Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA-seq data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.1.7 dated 2025-03-30 and 1.2.0 dated 2025-10-15
inferCSN-1.1.7/inferCSN/R/import.R |only inferCSN-1.1.7/inferCSN/man/as_matrix.Rd |only inferCSN-1.1.7/inferCSN/man/check_sparsity.Rd |only inferCSN-1.1.7/inferCSN/man/coef.srm.Rd |only inferCSN-1.1.7/inferCSN/man/grapes-ss-grapes.Rd |only inferCSN-1.1.7/inferCSN/man/log_message.Rd |only inferCSN-1.1.7/inferCSN/man/matrix_to_table.Rd |only inferCSN-1.1.7/inferCSN/man/normalization.Rd |only inferCSN-1.1.7/inferCSN/man/parallelize_fun.Rd |only inferCSN-1.1.7/inferCSN/man/pearson_correlation.Rd |only inferCSN-1.1.7/inferCSN/man/plot_all_metrics.Rd |only inferCSN-1.1.7/inferCSN/man/predict.srm.Rd |only inferCSN-1.1.7/inferCSN/man/print.srm.Rd |only inferCSN-1.1.7/inferCSN/man/r_square.Rd |only inferCSN-1.1.7/inferCSN/man/simulate_sparse_matrix.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_cor.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_cov_cor.Rd |only inferCSN-1.1.7/inferCSN/man/sparse_regression.Rd |only inferCSN-1.1.7/inferCSN/man/split_indices.Rd |only inferCSN-1.1.7/inferCSN/man/table_to_matrix.Rd |only inferCSN-1.1.7/inferCSN/src/BetaVector.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012LogisticSwaps.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012SquaredHingeSwaps.cpp |only inferCSN-1.1.7/inferCSN/src/CDL012Swaps.cpp |only inferCSN-1.1.7/inferCSN/src/Grid.cpp |only inferCSN-1.1.7/inferCSN/src/Grid1D.cpp |only inferCSN-1.1.7/inferCSN/src/Grid2D.cpp |only inferCSN-1.1.7/inferCSN/src/Interface.cpp |only inferCSN-1.1.7/inferCSN/src/Makevars |only inferCSN-1.1.7/inferCSN/src/Makevars.win |only inferCSN-1.1.7/inferCSN/src/Normalize.cpp |only inferCSN-1.1.7/inferCSN/src/Test_Interface.cpp |only inferCSN-1.1.7/inferCSN/src/asMatrix.cpp |only inferCSN-1.1.7/inferCSN/src/include |only inferCSN-1.1.7/inferCSN/src/matrix_to_table.cpp |only inferCSN-1.1.7/inferCSN/src/split_indices.cpp |only inferCSN-1.1.7/inferCSN/src/table_to_matrix.cpp |only inferCSN-1.1.7/inferCSN/src/utils.cpp |only inferCSN-1.2.0/inferCSN/DESCRIPTION | 21 inferCSN-1.2.0/inferCSN/MD5 | 168 +-- inferCSN-1.2.0/inferCSN/NAMESPACE | 24 inferCSN-1.2.0/inferCSN/R/RcppExports.R | 188 --- inferCSN-1.2.0/inferCSN/R/calculate_gene_rank.R | 2 inferCSN-1.2.0/inferCSN/R/inferCSN-package.R | 109 +- inferCSN-1.2.0/inferCSN/R/inferCSN.R | 69 - inferCSN-1.2.0/inferCSN/R/meta_cells.R | 54 - inferCSN-1.2.0/inferCSN/R/network_evaluation.R | 92 - inferCSN-1.2.0/inferCSN/R/network_sift.R | 41 inferCSN-1.2.0/inferCSN/R/network_visualization.R | 80 - inferCSN-1.2.0/inferCSN/R/plotting_functions.R | 31 inferCSN-1.2.0/inferCSN/R/reexports.R |only inferCSN-1.2.0/inferCSN/R/single_network.R | 12 inferCSN-1.2.0/inferCSN/R/sparse_regression_model.R | 361 ------ inferCSN-1.2.0/inferCSN/R/subsampling.R | 14 inferCSN-1.2.0/inferCSN/R/utils.R | 857 ---------------- inferCSN-1.2.0/inferCSN/README.md | 29 inferCSN-1.2.0/inferCSN/man/calculate_accuracy.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auprc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_auroc.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_f1.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_gene_rank.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_ji.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_metrics.Rd | 47 inferCSN-1.2.0/inferCSN/man/calculate_precision.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_recall.Rd | 2 inferCSN-1.2.0/inferCSN/man/calculate_si.Rd | 2 inferCSN-1.2.0/inferCSN/man/figures/logo.svg | 538 ++-------- inferCSN-1.2.0/inferCSN/man/filter_sort_matrix.Rd | 5 inferCSN-1.2.0/inferCSN/man/fit_srm.Rd | 28 inferCSN-1.2.0/inferCSN/man/inferCSN-package.Rd | 8 inferCSN-1.2.0/inferCSN/man/inferCSN.Rd | 46 inferCSN-1.2.0/inferCSN/man/infercsn_logo.Rd |only inferCSN-1.2.0/inferCSN/man/meta_cells.Rd | 48 inferCSN-1.2.0/inferCSN/man/network_format.Rd | 2 inferCSN-1.2.0/inferCSN/man/network_sift.Rd | 26 inferCSN-1.2.0/inferCSN/man/plot_coefficient.Rd | 22 inferCSN-1.2.0/inferCSN/man/plot_coefficients.Rd | 10 inferCSN-1.2.0/inferCSN/man/plot_contrast_networks.Rd | 13 inferCSN-1.2.0/inferCSN/man/plot_dynamic_networks.Rd | 44 inferCSN-1.2.0/inferCSN/man/plot_edges_comparison.Rd | 10 inferCSN-1.2.0/inferCSN/man/plot_embedding.Rd | 4 inferCSN-1.2.0/inferCSN/man/plot_histogram.Rd | 2 inferCSN-1.2.0/inferCSN/man/plot_network_heatmap.Rd | 29 inferCSN-1.2.0/inferCSN/man/plot_scatter.Rd | 2 inferCSN-1.2.0/inferCSN/man/plot_static_networks.Rd | 2 inferCSN-1.2.0/inferCSN/man/print.infercsn_logo.Rd |only inferCSN-1.2.0/inferCSN/man/single_network.Rd | 28 inferCSN-1.2.0/inferCSN/man/subsampling.Rd | 14 inferCSN-1.2.0/inferCSN/man/weight_sift.Rd | 2 inferCSN-1.2.0/inferCSN/src/RcppExports.cpp | 463 -------- inferCSN-1.2.0/inferCSN/src/filter_sort_matrix.cpp | 41 inferCSN-1.2.0/inferCSN/src/network_format.cpp | 4 inferCSN-1.2.0/inferCSN/src/network_format.h |only inferCSN-1.2.0/inferCSN/src/weight_sift.cpp | 2 95 files changed, 845 insertions(+), 2767 deletions(-)
Title: The Directed Prediction Index for Causal Inference from
Observational Data
Description: The Directed Prediction Index ('DPI') is
a quasi-causal inference (causal discovery) method for observational data
designed to quantify the relative endogeneity (relative dependence)
of outcome (Y) versus predictor (X) variables in regression models.
By comparing the proportion of variance explained (R-squared)
between the Y-as-outcome model and the X-as-outcome model
while controlling for a sufficient number of possible confounders,
it can suggest a plausible (admissible) direction of influence
from a more exogenous variable (X) to a more endogenous variable (Y).
Methodological details are provided at
<https://psychbruce.github.io/DPI/>.
This package also provides functions for data simulation and network
analysis (correlation, partial correlation, and Bayesian networks).
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between DPI versions 2025.9 dated 2025-09-20 and 2025.10 dated 2025-10-15
DPI-2025.10/DPI/DESCRIPTION | 20 DPI-2025.10/DPI/MD5 | 28 DPI-2025.10/DPI/NAMESPACE | 18 DPI-2025.10/DPI/NEWS.md | 17 DPI-2025.10/DPI/R/DPI.R | 987 +++++++++++++++++++++++--------- DPI-2025.10/DPI/README.md | 128 +++- DPI-2025.10/DPI/man/BNs_dag.Rd |only DPI-2025.10/DPI/man/DPI-package.Rd | 4 DPI-2025.10/DPI/man/DPI.Rd | 87 ++ DPI-2025.10/DPI/man/DPI_curve.Rd | 46 + DPI-2025.10/DPI/man/DPI_dag.Rd |only DPI-2025.10/DPI/man/S3method.network.Rd | 83 ++ DPI-2025.10/DPI/man/cor_matrix.Rd |only DPI-2025.10/DPI/man/cor_net.Rd |only DPI-2025.10/DPI/man/p_to_bf.Rd |only DPI-2025.10/DPI/man/sim_data.Rd | 10 DPI-2025.9/DPI/man/cor_network.Rd |only DPI-2025.9/DPI/man/dag_network.Rd |only DPI-2025.9/DPI/man/matrix_cor.Rd |only 19 files changed, 1040 insertions(+), 388 deletions(-)
Title: 'StreamCatTools'
Description: Tools for using the 'StreamCat' and 'LakeCat' API and
interacting with the 'StreamCat' and 'LakeCat' database.
Convenience functions in the package wrap the API for 'StreamCat'
on <https://api.epa.gov/StreamCat/streams/metrics>.
Author: Marc Weber [aut, cre],
Ryan Hill [ctb],
Travis Hudson [ctb],
Allen Brookes [ctb],
David Rebhuhn [ctb],
Michael Dumelle [ctb],
Zachary Smith [ctb]
Maintainer: Marc Weber <weber.marc@epa.gov>
Diff between StreamCatTools versions 0.8.0 dated 2025-10-09 and 0.9.0 dated 2025-10-15
DESCRIPTION | 6 - MD5 | 36 +++++----- NEWS.md | 6 + R/lc_get_data.R | 27 +++++-- R/lc_get_params.R | 129 +++++++++++++++++++----------------- R/sc_get_data.R | 15 +++- R/sc_get_params.R | 129 +++++++++++++++++++----------------- inst/doc/Applications.html | 4 - inst/doc/Introduction.R | 4 + inst/doc/Introduction.Rmd | 8 ++ inst/doc/Introduction.html | 76 +++++++++++++-------- inst/doc/LakeCat.R | 4 + inst/doc/LakeCat.Rmd | 7 + inst/doc/LakeCat.html | 38 +++++++--- man/lc_get_metric_names.Rd | 2 man/sc_get_metric_names.Rd | 2 tests/testthat/test-lc_get_params.R | 2 vignettes/Introduction.Rmd | 8 ++ vignettes/LakeCat.Rmd | 7 + 19 files changed, 321 insertions(+), 189 deletions(-)
More information about StreamCatTools at CRAN
Permanent link
Title: Interactive Plotting for Functional Data Analyses
Description: Produces Shiny applications for different types of popular functional data analyses. The functional data analyses are implemented in the refund package, then refund.shiny reads in the refund object and implements an object-specific set of plots based on the object class using S3.
Author: Julia Wrobel [aut, cre],
Jeff Goldsmith [aut]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund.shiny versions 1.0 dated 2022-10-10 and 1.1 dated 2025-10-15
DESCRIPTION | 16 +++++++++------- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/plot_shiny.R | 8 ++++---- R/plot_shiny.lfpca.R | 4 ++++ README.md | 4 +--- man/plot_shiny.Rd | 8 ++++---- 8 files changed, 36 insertions(+), 25 deletions(-)
Title: Community Estimation in G-Models via CORD
Description: Partitions data points (variables) into communities/clusters,
similar to clustering algorithms such as k-means and hierarchical
clustering. This package implements a clustering algorithm based on a new
metric CORD, defined for high-dimensional parametric or semiparametric
distributions. For more details see Bunea et al. (2020), Annals of Statistics
<doi:10.1214/18-AOS1794>.
Author: Xi LUO [aut, cre],
Florentina Bunea [aut],
Christophe Giraud [aut]
Maintainer: Xi (Rossi) LUO <xi.rossi.luo@gmail.com>
Diff between cord versions 0.1.1 dated 2015-09-20 and 0.2.0 dated 2025-10-15
ChangeLog | 4 ++ DESCRIPTION | 32 +++++++++++++++----- MD5 | 17 +++++----- R/RcppExports.R | 6 +-- R/cord.R | 41 ++++++++++++-------------- build |only man/cord.Rd | 14 +++++--- src/RcppExports.cpp | 38 +++++++++++++++++------- src/cordDist.cpp | 35 ++++++++++++++++++++-- src/greedyCord.cpp | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++-- 10 files changed, 209 insertions(+), 60 deletions(-)
Title: Fully Parameterized Generalized Wendland Covariance Function
Description: A fully parameterized Generalized Wendland covariance function for use in Gaussian process models, as well as multiple methods for approximating it via covariance interpolation. The available methods are linear interpolation, polynomial interpolation, and cubic spline interpolation.
Moreno Bevilacqua and Reinhard Furrer and Tarik Faouzi and Emilio Porcu (2019) <url:<https://projecteuclid.org/journalArticle/Download?urlId=10.1214%2F17-AOS1652 >>.
Moreno Bevilacqua and Christian Caamaño-Carrillo and Emilio Porcu (2022) <doi:10.48550/arXiv.2008.02904>.
Reinhard Furrer and Roman Flury and Florian Gerber (2022) <url:<https://CRAN.R-project.org/package=spam >>.
Author: Thomas C. Fischer [aut, cre],
Reinhard Furrer [aut, ths],
Josef Stocker [aut]
Maintainer: Thomas C. Fischer <thomascasparfischer@gmail.com>
Diff between GeneralizedWendland versions 0.6.0 dated 2024-02-18 and 0.6.1 dated 2025-10-15
DESCRIPTION | 10 - MD5 | 34 ++--- R/helper_functions.R | 70 +++++------ build/vignette.rds |binary man/GeneralizedWendland-package.Rd | 60 +++++----- man/Rcpp_Wendland.Rd | 138 +++++++++++------------ man/cov.askey.Rd | 98 ++++++++-------- man/cov.wendland.Rd | 178 ++++++++++++++--------------- man/factory-choleskyFactory.Rd | 114 +++++++++---------- man/factory-covDiag.Rd | 220 ++++++++++++++++++------------------- man/factory-covarianceFactory.Rd | 124 ++++++++++---------- man/factory-mleFactory.Rd | 85 ++++++++++---- man/factory-neg2loglikDiag.Rd | 134 +++++++++++----------- man/factory-neg2loglikFactory.Rd | 172 ++++++++++++++-------------- man/factory-optimFactory.Rd | 204 ++++++++++++++++++++-------------- man/factory_predict.Rd | 152 ++++++++++++------------- man/generalizedwendland-error.Rd | 56 ++++----- man/generalizedwendland-warning.Rd | 58 ++++----- 18 files changed, 990 insertions(+), 917 deletions(-)
More information about GeneralizedWendland at CRAN
Permanent link
Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process
Emulations
Description: Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process,
and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI).
The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and
Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and
Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package,
see <https://mingdeyu.github.io/dgpsi-R/>.
Author: Deyu Ming [aut, cre, cph],
Daniel Williamson [aut]
Maintainer: Deyu Ming <deyu.ming.16@ucl.ac.uk>
Diff between dgpsi versions 2.5.0 dated 2024-12-14 and 2.6.0 dated 2025-10-15
dgpsi-2.5.0/dgpsi/man/combine.Rd |only dgpsi-2.5.0/dgpsi/man/set_linked_idx.Rd |only dgpsi-2.6.0/dgpsi/DESCRIPTION | 8 dgpsi-2.6.0/dgpsi/MD5 | 88 ++---- dgpsi-2.6.0/dgpsi/NAMESPACE | 2 dgpsi-2.6.0/dgpsi/NEWS.md | 21 + dgpsi-2.6.0/dgpsi/R/alm.R | 15 - dgpsi-2.6.0/dgpsi/R/design.R | 215 ++++++++++---- dgpsi-2.6.0/dgpsi/R/dgp.R | 303 +++++++++++--------- dgpsi-2.6.0/dgpsi/R/draw.R | 76 +++-- dgpsi-2.6.0/dgpsi/R/gp.R | 101 +----- dgpsi-2.6.0/dgpsi/R/initi_py.R | 36 +- dgpsi-2.6.0/dgpsi/R/lgp.R | 106 +------ dgpsi-2.6.0/dgpsi/R/mice.R | 15 - dgpsi-2.6.0/dgpsi/R/plot.R | 465 ++++++++++++++++---------------- dgpsi-2.6.0/dgpsi/R/prediction.R | 339 ++++------------------- dgpsi-2.6.0/dgpsi/R/serialization.R | 231 +++++++++------ dgpsi-2.6.0/dgpsi/R/update.R | 22 - dgpsi-2.6.0/dgpsi/R/utils.R | 369 +++++++++++-------------- dgpsi-2.6.0/dgpsi/R/validation.R | 427 +++++++++-------------------- dgpsi-2.6.0/dgpsi/R/vigf.R | 39 +- dgpsi-2.6.0/dgpsi/README.md | 8 dgpsi-2.6.0/dgpsi/inst/WORDLIST | 7 dgpsi-2.6.0/dgpsi/inst/doc/dgpsi.Rmd | 6 dgpsi-2.6.0/dgpsi/inst/doc/dgpsi.html | 2 dgpsi-2.6.0/dgpsi/man/alm.Rd | 8 dgpsi-2.6.0/dgpsi/man/deserialize.Rd | 39 -- dgpsi-2.6.0/dgpsi/man/design.Rd | 16 - dgpsi-2.6.0/dgpsi/man/dgp.Rd | 134 ++++----- dgpsi-2.6.0/dgpsi/man/draw.Rd | 4 dgpsi-2.6.0/dgpsi/man/get_thread_num.Rd | 2 dgpsi-2.6.0/dgpsi/man/gp.Rd | 52 --- dgpsi-2.6.0/dgpsi/man/init_py.Rd | 4 dgpsi-2.6.0/dgpsi/man/lgp.Rd | 31 -- dgpsi-2.6.0/dgpsi/man/mice.Rd | 8 dgpsi-2.6.0/dgpsi/man/plot.Rd | 23 - dgpsi-2.6.0/dgpsi/man/predict.Rd | 95 +----- dgpsi-2.6.0/dgpsi/man/serialize.Rd | 32 +- dgpsi-2.6.0/dgpsi/man/set_id.Rd | 2 dgpsi-2.6.0/dgpsi/man/set_thread_num.Rd | 2 dgpsi-2.6.0/dgpsi/man/set_vecchia.Rd | 18 - dgpsi-2.6.0/dgpsi/man/summary.Rd | 5 dgpsi-2.6.0/dgpsi/man/update.Rd | 2 dgpsi-2.6.0/dgpsi/man/validate.Rd | 51 +-- dgpsi-2.6.0/dgpsi/man/vigf.Rd | 10 dgpsi-2.6.0/dgpsi/vignettes/dgpsi.Rmd | 6 46 files changed, 1487 insertions(+), 1958 deletions(-)
Title: Multivariate Histograms
Description: Tabulate and plot directional and other multivariate histograms.
Author: John P. Nolan [aut, cre, cph]
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvhist versions 1.1 dated 2023-10-03 and 1.2 dated 2025-10-15
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- man/mvhist.Rd | 28 +++++++++++----------------- man/mvhistDirectional.Rd | 17 ++++++++++++++--- man/mvhistMisc.Rd | 6 +++--- 6 files changed, 39 insertions(+), 34 deletions(-)
Title: A 'shiny' App to Evaluate Diagnostic Tests Performance
Description: Evaluate diagnostic test performance using data from laboratory or diagnostic research. It supports both binary and continuous test variables. It allows users to compute key performance indicators and visualize Receiver Operating Characteristic (ROC) curves, determine optimal cut-off thresholds, display confusion matrix, and export publication-ready plot. It aims to facilitate the application of statistical methods in diagnostic test evaluation by healthcare professionals. The methodology used to compute the performance indicators follows the overview described by Habibzadeh (2025) <doi:10.11613/BM.2025.010101>. Thanks to 'shiny' package.
Author: Nassim AYAD [aut, cre]
Maintainer: Nassim AYAD <nassim.ayad.ph@gmail.com>
Diff between EvalTest versions 1.0.2 dated 2025-09-14 and 1.0.3 dated 2025-10-15
DESCRIPTION | 8 MD5 | 19 - NEWS.md |only README.md | 31 + inst/app/app.R | 714 +++++++++++++++++++++--------------------- inst/doc/introduction.R | 5 inst/doc/introduction.Rmd | 40 +- inst/doc/introduction.html | 60 ++- vignettes/img/screenshot2.png |binary vignettes/img/screenshot3.png |binary vignettes/introduction.Rmd | 40 +- 11 files changed, 503 insertions(+), 414 deletions(-)
Title: Simultaneous Confidence Intervals for Multinomial Proportions
Description: Several authors have proposed methods for constructing simultaneous confidence intervals for multinomial proportions. The package implements seven classical approaches—Wilson, Quesenberry and Hurst, Goodman, Wald (with and without continuity correction), Fitzpatrick and Scott, and Sison and Glaz—along with Bayesian methods based on Dirichlet models. Both equal and unequal Dirichlet priors are supported, providing a broad framework for inference, data analysis, and sensitivity evaluation.
Author: Subbiah M [aut, cre]
Maintainer: Subbiah M <sisufive@gmail.com>
This is a re-admission after prior archival of version 1.1 dated 2013-05-28
Diff between CoinMinD versions 1.1 dated 2013-05-28 and 1.2.1 dated 2025-10-15
CoinMinD-1.1/CoinMinD/man/CoinMinD-package.Rd |only CoinMinD-1.2.1/CoinMinD/DESCRIPTION | 34 +-- CoinMinD-1.2.1/CoinMinD/MD5 | 41 ++-- CoinMinD-1.2.1/CoinMinD/NAMESPACE | 22 +- CoinMinD-1.2.1/CoinMinD/R/BMDE.R | 95 ++++++---- CoinMinD-1.2.1/CoinMinD/R/BMDU.R | 112 +++++++----- CoinMinD-1.2.1/CoinMinD/R/FS.R | 89 ++++++--- CoinMinD-1.2.1/CoinMinD/R/GM.R | 106 ++++++++--- CoinMinD-1.2.1/CoinMinD/R/QH.R | 104 ++++++++--- CoinMinD-1.2.1/CoinMinD/R/SG.R | 240 +++++++++++++------------- CoinMinD-1.2.1/CoinMinD/R/WALD.R | 95 +++++++--- CoinMinD-1.2.1/CoinMinD/R/WALDCC.R | 96 +++++++--- CoinMinD-1.2.1/CoinMinD/R/WS.R | 97 +++++++--- CoinMinD-1.2.1/CoinMinD/man/BMDE.Rd | 63 +++--- CoinMinD-1.2.1/CoinMinD/man/BMDU.Rd | 62 +++--- CoinMinD-1.2.1/CoinMinD/man/FS.Rd | 65 +++---- CoinMinD-1.2.1/CoinMinD/man/GM.Rd | 79 +++++--- CoinMinD-1.2.1/CoinMinD/man/QH.Rd | 81 +++++--- CoinMinD-1.2.1/CoinMinD/man/SG.Rd | 84 +++++---- CoinMinD-1.2.1/CoinMinD/man/WALD.Rd | 77 ++++---- CoinMinD-1.2.1/CoinMinD/man/WALDCC.Rd | 76 ++++---- CoinMinD-1.2.1/CoinMinD/man/WS.Rd | 79 ++++---- 22 files changed, 1083 insertions(+), 714 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Candace Savonen [aut, cre]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between rsynthbio versions 2.2.1 dated 2025-09-12 and 3.0.0 dated 2025-10-15
DESCRIPTION | 8 MD5 | 40 +- NAMESPACE | 4 NEWS.md | 56 +++ R/call_model_api.R | 455 +++++++++++++++++++++++++++----- R/utils.R | 30 +- README.md | 54 +++ build/vignette.rds |binary inst/doc/getting-started.R | 28 + inst/doc/getting-started.Rmd | 72 ++++- inst/doc/getting-started.html | 173 +++++++----- man/DEFAULT_POLL_INTERVAL_SECONDS.Rd |only man/DEFAULT_POLL_TIMEOUT_SECONDS.Rd |only man/DEFAULT_TIMEOUT.Rd |only man/MODEL_MODALITIES.Rd | 3 man/get_json.Rd |only man/get_valid_query.Rd | 14 man/poll_model_query.Rd |only man/predict_query.Rd | 33 +- man/resolve_api_slug.Rd |only man/start_model_query.Rd |only man/transform_result_to_frames.Rd |only tests/testthat/helper-mocks.R |only tests/testthat/test-call_model_api.R | 496 ++++++++++++++++++++++++++--------- tests/testthat/test-live-api.R |only vignettes/getting-started.Rmd | 72 ++++- 26 files changed, 1178 insertions(+), 360 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression or any other function. Also includes a comprehensive framework for discrete-time
simulation, and networks-based simulation which can generate even more complex longitudinal and dependent data.
For more details, see Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.4.0 dated 2025-08-27 and 0.4.1 dated 2025-10-15
DESCRIPTION | 9 MD5 | 77 ++-- NAMESPACE | 3 NEWS.md | 16 R/dag.r | 32 + R/input_checks.r | 44 ++ R/node.r | 8 R/node_binomial.r | 19 - R/node_gaussian.r | 15 R/node_lmer.r | 3 R/node_negative_binomial.r | 13 R/node_poisson.r | 14 R/node_zeroinfl.r | 7 R/sim_n_datasets.r | 2 R/structural_equations.r | 86 ++++- inst/doc/simDAG.html | 2 inst/doc/v_cookbook.R | 46 ++ inst/doc/v_cookbook.Rmd | 71 ++++ inst/doc/v_cookbook.html | 363 ++++++++++++++-------- inst/doc/v_covid_example.html | 2 man/as.dagitty.DAG.Rd |only man/as.igraph.DAG.Rd | 6 man/node_binomial.Rd | 13 man/node_gaussian.Rd | 7 man/node_negative_binomial.Rd | 7 man/node_poisson.Rd | 9 man/node_zeroinfl.Rd | 7 man/sim_n_datasets.Rd | 7 tests/testthat/test_as.dagitty.DAG.r |only tests/testthat/test_node.r | 30 + tests/testthat/test_node_binomial.r | 72 ++++ tests/testthat/test_node_gaussian.r | 40 ++ tests/testthat/test_node_lmer.r | 31 + tests/testthat/test_node_negative_binomial.r | 27 + tests/testthat/test_node_poisson.r | 38 ++ tests/testthat/test_node_zeroinfl.r | 31 + tests/testthat/test_str_eq_binomial.r | 24 + tests/testthat/test_str_eq_gaussian.r | 4 tests/testthat/test_str_eq_poisson.r | 11 vignettes/images_v_joss/disc_time_sim.bib.sav.tmp |only vignettes/v_cookbook.Rmd | 71 ++++ 41 files changed, 1037 insertions(+), 230 deletions(-)
Title: Processing Agro-Environmental Data
Description: A set of tools for processing and analyzing data developed in the
context of the "Who Has Eaten the Planet" (WHEP) project, funded by the
European Research Council (ERC). For more details on multi-regional
input–output model "Food and Agriculture Biomass Input–Output" (FABIO) see
Bruckner et al. (2019) <doi:10.1021/acs.est.9b03554>.
Author: Catalin Covaci [aut, cre] ,
Eduardo Aguilera [aut, cph] ,
Joao Serra [ctb] ,
European Research Council [fnd]
Maintainer: Catalin Covaci <catalin.covaci@csic.es>
Diff between whep versions 0.1.0 dated 2025-07-25 and 0.2.0 dated 2025-10-15
whep-0.1.0/whep/inst/doc/workflow-intro.R |only whep-0.1.0/whep/inst/doc/workflow-intro.Rmd |only whep-0.1.0/whep/inst/doc/workflow-intro.html |only whep-0.1.0/whep/tests/testthat/test_scrape_faostat.R |only whep-0.1.0/whep/vignettes/workflow-intro.Rmd |only whep-0.2.0/whep/DESCRIPTION | 8 whep-0.2.0/whep/MD5 | 100 ++- whep-0.2.0/whep/NAMESPACE | 4 whep-0.2.0/whep/NEWS.md | 5 whep-0.2.0/whep/R/bilateral_trade.R | 10 whep-0.2.0/whep/R/code_names.R | 42 - whep-0.2.0/whep/R/commodity_balance_sheet.R | 4 whep-0.2.0/whep/R/gapfilling.R |only whep-0.2.0/whep/R/input_files.R | 54 + whep-0.2.0/whep/R/livestock.R | 2 whep-0.2.0/whep/R/pins_internal.R | 37 - whep-0.2.0/whep/R/production.R | 4 whep-0.2.0/whep/R/scrape_faostat.R | 4 whep-0.2.0/whep/R/sources.R | 4 whep-0.2.0/whep/R/supply_use.R | 52 - whep-0.2.0/whep/R/utils.R | 8 whep-0.2.0/whep/README.md | 31 - whep-0.2.0/whep/build/partial.rdb |binary whep-0.2.0/whep/build/vignette.rds |binary whep-0.2.0/whep/inst/doc/trade-sources-coverage.html | 2 whep-0.2.0/whep/inst/extdata/examples |only whep-0.2.0/whep/inst/scripts/check_lint.R | 5 whep-0.2.0/whep/man/build_supply_use.Rd | 10 whep-0.2.0/whep/man/get_bilateral_trade.Rd | 4 whep-0.2.0/whep/man/get_feed_intake.Rd | 2 whep-0.2.0/whep/man/get_primary_production.Rd | 2 whep-0.2.0/whep/man/get_primary_residues.Rd | 2 whep-0.2.0/whep/man/get_processing_coefs.Rd | 2 whep-0.2.0/whep/man/get_wide_cbs.Rd | 2 whep-0.2.0/whep/man/linear_fill.Rd |only whep-0.2.0/whep/man/proxy_fill.Rd |only whep-0.2.0/whep/man/sum_fill.Rd |only whep-0.2.0/whep/tests/testthat/test_bilateral_trade.R | 71 +- whep-0.2.0/whep/tests/testthat/test_commodity_balance_sheet.R | 101 +-- whep-0.2.0/whep/tests/testthat/test_gapfilling.R |only whep-0.2.0/whep/tests/testthat/test_input_files.R | 39 - whep-0.2.0/whep/tests/testthat/test_sources.R | 11 whep-0.2.0/whep/tests/testthat/test_supply_use.R | 295 ++++------ 43 files changed, 510 insertions(+), 407 deletions(-)
Title: Automatically Builds 12 Classification Models
Description: Automatically builds 12 classification models from data. The package returns 26 plots, 5 tables and a summary report.
The package automatically builds six individual classification models, including error (RMSE) and predictions. That data is used to create an ensemble, which is then modeled using six methods.
The process is repeated as many times as the user requests. The mean of the results are presented in a summary table.
The package returns the confusion matrices for all 12 models, tables of the correlation of the numeric data, the results of the variance inflation process, the head of the ensemble and the head of the data frame.
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between ClassificationEnsembles versions 0.7.0 dated 2025-10-12 and 0.7.1 dated 2025-10-15
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 3 ++ R/ClassificationEnsembles.R | 48 ++++++++++++++++++++++---------------------- 4 files changed, 33 insertions(+), 30 deletions(-)
More information about ClassificationEnsembles at CRAN
Permanent link
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Impect GmbH [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@impect.com>
Diff between impectR versions 2.4.3 dated 2025-09-08 and 2.5.1 dated 2025-10-15
impectR-2.4.3/impectR/R/getPlayerMatchSums.R |only impectR-2.4.3/impectR/R/getSquadMatchSums.R |only impectR-2.5.1/impectR/DESCRIPTION | 8 impectR-2.5.1/impectR/MD5 | 84 ++-- impectR-2.5.1/impectR/NAMESPACE | 1 impectR-2.5.1/impectR/NEWS.md | 20 + impectR-2.5.1/impectR/R/getAccessToken.R | 11 impectR-2.5.1/impectR/R/getEvents.R | 156 +++++++- impectR-2.5.1/impectR/R/getFormations.R | 18 - impectR-2.5.1/impectR/R/getIterations.R | 6 impectR-2.5.1/impectR/R/getMatches.R | 12 impectR-2.5.1/impectR/R/getPlayerIterationAverages.R | 21 - impectR-2.5.1/impectR/R/getPlayerIterationScores.R | 221 ++++++++---- impectR-2.5.1/impectR/R/getPlayerMatchScores.R | 285 ++++++++++++---- impectR-2.5.1/impectR/R/getPlayerMatchsums.R |only impectR-2.5.1/impectR/R/getPlayerProfileScores.R | 22 - impectR-2.5.1/impectR/R/getSetPieces.R | 20 - impectR-2.5.1/impectR/R/getSquadCoefficients.R |only impectR-2.5.1/impectR/R/getSquadIterationAverages.R | 18 - impectR-2.5.1/impectR/R/getSquadIterationScores.R | 18 - impectR-2.5.1/impectR/R/getSquadMatchScores.R | 127 ++++++- impectR-2.5.1/impectR/R/getSquadMatchsums.R |only impectR-2.5.1/impectR/R/getSquadRatings.R | 15 impectR-2.5.1/impectR/R/getStartingPositions.R | 21 - impectR-2.5.1/impectR/R/getSubstitutions.R | 21 - impectR-2.5.1/impectR/R/utils.R | 14 impectR-2.5.1/impectR/README.md | 65 +++ impectR-2.5.1/impectR/man/getAccessToken.Rd | 9 impectR-2.5.1/impectR/man/getEvents.Rd | 10 impectR-2.5.1/impectR/man/getFormations.Rd | 4 impectR-2.5.1/impectR/man/getIterations.Rd | 4 impectR-2.5.1/impectR/man/getMatches.Rd | 4 impectR-2.5.1/impectR/man/getPlayerIterationAverages.Rd | 4 impectR-2.5.1/impectR/man/getPlayerIterationScores.Rd | 16 impectR-2.5.1/impectR/man/getPlayerMatchScores.Rd | 16 impectR-2.5.1/impectR/man/getPlayerMatchsums.Rd | 6 impectR-2.5.1/impectR/man/getPlayerProfileScores.Rd | 9 impectR-2.5.1/impectR/man/getSetPieces.Rd | 4 impectR-2.5.1/impectR/man/getSquadCoefficients.Rd |only impectR-2.5.1/impectR/man/getSquadIterationAverages.Rd | 4 impectR-2.5.1/impectR/man/getSquadIterationScores.Rd | 4 impectR-2.5.1/impectR/man/getSquadMatchScores.Rd | 4 impectR-2.5.1/impectR/man/getSquadMatchsums.Rd | 6 impectR-2.5.1/impectR/man/getSquadRatings.Rd | 4 impectR-2.5.1/impectR/man/getStartingPositions.Rd | 4 impectR-2.5.1/impectR/man/getSubstitutions.Rd | 4 46 files changed, 961 insertions(+), 339 deletions(-)
Title: Fast Approximation of Time-Varying Infectious Disease
Transmission Rates
Description: A fast method for approximating time-varying infectious disease
transmission rates from disease incidence time series and other
data, based on a discrete time approximation of an SEIR model, as
analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.4.0 dated 2025-04-28 and 0.5.0 dated 2025-10-15
fastbeta-0.4.0/fastbeta/R/lambertW.R |only fastbeta-0.5.0/fastbeta/DESCRIPTION | 11 fastbeta-0.5.0/fastbeta/MD5 | 42 - fastbeta-0.5.0/fastbeta/NAMESPACE | 1 fastbeta-0.5.0/fastbeta/R/aoi.R | 296 ++++++---- fastbeta-0.5.0/fastbeta/R/cbind.ts.R |only fastbeta-0.5.0/fastbeta/R/deconvolve.R | 7 fastbeta-0.5.0/fastbeta/R/fastbeta.R | 3 fastbeta-0.5.0/fastbeta/data/datalist | 1 fastbeta-0.5.0/fastbeta/data/pneumonia.rda |only fastbeta-0.5.0/fastbeta/inst/NEWS.Rd | 152 +++-- fastbeta-0.5.0/fastbeta/inst/de.R |only fastbeta-0.5.0/fastbeta/inst/scripts/1918KeatCush-Chart2-SolidLine.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/1979MoseBend-Figure1-Bars.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/2009GoldDush-SupplementFigure1-Points.csv |only fastbeta-0.5.0/fastbeta/inst/scripts/pneumonia.R |only fastbeta-0.5.0/fastbeta/inst/scripts/pneumonia.csv |only fastbeta-0.5.0/fastbeta/inst/test.R |only fastbeta-0.5.0/fastbeta/man/cbind.ts.Rd |only fastbeta-0.5.0/fastbeta/man/deconvolve.Rd | 99 ++- fastbeta-0.5.0/fastbeta/man/fastbeta.Rd | 3 fastbeta-0.5.0/fastbeta/man/fastbeta.bootstrap.Rd | 3 fastbeta-0.5.0/fastbeta/man/fastbeta.matrix.Rd | 3 fastbeta-0.5.0/fastbeta/man/pneumonia.Rd |only fastbeta-0.5.0/fastbeta/man/ptpi.Rd | 3 fastbeta-0.5.0/fastbeta/man/seir.Rd | 4 fastbeta-0.5.0/fastbeta/man/sir.aoi.Rd | 226 ++++--- fastbeta-0.5.0/fastbeta/man/smallpox.Rd | 8 28 files changed, 560 insertions(+), 302 deletions(-)
Title: NPMLE for Logistic-Cox Cure-Rate Model
Description: Expectation-Maximization (EM) algorithm for point estimation and variance estimation to
the nonparametric maximum likelihood estimator (NPMLE) for
logistic-Cox cure-rate model with left truncation and right-
censoring. See Hou, Chambers and Xu (2017) <doi:10.1007/s10985-017-9415-2>.
Author: Evan Ren [aut],
Jue Hou [cre]
Maintainer: Jue Hou <hou00123@umn.edu>
Diff between curephEM versions 0.3.0 dated 2024-02-02 and 0.3.2 dated 2025-10-15
DESCRIPTION | 25 +++++-- MD5 | 18 ++--- build/vignette.rds |binary data/sim.cureph.data.rda |binary inst/doc/curephEM-vignette.R | 33 +-------- inst/doc/curephEM-vignette.Rmd | 83 +++++------------------ inst/doc/curephEM-vignette.html | 141 ++-------------------------------------- man/Survcure.Rd | 2 tests |only vignettes/curephEM-vignette.Rmd | 83 +++++------------------ 10 files changed, 83 insertions(+), 302 deletions(-)
Title: Computerized Adaptive Testing for Survey Research
Description: Provides methods of computerized adaptive testing for survey researchers. See Montgomery and Rossiter (2020) <doi:10.1093/jssam/smz027>. Includes functionality for data fit with the classic item response methods including the latent trait model, the Birnbaum three parameter model, the graded response, and the generalized partial credit model. Additionally, includes several ability parameter estimation and item selection routines. During item selection, all calculations are done in compiled C++ code.
Author: Jacob Montgomery [aut],
Erin Rossiter [aut, cre]
Maintainer: Erin Rossiter <erossite@nd.edu>
Diff between catSurv versions 1.5.0 dated 2022-12-03 and 1.6.0 dated 2025-10-15
DESCRIPTION | 15 ++++++------ MD5 | 56 ++++++++++++++++++++++----------------------- NEWS.md | 8 ++++++ R/data.R | 44 +++++++++++++++++------------------ R/simulateFisherInfo.R | 3 ++ R/simulateThetas.R | 3 ++ man/agree_cat.Rd | 2 - man/consc_cat.Rd | 2 - man/empathy_cat.Rd | 2 - man/extra_cat.Rd | 2 - man/mach_cat.Rd | 2 - man/neuro_cat.Rd | 2 - man/nfa_cat.Rd | 4 +-- man/nfc_cat.Rd | 4 +-- man/npi_cat.Rd | 2 - man/nte_cat.Rd | 4 +-- man/open_cat.Rd | 2 - man/polknowMT.Rd | 2 - man/rwa_cat.Rd | 2 - man/sdo_cat.Rd | 2 - man/simulateFisherInfo.Rd | 3 ++ man/simulateThetas.Rd | 3 ++ man/sv_conservation_cat.Rd | 2 - man/sv_open_cat.Rd | 2 - man/sv_selfenhance_cat.Rd | 2 - man/sv_selftransc_cat.Rd | 2 - man/systemizing_cat.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 3 -- 29 files changed, 102 insertions(+), 82 deletions(-)
Title: Ridge Redundancy Analysis for High-Dimensional Omics Data
Description: Efficient framework for ridge redundancy analysis (rrda),
tailored for high-dimensional omics datasets where the number of
predictors exceeds the number of samples. The method leverages
Singular Value Decomposition (SVD) to avoid direct inversion of the
covariance matrix, enhancing scalability and performance. It also
introduces a memory-efficient storage strategy for coefficient
matrices, enabling practical use in large-scale applications. The
package supports cross-validation for selecting regularization
parameters and reduced-rank dimensions, making it a robust and
flexible tool for multivariate analysis in omics research. Please
refer to our article (Yoshioka et al., 2025) for more details.
Author: Hayato Yoshioka [aut] ,
Julie Aubert [aut, cre] ,
Tristan Mary-Huard [aut]
Maintainer: Julie Aubert <julie.aubert@inrae.fr>
Diff between rrda versions 0.1.1 dated 2025-04-29 and 0.2.3 dated 2025-10-15
DESCRIPTION | 17 +- MD5 | 22 +-- NAMESPACE | 3 R/cv.R | 18 +- R/graphs.R | 236 ++++++++++++++++++++++++++++++++++++++- man/figures |only man/get_lambda.Rd | 11 + man/rrda.cv.Rd | 11 + man/rrda.heatmap.Rd | 4 man/rrda.plot.Rd | 4 man/rrda.top.Rd |only tests/testing_RCMD_hayato.Rmd | 4 tests/testthat/test-rrda_graph.R | 98 ++++++++++++++++ 13 files changed, 397 insertions(+), 31 deletions(-)
Title: R Bindings for Calling the 'Earth Engine' API
Description: Earth Engine <https://earthengine.google.com/> client library for R. All
of the 'Earth Engine' API classes, modules, and functions are made available. Additional
functions implemented include importing (exporting) of Earth Engine spatial objects,
extraction of time series, interactive map display, assets management interface,
and metadata display. See <https://r-spatial.github.io/rgee/> for further details.
Author: Cesar Aybar [aut] ,
Wu Qiusheng [ctb] ,
Lesly Bautista [ctb] ,
Roy Yali [ctb] ,
Antony Barja [ctb] ,
Kevin Ushey [ctb],
Jeroen Ooms [ctb] ,
Tim Appelhans [ctb],
JJ Allaire [ctb],
Yuan Tang [ctb],
Samapriya Roy [ctb],
MariaElena Adauto [ctb] ,
Gabriel [...truncated...]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between rgee versions 1.1.7 dated 2023-09-27 and 1.1.8 dated 2025-10-15
rgee-1.1.7/rgee/inst/python/__pycache__ |only rgee-1.1.8/rgee/DESCRIPTION | 48 rgee-1.1.8/rgee/MD5 | 104 rgee-1.1.8/rgee/NEWS.md | 13 rgee-1.1.8/rgee/R/Deprecated.R | 18 rgee-1.1.8/rgee/R/ee_Initialize.R | 10 rgee-1.1.8/rgee/R/ee_as_sf.R | 18 rgee-1.1.8/rgee/R/ee_check.R | 2 rgee-1.1.8/rgee/R/ee_download.R | 4 rgee-1.1.8/rgee/R/ee_image.R | 64 rgee-1.1.8/rgee/R/ee_imagecollection.R | 42 rgee-1.1.8/rgee/R/ee_install.R | 8 rgee-1.1.8/rgee/R/ee_utils.R | 9 rgee-1.1.8/rgee/R/ee_version.R | 2 rgee-1.1.8/rgee/R/utils-auth.R | 2 rgee-1.1.8/rgee/R/utils-upload.R | 20 rgee-1.1.8/rgee/build/vignette.rds |binary rgee-1.1.8/rgee/inst/WORDLIST | 506 ++-- rgee-1.1.8/rgee/inst/dataset.json | 2 rgee-1.1.8/rgee/inst/devtools_internal_tests.R |only rgee-1.1.8/rgee/inst/doc/rgee01.R | 52 rgee-1.1.8/rgee/inst/doc/rgee01.html | 8 rgee-1.1.8/rgee/inst/doc/rgee02.R | 2 rgee-1.1.8/rgee/inst/doc/rgee02.html | 4 rgee-1.1.8/rgee/inst/doc/rgee03.R | 1412 ++++++------- rgee-1.1.8/rgee/inst/doc/rgee03.html | 28 rgee-1.1.8/rgee/inst/doc/rgee04.R | 74 rgee-1.1.8/rgee/inst/doc/rgee04.Rmd | 3 rgee-1.1.8/rgee/inst/doc/rgee04.html | 16 rgee-1.1.8/rgee/inst/doc/rgee05.R | 148 - rgee-1.1.8/rgee/inst/doc/rgee05.html | 50 rgee-1.1.8/rgee/inst/doc/rgee06.R | 140 - rgee-1.1.8/rgee/inst/doc/rgee06.Rmd | 10 rgee-1.1.8/rgee/inst/doc/rgee06.html | 21 rgee-1.1.8/rgee/man/ee_Authenticate.Rd | 2 rgee-1.1.8/rgee/man/ee_Initialize.Rd | 2 rgee-1.1.8/rgee/man/ee_as_rast.Rd | 18 rgee-1.1.8/rgee/man/ee_as_raster.Rd | 18 rgee-1.1.8/rgee/man/ee_as_sf.Rd | 18 rgee-1.1.8/rgee/man/ee_as_stars.Rd | 50 rgee-1.1.8/rgee/man/ee_as_thumbnail.Rd | 2 rgee-1.1.8/rgee/man/ee_drive_to_local.Rd | 2 rgee-1.1.8/rgee/man/ee_gcs_to_local.Rd | 2 rgee-1.1.8/rgee/man/ee_imagecollection_to_local.Rd | 46 rgee-1.1.8/rgee/man/ee_install.Rd | 6 rgee-1.1.8/rgee/man/ee_install_set_pyenv.Rd | 6 rgee-1.1.8/rgee/man/ee_install_upgrade.Rd | 4 rgee-1.1.8/rgee/man/ee_utils_cog_metadata.Rd | 6 rgee-1.1.8/rgee/man/rgee-package.Rd | 7 rgee-1.1.8/rgee/tests/testthat/test-ee_utils_get_crs_web.R |only rgee-1.1.8/rgee/vignettes/rgee04.Rmd | 3 rgee-1.1.8/rgee/vignettes/rgee06.Rmd | 10 52 files changed, 1527 insertions(+), 1515 deletions(-)
Title: Develop Clinical Prediction Models Using the Common Data Model
Description: A user friendly way to create patient level prediction models using
the Observational Medical Outcomes Partnership Common Data Model. Given a cohort
of interest and an outcome of interest, the package can use data in the Common
Data Model to build a large set of features. These features can then be used to
fit a predictive model with a number of machine learning algorithms. This is
further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Author: Egill Fridgeirsson [aut, cre],
Jenna Reps [aut],
Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Peter Rijnbeek [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Egill Fridgeirsson <e.fridgeirsson@erasmusmc.nl>
Diff between PatientLevelPrediction versions 6.5.0 dated 2025-07-25 and 6.5.1 dated 2025-10-15
PatientLevelPrediction-6.5.0/PatientLevelPrediction/inst/sql/postgresql/Migration_1-store_version.sql |only PatientLevelPrediction-6.5.1/PatientLevelPrediction/DESCRIPTION | 18 PatientLevelPrediction-6.5.1/PatientLevelPrediction/MD5 | 145 +++---- PatientLevelPrediction-6.5.1/PatientLevelPrediction/NEWS.md | 10 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/AdditionalCovariates.R | 15 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/DatabaseMigration.R | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/ExistingSklearn.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/ExtractData.R | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/GradientBoostingMachine.R | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/HelperFunctions.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/Plotting.R | 195 +++++++--- PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/SaveLoadPlp.R | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/R/SklearnClassifierHelpers.R | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/build/vignette.rds |binary PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomFeatureEngineering.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomSamples.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/AddingCustomSplitting.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BenchmarkTasks.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BestPractices.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BuildingMultiplePredictiveModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/BuildingPredictiveModels.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/ClinicalModels.html | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/ConstrainedPredictors.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingLearningCurves.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.Rmd | 54 -- PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.html | 195 +--------- PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/GISExample.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/doc/InstallationGuide.html | 6 PatientLevelPrediction-6.5.1/PatientLevelPrediction/inst/sql/postgresql/migrations |only PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createDatabaseDetails.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createLearningCurve.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createPlpResultTables.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createRareFeatureRemover.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/createSampleSettings.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/diagnosePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/externalValidateDbPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getCohortCovariateData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getEunomiaPlpData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/getPlpData.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/insertResultsToSqlite.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/outcomeSurvivalPlot.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotDemographicSummary.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotF1Measure.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotGeneralizability.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotLearningCurve.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotNetBenefit.Rd | 14 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPrecisionRecall.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPredictedPDF.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPredictionDistribution.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotPreferencePDF.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSmoothCalibration.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseCalibration.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseCalibration2.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotSparseRoc.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/plotVariableScatterplot.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/runMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setGradientBoostingMachine.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setIterativeHardThresholding.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/setLightGBM.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/validateExternal.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/validateMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewDatabaseResultPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewMultiplePlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/man/viewPlp.Rd | 2 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/setup.R | 124 +++++- PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-UploadToDatabase.R | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-evaluation.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-plotting.R | 38 + PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnClassifier.R | 3 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnClassifierSettings.R | 4 PatientLevelPrediction-6.5.1/PatientLevelPrediction/tests/testthat/test-sklearnJson.R | 1 PatientLevelPrediction-6.5.1/PatientLevelPrediction/vignettes/CreatingNetworkStudies.Rmd | 54 -- PatientLevelPrediction-6.5.1/PatientLevelPrediction/vignettes/maintainers |only 75 files changed, 537 insertions(+), 520 deletions(-)
More information about PatientLevelPrediction at CRAN
Permanent link
Title: Machine Learning Experiments
Description: Provides 'R6' objects to perform parallelized hyperparameter
optimization and cross-validation. Hyperparameter optimization can be
performed with Bayesian optimization (via 'ParBayesianOptimization'
<https://cran.r-project.org/package=ParBayesianOptimization>) and grid
search. The optimized hyperparameters can be validated using k-fold
cross-validation. Alternatively, hyperparameter optimization and
validation can be performed with nested cross-validation. While
'mlexperiments' focuses on core wrappers for machine learning
experiments, additional learner algorithms can be supplemented by
inheriting from the provided learner base class.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlexperiments versions 0.0.7 dated 2025-09-09 and 0.0.8 dated 2025-10-15
DESCRIPTION | 7 MD5 | 32 - R/MLNestedCV.R | 13 R/MLTuneParameters.R | 21 R/cv_helper_base.R | 29 - R/cv_helper_nested.R | 20 R/ml_helper_base.R | 50 +- R/optimizer_helper_bayesian.R | 62 +- R/tune_helper_base.R | 55 +- R/utils_metrics.R | 668 +++++++++++++-------------- build/vignette.rds |binary inst/doc/mlexperiments_knn_binary.html | 180 +++++-- inst/doc/mlexperiments_knn_multiclass.html | 180 +++++-- inst/doc/mlexperiments_rpart_binary.html | 180 +++++-- inst/doc/mlexperiments_rpart_multiclass.html | 180 +++++-- inst/doc/mlexperiments_rpart_regression.html | 180 +++++-- inst/doc/mlexperiments_starter.html | 180 +++++-- 17 files changed, 1376 insertions(+), 661 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.6.1 dated 2025-09-25 and 0.6.2 dated 2025-10-15
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- R/alloc_dmd.R | 3 ++ README.md | 2 + inst/doc/get_started.html | 24 ++++++++++----------- inst/doc/user_cases.html | 52 +++++++++++++++++++++++----------------------- 6 files changed, 51 insertions(+), 46 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.5 dated 2025-10-10 and 1.5.1 dated 2025-10-15
gdverse-1.5.1/gdverse/DESCRIPTION | 6 gdverse-1.5.1/gdverse/MD5 | 45 - gdverse-1.5.1/gdverse/NEWS.md | 214 +++-- gdverse-1.5.1/gdverse/R/rgd.R | 13 gdverse-1.5.1/gdverse/R/rid.R | 13 gdverse-1.5.1/gdverse/R/robustdisc.R | 13 gdverse-1.5.1/gdverse/inst/doc/consistency.html | 5 gdverse-1.5.1/gdverse/inst/doc/gd.Rmd | 862 ++++++++++++------------ gdverse-1.5.1/gdverse/inst/doc/gd.html | 5 gdverse-1.5.1/gdverse/inst/doc/idsa.Rmd | 2 gdverse-1.5.1/gdverse/inst/doc/idsa.html | 7 gdverse-1.5.1/gdverse/inst/doc/opgd.html | 5 gdverse-1.5.1/gdverse/inst/doc/rgdrid.html | 5 gdverse-1.5.1/gdverse/inst/doc/sesu.html | 5 gdverse-1.5.1/gdverse/inst/doc/shegd.html | 5 gdverse-1.5.1/gdverse/inst/doc/spade.Rmd | 441 ++++++------ gdverse-1.5.1/gdverse/inst/doc/spade.html | 34 gdverse-1.5.1/gdverse/man/rgd.Rd | 13 gdverse-1.5.1/gdverse/man/rid.Rd | 13 gdverse-1.5.1/gdverse/man/robust_disc.Rd | 13 gdverse-1.5.1/gdverse/vignettes/gd.Rmd | 862 ++++++++++++------------ gdverse-1.5.1/gdverse/vignettes/idsa.Rmd | 2 gdverse-1.5.1/gdverse/vignettes/spade.Rmd | 441 ++++++------ gdverse-1.5/gdverse/inst/python/__pycache__ |only 24 files changed, 1519 insertions(+), 1505 deletions(-)
Title: Globally-Applicable Area Disaggregated General Ecosystem Toolbox
V3
Description: A framework to assist creation of marine ecosystem models,
generating either 'R' or 'C++' code which can then be optimised using
the 'TMB' package and standard 'R' tools. Principally designed to
reproduce gadget2 models in 'TMB', but can be extended beyond
gadget2's capabilities.
Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.".
Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Author: Jamie Lentin [aut, cre] ,
Bjarki Thor Elvarsson [aut] ,
William Butler [aut] ,
Marine and Freshwater Research Institute [cph]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between gadget3 versions 0.13-0 dated 2025-04-19 and 0.14-0 dated 2025-10-15
gadget3-0.13-0/gadget3/inst/doc/random-effects.R |only gadget3-0.13-0/gadget3/inst/doc/random-effects.Rmd |only gadget3-0.13-0/gadget3/inst/doc/random-effects.html |only gadget3-0.13-0/gadget3/vignettes/random-effects.Rmd |only gadget3-0.14-0/gadget3/DESCRIPTION | 16 gadget3-0.14-0/gadget3/MD5 | 228 ++++----- gadget3-0.14-0/gadget3/NAMESPACE | 9 gadget3-0.14-0/gadget3/NEWS.md | 21 gadget3-0.14-0/gadget3/R/aab_env.R | 25 gadget3-0.14-0/gadget3/R/action_age.R | 7 gadget3-0.14-0/gadget3/R/action_grow.R | 38 + gadget3-0.14-0/gadget3/R/action_mature.R | 123 +--- gadget3-0.14-0/gadget3/R/action_migrate.R | 9 gadget3-0.14-0/gadget3/R/action_predate.R | 24 gadget3-0.14-0/gadget3/R/action_renewal.R | 27 - gadget3-0.14-0/gadget3/R/action_spawn.R | 9 gadget3-0.14-0/gadget3/R/action_tagging.R | 2 gadget3-0.14-0/gadget3/R/action_time.R | 2 gadget3-0.14-0/gadget3/R/action_trace.R |only gadget3-0.14-0/gadget3/R/action_weightloss.R | 4 gadget3-0.14-0/gadget3/R/array_utils.R | 50 + gadget3-0.14-0/gadget3/R/debug_utils.R | 2 gadget3-0.14-0/gadget3/R/eval.R | 4 gadget3-0.14-0/gadget3/R/formula_utils.R | 3 gadget3-0.14-0/gadget3/R/headtail.R |only gadget3-0.14-0/gadget3/R/init_val.R | 25 gadget3-0.14-0/gadget3/R/param_project.R | 252 +++++----- gadget3-0.14-0/gadget3/R/params.R | 12 gadget3-0.14-0/gadget3/R/quota.R | 53 +- gadget3-0.14-0/gadget3/R/run.R | 25 gadget3-0.14-0/gadget3/R/run_r.R | 9 gadget3-0.14-0/gadget3/R/run_tmb.R | 100 +++ gadget3-0.14-0/gadget3/R/step.R | 149 ++++- gadget3-0.14-0/gadget3/R/test_utils.R | 110 ++-- gadget3-0.14-0/gadget3/R/timedata.R | 2 gadget3-0.14-0/gadget3/README.md | 5 gadget3-0.14-0/gadget3/build/vignette.rds |binary gadget3-0.14-0/gadget3/inst/doc/incorporating-observation-data.R | 30 - gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.R | 56 +- gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.Rmd | 13 gadget3-0.14-0/gadget3/inst/doc/introduction-single-stock.html | 45 + gadget3-0.14-0/gadget3/inst/doc/model-customisation.R | 10 gadget3-0.14-0/gadget3/inst/doc/model-debugging.R | 82 ++- gadget3-0.14-0/gadget3/inst/doc/model-debugging.Rmd | 120 +++- gadget3-0.14-0/gadget3/inst/doc/model-debugging.html | 158 ++++-- gadget3-0.14-0/gadget3/inst/doc/model-structure.html | 66 ++ gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.R | 137 +++-- gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.Rmd | 115 ++-- gadget3-0.14-0/gadget3/inst/doc/multiple-substocks.html | 136 +++-- gadget3-0.14-0/gadget3/inst/doc/writing_actions.R | 24 gadget3-0.14-0/gadget3/inst/doc/writing_actions.html | 11 gadget3-0.14-0/gadget3/man/aaa_lang.Rd | 6 gadget3-0.14-0/gadget3/man/aab_env.Rd | 4 gadget3-0.14-0/gadget3/man/action_renewal.Rd | 22 gadget3-0.14-0/gadget3/man/action_trace.Rd |only gadget3-0.14-0/gadget3/man/action_weightloss.Rd | 2 gadget3-0.14-0/gadget3/man/array_utils.Rd | 14 gadget3-0.14-0/gadget3/man/init_val.Rd | 1 gadget3-0.14-0/gadget3/man/param_project.Rd | 58 +- gadget3-0.14-0/gadget3/man/quota.Rd | 130 +++-- gadget3-0.14-0/gadget3/man/run_tmb.Rd | 46 + gadget3-0.14-0/gadget3/man/step.Rd | 9 gadget3-0.14-0/gadget3/tests/test-aab_env.R | 70 +- gadget3-0.14-0/gadget3/tests/test-action_age.R | 47 - gadget3-0.14-0/gadget3/tests/test-action_grow-methods.R | 4 gadget3-0.14-0/gadget3/tests/test-action_grow-weightjones.R |only gadget3-0.14-0/gadget3/tests/test-action_grow.R | 53 -- gadget3-0.14-0/gadget3/tests/test-action_mature.R | 52 -- gadget3-0.14-0/gadget3/tests/test-action_migrate.R | 31 - gadget3-0.14-0/gadget3/tests/test-action_naturalmortality.R | 27 - gadget3-0.14-0/gadget3/tests/test-action_predate-catchability.R | 22 gadget3-0.14-0/gadget3/tests/test-action_predate-catchability_project.R |only gadget3-0.14-0/gadget3/tests/test-action_predate-numberfleet.R | 13 gadget3-0.14-0/gadget3/tests/test-action_predate-predator.R | 10 gadget3-0.14-0/gadget3/tests/test-action_predate-timebasedsuitability.R | 4 gadget3-0.14-0/gadget3/tests/test-action_predate.R | 70 -- gadget3-0.14-0/gadget3/tests/test-action_renewal-otherfood.R | 7 gadget3-0.14-0/gadget3/tests/test-action_renewal.R | 51 -- gadget3-0.14-0/gadget3/tests/test-action_report.R | 39 - gadget3-0.14-0/gadget3/tests/test-action_spawn-multipleoutputs.R | 8 gadget3-0.14-0/gadget3/tests/test-action_spawn.R | 16 gadget3-0.14-0/gadget3/tests/test-action_tagging.R | 36 - gadget3-0.14-0/gadget3/tests/test-action_time.R | 72 -- gadget3-0.14-0/gadget3/tests/test-action_trace-timing.R |only gadget3-0.14-0/gadget3/tests/test-action_weightloss.R | 6 gadget3-0.14-0/gadget3/tests/test-array_utils.R | 33 + gadget3-0.14-0/gadget3/tests/test-env_dif.R | 5 gadget3-0.14-0/gadget3/tests/test-formula_utils.R | 4 gadget3-0.14-0/gadget3/tests/test-init_val.R | 25 gadget3-0.14-0/gadget3/tests/test-likelihood_bounds.R | 44 + gadget3-0.14-0/gadget3/tests/test-likelihood_distribution-surveyindices.R | 13 gadget3-0.14-0/gadget3/tests/test-likelihood_distribution.R | 93 +-- gadget3-0.14-0/gadget3/tests/test-likelihood_random.R | 25 gadget3-0.14-0/gadget3/tests/test-likelihood_sparsesample.R | 4 gadget3-0.14-0/gadget3/tests/test-likelihood_tagging_ckmr.R | 27 - gadget3-0.14-0/gadget3/tests/test-param_project-ar1.R | 174 ++++-- gadget3-0.14-0/gadget3/tests/test-param_project-logar1.R | 190 ++++--- gadget3-0.14-0/gadget3/tests/test-param_project.R | 181 ++++--- gadget3-0.14-0/gadget3/tests/test-params.R | 15 gadget3-0.14-0/gadget3/tests/test-quota-assess.R | 10 gadget3-0.14-0/gadget3/tests/test-quota-hockeyfleet.R | 243 ++++++--- gadget3-0.14-0/gadget3/tests/test-regression.R | 4 gadget3-0.14-0/gadget3/tests/test-run_r.R | 16 gadget3-0.14-0/gadget3/tests/test-run_tmb-reporting_enabled.R | 4 gadget3-0.14-0/gadget3/tests/test-run_tmb.R | 130 +++-- gadget3-0.14-0/gadget3/tests/test-step.R | 100 +++ gadget3-0.14-0/gadget3/tests/test-stock.R | 23 gadget3-0.14-0/gadget3/tests/test-stock_age.R | 31 - gadget3-0.14-0/gadget3/tests/test-stock_areas.R | 15 gadget3-0.14-0/gadget3/tests/test-stock_tag.R | 7 gadget3-0.14-0/gadget3/tests/test-stock_time-fishingyear.R | 3 gadget3-0.14-0/gadget3/tests/test-stock_time.R | 26 - gadget3-0.14-0/gadget3/tests/test-suitability-report.R | 10 gadget3-0.14-0/gadget3/tests/test-suitability.R | 24 gadget3-0.14-0/gadget3/tests/test-timedata.R | 22 gadget3-0.14-0/gadget3/tests/test-timevariable.R | 18 gadget3-0.14-0/gadget3/vignettes/introduction-single-stock.Rmd | 13 gadget3-0.14-0/gadget3/vignettes/model-debugging.Rmd | 120 +++- gadget3-0.14-0/gadget3/vignettes/multiple-substocks.Rmd | 115 ++-- gadget3-0.14-0/gadget3/vignettes/random-effect-recruitment.R |only gadget3-0.14-0/gadget3/vignettes/random-effect-recruitment.html |only 121 files changed, 2932 insertions(+), 2113 deletions(-)
Title: Estimation of Cell Infiltration Based on Cell Crosstalk
Description: A systematic biology tool was developed to identify cell infiltration via Individualized Cell-Cell interaction network. 'CITMIC' first constructed a weighted cell interaction network through integrating Cell-target interaction information, molecular function data from Gene Ontology (GO) database and gene transcriptomic data in specific sample, and then, it used a network propagation algorithm on the network to identify cell infiltration for the sample. Ultimately, cell infiltration in the patient dataset was obtained by normalizing the centrality scores of the cells.
Author: Junwei Han [aut, cre, cph],
Xilong Zhao [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between CITMIC versions 0.1.2 dated 2024-11-08 and 0.1.3 dated 2025-10-15
CITMIC-0.1.2/CITMIC/man/figures |only CITMIC-0.1.3/CITMIC/DESCRIPTION | 8 +-- CITMIC-0.1.3/CITMIC/MD5 | 17 +++----- CITMIC-0.1.3/CITMIC/R/CITMIC.R | 32 +++++++-------- CITMIC-0.1.3/CITMIC/build/vignette.rds |binary CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.R | 7 --- CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.Rmd | 13 ++---- CITMIC-0.1.3/CITMIC/inst/doc/CITMIC.html | 63 ++++++++++++------------------- CITMIC-0.1.3/CITMIC/man/CITMIC.Rd | 2 CITMIC-0.1.3/CITMIC/vignettes/CITMIC.Rmd | 13 ++---- 10 files changed, 65 insertions(+), 90 deletions(-)
Title: Testing for Partial Copulas and the Simplifying Assumption in
Vine Copulas
Description: Routines for two different test types, the Constant Conditional Correlation (CCC) test and the Vectorial Independence (VI) test are provided (Kurz and Spanhel (2022) <doi:10.1214/22-EJS2051>). The tests can be applied to check whether a conditional copula coincides with its partial copula. Functions to test whether a regular vine copula satisfies the so-called simplifying assumption or to test a single copula within a regular vine copula to be a (j-1)-th order partial copula are available. The CCC test comes with a decision tree approach to allow testing in high-dimensional settings.
Author: Malte S. Kurz [aut, cre]
Maintainer: Malte S. Kurz <mkurz-software@gmx.de>
Diff between pacotest versions 0.4.2 dated 2022-11-04 and 0.4.3 dated 2025-10-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 +++++- README.md | 2 +- inst/CITATION | 9 ++++----- src/Grouping.cpp | 21 ++++++++++++++++----- src/pacotestFunctions.cpp | 2 +- 7 files changed, 36 insertions(+), 22 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 Neste [...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 3.7.0 dated 2025-03-06 and 3.7.1 dated 2025-10-15
DESCRIPTION | 13 MD5 | 18 NEWS | 3 R/longiPenal.R | 217 ++-- build/vignette.rds |binary inst/doc/Package_summary.html | 2276 +++++++++++++++++++++--------------------- man/frailtypack-package.Rd | 2 man/longiPenal.Rd | 113 +- src/funcpajlongisplines.f90 | 2 src/joint_longi.f90 | 4 10 files changed, 1405 insertions(+), 1243 deletions(-)
Title: Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Description: Package computes and displays tables with support for 'SPSS'-style
labels, multiple and nested banners, weights, multiple-response variables
and significance testing. There are facilities for nice output of tables
in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods
for labelled variables add value labels support to base R functions and to
some functions from other packages. Additionally, the package brings
popular data transformation functions from 'SPSS' Statistics and 'Excel':
'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc.
These functions are very useful for data processing in marketing research
surveys. Package intended to help people to move data
processing from 'Excel' and 'SPSS' to R.
Author: Gregory Demin [aut, cre],
Sebastian Jeworutzki [ctb] ,
Dan Chaltiel [ctb],
John Williams [ctb],
Tom Elliott [ctb]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.11.6 dated 2023-07-15 and 0.11.7 dated 2025-10-15
DESCRIPTION | 11 ++- MD5 | 112 +++++++++++++++++++-------------------- NAMESPACE | 7 ++ NEWS | 6 +- R/S3_methods.R | 4 - R/compute.R | 12 ++-- R/count_if.R | 8 +- R/criteria_functions.R | 72 ++++++++++++------------- R/cross.R | 32 +++++------ R/cross_fun.R | 29 +++++----- R/custom_tables.R | 72 ++++++++++++------------- R/dichotomy.R | 10 +-- R/expss.R | 50 ++++++++--------- R/expss_options.R | 20 +++--- R/if_na.R | 12 ++-- R/labels.R | 32 +++++------ R/mrset.R | 12 ++-- R/product_test.R | 38 ++++++------- R/qc.R | 6 +- R/recode.R | 24 ++++---- R/selectors.R | 32 +++++------ R/significance_cpct.R | 47 ++++++++-------- R/sum.R | 2 R/vec_ops.R | 32 +++++------ R/weighted_stats.R | 26 ++++----- R/window_fun.R | 3 - R/write_labelled.R | 41 ++++++-------- build/vignette.rds |binary inst/doc/examples.R | 50 ++++++++--------- inst/doc/examples.html | 4 - inst/doc/labels-support.R | 20 +++--- inst/doc/labels-support.html | 10 +-- inst/doc/tables-with-labels.R | 10 +-- inst/doc/tables-with-labels.html | 4 - inst/doc/xlsx-export.R | 8 +- inst/doc/xlsx-export.html | 8 +- man/as.dichotomy.Rd | 10 +-- man/compute.Rd | 12 ++-- man/count_if.Rd | 8 +- man/criteria.Rd | 70 ++++++++++++------------ man/cross_cases.Rd | 24 ++++---- man/cross_fun.Rd | 27 ++++----- man/expss.Rd | 52 +++++++++--------- man/expss.options.Rd | 20 +++--- man/if_na.Rd | 12 ++-- man/mrset.Rd | 12 ++-- man/product_test.Rd | 38 ++++++------- man/qc.Rd | 6 +- man/recode.Rd | 24 ++++---- man/significance.Rd | 48 ++++++++-------- man/tables.Rd | 72 ++++++++++++------------- man/val_lab.Rd | 18 +++--- man/var_lab.Rd | 14 ++-- man/vars.Rd | 32 +++++------ man/vectors.Rd | 32 +++++------ man/w_mean.Rd | 26 ++++----- man/write_labelled_csv.Rd | 41 ++++++-------- 57 files changed, 741 insertions(+), 723 deletions(-)
Title: Proximity Measure Based Diagnostics for Standard, Soft, and
Multi-Way Clustering
Description: Quantifies clustering quality by measuring both cohesion within clusters and separation between clusters. Implements advanced silhouette width computations for diverse clustering structures, including: simplified silhouette (Van der Laan et al., 2003) <doi:10.1080/0094965031000136012>, Probability of Alternative Cluster normalization methods (Raymaekers & Rousseeuw, 2022) <doi:10.1080/10618600.2022.2050249>, fuzzy clustering and silhouette diagnostics using membership probabilities (Campello & Hruschka, 2006; Menardi, 2011; Bhat & Kiruthika, 2024) <doi:10.1016/j.fss.2006.07.006>, <doi:10.1007/s11222-010-9169-0>, <doi:10.1080/23737484.2024.2408534>, and multi-way clustering extensions such as block and tensor clustering (Schepers et al., 2008; Bhat & Kiruthika, 2025) <doi:10.1007/s00357-008-9005-9>, <doi:10.21203/rs.3.rs-6973596/v1>. Provides tools for computation and visualization (Rousseeuw, 1987) <doi:10.1016/0377-0427(87)9 [...truncated...]
Author: Shrikrishna Bhat K [aut, cre, cph] ,
Kiruthika C [aut]
Maintainer: Shrikrishna Bhat K <skbhat.in@gmail.com>
Diff between Silhouette versions 0.9.4 dated 2025-07-30 and 0.9.6 dated 2025-10-15
Silhouette-0.9.4/Silhouette/R/summary.silhouette.R |only Silhouette-0.9.6/Silhouette/DESCRIPTION | 19 Silhouette-0.9.6/Silhouette/MD5 | 68 Silhouette-0.9.6/Silhouette/NAMESPACE | 27 Silhouette-0.9.6/Silhouette/NEWS.md | 47 Silhouette-0.9.6/Silhouette/R/Silhouette-package.R |only Silhouette-0.9.6/Silhouette/R/Silhouette.R | 216 -- Silhouette-0.9.6/Silhouette/R/calSilhouette.R |only Silhouette-0.9.6/Silhouette/R/cerSilhouette.R |only Silhouette-0.9.6/Silhouette/R/dbSilhouette.R |only Silhouette-0.9.6/Silhouette/R/extSilhouette.R | 9 Silhouette-0.9.6/Silhouette/R/getSilhouette.R |only Silhouette-0.9.6/Silhouette/R/is.Silhouette.R |only Silhouette-0.9.6/Silhouette/R/plotSilhouette.R | 497 ++-- Silhouette-0.9.6/Silhouette/R/softSilhouette.R | 106 Silhouette-0.9.6/Silhouette/R/summary.Silhouette.R |only Silhouette-0.9.6/Silhouette/README.md | 75 Silhouette-0.9.6/Silhouette/inst/CITATION |only Silhouette-0.9.6/Silhouette/inst/WORDLIST | 20 Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.R | 327 ++- Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.Rmd | 641 +++++ Silhouette-0.9.6/Silhouette/inst/doc/Silhouette.html | 1071 +++++++--- Silhouette-0.9.6/Silhouette/man/Silhouette-package.Rd |only Silhouette-0.9.6/Silhouette/man/Silhouette.Rd | 68 Silhouette-0.9.6/Silhouette/man/calSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/cerSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/dbSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/extSilhouette.Rd | 5 Silhouette-0.9.6/Silhouette/man/figures |only Silhouette-0.9.6/Silhouette/man/getSilhouette.Rd |only Silhouette-0.9.6/Silhouette/man/is.Silhouette.Rd |only Silhouette-0.9.6/Silhouette/man/plotSilhouette.Rd | 251 +- Silhouette-0.9.6/Silhouette/man/softSilhouette.Rd | 37 Silhouette-0.9.6/Silhouette/tests/testthat.R | 24 Silhouette-0.9.6/Silhouette/tests/testthat/test-cerSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-dbSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-extSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-getSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-is.Silhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-plotSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-silhouette.R | 305 ++ Silhouette-0.9.6/Silhouette/tests/testthat/test-softSilhouette.R |only Silhouette-0.9.6/Silhouette/tests/testthat/test-summary.silhouette.R |only Silhouette-0.9.6/Silhouette/vignettes/Silhouette.Rmd | 641 +++++ Silhouette-0.9.6/Silhouette/vignettes/references.bib | 11 45 files changed, 3327 insertions(+), 1138 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
This is a re-admission after prior archival of version 0.7.5 dated 2025-09-29
Diff between sentopics versions 0.7.5 dated 2025-09-29 and 0.7.6 dated 2025-10-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/conversions.R | 1 + man/as.LDA.Rd | 1 + tests/testthat.R | 4 +++- 6 files changed, 18 insertions(+), 10 deletions(-)
Title: Rho for Inter Rater Reliability
Description: Rho is used to test the generalization of inter rater reliability
(IRR) statistics. Calculating rho starts by generating a large number of
simulated, fully-coded data sets: a sizable collection of hypothetical
populations, all of which have a kappa value below a given threshold -- which
indicates unacceptable agreement. Then kappa is calculated on a sample from
each of those sets in the collection to see if it is equal to or higher than
the kappa in then real sample. If less than five percent of the distribution
of samples from the simulated data sets is greater than actual observed kappa,
the null hypothesis is rejected and one can conclude that if the two raters had
coded the rest of the data, we would have acceptable agreement (kappa above the
threshold).
Author: Brendan Eagan [aut],
Brad Rogers [aut],
Rebecca Pozen [aut],
Cody L Marquart [cre, aut] ,
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rhoR versions 1.3.0.3 dated 2020-09-13 and 1.3.1 dated 2025-10-15
rhoR-1.3.0.3/rhoR/data/codeSet.csv |only rhoR-1.3.0.3/rhoR/data/contingencyTable.csv |only rhoR-1.3.1/rhoR/DESCRIPTION | 11 +++--- rhoR-1.3.1/rhoR/MD5 | 34 ++++++++++----------- rhoR-1.3.1/rhoR/NEWS.md | 3 + rhoR-1.3.1/rhoR/R/rho.R | 3 + rhoR-1.3.1/rhoR/R/rho.file.R | 3 + rhoR-1.3.1/rhoR/R/rhoCT.R | 3 + rhoR-1.3.1/rhoR/R/rhoSet.R | 6 ++- rhoR-1.3.1/rhoR/README.md | 19 ++++++++--- rhoR-1.3.1/rhoR/data/codeSet.csv.gz |only rhoR-1.3.1/rhoR/data/contingencyTable.csv.gz |only rhoR-1.3.1/rhoR/inst/_pkgdown.yml | 8 ++-- rhoR-1.3.1/rhoR/man/rho.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rho.file.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rhoCT.Rd | 7 +++- rhoR-1.3.1/rhoR/man/rhoK.Rd | 2 - rhoR-1.3.1/rhoR/man/rhoSet.Rd | 7 +++- rhoR-1.3.1/rhoR/src/RcppExports.cpp | 5 +++ rhoR-1.3.1/rhoR/tests/testthat/test-util-methods.R | 6 +-- 20 files changed, 82 insertions(+), 49 deletions(-)
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Sebastian Fischer [aut, cre] ,
Maximilian Muecke [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3fda versions 0.2.0 dated 2024-07-22 and 0.3.0 dated 2025-10-15
mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpCor.R |only mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpScaleRange.R |only mlr3fda-0.3.0/mlr3fda/DESCRIPTION | 30 ++- mlr3fda-0.3.0/mlr3fda/MD5 | 81 ++++++---- mlr3fda-0.3.0/mlr3fda/NAMESPACE | 6 mlr3fda-0.3.0/mlr3fda/NEWS.md | 10 + mlr3fda-0.3.0/mlr3fda/R/PipeOpFDABsignal.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDACor.R | 4 mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAExtract.R | 27 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAFlatten.R | 26 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAInterpol.R | 58 +++---- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDARandomEffect.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAScaleRange.R | 28 +-- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDASmooth.R | 24 +- mlr3fda-0.3.0/mlr3fda/R/PipeOpFDATsfeatures.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAWavelets.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFDAZoom.R |only mlr3fda-0.3.0/mlr3fda/R/PipeOpFPCA.R | 13 - mlr3fda-0.3.0/mlr3fda/R/TaskRegr_dti.R | 2 mlr3fda-0.3.0/mlr3fda/R/TaskRegr_fuel.R | 2 mlr3fda-0.3.0/mlr3fda/R/bibentries.R | 3 mlr3fda-0.3.0/mlr3fda/R/zzz.R | 39 +--- mlr3fda-0.3.0/mlr3fda/README.md | 45 +++-- mlr3fda-0.3.0/mlr3fda/build/partial.rdb |binary mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.bsignal.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.cor.Rd | 4 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.extract.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.flatten.Rd | 2 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.fpca.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.interpol.Rd | 10 - mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.random_effect.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.scalerange.Rd | 8 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.smooth.Rd | 4 mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.tsfeats.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.wavelets.Rd |only mlr3fda-0.3.0/mlr3fda/man/mlr_pipeops_fda.zoom.Rd |only mlr3fda-0.3.0/mlr3fda/tests/testthat/_snaps |only mlr3fda-0.3.0/mlr3fda/tests/testthat/helper.R | 6 mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDABsignal.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDACor.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAExtract.R | 33 +--- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAFlatten.R | 20 +- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAInterpolate.R | 57 +++---- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDARandomEffect.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAScaleRange.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDASmooth.R | 32 ++- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDATsfeatures.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAWavelets.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAZoom.R |only mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFPCA.R | 17 +- mlr3fda-0.3.0/mlr3fda/tests/testthat/test_tf.R | 2 51 files changed, 327 insertions(+), 282 deletions(-)
Title: Synthesizing Causal Evidence in a Distributed Research Network
Description: Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data.
Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
Author: Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Fan Bu [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EvidenceSynthesis versions 1.0.0 dated 2025-08-26 and 1.1.0 dated 2025-10-15
DESCRIPTION | 16 MD5 | 61 +-- NAMESPACE | 1 NEWS.md | 12 R/BayesianMetaAnalysis.R | 34 + R/EvidenceSynthesis.R | 2 R/FixedEffectMetaAnalysis.R | 5 R/LikelihoodApproximation.R | 2 R/MetaAnalysis.R | 301 +++++++++------- R/Plots.R | 26 - README.md | 4 inst/doc/BayesianBiasCorrection.pdf |binary inst/doc/NonNormalEffectSynthesis.pdf |binary inst/doc/VideoVignette.pdf |binary man/computeBayesianMetaAnalysis.Rd | 5 man/computeFixedEffectMetaAnalysis.Rd | 5 man/plotLikelihoodFit.Rd | 4 man/plotMcmcTrace.Rd | 5 man/plotMetaAnalysisForest.Rd | 11 man/plotPerDbMcmcTrace.Rd | 5 man/plotPerDbPosterior.Rd | 5 man/plotPosterior.Rd | 5 tests/testthat/resources/gsPredictionInterval.rds |only tests/testthat/resources/pooledFixedFxEstimate.rds |binary tests/testthat/resources/pooledRandomFxEstimate.rds |binary tests/testthat/resources/populations.rds |binary tests/testthat/resources/sccsPooledFixedFxEstimate.rds |binary tests/testthat/resources/sccsPooledRandomFxEstimate.rds |binary tests/testthat/resources/sccsPopulations.rds |binary tests/testthat/resources/tracesForPi.rds |only tests/testthat/test-nonNormalMetaAnalysis.R | 28 - tests/testthat/test-plots.R | 10 tests/testthat/test_predictionInterval.R |only 33 files changed, 340 insertions(+), 207 deletions(-)
More information about EvidenceSynthesis at CRAN
Permanent link
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut] ,
Jasper Cooper [aut] ,
Alexander Coppock [aut, cre] ,
Macartan Humphreys [aut] ,
Neal Fultz [aut]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between DeclareDesign versions 1.0.10 dated 2024-04-21 and 1.1.0 dated 2025-10-15
DeclareDesign-1.0.10/DeclareDesign/man/edit.Rd |only DeclareDesign-1.0.10/DeclareDesign/man/expand_conditions.Rd |only DeclareDesign-1.1.0/DeclareDesign/DESCRIPTION | 36 DeclareDesign-1.1.0/DeclareDesign/MD5 | 152 +-- DeclareDesign-1.1.0/DeclareDesign/NAMESPACE | 12 DeclareDesign-1.1.0/DeclareDesign/NEWS.md | 7 DeclareDesign-1.1.0/DeclareDesign/R/DeclareDesign.R | 2 DeclareDesign-1.1.0/DeclareDesign/R/aaa.R | 434 ++++++++-- DeclareDesign-1.1.0/DeclareDesign/R/compare_diagnoses.R | 364 ++++---- DeclareDesign-1.1.0/DeclareDesign/R/declare_assignment.R | 4 DeclareDesign-1.1.0/DeclareDesign/R/declare_diagnosands.R | 2 DeclareDesign-1.1.0/DeclareDesign/R/declare_estimator.R | 215 ++-- DeclareDesign-1.1.0/DeclareDesign/R/declare_inquiry.R | 17 DeclareDesign-1.1.0/DeclareDesign/R/declare_measurement.R | 8 DeclareDesign-1.1.0/DeclareDesign/R/declare_model.R | 58 - DeclareDesign-1.1.0/DeclareDesign/R/declare_potential_outcomes.R | 322 ++----- DeclareDesign-1.1.0/DeclareDesign/R/declare_sampling.R | 3 DeclareDesign-1.1.0/DeclareDesign/R/declare_test.R | 5 DeclareDesign-1.1.0/DeclareDesign/R/design_helper_functions.R | 3 DeclareDesign-1.1.0/DeclareDesign/R/design_print_summary.R | 22 DeclareDesign-1.1.0/DeclareDesign/R/diagnose_design.R | 380 +++++--- DeclareDesign-1.1.0/DeclareDesign/R/diagnosis_helper_functions.R | 7 DeclareDesign-1.1.0/DeclareDesign/R/expand_design.R | 24 DeclareDesign-1.1.0/DeclareDesign/R/modify_design.R | 4 DeclareDesign-1.1.0/DeclareDesign/R/modify_edit.R | 152 ++- DeclareDesign-1.1.0/DeclareDesign/R/object_handlers.R |only DeclareDesign-1.1.0/DeclareDesign/R/redesign.R | 36 DeclareDesign-1.1.0/DeclareDesign/R/select_diagnosands.R |only DeclareDesign-1.1.0/DeclareDesign/R/simulate_design.R | 19 DeclareDesign-1.1.0/DeclareDesign/R/utilities.R | 24 DeclareDesign-1.1.0/DeclareDesign/build |only DeclareDesign-1.1.0/DeclareDesign/inst/doc |only DeclareDesign-1.1.0/DeclareDesign/man/DeclareDesign-deprecated.Rd | 6 DeclareDesign-1.1.0/DeclareDesign/man/DeclareDesign.Rd | 38 DeclareDesign-1.1.0/DeclareDesign/man/compare_diagnoses.Rd | 10 DeclareDesign-1.1.0/DeclareDesign/man/declare_assignment.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/declare_estimator.Rd | 42 DeclareDesign-1.1.0/DeclareDesign/man/declare_inquiry.Rd | 11 DeclareDesign-1.1.0/DeclareDesign/man/declare_internal_inherit_params.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/declare_measurement.Rd | 15 DeclareDesign-1.1.0/DeclareDesign/man/declare_model.Rd | 58 - DeclareDesign-1.1.0/DeclareDesign/man/declare_potential_outcomes.Rd | 28 DeclareDesign-1.1.0/DeclareDesign/man/declare_reveal.Rd | 12 DeclareDesign-1.1.0/DeclareDesign/man/declare_sampling.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/declare_test.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/diagnose_design.Rd | 71 - DeclareDesign-1.1.0/DeclareDesign/man/expand_design.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/find_all_objects.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/modify_design.Rd | 4 DeclareDesign-1.1.0/DeclareDesign/man/modify_edit.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/redesign.Rd | 8 DeclareDesign-1.1.0/DeclareDesign/man/select_diagnosands.Rd |only DeclareDesign-1.1.0/DeclareDesign/man/simulate_design.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/man/tidy.diagnosis.Rd | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat.R | 10 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-allow-custom-functions.R | 4 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-alternative-df-compatibility.R | 24 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-assignment.R | 10 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-bootstrap-diagnosands.R | 9 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-citation.R | 3 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-compare-designs.R | 3 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-compare-diagnoses.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-demo.R | 13 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-describe_variable.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-design-library.R | 171 +++ DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-design-summary.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-diagnosands.R | 15 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-diagnose-design.R | 24 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-environment-issues.R | 15 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-environments.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-fanout.R | 6 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-find-objects.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-multiple-estimands-one-estimator.R | 2 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-multiple-pos.R | 12 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-potential-outcomes.R | 282 ++++-- DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-redesign.R | 223 ++++- DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-reshape-diagnosis.R | 21 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-reveal-outcomes.R | 14 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-select-diagnosands.R |only DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-simulate-design.R | 33 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-test.R | 7 DeclareDesign-1.1.0/DeclareDesign/tests/testthat/test-utilities.R | 14 DeclareDesign-1.1.0/DeclareDesign/vignettes |only 83 files changed, 2311 insertions(+), 1237 deletions(-)
Title: Tools to Use and Explore the 'BioTIME' Database
Description: The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.
Author: Alban Sagouis [aut, cre] ,
Faye Moyes [aut] ,
Ines S. Martins [aut, rev] ,
Shane A. Blowes [ctb] ,
Viviana Brambilla [ctb] ,
Cher F. Y. Chow [ctb] ,
Ada Fontrodona-Eslava [ctb] ,
Laura Antao [ctb, rev] ,
Jonathan M. Chase [fnd] ,
Maria Dornelas [fnd, [...truncated...]
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
Diff between BioTIMEr versions 0.2.5 dated 2025-09-19 and 0.2.6 dated 2025-10-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/vignette1.html | 10 +++++----- tests/testthat/test-metrics.R | 8 ++++---- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: Background-Parallel Jobs
Description: Easily launch, track, and control functions as
background-parallel jobs. Includes robust utilities for job status,
error handling, resource monitoring, and result collection. Designed
for scalable workflows in interactive and automated settings (local or
remote). Integrates with multiple backends; supports flexible
automation pipelines and live job tracking. For more information, see
<https://anirbanshaw24.github.io/bakerrr/>.
Author: Anirban Shaw [aut, cre]
Maintainer: Anirban Shaw <anirbanshaw24@gmail.com>
Diff between bakerrr versions 0.1.0 dated 2025-10-01 and 0.2.0 dated 2025-10-15
DESCRIPTION | 10 + MD5 | 35 +++--- NEWS.md | 6 - R/01_bakerrr.R | 78 +++++++++++++-- R/print.R | 36 +++--- R/summary.R | 28 ++--- README.md | 182 ++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/multi_function.R |only inst/doc/multi_function.Rmd |only inst/doc/multi_function.html |only inst/doc/simple_example.html | 80 +++++++++------ inst/doc/vs_mirai.R | 20 +-- inst/doc/vs_mirai.Rmd | 20 +-- inst/doc/vs_mirai.html | 117 ++++++++++------------ inst/pkgdown.yml | 3 tests/testthat/test-bakerrr_class.R | 2 tests/testthat/test-multi_function.R |only vignettes/multi_function.Rmd |only vignettes/vs_mirai.Rmd | 20 +-- 21 files changed, 433 insertions(+), 208 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-26 2.1.0
2024-11-15 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-29 0.7.5
2024-09-20 0.7.4
2024-04-18 0.7.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-01 2.0
2023-02-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-16 1.2.0
2025-02-21 1.1.0
2025-01-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-08 1.15.1
2025-01-12 1.14.1
2024-08-16 1.13.11
2023-12-18 1.13.10
2023-09-22 1.13.8
2023-08-25 1.13.6
2023-06-19 1.13.3
2023-03-23 1.13.1
2022-11-07 1.12.2
2022-08-31 1.12.0
2022-06-16 1.11.1
2022-03-22 1.10.3
2022-02-22 1.10.1
2021-11-21 1.9.2
2021-11-12 1.9.1
2021-08-11 1.8.1
2021-04-26 1.7.2
2021-03-25 1.7.1
2021-01-10 1.6.5
2020-12-17 1.6.2
2020-12-17 1.6.3
2020-08-10 1.5.1
2020-06-11 1.4.1
2020-05-13 1.3.1
2020-01-09 1.2.1
2019-10-29 1.1.1
2019-06-28 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-05 1.2.1
2025-01-10 1.1.1
2024-12-19 1.1.0
2024-08-20 1.0.2
2024-04-08 1.0.1
2024-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-17 1.2.1
2024-01-20 1.2.0
2023-03-19 1.1.0
2023-02-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-29 0.1.1
2024-01-29 0.1.2
2024-01-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 0.1.9
2020-03-13 0.1.8
2020-02-01 0.1.7
2019-12-16 0.1.6
2019-11-16 0.1.5
2019-08-01 0.1.4
2019-06-24 0.1.3
2019-06-09 0.1.2
2019-04-22 0.1.1
2019-04-07 0.1.0
Title: Robust Regression and Estimation Through Maximum Mean
Discrepancy Minimization
Description: The functions in this package compute robust estimators by minimizing a kernel-based distance known as MMD (Maximum Mean Discrepancy) between the sample and a statistical model. Recent works proved that these estimators enjoy a universal consistency property, and are extremely robust to outliers. Various optimization algorithms are implemented: stochastic gradient is available for most models, but the package also allows gradient descent in a few models for which an exact formula is available for the gradient. In terms of distribution fit, a large number of continuous and discrete distributions are available: Gaussian, exponential, uniform, gamma, Poisson, geometric, etc. In terms of regression, the models available are: linear, logistic, gamma, beta and Poisson.
Alquier, P. and Gerber, M. (2024) <doi:10.1093/biomet/asad031>
Cherief-Abdellatif, B.-E. and Alquier, P. (2022) <doi:10.3150/21-BEJ1338>.
Author: Pierre Alquier [aut, cre] ,
Mathieu Gerber [aut]
Maintainer: Pierre Alquier <pierre.alquier.stat@gmail.com>
Diff between regMMD versions 0.0.1 dated 2024-10-25 and 0.0.2 dated 2025-10-15
DESCRIPTION | 11 ++++---- MD5 | 56 +++++++++++++++++++++--------------------- R/Beta_hat.R | 4 +-- R/Beta_tilde.R | 4 +-- R/Gamma_hat.R | 4 +-- R/Gamma_tilde.R | 4 +-- R/LG_hat.R | 8 +++--- R/LG_tilde.R | 8 +++--- R/Logistic_hat.R | 2 - R/Logistic_tilde.R | 2 - R/Poisson_hat.R | 2 - R/Poisson_tilde.R | 2 - R/estimation_function.R | 3 +- R/models_Cauchy.R | 6 +++- R/models_Dirac.R | 6 +++- R/models_Gaussian.R | 20 ++++++++++++--- R/models_Pareto.R | 6 +++- R/models_Poisson.R | 8 +++++- R/models_beta.R | 6 +++- R/models_binomial.R | 33 +++++++++++++++++++----- R/models_continuous_uniform.R | 24 +++++++++++++++--- R/models_discrete_uniform.R | 4 ++- R/models_gamma.R | 18 +++++++++++-- R/models_geometric.R | 8 +++++- R/models_multidim_Dirac.R | 6 +++- R/models_multidim_Gaussian.R | 26 ++++++++++++++++--- R/reg_function.R | 28 ++++++++++----------- build/partial.rdb |binary man/mmd_est.Rd | 1 29 files changed, 212 insertions(+), 98 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.16.0 dated 2025-09-19 and 0.17.0 dated 2025-10-15
progressr-0.16.0/progressr/tests/debug.R |only progressr-0.16.0/progressr/tests/demo.R |only progressr-0.16.0/progressr/tests/exceptions.R |only progressr-0.16.0/progressr/tests/globals,relay.R |only progressr-0.16.0/progressr/tests/handler_cli.R |only progressr-0.16.0/progressr/tests/handler_filesize.R |only progressr-0.16.0/progressr/tests/handler_make_progression.R |only progressr-0.16.0/progressr/tests/handler_pbmcapply.R |only progressr-0.16.0/progressr/tests/handler_progress.R |only progressr-0.16.0/progressr/tests/handler_rstudio.R |only progressr-0.16.0/progressr/tests/handler_shiny.R |only progressr-0.16.0/progressr/tests/handler_tkprogressbar.R |only progressr-0.16.0/progressr/tests/handler_txtprogressbar.R |only progressr-0.16.0/progressr/tests/handlers.R |only progressr-0.16.0/progressr/tests/incl |only progressr-0.16.0/progressr/tests/progress_aggregator.R |only progressr-0.16.0/progressr/tests/progression.R |only progressr-0.16.0/progressr/tests/progressor.R |only progressr-0.16.0/progressr/tests/utils.R |only progressr-0.16.0/progressr/tests/with_progress,delay.R |only progressr-0.16.0/progressr/tests/with_progress,relay.R |only progressr-0.16.0/progressr/tests/with_progress.R |only progressr-0.16.0/progressr/tests/without_progress.R |only progressr-0.16.0/progressr/tests/zzz,doFuture.R |only progressr-0.16.0/progressr/tests/zzz,foreach_do.R |only progressr-0.16.0/progressr/tests/zzz,furrr.R |only progressr-0.16.0/progressr/tests/zzz,future.apply.R |only progressr-0.16.0/progressr/tests/zzz,plyr.R |only progressr-0.16.0/progressr/tests/zzz,purrr.R |only progressr-0.16.0/progressr/tests/zzz,shiny.R |only progressr-0.17.0/progressr/DESCRIPTION | 6 progressr-0.17.0/progressr/MD5 | 136 ++++++---- progressr-0.17.0/progressr/NEWS.md | 19 + progressr-0.17.0/progressr/R/global_progression_handler.R | 15 - progressr-0.17.0/progressr/R/handler_cli.R | 2 progressr-0.17.0/progressr/R/handler_rpushbullet.R | 4 progressr-0.17.0/progressr/R/make_calling_handler.R | 2 progressr-0.17.0/progressr/R/options.R | 4 progressr-0.17.0/progressr/R/progress_aggregator.R | 7 progressr-0.17.0/progressr/R/rstudio-console.R | 15 - progressr-0.17.0/progressr/R/testme.R |only progressr-0.17.0/progressr/R/warn_about_too_many_progressions.R |only progressr-0.17.0/progressr/R/with_progress.R | 29 +- progressr-0.17.0/progressr/R/without_progress.R | 5 progressr-0.17.0/progressr/inst/doc/progressr-91-appendix.html | 12 progressr-0.17.0/progressr/inst/doc/progressr-91-appendix.md | 10 progressr-0.17.0/progressr/inst/testme |only progressr-0.17.0/progressr/man/with_progress.Rd | 5 progressr-0.17.0/progressr/tests/test-debug.R |only progressr-0.17.0/progressr/tests/test-demo.R |only progressr-0.17.0/progressr/tests/test-exceptions.R |only progressr-0.17.0/progressr/tests/test-globals,relay.R |only progressr-0.17.0/progressr/tests/test-handler_cli.R |only progressr-0.17.0/progressr/tests/test-handler_filesize.R |only progressr-0.17.0/progressr/tests/test-handler_make_progression.R |only progressr-0.17.0/progressr/tests/test-handler_pbmcapply.R |only progressr-0.17.0/progressr/tests/test-handler_progress.R |only progressr-0.17.0/progressr/tests/test-handler_rstudio.R |only progressr-0.17.0/progressr/tests/test-handler_shiny.R |only progressr-0.17.0/progressr/tests/test-handler_tkprogressbar.R |only progressr-0.17.0/progressr/tests/test-handler_txtprogressbar.R |only progressr-0.17.0/progressr/tests/test-handlers.R |only progressr-0.17.0/progressr/tests/test-progress_aggregator.R |only progressr-0.17.0/progressr/tests/test-progression.R |only progressr-0.17.0/progressr/tests/test-progressor.R |only progressr-0.17.0/progressr/tests/test-utils.R |only progressr-0.17.0/progressr/tests/test-with_progress,delay.R |only progressr-0.17.0/progressr/tests/test-with_progress,relay.R |only progressr-0.17.0/progressr/tests/test-with_progress.R |only progressr-0.17.0/progressr/tests/test-without_progress.R |only progressr-0.17.0/progressr/tests/test-zzz,doFuture.R |only progressr-0.17.0/progressr/tests/test-zzz,foreach_do.R |only progressr-0.17.0/progressr/tests/test-zzz,furrr.R |only progressr-0.17.0/progressr/tests/test-zzz,future.apply.R |only progressr-0.17.0/progressr/tests/test-zzz,plyr.R |only progressr-0.17.0/progressr/tests/test-zzz,purrr.R |only progressr-0.17.0/progressr/tests/test-zzz,shiny.R |only progressr-0.17.0/progressr/vignettes/progressr-91-appendix.md | 10 78 files changed, 188 insertions(+), 93 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering several procedures), omnibus tests for
univariate normality, functions to compute the multivariate skewness, kurtosis, the
Mahalanobis distance (checking the positive defineteness), and t [...truncated...]
Author: Felipe Osorio [aut, cre] ,
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <faosorios.stat@gmail.com>
Diff between fastmatrix versions 0.6 dated 2025-07-07 and 0.6-2 dated 2025-10-15
ChangeLog | 8 +++++ DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++++++----------------- NAMESPACE | 6 ++-- R/RNG.R | 6 ++-- R/bezier.R | 4 +- R/ccc.R | 20 +++++++------- R/condition.R | 2 - R/floyd.R |only R/fnc_matrix.R |only R/harris.R | 12 +++++--- R/jarque.bera.R | 4 ++ R/krylov.R | 2 - R/polymat.R | 2 - R/root_matrix.R | 38 +++++++++++++++++----------- R/schur.R |only R/symmetrizer.R | 2 - R/whitening.R | 2 - R/wilson_hilferty.R | 4 +- inst/CITATION | 4 +- inst/include/fastmatrix.h | 3 +- inst/include/fastmatrix_API.h | 11 +++++++- man/floyd.Rd |only man/matrix.fun.Rd |only man/matrix.sqrt.Rd | 18 +++++++++---- man/schur.Rd |only src/R_init_fastmatrix.c | 12 +++++++- src/fastmatrix.h | 16 ++++++++++- src/floyd_warshall.f |only src/fnc_matrix.f |only src/matrix_API.c | 21 ++++++++++++++- src/schur.c |only src/schur_decomp.f |only src/sqrt_matrix.c | 57 +++++++++++++++++++++++++++++++++++++----- 34 files changed, 226 insertions(+), 92 deletions(-)
Title: Finding Recurrent DNA Copy Number Alterations and Differences
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. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
can be found at <doi: 10.1093/bioinformatics/ [...truncated...]
Author: Vonn Walter [aut, cre] ,
Hyo Young Choi [aut] ,
Xiaobei Zhao [aut] ,
Yan Gao [aut] ,
David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between DiNAMIC.Duo versions 1.0.3 dated 2025-04-03 and 1.0.4 dated 2025-10-15
DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS.md | 9 +++++++++ R/dataPrep.R | 19 ++++++++++++------- R/findNull.R | 2 +- man/dataPrep.Rd | 8 ++++---- man/findNull.Rd | 2 +- 8 files changed, 45 insertions(+), 31 deletions(-)
Title: Crop Growing Degree Days and Agrometeorological Calculations
Description: Calculate agrometeorological variables for crops
including growing degree days (McMaster, GS & Wilhelm, WW
(1997) <doi:10.1016/S0168-1923(97)00027-0>), cumulative
rainfall, number of stress days and cumulative or mean
radiation and evaporation. Convert dates to day of year
and vice versa. Also, download curated and interpolated
Australian weather data from the Queensland Government
DES longpaddock website
<https://www.longpaddock.qld.gov.au/>. This data is
freely available under the Creative Commons 4.0 licence.
Author: Peter Baker [aut, cre] ,
Miranda Mortlock [aut]
Maintainer: Peter Baker <drpetebaker@gmail.com>
Diff between cropgrowdays versions 0.2.1 dated 2024-03-12 and 0.2.2 dated 2025-10-15
DESCRIPTION | 12 +++++----- MD5 | 34 ++++++++++++++--------------- NEWS.md | 9 +++++++ R/cumulative.R | 2 - R/get_multi_silodata.R | 2 - R/growing_degree_days.R | 4 +-- README.md | 8 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/crop-grow-days.R | 42 ++++++++++++++++++------------------- inst/doc/crop-grow-days.html | 7 ++---- inst/doc/getting-weather-data.R | 30 +++++++++++++------------- man/cumulative.Rd | 2 - man/fragments/agro_met_calcs.Rmd | 2 - man/fragments/auto/cropgrowdays.el | 6 ++++- man/fragments/cropgrowdays.bib | 17 +++++++------- man/get_multi_silodata.Rd | 2 - man/growing_degree_days.Rd | 4 +-- 18 files changed, 97 insertions(+), 86 deletions(-)