Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.32.2 dated 2024-02-20 and 0.34.2 dated 2024-07-27
rayrender-0.32.2/rayrender/src/stb_image.h |only rayrender-0.32.2/rayrender/src/stb_image_resize.h |only rayrender-0.34.2/rayrender/DESCRIPTION | 13 rayrender-0.34.2/rayrender/MD5 | 116 ++-- rayrender-0.34.2/rayrender/NAMESPACE | 1 rayrender-0.34.2/rayrender/R/RcppExports.R | 16 rayrender-0.34.2/rayrender/R/create_instances.R |only rayrender-0.34.2/rayrender/R/generate_camera_motion.R | 3 rayrender-0.34.2/rayrender/R/group_objects.R | 12 rayrender-0.34.2/rayrender/R/materials.R | 257 ++++----- rayrender-0.34.2/rayrender/R/objects.R | 161 ++++- rayrender-0.34.2/rayrender/R/prepare_scene_list.R | 272 --------- rayrender-0.34.2/rayrender/R/process_scene.R |only rayrender-0.34.2/rayrender/R/r_obj.R | 14 rayrender-0.34.2/rayrender/R/ray_scene.R | 4 rayrender-0.34.2/rayrender/R/render_animation.R | 18 rayrender-0.34.2/rayrender/R/render_scene.R | 12 rayrender-0.34.2/rayrender/inst/extdata/3d_r_logo.txt |only rayrender-0.34.2/rayrender/inst/extdata/3d_r_logo_mat.txt |only rayrender-0.34.2/rayrender/man/check_image_texture.Rd |only rayrender-0.34.2/rayrender/man/create_instances.Rd |only rayrender-0.34.2/rayrender/man/glossy.Rd | 6 rayrender-0.34.2/rayrender/man/mesh3d_model.Rd | 24 rayrender-0.34.2/rayrender/man/obj_model.Rd | 72 +- rayrender-0.34.2/rayrender/man/ply_model.Rd | 8 rayrender-0.34.2/rayrender/man/process_scene.Rd |only rayrender-0.34.2/rayrender/man/r_obj.Rd | 10 rayrender-0.34.2/rayrender/man/raymesh_model.Rd | 21 rayrender-0.34.2/rayrender/man/render_animation.Rd | 2 rayrender-0.34.2/rayrender/src/PrintClassSizes.cpp |only rayrender-0.34.2/rayrender/src/RcppExports.cpp | 38 - rayrender-0.34.2/rayrender/src/assert.cpp |only rayrender-0.34.2/rayrender/src/assert.h |only rayrender-0.34.2/rayrender/src/buildscene.cpp | 396 +++++++++++--- rayrender-0.34.2/rayrender/src/buildscene.h | 41 - rayrender-0.34.2/rayrender/src/bvh_node.cpp | 4 rayrender-0.34.2/rayrender/src/calcnormals.cpp |only rayrender-0.34.2/rayrender/src/calcnormals.h |only rayrender-0.34.2/rayrender/src/calctangents.cpp |only rayrender-0.34.2/rayrender/src/calctangents.h |only rayrender-0.34.2/rayrender/src/debug.cpp | 6 rayrender-0.34.2/rayrender/src/debug.h | 8 rayrender-0.34.2/rayrender/src/displacement.cpp |only rayrender-0.34.2/rayrender/src/displacement.h |only rayrender-0.34.2/rayrender/src/instance.cpp |only rayrender-0.34.2/rayrender/src/instance.h |only rayrender-0.34.2/rayrender/src/loopsubdiv.cpp |only rayrender-0.34.2/rayrender/src/loopsubdiv.h |only rayrender-0.34.2/rayrender/src/material.cpp | 2 rayrender-0.34.2/rayrender/src/mathinline.h | 11 rayrender-0.34.2/rayrender/src/mesh3d.cpp | 50 + rayrender-0.34.2/rayrender/src/mesh3d.h | 7 rayrender-0.34.2/rayrender/src/normal.h | 2 rayrender-0.34.2/rayrender/src/plymesh.cpp | 19 rayrender-0.34.2/rayrender/src/plymesh.h | 4 rayrender-0.34.2/rayrender/src/point2.h | 4 rayrender-0.34.2/rayrender/src/raymesh.cpp | 54 + rayrender-0.34.2/rayrender/src/raymesh.h | 20 rayrender-0.34.2/rayrender/src/render_animation_rcpp.cpp | 260 ++------- rayrender-0.34.2/rayrender/src/render_scene_rcpp.cpp | 298 ++-------- rayrender-0.34.2/rayrender/src/stb |only rayrender-0.34.2/rayrender/src/texturecache.cpp |only rayrender-0.34.2/rayrender/src/texturecache.h |only rayrender-0.34.2/rayrender/src/tinyobj/earcut.hpp | 3 rayrender-0.34.2/rayrender/src/tinyobj/tinyexr.h |only rayrender-0.34.2/rayrender/src/triangle.cpp | 79 +- rayrender-0.34.2/rayrender/src/trianglemesh.cpp | 291 +++++----- rayrender-0.34.2/rayrender/src/trianglemesh.h | 27 rayrender-0.34.2/rayrender/src/trimesh.cpp | 55 + rayrender-0.34.2/rayrender/src/trimesh.h | 9 rayrender-0.34.2/rayrender/src/vec2.h | 4 71 files changed, 1451 insertions(+), 1283 deletions(-)
Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized (adaptive) elastic net S and M estimators for
linear regression. The methods are proposed in
Cohen Freue, G. V., Kepplinger, D., Salibián-Barrera, M., and Smucler, E.
(2019) <https://projecteuclid.org/euclid.aoas/1574910036>.
The package implements the extensions and algorithms described in
Kepplinger, D. (2020) <doi:10.14288/1.0392915>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pense versions 2.2.0 dated 2023-02-07 and 2.2.2 dated 2024-07-27
pense-2.2.0/pense/build/pense.pdf |only pense-2.2.0/pense/tests/testthat/Rplots.pdf |only pense-2.2.0/pense/vignettes/migration_guide_cache |only pense-2.2.2/pense/DESCRIPTION | 10 pense-2.2.2/pense/MD5 | 39 +- pense-2.2.2/pense/NEWS.md | 7 pense-2.2.2/pense/build/stage23.rdb |only pense-2.2.2/pense/build/vignette.rds |binary pense-2.2.2/pense/inst/doc/computing_adapense.R | 16 - pense-2.2.2/pense/inst/doc/computing_adapense.html | 268 ++++++++++---------- pense-2.2.2/pense/inst/doc/lambda_grids.R | 14 - pense-2.2.2/pense/inst/doc/lambda_grids.html | 56 ++-- pense-2.2.2/pense/inst/doc/migration_guide.R | 12 pense-2.2.2/pense/inst/doc/migration_guide.html | 169 ++++++------ pense-2.2.2/pense/man/mscale.Rd | 2 pense-2.2.2/pense/man/tau_size.Rd | 2 pense-2.2.2/pense/src/autoconfig.hpp.win | 8 pense-2.2.2/pense/src/nsoptim/optimizer/auglars.hpp | 10 18 files changed, 307 insertions(+), 306 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant
versions of 'install.packages' and `require` for CRAN packages, packages
no longer on CRAN (i.e., archived), specific versions of packages,
and GitHub packages. This approach is developed to create reproducible
workflows that are flexible and fast enough to use while in development stages,
while able to build snapshots once a stable package collection is found.
As with other functions in a reproducible workflow, this package
emphasizes functions that return the same result whether it is
the first or subsequent times running the function, with subsequent times being
sufficiently fast that they can be run every time without undue waiting burden on
the user or developer.
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [ctb] ,
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.3.1 dated 2023-05-22 and 1.0.0 dated 2024-07-27
Require-0.3.1/Require/man/RequireCacheDir.Rd |only Require-0.3.1/Require/man/getOptionRPackageCache.Rd |only Require-0.3.1/Require/tests/test-all.R |only Require-0.3.1/Require/tests/test-helpers.R |only Require-0.3.1/Require/tests/testit |only Require-1.0.0/Require/DESCRIPTION | 22 Require-1.0.0/Require/MD5 | 127 Require-1.0.0/Require/NAMESPACE | 21 Require-1.0.0/Require/NEWS.md | 630 +- Require-1.0.0/Require/R/CRAN.R | 5 Require-1.0.0/Require/R/Require-helpers.R | 1077 ++- Require-1.0.0/Require/R/Require2.R | 3597 ++++++++---- Require-1.0.0/Require/R/RequireOptions.R | 38 Require-1.0.0/Require/R/envs.R |only Require-1.0.0/Require/R/extract.R | 9 Require-1.0.0/Require/R/helpers.R | 157 Require-1.0.0/Require/R/messages.R |only Require-1.0.0/Require/R/pak.R |only Require-1.0.0/Require/R/pkgDep.R | 2131 ++----- Require-1.0.0/Require/R/pkgDep3.R |only Require-1.0.0/Require/R/pkgSnapshot.R | 78 Require-1.0.0/Require/R/setup.R | 158 Require-1.0.0/Require/R/zzz.R | 36 Require-1.0.0/Require/README.md | 133 Require-1.0.0/Require/build |only Require-1.0.0/Require/inst/WORDLIST | 34 Require-1.0.0/Require/inst/doc |only Require-1.0.0/Require/inst/snapshot.txt |only Require-1.0.0/Require/inst/timings.csv |only Require-1.0.0/Require/man/DESCRIPTION-helpers.Rd | 11 Require-1.0.0/Require/man/GitHubTools.Rd | 5 Require-1.0.0/Require/man/Require.Rd | 110 Require-1.0.0/Require/man/RequireOptions.Rd | 6 Require-1.0.0/Require/man/availablePackagesOverride.Rd | 14 Require-1.0.0/Require/man/availableVersions.Rd | 25 Require-1.0.0/Require/man/cacheDefaultDir.Rd |only Require-1.0.0/Require/man/cacheDir.Rd |only Require-1.0.0/Require/man/cacheGetOptionCachePkgDir.Rd |only Require-1.0.0/Require/man/cachePurge.Rd |only Require-1.0.0/Require/man/checkLibPaths.Rd |only Require-1.0.0/Require/man/checkPath.Rd | 2 Require-1.0.0/Require/man/clearRequire.Rd | 18 Require-1.0.0/Require/man/compareVersion2.Rd |only Require-1.0.0/Require/man/dealWithMissingLibPaths.Rd |only Require-1.0.0/Require/man/detachAll.Rd | 8 Require-1.0.0/Require/man/doLibPaths.Rd |only Require-1.0.0/Require/man/dot-downloadFileMasterMainAuth.Rd | 5 Require-1.0.0/Require/man/dot-installed.pkgs.Rd |only Require-1.0.0/Require/man/envPkgCreate.Rd |only Require-1.0.0/Require/man/envPkgDepDESCFileCreate.Rd |only Require-1.0.0/Require/man/envPkgDepDepsCreate.Rd |only Require-1.0.0/Require/man/getDeps.Rd |only Require-1.0.0/Require/man/joinToAvailablePackages.Rd |only Require-1.0.0/Require/man/masterMainToHead.Rd |only Require-1.0.0/Require/man/messageVerbose.Rd | 5 Require-1.0.0/Require/man/normPath.Rd | 2 Require-1.0.0/Require/man/pakEnv.Rd |only Require-1.0.0/Require/man/pkgDep.Rd | 251 Require-1.0.0/Require/man/pkgDepEnv.Rd |only Require-1.0.0/Require/man/pkgDepIfDepRemoved.Rd | 5 Require-1.0.0/Require/man/pkgSnapshot.Rd | 20 Require-1.0.0/Require/man/rmBase.Rd |only Require-1.0.0/Require/man/setLibPaths.Rd | 5 Require-1.0.0/Require/man/setLinuxBinaryRepo.Rd | 2 Require-1.0.0/Require/man/setup.Rd | 7 Require-1.0.0/Require/man/splitKeepOrderAndDTIntegrity.Rd |only Require-1.0.0/Require/man/sysInstallAndDownload.Rd |only Require-1.0.0/Require/man/updatePackages.Rd |only Require-1.0.0/Require/tests/testthat |only Require-1.0.0/Require/tests/testthat.R |only Require-1.0.0/Require/vignettes |only 71 files changed, 5078 insertions(+), 3676 deletions(-)
Title: Ask Yes-No Questions
Description: Asks Yes-No questions with variable or custom responses.
Author: Ayla Pearson [cre] ,
Joe Thorley [aut, cph] ,
Hadley Wickham [aut, cph]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between yesno versions 0.1.2 dated 2020-07-10 and 0.1.3 dated 2024-07-26
DESCRIPTION | 34 ++++++++++++++----------- LICENSE |only MD5 | 14 +++++----- NEWS.md | 10 +++++++ README.md | 58 ++++++++++++++++++++----------------------- man/figures |only tests/testthat.R | 8 +++++ tests/testthat/test-yesno.R | 2 - tests/testthat/test-yesno2.R | 2 - 9 files changed, 74 insertions(+), 54 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parameteric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.1.0 dated 2024-05-04 and 1.2.0 dated 2024-07-26
WeightIt-1.1.0/WeightIt/R/mlogit_weightit.R |only WeightIt-1.1.0/WeightIt/build/WeightIt.pdf |only WeightIt-1.2.0/WeightIt/DESCRIPTION | 24 WeightIt-1.2.0/WeightIt/MD5 | 115 - WeightIt-1.2.0/WeightIt/NAMESPACE | 38 WeightIt-1.2.0/WeightIt/NEWS.md | 80 WeightIt-1.2.0/WeightIt/R/SHARED.R | 114 - WeightIt-1.2.0/WeightIt/R/calibrate.R | 9 WeightIt-1.2.0/WeightIt/R/chk-utilities.R | 18 WeightIt-1.2.0/WeightIt/R/dist_functions.R | 10 WeightIt-1.2.0/WeightIt/R/functions_for_processing.R | 354 ++- WeightIt-1.2.0/WeightIt/R/get_w_from_ps.R | 245 +- WeightIt-1.2.0/WeightIt/R/glm_weightit-methods.R |only WeightIt-1.2.0/WeightIt/R/glm_weightit.R | 1058 +++------- WeightIt-1.2.0/WeightIt/R/make_full_rank.R | 2 WeightIt-1.2.0/WeightIt/R/multinom_weightit.R |only WeightIt-1.2.0/WeightIt/R/ordinal_weightit.R |only WeightIt-1.2.0/WeightIt/R/plot.weightit.R |only WeightIt-1.2.0/WeightIt/R/predict.glm_weightit.R |only WeightIt-1.2.0/WeightIt/R/sbps.R | 94 WeightIt-1.2.0/WeightIt/R/summary.weightit.R | 68 WeightIt-1.2.0/WeightIt/R/weightit.R | 44 WeightIt-1.2.0/WeightIt/R/weightit.fit.R | 16 WeightIt-1.2.0/WeightIt/R/weightit2bart.R | 17 WeightIt-1.2.0/WeightIt/R/weightit2cbps.R | 769 ++----- WeightIt-1.2.0/WeightIt/R/weightit2ebal.R | 32 WeightIt-1.2.0/WeightIt/R/weightit2energy.R | 103 WeightIt-1.2.0/WeightIt/R/weightit2gbm.R | 393 ++- WeightIt-1.2.0/WeightIt/R/weightit2glm.R | 171 - WeightIt-1.2.0/WeightIt/R/weightit2ipt.R | 88 WeightIt-1.2.0/WeightIt/R/weightit2npcbps.R | 3 WeightIt-1.2.0/WeightIt/R/weightit2ps.R | 4 WeightIt-1.2.0/WeightIt/R/weightit2super.R | 50 WeightIt-1.2.0/WeightIt/R/weightit2user.R | 9 WeightIt-1.2.0/WeightIt/R/weightitMSM.R | 93 WeightIt-1.2.0/WeightIt/build/stage23.rdb |binary WeightIt-1.2.0/WeightIt/build/vignette.rds |binary WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.R | 3 WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.Rmd | 3 WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.html | 46 WeightIt-1.2.0/WeightIt/inst/doc/estimating-effects.Rmd | 20 WeightIt-1.2.0/WeightIt/inst/doc/estimating-effects.html | 397 +-- WeightIt-1.2.0/WeightIt/inst/doc/installing-packages.html | 6 WeightIt-1.2.0/WeightIt/man/WeightIt-package.Rd | 2 WeightIt-1.2.0/WeightIt/man/get_w_from_ps.Rd | 87 WeightIt-1.2.0/WeightIt/man/glm_weightit-methods.Rd |only WeightIt-1.2.0/WeightIt/man/glm_weightit.Rd | 101 WeightIt-1.2.0/WeightIt/man/method_bart.Rd | 15 WeightIt-1.2.0/WeightIt/man/method_ebal.Rd | 2 WeightIt-1.2.0/WeightIt/man/method_energy.Rd | 14 WeightIt-1.2.0/WeightIt/man/method_gbm.Rd | 48 WeightIt-1.2.0/WeightIt/man/method_glm.Rd | 22 WeightIt-1.2.0/WeightIt/man/method_ipt.Rd | 2 WeightIt-1.2.0/WeightIt/man/method_npcbps.Rd | 3 WeightIt-1.2.0/WeightIt/man/method_super.Rd | 22 WeightIt-1.2.0/WeightIt/man/method_user.Rd | 9 WeightIt-1.2.0/WeightIt/man/plot.weightit.Rd |only WeightIt-1.2.0/WeightIt/man/predict.glm_weightit.Rd |only WeightIt-1.2.0/WeightIt/tests/testthat/test-get_w_from_ps.R |only WeightIt-1.2.0/WeightIt/tests/testthat/test-glm_weightit.R | 71 WeightIt-1.2.0/WeightIt/tests/testthat/test-method_glm.R | 63 WeightIt-1.2.0/WeightIt/tests/testthat/test-multinom_weightit.R |only WeightIt-1.2.0/WeightIt/tests/testthat/test-ordinal_weightit.R |only WeightIt-1.2.0/WeightIt/vignettes/WeightIt.Rmd | 3 WeightIt-1.2.0/WeightIt/vignettes/estimating-effects.Rmd | 20 65 files changed, 2627 insertions(+), 2353 deletions(-)
Title: Single Sample Directional Gene Set Analysis
Description: A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed.
Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.
Author: Xingpeng Li [aut, cre],
Qi Qian [aut]
Maintainer: Xingpeng Li <xingpeng.li@pfizer.com>
Diff between ssdGSA versions 0.1.0 dated 2024-07-22 and 0.1.1 dated 2024-07-26
DESCRIPTION | 15 ++++++++------- MD5 | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-)
Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique
for determining the overall within-individual relationship among paired measures
assessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence
interval including optional bootstrapping, as well as graphing. Also includes
several example datasets. For more details, see the web documentation
<https://lmarusich.github.io/rmcorr/index.html> and the
original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash [aut] ,
Laura R. Marusich [aut, cre]
Maintainer: Laura R. Marusich <lmarusich@gmail.com>
Diff between rmcorr versions 0.6.0 dated 2023-08-09 and 0.7.0 dated 2024-07-26
rmcorr-0.6.0/rmcorr/tests/HCAPHS.csv |only rmcorr-0.7.0/rmcorr/DESCRIPTION | 15 - rmcorr-0.7.0/rmcorr/MD5 | 81 +++-- rmcorr-0.7.0/rmcorr/NAMESPACE | 1 rmcorr-0.7.0/rmcorr/NEWS.md | 11 rmcorr-0.7.0/rmcorr/R/data.R | 4 rmcorr-0.7.0/rmcorr/R/geom_rmc.R |only rmcorr-0.7.0/rmcorr/R/plot.rmc.R | 33 -- rmcorr-0.7.0/rmcorr/R/rmcorr-package.R | 4 rmcorr-0.7.0/rmcorr/R/rmcorr.R | 2 rmcorr-0.7.0/rmcorr/README.md | 4 rmcorr-0.7.0/rmcorr/build/partial.rdb |binary rmcorr-0.7.0/rmcorr/build/vignette.rds |binary rmcorr-0.7.0/rmcorr/inst/doc/CI_fix.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/CI_fix.html | 6 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.Rmd | 2 rmcorr-0.7.0/rmcorr/inst/doc/FAQ_and_limitations.html | 11 rmcorr-0.7.0/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.R | 22 - rmcorr-0.7.0/rmcorr/inst/doc/New_rmcorr_paper_analyses_figures.html | 8 rmcorr-0.7.0/rmcorr/inst/doc/compcor.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/compcor.html | 9 rmcorr-0.7.0/rmcorr/inst/doc/estimates_w_NaN.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/estimates_w_NaN.html | 48 +-- rmcorr-0.7.0/rmcorr/inst/doc/model_diag.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/model_diag.html | 11 rmcorr-0.7.0/rmcorr/inst/doc/overfitting.R |only rmcorr-0.7.0/rmcorr/inst/doc/overfitting.Rmd |only rmcorr-0.7.0/rmcorr/inst/doc/overfitting.html |only rmcorr-0.7.0/rmcorr/inst/doc/repro_bootstrapping.R | 2 rmcorr-0.7.0/rmcorr/inst/doc/repro_bootstrapping.html | 6 rmcorr-0.7.0/rmcorr/inst/doc/rmcorr_mat.R | 4 rmcorr-0.7.0/rmcorr/inst/doc/rmcorr_mat.html | 9 rmcorr-0.7.0/rmcorr/man/HCAHPS2022.Rd | 4 rmcorr-0.7.0/rmcorr/man/geom_rmc.Rd |only rmcorr-0.7.0/rmcorr/man/plot.rmc.Rd | 38 -- rmcorr-0.7.0/rmcorr/man/rmcorr-package.Rd | 22 + rmcorr-0.7.0/rmcorr/man/rmcorr.Rd | 2 rmcorr-0.7.0/rmcorr/tests/testthat/Rplots.pdf |binary rmcorr-0.7.0/rmcorr/tests/testthat/_snaps/geom_rmc |only rmcorr-0.7.0/rmcorr/tests/testthat/_snaps/rmcorr.md | 42 +- rmcorr-0.7.0/rmcorr/tests/testthat/test-geom_rmc.R |only rmcorr-0.7.0/rmcorr/vignettes/FAQ_and_limitations.Rmd | 2 rmcorr-0.7.0/rmcorr/vignettes/overfitting.Rmd |only rmcorr-0.7.0/rmcorr/vignettes/references.bib | 149 ++++++++++ 45 files changed, 357 insertions(+), 211 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.0 dated 2024-07-24 and 1.2.1 dated 2024-07-26
DESCRIPTION | 11 +++-- MD5 | 16 ++++---- NEWS.md | 4 ++ R/import_methods.R | 2 - R/sysdata.rda |binary README.md | 2 - inst/doc/labelled.html | 4 +- inst/doc/rio.html | 70 +++++++++++++++++------------------ tests/testthat/test_format_parquet.R | 2 - 9 files changed, 58 insertions(+), 53 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.3 dated 2024-07-09 and 3.6.4 dated 2024-07-26
DESCRIPTION | 6 MD5 | 90 ++--- NEWS.md | 23 + R/gsDesign.R | 4 R/gsMethods.R | 17 R/gsSurv.R | 2 build/vignette.rds |binary inst/doc/ConditionalErrorSpending.Rmd | 4 inst/doc/ConditionalErrorSpending.html | 427 +++++++++++++----------- inst/doc/ConditionalPowerPlot.Rmd | 4 inst/doc/ConditionalPowerPlot.html | 6 inst/doc/GentleIntroductionToGSD.Rmd | 6 inst/doc/GentleIntroductionToGSD.html | 8 inst/doc/PoissonMixtureModel.Rmd | 32 - inst/doc/PoissonMixtureModel.html | 170 +++++---- inst/doc/SpendingFunctionOverview.Rmd | 6 inst/doc/SpendingFunctionOverview.html | 12 inst/doc/SurvivalOverview.Rmd | 12 inst/doc/SurvivalOverview.html | 12 inst/doc/VaccineEfficacy.Rmd | 32 - inst/doc/VaccineEfficacy.html | 568 +++++++++++++++++---------------- inst/doc/binomialSPRTExample.Rmd | 12 inst/doc/binomialSPRTExample.html | 250 +++++++------- inst/doc/gsDesignPackageOverview.Rmd | 6 inst/doc/gsDesignPackageOverview.html | 12 inst/doc/gsSurvBasicExamples.Rmd | 30 - inst/doc/gsSurvBasicExamples.html | 463 ++++++++++++++------------ inst/doc/nNormal.Rmd | 24 - inst/doc/nNormal.html | 44 +- inst/doc/toInteger.Rmd | 14 inst/doc/toInteger.html | 30 - man/gsDesign.Rd | 6 man/nSurv.Rd | 4 vignettes/ConditionalErrorSpending.Rmd | 4 vignettes/ConditionalPowerPlot.Rmd | 4 vignettes/GentleIntroductionToGSD.Rmd | 6 vignettes/PoissonMixtureModel.Rmd | 32 - vignettes/SpendingFunctionOverview.Rmd | 6 vignettes/SurvivalOverview.Rmd | 12 vignettes/VaccineEfficacy.Rmd | 32 - vignettes/binomialSPRTExample.Rmd | 12 vignettes/gsDesign.bib | 9 vignettes/gsDesignPackageOverview.Rmd | 6 vignettes/gsSurvBasicExamples.Rmd | 30 - vignettes/nNormal.Rmd | 24 - vignettes/toInteger.Rmd | 14 46 files changed, 1331 insertions(+), 1196 deletions(-)
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.0-10 dated 2023-12-07 and 1.1-0 dated 2024-07-26
cartogramR-1.0-10/cartogramR/man/geom_cartogramR.Rd |only cartogramR-1.1-0/cartogramR/DESCRIPTION | 10 - cartogramR-1.1-0/cartogramR/MD5 | 54 ++++--- cartogramR-1.1-0/cartogramR/NAMESPACE | 1 cartogramR-1.1-0/cartogramR/R/as.sf.cartogramR.R | 12 - cartogramR-1.1-0/cartogramR/R/as.sfc.cartogramR.R | 2 cartogramR-1.1-0/cartogramR/R/cartogramR-deprecated.R |only cartogramR-1.1-0/cartogramR/R/cartogramR.R | 52 ++++--- cartogramR-1.1-0/cartogramR/R/cartogramR_options.R | 6 cartogramR-1.1-0/cartogramR/R/from_coord_polygon.R | 6 cartogramR-1.1-0/cartogramR/R/geom_cartogramR.R | 68 ---------- cartogramR-1.1-0/cartogramR/R/make_layer.R | 18 +- cartogramR-1.1-0/cartogramR/R/plot.cartogramR.R | 2 cartogramR-1.1-0/cartogramR/R/print.cartogramR.R | 8 - cartogramR-1.1-0/cartogramR/R/print.summary.cartogramR.R | 8 - cartogramR-1.1-0/cartogramR/R/residuals.cartogramR.R | 41 +++--- cartogramR-1.1-0/cartogramR/R/summary.cartogramR.R | 12 + cartogramR-1.1-0/cartogramR/R/to_coord_polygon.R | 6 cartogramR-1.1-0/cartogramR/R/warp_features.R |only cartogramR-1.1-0/cartogramR/man/cartogramR-deprecated.Rd |only cartogramR-1.1-0/cartogramR/man/cartogramR.Rd | 19 +- cartogramR-1.1-0/cartogramR/man/cartogramR_options.Rd | 35 +---- cartogramR-1.1-0/cartogramR/man/france_rivers.Rd | 2 cartogramR-1.1-0/cartogramR/man/geom_cartogramR-deprecated.Rd |only cartogramR-1.1-0/cartogramR/man/grid_analysis.Rd | 2 cartogramR-1.1-0/cartogramR/man/make_layer.Rd | 4 cartogramR-1.1-0/cartogramR/man/plot.dbv.cartogramR.Rd | 3 cartogramR-1.1-0/cartogramR/man/residuals.cartogramR.Rd | 10 - cartogramR-1.1-0/cartogramR/man/summary.cartogramR.Rd | 7 - cartogramR-1.1-0/cartogramR/man/summary.gridanalysis.cartogramR.Rd | 3 cartogramR-1.1-0/cartogramR/man/warp_features.Rd |only 31 files changed, 169 insertions(+), 222 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 9.1.1 dated 2024-06-14 and 10.0.0 dated 2024-07-26
ggblanket-10.0.0/ggblanket/DESCRIPTION | 14 ggblanket-10.0.0/ggblanket/MD5 | 458 ++-- ggblanket-10.0.0/ggblanket/NAMESPACE | 21 ggblanket-10.0.0/ggblanket/NEWS.md | 25 ggblanket-10.0.0/ggblanket/R/aes.R |only ggblanket-10.0.0/ggblanket/R/dark_mode.R | 162 - ggblanket-10.0.0/ggblanket/R/flex_mode.R | 206 - ggblanket-10.0.0/ggblanket/R/gg_area.R | 56 ggblanket-10.0.0/ggblanket/R/gg_bar.R | 60 ggblanket-10.0.0/ggblanket/R/gg_bin_2d.R | 56 ggblanket-10.0.0/ggblanket/R/gg_blanket.R | 1035 +++------ ggblanket-10.0.0/ggblanket/R/gg_boxplot.R | 63 ggblanket-10.0.0/ggblanket/R/gg_col.R | 59 ggblanket-10.0.0/ggblanket/R/gg_contour.R | 56 ggblanket-10.0.0/ggblanket/R/gg_contour_filled.R | 56 ggblanket-10.0.0/ggblanket/R/gg_crossbar.R | 56 ggblanket-10.0.0/ggblanket/R/gg_density.R | 59 ggblanket-10.0.0/ggblanket/R/gg_density_2d.R | 56 ggblanket-10.0.0/ggblanket/R/gg_density_2d_filled.R | 56 ggblanket-10.0.0/ggblanket/R/gg_errorbar.R | 56 ggblanket-10.0.0/ggblanket/R/gg_freqpoly.R | 59 ggblanket-10.0.0/ggblanket/R/gg_function.R | 58 ggblanket-10.0.0/ggblanket/R/gg_hex.R | 58 ggblanket-10.0.0/ggblanket/R/gg_histogram.R | 59 ggblanket-10.0.0/ggblanket/R/gg_jitter.R | 56 ggblanket-10.0.0/ggblanket/R/gg_label.R | 56 ggblanket-10.0.0/ggblanket/R/gg_line.R | 56 ggblanket-10.0.0/ggblanket/R/gg_linerange.R | 56 ggblanket-10.0.0/ggblanket/R/gg_path.R | 56 ggblanket-10.0.0/ggblanket/R/gg_point.R | 59 ggblanket-10.0.0/ggblanket/R/gg_pointrange.R | 56 ggblanket-10.0.0/ggblanket/R/gg_polygon.R | 56 ggblanket-10.0.0/ggblanket/R/gg_qq.R | 56 ggblanket-10.0.0/ggblanket/R/gg_quantile.R | 56 ggblanket-10.0.0/ggblanket/R/gg_raster.R | 56 ggblanket-10.0.0/ggblanket/R/gg_rect.R | 56 ggblanket-10.0.0/ggblanket/R/gg_ribbon.R | 56 ggblanket-10.0.0/ggblanket/R/gg_rug.R | 59 ggblanket-10.0.0/ggblanket/R/gg_segment.R | 56 ggblanket-10.0.0/ggblanket/R/gg_sf.R | 56 ggblanket-10.0.0/ggblanket/R/gg_smooth.R | 60 ggblanket-10.0.0/ggblanket/R/gg_step.R | 59 ggblanket-10.0.0/ggblanket/R/gg_text.R | 56 ggblanket-10.0.0/ggblanket/R/gg_tile.R | 57 ggblanket-10.0.0/ggblanket/R/gg_violin.R | 61 ggblanket-10.0.0/ggblanket/R/light_mode.R | 161 - ggblanket-10.0.0/ggblanket/R/mode_defaults.R | 9 ggblanket-10.0.0/ggblanket/R/mode_orientation.R |only ggblanket-10.0.0/ggblanket/R/scale_symmetric.R |only ggblanket-10.0.0/ggblanket/R/set_blanket.R | 175 + ggblanket-10.0.0/ggblanket/R/unexported.R |only ggblanket-10.0.0/ggblanket/R/weave.R | 381 +-- ggblanket-10.0.0/ggblanket/inst/WORDLIST | 7 ggblanket-10.0.0/ggblanket/inst/doc/ggblanket.R | 21 ggblanket-10.0.0/ggblanket/inst/doc/ggblanket.Rmd | 84 ggblanket-10.0.0/ggblanket/inst/doc/ggblanket.html | 170 - ggblanket-10.0.0/ggblanket/man/aes_colour_contrast.Rd |only ggblanket-10.0.0/ggblanket/man/aes_colour_darken.Rd |only ggblanket-10.0.0/ggblanket/man/dark_mode_r.Rd | 360 +-- ggblanket-10.0.0/ggblanket/man/flex_mode_b.Rd | 244 +- ggblanket-10.0.0/ggblanket/man/flex_mode_base.Rd | 238 +- ggblanket-10.0.0/ggblanket/man/flex_mode_r.Rd | 244 +- ggblanket-10.0.0/ggblanket/man/flex_mode_t.Rd | 244 +- ggblanket-10.0.0/ggblanket/man/gg_area.Rd | 346 +-- ggblanket-10.0.0/ggblanket/man/gg_bar.Rd | 350 +-- ggblanket-10.0.0/ggblanket/man/gg_bin_2d.Rd | 344 +-- ggblanket-10.0.0/ggblanket/man/gg_blanket.Rd | 364 +-- ggblanket-10.0.0/ggblanket/man/gg_boxplot.Rd | 351 +-- ggblanket-10.0.0/ggblanket/man/gg_col.Rd | 359 +-- ggblanket-10.0.0/ggblanket/man/gg_contour.Rd | 346 +-- ggblanket-10.0.0/ggblanket/man/gg_contour_filled.Rd | 348 +-- ggblanket-10.0.0/ggblanket/man/gg_crossbar.Rd | 368 +-- ggblanket-10.0.0/ggblanket/man/gg_density.Rd | 349 +-- ggblanket-10.0.0/ggblanket/man/gg_density_2d.Rd | 350 +-- ggblanket-10.0.0/ggblanket/man/gg_density_2d_filled.Rd | 350 +-- ggblanket-10.0.0/ggblanket/man/gg_errorbar.Rd | 368 +-- ggblanket-10.0.0/ggblanket/man/gg_freqpoly.Rd | 349 +-- ggblanket-10.0.0/ggblanket/man/gg_function.Rd | 344 +-- ggblanket-10.0.0/ggblanket/man/gg_hex.Rd | 348 +-- ggblanket-10.0.0/ggblanket/man/gg_histogram.Rd | 351 +-- ggblanket-10.0.0/ggblanket/man/gg_jitter.Rd | 358 +-- ggblanket-10.0.0/ggblanket/man/gg_label.Rd | 40 ggblanket-10.0.0/ggblanket/man/gg_line.Rd | 348 +-- ggblanket-10.0.0/ggblanket/man/gg_linerange.Rd | 366 +-- ggblanket-10.0.0/ggblanket/man/gg_path.Rd | 352 +-- ggblanket-10.0.0/ggblanket/man/gg_point.Rd | 349 +-- ggblanket-10.0.0/ggblanket/man/gg_pointrange.Rd | 368 +-- ggblanket-10.0.0/ggblanket/man/gg_polygon.Rd | 390 +-- ggblanket-10.0.0/ggblanket/man/gg_qq.Rd | 354 +-- ggblanket-10.0.0/ggblanket/man/gg_quantile.Rd | 348 +-- ggblanket-10.0.0/ggblanket/man/gg_raster.Rd | 346 +-- ggblanket-10.0.0/ggblanket/man/gg_rect.Rd | 372 +-- ggblanket-10.0.0/ggblanket/man/gg_ribbon.Rd | 356 +-- ggblanket-10.0.0/ggblanket/man/gg_rug.Rd | 349 +-- ggblanket-10.0.0/ggblanket/man/gg_segment.Rd | 350 +-- ggblanket-10.0.0/ggblanket/man/gg_sf.Rd | 346 +-- ggblanket-10.0.0/ggblanket/man/gg_smooth.Rd | 352 +-- ggblanket-10.0.0/ggblanket/man/gg_step.Rd | 351 +-- ggblanket-10.0.0/ggblanket/man/gg_text.Rd | 40 ggblanket-10.0.0/ggblanket/man/gg_tile.Rd | 353 +-- ggblanket-10.0.0/ggblanket/man/gg_violin.Rd | 353 +-- ggblanket-10.0.0/ggblanket/man/light_mode_r.Rd | 360 +-- ggblanket-10.0.0/ggblanket/man/lightness.Rd | 7 ggblanket-10.0.0/ggblanket/man/mode_orientation_to_x.Rd |only ggblanket-10.0.0/ggblanket/man/scale_x_symmetric.Rd |only ggblanket-10.0.0/ggblanket/man/scale_y_symmetric.Rd |only ggblanket-10.0.0/ggblanket/man/set_blanket.Rd | 129 - 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Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation,
model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs,
correlation between graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Grover E. Castro Guzman [aut],
Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 1.0.2 dated 2024-07-03 and 1.0.3 dated 2024-07-26
DESCRIPTION | 10 - MD5 | 70 ++++---- NAMESPACE | 3 R/GIC.R | 88 +++++----- R/anogva.R | 94 +++++------ R/graph.acf.R | 13 - R/graph.cem.R | 190 +++++++++++----------- R/graph.cor.test.R | 44 ++--- R/graph.dist.R | 97 +++++------ R/graph.entropy.R | 35 ++-- R/graph.hclust.R | 43 ++--- R/graph.kmeans.R | 154 +++++++++--------- R/graph.model.selection.R | 85 ++++------ R/graph.models.R | 265 +++++++++++++++---------------- R/graph.mult.scaling.R | 60 +++---- R/graph.param.estimator.R | 205 ++++++++++++------------ R/graph.spectral.density.R | 355 +++++++++++++++++++++--------------------- R/graph.takahashi.test.R | 100 ++++++----- R/plot.statGraph.R |only R/print.statGraph.R | 84 +++++---- R/sp.anogva.R | 108 ++++++------ R/summary.statGraph.R |only R/utils.R | 210 ++++++++++++------------ man/GIC.Rd | 30 +-- man/anogva.Rd | 6 man/graph.cem.Rd | 12 - man/graph.cor.test.Rd | 6 man/graph.dist.Rd | 6 man/graph.entropy.Rd | 2 man/graph.hclust.Rd | 22 +- man/graph.kmeans.Rd | 12 - man/graph.model.selection.Rd | 16 - man/graph.mult.scaling.Rd | 10 - man/graph.param.estimator.Rd | 32 +-- man/graph.spectral.density.Rd | 8 man/graph.takahashi.test.Rd | 18 +- man/sp.anogva.Rd | 10 - 37 files changed, 1271 insertions(+), 1232 deletions(-)
Title: A Shiny App for Design of Experiments in Life Sciences
Description: A shiny design of experiments (DOE) app that aids in the creation of traditional,
un-replicated, augmented and partially-replicated designs applied to agriculture,
plant breeding, forestry, animal and biological sciences.
Author: Didier Murillo [cre, aut],
Salvador Gezan [aut],
Ana Heilman [ctb],
Thomas Walk [ctb],
Johan Aparicio [ctb],
Matthew Seefeldt [ctb],
Jean-Marc Montpetit [ctb],
Richard Horsley [ctb],
North Dakota State University [cph]
Maintainer: Didier Murillo <didier.murilloflorez@ndsu.edu>
Diff between FielDHub versions 1.4.0 dated 2024-07-09 and 1.4.2 dated 2024-07-26
FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.R |only FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.Rmd |only FielDHub-1.4.0/FielDHub/inst/doc/optimized_arrangement.html |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.R |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.Rmd |only FielDHub-1.4.0/FielDHub/inst/doc/sparse_allocation.html |only FielDHub-1.4.0/FielDHub/vignettes/optimized_arrangement.Rmd |only FielDHub-1.4.0/FielDHub/vignettes/sparse_allocation.Rmd |only FielDHub-1.4.2/FielDHub/DESCRIPTION | 6 FielDHub-1.4.2/FielDHub/MD5 | 53 +- FielDHub-1.4.2/FielDHub/R/app_ui.R | 4 FielDHub-1.4.2/FielDHub/R/fct_incomplete_blocks.R | 9 FielDHub-1.4.2/FielDHub/R/fct_row_column.R | 227 ++++++++---- FielDHub-1.4.2/FielDHub/R/globals.R | 5 FielDHub-1.4.2/FielDHub/R/mod_RowCol.R | 22 + FielDHub-1.4.2/FielDHub/R/utils_S3_methods.R | 28 - FielDHub-1.4.2/FielDHub/R/utils_plot_latinSQ.R | 2 FielDHub-1.4.2/FielDHub/R/utils_row_col_optimization.R |only FielDHub-1.4.2/FielDHub/build/vignette.rds |binary FielDHub-1.4.2/FielDHub/inst/WORDLIST | 6 FielDHub-1.4.2/FielDHub/inst/doc/RCBD_augmented.html | 6 FielDHub-1.4.2/FielDHub/inst/doc/alpha_lattice.html | 46 +- FielDHub-1.4.2/FielDHub/inst/doc/diagonal_arrangement.html | 9 FielDHub-1.4.2/FielDHub/inst/doc/full_factorial.html | 4 FielDHub-1.4.2/FielDHub/inst/doc/multi_location_prep.html | 73 +-- FielDHub-1.4.2/FielDHub/inst/doc/partially_replicated.html | 7 FielDHub-1.4.2/FielDHub/inst/doc/rcbd.html | 4 FielDHub-1.4.2/FielDHub/inst/doc/row_column.Rmd | 24 + FielDHub-1.4.2/FielDHub/inst/doc/row_column.html | 81 ++-- FielDHub-1.4.2/FielDHub/inst/doc/split_plot.html | 4 FielDHub-1.4.2/FielDHub/man/row_column.Rd | 76 ++-- FielDHub-1.4.2/FielDHub/vignettes/row_column.Rmd | 24 + 32 files changed, 469 insertions(+), 251 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt).
FishPar(): Calculates length-based indicators (LBIs) proposed by Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> such as the percentage of mature fish (Pmat), percentage of optimal length fish (Popt), percentage of mega spawners (Pmega), and the sum of these as Pobj. This function also estimates confidence intervals for different lengths, visualizes length frequency distributions, a [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.4 dated 2024-07-09 and 0.1.5 dated 2024-07-26
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/FishPar.R | 3 ++- inst/doc/Introduction.html | 20 ++++++++++---------- 4 files changed, 20 insertions(+), 19 deletions(-)
More information about SampleSizeDiagnostics at CRAN
Permanent link
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.4-2 dated 2024-02-02 and 4.5 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 9 ++++++++- src/emf+.h | 33 +++++++++++++++++++++++++-------- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.1.1 dated 2024-06-17 and 0.1.2 dated 2024-07-26
DESCRIPTION | 8 MD5 | 46 R/summariseTemporalSymmetry.R | 232 +- inst/doc/a02_Generate_a_sequence_cohort_set.R | 22 inst/doc/a02_Generate_a_sequence_cohort_set.Rmd | 23 inst/doc/a02_Generate_a_sequence_cohort_set.html | 104 - inst/doc/a03_Summarise_sequence_ratios.R | 22 inst/doc/a03_Summarise_sequence_ratios.Rmd | 263 +- inst/doc/a03_Summarise_sequence_ratios.html | 11 inst/doc/a04_Visualise_sequence_ratios.R | 22 inst/doc/a04_Visualise_sequence_ratios.Rmd | 23 inst/doc/a04_Visualise_sequence_ratios.html | 457 ++--- inst/doc/a05_Summarise_temporal_symmetry.R | 22 inst/doc/a05_Summarise_temporal_symmetry.Rmd | 23 inst/doc/a05_Summarise_temporal_symmetry.html | 31 inst/doc/a06_Visualise_temporal_symmetry.R | 22 inst/doc/a06_Visualise_temporal_symmetry.Rmd | 269 +-- inst/doc/a06_Visualise_temporal_symmetry.html | 9 tests/testthat/test-generateSequenceCohortSet.R | 2024 +++++++++++------------ vignettes/a02_Generate_a_sequence_cohort_set.Rmd | 23 vignettes/a03_Summarise_sequence_ratios.Rmd | 263 +- vignettes/a04_Visualise_sequence_ratios.Rmd | 23 vignettes/a05_Summarise_temporal_symmetry.Rmd | 23 vignettes/a06_Visualise_temporal_symmetry.Rmd | 269 +-- 24 files changed, 2235 insertions(+), 1999 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Streamline Population Genomic and Genetic Analyses
Description: Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Author: Keaka Farleigh [aut, cph, cre]
,
Mason Murphy [aut, cph, ctb] ,
Christopher Blair [aut, cph, ctb]
,
Tereza Jezkova [aut, cph, ctb]
Maintainer: Keaka Farleigh <keakafarleigh@gmail.com>
Diff between PopGenHelpR versions 1.3.0 dated 2024-05-09 and 1.3.1 dated 2024-07-26
PopGenHelpR-1.3.0/PopGenHelpR/R/Dif_stats.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Dif_stats_Map.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Div_Stats.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Div_Stats_Map.R |only PopGenHelpR-1.3.0/PopGenHelpR/R/Plot_ancestry.R |only PopGenHelpR-1.3.0/PopGenHelpR/man/Dif_Stats_Map.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Dif_stats.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Div_Stats_Map.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Div_stats.Rd |only PopGenHelpR-1.3.0/PopGenHelpR/man/Plot_ancestry.Rd |only PopGenHelpR-1.3.1/PopGenHelpR/DESCRIPTION | 11 PopGenHelpR-1.3.1/PopGenHelpR/MD5 | 28 -- PopGenHelpR-1.3.1/PopGenHelpR/NAMESPACE | 5 PopGenHelpR-1.3.1/PopGenHelpR/NEWS.md | 82 +++--- PopGenHelpR-1.3.1/PopGenHelpR/R/data.R | 241 ++++++++---------- PopGenHelpR-1.3.1/PopGenHelpR/man/Fst_dat.Rd | 6 PopGenHelpR-1.3.1/PopGenHelpR/man/Het_dat.Rd | 6 PopGenHelpR-1.3.1/PopGenHelpR/man/HornedLizard_Pop.Rd | 5 PopGenHelpR-1.3.1/PopGenHelpR/man/HornedLizard_VCF.Rd | 5 PopGenHelpR-1.3.1/PopGenHelpR/man/Q_dat.Rd | 5 20 files changed, 186 insertions(+), 208 deletions(-)
Title: Power in a Group Sequential Design
Description: Tools for the evaluation of interim analysis plans for sequentially
monitored trials on a survival endpoint; tools to construct efficacy and
futility boundaries, for deriving power of a sequential design at a specified
alternative, template for evaluating the performance of candidate plans at a
set of time varying alternatives. See Izmirlian, G. (2014) <doi:10.4310/SII.2014.v7.n1.a4>.
Author: Grant Izmirlian <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between PwrGSD versions 2.3.6 dated 2021-12-10 and 2.3.7 dated 2024-07-26
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/PwrGSD.R | 20 ++++++++++++-------- build/vignette.rds |binary inst/CITATION |only inst/doc/GrpSeqBnds-vignette.pdf |binary inst/doc/PwrGSD-vignette.pdf |binary inst/doc/cpd-PwrGSD-vignette.pdf |binary man/Ch0C-plot.cpd.PwrGSD.Rd | 2 +- man/Ch17-CRRtoRR.Rd | 6 +++--- src/SimPwrGSD.c | 2 -- 11 files changed, 29 insertions(+), 26 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.1-0 dated 2023-01-23 and 2.1-1 dated 2024-07-26
colorspace-2.1-0/colorspace/inst/hclwizard/html/python-example.html |only colorspace-2.1-1/colorspace/DESCRIPTION | 10 colorspace-2.1-1/colorspace/MD5 | 55 ++-- colorspace-2.1-1/colorspace/NAMESPACE | 1 colorspace-2.1-1/colorspace/NEWS.md | 31 ++ colorspace-2.1-1/colorspace/R/adjust_hcl.R | 10 colorspace-2.1-1/colorspace/R/adjust_transparency.R | 16 - colorspace-2.1-1/colorspace/R/cvd_image.R | 57 ++-- colorspace-2.1-1/colorspace/R/desaturate.R | 117 ++++++---- colorspace-2.1-1/colorspace/R/divergingx_hcl.R | 2 colorspace-2.1-1/colorspace/R/hcl_palettes.R | 4 colorspace-2.1-1/colorspace/R/hclplot.R | 66 +++-- colorspace-2.1-1/colorspace/R/lighten.R | 7 colorspace-2.1-1/colorspace/R/simulate_cvd.R | 13 - colorspace-2.1-1/colorspace/build/partial.rdb |binary colorspace-2.1-1/colorspace/build/vignette.rds |binary colorspace-2.1-1/colorspace/inst/CITATION | 80 +++--- colorspace-2.1-1/colorspace/inst/doc/colorspace.Rmd | 5 colorspace-2.1-1/colorspace/inst/doc/colorspace.html | 34 +- colorspace-2.1-1/colorspace/inst/doc/hcl-colors.pdf |binary colorspace-2.1-1/colorspace/inst/hclcolorpicker/server.R | 8 colorspace-2.1-1/colorspace/inst/hclwizard/html/python.html | 18 - colorspace-2.1-1/colorspace/inst/hclwizard/server.R | 114 ++++++++- colorspace-2.1-1/colorspace/inst/hclwizard/ui.R | 3 colorspace-2.1-1/colorspace/man/cvd_image.Rd | 11 colorspace-2.1-1/colorspace/man/desaturate.Rd | 19 - colorspace-2.1-1/colorspace/man/hcl_palettes.Rd | 2 colorspace-2.1-1/colorspace/vignettes/color.bib | 4 colorspace-2.1-1/colorspace/vignettes/colorspace.Rmd | 5 29 files changed, 433 insertions(+), 259 deletions(-)
Title: A Configurable 'shiny' Portal for Sharing Analysis of Molecular
Expression Data
Description: Enables deploying configuration file-based 'shiny' apps with minimal programming for interactive exploration and analysis showcase of molecular expression data. For exploration, supports visualization of correlations between rows of an expression matrix and a table of observations, such as clinical measures, and comparison of changes in expression over time. For showcase, enables visualizing the results of differential expression from package such as 'limma', co-expression modules from 'WGCNA' and lower dimensional projections.
Author: Rafael Henkin [cre, aut, cph]
Maintainer: Rafael Henkin <r.henkin@qmul.ac.uk>
Diff between shinyExprPortal versions 1.1.0 dated 2024-02-06 and 1.2.0 dated 2024-07-26
DESCRIPTION | 8 - MD5 | 42 +++++----- NEWS.md | 6 + R/app_config.R | 2 R/app_server.R | 2 R/create_example.R | 4 R/create_mod_template.R | 6 - R/mod_compareTrajGroups.R | 6 - R/mod_geneModulesHeatmap.R | 23 +++-- R/mod_geneModulesHeatmap_utils.R | 3 R/mod_geneProjectionOverlay.R | 3 R/mod_multiMeasureCorr.R | 6 - R/mod_singleGeneCorr.R | 9 +- R/mod_singleMeasureCorr.R | 3 build/vignette.rds |binary inst/doc/config.html | 80 +++++++++---------- inst/doc/customization.html | 4 inst/doc/dataprep.html | 142 +++++++++++++++++----------------- inst/doc/shinyExprPortal.Rmd | 6 - inst/doc/shinyExprPortal.html | 159 +++++++++++++++++++-------------------- man/create_module_template.Rd | 5 - vignettes/shinyExprPortal.Rmd | 6 - 22 files changed, 279 insertions(+), 246 deletions(-)
More information about shinyExprPortal at CRAN
Permanent link
Title: Analysis of Chronological Patterns from Archaeological Count
Data
Description: A toolkit for absolute and relative dating and analysis of
chronological patterns. This package includes functions for
chronological modeling and dating of archaeological assemblages from
count data. It provides methods for matrix seriation. It also allows
to compute time point estimates and density estimates of the
occupation and duration of an archaeological site.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kairos versions 2.1.0 dated 2024-02-26 and 2.1.1 dated 2024-07-26
DESCRIPTION | 20 ++++++------- MD5 | 56 +++++++++++++++++++------------------- NEWS.md | 4 ++ R/AllClasses.R | 2 - R/AllGenerics.R | 55 +++++++++++++++++++++---------------- R/kairos-package.R | 4 +- R/mcd.R | 21 ++++++++++++-- README.md | 36 ++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/event.html | 14 ++++----- inst/doc/seriation.html | 6 ---- man/AoristicSum-class.Rd | 2 - man/aoristic.Rd | 4 +- man/data.frame.Rd | 4 +- man/event.Rd | 4 +- man/figures/README-aoristic-2.png |binary man/fit.Rd | 4 +- man/kairos-package.Rd | 4 +- man/mcd.Rd | 4 +- man/model.Rd | 5 ++- man/plot_aoristic.Rd | 6 ++-- man/plot_event.Rd | 4 +- man/plot_fit.Rd | 4 +- man/plot_mcd.Rd | 4 +- man/plot_time.Rd | 4 +- man/predict_event.Rd | 5 ++- man/resample_mcd.Rd | 4 +- man/series.Rd | 5 ++- 29 files changed, 152 insertions(+), 133 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb],
Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb],
Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb],
Michael Quinn [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between yaml versions 2.3.9 dated 2024-07-05 and 2.3.10 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/verbatim_logical.Rd | 12 ++++++------ src/dumper.c | 1 + src/implicit.c | 1 + 5 files changed, 16 insertions(+), 14 deletions(-)
Title: R-Language Based Calculus Operations for Teaching
Description: Software to support the introductory *MOSAIC Calculus*
textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>),
one of many data- and modeling-oriented educational resources developed by
Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and
numerical differentiation and integration, as well as support for
applied linear algebra (for data science), and differential equations/dynamics.
Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc.
The software is suitable for general use, but intended mainly for teaching calculus.
Author: Daniel T. Kaplan <kaplan@macalester.edu>, Randall Pruim <rpruim@calvin.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Daniel Kaplan <kaplan@macalester.edu>
Diff between mosaicCalc versions 0.6.1 dated 2024-03-16 and 0.6.4 dated 2024-07-26
DESCRIPTION | 21 +++++++++++---------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 5 +---- NEWS.md | 11 +++++++++++ R/Calculus.R | 4 ++-- R/Integrate.R | 13 ++++++++++--- R/Zeros.R | 2 +- R/argM.R | 2 +- R/interactive_plot.R | 4 +++- R/makeODE.R | 10 +++++++--- R/numD.R | 2 +- R/symbolicD.R | 2 +- R/traj_plot_3D.R | 4 ++++ inst/doc/Calculus_with_R.html | 8 ++++---- inst/doc/Instructors.html | 13 +++++++------ inst/doc/quick-reference.html | 4 ++-- man/makeODE.Rd | 4 +++- man/symbolicD.Rd | 2 +- 18 files changed, 87 insertions(+), 58 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-18 1.1.31
2024-01-23 1.1.30
2023-09-05 1.1.29
2022-12-09 1.1.28
2022-02-23 1.1.27
2021-03-09 1.1.26
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-17 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-21 1.0.13
2021-03-09 1.0.12
Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed.
The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.1-0 dated 2024-05-14 and 2.1-1 dated 2024-07-26
DESCRIPTION | 13 +++++------ MD5 | 50 ++++++++++++++++++++++----------------------- NEWS | 6 +++++ R/intercept.r | 10 +++++---- R/plot.segmented.lme.r | 16 ++++++++++---- R/seg.Ar.fit.boot.r | 7 ++++-- R/seg.def.fit.boot.r | 5 +++- R/seg.glm.fit.boot.r | 7 +++++- R/seg.lm.fit.boot.r | 7 +++++- R/seg.num.fit.boot.r | 7 +++--- R/segConstr.glm.fit.boot.r | 8 ++++--- R/segConstr.lm.fit.boot.r | 8 ++++--- R/segmented.lme.r | 2 + R/segreg.r | 18 ++++++++++++++++ R/selgmented.R | 1 R/slope.R | 2 + R/step.glm.fit.boot.r | 25 ++++++++++++++++++---- R/step.lm.fit.boot.r | 7 +++++- R/step.num.fit.boot.r | 6 ++++- R/step.ts.fit.boot.r | 8 +++++-- R/stepreg.r | 14 ++++++++++++ man/seg.control.Rd | 4 +-- man/segmented-package.Rd | 4 +-- man/segmented.Rd | 10 ++++----- man/segreg.Rd | 4 +-- man/selgmented.Rd | 2 - 26 files changed, 176 insertions(+), 75 deletions(-)
Title: Bayesian Deming Regression for Method Comparison
Description: Regression methods to quantify the relation
between two measurement methods are provided by this package. The
focus is on a Bayesian Deming regressions family. With a Bayesian
method the Deming regression can be run in a traditional fashion or
can be run in a robust way just decreasing the degree of freedom
d.f. of the sampling distribution. With d.f. = 1 an extremely robust
Cauchy distribution can be sampled. Moreover, models for dealing
with heteroscedastic data are also provided. For reference see
G. Pioda (2024) <https://piodag.github.io/bd1/>.
Author: Giorgio Pioda [aut, cre]
Maintainer: Giorgio Pioda <gfwp@ticino.com>
Diff between rstanbdp versions 0.0.2 dated 2024-02-23 and 0.0.3 dated 2024-07-26
DESCRIPTION | 6 MD5 | 43 +++--- NAMESPACE | 1 NEWS.md | 15 ++ R/bdpCalcResponse.R | 18 +- R/bdpExtract.R | 9 + R/bdpPlot.R | 26 ++- R/bdpPlotResiduals.R | 23 ++- R/bdpSummary.R |only R/bdpreg.R | 18 +- R/plotBoxEllipses.R | 31 ++-- R/stanmodels.R | 3 inst/stan/bdpreg_exphettrunc.stan |only inst/stan/bdpreg_linhet.stan | 5 inst/stan/bdpreg_linhettrunc.stan | 5 man/bdpPlot.Rd | 4 man/bdpPlotBE.Rd | 4 man/bdpPlotResiduals.Rd | 8 - man/bdpSummary.Rd |only man/bdpreg.Rd | 5 src/RcppExports.cpp | 2 src/stanExports_bdpreg_exphettrunc.cc |only src/stanExports_bdpreg_exphettrunc.h |only src/stanExports_bdpreg_linhet.h | 219 ++++++++++++++++-------------- src/stanExports_bdpreg_linhettrunc.h | 243 ++++++++++++++++++---------------- 25 files changed, 397 insertions(+), 291 deletions(-)
Title: Multivariate Statistical Methods
Description: Algorithms to build set partitions and commutator matrices and their use in the
construction of multivariate d-Hermite polynomials; estimation and derivation of theoretical vector moments and vector
cumulants of multivariate distributions; conversion formulae for multivariate moments and cumulants. Applications to
estimation and derivation of multivariate measures of skewness and kurtosis; estimation and derivation of asymptotic
covariances for d-variate Hermite polynomials, multivariate moments and cumulants and measures of skewness and kurtosis.
The formulae implemented are discussed in Terdik (2021, ISBN:9783030813925), "Multivariate Statistical Methods".
Author: Gyorgy Terdik [aut],
Emanuele Taufer [aut, cre]
Maintainer: Emanuele Taufer <emanuele.taufer@unitn.it>
Diff between MultiStatM versions 1.2.1 dated 2024-01-31 and 2.0.0 dated 2024-07-26
MultiStatM-1.2.1/MultiStatM/man/Esti_EVSK.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Gram_Charlier.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Hermite_Poly_HN_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_MRSz.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Mardia.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Total.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Kurt_Variance_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_MMom_MCum.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_MRSz.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_Mardia.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Skew_Variance_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/Esti_Variance_Skew_Kurt.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Coeff.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_CoeffMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_N_Cov_X1_X2.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Nth.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_HN.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_HN_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_NH_Inv.Rd |only MultiStatM-1.2.1/MultiStatM/man/Hermite_Poly_NH_Multi_Inv.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_2Perm.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_DiagramsClosedNoLoops.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Indecomposable.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Pairs.Rd |only MultiStatM-1.2.1/MultiStatM/man/Partition_Type_All.Rd |only MultiStatM-1.2.1/MultiStatM/man/Permutation_Inverse.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Cum2Mom.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Cum2MomMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Mom2Cum.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Mom2CumMulti.Rd |only MultiStatM-1.2.1/MultiStatM/man/conv_Stand_Multi.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSN_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSN_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_CFUSSD_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_SkewNorm_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_UniAbs_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_EVSK_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Uni_Rand.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_ZabsM_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/distr_Zabs_MomCum_Th.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Kmn.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Kperm.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Mixing.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Commutator_Moment.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Elimination.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Qplication.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_Symmetry.Rd |only MultiStatM-1.2.1/MultiStatM/man/indx_UnivMomCum.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Kmn.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Kperm.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Mixing.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Commutator_Moment.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Elimination.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Qplication.Rd |only MultiStatM-1.2.1/MultiStatM/man/matr_Symmetry.Rd |only MultiStatM-2.0.0/MultiStatM/DESCRIPTION | 8 MultiStatM-2.0.0/MultiStatM/MD5 | 123 - 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Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 2.0.11 dated 2024-02-23 and 2.0.12 dated 2024-07-26
DESCRIPTION | 8 MD5 | 18 NEWS | 27 NEWS.md | 27 R/gamTestSeason.r | 14 R/imputeCensored.R | 10 build/vignette.rds |binary inst/doc/Detrending_Flow_and_Salinity_Data.html | 14 inst/doc/Processing_Censored_Data.html | 8 inst/extdata/baytrends_install.nb.html | 6276 ++++++++++++------------ 10 files changed, 3226 insertions(+), 3176 deletions(-)
Title: Archaeological Time Series
Description: A toolkit for archaeological time series. This package
provides a system of classes and methods to represent and work with
archaeological time series. Dates are represented as "rata die" and
can be converted to (virtually) any calendar defined by Reingold and
Dershowitz (2018) <doi:10.1017/9781107415058>. This packages offers a
simple API that can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] ,
Joe Roe [aut] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between aion versions 1.0.2 dated 2023-10-26 and 1.0.4 dated 2024-07-26
DESCRIPTION | 22 MD5 | 74 +- NEWS.md | 6 R/AllGenerics.R | 2 R/aion-internal.R | 10 R/aion-package.R | 2 README.md | 71 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 19 inst/doc/aion.R | 30 - inst/doc/aion.Rmd | 44 + inst/doc/aion.html | 879 ++++++++++++----------------------- inst/doc/bibliography.Rmd | 10 inst/doc/bibliography.html | 341 ++----------- inst/doc/extending.R | 2 inst/doc/extending.Rmd | 14 inst/doc/extending.html | 751 +++++++++-------------------- man/aion-package.Rd | 3 man/arithmetic.Rd | 2 man/as_date.Rd | 2 man/as_decimal.Rd | 2 man/as_fixed.Rd | 2 man/as_year.Rd | 2 man/convert.Rd | 2 man/figures/README-time-series-1.png |binary man/fixed_gregorian.Rd | 2 man/fixed_julian.Rd | 2 man/format.Rd | 2 man/gregorian.Rd | 2 man/is.Rd | 2 man/julian.Rd | 2 man/plot.Rd | 2 man/pretty.Rd | 2 man/subset.Rd | 6 vignettes/aion.Rmd | 44 + vignettes/bibliography.Rmd | 10 vignettes/extending.Rmd | 14 38 files changed, 872 insertions(+), 1510 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-09 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-22 1.2.3
2024-05-17 1.2.1
2024-04-15 1.1.5
2024-02-06 1.1.4
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.11.0.1 dated 2024-02-14 and 1.12.0 dated 2024-07-26
DESCRIPTION | 13 MD5 | 89 - NAMESPACE | 1 R/corColumnOrder.R | 23 R/extractTestingResults.R | 8 R/getUPS1acc.R | 8 R/matrixNAneighbourImpute.R | 2 R/readAlphaPeptFile.R | 62 R/readDiaNNFile.R | 51 R/readDiaNNPeptides.R | 48 R/readFasta2.R | 51 R/readFragpipeFile.R | 55 R/readIonbotPeptides.R |only R/readMassChroQFile.R | 54 R/readMaxQuantFile.R | 66 R/readMaxQuantPeptides.R | 120 + R/readProlineFile.R | 83 - R/readProteomeDiscovererFile.R | 417 +++-- R/readProteomeDiscovererPeptides.R | 95 - R/readSampleMetaData.R | 460 +++-- R/readSdrf.R | 51 R/readWombatNormFile.R | 50 R/shortSoftwName.R | 4 build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 6 inst/doc/wrProteoVignette1.Rmd | 24 inst/doc/wrProteoVignette1.html | 1546 +++++++----------- inst/doc/wrProteoVignetteUPS1.R | 68 inst/doc/wrProteoVignetteUPS1.Rmd | 151 + inst/doc/wrProteoVignetteUPS1.html | 2939 +++++++++++++++--------------------- inst/extdata/tinyIonbotFile1.tsv.gz |only man/corColumnOrder.Rd | 19 man/extractTestingResults.Rd | 8 man/getUPS1acc.Rd | 8 man/readAlphaPeptFile.Rd | 10 man/readFasta2.Rd | 20 man/readFragpipeFile.Rd | 6 man/readIonbotPeptides.Rd |only man/readMassChroQFile.Rd | 6 man/readMaxQuantFile.Rd | 6 man/readMaxQuantPeptides.Rd | 14 man/readProlineFile.Rd | 8 man/readProteomeDiscovererFile.Rd | 6 man/readSampleMetaData.Rd | 22 man/readSdrf.Rd | 4 vignettes/wrProteoVignette1.Rmd | 24 vignettes/wrProteoVignetteUPS1.Rmd | 151 + 47 files changed, 3537 insertions(+), 3320 deletions(-)
Title: Accesses Weather Data from the Iowa Environment Mesonet
Description: Allows to get weather data from Automated Surface Observing
System (ASOS) stations (airports) in the whole world thanks to the
Iowa Environment Mesonet website.
Author: Maelle Salmon [aut, cre] ,
Brooke Anderson [rev] ,
CHAI Project [fnd] ,
rOpenSci [fnd] ,
Daryl Herzmann [ctb]
Maintainer: Maelle Salmon <maelle.salmon@yahoo.se>
Diff between riem versions 0.3.1 dated 2024-04-04 and 0.3.2 dated 2024-07-26
riem-0.3.1/riem/tests/testthat/fixtures/networks-error |only riem-0.3.2/riem/DESCRIPTION | 8 riem-0.3.2/riem/MD5 | 18 riem-0.3.2/riem/NEWS.md | 4 riem-0.3.2/riem/tests/testthat/fixtures/networks/mesonet.agron.iastate.edu/api/1/networks.json.json | 2716 ++++++---- riem-0.3.2/riem/tests/testthat/fixtures/stations/mesonet.agron.iastate.edu/api/1/network/IN__ASOS.json.json | 1905 +++++-- riem-0.3.2/riem/tests/testthat/fixtures/stations/mesonet.agron.iastate.edu/api/1/networks.json.json | 2716 ++++++---- riem-0.3.2/riem/tests/testthat/fixtures/warnings |only riem-0.3.2/riem/tests/testthat/helper-riem.R | 6 riem-0.3.2/riem/tests/testthat/setup.R | 1 riem-0.3.2/riem/tests/testthat/test-measures.R | 2 11 files changed, 4914 insertions(+), 2462 deletions(-)
Title: National Library of Norway Quantitative Text Data API Tools
Description: Tools for accessing data from National Library of Norway's dhlab (digital humanities laboratory).
Provides wrappers for accessing our API services at <https://api.nb.no/dhlab/>.
To learn more about dhlab, visit out site <https://www.nb.no/dh-lab/>.
Author: Ingerid Dale [aut, cre],
Lars Johnsen [aut, cph],
Lars Tungland [aut],
Andre Kasen [aut]
Maintainer: Ingerid Dale <ingerid.dale@nb.no>
Diff between dhlabR versions 1.0.2 dated 2023-06-09 and 1.0.6 dated 2024-07-26
DESCRIPTION | 22 +++++++++++++--------- MD5 | 32 +++++++++++++++++--------------- NEWS.md | 9 +++++++++ R/api_tools.R |only R/get_collocations.R | 7 ++++++- R/get_concordance.R | 9 +++++++-- R/get_dispersion.R | 8 +++++++- R/get_document_corpus.R | 8 +++++++- R/get_document_frequencies.R | 7 ++++++- R/get_metadata.R | 7 ++++++- R/get_ngram_from_book.R | 9 +++++++-- R/get_ngram_from_newspapers.R | 9 +++++++-- R/get_reference_words.R | 7 ++++++- R/get_urn_frequencies.R | 7 ++++++- R/ngram.R | 3 ++- man/get_concordance.Rd | 2 +- tests/testthat/test-api_tools.R |only tests/testthat/test-ngram.R | 2 +- 18 files changed, 108 insertions(+), 40 deletions(-)
Title: Pre-Processing XY Data from Experimental Methods
Description: A lightweight, dependency-free toolbox for pre-processing XY
data from experimental methods (i.e. any signal that can be measured
along a continuous variable). This package provides methods for
baseline estimation and correction, smoothing, normalization,
integration and peaks detection. Baseline correction methods includes
polynomial fitting as described in Lieber and Mahadevan-Jansen (2003)
<doi:10.1366/000370203322554518>, Rolling Ball algorithm after Kneen
and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>, SNIP algorithm
after Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, 4S Peak
Filling after Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between alkahest versions 1.1.1 dated 2023-06-13 and 1.2.0 dated 2024-07-26
alkahest-1.1.1/alkahest/inst/doc/bibliography.R |only alkahest-1.1.1/alkahest/inst/doc/bibliography.Rmd |only alkahest-1.1.1/alkahest/inst/doc/bibliography.html |only alkahest-1.1.1/alkahest/vignettes/bibliography.Rmd |only alkahest-1.2.0/alkahest/DESCRIPTION | 19 - alkahest-1.2.0/alkahest/MD5 | 99 +++--- alkahest-1.2.0/alkahest/NAMESPACE | 2 alkahest-1.2.0/alkahest/NEWS.md | 6 alkahest-1.2.0/alkahest/R/AllGenerics.R | 65 ++++ alkahest-1.2.0/alkahest/R/alkahest-internal.R | 30 +- alkahest-1.2.0/alkahest/R/alkahest-package.R | 2 alkahest-1.2.0/alkahest/R/baseline.R | 67 ++++ alkahest-1.2.0/alkahest/R/data.R | 14 alkahest-1.2.0/alkahest/R/integrate.R | 4 alkahest-1.2.0/alkahest/R/peaks.R | 3 alkahest-1.2.0/alkahest/R/replace.R | 4 alkahest-1.2.0/alkahest/R/resample.R | 5 alkahest-1.2.0/alkahest/R/rescale.R | 40 ++ alkahest-1.2.0/alkahest/R/signal.R | 21 + alkahest-1.2.0/alkahest/R/smooth.R | 18 - alkahest-1.2.0/alkahest/R/xrd.R | 9 alkahest-1.2.0/alkahest/README.md | 149 ++++++++-- alkahest-1.2.0/alkahest/build/partial.rdb |binary alkahest-1.2.0/alkahest/build/vignette.rds |binary alkahest-1.2.0/alkahest/data/Raman.rda |only alkahest-1.2.0/alkahest/inst/CITATION | 2 alkahest-1.2.0/alkahest/inst/doc/baseline.R |only alkahest-1.2.0/alkahest/inst/doc/baseline.Rmd |only alkahest-1.2.0/alkahest/inst/doc/baseline.html |only alkahest-1.2.0/alkahest/inst/doc/smoothing.R |only alkahest-1.2.0/alkahest/inst/doc/smoothing.Rmd |only alkahest-1.2.0/alkahest/inst/doc/smoothing.html |only alkahest-1.2.0/alkahest/inst/examples/ex-baseline-asls.R |only alkahest-1.2.0/alkahest/inst/examples/ex-normalize.R |only alkahest-1.2.0/alkahest/inst/tinytest/_snaps/baseline_asls.rds |only alkahest-1.2.0/alkahest/inst/tinytest/test_baseline.R | 8 alkahest-1.2.0/alkahest/inst/tinytest/test_helpers.R | 4 alkahest-1.2.0/alkahest/inst/tinytest/test_rescale.R | 6 alkahest-1.2.0/alkahest/man/BEGe.Rd | 1 alkahest-1.2.0/alkahest/man/LaBr.Rd | 1 alkahest-1.2.0/alkahest/man/Raman.Rd |only alkahest-1.2.0/alkahest/man/XRD.Rd | 3 alkahest-1.2.0/alkahest/man/alkahest-package.Rd | 3 alkahest-1.2.0/alkahest/man/baseline_asls.Rd |only alkahest-1.2.0/alkahest/man/baseline_linear.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_peakfilling.Rd | 6 alkahest-1.2.0/alkahest/man/baseline_polynomial.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_rollingball.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_rubberband.Rd | 1 alkahest-1.2.0/alkahest/man/baseline_snip.Rd | 1 alkahest-1.2.0/alkahest/man/replace_threshold.Rd | 4 alkahest-1.2.0/alkahest/man/rescale_area.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_range.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_snv.Rd |only alkahest-1.2.0/alkahest/man/rescale_total.Rd | 1 alkahest-1.2.0/alkahest/man/rescale_transform.Rd | 1 alkahest-1.2.0/alkahest/man/signal_correct.Rd | 21 + alkahest-1.2.0/alkahest/vignettes/baseline.Rmd |only alkahest-1.2.0/alkahest/vignettes/bibliography.bib | 38 ++ alkahest-1.2.0/alkahest/vignettes/smoothing.Rmd |only 60 files changed, 542 insertions(+), 121 deletions(-)
Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] ,
Kaio Dias [aut, cph] ,
Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>
Diff between ProbBreed versions 1.0.4.0 dated 2024-07-17 and 1.0.4.1 dated 2024-07-26
DESCRIPTION | 19 MD5 | 98 + NAMESPACE | 6 NEWS.md | 17 R/ProbBreed-package.R | 31 R/bayes_met.R | 2273 ------------------------------ R/extr_outs.R | 14 R/prob_sup.R | 6 R/stanmodels.R |only README.md | 513 +++--- build/partial.rdb |binary configure |only configure.win |only inst/include |only inst/stan |only man/ProbBreed-package.Rd | 20 man/bayes_met.Rd | 4 man/extr_outs.Rd | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/plot.extr.Rd | 12 man/plot.probsup.Rd | 4 man/prob_sup.Rd | 2 src |only 27 files changed, 472 insertions(+), 2549 deletions(-)
Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] ,
OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between IceSat2R versions 1.0.4 dated 2022-11-17 and 1.0.5 dated 2024-07-26
DESCRIPTION | 14 MD5 | 59 +-- NAMESPACE | 2 NEWS.md | 12 R/API_utils.R | 64 +++ R/IceSat2R.R | 2 R/get_Atlas_data.R | 289 ++++++++++++++++-- R/get_Tracks_data.R | 4 R/mission_orbits.R | 49 ++- README.md | 19 - build/vignette.rds |binary data/RGT_cycle_14.rda |binary data/datalist | 2 data/ne_10m_glaciated_areas.rda |binary inst/data_files/technical_specs_urls.csv | 9 inst/doc/IceSat-2_Atlas_products_PDF.R | 34 +- inst/doc/IceSat-2_Atlas_products_PDF.pdf |binary inst/doc/IceSat-2_Mission_Orbits_PDF.R | 10 inst/doc/IceSat-2_Mission_Orbits_PDF.pdf |binary inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.R | 29 + inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.Rmd | 27 + inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.pdf |binary man/IceSat2R.Rd | 2 man/download_file.Rd |only man/getTracks.Rd | 2 man/get_atlas_data.Rd | 218 +++++++++++++ man/get_level3a_data.Rd | 6 man/vsi_nominal_orbits_wkt.Rd | 4 tests/testthat/setup.R | 6 tests/testthat/test-get_Atlas_data.R | 2 vignettes/IceSat-2_Virtual_File_System_Orbits_PDF.Rmd | 27 + 31 files changed, 747 insertions(+), 145 deletions(-)
Title: Estimation of the Weights Attached to the Two-Way Fixed Effects
Regressions
Description: Estimates the weights and measure of robustness to treatment effect heterogeneity attached to two-way fixed effects regressions.
Clément de Chaisemartin, Xavier D'Haultfœuille (2020) <DOI: 10.1257/aer.20181169>.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Shuo Zhang [aut],
Clement de Chaisemartin [aut],
Grant McDermott [ctb]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between TwoWayFEWeights versions 2.0.3 dated 2024-04-25 and 2.0.4 dated 2024-07-26
DESCRIPTION | 15 +++++++++------ MD5 | 3 ++- NEWS.md |only 3 files changed, 11 insertions(+), 7 deletions(-)
More information about TwoWayFEWeights at CRAN
Permanent link
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between nser versions 1.5.2 dated 2024-05-02 and 1.5.3 dated 2024-07-26
DESCRIPTION | 12 ++++++------ MD5 | 27 ++++++++++++++++----------- NAMESPACE | 4 ++++ R/bhav.R | 37 +++++++++++++++++++++---------------- R/bhav1.R |only R/bhavpr.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/bhav.Rmd | 15 ++++++--------- inst/doc/bhav.html | 17 ++++++++--------- inst/doc/bhav1.Rmd |only inst/doc/bhav1.html |only man/bhav.Rd | 8 ++++---- man/bhav1.Rd |only man/bhavpr.Rd | 2 +- vignettes/bhav.Rmd | 15 ++++++--------- vignettes/bhav1.Rmd |only 17 files changed, 74 insertions(+), 67 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 5.0.2 dated 2024-07-07 and 5.0.4 dated 2024-07-26
ChangeLog | 5 ++--- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/ETSmodel.R | 1 - R/TETScomponents.R | 10 ++++++++-- R/TETSmodel.R | 4 +--- R/TETSvalidate.R | 15 +++++++++++---- 7 files changed, 32 insertions(+), 23 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.7.0 dated 2023-10-25 and 2.8.0 dated 2024-07-26
DESCRIPTION | 25 MD5 | 186 +- NAMESPACE | 381 ++--- NEWS.md | 445 +++-- R/Information.R | 10 R/Islands.R |only R/MSTSegments.R | 6 R/Plot3.R | 2 R/RcppExports.R | 32 R/Reduce.R |only R/TreeDist-package.R | 4 R/VisualizeMatching.R | 8 R/cluster_stats.R | 14 R/kmeanspp.R | 6 R/lap.R | 5 R/median.R | 8 R/parallel.R | 2 R/plot.R | 28 R/spectral_clustering.R | 6 R/tree_distance.R | 30 R/tree_distance_info.R | 728 +++++---- R/tree_distance_kendall-colijn.R | 64 R/tree_distance_mast.R | 16 R/tree_distance_msi.R | 2 R/tree_distance_nni.R | 6 R/tree_distance_nye.R | 428 ++--- R/tree_distance_path.R | 64 R/tree_distance_rf.R | 322 ++-- R/tree_distance_spr.R | 172 +- R/tree_distance_utilities.R | 84 - R/tree_information.R | 2 R/trustworthiness.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 54 inst/WORDLIST | 2 inst/doc/Generalized-RF.R | 26 inst/doc/Generalized-RF.Rmd | 11 inst/doc/Generalized-RF.html | 67 inst/doc/Robinson-Foulds.R | 43 inst/doc/Robinson-Foulds.Rmd | 27 inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.R | 2 inst/doc/Using-TreeDist.html | 8 inst/doc/compare-treesets.html | 1081 ++++++++++++++ inst/doc/different-leaves.html | 2 inst/doc/information.html | 43 inst/doc/landscapes.html | 31 inst/doc/tree-islands.R |only inst/doc/tree-islands.Rmd |only inst/doc/tree-islands.html |only inst/doc/treespace.R | 29 inst/doc/treespace.Rmd | 41 inst/doc/treespace.html | 239 +-- inst/doc/using-distances.R | 12 inst/doc/using-distances.html | 7 inst/treespace/app.R | 18 man/CalculateTreeDistance.Rd | 3 man/Islands.Rd |only man/JaccardRobinsonFoulds.Rd | 3 man/KMeansPP.Rd | 110 - man/KendallColijn.Rd | 5 man/LAPJV.Rd | 4 man/MSTSegments.Rd | 1 man/MapTrees.Rd | 1 man/MappingQuality.Rd | 1 man/MatchingSplitDistance.Rd | 3 man/NormalizeInfo.Rd | 75 - man/NyeSimilarity.Rd | 3 man/PathDist.Rd | 13 man/ReduceTrees.Rd |only man/Robinson-Foulds.Rd | 27 man/SPRDist.Rd | 61 man/SpectralEigens.Rd | 1 man/StartParallel.Rd | 2 man/TreeDist-package.Rd | 4 man/TreeDistance.Rd | 40 man/cluster-statistics.Rd | 1 man/median.multiPhylo.Rd | 1 src/RcppExports.cpp | 105 + src/day_1985.cpp | 2 src/lap.cpp | 16 src/path_vector.cpp |only src/reduce_tree.cpp |only src/reduce_tree.h |only src/spr.cpp |only tests/benchmark/benchmark.R | 12 tests/testthat/test-Islands.R |only tests/testthat/test-MSTSegments.R | 2 tests/testthat/test-Reduce.R |only tests/testthat/test-different-tips.R | 3 tests/testthat/test-information.R | 21 tests/testthat/test-tree_distance.R | 1947 +++++++++++++------------- tests/testthat/test-tree_distance_kc.R | 13 tests/testthat/test-tree_distance_path.R | 40 tests/testthat/test-tree_distance_spr.R | 213 ++ tests/testthat/test-tree_distance_utilities.R | 4 vignettes/Generalized-RF.Rmd | 11 vignettes/Robinson-Foulds.Rmd | 27 vignettes/tree-islands.Rmd |only vignettes/treespace.Rmd | 41 101 files changed, 4838 insertions(+), 2814 deletions(-)
Title: Game of 'tetRys'
Description: A game inspired by 'Tetris'. Opens a plot window device and starts a game of 'tetRys' in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.
Author: Carsten Croonenbroeck [aut, cre]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between tetRys versions 1.0 dated 2024-07-21 and 1.1 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ R/tetRys.R | 21 ++++++++++++++------- 4 files changed, 28 insertions(+), 14 deletions(-)
Title: Client for 'AcademyOcean API'
Description: Provide function for work with 'AcademyOcean API'
<https://academyocean.com/api>.
Author: Alexey Seleznev [aut, cre] ,
Netpeak [cph],
AcademyOcean [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between racademyocean versions 0.3.2 dated 2023-02-09 and 0.3.3 dated 2024-07-26
DESCRIPTION | 6 +- MD5 | 6 +- NEWS.md | 8 +++ R/utils.R | 134 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 81 insertions(+), 73 deletions(-)
Title: Identifying Infection with Machine Intelligence
Description: A novel machine learning method for plant viruses diagnostic using
genome sequencing data. This package includes three different machine
learning models, random forest, XGBoost, and elastic net, to train and
predict mapped genome samples. Mappability profile and unreliable regions
are introduced to the algorithm, and users can build a mappability profile
from scratch with functions included in the package. Plotting mapped sample
coverage information is provided.
Author: Haochen Ning [aut],
Ian Boyes [aut],
Ibrahim Numanagic [aut] ,
Michael Rott [aut],
Li Xing [aut] ,
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Diff between iimi versions 1.1.0 dated 2024-07-18 and 1.1.1 dated 2024-07-26
DESCRIPTION | 6 MD5 | 10 - inst/doc/package_vignette.R | 54 ++++--- inst/doc/package_vignette.Rmd | 155 ++++++++++++-------- inst/doc/package_vignette.html | 304 ++++++++++++++++++++++------------------- vignettes/package_vignette.Rmd | 155 ++++++++++++-------- 6 files changed, 394 insertions(+), 290 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.4.1 dated 2024-04-28 and 1.4.2 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/glmm.gei.R | 6 +++--- inst/doc/MAGEE.Rnw | 9 +++++++-- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- man/glmm.gei.Rd | 9 ++++++--- vignettes/MAGEE.Rnw | 9 +++++++-- 8 files changed, 36 insertions(+), 23 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.1.1 dated 2024-01-15 and 0.2.0 dated 2024-07-26
SSN2-0.1.1/SSN2/R/create_netgeometry.R |only SSN2-0.1.1/SSN2/R/names.SSN.R |only SSN2-0.1.1/SSN2/R/ssn_get_netgeometry.R |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/CapeHorn.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/Knapp.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/distance/Knapp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/edges.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/pred1km.shx |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.dbf |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.prj |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.shp |only SSN2-0.1.1/SSN2/inst/lsndata/MiddleFork04.ssn/sites.shx |only SSN2-0.1.1/SSN2/man/names.SSN.Rd |only SSN2-0.2.0/SSN2/DESCRIPTION | 12 SSN2-0.2.0/SSN2/MD5 | 247 +- SSN2-0.2.0/SSN2/NAMESPACE | 8 SSN2-0.2.0/SSN2/NEWS.md | 68 SSN2-0.2.0/SSN2/R/SSN2.R | 44 SSN2-0.2.0/SSN2/R/SSN_to_SSN2.R | 269 +- SSN2-0.2.0/SSN2/R/Torgegram.R | 344 +-- SSN2-0.2.0/SSN2/R/amongSitesDistMat.R | 17 SSN2-0.2.0/SSN2/R/anova.R | 18 SSN2-0.2.0/SSN2/R/checks.R | 58 SSN2-0.2.0/SSN2/R/cov_betahat_adjust.R | 29 SSN2-0.2.0/SSN2/R/cov_initial_search.R | 359 +-- SSN2-0.2.0/SSN2/R/cov_initial_search_glm.R | 375 ++- SSN2-0.2.0/SSN2/R/cov_matrix.R | 619 +++--- SSN2-0.2.0/SSN2/R/cov_vector.R | 536 ++--- SSN2-0.2.0/SSN2/R/createBinaryID.R | 127 - SSN2-0.2.0/SSN2/R/create_netgeom.R |only SSN2-0.2.0/SSN2/R/data.R | 52 SSN2-0.2.0/SSN2/R/get.rid.fc.R | 23 SSN2-0.2.0/SSN2/R/getObsRelationshipsDF.R | 122 - SSN2-0.2.0/SSN2/R/getPredRelationshipsDF.R | 77 SSN2-0.2.0/SSN2/R/get_Torgegram_initial_object.R | 61 SSN2-0.2.0/SSN2/R/get_anisotropy_corrected.R | 76 SSN2-0.2.0/SSN2/R/get_cholprods.R | 108 - SSN2-0.2.0/SSN2/R/get_cov_matrix.R | 178 - SSN2-0.2.0/SSN2/R/get_cov_vector.R | 115 - SSN2-0.2.0/SSN2/R/get_data_object.R | 474 ++-- SSN2-0.2.0/SSN2/R/get_data_object_glm.R | 534 ++--- SSN2-0.2.0/SSN2/R/get_dist_object.R | 639 +++--- SSN2-0.2.0/SSN2/R/get_dist_pred_object.R | 47 SSN2-0.2.0/SSN2/R/get_dist_predbk_object.R | 303 +-- SSN2-0.2.0/SSN2/R/get_eigenprods.R | 132 - SSN2-0.2.0/SSN2/R/get_model_stats.R | 583 ++--- SSN2-0.2.0/SSN2/R/get_model_stats_glm.R | 957 ++++----- SSN2-0.2.0/SSN2/R/get_sf_obj.R |only SSN2-0.2.0/SSN2/R/gloglik.R | 62 SSN2-0.2.0/SSN2/R/gloglik_products.R | 154 - SSN2-0.2.0/SSN2/R/initial.R | 598 +++--- SSN2-0.2.0/SSN2/R/initial_NA.R | 385 ++- SSN2-0.2.0/SSN2/R/laploglik.R | 72 SSN2-0.2.0/SSN2/R/laploglik_products.R | 768 ++++--- SSN2-0.2.0/SSN2/R/local.R | 312 +-- SSN2-0.2.0/SSN2/R/loocv.R | 568 ++--- SSN2-0.2.0/SSN2/R/loocv_glm.R | 423 ++-- SSN2-0.2.0/SSN2/R/optim.R | 231 +- SSN2-0.2.0/SSN2/R/optim2orig.R | 166 - 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Title: Discrete Global Grids
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut],
Kevin Sahr [aut, cph],
Gerald Evenden [cph],
Angus Johnson [cph],
Frank Warmerdam [cph],
Even Rouault [cph],
Lian Song [ctb],
Sebastian Krantz [ctb, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dggridR versions 3.0.0 dated 2023-01-18 and 3.1.0 dated 2024-07-26
DESCRIPTION | 33 ++-- MD5 | 44 ++--- NAMESPACE | 22 +- NEWS | 14 + R/cwrapper.R | 140 +++++++++--------- R/dggridR.R | 152 ++++++++++++-------- R/zzz.R | 7 README.md | 4 build/vignette.rds |binary inst/doc/dggridR.R | 41 ++--- inst/doc/dggridR.Rmd | 19 +- inst/doc/dggridR.html | 375 +++++++++++++++++++++++++------------------------- man/dgcellstogrid.Rd | 4 man/dgearthgrid.Rd | 6 man/dgrectgrid.Rd | 7 man/dgshptogrid.Rd | 11 - src/DgBoundedRF.h | 8 - src/DgDmdIDGG.cpp | 3 src/DgHexIDGG.cpp | 4 src/DgParamList.h | 4 src/DgTriIDGG.cpp | 3 src/shputils.c | 4 vignettes/dggridR.Rmd | 19 +- 23 files changed, 490 insertions(+), 434 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-12 0.5.1
2022-12-08 0.4.3
2022-05-24 0.4.2
2018-08-06 0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-25 0.3.2
2023-03-22 0.3.1
2023-02-20 0.3
2022-09-08 0.2.2
2022-05-26 0.2.1
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.1.4 dated 2024-01-28 and 0.1.5 dated 2024-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- NAMESPACE | 1 + NEWS.md | 4 ++++ R/yulab-msg.R |only R/yulab-utils-package.R |only man/yulab.utils-package.Rd |only man/yulab_msg.Rd |only 8 files changed, 16 insertions(+), 7 deletions(-)
Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks.
'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
This package offers an R interface to work with it.
It is designed to be distributed and efficient with the following advantages:
1. Faster training speed and higher efficiency.
2. Lower memory usage.
3. Better accuracy.
4. Parallel learning supported.
5. Capable of handling large-scale data.
In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple m [...truncated...]
Author: Yu Shi [aut],
Guolin Ke [aut],
Damien Soukhavong [aut],
James Lamb [aut, cre],
Qi Meng [aut],
Thomas Finley [aut],
Taifeng Wang [aut],
Wei Chen [aut],
Weidong Ma [aut],
Qiwei Ye [aut],
Tie-Yan Liu [aut],
Nikita Titov [aut],
Yachen Yan [ctb],
Microsof [...truncated...]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between lightgbm versions 4.4.0 dated 2024-06-15 and 4.5.0 dated 2024-07-26
DESCRIPTION | 10 - MD5 | 52 ++++----- R/lgb.Booster.R | 40 ++++++ R/lgb.Dataset.R | 9 + README.md | 2 configure | 18 +-- configure.ac | 2 inst/doc/basic_walkthrough.html | 3 man/lgb.Dataset.Rd | 8 + src/boosting/gbdt.cpp | 18 +-- src/boosting/gbdt.h | 2 src/c_api.cpp | 12 -- src/include/LightGBM/arrow.h | 2 src/include/LightGBM/boosting.h | 2 src/include/LightGBM/config.h | 19 +-- src/include/LightGBM/utils/log.h | 7 + src/io/config.cpp | 21 +++ src/io/dataset_loader.cpp | 4 src/io/dense_bin.hpp | 2 src/io/file_io.cpp | 129 ---------------------- src/io/metadata.cpp | 2 src/io/multi_val_dense_bin.hpp | 2 src/io/multi_val_sparse_bin.hpp | 3 src/io/sparse_bin.hpp | 2 src/lightgbm_R.cpp | 219 +++++++++++++++++++++----------------- src/lightgbm_R.h | 28 ++++ tests/testthat/test_lgb.Booster.R | 168 +++++++++++++++++++++++++++++ 27 files changed, 473 insertions(+), 313 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.4.1 dated 2024-02-13 and 1.5.1 dated 2024-07-26
DESCRIPTION | 12 +-- MD5 | 117 +++++++++++++++++++++++++++----------- NAMESPACE | 6 + NEWS.md | 43 +++++++++++++ R/Aaaa.R | 4 - R/class_ev.R | 16 ++++- R/class_evd.R | 4 + R/class_mrgmod.R | 1 R/data_set.R | 60 ++++++++++++------- R/events.R | 27 +++++--- R/mrgindata.R | 89 ++++++++++++++++++---------- R/mrgsolve.R | 10 ++- R/mwrite.R |only R/print.R | 5 - R/utils.R | 3 inst/WORDLIST | 3 inst/base/modelheader.h | 4 + inst/base/mrgsolv.h | 4 - inst/base/mrgsolve-evtools.h | 15 ++++ inst/include/datarecord.h | 16 +++-- inst/include/odeproblem.h | 7 -- inst/maintenance |only man/as_data_set.Rd | 38 ++++++++---- man/mread_yaml.Rd |only man/mwrite_cpp.Rd |only man/mwrite_yaml.Rd |only man/omega.Rd | 2 man/sigma.Rd | 2 man/valid_data_set.Rd | 37 +++++++----- man/valid_idata_set.Rd | 23 +++++-- src/dataobject.cpp | 4 - src/datarecord.cpp | 41 +++++++++++-- src/devtran.cpp | 29 ++++----- src/mrgsolve.cpp | 4 - src/odeproblem.cpp | 8 ++ tests/testthat/test-as_data_set.R | 94 ++++++++++++++++++++++++++++++ tests/testthat/test-carry_out.R | 30 +++++++++ tests/testthat/test-data_set.R | 4 - tests/testthat/test-mrgindata.R | 24 +++---- tests/testthat/test-mwrite.R |only 40 files changed, 582 insertions(+), 204 deletions(-)
Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance
for Generalized Additive Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of gam()in 'mgcv' package, applying the algorithm in this paper: Lai(2024) <doi:10.1016/j.pld.2024.06.002>.
Author: Jiangshan Lai [aut, cre] ,
Jing Tang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between gam.hp versions 0.0-1 dated 2024-03-14 and 0.0-2 dated 2024-07-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/gam.hp.r | 1 + inst/CITATION | 37 +++++++++++-------------------------- man/gam.hp.Rd | 1 + 5 files changed, 22 insertions(+), 35 deletions(-)
Title: Systematically Run R CMD Checks
Description: Systematically Run R checks against multiple packages. Checks are run in
parallel with strategies to minimize dependency installation. Provides
out of the box interface for running reverse dependency check.
Author: Szymon Maksymiuk [cre, aut] ,
Doug Kelkhoff [aut] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between checked versions 0.1.0 dated 2024-07-10 and 0.2.0 dated 2024-07-25
checked-0.1.0/checked/man/message_possible_isolation_problems.Rd |only checked-0.2.0/checked/DESCRIPTION | 8 checked-0.2.0/checked/LICENSE | 2 checked-0.2.0/checked/MD5 | 48 +-- checked-0.2.0/checked/NAMESPACE | 9 checked-0.2.0/checked/NEWS.md | 29 +- checked-0.2.0/checked/R/check.R | 2 checked-0.2.0/checked/R/check_design.R | 138 ++++----- checked-0.2.0/checked/R/check_process.R | 41 +- checked-0.2.0/checked/R/checks_df.R | 83 +++-- checked-0.2.0/checked/R/cli.R | 5 checked-0.2.0/checked/R/install.R | 23 + checked-0.2.0/checked/R/next_task.R | 2 checked-0.2.0/checked/R/reporter_ansi_tty.R | 71 ++++ checked-0.2.0/checked/R/reporter_basic_tty.R | 23 + checked-0.2.0/checked/R/results.R | 143 ++++++---- checked-0.2.0/checked/R/task_graph.R | 11 checked-0.2.0/checked/R/utils.R | 11 checked-0.2.0/checked/README.md | 4 checked-0.2.0/checked/man/check_design.Rd | 92 ------ checked-0.2.0/checked/man/checked-package.Rd | 15 + checked-0.2.0/checked/man/checks_df.Rd | 10 checked-0.2.0/checked/man/print.checked_results.Rd |only checked-0.2.0/checked/man/results.Rd | 13 checked-0.2.0/checked/tests/testthat/test-check.R | 11 checked-0.2.0/checked/tests/testthat/test-checks_df.R | 2 26 files changed, 480 insertions(+), 316 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.6.3 dated 2024-03-20 and 1.6.5 dated 2024-07-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/acs.R | 3 +++ R/estimates.R | 29 +++++++++++++++++------------ R/utils.R | 7 ++++++- man/tidycensus.Rd | 9 +++++++++ 6 files changed, 45 insertions(+), 23 deletions(-)
Title: Computing P-Values of the One-Sample K-S Test and the Two-Sample
K-S and Kuiper Tests for (Dis)Continuous Null Distribution
Description: Contains functions to compute p-values for the one-sample and two-sample Kolmogorov-Smirnov (KS) tests and the two-sample Kuiper test for any fixed critical level and arbitrary (possibly very large) sample sizes. For the one-sample KS test, this package implements a novel, accurate and efficient method named Exact-KS-FFT, which allows the pre-specified cumulative distribution function under the null hypothesis to be continuous, purely discrete or mixed. In the two-sample case, it is assumed that both samples come from an unspecified (unknown) continuous, purely discrete or mixed distribution, i.e. ties (repeated observations) are allowed, and exact p-values of the KS and the Kuiper tests are computed. Note, the two-sample Kuiper test is often used when data samples are on the line or on the circle (circular data). To cite this package in publication: (for the use of the one-sample KS test) Dimitrina S. Dimitrova, Vladimir K. Kaishev, and Senren Tan. Computing the Kolmogorov-Smirnov Dis [...truncated...]
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Yun Jia <yunjia2019@gmail.com>,
Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk>,
Senren Tan <raymondtsrtsr@outlook.com>
Maintainer: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>
Diff between KSgeneral versions 2.0.0 dated 2024-05-21 and 2.0.1 dated 2024-07-25
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/KS2sample.R | 2 +- R/Kuiper2sample.R | 2 +- build/partial.rdb |binary man/KS2sample.Rd | 6 +++--- man/KS2sample_Rcpp.Rd | 2 +- man/KS2sample_c_Rcpp.Rd | 2 +- man/Kuiper2sample.Rd | 6 +++--- man/Kuiper2sample_Rcpp.Rd | 2 +- man/Kuiper2sample_c_Rcpp.Rd | 2 +- man/ksgeneral-package.Rd | 6 +++--- 12 files changed, 29 insertions(+), 29 deletions(-)
Title: Modern Database Engine for Complex Data Based on
Multi-Dimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for storing and accessing any complex data based on multi-dimensional
arrays. It supports dense and sparse arrays, dataframes and key-values stores,
cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded implementation,
supports parallel I/O, data versioning ('time travel'), metadata and groups.
It is implemented as an embeddable cross-platform C++ library with APIs from
several languages, and integrations. This package provides the R support.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.28.0 dated 2024-06-07 and 0.29.0 dated 2024-07-25
DESCRIPTION | 8 MD5 | 90 +- NAMESPACE | 14 NEWS.md | 41 + R/Array.R | 38 + R/ArraySchema.R | 33 + R/ArraySchemaEvolution.R | 16 R/CurrentDomain.R |only R/DataFrame.R | 16 R/NDRectangle.R |only R/RcppExports.R | 48 + R/TileDBArray.R | 9 README.md | 2 build/vignette.rds |binary cleanup | 1 configure | 27 configure.ac | 10 inst/doc/data-ingestion-from-sql.html | 150 ++-- inst/doc/documentation.html | 224 +++---- inst/doc/installation-options.html | 150 ++-- inst/doc/introduction.html | 152 ++-- inst/doc/tiledb-mariadb-examples.html | 150 ++-- inst/include/tiledb.h | 13 inst/tinytest/test_arrayschema.R | 42 + inst/tinytest/test_arrayschemaevolution.R | 16 inst/tinytest/test_currentdomain.R |only inst/tinytest/test_dataframe.R | 25 inst/tinytest/test_fragmentinfo.R | 57 + inst/tinytest/test_ndrectangle.R |only inst/tinytest/test_timetravel.R | 2 man/fromDataFrame.Rd | 8 man/tiledb_array_delete_fragments_list.Rd |only man/tiledb_array_schema_evolution_expand_current_domain.Rd |only man/tiledb_array_schema_evolution_extend_enumeration.Rd | 3 man/tiledb_array_schema_get_current_domain.Rd |only man/tiledb_array_schema_set_current_domain.Rd |only man/tiledb_current_domain-class.Rd |only man/tiledb_current_domain.Rd |only man/tiledb_current_domain_get_ndrectangle.Rd |only man/tiledb_current_domain_get_type.Rd |only man/tiledb_current_domain_is_empty.Rd |only man/tiledb_current_domain_set_ndrectangle.Rd |only man/tiledb_ndrectangle-class.Rd |only man/tiledb_ndrectangle.Rd |only man/tiledb_ndrectangle_get_range.Rd |only man/tiledb_ndrectangle_set_range.Rd |only man/vfs_file.Rd | 8 src/Makevars.in | 6 src/RcppExports.cpp | 156 ++++ src/deprecation.cpp | 12 src/libtiledb.cpp | 234 +++++++ src/nanoarrow.c | 370 ++++++++++- src/nanoarrow.h | 213 ++++-- src/nanoarrow.hpp | 415 ++++++++++++- tools/tiledbVersion.txt | 4 55 files changed, 2191 insertions(+), 572 deletions(-)
Title: R Wrapper to Access a Wide Range of Germany's Federal
Statistical System Databases Based on the GENESIS Web Service
RESTful API of the German Federal Statistical Office
(Statistisches Bundesamt/Destatis)
Description: A RESTful API wrapper for accessing the GENESIS database of
the German Federal Statistical Office (Destatis) as well as its Census
Database and the database of Germany's regional statistics. Supports data
search functions, credential management, result caching, and handling
remote background jobs for large datasets.
Author: Yannik Buhl [aut, cre],
Zoran Kovacevic [aut] ,
Dorian Le Jeune [aut],
Long Nguyen [aut] ,
Johannes Ritter [aut]
Maintainer: Yannik Buhl <ybuhl@posteo.de>
Diff between restatis versions 0.1.0 dated 2023-06-30 and 0.2.0 dated 2024-07-25
restatis-0.1.0/restatis/R/gen_list_jobs.R |only restatis-0.1.0/restatis/data/evas_list_long_20220724.rda |only restatis-0.1.0/restatis/man/evas_list_long_20220724.Rd |only restatis-0.1.0/restatis/tests/testthat/catalogue1/api/catalogue/tables-c47d1c.json |only restatis-0.1.0/restatis/tests/testthat/catalogue3/api/catalogue/cubes-b8e23a.json |only restatis-0.1.0/restatis/tests/testthat/catalogue4/api/catalogue/cubes-6cb32c.json |only restatis-0.1.0/restatis/tests/testthat/catalogue4/api/catalogue/tables-c47d1c.json |only restatis-0.1.0/restatis/tests/testthat/catalogue5/api/catalogue/tables-d53922.json |only restatis-0.1.0/restatis/tests/testthat/catalogue6/api/catalogue/tables-d53922.json |only restatis-0.1.0/restatis/tests/testthat/cube1/api/data/cubefile-f31506.csv |only restatis-0.1.0/restatis/tests/testthat/meta1/api/metadata/table-7837de.json |only restatis-0.1.0/restatis/tests/testthat/meta2_fake/api/metadata/cube-8d0bb5.json |only restatis-0.1.0/restatis/tests/testthat/meta3/api/metadata/table-7837de.json |only restatis-0.1.0/restatis/tests/testthat/modified2/api/catalogue/modifieddata-ceb5a8.json |only restatis-0.1.0/restatis/tests/testthat/searchvars1/api/catalogue/variables-a1a6d0.json |only restatis-0.1.0/restatis/tests/testthat/searchvars2_fake |only restatis-0.1.0/restatis/tests/testthat/table1/api/data/tablefile-6dd2df.csv |only restatis-0.1.0/restatis/tests/testthat/values1/api/catalogue/values2variable-886f37.json |only restatis-0.1.0/restatis/tests/testthat/values2/api/catalogue/values2variable-cb5890.json |only restatis-0.1.0/restatis/tests/testthat/variables1/api/catalogue/variables2statistic-476d62.json |only restatis-0.1.0/restatis/tests/testthat/variables2_fake/api/catalogue/variables2statistic-3d1ffb.json |only restatis-0.1.0/restatis/tests/testthat/variables3/api/catalogue/variables2statistic-8da08f.json |only 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Title: R Interface to the Data Retriever
Description: Provides an R interface to the Data Retriever
<https://retriever.readthedocs.io/en/latest/> via the Data Retriever's
command line interface. The Data Retriever automates the
tasks of finding, downloading, and cleaning public datasets,
and then stores them in a local database.
Author: Henry Senyondo [aut, cre] ,
Daniel McGlinn [aut] ,
Pranita Sharma [aut] ,
David J Harris [aut] ,
Hao Ye [aut] ,
Shawn Taylor [aut] ,
Jeroen Ooms [aut] ,
Francisco Rodriguez-Sanchez Ooms [aut]
,
Karthik Ram [aut] ,
Apoorva Pandey [aut] ,
Harshit Bansa [...truncated...]
Maintainer: Henry Senyondo <henrykironde@gmail.com>
Diff between rdataretriever versions 3.1.0 dated 2022-05-18 and 3.1.1 dated 2024-07-25
DESCRIPTION | 12 MD5 | 18 - README.md | 6 build/vignette.rds |binary inst/CITATION | 36 +- inst/doc/breed-bird-survey-analysis.R | 24 - inst/doc/breed-bird-survey-analysis.html | 406 +++++++++++++++++++------------ inst/doc/provenance.R | 2 inst/doc/provenance.html | 237 +++++++++++------- man/install_retriever.Rd | 4 10 files changed, 462 insertions(+), 283 deletions(-)
More information about rdataretriever at CRAN
Permanent link
Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.10.5 dated 2024-06-30 and 0.10.6 dated 2024-07-25
DESCRIPTION | 10 - MD5 | 24 +- NEWS.md | 9 + R/create.R | 5 R/delete.R | 42 ++-- R/query.R | 75 +++++--- R/src_duckdb.R | 4 R/src_sqlite.R | 5 R/zzz.R | 59 +++---- build/vignette.rds |binary inst/doc/nodbi-overview.html | 362 +++++++++++++++++++++---------------------- tests/testthat/core-nodbi.R | 2 tests/testthat/helper.R | 2 13 files changed, 319 insertions(+), 280 deletions(-)
Title: Easy-to-Use, Dependencyless Logger
Description: An easy-to-use 'ndjson' (newline-delimited 'JSON') logger.
It provides a set of wrappers for base R's message(), warning(), and
stop() functions that maintain identical functionality, but also log
the handler message to an 'ndjson' log file.
No change in existing code is necessary to use this package,
and only a few additional adjustments are needed to fully
utilize its potential.
Author: Matthias Ollech [cre, aut],
Ryan Price [fnd, aut]
Maintainer: Matthias Ollech <ollech@gmx.com>
Diff between loggit2 versions 2.3.0 dated 2024-06-08 and 2.3.1 dated 2024-07-25
DESCRIPTION | 13 - LICENSE | 2 MD5 | 120 +++++----- NAMESPACE | 40 +-- NEWS.md | 167 +++++++------- R/configurations.R | 338 ++++++++++++++-------------- R/handlers.R | 406 +++++++++++++++++----------------- R/json.R | 282 ++++++++++++------------ R/loggit.R | 201 ++++++++++------- R/setup.R | 154 ++++++------- R/split_json.R | 32 +- R/utils.R | 312 +++++++++++++------------- R/whit_loggit.R | 110 ++++----- R/zzz.R | 14 - inst/doc/further_configurations.html | 32 +- inst/doc/further_configurations.rmd | 273 +++++++++++------------ inst/doc/loggit2.Rmd | 411 +++++++++++++++++------------------ inst/doc/loggit2.html | 80 +++--- man/convert_lvl_input.Rd | 36 +-- man/convert_to_csv.Rd | 84 +++---- man/find_call.Rd | 32 +- man/get_echo.Rd | 28 +- man/get_log_level.Rd | 28 +- man/get_logfile.Rd | 36 +-- man/get_lvl_int.Rd | 36 +-- man/get_lvl_name.Rd | 36 +-- man/get_timestamp_format.Rd | 36 +-- man/loggit.Rd | 104 ++++---- man/loggit_dots.Rd |only man/loggit_internal.Rd |only man/message.Rd | 90 +++---- man/read_logs.Rd | 64 ++--- man/read_ndjson.Rd | 44 +-- man/rotate_logs.Rd | 56 ++-- man/sanitizers.Rd | 80 +++--- man/set_echo.Rd | 52 ++-- man/set_log_level.Rd | 74 +++--- man/set_logfile.Rd | 64 ++--- man/set_timestamp_format.Rd | 66 ++--- man/setup_echo.Rd | 40 +-- man/setup_log_level.Rd | 40 +-- man/setup_logfile.Rd | 34 +- man/setup_timestamp_format.Rd | 34 +- man/split_ndjson.Rd | 46 +-- man/stop.Rd | 92 +++---- man/stopifnot.Rd | 116 ++++----- man/warning.Rd | 120 +++++----- man/with_loggit.Rd | 100 ++++---- man/write_ndjson.Rd | 58 ++-- src/split_json.cpp | 14 - tests/testthat.R | 8 tests/testthat/setup.R | 150 ++++++------ tests/testthat/test-configurations.R | 188 ++++++++-------- tests/testthat/test-handlers.R | 329 ++++++++++++++-------------- tests/testthat/test-json.R | 84 +++---- tests/testthat/test-loggit.R | 116 ++++----- tests/testthat/test-utils.R | 292 ++++++++++++------------ tests/testthat/test-whit_loggit.R | 158 ++++++------- tests/testthat/testdata/test.loggit | 12 - vignettes/articles/fork.rmd | 243 ++++++++++---------- vignettes/further_configurations.rmd | 273 +++++++++++------------ vignettes/loggit2.Rmd | 411 +++++++++++++++++------------------ 62 files changed, 3537 insertions(+), 3454 deletions(-)
Title: Fitting Second-Order Tensor Data
Description: An implementation of fitting generalized linear models on
second-order tensor type data. The functions within this package mainly focus on
parameter estimation, including parameter coefficients and standard deviation.
Author: Mark Chen [aut, cre],
Sheng-Mao Chang [aut],
Wenbin Lu [aut],
Jung-Ying Tzeng [aut],
Ping-Yang Chen [aut]
Maintainer: Mark Chen <l501l501l@gmail.com>
Diff between TensorTest2D versions 1.1.1 dated 2022-01-03 and 1.1.2 dated 2024-07-25
DESCRIPTION | 10 MD5 | 50 - R/TensorTest2D.R | 2 R/mnist_mp2c2-data.R | 86 +-- R/omics-data.R | 112 ++-- R/summary.tsglm.R | 382 +++++++------- R/tensorReg2D.R | 1262 ++++++++++++++++++++++++------------------------ R/util.tsglm.R | 602 +++++++++++----------- README.md | 53 +- man/ALS.Rd | 68 +- man/Calculate_IC_Dev.Rd | 68 +- man/Check_tidy_input.Rd | 68 +- man/TensorTest2D.Rd | 61 +- man/VAR_ALS.Rd | 68 +- man/draw.coef.Rd | 100 +-- man/getGLMCoef.Rd | 48 - man/grapes-b-grapes.Rd | 42 - man/grapes-hp-grapes.Rd | 48 - man/grapes-w-grapes.Rd | 44 - man/grapes-wt-grapes.Rd | 44 - man/mnist_mp2c2.Rd | 100 +-- man/omics.Rd | 122 ++-- man/plot.tsglm.Rd | 186 +++---- man/predict.tsglm.Rd | 166 +++--- man/summary.tsglm.Rd | 198 +++---- man/tensorReg2D.Rd | 358 ++++++------- 26 files changed, 2200 insertions(+), 2148 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Phil Chalmers [aut] ,
Georges Monette [ctb] ,
Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.9.6 dated 2022-12-08 and 0.9.8 dated 2024-07-25
DESCRIPTION | 32 - MD5 | 85 +-- NAMESPACE | 6 NEWS.md | 12 R/GramSchmidt.R | 22 R/circle.R |only R/gaussian-elimination.R | 9 R/matlib-package.R | 2 R/matrix2latex.R | 65 +- R/util.R | 5 R/vectors.R | 7 R/vectors3d.R | 2 build/vignette.rds |binary inst/doc/data-beta.html | 1130 ++++++++++++++++++++++------------------ inst/doc/det-ex1.html | 126 ++-- inst/doc/det-ex2.html | 80 +- inst/doc/eigen-ex1.R | 2 inst/doc/eigen-ex1.html | 54 - inst/doc/eigen-ex2.R | 2 inst/doc/eigen-ex2.html | 68 +- inst/doc/ginv.html | 50 - inst/doc/gramreg.html | 104 +-- inst/doc/inv-ex1.html | 140 ++-- inst/doc/inv-ex2.html | 78 +- inst/doc/linear-equations.R | 4 inst/doc/linear-equations.html | 1062 +++++++++++++++++++++---------------- man/GramSchmidt.Rd | 13 man/Inverse.Rd | 76 +- man/Proj.Rd | 4 man/arc.Rd | 4 man/arrows3d.Rd | 4 man/circle.Rd |only man/circle3d.Rd | 4 man/corner.Rd | 4 man/figures/logo.png |only man/getYmult.Rd |only man/matlib-package.Rd | 133 ++-- man/matrix2latex.Rd | 33 - man/plot.regvec3d.Rd | 4 man/pointOnLine.Rd | 4 man/regvec3d.Rd | 4 man/swp.Rd | 94 +-- man/vectors3d.Rd | 2 vignettes/file75fc193c2d21.html |only vignettes/file75fc2d985765.html |only vignettes/file75fc37d71f65.html |only vignettes/file75fc68d870a4.html |only vignettes/file75fc756d1ecc.html |only 48 files changed, 1980 insertions(+), 1550 deletions(-)
Title: Set of Tools to Data Analysis using Generalized Linear Models
Description: Set of tools for the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized nonlinear models; (7) generalized estimating equations for cluster correlated data.
Author: Luis Hernando Vanegas [aut, cre],
Luz Marina Rondon [aut],
Gilberto A. Paula [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between glmtoolbox versions 0.1.11 dated 2024-04-12 and 0.1.12 dated 2024-07-25
DESCRIPTION | 8 +- MD5 | 70 ++++++++++++----------- NAMESPACE | 4 + R/data.R | 109 ++++++++++++++++++++++++++++++++---- R/geeglm.R | 39 +++++++----- R/glms.R | 12 +-- R/overglm3.R | 14 ++-- data/paramecium.rda |only man/BoxTidwell.Rd | 2 man/BoxTidwell.glm.Rd | 2 man/BoxTidwell.lm.Rd | 2 man/QIC.Rd | 2 man/cooks.distance.glmgee.Rd | 2 man/cooks.distance.gnm.Rd | 2 man/cooks.distance.overglm.Rd | 2 man/cooks.distance.zeroinflation.Rd | 2 man/envelope.glm.Rd | 2 man/envelope.gnm.Rd | 2 man/glance.glmgee.Rd |only man/glmgee.Rd | 5 - man/gnm.Rd | 6 + man/gnmgee.Rd | 12 ++- man/leverage.glmgee.Rd | 2 man/localInfluence.glm.Rd | 2 man/localInfluence.glmgee.Rd | 2 man/localInfluence.gnm.Rd | 2 man/localInfluence.overglm.Rd | 2 man/paramecium.Rd |only man/predict.glmgee.Rd | 2 man/residuals.glmgee.Rd | 2 man/residuals.gnm.Rd | 4 - man/residuals.overglm.Rd | 2 man/residuals.zeroinflation.Rd | 2 man/residuals2.Rd | 4 - man/tidy.glmgee.Rd |only man/wglmgee.Rd | 2 man/zeroalt.Rd | 2 man/zeroinf.Rd | 2 38 files changed, 224 insertions(+), 107 deletions(-)
Title: Convert R Models to PMML
Description: R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>,
which converts R models to Predictive Model Markup Language (PMML).
Author: Villu Ruusmann <villu.ruusmann@gmail.com>
Maintainer: Villu Ruusmann <villu.ruusmann@gmail.com>
Diff between r2pmml versions 0.27.1 dated 2023-04-05 and 0.28.0 dated 2024-07-25
r2pmml-0.27.1/r2pmml/inst/java/gson-2.10.jar |only r2pmml-0.27.1/r2pmml/inst/java/guava-21.0-minified.jar |only r2pmml-0.27.1/r2pmml/inst/java/jackson-annotations-2.13.3.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-converter-1.5.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-model-1.6.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-model-metro-1.6.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-rexp-1.5.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-rexp-xgboost-1.5.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-xgboost-1.7.3.jar |only r2pmml-0.27.1/r2pmml/java/pmml-converter-1.5.4-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-rexp-1.5.2-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-rexp-xgboost-1.5.2-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-xgboost-1.7.3-sources.jar |only r2pmml-0.28.0/r2pmml/DESCRIPTION | 8 +- r2pmml-0.28.0/r2pmml/MD5 | 32 +++++----- r2pmml-0.28.0/r2pmml/NEWS.md |only r2pmml-0.28.0/r2pmml/README.md | 2 r2pmml-0.28.0/r2pmml/inst/java/gson-2.9.1.jar |only r2pmml-0.28.0/r2pmml/inst/java/guava-15.0-minified.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-converter-1.5.7.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-model-1.6.5.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-model-metro-1.6.5.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-rexp-1.5.6.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-rexp-xgboost-1.5.6.jar |only r2pmml-0.28.0/r2pmml/inst/java/pmml-xgboost-1.8.6.jar |only r2pmml-0.28.0/r2pmml/inst/java/r2pmml-1.0-SNAPSHOT.jar |binary r2pmml-0.28.0/r2pmml/java/pmml-converter-1.5.7-sources.jar |only r2pmml-0.28.0/r2pmml/java/pmml-rexp-1.5.6-sources.jar |only r2pmml-0.28.0/r2pmml/java/pmml-rexp-xgboost-1.5.6-sources.jar |only r2pmml-0.28.0/r2pmml/java/pmml-xgboost-1.8.6-sources.jar |only 30 files changed, 21 insertions(+), 21 deletions(-)
Title: Regulatory Tables for Clinical Research
Description: Creates tables suitable for regulatory agency submission by
leveraging the 'gtsummary' package as the back end. Tables can be exported
to HTML, Word, PDF and more. Highly customized outputs are
available by utilizing existing styling functions from 'gtsummary' as
well as custom options designed for regulatory tables.
Author: Shannon Pileggi [aut, cre, cph]
,
Daniel D. Sjoberg [aut]
Maintainer: Shannon Pileggi <shannon.pileggi@gmail.com>
Diff between gtreg versions 0.3.0 dated 2023-11-17 and 0.4.0 dated 2024-07-25
DESCRIPTION | 8 MD5 | 32 NAMESPACE | 2 NEWS.md | 98 +- R/reexport.R | 4 R/selectors.R | 178 +--- R/tbl_listing.R | 4 R/tbl_reg_summary.R | 150 +-- R/utils-tbl_ae.R | 38 README.md | 3 build/vignette.rds |binary inst/doc/further_documentation.R | 2 man/reexports.Rd | 5 man/tbl_reg_summary.Rd | 68 - tests/testthat/_snaps/style_xxx.md | 1645 +------------------------------------ tests/testthat/test-style_xxx.R | 6 tests/testthat/test-tbl_ae.R | 1508 ++++++++++++++++----------------- 17 files changed, 1146 insertions(+), 2605 deletions(-)
Title: Create Ternary and Holdridge Plots
Description: Plots ternary diagrams (simplex plots / Gibbs triangles) and
Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the
standard graphics functions.
Allows custom annotation, interpolating, contouring and scaling of plotting
region.
Includes a 'Shiny' user interface for point-and-click ternary plotting.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting
functions.
Author: Martin R. Smith [aut, cre, cph]
,
Lilian Sanselme [ctb]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 2.3.1 dated 2024-02-06 and 2.3.2 dated 2024-07-25
DESCRIPTION | 12 +++-- MD5 | 62 ++++++++++++++--------------- NEWS.md | 4 + R/Contours.R | 5 +- R/Holdridge.R | 3 - R/TernaryPlot.R | 5 +- R/data.R | 7 +-- R/dot-TrianglePlot.R | 7 +-- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/Holdridge.R | 8 +++ inst/doc/Holdridge.Rmd | 86 +++++++++++++++++++++++++++++++++++++++-- inst/doc/Holdridge.html | 76 +++++++++++++++++++++++++++++++++--- inst/doc/Ternary.R | 2 inst/doc/Ternary.Rmd | 2 inst/doc/Ternary.html | 10 ++-- inst/doc/annotation.html | 4 - inst/doc/interpolation.html | 4 - inst/doc/new-users.Rmd | 39 ++++++++++++++++++ inst/doc/new-users.html | 41 ++++++++++++++++++- man/AddToTernary.Rd | 4 - man/ColourTernary.Rd | 3 - man/HoldridgeHypsometricCol.Rd | 4 - man/HoldridgePlot.Rd | 11 ++--- man/TernaryContour.Rd | 2 man/TernaryPlot.Rd | 5 +- man/holdridgeClasses.Rd | 5 -- tests/testthat/Rplots.pdf |binary vignettes/Holdridge.Rmd | 86 +++++++++++++++++++++++++++++++++++++++-- vignettes/Ternary.Rmd | 2 vignettes/new-users.Rmd | 39 ++++++++++++++++++ 32 files changed, 446 insertions(+), 93 deletions(-)
Title: 'Amazon Web Service S3' File System
Description: Access 'Amazon Web Service Simple Storage Service' ('S3') <https://aws.amazon.com/s3/>
as if it were a file system. Interface based on the R package 'fs'.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between s3fs versions 0.1.5 dated 2024-03-15 and 0.1.6 dated 2024-07-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/s3filesystem_class.R | 18 ++++++++++-------- 4 files changed, 21 insertions(+), 15 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut, cph]
,
Fani Kostourou [aut, ctb, cph]
,
Kimon Krenz [ctb, cph] ,
Alasdair Turner [ctb, cph] ,
Tasos Varoudis [ctb, cph] ,
Christian Sailer [ctb, cph] ,
Eva Friedrich [ctb, cph] ,
University College London [fnd],
Spacel [...truncated...]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.3.0 dated 2024-06-19 and 0.4.0 dated 2024-07-25
alcyon-0.3.0/alcyon/src/libs/genlib/linreg.h |only alcyon-0.3.0/alcyon/src/libs/salalib/agents/agentengine.cpp |only alcyon-0.3.0/alcyon/src/libs/salalib/agents/agentengine.h |only alcyon-0.3.0/alcyon/src/libs/salalib/agents/agenthelpers.h |only alcyon-0.3.0/alcyon/src/libs/salalib/agents/agentset.cpp |only alcyon-0.3.0/alcyon/src/libs/salalib/agents/agentset.h |only alcyon-0.3.0/alcyon/src/libs/salalib/mgraph.cpp |only alcyon-0.3.0/alcyon/src/libs/salalib/mgraph.h |only alcyon-0.3.0/alcyon/src/libs/salalib/options.h |only alcyon-0.3.0/alcyon/src/libs/salalib/pointdata.cpp |only alcyon-0.3.0/alcyon/src/libs/salalib/pointdata.h |only alcyon-0.3.0/alcyon/src/libs/salalib/spacepixfile.cpp |only alcyon-0.3.0/alcyon/src/libs/salalib/spacepixfile.h |only alcyon-0.4.0/alcyon/DESCRIPTION | 11 alcyon-0.4.0/alcyon/MD5 | 335 ++--- alcyon-0.4.0/alcyon/NAMESPACE | 1 alcyon-0.4.0/alcyon/NEWS.md | 5 alcyon-0.4.0/alcyon/R/RcppExports.R | 20 alcyon-0.4.0/alcyon/R/allFewestLineMap.R | 13 alcyon-0.4.0/alcyon/R/isovist.R | 4 alcyon-0.4.0/alcyon/R/oneToOneTraverse.R |only alcyon-0.4.0/alcyon/inst/WORDLIST | 1 alcyon-0.4.0/alcyon/inst/doc/segmentAnalysis.R | 13 alcyon-0.4.0/alcyon/inst/doc/segmentAnalysis.Rmd | 12 alcyon-0.4.0/alcyon/inst/doc/segmentAnalysis.html | 12 alcyon-0.4.0/alcyon/inst/doc/vga.R | 75 + alcyon-0.4.0/alcyon/inst/doc/vga.Rmd | 80 + alcyon-0.4.0/alcyon/inst/doc/vga.html | 70 + alcyon-0.4.0/alcyon/man/oneToOneTraverse.Rd |only alcyon-0.4.0/alcyon/src/AgentLookMode.h | 2 alcyon-0.4.0/alcyon/src/Makevars | 4 alcyon-0.4.0/alcyon/src/Makevars.win | 8 alcyon-0.4.0/alcyon/src/PointMap.h | 2 alcyon-0.4.0/alcyon/src/RcppExports.cpp | 83 + alcyon-0.4.0/alcyon/src/agentAnalysis.cpp | 87 - alcyon-0.4.0/alcyon/src/alcyon_types.h | 2 alcyon-0.4.0/alcyon/src/allFewest.cpp | 29 alcyon-0.4.0/alcyon/src/axialAnalysis.cpp | 5 alcyon-0.4.0/alcyon/src/isovist.cpp | 6 alcyon-0.4.0/alcyon/src/libs/genlib/CMakeLists.txt | 4 alcyon-0.4.0/alcyon/src/libs/genlib/bsptree.cpp | 45 alcyon-0.4.0/alcyon/src/libs/genlib/bsptree.h | 11 alcyon-0.4.0/alcyon/src/libs/genlib/comm.h | 2 alcyon-0.4.0/alcyon/src/libs/genlib/p2dpoly.cpp | 32 alcyon-0.4.0/alcyon/src/libs/genlib/p2dpoly.h | 22 alcyon-0.4.0/alcyon/src/libs/genlib/pafmath.cpp | 35 alcyon-0.4.0/alcyon/src/libs/genlib/pafmath.h | 109 - alcyon-0.4.0/alcyon/src/libs/genlib/readwritehelpers.h | 2 alcyon-0.4.0/alcyon/src/libs/genlib/simplematrix.h | 6 alcyon-0.4.0/alcyon/src/libs/salalib/CMakeLists.txt | 39 alcyon-0.4.0/alcyon/src/libs/salalib/agents/CMakeLists.txt | 20 alcyon-0.4.0/alcyon/src/libs/salalib/agents/agent.cpp | 49 alcyon-0.4.0/alcyon/src/libs/salalib/agents/agent.h | 4 alcyon-0.4.0/alcyon/src/libs/salalib/agents/agentanalysis.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/agents/agentanalysis.h |only alcyon-0.4.0/alcyon/src/libs/salalib/agents/agentga.cpp | 2 alcyon-0.4.0/alcyon/src/libs/salalib/agents/agentprogram.cpp | 18 alcyon-0.4.0/alcyon/src/libs/salalib/alllinemap.cpp | 182 +- alcyon-0.4.0/alcyon/src/libs/salalib/alllinemap.h | 36 alcyon-0.4.0/alcyon/src/libs/salalib/analysisresult.h | 19 alcyon-0.4.0/alcyon/src/libs/salalib/analysistype.h |only alcyon-0.4.0/alcyon/src/libs/salalib/attributemap.h |only alcyon-0.4.0/alcyon/src/libs/salalib/attributetable.cpp | 21 alcyon-0.4.0/alcyon/src/libs/salalib/attributetable.h | 20 alcyon-0.4.0/alcyon/src/libs/salalib/attributetablehelpers.h | 10 alcyon-0.4.0/alcyon/src/libs/salalib/axialminimiser.cpp | 4 alcyon-0.4.0/alcyon/src/libs/salalib/axialminimiser.h | 7 alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axialintegration.cpp | 370 +++-- alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axialintegration.h | 70 + alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axiallocal.cpp | 12 alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axiallocal.h | 6 alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axialstepdepth.cpp | 10 alcyon-0.4.0/alcyon/src/libs/salalib/axialmodules/axialstepdepth.h | 10 alcyon-0.4.0/alcyon/src/libs/salalib/axialpolygons.cpp | 14 alcyon-0.4.0/alcyon/src/libs/salalib/bspnodetree.h |only alcyon-0.4.0/alcyon/src/libs/salalib/connector.cpp | 4 alcyon-0.4.0/alcyon/src/libs/salalib/connector.h | 2 alcyon-0.4.0/alcyon/src/libs/salalib/exportutils.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/exportutils.h |only alcyon-0.4.0/alcyon/src/libs/salalib/fileproperties.h | 4 alcyon-0.4.0/alcyon/src/libs/salalib/gridproperties.cpp | 2 alcyon-0.4.0/alcyon/src/libs/salalib/importtypedefs.h | 2 alcyon-0.4.0/alcyon/src/libs/salalib/importutils.cpp | 303 +++- alcyon-0.4.0/alcyon/src/libs/salalib/importutils.h | 10 alcyon-0.4.0/alcyon/src/libs/salalib/isegment.h | 8 alcyon-0.4.0/alcyon/src/libs/salalib/isovist.cpp | 2 alcyon-0.4.0/alcyon/src/libs/salalib/isovist.h | 1 alcyon-0.4.0/alcyon/src/libs/salalib/isovistutils.h |only alcyon-0.4.0/alcyon/src/libs/salalib/ivga.h | 2 alcyon-0.4.0/alcyon/src/libs/salalib/linkutils.h | 2 alcyon-0.4.0/alcyon/src/libs/salalib/mapconverter.cpp | 126 - 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alcyon-0.4.0/alcyon/src/libs/salalib/shapegraph.h | 33 alcyon-0.4.0/alcyon/src/libs/salalib/shapemap.cpp | 654 ++-------- alcyon-0.4.0/alcyon/src/libs/salalib/shapemap.h | 396 +----- alcyon-0.4.0/alcyon/src/libs/salalib/shapemapgroupdata.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/shapemapgroupdata.h |only alcyon-0.4.0/alcyon/src/libs/salalib/shaperef.h |only alcyon-0.4.0/alcyon/src/libs/salalib/spacepix.cpp | 100 - alcyon-0.4.0/alcyon/src/libs/salalib/sparksieve2.cpp | 2 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/CMakeLists.txt | 27 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/extractlinkdata.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/extractlinkdata.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangular.cpp | 38 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangular.h | 24 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.cpp | 14 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.h | 12 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.cpp | 61 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.h | 16 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametric.cpp | 41 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametric.h | 25 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.cpp | 30 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.h | 14 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.cpp | 22 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.h | 8 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.cpp | 30 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.h | 21 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.cpp | 12 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.h | 12 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.cpp | 23 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.h | 10 alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.h |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.cpp |only alcyon-0.4.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.h |only alcyon-0.4.0/alcyon/src/link.cpp | 12 alcyon-0.4.0/alcyon/src/metagraphdata.cpp | 37 alcyon-0.4.0/alcyon/src/segmentAnalysis.cpp | 152 -- alcyon-0.4.0/alcyon/src/segmentDepth.cpp |only alcyon-0.4.0/alcyon/src/segmentShortestPath.cpp |only alcyon-0.4.0/alcyon/src/vga.cpp | 108 - 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Title: Methods to Analyse Seasonal Radial Tree Growth Data
Description: Methods for comparing different regression algorithms for
describing the temporal dynamics of secondary tree growth (xylem and
phloem). Users can compare the accuracy of the most common fitting methods
usually used to analyse xylem and phloem data, i.e., Gompertz function,
Double Gompertz function, General Additive Models (GAMs); and an algorithm
newly introduced to the field, i.e., Bayesian Regularised Neural Networks
(brnn). The core function of the package is XPSgrowth(), while the results
can be interpreted using implemented generic S3 methods, such as plot() and
summary().
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between rTG versions 1.0.2 dated 2024-02-03 and 1.0.3 dated 2024-07-25
DESCRIPTION | 6 - MD5 | 12 +- NAMESPACE | 2 NEWS.md | 5 + R/XPSgrowth.R | 178 ++++++++++++++++++++++++++++++++++++++---- man/XPSgrowth.Rd | 34 +++++--- tests/testthat/test_general.R | 5 - 7 files changed, 205 insertions(+), 37 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.3.0 dated 2024-06-25 and 3.3.1 dated 2024-07-25
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + R/generic.predict.rfsrc.R | 5 ++--- R/plot.quantreg.rfsrc.R | 11 +++++++++-- R/predict.rfsrc.R | 2 ++ R/rfsrc.R | 8 +++----- R/utilities.R | 8 -------- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS | 12 +++++++++--- man/plot.quantreg.rfsrc.Rd | 4 +++- man/predict.rfsrc.Rd | 7 ++++++- man/rfsrc.Rd | 5 +++++ src/randomForestSRC.c | 3 +++ 15 files changed, 72 insertions(+), 52 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.11.1 dated 2024-06-07 and 1.12.0 dated 2024-07-25
DESCRIPTION | 19 MD5 | 94 +- NAMESPACE | 944 +++++++++++++------------ NEWS.md | 18 R/AddTip.R | 4 R/RUtreebalance.R |only R/SplitFunctions.R | 2 R/TopologyOnly.R |only R/TotalCopheneticIndex.R | 17 R/TreeNumber.R | 4 R/helper_functions.R | 2 R/parse_files.R | 7 R/phylo.R | 11 R/tree_generation.R | 1057 ++++++++++++++--------------- R/tree_shape.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 12 inst/WORDLIST | 4 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.html | 4 inst/doc/load-trees.html | 10 inst/include/TreeTools/root_tree.h | 14 man/AddTip.Rd | 4 man/AncestorEdge.Rd | 6 man/CladisticInfo.Rd | 1 man/Consensus.Rd | 1 man/DescendantEdges.Rd | 6 man/EdgeAncestry.Rd | 6 man/J1Index.Rd |only man/ListAncestors.Rd | 6 man/Neworder.Rd | 6 man/ReadCharacters.Rd | 3 man/Reorder.Rd | 6 man/Stemwardness.Rd | 1 man/Subtree.Rd | 6 man/TipLabels.Rd | 2 man/TopologyOnly.Rd |only man/TotalCopheneticIndex.Rd | 11 man/TreeShape.Rd | 2 man/TreeTools-package.Rd | 1 man/figures/Stemwardness.png |binary man/sapply64.Rd | 2 src/ape_reorder.cpp | 1 tests/testthat/test-RUtreebalance.R |only tests/testthat/test-TopologyOnly.R |only tests/testthat/test-TotalCopheneticIndex.R | 20 tests/testthat/test-phylo.R | 11 tests/testthat/test-root_tree.h.R | 13 tests/testthat/test-tree_generation.R | 12 tests/testthat/test-tree_properties.R | 2 51 files changed, 1256 insertions(+), 1102 deletions(-)
Title: Perform Structural Missing Data Investigations
Description: An easy to use implementation of routine structural missing data diagnostics with functions to visualize the proportions of missing observations, investigate missing data patterns and conduct various empirical missing data diagnostic tests. Reference: Weberpals J, Raman SR, Shaw PA, Lee H, Hammill BG, Toh S, Connolly JG, Dandreo KJ, Tian F, Liu W, Li J, Hernández-Muñoz JJ, Glynn RJ, Desai RJ. smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies. JAMIA Open. 2024 Jan 31;7(1):ooae008. <doi:10.1093/jamiaopen/ooae008>.
Author: Janick Weberpals [aut, cre, cph]
Maintainer: Janick Weberpals <janick.developer@gmail.com>
Diff between smdi versions 0.2.2 dated 2023-07-17 and 0.3.0 dated 2024-07-25
DESCRIPTION | 27 MD5 | 95 - NAMESPACE | 16 NEWS.md | 18 R/smdi_asmd.R | 12 R/smdi_check_covar.R | 14 R/smdi_diagnose.R | 8 R/smdi_hotelling.R | 34 R/smdi_little.R | 32 R/smdi_na_indicator.R | 6 R/smdi_outcome.R | 49 R/smdi_rf.R | 66 + R/smdi_style_gt.R | 16 R/smdi_summarize.R | 4 build/partial.rdb |only build/vignette.rds |binary data/smdi_data.rda |binary data/smdi_data_complete.rda |binary inst/doc/a_data_generation.R | 137 +- inst/doc/a_data_generation.Rmd | 109 +- inst/doc/a_data_generation.html | 1434 ++++++++++++++++------------ inst/doc/b_routine_diagnostics.R | 26 inst/doc/b_routine_diagnostics.Rmd | 18 inst/doc/b_routine_diagnostics.html | 135 +- inst/doc/c_multivariate_missingness.R | 13 inst/doc/c_multivariate_missingness.Rmd | 5 inst/doc/c_multivariate_missingness.html | 632 +++++++----- inst/doc/d_narfcs_sensitivity_analysis.R | 56 - inst/doc/d_narfcs_sensitivity_analysis.Rmd | 48 inst/doc/d_narfcs_sensitivity_analysis.html | 144 +- inst/doc/smdi.R | 2 inst/doc/smdi.html | 89 + man/smdi-package.Rd | 4 man/smdi_asmd.Rd | 2 man/smdi_diagnose.Rd | 8 man/smdi_hotelling.Rd | 9 man/smdi_little.Rd | 2 man/smdi_outcome.Rd | 15 man/smdi_rf.Rd | 8 man/smdi_style_gt.Rd | 2 tests/testthat/test-smdi_asmd.R | 4 tests/testthat/test-smdi_hotelling.R | 4 tests/testthat/test-smdi_little.R | 12 tests/testthat/test-smdi_outcome.R | 83 + tests/testthat/test-smdi_rf.R | 19 vignettes/a_data_generation.Rmd | 109 +- vignettes/b_routine_diagnostics.Rmd | 18 vignettes/c_multivariate_missingness.Rmd | 5 vignettes/d_narfcs_sensitivity_analysis.Rmd | 48 49 files changed, 2161 insertions(+), 1436 deletions(-)
Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with
complex sampling and assessment design (see 'Rutkowski', 2010
<doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the
package, see 'Mirazchiyski', 2021b (<doi:10.339 [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.4.5 dated 2024-04-26 and 1.4.7 dated 2024-07-25
DESCRIPTION | 10 MD5 | 42 NEWS.md | 20 R/common.r | 203 R/lsa.bench.r | 3 R/lsa.bin.log.reg.r | 7 R/lsa.convert.data.r | 9 R/lsa.corr.r | 3 R/lsa.crosstabs.r | 6 R/lsa.lin.reg.r | 83 R/lsa.pcts.means.r | 3 R/lsa.prctls.r | 3 README.md | 2 inst/shiny/GUI/server.r |18110 ++++++++++++++++++++++++------------------------ inst/shiny/GUI/ui.r | 3 man/lsa.bench.Rd | 1 man/lsa.bin.log.reg.Rd | 5 man/lsa.corr.Rd | 1 man/lsa.crosstabs.Rd | 4 man/lsa.lin.reg.Rd | 21 man/lsa.pcts.means.Rd | 1 man/lsa.prctls.Rd | 1 22 files changed, 9425 insertions(+), 9116 deletions(-)
Title: Concise Spatial Query and Representation System (c-Squares)
Description: Encode and decode c-squares, from and to simple feature (sf)
or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly
join or query spatial data.
Author: Pepijn de Vries [aut, cre]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between csquares versions 0.0.6 dated 2024-07-19 and 0.0.7 dated 2024-07-25
csquares-0.0.6/csquares/inst/doc/Wildcards.R |only csquares-0.0.6/csquares/inst/doc/Wildcards.Rmd |only csquares-0.0.6/csquares/inst/doc/Wildcards.html |only csquares-0.0.6/csquares/vignettes/Wildcards.Rmd |only csquares-0.0.7/csquares/DESCRIPTION | 15 +- csquares-0.0.7/csquares/MD5 | 75 ++++++---- csquares-0.0.7/csquares/NAMESPACE | 15 ++ csquares-0.0.7/csquares/NEWS.md | 14 + csquares-0.0.7/csquares/R/as_csquares.R | 14 + csquares-0.0.7/csquares/R/as_stars.R | 4 csquares-0.0.7/csquares/R/csquares_methods.R | 61 +++++--- csquares-0.0.7/csquares/R/expand.R | 2 csquares-0.0.7/csquares/R/helpers.R | 1 csquares-0.0.7/csquares/R/ices.R |only csquares-0.0.7/csquares/R/in.R | 2 csquares-0.0.7/csquares/R/init.R | 18 ++ csquares-0.0.7/csquares/R/joins_tidy.R |only csquares-0.0.7/csquares/R/resample.R | 4 csquares-0.0.7/csquares/R/tidyverse.R | 43 +++++ csquares-0.0.7/csquares/R/validate.R | 5 csquares-0.0.7/csquares/R/vctrs.R |only csquares-0.0.7/csquares/build/vignette.rds |binary csquares-0.0.7/csquares/inst/doc/csquares-objects.R |only csquares-0.0.7/csquares/inst/doc/csquares-objects.Rmd |only csquares-0.0.7/csquares/inst/doc/csquares-objects.html |only csquares-0.0.7/csquares/inst/doc/ices.R |only csquares-0.0.7/csquares/inst/doc/ices.Rmd |only csquares-0.0.7/csquares/inst/doc/ices.html |only csquares-0.0.7/csquares/inst/doc/tidy.R |only csquares-0.0.7/csquares/inst/doc/tidy.Rmd |only csquares-0.0.7/csquares/inst/doc/tidy.html |only csquares-0.0.7/csquares/inst/doc/wildcards.R |only csquares-0.0.7/csquares/inst/doc/wildcards.Rmd |only csquares-0.0.7/csquares/inst/doc/wildcards.html |only csquares-0.0.7/csquares/man/as_csquares.Rd | 3 csquares-0.0.7/csquares/man/csquares-methods.Rd | 8 - csquares-0.0.7/csquares/man/expand_wildcards.Rd | 2 csquares-0.0.7/csquares/man/figures/lifecycle-archived.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-defunct.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-deprecated.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-experimental.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-maturing.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-questioning.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-soft-deprecated.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-stable.svg |only csquares-0.0.7/csquares/man/figures/lifecycle-superseded.svg |only csquares-0.0.7/csquares/man/ices_columns.Rd |only csquares-0.0.7/csquares/man/ices_geom.Rd |only csquares-0.0.7/csquares/man/in_csquares.Rd | 2 csquares-0.0.7/csquares/man/tidyjoins.Rd |only csquares-0.0.7/csquares/man/tidyverse.Rd | 10 - csquares-0.0.7/csquares/man/vctrs.Rd |only csquares-0.0.7/csquares/tests/testthat/test-ices.R |only csquares-0.0.7/csquares/vignettes/csquares-objects.Rmd |only csquares-0.0.7/csquares/vignettes/ices.Rmd |only csquares-0.0.7/csquares/vignettes/tidy.Rmd |only csquares-0.0.7/csquares/vignettes/wildcards.Rmd |only 57 files changed, 227 insertions(+), 71 deletions(-)
Title: Workflow for Cluster Randomised Trials with Spillover
Description: Design, workflow and statistical analysis of Cluster Randomised Trials of (health) interventions where there may be spillover between the arms (see <https://thomasasmith.github.io/index.html>).
Author: Thomas Smith [aut, cre, cph] ,
Lea Multerer [ctb],
Mariah Silkey [ctb]
Maintainer: Thomas Smith <Thomas-a.Smith@unibas.ch>
Diff between CRTspat versions 1.2.0 dated 2024-02-12 and 1.3.0 dated 2024-07-25
CRTspat-1.2.0/CRTspat/tests/testthat/test3..R |only CRTspat-1.3.0/CRTspat/DESCRIPTION | 8 CRTspat-1.3.0/CRTspat/MD5 | 102 CRTspat-1.3.0/CRTspat/NAMESPACE | 1 CRTspat-1.3.0/CRTspat/NEWS.md | 5 CRTspat-1.3.0/CRTspat/R/CRTsp.R | 129 CRTspat-1.3.0/CRTspat/R/CRTspat-package.R | 1 CRTspat-1.3.0/CRTspat/R/analyseCRT.R | 9 CRTspat-1.3.0/CRTspat/R/designCRT.R | 167 CRTspat-1.3.0/CRTspat/R/simulateCRT.R | 43 CRTspat-1.3.0/CRTspat/R/surround.R | 188 CRTspat-1.3.0/CRTspat/R/utils.R | 90 CRTspat-1.3.0/CRTspat/inst/doc/Usecase1.Rmd | 107 CRTspat-1.3.0/CRTspat/inst/doc/Usecase1.html | 105 CRTspat-1.3.0/CRTspat/inst/doc/Usecase2.Rmd | 152 CRTspat-1.3.0/CRTspat/inst/doc/Usecase2.html | 163 CRTspat-1.3.0/CRTspat/inst/doc/Usecase3.Rmd | 18 CRTspat-1.3.0/CRTspat/inst/doc/Usecase3.html | 16 CRTspat-1.3.0/CRTspat/inst/doc/Usecase4.Rmd | 18 CRTspat-1.3.0/CRTspat/inst/doc/Usecase4.html | 2 CRTspat-1.3.0/CRTspat/inst/doc/Usecase5.Rmd | 46 CRTspat-1.3.0/CRTspat/inst/doc/Usecase5.html | 39 CRTspat-1.3.0/CRTspat/inst/doc/Usecase6.Rmd | 16 CRTspat-1.3.0/CRTspat/inst/doc/Usecase6.html | 4 CRTspat-1.3.0/CRTspat/inst/doc/Usecase7.Rmd | 32 CRTspat-1.3.0/CRTspat/inst/doc/Usecase7.html | 24 CRTspat-1.3.0/CRTspat/inst/doc/Usecase8.Rmd | 24 CRTspat-1.3.0/CRTspat/inst/doc/Usecase8.html | 18 CRTspat-1.3.0/CRTspat/inst/extdata/exampleCRT.txt | 3711 +++++++++--------- CRTspat-1.3.0/CRTspat/inst/extdata/example_design.txt | 10 CRTspat-1.3.0/CRTspat/man/CRTpower.Rd | 52 CRTspat-1.3.0/CRTspat/man/CRTsp.Rd | 16 CRTspat-1.3.0/CRTspat/man/CRTspat-package.Rd | 42 CRTspat-1.3.0/CRTspat/man/compute_distance.Rd | 18 CRTspat-1.3.0/CRTspat/man/compute_mesh.Rd | 2 CRTspat-1.3.0/CRTspat/man/figures/manual.pdf |binary CRTspat-1.3.0/CRTspat/man/plotCRT.Rd | 260 - CRTspat-1.3.0/CRTspat/man/randomizeCRT.Rd | 6 CRTspat-1.3.0/CRTspat/man/simulateCRT.Rd | 292 - CRTspat-1.3.0/CRTspat/man/specify_clusters.Rd | 18 CRTspat-1.3.0/CRTspat/tests/testthat/test3.R |only CRTspat-1.3.0/CRTspat/tests/testthat/test9.R | 6 CRTspat-1.3.0/CRTspat/vignettes/Usecase1.Rmd | 107 CRTspat-1.3.0/CRTspat/vignettes/Usecase2.Rmd | 152 CRTspat-1.3.0/CRTspat/vignettes/Usecase2.Rmd.orig | 8 CRTspat-1.3.0/CRTspat/vignettes/Usecase3.Rmd | 18 CRTspat-1.3.0/CRTspat/vignettes/Usecase4.Rmd | 18 CRTspat-1.3.0/CRTspat/vignettes/Usecase5.Rmd | 46 CRTspat-1.3.0/CRTspat/vignettes/Usecase6.Rmd | 16 CRTspat-1.3.0/CRTspat/vignettes/Usecase7.Rmd | 32 CRTspat-1.3.0/CRTspat/vignettes/Usecase7.Rmd.orig | 22 CRTspat-1.3.0/CRTspat/vignettes/Usecase8.Rmd | 24 CRTspat-1.3.0/CRTspat/vignettes/Usecase8.Rmd.orig | 16 53 files changed, 3406 insertions(+), 3013 deletions(-)
Title: Analyze Interconnection Structure of Multilayer Interaction
Networks
Description: In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network.
To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer networks by functions of this R package.
Author: WeiCheng Sun [aut, cre],
Chuan Yan [aut],
Yangyang Zhao [aut]
Maintainer: WeiCheng Sun <sunwch2023@lzu.edu.cn>
Diff between ILSM versions 1.0.2 dated 2024-04-07 and 1.0.3.1 dated 2024-07-25
ILSM-1.0.2/ILSM/R/Hc.R |only ILSM-1.0.2/ILSM/R/Node_versatility.R |only ILSM-1.0.2/ILSM/R/Prc.R |only ILSM-1.0.2/ILSM/R/Psc.R |only ILSM-1.0.2/ILSM/R/motif_count.R |only ILSM-1.0.2/ILSM/R/role.R |only ILSM-1.0.2/ILSM/man/Hc.Rd |only ILSM-1.0.2/ILSM/man/Midlayer_role.Rd |only ILSM-1.0.2/ILSM/man/Node_versatility.Rd |only ILSM-1.0.2/ILSM/man/Prc.Rd |only ILSM-1.0.2/ILSM/man/Psc.Rd |only ILSM-1.0.2/ILSM/man/figure/conbine_1.png |only ILSM-1.0.2/ILSM/man/figure/example.png |only ILSM-1.0.2/ILSM/man/figure/motif_motify.png |only ILSM-1.0.2/ILSM/man/motif_count.Rd |only ILSM-1.0.2/ILSM/tests/testthat/test-Midlayer_role.R |only ILSM-1.0.2/ILSM/tests/testthat/test-Node_versatility.R |only ILSM-1.0.2/ILSM/tests/testthat/test-motif_count.R |only ILSM-1.0.3.1/ILSM/DESCRIPTION | 11 ILSM-1.0.3.1/ILSM/MD5 | 90 +++--- ILSM-1.0.3.1/ILSM/NAMESPACE | 14 - ILSM-1.0.3.1/ILSM/NEWS.md | 36 ++ ILSM-1.0.3.1/ILSM/R/Multi_motif.R | 110 ++++++-- ILSM-1.0.3.1/ILSM/R/build_net.R | 2 ILSM-1.0.3.1/ILSM/R/coid.R |only ILSM-1.0.3.1/ILSM/R/cois.R |only ILSM-1.0.3.1/ILSM/R/edgelist_from_matrices.R | 51 +-- ILSM-1.0.3.1/ILSM/R/hc.R |only ILSM-1.0.3.1/ILSM/R/icmotif_count.R |only ILSM-1.0.3.1/ILSM/R/icmotif_role.R |only ILSM-1.0.3.1/ILSM/R/igraph_from_matrices.R | 58 +--- ILSM-1.0.3.1/ILSM/R/node_cv.R |only ILSM-1.0.3.1/ILSM/R/null_model.R | 6 ILSM-1.0.3.1/ILSM/R/pc.R |only ILSM-1.0.3.1/ILSM/R/poc.R |only ILSM-1.0.3.1/ILSM/R/role_sim.R | 8 ILSM-1.0.3.1/ILSM/R/subnet_cor.R | 100 ++----- ILSM-1.0.3.1/ILSM/README.md | 63 ++-- ILSM-1.0.3.1/ILSM/build/vignette.rds |binary ILSM-1.0.3.1/ILSM/inst/doc/motif_guideline.R | 23 + ILSM-1.0.3.1/ILSM/inst/doc/motif_guideline.Rmd | 32 +- ILSM-1.0.3.1/ILSM/inst/doc/motif_guideline.html | 149 ++++++++++- ILSM-1.0.3.1/ILSM/man/Multi_motif.Rd | 36 +- ILSM-1.0.3.1/ILSM/man/build_net.Rd | 2 ILSM-1.0.3.1/ILSM/man/coid.Rd |only ILSM-1.0.3.1/ILSM/man/cois.Rd |only ILSM-1.0.3.1/ILSM/man/figure/conbine.png |only ILSM-1.0.3.1/ILSM/man/figure/motif_ILSM.png |only ILSM-1.0.3.1/ILSM/man/figure/motif_ILSM.tif |only ILSM-1.0.3.1/ILSM/man/hc.Rd |only ILSM-1.0.3.1/ILSM/man/icmotif_count.Rd |only ILSM-1.0.3.1/ILSM/man/icmotif_role.Rd |only ILSM-1.0.3.1/ILSM/man/igraph_from_matrices.Rd | 4 ILSM-1.0.3.1/ILSM/man/node_cv.Rd |only ILSM-1.0.3.1/ILSM/man/null_model.Rd | 6 ILSM-1.0.3.1/ILSM/man/pc.Rd |only ILSM-1.0.3.1/ILSM/man/poc.Rd |only ILSM-1.0.3.1/ILSM/man/role_sim.Rd | 8 ILSM-1.0.3.1/ILSM/man/subnet_cor.Rd | 2 ILSM-1.0.3.1/ILSM/tests/testthat/test-Multi_motif.R | 18 - ILSM-1.0.3.1/ILSM/tests/testthat/test-adject_net.R | 2 ILSM-1.0.3.1/ILSM/tests/testthat/test-icmotif_count.R |only ILSM-1.0.3.1/ILSM/tests/testthat/test-icmotif_role.R |only ILSM-1.0.3.1/ILSM/tests/testthat/test-igraph_from_matrices.R | 12 ILSM-1.0.3.1/ILSM/tests/testthat/test-node_cv.R |only ILSM-1.0.3.1/ILSM/vignettes/motif_guideline.Rmd | 32 +- 66 files changed, 570 insertions(+), 305 deletions(-)
Title: Analyzing Animal's Rhythmicity
Description: Analyze and visualize the rhythmic behavior of animals using the
degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>),
compute and visualize harmonic power, actograms, average activity and diurnality
index.
Author: Hassan-Roland Nasser [aut, cre],
Marie Schneider [aut, ctb],
Joanna Stachowicz [aut, rev],
Christina Umstaetter [aut, ths]
Maintainer: Hassan-Roland Nasser <hassan.nasser@me.com>
Diff between digiRhythm versions 2.0 dated 2024-07-16 and 2.1 dated 2024-07-25
DESCRIPTION | 6 MD5 | 55 - R/actogram.R | 16 R/daily_acticity_wrap_plot.R | 15 R/daily_average_activity.R | 13 R/data.R | 3 R/dfc.R | 64 -- R/diurnality.R | 22 R/import_raw_activity_data.R | 40 + R/is_dgm_friendly.R | 31 - R/lomb_scargle_periodogram.R | 118 ++-- R/resample_dgm.R | 11 R/sliding_DI.R | 41 - R/utils.R | 24 inst/doc/Actgram_diurnality_avg_activity.html | 4 inst/doc/DFC_and_HP_and_changing_plots.html | 380 +++++++------ inst/doc/Loading_and_preprocessing_data_in_DigiRhythm.html | 20 inst/doc/Visualisation.html | 4 man/actogram.Rd | 3 man/daily_average_activity.Rd | 4 man/dfc.Rd | 17 man/diurnality.Rd | 11 man/import_raw_activity_data.Rd | 11 man/is_dgm_friendly.Rd | 6 man/lomb_scargle_periodogram.Rd | 42 - man/lowest_possible_harmonic_period.Rd |only man/resample_dgm.Rd | 8 man/sliding_DI.Rd | 3 man/timedata.Rd | 3 29 files changed, 595 insertions(+), 380 deletions(-)
Title: Calibration, Validation, and Simulation of TKTD Models
Description: Eases the use of ecotoxicological effect models. Can simulate
common toxicokinetic-toxicodynamic (TK/TD) models such as
General Unified Threshold models of Survival (GUTS) and Lemna. It can
derive effects and effect profiles (EPx) from scenarios. It supports the
use of 'tidyr' workflows employing the pipe symbol. Time-consuming
tasks can be parallelized.
Author: Nils Kehrein [aut, cre],
Dirk Nickisch [aut],
Peter Vermeiren [aut],
Torben Wittwer [ctb],
Johannes Witt [ctb],
Andre Gergs [ctb]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between cvasi versions 1.1.0 dated 2024-05-30 and 1.1.3 dated 2024-07-25
DESCRIPTION | 8 MD5 | 72 ++-- NAMESPACE | 225 +++++++------- NEWS.md | 15 R/class-Algae.R | 61 ++- R/data.R | 26 + R/globals.R | 6 R/import_toxswa.R | 11 R/plotting.r | 429 ++++++++++++++++++---------- R/simulate.R | 20 + R/solver.R | 22 - inst/doc/cvasi-1-manual.R | 2 inst/doc/cvasi-1-manual.Rmd | 2 inst/doc/cvasi-2-howto.html | 8 man/Algae_Simple.Rd | 25 + man/Algae_TKTD.Rd | 28 + man/Algae_Weber.Rd | 14 man/CalibrationSet.Rd | 140 ++++----- man/effect.Rd | 132 ++++---- man/epx.Rd | 182 +++++------ man/minnow_it.Rd | 13 man/minnow_sd.Rd | 13 man/plot_epx.Rd | 10 man/plot_ppc.Rd | 90 +++-- man/plot_ppc_combi.Rd | 57 ++- man/plot_scenario.Rd |only man/plot_sd.Rd | 33 +- man/set_window.Rd | 64 ++-- man/simulate_batch.Rd | 13 src/algae_TKTD.c | 16 - src/algae_simple.c | 8 src/algae_weber.c | 17 - tests/data/TOXSWA |only tests/testthat/test-GUTS_ring_test.R | 4 tests/testthat/test-import_toxswa.R |only tests/testthat/test-simulate_Algae_simple.R | 9 tests/testthat/test-simulate_batch.R |only tests/testthat/test-survival.R | 18 + vignettes/cvasi-1-manual.Rmd | 2 39 files changed, 1047 insertions(+), 748 deletions(-)
Title: Water and Measurements Quality
Description: The functions proposed in this package allows to graphically evaluate the process of measurement of the chemical components of water. TSSS() and ICHS functions are useful to control the quality of measurements of chemical components of a sample of water. If one or more measurements include an error, the generated graph will indicate it with a position of the point that represents the sample outside the confidence interval.
Author: Maela Lupo [aut, cre],
Andrea Porpatto [aut],
Alfredo Rigalli [aut]
Maintainer: Maela Lupo <maela.lupo@gmail.com>
Diff between AQuality versions 1.0 dated 2024-05-15 and 1.1 dated 2024-07-25
AQuality-1.0/AQuality/data/data.rda |only AQuality-1.0/AQuality/man/data.Rd |only AQuality-1.1/AQuality/DESCRIPTION | 10 +++++----- AQuality-1.1/AQuality/MD5 | 18 +++++++++++------- AQuality-1.1/AQuality/NAMESPACE | 2 +- AQuality-1.1/AQuality/R/ICHS.R |only AQuality-1.1/AQuality/build/partial.rdb |binary AQuality-1.1/AQuality/data/dataICHS.rda |only AQuality-1.1/AQuality/data/dataTSSS.rda |only AQuality-1.1/AQuality/man/AQuality-package.Rd | 2 +- AQuality-1.1/AQuality/man/ICHS.Rd |only AQuality-1.1/AQuality/man/TSSS.Rd | 8 ++++---- AQuality-1.1/AQuality/man/dataICHS.Rd |only AQuality-1.1/AQuality/man/dataTSSS.Rd |only 14 files changed, 22 insertions(+), 18 deletions(-)
Title: Score Matching Estimation by Automatic Differentiation
Description: Hyvärinen's score matching (Hyvärinen, 2005) <https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful estimation technique when the normalising constant for a probability distribution is difficult to compute. This package implements score matching estimators using automatic differentiation in the 'CppAD' library <https://github.com/coin-or/CppAD> and is designed for quickly implementing score matching estimators for new models. Also available is general robustification (Windham, 1995) <https://www.jstor.org/stable/2346159>. Already in the package are estimators for directional distributions (Mardia, Kent and Laha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible Polynomially-Tilted Pairwise Interaction model for compositional data. The latter estimators perform well when there are zeros in the compositions (Scealy and Wood, 2023) <doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy, Hingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-1 [...truncated...]
Author: Kassel Liam Hingee [aut, cre] ,
Janice Scealy [aut] ,
Bradley M. Bell [cph]
Maintainer: Kassel Liam Hingee <kassel.hingee@anu.edu.au>
Diff between scorematchingad versions 0.0.64 dated 2024-06-27 and 0.0.67 dated 2024-07-24
scorematchingad-0.0.64/scorematchingad/inst/include/cppad |only scorematchingad-0.0.64/scorematchingad/src/Makevars |only scorematchingad-0.0.67/scorematchingad/DESCRIPTION | 10 scorematchingad-0.0.67/scorematchingad/MD5 | 1654 +++++++--- scorematchingad-0.0.67/scorematchingad/NEWS.md | 12 scorematchingad-0.0.67/scorematchingad/R/Windham.R | 2 scorematchingad-0.0.67/scorematchingad/R/buildsmdtape.R | 2 scorematchingad-0.0.67/scorematchingad/R/inlineCxxPlugin.R | 2 scorematchingad-0.0.67/scorematchingad/R/ppi_cW.R | 2 scorematchingad-0.0.67/scorematchingad/R/ppi_robust.R | 2 scorematchingad-0.0.67/scorematchingad/R/rppi.R | 4 scorematchingad-0.0.67/scorematchingad/R/vMF_robust.R | 4 scorematchingad-0.0.67/scorematchingad/README.md |only scorematchingad-0.0.67/scorematchingad/build/partial.rdb |binary scorematchingad-0.0.67/scorematchingad/cleanup |only scorematchingad-0.0.67/scorematchingad/configure |only scorematchingad-0.0.67/scorematchingad/configure.ac |only scorematchingad-0.0.67/scorematchingad/configure.win |only scorematchingad-0.0.67/scorematchingad/inst/cppad |only scorematchingad-0.0.67/scorematchingad/inst/include/CppAD_LICENSE | 2 scorematchingad-0.0.67/scorematchingad/inst/include/scorematchingad.h | 71 scorematchingad-0.0.67/scorematchingad/inst/include/scorematchingad_forward.h |only scorematchingad-0.0.67/scorematchingad/inst/include/utils/wrapas.hpp | 2 scorematchingad-0.0.67/scorematchingad/man/ADFun.Rd | 2 scorematchingad-0.0.67/scorematchingad/man/buildsmdtape.Rd | 2 scorematchingad-0.0.67/scorematchingad/man/scorematchingad-package.Rd | 8 scorematchingad-0.0.67/scorematchingad/src/approxwrap.h | 2 scorematchingad-0.0.67/scorematchingad/src/cppad_interface.h | 4 scorematchingad-0.0.67/scorematchingad/src/exposemanifold.cpp | 4 scorematchingad-0.0.67/scorematchingad/src/exposemanifold.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapebdryweight.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapell.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapesmd.h | 3 33 files changed, 1317 insertions(+), 483 deletions(-)
More information about scorematchingad at CRAN
Permanent link
Title: Statistical Functions for the
Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of
Distributions
Description: Provides probability mass, distribution, quantile, random variate
generation, and method-of-moments parameter fitting for the MBBEFD family of
distributions used in insurance modeling as described in Bernegger (1997)
<doi:10.2143/AST.27.1.563208> without any external dependencies.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between MBBEFDLite versions 0.0.3 dated 2024-06-20 and 0.0.4 dated 2024-07-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 14 ++++++++++++++ inst/tinytest/test_package_metadata.R | 2 +- man/ecmb.Rd | 11 ++++++----- src/dmb.c | 5 +++-- src/ecmb.c | 2 +- 9 files changed, 37 insertions(+), 21 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 1.7.7.1 dated 2024-01-25 and 1.7.8.1 dated 2024-07-24
DESCRIPTION | 8 - MD5 | 34 +++---- build/vignette.rds |binary configure | 18 ++-- configure.ac | 2 inst/doc/discoverYourData.Rmd | 2 inst/doc/discoverYourData.html | 57 ++++++------ inst/doc/xgboost.Rnw | 10 +- inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.Rmd | 6 - inst/doc/xgboostPresentation.html | 21 ++-- inst/doc/xgboostfromJSON.html | 4 src/include/xgboost/parameter.h | 2 src/xgboost_R.cc | 169 ++++++++++++++++++-------------------- src/xgboost_R.h | 3 vignettes/discoverYourData.Rmd | 2 vignettes/xgboost.Rnw | 10 +- vignettes/xgboostPresentation.Rmd | 6 - 18 files changed, 178 insertions(+), 176 deletions(-)
Title: ROC Surface Analysis Under the Three-Class Problems
Description: Receiver Operating Characteristic (ROC) analysis is performed assuming samples are from the proposed distributions. In addition, the volume under the ROC surface and true positive fractions values are evaluated by ROC surface analysis.
Author: Ertan Akgenc [cre, aut, cph]
,
Coskun Kus [aut, ctb]
Maintainer: Ertan Akgenc <statistician.ertan@gmail.com>
Diff between ROCsurf versions 0.1.0 dated 2024-07-21 and 0.1.1 dated 2024-07-24
DESCRIPTION | 6 ++-- MD5 | 4 +- tests/testthat/testfunction.R | 60 +++++++++++++++++++++--------------------- 3 files changed, 35 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-19 1.9
2023-08-27 1.8
2023-07-07 1.7
2023-04-07 1.6
2023-01-30 1.5
2023-01-15 1.4
2022-10-23 1.3
2022-09-12 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-17 1.1.3
2023-04-27 1.1.2
2023-03-21 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-27 1.2
2024-01-10 1.1
2022-12-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-03 2.0.2.3.1
2023-09-05 2.0.2.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-12 2.0
2023-01-26 1.6
2022-07-21 1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-09 0.9
2024-04-06 0.8
2024-03-03 0.7
2023-12-03 0.6
2023-10-19 0.5
2023-10-01 0.4
2023-09-02 0.3
2023-08-08 0.2
2023-07-18 0.1
Title: Bayesian Cure Rate Modeling for Time-to-Event Data
Description: A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2023) <doi:10.48550/arXiv.2310.06926>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of Gamma distributions. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.
Author: Panagiotis Papastamoulis [aut, cre]
,
Fotios Milienos [aut]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between bayesCureRateModel versions 1.0 dated 2024-06-27 and 1.1 dated 2024-07-24
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 1 R/bayesian_cure_rate_model.R | 221 ++++++++++++++++++++++++++++++-------- build/partial.rdb |binary man/bayesCureRateModel-package.Rd | 3 man/cure_rate_MC3.Rd | 7 - man/plot.bayesCureModel.Rd | 10 + man/summary.bayesCureModel.Rd | 1 9 files changed, 203 insertions(+), 66 deletions(-)
More information about bayesCureRateModel at CRAN
Permanent link
Title: Analyzing the Behaviour of Wind Generated by Tropical Storms and
Cyclones
Description: Set of functions to quantify and map the
behaviour of winds generated by tropical storms and cyclones in space
and time. It includes functions to compute and analyze fields such as the maximum sustained wind field, power dissipation index and duration of exposure to winds above a given threshold. It also includes functions to map the trajectories as well as characteristics of the storms.
Author: Baptiste Delaporte [aut],
Thomas Ibanez [aut] ,
Gunnar Keppel [aut] ,
Swen Jullien [aut] ,
Christophe Menkes [aut] ,
Thomas Arsouze [aut, cre]
Maintainer: Thomas Arsouze <thomas.arsouze@cirad.fr>
Diff between StormR versions 0.1.1 dated 2023-11-24 and 0.2.1 dated 2024-07-24
StormR-0.1.1/StormR/man/getSSHS-methods.Rd |only StormR-0.2.1/StormR/DESCRIPTION | 12 StormR-0.2.1/StormR/MD5 | 90 StormR-0.2.1/StormR/NAMESPACE | 3 StormR-0.2.1/StormR/NEWS.md | 13 StormR-0.2.1/StormR/R/defStormsDataset.R | 571 - StormR-0.2.1/StormR/R/defStormsList.R | 194 StormR-0.2.1/StormR/R/plotBehaviour.R | 224 StormR-0.2.1/StormR/R/plotStorms.R | 245 StormR-0.2.1/StormR/R/plotTemporal.R |only StormR-0.2.1/StormR/R/spatialBehaviour.R | 206 StormR-0.2.1/StormR/R/sysdata.rda |binary StormR-0.2.1/StormR/R/temporalBehaviour.R | 50 StormR-0.2.1/StormR/README.md | 31 StormR-0.2.1/StormR/build/vignette.rds |binary StormR-0.2.1/StormR/inst/doc/Behaviour.html | 7 StormR-0.2.1/StormR/inst/doc/ExtractStorms.R | 38 StormR-0.2.1/StormR/inst/doc/ExtractStorms.Rmd | 70 StormR-0.2.1/StormR/inst/doc/ExtractStorms.html | 5324 +++++++++++- StormR-0.2.1/StormR/inst/doc/Models.html | 27 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.R | 5 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.Rmd | 13 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.html | 5269 +++++++++++ StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.R | 24 StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.Rmd | 26 StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.html | 72 StormR-0.2.1/StormR/inst/extdata/test_dataset.csv |only StormR-0.2.1/StormR/man/defStormsDataset.Rd | 35 StormR-0.2.1/StormR/man/defStormsList.Rd | 15 StormR-0.2.1/StormR/man/getScale-methods.Rd |only StormR-0.2.1/StormR/man/plotBehaviour.Rd | 12 StormR-0.2.1/StormR/man/plotStorms.Rd | 30 StormR-0.2.1/StormR/man/plotTemporal.Rd |only StormR-0.2.1/StormR/man/spatialBehaviour.Rd | 15 StormR-0.2.1/StormR/man/storm-class.Rd | 7 StormR-0.2.1/StormR/man/stormsDataset-class.Rd | 13 StormR-0.2.1/StormR/man/stormsList-class.Rd | 6 StormR-0.2.1/StormR/man/temporalBehaviour.Rd | 17 StormR-0.2.1/StormR/tests/testthat/test-plotBehaviour.R | 909 +- StormR-0.2.1/StormR/tests/testthat/test-plotStorms.R | 1013 +- StormR-0.2.1/StormR/tests/testthat/test-plotTemporal.R |only StormR-0.2.1/StormR/tests/testthat/test-spatialBehaviour.R | 423 StormR-0.2.1/StormR/tests/testthat/test-stormsDataset.R | 2019 ++-- StormR-0.2.1/StormR/tests/testthat/test-stormsList.R | 884 + StormR-0.2.1/StormR/tests/testthat/test-temporalBehaviour.R | 109 StormR-0.2.1/StormR/tests/testthat/test-writeRast.R | 2 StormR-0.2.1/StormR/vignettes/ExtractStorms.Rmd | 70 StormR-0.2.1/StormR/vignettes/SpatialBehaviour.Rmd | 13 StormR-0.2.1/StormR/vignettes/TemporalBehaviour.Rmd | 26 49 files changed, 15203 insertions(+), 2929 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Pius [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 1.0.7 dated 2023-11-16 and 1.0.8 dated 2024-07-24
DESCRIPTION | 8 +- MD5 | 55 +++++++------- NAMESPACE | 5 + NEWS.md | 13 +++ R/coefficient_plot.R | 29 +++++-- R/ff_label.R | 2 R/ff_newdata.R | 105 ++++++++++++++++++++++++++- R/ff_plot.R | 2 R/finalfit.R | 2 R/finalfit_internal_functions.R | 2 R/or_plot.R | 31 +++++--- README.md | 2 inst/doc/all_plots_examples.html | 10 +- inst/doc/all_tables_examples.R | 6 - inst/doc/all_tables_examples.Rmd | 6 - inst/doc/all_tables_examples.html | 94 ++++++++++++------------ inst/doc/bootstrap.R | 6 + inst/doc/bootstrap.Rmd | 16 +++- inst/doc/bootstrap.html | 147 +++++++++++++++++++++++--------------- inst/doc/survival.html | 8 +- man/coefficient_plot.Rd | 5 + man/ff_expand.Rd |only man/ff_mode.Rd |only man/ff_plot.Rd | 2 man/finalfit.Rd | 2 man/or_plot.Rd | 5 + man/summary_df.Rd |only tests/testthat/Rplots.pdf |binary vignettes/all_tables_examples.Rmd | 6 - vignettes/bootstrap.Rmd | 16 +++- 30 files changed, 403 insertions(+), 182 deletions(-)
Title: Analysis of fMRI Experiments
Description: Contains R-functions to perform an fMRI analysis as described in
Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>,
Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>,
Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Brandon Whitcher [ctb],
Dames Sibylle [ctb]
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between fmri versions 1.9.12 dated 2023-09-06 and 1.9.12.1 dated 2024-07-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/aws.r | 2 +- man/fmri.lmePar.Rd | 12 ++++++------ man/fmri.metaPar.Rd | 8 ++++---- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Michael D. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gr [...truncated...]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.13.2 dated 2024-02-12 and 0.14.0 dated 2024-07-24
DESCRIPTION | 30 ++++---- MD5 | 80 +++++++++++----------- NEWS.md | 29 +++++++- R/area_under_curve.R | 6 - R/bayesfactor_models.R | 36 ++++----- R/bayesfactor_parameters.R | 55 +++++++-------- R/check_prior.R | 42 ++++++----- R/contr.equalprior.R | 12 --- R/convert_bayesian_to_frequentist.R | 94 ++++++++++++++++---------- R/describe_posterior.R | 2 R/diagnostic_posterior.R | 14 +-- R/effective_sample.R | 14 ++- R/equivalence_test.R | 29 ++++---- R/estimate_density.R | 83 ++++++++++++---------- R/mediation.R | 7 - R/rope_range.R | 13 +++ R/sexit.R | 73 +++++++++++--------- R/si.R | 4 - R/simulate_data.R | 44 ++++++------ R/simulate_simpson.R | 6 - R/utils.R | 8 +- R/utils_bayesfactor.R | 8 +- R/weighted_posteriors.R | 12 +-- inst/WORDLIST | 12 --- man/bayesfactor_parameters.Rd | 6 + man/bayesfactor_restricted.Rd | 6 + man/check_prior.Rd | 38 +++++----- man/effective_sample.Rd | 7 + man/equivalence_test.Rd | 8 +- man/estimate_density.Rd | 18 ++-- man/mediation.Rd | 1 man/sexit.Rd | 41 ++++++----- man/si.Rd | 6 + man/simulate_correlation.Rd | 2 man/weighted_posteriors.Rd | 4 - tests/testthat/test-bayesian_as_frequentist.R | 77 +++++++++++++++++++-- tests/testthat/test-blavaan.R | 11 --- tests/testthat/test-check_prior.R | 4 - tests/testthat/test-describe_posterior.R | 20 +++-- tests/testthat/test-estimate_density.R | 18 ++-- tests/testthat/test-simulate_data.R | 2 41 files changed, 571 insertions(+), 411 deletions(-)
Title: Spatiotemporal Point Patterns Simulation
Description: Generates artificial point patterns marked by their
spatial and temporal signatures. The resulting point cloud
may exhibit inherent interactions between both signatures.
The simulation integrates microsimulation
(Holm, E., (2017)<doi:10.1002/9781118786352.wbieg0320>)
and agent-based models (Bonabeau, E., (2002)<doi:10.1073/pnas.082080899>),
beginning with the configuration of movement characteristics for
the specified agents (referred to as 'walkers') and their interactions
within the simulation environment. These interactions
(Quaglietta, L. and Porto, M., (2019)<doi:10.1186/s40462-019-0154-8>)
result in specific spatiotemporal patterns that can be visualized,
analyzed, and used for various analytical purposes.
Given the growing scarcity of detailed spatiotemporal data
across many domains, this package provides an alternative data source
for applications in social and life sciences.
Author: Monsuru Adepeju [cre, aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>
Diff between stppSim versions 1.3.2 dated 2023-10-29 and 1.3.4 dated 2024-07-24
DESCRIPTION | 34 +++++++++++++++++----------------- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/make_grids.R | 8 ++++---- inst/doc/stppSim-vignette.Rmd | 2 +- inst/doc/stppSim-vignette.html | 4 ++-- man/make_grids.Rd | 6 +++--- vignettes/stppSim-vignette.Rmd | 2 +- 8 files changed, 43 insertions(+), 35 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)
Author: Philip Leifeld [aut, cre],
Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between texreg versions 1.39.3 dated 2023-11-09 and 1.39.4 dated 2024-07-24
texreg-1.39.3/texreg/man/extract-Zelig-method.Rd |only texreg-1.39.3/texreg/man/extract-maBina-method.Rd |only texreg-1.39.3/texreg/man/extract-mnlogit-method.Rd |only texreg-1.39.4/texreg/DESCRIPTION | 34 - texreg-1.39.4/texreg/MD5 | 22 texreg-1.39.4/texreg/NAMESPACE | 1 texreg-1.39.4/texreg/R/extract.R | 585 +++--------------- texreg-1.39.4/texreg/R/texreg.R | 4 texreg-1.39.4/texreg/build/partial.rdb |binary texreg-1.39.4/texreg/build/vignette.rds |binary texreg-1.39.4/texreg/inst/doc/texreg.pdf |binary texreg-1.39.4/texreg/man/extract-remstimate-method.Rd |only texreg-1.39.4/texreg/man/texreg-package.Rd | 2 texreg-1.39.4/texreg/tests/testthat/test-extract.R | 89 ++ 14 files changed, 219 insertions(+), 518 deletions(-)
Title: How to Add Two R Tables
Description: Methods to "add" two R tables; also an alternative
interpretation of named vectors as generalized R tables, so that
c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses
'disordR' discipline (Hankin, 2022,
<doi:10.48550/arXiv.2210.03856>). Extraction and replacement
methods are provided. The underlying mathematical structure is
the Free Abelian group, hence the name. To cite in publications
please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between frab versions 0.0-5 dated 2024-06-21 and 0.0-6 dated 2024-07-24
frab-0.0-5/frab/inst/frab.bib |only frab-0.0-5/frab/inst/frab_arxiv.Rnw |only frab-0.0-5/frab/inst/read.me |only frab-0.0-6/frab/DESCRIPTION | 8 +++--- frab-0.0-6/frab/MD5 | 15 +++++------- frab-0.0-6/frab/NAMESPACE | 1 frab-0.0-6/frab/NEWS.md | 5 ++++ frab-0.0-6/frab/R/frab.R | 3 +- frab-0.0-6/frab/build/partial.rdb |binary frab-0.0-6/frab/vignettes/frab.bib | 43 ++++++++++++++++++++++++++++++++++++ 10 files changed, 60 insertions(+), 15 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.0.0 dated 2024-06-28 and 1.0.1 dated 2024-07-24
DESCRIPTION | 8 - MD5 | 26 +-- NEWS.md | 4 R/OptimInstanceAsyncMultiCrit.R | 6 R/OptimInstanceAsyncSingleCrit.R | 4 R/OptimInstanceBatchMultiCrit.R | 4 R/OptimInstanceBatchSingleCrit.R | 4 R/Optimizer.R | 6 R/OptimizerBatchFocusSearch.R | 2 inst/doc/bbotk.html | 240 ++++++++++++++++++------------------ man/OptimInstanceAsyncMultiCrit.Rd | 5 man/OptimInstanceAsyncSingleCrit.Rd | 5 man/OptimInstanceBatchMultiCrit.Rd | 5 man/OptimInstanceBatchSingleCrit.Rd | 5 14 files changed, 176 insertions(+), 148 deletions(-)
Title: Create Visualisations for BART Models
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut],
Claus Wilke [ctb]
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Diff between bartMan versions 0.1.0 dated 2024-04-15 and 0.1.1 dated 2024-07-24
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 2 R/bartDiag.R | 6 + R/mdsBart.R | 4 R/vimpBart.R | 3 R/viviBartMatrix.R | 252 ++++++++++++++++++++++++++++--------------------- R/viviBartPlot.R | 11 ++ README.md | 8 + man/bivariate_scale.Rd | 9 - 10 files changed, 190 insertions(+), 129 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph]
,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.1.1 dated 2023-09-29 and 1.1.2 dated 2024-07-24
DESCRIPTION | 12 MD5 | 32 +- NEWS.md | 4 R/data.R | 8 README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_usage.html | 62 ++-- inst/doc/data_formatting.html | 4 inst/doc/interactions.html | 22 - inst/doc/mnl_models.html | 72 ++--- inst/doc/mnl_models_weighted.html | 116 ++++----- inst/doc/mxl_models.html | 18 - inst/doc/summarizing_results.html | 478 +++++++++++++++++++------------------- man/apolloModeChoiceData.Rd | 2 man/electricity.Rd | 2 man/runtimes.Rd | 4 17 files changed, 430 insertions(+), 407 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-638 dated 2022-09-01 and 0.1-639 dated 2024-07-24
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ inst/CITATION | 32 +++++++++++++++++--------------- inst/doc/CheddarQuickstart.pdf |binary inst/doc/Collections.pdf |binary inst/doc/Community.pdf |binary inst/doc/ImportExport.pdf |binary inst/doc/PlotsAndStats.pdf |binary man/LoadCollection.Rd | 2 +- man/ShortestPaths.Rd | 3 ++- man/TL84.Rd | 2 +- man/YthanEstuary.Rd | 5 +++-- man/cheddar.Rd | 4 ++-- 13 files changed, 42 insertions(+), 38 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.1.1 dated 2024-06-05 and 1.2.0 dated 2024-07-24
DESCRIPTION | 16 +++--- MD5 | 58 ++++++++++++------------ NEWS.md | 12 ++++- R/compression.R | 25 +++++----- R/export.R | 4 - R/export_methods.R | 10 ++-- R/extensions.R | 2 R/gather_attrs.R | 4 - R/import.R | 3 - R/import_list.R | 3 - R/import_methods.R | 18 +++---- R/onLoad.R | 2 R/remote_to_local.R | 6 +- R/standardize_attributes.R | 4 - R/sysdata.rda |binary R/utils.R | 5 +- README.md | 93 +++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/labelled.html | 22 ++++----- inst/doc/remap.R | 5 -- inst/doc/rio.R | 2 inst/doc/rio.html | 64 +++++++++++++++----------- man/export.Rd | 2 man/import.Rd | 2 man/rio.Rd | 1 tests/testthat/test_check_file.R | 4 + tests/testthat/test_compress.R | 21 ++++++++ tests/testthat/test_format_csv.R | 10 ++++ vignettes/remap.Rmd | 2 vignettes/rio.Rmd | 2 30 files changed, 227 insertions(+), 175 deletions(-)
Title: Parameter Space Partitioning MCMC for Global Model Evaluation
Description: Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.
Author: Lenard Dome [aut, cre],
Andy Wills [aut]
Maintainer: Lenard Dome <lenarddome@gmail.com>
Diff between psp versions 1.0.0 dated 2023-08-16 and 1.0.2 dated 2024-07-24
DESCRIPTION | 8 ++-- MD5 | 9 ++--- build |only man/psp.Rd | 2 - man/pspGlobal.Rd | 93 +++++++++++++++++++++++------------------------------- src/pspGlobal.cpp | 4 +- 6 files changed, 54 insertions(+), 62 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 2.1.24 dated 2024-02-28 and 2.1.25 dated 2024-07-24
DESCRIPTION | 8 ++-- MD5 | 60 ++++++++++++++++++------------------- R/byIndv4Times.r | 7 ++++ R/traitSmooth.r | 2 + build/partial.rdb |binary build/vignette.rds |binary inst/News.Rd | 5 +++ inst/doc/Rice.pdf |binary inst/doc/Tomato.pdf |binary inst/doc/growthPheno-manual.pdf |binary man/args4chosen_plot.Rd | 12 +++---- man/args4devnboxes_plot.Rd | 16 ++++----- man/args4meddevn_plot.Rd | 17 +++++----- man/args4profile_plot.Rd | 16 ++++----- man/byIndv4Times_GRsDiff.Rd | 5 +++ man/plotAnom.Rd | 2 - man/plotCorrmatrix.Rd | 17 +++++----- man/plotDeviationsBoxes.Rd | 21 ++++++------ man/plotImagetimes.Rd | 13 ++++---- man/plotLongitudinal.Rd | 21 ++++++------ man/plotMedianDeviations.Rd | 21 ++++++------ man/plotProfiles.Rd | 21 ++++++------ man/plotSmoothsComparison.Rd | 12 +++---- man/plotSmoothsDevnBoxplots.Rd | 10 +++--- man/plotSmoothsMedianDevns.Rd | 4 +- man/probeSmoothing.Rd | 22 ++++++------- man/probeSmooths.Rd | 4 +- man/traitSmooth.Rd | 2 - tests/testthat/testProbeSmooths.r | 6 +-- tests/testthat/testTraitWrappers.r | 8 ++-- tests/testthat/testexampleData.r | 4 +- 31 files changed, 181 insertions(+), 155 deletions(-)
Title: Mediterranean Landscape Simulation
Description: Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.
Author: Miquel De Caceres [aut, cre],
Aitor Ameztegui [aut] ,
Maria Gonzalez [aut] ,
Nuria Aquilue [aut],
Daniel Caviedes-Voullieme [aut],
Mario Morales-Hernandez [aut],
Mario Beltran [ctb],
Rodrigo Balaguer-Romano [ctb] ,
Roberto Molowny-Horas [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfateland versions 2.4.3 dated 2024-06-02 and 2.4.5 dated 2024-07-24
DESCRIPTION | 17 +++--- MD5 | 98 +++++++++++++++++------------------ NAMESPACE | 1 R/add_forests.R | 14 ++--- R/add_soilgrids.R | 8 +- R/add_topography.R | 10 +-- R/create_management_scenario.R | 4 - R/dataset_documentation.R | 10 +-- R/default_volume_function.R | 2 R/dispersal.R | 9 +-- R/extract_variables.R | 10 +-- R/fire_regime_instance.R | 4 - R/fordyn_scenario.R | 18 +++--- R/impute_forests.R | 84 ++++++++++++++++++------------ R/initialize_landscape.R | 26 +++++---- R/landscape_summary.R | 10 +-- R/medfateland-package.R | 5 + R/model_land.R | 55 ++++++++++--------- R/model_spatial.R | 26 ++++----- R/model_spatial_day.R | 12 ++-- R/parse_forestable.R |only R/plot_summary.R | 6 +- R/shinyplot_land.R | 8 +- R/simulation_summary.R | 6 +- R/sysdata.rda |binary R/update_landscape.R | 4 - man/add_forests.Rd | 15 +++-- man/add_topography.Rd | 10 +-- man/create_management_scenario.Rd | 4 - man/defaultPrescriptionsBySpecies.Rd | 4 - man/default_volume_function.Rd | 2 man/dispersal.Rd | 8 +- man/example_ifn.Rd | 2 man/example_watershed.Rd | 4 - man/extract_variables.Rd | 10 +-- man/fire_regime_instance.Rd | 4 - man/fordyn_scenario.Rd | 18 +++--- man/forest_parametrization.Rd | 41 ++++++++------ man/initialize_landscape.Rd | 26 +++++---- man/landscape_summary.Rd | 10 +-- man/medfateland-package.Rd | 5 + man/parse_forestable.Rd |only man/plot_summary.Rd | 6 +- man/shinyplot_land.Rd | 8 +- man/simulation_summary.Rd | 6 +- man/soil_parametrization.Rd | 8 +- man/spwb_land.Rd | 41 +++++++------- man/spwb_land_day.Rd | 14 ++--- man/spwb_spatial.Rd | 26 ++++----- man/spwb_spatial_day.Rd | 12 ++-- man/update_landscape.Rd | 4 - 51 files changed, 400 insertions(+), 335 deletions(-)
Title: Compact Standard for Australian Phone Numbers
Description: Phone numbers are often represented as strings because there
is no obvious and suitable native representation for them. This leads
to high memory use and a lack of standard representation. The package
provides integer representation of Australian phone numbers with optional
raw vector calling code. The package name is an extension of 'au' and 'ph'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between dauphin versions 0.3.1 dated 2023-11-28 and 0.3.2 dated 2024-07-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/CMobileCleaning.c | 8 ++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.39 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.3.0 dated 2024-02-17 and 1.3.4 dated 2024-07-24
DESCRIPTION | 16 - MD5 | 42 +- NAMESPACE | 3 R/ReadConQuestState_createDF.R | 4 R/conquestr.R | 10 R/conquestrFunc.R | 80 ++--- R/generateHelpers.R | 65 +++- R/itanalHelpers.R | 6 R/plotRout.R | 45 +++ build/vignette.rds |binary inst/doc/data-cleaning-functions-in-conquestr.html | 40 +- inst/doc/generateResponses.html | 59 ++- inst/doc/intro-to-conquestr.html | 312 ++++++++++----------- inst/doc/itanal-in-conquestr.html | 40 +- inst/doc/plotting.html | 16 - inst/doc/responseProbs.html | 6 inst/doc/test_item_review_sheet_markdown.html | 34 +- inst/extdata/myicc.rout |binary inst/extdata/mysysfile.cqs |binary man/genResponses.Rd | 17 - man/plotRout.Rd | 3 man/transformPvs.Rd | 18 - 22 files changed, 458 insertions(+), 358 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen , Terry Leitch
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.22 dated 2024-04-25 and 0.4.23 dated 2024-07-23
ChangeLog | 59 +++++++ DESCRIPTION | 8 - MD5 | 40 ++--- README.md | 8 - configure | 18 +- configure.ac | 2 data/tsQuotes.RData |binary data/vcube.RData |binary inst/include/rquantlib_internal.h | 15 +- inst/tinytest/test_options.R | 1 src/affine.cpp | 72 ++++----- src/asian.cpp | 63 +++----- src/barrier_binary.cpp | 158 +++++++-------------- src/bermudan.cpp | 181 +++++++++++------------- src/bonds.cpp | 177 +++++++++-------------- src/discount.cpp | 15 -- src/hullwhite.cpp | 39 ++--- src/implieds.cpp | 82 +++-------- src/utils.cpp | 282 ++++++++++++++++++-------------------- src/vanilla.cpp | 186 ++++++++----------------- src/zero.cpp | 19 +- 21 files changed, 632 insertions(+), 793 deletions(-)
Title: Decision Curve Analysis for Model Evaluation
Description: Diagnostic and prognostic models are typically evaluated with
measures of accuracy that do not address clinical consequences.
Decision-analytic techniques allow assessment of clinical outcomes,
but often require collection of additional information may be
cumbersome to apply to models that yield a continuous result. Decision
curve analysis is a method for evaluating and comparing prediction
models that incorporates clinical consequences, requires only the data
set on which the models are tested, and can be applied to models that
have either continuous or dichotomous results. See the following references
for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>,
Vickers (2008) <doi:10.1186/1472-6947-8-53>,
and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.
Author: Daniel D. Sjoberg [aut, cre, cph]
,
Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between dcurves versions 0.4.0 dated 2022-12-23 and 0.5.0 dated 2024-07-23
DESCRIPTION | 18 LICENSE | 4 MD5 | 86 NAMESPACE | 78 NEWS.md | 4 R/as_tibble.R | 32 R/data.r | 88 R/dca.r | 525 ++-- R/dcurves-package.R | 28 R/net_intervention_avoided.R | 107 R/plot.R | 316 +- R/print.R | 52 R/reexport.R | 94 R/standardize_net_benefit.R | 63 R/test_consequences.R | 624 ++-- README.md | 206 - build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 56 inst/doc/dca.R | 296 +- inst/doc/dca.Rmd | 702 ++--- inst/doc/dca.html | 3209 ++++++++++++------------- man/as_tibble.dca.Rd | 58 man/dca.Rd | 202 - man/dcurves-package.Rd | 58 man/df_binary.Rd | 52 man/df_case_control.Rd | 50 man/df_surv.Rd | 54 man/net_intervention_avoided.Rd | 78 man/plot.dca.Rd | 128 man/print.dca.Rd | 48 man/reexports.Rd | 64 man/standardized_net_benefit.Rd | 54 man/test_consequences.Rd | 142 - tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-as_tibble.R | 16 tests/testthat/test-dca.R | 250 - tests/testthat/test-net_intervention_avoided.R | 40 tests/testthat/test-plot.R | 102 tests/testthat/test-standardize_net_benefit.R | 52 tests/testthat/test-test_consequences.R | 90 vignettes/dca.Rmd | 702 ++--- vignettes/references.bib | 64 44 files changed, 4501 insertions(+), 4405 deletions(-)
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.2.4 dated 2024-07-01 and 0.3.0 dated 2024-07-23
DESCRIPTION | 8 MD5 | 81 - NAMESPACE | 5 NEWS.md | 7 R/bivariate.R |only R/caterpillar.R |only R/density.R |only R/diagnostic_plots.R |only R/envelope.R |only R/jagshelper1.R | 2006 -------------------------------------- R/summarize.R |only R/trace.R |only README.md | 9 inst/doc/jagshelper-vignette.R | 25 inst/doc/jagshelper-vignette.Rmd | 45 inst/doc/jagshelper-vignette.html | 66 + man/caterpillar.Rd | 4 man/chaindens_df.Rd | 2 man/chaindens_jags.Rd | 2 man/chaindens_line.Rd | 2 man/check_Rhat.Rd | 2 man/check_neff.Rd | 2 man/comparecat.Rd | 4 man/comparedens.Rd | 2 man/comparepriors.Rd | 2 man/cor_jags.Rd | 2 man/crossplot.Rd |only man/envelope.Rd | 2 man/jagshelper-package.Rd | 8 man/nbyname.Rd | 2 man/nparam.Rd | 2 man/overlayenvelope.Rd | 4 man/pairstrace_jags.Rd | 4 man/plotRhats.Rd | 4 man/plot_postpred.Rd |only man/plotcor_jags.Rd | 2 man/plotdens.Rd | 2 man/qq_postpred.Rd | 4 man/trace_df.Rd | 2 man/trace_jags.Rd | 2 man/trace_line.Rd | 2 man/tracedens_jags.Rd | 2 man/traceworstRhat.Rd | 4 man/ts_postpred.Rd | 11 tests/testthat/test_jagshelper.R | 72 + vignettes/jagshelper-vignette.Rmd | 45 46 files changed, 359 insertions(+), 2091 deletions(-)
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
R package for matching 'HTTP' requests by various rules ('HTTP' method,
'URL', query parameters, headers, body, etc.), and then caching
real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
matching any previous requests in the same 'cassette' use a cached
'HTTP' response.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [aut] ,
Maelle Salmon [aut] ,
Daniel Possenriede [aut] ,
rOpenSci [fnd]
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between vcr versions 1.2.2 dated 2023-06-25 and 1.6.0 dated 2024-07-23
vcr-1.2.2/vcr/man/vcr.Rd |only vcr-1.6.0/vcr/DESCRIPTION | 19 +- vcr-1.6.0/vcr/MD5 | 118 +++++++-------- vcr-1.6.0/vcr/NAMESPACE | 3 vcr-1.6.0/vcr/NEWS.md | 20 ++ vcr-1.6.0/vcr/R/cassette_class.R | 35 +++- vcr-1.6.0/vcr/R/errors.R | 5 vcr-1.6.0/vcr/R/http_interaction.R | 2 vcr-1.6.0/vcr/R/http_interaction_list.R | 2 vcr-1.6.0/vcr/R/http_interactions.R | 2 vcr-1.6.0/vcr/R/insert_cassette.R | 2 vcr-1.6.0/vcr/R/lightswitch.R | 4 vcr-1.6.0/vcr/R/request_class.R | 15 + vcr-1.6.0/vcr/R/request_handler-crul.R | 2 vcr-1.6.0/vcr/R/request_handler-httr.R | 2 vcr-1.6.0/vcr/R/request_handler-httr2.R |only vcr-1.6.0/vcr/R/request_response.R | 2 vcr-1.6.0/vcr/R/serialize_to_httr2.R |only vcr-1.6.0/vcr/R/use_cassette.R | 6 vcr-1.6.0/vcr/R/vcr-package.R | 26 +-- vcr-1.6.0/vcr/R/vcr_setup.R | 2 vcr-1.6.0/vcr/build/vignette.rds |binary vcr-1.6.0/vcr/inst/doc/cassette-manual-editing.R | 2 vcr-1.6.0/vcr/inst/doc/cassette-manual-editing.html | 16 +- vcr-1.6.0/vcr/inst/doc/configuration.html | 23 +- vcr-1.6.0/vcr/inst/doc/debugging.R | 2 vcr-1.6.0/vcr/inst/doc/debugging.html | 4 vcr-1.6.0/vcr/inst/doc/design.R | 2 vcr-1.6.0/vcr/inst/doc/design.html | 11 - vcr-1.6.0/vcr/inst/doc/internals.R | 2 vcr-1.6.0/vcr/inst/doc/internals.html | 19 +- vcr-1.6.0/vcr/inst/doc/lightswitch.R | 4 vcr-1.6.0/vcr/inst/doc/lightswitch.html | 4 vcr-1.6.0/vcr/inst/doc/record-modes.html | 4 vcr-1.6.0/vcr/inst/doc/request_matching.html | 4 vcr-1.6.0/vcr/inst/doc/vcr.R | 8 - vcr-1.6.0/vcr/inst/doc/vcr.Rmd | 2 vcr-1.6.0/vcr/inst/doc/vcr.html | 8 - vcr-1.6.0/vcr/inst/doc/write-to-disk.html | 10 - vcr-1.6.0/vcr/man/Cassette.Rd | 8 - vcr-1.6.0/vcr/man/HTTPInteraction.Rd | 2 vcr-1.6.0/vcr/man/HTTPInteractionList.Rd | 2 vcr-1.6.0/vcr/man/Request.Rd | 24 ++- vcr-1.6.0/vcr/man/RequestHandlerCrul.Rd | 2 vcr-1.6.0/vcr/man/RequestHandlerHttr.Rd | 2 vcr-1.6.0/vcr/man/RequestHandlerHttr2.Rd |only vcr-1.6.0/vcr/man/UnhandledHTTPRequestError.Rd | 4 vcr-1.6.0/vcr/man/http_interactions.Rd | 2 vcr-1.6.0/vcr/man/insert_cassette.Rd | 2 vcr-1.6.0/vcr/man/lightswitch.Rd | 4 vcr-1.6.0/vcr/man/request_response.Rd | 2 vcr-1.6.0/vcr/man/rmdhunks/cassette-editing-vignette.Rmd | 12 - vcr-1.6.0/vcr/man/rmdhunks/configuration-vignette.Rmd | 8 - vcr-1.6.0/vcr/man/rmdhunks/internals-vignette.Rmd | 2 vcr-1.6.0/vcr/man/rmdhunks/vcr-design.Rmd | 10 - vcr-1.6.0/vcr/man/use_cassette.Rd | 6 vcr-1.6.0/vcr/man/vcr-package.Rd |only vcr-1.6.0/vcr/tests/testthat/helper-vcr.R | 36 +++- vcr-1.6.0/vcr/tests/testthat/httr2_obj.rda |only vcr-1.6.0/vcr/tests/testthat/test-ause_cassette.R | 8 - vcr-1.6.0/vcr/tests/testthat/test-httr2.R |only vcr-1.6.0/vcr/tests/testthat/test-localhost_port.R |only vcr-1.6.0/vcr/tests/testthat/test-request_summary.R | 8 - vcr-1.6.0/vcr/vignettes/vcr.Rmd | 2 64 files changed, 312 insertions(+), 226 deletions(-)
Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit
conversion and formatting of Global Surface Summary of the Day
('GSOD') weather data from the from the USA National Centers for
Environmental Information ('NCEI'). Units are converted from from
United States Customary System ('USCS') units to International System
of Units ('SI'). Stations may be individually checked for number of
missing days defined by the user, where stations with too many missing
observations are omitted. Only stations with valid reported latitude
and longitude values are permitted in the final data. Additional
useful elements, saturation vapour pressure ('es'), actual vapour
pressure ('ea') and relative humidity ('RH') are calculated from the
original data using the improved August-Roche-Magnus approximation
(Alduchov & Eskridge 1996) and included in the final data set. The
resulting metadata include station identification information,
country, state, latitude, longitude, elevation, weather observatio [...truncated...]
Author: Adam H. Sparks [aut, cre] ,
Tomislav Hengl [aut] ,
Andrew Nelson [aut] ,
Hugh Parsonage [cph, ctb] ,
Taras Kaduk [ctb] ,
Gwenael Giboire [ctb] ,
Lukasz Pawlik [ctb] ,
Ross Darnell [ctb] ,
Tyler Widdison [ctb] ` did not
return stations in order of nea [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 4.1.0 dated 2024-07-21 and 4.1.1 dated 2024-07-23
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 13 +++ R/globals.R | 1 R/process_csv.R | 2 README.md | 14 ++-- inst/doc/GSODR.Rmd | 180 ++++++++++++++++++++++++++++------------------------ inst/doc/GSODR.html | 180 ++++++++++++++++++++++++++++------------------------ vignettes/GSODR.Rmd | 180 ++++++++++++++++++++++++++++------------------------ 9 files changed, 332 insertions(+), 260 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.3.0 dated 2024-02-21 and 0.4.0 dated 2024-07-23
DESCRIPTION | 18 LICENSE | 4 MD5 | 176 - NAMESPACE | 12 NEWS.md | 264 +- R/altdoc_variables.R | 108 R/check.R | 110 R/freeze.R | 128 - R/import_man.R | 430 +-- R/import_misc.R | 301 +- R/import_readme.R | 212 - R/import_vignettes.R | 476 ++-- R/preview_docs.R | 58 R/qmd2md.R | 99 R/rd2qmd.R | 203 - R/render_docs.R | 228 +- R/settings.R | 122 - R/settings_docsify.R | 176 - R/settings_docute.R | 186 - R/settings_mkdocs.R | 334 +- R/settings_quarto_website.R | 271 +- R/setup_docs.R | 369 +-- R/setup_github_actions.R | 95 R/utils.R | 384 +-- README.md | 473 ++-- build/vignette.rds |binary inst/WORDLIST | 71 inst/doc/get-started.R | 6 inst/doc/get-started.Rmd | 390 +-- inst/doc/get-started.html | 1132 +++++----- inst/docsify/docsify.html | 90 inst/docsify/docsify.md | 18 inst/docute/docute.html | 104 inst/gha/altdoc.yaml | 146 - inst/mkdocs/mkdocs.yml | 80 inst/preamble/preamble_man_qmd.yml | 12 inst/preamble/preamble_vignettes_qmd.yml | 12 inst/preamble/preamble_vignettes_rmd.yml | 8 inst/quarto_website/quarto_website.yml | 77 man/preview_docs.Rd | 62 man/render_docs.Rd | 218 + man/setup_docs.Rd | 168 - man/setup_github_actions.Rd | 50 tests/spelling.R | 12 tests/testthat.R | 8 tests/testthat/_snaps/docsify/render_docs.md | 153 + tests/testthat/_snaps/docute/render_docs.md | 133 + tests/testthat/_snaps/mkdocs/render_docs.md | 43 tests/testthat/examples/examples-man/between.Rd | 36 tests/testthat/examples/examples-man/between.md | 80 tests/testthat/examples/examples-man/is-internal.Rd | 36 tests/testthat/examples/examples-man/should-fail.Rd | 34 tests/testthat/examples/examples-qmd/with-preamble.qmd | 26 tests/testthat/examples/examples-qmd/without-preamble.qmd | 16 tests/testthat/examples/examples-vignettes/basic.Rmd | 36 tests/testthat/examples/examples-vignettes/several-outputs.Rmd | 48 tests/testthat/examples/examples-vignettes/with-figure.Rmd | 50 tests/testthat/examples/examples-yaml/basic.Rmd | 20 tests/testthat/examples/examples-yaml/options.Rmd | 28 tests/testthat/examples/examples-yaml/several-outputs.Rmd | 32 tests/testthat/examples/testpkg.altdoc/DESCRIPTION | 32 tests/testthat/examples/testpkg.altdoc/NAMESPACE | 12 tests/testthat/examples/testpkg.altdoc/NEWS.md | 18 tests/testthat/examples/testpkg.altdoc/R/examplesIf_false.R |only tests/testthat/examples/testpkg.altdoc/R/examplesIf_true.R |only tests/testthat/examples/testpkg.altdoc/R/hello_base.R | 40 tests/testthat/examples/testpkg.altdoc/R/hello_r6.R | 60 tests/testthat/examples/testpkg.altdoc/README.Rmd | 82 tests/testthat/examples/testpkg.altdoc/README.md | 72 tests/testthat/examples/testpkg.altdoc/man/examplesIf_false.Rd |only tests/testthat/examples/testpkg.altdoc/man/examplesIf_true.Rd |only tests/testthat/examples/testpkg.altdoc/man/hello_base.Rd | 65 tests/testthat/examples/testpkg.altdoc/man/hello_r6.Rd | 178 - tests/testthat/examples/testpkg.altdoc/vignettes/test.Rmd | 42 tests/testthat/helper.R | 174 - tests/testthat/test-check_md_structure.R | 60 tests/testthat/test-freeze.R | 46 tests/testthat/test-import_man.R | 110 tests/testthat/test-parallel.R | 18 tests/testthat/test-preview_docs.R | 26 tests/testthat/test-qmd2md.R | 72 tests/testthat/test-rd2qmd.R | 62 tests/testthat/test-render_docs.R | 350 +-- tests/testthat/test-settings.R | 34 tests/testthat/test-setup_docs.R | 124 - tests/testthat/test-setup_github_actions.R | 62 tests/testthat/test-update.R | 240 +- tests/testthat/test-utils.R | 116 - vignettes/customize.qmd | 546 ++-- vignettes/deploy.qmd | 176 - vignettes/get-started.Rmd | 390 +-- 91 files changed, 6158 insertions(+), 5721 deletions(-)
Title: Young Tableaux
Description: Deals with Young tableaux (field of combinatorics). For standard
Young tabeaux, performs enumeration, counting, random generation, the
Robinson-Schensted correspondence, and conversion to and from paths on
the Young lattice. Also performs enumeration and counting of
semistandard Young tableaux, enumeration of skew semistandard Young
tableaux, enumeration of Gelfand-Tsetlin patterns, and computation of
Kostka numbers.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between syt versions 0.4.0 dated 2024-04-23 and 0.5.0 dated 2024-07-23
DESCRIPTION | 11 - MD5 | 106 ++++++---- NAMESPACE | 10 + NEWS.md | 28 ++ R/GelfandTsetlin.R |only R/Kostka.R | 280 ++++++++++++++++++++++++++++- R/RSK.R | 4 R/enumeration.R | 26 +- R/hooks.R | 14 - R/internal.R | 87 ++++++++- R/isSYT.R | 4 R/plancherel.R | 8 R/randomsyt.R | 2 R/skewGelfandTsetlin.R |only R/skewKostkaNumbers.R |only R/skewTableaux.R | 38 +++ R/ssyt.R | 25 ++ R/syt2matrix.R | 10 - R/syt2path.R | 8 R/tableaux.R | 4 man/GelfandTsetlinPatterns.Rd |only man/KostkaNumber.Rd | 76 ++++--- man/KostkaNumbers.Rd |only man/KostkaNumbersWithGivenLambda.Rd |only man/KostkaNumbersWithGivenMu.Rd |only man/RS.Rd | 2 man/all_ssSkewTableaux.Rd | 60 +++--- man/all_ssytx.Rd | 55 +++-- man/all_sytx.Rd | 2 man/count_ssytx.Rd | 53 ++--- man/count_sytx.Rd | 6 man/dualSkewTableau.Rd | 44 ++-- man/firstsyt.Rd | 2 man/gprocess2syt.Rd | 2 man/hooklengths.Rd | 4 man/hooks.Rd | 4 man/isSSYT.Rd | 2 man/isSYT.Rd | 2 man/isSemistandardSkewTableau.Rd | 42 ++-- man/isSkewTableau.Rd | 42 ++-- man/isStandardSkewTableau.Rd | 42 ++-- man/matrix2syt.Rd | 2 man/nextsyt.Rd | 4 man/prettyGT.Rd |only man/prettySkewTableau.Rd | 42 ++-- man/prettyTableau.Rd | 42 ++-- man/rgprocess.Rd | 4 man/rsyt.Rd | 2 man/skewGelfandTsetlinPatterns.Rd |only man/skewKostkaNumbers.Rd |only man/skewTableauxWithGivenShapeAndWeight.Rd |only man/ssytx_withGivenShapeAndWeight.Rd |only man/syt2gprocess.Rd | 6 man/syt2matrix.Rd | 4 man/tableau2matrix.Rd | 4 man/tableauShape.Rd | 4 tests/testthat/helper-00.R |only tests/testthat/test-Gelfand-Tsetlin.R |only tests/testthat/test-Kostka.R | 34 +++ tests/testthat/test-skewTableaux.R | 27 ++ tests/testthat/test-ssyt.R | 27 ++ 61 files changed, 941 insertions(+), 366 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.6 dated 2024-07-23 and 4.2.6.1 dated 2024-07-23
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/Formatting.html | 4 ++-- inst/doc/Introduction.html | 4 ++-- tests/testthat/test-writeData.R | 7 ++----- 5 files changed, 15 insertions(+), 18 deletions(-)
Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between DIDmultiplegtDYN versions 1.0.13 dated 2024-06-28 and 1.0.15 dated 2024-07-23
DESCRIPTION | 12 ++--- MD5 | 14 +++--- NEWS.md | 4 + R/did_multiplegt_dyn.R | 2 R/did_multiplegt_dyn_by_check.R | 2 R/did_multiplegt_dyn_design.R | 2 R/did_multiplegt_main.R | 84 +++++++++++++++++++++++++++++++++++++--- R/print.R | 4 + 8 files changed, 103 insertions(+), 21 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] ,
Laurent Coron [aut] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.3.2 dated 2023-07-12 and 0.3.3 dated 2024-07-23
DESCRIPTION | 8 MD5 | 93 +- NAMESPACE | 10 NEWS.md | 19 R/ShinyGR.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 42 - inst/ShinyGR/server.R | 48 - inst/ShinyGR/ui.R | 4 inst/ShinyGR/www/tab_about.rmd |only inst/ShinyGR/www/tab_authors.rmd |only inst/ShinyGR/www/tab_fun.rmd |only inst/doc/get_started.R | 30 inst/doc/get_started.html | 145 ++-- inst/doc/v00_teaching_hydrology.R | 68 +- inst/doc/v00_teaching_hydrology.html | 1028 +++++++++++++++---------------- inst/doc/v00_teaching_hydrology.rmd | 48 - inst/doc/v01_EN_flow_reconstruction.R | 54 - inst/doc/v01_EN_flow_reconstruction.html | 350 +++++----- inst/doc/v01_EN_flow_reconstruction.rmd | 14 inst/doc/v01_FR_flow_reconstruction.R | 54 - inst/doc/v01_FR_flow_reconstruction.html | 332 ++++------ inst/doc/v01_FR_flow_reconstruction.rmd | 6 inst/doc/v02_EN_flow_forecasting.R | 126 +-- inst/doc/v02_EN_flow_forecasting.html | 532 +++++++--------- inst/doc/v02_EN_flow_forecasting.rmd | 22 inst/doc/v02_FR_flow_forecasting.R | 126 +-- inst/doc/v02_FR_flow_forecasting.html | 516 +++++++-------- inst/doc/v02_FR_flow_forecasting.rmd | 12 inst/doc/v03_EN_impact_CC_flow.R | 58 - inst/doc/v03_EN_impact_CC_flow.html | 488 +++++++------- inst/doc/v03_EN_impact_CC_flow.rmd | 20 inst/doc/v03_FR_impact_CC_flow.R | 58 - inst/doc/v03_FR_impact_CC_flow.html | 478 +++++++------- inst/doc/v03_FR_impact_CC_flow.rmd | 14 man/ShinyGR.Rd | 4 man/SimGR.Rd | 2 man/airGRteaching.Rd | 2 tests/testthat/test-plot.R | 2 vignettes/V00_airGRteaching_ref.bib | 3 vignettes/v00_teaching_hydrology.rmd | 48 - vignettes/v01_EN_flow_reconstruction.rmd | 14 vignettes/v01_FR_flow_reconstruction.rmd | 6 vignettes/v02_EN_flow_forecasting.rmd | 22 vignettes/v02_FR_flow_forecasting.rmd | 12 vignettes/v03_EN_impact_CC_flow.rmd | 20 vignettes/v03_FR_impact_CC_flow.rmd | 14 49 files changed, 2462 insertions(+), 2496 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre] ,
Stefan Voigt [aut] ,
Patrick Weiss [aut]
Maintainer: Christoph Scheuch <christoph.scheuch@gmail.com>
Diff between tidyfinance versions 0.2.1 dated 2024-07-03 and 0.3.0 dated 2024-07-23
DESCRIPTION | 55 ++-- MD5 | 119 +++++----- NAMESPACE | 21 - NEWS.md | 23 ++ R/assign_portfolio.R | 13 - R/check_if_package_installed.R | 6 R/check_supported_type.R | 6 R/create_summary_statistics.R | 38 +-- R/create_wrds_dummy_database.R | 15 - R/disconnect_connection.R | 7 R/download_data.R | 16 - R/download_data_factors.R | 120 ++++++---- R/download_data_macro_predictors.R | 46 ++-- R/download_data_stocks.R |only R/download_data_wrds.R | 13 - R/download_data_wrds_ccm_links.R | 15 - R/download_data_wrds_clean_trace.R | 70 +++--- R/download_data_wrds_compustat.R | 94 ++++++-- R/download_data_wrds_crsp.R | 184 +++++++++------- R/download_data_wrds_fisd.R | 32 +- R/estimate_model.R | 13 - R/get_wrds_connection.R | 25 -- R/global_variables.R | 5 R/list_supported_types.R | 378 ++++++++++++++++++++++++++++++++-- R/list_tidy_finance_chapters.R | 11 R/open_tidy_finance_website.R | 13 - R/set_wrds_credentials.R | 5 R/tidyfinance-package.R | 5 R/trim.R | 7 R/winsorize.R | 11 README.md | 7 build/vignette.rds |binary inst/doc/dates-in-tidyfinance.R |only inst/doc/dates-in-tidyfinance.Rmd |only inst/doc/dates-in-tidyfinance.html |only inst/doc/using-tidyfinance.R | 17 - inst/doc/using-tidyfinance.Rmd | 21 - inst/doc/using-tidyfinance.html | 126 +++++------ man/assign_portfolio.Rd | 1 man/create_summary_statistics.Rd | 2 man/create_wrds_dummy_database.Rd | 3 man/download_data.Rd | 12 - man/download_data_factors.Rd | 4 man/download_data_factors_ff.Rd | 20 + man/download_data_factors_q.Rd | 8 man/download_data_macro_predictors.Rd | 9 man/download_data_stocks.Rd |only man/download_data_stocks_yf.Rd |only man/download_data_wrds.Rd | 9 man/download_data_wrds_ccm_links.Rd | 1 man/download_data_wrds_clean_trace.Rd | 9 man/download_data_wrds_compustat.Rd | 18 - man/download_data_wrds_crsp.Rd | 7 man/download_data_wrds_fisd.Rd | 10 man/estimate_model.Rd | 1 man/get_wrds_connection.Rd | 1 man/list_supported_types.Rd | 1 man/list_supported_types_ff_legacy.Rd |only man/list_supported_types_stocks.Rd |only man/list_tidy_finance_chapters.Rd | 1 man/open_tidy_finance_website.Rd | 5 man/trim.Rd | 1 man/winsorize.Rd | 1 vignettes/dates-in-tidyfinance.Rmd |only vignettes/using-tidyfinance.Rmd | 21 - 65 files changed, 1051 insertions(+), 631 deletions(-)
Title: Provides Progress Bars in 'knitr'
Description: Provides a progress bar similar to 'dplyr' that can write progress out to a
variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown',
and you still want to see progress of calculations in the terminal.
Author: Robert M Flight [aut, cre],
Hadley Wickham [ctb] ,
Romain Francois [ctb] ,
Lionel Henry [ctb] ,
Kirill Mueller [ctb] ,
RStudio [cph]
Maintainer: Robert M Flight <rflight79@gmail.com>
Diff between knitrProgressBar versions 1.1.0 dated 2018-02-19 and 1.1.1 dated 2024-07-23
DESCRIPTION | 11 MD5 | 22 - R/progress.R | 2 README.md | 95 +++-- build/vignette.rds |binary inst/doc/example_progress_bars.R | 18 inst/doc/example_progress_bars.html | 637 +++++++++++++++++++++-------------- inst/doc/multiprocessing.R | 10 inst/doc/multiprocessing.html | 557 +++++++++++++++++++----------- man/progress_estimated.Rd | 7 man/watch_progress_mp.Rd | 8 tests/testthat/test-decision-logic.R | 35 - 12 files changed, 864 insertions(+), 538 deletions(-)
More information about knitrProgressBar at CRAN
Permanent link
Title: Discovery, Retrieval, and Analysis of Water Isotope Data
Description: The wiDB...() functions provide an interface to the public API
of the wiDB <https://github.com/SPATIAL-Lab/isoWater/blob/master/Protocol.md>:
build, check and submit queries, and receive and
unpack responses. Data analysis functions support Bayesian
inference of the source and source isotope composition of water
samples that may have experienced evaporation. Algorithms
adapted from Bowen et al. (2018, <doi:10.1007/s00442-018-4192-5>).
Author: Gabe Bowen [aut, cre]
Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
Diff between isoWater versions 1.1.2 dated 2023-08-18 and 1.2.0 dated 2024-07-23
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS.md | 4 + R/constructors.R | 23 +++++ R/sysdata.rda |binary R/watercomp.R | 78 +++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/isoWater.R | 2 inst/doc/isoWater.Rmd | 2 inst/doc/isoWater.html | 196 ++++++++++++++++++++++++------------------------- man/iso.Rd | 10 +- man/mixSource.Rd | 9 +- man/mwlSource.Rd | 9 ++ vignettes/isoWater.Rmd | 2 15 files changed, 216 insertions(+), 155 deletions(-)
Title: Joint Estimation of Latent Groups and Group-Specific
Coefficients in Panel Data Models
Description: Latent group structures are a common challenge in panel data analysis. Disregarding group-level heterogeneity can introduce bias. Conversely, estimating individual coefficients for each cross-sectional unit is inefficient and may lead to high uncertainty.
This package addresses the issue of unobservable group structures by implementing the pairwise adaptive group fused Lasso (PAGFL) by Mehrabani (2023) <doi:10.1016/j.jeconom.2022.12.002>. PAGFL identifies latent group structures and group-specific coefficients in a single step.
On top of that, we extend the PAGFL to time-varying coefficient functions.
Author: Paul Haimerl [aut, cre] ,
Stephan Smeekes [ctb] ,
Ines Wilms [ctb] ,
Ali Mehrabani [ctb]
Maintainer: Paul Haimerl <p.haimerl@student.maastrichtuniversity.nl>
Diff between PAGFL versions 1.1.0 dated 2024-06-08 and 1.1.1 dated 2024-07-23
PAGFL-1.1.0/PAGFL/tests/testthat/test-results.R |only PAGFL-1.1.1/PAGFL/DESCRIPTION | 6 PAGFL-1.1.1/PAGFL/MD5 | 61 - PAGFL-1.1.1/PAGFL/NAMESPACE | 18 PAGFL-1.1.1/PAGFL/NEWS.md | 9 PAGFL-1.1.1/PAGFL/R/RcppExports.R | 12 PAGFL-1.1.1/PAGFL/R/checks.R | 55 - PAGFL-1.1.1/PAGFL/R/grouped_plm.R |only PAGFL-1.1.1/PAGFL/R/grouped_tv_plm.R |only PAGFL-1.1.1/PAGFL/R/helper.R |only PAGFL-1.1.1/PAGFL/R/pagfl.R | 100 +- PAGFL-1.1.1/PAGFL/R/pagfl_tv.R | 157 +-- PAGFL-1.1.1/PAGFL/R/s3_methods.R | 7 PAGFL-1.1.1/PAGFL/R/s3_methods_grouped_plm.R |only PAGFL-1.1.1/PAGFL/R/s3_methods_grouped_tv_plm.R |only PAGFL-1.1.1/PAGFL/R/s3_methods_tv.R | 4 PAGFL-1.1.1/PAGFL/R/sim.R | 33 PAGFL-1.1.1/PAGFL/R/sim_tv.R | 45 - PAGFL-1.1.1/PAGFL/README.md | 84 +- PAGFL-1.1.1/PAGFL/man/figures/README-unnamed-chunk-8-1.png |binary PAGFL-1.1.1/PAGFL/man/figures/README-unnamed-chunk-9-1.png |binary PAGFL-1.1.1/PAGFL/man/grouped_plm.Rd |only PAGFL-1.1.1/PAGFL/man/grouped_tv_plm.Rd |only PAGFL-1.1.1/PAGFL/man/pagfl.Rd | 65 - PAGFL-1.1.1/PAGFL/man/sim_DGP.Rd | 27 PAGFL-1.1.1/PAGFL/man/sim_tv_DGP.Rd | 24 PAGFL-1.1.1/PAGFL/man/tv_pagfl.Rd | 72 - PAGFL-1.1.1/PAGFL/src/PAGFL-package.cpp | 402 ++++++---- PAGFL-1.1.1/PAGFL/src/RcppExports.cpp | 53 + PAGFL-1.1.1/PAGFL/tests/testthat/_snaps/methods.md | 226 +++++ PAGFL-1.1.1/PAGFL/tests/testthat/fixtures/pagfl_pls_sim_smallNk.rds |only PAGFL-1.1.1/PAGFL/tests/testthat/fixtures/test_helper.R | 49 - PAGFL-1.1.1/PAGFL/tests/testthat/test-inputs.R | 69 + PAGFL-1.1.1/PAGFL/tests/testthat/test-methods.R | 112 ++ PAGFL-1.1.1/PAGFL/tests/testthat/test-oracle.R |only PAGFL-1.1.1/PAGFL/tests/testthat/test-pagfl_results.R |only PAGFL-1.1.1/PAGFL/tests/testthat/test-sim.R | 46 - 37 files changed, 1148 insertions(+), 588 deletions(-)
Title: Enable the Use of 'metacore' to Help Create and Check Dataset
Description: Uses the metadata information stored in 'metacore' objects to check and build metadata associated columns.
Author: Christina Fillmore [aut, cre] ,
Mike Stackhouse [aut] ,
Jana Stoilova [aut],
Tamara Senior [aut],
GlaxoSmithKline LLC [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
Atorus Research LLC [cph, fnd]
Maintainer: Christina Fillmore <christina.e.fillmore@gsk.com>
Diff between metatools versions 0.1.5 dated 2023-03-13 and 0.1.6 dated 2024-07-23
DESCRIPTION | 25 +++++-- MD5 | 29 ++++---- NAMESPACE | 7 ++ NEWS.md | 12 ++- R/build.R | 38 +++++++++-- R/checks.R | 141 ++++++++++++++++++++++++++++++++++++++----- R/supp.R | 126 +++++++++++++++++++++++++++++++++----- inst/WORDLIST |only man/build_from_derived.Rd | 8 +- man/check_ct_data.Rd | 22 +++++- man/check_unique_keys.Rd |only man/check_variables.Rd | 4 - man/get_bad_ct.Rd | 13 +++ tests/spelling.R |only tests/testthat/test-build.R | 34 +++++++++- tests/testthat/test-checks.R | 44 +++++++++++++ tests/testthat/test-supp.R | 50 +++++++++++---- 17 files changed, 466 insertions(+), 87 deletions(-)
Title: Functions to Calculate Common Laterality Statistics in
Primatology
Description: Calculates and plots Handedness index (HI), absolute HI, mean HI and z-score which are commonly used indexes for the study of hand preference (laterality) in non-human primates.
Author: Borel A., Pouydebat E., Reghem E.
Maintainer: Antony Borel <antony.borel@gmail.com>
Diff between Laterality versions 0.9.4 dated 2022-06-06 and 0.9.5 dated 2024-07-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/Laterality-package.Rd | 8 -------- 3 files changed, 6 insertions(+), 14 deletions(-)
Title: Yatchew (1997), De Chaisemartin & D'Haultfoeuille (2024)
Linearity Test
Description: Test of linearity originally proposed by Yatchew (1997) <doi:10.1016/S0165-1765(97)00218-8> and improved by de Chaisemartin & D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> to be robust under heteroskedasticity.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut],
Xavier D'Haultfoeuille [aut]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between YatchewTest versions 1.1.0 dated 2024-06-11 and 1.1.1 dated 2024-07-23
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Generalised Additive Point Process Models
Description: Methods for fitting point processes with parameters of generalised additive
model (GAM) form are provided. For an introduction to point processes see Cox, D.R &
Isham, V. (Point Processes, 1980, CRC Press), GAMs see Wood, S.N. (2017)
<doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. &
Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>.
Author: Ben Youngman [aut, cre], Theo Economou [aut]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between ppgam versions 1.0.1 dated 2020-04-19 and 1.0.2 dated 2024-07-23
DESCRIPTION | 10 ++-- MD5 | 23 ++++++---- NAMESPACE | 8 +++ NEWS.md | 8 +++ R/data.R | 2 R/nohelp.R | 114 ++++++++++++++++++++++++++++++++++++++------------ R/ppgam.R | 25 +++++++--- R/s3.R |only man/coef.ppgam.Rd |only man/fitted.ppgam.Rd |only man/plot.ppgam.Rd |only man/ppgam.Rd | 13 ++++- man/predict.ppgam.Rd |only man/print.ppgam.Rd |only man/simulate.ppgam.Rd |only man/windstorm.Rd | 2 16 files changed, 152 insertions(+), 53 deletions(-)
Title: Difference-in-Differences in Heterogeneous Adoption Designs with
Quasi Stayers
Description: Estimation of Difference-in-Differences (DiD) estimators from de Chaisemartin and D'Haultfoeuille (2024) <doi:10.2139/ssrn.4284811> in Heterogeneous Adoption Designs with no stayers but with quasi stayers.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut],
Xavier D'Haultfoeuille [aut]
Maintainer: Diego Ciccia <diego.ciccia@kellogg.northwestern.edu>
Diff between DIDHAD versions 1.0.0 dated 2024-06-18 and 1.0.1 dated 2024-07-23
DESCRIPTION | 12 +++--- MD5 | 10 ++--- R/did_had.R | 7 +++ R/did_had_est.R | 10 ++++- R/did_het_adoption_main.R | 86 +++++++++++++++++++++++++++++++++++++++++----- man/did_had.Rd | 6 +++ 6 files changed, 109 insertions(+), 22 deletions(-)
Title: Flexible Framework for Developing Spatial Interaction Models
Description: Develop spatial interaction models (SIMs). SIMs predict the
amount of interaction, for example number of trips per day, between
geographic entities representing trip origins and destinations.
Contains functions for creating origin-destination datasets
from geographic input datasets and calculating movement between
origin-destination pairs with constrained, production-constrained,
and attraction-constrained models (Wilson 1979) <doi:10.1068/a030001>.
Author: Robin Lovelace [aut, cre] ,
Jakub Nowosad [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between simodels versions 0.0.5 dated 2022-08-31 and 0.1.0 dated 2024-07-23
simodels-0.0.5/simodels/data/od_aus.rda |only simodels-0.0.5/simodels/data/zones_aus.rda |only simodels-0.0.5/simodels/man/od_aus.Rd |only simodels-0.0.5/simodels/man/zones_aus.Rd |only simodels-0.1.0/simodels/DESCRIPTION | 6 simodels-0.1.0/simodels/MD5 | 32 simodels-0.1.0/simodels/NEWS.md | 6 simodels-0.1.0/simodels/R/si_model.R | 22 simodels-0.1.0/simodels/README.md | 33 simodels-0.1.0/simodels/build/partial.rdb |binary simodels-0.1.0/simodels/build/vignette.rds |binary simodels-0.1.0/simodels/inst/doc/simodels.R | 215 simodels-0.1.0/simodels/inst/doc/simodels.Rmd | 5 simodels-0.1.0/simodels/inst/doc/simodels.html | 5293 ------------ simodels-0.1.0/simodels/inst/doc/sims-first-principles.R | 4 simodels-0.1.0/simodels/inst/doc/sims-first-principles.Rmd | 2 simodels-0.1.0/simodels/inst/doc/sims-first-principles.html | 5195 ----------- simodels-0.1.0/simodels/vignettes/simodels.Rmd | 5 simodels-0.1.0/simodels/vignettes/sims-first-principles.Rmd | 2 19 files changed, 481 insertions(+), 10339 deletions(-)
Title: Model Wrappers for Tree-Based Models
Description: Bindings for additional tree-based model engines for use with
the 'parsnip' package. Models include gradient boosted decision trees
with 'LightGBM' (Ke et al, 2017.),
conditional inference trees and conditional random forests with
'partykit' (Hothorn and Zeileis, 2015. and
Hothorn et al, 2006. <doi:10.1198/106186006X133933>), and accelerated
oblique random forests with 'aorsf' (Jaeger et al, 2022
<doi:10.5281/zenodo.7116854>).
Author: Daniel Falbel [aut],
Athos Damiani [aut],
Roel M. Hogervorst [aut] ,
Max Kuhn [aut] ,
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between bonsai versions 0.3.0 dated 2024-06-23 and 0.3.1 dated 2024-07-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/aorsf_data.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary 6 files changed, 17 insertions(+), 8 deletions(-)
Title: Binscatter Estimation and Inference
Description: Provides tools for statistical analysis using the binscatter methods developed by Cattaneo, Crump, Farrell and Feng (2024a) <doi:10.48550/arXiv.1902.09608>, Cattaneo, Crump, Farrell and Feng (2024b) <https://nppackages.github.io/references/Cattaneo-Crump-Farrell-Feng_2024_NonlinearBinscatter.pdf> and Cattaneo, Crump, Farrell and Feng (2024c) <doi:10.48550/arXiv.1902.09615>. Binscatter provides a flexible way of describing the relationship between two variables based on partitioning/binning of the independent variable of interest. binsreg(), binsqreg() and binsglm() implement binscatter least squares regression, quantile regression and generalized linear regression respectively, with particular focus on constructing binned scatter plots. They also implement robust (pointwise and uniform) inference of regression functions and derivatives thereof. binstest() implements hypothesis testing procedures for parametric functional forms of and nonparametric shape restrictions o [...truncated...]
Author: Matias D. Cattaneo, Richard K. Crump, Max H. Farrell, Yingjie Feng
Maintainer: Yingjie Feng <fengyingjiepku@gmail.com>
Diff between binsreg versions 1.0 dated 2023-07-11 and 1.1 dated 2024-07-23
DESCRIPTION | 12 MD5 | 32 R/binsglm.R | 3627 ++++++++++++++++++++++++------------------------- R/binspwc.R | 2324 ++++++++++++++++--------------- R/binsqreg.R | 3355 ++++++++++++++++++++++----------------------- R/binsreg-package.R | 103 - R/binsreg.R | 3353 ++++++++++++++++++++++----------------------- R/binsreg_functions.R | 18 R/binsregselect.R | 1544 ++++++++++---------- R/binstest.R | 2475 ++++++++++++++++----------------- man/binsglm.Rd | 14 man/binspwc.Rd | 57 man/binsqreg.Rd | 20 man/binsreg-package.Rd | 16 man/binsreg.Rd | 12 man/binsregselect.Rd | 10 man/binstest.Rd | 23 17 files changed, 8616 insertions(+), 8379 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] ,
Martin Huber [aut] ,
Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 1.1.0 dated 2024-01-24 and 1.1.1 dated 2024-07-23
DESCRIPTION | 10 +- MD5 | 24 ++++-- NAMESPACE | 107 ++++++++++++++++-------------- R/didDML.R |only R/didcontDML.R |only R/didcontDMLpanel.R |only R/didweight.R | 2 R/functions.R | 87 ++++++++++++++++++++++++ R/paneltestDML.R |only R/testmedident.R |only man/didDML.Rd |only man/didcontDML.Rd |only man/didcontDMLpanel.Rd |only man/didweight.Rd | 2 man/india.Rd | 88 ++++++++++++------------- man/paneltestDML.Rd |only man/rkd.Rd | 172 ++++++++++++++++++++++++------------------------- man/testmedident.Rd |only 18 files changed, 298 insertions(+), 194 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.5.2 dated 2023-02-06 and 4.2.6 dated 2024-07-23
DESCRIPTION | 32 LICENSE | 4 MD5 | 379 NAMESPACE | 222 NEWS.md | 996 +- R/CommentClass.R | 468 - R/HyperlinkClass.R | 218 R/RcppExports.R | 288 R/StyleClass.R | 586 - R/WorkbookClass.R | 8750 +++++++++---------- R/asserts.R | 192 R/baseXML.R | 970 +- R/borderFunctions.R | 1192 +- R/build_workbook.R | 306 R/chartsheet_class.R | 110 R/class_definitions.R | 322 R/conditional_formatting.R | 1360 +-- R/data-fontSizeLookupTables.R | 23 R/helperFunctions.R | 1970 ++-- R/loadWorkbook.R | 2094 ++-- R/onUnload.R | 6 R/openXL.R | 210 R/openxlsx-package.R | 6 R/openxlsx.R | 336 R/openxlsxCoerce.R | 474 - R/readWorkbook.R | 1213 +- R/sheet_data_class.R | 204 R/sysdata.rda |binary R/utils.R | 112 R/workbook_column_widths.R | 394 R/workbook_read_workbook.R | 722 - R/workbook_write_data.R | 616 - R/worksheet_class.R | 552 - R/wrappers.R | 9432 ++++++++++----------- R/writeData.R | 1119 +- R/writeDataTable.R | 657 - R/writexlsx.R | 135 R/zzz.R | 14 README.md | 84 build/vignette.rds |binary data |only inst/WORDLIST | 276 inst/doc/Formatting.R | 27 inst/doc/Formatting.Rmd | 648 - inst/doc/Formatting.html | 657 - inst/doc/Introduction.R | 56 inst/doc/Introduction.Rmd | 1024 +- inst/doc/Introduction.html | 865 - inst/extdata/build_font_size_lookup.R | 128 inst/extdata/conditional_formatting_testing.R | 160 inst/extdata/load_xlsx_testing.R | 350 inst/extdata/stack_style_testing.R | 252 man/NamedRegion.Rd | 152 man/activeSheet.Rd | 76 man/addCreator.Rd | 48 man/addFilter.Rd | 96 man/addStyle.Rd | 122 man/addWorksheet.Rd | 254 man/all.equal.Rd | 38 man/as.character.formula.Rd |only man/buildWorkbook.Rd | 202 man/cloneWorksheet.Rd | 74 man/col2int.Rd | 34 man/conditionalFormat.Rd | 94 man/conditionalFormatting.Rd | 651 - man/convertFromExcelRef.Rd | 42 man/convertToDate.Rd | 58 man/convertToDateTime.Rd | 56 man/copyWorkbook.Rd | 58 man/createComment.Rd | 102 man/createStyle.Rd | 344 man/createWorkbook.Rd | 108 man/dataValidation.Rd | 196 man/deleteData.Rd | 82 man/deleteDataColumn.Rd |only man/freezePane.Rd | 110 man/getBaseFont.Rd | 58 man/getCellRefs.Rd | 52 man/getCreators.Rd | 52 man/getDateOrigin.Rd | 78 man/getNamedRegions.Rd | 106 man/getSheetNames.Rd | 46 man/getStyles.Rd | 44 man/getTables.Rd | 56 man/groupColumns.Rd | 62 man/groupRows.Rd | 52 man/if_null_then.Rd | 50 man/insertImage.Rd | 132 man/insertPlot.Rd | 160 man/int2col.Rd | 34 man/loadWorkbook.Rd | 84 man/makeHyperlinkString.Rd | 194 man/mergeCells.Rd | 116 man/modifyBaseFont.Rd | 80 man/names.Rd | 64 man/openXL.Rd | 86 man/openxlsx.Rd | 125 man/openxlsxFontSizeLookupTable.Rd | 42 man/openxlsx_options.Rd | 90 man/pageBreak.Rd | 72 man/pageSetup.Rd | 330 man/protectWorkbook.Rd | 94 man/protectWorksheet.Rd | 180 man/read.xlsx.Rd | 228 man/readWorkbook.Rd | 168 man/removeCellMerge.Rd | 54 man/removeColWidths.Rd | 68 man/removeComment.Rd | 56 man/removeFilter.Rd | 76 man/removeRowHeights.Rd | 68 man/removeTable.Rd | 96 man/removeWorksheet.Rd | 66 man/renameWorksheet.Rd | 96 man/replaceStyle.Rd | 88 man/saveWorkbook.Rd | 90 man/setColWidths.Rd | 142 man/setFooter.Rd | 80 man/setHeader.Rd | 80 man/setHeaderFooter.Rd | 202 man/setLastModifiedBy.Rd | 48 man/setRowHeights.Rd | 88 man/sheetVisibility.Rd | 74 man/sheetVisible.Rd | 76 man/sheets.Rd | 88 man/showGridLines.Rd | 60 man/temp_xlsx.Rd | 28 man/ungroupColumns.Rd | 54 man/ungroupRows.Rd | 54 man/worksheetOrder.Rd | 98 man/write.xlsx.Rd | 264 man/writeComment.Rd | 94 man/writeData.Rd | 426 man/writeDataTable.Rd | 390 man/writeFormula.Rd | 230 src/read_workbook.cpp | 18 src/write_data.cpp | 2 tests/testthat.R | 8 tests/testthat/test-CommentClass.R | 36 tests/testthat/test-Workbook_properties.R | 100 tests/testthat/test-Worksheet_naming.R | 92 tests/testthat/test-activeSheet.R | 66 tests/testthat/test-border_parsing.R | 642 - tests/testthat/test-build_workbook.R | 84 tests/testthat/test-cloneWorksheet.R | 64 tests/testthat/test-conditionalFormatting.R | 145 tests/testthat/test-date_time_conversion.R | 70 tests/testthat/test-deleting_tables.R | 444 tests/testthat/test-encoding.R | 182 tests/testthat/test-fill_merged_cells.R | 88 tests/testthat/test-fontSizeLookupTables.R | 8 tests/testthat/test-freeze_pane.R | 222 tests/testthat/test-getBaseFont.R | 44 tests/testthat/test-getCellRefs.R | 48 tests/testthat/test-load_read_file_read_equality.R | 86 tests/testthat/test-loading_workbook.R | 2088 ++-- tests/testthat/test-loading_workbook_tables.R | 76 tests/testthat/test-loading_workbook_unzipped.R | 64 tests/testthat/test-named_regions.R | 828 - tests/testthat/test-options.R | 102 tests/testthat/test-outlines.R | 282 tests/testthat/test-page_setup.R | 80 tests/testthat/test-protect-workbook.R | 66 tests/testthat/test-protect-worksheet.R | 40 tests/testthat/test-read_from_created_wb.R | 722 - tests/testthat/test-read_from_loaded_workbook.R | 646 - tests/testthat/test-read_sources.R | 133 tests/testthat/test-read_write_logicals.R | 94 tests/testthat/test-read_xlsx_correct_sheet.R | 64 tests/testthat/test-read_xlsx_random_seed.R | 22 tests/testthat/test-remove_worksheets.R | 124 tests/testthat/test-saveWorkbook.R | 126 tests/testthat/test-skip_empty_cols.R | 494 - tests/testthat/test-skip_empty_rows.R | 642 - tests/testthat/test-styles.R | 100 tests/testthat/test-table_overlaps.R | 206 tests/testthat/test-trying_to_break_openxlsx.R | 424 tests/testthat/test-v3_0_0_bugs.R | 28 tests/testthat/test-validate_table_name.R | 98 tests/testthat/test-worksheet_ordering.R | 568 - tests/testthat/test-worksheet_renaming.R | 116 tests/testthat/test-wrappers.R | 156 tests/testthat/test-write-permissions.R | 38 tests/testthat/test-writeData.R | 109 tests/testthat/test-writeDataTable.R |only tests/testthat/test-write_data_to_sheetData.R | 622 - tests/testthat/test-write_data_to_sheetData_NAs.R | 278 tests/testthat/test-write_read_equality.R | 588 - tests/testthat/test-write_xlsx_vector_args.R | 236 tests/testthat/test-writing_posixct.R | 198 tests/testthat/test-writing_sheet_data.R | 446 vignettes/Formatting.Rmd | 648 - vignettes/Introduction.Rmd | 1024 +- 192 files changed, 33008 insertions(+), 32494 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph]
,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Julien Ruffault [ctb],
Francois Pimont [ctb] ,
Herve Cochard [ctb] ,
Aitor Amezte [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.3.1 dated 2024-05-25 and 4.4.0 dated 2024-07-23
medfate-4.3.1/medfate/R/forest.R |only medfate-4.3.1/medfate/man/exampleforest.Rd |only medfate-4.4.0/medfate/DESCRIPTION | 10 medfate-4.4.0/medfate/MD5 | 211 - medfate-4.4.0/medfate/R/RcppExports.R | 345 +- medfate-4.4.0/medfate/R/VerticalProfiles.R | 6 medfate-4.4.0/medfate/R/dataset_documentation.R | 68 medfate-4.4.0/medfate/R/defaultControl.R | 20 medfate-4.4.0/medfate/R/emptyforest.R |only medfate-4.4.0/medfate/R/evaluation.R | 2 medfate-4.4.0/medfate/R/hydraulics_supplyFunctionPlot.R | 1 medfate-4.4.0/medfate/R/hydraulics_vulnerabilityCurvePlot.R | 1 medfate-4.4.0/medfate/R/moisture_pressureVolumeCurvePlot.R | 1 medfate-4.4.0/medfate/R/plot.forest.R | 2 medfate-4.4.0/medfate/R/plot.spwb.R | 3 medfate-4.4.0/medfate/R/plot_internals.R | 16 medfate-4.4.0/medfate/R/regeneration.R | 5 medfate-4.4.0/medfate/R/stand_metrics.R | 8 medfate-4.4.0/medfate/R/summary.forest.R |only medfate-4.4.0/medfate/R/summary.spwb.R | 3 medfate-4.4.0/medfate/R/transp_maximumTranspirationModel.R | 1 medfate-4.4.0/medfate/R/transp_stomatalRegulationPlot.R | 1 medfate-4.4.0/medfate/R/tree2forest.R | 3 medfate-4.4.0/medfate/build/partial.rdb |binary medfate-4.4.0/medfate/data/SpParamsDefinition.rda |binary medfate-4.4.0/medfate/inst/include/medfate_RcppExports.h | 23 medfate-4.4.0/medfate/man/SpParams.Rd | 4 medfate-4.4.0/medfate/man/aspwb.Rd | 1 medfate-4.4.0/medfate/man/biophysics.Rd | 3 medfate-4.4.0/medfate/man/carbon.Rd | 1 medfate-4.4.0/medfate/man/defaultControl.Rd | 11 medfate-4.4.0/medfate/man/emptyforest.Rd |only medfate-4.4.0/medfate/man/evaluation.Rd | 2 medfate-4.4.0/medfate/man/fire_behaviour.Rd | 24 medfate-4.4.0/medfate/man/fire_severity.Rd | 1 medfate-4.4.0/medfate/man/forest.Rd | 64 medfate-4.4.0/medfate/man/forest2aboveground.Rd | 3 medfate-4.4.0/medfate/man/fuel_properties.Rd | 32 medfate-4.4.0/medfate/man/fuel_windAdjustmentFactor.Rd |only medfate-4.4.0/medfate/man/growth.Rd | 2 medfate-4.4.0/medfate/man/herb_values.Rd | 1 medfate-4.4.0/medfate/man/hydraulics_conductancefunctions.Rd | 1 medfate-4.4.0/medfate/man/hydraulics_defoliation.Rd | 1 medfate-4.4.0/medfate/man/hydraulics_scalingconductance.Rd | 1 medfate-4.4.0/medfate/man/hydraulics_supplyfunctions.Rd | 1 medfate-4.4.0/medfate/man/hydrology_infiltration.Rd | 1 medfate-4.4.0/medfate/man/hydrology_interception.Rd | 1 medfate-4.4.0/medfate/man/hydrology_soilEvaporation.Rd | 1 medfate-4.4.0/medfate/man/hydrology_soilWaterBalance.Rd | 26 medfate-4.4.0/medfate/man/hydrology_verticalInputs.Rd | 1 medfate-4.4.0/medfate/man/light_advanced.Rd | 1 medfate-4.4.0/medfate/man/light_basic.Rd | 1 medfate-4.4.0/medfate/man/modelInput.Rd | 47 medfate-4.4.0/medfate/man/moisture.Rd | 1 medfate-4.4.0/medfate/man/mortality_dailyProbability.Rd | 1 medfate-4.4.0/medfate/man/pheno_updateLeaves.Rd | 1 medfate-4.4.0/medfate/man/photo.Rd | 1 medfate-4.4.0/medfate/man/plant_values.Rd | 1 medfate-4.4.0/medfate/man/plot.forest.Rd | 2 medfate-4.4.0/medfate/man/plot.spwb.Rd | 3 medfate-4.4.0/medfate/man/regeneration.Rd | 1 medfate-4.4.0/medfate/man/root.Rd | 1 medfate-4.4.0/medfate/man/soil_texture.Rd | 1 medfate-4.4.0/medfate/man/soil_thermodynamics.Rd | 1 medfate-4.4.0/medfate/man/species_values.Rd | 1 medfate-4.4.0/medfate/man/spwb.Rd | 2 medfate-4.4.0/medfate/man/stand_values.Rd | 2 medfate-4.4.0/medfate/man/summary.forest.Rd |only medfate-4.4.0/medfate/man/summary.spwb.Rd | 3 medfate-4.4.0/medfate/man/sureau_ecos.Rd | 1 medfate-4.4.0/medfate/man/transp_maximumTranspirationModel.Rd | 1 medfate-4.4.0/medfate/man/transp_modes.Rd | 1 medfate-4.4.0/medfate/man/transp_stomatalregulation.Rd | 1 medfate-4.4.0/medfate/man/tree2forest.Rd | 3 medfate-4.4.0/medfate/man/vprofile_leafAreaDensity.Rd | 1 medfate-4.4.0/medfate/man/wind.Rd | 1 medfate-4.4.0/medfate/man/woodformation.Rd | 1 medfate-4.4.0/medfate/src/RcppExports.cpp | 46 medfate-4.4.0/medfate/src/aspwb.cpp | 3 medfate-4.4.0/medfate/src/biophysicsutils.cpp | 9 medfate-4.4.0/medfate/src/carbon.cpp | 10 medfate-4.4.0/medfate/src/firebehaviour.cpp | 24 medfate-4.4.0/medfate/src/fireseverity.cpp | 6 medfate-4.4.0/medfate/src/forestutils.cpp | 34 medfate-4.4.0/medfate/src/fuelstructure.cpp | 21 medfate-4.4.0/medfate/src/fuelstructure.h | 1 medfate-4.4.0/medfate/src/growth.cpp | 3 medfate-4.4.0/medfate/src/hydraulics.cpp | 33 medfate-4.4.0/medfate/src/hydrology.cpp | 1538 +++++----- medfate-4.4.0/medfate/src/hydrology.h | 2 medfate-4.4.0/medfate/src/inner_sperry.cpp | 1 medfate-4.4.0/medfate/src/inner_sureau.cpp | 22 medfate-4.4.0/medfate/src/lightextinction_advanced.cpp | 10 medfate-4.4.0/medfate/src/lightextinction_basic.cpp | 4 medfate-4.4.0/medfate/src/modelInput.cpp | 62 medfate-4.4.0/medfate/src/paramutils.cpp | 27 medfate-4.4.0/medfate/src/phenology.cpp | 5 medfate-4.4.0/medfate/src/photosynthesis.cpp | 8 medfate-4.4.0/medfate/src/root.cpp | 15 medfate-4.4.0/medfate/src/soil.cpp | 30 medfate-4.4.0/medfate/src/soil.h | 2 medfate-4.4.0/medfate/src/soil_thermodynamics.cpp | 4 medfate-4.4.0/medfate/src/spwb.cpp | 59 medfate-4.4.0/medfate/src/tissuemoisture.cpp | 9 medfate-4.4.0/medfate/src/transpiration_advanced.cpp | 26 medfate-4.4.0/medfate/src/transpiration_basic.cpp | 8 medfate-4.4.0/medfate/src/windKatul.cpp | 2 medfate-4.4.0/medfate/src/windextinction.cpp | 27 medfate-4.4.0/medfate/src/woodformation.cpp | 4 medfate-4.4.0/medfate/tests/testthat/Rplots.pdf |binary 110 files changed, 1863 insertions(+), 1186 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb] ,
Stephanie Lobaugh [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.7.2 dated 2023-07-15 and 2.0.0 dated 2024-07-23
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gtsummary-2.0.0/gtsummary/tests/testthat/test-add_n.tbl_uvregression.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_nevent.tbl_regression.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_nevent.tbl_survfit.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_nevent.tbl_uvregression.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_overall.tbl_continuous.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_overall.tbl_summary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_overall.tbl_svysummary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_p.tbl_continuous.R | 146 - gtsummary-2.0.0/gtsummary/tests/testthat/test-add_p.tbl_cross.R | 104 gtsummary-2.0.0/gtsummary/tests/testthat/test-add_p.tbl_summary.R | 460 +-- gtsummary-2.0.0/gtsummary/tests/testthat/test-add_p.tbl_survfit.R | 152 - gtsummary-2.0.0/gtsummary/tests/testthat/test-add_p.tbl_svysummary.R | 447 +-- gtsummary-2.0.0/gtsummary/tests/testthat/test-add_q.R | 89 gtsummary-2.0.0/gtsummary/tests/testthat/test-add_significance_stars.R | 82 gtsummary-2.0.0/gtsummary/tests/testthat/test-add_stat.R | 229 + gtsummary-2.0.0/gtsummary/tests/testthat/test-add_stat_label.R | 138 gtsummary-2.0.0/gtsummary/tests/testthat/test-add_stat_label.tbl_svysummary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-add_vif.R | 62 gtsummary-2.0.0/gtsummary/tests/testthat/test-as_flex_table.R | 475 ++- gtsummary-2.0.0/gtsummary/tests/testthat/test-as_gt.R | 516 +++ gtsummary-2.0.0/gtsummary/tests/testthat/test-as_hux_table.R | 298 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-as_kable.R | 320 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-as_kable_extra.R | 367 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-as_tibble.R | 274 + gtsummary-2.0.0/gtsummary/tests/testthat/test-bold_italicize_labels_levels.R | 231 + gtsummary-2.0.0/gtsummary/tests/testthat/test-bold_p.R | 97 gtsummary-2.0.0/gtsummary/tests/testthat/test-combine_terms.R | 297 -- gtsummary-2.0.0/gtsummary/tests/testthat/test-custom_tidiers.R | 109 gtsummary-2.0.0/gtsummary/tests/testthat/test-inline_text.R | 393 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-label_style.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_caption.R | 112 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_column_alignment.R | 23 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_column_hide.R | 12 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_column_indent.R | 76 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_column_merge.R | 21 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_fmt_fun.R | 57 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_footnote.R | 256 + gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_header.R | 274 + gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_spanning_header.R | 217 + gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_table_body.R | 45 gtsummary-2.0.0/gtsummary/tests/testthat/test-modify_table_styling.R | 416 ++ gtsummary-2.0.0/gtsummary/tests/testthat/test-plot.tbl_regression.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-plot.tbl_uvregression.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-remove_row_type.R | 97 gtsummary-2.0.0/gtsummary/tests/testthat/test-scoping_gtsummary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-select_helpers.R | 159 - gtsummary-2.0.0/gtsummary/tests/testthat/test-separate_p_footnotes.R | 62 gtsummary-2.0.0/gtsummary/tests/testthat/test-show_header_names.R | 10 gtsummary-2.0.0/gtsummary/tests/testthat/test-sort_filter_p.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-style_percent.R | 25 gtsummary-2.0.0/gtsummary/tests/testthat/test-style_pvalue.R | 54 gtsummary-2.0.0/gtsummary/tests/testthat/test-style_ratio.R | 8 gtsummary-2.0.0/gtsummary/tests/testthat/test-style_sigfig.R | 8 gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_ard_continuous.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_ard_summary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_ard_wide_summary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_butcher.R | 21 gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_continuous.R | 218 + gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_cross.R | 256 - gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_custom_summary.R | 180 - gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_merge.R | 234 - gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_regression.R | 362 -- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_regression_methods.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_split.R | 19 gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_stack.R | 334 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_strata.R | 353 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_summary.R | 1091 +++---- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_survfit.R | 338 +- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_svysummary.R | 983 +++--- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_uvregression.R | 700 ++-- gtsummary-2.0.0/gtsummary/tests/testthat/test-tbl_wide_summary.R |only gtsummary-2.0.0/gtsummary/tests/testthat/test-theme_gtsummary.R |only gtsummary-2.0.0/gtsummary/vignettes/gtsummary_definition.Rmd | 54 gtsummary-2.0.0/gtsummary/vignettes/inline_text.Rmd | 2 gtsummary-2.0.0/gtsummary/vignettes/themes.Rmd | 59 477 files changed, 21832 insertions(+), 27455 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.6 dated 2024-04-25 and 0.9.7 dated 2024-07-23
finbif-0.9.6/finbif/tests/testthat/helper-finbif.R |only finbif-0.9.6/finbif/tests/testthat/test-finbif_api_get.R |only finbif-0.9.6/finbif/tests/testthat/test-finbif_coords.R |only finbif-0.9.6/finbif/tests/testthat/test-finbif_dates.R |only finbif-0.9.6/finbif/tests/testthat/test-finbif_last_mod.R |only finbif-0.9.6/finbif/tests/testthat/test-finbif_occurrence-db.R |only finbif-0.9.6/finbif/tests/testthat/test-metadata.R |only finbif-0.9.6/finbif/tests/testthat/test-onload.R |only finbif-0.9.6/finbif/tests/testthat/test-sysdata.R |only finbif-0.9.6/finbif/tests/testthat/test-utils.R |only finbif-0.9.6/finbif/tests/write-files |only finbif-0.9.7/finbif/DESCRIPTION | 13 finbif-0.9.7/finbif/MD5 | 106 finbif-0.9.7/finbif/NEWS.md | 132 finbif-0.9.7/finbif/R/api_get.R | 8 finbif-0.9.7/finbif/R/dates.R | 10 finbif-0.9.7/finbif/R/finbif_collections.R | 2 finbif-0.9.7/finbif/R/finbif_occurrence.R | 78 finbif-0.9.7/finbif/R/finbif_records.R | 283 - finbif-0.9.7/finbif/R/finbif_request_token.R | 4 finbif-0.9.7/finbif/R/finbif_taxa.R | 4 finbif-0.9.7/finbif/R/methods.R | 6 finbif-0.9.7/finbif/R/sysdata.R | 2 finbif-0.9.7/finbif/R/sysdata.rda |binary finbif-0.9.7/finbif/R/utils.R | 39 finbif-0.9.7/finbif/README.md | 14 finbif-0.9.7/finbif/build/vignette.rds |binary finbif-0.9.7/finbif/inst/CITATION | 12 finbif-0.9.7/finbif/inst/NEWS.Rd | 27 finbif-0.9.7/finbif/inst/doc/finbif.html | 2 finbif-0.9.7/finbif/inst/doc/v02_occurrence_data.html | 2 finbif-0.9.7/finbif/inst/doc/v03_selecting_variables.html | 2 finbif-0.9.7/finbif/inst/doc/v04_metadata.html | 2 finbif-0.9.7/finbif/inst/doc/v05_filtering.html | 2 finbif-0.9.7/finbif/man/finbif_taxa.Rd | 4 finbif-0.9.7/finbif/tests/fixtures |only finbif-0.9.7/finbif/tests/testthat/HBF.6960.zip |only finbif-0.9.7/finbif/tests/testthat/_snaps/caching.md |only finbif-0.9.7/finbif/tests/testthat/_snaps/finbif_collections.md |only finbif-0.9.7/finbif/tests/testthat/_snaps/finbif_metadata.md |only finbif-0.9.7/finbif/tests/testthat/_snaps/finbif_occurrence.md |only finbif-0.9.7/finbif/tests/testthat/_snaps/finbif_occurrence_load.md | 2409 ++++++---- finbif-0.9.7/finbif/tests/testthat/helper.R |only finbif-0.9.7/finbif/tests/testthat/laji-data-pap.tsv | 8 finbif-0.9.7/finbif/tests/testthat/test-caching.R |only finbif-0.9.7/finbif/tests/testthat/test-finbif_check_taxa.R | 49 finbif-0.9.7/finbif/tests/testthat/test-finbif_clear_cache.R | 33 finbif-0.9.7/finbif/tests/testthat/test-finbif_collections.R | 54 finbif-0.9.7/finbif/tests/testthat/test-finbif_informal_groups.R |only finbif-0.9.7/finbif/tests/testthat/test-finbif_metadata.R |only finbif-0.9.7/finbif/tests/testthat/test-finbif_occurrence.R | 772 +-- finbif-0.9.7/finbif/tests/testthat/test-finbif_occurrence_load.R | 400 - finbif-0.9.7/finbif/tests/testthat/test-finbif_request_token.R | 97 finbif-0.9.7/finbif/tests/testthat/test-finbif_taxa.R | 50 finbif-0.9.7/finbif/tests/testthat/test-finbif_update_cache.R |only finbif-0.9.7/finbif/tests/testthat/test-to_dwc.R |only finbif-0.9.7/finbif/tests/testthat/test-zzz.R |only 57 files changed, 2389 insertions(+), 2237 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph]
,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.0.1 dated 2024-04-09 and 1.1.0 dated 2024-07-23
DESCRIPTION | 8 MD5 | 60 - NEWS.md | 14 R/cff.R | 4 R/cff_read.R | 4 R/deprecated.R | 18 R/utils-cff_read.R | 20 R/utils-create.R | 25 R/utils-schema.R | 4 README.md | 132 +++ build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/WORDLIST | 1 inst/doc/cffr.html | 18 inst/doc/crosswalk.R | 14 inst/doc/crosswalk.Rmd | 46 - inst/doc/crosswalk.html | 1364 +++++++++++++++++++--------------- inst/extdata/cran_licenses.csv | 326 +++----- inst/schemaorg.json | 4 man/cff.Rd | 4 man/cff_class.Rd | 16 man/cran_to_spdx.Rd | 2 tests/testthat/_snaps/cff.md | 20 tests/testthat/_snaps/cff_create.md | 42 - tests/testthat/_snaps/cff_read.md | 1 tests/testthat/_snaps/mock-package.md | 14 tests/testthat/_snaps/utils-create.md | 22 tests/testthat/_snaps/utils-schema.md | 10 tests/testthat/test-cff_create.R | 4 vignettes/crosswalk.Rmd | 46 - 31 files changed, 1327 insertions(+), 916 deletions(-)
Title: A Simple XML Tree Parser and Generator
Description: Provides a simple XML tree parser/generator. It includes
functions to read XML files into R objects, get information out of
and into nodes, and write R objects back to XML code. It's not as
powerful as the 'XML' package and doesn't aim to be, but for simple
XML handling it could be useful. It was originally developed for
the R GUI and IDE 'RKWard' <https://rkward.kde.org>, to make plugin
development easier.
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between XiMpLe versions 0.11-2 dated 2023-08-22 and 0.11-3 dated 2024-07-23
ChangeLog | 129 +++++++++++++++++++++--------------------- DESCRIPTION | 27 +++++--- MD5 | 28 ++++----- R/XMLNode.R | 2 R/XiMpLe-package.R | 4 - R/zzz_is_get_utils.R | 8 +- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 8 +- inst/NEWS.Rd | 32 +++++++--- inst/doc/XiMpLe_vignette.R | 10 +-- inst/doc/XiMpLe_vignette.html | 4 - man/XMLGetters-methods.Rd | 6 - man/XiMpLe-package.Rd | 4 - 15 files changed, 143 insertions(+), 121 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.11 dated 2024-04-27 and 0.0.12 dated 2024-07-23
ChangeLog | 24 ++++++++++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 26 +++++++++++------------ README.md | 9 +++++++- build/partial.rdb |binary inst/NEWS.Rd | 7 ++++++ src/ql/time/calendar.cpp | 4 +-- src/ql/time/calendars/brazil.cpp | 4 +-- src/ql/time/calendars/brazil.hpp | 4 +-- src/ql/time/calendars/chile.cpp | 36 ++++++++++++++++++++++++++++++++- src/ql/time/calendars/chile.hpp | 2 - src/ql/time/calendars/india.cpp | 10 ++++++--- src/ql/time/calendars/india.hpp | 4 +-- src/ql/time/calendars/unitedstates.cpp | 17 +++++++++++---- 14 files changed, 120 insertions(+), 35 deletions(-)
Title: Harmonised Index of Consumer Prices
Description: The Harmonised Index of Consumer Prices (HICP) is the key economic figure to measure inflation in the euro area.
The methodology underlying the HICP is documented in the HICP Methodological Manual (<https://ec.europa.eu/eurostat/web/products-manuals-and-guidelines/w/ks-gq-24-003>).
Based on the manual, this package provides functions to access and work with HICP data from Eurostat's public database (<https://ec.europa.eu/eurostat/data/database>).
Author: Sebastian Weinand [aut, cre]
Maintainer: Sebastian Weinand <sebastian.weinand@ec.europa.eu>
Diff between hicp versions 0.6.0 dated 2024-07-19 and 0.6.1 dated 2024-07-23
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 inst/doc/hicp_intro.R | 15 -- inst/doc/hicp_intro.Rmd | 15 -- inst/doc/hicp_intro.html | 346 +++++++++++++++++++++++------------------------ vignettes/hicp_intro.Rmd | 15 -- 7 files changed, 202 insertions(+), 211 deletions(-)
Title: A Clustering Method for Time-Series Whole-Brain Activity Data of
'C. elegans'
Description: A toolkit to detect clusters from distance matrices.
The distance matrices are assumed to be calculated between the cells of
multiple animals ('Caenorhabditis elegans') from input time-series matrices.
Some functions for generating distance matrices, performing clustering,
evaluating the clustering, and visualizing the results of clustering and
evaluation are available. We're also providing the download function to
retrieve the calculated distance matrices from
'figshare' <https://figshare.com>.
Author: Kentaro Yamamoto [aut, cre],
Koki Tsuyuzaki [aut],
Itoshi Nikaido [aut]
Maintainer: Kentaro Yamamoto <yamaken37.the.answer@gmail.com>
Diff between WormTensor versions 0.1.0 dated 2022-09-08 and 0.1.1 dated 2024-07-23
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 4 ++ R/as_worm_tensor.R | 2 - inst/doc/WormTensor.R | 2 - inst/doc/WormTensor.html | 64 +++++++++++++++++++----------------- tests/testthat/test-worm_distance.R | 8 +--- tests/testthat/test-worm_download.R | 10 ++--- 8 files changed, 58 insertions(+), 52 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.12 dated 2023-02-28 and 6.0.0 dated 2024-07-23
dtwclust-5.5.12/dtwclust/tests/testthat/acceptance |only dtwclust-5.5.12/dtwclust/tests/testthat/integration |only dtwclust-5.5.12/dtwclust/tests/testthat/regression |only dtwclust-5.5.12/dtwclust/tests/testthat/system |only dtwclust-5.5.12/dtwclust/tests/testthat/test-01-unit.R |only dtwclust-5.5.12/dtwclust/tests/testthat/test-02-integration.R |only dtwclust-5.5.12/dtwclust/tests/testthat/test-03-acceptance.R |only dtwclust-5.5.12/dtwclust/tests/testthat/test-04-system.R |only dtwclust-5.5.12/dtwclust/tests/testthat/test-05-regression.R |only dtwclust-5.5.12/dtwclust/tests/testthat/unit |only dtwclust-6.0.0/dtwclust/DESCRIPTION | 20 dtwclust-6.0.0/dtwclust/MD5 | 212 +++---- dtwclust-6.0.0/dtwclust/NAMESPACE | 17 dtwclust-6.0.0/dtwclust/R/CENTROIDS-dba.R | 8 dtwclust-6.0.0/dtwclust/R/CENTROIDS-pam.R | 27 - dtwclust-6.0.0/dtwclust/R/CENTROIDS-sdtw-cent.R | 6 dtwclust-6.0.0/dtwclust/R/CENTROIDS-shape-extraction.R | 10 dtwclust-6.0.0/dtwclust/R/CLUSTERING-all-cent2.R | 15 dtwclust-6.0.0/dtwclust/R/CLUSTERING-compare-clusterings.R | 20 dtwclust-6.0.0/dtwclust/R/CLUSTERING-cvi-evaluators.R | 4 dtwclust-6.0.0/dtwclust/R/CLUSTERING-ddist2.R | 28 - dtwclust-6.0.0/dtwclust/R/CLUSTERING-repeat-clustering.R | 267 +++++----- dtwclust-6.0.0/dtwclust/R/CLUSTERING-tadpole.R | 6 dtwclust-6.0.0/dtwclust/R/CLUSTERING-tsclust.R | 80 +- dtwclust-6.0.0/dtwclust/R/DISTANCES-dtw-basic.R | 18 dtwclust-6.0.0/dtwclust/R/DISTANCES-dtw-lb.R | 6 dtwclust-6.0.0/dtwclust/R/DISTANCES-dtw2.R | 116 ++-- dtwclust-6.0.0/dtwclust/R/DISTANCES-gak.R | 32 + dtwclust-6.0.0/dtwclust/R/DISTANCES-lb-improved.R | 11 dtwclust-6.0.0/dtwclust/R/DISTANCES-lb-keogh.R | 7 dtwclust-6.0.0/dtwclust/R/DISTANCES-sbd.R | 17 dtwclust-6.0.0/dtwclust/R/DISTANCES-sdtw.R | 67 ++ dtwclust-6.0.0/dtwclust/R/RD-helpers.R |only dtwclust-6.0.0/dtwclust/R/S4-Distmat.R | 3 dtwclust-6.0.0/dtwclust/R/S4-DistmatLowerTriangular.R |only dtwclust-6.0.0/dtwclust/R/S4-SparseDistmat.R | 4 dtwclust-6.0.0/dtwclust/R/S4-TSClusters-methods.R | 84 +-- dtwclust-6.0.0/dtwclust/R/S4-tsclustFamily.R | 34 - dtwclust-6.0.0/dtwclust/R/SHINY-utils.R | 11 dtwclust-6.0.0/dtwclust/R/UTILS-compute-envelope.R | 6 dtwclust-6.0.0/dtwclust/R/UTILS-expressions.R | 29 - dtwclust-6.0.0/dtwclust/R/UTILS-nccc.R | 2 dtwclust-6.0.0/dtwclust/R/UTILS-utils.R | 90 ++- dtwclust-6.0.0/dtwclust/R/UTILS-zscore.R | 2 dtwclust-6.0.0/dtwclust/build/partial.rdb |binary dtwclust-6.0.0/dtwclust/build/vignette.rds |binary dtwclust-6.0.0/dtwclust/inst/COPYRIGHTS | 2 dtwclust-6.0.0/dtwclust/inst/NEWS.Rd | 6 dtwclust-6.0.0/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-6.0.0/dtwclust/inst/doc/parallelization-considerations.html | 22 dtwclust-6.0.0/dtwclust/inst/doc/timing-experiments.html | 43 - dtwclust-6.0.0/dtwclust/inst/interactive-clustering/main.R | 2 dtwclust-6.0.0/dtwclust/inst/ssdtwclust/main.R | 2 dtwclust-6.0.0/dtwclust/man/DBA.Rd | 35 - dtwclust-6.0.0/dtwclust/man/DistmatLowerTriangular-class.Rd |only dtwclust-6.0.0/dtwclust/man/DistmatLowerTriangular-generics.Rd |only dtwclust-6.0.0/dtwclust/man/GAK.Rd | 34 - dtwclust-6.0.0/dtwclust/man/SBD.Rd | 36 - dtwclust-6.0.0/dtwclust/man/TADPole.Rd | 33 - dtwclust-6.0.0/dtwclust/man/compute_envelope.Rd | 9 dtwclust-6.0.0/dtwclust/man/dtw2.Rd | 9 dtwclust-6.0.0/dtwclust/man/dtw_basic.Rd | 45 - dtwclust-6.0.0/dtwclust/man/dtw_lb.Rd | 33 - dtwclust-6.0.0/dtwclust/man/lb_improved.Rd | 28 - dtwclust-6.0.0/dtwclust/man/lb_keogh.Rd | 28 - dtwclust-6.0.0/dtwclust/man/sdtw.Rd | 40 - dtwclust-6.0.0/dtwclust/man/sdtw_cent.Rd | 26 dtwclust-6.0.0/dtwclust/man/tsclust.Rd | 6 dtwclust-6.0.0/dtwclust/man/tsclustFamily-class.Rd | 1 dtwclust-6.0.0/dtwclust/man/tsclusters-methods.Rd | 5 dtwclust-6.0.0/dtwclust/src/Makevars | 1 dtwclust-6.0.0/dtwclust/src/Makevars.win | 2 dtwclust-6.0.0/dtwclust/src/centroids/R-gateways.h | 1 dtwclust-6.0.0/dtwclust/src/centroids/dba.cpp | 3 dtwclust-6.0.0/dtwclust/src/centroids/sdtw-cent.cpp | 3 dtwclust-6.0.0/dtwclust/src/distances/R-gateways.h | 1 dtwclust-6.0.0/dtwclust/src/distances/calculators.cpp | 23 dtwclust-6.0.0/dtwclust/src/distances/calculators.h | 4 dtwclust-6.0.0/dtwclust/src/distmat/R-gateways.h | 1 dtwclust-6.0.0/dtwclust/src/distmat/distmat-loop.cpp | 12 dtwclust-6.0.0/dtwclust/src/distmat/distmat.h | 1 dtwclust-6.0.0/dtwclust/src/distmat/fillers.cpp | 186 ++++++ dtwclust-6.0.0/dtwclust/src/distmat/fillers.h | 42 + dtwclust-6.0.0/dtwclust/src/tadpole/R-gateways.h | 1 dtwclust-6.0.0/dtwclust/src/utils/R-gateways.h | 1 dtwclust-6.0.0/dtwclust/tests/testthat/Rplots.pdf |binary dtwclust-6.0.0/dtwclust/tests/testthat/helper-all.R | 24 dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-01-methods.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-02-misc.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-03-distances.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-04-centroids.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-05-cvis.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-01-unit-06-configs.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-02-integration-01-proxy.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-02-integration-02-families.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-02-integration-03-custom-dist.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-03-acceptance-01-dtwb.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-03-acceptance-02-gak.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-03-acceptance-03-lbs.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-03-acceptance-04-symmetric-proxy.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-01-invalid-inputs.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-02-data-formats.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-03-preproc.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-04-fuzzy.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-05-hierarchical.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-06-partitional.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-07-comparisons.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-04-system-99-rng.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-01-proxy.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-02-dtwb.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-03-family-distmat.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-04-family-centroids.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-05-custom-dist.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-06-cvis.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-07-clusterings.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-05-regression-08-comparisons.R |only dtwclust-6.0.0/dtwclust/tests/testthat/test-06-parallel.R | 1 117 files changed, 1218 insertions(+), 793 deletions(-)
Title: Polygon Clipping
Description: R port of Angus Johnson's open source library 'Clipper'. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
Author: Angus Johnson [aut] ,
Adrian Baddeley [aut, trl, cre],
Kurt Hornik [ctb],
Brian D. Ripley [ctb],
Elliott Sales de Andrade [ctb],
Paul Murrell [ctb],
Ege Rubak [ctb],
Mark Padgham [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between polyclip versions 1.10-6 dated 2023-09-27 and 1.10-7 dated 2024-07-23
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS | 20 ++++++++++++++++++++ src/clipper.cpp | 2 +- src/interface.cpp | 16 +++++++++------- 5 files changed, 40 insertions(+), 18 deletions(-)
Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests.
Includes tools for stubbing 'HTTP' requests, including expected
request conditions and response conditions. Match on
'HTTP' method, query parameters, request body, headers and
more. Can be used for unit tests or outside of a testing
context.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [ctb] ,
rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between webmockr versions 0.9.0 dated 2023-02-28 and 1.0.0 dated 2024-07-23
webmockr-0.9.0/webmockr/R/webmockr.R |only webmockr-1.0.0/webmockr/DESCRIPTION | 16 - webmockr-1.0.0/webmockr/MD5 | 121 +++++----- webmockr-1.0.0/webmockr/NAMESPACE | 4 webmockr-1.0.0/webmockr/NEWS.md | 10 webmockr-1.0.0/webmockr/R/HttpLibAdapterRegistry.R | 2 webmockr-1.0.0/webmockr/R/RequestPattern.R | 27 -- webmockr-1.0.0/webmockr/R/Response.R | 8 webmockr-1.0.0/webmockr/R/adapter-httr.R | 5 webmockr-1.0.0/webmockr/R/adapter-httr2.R |only webmockr-1.0.0/webmockr/R/adapter.R | 59 +++- webmockr-1.0.0/webmockr/R/flipswitch.R | 20 - webmockr-1.0.0/webmockr/R/mocking-disk-writing.R | 67 ++++- webmockr-1.0.0/webmockr/R/onload.R | 3 webmockr-1.0.0/webmockr/R/pluck_body.R | 2 webmockr-1.0.0/webmockr/R/to_raise.R | 4 webmockr-1.0.0/webmockr/R/webmockr-opts.R | 1 webmockr-1.0.0/webmockr/R/webmockr-package.R |only webmockr-1.0.0/webmockr/R/wi_th.R | 4 webmockr-1.0.0/webmockr/man/Adapter.Rd | 52 ++++ webmockr-1.0.0/webmockr/man/StubRegistry.Rd | 4 webmockr-1.0.0/webmockr/man/build_httr2_request.Rd |only webmockr-1.0.0/webmockr/man/build_httr2_response.Rd |only webmockr-1.0.0/webmockr/man/enable.Rd | 10 webmockr-1.0.0/webmockr/man/httr2_mock.Rd |only webmockr-1.0.0/webmockr/man/httr_mock.Rd | 6 webmockr-1.0.0/webmockr/man/mocking-disk-writing.Rd | 49 +++- webmockr-1.0.0/webmockr/man/pluck_body.Rd | 2 webmockr-1.0.0/webmockr/man/remove_request_stub.Rd | 4 webmockr-1.0.0/webmockr/man/to_raise.Rd | 4 webmockr-1.0.0/webmockr/man/to_return.Rd | 4 webmockr-1.0.0/webmockr/man/webmockr-package.Rd | 35 ++ webmockr-1.0.0/webmockr/man/wi_th.Rd | 4 webmockr-1.0.0/webmockr/tests/testthat/helper-webmockr.R | 3 webmockr-1.0.0/webmockr/tests/testthat/httr2_obj.rda |only webmockr-1.0.0/webmockr/tests/testthat/httr2_obj_auth.rda |only webmockr-1.0.0/webmockr/tests/testthat/httr_obj.rda |binary webmockr-1.0.0/webmockr/tests/testthat/httr_obj_auth.rda |binary webmockr-1.0.0/webmockr/tests/testthat/test-CrulAdapter.R | 6 webmockr-1.0.0/webmockr/tests/testthat/test-HashCounter.R | 2 webmockr-1.0.0/webmockr/tests/testthat/test-HttpLibAdapaterRegistry.R | 14 + webmockr-1.0.0/webmockr/tests/testthat/test-Httr2Adapter.R |only webmockr-1.0.0/webmockr/tests/testthat/test-HttrAdapter.R | 69 ++--- webmockr-1.0.0/webmockr/tests/testthat/test-RequestPattern.R | 16 - webmockr-1.0.0/webmockr/tests/testthat/test-RequestSignature.R | 8 webmockr-1.0.0/webmockr/tests/testthat/test-Response.R | 19 - webmockr-1.0.0/webmockr/tests/testthat/test-StubRegistry.R | 2 webmockr-1.0.0/webmockr/tests/testthat/test-StubbedRequest.R | 32 +- webmockr-1.0.0/webmockr/tests/testthat/test-b-no-cassette-in-use.R | 2 webmockr-1.0.0/webmockr/tests/testthat/test-flipswitch.R | 12 webmockr-1.0.0/webmockr/tests/testthat/test-onload.R | 8 webmockr-1.0.0/webmockr/tests/testthat/test-remove_request_stub.R | 4 webmockr-1.0.0/webmockr/tests/testthat/test-request_registry.R | 4 webmockr-1.0.0/webmockr/tests/testthat/test-stub_registry.R | 6 webmockr-1.0.0/webmockr/tests/testthat/test-stub_request.R | 6 webmockr-1.0.0/webmockr/tests/testthat/test-stub_requests_crul.R | 16 - webmockr-1.0.0/webmockr/tests/testthat/test-to_raise.R | 6 webmockr-1.0.0/webmockr/tests/testthat/test-to_return.R | 95 ++++++- webmockr-1.0.0/webmockr/tests/testthat/test-to_return_then.R | 10 webmockr-1.0.0/webmockr/tests/testthat/test-to_timeout.R | 4 webmockr-1.0.0/webmockr/tests/testthat/test-uri_regex.R | 56 ++++ webmockr-1.0.0/webmockr/tests/testthat/test-wi_th.R | 47 ++- webmockr-1.0.0/webmockr/tests/testthat/test-within_test_that_blocks.R | 12 webmockr-1.0.0/webmockr/tests/testthat/test-writing-to-disk-write_disk_path.R | 12 webmockr-1.0.0/webmockr/tests/testthat/test-writing-to-disk.R | 73 +++++- webmockr-1.0.0/webmockr/tests/testthat/test-zutils.R | 2 66 files changed, 730 insertions(+), 343 deletions(-)
Title: Distributional Synthetic Controls Estimation
Description: The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.
Author: David Van Dijcke [aut, cre] ,
Florian Gunsilius [aut] ,
Siyun He [aut]
Maintainer: David Van Dijcke <dvdijcke@umich.edu>
Diff between DiSCos versions 0.1.0 dated 2024-05-13 and 0.1.1 dated 2024-07-22
DESCRIPTION | 16 ++-- MD5 | 20 ++--- R/DiSCo.R | 6 + R/DiSCoTEA.R | 6 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/Dube2019.R | 2 inst/doc/Dube2019.Rmd | 2 inst/doc/Dube2019.html | 142 +---------------------------------------- tests/testthat/test-DiSCoTEA.R | 2 vignettes/Dube2019.Rmd | 2 11 files changed, 37 insertions(+), 161 deletions(-)
Title: Access Databases from the Federal Statistical Office of Germany
Description: Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service <https://www-genesis.destatis.de/>.
Author: Moritz Marbach [aut, cre]
Maintainer: Moritz Marbach <m.marbach@ucl.ac.uk>
Diff between wiesbaden versions 1.2.9 dated 2023-02-17 and 1.2.10 dated 2024-07-22
DESCRIPTION | 13 +++-- MD5 | 32 +++++++------- NAMESPACE | 1 NEWS.md | 5 ++ R/read_gv100.R | 10 +--- R/read_header_genesis.R | 2 R/retrieve_data.R | 4 + R/save_credentials.R | 4 - R/wiesbaden-package.R | 4 - build/vignette.rds |binary inst/doc/wiesbaden.R | 2 inst/doc/wiesbaden.html | 100 ++++++++++++++++++++++----------------------- man/read_gv100.Rd | 7 +-- man/read_header_genesis.Rd | 2 man/retrieve_data.Rd | 4 + man/save_credentials.Rd | 5 -- man/wiesbaden-package.Rd | 2 17 files changed, 104 insertions(+), 93 deletions(-)
Title: 'WebSocket' Client Library
Description: Provides a 'WebSocket' client interface for R.
'WebSocket' is a protocol for low-overhead real-time communication:
<https://en.wikipedia.org/wiki/WebSocket>.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit, PBC [cph],
Peter Thorson [ctb, cph] ,
Rene Nyffenegger [ctb, cph] ,
Micael Hildenborg [ctb, cph] ,
Aladdin Enterprises [cph] ,
Bjoern Hoehrmann [ctb, cph]
Maintainer: Winston Chang <winston@posit.co>
Diff between websocket versions 1.4.1 dated 2021-08-18 and 1.4.2 dated 2024-07-22
websocket-1.4.1/websocket/man/figures/websocket_logo.svg |only websocket-1.4.2/websocket/DESCRIPTION | 20 websocket-1.4.2/websocket/MD5 | 28 websocket-1.4.2/websocket/NEWS.md | 6 websocket-1.4.2/websocket/README.md | 4 websocket-1.4.2/websocket/build/vignette.rds |binary websocket-1.4.2/websocket/cleanup | 2 websocket-1.4.2/websocket/inst/doc/overview.R | 10 websocket-1.4.2/websocket/inst/doc/overview.html | 325 ++++++---- websocket-1.4.2/websocket/man/figures/logo.svg |only websocket-1.4.2/websocket/src/Makevars.in | 3 websocket-1.4.2/websocket/src/Makevars.win | 2 websocket-1.4.2/websocket/src/cpp11.cpp | 14 websocket-1.4.2/websocket/src/lib/websocketpp/endpoint.hpp | 2 websocket-1.4.2/websocket/src/lib/websocketpp/logger/basic.hpp | 14 websocket-1.4.2/websocket/src/websocket.cpp | 2 16 files changed, 246 insertions(+), 186 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 6.5.0-4 dated 2023-12-08 and 6.5.0-5 dated 2024-07-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ build/partial.rdb |binary cleanup | 2 +- inst/include/r2sundials.h | 2 +- inst/unitTests/runit.r2cvodes.R | 2 +- src/r2sundials.cpp | 6 +++--- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Efficiently Impute Large Scale Incomplete Matrix
Description: Efficiently impute large scale matrix with missing values via its unbiased low-rank matrix approximation. Our main approach is Hard-Impute algorithm proposed in <https://www.jmlr.org/papers/v11/mazumder10a.html>, which achieves highly computational advantage by truncated singular-value decomposition.
Author: Zhe Gao [aut, cre],
Jin Zhu [aut],
Junxian Zhu [aut],
Xueqin Wang [aut],
Yixuan Qiu [cph],
Gael Guennebaud [cph, ctb],
Jitse Niesen [cph, ctb],
Ray Gardner [ctb]
Maintainer: Zhe Gao <gaozh8@mail.ustc.edu.cn>
Diff between eimpute versions 0.2.3 dated 2024-02-18 and 0.2.4 dated 2024-07-22
DESCRIPTION | 14 +++---- MD5 | 19 +++++---- NEWS.md | 8 +--- R/r.search.R | 6 +-- build/vignette.rds |binary inst/doc/eimpute.R | 6 +-- inst/doc/eimpute.html | 48 ++++++++++++------------ inst/include/Spectra/MatOp/internal/ArnoldiOp.h | 2 - src/Makevars | 7 --- src/Makevars.win | 7 --- vignettes/toyex.png |only 11 files changed, 49 insertions(+), 68 deletions(-)
Title: Download, Wrangle, and Analyse Vessel Monitoring System Data
Description: Allows to download, clean and analyse raw Vessel Monitoring System, VMS, data from
Mexican government. You can use the vms_download() function to
download raw data, or you can use the sample_dataset provided within
the package. You can follow the tutorial in the vignette available at
<https://cbmc-gcmp.github.io/dafishr/index.html>.
Author: Fabio Favoretto [aut, cre] ,
Eduardo Leon Solorzano [ctb]
Maintainer: Fabio Favoretto <fabio@gocmarineprogram.org>
Diff between dafishr versions 1.0.0 dated 2022-12-06 and 1.0.1 dated 2024-07-22
DESCRIPTION | 13 +++++------ MD5 | 16 +++++++------- R/all_mpas.R | 2 - R/remote_mpas.R | 2 - README.md | 8 +++++-- build/vignette.rds |binary inst/doc/dafisr.html | 56 +++++++++++++++++++++++++-------------------------- man/all_mpas.Rd | 2 - man/remote_mpas.Rd | 2 - 9 files changed, 52 insertions(+), 49 deletions(-)
Title: Tidy Model Stacking
Description: Model stacking is an ensemble technique that involves
training a model to combine the outputs of many diverse statistical
models, and has been shown to improve predictive performance in a
variety of settings. 'stacks' implements a grammar for
'tidymodels'-aligned model stacking.
Author: Simon Couch [aut, cre],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between stacks versions 1.0.4 dated 2024-03-21 and 1.0.5 dated 2024-07-22
DESCRIPTION | 6 ++-- MD5 | 20 +++++++-------- NEWS.md | 7 +++++ R/blend_predictions.R | 5 +++ R/butcher.R | 3 +- R/collect_parameters.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/basics.html | 54 +++++++++++++++++++++---------------------- inst/doc/classification.html | 10 +++---- man/axe_model_stack.Rd | 2 - 11 files changed, 61 insertions(+), 48 deletions(-)
Title: Bayesian Recurrent Events Analysis
Description: Functions to produce MCMC samples for posterior inference in semiparametric Bayesian discrete time competing risks recurrent events models and multistate models.
Author: Adam J King
Maintainer: Adam J King <king@cpp.edu>
Diff between brea versions 0.3.0 dated 2024-07-02 and 0.3.1 dated 2024-07-22
DESCRIPTION | 10 ++++++---- MD5 | 8 +++++++- build |only inst |only vignettes |only 5 files changed, 13 insertions(+), 5 deletions(-)
Title: Bayesian Estimation of Multivariate Threshold Autoregressive
Models
Description: Estimation, inference and forecasting using the Bayesian approach for multivariate threshold autoregressive (TAR) models in which the distribution used to describe the noise process belongs to the class of Gaussian variance mixtures.
Author: Luis Hernando Vanegas [aut, cre],
Sergio Alejandro Calderon [aut],
Luz Marina Rondon [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between mtarm versions 0.1.1 dated 2024-06-04 and 0.1.2 dated 2024-07-22
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NAMESPACE | 1 R/mtar.R | 71 ++++++++++++++++++++++++++++++++++++++++------------ data/riverflows.rda |binary 5 files changed, 63 insertions(+), 23 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Lane Burgette <burgette@rand.org>
Diff between twang versions 2.6 dated 2023-12-05 and 2.6.1 dated 2024-07-22
DESCRIPTION | 10 - MD5 | 26 ++-- R/bal.stat.fast.R | 227 ++++++++++++++++++++--------------------- R/iptw.R | 23 ++-- R/mnps.R | 22 ++-- R/mnps.fast.R | 288 ++++++++++++++++++++++++++--------------------------- R/ps.R | 23 ++-- build/vignette.rds |binary inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.pdf |binary man/iptw.Rd | 21 ++- man/mnps.Rd | 22 ++-- man/ps.Rd | 23 ++-- 14 files changed, 347 insertions(+), 338 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 0.20.0 dated 2024-06-28 and 0.20.1 dated 2024-07-22
DESCRIPTION | 10 +-- MD5 | 84 ++++++++++++++++---------------- NEWS.md | 4 + R/Learner.R | 2 R/MeasureSimple.R | 8 +-- R/set_validate.R | 2 R/worker.R | 3 + README.md | 8 +-- man/Learner.Rd | 2 man/mlr_measures_classif.acc.Rd | 3 - man/mlr_measures_classif.auc.Rd | 1 man/mlr_measures_classif.bacc.Rd | 3 - man/mlr_measures_classif.bbrier.Rd | 1 man/mlr_measures_classif.ce.Rd | 3 - man/mlr_measures_classif.costs.Rd | 3 - man/mlr_measures_classif.dor.Rd | 1 man/mlr_measures_classif.fbeta.Rd | 1 man/mlr_measures_classif.fdr.Rd | 1 man/mlr_measures_classif.fn.Rd | 1 man/mlr_measures_classif.fnr.Rd | 1 man/mlr_measures_classif.fomr.Rd | 1 man/mlr_measures_classif.fp.Rd | 1 man/mlr_measures_classif.fpr.Rd | 1 man/mlr_measures_classif.logloss.Rd | 3 - man/mlr_measures_classif.mauc_au1p.Rd | 3 - man/mlr_measures_classif.mauc_au1u.Rd | 3 - man/mlr_measures_classif.mauc_aunp.Rd | 3 - man/mlr_measures_classif.mauc_aunu.Rd | 3 - man/mlr_measures_classif.mbrier.Rd | 3 - man/mlr_measures_classif.mcc.Rd | 63 ++++++++++++------------ man/mlr_measures_classif.npv.Rd | 1 man/mlr_measures_classif.ppv.Rd | 1 man/mlr_measures_classif.prauc.Rd | 1 man/mlr_measures_classif.precision.Rd | 1 man/mlr_measures_classif.recall.Rd | 1 man/mlr_measures_classif.sensitivity.Rd | 1 man/mlr_measures_classif.specificity.Rd | 1 man/mlr_measures_classif.tn.Rd | 1 man/mlr_measures_classif.tnr.Rd | 1 man/mlr_measures_classif.tp.Rd | 1 man/mlr_measures_classif.tpr.Rd | 1 man/mlr_sugar.Rd | 2 tests/testthat/test_Learner.R | 7 ++ 43 files changed, 126 insertions(+), 120 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.15.0.3 dated 2024-05-10 and 1.15.1 dated 2024-07-22
DESCRIPTION | 8 - MD5 | 30 +++---- NAMESPACE | 1 R/asSepList.R | 21 ++--- R/makeNRedMatr.R | 66 ++++++++++------ R/rmOrphans.R |only R/summarizeCols.R | 144 ++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 27 ++++++ inst/doc/wrMiscVignette1.Rmd | 48 +++++++++++ inst/doc/wrMiscVignette1.html | 171 ++++++++++++++++++++++++++++++------------ man/dot-sortMid.Rd | 3 man/dot-summarizeCols.Rd | 23 ++++- man/makeNRedMatr.Rd | 24 ++++- man/rmOrphans.Rd |only man/summarizeCols.Rd | 22 +++-- vignettes/wrMiscVignette1.Rmd | 48 +++++++++++ 17 files changed, 475 insertions(+), 161 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition.
The method is based on a Principal Component Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut, cre],
Remi Servien [aut] ,
Nathalie Vialaneix [aut]
Maintainer: Camille Guilmineau <camille.guilmineau@inrae.fr>
Diff between phoenics versions 0.2 dated 2024-06-27 and 0.3 dated 2024-07-22
DESCRIPTION | 8 MD5 | 6 NEWS.md | 14 + inst/adddata/ASICS_library_codes.txt | 407 ++++++++++++++++++----------------- 4 files changed, 236 insertions(+), 199 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current
literature on landscape metrics. This package supports 'terra' SpatRaster objects
as input arguments. It further provides utility functions to visualize patches,
select metrics and building blocks to develop new metrics.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Jakub Nowosad [aut] ,
Sebastian Hanss [aut] ,
Laura J. Graham [ctb] ,
Jeffrey Hollister [ctb] ,
Kimberly A. With [ctb] ,
Florian Prive [ctb] function),
Project Nayuki [ctb] ,
Matt Strima [...truncated...]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between landscapemetrics versions 2.1.3 dated 2024-06-26 and 2.1.4 dated 2024-07-22
DESCRIPTION | 8 MD5 | 20 NAMESPACE | 1 NEWS.md | 586 +++++++------ R/RcppExports.R | 218 ++--- R/landscape_as_list.R | 14 build/vignette.rds |binary inst/doc/get_started.R | 198 ++-- inst/doc/get_started.html | 1344 ++++++++++++++++---------------- man/landscape_as_list.Rd | 3 tests/testthat/test-landscape_as_list.R | 1 11 files changed, 1208 insertions(+), 1185 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Sebastian Fischer [aut, cre] ,
Maximilian Muecke [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3fda versions 0.1.2 dated 2024-05-30 and 0.2.0 dated 2024-07-22
mlr3fda-0.1.2/mlr3fda/tests/testhat |only mlr3fda-0.1.2/mlr3fda/tests/testthat/helper_mlr3pipelines.R |only mlr3fda-0.2.0/mlr3fda/DESCRIPTION | 42 +++-- mlr3fda-0.2.0/mlr3fda/MD5 | 73 +++++----- mlr3fda-0.2.0/mlr3fda/NAMESPACE | 2 mlr3fda-0.2.0/mlr3fda/NEWS.md | 8 - mlr3fda-0.2.0/mlr3fda/R/PipeOpFDACor.R |only mlr3fda-0.2.0/mlr3fda/R/PipeOpFDAExtract.R | 10 - mlr3fda-0.2.0/mlr3fda/R/PipeOpFDAFlatten.R | 8 - mlr3fda-0.2.0/mlr3fda/R/PipeOpFDAInterpol.R | 12 - mlr3fda-0.2.0/mlr3fda/R/PipeOpFDAScaleRange.R |only mlr3fda-0.2.0/mlr3fda/R/PipeOpFDASmooth.R | 23 +-- mlr3fda-0.2.0/mlr3fda/R/PipeOpFPCA.R | 24 ++- mlr3fda-0.2.0/mlr3fda/R/TaskClassif_phoneme.R | 2 mlr3fda-0.2.0/mlr3fda/R/TaskRegr_dti.R | 2 mlr3fda-0.2.0/mlr3fda/R/TaskRegr_fuel.R | 2 mlr3fda-0.2.0/mlr3fda/R/zzz.R | 6 mlr3fda-0.2.0/mlr3fda/README.md | 18 +- mlr3fda-0.2.0/mlr3fda/build/partial.rdb |binary mlr3fda-0.2.0/mlr3fda/man/mlr3fda-package.Rd | 4 mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.cor.Rd |only mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.extract.Rd | 6 mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.flatten.Rd | 4 mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.fpca.Rd | 7 mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.interpol.Rd | 8 - mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.scalerange.Rd |only mlr3fda-0.2.0/mlr3fda/man/mlr_pipeops_fda.smooth.Rd | 14 - mlr3fda-0.2.0/mlr3fda/man/mlr_tasks_dti.Rd | 9 - mlr3fda-0.2.0/mlr3fda/man/mlr_tasks_fuel.Rd | 9 - mlr3fda-0.2.0/mlr3fda/man/mlr_tasks_phoneme.Rd | 9 - mlr3fda-0.2.0/mlr3fda/tests/testthat/helper.R | 5 mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpCor.R |only mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpFDAExtract.R | 58 +++---- mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpFDAFlatten.R | 2 mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpFDAInterpolate.R | 12 + mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpFDASmooth.R | 13 + mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpFPCA.R | 38 ++--- mlr3fda-0.2.0/mlr3fda/tests/testthat/test_PipeOpScaleRange.R |only mlr3fda-0.2.0/mlr3fda/tests/testthat/test_TaskClassif_phoneme.R |only mlr3fda-0.2.0/mlr3fda/tests/testthat/test_TaskRegr_dti.R | 2 mlr3fda-0.2.0/mlr3fda/tests/testthat/test_hash_input.R | 4 mlr3fda-0.2.0/mlr3fda/tests/testthat/test_tf.R | 4 42 files changed, 227 insertions(+), 213 deletions(-)
Title: Sensitivity Analysis Tools for Regression Models
Description: Implements a suite of sensitivity analysis tools
that extends the traditional omitted variable bias framework and makes it easier
to understand the impact of omitted variables in regression models, as discussed in Cinelli, C. and Hazlett, C. (2020), "Making Sense of Sensitivity: Extending Omitted Variable Bias." Journal of the Royal Statistical Society, Series B (Statistical Methodology) <doi:10.1111/rssb.12348>.
Author: Carlos Cinelli [aut, cre],
Jeremy Ferwerda [aut],
Chad Hazlett [aut],
Danielle Tsao [ctb],
Aaron Rudkin [ctb],
Grigorij Ljubownikow [ctb]
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sensemakr versions 0.1.4 dated 2021-10-08 and 0.1.6 dated 2024-07-22
sensemakr-0.1.4/sensemakr/vignettes/darfur_dag.png |only sensemakr-0.1.6/sensemakr/DESCRIPTION | 20 sensemakr-0.1.6/sensemakr/MD5 | 90 - sensemakr-0.1.6/sensemakr/NAMESPACE | 35 sensemakr-0.1.6/sensemakr/R/bias_functions.R | 285 +++ sensemakr-0.1.6/sensemakr/R/data.R | 1 sensemakr-0.1.6/sensemakr/R/other.R | 1 sensemakr-0.1.6/sensemakr/R/ovb_bounds.R | 205 ++ sensemakr-0.1.6/sensemakr/R/ovb_plots.R | 375 ++++ sensemakr-0.1.6/sensemakr/R/print.R | 2 sensemakr-0.1.6/sensemakr/R/sensemakr.R | 213 ++ sensemakr-0.1.6/sensemakr/R/sensitivity_stats.R | 499 +++++ sensemakr-0.1.6/sensemakr/build/vignette.rds |binary sensemakr-0.1.6/sensemakr/inst/doc/informal_benchmarking.R | 12 sensemakr-0.1.6/sensemakr/inst/doc/informal_benchmarking.html | 598 +++++-- sensemakr-0.1.6/sensemakr/inst/doc/sensemakr.R | 16 sensemakr-0.1.6/sensemakr/inst/doc/sensemakr.html | 834 +++++++--- sensemakr-0.1.6/sensemakr/man/add_bound_to_contour.Rd | 34 sensemakr-0.1.6/sensemakr/man/adjusted_critical_value.Rd |only sensemakr-0.1.6/sensemakr/man/adjusted_estimate.Rd | 100 + sensemakr-0.1.6/sensemakr/man/darfur.Rd | 2 sensemakr-0.1.6/sensemakr/man/figures/figures-basic-usage-2.png |binary sensemakr-0.1.6/sensemakr/man/figures/figures-basic-usage-3.png |binary sensemakr-0.1.6/sensemakr/man/figures/figures-basic-usage-4.png |only sensemakr-0.1.6/sensemakr/man/group_partial_r2.Rd | 9 sensemakr-0.1.6/sensemakr/man/model_helper.Rd | 1 sensemakr-0.1.6/sensemakr/man/ovb_bounds.Rd | 53 sensemakr-0.1.6/sensemakr/man/ovb_contour_plot.Rd | 70 sensemakr-0.1.6/sensemakr/man/ovb_extreme_plot.Rd | 39 sensemakr-0.1.6/sensemakr/man/partial_r2.Rd | 26 sensemakr-0.1.6/sensemakr/man/resid_maker.Rd | 1 sensemakr-0.1.6/sensemakr/man/robustness_value.Rd | 107 + sensemakr-0.1.6/sensemakr/man/sensemakr-package.Rd | 2 sensemakr-0.1.6/sensemakr/man/sensemakr.Rd | 46 sensemakr-0.1.6/sensemakr/man/sensitivity_stats.Rd | 39 sensemakr-0.1.6/sensemakr/tests/testthat/Rplots.pdf |binary sensemakr-0.1.6/sensemakr/tests/testthat/test-01-manual-tests.R | 18 sensemakr-0.1.6/sensemakr/tests/testthat/test-02-darfur.R | 30 sensemakr-0.1.6/sensemakr/tests/testthat/test-03-contour.R | 2 sensemakr-0.1.6/sensemakr/tests/testthat/test-05-robustness_value.R | 41 sensemakr-0.1.6/sensemakr/tests/testthat/test-07-bounds.R | 2 sensemakr-0.1.6/sensemakr/tests/testthat/test-10-rv-xrv.R | 148 + sensemakr-0.1.6/sensemakr/tests/testthat/test-12-reduce-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-13-darfur-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-14-contour-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-15-extreme_fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-16-robustness_value-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-17-misc-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-18-bounds-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-19-bias_functions-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-20-plots-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-21-print-fixest.R |only sensemakr-0.1.6/sensemakr/tests/testthat/test-22-t-dagger.R |only 53 files changed, 3279 insertions(+), 677 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding and decoding. Performs direct hashing of strings and raw vectors.
Stream hashes files potentially larger than memory, as well as in-memory
objects through R's serialization mechanism. Implementations include the
SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256
extendable-output function (XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.0 dated 2024-06-16 and 1.0.1 dated 2024-07-22
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- NEWS.md | 4 ++ README.md | 105 ++++++++++++++++++++++++++++-------------------------- build/partial.rdb |binary src/base.c | 72 +++++++++++++++++++------------------ src/secret.c | 43 +++++++++++++--------- src/secret.h | 17 +++++++- src/secret2.c | 24 ++++++------ src/secret3.c | 18 ++++----- tests/tests.R | 13 ++++-- 11 files changed, 184 insertions(+), 140 deletions(-)
Title: Propensity Score Matching for Unordered 3-Group Data
Description: You can use this program for 3 sets of categorical data for propensity score matching.
Assume that the data has 3 different categorical variables. You can use it to perform propensity matching of baseline indicator groupings.
The matching will make the differences in the baseline data smaller.
This method was described by Alvaro Fuentes (2022) <doi:10.1080/00273171.2021.1925521>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between pm3 versions 0.1.9 dated 2023-06-17 and 0.2.0 dated 2024-07-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/datach.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Analyze and Create Elegant Directed Acyclic Graphs
Description: Tidy, analyze, and plot directed acyclic graphs (DAGs).
'ggdag' is built on top of 'dagitty', an R package that uses the
'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing
DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using
'ggplot2' and 'ggraph', as well as common analytic and graphical
functions, such as determining adjustment sets and node relationships.
Author: Malcolm Barrett [aut, cre]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ggdag versions 0.2.12 dated 2024-03-08 and 0.2.13 dated 2024-07-22
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 2 ++ R/tidy_dag.R | 9 +++++---- R/utils.R | 8 ++++++++ inst/doc/bias-structures.html | 4 ++-- inst/doc/intro-to-dags.Rmd | 2 +- inst/doc/intro-to-dags.html | 6 +++--- inst/doc/intro-to-ggdag.html | 31 +++++-------------------------- tests/testthat/test-tidy_dag.R | 5 +++++ vignettes/intro-to-dags.Rmd | 2 +- 11 files changed, 45 insertions(+), 50 deletions(-)
Title: Framework for Easy Statistical Modeling, Visualization, and
Reporting
Description: A meta-package that installs and loads a set of packages from
'easystats' ecosystem in a single step. This collection of packages provide
a unifying and consistent framework for statistical modeling, visualization,
and reporting. Additionally, it provides articles targeted at instructors for
teaching 'easystats', and a dashboard targeted at new R users for easily
conducting statistical analysis by accessing summary results, model fit indices,
and visualizations with minimal programming.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Etienne Bacher [aut] ,
Remi Theriault [aut]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between easystats versions 0.7.2 dated 2024-06-06 and 0.7.3 dated 2024-07-22
easystats-0.7.2/easystats/man/figures/unnamed-chunk-8-1.png |only easystats-0.7.3/easystats/DESCRIPTION | 37 easystats-0.7.3/easystats/MD5 | 50 - easystats-0.7.3/easystats/NAMESPACE | 1 easystats-0.7.3/easystats/NEWS.md | 15 easystats-0.7.3/easystats/R/easystats_update.R | 28 easystats-0.7.3/easystats/R/install_easystats.R | 2 easystats-0.7.3/easystats/R/install_suggested.R | 65 - easystats-0.7.3/easystats/R/utils.R | 87 -- easystats-0.7.3/easystats/R/zzz.R | 2 easystats-0.7.3/easystats/README.md | 24 easystats-0.7.3/easystats/build/vignette.rds |binary easystats-0.7.3/easystats/inst/CITATION | 3 easystats-0.7.3/easystats/inst/WORDLIST | 6 easystats-0.7.3/easystats/inst/doc/citation.Rmd | 4 easystats-0.7.3/easystats/inst/doc/list_of_functions.R | 4 easystats-0.7.3/easystats/inst/doc/list_of_functions.Rmd | 4 easystats-0.7.3/easystats/inst/doc/list_of_functions.html | 4 easystats-0.7.3/easystats/inst/doc/workflow_performance.html | 428 +++++------ easystats-0.7.3/easystats/inst/templates/easydashboard.Rmd | 16 easystats-0.7.3/easystats/man/easystats_packages.Rd |only easystats-0.7.3/easystats/man/figures/depnetwork-1.png |binary easystats-0.7.3/easystats/man/figures/logo_wall.png |binary easystats-0.7.3/easystats/man/figures/unnamed-chunk-7-1.png |binary easystats-0.7.3/easystats/man/install_suggested.Rd | 3 easystats-0.7.3/easystats/vignettes/citation.Rmd | 4 easystats-0.7.3/easystats/vignettes/list_of_functions.Rmd | 4 27 files changed, 368 insertions(+), 423 deletions(-)
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Description: A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Author: Massimo Andreatta [aut, cre] ,
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>
Diff between GeneNMF versions 0.4.0 dated 2024-02-29 and 0.6.0 dated 2024-07-22
DESCRIPTION | 14 +- MD5 | 37 +++--- NAMESPACE | 9 + R/main.R | 276 +++++++++++++++++++++++++++++++++++------------ R/utils.R | 169 +++++++++++++++++++++++----- README.md | 54 ++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 10 + inst/doc/make.index.Rmd | 4 inst/doc/make.index.html | 9 + man/getDataMatrix.Rd | 10 + man/getMetaPrograms.Rd | 31 +++-- man/getNMFgenes.Rd | 19 ++- man/multiNMF.Rd | 7 - man/multiPCA.Rd |only man/plotMetaPrograms.Rd | 10 - man/runGSEA.Rd | 13 +- man/runNMF.Rd | 7 - vignettes/make.index.Rmd | 4 20 files changed, 514 insertions(+), 169 deletions(-)
Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad
Networks
Description: Many tools for making, modifying, mapping, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.0.1 dated 2024-07-17 and 1.0.2 dated 2024-07-22
DESCRIPTION | 13 MD5 | 41 NEWS.md | 70 + R/reexports_classes.R | 2 README.md | 164 ++- build/partial.rdb |binary inst/tutorials/tutorial0/tutorial0.Rmd | 257 +++-- inst/tutorials/tutorial0/tutorial0.html |only inst/tutorials/tutorial1/data.Rmd | 330 +++++-- inst/tutorials/tutorial1/data.html | 1197 ++++++++++++++++++------- inst/tutorials/tutorial2/visualisation.Rmd | 433 ++++++--- inst/tutorials/tutorial2/visualisation.html | 1298 ++++++++++++++++++++++------ inst/tutorials/tutorial3/centrality.Rmd | 150 ++- inst/tutorials/tutorial3/centrality.html | 510 ++++++++--- inst/tutorials/tutorial4/community.Rmd | 77 - inst/tutorials/tutorial4/community.html | 645 ++++++------- inst/tutorials/tutorial5/position.Rmd | 29 inst/tutorials/tutorial5/position.html | 262 ++--- inst/tutorials/tutorial6/topology.Rmd | 33 inst/tutorials/tutorial6/topology.html | 330 +++---- inst/tutorials/tutorial7/diffusion.Rmd | 22 inst/tutorials/tutorial7/diffusion.html | 152 +-- 22 files changed, 4048 insertions(+), 1967 deletions(-)
Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.2.1 dated 2024-04-02 and 1.3.0 dated 2024-07-22
DESCRIPTION | 10 ++-- MD5 | 22 ++++----- NEWS.md | 6 ++ R/dsem.R | 30 ++++++++++++- README.md | 1 build/vignette.rds |binary inst/doc/dynamic_factor_analysis.html | 36 +++++++--------- inst/doc/vignette.html | 20 ++++----- man/as_fitted_DAG.Rd | 7 ++- man/dsem_control.Rd | 16 +++++++ src/dsem.cpp | 61 ++++++++++++++++++++++++++- tests/testthat/test-gmrf-versions.R | 75 ++++++++++++++++++++++++++++++++++ 12 files changed, 232 insertions(+), 52 deletions(-)
Title: UK Biobank COVID-19 Data Processing and Risk Factor Association
Tests
Description: Process UK Biobank COVID-19 test result data for susceptibility, severity and mortality analyses, perform potential non-genetic COVID-19 risk factor and co-morbidity association tests. Wang et al. (2021) <doi:10.5281/zenodo.5174381>.
Author: Longfei Wang [aut, cre]
Maintainer: Longfei Wang <wang.lo@wehi.edu.au>
Diff between UKB.COVID19 versions 0.1.4 dated 2024-01-24 and 0.1.5 dated 2024-07-22
DESCRIPTION | 13 +++++++------ MD5 | 9 +++++++-- NEWS.md | 12 ++++++++++++ build |only inst/doc |only vignettes |only 6 files changed, 26 insertions(+), 8 deletions(-)
Title: Network Analysis and Causal Inference Through Structural
Equation Modeling
Description: Estimate networks and causal relationships in complex systems through
Structural Equation Modeling. This package also includes functions to import,
weight, manipulate, and fit biological network models within the
Structural Equation Modeling framework proposed in
Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.
Author: Mario Grassi [aut],
Fernando Palluzzi [aut],
Barbara Tarantino [aut, cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMgraph versions 1.2.1 dated 2024-02-06 and 1.2.2 dated 2024-07-22
SEMgraph-1.2.1/SEMgraph/man/predictSink.Rd |only SEMgraph-1.2.2/SEMgraph/DESCRIPTION | 8 SEMgraph-1.2.2/SEMgraph/MD5 | 45 +-- SEMgraph-1.2.2/SEMgraph/NAMESPACE | 1 SEMgraph-1.2.2/SEMgraph/NEWS.md | 20 + SEMgraph-1.2.2/SEMgraph/R/ALSdata.R | 2 SEMgraph-1.2.2/SEMgraph/R/semCluster.R | 8 SEMgraph-1.2.2/SEMgraph/R/semFit.R | 50 +-- SEMgraph-1.2.2/SEMgraph/R/semLearn.R | 10 SEMgraph-1.2.2/SEMgraph/R/semPaths.R | 2 SEMgraph-1.2.2/SEMgraph/R/semTools.R | 342 ------------------------- SEMgraph-1.2.2/SEMgraph/R/semUtils.R | 4 SEMgraph-1.2.2/SEMgraph/man/SEMrun.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/SEMtree.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/Shipley.test.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/alsData.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/clusterGraph.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/colorGraph.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/cplot.Rd | 4 SEMgraph-1.2.2/SEMgraph/man/extractClusters.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/modelSearch.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/pathFinder.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/resizeGraph.Rd | 2 SEMgraph-1.2.2/SEMgraph/man/transformData.Rd | 25 - 24 files changed, 91 insertions(+), 450 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-17 1.1.5
2022-03-10 1.1.4
2022-01-19 1.1.3
2021-10-06 1.1.2
2021-09-16 1.1.1
2021-06-04 1.1.0
Title: 3D Software Rasterizer
Description: Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Vilya Harvey [ctb, cph],
G-Truc Creation [ctb, cph],
Sean Barrett [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayvertex versions 0.10.4 dated 2023-12-16 and 0.11.4 dated 2024-07-22
rayvertex-0.10.4/rayvertex/src/earcut.h |only rayvertex-0.10.4/rayvertex/src/stb_image.h |only rayvertex-0.10.4/rayvertex/src/tiny_obj_loader.h |only rayvertex-0.11.4/rayvertex/DESCRIPTION | 13 rayvertex-0.11.4/rayvertex/MD5 | 140 ++++++---- rayvertex-0.11.4/rayvertex/NAMESPACE | 4 rayvertex-0.11.4/rayvertex/R/RcppExports.R | 16 + rayvertex-0.11.4/rayvertex/R/add_plane_uv_mesh.R | 71 ++++- rayvertex-0.11.4/rayvertex/R/add_shape.R | 26 + rayvertex-0.11.4/rayvertex/R/construct_mesh.R | 24 - rayvertex-0.11.4/rayvertex/R/displace_mesh.R |only rayvertex-0.11.4/rayvertex/R/displacement_sphere.R |only rayvertex-0.11.4/rayvertex/R/generate_surface.R |only rayvertex-0.11.4/rayvertex/R/lines.R | 2 rayvertex-0.11.4/rayvertex/R/material_functions.R | 67 +++- rayvertex-0.11.4/rayvertex/R/merge_scene.R | 2 rayvertex-0.11.4/rayvertex/R/objects.R | 64 ++-- rayvertex-0.11.4/rayvertex/R/r_obj.R | 22 + rayvertex-0.11.4/rayvertex/R/rasterize_scene.R | 69 ++-- rayvertex-0.11.4/rayvertex/R/rayvertex_classes.R |only rayvertex-0.11.4/rayvertex/R/readobj.R | 44 ++- rayvertex-0.11.4/rayvertex/R/remove_duplicate_materials.R | 21 - rayvertex-0.11.4/rayvertex/R/scene_from_list.R | 39 +- rayvertex-0.11.4/rayvertex/R/smooth_normals_mesh.R | 22 + rayvertex-0.11.4/rayvertex/R/subdivide_mesh.R |only rayvertex-0.11.4/rayvertex/R/swap_yz.R | 20 + rayvertex-0.11.4/rayvertex/R/transform_mesh_functions.R | 79 ++--- rayvertex-0.11.4/rayvertex/R/util_functions.R | 3 rayvertex-0.11.4/rayvertex/R/validate_mesh.R | 5 rayvertex-0.11.4/rayvertex/R/write_scene_to_obj.R | 8 rayvertex-0.11.4/rayvertex/R/zzz.R | 66 ++++ rayvertex-0.11.4/rayvertex/inst/extdata/3d_r_logo.txt |only rayvertex-0.11.4/rayvertex/inst/extdata/3d_r_logo_mat.txt |only rayvertex-0.11.4/rayvertex/inst/extdata/cube.txt | 4 rayvertex-0.11.4/rayvertex/man/add_plane_uv_mesh.Rd | 6 rayvertex-0.11.4/rayvertex/man/add_sphere_uv_mesh.Rd |only rayvertex-0.11.4/rayvertex/man/cat_color.Rd |only rayvertex-0.11.4/rayvertex/man/change_material.Rd | 14 - rayvertex-0.11.4/rayvertex/man/convert_rgb_to_ansi.Rd |only rayvertex-0.11.4/rayvertex/man/displace_mesh.Rd |only rayvertex-0.11.4/rayvertex/man/displacement_sphere.Rd |only rayvertex-0.11.4/rayvertex/man/format_pillar_shp.Rd |only rayvertex-0.11.4/rayvertex/man/generate_cornell_mesh.Rd | 8 rayvertex-0.11.4/rayvertex/man/generate_line.Rd | 2 rayvertex-0.11.4/rayvertex/man/generate_surface.Rd |only rayvertex-0.11.4/rayvertex/man/get_mesh_center.Rd | 2 rayvertex-0.11.4/rayvertex/man/material_list.Rd | 6 rayvertex-0.11.4/rayvertex/man/mesh3d_mesh.Rd | 15 - rayvertex-0.11.4/rayvertex/man/obj_mesh.Rd | 2 rayvertex-0.11.4/rayvertex/man/pillar_shaft.ray_shape.Rd |only rayvertex-0.11.4/rayvertex/man/pillar_shaft.ray_shape_list.Rd |only rayvertex-0.11.4/rayvertex/man/print.ray_shape.Rd |only rayvertex-0.11.4/rayvertex/man/print.ray_vertex_data.Rd |only rayvertex-0.11.4/rayvertex/man/r_obj.Rd | 18 - rayvertex-0.11.4/rayvertex/man/rasterize_scene.Rd | 5 rayvertex-0.11.4/rayvertex/man/ray_mesh.Rd |only rayvertex-0.11.4/rayvertex/man/ray_shape.Rd |only rayvertex-0.11.4/rayvertex/man/ray_shape_list.Rd |only rayvertex-0.11.4/rayvertex/man/ray_vertex_data.Rd |only rayvertex-0.11.4/rayvertex/man/rotate_mesh.Rd | 14 - rayvertex-0.11.4/rayvertex/man/scale_mesh.Rd | 8 rayvertex-0.11.4/rayvertex/man/scale_unit_mesh.Rd | 10 rayvertex-0.11.4/rayvertex/man/set_material.Rd | 4 rayvertex-0.11.4/rayvertex/man/smooth_normals_mesh.Rd | 4 rayvertex-0.11.4/rayvertex/man/sphere_mesh.Rd | 3 rayvertex-0.11.4/rayvertex/man/subdivide_mesh.Rd |only rayvertex-0.11.4/rayvertex/man/swap_yz.Rd | 17 - rayvertex-0.11.4/rayvertex/man/translate_mesh.Rd | 8 rayvertex-0.11.4/rayvertex/man/vec_ptype_abbr.ray_shape.Rd |only rayvertex-0.11.4/rayvertex/man/vec_ptype_abbr.ray_shape_list.Rd |only rayvertex-0.11.4/rayvertex/man/yz_rect_mesh.Rd | 6 rayvertex-0.11.4/rayvertex/src/RcppExports.cpp | 62 ++++ rayvertex-0.11.4/rayvertex/src/assert.cpp |only rayvertex-0.11.4/rayvertex/src/assert.h |only rayvertex-0.11.4/rayvertex/src/calcnormals.cpp |only rayvertex-0.11.4/rayvertex/src/calcnormals.h |only rayvertex-0.11.4/rayvertex/src/calctangents.cpp |only rayvertex-0.11.4/rayvertex/src/calctangents.h |only rayvertex-0.11.4/rayvertex/src/displacement.cpp |only rayvertex-0.11.4/rayvertex/src/displacement.h |only rayvertex-0.11.4/rayvertex/src/filltri.h | 4 rayvertex-0.11.4/rayvertex/src/load_obj.cpp | 14 - rayvertex-0.11.4/rayvertex/src/loopsubdiv.cpp |only rayvertex-0.11.4/rayvertex/src/loopsubdiv.h |only rayvertex-0.11.4/rayvertex/src/rayraster.cpp | 4 rayvertex-0.11.4/rayvertex/src/shaders.cpp | 55 ++- rayvertex-0.11.4/rayvertex/src/shaders.h | 24 - rayvertex-0.11.4/rayvertex/src/stb |only rayvertex-0.11.4/rayvertex/src/tinyobj |only 89 files changed, 779 insertions(+), 367 deletions(-)
Title: High-Dimensional Robust Factor Analysis
Description: Factor models have been widely applied in areas such as economics and finance, and the well-known heavy-tailedness of macroeconomic/financial data should be taken into account when conducting factor analysis. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's L2 norm, which turns out to do Principal Component Analysis (PCA) on the weighted sample covariance matrix and thereby named as Huber PCA. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm. In this package we also provide the code for traditional PCA, the Robust Two Step (RTS) method by He et al. (2022) and the Quantile Factor Analysis (QFA) method by Chen et al. (2021) and He et al. (2023).
Author: Yong He [aut],
Lingxiao Li [aut],
Dong Liu [aut, cre],
Wenxin Zhou [aut]
Maintainer: Dong Liu <liudong_stat@163.com>
Diff between HDRFA versions 0.1.4 dated 2023-11-07 and 0.1.5 dated 2024-07-22
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/HPCA.R | 46 +++++++++++++++++++++------------------------- R/IQR.R | 27 +++++++++++---------------- R/Myrlm.R | 4 ++++ R/PCA.R | 4 ++-- R/RTS.R | 2 +- R/function_all.R | 48 ++++++++++++++++++++---------------------------- man/HPCA.Rd | 12 +++++++----- man/HPCA_FN.Rd | 11 +++++++++-- 10 files changed, 87 insertions(+), 91 deletions(-)
Title: A Multivariate Meta-Analysis Model for Metabolomics Data
Description: Performs multivariate meta-analysis for high-dimensional metabolomics data for integrating and collectively analysing individual-level metabolomics data generated from multiple studies as well as for combining summary estimates. This approach accounts for correlation between metabolites, considers variability within and between studies, handles missing values and uses shrinkage estimation to allow for high dimensionality. A detailed vignette with example datasets and code to prepare data and analyses are available on <https://bookdown.org/a2delivera/MetaHD/>.
Author: Jayamini Liyanage [aut, cre],
Alysha De Livera [aut]
Maintainer: Jayamini Liyanage <j.liyanage@latrobe.edu.au>
Diff between MetaHD versions 0.1.1 dated 2024-06-25 and 0.1.2 dated 2024-07-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MetaHD.R | 24 +++++++++++++----------- data/realdata.rda |binary man/MetaHDInput.Rd | 9 ++++----- man/realdata.Rd | 13 +++---------- 6 files changed, 29 insertions(+), 35 deletions(-)
Title: Access Women's Basketball Play by Play Data
Description: A utility for working with women's basketball data. A scraping and aggregating interface for the WNBA Stats API <https://stats.wnba.com/> and ESPN's <https://www.espn.com> women's college basketball and WNBA statistics. It provides users with the capability to access the game play-by-plays, box scores, standings and results to analyze the data for themselves.
Author: Saiem Gilani [aut, cre],
Geoffery Hutchinson [aut]
Maintainer: Saiem Gilani <saiem.gilani@gmail.com>
Diff between wehoop versions 2.0.0 dated 2023-11-25 and 2.1.0 dated 2024-07-21
DESCRIPTION | 10 MD5 | 150 +-- NAMESPACE | 1 NEWS.md | 8 R/espn_wbb_data.R | 97 +- R/espn_wnba_data.R | 70 + R/ncaa_wbb_data.R | 10 R/utils_wnba_stats.R | 20 R/wnba_data_pbp.R | 4 R/wnba_stats_boxscore.R | 36 R/wnba_stats_boxscore_v3.R | 38 R/wnba_stats_cume.R | 16 R/wnba_stats_draft.R | 30 R/wnba_stats_franchise.R | 18 R/wnba_stats_hustle.R | 18 R/wnba_stats_leaders.R | 838 ++++++++++++++++++--- R/wnba_stats_league.R | 14 R/wnba_stats_league_dash.R | 28 R/wnba_stats_lineups.R | 20 R/wnba_stats_pbp.R | 12 R/wnba_stats_player.R | 68 + R/wnba_stats_player_dash.R | 32 R/wnba_stats_roster.R | 16 R/wnba_stats_scoreboard.R | 85 +- R/wnba_stats_shotchart.R | 12 R/wnba_stats_team.R | 112 +- R/wnba_stats_team_dash.R | 36 R/wnba_stats_video.R | 16 man/wnba_alltimeleadersgrids.Rd | 4 man/wnba_assistleaders.Rd | 4 man/wnba_assisttracker.Rd | 4 man/wnba_homepageleaders.Rd | 11 man/wnba_homepagev2.Rd | 11 man/wnba_homepagewidget.Rd |only man/wnba_leaderstiles.Rd | 11 man/wnba_leaguedashteamstats.Rd | 1 man/wnba_leagueleaders.Rd | 4 man/wnba_schedule.Rd | 1 man/wnba_scoreboard.Rd | 9 man/wnba_scoreboardv2.Rd | 1 man/wnba_scoreboardv3.Rd | 1 man/wnba_teamdashboardbyclutch.Rd | 1 man/wnba_teamdashboardbygamesplits.Rd | 1 man/wnba_teamdashboardbygeneralsplits.Rd | 1 man/wnba_teamdashboardbylastngames.Rd | 1 man/wnba_teamdashboardbyopponent.Rd | 1 man/wnba_teamdashboardbyshootingsplits.Rd | 1 man/wnba_teamdashboardbyteamperformance.Rd | 1 man/wnba_teamdashboardbyyearoveryear.Rd | 1 man/wnba_teamdashlineups.Rd | 1 man/wnba_teamdetails.Rd | 1 man/wnba_teamestimatedmetrics.Rd | 1 man/wnba_teamgamelog.Rd | 1 man/wnba_teamgamelogs.Rd | 1 man/wnba_teamgamestreakfinder.Rd | 1 man/wnba_teamhistoricalleaders.Rd | 1 man/wnba_teaminfocommon.Rd | 27 man/wnba_teamplayerdashboard.Rd | 1 man/wnba_teamplayeronoffdetails.Rd | 1 man/wnba_teamplayeronoffsummary.Rd | 1 man/wnba_teams.Rd | 1 man/wnba_teamvsplayer.Rd | 1 man/wnba_teamyearbyyearstats.Rd | 1 man/wnba_todays_scoreboard.Rd | 3 tests/testthat/test-espn_wbb_game_all.R | 4 tests/testthat/test-espn_wbb_player_stats.R | 9 tests/testthat/test-espn_wbb_team_box.R | 4 tests/testthat/test-espn_wbb_team_stats.R | 17 tests/testthat/test-wnba_homepageleaders.R | 1 tests/testthat/test-wnba_homepagev2.R | 1 tests/testthat/test-wnba_homepagewidget.R |only tests/testthat/test-wnba_leaderstiles.R | 1 tests/testthat/test-wnba_playerdashboardbyclutch.R | 2 tests/testthat/test-wnba_schedule.R | 6 tests/testthat/test-wnba_scoreboard.R | 1 tests/testthat/test-wnba_scoreboardv3.R | 2 tests/testthat/test-wnba_teaminfocommon.R | 2 77 files changed, 1426 insertions(+), 552 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [ctb],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut],
Eric Dal Moro [au [...truncated...]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.18 dated 2023-06-27 and 0.2.19 dated 2024-07-21
DESCRIPTION | 8 ++-- MD5 | 22 +++++------ NEWS.md | 6 ++- README.md | 4 +- build/vignette.rds |binary inst/doc/ChainLadder.R | 2 - inst/doc/ChainLadder.Rmd | 2 - inst/doc/ChainLadder.html | 83 ++++++++++++++++++++++---------------------- man/Triangles.Rd | 2 - man/plot.MackChainLadder.Rd | 2 - man/tweedieReserve.Rd | 2 - vignettes/ChainLadder.Rmd | 2 - 12 files changed, 70 insertions(+), 65 deletions(-)
Title: Build a Metric Subspaces Data Model for a Data Source
Description: Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.
Author: Werner Mueller
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganDataModel versions 1.1.6 dated 2024-01-21 and 1.1.7 dated 2024-07-21
DESCRIPTION | 8 ++--- MD5 | 26 +++++++++-------- R/dmBuildMetricSubspaces.R | 2 - man/dmGetContainedInMetricSubspaces.Rd | 2 - man/ganDataModel-package.Rd | 10 +++--- src/column.h | 6 +++- src/dataSource.h | 49 ++++++++++++++++++++------------- src/density.h |only src/dmInt.cpp | 2 - src/generativeData.h | 32 ++++++++++++++++++++- src/inOut.h | 5 ++- src/normalizeData.h | 24 ++++++++++++---- src/numberArrayColumn.h |only src/stringColumn.h | 30 ++++++++++++++------ src/utils.h | 2 - 15 files changed, 136 insertions(+), 62 deletions(-)
Title: Generating Various Numerical Representation Schemes for Protein
Sequences
Description: Comprehensive toolkit for generating various numerical
features of protein sequences described in Xiao et al. (2015)
<DOI:10.1093/bioinformatics/btv042>. For full functionality,
the software 'ncbi-blast+' is needed, see
<https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html>
for more information.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Dong-Sheng Cao [aut],
Sebastian Mueller [ctb]
Maintainer: Nan Xiao <me@nanx.me>
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More information about serocalculator at CRAN
Permanent link
Title: Portfolio Management with R
Description: Tools for the practical management of financial
portfolios: backtesting investment and trading strategies,
computing profit/loss and returns, analysing trades,
handling lists of transactions, reporting, and more. The
package provides a small set of reliable, efficient and
convenient tools for processing and analysing
trade/portfolio data. The Manual provides all the details;
it is available from
<https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>.
Examples and descriptions of new features are provided at
<https://enricoschumann.net/notes/PMwR/>.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 0.19-3 dated 2023-10-19 and 0.19-5 dated 2024-07-21
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Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>. Different research methods during Q-matrix validating are available.
Author: Haijiang Qin [aut, cre, cph],
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 0.1.6 dated 2024-04-14 and 0.1.7 dated 2024-07-21
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