColSeeker.Rd | 2 man/FindVars.Rd | 7 man/WINratio.Rd |only man/detect_outliers.Rd |only man/eGFR.Rd |only man/flex2rmd.Rd |only man/glmCI.Rd | 2 man/ksnormal.Rd | 3 man/label_outliers.Rd |only man/median_cl_boot_gg.Rd |only man/print_kable.Rd | 5 man/wrappedtools-package.Rd | 8 tests/testthat/meanseout.rda |binary tests/testthat/test-FindVars.R | 2 27 files changed, 487 insertions(+), 271 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.1.22 dated 2024-01-25 and 9.3.3 dated 2024-03-16
DESCRIPTION | 8 MD5 | 255 - NEWS.md | 13 README.md | 5 src/Makevars | 10 src/Makevars.win | 6 src/swipl-devel/CMAKE.md | 10 src/swipl-devel/VERSION | 2 src/swipl-devel/app/pack.pl | 18 src/swipl-devel/app/qlf.pl | 296 - src/swipl-devel/bench/run.pl | 18 src/swipl-devel/boot/autoload.pl | 5 src/swipl-devel/boot/init.pl | 56 src/swipl-devel/boot/messages.pl | 6 src/swipl-devel/boot/toplevel.pl | 45 src/swipl-devel/boot/topvars.pl | 17 src/swipl-devel/cmake/Locations.cmake | 13 src/swipl-devel/cmake/LocationsPostPorts.cmake | 4 src/swipl-devel/cmake/QLF.cmake | 2 src/swipl-devel/cmake/cross/linux_i386.cmake | 27 src/swipl-devel/cmake/port/Darwin.cmake | 11 src/swipl-devel/cmake/port/MSYS2.cmake |only src/swipl-devel/cmake/port/Windows.cmake | 2 src/swipl-devel/doc/Release.md | 28 src/swipl-devel/library/check_installation.pl | 24 src/swipl-devel/library/dom.pl | 37 src/swipl-devel/library/help.pl | 43 src/swipl-devel/library/main.pl | 6 src/swipl-devel/library/prolog_colour.pl | 4 src/swipl-devel/library/prolog_coverage.pl | 345 + src/swipl-devel/library/prolog_deps.pl | 123 src/swipl-devel/library/prolog_pack.pl | 238 - src/swipl-devel/library/prolog_trace.pl | 162 src/swipl-devel/library/prolog_versions.pl | 14 src/swipl-devel/library/prolog_xref.pl | 47 src/swipl-devel/library/qsave.pl | 3 src/swipl-devel/library/sandbox.pl | 10 src/swipl-devel/packages/clib/process.c | 2 src/swipl-devel/packages/clib/unix.c | 1 src/swipl-devel/packages/cpp/SWI-cpp2-atommap.h | 2 src/swipl-devel/packages/cpp/SWI-cpp2-plx.h | 8 src/swipl-devel/packages/cpp/SWI-cpp2.cpp | 146 src/swipl-devel/packages/cpp/SWI-cpp2.h | 271 - src/swipl-devel/packages/cpp/pl2cpp2.doc | 1787 +++++++--- src/swipl-devel/packages/cpp/test_cpp.cpp | 552 ++- src/swipl-devel/packages/cpp/test_cpp.pl | 230 + src/swipl-devel/packages/cpp/test_ffi.c | 12 src/swipl-devel/packages/cpp/test_ffi.pl | 2 src/swipl-devel/packages/http/CMakeLists.txt | 7 src/swipl-devel/packages/http/config.h.cmake | 7 src/swipl-devel/packages/http/http.doc | 1 src/swipl-devel/packages/http/http_client.pl | 4 src/swipl-devel/packages/http/http_cors.pl | 2 src/swipl-devel/packages/http/http_files.pl | 6 src/swipl-devel/packages/http/http_header.pl | 12 src/swipl-devel/packages/http/http_open.pl | 24 src/swipl-devel/packages/http/http_redis_plugin.pl | 123 src/swipl-devel/packages/http/http_server_health.pl |only src/swipl-devel/packages/http/http_session.pl | 105 src/swipl-devel/packages/http/json.c | 42 src/swipl-devel/packages/http/stream_range.c | 9 src/swipl-devel/packages/http/test_proxy.pl | 77 src/swipl-devel/packages/http/thread_httpd.pl | 32 src/swipl-devel/packages/http/websocket.pl | 29 src/swipl-devel/packages/plunit/plunit.pl | 34 src/swipl-devel/packages/sgml/catalog.c | 4 src/swipl-devel/packages/ssl/crypto4pl.c | 51 src/swipl-devel/packages/ssl/cryptolib.c | 2 src/swipl-devel/packages/ssl/ssl4pl.c | 1 src/swipl-devel/packages/ssl/test_ssl.pl | 7 src/swipl-devel/packages/zlib/zlib4pl.c | 10 src/swipl-devel/scripts/configure | 52 src/swipl-devel/scripts/macos-deps.sh | 48 src/swipl-devel/scripts/macosx_bundle_fixup.sh | 44 src/swipl-devel/scripts/make-distribution | 36 src/swipl-devel/scripts/make-ppa | 2 src/swipl-devel/src/SWI-Prolog.h | 8 src/swipl-devel/src/Tests/core/test_answer.pl | 6 src/swipl-devel/src/Tests/library/test_date.pl | 4 src/swipl-devel/src/Tests/tabling/test_tabled_shortest_path.pl |only src/swipl-devel/src/minizip/MiniZip64_Changes.txt | 2 src/swipl-devel/src/minizip/configure.ac | 2 src/swipl-devel/src/minizip/crypt.h | 29 src/swipl-devel/src/minizip/ioapi.c | 77 src/swipl-devel/src/minizip/ioapi.h | 44 src/swipl-devel/src/minizip/iowin32.c | 70 src/swipl-devel/src/minizip/iowin32.h | 8 src/swipl-devel/src/minizip/miniunz.c | 101 src/swipl-devel/src/minizip/minizip.c | 85 src/swipl-devel/src/minizip/mztools.c | 8 src/swipl-devel/src/minizip/unzip.c | 556 +-- src/swipl-devel/src/minizip/unzip.h | 154 src/swipl-devel/src/minizip/zip.c | 351 - src/swipl-devel/src/minizip/zip.h | 310 - src/swipl-devel/src/os/SWI-Stream.h | 3 src/swipl-devel/src/os/pl-file.c | 166 src/swipl-devel/src/os/pl-file.h | 18 src/swipl-devel/src/os/pl-fmt.c | 4 src/swipl-devel/src/os/pl-prologflag.c | 10 src/swipl-devel/src/os/pl-stream.c | 71 src/swipl-devel/src/os/pl-stream.h | 9 src/swipl-devel/src/pl-atom.c | 6 src/swipl-devel/src/pl-bag.c | 81 src/swipl-devel/src/pl-bag.h | 4 src/swipl-devel/src/pl-coverage.c | 4 src/swipl-devel/src/pl-debug.c | 2 src/swipl-devel/src/pl-debug.h | 2 src/swipl-devel/src/pl-ext.c | 2 src/swipl-devel/src/pl-fli.c | 12 src/swipl-devel/src/pl-global.h | 20 src/swipl-devel/src/pl-init.c | 237 - src/swipl-devel/src/pl-init.h | 2 src/swipl-devel/src/pl-nt.c | 21 src/swipl-devel/src/pl-ntmain.c | 29 src/swipl-devel/src/pl-qlf.c | 64 src/swipl-devel/src/pl-segstack.c | 40 src/swipl-devel/src/pl-segstack.h | 7 src/swipl-devel/src/pl-setup.c | 10 src/swipl-devel/src/pl-string.c | 4 src/swipl-devel/src/pl-thread.c | 87 src/swipl-devel/src/pl-thread.h | 8 src/swipl-devel/src/pl-trace.c | 2 src/swipl-devel/src/pl-write.c | 5 src/swipl-devel/src/test.pl | 30 src/swipl-devel/src/wasm/README.md |only src/swipl-devel/src/wasm/bind.html |only src/swipl-devel/src/wasm/index.html | 1 src/swipl-devel/src/wasm/prolog.js | 1 src/swipl-devel/src/wasm/runtime_exports.json | 1 src/swipl-devel/src/wasm/server.pl | 34 src/swipl-devel/src/wasm/shell.html | 4 131 files changed, 5506 insertions(+), 3007 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can
check if a background process is running; wait on a background process
to finish; get the exit status of finished processes; kill background
processes. It can read the standard output and error of the processes,
using non-blocking connections. 'processx' can poll a process for
standard output or error, with a timeout. It can also poll several
processes at once.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
Posit Software, PBC [cph, fnd],
Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between processx versions 3.8.3 dated 2023-12-10 and 3.8.4 dated 2024-03-16
DESCRIPTION | 12 ++++++------ LICENSE | 4 ++-- MD5 | 13 +++++++------ NEWS.md | 4 ++++ README.md | 2 +- inst/COPYRIGHTS |only man/processx-package.Rd | 2 +- src/init.c | 19 +++++++++++++++++++ 8 files changed, 40 insertions(+), 16 deletions(-)
Title: High Performance Implementation of the Naive Bayes Algorithm
Description: In this implementation of the Naive Bayes classifier
following class conditional distributions are available: 'Bernoulli',
'Categorical', 'Gaussian', 'Poisson', 'Multinomial' and non-parametric
representation of the class conditional density estimated via Kernel
Density Estimation. Implemented classifiers handle missing data and
can take advantage of sparse data.
Author: Michal Majka [aut, cre]
Maintainer: Michal Majka <michalmajka@hotmail.com>
Diff between naivebayes versions 0.9.7 dated 2020-03-08 and 1.0.0 dated 2024-03-16
DESCRIPTION | 29 + MD5 | 64 +-- R/bernoulli_naive_bayes.R | 17 - R/gaussian_naive_bayes.R | 12 R/misc.R | 9 R/multinomial_naive_bayes.R | 15 R/nonparametric_naive_bayes.R | 15 R/poisson_naive_bayes.R | 17 - R/predict.naive_bayes.R | 21 - R/print.naive_bayes.R | 12 R/print.naive_bayes_tables.R | 33 - R/summary.naive_bayes.R | 5 build/vignette.rds |binary inst/CITATION | 2 inst/NEWS.Rd | 13 inst/doc/intro_naivebayes.R | 246 +++++++++----- inst/doc/intro_naivebayes.Rnw | 493 +++++++++++++++++++---------- inst/doc/intro_naivebayes.pdf |binary man/bernoulli_naive_bayes.Rd | 1 man/figures/kde-1.png |binary man/figures/kde-2.png |binary man/figures/kde_adjust-1.png |binary man/figures/kde_bw-1.png |binary man/figures/kde_kernel-1.png |binary man/figures/poisson-1.png |binary man/figures/poisson-2.png |binary man/gaussian_naive_bayes.Rd | 2 man/multinomial_naive_bayes.Rd | 29 + man/naivebayes.Rd | 31 + man/nonparametric_naive_bayes.Rd | 2 man/poisson_naive_bayes.Rd | 1 vignettes/intro_naivebayes-concordance.tex | 4 vignettes/intro_naivebayes.Rnw | 493 +++++++++++++++++++---------- 33 files changed, 1026 insertions(+), 540 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.15-4 dated 2023-10-22 and 2.16-1 dated 2024-03-16
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + R/treegoer.R |only inst/ChangeLog | 12 +++++++++++- man/treegoer.Rd |only 6 files changed, 21 insertions(+), 8 deletions(-)
Title: Wrapper for 'Visa Chart Components'
Description: Provides a set of wrapper functions for 'Visa Chart Components'.
'Visa Chart Components' <https://github.com/visa/visa-chart-components> is an accessibility focused,
framework agnostic set of data experience design systems components for the web.
Author: Christopher DeMartini [aut, cre],
Stephanie Modica [aut],
David Kutas [aut],
Jaime Tanner [aut],
Frank Elavsky [aut],
Wojtek Kostelecki [ctb],
Visa Data Experience Team [aut, fnd],
Visa, Inc. [cph]
Maintainer: Christopher DeMartini <chris.demartini.npm@gmail.com>
Diff between visachartR versions 3.2.0 dated 2023-10-06 and 3.3.0 dated 2024-03-16
visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-02a12e6e.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-033e8797.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-0a4325d4.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-10e6839b.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-10f35386.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-13680a52.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-17a4b994.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-19a4f06b.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-1c8b622e.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-2c07c4b3.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-38713fe1.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-3e62422c.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-48149074.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-49b3e656.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-4b199693.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-4ca387c2.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-4d739442.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-57d3a351.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-595f70a7.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-5aee2b76.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-5e793f5c.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-640145c6.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-66dbebec.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-6737e9f6.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-706fbd75.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-79a60478.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7b3191f4.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7d3d6ab8.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-818eb7ff.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-83dc6199.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-89f93093.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a21b1bc0.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a2704cb7.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a2cbd5ab.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-b11333b4.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-b9c5f66c.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-bc68d7f5.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-be615bb3.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-c555bdb7.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-cc34c52b.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-d1b352ab.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-df51eb7c.system.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-ed125cb5.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-efcb8e13.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-f3fa3b46.system.entry.js |only visachartR-3.2.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-f54e8bed.system.js |only visachartR-3.3.0/visachartR/DESCRIPTION | 8 visachartR-3.3.0/visachartR/MD5 | 108 +++++----- visachartR-3.3.0/visachartR/NEWS.md | 14 + visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/charts.esm.js | 4 visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-080aaab6.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-0b96172d.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-0c4cf0fa.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-0ed8b3b5.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-11aac691.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-1f775dc3.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-27f768e1.system.js | 4 visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-2918efe2.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-2ce88f16.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-2f90bdc4.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-32bc4b3b.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-38153388.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-3867c5ab.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-3dae7af0.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-45691346.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-4658b73a.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-5783562f.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-5c4b9788.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-63ec12bd.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-6812b7e2.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-6f1df621.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7494cafb.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7658b7d7.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-78b70151.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7b0b7a9e.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7be0a444.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7c7ee7e9.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-7cef192e.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-85d34e7b.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-8e11a6c4.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-8eb67ad8.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-937c7e2a.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-96722878.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-9cc83250.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a01feafa.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a480705f.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a494a9b5.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-a84a9dfe.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-aa9e3d3e.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-ae865b4c.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-b3cc0ee5.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-b62f42bc.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-b7c1501d.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-bdfdaf83.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-cb36b831.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-d2fbb372.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-e6f1019b.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-ea8eb695.system.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-f19973de.system.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-fef5c4ba.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/lib/visa-chart-components/p-ff55a283.entry.js |only visachartR-3.3.0/visachartR/inst/htmlwidgets/visaChart.yaml | 4 visachartR-3.3.0/visachartR/inst/htmlwidgets/visaNodeLinkChart.yaml | 4 103 files changed, 82 insertions(+), 64 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <ByrneL54@tcd.ie>
Diff between DImodelsMulti versions 1.0 dated 2024-01-16 and 1.0.1 dated 2024-03-16
DESCRIPTION | 6 MD5 | 20 - R/DImulti_fit.R | 32 +- R/DImulti_vcov.R | 4 build/vignette.rds |binary inst/doc/DImulti_onTheta.Rmd | 2 inst/doc/DImulti_workflow.R | 17 - inst/doc/DImulti_workflow.Rmd | 36 +- inst/doc/DImulti_workflow.html | 525 +++++++++++++++++------------------------ vignettes/DImulti_onTheta.Rmd | 2 vignettes/DImulti_workflow.Rmd | 36 +- 11 files changed, 297 insertions(+), 383 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-01 2.4
2022-11-15 2.3
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.49 dated 2023-11-22 and 0.50 dated 2024-03-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/install.R | 12 ++++++++++-- R/tlmgr.R | 2 +- man/install_tinytex.Rd | 3 ++- 5 files changed, 21 insertions(+), 12 deletions(-)
Title: Generalized Two Arms Clinical Trial Sample Size Calculation
Description: Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19%3C2689::aid-sim555%3E3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.
Author: Mohsen Soltanifar [aut] ,
Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>
Diff between GenTwoArmsTrialSize versions 0.0.4.5 dated 2023-12-11 and 0.0.5 dated 2024-03-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/main.R | 36 ++++++++++++++++++------------------ inst/doc/tutorial.html | 4 ++-- 4 files changed, 26 insertions(+), 26 deletions(-)
More information about GenTwoArmsTrialSize at CRAN
Permanent link
Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate
abundance and run-timing from temporally-stratified
Petersen mark-recapture experiments. Methods include
hierarchical modelling of the capture probabilities
and spline smoothing of the daily run size. Theory
described in Bonner and Schwarz (2011)
<doi:10.1111/j.1541-0420.2011.01599.x>.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and
Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between BTSPAS versions 2021.11.2 dated 2021-10-25 and 2024.4.1 dated 2024-03-15
DESCRIPTION | 10 ++-- MD5 | 42 ++++++++++---------- NEWS.md | 9 ++++ R/TimeStratPetersenDiagError_fit.R | 11 ----- R/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.R | 10 ---- R/TimeStratPetersenNonDiagErrorNP_fit.R | 10 ---- R/TimeStratPetersenNonDiagError_fit.R | 10 ---- R/TimeToTargetRunSize.r | 2 R/plot_trace.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 +++++++++--------- man/RunTime.Rd | 2 man/TimeStratPetersenDiagErrorWHChinook_fit.Rd | 2 man/TimeStratPetersenDiagErrorWHSteel_fit.Rd | 2 man/TimeStratPetersenDiagError_fit.Rd | 4 - man/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.Rd | 2 man/TimeStratPetersenNonDiagErrorNP_fit.Rd | 2 man/TimeStratPetersenNonDiagError_fit.Rd | 2 man/TimeToTargetRunSize.Rd | 2 man/plot_trace.Rd | 2 vignettes/a-Diagonal-model.Rmd | 2 22 files changed, 72 insertions(+), 94 deletions(-)
Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation
of 'rmarkdown' reports, supporting reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre] ,
Kartikeya Kirar [aut] ,
Marcin Kosinski [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Mahmoud Hallal [aut],
Chendi Liao [rev],
Dony Unardi [rev],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.reporter versions 0.3.0 dated 2024-02-16 and 0.3.1 dated 2024-03-15
teal.reporter-0.3.0/teal.reporter/man/add_card_button_srv.Rd |only teal.reporter-0.3.0/teal.reporter/man/add_card_button_ui.Rd |only teal.reporter-0.3.0/teal.reporter/man/download_report_button_srv.Rd |only teal.reporter-0.3.0/teal.reporter/man/download_report_button_ui.Rd |only teal.reporter-0.3.0/teal.reporter/man/reporter_previewer_srv.Rd |only teal.reporter-0.3.0/teal.reporter/man/reporter_previewer_ui.Rd |only teal.reporter-0.3.0/teal.reporter/man/reset_report_button_srv.Rd |only teal.reporter-0.3.0/teal.reporter/man/reset_report_button_ui.Rd |only teal.reporter-0.3.0/teal.reporter/man/simple_reporter_srv.Rd |only teal.reporter-0.3.0/teal.reporter/man/simple_reporter_ui.Rd |only teal.reporter-0.3.1/teal.reporter/DESCRIPTION | 27 - teal.reporter-0.3.1/teal.reporter/MD5 | 142 +++---- teal.reporter-0.3.1/teal.reporter/NEWS.md | 6 teal.reporter-0.3.1/teal.reporter/R/AddCardModule.R | 77 +-- teal.reporter-0.3.1/teal.reporter/R/Archiver.R | 58 ++ teal.reporter-0.3.1/teal.reporter/R/ContentBlock.R | 25 - teal.reporter-0.3.1/teal.reporter/R/DownloadModule.R | 76 ++- teal.reporter-0.3.1/teal.reporter/R/FileBlock.R | 15 teal.reporter-0.3.1/teal.reporter/R/NewpageBlock.R | 8 teal.reporter-0.3.1/teal.reporter/R/PictureBlock.R | 45 +- teal.reporter-0.3.1/teal.reporter/R/Previewer.R | 46 +- teal.reporter-0.3.1/teal.reporter/R/RcodeBlock.R | 27 - teal.reporter-0.3.1/teal.reporter/R/Renderer.R | 57 +- teal.reporter-0.3.1/teal.reporter/R/ReportCard.R | 99 ++-- teal.reporter-0.3.1/teal.reporter/R/Reporter.R | 148 ++++--- teal.reporter-0.3.1/teal.reporter/R/ResetModule.R | 30 - teal.reporter-0.3.1/teal.reporter/R/SimpleReporter.R | 50 +- teal.reporter-0.3.1/teal.reporter/R/TableBlock.R | 20 teal.reporter-0.3.1/teal.reporter/R/TextBlock.R | 28 - teal.reporter-0.3.1/teal.reporter/R/utils.R | 38 - teal.reporter-0.3.1/teal.reporter/R/yaml_utils.R | 106 +++-- teal.reporter-0.3.1/teal.reporter/README.md | 2 teal.reporter-0.3.1/teal.reporter/build/vignette.rds |binary teal.reporter-0.3.1/teal.reporter/inst/WORDLIST | 2 teal.reporter-0.3.1/teal.reporter/inst/css/Previewer.css | 12 teal.reporter-0.3.1/teal.reporter/inst/doc/previewerReporter.R | 19 teal.reporter-0.3.1/teal.reporter/inst/doc/previewerReporter.Rmd | 53 +- teal.reporter-0.3.1/teal.reporter/inst/doc/previewerReporter.html | 189 ++++----- teal.reporter-0.3.1/teal.reporter/inst/doc/simpleReporter.R | 32 - teal.reporter-0.3.1/teal.reporter/inst/doc/simpleReporter.Rmd | 66 +-- teal.reporter-0.3.1/teal.reporter/inst/doc/simpleReporter.html | 202 +++++----- teal.reporter-0.3.1/teal.reporter/inst/doc/teal-reporter.R | 6 teal.reporter-0.3.1/teal.reporter/inst/doc/teal-reporter.Rmd | 32 - teal.reporter-0.3.1/teal.reporter/inst/doc/teal-reporter.html | 182 ++++----- teal.reporter-0.3.1/teal.reporter/man/Archiver.Rd | 17 teal.reporter-0.3.1/teal.reporter/man/ContentBlock.Rd | 25 - teal.reporter-0.3.1/teal.reporter/man/FileArchiver.Rd | 15 teal.reporter-0.3.1/teal.reporter/man/FileBlock.Rd | 16 teal.reporter-0.3.1/teal.reporter/man/JSONArchiver.Rd | 41 +- teal.reporter-0.3.1/teal.reporter/man/NewpageBlock.Rd | 9 teal.reporter-0.3.1/teal.reporter/man/PictureBlock.Rd |only teal.reporter-0.3.1/teal.reporter/man/RcodeBlock.Rd | 28 - teal.reporter-0.3.1/teal.reporter/man/Renderer.Rd | 85 ++-- teal.reporter-0.3.1/teal.reporter/man/ReportCard.Rd | 121 +++-- teal.reporter-0.3.1/teal.reporter/man/Reporter.Rd | 197 +++++---- teal.reporter-0.3.1/teal.reporter/man/TableBlock.Rd | 21 - teal.reporter-0.3.1/teal.reporter/man/TextBlock.Rd | 29 - teal.reporter-0.3.1/teal.reporter/man/add_card_button.Rd |only teal.reporter-0.3.1/teal.reporter/man/as_yaml_auto.Rd | 31 - teal.reporter-0.3.1/teal.reporter/man/conv_str_logi.Rd | 14 teal.reporter-0.3.1/teal.reporter/man/download_report_button.Rd |only teal.reporter-0.3.1/teal.reporter/man/get_yaml_field.Rd | 9 teal.reporter-0.3.1/teal.reporter/man/md_header.Rd | 9 teal.reporter-0.3.1/teal.reporter/man/panel_item.Rd | 8 teal.reporter-0.3.1/teal.reporter/man/print.rmd_yaml_header.Rd | 6 teal.reporter-0.3.1/teal.reporter/man/report_render_and_compress.Rd | 12 teal.reporter-0.3.1/teal.reporter/man/reporter_download_inputs.Rd | 12 teal.reporter-0.3.1/teal.reporter/man/reporter_previewer.Rd |only teal.reporter-0.3.1/teal.reporter/man/reset_report_button.Rd |only teal.reporter-0.3.1/teal.reporter/man/rmd_output_arguments.Rd | 7 teal.reporter-0.3.1/teal.reporter/man/rmd_outputs.Rd | 4 teal.reporter-0.3.1/teal.reporter/man/simple_reporter.Rd |only teal.reporter-0.3.1/teal.reporter/man/split_text_block.Rd | 8 teal.reporter-0.3.1/teal.reporter/man/teal.reporter-package.Rd | 2 teal.reporter-0.3.1/teal.reporter/man/to_flextable.Rd | 15 teal.reporter-0.3.1/teal.reporter/man/yaml_quoted.Rd | 10 teal.reporter-0.3.1/teal.reporter/tests/testthat/test-PictureBlock.R | 2 teal.reporter-0.3.1/teal.reporter/vignettes/previewerReporter.Rmd | 53 +- teal.reporter-0.3.1/teal.reporter/vignettes/simpleReporter.Rmd | 66 +-- teal.reporter-0.3.1/teal.reporter/vignettes/teal-reporter.Rmd | 32 - 80 files changed, 1572 insertions(+), 1257 deletions(-)
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks
Description: Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between SpatialDDLS versions 1.0.0 dated 2023-12-06 and 1.0.1 dated 2024-03-15
DESCRIPTION | 8 MD5 | 65 ++- NEWS.md | 8 R/SpatialDDLS.R | 4 R/interGradientsDL.R | 10 R/loadData.R | 13 R/simSingleCell.R | 4 README.md | 13 build/vignette.rds |binary inst/doc/realModelExample.Rmd | 214 ++++++++---- inst/doc/realModelExample.html | 495 ++++++++++++++++------------- man/SpatialDDLS-Rpackage.Rd | 4 man/createSpatialDDLSobject.Rd | 4 man/figures/summary.png |binary vignettes/abserr-celltype-1.png |binary vignettes/abserr-celltype-sep-1.png |binary vignettes/clustering-1.png |binary vignettes/corr-pred-1.png |binary vignettes/distances-1.png |binary vignettes/negative-grad-1.png |binary vignettes/positive-grad-1.png |binary vignettes/pred-spatial-1.png |binary vignettes/pred-spatial-sep-1.png |binary vignettes/pred-spatial-sep-2.png |binary vignettes/pred-spatial-sep-3.png |binary vignettes/pred-spatial-sep-extrinsic-1.png |binary vignettes/pred-spatial-sep-extrinsic-2.png |binary vignettes/pred-spatial-sep-extrinsic-3.png |binary vignettes/realModelExample.Rmd | 214 ++++++++---- vignettes/realModelExample.Rmd.orig | 72 ++-- vignettes/references.bib | 17 vignettes/top-genes-spatial-1.png |only vignettes/top-genes-spatial-2.png |only vignettes/top-genes-spatial-3.png |only vignettes/top-genes-spatial-4.png |only vignettes/top-genes-spatial-5.png |only 36 files changed, 691 insertions(+), 454 deletions(-)
Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] ,
Barret Schloerke [aut] ,
Carson Sievert [aut, cre] ,
Christophe Dervieux [ctb] ,
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] ,
Greter Marcel [ctb, cph] ,
Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.4.8 dated 2023-12-05 and 0.4.9 dated 2024-03-15
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NEWS.md | 4 ++ R/fonts.R | 29 +++++++++++++----- inst/doc/sass.Rmd | 2 - inst/doc/sass.html | 43 +++++++++++++--------------- man/font_face.Rd | 2 - src/libsass/src/memory/shared_ptr.hpp | 2 - tests/testthat/_snaps/font-objects/font-css | 40 +++++++++++++++++++++++++- tests/testthat/test-font-objects.R | 21 ++++++++++++- vignettes/sass.Rmd | 2 - 11 files changed, 121 insertions(+), 52 deletions(-)
Title: Computing P-Values of the K-S Test for (Dis)Continuous Null
Distribution
Description: Computes a p-value of the one-sample two-sided (or one-sided, as a special case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an arbitrary, possibly large sample size for a pre-specified purely discrete, mixed or continuous cumulative distribution function (cdf) under the null hypothesis. If a data sample is supplied, 'KSgeneral' computes the p-value corresponding to the value of the KS test statistic computed based on the user provided data sample. The package 'KSgeneral' implements a novel, accurate and efficient method named Exact-KS-FFT, expressing the p-value as a double-boundary non-crossing probability for a homogeneous Poisson process, which is then efficiently computed using Fast Fourier Transform (FFT). The package can also be used to compute and plot the complementary cdf of the KS statistic which is known to depend on the hypothesized distribution when the latter is discontinuous (i.e. purely discrete or mixed). To cite this package in publication us [...truncated...]
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Yun Jia <yunjia2019@gmail.com>,
Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk> and
Senren Tan <raymondtsrtsr@outlook.com>
Maintainer: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>
Diff between KSgeneral versions 1.1.2 dated 2023-07-10 and 1.1.3 dated 2024-03-15
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/RcppExports.R | 14 +++++++------- build/partial.rdb |binary 4 files changed, 15 insertions(+), 14 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.19.8 dated 2024-01-31 and 0.19.9 dated 2024-03-15
DESCRIPTION | 17 +- MD5 | 90 ++++++------ NAMESPACE | 9 + NEWS.md | 22 +++ R/apply_table_theme.R | 16 -- R/compute_variances.R | 231 +++++++++++++++----------------- R/find_parameters_mixed.R | 2 R/find_predictors.R | 22 ++- R/find_statistic.R | 20 +- R/format_ci.R | 119 ++++++++++++---- R/get_df.R | 9 - R/get_df_residual.R | 21 +- R/get_modelmatrix.R | 24 ++- R/get_parameters.R | 2 R/get_parameters_mixed.R | 35 ++-- R/get_predicted_args.R | 42 ++--- R/get_predicted_ci.R | 8 - R/get_statistic.R | 44 +++--- R/get_varcov.R | 113 +++++++++------ R/is_model.R | 2 R/is_model_supported.R | 4 R/is_multivariate.R | 11 - R/link_function.R | 18 +- R/link_inverse.R | 18 +- R/model_info.R | 3 R/null_model.R | 4 R/standardize_names.R | 1 R/utils_model_info.R | 2 README.md | 106 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/display.html | 214 ++++++++++++++--------------- inst/doc/export.html | 2 inst/doc/insight.html | 2 man/export_table.Rd | 2 man/format_ci.Rd | 19 ++ tests/testthat/test-BayesFactorBF.R | 1 tests/testthat/test-PROreg.R |only tests/testthat/test-apply_table_theme.R |only tests/testthat/test-coxme.R | 6 tests/testthat/test-format.R | 36 ++++ tests/testthat/test-get_varcov.R | 7 tests/testthat/test-marginaleffects.R | 11 + tests/testthat/test-mgcv.R |only tests/testthat/test-rqss.R | 15 +- tests/testthat/test-serp.R |only tests/testthat/test-vgam.R | 4 48 files changed, 769 insertions(+), 568 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: Provide the EMU Speech Database Management System (EMU-SDMS) with
database management, data extraction, data preparation and data
visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/>
for more details.
Author: Markus Jochim [aut, cre] ,
Raphael Winkelmann [aut],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Markus Jochim <markusjochim@phonetik.uni-muenchen.de>
Diff between emuR versions 2.4.2 dated 2023-11-03 and 2.5.0 dated 2024-03-15
DESCRIPTION | 10 MD5 | 26 - NAMESPACE | 1 NEWS.md | 12 R/emuR-annotations_crud.R | 512 +++++++++++++++++++++------- R/emuR-crud-helpers.R | 35 + R/emuR-emuRsegs.R | 2 R/emuR-packageDocs.R | 3 R/emusegs.R | 8 man/create_itemsInLevel.Rd | 166 ++++++--- man/delete_itemsInLevel.Rd | 51 ++ man/emuR-package.Rd | 21 + man/update_itemsInLevel.Rd | 37 +- tests/testthat/test_emuR-annotations_crud.R | 3 14 files changed, 661 insertions(+), 226 deletions(-)
Title: LiDAR Data Voxelisation
Description: Read, manipulate and write voxel spaces. Voxel spaces are
read from text-based output files of the 'AMAPVox' software. 'AMAPVox'
is a LiDAR point cloud voxelisation software that aims at estimating
leaf area through several theoretical/numerical approaches. See more
in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the
technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.
Author: Gregoire Vincent [aut],
Julien Heurtebize [aut],
Philippe Verley [aut, cre]
Maintainer: Philippe Verley <philippe.verley@ird.fr>
Diff between AMAPVox versions 1.0.1 dated 2023-06-22 and 2.2.1 dated 2024-03-15
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/AMAPVox.R | 2 +- R/VersionManager.R | 30 ++++++++++++++++++++---------- build/partial.rdb |binary inst/doc/AMAPVox.R | 2 +- inst/doc/Installation.R | 2 +- inst/doc/Publications.R | 6 +++--- inst/doc/Voxelization.R | 2 +- inst/doc/amapvox-gui.R | 2 +- man/AMAPVox.Rd | 6 +++--- man/installVersion.Rd | 6 +++++- 13 files changed, 62 insertions(+), 39 deletions(-)
Title: Clinical Graphs and Tables Adhering to Graphical Principles
Description: To enable fit-for-purpose, reusable clinical and medical
research focused visualizations and tables with sensible defaults and
based on graphical principles as described in: "Vandemeulebroecke et
al. (2018)" <doi:10.1002/pst.1912>, "Vandemeulebroecke et al. (2019)"
<doi:10.1002/psp4.12455>, and "Morris et al. (2019)"
<doi:10.1136/bmjopen-2019-030215>.
Author: Mark Baillie [aut, cre, cph],
Diego Saldana [aut],
Charlotta Fruechtenicht [aut],
Marc Vandemeulebroecke [aut],
Thanos Siadimas [aut],
Pawel Kawski [aut],
Steven Haesendonckx [aut],
James Black [aut],
Pelagia Alexandra Papadopoulou [aut],
Tim Treis [ [...truncated...]
Maintainer: Mark Baillie <bailliem@gmail.com>
Diff between visR versions 0.4.0 dated 2023-11-20 and 0.4.1 dated 2024-03-15
DESCRIPTION | 9 MD5 | 20 NEWS.md | 2 R/add_highlight.R | 42 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/CDISC_ADaM.html | 212 +++--- inst/doc/Time_to_event_analysis.html | 1072 ++++++++++++++--------------------- man/visR-package.Rd | 1 tests/testthat/helper.R | 5 tests/testthat/test-utils_visR.R | 4 11 files changed, 600 insertions(+), 767 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested fra [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.5.1 dated 2023-11-25 and 3.6.0 dated 2024-03-15
DESCRIPTION | 17 MD5 | 75 NAMESPACE | 12 NEWS | 5 R/SurvIC.R | 3 R/dataHelp.R | 31 R/frailtyPenal.R | 3 R/frailtypack-package.R | 75 R/jointRecCompet.R |only R/longiPenal.R | 547 ++ R/plot.jointRecCompet.R |only R/plot.longiPenal.R | 210 - R/print.jointRecCompet.R |only R/print.longiPenal.R | 134 R/simulatejointRecCompet.R |only R/summary.jointRecCompet.R |only R/summary.longiPenal.R | 31 R/trivPenal.R | 62 data/reduce.rda |only man/figures/logo.png |only man/frailtyPenal.Rd | 3 man/frailtypack-package.Rd | 75 man/jointRecCompet.Rd |only man/longiPenal.Rd | 95 man/plot.jointRecCompet.Rd |only man/plot.longiPenal.Rd | 13 man/print.jointRecCompet.Rd |only man/print.longiPenal.Rd | 7 man/reduce.Rd |only man/simulatejointRecCompet.Rd |only man/summary.jointRecCompet.Rd |only man/summary.longiPenal.Rd | 6 src/Adonnees.f90 | 832 ++++ src/AparamMultive.f90 | 217 - src/Aparameters.f90 | 14 src/Integrale_mult_scl.f90 | 4 src/aaUseFunction.f90 | 202 src/distance.f90 | 69 src/frailtypack.h | 17 src/funcpajcompetingsplines.f90 |only src/funcpajcompetingweib.f90 |only src/funcpajlongisplines.f90 | 3 src/funcpajlongisplines2.f90 |only src/init.c | 1 src/joint_competing.f90 |only src/joint_longi.f90 | 8175 ++++++++++++++++++++++------------------ src/natural_effects.f90 | 658 +++ 47 files changed, 7540 insertions(+), 4056 deletions(-)
Title: Standardized Folder Names
Description: Supports the use of standardized folder names.
Author: Brian High [aut, cre],
University of Washington [cph, fnd]
Maintainer: Brian High <bhigh@live.com>
Diff between folders versions 0.0.6 dated 2023-03-14 and 0.1.0 dated 2024-03-15
DESCRIPTION | 6 - MD5 | 22 ++-- R/cleanup_folders.R | 45 ++++++--- R/create_folders.R | 19 ++- R/get_folders.R | 25 ++--- README.md | 166 +++++++++++++++++++++++----------- man/cleanup_folders.Rd | 28 +++-- man/create_folders.Rd | 19 ++- man/get_folders.Rd | 20 +--- tests/testthat/test-cleanup_folders.R | 111 +++++++++++++++++++--- tests/testthat/test-create_folders.R | 9 + tests/testthat/test-get_folders.R | 29 ++++- 12 files changed, 353 insertions(+), 146 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in the educational and social sciences,
data is often unbalanced in terms of
frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'keras',
'tensorflow', and 'pytorch' to deal with natural language problems. In addition,
the package ships with a shiny app, providing a graphical user interface.
This allows the usage of AI for people without skills in writing python/R scripts.
The tools integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Lee (2013)
<https://www.researchgate.net/publication/280581078_Pseudo-Label_The_Simple_and_Efficie [...truncated...]
Author: Berding Florian [aut, cre] ,
Pargmann Julia [ctb],
Riebenbauer Elisabeth [ctb],
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 0.3.1 dated 2024-02-18 and 0.3.2 dated 2024-03-15
DESCRIPTION | 6 MD5 | 78 +++--- NAMESPACE | 2 NEWS.md | 42 +++ R/aif_gui.R | 159 +++++++++++-- R/aux_fct.R | 68 +++++ R/install_and_config.R | 14 - R/onLoad.R | 2 R/te_classifier_neuralnet_model.R | 2 R/text_embedding_model.R | 324 ++++++++++++++++++++++----- R/transformer_bert.R | 29 ++ R/transformer_deberta_v2.R | 24 +- R/transformer_funnel.R | 22 + R/transformer_longformer.R | 24 +- R/transformer_roberta.R | 24 +- inst/python/pytorch_te_classifier.py | 24 +- inst/python/pytorch_transformer_callbacks.py | 3 man/EmbeddedText.Rd | 15 + man/TextEmbeddingClassifierNeuralNet.Rd | 2 man/TextEmbeddingModel.Rd | 40 ++- man/array_to_matrix.Rd | 2 man/calc_standard_classification_measures.Rd | 2 man/check_embedding_models.Rd | 2 man/clean_pytorch_log_transformers.Rd |only man/create_iota2_mean_object.Rd | 2 man/create_synthetic_units.Rd | 2 man/generate_id.Rd | 2 man/get_coder_metrics.Rd | 2 man/get_folds.Rd | 2 man/get_n_chunks.Rd | 2 man/get_stratified_train_test_split.Rd | 2 man/get_synthetic_cases.Rd | 2 man/get_train_test_split.Rd | 2 man/install_py_modules.Rd | 114 ++++----- man/is.null_or_na.Rd |only man/matrix_to_array_c.Rd | 2 man/split_labeled_unlabeled.Rd | 2 man/summarize_tracked_sustainability.Rd | 2 man/to_categorical_c.Rd | 2 tests/testthat/test-02_basic_text_rep.R | 2 tests/testthat/test-04_transformer_models.R | 116 ++++++++- 41 files changed, 927 insertions(+), 241 deletions(-)
Title: Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait
data associated with the tips of a phylogenetic tree. Examples of such models
are Gaussian continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the
tips of the tree as an observed (final) state of a Markov process starting from
an initial state at the root and evolving along the branches of the tree. The
PCMBase R package provides a general framework for manipulating such models.
This framework consists of an application programming interface for specifying
data and model parameters, and efficient algorithms for simulating trait evolution
under a model and calculating the likelihood of model parameters for an assumed
model and trait data. The package implements a growing collection of models,
which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed
Gaussian models, in which different types of the above model [...truncated...]
Author: Venelin Mitov [aut, cre, cph] ,
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBase versions 1.2.13 dated 2022-11-18 and 1.2.14 dated 2024-03-15
PCMBase-1.2.13/PCMBase/vignettes/PCMBMkappa.zip |only PCMBase-1.2.14/PCMBase/DESCRIPTION | 14 PCMBase-1.2.14/PCMBase/MD5 | 379 PCMBase-1.2.14/PCMBase/NAMESPACE | 2562 - PCMBase-1.2.14/PCMBase/NEWS.md | 164 PCMBase-1.2.14/PCMBase/R/AutoGeneratedModelTypes.R |21380 +++++----- PCMBase-1.2.14/PCMBase/R/BM.R | 234 PCMBase-1.2.14/PCMBase/R/BMdrift.R | 268 PCMBase-1.2.14/PCMBase/R/DOU.R | 348 PCMBase-1.2.14/PCMBase/R/DefaultModelTypes.R | 346 PCMBase-1.2.14/PCMBase/R/GaussianPCM.R | 2532 - PCMBase-1.2.14/PCMBase/R/JOU.R | 354 PCMBase-1.2.14/PCMBase/R/LatexTools.R | 204 PCMBase-1.2.14/PCMBase/R/MixedGaussian.R | 856 PCMBase-1.2.14/PCMBase/R/OU.R | 392 PCMBase-1.2.14/PCMBase/R/PCM.R | 4438 +- PCMBase-1.2.14/PCMBase/R/PCMBaseTestObjects.R | 144 PCMBase-1.2.14/PCMBase/R/PCMParam.R | 3097 - PCMBase-1.2.14/PCMBase/R/PCMTable.R | 394 PCMBase-1.2.14/PCMBase/R/PCMTree.R | 5349 +- PCMBase-1.2.14/PCMBase/R/Utilities.R | 908 PCMBase-1.2.14/PCMBase/R/White.R | 228 PCMBase-1.2.14/PCMBase/R/matrixparametrizations.R | 1224 PCMBase-1.2.14/PCMBase/R/zzz.R | 46 PCMBase-1.2.14/PCMBase/README.md | 469 PCMBase-1.2.14/PCMBase/build/vignette.rds |binary PCMBase-1.2.14/PCMBase/inst/CITATION | 118 PCMBase-1.2.14/PCMBase/inst/doc/PCMBase.R | 325 PCMBase-1.2.14/PCMBase/inst/doc/PCMBase.Rmd | 654 PCMBase-1.2.14/PCMBase/inst/doc/PCMBase.html | 1910 PCMBase-1.2.14/PCMBase/inst/doc/PCMCreateModel.R | 469 PCMBase-1.2.14/PCMBase/inst/doc/PCMCreateModel.Rmd | 877 PCMBase-1.2.14/PCMBase/inst/doc/PCMCreateModel.html | 1485 PCMBase-1.2.14/PCMBase/inst/doc/PCMParam.R | 342 PCMBase-1.2.14/PCMBase/inst/doc/PCMParam.Rmd | 580 PCMBase-1.2.14/PCMBase/inst/doc/PCMParam.html | 2086 PCMBase-1.2.14/PCMBase/inst/doc/PCMTracePruning.R | 796 PCMBase-1.2.14/PCMBase/inst/doc/PCMTracePruning.Rmd | 978 PCMBase-1.2.14/PCMBase/inst/doc/PCMTracePruning.html | 8666 ++-- PCMBase-1.2.14/PCMBase/man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd | 48 PCMBase-1.2.14/PCMBase/man/Args_MixedGaussian_MGPMScalarOUType.Rd | 28 PCMBase-1.2.14/PCMBase/man/Args_MixedGaussian_MGPMSurfaceOUType.Rd | 28 PCMBase-1.2.14/PCMBase/man/FormatCellAsLatex.Rd | 36 PCMBase-1.2.14/PCMBase/man/FormatTableAsLatex.Rd | 60 PCMBase-1.2.14/PCMBase/man/MGPMScalarOUType.Rd | 28 PCMBase-1.2.14/PCMBase/man/MGPMSurfaceOUType.Rd | 28 PCMBase-1.2.14/PCMBase/man/MatchListMembers.Rd | 88 PCMBase-1.2.14/PCMBase/man/MixedGaussian.Rd | 162 PCMBase-1.2.14/PCMBase/man/MixedGaussianTemplate.Rd | 72 PCMBase-1.2.14/PCMBase/man/PCM.Rd | 272 PCMBase-1.2.14/PCMBase/man/PCMAbCdEf.Rd | 102 PCMBase-1.2.14/PCMBase/man/PCMAddToListAttribute.Rd | 98 PCMBase-1.2.14/PCMBase/man/PCMApplyTransformation.Rd | 58 PCMBase-1.2.14/PCMBase/man/PCMBaseIsADevRelease.Rd | 28 PCMBase-1.2.14/PCMBase/man/PCMBaseTestObjects.Rd | 110 PCMBase-1.2.14/PCMBase/man/PCMColorPalette.Rd | 60 PCMBase-1.2.14/PCMBase/man/PCMCombineListAttribute.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMCond.GaussianPCM.Rd | 82 PCMBase-1.2.14/PCMBase/man/PCMCond.Rd | 76 PCMBase-1.2.14/PCMBase/man/PCMCondVOU.Rd | 92 PCMBase-1.2.14/PCMBase/man/PCMCreateLikelihood.Rd | 144 PCMBase-1.2.14/PCMBase/man/PCMDefaultModelTypes.Rd | 92 PCMBase-1.2.14/PCMBase/man/PCMDefaultObject.Rd | 48 PCMBase-1.2.14/PCMBase/man/PCMDescribe.Rd | 44 PCMBase-1.2.14/PCMBase/man/PCMDescribeParameters.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMExtractDimensions.Rd | 60 PCMBase-1.2.14/PCMBase/man/PCMExtractRegimes.Rd | 50 PCMBase-1.2.14/PCMBase/man/PCMFindMethod.Rd | 44 PCMBase-1.2.14/PCMBase/man/PCMFixParameter.Rd | 40 PCMBase-1.2.14/PCMBase/man/PCMGenerateModelTypes.Rd | 78 PCMBase-1.2.14/PCMBase/man/PCMGenerateParameterizations.Rd | 102 PCMBase-1.2.14/PCMBase/man/PCMGetAttribute.Rd | 64 PCMBase-1.2.14/PCMBase/man/PCMGetVecParamsRegimesAndModels.Rd | 66 PCMBase-1.2.14/PCMBase/man/PCMInfo.Rd | 168 PCMBase-1.2.14/PCMBase/man/PCMLik.Rd | 236 PCMBase-1.2.14/PCMBase/man/PCMLikDmvNorm.Rd | 132 PCMBase-1.2.14/PCMBase/man/PCMLikTrace.Rd | 150 PCMBase-1.2.14/PCMBase/man/PCMListMembers.Rd | 66 PCMBase-1.2.14/PCMBase/man/PCMListParameterizations.Rd | 80 PCMBase-1.2.14/PCMBase/man/PCMLmr.Rd | 134 PCMBase-1.2.14/PCMBase/man/PCMMapModelTypesToRegimes.Rd | 58 PCMBase-1.2.14/PCMBase/man/PCMMean.Rd | 118 PCMBase-1.2.14/PCMBase/man/PCMMeanAtTime.Rd | 106 PCMBase-1.2.14/PCMBase/man/PCMModelTypes.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMModels.Rd | 58 PCMBase-1.2.14/PCMBase/man/PCMNumRegimes.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMNumTraits.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMOptions.Rd | 178 PCMBase-1.2.14/PCMBase/man/PCMPExpxMeanExp.Rd | 74 PCMBase-1.2.14/PCMBase/man/PCMPLambdaP_1.Rd | 50 PCMBase-1.2.14/PCMBase/man/PCMPairSums.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMParam.Rd | 46 PCMBase-1.2.14/PCMBase/man/PCMParamBindRegimeParams.Rd |only PCMBase-1.2.14/PCMBase/man/PCMParamCount.Rd | 92 PCMBase-1.2.14/PCMBase/man/PCMParamGetShortVector.Rd | 52 PCMBase-1.2.14/PCMBase/man/PCMParamLoadOrStore.Rd | 70 PCMBase-1.2.14/PCMBase/man/PCMParamLocateInShortVector.Rd | 76 PCMBase-1.2.14/PCMBase/man/PCMParamLowerLimit.Rd | 50 PCMBase-1.2.14/PCMBase/man/PCMParamRandomVecParams.Rd | 78 PCMBase-1.2.14/PCMBase/man/PCMParamSetByName.Rd | 96 PCMBase-1.2.14/PCMBase/man/PCMParamType.Rd | 332 PCMBase-1.2.14/PCMBase/man/PCMParamUpperLimit.Rd | 50 PCMBase-1.2.14/PCMBase/man/PCMParentClasses.Rd | 44 PCMBase-1.2.14/PCMBase/man/PCMParseErrorMessage.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMPlotGaussianDensityGrid2D.Rd | 66 PCMBase-1.2.14/PCMBase/man/PCMPlotGaussianSample2D.Rd | 56 PCMBase-1.2.14/PCMBase/man/PCMPlotMath.Rd | 46 PCMBase-1.2.14/PCMBase/man/PCMPlotTraitData2D.Rd | 116 PCMBase-1.2.14/PCMBase/man/PCMPresentCoordinates.Rd | 86 PCMBase-1.2.14/PCMBase/man/PCMRegimes.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMSetAttribute.Rd | 102 PCMBase-1.2.14/PCMBase/man/PCMSim.Rd | 146 PCMBase-1.2.14/PCMBase/man/PCMSpecify.Rd | 44 PCMBase-1.2.14/PCMBase/man/PCMTable.Rd | 70 PCMBase-1.2.14/PCMBase/man/PCMTableParameterizations.Rd | 60 PCMBase-1.2.14/PCMBase/man/PCMTrajectory.Rd | 232 PCMBase-1.2.14/PCMBase/man/PCMTree.Rd | 212 PCMBase-1.2.14/PCMBase/man/PCMTreeBackbonePartition.Rd | 191 PCMBase-1.2.14/PCMBase/man/PCMTreeDropClade.Rd | 144 PCMBase-1.2.14/PCMBase/man/PCMTreeDtNodes.Rd | 66 PCMBase-1.2.14/PCMBase/man/PCMTreeEdgeTimes.Rd | 28 PCMBase-1.2.14/PCMBase/man/PCMTreeEvalNestedEDxOnTree.Rd | 144 PCMBase-1.2.14/PCMBase/man/PCMTreeExtractClade.Rd | 130 PCMBase-1.2.14/PCMBase/man/PCMTreeGetBranchLength.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMTreeGetDaughters.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMTreeGetLabels.Rd | 76 PCMBase-1.2.14/PCMBase/man/PCMTreeGetParent.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMTreeGetPartNames.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMTreeGetPartRegimes.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMTreeGetPartition.Rd | 62 PCMBase-1.2.14/PCMBase/man/PCMTreeGetPartsForNodes.Rd | 42 PCMBase-1.2.14/PCMBase/man/PCMTreeGetRegimesForEdges.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMTreeGetRegimesForNodes.Rd | 42 PCMBase-1.2.14/PCMBase/man/PCMTreeGetTipsInPart.Rd | 71 PCMBase-1.2.14/PCMBase/man/PCMTreeGetTipsInRegime.Rd | 71 PCMBase-1.2.14/PCMBase/man/PCMTreeInsertSingletons.Rd | 284 PCMBase-1.2.14/PCMBase/man/PCMTreeJumps.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMTreeListAllPartitions.Rd | 111 PCMBase-1.2.14/PCMBase/man/PCMTreeListCladePartitions.Rd | 104 PCMBase-1.2.14/PCMBase/man/PCMTreeListDescendants.Rd | 54 PCMBase-1.2.14/PCMBase/man/PCMTreeListRootPaths.Rd | 56 PCMBase-1.2.14/PCMBase/man/PCMTreeLocateEpochOnBranches.Rd | 42 PCMBase-1.2.14/PCMBase/man/PCMTreeLocateMidpointsOnBranches.Rd | 44 PCMBase-1.2.14/PCMBase/man/PCMTreeMatchLabels.Rd | 58 PCMBase-1.2.14/PCMBase/man/PCMTreeMatrixNodesInSamePart.Rd | 150 PCMBase-1.2.14/PCMBase/man/PCMTreeNearestNodesToEpoch.Rd | 38 PCMBase-1.2.14/PCMBase/man/PCMTreeNodeTimes.Rd | 42 PCMBase-1.2.14/PCMBase/man/PCMTreeNumNodes.Rd | 40 PCMBase-1.2.14/PCMBase/man/PCMTreeNumParts.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMTreeNumTips.Rd | 34 PCMBase-1.2.14/PCMBase/man/PCMTreePlot.Rd | 62 PCMBase-1.2.14/PCMBase/man/PCMTreePostorder.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMTreePreorder.Rd | 36 PCMBase-1.2.14/PCMBase/man/PCMTreeSetLabels.Rd | 122 PCMBase-1.2.14/PCMBase/man/PCMTreeSetPartRegimes.Rd | 184 PCMBase-1.2.14/PCMBase/man/PCMTreeSetPartition.Rd | 137 PCMBase-1.2.14/PCMBase/man/PCMTreeSetRegimesForEdges.Rd | 72 PCMBase-1.2.14/PCMBase/man/PCMTreeSplitAtNode.Rd | 116 PCMBase-1.2.14/PCMBase/man/PCMTreeTableAncestors.Rd | 56 PCMBase-1.2.14/PCMBase/man/PCMTreeToString.Rd | 42 PCMBase-1.2.14/PCMBase/man/PCMTreeVCV.Rd | 48 PCMBase-1.2.14/PCMBase/man/PCMUnfixParameter.Rd | 40 PCMBase-1.2.14/PCMBase/man/PCMVar.Rd | 176 PCMBase-1.2.14/PCMBase/man/PCMVarAtTime.Rd | 120 PCMBase-1.2.14/PCMBase/man/RequireSuggestedPackages.Rd |only PCMBase-1.2.14/PCMBase/man/TruePositiveRate.Rd | 78 PCMBase-1.2.14/PCMBase/man/UpperTriFactor.Rd | 76 PCMBase-1.2.14/PCMBase/man/White.Rd | 26 PCMBase-1.2.14/PCMBase/man/as.MixedGaussian.Rd | 76 PCMBase-1.2.14/PCMBase/man/dataFig3.Rd | 36 PCMBase-1.2.14/PCMBase/man/is.GaussianPCM.Rd | 34 PCMBase-1.2.14/PCMBase/man/is.MixedGaussian.Rd | 34 PCMBase-1.2.14/PCMBase/man/is.PCM.Rd | 34 PCMBase-1.2.14/PCMBase/man/is.PCMTree.Rd | 34 PCMBase-1.2.14/PCMBase/tests/README.txt | 6 PCMBase-1.2.14/PCMBase/tests/testthat.R | 8 PCMBase-1.2.14/PCMBase/tests/testthat/test-MixedGaussian.R | 352 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCM.R | 530 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMLik-BM.R | 160 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMLik-BMdrift.R | 282 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMLik-DOU.R | 154 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMLik-OU.R | 176 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMParam.R | 132 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMSim.R | 114 PCMBase-1.2.14/PCMBase/tests/testthat/test-PCMTree.R | 276 PCMBase-1.2.14/PCMBase/tests/testthat/test-Transformations.R | 130 PCMBase-1.2.14/PCMBase/vignettes/PCMBase.Rmd | 654 PCMBase-1.2.14/PCMBase/vignettes/PCMCreateModel.Rmd | 877 PCMBase-1.2.14/PCMBase/vignettes/PCMParam.Rmd | 580 PCMBase-1.2.14/PCMBase/vignettes/PCMTracePruning.Rmd | 978 PCMBase-1.2.14/PCMBase/vignettes/REFERENCES-R.bib | 279 PCMBase-1.2.14/PCMBase/vignettes/REFERENCES.bib | 652 192 files changed, 42043 insertions(+), 40508 deletions(-)
Title: A Method to Analyze Recurrent DNA Copy Number Aberrations in
Tumors
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage.
This package implements the DiNAMIC procedure for assessing the statistical significance of
recurrent DNA copy number aberrations (Bioinformatics (2011) 27(5) 678 - 685).
Author: Vonn Walter [aut, cre] ,
Andrew B. Nobel [aut],
Fred A. Wright [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between dinamic versions 1.0 dated 2011-11-09 and 1.0.1 dated 2024-03-15
dinamic-1.0.1/dinamic/DESCRIPTION | 49 ++++++++++++++++++++++------- dinamic-1.0.1/dinamic/MD5 | 36 ++++++++++++--------- dinamic-1.0.1/dinamic/NAMESPACE |only dinamic-1.0.1/dinamic/NEWS.md |only dinamic-1.0.1/dinamic/R/annot.file.R |only dinamic-1.0.1/dinamic/R/detailedLook.R |only dinamic-1.0.1/dinamic/R/makeCytoband.R |only dinamic-1.0.1/dinamic/R/peeling.R |only dinamic-1.0.1/dinamic/R/quickLook.R |only dinamic-1.0.1/dinamic/R/recodeBinary.R |only dinamic-1.0.1/dinamic/R/wilms.data.R |only dinamic-1.0.1/dinamic/R/wilms.markers.R |only dinamic-1.0.1/dinamic/README.md |only dinamic-1.0.1/dinamic/data/dinamic.RData |binary dinamic-1.0.1/dinamic/man/annot.file.Rd |only dinamic-1.0.1/dinamic/man/detailedLook.Rd |only dinamic-1.0.1/dinamic/man/makeCytoband.Rd |only dinamic-1.0.1/dinamic/man/peeling.Rd |only dinamic-1.0.1/dinamic/man/quickLook.Rd |only dinamic-1.0.1/dinamic/man/recodeBinary.Rd |only dinamic-1.0.1/dinamic/man/wilms.data.Rd |only dinamic-1.0.1/dinamic/man/wilms.markers.Rd |only dinamic-1.0/dinamic/data/annot.file.txt.gz |only dinamic-1.0/dinamic/data/wilms.data.rda |only dinamic-1.0/dinamic/data/wilms.markers.rda |only dinamic-1.0/dinamic/man/annot.file.rd |only dinamic-1.0/dinamic/man/detailedLook.rd |only dinamic-1.0/dinamic/man/dinamic-package.rd |only dinamic-1.0/dinamic/man/findNull.rd |only dinamic-1.0/dinamic/man/makeCytoband.rd |only dinamic-1.0/dinamic/man/peeling.rd |only dinamic-1.0/dinamic/man/quickLook.rd |only dinamic-1.0/dinamic/man/recodeBinary.rd |only dinamic-1.0/dinamic/man/wilms.data.rd |only dinamic-1.0/dinamic/man/wilms.markers.rd |only 35 files changed, 59 insertions(+), 26 deletions(-)
Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to Analysis
Results Datasets (ARDs). The use of 'tfrmt' allows users to define table
format and styling without the data, and later apply the format to the data.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
GlaxoSmithKline Research & Development Limited [cph, fnd],
Atorus Research LLC [cph, fnd],
Ellis Hughes [aut] ,
Karima Ahmad [aut] ,
Shannon Haughton [aut]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmt versions 0.1.0 dated 2023-10-17 and 0.1.1 dated 2024-03-15
DESCRIPTION | 8 MD5 | 199 + NAMESPACE | 523 ++--- NEWS.md | 11 R/JSON.R | 882 ++++---- R/apply_col_plan.R | 762 +++---- R/apply_footnote_meta.R | 476 ++-- R/apply_footnote_plan.R | 388 +-- R/apply_frmt_methods.R | 686 +++--- R/apply_page_plan.R | 795 +++---- R/apply_row_grp_plan.R | 680 +++--- R/apply_table_frmt_plan.R | 394 +-- R/apply_tfrmt.R | 1012 +++++----- R/big_n.R | 342 +-- R/body_plan.R | 258 +- R/col_style_plan.R | 344 +-- R/data.R | 148 - R/display_insights.R | 432 ++-- R/display_row_frmts.R | 238 +- R/eval_tidyselect.R | 60 R/frmt_utils.R | 752 +++---- R/mock_tbl.R | 487 ++-- R/page_plan.R | 170 - R/print_to_ggplot.R | 398 +-- R/print_to_gt.R | 74 R/row_group_plan.R | 202 +- R/struct_utils.R |only R/tfrmt.R | 954 ++++----- R/tfrmt_checks.R | 611 +++--- R/tfrmt_layer.R | 560 ++--- R/tfrmt_n_pct.R | 152 - R/theme_element.R | 8 R/utils-pipe.R | 32 R/zzz.R | 14 README.md | 208 +- inst/WORDLIST | 114 - inst/create_json_example_tfrmts.R |only inst/json_examples |only man/apply_frmt.Rd | 130 - man/as_json.Rd | 42 man/big_n_structure.Rd | 62 man/body_plan.Rd | 80 man/cleaned_data_to_gt.Rd | 65 man/col_plan.Rd | 232 +- man/col_style_plan.Rd | 68 man/data_ae.Rd | 54 man/data_demog.Rd | 54 man/data_efficacy.Rd | 52 man/data_labs.Rd | 58 man/display_row_frmts.Rd | 164 - man/display_val_frmts.Rd | 100 - man/element_block.Rd | 85 man/element_row_grp_loc.Rd | 120 - man/footnote_plan.Rd | 72 man/footnote_structure.Rd | 90 man/frmt.Rd | 226 +- man/frmt_structure.Rd | 110 - man/frmt_utils.Rd | 122 - man/json_to_tfrmt.Rd | 36 man/layer_tfrmt.Rd | 88 man/make_mock_data.Rd | 78 man/page_plan.Rd | 84 man/page_structure.Rd | 58 man/param_set.Rd | 82 man/pipe.Rd | 40 man/print_mock_gt.Rd | 124 - man/print_to_ggplot.Rd | 94 man/print_to_gt.Rd | 110 - man/row_grp_plan.Rd | 92 man/row_grp_structure.Rd | 74 man/tfrmt.Rd | 428 ++-- man/tfrmt_n_pct.Rd | 90 man/tfrmt_sigdig.Rd | 206 +- man/tfrmt_to_json.Rd | 56 man/theme_element.Rd | 146 - man/update_group.Rd | 84 tests/testthat.R | 8 tests/testthat/_snaps/JSON.md | 12 tests/testthat/test-JSON.R | 1126 +++++------ tests/testthat/test-apply_footnote_meta.R | 914 ++++----- tests/testthat/test-apply_footnote_plan.R | 578 ++--- tests/testthat/test-apply_frmt.R | 1428 +++++++------- tests/testthat/test-apply_page_plan.R | 1240 ++++++------ tests/testthat/test-apply_row_grp_plan.R | 1949 ++++++++++--------- tests/testthat/test-apply_tfrmt.R | 396 +-- tests/testthat/test-big_ns.R | 1454 +++++++------- tests/testthat/test-check_order_vars.R | 126 - tests/testthat/test-col_plan.R | 2993 +++++++++++++++--------------- tests/testthat/test-col_style_structure.R | 1768 ++++++++--------- tests/testthat/test-display_row_frmts.R | 318 +-- tests/testthat/test-expr_to_filter.R | 134 - tests/testthat/test-footnote_plan.R | 350 +-- tests/testthat/test-make_mock_data.R | 1435 +++++++------- tests/testthat/test-mrkdown_labels.R | 424 ++-- tests/testthat/test-quo_get.R | 236 +- tests/testthat/test-tfmt.R | 2334 +++++++++++------------ tests/testthat/test-tfrmt_checks.R | 157 + tests/testthat/test-tfrmt_n_pct.R | 126 - tests/testthat/test-tfrmt_sigdig.R | 670 +++--- tests/testthat/test-utils_tfrmt.R | 802 ++++---- tests/testthat/test_print_to_ggplot.R | 448 ++-- 101 files changed, 19543 insertions(+), 19213 deletions(-)
Title: Easily Create Fully Randomized 'Moodle' Test Questions
Description: Routines to generate fully randomized 'moodle' quizzes. It also contains 12 examples and a 'shiny' app.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between moodlequizR versions 1.0.3 dated 2023-09-12 and 2.0.2 dated 2024-03-15
DESCRIPTION | 10 MD5 | 119 +++++--- NAMESPACE | 1 NEWS.md | 3 R/RtoHTML.R |only R/genquiz.R | 14 - R/make.xml.R | 2 R/moodleRexample1.R | 4 R/moodleRexample10.R | 4 R/moodleRexample11.R | 4 R/moodleRexample12.R | 4 R/moodleRexample13.R |only R/moodleRexample14.R |only R/moodleRexample15.R |only R/moodleRexample2.R | 4 R/moodleRexample3.R | 4 R/moodleRexample4.R | 4 R/moodleRexample5.R | 4 R/moodleRexample6.R | 4 R/moodleRexample7.R | 4 R/moodleRexample8.R | 4 R/moodleRexample9.R | 4 R/paste.data.R | 10 R/qamatrix.R | 4 data/moodleRexample1.rda |binary data/moodleRexample10.rda |binary data/moodleRexample11.rda |binary data/moodleRexample12.rda |binary data/moodleRexample13.rda |only data/moodleRexample14.rda |only data/moodleRexample15.rda |only data/moodleRexample2.rda |binary data/moodleRexample3.rda |binary data/moodleRexample4.rda |binary data/moodleRexample5.rda |binary data/moodleRexample6.rda |binary data/moodleRexample7.rda |binary data/moodleRexample8.rda |binary data/moodleRexample9.rda |binary inst/doc/moodlequizR.R | 19 - inst/doc/moodlequizR.Rmd | 186 ++++++++++--- inst/doc/moodlequizR.html | 549 ++++++++++++++++++++++++++++------------- inst/shinymoodlequizR/server.R | 223 +++++++++++----- inst/shinymoodlequizR/ui.R | 64 ++-- man/RtoHTML.Rd |only man/genquiz.Rd | 10 man/moodleRexample1.Rd | 4 man/moodleRexample10.Rd | 4 man/moodleRexample11.Rd | 4 man/moodleRexample12.Rd | 4 man/moodleRexample13.Rd |only man/moodleRexample14.Rd |only man/moodleRexample15.Rd |only man/moodleRexample2.Rd | 4 man/moodleRexample3.Rd | 4 man/moodleRexample4.Rd | 4 man/moodleRexample5.Rd | 4 man/moodleRexample6.Rd | 4 man/moodleRexample7.Rd | 4 man/moodleRexample8.Rd | 4 man/moodleRexample9.Rd | 4 man/qamatrix.Rd | 2 vignettes/figure1.png |only vignettes/figure2.png |only vignettes/figure3.png |only vignettes/figure4.png |only vignettes/figure5.png |only vignettes/figure6.png |only vignettes/moodlequizR.Rmd | 186 ++++++++++--- 69 files changed, 1028 insertions(+), 470 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Map Myriad Networks
Description: A set of tools for making, modifying, marking, and mapping many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 0.4.1 dated 2024-01-24 and 0.4.4 dated 2024-03-15
manynet-0.4.1/manynet/man/autographing.Rd |only manynet-0.4.4/manynet/DESCRIPTION | 10 manynet-0.4.4/manynet/MD5 | 56 - manynet-0.4.4/manynet/NAMESPACE | 5 manynet-0.4.4/manynet/NEWS.md | 39 + manynet-0.4.4/manynet/R/make_generate.R | 2 manynet-0.4.4/manynet/R/make_play.R | 8 manynet-0.4.4/manynet/R/manip_reformat.R | 2 manynet-0.4.4/manynet/R/manip_reformed.R | 2 manynet-0.4.4/manynet/R/map_autographr.R | 388 +++++++------ manynet-0.4.4/manynet/R/map_layout_configurations.R | 17 manynet-0.4.4/manynet/R/map_layout_partition.R | 74 +- manynet-0.4.4/manynet/R/map_palettes.R | 4 manynet-0.4.4/manynet/R/map_theme.R | 83 +- manynet-0.4.4/manynet/R/mark_nodes.R | 47 - manynet-0.4.4/manynet/man/attributes.Rd | 4 manynet-0.4.4/manynet/man/autographr.Rd |only manynet-0.4.4/manynet/man/autographs.Rd |only manynet-0.4.4/manynet/man/autographt.Rd |only manynet-0.4.4/manynet/man/configuration_layouts.Rd | 13 manynet-0.4.4/manynet/man/features.Rd | 4 manynet-0.4.4/manynet/man/learning.Rd | 2 manynet-0.4.4/manynet/man/many_palettes.Rd | 6 manynet-0.4.4/manynet/man/partition_layouts.Rd | 18 manynet-0.4.4/manynet/man/play.Rd | 1 manynet-0.4.4/manynet/man/properties.Rd | 4 manynet-0.4.4/manynet/man/themes.Rd | 9 manynet-0.4.4/manynet/man/to_scope.Rd | 4 manynet-0.4.4/manynet/tests/testthat/test-manip_reformat.R | 2 manynet-0.4.4/manynet/tests/testthat/test-map_autographr.R | 4 manynet-0.4.4/manynet/tests/testthat/test-map_theme.R | 15 31 files changed, 471 insertions(+), 352 deletions(-)
Title: Create Flashcards of Terms and Definitions
Description: Provides functions for creating flashcard decks of terms and
definitions. This package creates HTML slides using 'revealjs' that can be
viewed in the 'RStudio' viewer or a web browser. Users can create
flashcards from either existing built-in decks or create their own from CSV
files or vectors of function names.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between flashr versions 0.1.1 dated 2023-03-28 and 0.1.2 dated 2024-03-15
DESCRIPTION | 8 - MD5 | 22 +- NEWS.md | 5 R/flashcard.R | 8 - README.md | 9 - build/vignette.rds |binary inst/doc/flashr.R | 2 inst/doc/flashr.Rmd | 2 inst/doc/flashr.html | 308 ++++++++++++++++++++-------------------- inst/extdata/operators.csv | 47 +++--- tests/testthat/test-flashcard.R | 18 +- vignettes/flashr.Rmd | 2 12 files changed, 227 insertions(+), 204 deletions(-)
Title: R Client for 'iRODS'
Description: The open sourced data management software 'Integrated
Rule-Oriented Data System' ('iRODS') offers solutions for the whole
data life cycle (<https://irods.org/>). The loosely constructed and
highly configurable architecture of 'iRODS' frees the user from strict
formatting constraints and single-vendor solutions. This package
provides an interface to the 'iRODS' HTTP API, allowing you to manage
your data and metadata in 'iRODS' with R. Storage of annotated files
and R objects in 'iRODS' ensures findability, accessibility,
interoperability, and reusability of data.
Author: Martin Schobben [aut, cre, cph]
,
Mariana Montes [aut],
Terrell Russell [ctb],
Christine Staiger [ctb],
Ton Smeele [ctb],
Alan King [ctb]
Maintainer: Martin Schobben <schobbenmartin@gmail.com>
Diff between rirods versions 0.1.2 dated 2023-11-02 and 0.2.0 dated 2024-03-15
rirods-0.1.2/rirods/R/irods-rest.R |only rirods-0.1.2/rirods/inst/irods_demo/irods_catalog_provider/setup-4.3.0.input |only rirods-0.1.2/rirods/inst/shell_scripts/docker-images-remove.sh |only rirods-0.1.2/rirods/inst/shell_scripts/iadmin.sh |only rirods-0.1.2/rirods/inst/shell_scripts/iauth.sh |only rirods-0.1.2/rirods/inst/shell_scripts/iget.sh |only rirods-0.1.2/rirods/inst/shell_scripts/ils.sh |only rirods-0.1.2/rirods/inst/shell_scripts/imeta.sh |only rirods-0.1.2/rirods/inst/shell_scripts/imkdir.sh |only rirods-0.1.2/rirods/inst/shell_scripts/iput.sh |only rirods-0.1.2/rirods/inst/shell_scripts/iquery.sh |only rirods-0.1.2/rirods/inst/shell_scripts/irm.sh |only rirods-0.1.2/rirods/inst/shell_scripts/urlencode.sh |only rirods-0.1.2/rirods/man/irods_rest_call.Rd |only rirods-0.1.2/rirods/man/local_create_irods.Rd |only rirods-0.1.2/rirods/man/new_irods_df.Rd |only rirods-0.1.2/rirods/man/remove_docker_images.Rd |only rirods-0.1.2/rirods/man/remove_mock_files.Rd |only rirods-0.1.2/rirods/tests/testthat/_snaps/irods-print.md |only rirods-0.1.2/rirods/tests/testthat/_snaps/irods-s3.md |only rirods-0.1.2/rirods/tests/testthat/_snaps/local-path.md |only rirods-0.1.2/rirods/tests/testthat/add-data-collections |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/list-e12d92.R |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/logicalpath-b947e4-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/metadata-8584b1-POST.R |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/stream-07de5f-PUT.R |only rirods-0.1.2/rirods/tests/testthat/coerce-irods_df/stream-322103-PUT.R |only rirods-0.1.2/rirods/tests/testthat/expand-path/list-20ba52.R |only rirods-0.1.2/rirods/tests/testthat/expand-path/list-f91c86.R |only rirods-0.1.2/rirods/tests/testthat/ils |only rirods-0.1.2/rirods/tests/testthat/irods-rest-call |only rirods-0.1.2/rirods/tests/testthat/large-data-objects |only rirods-0.1.2/rirods/tests/testthat/metadata-1/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/metadata-1/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/metadata-1/metadata-b357da-POST.R |only rirods-0.1.2/rirods/tests/testthat/metadata-1/stream-3b4fe7-PUT.R |only rirods-0.1.2/rirods/tests/testthat/metadata-1/stream-560aa9-PUT.R |only rirods-0.1.2/rirods/tests/testthat/metadata-2/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/metadata-2/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/metadata-2/metadata-02d501-POST.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/list-7f041c.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/logicalpath-9f16e8-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/metadata-02d501-POST.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/stream-012c54-PUT.R |only rirods-0.1.2/rirods/tests/testthat/metadata-3/stream-e4f82a-PUT.R |only rirods-0.1.2/rirods/tests/testthat/metadata-errors/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/metadata-query |only rirods-0.1.2/rirods/tests/testthat/metadata-remove/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/metadata-remove/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/metadata-remove/logicalpath-add13d-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/metadata-remove/metadata-1956b8-POST.R |only rirods-0.1.2/rirods/tests/testthat/navigation/list-79a573.R |only rirods-0.1.2/rirods/tests/testthat/navigation/list-9de04e.R |only rirods-0.1.2/rirods/tests/testthat/navigation/list-f91c86.R |only rirods-0.1.2/rirods/tests/testthat/navigation/list-fe4aa0.R |only rirods-0.1.2/rirods/tests/testthat/navigation/logicalpath-b87c6d-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/navigation/stream-178e79-PUT.R |only rirods-0.1.2/rirods/tests/testthat/navigation/stream-9b29ff-PUT.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/list-20ba52.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/list-2adf82.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/list-d4592f.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/list-ec443a.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/logicalpath-add13d-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/stream-3b4fe7-PUT.R |only rirods-0.1.2/rirods/tests/testthat/object-helpers/stream-560aa9-PUT.R |only rirods-0.1.2/rirods/tests/testthat/overwrite-data-objects-errors |only rirods-0.1.2/rirods/tests/testthat/print-1/list-f91c86.R |only rirods-0.1.2/rirods/tests/testthat/print-2/list-426d3d.R |only rirods-0.1.2/rirods/tests/testthat/print-2/list-45dbe0.R |only rirods-0.1.2/rirods/tests/testthat/print-2/list-c54ec9.R |only rirods-0.1.2/rirods/tests/testthat/print-2/list-f91c86.R |only rirods-0.1.2/rirods/tests/testthat/print-2/metadata-a30c47-POST.R |only rirods-0.1.2/rirods/tests/testthat/print-2/stream-0c01b5-PUT.R |only rirods-0.1.2/rirods/tests/testthat/print-2/stream-45c328-PUT.R |only rirods-0.1.2/rirods/tests/testthat/print-2/stream-57f480-PUT.R |only rirods-0.1.2/rirods/tests/testthat/print-2/stream-92b2f2-PUT.R |only rirods-0.1.2/rirods/tests/testthat/print-3 |only rirods-0.1.2/rirods/tests/testthat/print-4 |only rirods-0.1.2/rirods/tests/testthat/remove-objects/list-381167.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/list-d8627f.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/list-f91c86.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/logicalpath-745fc8-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/logicalpath-a7251e-DELETE.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/stream-07e6a3-PUT.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/stream-24b999-PUT.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/stream-2bdbf2-PUT.R |only rirods-0.1.2/rirods/tests/testthat/remove-objects/stream-bfee42-PUT.R |only rirods-0.1.2/rirods/tests/testthat/small-data-objects |only rirods-0.1.2/rirods/tests/testthat/test-irods-rest.R |only rirods-0.1.2/rirods/vignettes/demo |only rirods-0.2.0/rirods/DESCRIPTION | 43 rirods-0.2.0/rirods/LICENSE | 2 rirods-0.2.0/rirods/MD5 | 449 ++++----- rirods-0.2.0/rirods/NEWS.md | 11 rirods-0.2.0/rirods/R/admin.R | 82 - rirods-0.2.0/rirods/R/authentication.R | 60 - rirods-0.2.0/rirods/R/collections.R | 92 + rirods-0.2.0/rirods/R/create-irods.R | 14 rirods-0.2.0/rirods/R/data-objects.R | 489 ++++++---- rirods-0.2.0/rirods/R/dev-helpers.R | 49 - rirods-0.2.0/rirods/R/irods-conf.R | 35 rirods-0.2.0/rirods/R/irods-demo.R | 265 +++-- rirods-0.2.0/rirods/R/irods-http.R |only rirods-0.2.0/rirods/R/irods-path.R | 124 +- rirods-0.2.0/rirods/R/irods-print.R | 79 - rirods-0.2.0/rirods/R/irods-s3.R | 77 - rirods-0.2.0/rirods/R/irods-utils.R |only rirods-0.2.0/rirods/R/local-path.R | 63 - rirods-0.2.0/rirods/R/metadata.R | 153 ++- rirods-0.2.0/rirods/R/navigation.R | 175 ++- rirods-0.2.0/rirods/R/zzz.R | 5 rirods-0.2.0/rirods/README.md | 45 rirods-0.2.0/rirods/build/partial.rdb |only rirods-0.2.0/rirods/build/vignette.rds |binary rirods-0.2.0/rirods/inst/CITATION | 8 rirods-0.2.0/rirods/inst/WORDLIST | 8 rirods-0.2.0/rirods/inst/doc/demo.R | 12 rirods-0.2.0/rirods/inst/doc/demo.Rmd | 16 rirods-0.2.0/rirods/inst/doc/demo.html | 14 rirods-0.2.0/rirods/inst/doc/develop.R | 3 rirods-0.2.0/rirods/inst/doc/develop.Rmd | 24 rirods-0.2.0/rirods/inst/doc/develop.html | 40 rirods-0.2.0/rirods/inst/doc/icommands.R | 26 rirods-0.2.0/rirods/inst/doc/icommands.Rmd | 26 rirods-0.2.0/rirods/inst/doc/icommands.html | 18 rirods-0.2.0/rirods/inst/doc/local-irods.R | 12 rirods-0.2.0/rirods/inst/doc/local-irods.Rmd | 12 rirods-0.2.0/rirods/inst/doc/local-irods.html | 6 rirods-0.2.0/rirods/inst/doc/metadata.R | 28 rirods-0.2.0/rirods/inst/doc/metadata.Rmd | 28 rirods-0.2.0/rirods/inst/doc/metadata.html | 37 rirods-0.2.0/rirods/inst/httptest2/redact.R | 53 - rirods-0.2.0/rirods/inst/irods_demo/README.md | 12 rirods-0.2.0/rirods/inst/irods_demo/docker-compose.yml | 28 rirods-0.2.0/rirods/inst/irods_demo/irods_catalog_provider/Dockerfile | 4 rirods-0.2.0/rirods/inst/irods_demo/irods_catalog_provider/setup-4.3.1.input |only rirods-0.2.0/rirods/inst/irods_demo/irods_client_http_api |only rirods-0.2.0/rirods/inst/shell_scripts/docker-images.sh | 2 rirods-0.2.0/rirods/inst/shell_scripts/dry-run-irods-curl.sh |only rirods-0.2.0/rirods/inst/shell_scripts/dry-run-irods-icommands.sh |only rirods-0.2.0/rirods/inst/shell_scripts/iadmin-docker-icommand.sh | 6 rirods-0.2.0/rirods/man/as.data.frame.irods_df.Rd | 14 rirods-0.2.0/rirods/man/create_irods.Rd | 5 rirods-0.2.0/rirods/man/iadmin.Rd | 45 rirods-0.2.0/rirods/man/iauth.Rd | 12 rirods-0.2.0/rirods/man/icd.Rd | 15 rirods-0.2.0/rirods/man/iget.Rd | 28 rirods-0.2.0/rirods/man/ils.Rd | 30 rirods-0.2.0/rirods/man/imeta.Rd | 19 rirods-0.2.0/rirods/man/imkdir.Rd | 20 rirods-0.2.0/rirods/man/iput.Rd | 28 rirods-0.2.0/rirods/man/iquery.Rd | 43 rirods-0.2.0/rirods/man/irm.Rd | 33 rirods-0.2.0/rirods/man/print.irods_df.Rd | 19 rirods-0.2.0/rirods/man/use_irods_demo.Rd | 3 rirods-0.2.0/rirods/tests/testthat/_snaps/data-objects.md |only rirods-0.2.0/rirods/tests/testthat/add-data-collections-1 |only rirods-0.2.0/rirods/tests/testthat/add-data-collections-2 |only rirods-0.2.0/rirods/tests/testthat/admin-http |only rirods-0.2.0/rirods/tests/testthat/chunked-write |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/collections-3e83a9.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/data-objects-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/data-objects-a36303-POST.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/data-objects-bef74d-POST.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/query-9a9228.R |only rirods-0.2.0/rirods/tests/testthat/coerce-irods_df/query-e6da8c.R |only rirods-0.2.0/rirods/tests/testthat/collection-http |only rirods-0.2.0/rirods/tests/testthat/expand-path/collections-84f63d.R |only rirods-0.2.0/rirods/tests/testthat/expand-path/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/http-erros |only rirods-0.2.0/rirods/tests/testthat/info-http |only rirods-0.2.0/rirods/tests/testthat/list |only rirods-0.2.0/rirods/tests/testthat/list-limit-number-rows |only rirods-0.2.0/rirods/tests/testthat/list-metadata-0 |only rirods-0.2.0/rirods/tests/testthat/list-metadata-1 |only rirods-0.2.0/rirods/tests/testthat/list-metadata-2 |only rirods-0.2.0/rirods/tests/testthat/list-metadata-3 |only rirods-0.2.0/rirods/tests/testthat/list-stats |only rirods-0.2.0/rirods/tests/testthat/metadata-1/collections-2dc723-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-1/collections-84f63d.R |only rirods-0.2.0/rirods/tests/testthat/metadata-1/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/metadata-1/query-162cfa.R |only rirods-0.2.0/rirods/tests/testthat/metadata-1/query-d5855b.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/data-objects-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/data-objects-884272-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/data-objects-f8db01-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-2/query-e6ba3e.R |only rirods-0.2.0/rirods/tests/testthat/metadata-3/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/metadata-3/data-objects-29c6eb-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-3/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-3/query-9a9228.R |only rirods-0.2.0/rirods/tests/testthat/metadata-errors/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/data-objects-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/data-objects-a23ace-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/data-objects-ba2faa-POST.R |only rirods-0.2.0/rirods/tests/testthat/metadata-remove/query-9a9228.R |only rirods-0.2.0/rirods/tests/testthat/navigation/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/navigation/collections-3e83a9.R |only rirods-0.2.0/rirods/tests/testthat/navigation/collections-6085b0.R |only rirods-0.2.0/rirods/tests/testthat/navigation/collections-84f63d.R |only rirods-0.2.0/rirods/tests/testthat/navigation/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/navigation/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/navigation/data-objects-ba2faa-POST.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/collections-58613e.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/data-objects-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/data-objects-58613e.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/object-helpers/data-objects-ba2faa-POST.R |only rirods-0.2.0/rirods/tests/testthat/parallel-write-handle |only rirods-0.2.0/rirods/tests/testthat/print-1/collections-3e83a9.R |only rirods-0.2.0/rirods/tests/testthat/print-2/collections-3e83a9.R |only rirods-0.2.0/rirods/tests/testthat/print-2/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/print-2/collections-d0edea.R |only rirods-0.2.0/rirods/tests/testthat/print-2/collections-fe78e7.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-a91479-POST.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-c3f5dd-POST.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-d0edea.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-ed5572-POST.R |only rirods-0.2.0/rirods/tests/testthat/print-2/data-objects-fe78e7.R |only rirods-0.2.0/rirods/tests/testthat/print-2/query-9a9228.R |only rirods-0.2.0/rirods/tests/testthat/print-2/query-e6da8c.R |only rirods-0.2.0/rirods/tests/testthat/remove-data-collections-1 |only rirods-0.2.0/rirods/tests/testthat/remove-data-collections-2 |only rirods-0.2.0/rirods/tests/testthat/remove-objects/collections-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/remove-objects/collections-3e83a9.R |only rirods-0.2.0/rirods/tests/testthat/remove-objects/collections-c3fee2.R |only rirods-0.2.0/rirods/tests/testthat/remove-objects/data-objects-00f0ca.R |only rirods-0.2.0/rirods/tests/testthat/remove-objects/data-objects-POST.R |only rirods-0.2.0/rirods/tests/testthat/remove-objects/data-objects-a36303-POST.R |only rirods-0.2.0/rirods/tests/testthat/server-info |only rirods-0.2.0/rirods/tests/testthat/setup.R | 88 - rirods-0.2.0/rirods/tests/testthat/single-write |only rirods-0.2.0/rirods/tests/testthat/test-admin.R | 47 rirods-0.2.0/rirods/tests/testthat/test-authentication.R | 37 rirods-0.2.0/rirods/tests/testthat/test-collections.R | 74 - rirods-0.2.0/rirods/tests/testthat/test-data-objects.R | 249 +++-- rirods-0.2.0/rirods/tests/testthat/test-irods-conf.R | 36 rirods-0.2.0/rirods/tests/testthat/test-irods-demo.R | 63 + rirods-0.2.0/rirods/tests/testthat/test-irods-http.R |only rirods-0.2.0/rirods/tests/testthat/test-irods-path.R | 57 - rirods-0.2.0/rirods/tests/testthat/test-irods-print.R | 89 - rirods-0.2.0/rirods/tests/testthat/test-irods-s3.R | 82 - rirods-0.2.0/rirods/tests/testthat/test-irods-utils.R |only rirods-0.2.0/rirods/tests/testthat/test-local-path.R | 23 rirods-0.2.0/rirods/tests/testthat/test-metadata.R | 227 ++-- rirods-0.2.0/rirods/tests/testthat/test-navigation.R | 185 ++- rirods-0.2.0/rirods/tests/testthat/write-read-data-objects |only rirods-0.2.0/rirods/vignettes/demo.Rmd | 16 rirods-0.2.0/rirods/vignettes/develop.Rmd | 24 rirods-0.2.0/rirods/vignettes/icommands.Rmd | 26 rirods-0.2.0/rirods/vignettes/local-irods.Rmd | 12 rirods-0.2.0/rirods/vignettes/metadata.Rmd | 28 266 files changed, 2562 insertions(+), 1850 deletions(-)
Title: Power Analysis and Data Simulation for Multilevel Models
Description: A declarative language for specifying multilevel models,
solving for population parameters based on specified variance-explained effect
size measures, generating data, and conducting power analyses to determine
sample size recommendations. The specification allows for any number of
within-cluster effects, between-cluster effects, covariate effects
at either level, and random coefficients. Moreover, the models do not
assume orthogonal effects, and predictors can correlate at either level
and accommodate models with multiple interaction effects.
Author: Brian T. Keller [aut, cre, cph]
Maintainer: Brian T. Keller <btkeller@missouri.edu>
Diff between mlmpower versions 1.0.5 dated 2024-01-29 and 1.0.6 dated 2024-03-15
DESCRIPTION | 8 +- MD5 | 21 +++--- NAMESPACE | 1 NEWS.md | 4 + R/model.R | 2 R/parameters.R | 3 R/simulation.R | 155 ++++++++++++++++++++++++++++++++++++++++++++++++- R/variables.R | 6 + build/vignette.rds |binary inst/doc/mlmpower.html | 2 man/center.Rd |only man/mlmpower.Rd | 2 12 files changed, 184 insertions(+), 20 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Originally described in Kamvar, Tabima, and Grünwald (2014)
<doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and
Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] ,
Javier F. Tabima [aut] ,
Sydney E. Everhart [ctb, dtc] ,
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
,
Erik Sotka [ctb],
Brian J. Knaus [ctb] ,
Patrick G. Meirmans [ctb] ,
Frederic D. Chevalier [ctb] ,
David Fo [...truncated...]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.9.5 dated 2024-01-15 and 2.9.6 dated 2024-03-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 9 +++++++++ R/zzz.r | 10 ++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/algo.pdf |binary 7 files changed, 24 insertions(+), 13 deletions(-)
Title: Create Custom Plots for Viewing Genetic Association Results
Description: A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Author: Thorhildur Juliusdottir [cph, aut, cre],
Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <totajuliusd@gmail.com>
Diff between topr versions 2.0.0 dated 2024-02-04 and 2.0.1 dated 2024-03-15
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/dat_checks.R | 4 ++-- R/get_plots.R | 2 +- R/manhattan.R | 7 +++++-- R/miscellaneous.R | 7 +++++++ R/plot_functions.R | 2 +- R/regionplot.R | 8 +++++++- man/topr.Rd | 18 ++++++++++++++++++ 10 files changed, 58 insertions(+), 20 deletions(-)
Title: Data Visualization for QTL Experiments
Description: Functions to plot QTL (quantitative trait loci) analysis
results and related diagnostics.
Part of 'qtl2', an upgrade of the 'qtl'
package to better handle high-dimensional data and complex cross
designs.
Author: Brian S Yandell [aut, cre],
Karl W Broman [aut]
Maintainer: Brian S Yandell <brian.yandell@wisc.edu>
Diff between qtl2ggplot versions 1.2.2 dated 2023-03-11 and 1.2.4 dated 2024-03-15
DESCRIPTION | 10 - MD5 | 16 +- R/ggplot_coef.R | 2 R/ggplot_coef_and_lod.R | 3 R/ggplot_listof_scan1coef.R | 14 + R/ggplot_snpasso.R | 2 build/vignette.rds |binary inst/doc/qtl2ggplot.html | 334 ++++++++++++++++++++++---------------------- man/ggplot_snpasso.Rd | 2 9 files changed, 194 insertions(+), 189 deletions(-)
Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information
System of the Commission) Eurostat database
<https://ec.europa.eu/eurostat/web/gisco>. Global and European map
data available. This package is in no way officially related to or
endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph]
,
EuroGeographics [cph] ,
Vincent Arel-Bundock [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 0.4.0 dated 2023-10-30 and 0.4.1 dated 2024-03-15
giscoR-0.4.0/giscoR/data/tgs00026.rda |only giscoR-0.4.0/giscoR/man/gisco_detect_cache_dir.Rd |only giscoR-0.4.0/giscoR/man/tgs00026.Rd |only giscoR-0.4.1/giscoR/DESCRIPTION | 21 giscoR-0.4.1/giscoR/MD5 | 119 - giscoR-0.4.1/giscoR/NEWS.md | 8 giscoR-0.4.1/giscoR/R/data.R | 521 +++---- giscoR-0.4.1/giscoR/R/gisco_attributions.R | 240 +-- giscoR-0.4.1/giscoR/R/gisco_bulk_download.R | 33 giscoR-0.4.1/giscoR/R/gisco_cache.R | 489 +++--- giscoR-0.4.1/giscoR/R/gisco_check_access.R | 100 - giscoR-0.4.1/giscoR/R/gisco_clear_cache.R | 139 - giscoR-0.4.1/giscoR/R/gisco_get_airports.R | 292 ++-- giscoR-0.4.1/giscoR/R/gisco_get_coastallines.R | 174 +- giscoR-0.4.1/giscoR/R/gisco_get_countries.R | 378 ++--- giscoR-0.4.1/giscoR/R/gisco_get_grid.R | 380 ++--- giscoR-0.4.1/giscoR/R/gisco_get_healthcare.R | 19 giscoR-0.4.1/giscoR/R/gisco_get_lau.R | 553 +++---- giscoR-0.4.1/giscoR/R/gisco_get_nuts.R | 359 ++--- giscoR-0.4.1/giscoR/R/gisco_get_postalcodes.R | 310 ++-- giscoR-0.4.1/giscoR/R/gisco_get_units.R | 713 ++++------ giscoR-0.4.1/giscoR/R/gisco_get_urban_audit.R | 184 +- giscoR-0.4.1/giscoR/R/utils_downloads.R | 22 giscoR-0.4.1/giscoR/R/utils_names.R | 233 +-- giscoR-0.4.1/giscoR/README.md | 151 -- giscoR-0.4.1/giscoR/build/vignette.rds |binary giscoR-0.4.1/giscoR/data/gisco_coastallines.rda |binary giscoR-0.4.1/giscoR/data/gisco_countries.rda |binary giscoR-0.4.1/giscoR/data/gisco_countrycode.rda |binary giscoR-0.4.1/giscoR/data/gisco_db.rda |binary giscoR-0.4.1/giscoR/data/gisco_nuts.rda |binary giscoR-0.4.1/giscoR/inst/WORDLIST | 25 giscoR-0.4.1/giscoR/inst/doc/giscoR.Rmd | 259 +-- giscoR-0.4.1/giscoR/inst/doc/giscoR.html | 353 ++-- giscoR-0.4.1/giscoR/inst/schemaorg.json | 4 giscoR-0.4.1/giscoR/man/figures/logo.png |binary giscoR-0.4.1/giscoR/man/gisco_attributions.Rd | 47 giscoR-0.4.1/giscoR/man/gisco_bulk_download.Rd | 35 giscoR-0.4.1/giscoR/man/gisco_check_access.Rd | 6 giscoR-0.4.1/giscoR/man/gisco_clear_cache.Rd | 11 giscoR-0.4.1/giscoR/man/gisco_coastallines.Rd | 11 giscoR-0.4.1/giscoR/man/gisco_countries.Rd | 13 giscoR-0.4.1/giscoR/man/gisco_countrycode.Rd | 10 giscoR-0.4.1/giscoR/man/gisco_db.Rd | 9 giscoR-0.4.1/giscoR/man/gisco_get.Rd | 52 giscoR-0.4.1/giscoR/man/gisco_get_airports.Rd | 8 giscoR-0.4.1/giscoR/man/gisco_get_coastallines.Rd | 33 giscoR-0.4.1/giscoR/man/gisco_get_grid.Rd | 71 giscoR-0.4.1/giscoR/man/gisco_get_healthcare.Rd | 8 giscoR-0.4.1/giscoR/man/gisco_get_lau.Rd | 46 giscoR-0.4.1/giscoR/man/gisco_get_nuts.Rd | 65 giscoR-0.4.1/giscoR/man/gisco_get_postalcodes.Rd | 8 giscoR-0.4.1/giscoR/man/gisco_get_units.Rd | 48 giscoR-0.4.1/giscoR/man/gisco_get_urban_audit.Rd | 29 giscoR-0.4.1/giscoR/man/gisco_nuts.Rd | 8 giscoR-0.4.1/giscoR/man/gisco_set_cache_dir.Rd | 28 giscoR-0.4.1/giscoR/tests/testthat/test-gisco_bulk_download.R | 209 +- giscoR-0.4.1/giscoR/tests/testthat/test-utils.R | 4 giscoR-0.4.1/giscoR/vignettes/africa-1.png |binary giscoR-0.4.1/giscoR/vignettes/country-1.png |binary giscoR-0.4.1/giscoR/vignettes/giscoR-1.png |binary giscoR-0.4.1/giscoR/vignettes/giscoR.Rmd | 259 +-- 62 files changed, 3430 insertions(+), 3667 deletions(-)
Title: Formatting Tools for 'rmarkdown' Documents
Description: Provides a small set of tools for formatting tasks when creating
documents in R Markdown or Quarto Markdown. Convert the elements of a
numerical vector to character strings in one of several forms: powers-of-ten
notation in engineering or scientific form delimited for rendering as inline
equations; integer or decimal notation delimited for equation rendering;
numbers with measurement units (non-delimited) where units are selected to
eliminate the need for powers-of-ten or scientific notation. Useful for
rendering a numerical scalar in an inline R code chunk as well as formatting
columns of data frames displayed in a table.
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>
Diff between formatdown versions 0.1.2 dated 2023-06-21 and 0.1.3 dated 2024-03-15
DESCRIPTION | 8 MD5 | 56 - NAMESPACE | 1 NEWS.md | 28 R/format_power.R | 97 + R/format_text.R |only R/formatdown-package.R | 2 R/utils.R | 3 README.md | 39 build/vignette.rds |binary inst/WORDLIST | 8 inst/doc/format_integers_and_decimals.html | 206 ++-- inst/doc/format_powers_of_ten.R | 74 + inst/doc/format_powers_of_ten.Rmd | 154 ++- inst/doc/format_powers_of_ten.html | 1121 +++++++++++++---------- inst/doc/format_text.R |only inst/doc/format_text.Rmd |only inst/doc/format_text.html |only inst/doc/format_units.R | 49 + inst/doc/format_units.Rmd | 76 + inst/doc/format_units.html | 389 +++++-- inst/tinytest/test_format_power.R | 65 - inst/tinytest/test_format_text.R |only man/examples/examples_format_text.R |only man/figures/latex_math_formatting_text_table.png |only man/figures/si-base-units-v2.png |only man/format_decimal.Rd | 1 man/format_power.Rd | 33 man/format_text.Rd |only man/format_units.Rd | 3 man/formatdown-package.Rd | 1 vignettes/format_powers_of_ten.Rmd | 154 ++- vignettes/format_text.Rmd |only vignettes/format_units.Rmd | 76 + 34 files changed, 1779 insertions(+), 865 deletions(-)
Title: Robust Small Area Estimation
Description: Methods to fit robust alternatives to commonly used models used in
Small Area Estimation. The methods here used are based on best linear
unbiased predictions and linear mixed models. At this time available models
include area level models incorporating spatial and temporal correlation in
the random effects.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between saeRobust versions 0.4.0 dated 2023-01-18 and 0.5.0 dated 2024-03-15
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 5 +++++ R/print.R | 4 +++- build/vignette.rds |binary inst/doc/fixedPoint.html | 8 ++++---- 6 files changed, 20 insertions(+), 13 deletions(-)
Title: Calculate How many Imputations are Needed for Multiple
Imputation
Description: When performing multiple imputations, while 5-10 imputations are
sufficient for obtaining point estimates, a larger number of
imputations are needed for proper standard error estimates.
This package allows you to calculate how many imputations are
needed, following the work of von Hippel (2020)
<doi:10.1177/0049124117747303>.
Author: Josh Errickson [aut, cre]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between howManyImputations versions 0.2.4 dated 2023-02-05 and 0.2.5 dated 2024-03-15
howManyImputations-0.2.4/howManyImputations/man/howManyImputations.Rd |only howManyImputations-0.2.4/howManyImputations/tests/testthat |only howManyImputations-0.2.4/howManyImputations/tests/testthat.R |only howManyImputations-0.2.5/howManyImputations/DESCRIPTION | 10 +- howManyImputations-0.2.5/howManyImputations/MD5 | 13 +-- howManyImputations-0.2.5/howManyImputations/NEWS.md | 9 ++ howManyImputations-0.2.5/howManyImputations/R/how_many_imputations.R | 39 ++++------ howManyImputations-0.2.5/howManyImputations/inst/tinytest |only howManyImputations-0.2.5/howManyImputations/man/how_many_imputations.Rd | 25 ++++-- howManyImputations-0.2.5/howManyImputations/tests/tinytest.R |only 10 files changed, 57 insertions(+), 39 deletions(-)
More information about howManyImputations at CRAN
Permanent link
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.4 dated 2024-01-12 and 0.9.5 dated 2024-03-15
DESCRIPTION | 8 ++-- MD5 | 30 +++++++-------- NEWS.md | 14 +++++++ R/filters.R | 31 +++++++--------- R/finbif_occurrence_load.R | 4 +- R/finbif_records.R | 2 - R/finbif_request_token.R | 11 ++--- R/sysdata.rda |binary README.md | 4 +- build/vignette.rds |binary inst/NEWS.Rd | 16 ++++++++ inst/doc/v05_filtering.Rmd | 51 +++++++++----------------- inst/doc/v05_filtering.html | 62 ++++++++++++-------------------- man/filters.Rd | 31 +++++++--------- tests/testthat/test-finbif_occurrence.R | 16 +++++++- vignettes/v05_filtering.Rmd | 51 +++++++++----------------- 16 files changed, 168 insertions(+), 163 deletions(-)
Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate
time series forecasting models including automatically selected exponential
smoothing (ETS) and autoregressive integrated moving average (ARIMA) models.
These models work within the 'fable' framework provided by the 'fabletools'
package, which provides the tools to evaluate, visualise, and combine models
in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Gabriel Caceres [ctb] ,
Christoph Bergmeir [ctb] ,
Tim-Gunnar Hensel [ctb],
Timothy Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fable versions 0.3.3 dated 2023-03-22 and 0.3.4 dated 2024-03-15
DESCRIPTION | 8 MD5 | 30 +-- NEWS.md | 6 R/ar.R | 6 R/nnetar.R | 6 README.md | 28 +-- build/partial.rdb |binary inst/WORDLIST | 1 inst/doc/fable.R | 4 inst/doc/fable.html | 316 +++++++++++++++++++-------------------- inst/doc/transformations.html | 112 ++++++------- man/figures/README-example-1.png |binary man/forecast.NNETAR.Rd | 8 src/Makevars | 4 src/Makevars.win | 6 tests/testthat/test-rw.R | 1 16 files changed, 273 insertions(+), 263 deletions(-)
Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification
(IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are
available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>)
simplified and advanced endpoints to easily download the data in a clean and
tidy format.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>
Diff between ripc versions 0.2.0 dated 2023-09-06 and 0.2.1 dated 2024-03-15
DESCRIPTION | 6 ++--- MD5 | 32 +++++++++++++-------------- NEWS.md | 13 ++++++++++- R/asserts.R | 2 - R/ipc_get.R | 10 ++++++-- R/ipc_get_analyses.R | 5 ++-- R/ipc_get_areas.R | 15 ++++++------ R/ipc_get_country.R | 15 +++++++----- R/ipc_get_icons.R | 5 +++- R/ipc_get_points.R | 20 +++++++++++++++-- R/ipc_get_population.R | 54 ++++++++++++++++++++++++++++------------------ build/vignette.rds |binary man/ipc_get_analyses.Rd | 2 - man/ipc_get_areas.Rd | 2 - man/ipc_get_icons.Rd | 2 - man/ipc_get_points.Rd | 2 - man/ipc_get_population.Rd | 2 - 17 files changed, 121 insertions(+), 66 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.0.4 dated 2024-01-22 and 2.0.5 dated 2024-03-15
DESCRIPTION | 21 MD5 | 46 - NAMESPACE | 6 NEWS | 23 R/EBICglasso.qgraph.R | 202 ++--- R/auto.correlate.R | 206 ++--- R/bootEGA.R | 777 ++++++++++---------- R/community.compare.R | 242 +++--- R/helpers.R | 1502 +++++++++++++++++++++++----------------- R/hierEGA.R | 491 ++++++------- R/infoCluster.R | 136 ++- R/invariance.R | 448 +++++------ R/net.loads.R | 454 ++++++------ R/network.generalizability.R |only R/network.predictability.R |only inst/CITATION | 8 man/EBICglasso.qgraph.Rd | 10 man/auto.correlate.Rd | 14 man/bootEGA.Rd | 51 - man/community.compare.Rd | 41 - man/hierEGA.Rd | 56 - man/infoCluster.Rd | 4 man/invariance.Rd | 28 man/net.loads.Rd | 2 man/network.generalizability.Rd |only man/network.predictability.Rd |only 26 files changed, 2598 insertions(+), 2170 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre], Tomi Silander [ctb], Robert Ness [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 4.9.2 dated 2024-03-12 and 4.9.3 dated 2024-03-15
Changelog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/classifiers.R | 1 + 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Distribution of the 'BayesX' C++ Sources
Description: 'BayesX' performs Bayesian inference in structured additive regression (STAR) models.
The R package BayesXsrc provides the 'BayesX' command line tool for easy installation.
A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre] ,
Daniel Adler [aut],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesXsrc versions 3.0-4 dated 2023-02-03 and 3.0-5 dated 2024-03-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/bayesxsrc/psplines/spline_basis.cpp | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.1.0 dated 2024-03-13 and 2.1.1 dated 2024-03-15
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 5 ++++ R/compute_mallows_sequentially.R | 7 ++++++ build/partial.rdb |binary inst/examples/compute_mallows_sequentially_example.R | 2 - man/compute_mallows_sequentially.Rd | 2 - tests/testthat/test-compute_mallows_sequentially.R | 21 +++++++++++++++++++ 8 files changed, 45 insertions(+), 12 deletions(-)
Title: A System for Working with Templates
Description: Provides tools to work with template code and text in R. It aims to
provide a simple substitution mechanism for R-expressions inside these
templates. Templates can be written in other languages like 'SQL', can
simply be represented by characters in R, or can themselves be R-expressions
or functions.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between templates versions 0.3.0 dated 2018-05-22 and 0.4.0 dated 2024-03-15
DESCRIPTION | 11 MD5 | 18 - NAMESPACE | 4 NEWS | 6 R/NAMESPACE.R | 6 R/templateUtilities.R | 6 build/vignette.rds |binary inst/doc/Template_Programming_in_R.R | 14 inst/doc/Template_Programming_in_R.html | 455 ++++++++++++++++++++++++++------ tests/testthat/test-utils.R | 20 + 10 files changed, 427 insertions(+), 113 deletions(-)
Title: 'Amazon Web Service S3' File System
Description: Access 'Amazon Web Service Simple Storage Service' ('S3') <https://aws.amazon.com/s3/>
as if it were a file system. Interface based on the R package 'fs'.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between s3fs versions 0.1.4 dated 2023-10-23 and 0.1.5 dated 2024-03-15
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 6 +++ R/s3filesystem_class.R | 30 ++++++++-------- R/utils.R | 88 +++++++++++++++++++++---------------------------- 5 files changed, 67 insertions(+), 71 deletions(-)
Title: Decode Information from Neural Activity
Description: Neural decoding is method of analyzing neural data that
uses a pattern classifiers to predict experimental conditions based
on neural activity. 'NeuroDecodeR' is a system of objects that
makes it easy to run neural decoding analyses. For more information
on neural decoding see Meyers & Kreiman (2011)
<doi:10.7551/mitpress/8404.003.0024>.
Author: Ethan Meyers [aut, cre]
Maintainer: Ethan Meyers <ethan.meyers@gmail.com>
Diff between NeuroDecodeR versions 0.1.0 dated 2022-09-29 and 0.2.0 dated 2024-03-15
NeuroDecodeR-0.1.0/NeuroDecodeR/vignettes/ZD_400bins_400sampled_start100_end500.Rda |only NeuroDecodeR-0.1.0/NeuroDecodeR/vignettes/position_invariance_results |only NeuroDecodeR-0.1.0/NeuroDecodeR/vignettes/results |only NeuroDecodeR-0.2.0/NeuroDecodeR/DESCRIPTION | 13 NeuroDecodeR-0.2.0/NeuroDecodeR/MD5 | 276 - NeuroDecodeR-0.2.0/NeuroDecodeR/NAMESPACE | 138 NeuroDecodeR-0.2.0/NeuroDecodeR/R/NeuroDecodeR.R | 120 NeuroDecodeR-0.2.0/NeuroDecodeR/R/cl_max_correlation.R | 300 - NeuroDecodeR-0.2.0/NeuroDecodeR/R/cl_poisson_naive_bayes.R | 374 +- NeuroDecodeR-0.2.0/NeuroDecodeR/R/cl_svm.R | 412 +- NeuroDecodeR-0.2.0/NeuroDecodeR/R/create_binned_data.R | 566 +-- NeuroDecodeR-0.2.0/NeuroDecodeR/R/cv_standard.R | 1046 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/R/ds_basic.R | 950 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/R/ds_generalization.R | 578 +-- NeuroDecodeR-0.2.0/NeuroDecodeR/R/fp_select_k_features.R | 332 +- NeuroDecodeR-0.2.0/NeuroDecodeR/R/fp_zscore.R | 212 - NeuroDecodeR-0.2.0/NeuroDecodeR/R/generic_functions.R | 486 +-- NeuroDecodeR-0.2.0/NeuroDecodeR/R/get_num_label_repetitions.R | 1052 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/R/log_and_save_decoding_results.R | 733 ++-- NeuroDecodeR-0.2.0/NeuroDecodeR/R/ndr_container.R | 276 - NeuroDecodeR-0.2.0/NeuroDecodeR/R/private_helper_functions.R | 526 +-- NeuroDecodeR-0.2.0/NeuroDecodeR/R/raster_data_functions.R | 1305 ++++---- NeuroDecodeR-0.2.0/NeuroDecodeR/R/rm_confusion_matrix.R | 1100 +++---- NeuroDecodeR-0.2.0/NeuroDecodeR/R/rm_main_results.R | 1566 +++++----- NeuroDecodeR-0.2.0/NeuroDecodeR/R/test_valid_NDR_objects.R | 1006 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/README.md | 254 - NeuroDecodeR-0.2.0/NeuroDecodeR/build/vignette.rds |binary NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/NDR_object_specification.R | 172 - NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/NDR_object_specification.Rmd | 836 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/NDR_object_specification.html | 1459 ++++----- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.R | 56 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.Rmd | 350 +- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.html | 1091 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.R | 28 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.Rmd | 288 - NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.html | 917 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.R | 360 +- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.Rmd | 716 ++-- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.html | 1447 ++++----- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/introduction_tutorial.R | 254 - NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/introduction_tutorial.Rmd | 992 +++--- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/introduction_tutorial.html | 1461 ++++----- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/extdata/Zhang_Desimone_7object_raster_data_small_csv/bp1001spk_01A_raster_data.csv | 842 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/inst/extdata/Zhang_Desimone_7object_raster_data_small_csv/bp1001spk_02A_raster_data.csv | 842 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/man/NeuroDecodeR.Rd | 82 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_CV_split_results.Rd | 74 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_CV_split_results.rm_confusion_matrix.Rd | 74 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_CV_split_results.rm_main_results.Rd | 74 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_resample_run_results.Rd | 52 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_resample_run_results.rm_confusion_matrix.Rd | 52 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_resample_run_results.rm_main_results.Rd | 52 NeuroDecodeR-0.2.0/NeuroDecodeR/man/cl_max_correlation.Rd | 156 NeuroDecodeR-0.2.0/NeuroDecodeR/man/cl_poisson_naive_bayes.Rd | 182 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/cl_svm.Rd | 154 NeuroDecodeR-0.2.0/NeuroDecodeR/man/convert_matlab_raster_data.Rd | 160 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/create_binned_data.Rd | 164 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/cv_standard.Rd | 246 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/ds_basic.Rd | 232 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/ds_generalization.Rd | 236 - NeuroDecodeR-0.2.0/NeuroDecodeR/man/figures/README-TCD_plot-1.png |binary NeuroDecodeR-0.2.0/NeuroDecodeR/man/figures/README-line_plot-1.png |binary NeuroDecodeR-0.2.0/NeuroDecodeR/man/figures/README-pipe_example-1.png |binary NeuroDecodeR-0.2.0/NeuroDecodeR/man/fp_select_k_features.Rd | 124 NeuroDecodeR-0.2.0/NeuroDecodeR/man/fp_zscore.Rd | 102 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.Rd | 70 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.ds_basic.Rd | 70 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.ds_generalization.Rd | 70 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_num_label_repetitions.Rd | 112 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_num_label_repetitions_each_site.Rd | 68 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_max_correlation.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_poisson_naive_bayes.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_svm.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cv_standard.Rd | 62 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.ds_basic.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.ds_generalization.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.fp_select_k_features.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.fp_zscore.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.rm_confusion_matrix.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.rm_main_results.Rd | 64 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.Rd | 94 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_max_correlation.Rd | 94 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_poisson_naive_bayes.Rd | 94 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_svm.Rd | 94 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_siteIDs_with_k_label_repetitions.Rd | 86 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_check_results_already_exist.Rd | 44 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_load_results_from_params.Rd | 48 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_load_results_from_result_name.Rd | 54 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_save_results.Rd | 66 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.label_repetition.Rd | 56 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.raster_data.Rd | 54 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.rm_confusion_matrix.Rd | 120 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.rm_main_results.Rd | 91 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot_main_results.Rd | 126 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.Rd | 86 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.fp_select_k_features.Rd | 86 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.fp_zscore.Rd | 86 NeuroDecodeR-0.2.0/NeuroDecodeR/man/read_matlab_raster_data.Rd | 138 NeuroDecodeR-0.2.0/NeuroDecodeR/man/read_raster_data.Rd | 94 NeuroDecodeR-0.2.0/NeuroDecodeR/man/rm_confusion_matrix.Rd | 132 NeuroDecodeR-0.2.0/NeuroDecodeR/man/rm_main_results.Rd | 134 NeuroDecodeR-0.2.0/NeuroDecodeR/man/run_decoding.Rd | 60 NeuroDecodeR-0.2.0/NeuroDecodeR/man/run_decoding.cv_standard.Rd | 58 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_binned_format.Rd | 48 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_ndr_object.Rd | 50 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_raster_format.Rd | 87 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat.R | 8 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/example_DECODING_RESULTS.Rda |binary NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/generate_data_to_test_NDR.R | 370 +- NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-bin_convert_data.R | 622 +-- NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-classifiers.R | 344 +- NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-datasources.R | 849 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-feature_preprocessors.R | 290 - NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-full_decoding.R | 152 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-log_save_results.R | 310 - NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-ndr_container.R | 74 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-result_metrics.R | 240 - NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/NDR_object_specification.Rmd | 836 ++--- NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/data_formats.Rmd | 350 +- NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/datasets.Rmd | 288 - NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/generalization_tutorial.Rmd | 716 ++-- NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/introduction_tutorial.Rmd | 992 +++--- 122 files changed, 18938 insertions(+), 18723 deletions(-)
Title: Interact with the 'Databrary.org' API
Description: 'Databrary.org' is a restricted access repository for research data, especially video and audio.
This package provides commands to interact with the data stored on 'Databrary.org'.
Author: Rick O. Gilmore [aut, cre, cph],
Jeffrey Spies [aut],
National Science Foundation OAC-2032713 [fnd],
National Institutes of Health R01HD094830 [fnd]
Maintainer: Rick O. Gilmore <rog1@psu.edu>
Diff between databraryr versions 0.6.1 dated 2024-02-22 and 0.6.2 dated 2024-03-15
DESCRIPTION | 6 +-- MD5 | 18 +++++----- NEWS.md | 2 + R/list_party_sponsors.R | 2 - R/list_party_volumes.R | 69 +++++++++++++++++++++++++++++++---------- inst/doc/authorized-users.R | 8 ++-- inst/doc/authorized-users.Rmd | 8 ++-- inst/doc/authorized-users.html | 8 ++-- inst/doc/databrary.html | 2 - vignettes/authorized-users.Rmd | 8 ++-- 10 files changed, 84 insertions(+), 47 deletions(-)
Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi_reiichiro33@fra.go.jp>
Diff between FinePop versions 1.5.1 dated 2018-10-26 and 1.5.2 dated 2024-03-15
DESCRIPTION | 14 +++++++------- MD5 | 34 +++++++++++++++++----------------- build/partial.rdb |binary data/herring.rda |binary data/jsmackerel.rda |binary man/DJ.Rd | 11 ++++++----- man/EBDJ.Rd | 11 ++++++----- man/EBFST.Rd | 11 ++++++----- man/EBGstH.Rd | 11 ++++++----- man/GstH.Rd | 11 ++++++----- man/GstN.Rd | 11 ++++++----- man/GstNC.Rd | 11 ++++++----- man/clip.genepop.Rd | 27 ++++++++++++++++++++------- man/herring.Rd | 15 ++++++++++----- man/jsmackerel.Rd | 22 ++++++++++++++-------- man/read.frequency.Rd | 18 +++++++----------- man/read.genepop.Rd | 17 ++++++++--------- man/thetaWC.pair.Rd | 11 ++++++----- 18 files changed, 131 insertions(+), 104 deletions(-)
Title: Epilepsy Ontologies' Similarities
Description: Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.
Author: Bernd Mueller
Maintainer: Bernd Mueller <bernd.mueller@zbmed.de>
Diff between epos versions 1.0 dated 2021-02-19 and 1.1 dated 2024-03-15
epos-1.0/epos/LICENSE |only epos-1.0/epos/inst/extdata/DCh-Miner_miner-disease-chemical.tsv.gz |only epos-1.1/epos/DESCRIPTION | 14 epos-1.1/epos/MD5 | 70 ++-- epos-1.1/epos/NAMESPACE | 119 ++++---- epos-1.1/epos/R/data.R | 35 +- epos-1.1/epos/R/doThePlotDrugVectors.R | 86 ++--- epos-1.1/epos/R/drawVennDiagramms.R | 60 ++-- epos-1.1/epos/R/main.R | 1 epos-1.1/epos/R/writeNeuroTable.R | 51 ++- epos-1.1/epos/README.md | 15 - epos-1.1/epos/man/calcDSEA.Rd | 44 +-- epos-1.1/epos/man/calcEnrichment.Rd | 40 +- epos-1.1/epos/man/createNeuroTable.Rd | 12 epos-1.1/epos/man/drawVenn4.Rd | 44 +-- epos-1.1/epos/man/drawVenn4Doc.Rd | 44 +-- epos-1.1/epos/man/drawVenn4DrugDoc.Rd | 44 +-- epos-1.1/epos/man/drawVenn4Syn.Rd | 44 +-- epos-1.1/epos/man/drawVenn5.Rd | 44 +-- epos-1.1/epos/man/drawVenn5Doc.Rd | 44 +-- epos-1.1/epos/man/drawVenn5DrugDoc.Rd | 44 +-- epos-1.1/epos/man/drawVenn5Syn.Rd | 44 +-- epos-1.1/epos/man/drawVennGrid.Rd | 102 +++---- epos-1.1/epos/man/getRefAll.Rd | 34 +- epos-1.1/epos/man/getTermMatrix.Rd | 56 +-- epos-1.1/epos/man/plotDSEA.Rd | 144 +++++----- epos-1.1/epos/man/plotEnrichment.Rd | 134 ++++----- epos-1.1/epos/man/printTop10Drugs.Rd | 112 +++---- epos-1.1/epos/man/rawDrugNamesCoOcEPILONT.Rd | 63 ++-- epos-1.1/epos/man/rawDrugNamesCoOcEPISEM.Rd | 63 ++-- epos-1.1/epos/man/rawDrugNamesCoOcESSO.Rd | 63 ++-- epos-1.1/epos/man/rawDrugNamesCoOcEpSO.Rd | 64 ++-- epos-1.1/epos/man/rawDrugNamesCoOcFENICS.Rd | 64 ++-- epos-1.1/epos/man/sortTableByRefMatches.Rd | 113 ++++--- epos-1.1/epos/tests/testthat/test_createBaseTable.R | 11 epos-1.1/epos/tests/testthat/test_createNeuroTable.R | 2 epos-1.1/epos/tests/testthat/test_createTanimotoBaseline.R | 24 + 37 files changed, 996 insertions(+), 952 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative
divide in social science research. It uses a Boolean minimization
algorithm, resulting in a minimal causal configuration associated
with a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] ,
Ciprian Paduraru [ctb] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
Vasil Dinkov [ctb, cph] ,
Dmitry Baranovskiy [ctb, cph] ,
Emmanuel Quentin [ctb, cph] ,
Jimmy Breck-McKye [ctb, cph] ,
Alrik Thiem [aut] [...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.21 dated 2023-09-18 and 3.22 dated 2024-03-15
DESCRIPTION | 66 ++-- MD5 | 206 ++++++------- NAMESPACE | 1 R/XYplot.R | 15 - R/Xplot.R | 17 - R/allExpressions.R | 15 - R/calibrate.R | 23 - R/causalChain.R | 15 - R/combint.R | 15 - R/complexity.R | 15 - R/createMatrix.R | 15 - R/dimnames.R | 15 - R/findRows.R | 17 - R/findSubsets.R | 15 - R/findSupersets.R | 15 - R/findTh.R | 15 - R/findmin.R | 15 - R/fuzzyand.R | 67 ++-- R/fuzzyor.R | 65 ++-- R/generate.R | 15 - R/getRow.R | 15 - R/getSolution.R | 15 - R/makeChart.R | 15 - R/minimize.R | 38 +- R/modelFit.R | 62 +++- R/onAttach.R | 27 + R/onUnload.R | 15 - R/panel.R | 15 - R/pof.R | 46 +-- R/pofind.R | 15 - R/print.R | 23 - R/removeRedundants.R | 15 - R/replaceCategories.R | 15 - R/retention.R | 15 - R/rowDominance.R | 15 - R/runGUI.R | 15 - R/solveChart.R | 15 - R/sortMatrix.R | 15 - R/sortVector.R | 15 - R/string.R | 15 - R/superSubset.R | 19 - R/truthTable.R | 65 ++-- R/verifyQCA.R | 15 - R/writeSolution.R | 15 - build/partial.rdb |binary data/HarKem.rda |binary data/LC.rda |binary data/LF.rda |binary data/LM.rda |binary data/d.HK.rda |binary data/d.partybans.rda |binary inst/ChangeLog | 129 ++++---- inst/gui/server.R | 19 - inst/gui/www/js/maincode.js | 17 - inst/gui/www/js/utils.js | 15 - inst/staticdocs/CV.html | 4 inst/staticdocs/LegacyDatasets.html | 4 inst/staticdocs/Lipset.html | 4 inst/staticdocs/QCA_package.html | 106 +++---- inst/staticdocs/RS.html | 4 inst/staticdocs/SOPexpressions.html | 4 inst/staticdocs/XYplot.html | 4 inst/staticdocs/Xplot.html | 4 inst/staticdocs/calibrate.html | 4 inst/staticdocs/causalChain.html | 4 inst/staticdocs/chartFunctions.html | 4 inst/staticdocs/export.html | 4 inst/staticdocs/factorize.html | 4 inst/staticdocs/findRows.html | 58 +-- inst/staticdocs/findTh.html | 4 inst/staticdocs/fuzzyops.html | 38 +- inst/staticdocs/generate.html | 4 inst/staticdocs/implicantMatrixFunctions.html | 4 inst/staticdocs/index.html | 4 inst/staticdocs/intersection.html | 4 inst/staticdocs/minimize.html | 389 ++++++++++++-------------- inst/staticdocs/modelFit.html | 4 inst/staticdocs/negate.html | 4 inst/staticdocs/pof.html | 4 inst/staticdocs/retention.html | 4 inst/staticdocs/runGUI.html | 4 inst/staticdocs/subsetsAndSupersets.html | 4 inst/staticdocs/truthTable.html | 357 ++++++++++++----------- man/Lipset.Rd | 16 - man/QCA_package.Rd | 57 +-- man/findRows.Rd | 8 man/fuzzyops.Rd | 11 man/minimize.Rd | 21 - man/modelFit.Rd | 17 - man/truthTable.Rd | 23 - src/CCubes.c | 19 - src/QCA.c | 15 - src/consistency.c | 15 - src/consistent_solution.c | 15 - src/find_consistent_models.c | 15 - src/find_models.c | 15 - src/generate_matrix.c | 15 - src/registerDynamicSymbol.c | 15 - src/row_dominance.c | 15 - src/sort_cols.c | 15 - src/sort_matrix.c | 15 - src/super_rows.c | 15 - src/truthTable.c | 15 - src/utils.c | 15 - 104 files changed, 1431 insertions(+), 1333 deletions(-)
Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods,
statistical summaries and graphics functions for the analysing tidy time
series data. The package name 'feasts' is an acronym comprising of its key
features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Di Cook [ctb],
Thiyanga Talagala [ctb] ,
Leanne Chhay [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between feasts versions 0.3.1 dated 2023-03-22 and 0.3.2 dated 2024-03-15
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 15 ++ R/classical.R | 8 - R/graphics.R | 7 + R/zzz.R | 2 inst/doc/feasts.R | 2 inst/doc/feasts.html | 202 ++++++++++++++++++-------------------- man/generate.stl_decomposition.Rd | 4 tests/testthat/Rplots.pdf |binary 10 files changed, 140 insertions(+), 124 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut],
Indrajeet Patil [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 1.1-5 dated 2023-10-30 and 1.1-6 dated 2024-03-15
WRS2-1.1-5/WRS2/R/matl.R |only WRS2-1.1-5/WRS2/R/pdis.R |only WRS2-1.1-6/WRS2/DESCRIPTION | 8 ++++---- WRS2-1.1-6/WRS2/MD5 | 12 +++++------- WRS2-1.1-6/WRS2/R/utilities.R | 23 +---------------------- WRS2-1.1-6/WRS2/build/vignette.rds |binary WRS2-1.1-6/WRS2/inst/NEWS.Rd | 7 +++++++ WRS2-1.1-6/WRS2/inst/doc/WRS2.pdf |binary 8 files changed, 17 insertions(+), 33 deletions(-)
Title: Extended Rasch Modeling
Description: Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, simulation module for various binary data matrices.
Author: Patrick Mair [cre, aut],
Thomas Rusch [aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Rudolf Debelak [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between eRm versions 1.0-5 dated 2024-03-01 and 1.0-6 dated 2024-03-15
DESCRIPTION | 8 +++--- MD5 | 14 +++++------ R/anova.llra.R | 62 ++++++++++++++++++++++++++--------------------------- R/summary.llra.R | 34 ++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 8 +++++- inst/doc/eRm.pdf |binary 8 files changed, 65 insertions(+), 61 deletions(-)
Title: Configural Frequency Analysis (CFA)
Description: Analysis of configuration frequencies for simple and repeated measures, multiple-samples CFA, hierarchical CFA, bootstrap CFA, functional CFA, Kieser-Victor CFA, and Lindner's test using a conventional and an accelerated algorithm.
Author: Patrick Mair [aut, cre],
Stefan Funke [aut],
Joachim Harloff [ctb],
Alexander von Eye [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between cfa versions 0.10-0 dated 2017-05-01 and 0.10-1 dated 2024-03-15
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/PXisMclassic.R | 7 ------- 3 files changed, 6 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-15 4.2.9
2023-12-05 4.2.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 0.4.0
2024-01-14 0.3.8
2023-12-14 0.3.5
Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.0.0 dated 2024-02-09 and 1.0.1 dated 2024-03-15
inferCSN-1.0.0/inferCSN/R/compute.gene.rank.R |only inferCSN-1.0.0/inferCSN/man/coef.inferCSN.Rd |only inferCSN-1.0.0/inferCSN/man/compute.gene.rank.Rd |only inferCSN-1.0.0/inferCSN/man/inferCSN.fit.Rd |only inferCSN-1.0.0/inferCSN/man/predict.inferCSN.Rd |only inferCSN-1.0.0/inferCSN/man/print.inferCSN.Rd |only inferCSN-1.0.0/inferCSN/man/sub.inferCSN.Rd |only inferCSN-1.0.0/inferCSN/tests |only inferCSN-1.0.1/inferCSN/DESCRIPTION | 8 inferCSN-1.0.1/inferCSN/MD5 | 55 inferCSN-1.0.1/inferCSN/NAMESPACE | 19 inferCSN-1.0.1/inferCSN/R/RcppExports.R | 16 inferCSN-1.0.1/inferCSN/R/calculate.gene.rank.R |only inferCSN-1.0.1/inferCSN/R/inferCSN.R | 33 inferCSN-1.0.1/inferCSN/R/network.visualization.R | 168 +- inferCSN-1.0.1/inferCSN/R/sparse.regression.R | 233 +- inferCSN-1.0.1/inferCSN/R/utils.R | 199 +- inferCSN-1.0.1/inferCSN/README.md | 14 inferCSN-1.0.1/inferCSN/man/calculate.gene.rank.Rd |only inferCSN-1.0.1/inferCSN/man/coef.SRM_fit.Rd |only inferCSN-1.0.1/inferCSN/man/contrast.networks.Rd | 9 inferCSN-1.0.1/inferCSN/man/dynamic.networks.Rd | 35 inferCSN-1.0.1/inferCSN/man/figures/logo.svg | 1715 ++++++++++----------- inferCSN-1.0.1/inferCSN/man/filter.sort.matrix.Rd |only inferCSN-1.0.1/inferCSN/man/model.fit.Rd |only inferCSN-1.0.1/inferCSN/man/net.format.Rd | 37 inferCSN-1.0.1/inferCSN/man/network.heatmap.Rd | 89 - inferCSN-1.0.1/inferCSN/man/predict.SRM_fit.Rd |only inferCSN-1.0.1/inferCSN/man/print.SRM_fit.Rd |only inferCSN-1.0.1/inferCSN/man/single.network.Rd |only inferCSN-1.0.1/inferCSN/man/sparse.regression.Rd | 11 inferCSN-1.0.1/inferCSN/man/table.to.matrix.Rd | 28 inferCSN-1.0.1/inferCSN/src/Interface.cpp | 21 inferCSN-1.0.1/inferCSN/src/RcppExports.cpp | 40 inferCSN-1.0.1/inferCSN/src/include/Interface.h | 2 inferCSN-1.0.1/inferCSN/src/table_to_matrix.cpp | 190 +- 36 files changed, 1646 insertions(+), 1276 deletions(-)
Title: Clean Data Frames
Description: Provides a friendly interface for modifying data frames with a sequence of piped commands built upon the 'tidyverse' Wickham et al., (2019) <doi:10.21105/joss.01686> . The majority of commands wrap 'dplyr' mutate statements in a convenient way to concisely solve common issues that arise when tidying small to medium data sets. Includes smart defaults and allows flexible selection of columns via 'tidyselect'.
Author: Harrison Tietze [aut, cre]
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Diff between framecleaner versions 0.2.0 dated 2021-11-17 and 0.2.1 dated 2024-03-15
framecleaner-0.2.0/framecleaner/man/fct_or_prob.Rd |only framecleaner-0.2.0/framecleaner/vignettes/PackageIntroduction.R |only framecleaner-0.2.1/framecleaner/DESCRIPTION | 8 framecleaner-0.2.1/framecleaner/LICENSE | 4 framecleaner-0.2.1/framecleaner/MD5 | 140 + framecleaner-0.2.1/framecleaner/NAMESPACE | 100 - framecleaner-0.2.1/framecleaner/NEWS.md | 2 framecleaner-0.2.1/framecleaner/R/clean_frame.R | 82 - framecleaner-0.2.1/framecleaner/R/create_dummmies.R | 161 +- framecleaner-0.2.1/framecleaner/R/create_flag.R | 80 - framecleaner-0.2.1/framecleaner/R/fill_na.R | 122 - framecleaner-0.2.1/framecleaner/R/filter_for.R | 96 - framecleaner-0.2.1/framecleaner/R/filter_missing.R | 384 ++--- framecleaner-0.2.1/framecleaner/R/globals.R | 6 framecleaner-0.2.1/framecleaner/R/guess_id_col.R | 182 +- framecleaner-0.2.1/framecleaner/R/import_dir.R | 66 framecleaner-0.2.1/framecleaner/R/import_tibble.R | 70 framecleaner-0.2.1/framecleaner/R/make_na.R | 158 +- framecleaner-0.2.1/framecleaner/R/manipulate_dates.R |only framecleaner-0.2.1/framecleaner/R/pad_cols.R | 136 - framecleaner-0.2.1/framecleaner/R/recode_item.R | 96 - framecleaner-0.2.1/framecleaner/R/relocate_all.R | 96 - framecleaner-0.2.1/framecleaner/R/remove_whitespace.R | 50 framecleaner-0.2.1/framecleaner/R/select_otherwise.R | 124 - framecleaner-0.2.1/framecleaner/R/set_chr.R | 44 framecleaner-0.2.1/framecleaner/R/set_date.R | 180 +- framecleaner-0.2.1/framecleaner/R/set_dbl.R | 187 +- framecleaner-0.2.1/framecleaner/R/set_fct.R | 169 +- framecleaner-0.2.1/framecleaner/R/set_int.R | 274 +-- framecleaner-0.2.1/framecleaner/R/set_lgl.R | 130 - framecleaner-0.2.1/framecleaner/R/setters.R | 92 - framecleaner-0.2.1/framecleaner/R/utilities.R | 120 - framecleaner-0.2.1/framecleaner/R/utils-pipe.R | 22 framecleaner-0.2.1/framecleaner/README.md | 82 - framecleaner-0.2.1/framecleaner/build/vignette.rds |binary framecleaner-0.2.1/framecleaner/inst/doc/cleanYourFrame.R | 74 - framecleaner-0.2.1/framecleaner/inst/doc/cleanYourFrame.Rmd | 164 +- framecleaner-0.2.1/framecleaner/inst/doc/cleanYourFrame.html | 709 ++++++---- framecleaner-0.2.1/framecleaner/man/as_integer16_or_64.Rd | 34 framecleaner-0.2.1/framecleaner/man/auto_setwd.Rd | 30 framecleaner-0.2.1/framecleaner/man/clean_frame.Rd | 72 - framecleaner-0.2.1/framecleaner/man/create_dummies.Rd | 113 - framecleaner-0.2.1/framecleaner/man/create_flag.Rd | 70 framecleaner-0.2.1/framecleaner/man/date_yh.Rd |only framecleaner-0.2.1/framecleaner/man/date_ym.Rd |only framecleaner-0.2.1/framecleaner/man/date_yq.Rd |only framecleaner-0.2.1/framecleaner/man/fill_na.Rd | 76 - framecleaner-0.2.1/framecleaner/man/filter_for.Rd | 88 - framecleaner-0.2.1/framecleaner/man/filter_missing.data.frame.Rd | 100 - framecleaner-0.2.1/framecleaner/man/import_dir.Rd | 58 framecleaner-0.2.1/framecleaner/man/import_tibble.Rd | 58 framecleaner-0.2.1/framecleaner/man/is_integerish_character.Rd | 36 framecleaner-0.2.1/framecleaner/man/is_integery.Rd | 38 framecleaner-0.2.1/framecleaner/man/is_missing_or_inf.Rd | 36 framecleaner-0.2.1/framecleaner/man/is_probability.Rd | 36 framecleaner-0.2.1/framecleaner/man/make_na.data.frame.Rd | 68 framecleaner-0.2.1/framecleaner/man/pad_auto.Rd | 62 framecleaner-0.2.1/framecleaner/man/pad_col.Rd | 70 framecleaner-0.2.1/framecleaner/man/pipe.Rd | 24 framecleaner-0.2.1/framecleaner/man/recode_chr.Rd | 100 - framecleaner-0.2.1/framecleaner/man/relocate_all.Rd | 58 framecleaner-0.2.1/framecleaner/man/remove_infs.Rd | 36 framecleaner-0.2.1/framecleaner/man/remove_nans.Rd | 36 framecleaner-0.2.1/framecleaner/man/remove_nas.Rd | 36 framecleaner-0.2.1/framecleaner/man/remove_whitespace.Rd | 56 framecleaner-0.2.1/framecleaner/man/select_otherwise.Rd | 76 - framecleaner-0.2.1/framecleaner/man/set_chr.Rd | 52 framecleaner-0.2.1/framecleaner/man/set_date.Rd | 88 - framecleaner-0.2.1/framecleaner/man/set_dbl.data.frame.Rd | 117 - framecleaner-0.2.1/framecleaner/man/set_fct.data.frame.Rd | 97 - framecleaner-0.2.1/framecleaner/man/set_int.data.frame.Rd | 108 - framecleaner-0.2.1/framecleaner/man/set_lgl.data.frame.Rd | 80 - framecleaner-0.2.1/framecleaner/man/set_type_groups.Rd | 44 framecleaner-0.2.1/framecleaner/vignettes/cleanYourFrame.Rmd | 164 +- 74 files changed, 3435 insertions(+), 3192 deletions(-)
Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rwhois versions 1.0.14 dated 2023-05-24 and 1.0.16 dated 2024-03-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/functions.R | 11 +++++++++-- README.md | 2 +- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: RDAP Server Querying
Description: Queries data from RDAP servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rrdap versions 1.0.6 dated 2022-07-14 and 1.0.7 dated 2024-03-14
DESCRIPTION | 8 +-- MD5 | 6 +- R/functions.R | 119 ++++++++++++++++++++++++++++++++++------------------------ README.md | 2 4 files changed, 79 insertions(+), 56 deletions(-)
Title: False Discovery Control Procedure Integrating the Prior
Structure Information
Description: Perform more powerful false discovery control (FDR) for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. As a general methodology, it is applicable to any type of (genomic) data with prior structure information.
Author: Jun Chen
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between StructFDR versions 1.3 dated 2018-05-29 and 1.4 dated 2024-03-14
StructFDR-1.3/StructFDR/man/StructFDR-package.Rd |only StructFDR-1.4/StructFDR/DESCRIPTION | 8 StructFDR-1.4/StructFDR/MD5 | 27 StructFDR-1.4/StructFDR/build/vignette.rds |binary StructFDR-1.4/StructFDR/data/alcohol.rda |binary StructFDR-1.4/StructFDR/data/throat.parameter.rda |binary StructFDR-1.4/StructFDR/inst/doc/StructFDR.R | 20 StructFDR-1.4/StructFDR/inst/doc/StructFDR.html | 949 +++++++++++--------- StructFDR-1.4/StructFDR/man/AdjStats.Rd | 2 StructFDR-1.4/StructFDR/man/EstHyper.Rd | 2 StructFDR-1.4/StructFDR/man/MicrobiomeSeqTreeFDR.Rd | 5 StructFDR-1.4/StructFDR/man/SimulateData.Rd | 3 StructFDR-1.4/StructFDR/man/StructFDR.Rd | 2 StructFDR-1.4/StructFDR/man/TreeFDR.Rd | 2 StructFDR-1.4/StructFDR/man/Ztransform.Rd | 2 15 files changed, 560 insertions(+), 462 deletions(-)
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.1.8 dated 2023-06-26 and 0.1.9 dated 2024-03-14
PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-32-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-35-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-36-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-41-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-42-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-60-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-67-1.png |only PriceIndices-0.1.8/PriceIndices/man/figures/README-unnamed-chunk-68-1.png |only PriceIndices-0.1.9/PriceIndices/DESCRIPTION | 6 PriceIndices-0.1.9/PriceIndices/MD5 | 77 +- PriceIndices-0.1.9/PriceIndices/NAMESPACE | 2 PriceIndices-0.1.9/PriceIndices/NEWS.md | 15 PriceIndices-0.1.9/PriceIndices/R/PriceIndices.R | 74 -- PriceIndices-0.1.9/PriceIndices/R/dataDOWNSIZED.R |only PriceIndices-0.1.9/PriceIndices/R/f_Machine_Learning.R | 85 +- PriceIndices-0.1.9/PriceIndices/R/f_bilateral_indicators.R | 75 ++ PriceIndices-0.1.9/PriceIndices/R/f_data_processing.R | 298 +++++++++- PriceIndices-0.1.9/PriceIndices/R/f_internal.R | 183 ++---- PriceIndices-0.1.9/PriceIndices/R/f_multilateral_indicators.R | 81 +- PriceIndices-0.1.9/PriceIndices/README.md | 191 ++++-- PriceIndices-0.1.9/PriceIndices/data/dataDOWNSIZED.rda |only PriceIndices-0.1.9/PriceIndices/data/dataU.rda |binary PriceIndices-0.1.9/PriceIndices/inst/doc/PriceIndices.R | 29 PriceIndices-0.1.9/PriceIndices/inst/doc/PriceIndices.Rmd | 47 + PriceIndices-0.1.9/PriceIndices/inst/doc/PriceIndices.html | 40 + PriceIndices-0.1.9/PriceIndices/man/PriceIndices.Rd | 80 -- PriceIndices-0.1.9/PriceIndices/man/dataDOWNSIZED.Rd |only PriceIndices-0.1.9/PriceIndices/man/data_classifying.Rd | 8 PriceIndices-0.1.9/PriceIndices/man/data_norm.Rd | 4 PriceIndices-0.1.9/PriceIndices/man/data_reducing.Rd |only PriceIndices-0.1.9/PriceIndices/man/data_unit.Rd | 17 PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-19-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-20-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-34-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-37-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-38-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-43-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-44-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-45-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-47-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-49-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-62-1.png |binary PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-64-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-69-1.png |only PriceIndices-0.1.9/PriceIndices/man/figures/README-unnamed-chunk-70-1.png |only PriceIndices-0.1.9/PriceIndices/man/load_model.Rd | 4 PriceIndices-0.1.9/PriceIndices/man/model_classification.Rd | 14 PriceIndices-0.1.9/PriceIndices/man/save_model.Rd | 2 PriceIndices-0.1.9/PriceIndices/man/shrinkflation.Rd |only PriceIndices-0.1.9/PriceIndices/vignettes/PriceIndices.Rmd | 47 + 50 files changed, 864 insertions(+), 515 deletions(-)
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021,
<doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a
single function for reading individual, batch, or map spectral data files
like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies
processing spectra, including smoothing, baseline correction,
range restriction and flattening, intensity conversions, wavenumber
alignment, and min-max normalization. Spectra can be identified in batch
using an onboard reference library (Cowger et al. 2020,
<doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available
via run_app() or online at <https://openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut, dtc] ,
Zacharias Steinmetz [aut] ,
Nick Leong [aut] ,
Andrea Faltynkova [aut, dtc] ,
Hannah Sherrod [aut] ,
Andrew B Gray [ctb] ,
Hannah Hapich [ctb] ,
Jennifer Lynch [ctb, dtc] ,
Hannah De Frond [ctb, dtc] ,
Keenan Munno [ctb, [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 1.0.7 dated 2024-03-11 and 1.0.8 dated 2024-03-14
DESCRIPTION | 8 +- MD5 | 48 +++++++------- NAMESPACE | 4 - NEWS.md | 6 + R/manage_na.R | 32 +++++---- R/manage_spec.R | 2 R/read_multi.R | 82 +++++++++++++----------- R/sig_noise.R | 2 R/spec_res.R | 3 README.md | 4 - inst/doc/sop.html | 108 ++++++++++++++++---------------- man/OpenSpecy-package.Rd | 1 man/manage_na.Rd | 16 ++-- man/read_multi.Rd | 21 +++--- tests/testthat/test-adj_range.R | 2 tests/testthat/test-interactive_plots.R | 2 tests/testthat/test-manage_na.R | 11 ++- tests/testthat/test-manage_spec.R | 2 tests/testthat/test-match_spec.R | 4 - tests/testthat/test-read_envi.R | 4 - tests/testthat/test-read_multi.R | 2 tests/testthat/test-share_spec.R | 3 tests/testthat/test-smooth_intens.R | 12 +-- tests/testthat/test-spec_res.R | 2 tests/testthat/test-workflows.R | 84 +++++++++++++----------- 25 files changed, 254 insertions(+), 211 deletions(-)
Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between EnrichIntersect versions 0.6 dated 2023-02-26 and 0.7 dated 2024-03-14
DESCRIPTION | 8 ++-- MD5 | 21 ++++++----- NEWS.md | 5 ++ R/enrichment.R | 11 +++-- README.md |only build/vignette.rds |binary inst/CITATION | 2 - inst/doc/EnrichIntersect.R | 6 ++- inst/doc/EnrichIntersect.Rmd | 4 +- inst/doc/EnrichIntersect.html | 78 +++++++++++++++++++++--------------------- man/figures |only vignettes/EnrichIntersect.Rmd | 4 +- 12 files changed, 78 insertions(+), 61 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to
develop continuous-time agent based models. Its high performance
allows it to simulate millions of agents efficiently. Agents are
defined by their states (arbitrary R lists). The events are handled in
chronological order. This avoids the multi-event interaction problem
in a time step of discrete-time simulations, and gives precise
outcomes. The states are modified by provided or user-defined events.
The framework provides a flexible and customizable implementation of
state transitions (either spontaneous or caused by agent
interactions), making the framework suitable to apply to epidemiology
and ecology, e.g., to model life history stages, competition and
cooperation, and disease and information spread. The agent
interactions are flexible and extensible. The framework provides
random mixing and network interactions, and supports multi-level
mixing patterns. It can be easily extended to other interactions such
as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>
Diff between ABM versions 0.3 dated 2023-03-24 and 0.4.1 dated 2024-03-14
ABM-0.3/ABM/R/ABM.R |only ABM-0.3/ABM/man/ABM.Rd |only ABM-0.4.1/ABM/DESCRIPTION | 8 +-- ABM-0.4.1/ABM/MD5 | 78 ++++++++++++++++---------------- ABM-0.4.1/ABM/R/ABM-package.R |only ABM-0.4.1/ABM/R/Agent.R | 26 ++-------- ABM-0.4.1/ABM/R/Contact.R | 14 ++++- ABM-0.4.1/ABM/R/Population.R | 18 ++----- ABM-0.4.1/ABM/R/RcppExports.R | 20 ++++---- ABM-0.4.1/ABM/R/Simulation.R | 10 ++-- ABM-0.4.1/ABM/README.md | 2 ABM-0.4.1/ABM/inst/include/Agent.h | 39 ++++++++++++++-- ABM-0.4.1/ABM/inst/include/Contact.h | 18 ++++--- ABM-0.4.1/ABM/inst/include/Counter.h | 4 - ABM-0.4.1/ABM/inst/include/Network.h | 12 ++-- ABM-0.4.1/ABM/inst/include/Population.h | 24 ++++----- ABM-0.4.1/ABM/inst/include/RNG.h | 1 ABM-0.4.1/ABM/inst/include/Simulation.h | 20 ++++++++ ABM-0.4.1/ABM/inst/include/XP.h | 2 ABM-0.4.1/ABM/man/ABM-package.Rd |only ABM-0.4.1/ABM/man/Agent.Rd | 6 +- ABM-0.4.1/ABM/man/Contact.Rd | 25 +++++++++- ABM-0.4.1/ABM/man/Population.Rd | 6 +- ABM-0.4.1/ABM/man/Simulation.Rd | 5 +- ABM-0.4.1/ABM/man/State.Rd | 2 ABM-0.4.1/ABM/man/addAgent.Rd | 3 - ABM-0.4.1/ABM/man/clearEvents.Rd | 3 - ABM-0.4.1/ABM/man/leave.Rd | 3 - ABM-0.4.1/ABM/man/schedule.Rd | 3 - ABM-0.4.1/ABM/man/setDeathTime.Rd | 3 - ABM-0.4.1/ABM/man/setState.Rd | 3 - ABM-0.4.1/ABM/man/setStates.Rd | 3 - ABM-0.4.1/ABM/man/unschedule.Rd | 3 - ABM-0.4.1/ABM/src/Agent.cpp | 53 +++++++++++++-------- ABM-0.4.1/ABM/src/Contact.cpp | 17 ++---- ABM-0.4.1/ABM/src/Counter.cpp | 9 +-- ABM-0.4.1/ABM/src/Network.cpp | 42 ++++++++--------- ABM-0.4.1/ABM/src/Population.cpp | 70 ++++++++++++++-------------- ABM-0.4.1/ABM/src/RNG.cpp | 2 ABM-0.4.1/ABM/src/RcppExports.cpp | 70 ++++++++++++---------------- ABM-0.4.1/ABM/src/Simulation.cpp | 20 ++++++-- ABM-0.4.1/ABM/src/Transition.cpp | 5 +- 42 files changed, 355 insertions(+), 297 deletions(-)
Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group
Structure
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Author: Yazdan Asgari [aut, cre],
Taban Baghfalaki [aut],
Benoit Liquet [aut],
Pierre-Emmanuel Sugier [aut],
Mohammed Sedki [aut],
Therese Truong [aut]
Maintainer: Yazdan Asgari <yazdan.asgari@inserm.fr>
Diff between GCPBayes versions 4.1.0 dated 2023-12-04 and 4.2.0 dated 2024-03-14
DESCRIPTION | 24 +++++++++++++++++++----- MD5 | 20 ++++++++++---------- NEWS.md | 19 +++++++++++++++++++ R/CS.R | 2 +- R/DS.R | 2 +- R/GCPBayes.R | 4 ++-- R/HS.R | 30 +++++++++++++++++++++++------- R/Simulated_individual_survival.R | 33 +++++++++++++++++---------------- R/summaryCS.R | 4 ++-- R/summaryDS.R | 2 +- R/summaryHS.R | 4 ++-- 11 files changed, 97 insertions(+), 47 deletions(-)
Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation,
dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via
bootstrap and recursive sandwich estimation. Estimation and
inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv).
Extension to continuous treatment variables. Wallace et al. (2017)
<DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020)
<DOI:10.1080/00949655.2020.1793341>.
Author: Michael Wallace, Erica E M Moodie, David A Stephens, Gabrielle Simoneau, Shannon T. Holloway and Juliana Schulz
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DTRreg versions 2.0 dated 2023-11-19 and 2.1 dated 2024-03-14
DESCRIPTION | 10 ++--- MD5 | 37 ++++++++++----------- NEWS | 10 +++++ R/Ahat.R | 4 +- R/DWsurv.R | 87 +++++++++++++++++++++++++++++++------------------- R/chooseM.R | 2 - R/dtrProcedure.R | 25 ++++++++++---- R/inputProcessing.R | 14 +++++--- R/s3-methods.R | 2 - R/sandwich.R | 2 - R/treatmentClasses.R | 36 +++++++++++++------- R/utils.R | 8 ++-- R/varest.R | 5 +- R/weights.R | 14 +++++--- man/DTRreg.Rd | 2 - man/DWSurv.Rd | 48 ++++++++++++++++----------- man/chooseM.Rd | 2 - man/plot.DTRreg.Rd | 2 - man/predict.DTRreg.Rd | 2 - tests |only 20 files changed, 194 insertions(+), 118 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb], Shaobo Li [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 3.2.1 dated 2023-08-24 and 3.2.2 dated 2024-03-14
DESCRIPTION | 8 LICENSE | 4 MD5 | 98 - NAMESPACE | 102 - NEWS | 310 +-- R/QICD_functions.R | 1366 ++++++++--------- R/mainFunctions.R | 43 R/rqPen.R | 52 R/workHorse.R | 2934 ++++++++++++++++++------------------ README.md | 116 - build/partial.rdb |binary inst/REFERENCES.bib | 3202 ++++++++++++++++++++-------------------- man/QICD.Rd | 112 - man/QICD.nonpen.Rd | 124 - man/beta_plots.Rd | 76 man/bytau.plot.Rd | 44 man/bytau.plot.rq.pen.seq.Rd | 74 man/bytau.plot.rq.pen.seq.cv.Rd | 88 - man/coef.cv.rq.group.pen.Rd | 44 man/coef.cv.rq.pen.Rd | 50 man/coef.rq.pen.seq.Rd | 98 - man/coef.rq.pen.seq.cv.Rd | 80 man/cv.rq.group.pen.Rd | 182 +- man/cv.rq.pen.Rd | 178 +- man/cv_plots.Rd | 54 man/plot.cv.rq.group.pen.Rd | 40 man/plot.rq.pen.seq.Rd | 124 - man/plot.rq.pen.seq.cv.Rd | 78 man/predict.cv.rq.pen.Rd | 48 man/predict.qic.select.Rd | 64 man/predict.rq.pen.Rd | 44 man/predict.rq.pen.seq.Rd | 106 - man/predict.rq.pen.seq.cv.Rd | 94 - man/print.cv.rq.pen.Rd | 60 man/print.qic.select.Rd | 44 man/print.rq.pen.Rd | 54 man/print.rq.pen.seq.Rd | 44 man/print.rq.pen.seq.cv.Rd | 38 man/qic.Rd | 86 - man/qic.select.Rd | 64 man/qic.select.rq.pen.seq.Rd | 112 - man/qic.select.rq.pen.seq.cv.Rd | 112 - man/rq.group.fit.Rd | 142 - man/rq.group.pen.Rd | 276 +-- man/rq.group.pen.cv.Rd | 174 +- man/rq.lasso.fit.Rd | 150 - man/rq.nc.fit.Rd | 180 +- man/rq.pen.Rd | 285 +-- man/rq.pen.cv.Rd | 206 +- man/rqPen.Rd | 34 50 files changed, 6047 insertions(+), 6051 deletions(-)
Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>)
by geography, state, measure, and release year. This package also contains a
function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>
Diff between CDCPLACES versions 1.1.4 dated 2024-01-24 and 1.1.5 dated 2024-03-14
DESCRIPTION | 8 MD5 | 15 - NAMESPACE | 5 NEWS.md |only R/get_places.R | 464 +++++++++++++++++++++++++++++---------- R/globals.R | 4 README.md | 9 man/get_places.Rd | 19 + tests/testthat/test-get_places.R | 12 - 9 files changed, 403 insertions(+), 133 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.5.1 dated 2024-01-10 and 0.5.2 dated 2024-03-14
DESCRIPTION | 9 +- MD5 | 172 +++++++++++++++++++-------------------- NEWS.md | 4 R/create_line.R | 26 +++-- README.md | 2 man/afterhours_dist.Rd | 4 man/afterhours_fizz.Rd | 4 man/afterhours_line.Rd | 4 man/afterhours_rank.Rd | 4 man/afterhours_summary.Rd | 4 man/afterhours_trend.Rd | 4 man/check_query.Rd | 2 man/collaboration_area.Rd | 4 man/collaboration_dist.Rd | 4 man/collaboration_fizz.Rd | 4 man/collaboration_line.Rd | 4 man/collaboration_rank.Rd | 4 man/collaboration_sum.Rd | 4 man/collaboration_trend.Rd | 4 man/create_bar.Rd | 4 man/create_bar_asis.Rd | 4 man/create_boxplot.Rd | 8 - man/create_bubble.Rd | 8 - man/create_density.Rd | 4 man/create_dist.Rd | 8 - man/create_fizz.Rd | 8 - man/create_hist.Rd | 4 man/create_inc.Rd | 8 - man/create_line.Rd | 4 man/create_line_asis.Rd | 4 man/create_period_scatter.Rd | 10 +- man/create_rank.Rd | 8 - man/create_sankey.Rd | 8 - man/create_scatter.Rd | 8 - man/create_stacked.Rd | 8 - man/create_tracking.Rd | 8 - man/create_trend.Rd | 10 +- man/email_dist.Rd | 4 man/email_fizz.Rd | 4 man/email_line.Rd | 4 man/email_rank.Rd | 4 man/email_summary.Rd | 4 man/email_trend.Rd | 4 man/external_dist.Rd | 4 man/external_fizz.Rd | 4 man/external_line.Rd | 4 man/external_rank.Rd | 4 man/external_sum.Rd | 4 man/extract_hr.Rd | 2 man/flag_ch_ratio.Rd | 2 man/flag_em_ratio.Rd | 2 man/flag_extreme.Rd | 2 man/flag_outlooktime.Rd | 2 man/g2g_data.Rd | 6 - man/hr_trend.Rd | 6 - man/hrvar_count.Rd | 4 man/hrvar_trend.Rd | 6 - man/identify_churn.Rd | 2 man/identify_holidayweeks.Rd | 2 man/identify_inactiveweeks.Rd | 2 man/identify_nkw.Rd | 2 man/identify_outlier.Rd | 2 man/identify_privacythreshold.Rd | 2 man/identify_shifts.Rd | 2 man/identify_tenure.Rd | 2 man/keymetrics_scan.Rd | 4 man/meeting_dist.Rd | 4 man/meeting_fizz.Rd | 4 man/meeting_line.Rd | 4 man/meeting_rank.Rd | 4 man/meeting_summary.Rd | 4 man/meeting_trend.Rd | 4 man/mt_data.Rd | 2 man/network_g2g.Rd | 4 man/network_p2p.Rd | 4 man/network_summary.Rd | 4 man/one2one_dist.Rd | 4 man/one2one_fizz.Rd | 4 man/one2one_freq.Rd | 4 man/one2one_line.Rd | 4 man/one2one_rank.Rd | 4 man/one2one_sum.Rd | 4 man/one2one_trend.Rd | 4 man/pq_data.Rd | 4 man/track_HR_change.Rd | 2 man/validation_report.Rd | 2 man/vivainsights-package.Rd | 1 87 files changed, 286 insertions(+), 276 deletions(-)
Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between bigrquery versions 1.5.0 dated 2024-01-22 and 1.5.1 dated 2024-03-14
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/bigrquery-package.R | 1 - R/bq-refs.R | 7 ++++++- R/dbi-connection.R | 41 +++++++++++++++++++++++++++++++++++++---- R/dplyr.R | 11 +++++++++-- R/zzz.R | 1 - README.md | 42 +++++++++++++++++++++--------------------- man/DBI.Rd | 35 +++++++++++++++++++++++++++++++++-- man/bigrquery-package.Rd | 2 +- man/bq_deauth.Rd | 4 ++-- tests/testthat/test-dplyr.R | 3 ++- 14 files changed, 134 insertions(+), 54 deletions(-)
Title: R6 Class for Structural Causal Models
Description: The implemented R6 class 'SCM' aims to simplify working with structural causal models. The missing data mechanism can be defined as a part of the structural model. The class contains methods for 1) defining a structural causal model via functions, text or conditional probability tables, 2) printing basic information on the model, 3) plotting the graph for the model using packages 'igraph' or 'qgraph', 4) simulating data from the model, 5) applying an intervention, 6) checking the identifiability of a query using the R packages 'causaleffect' and 'dosearch', 7) defining the missing data mechanism, 8) simulating incomplete data from the model according to the specified missing data mechanism and 9) checking the identifiability in a missing data problem using the R package 'dosearch'. In addition, there are functions for running experiments and doing counterfactual inference using simulation.
Author: Juha Karvanen [aut, cre]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>
Diff between R6causal versions 0.8.2 dated 2023-12-18 and 0.8.3 dated 2024-03-14
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NEWS.md | 4 + R/R6causal_counterfactual.R | 106 ++++++++++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/using_R6causal.R | 6 +- inst/doc/using_R6causal.Rmd | 8 +-- inst/doc/using_R6causal.pdf |binary man/counterfactual.Rd | 13 +++-- man/fairness.Rd | 18 ++++--- vignettes/using_R6causal.Rmd | 8 +-- 11 files changed, 123 insertions(+), 68 deletions(-)
Title: Data for Generalised Additive Models for Location Scale and
Shape
Description: Data used as examples in the current two books on Generalised Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.
Author: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>, Bob
Rigby, Fernanda De Bastiani
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss.data versions 6.0-2 dated 2021-11-07 and 6.0-6 dated 2024-03-14
DESCRIPTION | 12 +++--- MD5 | 13 ++++--- README.md |only build/partial.rdb |binary data/ultra.RData |only man/LGAclaims.Rd | 98 +++++++++++++++++++++++++----------------------------- man/brownfat.Rd | 4 +- man/leukemia.Rd | 3 + man/ultra.Rd |only 9 files changed, 64 insertions(+), 66 deletions(-)
Title: Model-Based Causal Feature Selection for General Response Types
Description: Extends invariant causal prediction (Peters et al., 2016,
<doi:10.1111/rssb.12167>) to generalized linear and transformation models
(Hothorn et al., 2018, <doi:10.1111/sjos.12291>).
The methodology is described in Kook et al. (2023,
<doi:10.48550/arXiv.2309.12833>).
Author: Lucas Kook [aut, cre] ,
Sorawit Saengkyongam [ctb],
Anton Rask Lundborg [ctb],
Torsten Hothorn [ctb],
Jonas Peters [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramicp versions 0.0-1 dated 2023-09-29 and 0.0-2 dated 2024-03-14
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NAMESPACE | 5 +++ R/alias.R | 69 ++++++++++++++++++++++++++++++++++++++++++---- R/controls.R | 2 - R/helpers.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++---- R/invariance-types.R | 4 +- R/tramicp.R | 4 +- build/partial.rdb |binary man/tramicp-alias.Rd | 53 +++++++++++++++++++++++++++++++++++- 10 files changed, 208 insertions(+), 30 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjaerde [trl],
Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 2.2.1 dated 2024-01-11 and 3.0.0 dated 2024-03-14
DESCRIPTION | 10 MD5 | 298 ++++++------ NAMESPACE | 15 NEWS.md | 11 R/Adjusted_inv_sinh_CI_OR_2x2.R | 2 R/Adjusted_inv_sinh_CI_ratio_2x2.R | 2 R/Adjusted_log_CI_2x2.R | 2 R/AgrestiCaffo_CI_2x2.R | 6 R/Arcsine_CI_1x2.R | 2 R/BaptistaPike_exact_conditional_CI_2x2.R | 2 R/BaptistaPike_midP_CI_2x2.R | 2 R/Bhapkar_test_paired_cxc.R | 2 R/Blaker_exact_CI_1x2.R | 2 R/Blaker_exact_test_1x2.R | 2 R/Blaker_midP_CI_1x2.R | 2 R/Blaker_midP_test_1x2.R | 2 R/BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2.R | 2 R/BonettPrice_hybrid_Wilson_score_CI_paired_2x2.R | 2 R/Bonferroni_type_CIs_paired_cxc.R | 4 R/Bonferroni_type_CIs_rxc.R | 2 R/Brant_test_2xc.R | 2 R/BreslowDay_homogeneity_test_stratified_2x2.R | 17 R/Chacko_test_1xc.R | 2 R/ClopperPearson_exact_CI_1x2.R | 2 R/ClopperPearson_exact_CI_1x2_beta_version.R | 2 R/ClopperPearson_midP_CI_1x2.R | 2 R/CochranArmitage_CI_rx2.R | 2 R/CochranArmitage_exact_cond_midP_tests_rx2.R | 2 R/CochranMantelHaenszel_test_stratified_2x2.R | 2 R/Cochran_Q_test_stratified_2x2.R | 2 R/Cornfield_exact_conditional_CI_2x2.R | 2 R/Cornfield_midP_CI_2x2.R | 2 R/Cumulative_models_for_2xc.R | 19 R/Cumulative_models_for_rxc.R | 8 R/Exact_binomial_test_1x2.R | 2 R/Exact_cond_midP_linear_rank_tests_2xc.R | 2 R/Exact_cond_midP_unspecific_ordering_rx2.R | 2 R/Exact_multinomial_test_1xc.R | 2 R/Exact_unconditional_test_2x2.R | 24 R/FisherFreemanHalton_asymptotic_test_rxc.R | 2 R/Fisher_exact_test_2x2.R | 8 R/Fisher_midP_test_2x2.R | 2 R/FleissEveritt_test_paired_cxc.R | 2 R/FleissLevinPaik_test_paired_cxc.R | 2 R/InverseVariance_estimate_stratified_2x2.R | 2 R/JonckheereTerpstra_test_rxc.R | 2 R/Katz_log_CI_2x2.R | 2 R/Kendalls_tau_b_rxc.R | 2 R/Kendalls_tau_b_rxc_bca.R | 2 R/Koopman_asymptotic_score_CI_2x2.R | 10 R/KruskalWallis_asymptotic_test_rxc.R | 2 R/LR_CI_1x2.R | 2 R/LR_test_1x2.R | 2 R/LR_test_1xc.R | 2 R/LR_test_2x2.R | 7 R/MOVER_R_Wilson_CI_OR_2x2.R | 2 R/MOVER_R_Wilson_CI_ratio_2x2.R | 2 R/MOVER_Wilson_score_CI_paired_2x2.R | 2 R/MantelHaenszel_estimate_stratified_2x2.R | 2 R/MantelHaenszel_test_2xc.R | 2 R/McNemarBowker_test_paired_cxc.R | 2 R/McNemar_asymptotic_test_CC_paired_2x2.R | 4 R/McNemar_asymptotic_test_paired_2x2.R | 4 R/McNemar_exact_cond_test_paired_2x2.R | 7 R/McNemar_exact_unconditional_test_paired_2x2.R | 7 R/Mee_asymptotic_score_CI_2x2.R | 37 - R/MidP_multinomial_test_1xc.R | 2 R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R | 12 R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R | 42 - R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R | 19 R/Newcombe_hybrid_score_CI_2x2.R | 2 R/Newcombe_square_and_add_CI_paired_2x2.R | 2 R/Pearson_LR_homogeneity_test_stratified_2x2.R | 14 R/Pearson_LR_test_common_effect_stratified_2x2.R | 11 R/Pearson_chi_squared_test_1xc.R | 2 R/Pearson_chi_squared_test_2x2.R | 2 R/Pearson_chi_squared_test_CC_2x2.R | 2 R/Pearson_correlation_coefficient_rxc.R | 2 R/Pearson_correlation_coefficient_rxc_bca.R | 2 R/Peto_OR_estimate_stratified_2x2.R | 6 R/Peto_homogeneity_test_stratified_2x2.R | 2 R/PriceBonett_approximate_Bayes_CI_2x2.R | 2 R/QuesenberryHurst_Wilson_score_CIs_1xc.R | 2 R/RBG_test_and_CI_stratified_2x2.R | 5 R/Scheffe_type_CIs_paired_cxc.R | 10 R/Scheffe_type_CIs_rxc.R | 8 R/Score_test_1x2.R | 2 R/Score_test_CC_1x2.R | 2 R/Score_test_and_CI_marginal_mean_scores_paired_cxc.R | 5 R/Score_test_for_effect_in_the_probit_model_2xc.R | 2 R/Spearman_correlation_coefficient_rxc.R | 3 R/Spearman_correlation_coefficient_rxc_bca.R | 2 R/Stuart_test_paired_cxc.R | 6 R/Tang_asymptotic_score_CI_paired_2x2.R | 2 R/Tango_asymptotic_score_CI_paired_2x2.R | 4 R/Transformed_Blaker_exact_CI_paired_2x2.R | 2 R/Transformed_Clopper_Pearson_exact_CI_paired_2x2.R | 2 R/Transformed_Clopper_Pearson_midP_CI_paired_2x2.R | 2 R/Transformed_Wilson_score_CI_paired_2x2.R | 2 R/Trend_estimate_CI_tests_rx2.R | 26 - R/Uncorrected_asymptotic_score_CI_2x2.R | 10 R/Wald_CI_2x2.R | 2 R/Wald_CI_AgrestiMin_paired_2x2.R | 4 R/Wald_CI_BonettPrice_paired_2x2.R | 2 R/Wald_CI_CC_2x2.R | 2 R/Wald_CI_OR_Laplace_paired_2x2.R | 2 R/Wald_CI_OR_paired_2x2.R | 2 R/Wald_CI_diff_CC_paired_2x2.R | 2 R/Wald_CI_diff_paired_2x2.R | 2 R/Wald_CI_ratio_paired_2x2.R | 2 R/Wald_test_1x2.R | 2 R/Wald_test_CC_1x2.R | 2 R/Wald_test_and_CI_common_diff_stratified_2x2.R | 5 R/Wald_test_and_CI_common_ratio_stratified_2x2.R | 3 R/Wald_test_and_CI_marginal_mean_scores_paired_cxc.R | 2 R/Woolf_logit_CI_2x2.R | 2 R/Woolf_test_and_CI_stratified_2x2.R | 2 R/Z_unpooled_test_2x2.R | 2 R/gamma_coefficient_rxc.R | 2 R/gamma_coefficient_rxc_bca.R | 2 R/generics.R | 64 -- R/linear_by_linear_test_rxc.R | 2 R/plot_functions.R |only R/the_2x2_table_tests.R | 32 - R/the_2xc_table.R | 31 - R/the_paired_2x2_table_tests.R | 4 R/the_paired_cxc_table_nominal.R | 2 R/validateArguments.R | 4 man/Cumulative_models_for_2xc.Rd | 2 man/Cumulative_models_for_rxc.Rd | 2 man/Exact_unconditional_test_2x2.Rd | 4 man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd | 4 man/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.Rd | 6 man/Scheffe_type_CIs_paired_cxc.Rd | 4 man/Scheffe_type_CIs_rxc.Rd | 4 man/calculate_limit_lower.Rd |only man/calculate_limit_upper.Rd |only man/contingencytables.Rd | 2 man/validateArguments.Rd | 2 tests/testthat/test-ch10.R | 4 tests/testthat/test-ch2.R | 24 tests/testthat/test-ch3.R | 11 tests/testthat/test-ch4.R | 89 +++ tests/testthat/test-ch5.R | 17 tests/testthat/test-ch6.R | 25 + tests/testthat/test-ch7.R | 18 tests/testthat/test-ch8.R | 46 + tests/testthat/test-ch9.R | 28 + tests/testthat/test-issue34.R | 10 tests/testthat/test-issue36.R | 2 tests/testthat/test-plotting.R |only tests/testthat/test-print.R | 6 152 files changed, 761 insertions(+), 545 deletions(-)
More information about contingencytables at CRAN
Permanent link
Title: Partitioning the Drivers of Stability of Ecological Communities
Description: Contains the basic functions to apply the unified framework
for partitioning the drivers of stability of ecological communities.
Segrestin et al. (2024) <doi:10.1111/geb.13828>.
Author: Jules Segrestin [aut, cre, cph]
Maintainer: Jules Segrestin <jsegrestin@gmail.com>
Diff between comstab versions 0.0.1 dated 2024-02-20 and 0.0.2 dated 2024-03-14
DESCRIPTION | 9 +--- MD5 | 12 ++--- NEWS.md | 12 ++++- R/partitionR.R | 116 ++++++++++++++++++++++++++++++++++-------------------- R/ternStab.R | 1 README.md | 4 + man/partitionR.Rd | 3 - 7 files changed, 99 insertions(+), 58 deletions(-)
Title: Clinical Indices and Outcomes Tools
Description: Collection of indices and tools relating to cardiovascular, nephrology, and hepatic research that aid epidemiological chort or retrospective chart review with big data. All indices and tools take commonly used lab values and patient demographics and measurements to compute various risk and predictive values for survival. References to original literature and validation contained in each function documentation.
Author: Neel Agarwal <nxa357@case.edu>
Maintainer: Neel Agarwal <neel.agarwal.216@gmail.com>
Diff between cliot versions 0.1.0 dated 2024-01-22 and 0.2.0 dated 2024-03-14
DESCRIPTION | 8 - MD5 | 17 ++- R/neelpackage.R | 213 +++++++++++++++++++++++++++++++++++++++++ man/aha_stroke.Rd |only man/albi.Rd | 4 man/ast_alt_ratio_interpret.Rd |only man/bard_score.Rd |only man/bard_score_interpret.Rd |only man/fli.Rd | 2 man/homair.Rd | 4 man/nafld_score.Rd |only man/rfactor.Rd |only man/rfactor_interpret.Rd |only 13 files changed, 234 insertions(+), 14 deletions(-)
Title: Import Origin(R) Project Files
Description: Read the data from Origin(R) project files ('*.opj')
<https://www.originlab.com/doc/User-Guide/Origin-File-Types>.
No write support is planned.
Author: Miquel Garriga [aut, cph],
Stefan Gerlach [aut, cph],
Ion Vasilief [aut, cph],
Alex Kargovsky [aut, cph],
Knut Franke [ctb, cph],
Alexander Semke [ctb, cph],
Tilman Benkert [ctb, cph],
Kasper Peeters [ctb, cph],
Russell Standish [ctb, cph],
Ivan Kryl [...truncated...]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>
Diff between Ropj versions 0.3-4 dated 2023-03-14 and 0.3-5 dated 2024-03-14
DESCRIPTION | 6 - MD5 | 16 +-- build/partial.rdb |binary inst/NEWS.Rd | 4 src/config.h | 2 src/liborigin/OriginAnyParser.cpp | 159 +++++++++++++++++++++++++------------- src/liborigin/OriginFile.cpp | 23 ++++- src/liborigin/OriginFile.h | 3 src/liborigin/OriginObj.h | 14 ++- 9 files changed, 150 insertions(+), 77 deletions(-)
Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using
Gaussian models, together with time-series power demand calculations.
The simulation methodology is published in
Cañigueral et al. (2023, ISBN:0957-4174) <doi:10.1016/j.eswa.2023.120318>.
Author: Marc Canigueral [aut, cre]
Maintainer: Marc Canigueral <marc.canigueral@udg.edu>
Diff between evsim versions 1.3.0 dated 2024-02-04 and 1.4.0 dated 2024-03-14
evsim-1.3.0/evsim/man/df_to_ts.Rd |only evsim-1.3.0/evsim/man/get_n_connections.Rd |only evsim-1.3.0/evsim/tests/testthat/test-get_n_connections.R |only evsim-1.4.0/evsim/DESCRIPTION | 8 evsim-1.4.0/evsim/MD5 | 48 ++-- evsim-1.4.0/evsim/NAMESPACE | 8 evsim-1.4.0/evsim/NEWS.md | 9 evsim-1.4.0/evsim/R/charging_infrastructure.R | 115 ++++++++-- evsim-1.4.0/evsim/R/demand.R | 59 ++--- evsim-1.4.0/evsim/R/evmodel.R | 15 + evsim-1.4.0/evsim/R/simulation.R | 28 +- evsim-1.4.0/evsim/man/adapt_charging_features.Rd | 24 +- evsim-1.4.0/evsim/man/add_charging_infrastructure.Rd | 24 +- evsim-1.4.0/evsim/man/get_charging_rates_distribution.Rd | 4 evsim-1.4.0/evsim/man/get_connection_models_from_parameters.Rd | 2 evsim-1.4.0/evsim/man/get_demand.Rd | 10 evsim-1.4.0/evsim/man/get_energy_models_from_parameters.Rd | 2 evsim-1.4.0/evsim/man/get_ev_model.Rd | 2 evsim-1.4.0/evsim/man/get_evmodel_parameters.Rd | 2 evsim-1.4.0/evsim/man/get_occupancy.Rd |only evsim-1.4.0/evsim/man/get_user_profiles_distribution.Rd | 3 evsim-1.4.0/evsim/man/plot_occupancy_duration_curve.Rd |only evsim-1.4.0/evsim/man/plot_ts.Rd | 19 - evsim-1.4.0/evsim/man/read_ev_model.Rd | 2 evsim-1.4.0/evsim/man/save_ev_model.Rd | 2 evsim-1.4.0/evsim/man/simulate_sessions.Rd | 4 evsim-1.4.0/evsim/tests/testthat/test-charging_infrastructure.R | 13 + evsim-1.4.0/evsim/tests/testthat/test-get_occupancy.R |only 28 files changed, 265 insertions(+), 138 deletions(-)
Title: Electric Vehicle Charging Sessions Profiling and Modelling
Description: Tools for modelling electric vehicle charging sessions into
generic groups with similar connection patterns called "user profiles",
using Gaussian Mixture Models clustering. The clustering and profiling
methodology is described in Cañigueral and Meléndez (2021, ISBN:0142-0615)
<doi:10.1016/j.ijepes.2021.107195>.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marc.canigueral@udg.edu>
Diff between evprof versions 1.1.1 dated 2024-02-05 and 1.1.2 dated 2024-03-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/exploration.R | 10 ++++++---- build/vignette.rds |binary 5 files changed, 18 insertions(+), 11 deletions(-)
Title: Statistical Methods for Composite Material Data
Description: An implementation of the statistical methods commonly
used for advanced composite materials in aerospace applications.
This package focuses on calculating basis values (lower tolerance
bounds) for material strength properties, as well as performing the
associated diagnostic tests. This package provides functions for
calculating basis values assuming several different distributions,
as well as providing functions for non-parametric methods of computing
basis values. Functions are also provided for testing the hypothesis
that there is no difference between strength and modulus data from an
alternate sample and that from a "qualification" or "baseline" sample.
For a discussion of these statistical methods and their use, see the
Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4).
Additional details about this package are available in the paper by
Kloppenborg (2020, <doi:10.21105/joss.02265>).
Author: Stefan Kloppenborg [aut, cre] ,
Billy Cheng [ctb],
Ally Fraser [ctb],
Jeffrey Borlik [ctb],
Comtek Advanced Structures, Ltd. [fnd]
Maintainer: Stefan Kloppenborg <stefan@kloppenborg.ca>
Diff between cmstatr versions 0.9.2 dated 2023-09-09 and 0.9.3 dated 2024-03-14
DESCRIPTION | 10 MD5 | 34 +- NEWS.md | 5 R/basis.R | 12 R/equiv.R | 4 build/vignette.rds |binary inst/doc/cmstatr_Graphing.html | 6 inst/doc/cmstatr_Tutorial.html | 2 inst/doc/cmstatr_Validation.html | 48 +- tests/testthat/_snaps/plot-nested/nested-data-plot-color-and-fill.svg | 162 +++++----- tests/testthat/_snaps/plot-nested/nested-data-plot-color.svg | 26 - tests/testthat/_snaps/plot-nested/nested-data-plot-single-grouping.svg | 6 tests/testthat/_snaps/plot-nested/nested-data-plot-single-obs-per-group.svg | 74 ++-- tests/testthat/_snaps/plot-nested/nested-data-plot-two-groupings.svg | 18 - tests/testthat/_snaps/plotting/stat-esf.svg | 2 tests/testthat/_snaps/plotting/stat-normal-surv-func-and-stat-esf.svg | 2 tests/testthat/_snaps/plotting/stat-normal-surv-func.svg | 2 tests/testthat/test-lintr.R | 3 18 files changed, 217 insertions(+), 199 deletions(-)
More information about CompositionalML at CRAN
Permanent link
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms, see
Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre],
Isaac Gravestock [aut],
Robert Davies [cph],
Stephen Moshier [cph],
Gareth Ambler [cph],
Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Diff between bfp versions 0.0-47 dated 2023-12-06 and 0.0-48 dated 2024-03-14
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/scrBesag.Rd | 8 ++++---- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: A Collection of Oversampling Techniques for Class Imbalance
Problem Based on SMOTE
Description: A collection of various oversampling techniques developed from SMOTE is provided. SMOTE is a oversampling technique which synthesizes a new minority instance between a pair of one minority instance and one of its K nearest neighbor. Other techniques adopt this concept with other criteria in order to generate balanced dataset for class imbalance problem.
Author: Wacharasak Siriseriwan [aut, cre]
Maintainer: Wacharasak Siriseriwan <wacharasak.s@gmail.com>
Diff between smotefamily versions 1.3.1 dated 2019-05-30 and 1.4.0 dated 2024-03-14
DESCRIPTION | 12 +++++----- MD5 | 8 +++--- NAMESPACE | 5 +++- man/SMOTE.Rd | 1 man/smotefamily-package.Rd | 52 +++++++++++++++++++++++++-------------------- 5 files changed, 44 insertions(+), 34 deletions(-)
Title: Recursive Display of Items in Nested Lists
Description: Recursive display of names and paths of all the items nested within sublists of a list object.
Author: Diego Ciccia [aut, cre]
Maintainer: Diego Ciccia <cicciadiego99@gmail.com>
Diff between rnames versions 1.0.0 dated 2024-03-11 and 1.0.1 dated 2024-03-14
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 1 + NEWS.md |only R/rnames.R | 17 +++++++++++++++-- man/rnames.Rd | 4 +++- man/rnames.list.Rd |only 7 files changed, 28 insertions(+), 10 deletions(-)
Title: Simulation and Resampling Methods for Epistemic Fuzzy Data
Description: Random simulations of fuzzy numbers are still a challenging problem. The aim of this package is to provide the respective
procedures to simulate fuzzy random variables, especially in the case of the piecewise linear fuzzy numbers (PLFNs,
see Coroianua et al. (2013) <doi:10.1016/j.fss.2013.02.005> for the further details).
Additionally, the special resampling algorithms known as the epistemic bootstrap are provided (see Grzegorzewski and Romaniuk
(2022) <doi:10.34768/amcs-2022-0021>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-031-08974-9_39>)
together with the functions to apply statistical tests and estimate various characteristics based on the epistemic bootstrap.
The package also includes a real-life data set of epistemic fuzzy triangular numbers.
The fuzzy numbers used in this package are consistent with the 'FuzzyNumbers' package.
Author: Maciej Romaniuk [cre, aut] ,
Przemyslaw Grzegorzewski [aut]
,
Abbas Parchami [aut] ,
Luis Carvalho [ctb, cph]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzySimRes versions 0.3.0 dated 2023-08-10 and 0.4.0 dated 2024-03-14
DESCRIPTION | 8 - MD5 | 90 +++++++------- NEWS.md | 8 + R/AntitheticBootstrap.R | 12 + R/AverageStatisticEpistemicTest.R | 26 ++-- R/CombinePValues.R | 4 R/EpistemicBootstrap.R | 12 + R/EpistemicCorrectedVariance.R | 76 +++++++++-- R/EpistemicEstimator.R | 75 +++++++++-- R/EpistemicMean.R | 23 ++- R/EpistemicTest.R | 16 +- R/MultiStatisticEpistemicTest.R | 26 ++-- R/ResamplingStatisticEpistemicTest.R | 26 ++-- R/SimulateFuzzyNumber.R | 108 ++++++++--------- R/SimulateSample.R | 91 +++++++------- README.md | 87 ++++++++----- man/AntitheticBootstrap.Rd | 12 + man/AverageStatisticEpistemicTest.Rd | 16 +- man/CombinePValues.Rd | 4 man/EpistemicBootstrap.Rd | 12 + man/EpistemicCorrectedVariance.Rd | 30 +++- man/EpistemicEstimator.Rd | 31 +++- man/EpistemicMean.Rd | 22 ++- man/EpistemicTest.Rd | 16 +- man/MultiStatisticEpistemicTest.Rd | 16 +- man/ResamplingStatisticEpistemicTest.Rd | 16 +- man/SimulateFuzzyNumber.Rd | 83 +++++++------ man/SimulateSample.Rd | 81 ++++++------ tests/testthat/_snaps/AntitheticBootstrap.md | 36 ++--- tests/testthat/_snaps/EpistemicBootstrap.md | 36 ++--- tests/testthat/_snaps/EpistemicCorrectedVariance.md | 47 ++++--- tests/testthat/_snaps/EpistemicEstimator.md | 92 +++++++++----- tests/testthat/_snaps/EpistemicMean.md | 52 +++----- tests/testthat/_snaps/SimulateFuzzyNumber.md | 34 ++--- tests/testthat/_snaps/SimulateSample.md | 34 ++--- tests/testthat/test-AntitheticBootstrap.R | 40 +++--- tests/testthat/test-AverageStatisticEpistemicTest.R | 40 +++--- tests/testthat/test-EpistemicBootstrap.R | 40 +++--- tests/testthat/test-EpistemicCorrectedVariance.R | 56 +++++--- tests/testthat/test-EpistemicEstimator.R | 87 +++++++++---- tests/testthat/test-EpistemicMean.R | 46 +++---- tests/testthat/test-EpistemicTest.R | 40 +++--- tests/testthat/test-MultiStatisticEpistemicTest.R | 40 +++--- tests/testthat/test-ResamplingStatisticEpistemicTest.R | 40 +++--- tests/testthat/test-SimulateFuzzyNumber.R | 72 +++++------ tests/testthat/test-SimulateSample.R | 66 +++++----- 46 files changed, 1095 insertions(+), 830 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] ,
Shensuo Li [aut],
Yi Xiong [aut] ,
Longfei Zhao [aut] ,
Kai Gu [aut] ,
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.10 dated 2023-02-28 and 2.0.0 dated 2024-03-13
UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/extdata/ccle_drug_response_extend.rda |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/home-pancan-search.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-target.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-genecor.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-search.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-file-upload.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-group-comparison.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-matrix-correlation.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-scatter-correlation.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-surv-analysis.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-anatomy.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-genecor.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-immune.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-radar.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search-cancer.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-til.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-unicox.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-genecor.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-search.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-survival-analysis.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-unicox.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/modules/modules-survival-analysis.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis.R |only UCSCXenaShiny-1.1.10/UCSCXenaShiny/man/UCSCXenaShiny.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/DESCRIPTION | 64 - UCSCXenaShiny-2.0.0/UCSCXenaShiny/MD5 | 267 ++++-- UCSCXenaShiny-2.0.0/UCSCXenaShiny/NAMESPACE | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/NEWS.md | 78 ++ UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/ccle.R | 22 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/data.R | 35 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/get_pancan_value.R | 181 +++- UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/get_pcawg_value.R | 10 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/globalVariables.R | 4 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/load_data.R | 23 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/query_general.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/query_tcga_group.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/query_value.R | 121 ++- UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/tcga_surv.R | 11 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/utils.R | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_ccle_value.R | 18 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_dim_dist.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_gene_pw_cor.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_identifier_dim_dist.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_pancan_value.R | 172 ++-- UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_pcawg_value.R | 29 UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/vis_toil_Mut.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/R/xenashiny.R | 11 UCSCXenaShiny-2.0.0/UCSCXenaShiny/README.md | 42 - UCSCXenaShiny-2.0.0/UCSCXenaShiny/build/vignette.rds |binary UCSCXenaShiny-2.0.0/UCSCXenaShiny/data/ccle_info_fine.rda |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/data/pcawg_info_fine.rda |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/data/tcga_clinical_fine.rda |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/doc/api.R | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/doc/api.Rmd | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/doc/api.html | 38 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/rmd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/App.R | 191 ++-- UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/PGdata.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/appdata.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/helper |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/PharmacoGenomics |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/ccle |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/general |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/other_page |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/pcawg |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/quick |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/tcga |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/modules/tpc_func |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/server/general-analysis.R | 49 - UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/server/home.R | 186 ++-- UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/server/modules.R | 201 ++++- UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/server/repository.R | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/citation2.md |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/datasets.md | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/shiny-doc/tmp.md |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/PharmacoGenomics.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/developers.R | 44 + UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/footer.R | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/general-analysis.R | 6 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/help.R | 55 - UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/home.R | 388 ++++++---- UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis-ccle.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis-pcawg.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis-quick.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis-tcga.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/pancan-download.R |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/ui/repository.R | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/www/20210708184045.png |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/inst/shinyapp/www/slick_img |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/UCSCXenaShiny-package.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/ccle_info_fine.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/dot-opt_pancan.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/get_pancan_value.Rd | 71 + UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/load_data.Rd | 10 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/mol_quick_analysis.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/pcawg_info_fine.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/query_general_value.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/query_pancan_value.Rd | 82 +- UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/query_tcga_group.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/tcga_clinical_fine.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/tcga_surv_analysis.Rd | 13 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_ccle_gene_cor.Rd | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_ccle_tpm.Rd | 9 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_dim_dist.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_TIL_cor.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_cor.Rd | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_cor_cancer.Rd | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_immune_cor.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_msi_cor.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_pw_cor.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_stemness_cor.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_gene_tmb_cor.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_identifier_dim_dist.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_identifier_grp_comparison.Rd | 11 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_identifier_multi_cor.Rd | 2 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_pancan_anatomy.Rd | 22 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_pcawg_dist.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_pcawg_gene_cor.Rd | 5 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_pcawg_unicox_tree.Rd | 7 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_toil_Mut.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_toil_Mut_cancer.Rd |only UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_toil_TvsN.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_toil_TvsN_cancer.Rd | 8 UCSCXenaShiny-2.0.0/UCSCXenaShiny/man/vis_unicox_tree.Rd | 7 UCSCXenaShiny-2.0.0/UCSCXenaShiny/vignettes/api.Rmd | 5 128 files changed, 1776 insertions(+), 821 deletions(-)
Title: A Pharmacometrics Data Transformation and Analysis Tool
Description: Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of 'ruminate' is to create a 'shiny' interface to make these tools more broadly available while creating reproducible results.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ruminate versions 0.2.1 dated 2023-12-11 and 0.2.2 dated 2024-03-13
DESCRIPTION | 18 - MD5 | 38 ++- NAMESPACE | 3 NEWS.md | 7 R/NCA_Server.R | 2 R/ruminate.R | 63 ++++-- R/simulate_rules.R |only README.md | 14 + inst/doc/deployment.R | 6 inst/doc/noncompartmental_analysis.R | 1 inst/doc/noncompartmental_analysis.Rmd | 1 inst/doc/noncompartmental_analysis.html | 293 ++++++------------------------ inst/templates/NCA.yaml | 6 inst/templates/ruminate.R | 34 --- inst/templates/ruminate_devel.R |only inst/test_apps/nca_app.R | 34 --- inst/test_apps/simulate_rules_ext_funcs.R |only inst/test_apps/simulate_rules_funcs.R |only inst/test_apps/test_rxode2_system.R |only man/NCA_Server.Rd | 34 --- man/ruminate.Rd | 7 vignettes/noncompartmental_analysis.Rmd | 1 vignettes/rmdhunks |only 23 files changed, 192 insertions(+), 370 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.1.0 dated 2024-03-04 and 0.1.9 dated 2024-03-13
DESCRIPTION | 8 ++-- MD5 | 25 ++++++++------ NAMESPACE | 2 + R/LIRI.R |only R/getplot.R | 77 +++++++++++++++++++++++++++++++++++++++------ R/modeldata.R | 8 ++++ R/randomForest.R |only R/scidca.R | 38 +++++++++++++++++++++- R/scidca.coxph.R | 26 ++++++++++++--- R/scidca.glm.R | 25 ++++++++++++-- data/LIRI.rda |only man/LIRI.Rd |only man/scidca.Rd | 57 ++++++++++++++++++++++++++++++++- man/scidca.coxph.Rd | 38 +++++++++++++++++++++- man/scidca.glm.Rd | 38 +++++++++++++++++++++- man/scidca.randomForest.Rd |only 16 files changed, 303 insertions(+), 39 deletions(-)
Title: Disease-Drived Differential Proteins Co-Expression Network
Analysis
Description: Functions designed to connect disease-related differential proteins and
co-expression network. It provides the basic statics analysis included t test, ANOVA analysis.
The network construction is not offered by the package, you can used 'WGCNA' package which you
can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis
included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and
hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>
Diff between DDPNA versions 0.3.1 dated 2022-05-17 and 0.3.3 dated 2024-03-13
DESCRIPTION | 8 - MD5 | 20 ++-- R/DEPextract.R | 16 +-- R/Moduleconstruction.R | 10 +- R/missing_value_impute.R | 111 ++------------------------- R/network.R | 165 +++++++++++------------------------------ man/DDPNA-package.Rd | 10 +- man/DEP_Mod_net_plot.Rd | 2 man/SoftThresholdScaleGraph.Rd | 5 - man/dataStatInf.Rd | 6 - man/missing_value_impute.Rd | 2 11 files changed, 101 insertions(+), 254 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.10.2 dated 2024-02-16 and 2.11.1 dated 2024-03-13
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Explore Brazilian Flora 2020 Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Brazilian Flora 2020 dataset. For more information about the dataset, please visit <https://floradobrasil.jbrj.gov.br/consulta/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Diff between florabr versions 1.0.1 dated 2023-12-10 and 1.1.0 dated 2024-03-13
DESCRIPTION | 9 MD5 | 53 - NAMESPACE | 5 NEWS.md | 6 R/check_names.R | 7 R/check_version.R | 202 +++--- R/filter_florabR.R | 956 +++++++++++++++---------------- R/get_florabr.R | 276 ++++---- R/get_pam.R |only R/get_spat_occ.R | 516 ++++++++-------- R/helpers.R | 1078 ++++++++++++++++++----------------- R/load_florabR.R | 226 +++---- README.md | 277 ++++---- build/vignette.rds |binary inst/doc/getting_pam.R |only inst/doc/getting_pam.Rmd |only inst/doc/getting_pam.html |only inst/doc/getting_started.R | 6 inst/doc/getting_started.Rmd | 309 +++++----- inst/doc/getting_started.html | 141 ++-- inst/doc/selecting_species.R | 26 inst/doc/selecting_species.Rmd | 842 +++++++++++++-------------- inst/doc/selecting_species.html | 32 - man/check_names.Rd | 5 man/get_florabr.Rd | 17 man/get_pam.Rd |only man/load_florabr.Rd | 2 vignettes/getting_pam.Rmd |only vignettes/getting_started.Rmd | 309 +++++----- vignettes/selecting_species.Rmd | 842 +++++++++++++-------------- vignettes/vignettes_img/Image_09.png |only 31 files changed, 3128 insertions(+), 3014 deletions(-)
Title: Describe Pedigree Relationships in Words
Description: Describe in words the genealogical relationship between two
members of a given pedigree, using the algorithm in Vigeland (2022)
<doi:10.1186/s12859-022-04759-y>. 'verbalisr' is part of the
'pedsuite' collection of packages for pedigree analysis. For a
demonstration of 'verbalisr', see the online app 'QuickPed' at
<https://magnusdv.shinyapps.io/quickped>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between verbalisr versions 0.5.1 dated 2023-08-19 and 0.5.2 dated 2024-03-13
DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- NEWS.md | 19 ++++++++++++------- R/data.R | 2 +- R/utils.R | 5 +---- man/habsburg.Rd | 2 +- tests/testthat/test-ped-lists.R | 3 --- tests/testthat/test-verbalise.R | 10 +--------- 8 files changed, 31 insertions(+), 39 deletions(-)
Title: Space-Filling Design under Maximin Distance
Description: Constructs a space-filling design under the criterion of maximum-minimum distance. Both discrete and continuous searches are provided.
Author: Furong Sun <furong.sun@gmail.com>, Robert B. Gramacy <rbg@vt.edu>
Maintainer: Furong Sun <furong.sun@gmail.com>
Diff between maximin versions 1.0-4 dated 2021-01-10 and 1.0-5 dated 2024-03-13
ChangeLog | 8 ++++++++ DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/maximin.R | 13 ++++--------- R/maximin_cand.R | 37 ++++++++++++++++--------------------- README | 2 +- man/maximin.Rd | 3 ++- 7 files changed, 44 insertions(+), 45 deletions(-)
Title: Goodness-of-Fit Methods for Complete and Right-Censored Data
Description: Graphical tools and goodness-of-fit tests for complete and right-censored data:
1. Kolmogorov-Smirnov, Cramér-von Mises, and Anderson-Darling tests,
which use the empirical distribution function for complete data
and are extended for right-censored data.
2. Generalized chi-squared-type test, which is based on the squared
differences between observed and expected counts using random
cells with right-censored data.
3. A series of graphical tools such as probability or cumulative hazard
plots to guide the decision about the most suitable parametric model
for the data.
Author: Klaus Langohr [aut, cre],
Mireia Besalu [aut],
Matilde Francisco [aut],
Guadalupe Gomez [aut]
Maintainer: Klaus Langohr <klaus.langohr@upc.edu>
Diff between GofCens versions 0.92 dated 2022-01-05 and 0.97 dated 2024-03-13
GofCens-0.92/GofCens/R/chisqcens1.R |only GofCens-0.92/GofCens/R/chisqcens2.R |only GofCens-0.92/GofCens/man/chisqcens1.Rd |only GofCens-0.92/GofCens/man/chisqcens2.Rd |only GofCens-0.97/GofCens/DESCRIPTION | 36 +- GofCens-0.97/GofCens/MD5 | 38 +- GofCens-0.97/GofCens/NAMESPACE | 9 GofCens-0.97/GofCens/R/ADcens.R |only GofCens-0.97/GofCens/R/CvMcens.R |only GofCens-0.97/GofCens/R/KScens.R | 341 ++++++++++++---------- GofCens-0.97/GofCens/R/chisqcens.R |only GofCens-0.97/GofCens/R/cumhazPlot.R | 425 ++++++++++++++-------------- GofCens-0.97/GofCens/R/gofcens.R | 268 ++++++++++------- GofCens-0.97/GofCens/R/kmPlot.R |only GofCens-0.97/GofCens/R/probPlot.R | 42 ++ GofCens-0.97/GofCens/data/nba.rda |binary GofCens-0.97/GofCens/man/ADcens.Rd |only GofCens-0.97/GofCens/man/CvMcens.Rd |only GofCens-0.97/GofCens/man/GofCens-package.Rd | 45 ++ GofCens-0.97/GofCens/man/KScens.Rd | 53 ++- GofCens-0.97/GofCens/man/chisqcens.Rd |only GofCens-0.97/GofCens/man/cumhazPlot.Rd | 30 + GofCens-0.97/GofCens/man/gofcens.Rd | 59 ++- GofCens-0.97/GofCens/man/kmPlot.Rd |only GofCens-0.97/GofCens/man/nba.Rd | 12 GofCens-0.97/GofCens/man/probPlot.Rd | 39 +- 26 files changed, 798 insertions(+), 599 deletions(-)
Title: Corrected Test Statistics for Comparing Machine Learning Models
on Correlated Samples
Description: Calculate a set of corrected test statistics for cases when samples
are not independent, such as when classification accuracy values are obtained
over resamples or through k-fold cross-validation, as proposed by Nadeau and Bengio (2003) <doi:10.1023/A:1024068626366>
and presented in Bouckaert and Frank (2004) <doi:10.1007/978-3-540-24775-3_3>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between correctR versions 0.1.3 dated 2023-08-20 and 0.2.1 dated 2024-03-13
DESCRIPTION | 8 LICENSE | 2 MD5 | 35 - R/correctR.R | 20 R/kfold_ttest.R | 132 ++-- R/repkfold_ttest.R | 167 +++-- R/resampled_ttest.R | 138 ++-- R/zzz.R |only README.md | 106 +-- build/vignette.rds |binary inst/doc/correctR.R | 80 +- inst/doc/correctR.Rmd | 233 ++++---- inst/doc/correctR.html | 1076 +++++++++++++++++++------------------- man/kfold_ttest.Rd | 14 man/repkfold_ttest.Rd | 80 +- man/resampled_ttest.Rd | 14 tests/testthat/helper-core_data.R | 24 tests/testthat/test-correctR.R | 31 - vignettes/correctR.Rmd | 233 ++++---- 19 files changed, 1288 insertions(+), 1105 deletions(-)
Title: Small Area Estimation for Continuous Zero Inflated Data
Description: Provides functionality to fit a zero-inflated estimator for small area estimation.
This estimator is a combines a linear mixed effects regression model and a logistic
mixed effects regression model via a two-stage modeling approach. The estimator's mean
squared error is estimated via a parametric bootstrap method. Chandra and others
(2012, <doi:10.1080/03610918.2011.598991>) introduce and describe this estimator and mean
squared error estimator. White and others (2024+, <arXiv:2402.03263>) describe the
applicability of this estimator to estimation of forest attributes and further assess the
estimator's properties.
Author: Josh Yamamoto [aut, cre],
Dinan Elsyad [aut],
Grayson White [aut],
Julian Schmitt [aut],
Niels Korsgaard [aut],
Kelly McConville [aut],
Kate Hu [aut]
Maintainer: Josh Yamamoto <joshuayamamoto5@gmail.com>
Diff between saeczi versions 0.1.0 dated 2024-02-13 and 0.1.1 dated 2024-03-13
saeczi-0.1.0/saeczi/tests/testthat/test-unit_zi.R |only saeczi-0.1.1/saeczi/DESCRIPTION | 24 - saeczi-0.1.1/saeczi/LICENSE |only saeczi-0.1.1/saeczi/MD5 | 23 - saeczi-0.1.1/saeczi/NAMESPACE | 7 saeczi-0.1.1/saeczi/NEWS.md | 2 saeczi-0.1.1/saeczi/R/RcppExports.R | 4 saeczi-0.1.1/saeczi/R/saeczi.R | 312 +++++++--------------- saeczi-0.1.1/saeczi/R/utils.R | 248 +++++++++++++++-- saeczi-0.1.1/saeczi/README.md | 47 +-- saeczi-0.1.1/saeczi/man/saeczi.Rd | 5 saeczi-0.1.1/saeczi/src/RcppExports.cpp | 9 saeczi-0.1.1/saeczi/src/helpers.cpp | 27 + saeczi-0.1.1/saeczi/tests/testthat/test-saeczi.R |only 14 files changed, 419 insertions(+), 289 deletions(-)
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Cankut Cubuk [ctb] ,
Katriona Goldmann [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.7.4 dated 2024-01-30 and 0.7.8 dated 2024-03-13
nestedcv-0.7.4/nestedcv/man/anova_filter.Rd |only nestedcv-0.7.4/nestedcv/man/correl_filter.Rd |only nestedcv-0.7.4/nestedcv/man/layer_filter.Rd |only nestedcv-0.7.4/nestedcv/man/wilcoxon_filter.Rd |only nestedcv-0.7.4/nestedcv/vignettes/boxplot.png |only nestedcv-0.7.8/nestedcv/DESCRIPTION | 27 + nestedcv-0.7.8/nestedcv/MD5 | 73 ++-- nestedcv-0.7.8/nestedcv/NAMESPACE | 15 - nestedcv-0.7.8/nestedcv/NEWS.md | 15 + nestedcv-0.7.8/nestedcv/R/complex_filters.R | 129 ++++---- nestedcv-0.7.8/nestedcv/R/cva.glmnet.R | 21 + nestedcv-0.7.8/nestedcv/R/filters.R | 141 +-------- nestedcv-0.7.8/nestedcv/R/metrics.R |only nestedcv-0.7.8/nestedcv/R/nestcv.train.R | 18 - nestedcv-0.7.8/nestedcv/R/nestcv_SuperLearner.R | 20 - nestedcv-0.7.8/nestedcv/R/nestedcv.R | 22 - nestedcv-0.7.8/nestedcv/R/outercv.R | 81 ++--- nestedcv-0.7.8/nestedcv/R/precision_recall.R |only nestedcv-0.7.8/nestedcv/R/repeatcv.R | 220 +++++++++++---- nestedcv-0.7.8/nestedcv/R/shap.R | 4 nestedcv-0.7.8/nestedcv/build/vignette.rds |binary nestedcv-0.7.8/nestedcv/inst/doc/nestedcv.R | 86 +++-- nestedcv-0.7.8/nestedcv/inst/doc/nestedcv.Rmd | 173 ++++++++--- nestedcv-0.7.8/nestedcv/inst/doc/nestedcv.html | 263 +++++++++++------- nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_hsstan.R | 5 nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_hsstan.Rmd | 7 nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_hsstan.html | 9 nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_shap.R | 36 +- nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_shap.Rmd | 43 ++ nestedcv-0.7.8/nestedcv/inst/doc/nestedcv_shap.html | 55 ++- nestedcv-0.7.8/nestedcv/man/coef.cva.glmnet.Rd | 3 nestedcv-0.7.8/nestedcv/man/lines.prc.Rd |only nestedcv-0.7.8/nestedcv/man/metrics.Rd |only nestedcv-0.7.8/nestedcv/man/outercv.Rd | 12 nestedcv-0.7.8/nestedcv/man/plot.prc.Rd |only nestedcv-0.7.8/nestedcv/man/pls_filter.Rd |only nestedcv-0.7.8/nestedcv/man/prc.Rd |only nestedcv-0.7.8/nestedcv/man/predict.cva.glmnet.Rd |only nestedcv-0.7.8/nestedcv/man/repeatcv.Rd | 52 ++- nestedcv-0.7.8/nestedcv/man/repeatfolds.Rd | 5 nestedcv-0.7.8/nestedcv/man/ttest_filter.Rd | 72 ++++ nestedcv-0.7.8/nestedcv/vignettes/nestedcv.Rmd | 173 ++++++++--- nestedcv-0.7.8/nestedcv/vignettes/nestedcv_hsstan.Rmd | 7 nestedcv-0.7.8/nestedcv/vignettes/nestedcv_shap.Rmd | 43 ++ 44 files changed, 1141 insertions(+), 689 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and
high-performance 2D drawing library. The 'ragg' package provides a set
of graphic devices based on AGG to use as alternative to the raster
devices provided through the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Maxim Shemanarev [aut, cph] ,
Tony Juricic [ctb, cph] ,
Milan Marusinec [ctb, cph] ,
Spencer Garrett [ctb] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ragg versions 1.2.7 dated 2023-12-11 and 1.3.0 dated 2024-03-13
DESCRIPTION | 8 MD5 | 59 +- NEWS.md | 9 R/agg_dev.R | 41 + README.md | 13 configure | 2 man/agg_capture.Rd | 5 man/agg_jpeg.Rd | 5 man/agg_png.Rd | 5 man/agg_ppm.Rd | 5 man/agg_supertransparent.Rd | 5 man/agg_tiff.Rd | 5 man/figures/README-unnamed-chunk-3-1.png |binary src/AggDevice.h | 647 +++++++++++++++++++++++++++---- src/AggDevice16.h | 4 src/AggDeviceCapture.h | 4 src/AggDeviceJpeg.h | 4 src/AggDevicePng.h | 8 src/AggDevicePpm.h | 4 src/AggDeviceTiff.h | 8 src/RenderBuffer.h | 72 +++ src/capture_dev.cpp | 5 src/group.h |only src/init.cpp | 12 src/init_device.h | 139 ++++++ src/jpeg_dev.cpp | 3 src/png_dev.cpp | 19 src/ppm_dev.cpp | 5 src/ragg.h | 13 src/text_renderer.h | 106 +++-- src/tiff_dev.cpp | 6 31 files changed, 1016 insertions(+), 205 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut],
Zachary Deane-Mayer [aut],
David Chudzicki [aut],
Dallin Akagi [aut],
Sergey Yurgenson [aut],
Thakur Raj Anand [aut],
Peter Hurford [aut],
Chester Ismay [aut],
AJ Alon [aut],
Andrew Watson [aut],
Gregory Williams [aut],
Anastasiia [...truncated...]
Maintainer: AJ Alon <api-maintainer@datarobot.com>
Diff between datarobot versions 2.18.5 dated 2023-11-02 and 2.18.6 dated 2024-03-13
DESCRIPTION | 6 - MD5 | 60 ++++++------- NEWS.md | 8 + R/GetPredictions.R | 9 -- R/ListModelJobs.R | 16 +-- R/MultiSeries.R | 7 - R/PredictionDatasets.R | 7 - R/Projects.R | 9 +- R/StartRetryWaiter.R | 6 - inst/doc/AdvancedTuning.html | 115 +++++++++++++------------ inst/doc/AdvancedVignette.html | 117 +++++++++++++------------- inst/doc/Calendars.html | 115 +++++++++++++------------ inst/doc/ComparingSubsets.html | 133 +++++++++++++++--------------- inst/doc/ComplianceDocumentation.html | 115 +++++++++++++------------ inst/doc/DatetimePartitionedProjects.html | 115 +++++++++++++------------ inst/doc/Deployment.html | 115 +++++++++++++------------ inst/doc/IntroductionToDataRobot.html | 115 +++++++++++++------------ inst/doc/Multiclass.Rmd | 4 inst/doc/Multiclass.html | 115 +++++++++++++------------ inst/doc/PartialDependence.html | 133 +++++++++++++++--------------- inst/doc/PredictionExplanations.html | 115 +++++++++++++------------ inst/doc/RatingTables.html | 115 +++++++++++++------------ inst/doc/TimeSeries.html | 115 +++++++++++++------------ inst/doc/TrainingPredictions.html | 115 +++++++++++++------------ inst/doc/VariableImportance.html | 133 +++++++++++++++--------------- man/GetModelJob.Rd | 32 +++---- man/ListModelJobs.Rd | 26 ++--- man/ListProjects.Rd | 6 - man/RequestPredictions.Rd | 6 - man/StartRetryWaiter.Rd | 6 - vignettes/Multiclass.Rmd | 4 31 files changed, 1008 insertions(+), 985 deletions(-)
Title: Preprocessing Experience Sampling Method (ESM) Data
Description: Tailored explicitly for Experience Sampling Method (ESM)
data, it contains a suite of functions designed to simplify
preprocessing steps and create subsequent reporting. It empowers
users with capabilities to extract critical insights during
preprocessing, conducts thorough data quality assessments (e.g., design
and sampling scheme checks, compliance rate, careless responses), and
generates visualizations and concise summary tables tailored
specifically for ESM data. Additionally, it streamlines the creation
of informative and interactive preprocessing reports, enabling
researchers to transparently share their dataset preprocessing
methodologies. Finally, it is part of a larger ecosystem which
includes a framework and a web gallery
(<https://preprocess.esmtools.com/>).
Author: Jordan Revol [aut, cre, cph] ,
Koen Niemeijer [ctb]
Maintainer: Jordan Revol <jordan.revol@kuleuven.be>
Diff between esmtools versions 1.0.0 dated 2024-01-11 and 1.0.1 dated 2024-03-13
DESCRIPTION | 6 MD5 | 28 NEWS.md | 8 R/txt.R | 28 R/vars_consist.R | 19 README.md | 20 data/esmdata_raw.rda |binary inst/extdata/esmdata_preprocessed.csv | 2400 +++++----- inst/extdata/esmdata_raw.csv | 4 inst/rmarkdown/templates/advanced_preprocess_report/skeleton/skeleton.Rmd | 33 inst/rmarkdown/templates/data_characteristics_report/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/preprocess_report/skeleton/skeleton.Rmd | 37 man/txt.Rd | 29 man/vars_consist.Rd | 4 tests/testthat/test-txt.R | 6 15 files changed, 1319 insertions(+), 1307 deletions(-)
Title: Bayesian Spectral Inference for Time Series
Description: Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126>, A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470> and Y. Tang et al (2023) <arXiv:2303.11561>. It was supported by DFG grants KI 1443/3-1 and KI 1443/3-2.
Author: Alexander Meier [aut],
Claudia Kirch [aut],
Matthew C. Edwards [aut],
Renate Meyer [aut, cre],
Yifu Tang [aut]
Maintainer: Renate Meyer <renate.meyer@auckland.ac.nz>
Diff between beyondWhittle versions 1.2.0 dated 2023-05-31 and 1.2.1 dated 2024-03-13
DESCRIPTION | 8 MD5 | 14 R/dynamicWhittle_miscellanea_zigzag.R | 2 R/dynamicWhittle_prior_and_mcmc_params.R | 2 R/psd_S3.R | 768 +++++++++++++++---------------- man/bdp_dw_bayes_factor_k1.Rd | 4 man/local_moving_FT_zigzag.Rd | 2 man/print_summary_gibbs_psd_help.Rd | 2 8 files changed, 401 insertions(+), 401 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.5.1 dated 2024-02-15 and 1.6.0 dated 2024-03-13
DESCRIPTION | 6 MD5 | 260 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 11 + R/class_glimpse.R | 8 R/class_inspection.R | 25 ++ R/class_mermaid.R | 10 - R/class_options.R | 27 ++- R/class_pattern.R | 4 R/class_process.R | 66 +++---- R/class_runtime.R | 18 +- R/class_settings.R | 10 + R/class_stem.R | 1 R/class_target.R | 4 R/class_visnetwork.R | 8 R/class_visual.R | 30 ++- R/tar_backoff.R | 16 - R/tar_branch_index.R | 2 R/tar_built.R | 4 R/tar_canceled.R | 4 R/tar_completed.R | 4 R/tar_config_get.R | 6 R/tar_config_set.R | 19 ++ R/tar_delete.R | 10 - R/tar_described_as.R |only R/tar_errored.R | 4 R/tar_exist_objects.R | 1 R/tar_glimpse.R | 17 + R/tar_invalidate.R | 6 R/tar_load.R | 7 R/tar_load_raw.R | 3 R/tar_make.R | 13 - R/tar_manifest.R | 29 +-- R/tar_mermaid.R | 13 + R/tar_network.R | 23 +- R/tar_newer.R | 7 R/tar_objects.R | 9 - R/tar_older.R | 7 R/tar_option_get.R | 1 R/tar_option_set.R | 2 R/tar_outdated.R | 8 R/tar_process.R | 7 R/tar_progress.R | 10 - R/tar_progress_branches.R | 6 R/tar_progress_summary.R | 4 R/tar_renv.R | 3 R/tar_sitrep.R | 6 R/tar_skipped.R | 4 R/tar_started.R | 4 R/tar_target.R | 14 + R/tar_target_raw.R | 9 - R/tar_unversion.R | 4 R/tar_visnetwork.R | 19 +- R/tar_workspaces.R | 4 R/utils_assert.R | 2 R/utils_callr.R | 28 ++- R/utils_character.R | 7 R/utils_cli.R | 20 +- R/utils_time.R | 20 +- inst/doc/overview.html | 155 +++++++++++++---- man/tar_active.Rd | 1 man/tar_backoff.Rd | 17 - man/tar_branch_index.Rd | 2 man/tar_built.Rd | 8 man/tar_call.Rd | 1 man/tar_callr_inner_try.Rd | 6 man/tar_cancel.Rd | 1 man/tar_canceled.Rd | 8 man/tar_completed.Rd | 8 man/tar_config_set.Rd | 8 man/tar_definition.Rd | 1 man/tar_delete.Rd | 8 man/tar_described_as.Rd |only man/tar_envir.Rd | 1 man/tar_errored.Rd | 8 man/tar_exist_objects.Rd | 3 man/tar_glimpse.Rd | 20 +- man/tar_group.Rd | 1 man/tar_invalidate.Rd | 6 man/tar_load.Rd | 7 man/tar_load_raw.Rd | 3 man/tar_make.Rd | 13 - man/tar_make_clustermq.Rd | 13 - man/tar_make_future.Rd | 13 - man/tar_manifest.Rd | 26 +-- man/tar_mermaid.Rd | 26 +-- man/tar_name.Rd | 1 man/tar_network.Rd | 23 +- man/tar_newer.Rd | 7 man/tar_objects.Rd | 9 - man/tar_older.Rd | 7 man/tar_option_set.Rd | 10 + man/tar_outdated.Rd | 8 man/tar_path.Rd | 1 man/tar_path_script.Rd | 1 man/tar_path_script_support.Rd | 1 man/tar_path_store.Rd | 1 man/tar_path_target.Rd | 1 man/tar_poll.Rd | 4 man/tar_process.Rd | 5 man/tar_progress.Rd | 10 - man/tar_progress_branches.Rd | 6 man/tar_progress_summary.Rd | 4 man/tar_renv.Rd | 4 man/tar_sitrep.Rd | 6 man/tar_skipped.Rd | 8 man/tar_source.Rd | 1 man/tar_started.Rd | 8 man/tar_store.Rd | 1 man/tar_target.Rd | 12 + man/tar_target_raw.Rd | 12 + man/tar_unversion.Rd | 6 man/tar_visnetwork.Rd | 24 +- man/tar_workspaces.Rd | 6 tests/interactive/test-mermaid.R | 45 ++++- tests/interactive/test-process.R | 15 + tests/interactive/test-visnetwork.R | 22 +- tests/testthat/test-class_glimpse.R | 4 tests/testthat/test-class_inspection.R | 27 ++- tests/testthat/test-class_options.R | 20 ++ tests/testthat/test-class_runtime.R | 10 + tests/testthat/test-class_target.R | 3 tests/testthat/test-tar_config_projects.R | 2 tests/testthat/test-tar_config_set.R | 27 ++- tests/testthat/test-tar_config_yaml.R | 2 tests/testthat/test-tar_described_as.R |only tests/testthat/test-tar_manifest.R | 7 tests/testthat/test-tar_network.R | 5 tests/testthat/test-tar_option_set.R | 12 + tests/testthat/test-tar_target.R | 7 tests/testthat/test-tar_target_raw.R | 7 tests/testthat/test-utils_character.R |only tests/testthat/test-utils_time.R | 28 ++- 133 files changed, 1119 insertions(+), 550 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 1.0.14 dated 2024-02-05 and 1.0.15 dated 2024-03-13
DESCRIPTION | 11 +++--- MD5 | 34 +++++++++++-------- NEWS.md | 4 ++ R/data.R | 37 +++++++++++++++++++++ build/vignette.rds |binary data/sotkadata_population.rda |only data/sotkadata_swedish_speaking_pop.rda |only data/statfi_zipcode_population.rda |only inst/doc/geofi_datasets.R | 7 +--- inst/doc/geofi_datasets.Rmd | 9 +---- inst/doc/geofi_datasets.html | 50 +++++++++++++---------------- inst/doc/geofi_joining_attribute_data.R | 13 ++----- inst/doc/geofi_joining_attribute_data.Rmd | 17 +++------ inst/doc/geofi_joining_attribute_data.html | 31 ++++++++--------- inst/doc/geofi_making_maps.html | 34 +++++++++---------- inst/doc/geofi_spatial_analysis.html | 14 ++++---- man/sotkadata_population.Rd |only man/sotkadata_swedish_speaking_pop.Rd |only man/statfi_zipcode_population.Rd |only vignettes/geofi_datasets.Rmd | 9 +---- vignettes/geofi_joining_attribute_data.Rmd | 17 +++------ 21 files changed, 153 insertions(+), 134 deletions(-)
Title: Excess Mortality
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Author: Rafael A. Irizarry [aut, cre],
Rolando Acosta [aut],
Ferenci Tamas [ctb]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between excessmort versions 0.6.1 dated 2021-10-11 and 0.7.0 dated 2024-03-13
DESCRIPTION | 14 MD5 | 46 +- NAMESPACE | 3 R/approx_demographics.R | 122 ++++-- R/compute_expected.R | 168 +++++--- R/excess_cumulative.R | 2 R/excess_model.R | 131 +++--- R/excess_stats.R | 4 R/expected_diagnostic.R | 100 +++- R/expected_plot.R | 20 build/vignette.rds |binary data/puerto_rico_counts.rda |binary data/puerto_rico_icd.rda |binary data/world_counts.rda |binary inst/doc/excessmort.R | 22 - inst/doc/excessmort.html | 894 +++++++++++++++++++++++++++++--------------- man/approx_demographics.Rd | 21 - man/compute_expected.Rd | 24 - man/excess_model.Rd | 11 man/excess_stats.Rd | 4 man/expected_diagnostic.Rd | 2 man/expected_plot.Rd | 2 man/puerto_rico_counts.Rd | 2 man/puerto_rico_icd.Rd | 2 24 files changed, 1054 insertions(+), 540 deletions(-)