Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference
using a spectral analysis of Gaussian process priors.
Gaussian processes are represented with a Fourier series
based on cosine basis functions. Currently the package
includes parametric linear models, partial linear additive
models with/without shape restrictions, generalized linear
additive models with/without shape restrictions, and
density estimation model. To maximize computational
efficiency, the actual Markov chain Monte Carlo sampling
for each model is done using codes written in FORTRAN 90.
This software has been developed using funding supported by
Basic Science Research Program through the National Research
Foundation of Korea (NRF) funded by the Ministry of Education
(no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut],
Taeryon Choi [aut],
Beomjo Park [aut, cre],
Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjop@gmail.com>
Diff between bsamGP versions 1.2.5 dated 2024-03-18 and 1.2.6 dated 2025-04-02
DESCRIPTION | 30 +++++++++++++++------ MD5 | 4 +- README.md | 82 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 64 insertions(+), 52 deletions(-)
Title: Tools for 'Box Geometry Model' (BGM) Files and Topology for the
Atlantis Ecosystem Model
Description: Facilities for working with Atlantis box-geometry model (BGM)
files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model.
Functions are provided to read from BGM files directly, preserving their
internal topology, as well as helper functions to generate spatial data from these
mesh forms. This functionality aims to simplify the creation and modification of box
and geometry as well as the ability to integrate with other data sources.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between rbgm versions 0.1.0 dated 2020-04-12 and 0.2.0 dated 2025-04-02
DESCRIPTION | 8 - MD5 | 26 +-- NEWS.md | 4 R/Spatial.R | 10 - R/rbgm.R | 9 - R/to_ll_hack.R | 1 README.md | 50 ------ build/vignette.rds |binary inst/doc/BGM_Spatial.R | 2 inst/doc/BGM_Spatial.html | 299 ++++++++++++++++++++++++----------------- inst/doc/BGM_examplefiles.R | 36 ++-- inst/doc/BGM_examplefiles.html | 233 +++++++++++++++++++------------ inst/doc/BGMfiles.html | 246 ++++++++++++++++++++------------- man/rbgm-package.Rd | 19 ++ 14 files changed, 538 insertions(+), 405 deletions(-)
Title: Generic Coordinate System Transformations Using 'PROJ'
Description: A wrapper around the generic coordinate transformation software 'PROJ'
that transforms coordinates from one coordinate reference system ('CRS')
to another. This includes cartographic projections as well as geodetic transformations. The intention is for this
package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5
pathways be provided by the 'proj4' package.
Author: Michael D. Sumner [aut, cre] ,
Jeroen Ooms [ctb] ,
Simon Urbanek [cph, ctb] ,
Dewey Dunnington [ctb] ,
Anthony North [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between PROJ versions 0.5.0 dated 2024-06-12 and 0.6.0 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/vignette.rds |binary configure | 5 ++--- configure.ac | 4 ++-- inst/doc/PROJ.html | 2 +- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 3.1.10 dated 2025-01-12 and 3.1.11 dated 2025-04-02
growthPheno-3.1.10/growthPheno/data/cart.dat.rda |only growthPheno-3.1.10/growthPheno/tests/testthat/testLongiPrime.r |only growthPheno-3.1.10/growthPheno/tests/testthat/testthat-problems.rds |only growthPheno-3.1.11/growthPheno/DESCRIPTION | 8 growthPheno-3.1.11/growthPheno/MD5 | 68 ++--- growthPheno-3.1.11/growthPheno/R/dataLongi_v10.r | 85 ++++-- growthPheno-3.1.11/growthPheno/R/traitSmooth.r | 1 growthPheno-3.1.11/growthPheno/build/partial.rdb |binary growthPheno-3.1.11/growthPheno/data/RicePrepped.dat.rda |binary growthPheno-3.1.11/growthPheno/data/RiceRaw.dat.rda |binary growthPheno-3.1.11/growthPheno/data/datalist | 3 growthPheno-3.1.11/growthPheno/data/exampleData.rda |binary growthPheno-3.1.11/growthPheno/data/tomato.dat.rda |binary growthPheno-3.1.11/growthPheno/inst/News.Rd | 10 growthPheno-3.1.11/growthPheno/inst/doc/Rice.pdf |binary growthPheno-3.1.11/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-3.1.11/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-3.1.11/growthPheno/man/RicePrepped.dat.Rd | 10 growthPheno-3.1.11/growthPheno/man/RiceRaw.dat.Rd | 2 growthPheno-3.1.11/growthPheno/man/calcTimes.Rd | 2 growthPheno-3.1.11/growthPheno/man/designFactors.Rd | 4 growthPheno-3.1.11/growthPheno/man/exampleData.Rd | 6 growthPheno-3.1.11/growthPheno/man/growthPheno-pkg.Rd | 2 growthPheno-3.1.11/growthPheno/man/importExcel.Rd | 19 - growthPheno-3.1.11/growthPheno/man/plotImagetimes.Rd | 6 growthPheno-3.1.11/growthPheno/man/prepImageData.Rd | 56 +++- growthPheno-3.1.11/growthPheno/tests/testthat/data/area.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/cart.dat.rda |only growthPheno-3.1.11/growthPheno/tests/testthat/data/chkpeadat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/dat1.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.19.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.RGB.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.fluo.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/testSpline.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/testContGRdiff.r | 30 +- growthPheno-3.1.11/growthPheno/tests/testthat/testImportXL.r | 14 - growthPheno-3.1.11/growthPheno/tests/testthat/testprepImageData.r | 130 +++++++--- 37 files changed, 286 insertions(+), 170 deletions(-)
Title: Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Description: Tools for detecting and summarize influential cases that
can affect exploratory and confirmatory factor analysis models as well as
structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>;
Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <doi:10.3389/fpsyg.2012.00055>).
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between faoutlier versions 0.7.6 dated 2021-01-10 and 0.7.7 dated 2025-04-02
DESCRIPTION | 9 +++---- MD5 | 38 +++++++++++++++--------------- NEWS.md | 6 ++-- R/GOF.R | 8 +++--- R/LD.R | 8 +++--- R/faoutlier.R | 20 +++++++-------- R/forward.search.R | 4 +-- R/gCD.R | 58 ++++++++++++++++++++++++++++++---------------- R/obs.resid.R | 4 +-- R/robustMD.R | 10 +++---- README.md | 2 - build/partial.rdb |binary inst/CITATION | 6 ++-- man/faoutlier.Rd | 8 +++--- man/gCD.Rd | 12 +++++++-- man/holzinger.Rd | 6 ++-- man/holzinger.outlier.Rd | 6 ++-- man/robustMD.Rd | 8 +++--- tests/testthat/test-GOF.R | 7 ++--- tests/testthat/test-gCD.R | 15 +++++++---- 20 files changed, 131 insertions(+), 104 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.10 dated 2024-09-26 and 1.1.11 dated 2025-04-02
glmmTMB-1.1.10/glmmTMB/inst/Matrix-version |only glmmTMB-1.1.10/glmmTMB/inst/TMB-version |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.R |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.csv |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.rda |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/tmbstan_traceplot.png |only glmmTMB-1.1.10/glmmTMB/vignettes/covstruct_files |only glmmTMB-1.1.10/glmmTMB/vignettes/lineno.sty |only glmmTMB-1.1.11/glmmTMB/DESCRIPTION | 13 glmmTMB-1.1.11/glmmTMB/MD5 | 152 ++-- glmmTMB-1.1.11/glmmTMB/NAMESPACE | 1 glmmTMB-1.1.11/glmmTMB/R/VarCorr.R | 2 glmmTMB-1.1.11/glmmTMB/R/diagnose.R | 4 glmmTMB-1.1.11/glmmTMB/R/enum.R | 4 glmmTMB-1.1.11/glmmTMB/R/family.R | 40 - glmmTMB-1.1.11/glmmTMB/R/glmmTMB.R | 141 ++-- glmmTMB-1.1.11/glmmTMB/R/methods.R | 51 + glmmTMB-1.1.11/glmmTMB/R/predict.R | 38 - glmmTMB-1.1.11/glmmTMB/R/profile.R | 2 glmmTMB-1.1.11/glmmTMB/R/utils.R | 100 +- glmmTMB-1.1.11/glmmTMB/build/partial.rdb |binary glmmTMB-1.1.11/glmmTMB/build/vignette.rds |binary glmmTMB-1.1.11/glmmTMB/inst/CITATION | 36 - glmmTMB-1.1.11/glmmTMB/inst/NEWS.Rd | 50 + glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.R | 352 +++++----- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.html | 96 +- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.R | 92 +- glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.R | 48 - glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.R | 251 ++++--- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.html | 270 ++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/inst/doc/miscEx.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.R | 30 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.R | 58 - glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.R | 26 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/sim.html | 6 glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.R | 154 ++-- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.html | 320 ++++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.rmd | 83 +- glmmTMB-1.1.11/glmmTMB/inst/test_data/models.rda |binary glmmTMB-1.1.11/glmmTMB/inst/test_data/sim_ar1.rds |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.R | 79 +- glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_bounds_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.R | 8 glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/volcano_data.png |binary glmmTMB-1.1.11/glmmTMB/man/dot-checkRankX.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/get_autopar.Rd |only glmmTMB-1.1.11/glmmTMB/man/get_cor.Rd | 22 glmmTMB-1.1.11/glmmTMB/man/glmmTMB.Rd | 5 glmmTMB-1.1.11/glmmTMB/man/glmmTMBControl.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/mkTMBStruc.Rd | 1 glmmTMB-1.1.11/glmmTMB/man/nbinom2.Rd | 14 glmmTMB-1.1.11/glmmTMB/man/predict.glmmTMB.Rd | 20 glmmTMB-1.1.11/glmmTMB/man/simulate_new.Rd | 42 - glmmTMB-1.1.11/glmmTMB/src/glmmTMB.cpp | 127 ++- glmmTMB-1.1.11/glmmTMB/tests/testthat/test-basics.R | 23 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-control.R | 30 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-diagnose.R | 13 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-downstream.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-families.R | 38 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-mapequal.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-methods.R | 46 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-predict.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-priors.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-propto.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-rr.R | 35 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-varstruc.R | 77 +- glmmTMB-1.1.11/glmmTMB/vignettes/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/vignettes/glmmTMB.bib | 6 glmmTMB-1.1.11/glmmTMB/vignettes/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/vignettes/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/vignettes/troubleshooting.rmd | 83 +- 83 files changed, 2477 insertions(+), 1113 deletions(-)
Title: Estimating Dynamic Correlation
Description: Implementations for two different Bayesian models of differential co-expression. scdeco.cop() fits the bivariate Gaussian copula model from Zichen Ma, Shannon W. Davis, Yen-Yi Ho (2023) <doi:10.1111/biom.13701>, while scdeco.pg() fits the bivariate Poisson-Gamma model from Zhen Yang, Yen-Yi Ho (2022) <doi:10.1111/biom.13457>.
Author: Anderson Bussing [aut, cre],
Yen-Yi Ho [aut, ths],
Zichen Ma [aut],
Zhen Yang [aut]
Maintainer: Anderson Bussing <abussing@email.sc.edu>
Diff between scDECO versions 0.1.0 dated 2024-06-04 and 0.1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 13 +++--- NEWS.md |only R/scdeco.cop.R | 70 +++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/scDECO-Copula.html | 28 +++++++------- inst/doc/scDECO-Poisson-Gamma.html | 22 +++++------ man/scdeco.cop.Rd | 16 +++++++- 8 files changed, 110 insertions(+), 47 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see Garrison et al. (2024) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.3 dated 2025-02-19 and 1.3.5 dated 2025-04-02
BGmisc-1.3.3/BGmisc/man/compute_transpose.Rd |only BGmisc-1.3.3/BGmisc/tests/testthat/Rplots.pdf |only BGmisc-1.3.5/BGmisc/DESCRIPTION | 14 BGmisc-1.3.5/BGmisc/MD5 | 109 +- BGmisc-1.3.5/BGmisc/NAMESPACE | 5 BGmisc-1.3.5/BGmisc/NEWS.md | 17 BGmisc-1.3.5/BGmisc/R/calculateFamilySize.R | 3 BGmisc-1.3.5/BGmisc/R/checkPedigree.R |only BGmisc-1.3.5/BGmisc/R/checkSex.R | 20 BGmisc-1.3.5/BGmisc/R/computeRelatedness.R | 2 BGmisc-1.3.5/BGmisc/R/convertPedigree.R | 430 +++++++--- BGmisc-1.3.5/BGmisc/R/documentData.R | 49 + BGmisc-1.3.5/BGmisc/R/makeLinks.R |only BGmisc-1.3.5/BGmisc/R/plotPedigree.R | 55 - BGmisc-1.3.5/BGmisc/R/readPedigree.R | 272 +++++- BGmisc-1.3.5/BGmisc/R/summarizePedigree.R | 24 BGmisc-1.3.5/BGmisc/README.md | 10 BGmisc-1.3.5/BGmisc/build/vignette.rds |binary BGmisc-1.3.5/BGmisc/data/ASOIAF.rda |only BGmisc-1.3.5/BGmisc/data/royal92.rda |only BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.R | 8 BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.html | 118 +- BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.html | 12 BGmisc-1.3.5/BGmisc/inst/doc/partial.R |only BGmisc-1.3.5/BGmisc/inst/doc/partial.Rmd |only BGmisc-1.3.5/BGmisc/inst/doc/partial.html |only BGmisc-1.3.5/BGmisc/inst/doc/pedigree.html | 225 ----- BGmisc-1.3.5/BGmisc/inst/doc/validation.R | 21 BGmisc-1.3.5/BGmisc/inst/doc/validation.Rmd | 45 - BGmisc-1.3.5/BGmisc/inst/doc/validation.html | 148 +-- BGmisc-1.3.5/BGmisc/man/ASOIAF.Rd |only BGmisc-1.3.5/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.3.5/BGmisc/man/assignParentIDs.Rd | 4 BGmisc-1.3.5/BGmisc/man/checkPedigreeNetwork.Rd |only BGmisc-1.3.5/BGmisc/man/com2links.Rd |only BGmisc-1.3.5/BGmisc/man/compute_parent_adjacency.Rd |only BGmisc-1.3.5/BGmisc/man/createFamilyToParentsMapping.Rd | 2 BGmisc-1.3.5/BGmisc/man/dot-computeTranspose.Rd |only BGmisc-1.3.5/BGmisc/man/extractSummaryText.Rd |only BGmisc-1.3.5/BGmisc/man/inferRelatedness.Rd | 2 BGmisc-1.3.5/BGmisc/man/makeLongTree.Rd |only BGmisc-1.3.5/BGmisc/man/matchMembers.Rd |only BGmisc-1.3.5/BGmisc/man/parseRelationships.Rd |only BGmisc-1.3.5/BGmisc/man/parseTree.Rd |only BGmisc-1.3.5/BGmisc/man/ped2add.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2cn.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2com.Rd | 8 BGmisc-1.3.5/BGmisc/man/ped2mit.Rd | 5 BGmisc-1.3.5/BGmisc/man/processParents.Rd | 2 BGmisc-1.3.5/BGmisc/man/readWikifamilytree.Rd |only BGmisc-1.3.5/BGmisc/man/repairSex.Rd | 4 BGmisc-1.3.5/BGmisc/man/royal92.Rd |only BGmisc-1.3.5/BGmisc/man/summarizePedigrees.Rd | 3 BGmisc-1.3.5/BGmisc/tests/testthat/test-calculateFamilySize.R | 22 BGmisc-1.3.5/BGmisc/tests/testthat/test-checkPedigreeNetwork.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-checkSex.R | 27 BGmisc-1.3.5/BGmisc/tests/testthat/test-convertPedigree.R | 209 ++++ BGmisc-1.3.5/BGmisc/tests/testthat/test-makeLinks.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-plotPedigree.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-readPedigrees.R | 33 BGmisc-1.3.5/BGmisc/tests/testthat/test-simulatePedigree.R | 29 BGmisc-1.3.5/BGmisc/tests/testthat/test-tweakPedigree.R | 12 BGmisc-1.3.5/BGmisc/vignettes/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/vignettes/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/vignettes/partial.Rmd |only BGmisc-1.3.5/BGmisc/vignettes/validation.Rmd | 45 - 68 files changed, 1413 insertions(+), 687 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types
of resampling objects (e.g. bootstrap, cross-validation).
Author: Hannah Frick [aut, cre] ,
Fanny Chow [aut],
Max Kuhn [aut],
Michael Mahoney [aut] ,
Julia Silge [aut] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between rsample versions 1.2.1 dated 2024-03-25 and 1.3.0 dated 2025-04-02
rsample-1.2.1/rsample/R/nest.R |only rsample-1.2.1/rsample/tests/testthat/_snaps/initial.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/nesting.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/strata.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/validation.md |only rsample-1.2.1/rsample/tests/testthat/test-for-pred.R |only rsample-1.2.1/rsample/tests/testthat/test-initial.R |only rsample-1.2.1/rsample/tests/testthat/test-make-splits.R |only rsample-1.2.1/rsample/tests/testthat/test-names.R |only rsample-1.2.1/rsample/tests/testthat/test-nesting.R |only rsample-1.2.1/rsample/tests/testthat/test-rolling.R |only rsample-1.2.1/rsample/tests/testthat/test-strata.R |only rsample-1.2.1/rsample/tests/testthat/test-validation.R |only rsample-1.3.0/rsample/DESCRIPTION | 12 rsample-1.3.0/rsample/MD5 | 213 +- rsample-1.3.0/rsample/NAMESPACE | 32 rsample-1.3.0/rsample/NEWS.md | 65 rsample-1.3.0/rsample/R/apparent.R | 5 rsample-1.3.0/rsample/R/boot.R | 8 rsample-1.3.0/rsample/R/bootci.R | 272 ++- rsample-1.3.0/rsample/R/caret.R | 33 rsample-1.3.0/rsample/R/clustering.R | 4 rsample-1.3.0/rsample/R/compat-vctrs-helpers.R | 53 rsample-1.3.0/rsample/R/complement.R | 9 rsample-1.3.0/rsample/R/fingerprint.R |only rsample-1.3.0/rsample/R/form_pred.R | 2 rsample-1.3.0/rsample/R/import-standalone-obj-type.R |only rsample-1.3.0/rsample/R/import-standalone-types-check.R |only rsample-1.3.0/rsample/R/initial_split.R | 52 rsample-1.3.0/rsample/R/initial_validation_split.R | 41 rsample-1.3.0/rsample/R/inner_split.R |only rsample-1.3.0/rsample/R/labels.R | 19 rsample-1.3.0/rsample/R/loo.R | 2 rsample-1.3.0/rsample/R/make_groups.R | 27 rsample-1.3.0/rsample/R/make_strata.R | 36 rsample-1.3.0/rsample/R/mc.R | 12 rsample-1.3.0/rsample/R/misc.R | 248 --- rsample-1.3.0/rsample/R/nested_cv.R |only rsample-1.3.0/rsample/R/permutations.R | 15 rsample-1.3.0/rsample/R/printing.R | 6 rsample-1.3.0/rsample/R/reg_intervals.R | 16 rsample-1.3.0/rsample/R/reshuffle_rset.R |only rsample-1.3.0/rsample/R/reverse_splits.R |only rsample-1.3.0/rsample/R/rolling_origin.R | 16 rsample-1.3.0/rsample/R/rsample-package.R | 11 rsample-1.3.0/rsample/R/rset.R | 14 rsample-1.3.0/rsample/R/rsplit.R | 37 rsample-1.3.0/rsample/R/slide.R | 46 rsample-1.3.0/rsample/R/tidy.R | 16 rsample-1.3.0/rsample/R/validation_set.R | 33 rsample-1.3.0/rsample/R/validation_split.R | 11 rsample-1.3.0/rsample/R/vfold.R | 81 - rsample-1.3.0/rsample/build/vignette.rds |binary rsample-1.3.0/rsample/inst/doc/Common_Patterns.R | 2 rsample-1.3.0/rsample/inst/doc/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/inst/doc/Common_Patterns.html | 16 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.Rmd | 9 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.html | 734 ++-------- rsample-1.3.0/rsample/inst/doc/rsample.html | 422 ----- rsample-1.3.0/rsample/man/add_resample_id.Rd | 2 rsample-1.3.0/rsample/man/as.data.frame.rsplit.Rd | 6 rsample-1.3.0/rsample/man/bootstraps.Rd | 2 rsample-1.3.0/rsample/man/dot-get_split_args.Rd |only rsample-1.3.0/rsample/man/form_pred.Rd | 2 rsample-1.3.0/rsample/man/get_fingerprint.Rd | 4 rsample-1.3.0/rsample/man/group_bootstraps.Rd | 2 rsample-1.3.0/rsample/man/initial_split.Rd | 11 rsample-1.3.0/rsample/man/initial_validation_split.Rd | 7 rsample-1.3.0/rsample/man/inner_split.Rd |only rsample-1.3.0/rsample/man/int_pctl.Rd | 56 rsample-1.3.0/rsample/man/labels.rset.Rd | 5 rsample-1.3.0/rsample/man/make_groups.Rd | 2 rsample-1.3.0/rsample/man/make_strata.Rd | 1 rsample-1.3.0/rsample/man/nested_cv.Rd | 24 rsample-1.3.0/rsample/man/permutations.Rd | 4 rsample-1.3.0/rsample/man/reg_intervals.Rd | 12 rsample-1.3.0/rsample/man/reshuffle_rset.Rd | 2 rsample-1.3.0/rsample/man/reverse_splits.Rd | 2 rsample-1.3.0/rsample/man/rolling_origin.Rd | 7 rsample-1.3.0/rsample/man/rsample2caret.Rd | 8 rsample-1.3.0/rsample/man/tidy.rsplit.Rd | 12 rsample-1.3.0/rsample/man/validation_set.Rd | 2 rsample-1.3.0/rsample/tests/testthat/_snaps/boot.md | 17 rsample-1.3.0/rsample/tests/testthat/_snaps/bootci.md | 224 ++- rsample-1.3.0/rsample/tests/testthat/_snaps/clustering.md | 48 rsample-1.3.0/rsample/tests/testthat/_snaps/form_pred.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_validation_split.md | 4 rsample-1.3.0/rsample/tests/testthat/_snaps/labels.md | 34 rsample-1.3.0/rsample/tests/testthat/_snaps/make_strata.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/mc.md | 87 + rsample-1.3.0/rsample/tests/testthat/_snaps/misc.md | 163 -- rsample-1.3.0/rsample/tests/testthat/_snaps/nested_cv.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/permutations.md | 39 rsample-1.3.0/rsample/tests/testthat/_snaps/reg_intervals.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reshuffle_rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reverse_splits.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rolling_origin.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rsplit.md | 70 rsample-1.3.0/rsample/tests/testthat/_snaps/slide.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/validation_set.md | 1 rsample-1.3.0/rsample/tests/testthat/_snaps/validation_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/vfold.md | 202 ++ rsample-1.3.0/rsample/tests/testthat/test-boot.R | 8 rsample-1.3.0/rsample/tests/testthat/test-bootci.R | 312 ++-- rsample-1.3.0/rsample/tests/testthat/test-caret.R | 405 +++-- rsample-1.3.0/rsample/tests/testthat/test-clustering.R | 31 rsample-1.3.0/rsample/tests/testthat/test-form_pred.R |only rsample-1.3.0/rsample/tests/testthat/test-initial_split.R |only rsample-1.3.0/rsample/tests/testthat/test-inner_split.R |only rsample-1.3.0/rsample/tests/testthat/test-labels.R | 16 rsample-1.3.0/rsample/tests/testthat/test-make_strata.R |only rsample-1.3.0/rsample/tests/testthat/test-mc.R | 44 rsample-1.3.0/rsample/tests/testthat/test-misc.R | 195 -- rsample-1.3.0/rsample/tests/testthat/test-nested_cv.R |only rsample-1.3.0/rsample/tests/testthat/test-permutations.R | 16 rsample-1.3.0/rsample/tests/testthat/test-reg_intervals.R |only rsample-1.3.0/rsample/tests/testthat/test-reshuffle_rset.R |only rsample-1.3.0/rsample/tests/testthat/test-reverse_splits.R |only rsample-1.3.0/rsample/tests/testthat/test-rolling_origin.R |only rsample-1.3.0/rsample/tests/testthat/test-rset.R | 31 rsample-1.3.0/rsample/tests/testthat/test-rsplit.R | 42 rsample-1.3.0/rsample/tests/testthat/test-slide.R | 72 rsample-1.3.0/rsample/tests/testthat/test-validation_split.R |only rsample-1.3.0/rsample/tests/testthat/test-vfold.R | 144 + rsample-1.3.0/rsample/vignettes/Applications/Intervals.Rmd | 2 rsample-1.3.0/rsample/vignettes/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/vignettes/Working_with_rsets.Rmd | 9 129 files changed, 2657 insertions(+), 2374 deletions(-)
Title: Friendly Input-Output Analysis
Description: Simplifies the process of importing and managing input-output
matrices from 'Microsoft Excel' into R, and provides a suite of functions for
analysis. It leverages the 'R6' class for clean, memory-efficient
object-oriented programming. Furthermore, all linear algebra computations are
implemented in 'Rust' to achieve highly optimized performance.
Author: Alberson da Silva Miranda [aut, cre, cph]
,
Celso Bissoli Sessa [dtc]
Maintainer: Alberson da Silva Miranda <albersonmiranda@hotmail.com>
Diff between fio versions 0.1.2 dated 2024-08-27 and 0.1.5 dated 2025-04-02
fio-0.1.2/fio/src/Makevars |only fio-0.1.2/fio/src/Makevars.ucrt |only fio-0.1.2/fio/src/Makevars.win |only fio-0.1.5/fio/DESCRIPTION | 14 fio-0.1.5/fio/MD5 | 52 +- fio-0.1.5/fio/NEWS.md | 16 fio-0.1.5/fio/R/extendr-wrappers.R | 1 fio-0.1.5/fio/R/import_iom.R | 2 fio-0.1.5/fio/R/r6.R | 91 ++-- fio-0.1.5/fio/README.md | 13 fio-0.1.5/fio/build/partial.rdb |binary fio-0.1.5/fio/build/vignette.rds |binary fio-0.1.5/fio/configure | 2 fio-0.1.5/fio/configure.win | 2 fio-0.1.5/fio/data/br_2020.rda |binary fio-0.1.5/fio/inst/doc/getting_started.html | 40 +- fio-0.1.5/fio/inst/extdata/iom/br/2020.xlsx |binary fio-0.1.5/fio/man/figures/example_leontief_inverse.png |binary fio-0.1.5/fio/man/import_element.Rd | 2 fio-0.1.5/fio/man/iom.Rd | 104 +++-- fio-0.1.5/fio/src/Makevars.in |only fio-0.1.5/fio/src/Makevars.win.in |only fio-0.1.5/fio/src/rust/Cargo.lock | 319 ++++++++++------- fio-0.1.5/fio/src/rust/Cargo.toml | 8 fio-0.1.5/fio/src/rust/src/lib.rs | 3 fio-0.1.5/fio/src/rust/vendor-config.toml | 5 fio-0.1.5/fio/src/rust/vendor.tar.xz |binary fio-0.1.5/fio/tests/testthat/test-computations.R | 13 fio-0.1.5/fio/tools/config.R |only fio-0.1.5/fio/tools/msrv.R | 4 30 files changed, 395 insertions(+), 296 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between AllelicSeries versions 0.1.1.2 dated 2024-11-23 and 0.1.1.5 dated 2025-04-02
DESCRIPTION | 10 - MD5 | 46 +++--- NAMESPACE | 2 NEWS.md | 3 R/allelic_series.R | 13 + R/generate_data.R | 17 ++ R/generate_sumstats.R | 15 +- R/input_checks.R | 1 R/utilities.R | 107 +++++++++++++++ build/vignette.rds |binary inst/doc/coast.R | 33 ++++ inst/doc/coast.Rmd | 48 ++++++ inst/doc/coast.html | 240 +++++++++++++++++++++------------- inst/doc/covariate_inference.R |only inst/doc/covariate_inference.Rmd |only inst/doc/covariate_inference.html |only man/AllelicSeries-package.Rd | 2 man/COAST.Rd | 4 man/CalcSumstats.Rd | 4 man/CollapseGeno.Rd |only man/ContainsInt.Rd |only man/DGP.Rd | 7 tests/testthat/test-allelic_series.R | 78 ++++++++++- tests/testthat/test-data_generation.R | 28 +++ tests/testthat/test-utils.R | 97 +++++++++++++ vignettes/coast.Rmd | 48 ++++++ vignettes/covariate_inference.Rmd |only 27 files changed, 675 insertions(+), 128 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.51 dated 2025-02-19 and 0.52 dated 2025-04-02
xfun-0.51/xfun/man/attr.Rd |only xfun-0.52/xfun/DESCRIPTION | 11 +-- xfun-0.52/xfun/MD5 | 64 ++++++++++---------- xfun-0.52/xfun/NAMESPACE | 3 xfun-0.52/xfun/NEWS.md | 18 +++++ xfun-0.52/xfun/R/algorithm.R |only xfun-0.52/xfun/R/cache.R | 13 +++- xfun-0.52/xfun/R/citation.R | 15 ++++ xfun-0.52/xfun/R/command.R | 11 --- xfun-0.52/xfun/R/data-structure.R | 2 xfun-0.52/xfun/R/image.R | 14 ---- xfun-0.52/xfun/R/io.R | 32 +++++++++- xfun-0.52/xfun/R/knitr.R | 17 ++++- xfun-0.52/xfun/R/markdown.R | 4 - xfun-0.52/xfun/R/packages.R | 2 xfun-0.52/xfun/R/record.R | 6 - xfun-0.52/xfun/R/utils.R | 14 +++- xfun-0.52/xfun/R/yaml.R | 17 +++-- xfun-0.52/xfun/build/vignette.rds |binary xfun-0.52/xfun/inst/doc/xfun.R | 6 - xfun-0.52/xfun/inst/doc/xfun.Rmd | 66 +------------------- xfun-0.52/xfun/inst/doc/xfun.html | 89 ++++++---------------------- xfun-0.52/xfun/man/attr2.Rd |only xfun-0.52/xfun/man/cache_exec.Rd | 4 + xfun-0.52/xfun/man/cache_rds.Rd | 11 +++ xfun-0.52/xfun/man/divide_chunk.Rd | 8 ++ xfun-0.52/xfun/man/pkg_bib.Rd | 10 ++- xfun-0.52/xfun/man/rand_unit.Rd |only xfun-0.52/xfun/man/upload_ftp.Rd | 6 - xfun-0.52/xfun/man/upload_imgur.Rd | 2 xfun-0.52/xfun/man/url_destination.Rd |only xfun-0.52/xfun/src/init.c | 2 xfun-0.52/xfun/src/rand_lcg.c |only xfun-0.52/xfun/tests/test-cran/test-utils.R | 6 - xfun-0.52/xfun/tests/test-cran/test-yaml.R | 4 + xfun-0.52/xfun/vignettes/xfun.Rmd | 66 +------------------- 36 files changed, 230 insertions(+), 293 deletions(-)
Title: Sample Size Calculation for Propensity Score Analysis
Description: Sample size calculations in causal inference with observational data are increasingly desired. This package is a tool to calculate sample size under prespecified power with minimal summary quantities needed.
Author: Bo Liu [aut, cre],
Xiaoxiao Zhou [ctb],
Fan Li [ctb]
Maintainer: Bo Liu <bl226@duke.edu>
Diff between PSpower versions 0.1.0 dated 2025-01-15 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 10 +- R/PSpower.R | 229 +++++++++++++++++++++++++--------------------------- R/util.R | 23 +---- man/PSpower.Rd | 29 ++---- man/plot.PSpower.Rd | 3 6 files changed, 143 insertions(+), 157 deletions(-)
Title: Tools for Summarising and Analysing Soundscape Data
Description: A variety of tools relevant to the analysis
of marine soundscape data. There are tools for downloading AIS (automatic identification system)
data from Marine Cadastre <https://hub.marinecadastre.gov>,
connecting AIS data to GPS coordinates, plotting summaries of various soundscape
measurements, and downloading relevant environmental variables (wind, swell height) from the
National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>.
Most tools were developed to work well with output from 'Triton' software, but can be adapted
to work with any similar measurements.
Author: Taiki Sakai [aut, cre],
Anne Simonis [ctb],
Shannon Rankin [ctb],
Megan McKenna [ctb],
Kaitlin Palmer [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMscapes versions 0.10.0 dated 2025-01-29 and 0.11.3 dated 2025-04-02
DESCRIPTION | 12 +- MD5 | 42 +++++---- NAMESPACE | 39 +++++++++ NEWS.md | 37 ++++++++ R/createOctaveLevel.R | 169 ++++++++++++--------------------------- R/evaluateDeployment.R |only R/evaluateRecordings.R |only R/formatEffort.R | 40 +++++++-- R/loadDetectionData.R | 128 ++++++++++++++++------------- R/loadMantaNc.R | 52 +++++++----- R/loadMultiscapeData.R | 13 +-- R/loadSoundscapeData.R | 109 ++++++++++++++++++++----- R/plotDetectionBoxplot.R | 6 + R/plotQAQC.R |only R/runQAQCReview.R |only R/utils.R | 13 ++- man/createOctaveLevel.Rd | 30 +++--- man/evaluateDeployment.Rd |only man/evaluateRecordings.Rd |only man/loadDetectionData.Rd | 11 +- man/loadMultiscapeData.Rd | 12 +- man/loadSoundscapeData.Rd | 7 + man/plotQAQC.Rd |only man/runQAQCReview.Rd |only tests/testthat/test-detection.R | 9 ++ tests/testthat/test-soundscape.R | 28 +++--- 26 files changed, 472 insertions(+), 285 deletions(-)
Title: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)
Description: This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tut [...truncated...]
Author: Matthew Mule [aut, cre] ,
Andrew Martins [aut] ,
John Tsang [pdr]
Maintainer: Matthew Mule <mattmule@gmail.com>
Diff between dsb versions 1.0.4 dated 2024-06-15 and 2.0.0 dated 2025-04-02
DESCRIPTION | 8 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 4 R/ModelNegativeADTnorm.r | 63 ++- R/dsb.r | 143 ++++---- README.md | 284 +++++++++------- build/vignette.rds |binary inst/doc/additional_topics.R | 22 - inst/doc/additional_topics.html | 356 ++++++++++----------- inst/doc/end_to_end_workflow.R | 36 +- inst/doc/end_to_end_workflow.html | 622 ++++++++++++++++++------------------- inst/doc/fastkm.R |only inst/doc/fastkm.Rmd |only inst/doc/fastkm.html |only inst/doc/no_empty_drops.R | 17 - inst/doc/no_empty_drops.Rmd | 12 inst/doc/no_empty_drops.html | 195 +++++------ inst/doc/understanding_dsb.R | 18 - inst/doc/understanding_dsb.html | 408 ++++++++++++------------ man/DSBNormalizeProtein.Rd | 47 +- man/ModelNegativeADTnorm.Rd | 11 man/figures/dsb_arguments.png |only man/figures/timingsfig2.png |only man/figures/vignette/compare.png |only man/figures/vignette/corr.png |only tests/testthat/test_dsb_function.R | 61 ++- vignettes/fastkm.Rmd |only vignettes/no_empty_drops.Rmd | 12 29 files changed, 1238 insertions(+), 1130 deletions(-)
Title: Parallel Numerical Derivatives, Gradients, Jacobians, and
Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations
can be calculated using the 'pnd' package with parallel capabilities and
optimal step-size selection to improve accuracy. These functions facilitate
efficient computation of derivatives, gradients, Jacobians, and Hessians,
allowing for more evaluations to reduce the mathematical and machine errors.
Designed for compatibility with the 'numDeriv' package,
which has not received updates in several years, it introduces advanced features
such as computing derivatives of arbitrary order, improving
the accuracy of Hessian approximations by avoiding repeated differencing,
and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between pnd versions 0.0.9 dated 2025-03-11 and 0.0.10 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 42 +++++----- NEWS.md | 1 R/gradient.R | 99 +++++++++++++------------ R/step-select.R | 118 +++++++++++++++--------------- R/zzz.R | 2 build/partial.rdb |binary inst/CITATION | 28 +++---- inst/doc/compatibility-with-numDeriv.html | 15 ++- inst/doc/fast-and-accurate.html | 7 + inst/doc/step-size-selection.html | 7 + man/GenD.Rd | 14 +++ man/Grad.Rd | 24 ++++-- man/Jacobian.Rd | 14 +++ man/checkDimensions.Rd | 6 + man/step.DV.Rd | 21 ++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-Grad.R | 14 +++ tests/testthat/test-Jacobian.R | 12 +++ tests/testthat/test-gradstep.R | 4 - tests/testthat/test-step.CR.R | 2 tests/testthat/test-step.DV.R | 9 +- 22 files changed, 262 insertions(+), 183 deletions(-)
Title: Methods for Penetrance Estimation in Family-Based Studies
Description: Implements statistical methods for estimating disease penetrance in
family-based studies. Penetrance refers to the probability of disease§
manifestation in individuals carrying specific genetic variants. The package
provides tools for age-specific penetrance estimation, handling missing data,
and accounting for ascertainment bias in family studies.
Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.
Author: Nicolas Kubista [aut, cre],
BayesMendel Lab [aut]
Maintainer: Nicolas Kubista <bmendel@jimmy.harvard.edu>
Diff between penetrance versions 0.1.0 dated 2025-03-03 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 14 +- R/helpers.R | 8 - R/mhChain.R | 187 ++++++++++++++++++++++++++--------- R/mhLoglikehood.r | 6 - R/penetranceMain.R | 277 ++++++++++++++++++++++++++++++++++++++++++----------- man/mhChain.Rd | 28 ++--- man/penetrance.Rd | 33 +++--- 8 files changed, 411 insertions(+), 148 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of
implementation can be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.2 dated 2024-12-07 and 3.0.3 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++++++-------- NAMESPACE | 4 ---- R/core_functions.R | 12 ------------ R/csi.R |only R/far.R |only R/nse.R |only R/pod.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/case_study.html | 4 ++-- inst/doc/introduction.html | 4 ++-- man/csi.Rd |only man/far.Rd |only man/nse.Rd |only man/pod.Rd |only man/reexports.Rd | 6 +----- 17 files changed, 24 insertions(+), 36 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.0 dated 2025-01-17 and 1.1 dated 2025-04-02
DESCRIPTION | 7 ++-- MD5 | 13 ++++--- NAMESPACE | 6 ++- R/diabetes.R |only R/main.R | 74 +++++++++++++++++++++++++++++++++++++-------- data |only man/create_kernel_plot.Rd | 14 ++++++-- man/diabetes.Rd |only tests/testthat/test-main.R | 27 +++++++++++++--- 9 files changed, 110 insertions(+), 31 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert
et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.
Author: Miika Ahdesmaki [aut, cre],
Konstantinos Fokianos [aut],
Korbinian Strimmer [aut]
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>
Diff between GeneCycle versions 1.1.5 dated 2021-01-05 and 1.1.6 dated 2025-04-02
CHANGES | 3 +++ DESCRIPTION | 26 ++++++++++++++++++++------ MD5 | 16 ++++++++-------- man/avpg.Rd | 2 +- man/dominant.freqs.Rd | 2 +- man/fisher.g.test.Rd | 2 +- man/is.constant.Rd | 2 +- man/periodogram.Rd | 2 +- man/robust.g.test.Rd | 2 +- 9 files changed, 37 insertions(+), 20 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-30 dated 2024-12-03 and 0.9-32 dated 2025-04-02
dbarts-0.9-30/dbarts/tests/testthat |only dbarts-0.9-30/dbarts/tests/testthat.R |only dbarts-0.9-32/dbarts/DESCRIPTION | 10 dbarts-0.9-32/dbarts/MD5 | 139 - dbarts-0.9-32/dbarts/R/A_class.R | 267 +- dbarts-0.9-32/dbarts/R/bart.R | 48 dbarts-0.9-32/dbarts/R/dbarts.R | 1333 +++++----- dbarts-0.9-32/dbarts/R/generics.R | 5 dbarts-0.9-32/dbarts/R/multipleAssignment.R | 1 dbarts-0.9-32/dbarts/R/partialDependence.R | 7 dbarts-0.9-32/dbarts/R/rbart.R | 14 dbarts-0.9-32/dbarts/build/vignette.rds |binary dbarts-0.9-32/dbarts/configure.ac | 2 dbarts-0.9-32/dbarts/inst/NEWS.Rd | 31 dbarts-0.9-32/dbarts/inst/doc/gibbs_sampler_mixture_model.pdf |binary dbarts-0.9-32/dbarts/inst/doc/working_with_saved_trees.pdf |binary dbarts-0.9-32/dbarts/inst/include/dbarts/R_C_interface.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/bartFit.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/control.hpp | 99 dbarts-0.9-32/dbarts/inst/tinytest |only dbarts-0.9-32/dbarts/man/bart.Rd | 4 dbarts-0.9-32/dbarts/man/dbartsSampler-class.Rd | 20 dbarts-0.9-32/dbarts/src/R_C_interface.cpp | 31 dbarts-0.9-32/dbarts/src/R_interface.cpp | 12 dbarts-0.9-32/dbarts/src/R_interface_common.cpp | 2 dbarts-0.9-32/dbarts/src/R_interface_sampler.cpp | 50 dbarts-0.9-32/dbarts/src/R_interface_sampler.hpp | 8 dbarts-0.9-32/dbarts/src/crossvalidate.cpp | 4 dbarts-0.9-32/dbarts/src/dbarts/bartFit.cpp | 339 +- dbarts-0.9-32/dbarts/src/dbarts/tree.cpp | 14 dbarts-0.9-32/dbarts/src/dbarts/tree.hpp | 4 dbarts-0.9-32/dbarts/src/external/randomBase.c | 10 dbarts-0.9-32/dbarts/src/include/external/random.h | 2 dbarts-0.9-32/dbarts/src/include/misc/thread.h | 3 dbarts-0.9-32/dbarts/src/misc/hierarchicalThreadManager.c | 4 dbarts-0.9-32/dbarts/src/misc/partition_body.c | 79 dbarts-0.9-32/dbarts/src/misc/partition_neon.c | 39 dbarts-0.9-32/dbarts/src/rc/bounds.c | 71 dbarts-0.9-32/dbarts/tests/tinytest.R |only 39 files changed, 1653 insertions(+), 1019 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Data sets of the Spanish National Forest Inventory <https://www.miteco.gob.es/es/biodiversidad/servicios/banco-datos-naturaleza/informacion-disponible.html> are processed to compute tree metrics and statistics. Function metrics2Vol() controls most of the routines.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.4 dated 2021-09-20 and 0.4.1 dated 2025-04-02
DESCRIPTION | 30 ++++++++++++++++++++++++------ MD5 | 22 +++++++++++----------- NEWS | 14 +++++++++++++- R/nfiMetrics.R | 2 +- R/readNFI.R | 6 +++--- R/urlToTemp.R | 2 +- man/dbhMetric.Rd | 2 +- man/dendroMetrics.Rd | 16 ++++++++-------- man/metrics2Vol.Rd | 2 +- man/nfiMetrics.Rd | 4 ++-- man/readNFI.Rd | 20 ++++++++++---------- man/urlToTemp.Rd | 4 ++-- 12 files changed, 77 insertions(+), 47 deletions(-)
More information about SecretsProvider at CRAN
Permanent link
Title: 'shiny' App for National Accounts
Description: Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
Author: Muhammad Yaseen [aut, cre, cph]
,
Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakNAcc versions 0.1.0 dated 2024-11-11 and 0.3.0 dated 2025-04-02
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 6 ++++ README.md | 17 +++++++++-- inst/shinyapp/GNIConstant.RDS |binary inst/shinyapp/GNICurrent.RDS |binary inst/shinyapp/NAConstant.RDS |binary inst/shinyapp/NACurrent.RDS |binary inst/shinyapp/rsconnect/shinyapps.io/myaseen208/PakNAcc.dcf | 2 - inst/shinyapp/ui.R | 8 ++--- 10 files changed, 37 insertions(+), 20 deletions(-)
Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working with vector space models of semantics/distributional semantic models/word embeddings.
Originally built for LSA models (hence the name), but can be used for all such vector-based models.
For actually building a vector semantic space, use the package 'lsa' or other specialized software.
Downloadable semantic spaces can be found at <https://sites.google.com/site/fritzgntr/software-resources>.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>
Diff between LSAfun versions 0.7.1 dated 2023-11-17 and 0.8.1 dated 2025-04-02
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 2 ++ R/Predication.r | 13 +++++++------ R/centroid_analysis.r |only man/centroid_analysis.Rd |only 7 files changed, 28 insertions(+), 15 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.32 dated 2025-02-05 and 0.1.35 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 8 + build/vignette.rds |binary src/core/isomorphism/foo.c |only src/core/isomorphism/lad.c | 136 ++++++++++++++++---------------- src/core/isomorphism/lad.c.org.20250205 |only 6 files changed, 76 insertions(+), 74 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both there 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [ctb]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>
Diff between dndR versions 2.0.0 dated 2024-04-26 and 3.0.0 dated 2025-04-02
DESCRIPTION | 27 +-- MD5 | 164 ++++++++++++---------- NEWS.md | 15 ++ R/ability_scores.R | 121 ++++++++-------- R/class_block.R | 120 ++++++++++------ R/cr_convert.R | 16 -- R/creature_list.R | 89 ++++++------ R/creature_text.R | 16 +- R/data-doc_creatures.R | 2 R/data-doc_monster-table.R | 2 R/data-doc_spells.R | 2 R/encounter_creator.R | 254 ++++++++++++++++++++++------------ R/mod_calc.R | 10 - R/monster_creator.R | 100 ++++++------- R/monster_stats.R | 21 +- R/npc_creator.R | 20 +- R/party_diagram.R | 131 +++++++++-------- R/pc_creator.R | 76 ++++++---- R/pc_level_calc.R | 18 -- R/probability_plot.R | 18 +- R/race_mods.R | 278 +++++++++++++++++++++++++------------- R/reference_functions.R | 6 R/reroll.R | 4 R/roll.R | 36 +++- R/spell_list.R | 19 +- R/spell_text.R | 16 +- R/xp_cost.R | 66 +++++---- R/xp_pool.R | 147 +++++++++++++------- README.md | 108 +------------- build/vignette.rds |binary data/creatures.rda |binary data/spells.rda |binary inst/doc/dndr_00_dice.html | 18 +- inst/doc/dndr_01_characters.html | 39 ++--- inst/doc/dndr_02_creatures.html | 50 ++++-- inst/doc/dndr_03_spells.html | 24 ++- inst/doc/dndr_04_encounters.R | 20 +- inst/doc/dndr_04_encounters.Rmd | 57 +++++-- inst/doc/dndr_04_encounters.html | 163 ++++++++++++++-------- inst/doc/dndr_05_visuals.html | 10 - inst/doc/dndr_99_dmg-vs-dndr.R | 5 inst/doc/dndr_99_dmg-vs-dndr.Rmd | 7 inst/doc/dndr_99_dmg-vs-dndr.html | 14 - man/ability_scores.Rd | 8 - man/class_block.Rd | 19 +- man/creature_list.Rd | 10 - man/creature_text.Rd | 8 - man/creatures.Rd | 2 man/dndR-package.Rd | 6 man/dnd_classes.Rd | 2 man/dnd_damage_types.Rd | 2 man/dnd_races.Rd | 2 man/encounter_creator.Rd | 26 +++ man/mod_calc.Rd | 2 man/monster_creator.Rd | 4 man/monster_stats.Rd | 8 + man/monster_table.Rd | 2 man/npc_creator.Rd | 2 man/party_diagram.Rd | 4 man/pc_creator.Rd | 23 +-- man/pc_level_calc.Rd | 2 man/probability_plot.Rd | 2 man/race_mods.Rd | 4 man/reroll.Rd | 4 man/roll.Rd | 6 man/spell_list.Rd | 9 - man/spell_text.Rd | 8 - man/spells.Rd | 2 man/xp_cost.Rd | 13 + man/xp_pool.Rd | 15 +- tests |only vignettes/dndr_04_encounters.Rmd | 57 +++++-- vignettes/dndr_99_dmg-vs-dndr.Rmd | 7 73 files changed, 1516 insertions(+), 1052 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.1.1 dated 2025-02-03 and 4.2.0 dated 2025-04-02
smooth-4.1.1/smooth/man/auto.ces.Rd |only smooth-4.1.1/smooth/man/auto.gum.Rd |only smooth-4.2.0/smooth/DESCRIPTION | 8 smooth-4.2.0/smooth/MD5 | 116 +++--- smooth-4.2.0/smooth/NAMESPACE | 2 smooth-4.2.0/smooth/NEWS | 11 smooth-4.2.0/smooth/R/RcppExports.R | 4 smooth-4.2.0/smooth/R/adam-ces.R |only smooth-4.2.0/smooth/R/adam-gum.R |only smooth-4.2.0/smooth/R/adam-sma.R | 2 smooth-4.2.0/smooth/R/adam.R | 383 +++++++++++++++------- smooth-4.2.0/smooth/R/adamGeneral.R | 43 ++ smooth-4.2.0/smooth/R/autoces.R | 283 +++++++--------- smooth-4.2.0/smooth/R/autogum.R | 288 +++++++--------- smooth-4.2.0/smooth/R/automsarima.R | 1 smooth-4.2.0/smooth/R/ces.R | 145 +------- smooth-4.2.0/smooth/R/es.R | 6 smooth-4.2.0/smooth/R/gum.R | 181 +--------- smooth-4.2.0/smooth/R/methods.R | 14 smooth-4.2.0/smooth/R/oes.R | 48 +- smooth-4.2.0/smooth/R/oesg.R | 79 ++-- smooth-4.2.0/smooth/R/smooth-package.R | 12 smooth-4.2.0/smooth/README.md | 2 smooth-4.2.0/smooth/build/partial.rdb |binary smooth-4.2.0/smooth/build/vignette.rds |binary smooth-4.2.0/smooth/inst/doc/adam.R | 6 smooth-4.2.0/smooth/inst/doc/adam.html | 228 ++++++------- smooth-4.2.0/smooth/inst/doc/ces.R | 11 smooth-4.2.0/smooth/inst/doc/ces.Rmd | 25 - smooth-4.2.0/smooth/inst/doc/ces.html | 137 +++---- smooth-4.2.0/smooth/inst/doc/es.R | 2 smooth-4.2.0/smooth/inst/doc/es.html | 18 - smooth-4.2.0/smooth/inst/doc/gum.R | 2 smooth-4.2.0/smooth/inst/doc/gum.Rmd | 2 smooth-4.2.0/smooth/inst/doc/gum.html | 137 ++----- smooth-4.2.0/smooth/inst/doc/oes.R | 7 smooth-4.2.0/smooth/inst/doc/oes.Rmd | 5 smooth-4.2.0/smooth/inst/doc/oes.html | 129 +++---- smooth-4.2.0/smooth/inst/doc/simulate.R | 2 smooth-4.2.0/smooth/inst/doc/simulate.Rmd | 4 smooth-4.2.0/smooth/inst/doc/simulate.html | 80 ++-- smooth-4.2.0/smooth/inst/doc/sma.html | 18 - smooth-4.2.0/smooth/inst/doc/smooth.html | 4 smooth-4.2.0/smooth/inst/doc/ssarima.R | 2 smooth-4.2.0/smooth/inst/doc/ssarima.html | 46 +- smooth-4.2.0/smooth/man/adam.Rd | 4 smooth-4.2.0/smooth/man/ces.Rd | 351 +++++++++----------- smooth-4.2.0/smooth/man/forecast.smooth.Rd | 7 smooth-4.2.0/smooth/man/gum.Rd | 352 ++++++++------------ smooth-4.2.0/smooth/man/msarima.Rd | 1 smooth-4.2.0/smooth/man/sim.ces.Rd | 8 smooth-4.2.0/smooth/man/smooth.Rd | 20 - smooth-4.2.0/smooth/src/RcppExports.cpp | 7 smooth-4.2.0/smooth/src/adamGeneral.cpp | 10 smooth-4.2.0/smooth/tests/testthat/test_ces.R | 30 - smooth-4.2.0/smooth/tests/testthat/test_gum.R | 28 - smooth-4.2.0/smooth/tests/testthat/test_ssarima.R | 2 smooth-4.2.0/smooth/vignettes/ces.Rmd | 25 - smooth-4.2.0/smooth/vignettes/gum.Rmd | 2 smooth-4.2.0/smooth/vignettes/oes.Rmd | 5 smooth-4.2.0/smooth/vignettes/simulate.Rmd | 4 61 files changed, 1563 insertions(+), 1786 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.20.4 dated 2025-03-15 and 2.21.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Consensus Clustering of Omic Data
Description: Procedures to perform consensus clustering starting from a dissimilarity matrix or a data matrix. It's allowed to select if the subsampling has to be by samples or features. In case of computational heavy load, the procedures can run in parallel.
Author: Stefano Maria Pagnotta [aut, cre, cph]
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>
Diff between yaConsensus versions 1.0 dated 2021-07-01 and 1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 19 ++++++---- NAMESPACE | 7 ++- R/cut_k_leaves.R |only R/get_ecdf.R |only R/monti.R |only R/plot.yaConsensus.R | 78 +++++++++++++++++++++++++++++++++++-------- R/print.yaConsensus.R | 29 ++++++++------- R/reduce_dist.R |only R/summary.yaConsensus_plot.R | 6 +++ man/monti.Rd |only man/plot.yaConsensus.Rd | 15 ++++++-- man/yaConsensus.Rd | 2 - 13 files changed, 118 insertions(+), 46 deletions(-)
Title: Terrestrial Water Cycle
Description: An open-access tool/framework that constitutes the core functions
to analyze terrestrial water cycle data across various spatio-temporal scales.
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between twc versions 0.0.1 dated 2024-12-02 and 0.0.2 dated 2025-04-02
twc-0.0.1/twc/R/csi.R |only twc-0.0.1/twc/R/far.R |only twc-0.0.1/twc/R/pod.R |only twc-0.0.1/twc/man/csi.Rd |only twc-0.0.1/twc/man/far.Rd |only twc-0.0.1/twc/man/pod.Rd |only twc-0.0.2/twc/DESCRIPTION | 8 ++++---- twc-0.0.2/twc/MD5 | 18 +++++++----------- twc-0.0.2/twc/NAMESPACE | 8 +++++--- twc-0.0.2/twc/R/fldmean.R | 8 ++++++-- twc-0.0.2/twc/R/globals.R | 8 +++++--- twc-0.0.2/twc/R/rank_repres.R |only twc-0.0.2/twc/README.md | 2 +- twc-0.0.2/twc/man/rank_repres.Rd |only 14 files changed, 28 insertions(+), 24 deletions(-)
Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based
on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre, cph]
,
Frank Harrell [ctb]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between tbrf versions 0.1.5 dated 2020-04-09 and 0.1.6 dated 2025-04-02
tbrf-0.1.5/tbrf/tests/spelling.R |only tbrf-0.1.6/tbrf/DESCRIPTION | 18 tbrf-0.1.6/tbrf/MD5 | 40 tbrf-0.1.6/tbrf/NEWS.md | 8 tbrf-0.1.6/tbrf/R/tbr_binom.R | 2 tbrf-0.1.6/tbrf/R/tbr_gmean.R | 33 tbrf-0.1.6/tbrf/R/tbr_mean.R | 14 tbrf-0.1.6/tbrf/R/tbr_median.R | 14 tbrf-0.1.6/tbrf/R/tbr_sd.R | 2 tbrf-0.1.6/tbrf/R/tbr_sum.R | 2 tbrf-0.1.6/tbrf/README.md | 149 +-- tbrf-0.1.6/tbrf/build/vignette.rds |binary tbrf-0.1.6/tbrf/inst/CITATION |only tbrf-0.1.6/tbrf/inst/WORDLIST | 4 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.R | 2 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.html | 526 ++++++----- tbrf-0.1.6/tbrf/man/figures/README-tbr_hour-1.png |binary tbrf-0.1.6/tbrf/man/figures/README-tbr_threehour-1.png |binary tbrf-0.1.6/tbrf/man/gm_mean_ci.Rd | 16 tbrf-0.1.6/tbrf/man/mean_ci.Rd | 12 tbrf-0.1.6/tbrf/man/median_ci.Rd | 12 tbrf-0.1.6/tbrf/tests/testthat/test-internalStatsFunctions.R | 28 22 files changed, 510 insertions(+), 372 deletions(-)
Title: Access the City of Toronto Open Data Portal
Description: Access data from the "City of Toronto
Open Data Portal" (<https://open.toronto.ca>) directly from R.
Author: Sharla Gelfand [aut, cre],
City of Toronto [cph, fnd]
Maintainer: Sharla Gelfand <sharla.gelfand@gmail.com>
Diff between opendatatoronto versions 0.1.5 dated 2022-04-13 and 0.1.6 dated 2025-04-02
opendatatoronto-0.1.5/opendatatoronto/vignettes/articles/multiple_resources_purrr.Rmd |only opendatatoronto-0.1.6/opendatatoronto/DESCRIPTION | 8 opendatatoronto-0.1.6/opendatatoronto/LICENSE | 2 opendatatoronto-0.1.6/opendatatoronto/MD5 | 29 - opendatatoronto-0.1.6/opendatatoronto/NEWS.md | 4 opendatatoronto-0.1.6/opendatatoronto/R/utils.R | 2 opendatatoronto-0.1.6/opendatatoronto/README.md | 140 +++--- opendatatoronto-0.1.6/opendatatoronto/build/vignette.rds |binary opendatatoronto-0.1.6/opendatatoronto/inst/doc/intro-opendatatoronto.html | 216 +++++++++- opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-browse.R | 15 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-get_resource.R | 16 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-list_package_resources.R | 20 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-packages.R | 21 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-utils.R | 7 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/opendatatoronto.Rmd | 4 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/spatial_data.Rmd | 87 ---- 16 files changed, 355 insertions(+), 216 deletions(-)
More information about opendatatoronto at CRAN
Permanent link
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-6 dated 2024-03-20 and 0.22-7 dated 2025-04-02
lattice-0.22-6/lattice/man/foo |only lattice-0.22-7/lattice/ChangeLog | 76 ++++++++++ lattice-0.22-7/lattice/DESCRIPTION | 8 - lattice-0.22-7/lattice/MD5 | 47 +++--- lattice-0.22-7/lattice/build/vignette.rds |binary lattice-0.22-7/lattice/data/barley.rda |binary lattice-0.22-7/lattice/data/environmental.rda |binary lattice-0.22-7/lattice/data/ethanol.rda |binary lattice-0.22-7/lattice/data/melanoma.rda |binary lattice-0.22-7/lattice/data/singer.rda |binary lattice-0.22-7/lattice/inst/doc/grid.pdf |binary lattice-0.22-7/lattice/inst/po/de/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/po/R-de.po | 30 ++- lattice-0.22-7/lattice/po/R-fr.po | 13 + lattice-0.22-7/lattice/po/R-it.po | 13 + lattice-0.22-7/lattice/po/R-ko.po | 13 + lattice-0.22-7/lattice/po/R-lattice.pot | 13 + lattice-0.22-7/lattice/po/R-pl.po | 17 +- lattice-0.22-7/lattice/tests/MASSch04.R | 6 lattice-0.22-7/lattice/tests/call.R | 2 lattice-0.22-7/lattice/tests/dataframe-methods.R | 2 lattice-0.22-7/lattice/tests/scales.R | 2 lattice-0.22-7/lattice/tests/temp.R | 6 lattice-0.22-7/lattice/tests/test.R | 12 - 25 files changed, 179 insertions(+), 81 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Camille Thabard [ctb] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.12.0 dated 2025-02-25 and 0.13.0 dated 2025-04-02
dimensio-0.12.0/dimensio/inst/examples/ex-envelopes.R |only dimensio-0.12.0/dimensio/inst/examples/ex-wrap.R |only dimensio-0.12.0/dimensio/man/viz_biplot.Rd |only dimensio-0.12.0/dimensio/man/wrap.Rd |only dimensio-0.13.0/dimensio/DESCRIPTION | 9 dimensio-0.13.0/dimensio/MD5 | 107 ++-- dimensio-0.13.0/dimensio/NEWS.md | 11 dimensio-0.13.0/dimensio/R/AllGenerics.R | 144 +++-- dimensio-0.13.0/dimensio/R/biplot.R | 55 +- dimensio-0.13.0/dimensio/R/ca.R | 19 dimensio-0.13.0/dimensio/R/dimensio-package.R | 2 dimensio-0.13.0/dimensio/R/export.R | 29 + dimensio-0.13.0/dimensio/R/pca.R | 4 dimensio-0.13.0/dimensio/R/pcoa.R | 8 dimensio-0.13.0/dimensio/R/plot.R | 33 + dimensio-0.13.0/dimensio/R/viz_ellipse.R | 80 +++ dimensio-0.13.0/dimensio/R/viz_hull.R | 75 ++- dimensio-0.13.0/dimensio/R/wrap_ellipses.R | 90 +++ dimensio-0.13.0/dimensio/R/wrap_hull.R | 38 + dimensio-0.13.0/dimensio/README.md | 4 dimensio-0.13.0/dimensio/inst/doc/pca.R | 20 dimensio-0.13.0/dimensio/inst/doc/pca.Rmd | 21 dimensio-0.13.0/dimensio/inst/doc/pca.html | 247 ++++------ dimensio-0.13.0/dimensio/inst/examples/ex-confidence.R |only dimensio-0.13.0/dimensio/inst/examples/ex-ellipses.R |only dimensio-0.13.0/dimensio/inst/examples/ex-hull.R |only dimensio-0.13.0/dimensio/inst/examples/ex-pcoa.R | 14 dimensio-0.13.0/dimensio/inst/examples/ex-plot.R | 2 dimensio-0.13.0/dimensio/inst/examples/ex-tolerance.R |only dimensio-0.13.0/dimensio/inst/tinytest/_snaps/pca_correlations.rds |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_contrib.svg | 200 ++++---- dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_eig.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quali.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quanti.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_ca.R | 26 - dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_pca.R | 18 dimensio-0.13.0/dimensio/inst/tinytest/test_ca.R | 1 dimensio-0.13.0/dimensio/inst/tinytest/test_pca.R | 4 dimensio-0.13.0/dimensio/inst/tinytest/test_pcoa.R | 34 + dimensio-0.13.0/dimensio/inst/tinytest/test_plot_ca.R | 2 dimensio-0.13.0/dimensio/inst/tinytest/test_plot_pca.R | 30 - dimensio-0.13.0/dimensio/man/PCOA-class.Rd | 14 dimensio-0.13.0/dimensio/man/biplot.Rd | 39 - dimensio-0.13.0/dimensio/man/ca.Rd | 12 dimensio-0.13.0/dimensio/man/dimensio-package.Rd | 2 dimensio-0.13.0/dimensio/man/export.Rd | 3 dimensio-0.13.0/dimensio/man/pcoa.Rd | 14 dimensio-0.13.0/dimensio/man/plot.Rd | 19 dimensio-0.13.0/dimensio/man/screeplot.Rd | 4 dimensio-0.13.0/dimensio/man/viz_confidence.Rd |only dimensio-0.13.0/dimensio/man/viz_contributions.Rd | 4 dimensio-0.13.0/dimensio/man/viz_ellipses.Rd | 115 ---- dimensio-0.13.0/dimensio/man/viz_hull.Rd |only dimensio-0.13.0/dimensio/man/viz_individuals.Rd | 6 dimensio-0.13.0/dimensio/man/viz_tolerance.Rd |only dimensio-0.13.0/dimensio/man/viz_variables.Rd | 6 dimensio-0.13.0/dimensio/vignettes/pca.Rmd | 21 67 files changed, 984 insertions(+), 602 deletions(-)
More information about D4TAlink.light at CRAN
Permanent link
Title: Timing, Anatomical, Therapeutic and Chemical Based Medication
Clustering
Description: Agglomerative hierarchical clustering with a bespoke distance
measure based on medication similarities in the Anatomical Therapeutic
Chemical Classification System, medication timing and
medication amount or dosage. Tools for summarizing, illustrating and
manipulating the cluster objects are also available.
Author: Anna Laksafoss [aut, cre]
Maintainer: Anna Laksafoss <adls@ssi.dk>
Diff between tame versions 0.0.1 dated 2023-02-23 and 0.2.0 dated 2025-04-02
tame-0.0.1/tame/R/is.medic.R |only tame-0.0.1/tame/R/medic_helpers.R |only tame-0.0.1/tame/R/summary_helpers.R |only tame-0.0.1/tame/man/amounts.Rd |only tame-0.0.1/tame/man/frequencies.Rd |only tame-0.0.1/tame/man/interactions.Rd |only tame-0.0.1/tame/man/medications.Rd |only tame-0.0.1/tame/man/trajectories.Rd |only tame-0.0.1/tame/tests/testthat/test-medic_helpers.R |only tame-0.0.1/tame/tests/testthat/test-summary_helpers.R |only tame-0.2.0/tame/DESCRIPTION | 16 tame-0.2.0/tame/LICENSE | 4 tame-0.2.0/tame/MD5 | 84 - tame-0.2.0/tame/NAMESPACE | 70 + tame-0.2.0/tame/R/crop.R |only tame-0.2.0/tame/R/documenting_data.R | 6 tame-0.2.0/tame/R/employ.R | 202 ++-- tame-0.2.0/tame/R/enrich.R | 5 tame-0.2.0/tame/R/extractors.R | 37 tame-0.2.0/tame/R/medic-utils.R |only tame-0.2.0/tame/R/medic.R | 223 ++-- tame-0.2.0/tame/R/plot-utils.R |only tame-0.2.0/tame/R/plot.R |only tame-0.2.0/tame/R/summary-utils.R |only tame-0.2.0/tame/R/summary.R | 905 +++++++++++++++--- tame-0.2.0/tame/R/tame_package.R | 6 tame-0.2.0/tame/README.md | 23 tame-0.2.0/tame/man/cluster_frequency.Rd |only tame-0.2.0/tame/man/cluster_selector.Rd | 8 tame-0.2.0/tame/man/comedication_count.Rd |only tame-0.2.0/tame/man/construct_color_scales.Rd |only tame-0.2.0/tame/man/construct_plot_data.Rd |only tame-0.2.0/tame/man/construct_time_scale.Rd |only tame-0.2.0/tame/man/default_atc_groups.Rd |only tame-0.2.0/tame/man/employ.Rd | 2 tame-0.2.0/tame/man/enrich.Rd | 4 tame-0.2.0/tame/man/flatten_trajctories.Rd |only tame-0.2.0/tame/man/is.medic.Rd | 2 tame-0.2.0/tame/man/medic.Rd | 12 tame-0.2.0/tame/man/medication_frequency.Rd |only tame-0.2.0/tame/man/method_selector.Rd | 8 tame-0.2.0/tame/man/parameters_constructor.Rd | 6 tame-0.2.0/tame/man/plot_cluster_frequency.Rd |only tame-0.2.0/tame/man/plot_comedication_count.Rd |only tame-0.2.0/tame/man/plot_medication_frequency.Rd |only tame-0.2.0/tame/man/plot_summary.Rd |only tame-0.2.0/tame/man/plot_timing_atc_group.Rd |only tame-0.2.0/tame/man/plot_timing_trajectory.Rd |only tame-0.2.0/tame/man/print.summary.medic.Rd |only tame-0.2.0/tame/man/str.summary.medic.Rd |only tame-0.2.0/tame/man/summary.medic.Rd | 60 - tame-0.2.0/tame/man/summary_crop.Rd |only tame-0.2.0/tame/man/timing_atc_group.Rd |only tame-0.2.0/tame/man/timing_trajectory.Rd |only tame-0.2.0/tame/tests/testthat/test-RcppExports.R | 30 tame-0.2.0/tame/tests/testthat/test-enrich.R | 6 tame-0.2.0/tame/tests/testthat/test-extractors.R | 18 tame-0.2.0/tame/tests/testthat/test-ismedic.R | 6 tame-0.2.0/tame/tests/testthat/test-medic-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary.R | 6 61 files changed, 1261 insertions(+), 488 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.4.0 dated 2025-01-14 and 1.4.2 dated 2025-04-02
DESCRIPTION | 9 - MD5 | 36 ++-- NEWS.md | 10 + R/formantplot.R | 50 ++++- R/intensityplot.R | 45 ++++- R/pitchplot.R | 90 +++++++--- R/praatpicture.R | 44 +++- R/specplot.R | 74 ++++++-- R/tgplot.R | 55 +++++- R/waveplot.R | 34 ++- inst/shiny/shiny_praatpicture/rsconnect/shinyapps.io/rpuggaardrode/praatpicture.dcf | 2 inst/shiny/shiny_praatpicture/server.R | 18 +- inst/shiny/shiny_praatpicture/ui.R | 3 man/formantplot.Rd | 3 man/intensityplot.Rd | 3 man/pitchplot.Rd | 3 man/praatpicture.Rd | 25 ++ man/tgplot.Rd | 13 + man/waveplot.Rd | 3 19 files changed, 399 insertions(+), 121 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-1 dated 2023-12-20 and 1.9-2 dated 2025-04-02
ChangeLog | 81 + DESCRIPTION | 14 MD5 | 98 - NAMESPACE | 14 R/bam.r | 692 ++++++++----- R/efam.r | 854 ++++++++++++++-- R/fast-REML.r | 372 +++++-- R/gam.fit3.r | 55 - R/gam.fit4.r | 76 - R/gamlss.r | 207 ++-- R/mgcv.r | 488 ++++++--- R/misc.r | 87 + R/mvam.r | 8 R/plots.r | 24 R/smooth.r | 158 ++- build/partial.rdb |binary inst/CITATION | 18 man/NCV.Rd | 36 man/Sl.setup.Rd | 7 man/XWXd.Rd | 16 man/bam.Rd | 11 man/clog.Rd |only man/cpois.Rd |only man/family.mgcv.Rd | 9 man/gam.Rd | 2 man/gam.side.Rd | 2 man/gammals.Rd | 2 man/gevlss.Rd | 11 man/ldetS.Rd | 12 man/lp.Rd |only man/mchol.Rd |only man/mgcv-package.Rd | 2 man/mgcv-parallel.Rd | 6 man/mroot.Rd | 12 man/pcls.Rd | 3 man/predict.gam.Rd | 22 man/slanczos.Rd | 2 man/smooth.construct.gp.smooth.spec.Rd | 2 man/twlss.Rd | 12 src/Makevars | 3 src/discrete.c | 1697 +++++++++++++++++++++++++++++++-- src/gdi.c | 58 - src/init.c | 13 src/magic.c | 6 src/mat.c | 286 ++++- src/matrix.c | 201 --- src/mgcv.c | 153 -- src/mgcv.h | 59 - src/ncv.c | 16 src/qp.c | 125 ++ src/sparse.c | 1 src/tprs.c | 5 52 files changed, 4611 insertions(+), 1427 deletions(-)
Title: Estimation and Testing for a Lognormal-Pareto Mixture
Description: Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>
Diff between LNPar versions 1.1.0 dated 2025-03-24 and 1.1.1 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/dpareto.r | 42 +++++++++++++++++++++--------------------- build/partial.rdb |binary man/dpareto.Rd | 2 +- 6 files changed, 33 insertions(+), 33 deletions(-)
Title: Boltzmann Entropy for Spatial Data
Description: Calculates several entropy metrics for spatial data
inspired by Boltzmann's entropy formula.
It includes metrics introduced by Cushman for landscape mosaics
(Cushman (2015) <doi:10.1007/s10980-015-0305-2>),
and landscape gradients and point patterns
(Cushman (2021) <doi:10.3390/e23121616>); by Zhao and Zhang for
landscape mosaics (Zhao and Zhang (2019) <doi:10.1007/s10980-019-00876-x>);
and by Gao et al. for landscape gradients
(Gao et al. (2018) <doi:10.1111/tgis.12315>; Gao and Li (2019) <doi:10.1007/s10980-019-00854-3>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between bespatial versions 0.1.2 dated 2024-06-07 and 0.1.3 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/get_distance.R | 2 +- README.md | 12 +++++++----- build/partial.rdb |binary man/figures/README-unnamed-chunk-3-1.png |binary 6 files changed, 17 insertions(+), 15 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 3.5-0 dated 2024-11-07 and 3.6-0 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/java/SDMX.jar |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.0 dated 2025-03-19 and 1.0.1 dated 2025-04-02
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 84 R/estimateSurvival.R | 3356 +++++++++++++-------------- R/tableSurvival.R | 843 +++--- README.md | 2 inst/doc/a01_Single_event_of_interest.R | 12 inst/doc/a01_Single_event_of_interest.Rmd | 649 ++--- inst/doc/a01_Single_event_of_interest.html | 1436 +++++------ inst/doc/a02_Competing_risk_survival.html | 220 - inst/doc/a03_Further_survival_analyses.html | 22 man/CohortSurvival-package.Rd | 2 tests/testthat/test-reexports-omopgenerics.R | 32 tests/testthat/test-tableSurvival.R | 237 + vignettes/a01_Single_event_of_interest.Rmd | 649 ++--- 15 files changed, 3871 insertions(+), 3715 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Description: Tools designed to perform and evaluate cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
A test for seed sample heterogeneity is now available. Mantel's permutation test can be found in this package.
A new approach for calculating its power is implemented. biotools also contains tests for genetic covariance components.
Heuristic approaches for performing non-parametric spatial predictions of generic response variables and
spatial gene diversity are implemented.
Author: Anderson Rodrigo da Silva [aut, cre]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between biotools versions 4.2 dated 2021-08-07 and 4.3 dated 2025-04-02
DESCRIPTION | 11 MD5 | 55 +- NEWS | 11 README.md |only build/vignette.rds |binary inst/CITATION | 41 -- inst/doc/overview.R | 30 - inst/doc/overview.html | 946 ++++++++++++++++++++++++++++-------------------- man/D2.disc.Rd | 10 man/D2.dist.Rd | 2 man/aer.Rd | 2 man/biotools-package.Rd | 26 - man/confusionmatrix.Rd | 2 man/cov2pcov.Rd | 6 man/distClust.Rd | 2 man/findSubsample.Rd | 4 man/fitplotsize.Rd | 6 man/gencovtest.Rd | 38 - man/mantelPower.Rd | 8 man/mantelTest.Rd | 14 man/multcor.test.Rd | 8 man/mvpaircomp.Rd | 14 man/optimumplotsize.Rd | 6 man/raise.matrix.rd | 2 man/sHe.Rd | 22 - man/samplesize.Rd | 24 - man/singh.Rd | 2 man/spatialpred.Rd | 10 man/tocher.Rd | 18 29 files changed, 750 insertions(+), 570 deletions(-)
Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between BigDataPE versions 0.0.95 dated 2025-02-17 and 0.0.96 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only R/BigDataPE.R | 47 ++++++++++++++++++++++++++--------------------- README.md | 2 +- man/bdpe_fetch_chunks.Rd | 10 +++++----- man/bdpe_fetch_data.Rd | 12 ++++++------ 7 files changed, 48 insertions(+), 42 deletions(-)
Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut],
Patrick Miller [aut],
Alexander M. Schoemann [aut] ,
Terrence D. Jorgensen [aut, cre]
,
Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between simsem versions 0.5-16 dated 2021-03-28 and 0.5-17 dated 2025-04-02
DESCRIPTION | 18 +- MD5 | 63 ++++----- NAMESPACE | 4 R/analyze.R | 79 ++++++----- R/anova-methods.R | 312 ++++++++++++++++++++++++++--------------------- R/bind.R | 2 R/drawParam.R | 6 R/find.R | 158 ++++++++++++----------- R/generate.R | 6 R/getPowerCoverage.R | 83 ++++++------ R/imposeMissing.R | 4 R/miss.R | 88 +++++++------ R/model.R | 31 +++- R/openMx.R | 4 R/sim.R | 89 +++++++++---- R/summarySimResult.R | 15 +- inst/CITATION |only man/SimDataDist-class.Rd | 116 ++++++++--------- man/SimMissing-class.Rd | 114 ++++++++--------- man/SimResult-class.Rd | 244 ++++++++++++++++++------------------ man/analyze.Rd | 24 +-- man/createData.Rd | 208 +++++++++++++++---------------- man/exportData.Rd | 60 ++++----- man/findPower.Rd | 10 - man/getExtraOutput.Rd | 8 - man/likRatioFit.Rd | 4 man/miss.Rd | 26 +-- man/model.Rd | 54 ++++---- man/modelLavaan.Rd | 4 man/pValue.Rd | 2 man/pValueNested.Rd | 4 man/pValueNonNested.Rd | 4 man/sim.Rd | 24 +-- 33 files changed, 989 insertions(+), 879 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] ,
Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.11 dated 2025-01-10 and 0.3.12 dated 2025-04-02
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/nanotime.R | 2 +- build/vignette.rds |binary inst/doc/nanotime-introduction.pdf |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 1.1-0 dated 2025-01-26 and 1.2-0 dated 2025-04-02
Changelog | 6 + DESCRIPTION | 9 -- MD5 | 38 ++++---- NAMESPACE | 2 R/kmSRdiagram.R |only R/kmbasisdiagram.R | 4 R/kmhasse.R | 4 R/kmsrvalidate.R |only R/kmsurmisefunction.R | 3 R/kmvalidate.R | 2 R/xpl.R | 11 +- build/vignette.rds |binary data/xpl.rda |binary inst/doc/kstMatrix.html | 210 +++++++++++++++++++----------------------------- man/kmSRdiagram.Rd |only man/kmSRvalidate.Rd |only man/kmbasisdiagram.Rd | 5 - man/kmdist.Rd | 1 man/kmhasse.Rd | 5 - man/kmvalidate.Rd | 3 man/xpl.Rd | 11 +- src/basis.c | 2 22 files changed, 144 insertions(+), 172 deletions(-)
Title: Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to
apply generalized additive models to bivariate dependence structures and
non-simplified vine copulas.
Author: Thomas Nagler [aut],
Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>
Diff between gamCopula versions 0.0-7 dated 2020-02-05 and 0.0-8 dated 2025-04-02
DESCRIPTION | 11 - MD5 | 87 ++++---- NEWS.md | 40 ++- R/AllClasses.R | 7 R/gamBiCop.R | 22 +- R/gamBiCopCDF.R | 2 R/gamBiCopFit.R | 6 R/gamBiCopPDF.R | 2 R/gamBiCopPredict.R | 6 R/gamBiCopSelect.R | 8 R/gamBiCopSimulate.R | 2 R/gamCopula-package.R |only R/gamVine.R | 19 - R/gamVineCopSelect.R | 4 R/gamVinePDF.R | 2 R/gamVineSeqFit.R | 2 R/gamVineStructureSelect.R | 2 R/utilsFamilies.R | 3 R/utilsPrivate.R | 4 R/utilsPublic.R | 11 - README.md | 110 +++++----- man/BiCopEta2Par.Rd | 5 man/BiCopPar2Eta.Rd | 6 man/EDF.gamBiCop-methods.Rd | 2 man/RVM2GVC.Rd | 6 man/formula.gamBiCop-methods.Rd | 6 man/gamBiCop-class.Rd | 4 man/gamBiCop.Rd | 4 man/gamBiCopCDF.Rd | 2 man/gamBiCopFit.Rd | 6 man/gamBiCopPDF.Rd | 2 man/gamBiCopPredict.Rd | 6 man/gamBiCopSelect.Rd | 6 man/gamBiCopSimulate.Rd | 2 man/gamCopula-package.Rd | 409 ++++++++++++++++++++-------------------- man/gamVine-class.Rd | 3 man/gamVine.Rd | 2 man/gamVineCopSelect.Rd | 4 man/gamVinePDF.Rd | 2 man/gamVineSeqFit.Rd | 2 man/gamVineStructureSelect.Rd | 2 man/plot.gamBiCop-methods.Rd | 6 man/plot.gamVine-methods.Rd | 6 man/summary.gamBiCop-methods.Rd | 4 man/summary.gamVine-methods.Rd | 4 45 files changed, 433 insertions(+), 418 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut],
Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.4 dated 2025-02-15 and 0.1.41 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/TDAvec_vignette.html | 7 ++++--- man/computePersistenceLandscape.Rd | 14 ++++++++------ src/PersistenceLandscape.cpp | 30 ++++++++++++++++-------------- 6 files changed, 36 insertions(+), 31 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.2.0 dated 2025-01-10 and 3.2.1 dated 2025-04-02
DESCRIPTION | 35 ++-- MD5 | 44 ++--- NEWS.md | 4 R/AllGenerics.R | 28 ++- R/tabula-package.R | 2 README.md | 13 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/alpha.Rmd | 1 inst/doc/alpha.html | 282 ++++++++++++++++------------------- inst/doc/beta.Rmd | 1 inst/doc/beta.html | 225 ++++++++++++--------------- inst/tinytest/test_index.R | 14 - man/figures/README-sample-size-1.png |binary man/figures/README-sample-size-2.png |binary man/index_bray.Rd | 2 man/index_jaccard.Rd | 4 man/index_sorenson.Rd | 8 man/similarity.Rd | 18 +- man/tabula-package.Rd | 6 vignettes/alpha.Rmd | 1 vignettes/beta.Rmd | 1 23 files changed, 328 insertions(+), 363 deletions(-)
Title: Conditional Process Analysis (CPA) via SEM Approach
Description: Utilizes the Reliability-Adjusted Product Indicator (RAPI) method to
estimate effects among latent variables, thus allowing for more precise definition and analysis of
mediation and moderation models. Our simulation studies reveal that while 'silp' may exhibit
instability with smaller sample sizes and lower reliability scores (e.g., N = 100, 'omega' = 0.7),
implementing nearest positive definite matrix correction and bootstrap confidence interval
estimation can significantly ameliorate this volatility. When these adjustments are applied,
'silp' achieves estimations akin in quality to those derived from LMS. In conclusion, the 'silp'
package is a valuable tool for researchers seeking to explore complex relational structures between
variables without resorting to commercial software.
Cheung et al.(2021)<doi:10.1007/s10869-020-09717-0>
Hsiao et al.(2018)<doi:10.1177/0013164416679877>.
Author: Yi-Hsuan Tseng [aut, cre],
Po-Hsien Huang [aut]
Maintainer: Yi-Hsuan Tseng <r12227115@g.ntu.edu.tw>
Diff between silp versions 1.0.1 dated 2025-03-11 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ R/resilp.R | 2 ++ R/silp.R | 5 ++--- R/utility.R | 4 ++-- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
,
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 2.1.0 dated 2024-01-15 and 2.1.2 dated 2025-04-02
DESCRIPTION | 8 MD5 | 276 ++++---- NAMESPACE | 190 ++--- NEWS | 153 ++-- R/LawTable.R | 220 +++--- R/LifeTable.R | 1162 +++++++++++++++++------------------ R/MortalityLaw_S3.R | 342 +++++----- R/MortalityLaw_check.R | 98 +- R/MortalityLaw_main.R | 824 ++++++++++++------------ R/MortalityLaw_models.R | 1094 ++++++++++++++++---------------- R/MortalityLaws-data.R | 92 +- R/MortalityLaws-package.R | 48 - R/availableHMD.R | 155 ++-- R/availableLF.R | 120 +-- R/availableLaws.R | 428 ++++++------ R/convertFx.R | 172 ++--- R/graphics.R | 336 +++++----- R/readAHMD.R | 393 +++++------ R/readCHMD.R | 502 +++++++-------- R/readHMD.R | 800 ++++++++++++------------ R/readJMD.R | 550 ++++++++-------- R/utils.R | 98 +- R/zzz.R | 18 README.md | 98 +- THANKS | 28 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Installation.R | 24 inst/doc/Installation.Rmd | 122 +-- inst/doc/Installation.pdf |binary inst/doc/Intro.R | 236 +++---- inst/doc/Intro.Rmd | 486 +++++++------- inst/doc/Intro.pdf |binary man/AHMD_sample.Rd | 42 - man/AIC.MortalityLaw.Rd | 36 - man/AUSregions.Rd | 30 man/CANregions.Rd | 30 man/CHMD_sample.Rd | 42 - man/HMD_sample.Rd | 42 - man/HMDcountries.Rd | 30 man/HMDindices.Rd | 30 man/HP.Rd | 48 - man/HP2.Rd | 48 - man/HP3.Rd | 48 - man/HP4.Rd | 48 - man/JMD_sample.Rd | 42 - man/JPNregions.Rd | 30 man/LawTable.Rd | 234 +++---- man/LifeTable.check.Rd | 36 - man/LifeTable.core.Rd | 92 +- man/MortalityLaw.Rd | 314 ++++----- man/MortalityLaws.Rd | 62 - man/ReadAHMD.Rd | 249 +++---- man/ReadCHMD.Rd | 250 +++---- man/ReadHMD.Rd | 274 ++++---- man/ReadHMD.core.Rd | 114 +-- man/ReadJMD.Rd | 262 +++---- man/addDetails.Rd | 58 - man/ageMsg.Rd | 36 - man/ahmd.Rd | 62 - man/availableHMD.Rd | 60 - man/availableLF.Rd | 52 - man/availableLaws.Rd | 227 +++--- man/beard.Rd | 48 - man/beard_makeham.Rd | 48 - man/bring_parameters.Rd | 46 - man/carriere1.Rd | 48 - man/carriere2.Rd | 48 - man/check.MortalityLaw.Rd | 36 - man/check_input_ReadAHMD.Rd | 36 - man/check_input_ReadCHMD.Rd | 36 - man/check_input_ReadHMD.Rd | 36 - man/check_input_ReadJMD.Rd | 36 - man/choose_optim.Rd | 36 - man/coale.demeny.ax.Rd | 70 +- man/compute.ax.Rd | 46 - man/convertFx.Rd | 126 +-- man/data_format.Rd | 30 man/deviance.MortalityLaw.Rd | 36 - man/df.residual.MortalityLaw.Rd | 36 - man/dx_lx.Rd | 40 - man/find.my.case.Rd | 62 - man/ggompertz.Rd | 48 - man/gompertz.Rd | 48 - man/gompertz0.Rd | 48 - man/head_tail.Rd | 60 - man/invgompertz.Rd | 50 - man/invweibull.Rd | 54 - man/kannisto.Rd | 48 - man/kannisto_makeham.Rd | 48 - man/kostaki.Rd | 48 - man/logLik.MortalityLaw.Rd | 36 - man/make_http_request.Rd | 36 - man/makeham.Rd | 48 - man/makeham0.Rd | 48 - man/martinelle.Rd | 48 - man/mx_qx.Rd | 50 - man/objective_fun.Rd | 82 +- man/opperman.Rd | 48 - man/perks.Rd | 48 - man/plot.MortalityLaw.Rd | 58 - man/predict.MortalityLaw.Rd | 76 +- man/print.MortalityLaw.Rd | 40 - man/print.ReadAHMD.Rd | 40 - man/print.ReadCHMD.Rd | 40 - man/print.ReadHMD.Rd | 40 - man/print.ReadJMD.Rd | 40 - man/print.availableLF.Rd | 40 - man/print.availableLaws.Rd | 40 - man/print.summary.MortalityLaw.Rd | 40 - man/quadratic.Rd | 48 - man/rogersplanck.Rd | 48 - man/saveMsg.Rd | 30 man/saveOutput.Rd | 42 - man/scale_x.Rd | 36 - man/siler.Rd | 48 - man/strehler_mildvan.Rd | 48 - man/substrRight.Rd | 40 - man/summary.MortalityLaw.Rd | 44 - man/thiele.Rd | 48 - man/uxAbove100.Rd | 54 - man/vandermaen.Rd | 48 - man/vandermaen2.Rd | 48 - man/weibull.Rd | 56 - man/wittstein.Rd | 48 - tests/testthat.R | 20 tests/testthat/test_LawTable.R | 64 - tests/testthat/test_LifeTable.R | 402 ++++++------ tests/testthat/test_MortalityLaws.R | 338 +++++----- tests/testthat/test_MortalityLaws2.R | 478 +++++++------- tests/testthat/test_ReadAHMD.R | 100 +-- tests/testthat/test_ReadCHMD.R | 100 +-- tests/testthat/test_ReadHMD.R | 186 ++--- tests/testthat/test_ReadJMD.R | 108 +-- tests/testthat/test_availableX.R | 56 - tests/testthat/test_convertFx.R | 124 +-- vignettes/Installation.Rmd | 122 +-- vignettes/Intro.Rmd | 486 +++++++------- vignettes/Mlaw_Refrences.bib | 420 ++++++------ 139 files changed, 8974 insertions(+), 8967 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] ,
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between clustvarsel versions 2.3.4 dated 2020-12-16 and 2.3.5 dated 2025-04-02
DESCRIPTION | 14 MD5 | 29 - NEWS.md | 5 R/clvarselgrbkw.R | 12 R/clvarselgrfwd.R | 42 + R/clvarselhlfwd.R | 16 README.md | 4 build/vignette.rds |binary inst/CITATION | 34 - inst/doc/clustvarsel.R | 422 +++++++++---------- inst/doc/clustvarsel.Rmd | 2 inst/doc/clustvarsel.html | 959 +++++++++++++++++++++++++++++---------------- man/clustvarsel.Rd | 6 vignettes/clustvarsel.Rmd | 2 vignettes/vignette.css | 39 - vignettes/vignette_old.css |only 16 files changed, 958 insertions(+), 628 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb],
Roger Bivand [ctb] ,
Andrew Brown [ctb],
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-29 dated 2025-02-26 and 1.8-42 dated 2025-04-02
terra-1.8-29/terra/R/plot_legend.R |only terra-1.8-29/terra/src/Makevars.win |only terra-1.8-42/terra/DESCRIPTION | 10 terra-1.8-42/terra/MD5 | 891 ++--- terra-1.8-42/terra/NAMESPACE | 2 terra-1.8-42/terra/NEWS.md | 44 terra-1.8-42/terra/R/Aclasses.R | 315 - terra-1.8-42/terra/R/Agenerics.R | 6 terra-1.8-42/terra/R/Arith_generics.R | 1534 ++++---- terra-1.8-42/terra/R/RGB.R | 458 +- terra-1.8-42/terra/R/RcppExports.R | 4 terra-1.8-42/terra/R/SpatRasterDataset.R | 871 ++-- terra-1.8-42/terra/R/SpatVectorCollection.R | 336 - terra-1.8-42/terra/R/Zdeprecated.R | 138 terra-1.8-42/terra/R/aggregate.R | 654 +-- terra-1.8-42/terra/R/animate.R | 64 terra-1.8-42/terra/R/app.R | 688 +-- terra-1.8-42/terra/R/approximate.R | 126 terra-1.8-42/terra/R/arith.R | 74 terra-1.8-42/terra/R/autocor.R | 408 +- terra-1.8-42/terra/R/cells.R | 194 - terra-1.8-42/terra/R/clean.R | 140 terra-1.8-42/terra/R/click.R | 318 - terra-1.8-42/terra/R/clip.R | 84 terra-1.8-42/terra/R/coerce.R | 1529 ++++---- terra-1.8-42/terra/R/colors.R | 194 - terra-1.8-42/terra/R/connect.R | 162 terra-1.8-42/terra/R/crosstab.R | 168 terra-1.8-42/terra/R/crs.R | 784 ++-- terra-1.8-42/terra/R/dimensions.R | 414 +- terra-1.8-42/terra/R/distance.R | 607 +-- terra-1.8-42/terra/R/draw.R | 176 - terra-1.8-42/terra/R/expand.R | 126 terra-1.8-42/terra/R/extent.R | 746 ++-- terra-1.8-42/terra/R/extract.R | 1195 +++--- terra-1.8-42/terra/R/extract_single.R | 612 +-- terra-1.8-42/terra/R/focal.R | 1714 ++++----- terra-1.8-42/terra/R/focalMat.R | 148 terra-1.8-42/terra/R/gcp.R | 90 terra-1.8-42/terra/R/gdal.R | 362 +- terra-1.8-42/terra/R/generics.R | 2621 +++++++-------- terra-1.8-42/terra/R/geocolors.R | 22 terra-1.8-42/terra/R/geom.R | 1625 ++++----- terra-1.8-42/terra/R/graticule.R | 452 +- terra-1.8-42/terra/R/hist.R | 212 - terra-1.8-42/terra/R/ifelse.R | 102 terra-1.8-42/terra/R/image.R | 54 terra-1.8-42/terra/R/init.R | 84 terra-1.8-42/terra/R/inset.R | 252 - terra-1.8-42/terra/R/interpolate.R | 154 terra-1.8-42/terra/R/k_means.R | 126 terra-1.8-42/terra/R/lapp.R | 650 +-- terra-1.8-42/terra/R/layerCor.R | 396 +- terra-1.8-42/terra/R/levels.R | 1015 ++--- terra-1.8-42/terra/R/lines.R | 322 - terra-1.8-42/terra/R/makeVRT.R | 244 - terra-1.8-42/terra/R/match.R | 126 terra-1.8-42/terra/R/math.R | 240 - terra-1.8-42/terra/R/merge.R | 154 terra-1.8-42/terra/R/mergeTime.R | 208 - terra-1.8-42/terra/R/messages.R | 156 terra-1.8-42/terra/R/names.R | 548 +-- terra-1.8-42/terra/R/ncdf.R | 1214 +++--- terra-1.8-42/terra/R/options.R | 433 +- terra-1.8-42/terra/R/panel.R | 222 - terra-1.8-42/terra/R/plotExtent.R | 76 terra-1.8-42/terra/R/plotRGB.R | 146 terra-1.8-42/terra/R/plot_2rasters.R | 404 +- terra-1.8-42/terra/R/plot_add.R |only terra-1.8-42/terra/R/plot_axes.R | 396 +- terra-1.8-42/terra/R/plot_cartogram.R | 44 terra-1.8-42/terra/R/plot_helper.R |only terra-1.8-42/terra/R/plot_legend_classes.R |only terra-1.8-42/terra/R/plot_legend_continuous.R |only terra-1.8-42/terra/R/plot_let.R | 16 terra-1.8-42/terra/R/plot_raster.R | 1907 ++++------ terra-1.8-42/terra/R/plot_scale.R | 562 +-- terra-1.8-42/terra/R/plot_vector.R | 1626 ++++----- terra-1.8-42/terra/R/predict.R | 541 +-- terra-1.8-42/terra/R/princomp.R | 88 terra-1.8-42/terra/R/rapp.R | 152 terra-1.8-42/terra/R/rast.R | 1203 +++--- terra-1.8-42/terra/R/rasterize.R | 731 ++-- terra-1.8-42/terra/R/rasterizeWin.R | 734 ++-- terra-1.8-42/terra/R/readsvg.R | 152 terra-1.8-42/terra/R/regress.R | 350 +- terra-1.8-42/terra/R/relate.R | 830 ++-- terra-1.8-42/terra/R/replace.R | 606 +-- terra-1.8-42/terra/R/replace_layer.R | 264 - terra-1.8-42/terra/R/replace_values.R | 732 ++-- terra-1.8-42/terra/R/roll.R | 148 terra-1.8-42/terra/R/rowSums.R | 186 - terra-1.8-42/terra/R/sample.R | 2010 +++++------ terra-1.8-42/terra/R/select.R | 92 terra-1.8-42/terra/R/selectHigh.R | 24 terra-1.8-42/terra/R/show.R | 29 terra-1.8-42/terra/R/spatDF.R | 194 - terra-1.8-42/terra/R/subset.R | 614 +-- terra-1.8-42/terra/R/tags.R | 448 +- terra-1.8-42/terra/R/tapp.R | 380 +- terra-1.8-42/terra/R/tempfiles.R | 138 terra-1.8-42/terra/R/tiles.R | 282 - terra-1.8-42/terra/R/time.R | 774 ++-- terra-1.8-42/terra/R/twoClasses.R | 152 terra-1.8-42/terra/R/update.R | 22 terra-1.8-42/terra/R/values.R | 1172 +++--- terra-1.8-42/terra/R/vect.R | 1066 +++--- terra-1.8-42/terra/R/watershed.R | 88 terra-1.8-42/terra/R/window.R | 68 terra-1.8-42/terra/R/wrap.R | 1038 ++--- terra-1.8-42/terra/R/write.R | 378 +- terra-1.8-42/terra/R/xapp.R | 144 terra-1.8-42/terra/R/xyRowColCell.R | 468 +- terra-1.8-42/terra/R/zonal.R | 1150 +++--- terra-1.8-42/terra/R/zoom.R | 100 terra-1.8-42/terra/R/zzz.R | 121 terra-1.8-42/terra/build/partial.rdb |binary terra-1.8-42/terra/configure | 693 ++- terra-1.8-42/terra/configure.ac | 80 terra-1.8-42/terra/inst/ex/test.grd | 52 terra-1.8-42/terra/inst/tinytest/test_aggregate.R | 26 terra-1.8-42/terra/inst/tinytest/test_arith.R | 14 terra-1.8-42/terra/inst/tinytest/test_cats.R | 118 terra-1.8-42/terra/inst/tinytest/test_classify.R | 48 terra-1.8-42/terra/inst/tinytest/test_crds.R | 14 terra-1.8-42/terra/inst/tinytest/test_crop.R | 58 terra-1.8-42/terra/inst/tinytest/test_equal.R | 32 terra-1.8-42/terra/inst/tinytest/test_extent.R | 6 terra-1.8-42/terra/inst/tinytest/test_extract.R | 470 +- terra-1.8-42/terra/inst/tinytest/test_flowAccumulation.R | 68 terra-1.8-42/terra/inst/tinytest/test_focal.R | 164 terra-1.8-42/terra/inst/tinytest/test_geom.R | 44 terra-1.8-42/terra/inst/tinytest/test_global.R | 22 terra-1.8-42/terra/inst/tinytest/test_matrix-input.R | 102 terra-1.8-42/terra/inst/tinytest/test_merge.R | 46 terra-1.8-42/terra/inst/tinytest/test_multivariate.R | 24 terra-1.8-42/terra/inst/tinytest/test_patches.R | 66 terra-1.8-42/terra/inst/tinytest/test_pitfinder.R | 104 terra-1.8-42/terra/inst/tinytest/test_plot.R | 10 terra-1.8-42/terra/inst/tinytest/test_raster-vector.R | 124 terra-1.8-42/terra/inst/tinytest/test_rasterize.R | 16 terra-1.8-42/terra/inst/tinytest/test_rds.R | 18 terra-1.8-42/terra/inst/tinytest/test_replace.R | 50 terra-1.8-42/terra/inst/tinytest/test_tags.R |only terra-1.8-42/terra/inst/tinytest/test_time.R | 8 terra-1.8-42/terra/inst/tinytest/test_vect-geom.R | 28 terra-1.8-42/terra/inst/tinytest/test_vector-subset.R | 34 terra-1.8-42/terra/inst/tinytest/test_weighted-mean.R | 32 terra-1.8-42/terra/inst/tinytest/test_window.R | 64 terra-1.8-42/terra/inst/tinytest/test_wkt_grd.R | 34 terra-1.8-42/terra/inst/tinytest/test_zonal.R | 48 terra-1.8-42/terra/inst/tinytest/tinytest.R | 8 terra-1.8-42/terra/man/NAflag.Rd | 92 terra-1.8-42/terra/man/NIPD.Rd | 196 - terra-1.8-42/terra/man/RGB.Rd | 168 terra-1.8-42/terra/man/SpatExtent-class.Rd | 70 terra-1.8-42/terra/man/SpatRaster-class.Rd | 90 terra-1.8-42/terra/man/SpatVector-class.Rd | 60 terra-1.8-42/terra/man/activeCat.Rd | 100 terra-1.8-42/terra/man/add.Rd | 86 terra-1.8-42/terra/man/add_mtext.Rd | 72 terra-1.8-42/terra/man/aggregate.Rd | 158 terra-1.8-42/terra/man/align.Rd | 92 terra-1.8-42/terra/man/all.equal.Rd | 114 terra-1.8-42/terra/man/animate.Rd | 88 terra-1.8-42/terra/man/app.Rd | 184 - terra-1.8-42/terra/man/approximate.Rd | 124 terra-1.8-42/terra/man/arith-generic.Rd | 156 terra-1.8-42/terra/man/as.character.Rd | 78 terra-1.8-42/terra/man/as.data.frame.Rd | 96 terra-1.8-42/terra/man/as.lines.Rd | 130 terra-1.8-42/terra/man/as.list.Rd | 102 terra-1.8-42/terra/man/as.points.Rd | 112 terra-1.8-42/terra/man/as.polygons.Rd | 114 terra-1.8-42/terra/man/as.raster.Rd | 76 terra-1.8-42/terra/man/atan2.Rd | 84 terra-1.8-42/terra/man/autocor.Rd | 156 terra-1.8-42/terra/man/barplot.Rd | 92 terra-1.8-42/terra/man/bestMatch.Rd | 132 terra-1.8-42/terra/man/boundaries.Rd | 88 terra-1.8-42/terra/man/box.Rd | 60 terra-1.8-42/terra/man/boxplot.Rd | 126 terra-1.8-42/terra/man/buffer.Rd | 134 terra-1.8-42/terra/man/c.Rd | 130 terra-1.8-42/terra/man/cartogram.Rd | 84 terra-1.8-42/terra/man/catalyze.Rd | 108 terra-1.8-42/terra/man/cellSize.Rd | 120 terra-1.8-42/terra/man/cells.Rd | 154 terra-1.8-42/terra/man/centroids.Rd | 66 terra-1.8-42/terra/man/clamp.Rd | 88 terra-1.8-42/terra/man/clamp_ts.Rd | 96 terra-1.8-42/terra/man/classify.Rd | 196 - terra-1.8-42/terra/man/click.Rd | 120 terra-1.8-42/terra/man/coerce.Rd | 136 terra-1.8-42/terra/man/collapse.Rd | 78 terra-1.8-42/terra/man/colors.Rd | 118 terra-1.8-42/terra/man/compare-generics.Rd | 200 - terra-1.8-42/terra/man/compareGeom.Rd | 126 terra-1.8-42/terra/man/concats.Rd | 104 terra-1.8-42/terra/man/contour.Rd | 140 terra-1.8-42/terra/man/convhull.Rd | 118 terra-1.8-42/terra/man/costDist.Rd | 116 terra-1.8-42/terra/man/cover.Rd | 134 terra-1.8-42/terra/man/crds.Rd | 120 terra-1.8-42/terra/man/crop.Rd | 168 terra-1.8-42/terra/man/crosstab.Rd | 104 terra-1.8-42/terra/man/crs.Rd | 164 terra-1.8-42/terra/man/datatype.Rd | 160 terra-1.8-42/terra/man/deepcopy.Rd | 88 terra-1.8-42/terra/man/densify.Rd | 124 terra-1.8-42/terra/man/density.Rd | 70 terra-1.8-42/terra/man/deprecated.Rd | 44 terra-1.8-42/terra/man/depth.Rd | 101 terra-1.8-42/terra/man/describe.Rd | 86 terra-1.8-42/terra/man/diff.Rd | 70 terra-1.8-42/terra/man/dimensions.Rd | 302 - terra-1.8-42/terra/man/direction.Rd | 94 terra-1.8-42/terra/man/disaggregate.Rd | 106 terra-1.8-42/terra/man/distance.Rd | 10 terra-1.8-42/terra/man/divide.Rd | 118 terra-1.8-42/terra/man/dots.Rd | 94 terra-1.8-42/terra/man/draw.Rd | 76 terra-1.8-42/terra/man/erase.Rd | 156 terra-1.8-42/terra/man/expanse.Rd | 190 - terra-1.8-42/terra/man/ext.Rd | 4 terra-1.8-42/terra/man/extract.Rd | 259 - terra-1.8-42/terra/man/extractAlong.Rd | 88 terra-1.8-42/terra/man/extractRange.Rd | 92 terra-1.8-42/terra/man/factors.Rd | 247 - terra-1.8-42/terra/man/fill.Rd | 96 terra-1.8-42/terra/man/fillTime.Rd | 96 terra-1.8-42/terra/man/flip.Rd | 108 terra-1.8-42/terra/man/flowAccumulation.Rd | 214 - terra-1.8-42/terra/man/focal.Rd | 232 - terra-1.8-42/terra/man/focal3D.Rd | 120 terra-1.8-42/terra/man/focalCpp.Rd | 202 - terra-1.8-42/terra/man/focalMat.Rd | 78 terra-1.8-42/terra/man/focalPairs.Rd | 128 terra-1.8-42/terra/man/focalReg.Rd | 100 terra-1.8-42/terra/man/focalValues.Rd | 76 terra-1.8-42/terra/man/forceCCW.Rd | 66 terra-1.8-42/terra/man/freq.Rd | 108 terra-1.8-42/terra/man/gaps.Rd | 84 terra-1.8-42/terra/man/gdal.Rd | 110 terra-1.8-42/terra/man/geometry.Rd | 132 terra-1.8-42/terra/man/geomtype.Rd | 108 terra-1.8-42/terra/man/global.Rd | 102 terra-1.8-42/terra/man/graticule.Rd | 90 terra-1.8-42/terra/man/grid.Rd | 68 terra-1.8-42/terra/man/gridDist.Rd | 120 terra-1.8-42/terra/man/halo.Rd | 82 terra-1.8-42/terra/man/headtail.Rd | 94 terra-1.8-42/terra/man/hist.Rd | 112 terra-1.8-42/terra/man/identical.Rd | 84 terra-1.8-42/terra/man/ifelse.Rd | 112 terra-1.8-42/terra/man/image.Rd | 78 terra-1.8-42/terra/man/impose.Rd | 76 terra-1.8-42/terra/man/init.Rd | 79 terra-1.8-42/terra/man/inplace.Rd | 226 - terra-1.8-42/terra/man/inset.Rd | 194 - terra-1.8-42/terra/man/interpIDW.Rd | 126 terra-1.8-42/terra/man/interpNear.Rd | 124 terra-1.8-42/terra/man/interpolate.Rd | 304 - terra-1.8-42/terra/man/intersect.Rd | 180 - terra-1.8-42/terra/man/is.bool.Rd | 168 terra-1.8-42/terra/man/is.empty.Rd | 80 terra-1.8-42/terra/man/is.flipped.Rd | 82 terra-1.8-42/terra/man/is.lonlat.Rd | 100 terra-1.8-42/terra/man/is.rotated.Rd | 84 terra-1.8-42/terra/man/is.valid.Rd | 112 terra-1.8-42/terra/man/k_means.Rd | 86 terra-1.8-42/terra/man/lapp.Rd | 202 - terra-1.8-42/terra/man/layerCor.Rd | 146 terra-1.8-42/terra/man/legend.Rd | 72 terra-1.8-42/terra/man/linearUnits.Rd | 102 terra-1.8-42/terra/man/lines.Rd | 172 terra-1.8-42/terra/man/makeTiles.Rd | 136 terra-1.8-42/terra/man/makeVRT.Rd | 94 terra-1.8-42/terra/man/map_extent.Rd | 66 terra-1.8-42/terra/man/mappal.Rd | 150 terra-1.8-42/terra/man/mask.Rd | 144 terra-1.8-42/terra/man/match.Rd | 98 terra-1.8-42/terra/man/math-generics.Rd | 206 - terra-1.8-42/terra/man/mem.Rd | 78 terra-1.8-42/terra/man/merge.Rd | 174 terra-1.8-42/terra/man/mergeTime.Rd | 98 terra-1.8-42/terra/man/meta.Rd | 58 terra-1.8-42/terra/man/metags.Rd | 136 terra-1.8-42/terra/man/minmax.Rd | 88 terra-1.8-42/terra/man/modal.Rd | 74 terra-1.8-42/terra/man/mosaic.Rd | 132 terra-1.8-42/terra/man/na.omit.Rd | 84 terra-1.8-42/terra/man/names.Rd | 148 terra-1.8-42/terra/man/nearby.Rd | 92 terra-1.8-42/terra/man/normalize.longitude.Rd | 68 terra-1.8-42/terra/man/north.Rd | 134 terra-1.8-42/terra/man/nseg.Rd | 66 terra-1.8-42/terra/man/origin.Rd | 78 terra-1.8-42/terra/man/pairs.Rd | 94 terra-1.8-42/terra/man/panel.Rd | 104 terra-1.8-42/terra/man/patches.Rd | 156 terra-1.8-42/terra/man/perim.Rd | 74 terra-1.8-42/terra/man/persp.Rd | 74 terra-1.8-42/terra/man/pitfinder.Rd | 162 terra-1.8-42/terra/man/plet.Rd | 256 - terra-1.8-42/terra/man/plot.Rd | 427 +- terra-1.8-42/terra/man/plotRGB.Rd | 118 terra-1.8-42/terra/man/plot_extent.Rd | 74 terra-1.8-42/terra/man/plot_graticule.Rd | 120 terra-1.8-42/terra/man/prcomp.Rd | 98 terra-1.8-42/terra/man/predict.Rd | 310 - terra-1.8-42/terra/man/princomp.Rd | 116 terra-1.8-42/terra/man/project.Rd | 248 - terra-1.8-42/terra/man/quantile.Rd | 114 terra-1.8-42/terra/man/query.Rd | 121 terra-1.8-42/terra/man/rangeFill.Rd | 96 terra-1.8-42/terra/man/rapp.Rd | 128 terra-1.8-42/terra/man/rast.Rd | 279 - terra-1.8-42/terra/man/rasterize.Rd | 175 - terra-1.8-42/terra/man/rasterizeGeom.Rd | 116 terra-1.8-42/terra/man/rasterizeWin.Rd | 144 terra-1.8-42/terra/man/rcl.Rd | 108 terra-1.8-42/terra/man/readwrite.Rd | 174 terra-1.8-42/terra/man/rectify.Rd | 74 terra-1.8-42/terra/man/regress.Rd | 88 terra-1.8-42/terra/man/rep.Rd | 78 terra-1.8-42/terra/man/replace_dollar.Rd | 98 terra-1.8-42/terra/man/replace_layers.Rd | 110 terra-1.8-42/terra/man/replace_values.Rd | 122 terra-1.8-42/terra/man/resample.Rd | 152 terra-1.8-42/terra/man/rescale.Rd | 88 terra-1.8-42/terra/man/roll.Rd | 124 terra-1.8-42/terra/man/rotate.Rd | 128 terra-1.8-42/terra/man/rowSums.Rd | 100 terra-1.8-42/terra/man/same.crs.Rd | 66 terra-1.8-42/terra/man/sample.Rd | 4 terra-1.8-42/terra/man/sapp.Rd | 104 terra-1.8-42/terra/man/sbar.Rd | 122 terra-1.8-42/terra/man/scale.Rd | 86 terra-1.8-42/terra/man/scale_linear.Rd | 78 terra-1.8-42/terra/man/scatter.Rd | 90 terra-1.8-42/terra/man/scoff.Rd | 104 terra-1.8-42/terra/man/sds.Rd | 145 terra-1.8-42/terra/man/segregate.Rd | 84 terra-1.8-42/terra/man/select.Rd | 138 terra-1.8-42/terra/man/selectRange.Rd | 102 terra-1.8-42/terra/man/serialize.Rd | 146 terra-1.8-42/terra/man/setValues.Rd | 144 terra-1.8-42/terra/man/shade.Rd | 118 terra-1.8-42/terra/man/sharedPaths.Rd | 106 terra-1.8-42/terra/man/shift.Rd | 94 terra-1.8-42/terra/man/simplify.Rd | 98 terra-1.8-42/terra/man/sort.Rd | 106 terra-1.8-42/terra/man/spin.Rd | 86 terra-1.8-42/terra/man/split.Rd | 111 terra-1.8-42/terra/man/sprc.Rd | 127 terra-1.8-42/terra/man/stretch.Rd | 106 terra-1.8-42/terra/man/subset.Rd | 152 terra-1.8-42/terra/man/subset_dollar.Rd | 130 terra-1.8-42/terra/man/subset_double.Rd | 160 terra-1.8-42/terra/man/subset_single.Rd | 228 - terra-1.8-42/terra/man/subst.Rd | 102 terra-1.8-42/terra/man/summarize-generics.Rd | 338 - terra-1.8-42/terra/man/summary.Rd | 96 terra-1.8-42/terra/man/surfArea.Rd | 82 terra-1.8-42/terra/man/svc.Rd | 137 terra-1.8-42/terra/man/symdif.Rd | 84 terra-1.8-42/terra/man/tapp.Rd | 120 terra-1.8-42/terra/man/terra-package.Rd | 1363 +++---- terra-1.8-42/terra/man/terrain.Rd | 166 terra-1.8-42/terra/man/text.Rd | 106 terra-1.8-42/terra/man/time.Rd | 156 terra-1.8-42/terra/man/tmpFile.Rd | 76 terra-1.8-42/terra/man/topology.Rd | 146 terra-1.8-42/terra/man/transpose.Rd | 94 terra-1.8-42/terra/man/trim.Rd | 78 terra-1.8-42/terra/man/unique.Rd | 124 terra-1.8-42/terra/man/units.Rd | 102 terra-1.8-42/terra/man/update.Rd | 78 terra-1.8-42/terra/man/values.Rd | 150 terra-1.8-42/terra/man/varnames.Rd | 142 terra-1.8-42/terra/man/vect.Rd | 5 terra-1.8-42/terra/man/vector_layers.Rd | 50 terra-1.8-42/terra/man/viewshed.Rd | 84 terra-1.8-42/terra/man/voronoi.Rd | 104 terra-1.8-42/terra/man/vrt.Rd | 128 terra-1.8-42/terra/man/vrt_tiles.Rd | 60 terra-1.8-42/terra/man/watershed.Rd | 82 terra-1.8-42/terra/man/weighted.mean.Rd | 120 terra-1.8-42/terra/man/where.Rd | 86 terra-1.8-42/terra/man/which.Rd | 72 terra-1.8-42/terra/man/width.Rd | 109 terra-1.8-42/terra/man/window.Rd | 126 terra-1.8-42/terra/man/wrap.Rd | 120 terra-1.8-42/terra/man/wrapCache.Rd | 92 terra-1.8-42/terra/man/writeCDF.Rd | 179 - terra-1.8-42/terra/man/writeRaster.Rd | 198 - terra-1.8-42/terra/man/writeVector.Rd | 96 terra-1.8-42/terra/man/xapp.Rd | 92 terra-1.8-42/terra/man/xmin.Rd | 198 - terra-1.8-42/terra/man/xyCellFrom.Rd | 266 - terra-1.8-42/terra/man/zonal.Rd | 218 - terra-1.8-42/terra/man/zoom.Rd | 80 terra-1.8-42/terra/src/Makevars.ucrt | 6 terra-1.8-42/terra/src/RcppExports.cpp | 11 terra-1.8-42/terra/src/RcppFunctions.cpp | 26 terra-1.8-42/terra/src/RcppModule.cpp | 35 terra-1.8-42/terra/src/arith.cpp | 85 terra-1.8-42/terra/src/crs.cpp | 2 terra-1.8-42/terra/src/distRaster.cpp | 59 terra-1.8-42/terra/src/distValueRaster.cpp | 6 terra-1.8-42/terra/src/distVector.cpp | 299 + terra-1.8-42/terra/src/distance.cpp | 2 terra-1.8-42/terra/src/extract.cpp | 66 terra-1.8-42/terra/src/focal.cpp | 2 terra-1.8-42/terra/src/gdal_algs.cpp | 50 terra-1.8-42/terra/src/gdalio.cpp | 4 terra-1.8-42/terra/src/geodesic.c | 66 terra-1.8-42/terra/src/geos_methods.cpp | 67 terra-1.8-42/terra/src/geos_spat.h | 20 terra-1.8-42/terra/src/math_utils.h | 34 terra-1.8-42/terra/src/memory.cpp | 3 terra-1.8-42/terra/src/raster_methods.cpp | 22 terra-1.8-42/terra/src/raster_stats.cpp | 63 terra-1.8-42/terra/src/rasterize.cpp | 4 terra-1.8-42/terra/src/read.cpp | 4 terra-1.8-42/terra/src/read_gdal.cpp | 142 terra-1.8-42/terra/src/read_ogr.cpp | 30 terra-1.8-42/terra/src/recycle.h | 8 terra-1.8-42/terra/src/sample.cpp | 278 + terra-1.8-42/terra/src/spatBase.cpp | 2 terra-1.8-42/terra/src/spatBase.h | 3 terra-1.8-42/terra/src/spatDataframe.cpp | 114 terra-1.8-42/terra/src/spatDataframe.h | 50 terra-1.8-42/terra/src/spatFactor.cpp | 14 terra-1.8-42/terra/src/spatFactor.h | 18 terra-1.8-42/terra/src/spatRaster.cpp | 106 terra-1.8-42/terra/src/spatRaster.h | 49 terra-1.8-42/terra/src/spatRasterMultiple.cpp | 124 terra-1.8-42/terra/src/spatRasterMultiple.h | 49 terra-1.8-42/terra/src/spatSources.cpp | 49 terra-1.8-42/terra/src/spatTime.cpp | 9 terra-1.8-42/terra/src/spatVector.cpp | 102 terra-1.8-42/terra/src/spatVector.h | 68 terra-1.8-42/terra/src/table_utils.cpp |only terra-1.8-42/terra/src/table_utils.h |only terra-1.8-42/terra/src/vecmath.h | 10 terra-1.8-42/terra/src/vector_methods.cpp | 4 terra-1.8-42/terra/src/write.cpp | 18 terra-1.8-42/terra/src/write_gdal.cpp | 78 terra-1.8-42/terra/tests/tinytest.R | 8 451 files changed, 44361 insertions(+), 42999 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 1.3-2 dated 2025-02-17 and 1.3-3 dated 2025-04-02
DESCRIPTION | 8 +- MD5 | 75 ++++++++++----------- NEWS.md | 6 + README.md | 42 ++++++++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/consistency.Rmd | 46 +++++++------ inst/doc/consistency.html | 76 +++++++++++---------- inst/doc/gd.Rmd | 18 ----- inst/doc/gd.html | 142 +++++++++++++++++------------------------ inst/doc/idsa.Rmd | 22 ------ inst/doc/idsa.html | 78 ++++++++-------------- inst/doc/opgd.Rmd | 4 - inst/doc/opgd.html | 28 +++----- inst/doc/rgdrid.Rmd | 2 inst/doc/rgdrid.html | 6 - inst/doc/sesu.Rmd | 20 ----- inst/doc/sesu.html | 48 ++++--------- inst/doc/shegd.Rmd | 12 --- inst/doc/shegd.html | 38 +++------- inst/doc/spade.Rmd | 20 ----- inst/doc/spade.html | 76 ++++++++------------- vignettes/consistency.Rmd | 46 +++++++------ vignettes/consistency.Rmd.orig | 21 +++--- vignettes/gd.Rmd | 18 ----- vignettes/gd.Rmd.orig | 1 vignettes/idsa.Rmd | 22 ------ vignettes/idsa.Rmd.orig | 1 vignettes/opgd.Rmd | 4 - vignettes/opgd.Rmd.orig | 1 vignettes/precompile.R | 2 vignettes/rgdrid.Rmd | 2 vignettes/rgdrid.Rmd.orig | 1 vignettes/sesu.Rmd | 20 ----- vignettes/sesu.Rmd.orig | 7 +- vignettes/shegd.Rmd | 12 --- vignettes/shegd.Rmd.orig | 1 vignettes/spade.Rmd | 20 ----- vignettes/spade.Rmd.orig | 1 39 files changed, 372 insertions(+), 575 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.6 dated 2025-02-28 and 5.1 dated 2025-04-02
ChangeLog | 4 DESCRIPTION | 8 MD5 | 16 - R/ETSvalidate.R | 30 + R/TETSvalidate.R | 30 + src/ETSmodel.h | 149 --------- src/TETSmodel.h | 873 ++++++++++++++++++++++++++++++++++++++++++++++--------- src/optim.h | 3 src/stats.h | 6 9 files changed, 812 insertions(+), 307 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak and area under the curve are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.1 dated 2024-08-28 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NEWS.md |only build/vignette.rds |binary inst/CITATION |only 5 files changed, 7 insertions(+), 5 deletions(-)
Title: Semi-Automatic Grading of R and Rmd Scripts
Description: A customisable set of tools for assessing and grading
R or R-markdown scripts from students. It allows for checking correctness
of code output, runtime statistics and static code analysis. The latter
feature is made possible by representing R expressions using a tree
structure.
Author: Vik Gopal [aut, cre],
Samuel Seah [aut],
Viknesh Jeya Kumar [aut],
Gabriel Ang [aut],
Ruofan Liu [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between autoharp versions 0.0.10 dated 2021-11-12 and 0.0.12 dated 2025-04-02
autoharp-0.0.10/autoharp/R/examplify_to_r.R |only autoharp-0.0.10/autoharp/R/lum_local_match.R |only autoharp-0.0.10/autoharp/man/examplify_to_r.Rd |only autoharp-0.0.10/autoharp/man/lum_local_match.Rd |only autoharp-0.0.12/autoharp/DESCRIPTION | 26 ++++++------ autoharp-0.0.12/autoharp/MD5 | 40 +++++++++---------- autoharp-0.0.12/autoharp/NAMESPACE | 4 - autoharp-0.0.12/autoharp/NEWS | 9 ++++ autoharp-0.0.12/autoharp/R/autoharp.R | 3 - autoharp-0.0.12/autoharp/R/extracton_section_text.R |only autoharp-0.0.12/autoharp/R/forestharp.R | 10 ++-- autoharp-0.0.12/autoharp/R/join_treeharp.R | 5 +- autoharp-0.0.12/autoharp/R/populate_soln_env.R | 37 +---------------- autoharp-0.0.12/autoharp/R/tree_routines.R | 19 +++++---- autoharp-0.0.12/autoharp/man/TreeHarp-class.Rd | 12 ++--- autoharp-0.0.12/autoharp/man/autoharp.Rd | 25 +++++++++++ autoharp-0.0.12/autoharp/man/extract_section_text.Rd |only autoharp-0.0.12/autoharp/man/forestharp-helpers.Rd | 30 +++++++------- autoharp-0.0.12/autoharp/man/get_adj_list.Rd | 4 - autoharp-0.0.12/autoharp/man/get_child_ids.Rd | 6 +- autoharp-0.0.12/autoharp/man/get_node_types.Rd | 4 - autoharp-0.0.12/autoharp/man/get_parent_id.Rd | 6 +- autoharp-0.0.12/autoharp/man/populate_soln_env.Rd | 10 +--- autoharp-0.0.12/autoharp/man/rmd_to_forestharp.Rd | 2 24 files changed, 128 insertions(+), 124 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Rodrigo Basa [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.10.1 dated 2024-09-20 and 1.11.0 dated 2025-04-02
DESCRIPTION | 17 + MD5 | 29 ++- NAMESPACE | 3 NEWS.md | 14 + R/destructure.R |only R/node.R | 12 - R/tools.R | 175 +++++++++++++++++++- inst/WORDLIST | 6 inst/templates/app_structure/app/static/favicon.ico |binary man/auto_test_r.Rd |only man/devmode.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/format_r.Rd | 4 man/grapes-set-grapes.Rd |only man/test_r.Rd | 5 tests/testthat/test-destructure.R |only tests/testthat/test-tools.R | 6 20 files changed, 237 insertions(+), 34 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-30 0.4.0
2024-02-14 0.3.0
2022-09-19 0.2.0
2022-02-02 0.1.0
2021-12-15 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-24 1.0.1
2023-09-28 1.0.0
2023-04-06 0.0.2
2022-11-03 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-27 0.1.1
2024-09-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-18 0.4.2
2023-03-21 0.4.0
2022-05-01 0.3.9
2021-02-01 0.3.8
2021-01-12 0.3.7
2020-07-21 0.3.6
2020-07-20 0.3.5
2020-04-24 0.3.4
2020-01-14 0.3.3
Title: The Double-Gap Life Expectancy Forecasting Model
Description: Life expectancy is highly correlated over time among countries and
between males and females. These associations can be used to improve forecasts.
Here we have implemented a method for forecasting female life expectancy based on
analysis of the gap between female life expectancy in a country compared with
the record level of female life expectancy in the world. Second, to forecast
male life expectancy, the gap between male life expectancy and female life
expectancy in a country is analysed. We named this method the Double-Gap model.
For a detailed description of the method see Pascariu et al. (2018).
<doi:10.1016/j.insmatheco.2017.09.011>.
Author: Marius D. Pascariu [aut, cre]
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between MortalityGaps versions 1.0.0 dated 2018-07-20 and 1.0.7 dated 2025-04-02
MortalityGaps-1.0.0/MortalityGaps/R/Utils.R |only MortalityGaps-1.0.0/MortalityGaps/R/data_and_imports.R |only MortalityGaps-1.0.0/MortalityGaps/man/onAttach.Rd |only MortalityGaps-1.0.7/MortalityGaps/DESCRIPTION | 28 MortalityGaps-1.0.7/MortalityGaps/MD5 | 75 MortalityGaps-1.0.7/MortalityGaps/NAMESPACE | 70 MortalityGaps-1.0.7/MortalityGaps/NEWS | 7 MortalityGaps-1.0.7/MortalityGaps/R/DGM_fit.R | 779 +++++----- MortalityGaps-1.0.7/MortalityGaps/R/DGM_predict.R | 310 +-- MortalityGaps-1.0.7/MortalityGaps/R/Graphics.R | 184 +- MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-data.R |only MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-package.R |only MortalityGaps-1.0.7/MortalityGaps/README.md | 115 - MortalityGaps-1.0.7/MortalityGaps/THANKS | 24 MortalityGaps-1.0.7/MortalityGaps/build/partial.rdb |only MortalityGaps-1.0.7/MortalityGaps/build/vignette.rds |binary MortalityGaps-1.0.7/MortalityGaps/inst/REFERENCES.bib |only MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.R | 56 MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.Rmd | 208 +- MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.pdf |binary MortalityGaps-1.0.7/MortalityGaps/inst/figures |only MortalityGaps-1.0.7/MortalityGaps/man/DoubleGap.Rd | 283 +-- MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.Rd |only MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.data.Rd | 64 MortalityGaps-1.0.7/MortalityGaps/man/bp_gap.model.Rd | 56 MortalityGaps-1.0.7/MortalityGaps/man/compute_CI.Rd | 58 MortalityGaps-1.0.7/MortalityGaps/man/find_fitted_values.Rd | 38 MortalityGaps-1.0.7/MortalityGaps/man/find_observed_values.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_record_ex.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_tau.Rd | 46 MortalityGaps-1.0.7/MortalityGaps/man/plot.predict.DoubleGap.Rd | 79 - MortalityGaps-1.0.7/MortalityGaps/man/predict.DoubleGap.Rd | 72 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data_for_prediction.Rd | 42 MortalityGaps-1.0.7/MortalityGaps/man/print.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.MortalityGaps.data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.predict.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/sex_gap.model.Rd | 52 MortalityGaps-1.0.7/MortalityGaps/man/summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/tests/testthat.R | 8 MortalityGaps-1.0.7/MortalityGaps/tests/testthat/testDGM.R | 208 +- MortalityGaps-1.0.7/MortalityGaps/vignettes/Manual.Rmd | 208 +- 43 files changed, 1690 insertions(+), 1644 deletions(-)
Title: Testing for Spatial Independence of Cross-Sectional Qualitative
Data
Description: Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
Author: Fernando Lopez [aut, cre] ,
Roman Minguez [aut] ,
Antonio Paez [aut] ,
Manuel Ruiz [aut]
Maintainer: Fernando Lopez <fernando.lopez@upct.es>
Diff between spqdep versions 0.1.3.5 dated 2025-01-08 and 0.1.3.6 dated 2025-04-02
DESCRIPTION | 13 +- MD5 | 28 +++--- NAMESPACE | 2 R/m.surround.R | 3 R/methods_qmap.R | 5 - R/plot.sprunstest.R | 69 ++++++++------ R/summary.spjctest.R | 20 ++-- R/summary.spqtest.R | 14 +-- R/utils-pipe.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 7 - inst/doc/user-guide.Rmd | 11 +- inst/doc/user-guide.html | 217 +++++++++++++++++++++++------------------------ man/pipe.Rd |only vignettes/user-guide.Rmd | 11 +- 16 files changed, 204 insertions(+), 196 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard '%dopar%' loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.8.6.1 dated 2025-01-13 and 1.8.6.2 dated 2025-04-02
doRNG-1.8.6.1/doRNG/build |only doRNG-1.8.6.1/doRNG/inst/doc |only doRNG-1.8.6.1/doRNG/vignettes |only doRNG-1.8.6.2/doRNG/DESCRIPTION | 9 ++++----- doRNG-1.8.6.2/doRNG/MD5 | 11 +++-------- doRNG-1.8.6.2/doRNG/man/doRNG-package.Rd | 2 +- doRNG-1.8.6.2/doRNG/man/grapes-dorng-grapes.Rd | 8 +++++--- 7 files changed, 13 insertions(+), 17 deletions(-)
Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API
<https://dev.elsevier.com/sc_apis.html> to download
information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between rscopus versions 0.6.6 dated 2019-09-17 and 0.8.1 dated 2025-04-02
rscopus-0.6.6/rscopus/R/read_cto.R |only rscopus-0.8.1/rscopus/DESCRIPTION | 15 rscopus-0.8.1/rscopus/MD5 | 106 +- rscopus-0.8.1/rscopus/NAMESPACE | 5 rscopus-0.8.1/rscopus/NEWS.md | 8 rscopus-0.8.1/rscopus/R/author_df.R | 12 rscopus-0.8.1/rscopus/R/author_retrieval.R | 8 rscopus-0.8.1/rscopus/R/author_search.R | 8 rscopus-0.8.1/rscopus/R/bibtex_core_data.R | 118 +- rscopus-0.8.1/rscopus/R/citation_retrieval.R | 48 rscopus-0.8.1/rscopus/R/elsevier_authenticate.R | 23 rscopus-0.8.1/rscopus/R/generic_elsevier_search.R | 6 rscopus-0.8.1/rscopus/R/get_affiliation_info.R | 4 rscopus-0.8.1/rscopus/R/get_all_coauthors.R |only rscopus-0.8.1/rscopus/R/get_author_info.R | 8 rscopus-0.8.1/rscopus/R/get_next.R | 2 rscopus-0.8.1/rscopus/R/object_retrieval.R | 11 rscopus-0.8.1/rscopus/R/read_cto.r |only rscopus-0.8.1/rscopus/R/scopus_search.R | 39 rscopus-0.8.1/rscopus/R/utils-pipe.R |only rscopus-0.8.1/rscopus/build/vignette.rds |binary rscopus-0.8.1/rscopus/inst/doc/api_key.R | 40 rscopus-0.8.1/rscopus/inst/doc/api_key.Rmd | 36 rscopus-0.8.1/rscopus/inst/doc/api_key.html | 285 +++-- rscopus-0.8.1/rscopus/inst/doc/multi_author.R | 32 rscopus-0.8.1/rscopus/inst/doc/multi_author.Rmd | 13 rscopus-0.8.1/rscopus/inst/doc/multi_author.html | 824 ++++++++-------- rscopus-0.8.1/rscopus/man/abstract_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/affil_df.Rd | 22 rscopus-0.8.1/rscopus/man/affil_search.Rd | 9 rscopus-0.8.1/rscopus/man/affiliation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/article_retrieval.Rd | 10 rscopus-0.8.1/rscopus/man/author_df.Rd | 51 rscopus-0.8.1/rscopus/man/author_retrieval.Rd | 42 rscopus-0.8.1/rscopus/man/author_search.Rd | 27 rscopus-0.8.1/rscopus/man/author_search_by_affil.Rd | 2 rscopus-0.8.1/rscopus/man/bibtex_core_data.Rd | 2 rscopus-0.8.1/rscopus/man/citation_retrieval.Rd | 27 rscopus-0.8.1/rscopus/man/complete_multi_author_info.Rd | 3 rscopus-0.8.1/rscopus/man/elsevier_authenticate.Rd | 22 rscopus-0.8.1/rscopus/man/embase_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/entitlement_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/generic_elsevier_api.Rd | 32 rscopus-0.8.1/rscopus/man/get_affiliation_info.Rd | 13 rscopus-0.8.1/rscopus/man/get_all_coauthors.Rd |only rscopus-0.8.1/rscopus/man/get_complete_author_info.Rd | 26 rscopus-0.8.1/rscopus/man/get_links.Rd | 5 rscopus-0.8.1/rscopus/man/object_retrieval.Rd | 30 rscopus-0.8.1/rscopus/man/pipe.Rd |only rscopus-0.8.1/rscopus/man/process_affiliation_name.Rd | 8 rscopus-0.8.1/rscopus/man/process_author_name.Rd | 16 rscopus-0.8.1/rscopus/man/read_cto.Rd | 2 rscopus-0.8.1/rscopus/man/recommendation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/scopus_search.Rd | 47 rscopus-0.8.1/rscopus/tests/testthat/test_author_df.R | 11 rscopus-0.8.1/rscopus/vignettes/api_key.Rmd | 36 rscopus-0.8.1/rscopus/vignettes/multi_author.Rmd | 13 57 files changed, 1285 insertions(+), 862 deletions(-)
Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with
absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre],
Brian Koch [ctb]
Maintainer: Bob Harlow <rharlow86@gmail.com>
Diff between quadprogXT versions 0.0.5 dated 2020-01-15 and 0.0.6 dated 2025-04-02
DESCRIPTION | 18 +++++---- MD5 | 10 ++--- R/convertToCompactQP.R | 68 +++++++++++++++++++++------------- inst/tinytest/test-convertToCompact.R | 17 ++++++-- man/convertToCompact.Rd | 9 ++-- man/solveQPXT.Rd | 23 +++++++++-- 6 files changed, 93 insertions(+), 52 deletions(-)
Title: Person Fit
Description: Several person-fit statistics
(PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>)
are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro [aut, cre]
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>
Diff between PerFit versions 1.4.6 dated 2021-10-15 and 1.4.7 dated 2025-04-02
DESCRIPTION | 17 +-- MD5 | 12 +- R/PerFitPFS.R | 180 ++++++++++++++++----------------- R/SanityChecks.R | 272 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/PerFit-package.Rd | 1 man/lz.Rd | 2 7 files changed, 244 insertions(+), 240 deletions(-)