Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.6.0 dated 2024-06-27 and 0.6.1 dated 2025-02-16
waywiser-0.6.0/waywiser/tests/testthat/_snaps/multi_scale.md |only waywiser-0.6.1/waywiser/DESCRIPTION | 8 - waywiser-0.6.1/waywiser/MD5 | 69 ++++------ waywiser-0.6.1/waywiser/NEWS.md | 6 waywiser-0.6.1/waywiser/R/multi_scale.R | 2 waywiser-0.6.1/waywiser/R/tidy_importance.R | 3 waywiser-0.6.1/waywiser/build/partial.rdb |binary waywiser-0.6.1/waywiser/build/vignette.rds |binary waywiser-0.6.1/waywiser/inst/doc/multi-scale-assessment.html | 12 - waywiser-0.6.1/waywiser/inst/doc/residual-autocorrelation.html | 6 waywiser-0.6.1/waywiser/inst/doc/waywiser.html | 56 ++++---- waywiser-0.6.1/waywiser/inst/srr_template_spatial_yardstick.R | 66 ++++++--- waywiser-0.6.1/waywiser/man/figures/README-unnamed-chunk-5-1.png |binary waywiser-0.6.1/waywiser/tests/testthat/_snaps/area_of_applicability.md | 18 +- waywiser-0.6.1/waywiser/tests/testthat/_snaps/misc.md | 9 + waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_geary_c.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_geary_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_moran_i.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_moran_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_geary_c.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_geary_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_getis_ord_g.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_getis_ord_g_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_moran_i.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_moran_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/test-multi_scale.R | 5 waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_geary_c.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_geary_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_moran_i.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_moran_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_geary_c.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_geary_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_getis_ord_g.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_getis_ord_g_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_moran_i.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_moran_pvalue.R | 66 ++++++--- 36 files changed, 948 insertions(+), 282 deletions(-)
Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor Analysis (EFA), making it easier to determine the number of factors. Traditional methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>, Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis (PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA are readily available. This package also implements several newer methods, such as the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017) <doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012) <doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011) <doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like Comparison Data Forest (CDF) by Goretzko and Ruscio (2024) <doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between EFAfactors versions 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-02-16
DESCRIPTION | 8 ++-- MD5 | 75 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 6 +++ R/CD.R | 28 +++++++------- R/CDF.R | 60 +++++++++++++++++++------------- R/EFAhclust.R | 16 ++++---- R/EFAindex.R | 4 +- R/EFAkmeans.R | 16 ++++---- R/EFAscreet.R | 4 +- R/EFAvote.R | 2 - R/EKC.R | 20 +++++----- R/GenData.R | 7 ++- R/Hull.R | 20 +++++----- R/KGC.R | 16 ++++---- R/PA.R | 20 +++++----- R/extractor.feature.DNN.R | 4 +- R/extractor.feature.FF.R | 32 +++++++++++++---- R/factor.analysis.R | 26 +++++++++---- man/CD.Rd | 28 +++++++------- man/CDF.Rd | 6 ++- man/EFAhclust.Rd | 16 ++++---- man/EFAindex.Rd | 4 +- man/EFAkmeans.Rd | 16 ++++---- man/EFAscreet.Rd | 4 +- man/EFAvote.Rd | 2 - man/EKC.Rd | 20 +++++----- man/GenData.Rd | 4 +- man/Hull.Rd | 20 +++++----- man/KGC.Rd | 16 ++++---- man/PA.Rd | 20 +++++----- man/extractor.feature.DNN.Rd | 4 +- man/extractor.feature.FF.Rd | 4 +- man/factor.analysis.Rd | 16 ++++---- src/Makevars | 2 - src/Makevars.win | 2 - tests/building.R | 2 - tests/testthat/demo_simulate.R | 14 +++---- tests/testthat/demo_simulate2.R |only 39 files changed, 306 insertions(+), 259 deletions(-)
Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on
sparse matrices - matrix factorizations, matrix completion,
elastic net regressions, factorization machines.
Also 'rsparse' enhances 'Matrix' package by providing methods for
multithreaded <sparse, dense> matrix products and native slicing of
the sparse matrices in Compressed Sparse Row (CSR) format.
List of the algorithms for regression problems:
1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL)
Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>)
2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>)
List of algorithms for matrix factorization and matrix completion:
1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least
Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>)
2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro
(2005, <doi:10.1145/110 [...truncated...]
Author: Dmitriy Selivanov [aut, cre, cph]
,
David Cortes [ctb],
Drew Schmidt [ctb] ,
Wei-Chen Chen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between rsparse versions 0.5.2 dated 2024-06-28 and 0.5.3 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/model_LinearFlow.R | 1 - R/zzz.R | 24 ++++++++++-------------- README.md | 4 ++-- man/LinearFlow.Rd | 1 - src/utils.cpp | 4 ++-- 7 files changed, 23 insertions(+), 29 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to
impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable
selection and statistical inference. In this package, we have implemented robust
Bayesian variable selection with spike-and-slab priors under high-dimensional
linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms
of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.5 dated 2025-02-05 and 1.1.0 dated 2025-02-16
pqrBayes-1.0.5/pqrBayes/R/Robust.R |only pqrBayes-1.0.5/pqrBayes/R/select.VC.R |only pqrBayes-1.0.5/pqrBayes/man/print.VCselect.Rd |only pqrBayes-1.0.5/pqrBayes/man/select.VC.Rd |only pqrBayes-1.1.0/pqrBayes/DESCRIPTION | 28 - pqrBayes-1.1.0/pqrBayes/MD5 | 68 ++- pqrBayes-1.1.0/pqrBayes/NAMESPACE | 24 - pqrBayes-1.1.0/pqrBayes/NEWS.md |only pqrBayes-1.1.0/pqrBayes/R/NonRobust.R | 150 ++++---- pqrBayes-1.1.0/pqrBayes/R/NonRobust_vc.R |only pqrBayes-1.1.0/pqrBayes/R/RcppExports.R | 16 pqrBayes-1.1.0/pqrBayes/R/Robust_vc.R |only pqrBayes-1.1.0/pqrBayes/R/coverage.R | 62 --- pqrBayes-1.1.0/pqrBayes/R/coverage_lin.R |only pqrBayes-1.1.0/pqrBayes/R/coverage_vc.R |only pqrBayes-1.1.0/pqrBayes/R/data.R | 40 +- pqrBayes-1.1.0/pqrBayes/R/estimation.R | 107 +----- pqrBayes-1.1.0/pqrBayes/R/estimation_lin.R |only pqrBayes-1.1.0/pqrBayes/R/estimation_vc.R |only pqrBayes-1.1.0/pqrBayes/R/nonrobust_lin.R |only pqrBayes-1.1.0/pqrBayes/R/pqrBayes-package.R | 120 +++--- pqrBayes-1.1.0/pqrBayes/R/pqrBayes.R | 194 ++++++----- pqrBayes-1.1.0/pqrBayes/R/pqrBayes_lin.R |only pqrBayes-1.1.0/pqrBayes/R/pqrBayes_vc.R |only pqrBayes-1.1.0/pqrBayes/R/predict.pqrBayes.R | 152 ++------ pqrBayes-1.1.0/pqrBayes/R/predict_lin.R |only pqrBayes-1.1.0/pqrBayes/R/predict_vc.R |only pqrBayes-1.1.0/pqrBayes/R/print.pqrBayes.R | 105 +++-- pqrBayes-1.1.0/pqrBayes/R/robust_lin.R |only pqrBayes-1.1.0/pqrBayes/R/select.pqrBayes.R |only pqrBayes-1.1.0/pqrBayes/R/select_lin.R |only pqrBayes-1.1.0/pqrBayes/R/select_vc.R |only pqrBayes-1.1.0/pqrBayes/README.md | 334 +++++++++++-------- pqrBayes-1.1.0/pqrBayes/data/data.rda |binary pqrBayes-1.1.0/pqrBayes/man/coverage.Rd | 18 - pqrBayes-1.1.0/pqrBayes/man/data.Rd | 36 +- pqrBayes-1.1.0/pqrBayes/man/estimation.pqrBayes.Rd | 20 - pqrBayes-1.1.0/pqrBayes/man/pqrBayes-package.Rd | 24 - pqrBayes-1.1.0/pqrBayes/man/pqrBayes.Rd | 76 ++-- pqrBayes-1.1.0/pqrBayes/man/predict.pqrBayes.Rd | 33 - pqrBayes-1.1.0/pqrBayes/man/print.pqrBayes.Rd | 6 pqrBayes-1.1.0/pqrBayes/man/print.pqrBayes.select.Rd |only pqrBayes-1.1.0/pqrBayes/man/select.pqrBayes.Rd |only pqrBayes-1.1.0/pqrBayes/src/BL.cpp |only pqrBayes-1.1.0/pqrBayes/src/BLSS.cpp |only pqrBayes-1.1.0/pqrBayes/src/BQL.cpp |only pqrBayes-1.1.0/pqrBayes/src/BQLSS.cpp |only pqrBayes-1.1.0/pqrBayes/src/RcppExports.cpp | 114 ++++++ 48 files changed, 907 insertions(+), 820 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.23 dated 2024-11-24 and 3.29 dated 2025-02-16
DESCRIPTION | 8 - MD5 | 48 +++++----- NAMESPACE | 5 - NEWS | 118 +++++++++++++++++++++++++ R/AUC.R | 70 ++++++++------- R/Boyce.R | 231 +++++++++++++++++++++++++------------------------- R/MillerCalib.R | 88 +++++++++---------- R/RsqGLM.R | 7 - R/lollipop.R | 93 ++++++++++++++------ R/optiPair.R | 141 +++++++++++++++--------------- R/optiThresh.R | 22 +--- R/plotCoeffs.R |only R/similarity.R | 4 R/threshMeasures.R | 6 - R/varImp.R | 151 +++++++++++++++++--------------- man/AUC.Rd | 4 man/Boyce.Rd | 160 +++++++++++++++++----------------- man/MillerCalib.Rd | 186 ++++++++++++++++++++-------------------- man/RMSE.Rd | 114 ++++++++++++------------ man/evaluate.Rd | 10 +- man/lollipop.Rd | 42 +++++---- man/modEvA-package.Rd | 4 man/optiPair.Rd | 165 ++++++++++++++++++----------------- man/optiThresh.Rd | 178 +++++++++++++++++++------------------- man/plotCoeffs.Rd |only man/varImp.Rd | 4 26 files changed, 1028 insertions(+), 831 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 1.3.0 dated 2024-10-30 and 2.0.0 dated 2025-02-16
mappeR-1.3.0/mappeR/R/stats_hub.R |only mappeR-1.3.0/mappeR/man/run_cluster_machine.Rd |only mappeR-1.3.0/mappeR/man/run_mapper.Rd |only mappeR-2.0.0/mappeR/DESCRIPTION | 6 mappeR-2.0.0/mappeR/LICENSE | 4 mappeR-2.0.0/mappeR/MD5 | 95 - mappeR-2.0.0/mappeR/NAMESPACE | 45 mappeR-2.0.0/mappeR/NEWS.md | 93 + mappeR-2.0.0/mappeR/R/art_studio.R | 112 +- mappeR-2.0.0/mappeR/R/baskin_robbins.R | 294 +++--- mappeR-2.0.0/mappeR/R/cartography_chamber.R | 530 +++++----- mappeR-2.0.0/mappeR/R/cluster_factory.R | 421 ++++---- mappeR-2.0.0/mappeR/R/clusterer_farm.R |only mappeR-2.0.0/mappeR/R/mappeR-package.R | 36 mappeR-2.0.0/mappeR/R/quilting_hut.R | 278 ++--- mappeR-2.0.0/mappeR/R/viewmaster-library.R | 56 - mappeR-2.0.0/mappeR/README.md | 586 ++++++------ mappeR-2.0.0/mappeR/man/assemble_mapper_object.Rd |only mappeR-2.0.0/mappeR/man/check_in_interval.Rd | 34 mappeR-2.0.0/mappeR/man/compute_tightness.Rd | 44 mappeR-2.0.0/mappeR/man/convert_to_clusters.Rd | 34 mappeR-2.0.0/mappeR/man/create_1D_mapper_object.Rd | 91 - mappeR-2.0.0/mappeR/man/create_ball_mapper_object.Rd | 58 - mappeR-2.0.0/mappeR/man/create_balls.Rd | 72 - mappeR-2.0.0/mappeR/man/create_bins.Rd | 42 mappeR-2.0.0/mappeR/man/create_clusterball_mapper_object.Rd | 83 - mappeR-2.0.0/mappeR/man/create_mapper_object.Rd | 112 +- mappeR-2.0.0/mappeR/man/create_single_bin.Rd | 42 mappeR-2.0.0/mappeR/man/create_width_balanced_cover.Rd | 70 - mappeR-2.0.0/mappeR/man/cut_dendrogram.Rd | 44 mappeR-2.0.0/mappeR/man/eccentricity_filter.Rd | 60 - mappeR-2.0.0/mappeR/man/get_bin_vector.Rd | 34 mappeR-2.0.0/mappeR/man/get_cluster_sizes.Rd | 34 mappeR-2.0.0/mappeR/man/get_cluster_tightness_vector.Rd | 38 mappeR-2.0.0/mappeR/man/get_clustered_data.Rd | 34 mappeR-2.0.0/mappeR/man/get_clusters.Rd | 44 mappeR-2.0.0/mappeR/man/get_edge_weights.Rd | 48 mappeR-2.0.0/mappeR/man/get_hierarchical_clusters.Rd | 40 mappeR-2.0.0/mappeR/man/get_raw_clusters.Rd |only mappeR-2.0.0/mappeR/man/get_tallest_branch.Rd | 34 mappeR-2.0.0/mappeR/man/hierarchical_clusterer.Rd |only mappeR-2.0.0/mappeR/man/is_in_ball.Rd | 34 mappeR-2.0.0/mappeR/man/mappeR-package.Rd | 46 mappeR-2.0.0/mappeR/man/mapper_object_to_igraph.Rd | 56 - mappeR-2.0.0/mappeR/man/process_dendrograms.Rd | 44 mappeR-2.0.0/mappeR/man/run_link.Rd | 38 mappeR-2.0.0/mappeR/man/subset_dists.Rd | 38 mappeR-2.0.0/mappeR/tests/testthat.R | 24 mappeR-2.0.0/mappeR/tests/testthat/test-binning.R | 50 - mappeR-2.0.0/mappeR/tests/testthat/test-covering.R | 176 +-- mappeR-2.0.0/mappeR/tests/testthat/test-igraph.R | 12 mappeR-2.0.0/mappeR/tests/testthat/test-inputs.R | 112 +- 52 files changed, 2143 insertions(+), 2135 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi'
(<https://www.jamovi.org>) aims to make statistical analyses easy and
intuitive. 'jamovi' produces syntax that can directly be used in R (in
connection with the R-package 'jmv'). Having import / export routines for
the data files 'jamovi' produces ('.omv') permits an easy transfer of
data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.4.9 dated 2025-01-16 and 0.4.10 dated 2025-02-16
DESCRIPTION | 6 MD5 | 24 +-- NEWS.md | 12 + R/describe_omv.R | 195 ++++++++++++++------------- R/globals.R | 94 ++++++++++--- R/read_omv.R | 279 +++++++++++++++++++--------------------- R/write_omv.R | 147 +++++++++------------ README.md | 4 inst/CITATION | 2 inst/doc/jmvReadWrite.html | 8 - tests/testthat/test-globals.R | 39 ++++- tests/testthat/test-read_omv.R | 163 +++++++++++++++++------ tests/testthat/test-write_omv.R | 94 ++++++++++++- 13 files changed, 653 insertions(+), 414 deletions(-)
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 4.2.0 dated 2024-10-15 and 4.2.1 dated 2025-02-16
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 7 +++++++ R/add_Cscale.R | 2 +- R/add_col.R | 4 ++-- R/add_labels.R | 2 +- R/create_Arrow.R | 5 +++++ R/load.R | 1 + README.md | 2 +- build/vignette.rds |binary data/Coast.RData |binary inst/doc/CCAMLRGIS.html | 4 ++-- man/add_Cscale.Rd | 2 +- man/add_col.Rd | 4 ++-- man/add_labels.Rd | 2 +- 15 files changed, 42 insertions(+), 29 deletions(-)
Title: Assessment Tools for Regression Models with Discrete and
Semicontinuous Outcomes
Description: Provides assessment tools for regression models with discrete and semicontinuous outcomes proposed in Yang (2023) <doi:10.48550/arXiv.2308.15596>. It calculates the double probability integral transform (DPIT) residuals, constructs QQ plots of residuals and the ordered curve for assessing mean structures.
Author: Lu Yang [aut],
Jeonghwan Lee [cre, aut]
Maintainer: Jeonghwan Lee <lee03938@umn.edu>
Diff between assessor versions 1.1.0 dated 2024-04-03 and 1.1.1 dated 2025-02-16
assessor-1.1.0/assessor/LICENSE |only assessor-1.1.1/assessor/DESCRIPTION | 12 ++++++------ assessor-1.1.1/assessor/MD5 | 6 ++++-- assessor-1.1.1/assessor/R/bballHR.R |only assessor-1.1.1/assessor/data/bballHR.rda |only assessor-1.1.1/assessor/man/bballHR.Rd |only 6 files changed, 10 insertions(+), 8 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.43 dated 2024-12-10 and 4.4.46 dated 2025-02-16
asremlPlus-4.4.43/asremlPlus/R/reml4.v11.r |only asremlPlus-4.4.43/asremlPlus/R/spatial.funcs.v10.r |only asremlPlus-4.4.43/asremlPlus/R/spatial.utilities.v3.r |only asremlPlus-4.4.46/asremlPlus/DESCRIPTION | 8 asremlPlus-4.4.46/asremlPlus/MD5 | 52 +-- asremlPlus-4.4.46/asremlPlus/R/REMLRTIC.v4.r | 14 asremlPlus-4.4.46/asremlPlus/R/asremlPlusObjUtils.r | 3 asremlPlus-4.4.46/asremlPlus/R/asremlPlusUtilities.r | 93 ++++- asremlPlus-4.4.46/asremlPlus/R/choose.r | 2 asremlPlus-4.4.46/asremlPlus/R/psplineUtilities.v2.R | 2 asremlPlus-4.4.46/asremlPlus/R/reml4.v13.r |only asremlPlus-4.4.46/asremlPlus/R/spatial.funcs.v11.r |only asremlPlus-4.4.46/asremlPlus/R/spatial.utilities.v4.r |only asremlPlus-4.4.46/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.46/asremlPlus/inst/NEWS.Rd | 18 + asremlPlus-4.4.46/asremlPlus/inst/doc/LadybirdEMMs.asreml.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/LadybirdEMMs.lm.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.46/asremlPlus/man/newfit.asreml.Rd | 16 asremlPlus-4.4.46/asremlPlus/man/setvarianceterms.call.Rd | 28 + asremlPlus-4.4.46/asremlPlus/tests/testthat/data/summ703.rda |binary asremlPlus-4.4.46/asremlPlus/tests/testthat/test42EstimateV.r | 36 +- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42GeneticCane.R | 19 - asremlPlus-4.4.46/asremlPlus/tests/testthat/test42REMLRTIC.r | 2 asremlPlus-4.4.46/asremlPlus/tests/testthat/test42Selection.r | 117 +++++- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42SpatialModels.r | 172 +++++++--- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 6 30 files changed, 426 insertions(+), 162 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.2 dated 2025-02-05 and 0.1.3 dated 2025-02-16
DESCRIPTION | 8 - MD5 | 40 ++--- inst/doc/a01_DatabaseDiagnostics.R | 2 inst/doc/a01_DatabaseDiagnostics.Rmd | 2 inst/doc/a01_DatabaseDiagnostics.html | 224 +++++++++++++++---------------- inst/doc/a02_CodelistDiagnostics.R | 2 inst/doc/a02_CodelistDiagnostics.Rmd | 2 inst/doc/a02_CodelistDiagnostics.html | 228 ++++++++++++++++---------------- inst/doc/a03_CohortDiagnostics.R | 2 inst/doc/a03_CohortDiagnostics.Rmd | 2 inst/doc/a03_CohortDiagnostics.html | 220 +++++++++++++++--------------- inst/doc/a04_MatchedDiagnostics.R | 2 inst/doc/a04_MatchedDiagnostics.Rmd | 2 inst/doc/a05_PopulationDiagnostics.R | 2 inst/doc/a05_PopulationDiagnostics.Rmd | 2 inst/doc/a05_PopulationDiagnostics.html | 226 +++++++++++++++---------------- vignettes/a01_DatabaseDiagnostics.Rmd | 2 vignettes/a02_CodelistDiagnostics.Rmd | 2 vignettes/a03_CohortDiagnostics.Rmd | 2 vignettes/a04_MatchedDiagnostics.Rmd | 2 vignettes/a05_PopulationDiagnostics.Rmd | 2 21 files changed, 488 insertions(+), 488 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library for reliable, high-performance messaging over in-process,
IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability
Protocols', a standard for common communications patterns including
publish/subscribe, request/reply and service discovery. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing. Intuitive 'aio' objects resolve automatically when
asynchronous operations complete, and synchronisation primitives allow R to
wait upon events signalled by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.5.0 dated 2025-01-27 and 1.5.1 dated 2025-02-16
nanonext-1.5.0/nanonext/cleanup.ucrt |only nanonext-1.5.0/nanonext/configure.ucrt |only nanonext-1.5.0/nanonext/src/Makevars.ucrt |only nanonext-1.5.0/nanonext/src/Makevars.win |only nanonext-1.5.1/nanonext/DESCRIPTION | 8 - nanonext-1.5.1/nanonext/MD5 | 64 +++++----- nanonext-1.5.1/nanonext/NAMESPACE | 1 nanonext-1.5.1/nanonext/NEWS.md | 10 + nanonext-1.5.1/nanonext/R/aio.R | 4 nanonext-1.5.1/nanonext/R/context.R | 4 nanonext-1.5.1/nanonext/R/listdial.R | 8 - nanonext-1.5.1/nanonext/R/nanonext-package.R | 10 + nanonext-1.5.1/nanonext/R/stream.R | 16 ++ nanonext-1.5.1/nanonext/R/sync.R | 60 --------- nanonext-1.5.1/nanonext/README.md | 20 +-- nanonext-1.5.1/nanonext/cleanup.win |only nanonext-1.5.1/nanonext/configure | 6 nanonext-1.5.1/nanonext/configure.win |only nanonext-1.5.1/nanonext/man/dial.Rd | 4 nanonext-1.5.1/nanonext/man/listen.Rd | 4 nanonext-1.5.1/nanonext/man/lock.Rd | 48 ------- nanonext-1.5.1/nanonext/man/pipe_notify.Rd | 14 -- nanonext-1.5.1/nanonext/man/recv_aio.Rd | 4 nanonext-1.5.1/nanonext/man/reply.Rd | 4 nanonext-1.5.1/nanonext/man/stream.Rd | 18 ++ nanonext-1.5.1/nanonext/src/aio.c | 26 ++-- nanonext-1.5.1/nanonext/src/comms.c | 34 ++--- nanonext-1.5.1/nanonext/src/init.c | 4 nanonext-1.5.1/nanonext/src/nanonext.h | 11 - nanonext-1.5.1/nanonext/src/ncurl.c | 10 - nanonext-1.5.1/nanonext/src/nng-110.tar.xz |binary nanonext-1.5.1/nanonext/src/proto.c | 21 +-- nanonext-1.5.1/nanonext/src/sync.c | 163 +++------------------------ nanonext-1.5.1/nanonext/src/thread.c | 6 nanonext-1.5.1/nanonext/src/utils.c | 34 ++--- nanonext-1.5.1/nanonext/tests/tests.R | 35 ----- 36 files changed, 217 insertions(+), 434 deletions(-)
Title: Regularized Joint Assignment Forest with Treatment Arm
Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] ,
Xinyi Zhang [aut, cre, cph] ,
Jann Spiess [aut, cph] ,
Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Diff between rjaf versions 0.1.1 dated 2024-12-08 and 0.1.2 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/residualize.R | 9 +++++---- R/rjaf.R | 40 +++++++++++++++++++++++++++------------- man/residualize.Rd | 7 ++++--- man/rjaf.Rd | 15 +++++++++------ src/rjaf.cpp | 10 ++++++++-- tests/testthat/test-rjaf.R | 2 +- 9 files changed, 66 insertions(+), 40 deletions(-)
Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening
Services
Description: Allows using two URL shortening services, which also provide
expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).
Author: John Malc [aut, cre] ,
Andrea Dodet [ctb] ,
Stephen Synchronicity [ctb]
Maintainer: John Malc <cincenko@outlook.com>
Diff between urlshorteneR versions 1.5.7 dated 2022-08-22 and 1.6.0 dated 2025-02-16
urlshorteneR-1.5.7/urlshorteneR/tests/testthat/test-GitHubIssue9.R |only urlshorteneR-1.6.0/urlshorteneR/DESCRIPTION | 24 - urlshorteneR-1.6.0/urlshorteneR/MD5 | 9 urlshorteneR-1.6.0/urlshorteneR/NEWS | 2 urlshorteneR-1.6.0/urlshorteneR/build/vignette.rds |binary urlshorteneR-1.6.0/urlshorteneR/inst/doc/Tutorial.html | 208 +++++----- 6 files changed, 125 insertions(+), 118 deletions(-)
Title: Access to Global Sub-National Income Data
Description: Provides access to granular sub-national income data from the
MCC-PIK Database Of Sub-national Economic Output (DOSE). The package
downloads and processes the data from its open repository on 'Zenodo'
(<https://zenodo.org/records/13773040>). Functions are provided to
fetch data at multiple geographic levels, match coordinates to
administrative regions, and access associated geometries.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Diff between subincomeR versions 0.2.2 dated 2024-12-19 and 0.3.0 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/getDOSE.R | 4 ++-- README.md | 13 ++++++++++++- inst/doc/regional-convergence.html | 8 ++++---- man/figures/map.png |binary 7 files changed, 35 insertions(+), 16 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.3.4 dated 2025-01-17 and 0.3.5 dated 2025-02-16
DESCRIPTION | 10 MD5 | 118 - NAMESPACE | 2 R/benchmark.R |only R/collapseCohorts.R | 207 +-- R/conceptCohort.R | 1182 ++++++++--------- R/copyCohorts.R |only R/demographicsCohort.R | 139 +- R/exitAtColumnDate.R | 580 ++++---- R/exitAtDate.R | 444 +++--- R/intersectCohorts.R | 1086 ++++++++-------- R/matchCohorts.R | 863 ++++++------ R/measurementCohort.R | 566 ++++---- R/padCohortDate.R | 646 ++++----- R/requireCohortIntersect.R | 355 ++--- R/requireConceptIntersect.R | 43 R/requireDateRange.R | 430 +++--- R/requireDeathFlag.R | 246 +-- R/requireDemographics.R | 1305 +++++++++---------- R/requireIsEntry.R | 443 +++--- R/requireMinCohortCount.R | 146 +- R/requireTableIntersect.R | 289 ++-- R/sampleCohorts.R | 167 +- R/stratifyCohorts.R | 491 +++---- R/subsetCohorts.R | 125 - R/sysdata.rda |binary R/trimDemographics.R | 833 ++++++------ R/unionCohorts.R | 208 +-- R/yearCohorts.R | 404 +++--- README.md | 4 inst/doc/a02_cohort_table_requirements.html | 20 inst/doc/a03_require_demographics.html | 20 inst/doc/a04_require_intersections.html | 20 inst/doc/a06_concatanate_cohorts.R | 13 inst/doc/a06_concatanate_cohorts.Rmd | 177 +- inst/doc/a06_concatanate_cohorts.html | 1746 +++++++------------------- inst/doc/a07_filter_cohorts.html | 24 inst/doc/a08_split_cohorts.R | 20 inst/doc/a08_split_cohorts.Rmd | 26 inst/doc/a08_split_cohorts.html | 88 - inst/doc/a09_combine_cohorts.R | 16 inst/doc/a09_combine_cohorts.Rmd | 19 inst/doc/a11_benchmark.R | 1 inst/doc/a11_benchmark.Rmd | 1 inst/doc/a11_benchmark.html | 440 +++--- man/benchmarkCohortConstructor.Rd |only man/copyCohorts.Rd |only man/measurementCohort.Rd | 2 tests/testthat/test-benchmark.R |only tests/testthat/test-collapseCohorts.R | 540 ++++---- tests/testthat/test-conceptCohort.R | 3 tests/testthat/test-copyCohorts.R |only tests/testthat/test-exitAtDate.R | 431 +++--- tests/testthat/test-measurementCohort.R | 16 tests/testthat/test-requireCohortIntersect.R | 724 +++++----- tests/testthat/test-requireConceptIntersect.R | 734 +++++----- tests/testthat/test-requireDateRange.R | 6 tests/testthat/test-requireIsEntry.R | 539 ++++---- tests/testthat/test-sampleCohorts.R | 30 vignettes/a06_concatanate_cohorts.Rmd | 177 +- vignettes/a08_split_cohorts.Rmd | 26 vignettes/a09_combine_cohorts.Rmd | 19 vignettes/a11_benchmark.Rmd | 1 63 files changed, 8334 insertions(+), 8877 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre],
Marcell T. Kurbucz [aut],
Attila I. Katona [aut],
Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between nda versions 0.1.15 dated 2024-10-14 and 0.2.4 dated 2025-02-16
DESCRIPTION | 8 MD5 | 42 - NAMESPACE | 8 R/biplot.nda.R | 14 R/fitted.ndrlm.R |only R/nda.R | 1431 +++++++++++++++++++++++++++++++++++++++++++++++-- R/ndr.R | 65 +- R/ndrlm.R |only R/plot.nda.R | 170 ++--- R/plot.ndrlm.R |only R/predict.nda.R |only R/predict.ndrlm.R |only R/print.nda.R | 8 R/print.ndrlm.R |only R/residuals.ndrlm.R |only R/summary.nda.R | 8 R/summary.ndrlm.R |only inst/NEWS | 24 man/fitted.ndrlm.Rd |only man/fs.dmred.Rd | 4 man/nda.Rd | 5 man/ndr.Rd | 211 ++++--- man/ndrlm.Rd |only man/plot.nda.Rd | 125 ++-- man/plot.ndrlm.Rd |only man/predict.nda.Rd |only man/predict.ndrlm.Rd |only man/print.ndrlm.Rd |only man/residuals.ndrlm.Rd |only man/summary.ndrlm.Rd |only 30 files changed, 1761 insertions(+), 362 deletions(-)
Title: An Alternative 'Rcpp' Wrapper of 'MeCab'
Description: A plain 'Rcpp' wrapper for 'MeCab' that can segment Chinese,
Japanese, and Korean text into tokens. The main goal of this package
is to provide an alternative to 'tidytext' using morphological
analysis.
Author: Akiru Kato [aut, cre],
Shogo Ichinose [aut],
Taku Kudo [aut],
Jorge Nocedal [ctb],
Nippon Telegraph and Telephone Corporation [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between gibasa versions 1.1.1 dated 2024-07-05 and 1.1.2 dated 2025-02-16
DESCRIPTION | 19 +++++----- MD5 | 42 +++++++++++----------- NEWS.md | 5 ++ R/RcppExports.R | 73 ++++++++++++++++++++++++++++---------- R/bind_tf_idf2.R | 8 ++-- R/mute_tokens.R | 2 - R/prettify.R | 2 - R/tokenize.R | 33 ++++++++++++----- R/utils.R | 11 +++-- README.md | 77 ++++++++++++----------------------------- build/partial.rdb |binary man/dictionary_info.Rd | 35 ++++++++++++++++-- man/get_transition_cost.Rd | 15 ++++--- man/gibasa-package.Rd | 2 - man/is_blank.Rd | 4 +- man/mute_tokens.Rd | 2 - man/posDebugRcpp.Rd | 12 +++--- man/posParallelRcpp.Rd | 15 ++++--- man/transition_cost.Rd | 14 ++++--- src/posDebug.cpp | 60 +++++++++++++++++++++++++------ src/posParallel.cpp | 17 +++++---- tests/testthat/test-tokenize.R | 24 +++++++++--- 22 files changed, 292 insertions(+), 180 deletions(-)
Title: Access Colombia's Public Data via 'API-Colombia'
Description: Provides a seamless interface to access diverse public data about
Colombia through the 'API-Colombia', a RESTful API. The package enables users
to explore various aspects of Colombia, including general information,
geography, and cultural insights. It includes five API-related functions to
retrieve data on topics such as Colombia's general information, airports,
departments, regions, and presidents. Additionally, 'ColombiAPI' offers a
built-in function to view the datasets available within the package. The
package also includes curated datasets covering Bogota air stations,
business and holiday dates, public schools, Colombian coffee exports,
cannabis licenses, Medellin rainfall, and malls in Bogota, making it a
comprehensive tool for exploring Colombia's data. For more details on the
'API-Colombia', see <https://api-colombia.com/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.1.0 dated 2025-01-09 and 0.1.1 dated 2025-02-16
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++----------- R/colombiapi-package.R | 2 R/data-documentation.R | 2 R/get_Colombia_info.R | 2 R/get_airports_list.R | 12 ++++- R/get_departments_list.R | 2 R/get_presidents_list.R | 2 R/get_regions_list.R | 2 R/utils.R | 2 R/view_datasets.R | 2 inst/CITATION | 2 tests/testthat/test-Bogota_airstations_df.R | 2 tests/testthat/test-Bogota_business_Date.R | 2 tests/testthat/test-Bogota_holidays_Date.R | 2 tests/testthat/test-Bogota_malls_tbl_df.R | 2 tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 tests/testthat/test-Colombia_coffee_tbl_df.R | 2 tests/testthat/test-Medellin_rain_tbl_df.R | 2 tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 tests/testthat/test-get_Colombia_info.R | 2 tests/testthat/test-get_airports_list.R | 6 +- tests/testthat/test-get_departments_list.R | 2 tests/testthat/test-get_presidents_list.R | 2 tests/testthat/test-get_regions_list.R | 2 tests/testthat/test-view_datasets.R | 2 26 files changed, 64 insertions(+), 56 deletions(-)