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 - 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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(-)