Title: Database Storage of Genotype Probabilities for QTL Mapping
Description: Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.
Author: Karl W Broman [aut, cre] ,
Brian S Yandell [aut] ,
Petr Simecek [aut]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2fst versions 0.28 dated 2024-07-16 and 0.30 dated 2024-11-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/fst_path.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/qtl2fst.html | 4 ++-- man/fst_restore.Rd | 4 ++-- man/probs2fst.Rd | 4 ++-- man/replace_path.Rd | 2 +- 10 files changed, 29 insertions(+), 22 deletions(-)
Title: Spatial Prediction Tools
Description: Methods for spatial predictive modeling, especially for spatial distribution models. This includes algorithms for model fitting and prediction, as well as methods for model evaluation.
Author: Robert J. Hijmans [cre, aut] ,
Steven Phillips [ctb],
Marcia Barbosa [ctb],
Chris Brunsdon [ctb],
Barry Rowlingson [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between predicts versions 0.1-16 dated 2024-10-07 and 0.1-17 dated 2024-11-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/divpol.R | 4 ++-- build/partial.rdb |binary man/maxent.Rd | 2 -- 5 files changed, 10 insertions(+), 12 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic heuristic algorithms for
global optimization of problems with and without general constraints.
The aim is to curate a collection of its variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it provides implementations of the algorithms 'jDE' by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
for multimodal optimization (single-objective problems with
multiple solutions).
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.1-3 dated 2023-10-07 and 1.1-3-1 dated 2024-11-23
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Download Forestry Data
Description: Functions for downloading forestry and land use data for use in spatial analysis. This packages offers a user-friendly solution to quickly obtain datasets such as forest height, forest types, tree species under various climate change scenarios, or land use data among others.
Author: Adrian Cidre Gonzalez [aut, cre]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between forestdata versions 0.1.0 dated 2024-09-10 and 0.2.0 dated 2024-11-23
forestdata-0.1.0/forestdata/R/canopy_height.R |only forestdata-0.1.0/forestdata/R/chorological_maps.R |only forestdata-0.1.0/forestdata/R/forest_country.R |only forestdata-0.1.0/forestdata/R/forest_inventory.R |only forestdata-0.1.0/forestdata/R/global_land_cover.R |only forestdata-0.1.0/forestdata/R/land_cover_explorer.R |only forestdata-0.1.0/forestdata/R/utils_notExported.R |only forestdata-0.2.0/forestdata/DESCRIPTION | 18 forestdata-0.2.0/forestdata/MD5 | 120 ++-- forestdata-0.2.0/forestdata/NAMESPACE | 42 - forestdata-0.2.0/forestdata/NEWS.md | 60 +- forestdata-0.2.0/forestdata/R/GLAD.R | 295 ++++++++-- forestdata-0.2.0/forestdata/R/allometry.R |only forestdata-0.2.0/forestdata/R/canopy-height.R |only forestdata-0.2.0/forestdata/R/chorological-maps.R |only forestdata-0.2.0/forestdata/R/eutrees4f.R | 34 - forestdata-0.2.0/forestdata/R/forest-country.R |only forestdata-0.2.0/forestdata/R/forest-inventory.R |only forestdata-0.2.0/forestdata/R/forestdata-package.R |only forestdata-0.2.0/forestdata/R/globals.R | 4 forestdata-0.2.0/forestdata/R/land-cover.R |only forestdata-0.2.0/forestdata/R/pathogens.R | 35 - forestdata-0.2.0/forestdata/R/sysdata.rda |binary forestdata-0.2.0/forestdata/R/utils-not-exported.R |only forestdata-0.2.0/forestdata/README.md | 18 forestdata-0.2.0/forestdata/build |only forestdata-0.2.0/forestdata/data/metadata_forestdata.rda |binary forestdata-0.2.0/forestdata/man/create_mfe50_table.Rd | 38 - forestdata-0.2.0/forestdata/man/fd_allometry_tallo.Rd |only forestdata-0.2.0/forestdata/man/fd_canopy_height.Rd | 129 ++-- forestdata-0.2.0/forestdata/man/fd_canopy_height_eth.Rd |only forestdata-0.2.0/forestdata/man/fd_canopy_height_meta.Rd |only forestdata-0.2.0/forestdata/man/fd_forest_chorological.Rd | 109 +-- forestdata-0.2.0/forestdata/man/fd_forest_eutrees4f.Rd | 244 ++++---- forestdata-0.2.0/forestdata/man/fd_forest_extent_glad.Rd | 125 ++-- forestdata-0.2.0/forestdata/man/fd_forest_france.Rd | 166 ++--- forestdata-0.2.0/forestdata/man/fd_forest_glad.Rd |only forestdata-0.2.0/forestdata/man/fd_forest_spain_mfe50.Rd | 87 +- forestdata-0.2.0/forestdata/man/fd_inventory_spain.Rd | 105 +-- forestdata-0.2.0/forestdata/man/fd_landcover_copernicus.Rd | 182 ++---- forestdata-0.2.0/forestdata/man/fd_landcover_esri.Rd | 72 +- forestdata-0.2.0/forestdata/man/fd_pathogens_defid2.Rd | 150 ++--- forestdata-0.2.0/forestdata/man/fdi_download_7zip.Rd | 70 +- forestdata-0.2.0/forestdata/man/fdi_download_raster.Rd | 40 - forestdata-0.2.0/forestdata/man/fdi_download_unzip.Rd | 70 +- forestdata-0.2.0/forestdata/man/fdi_fix_names.Rd | 38 - forestdata-0.2.0/forestdata/man/figures/functions_gt.png |binary forestdata-0.2.0/forestdata/man/figures/lifecycle-deprecated.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-experimental.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-stable.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-superseded.svg |only forestdata-0.2.0/forestdata/man/forestdata-package.Rd |only forestdata-0.2.0/forestdata/man/get_bdforet_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_chorological_tbl.Rd | 34 - forestdata-0.2.0/forestdata/man/get_combined_raster.Rd | 34 - forestdata-0.2.0/forestdata/man/get_combined_raster_2l.Rd | 34 - forestdata-0.2.0/forestdata/man/get_eutrees4f_tbl.Rd | 34 - forestdata-0.2.0/forestdata/man/get_forest_extent_tbl.Rd | 38 - forestdata-0.2.0/forestdata/man/get_gch_tbl.Rd | 41 - forestdata-0.2.0/forestdata/man/get_glad_tiles.Rd |only forestdata-0.2.0/forestdata/man/get_glc_tbl.Rd | 44 - forestdata-0.2.0/forestdata/man/get_landcoverexplorer_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_meta_tiles.Rd |only forestdata-0.2.0/forestdata/man/get_mfe50_ccaa_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_mfe50_provinces_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_spain_ifn2_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn3_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn4_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn_metadata_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/metadata_forestdata.Rd | 48 - forestdata-0.2.0/forestdata/tests/testthat/test-GLAD.R |only forestdata-0.2.0/forestdata/tests/testthat/test-allometry.R |only forestdata-0.2.0/forestdata/tests/testthat/test-canopy-height.R |only forestdata-0.2.0/forestdata/tests/testthat/test-chorological-maps.R |only forestdata-0.2.0/forestdata/tests/testthat/test-eutrees4f.R |only forestdata-0.2.0/forestdata/tests/testthat/test-forest-country.R |only forestdata-0.2.0/forestdata/tests/testthat/test-forest-inventory.R |only forestdata-0.2.0/forestdata/tests/testthat/test-land-cover.R |only forestdata-0.2.0/forestdata/tests/testthat/test-pathogens.R |only 79 files changed, 1565 insertions(+), 1239 deletions(-)
Title: Phase Portraits of Functions in the Complex Number Plane
Description: Functionality for creating phase portraits of functions in the
complex number plane. Works with R base graphics, whose full
functionality is available. Parallel processing is used for optimum
performance.
Author: Peter Biber [aut, cre]
Maintainer: Peter Biber <castor.fiber@gmx.de>
Diff between viscomplexr versions 1.1.1 dated 2021-09-18 and 1.1.2 dated 2024-11-23
DESCRIPTION | 14 MD5 | 18 NEWS.md | 24 R/VisComplex.R | 2 README.md | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/viscomplexr-vignette.R | 792 +++++++------- inst/doc/viscomplexr-vignette.html | 2073 ++++++++++++++++++++++++++----------- man/phasePortrait.Rd | 2 10 files changed, 1938 insertions(+), 997 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.20.0 dated 2024-11-22 and 0.21.0 dated 2024-11-23
DESCRIPTION | 10 +- MD5 | 25 ++--- NAMESPACE | 5 - R/0_globals.R | 5 - R/main.R | 169 +++++++++++++++++++++++++++++++++- R/utils.R | 16 ++- R/wordclouds.R | 25 +++++ README.md | 9 - man/topicsDtmEval.Rd |only tests/testthat/test_1_1_topicsGrams.R | 4 tests/testthat/test_1_2_topicsDtm.R | 1 tests/testthat/test_1_4_topicsPreds.R | 4 tests/testthat/test_1_5_topicsTest.R | 4 tests/testthat/test_1_6_topicsPlot.R | 6 - 14 files changed, 234 insertions(+), 49 deletions(-)
Title: Computing f-Statistics and Building Admixture Graphs Based on
Allele Count or Pool-Seq Read Count Data
Description: Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in TreeMix, BayPass and SelEstim format).
Author: Mathieu Gautier [aut, cre]
Maintainer: Mathieu Gautier <mathieu.gautier@inrae.fr>
Diff between poolfstat versions 2.2.0 dated 2023-09-06 and 3.0.0 dated 2024-11-23
poolfstat-2.2.0/poolfstat/man/compute_Ddenom.Rd |only poolfstat-2.2.0/poolfstat/man/compute_Ddenom_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/man/compute_F2_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/man/compute_Q_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/src/fast_block_averages.cpp |only poolfstat-3.0.0/poolfstat/ChangeLog | 15 poolfstat-3.0.0/poolfstat/DESCRIPTION | 19 poolfstat-3.0.0/poolfstat/MD5 | 76 + poolfstat-3.0.0/poolfstat/NAMESPACE | 21 poolfstat-3.0.0/poolfstat/R/RcppExports.R | 357 +++++++- poolfstat-3.0.0/poolfstat/R/add.leaf.R | 2 poolfstat-3.0.0/poolfstat/R/compute.F4ratio.R | 16 poolfstat-3.0.0/poolfstat/R/compute.pairwiseFST.R | 222 ++--- poolfstat-3.0.0/poolfstat/R/computeFST.R | 400 +++++----- poolfstat-3.0.0/poolfstat/R/countdata2genobaypass.R |only poolfstat-3.0.0/poolfstat/R/generate.graph.params.R | 2 poolfstat-3.0.0/poolfstat/R/graph.params2qpGraphFiles.R | 2 poolfstat-3.0.0/poolfstat/R/is.fitted.graph.R | 3 poolfstat-3.0.0/poolfstat/R/poolfstat-package.R | 8 poolfstat-3.0.0/poolfstat/R/sim.readcounts.R |only poolfstat-3.0.0/poolfstat/R/sliding.windows.fstat.R |only poolfstat-3.0.0/poolfstat/build/vignette.rds |binary poolfstat-3.0.0/poolfstat/inst/CITATION | 8 poolfstat-3.0.0/poolfstat/inst/doc/vignette.pdf |binary poolfstat-3.0.0/poolfstat/man/add.leaf.Rd | 2 poolfstat-3.0.0/poolfstat/man/block_sum.Rd |only poolfstat-3.0.0/poolfstat/man/block_sum2.Rd |only poolfstat-3.0.0/poolfstat/man/compute.f4ratio.Rd | 6 poolfstat-3.0.0/poolfstat/man/compute.pairwiseFST.Rd | 2 poolfstat-3.0.0/poolfstat/man/computeFST.Rd | 27 poolfstat-3.0.0/poolfstat/man/compute_snpFstAov.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpHierFstAov.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1onepop.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1rw.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2onepair.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2w.Rd |only poolfstat-3.0.0/poolfstat/man/countdata2genobaypass.Rd |only poolfstat-3.0.0/poolfstat/man/fitted.graph-class.Rd | 1 poolfstat-3.0.0/poolfstat/man/generate.graph.params.Rd | 2 poolfstat-3.0.0/poolfstat/man/graph.params2qpGraphFiles.Rd | 2 poolfstat-3.0.0/poolfstat/man/poolfstat.Rd | 7 poolfstat-3.0.0/poolfstat/man/sim.readcounts.Rd |only poolfstat-3.0.0/poolfstat/man/simureads_mono.Rd |only poolfstat-3.0.0/poolfstat/man/simureads_poly.Rd |only poolfstat-3.0.0/poolfstat/man/sliding.windows.fstat.Rd |only poolfstat-3.0.0/poolfstat/src/RcppExports.cpp | 190 +++- poolfstat-3.0.0/poolfstat/src/fst_utils.cpp |only poolfstat-3.0.0/poolfstat/src/fstats_utils.cpp |only poolfstat-3.0.0/poolfstat/src/simulate.readcounts.utils.cpp |only poolfstat-3.0.0/poolfstat/vignettes/poolfstat_vignette_6pops.pdf |binary 52 files changed, 911 insertions(+), 479 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian Multilevel Modelling for compositional data
in a multilevel framework. Compute multilevel compositional data and
Isometric log ratio (ILR) at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
References:
Le, Stanford, Dumuid, and Wiley (2024) <doi:10.48550/arXiv.2405.03985>,
Le, Dumuid, Stanford, and Wiley (2024) <doi:10.48550/arXiv.2411.12407>.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <floralebui@gmail.com>
Diff between multilevelcoda versions 1.3.0.2 dated 2024-07-09 and 1.3.1 dated 2024-11-23
multilevelcoda-1.3.0.2/multilevelcoda/R/basesub.R |only multilevelcoda-1.3.0.2/multilevelcoda/man/basesub.Rd |only multilevelcoda-1.3.1/multilevelcoda/DESCRIPTION | 19 multilevelcoda-1.3.1/multilevelcoda/MD5 | 99 - multilevelcoda-1.3.1/multilevelcoda/NAMESPACE | 12 multilevelcoda-1.3.1/multilevelcoda/NEWS.md | 44 multilevelcoda-1.3.1/multilevelcoda/R/brmcoda.R | 6 multilevelcoda-1.3.1/multilevelcoda/R/build.R |only multilevelcoda-1.3.1/multilevelcoda/R/coef.R |only multilevelcoda-1.3.1/multilevelcoda/R/complr-methods.R | 12 multilevelcoda-1.3.1/multilevelcoda/R/complr.R | 15 multilevelcoda-1.3.1/multilevelcoda/R/internal.R | 17 multilevelcoda-1.3.1/multilevelcoda/R/pivot-coord.R |only multilevelcoda-1.3.1/multilevelcoda/R/substitution-bsub.R | 7 multilevelcoda-1.3.1/multilevelcoda/R/substitution-bsubmargins.R | 3 multilevelcoda-1.3.1/multilevelcoda/R/substitution-helpers.R | 593 +++++----- multilevelcoda-1.3.1/multilevelcoda/R/substitution-sub-margins.R | 10 multilevelcoda-1.3.1/multilevelcoda/R/substitution-wsub.R | 7 multilevelcoda-1.3.1/multilevelcoda/R/substitution-wsubmargins.R | 3 multilevelcoda-1.3.1/multilevelcoda/R/substitution.R | 167 +- multilevelcoda-1.3.1/multilevelcoda/R/summary.R | 100 + multilevelcoda-1.3.1/multilevelcoda/R/update.R | 44 multilevelcoda-1.3.1/multilevelcoda/README.md | 29 multilevelcoda-1.3.1/multilevelcoda/build/vignette.rds |binary multilevelcoda-1.3.1/multilevelcoda/inst/doc/A-introduction.html | 8 multilevelcoda-1.3.1/multilevelcoda/inst/doc/B-composition-MLM.html | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/C-composition-MMLM.html | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/D-substitution.html | 8 multilevelcoda-1.3.1/multilevelcoda/inst/doc/E-simmodel-diag.Rmd | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/E-simmodel-diag.html | 13 multilevelcoda-1.3.1/multilevelcoda/man/bsub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/bsubmargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/build.basesub.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/build.sbp.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/complr.Rd | 2 multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord_refit.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord_rotate.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/sub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/submargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/substitution.Rd | 24 multilevelcoda-1.3.1/multilevelcoda/man/summary.complr.Rd | 3 multilevelcoda-1.3.1/multilevelcoda/man/summary.pivot_coord.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/var.complr.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/wsub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/wsubmargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-brmcoda.R | 2 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-bsub.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-bsubmargins.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-submargins.R | 20 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-substitution.R | 12 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-update.R | 76 - multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-wsub.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-wsubmargins.R | 24 multilevelcoda-1.3.1/multilevelcoda/vignettes/E-simmodel-diag.Rmd | 2 multilevelcoda-1.3.1/multilevelcoda/vignettes/E-simmodel-diag.Rmd.orig | 2 56 files changed, 885 insertions(+), 632 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>. The jti package is
part of the paper <doi:10.18637/jss.v111.i02>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <madslindskou@gmail.com>
Diff between jti versions 0.8.4 dated 2022-04-12 and 1.0.0 dated 2024-11-23
DESCRIPTION | 14 MD5 | 53 +- NAMESPACE | 15 NEWS.md | 9 R/api_compile.R | 7 R/api_jt.R | 18 R/helper_elimination_game.R | 6 R/helper_jt.R | 4 README.md | 30 - build/vignette.rds |binary inst/CITATION |only inst/doc/using_jti.R | 16 inst/doc/using_jti.Rmd | 8 inst/doc/using_jti.html | 653 ++++++++++++++++-------------- man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-22-1.png |binary man/figures/README-unnamed-chunk-23-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/jt.Rd | 8 man/jti-package.Rd | 2 man/par_lvs.Rd | 18 man/send_messages.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 vignettes/using_jti.Rmd | 8 28 files changed, 489 insertions(+), 393 deletions(-)
Title: Computing a New Informative Distribution Set of Asset Returns
Description: Estimation of the most-left informative set of gross returns
(i.e., the informative set).
The procedure to compute the informative set adjusts the method
proposed by
Mariani et al. (2022a) <doi:10.1007/s11205-020-02440-6>
and
Mariani et al. (2022b) <doi:10.1007/s10287-022-00422-2>
to gross returns of financial assets.
This is accomplished through an adaptive algorithm
that identifies sub-groups of gross returns in
each iteration by approximating their distribution with a
sequence of two-component log-normal mixtures.
These sub-groups emerge when a significant change
in the distribution occurs below the median of the
financial returns, with their boundary termed as
the “change point" of the mixture.
The process concludes when no further change points are detected.
The outcome encompasses parameters of the leftmost mixture
distributions and change points of the
analyzed financial time series.
The functionalities of the INFOSET package include: (i) modelling asset distribution [...truncated...]
Author: Gloria Polinesi [aut, cre],
Francesca Mariani [aut],
Maria Cristina Recchioni [aut]
Maintainer: Gloria Polinesi <g.polinesi@staff.univpm.it>
Diff between INFOSET versions 4.0.6 dated 2024-09-06 and 4.1 dated 2024-11-23
DESCRIPTION | 14 MD5 | 25 - NAMESPACE | 11 R/my_functions.R | 898 ++++++++++++++++++++++--------------- build |only inst |only man/LR_cp.Rd |only man/create_overlapping_windows.Rd |only man/infoset.Rd | 335 ------------- man/plot_LR_cp.Rd |only man/plot_ptf.Rd |only man/ptf_construction.Rd |only man/summary_ptf.Rd |only man/tail_mixture.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-my_functions.R | 8 vignettes |only 17 files changed, 607 insertions(+), 688 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R.
It further includes fast functions for common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated with base R classes, 'dplyr'/' [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.0.17 dated 2024-11-03 and 2.0.18 dated 2024-11-23
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------- NEWS.md | 8 +++++++ R/GRP.R | 5 ++-- R/pivot.R | 2 + inst/doc/collapse_and_sf.html | 4 +-- inst/doc/collapse_documentation.html | 4 +-- inst/doc/collapse_for_tidyverse_users.html | 6 ++--- inst/doc/collapse_object_handling.html | 6 ++--- src/data.table_subset.c | 4 ++- src/data.table_utils.c | 15 +++---------- src/kit.h | 2 - src/kit_dup.c | 32 ++++++++++++++--------------- src/pivot.c | 2 - tests/testthat/test-miscellaneous-issues.R | 4 +++ 15 files changed, 70 insertions(+), 60 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@insitro.com>
Diff between AllelicSeries versions 0.1.1.1 dated 2024-11-21 and 0.1.1.2 dated 2024-11-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-data_generation.R | 5 +++-- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Hierarchical Partitioning of R2 for Phylogenetic Linear
Regression
Description: Conducts hierarchical partitioning to calculate individual contributions of phylogenetic tree and predictors (groups) towards total R2 for phylogenetic linear regression models.
Author: Jiangshan Lai [aut, cre] ,
Gang Wang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between phylolm.hp versions 0.0-1 dated 2024-11-13 and 0.0-2 dated 2024-11-23
phylolm.hp-0.0-1/phylolm.hp/R/phylolmhp.r |only phylolm.hp-0.0-1/phylolm.hp/man/phylolm.hp.Rd |only phylolm.hp-0.0-2/phylolm.hp/DESCRIPTION | 10 - phylolm.hp-0.0-2/phylolm.hp/MD5 | 10 - phylolm.hp-0.0-2/phylolm.hp/NAMESPACE | 1 phylolm.hp-0.0-2/phylolm.hp/R/phyloglmhp.r | 155 +++++++++++++++++++------ phylolm.hp-0.0-2/phylolm.hp/man/phyloglm.hp.Rd | 30 +++- 7 files changed, 152 insertions(+), 54 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.8.0 dated 2024-10-25 and 0.9.0 dated 2024-11-23
DESCRIPTION | 6 +- MD5 | 68 ++++++++++++------------- NEWS.md | 6 ++ R/LearnerClassifLogReg.R | 8 -- R/LearnerClassifMultinom.R | 8 -- R/LearnerClassifRanger.R | 19 +++++- R/LearnerRegrLM.R | 8 -- R/LearnerRegrRanger.R | 6 +- R/helpers.R | 10 --- build/partial.rdb |binary inst/paramtest/test_paramtest_classif.ranger.R | 1 man/mlr_learners_classif.cv_glmnet.Rd | 1 man/mlr_learners_classif.glmnet.Rd | 1 man/mlr_learners_classif.kknn.Rd | 1 man/mlr_learners_classif.lda.Rd | 1 man/mlr_learners_classif.log_reg.Rd | 12 ---- man/mlr_learners_classif.multinom.Rd | 12 ---- man/mlr_learners_classif.naive_bayes.Rd | 1 man/mlr_learners_classif.nnet.Rd | 3 - man/mlr_learners_classif.qda.Rd | 1 man/mlr_learners_classif.ranger.Rd | 17 +++--- man/mlr_learners_classif.svm.Rd | 1 man/mlr_learners_classif.xgboost.Rd | 2 man/mlr_learners_regr.cv_glmnet.Rd | 1 man/mlr_learners_regr.glmnet.Rd | 1 man/mlr_learners_regr.kknn.Rd | 1 man/mlr_learners_regr.km.Rd | 1 man/mlr_learners_regr.lm.Rd | 12 ---- man/mlr_learners_regr.nnet.Rd | 3 - man/mlr_learners_regr.ranger.Rd | 15 +++-- man/mlr_learners_regr.svm.Rd | 1 man/mlr_learners_regr.xgboost.Rd | 2 tests/testthat/test_regr_lm.R | 2 tests/testthat/test_regr_ranger.R | 2 tests/testthat/test_regr_xgboost.R | 2 35 files changed, 110 insertions(+), 126 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-22 0.3.0
2024-09-19 0.2.0
2024-09-05 0.1.0
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.1 dated 2024-10-22 and 3.0.2 dated 2024-11-23
nlmixr2est-3.0.1/nlmixr2est/R/preProcessModel.R |only nlmixr2est-3.0.2/nlmixr2est/DESCRIPTION | 6 - nlmixr2est-3.0.2/nlmixr2est/MD5 | 46 ++++++---- nlmixr2est-3.0.2/nlmixr2est/NAMESPACE | 6 + nlmixr2est-3.0.2/nlmixr2est/NEWS.md | 12 ++ nlmixr2est-3.0.2/nlmixr2est/R/bobyqa.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/hook.R |only nlmixr2est-3.0.2/nlmixr2est/R/lbfgsb3c.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/n1qn1.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/newuoa.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/nlm.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/nlminb.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/nlmixr2.R | 9 + nlmixr2est-3.0.2/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-3.0.2/nlmixr2est/R/nls.R | 2 nlmixr2est-3.0.2/nlmixr2est/R/optim.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/preProcessDataUi.R |only nlmixr2est-3.0.2/nlmixr2est/R/preProcessLiteralFix.R |only nlmixr2est-3.0.2/nlmixr2est/R/preProcessZeroOmega.R |only nlmixr2est-3.0.2/nlmixr2est/R/uobyqa.R | 3 nlmixr2est-3.0.2/nlmixr2est/inst/tools/workaround.R | 22 +++- nlmixr2est-3.0.2/nlmixr2est/man/dot-nlmixrPreprocessLiteralFix.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/dot-preProcessDataUi.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/dot-preProcessZeroOmega.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/figures/README-example-1.png |binary nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooks.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooksAdd.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooksRm.Rd |only nlmixr2est-3.0.2/nlmixr2est/src/inner.cpp | 8 + nlmixr2est-3.0.2/nlmixr2est/tests/testthat/test-omega-boundary.R |only 30 files changed, 96 insertions(+), 44 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.28-1 dated 2024-09-14 and 0.4.29 dated 2024-11-22
DESCRIPTION | 8 +-- MD5 | 28 +++++----- NEWS.md | 5 + R/read-fmi-cum.R | 2 R/read-tuv-file.r | 99 +++++++++++++++++++++++++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 24 ++++----- inst/doc/user-guide.Rmd | 4 - inst/doc/user-guide.html | 114 ++++++++++++++++++++++---------------------- man/qtuv_s.e.irrad.Rd | 12 +++- man/read_fmi2mspct.Rd | 2 tests/testthat/test-macam.R | 6 +- tests/testthat/test-oo.R | 72 +++++++++++++-------------- vignettes/user-guide.Rmd | 4 - 15 files changed, 227 insertions(+), 153 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.3.2 dated 2024-02-08 and 1.4.0 dated 2024-11-22
toxEval-1.3.2/toxEval/man/figures/README-unnamed-chunk-6-1.png |only toxEval-1.3.2/toxEval/man/figures/README-unnamed-chunk-6-2.png |only toxEval-1.3.2/toxEval/man/figures/README-unnamed-chunk-6-3.png |only toxEval-1.4.0/toxEval/DESCRIPTION | 10 toxEval-1.4.0/toxEval/MD5 | 97 ++--- toxEval-1.4.0/toxEval/NAMESPACE | 1 toxEval-1.4.0/toxEval/NEWS | 6 toxEval-1.4.0/toxEval/R/clean_endPoint_info.R | 14 toxEval-1.4.0/toxEval/R/create_toxEval.R | 6 toxEval-1.4.0/toxEval/R/filter_endPoint_info.R | 24 - toxEval-1.4.0/toxEval/R/get_ACC.R | 44 +- toxEval-1.4.0/toxEval/R/get_chemical_summary.R | 99 +---- toxEval-1.4.0/toxEval/R/plot_tox_stacks.R | 3 toxEval-1.4.0/toxEval/R/sysdata.rda |binary toxEval-1.4.0/toxEval/R/toxEval.R | 85 +--- toxEval-1.4.0/toxEval/README.md | 76 +--- toxEval-1.4.0/toxEval/build/partial.rdb |binary toxEval-1.4.0/toxEval/build/vignette.rds |binary toxEval-1.4.0/toxEval/inst/doc/Chemical_names.R | 4 toxEval-1.4.0/toxEval/inst/doc/Chemical_names.Rmd | 6 toxEval-1.4.0/toxEval/inst/doc/Chemical_names.html | 21 - toxEval-1.4.0/toxEval/inst/doc/Introduction.R | 18 toxEval-1.4.0/toxEval/inst/doc/Introduction.Rmd | 7 toxEval-1.4.0/toxEval/inst/doc/Introduction.html | 25 - toxEval-1.4.0/toxEval/inst/doc/PrepareData.R | 32 + toxEval-1.4.0/toxEval/inst/doc/PrepareData.Rmd | 60 ++- toxEval-1.4.0/toxEval/inst/doc/PrepareData.html | 188 ++++++++-- toxEval-1.4.0/toxEval/inst/shiny/benchmarks.R | 10 toxEval-1.4.0/toxEval/inst/shiny/boxPlot.R | 1 toxEval-1.4.0/toxEval/inst/shiny/endpointGraph.R | 22 - toxEval-1.4.0/toxEval/inst/shiny/heatMap.R | 1 toxEval-1.4.0/toxEval/inst/shiny/server.R | 72 +-- toxEval-1.4.0/toxEval/inst/shiny/stackPlot.R | 1 toxEval-1.4.0/toxEval/inst/shiny/ui.R | 43 -- toxEval-1.4.0/toxEval/man/ToxCast_ACC.Rd | 18 toxEval-1.4.0/toxEval/man/clean_endPoint_info.Rd | 10 toxEval-1.4.0/toxEval/man/end_point_info.Rd | 59 +-- toxEval-1.4.0/toxEval/man/figures/README-unnamed-chunk-7-1.png |only toxEval-1.4.0/toxEval/man/figures/README-unnamed-chunk-7-2.png |only toxEval-1.4.0/toxEval/man/figures/README-unnamed-chunk-7-3.png |only toxEval-1.4.0/toxEval/man/filter_groups.Rd | 13 toxEval-1.4.0/toxEval/man/flags.Rd |only toxEval-1.4.0/toxEval/man/get_ACC.Rd | 6 toxEval-1.4.0/toxEval/man/plot_tox_stacks.Rd | 3 toxEval-1.4.0/toxEval/man/remove_flags.Rd | 39 +- toxEval-1.4.0/toxEval/man/tox_chemicals.Rd | 25 - toxEval-1.4.0/toxEval/tests/testthat/test_data.R | 50 -- toxEval-1.4.0/toxEval/tests/testthat/test_utils.R | 6 toxEval-1.4.0/toxEval/tests/testthat/tests_endpoint.R | 26 - toxEval-1.4.0/toxEval/tests/testthat/tests_summary.R | 74 ++- toxEval-1.4.0/toxEval/vignettes/Chemical_names.Rmd | 6 toxEval-1.4.0/toxEval/vignettes/Introduction.Rmd | 7 toxEval-1.4.0/toxEval/vignettes/PrepareData.Rmd | 60 ++- 53 files changed, 739 insertions(+), 639 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.9.1 dated 2024-02-21 and 1.0.0 dated 2024-11-22
slendr-0.9.1/slendr/R/engines.R |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.R |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.Rmd |only slendr-0.9.1/slendr/inst/doc/vignette-07-backends.html |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.R |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.Rmd |only slendr-0.9.1/slendr/inst/doc/vignette-09-paper.html |only slendr-0.9.1/slendr/vignettes/vignette-07-backends.Rmd |only slendr-0.9.1/slendr/vignettes/vignette-09-paper.Rmd |only slendr-1.0.0/slendr/DESCRIPTION | 8 slendr-1.0.0/slendr/MD5 | 263 +++--- slendr-1.0.0/slendr/NAMESPACE | 4 slendr-1.0.0/slendr/NEWS.md | 38 slendr-1.0.0/slendr/R/compilation.R | 158 ++- slendr-1.0.0/slendr/R/extensions.R |only slendr-1.0.0/slendr/R/extract_parameters.R |only slendr-1.0.0/slendr/R/interface.R | 67 - slendr-1.0.0/slendr/R/msprime.R |only slendr-1.0.0/slendr/R/print.R | 12 slendr-1.0.0/slendr/R/slim.R |only slendr-1.0.0/slendr/R/tree-sequences.R | 184 +++- slendr-1.0.0/slendr/R/tspop.R | 6 slendr-1.0.0/slendr/R/utils.R | 20 slendr-1.0.0/slendr/R/visualization.R | 33 slendr-1.0.0/slendr/R/zzz.R | 8 slendr-1.0.0/slendr/README.md | 35 slendr-1.0.0/slendr/build/partial.rdb |only slendr-1.0.0/slendr/build/vignette.rds |binary slendr-1.0.0/slendr/inst/doc/vignette-00-installation.Rmd | 6 slendr-1.0.0/slendr/inst/doc/vignette-00-installation.html | 28 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.R | 4 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 16 slendr-1.0.0/slendr/inst/doc/vignette-01-tutorial.html | 43 - slendr-1.0.0/slendr/inst/doc/vignette-02-grid-model.R | 2 slendr-1.0.0/slendr/inst/doc/vignette-02-grid-model.Rmd | 2 slendr-1.0.0/slendr/inst/doc/vignette-02-grid-model.html | 18 slendr-1.0.0/slendr/inst/doc/vignette-03-interactions.R | 2 slendr-1.0.0/slendr/inst/doc/vignette-03-interactions.Rmd | 2 slendr-1.0.0/slendr/inst/doc/vignette-03-interactions.html | 12 slendr-1.0.0/slendr/inst/doc/vignette-04-nonspatial-models.R | 32 slendr-1.0.0/slendr/inst/doc/vignette-04-nonspatial-models.Rmd | 47 - slendr-1.0.0/slendr/inst/doc/vignette-04-nonspatial-models.html | 122 ++ slendr-1.0.0/slendr/inst/doc/vignette-05-tree-sequences.R | 12 slendr-1.0.0/slendr/inst/doc/vignette-05-tree-sequences.Rmd | 24 slendr-1.0.0/slendr/inst/doc/vignette-05-tree-sequences.html | 286 +++--- slendr-1.0.0/slendr/inst/doc/vignette-06-locations.R | 2 slendr-1.0.0/slendr/inst/doc/vignette-06-locations.Rmd | 2 slendr-1.0.0/slendr/inst/doc/vignette-06-locations.html | 126 +-- slendr-1.0.0/slendr/inst/doc/vignette-07-engines.R |only slendr-1.0.0/slendr/inst/doc/vignette-07-engines.Rmd |only slendr-1.0.0/slendr/inst/doc/vignette-07-engines.html |only slendr-1.0.0/slendr/inst/doc/vignette-08-nonslendr-tskit.R | 24 slendr-1.0.0/slendr/inst/doc/vignette-08-nonslendr-tskit.Rmd | 32 slendr-1.0.0/slendr/inst/doc/vignette-08-nonslendr-tskit.html | 66 - slendr-1.0.0/slendr/inst/doc/vignette-10-tracts.R | 4 slendr-1.0.0/slendr/inst/doc/vignette-10-tracts.Rmd | 8 slendr-1.0.0/slendr/inst/doc/vignette-10-tracts.html | 17 slendr-1.0.0/slendr/inst/doc/vignette-11-extensions.R |only slendr-1.0.0/slendr/inst/doc/vignette-11-extensions.Rmd |only slendr-1.0.0/slendr/inst/doc/vignette-11-extensions.html |only slendr-1.0.0/slendr/inst/extdata/extension_introgression.txt |only slendr-1.0.0/slendr/inst/extdata/extension_purifying.txt |only slendr-1.0.0/slendr/inst/extdata/extension_sweep.txt |only slendr-1.0.0/slendr/inst/extdata/extension_trajectory.txt |only slendr-1.0.0/slendr/inst/extdata/extension_trajectory_params.txt |only slendr-1.0.0/slendr/inst/extdata/models/introgression/__pycache__ |only slendr-1.0.0/slendr/inst/extdata/models/introgression/checksums.tsv | 1 slendr-1.0.0/slendr/inst/extdata/models/introgression/script.py | 66 + slendr-1.0.0/slendr/inst/extdata/models/introgression/script.slim | 414 ++++++---- slendr-1.0.0/slendr/inst/extdata/models/introgression/time_units.txt |only slendr-1.0.0/slendr/inst/extdata/models/introgression_msprime.trees |binary slendr-1.0.0/slendr/inst/extdata/models/introgression_slim.trees |binary slendr-1.0.0/slendr/inst/extdata/models/msprime.trees |binary slendr-1.0.0/slendr/inst/pylib/pylib.py | 14 slendr-1.0.0/slendr/inst/scripts/__pycache__/script.cpython-312.pyc |binary slendr-1.0.0/slendr/inst/scripts/script.py | 62 + slendr-1.0.0/slendr/inst/scripts/script.slim | 412 ++++++--- slendr-1.0.0/slendr/man/compile_model.Rd | 70 - slendr-1.0.0/slendr/man/extract_parameters.Rd |only slendr-1.0.0/slendr/man/msprime.Rd | 47 - slendr-1.0.0/slendr/man/setup_env.Rd | 9 slendr-1.0.0/slendr/man/slim.Rd | 107 +- slendr-1.0.0/slendr/man/substitute_values.Rd |only slendr-1.0.0/slendr/man/ts_afs.Rd | 2 slendr-1.0.0/slendr/man/ts_ancestors.Rd | 2 slendr-1.0.0/slendr/man/ts_coalesced.Rd | 2 slendr-1.0.0/slendr/man/ts_descendants.Rd | 2 slendr-1.0.0/slendr/man/ts_divergence.Rd | 2 slendr-1.0.0/slendr/man/ts_diversity.Rd | 2 slendr-1.0.0/slendr/man/ts_draw.Rd | 2 slendr-1.0.0/slendr/man/ts_edges.Rd | 4 slendr-1.0.0/slendr/man/ts_f4ratio.Rd | 4 slendr-1.0.0/slendr/man/ts_fst.Rd | 2 slendr-1.0.0/slendr/man/ts_genotypes.Rd | 2 slendr-1.0.0/slendr/man/ts_ibd.Rd | 2 slendr-1.0.0/slendr/man/ts_load.Rd | 64 - slendr-1.0.0/slendr/man/ts_metadata.Rd | 2 slendr-1.0.0/slendr/man/ts_mutate.Rd | 13 slendr-1.0.0/slendr/man/ts_nodes.Rd | 2 slendr-1.0.0/slendr/man/ts_phylo.Rd | 2 slendr-1.0.0/slendr/man/ts_read.Rd |only slendr-1.0.0/slendr/man/ts_recapitate.Rd | 4 slendr-1.0.0/slendr/man/ts_samples.Rd | 2 slendr-1.0.0/slendr/man/ts_save.Rd | 25 slendr-1.0.0/slendr/man/ts_segregating.Rd | 2 slendr-1.0.0/slendr/man/ts_simplify.Rd | 2 slendr-1.0.0/slendr/man/ts_table.Rd | 9 slendr-1.0.0/slendr/man/ts_tajima.Rd | 2 slendr-1.0.0/slendr/man/ts_tracts.Rd | 4 slendr-1.0.0/slendr/man/ts_tree.Rd | 2 slendr-1.0.0/slendr/man/ts_write.Rd |only slendr-1.0.0/slendr/tests/testthat/afs_Darwin.tsv.gz |binary slendr-1.0.0/slendr/tests/testthat/afs_Linux.tsv.gz |binary slendr-1.0.0/slendr/tests/testthat/afs_Windows.tsv.gz |binary slendr-1.0.0/slendr/tests/testthat/distances.tsv.gz |binary slendr-1.0.0/slendr/tests/testthat/helper-functions.R | 32 slendr-1.0.0/slendr/tests/testthat/test-compilation.R | 108 ++ slendr-1.0.0/slendr/tests/testthat/test-coordinate-conversions.R | 3 slendr-1.0.0/slendr/tests/testthat/test-engines.R | 31 slendr-1.0.0/slendr/tests/testthat/test-extensions.R |only slendr-1.0.0/slendr/tests/testthat/test-future.R |only slendr-1.0.0/slendr/tests/testthat/test-ibd-squashing.R | 4 slendr-1.0.0/slendr/tests/testthat/test-interaction-changes.R | 44 - slendr-1.0.0/slendr/tests/testthat/test-manual-ts.R | 8 slendr-1.0.0/slendr/tests/testthat/test-msprime-geneflow.R | 90 +- slendr-1.0.0/slendr/tests/testthat/test-msprime-metadata.R | 58 - slendr-1.0.0/slendr/tests/testthat/test-msprime.R | 62 - slendr-1.0.0/slendr/tests/testthat/test-pure-msprime-vs-slendr.R | 8 slendr-1.0.0/slendr/tests/testthat/test-pure-slim-vs-slendr.R | 8 slendr-1.0.0/slendr/tests/testthat/test-runners.R | 38 slendr-1.0.0/slendr/tests/testthat/test-sampling.R | 56 - slendr-1.0.0/slendr/tests/testthat/test-serialization.R | 16 slendr-1.0.0/slendr/tests/testthat/test-simulation-runs.R | 2 slendr-1.0.0/slendr/tests/testthat/test-time-direction.R | 5 slendr-1.0.0/slendr/tests/testthat/test-trees.R | 36 slendr-1.0.0/slendr/tests/testthat/test-ts-ancestors-descendants.R | 6 slendr-1.0.0/slendr/tests/testthat/test-ts-pure-nonspatial.R | 44 - slendr-1.0.0/slendr/tests/testthat/test-ts-pure-spatial.R | 9 slendr-1.0.0/slendr/tests/testthat/test-ts.R | 217 ++--- slendr-1.0.0/slendr/vignettes/vignette-00-installation.Rmd | 6 slendr-1.0.0/slendr/vignettes/vignette-01-tutorial.Rmd | 16 slendr-1.0.0/slendr/vignettes/vignette-02-grid-model.Rmd | 2 slendr-1.0.0/slendr/vignettes/vignette-03-interactions.Rmd | 2 slendr-1.0.0/slendr/vignettes/vignette-04-nonspatial-models.Rmd | 47 - slendr-1.0.0/slendr/vignettes/vignette-05-tree-sequences.Rmd | 24 slendr-1.0.0/slendr/vignettes/vignette-06-locations.Rmd | 2 slendr-1.0.0/slendr/vignettes/vignette-07-engines.Rmd |only slendr-1.0.0/slendr/vignettes/vignette-08-nonslendr-tskit.Rmd | 32 slendr-1.0.0/slendr/vignettes/vignette-10-tracts.Rmd | 8 slendr-1.0.0/slendr/vignettes/vignette-11-extensions.Rmd |only 150 files changed, 2492 insertions(+), 1672 deletions(-)
Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Functions for
analysis of resulting respirometry data are also provided. This package
provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk [aut, cre]
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 2.0.0 dated 2024-07-18 and 2.0.1 dated 2024-11-22
DESCRIPTION | 20 +++++++++++++------- MD5 | 6 +++--- NEWS | 3 +++ R/import_firesting.R | 27 ++++++++++++++++++++++----- 4 files changed, 41 insertions(+), 15 deletions(-)
Title: Search Spaces for 'mlr3'
Description: Collection of search spaces for hyperparameter optimization in the
'mlr3' ecosystem. It features ready-to-use search spaces for many popular
machine learning algorithms. The search spaces are from scientific articles
and work for a wide range of data sets.
Author: Marc Becker [cre, aut] ,
Michel Lang [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuningspaces versions 0.5.1 dated 2024-06-21 and 0.5.2 dated 2024-11-22
DESCRIPTION | 12 +++---- MD5 | 20 ++++++------ NEWS.md | 4 ++ R/TuningSpace.R | 26 ++++++++++------ R/bibentries.R | 11 +++--- R/tuning_spaces_rbv1.R | 4 +- R/tuning_spaces_rbv2.R | 4 +- R/zzz.R | 2 + README.md | 62 ++++++++++++++++++++++----------------- man/TuningSpace.Rd | 24 +++++++++------ man/mlr_tuning_spaces_default.Rd | 5 +-- 11 files changed, 101 insertions(+), 73 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: Digitization of Phytosociological Relevés
Description: Simple and fast tool for transforming phytosociological
vegetation data into digital form for the following analysis.
Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786).
Hennekens, and Schaminée (2001) <doi:10.2307/3237010>.
Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>.
Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.
Author: Premysl Kral [aut, cre] ,
Jan Douda [aut]
Maintainer: Premysl Kral <kralp@fzp.czu.cz>
Diff between Rveg versions 0.1.5 dated 2024-06-26 and 0.1.6 dated 2024-11-22
Rveg-0.1.5/Rveg/inst/doc/Rveg.R |only Rveg-0.1.5/Rveg/man/tvToRveg.Rd |only Rveg-0.1.6/Rveg/DESCRIPTION | 6 Rveg-0.1.6/Rveg/MD5 | 45 Rveg-0.1.6/Rveg/NAMESPACE | 3 Rveg-0.1.6/Rveg/R/CreateChecklist.R | 8 Rveg-0.1.6/Rveg/R/RvegCheck.R | 7 Rveg-0.1.6/Rveg/R/RvegCombine.R | 1 Rveg-0.1.6/Rveg/R/RvegLoad.R |only Rveg-0.1.6/Rveg/R/RvegToJuice.R | 123 +- Rveg-0.1.6/Rveg/R/addReleve.R | 347 +++++- Rveg-0.1.6/Rveg/R/createTABLE.R | 233 +++- Rveg-0.1.6/Rveg/build/vignette.rds |binary Rveg-0.1.6/Rveg/inst/doc/Rveg.Rmd | 1359 +++++++++++++++++++----- Rveg-0.1.6/Rveg/inst/doc/Rveg.pdf |binary Rveg-0.1.6/Rveg/inst/extdata/example_dbHEAD.csv | 39 Rveg-0.1.6/Rveg/inst/extdata/example_dbREL.csv | 65 - Rveg-0.1.6/Rveg/inst/extdata/tvexport.csv | 146 +- Rveg-0.1.6/Rveg/man/CreateChecklist.Rd | 4 Rveg-0.1.6/Rveg/man/RvegCheck.Rd | 3 Rveg-0.1.6/Rveg/man/RvegCombine.Rd | 1 Rveg-0.1.6/Rveg/man/RvegLoad.Rd |only Rveg-0.1.6/Rveg/man/RvegToJuice.Rd | 1 Rveg-0.1.6/Rveg/man/TvToRveg.Rd |only Rveg-0.1.6/Rveg/man/addReleve.Rd | 9 Rveg-0.1.6/Rveg/vignettes/Rveg.Rmd | 1359 +++++++++++++++++++----- 26 files changed, 2983 insertions(+), 776 deletions(-)
Title: Interactive 3D Visualization of Molecular Structures
Description: Provides an 'htmlwidgets' <https://www.htmlwidgets.org/> interface to 'NGL.js' <http://nglviewer.org/ngl/api/>.
'NGLvieweR' can be used to visualize and interact with protein databank ('PDB') and structural files in R and Shiny applications.
It includes a set of API functions to manipulate the viewer after creation in Shiny.
Author: Niels van der Velden [aut, cre],
Alexander Rose [cph]
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Diff between NGLVieweR versions 1.3.1 dated 2021-06-01 and 1.4.0 dated 2024-11-22
DESCRIPTION | 10 MD5 | 90 - NAMESPACE | 76 NEWS.md | 30 R/NGLVieweR-shiny.R | 204 +- R/NGLVieweR.R | 1249 +++++++++----- R/NGLVieweR_example.R | 92 - R/api.R | 1727 ++++++++++--------- README.md | 111 - build/vignette.rds |binary inst/doc/NGLVieweR.R | 761 +++++--- inst/doc/NGLVieweR.Rmd | 1023 +++++++---- inst/doc/NGLVieweR.html | 2959 ++++++++++++++++++++++++++++------ inst/examples/API/app.R | 40 inst/examples/addSelection/app.R | 90 - inst/examples/multiStructureSelection |only inst/examples/updateColor/app.R | 3 inst/examples/updateZoomMove/app.R | 19 inst/htmlwidgets/NGLVieweR.js | 816 +++++---- inst/htmlwidgets/NGLVieweR.yaml | 24 man/NGLVieweR.Rd | 17 man/NGLVieweR_example.Rd | 7 man/addRepresentation.Rd | 30 man/addSelection.Rd | 20 man/addStructure.Rd |only man/figures/click_interaction.PNG |only man/removeSelection.Rd | 3 man/selectionParameters.Rd |only man/setFocus.Rd | 3 man/setPosition.Rd |only man/setQuality.Rd | 6 man/setRock.Rd | 6 man/setRotation.Rd |only man/setScale.Rd |only man/setSpin.Rd | 6 man/setSuperpose.Rd |only man/snapShot.Rd | 9 man/stageParameters.Rd | 9 man/updateColor.Rd | 10 man/updateFocus.Rd | 5 man/updateFullscreen.Rd | 3 man/updateRepresentation.Rd | 13 man/updateRock.Rd | 19 man/updateSelection.Rd | 10 man/updateSpin.Rd | 11 man/updateStage.Rd | 11 man/updateVisibility.Rd | 10 man/updateZoomMove.Rd | 30 man/zoomMove.Rd | 43 vignettes/NGLVieweR.Rmd | 1023 +++++++---- 50 files changed, 6938 insertions(+), 3690 deletions(-)
Title: Bayesian Estimation of the Additive Main Effects and
Multiplicative Interaction Model
Description: Performs Bayesian estimation of the additive main effects and multiplicative interaction (AMMI) model. The method is explained in Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J.M., Viele, K., Liu, G. and Cornelius, P.L. (2011) (<doi:10.2135/cropsci2010.06.0343>).
Author: Muhammad Yaseen [aut, cre],
Jose Crossa [aut, ctb],
Sergio Perez-Elizalde [aut, ctb],
Diego Jarquin [aut, ctb],
Jose Miguel Cotes [aut, ctb],
Kert Viele [aut, ctb],
Genzhou Liu [aut, ctb],
Paul L. Cornelius [aut, ctb],
Julian Garcia Abadillo Velasco [...truncated...]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between bayesammi versions 0.2.0 dated 2024-10-15 and 0.3.0 dated 2024-11-22
DESCRIPTION | 30 +++++++++++--------- MD5 | 14 +++++---- NAMESPACE | 13 +++++++++ NEWS.md | 11 +++++++ R/bayes_ammi.R | 78 ++++++++++++++++++++++++++++++++++++++---------------- R/biplots.R |only README.md | 26 +++++++----------- man/bayes_ammi.Rd | 2 - man/biplots.Rd |only 9 files changed, 114 insertions(+), 60 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.0.3 dated 2023-07-10 and 1.0.5 dated 2024-11-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/data.R | 2 +- build/vignette.rds |binary man/mock.vccc.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.2 dated 2024-09-23 and 3.7.3 dated 2024-11-22
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++++++----------- NAMESPACE | 7 +++++++ NEWS.md | 10 ++++++++++ R/Class_definitions.R | 14 ++++++++------ R/Data_Functions.R | 2 -- R/Empirical_MP.R |only R/MSE_functions.R | 4 +++- R/SAM2OM.R |only R/Splot.R |only R/popdyn.R | 5 ++--- R/runMSE.R | 3 ++- man/Emp.Rd |only man/Splot.Rd |only man/doHCR.Rd |only man/doIfreq.Rd |only man/doRec.Rd |only man/quantile_plot.Rd |only man/runMP.Rd | 3 --- man/select_MP.Rd | 38 +++++++++++++++++++------------------- man/smoothy.Rd |only src/LinInter.cpp | 3 ++- 22 files changed, 77 insertions(+), 50 deletions(-)
Title: Fast Approximation of Time-Varying Infectious Disease
Transmission Rates
Description: A fast method for approximating time-varying infectious disease
transmission rates from disease incidence time series and other
data, based on a discrete time approximation of an SEIR model, as
analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.3.0 dated 2024-05-17 and 0.3.1 dated 2024-11-22
fastbeta-0.3.0/fastbeta/R/fastbeta.affine.R |only fastbeta-0.3.0/fastbeta/R/fastbeta.bootstrap.R |only fastbeta-0.3.1/fastbeta/DESCRIPTION | 14 - fastbeta-0.3.1/fastbeta/MD5 | 54 ++-- fastbeta-0.3.1/fastbeta/NAMESPACE | 3 fastbeta-0.3.1/fastbeta/R/fastbeta.R | 228 ++++++++++++++++++++- fastbeta-0.3.1/fastbeta/R/ptpi.R | 9 fastbeta-0.3.1/fastbeta/R/seir.R | 211 +++++++++++++------ fastbeta-0.3.1/fastbeta/data/seir.ts01.R | 6 fastbeta-0.3.1/fastbeta/data/seir.ts02.R | 6 fastbeta-0.3.1/fastbeta/inst/NEWS.Rd | 55 ++++- fastbeta-0.3.1/fastbeta/man/deconvolve.Rd | 4 fastbeta-0.3.1/fastbeta/man/fastbeta-defunct.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-deprecated.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-notyet.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta-package.Rd |only fastbeta-0.3.1/fastbeta/man/fastbeta.Rd | 24 +- fastbeta-0.3.1/fastbeta/man/fastbeta.bootstrap.Rd | 12 - fastbeta-0.3.1/fastbeta/man/fastbeta.matrix.Rd |only fastbeta-0.3.1/fastbeta/man/ptpi.Rd | 16 - fastbeta-0.3.1/fastbeta/man/seir.Rd | 42 ++- fastbeta-0.3.1/fastbeta/man/seir.auxiliary.Rd |only fastbeta-0.3.1/fastbeta/man/seir.library.Rd | 2 fastbeta-0.3.1/fastbeta/man/smallpox.Rd | 2 fastbeta-0.3.1/fastbeta/src/Makevars |only fastbeta-0.3.1/fastbeta/src/fastbeta-win.def |only fastbeta-0.3.1/fastbeta/src/fastbeta.c | 19 - fastbeta-0.3.1/fastbeta/src/init.c | 25 +- fastbeta-0.3.1/fastbeta/src/ptpi.c | 52 ++-- fastbeta-0.3.1/fastbeta/src/seir.c | 47 ++-- fastbeta-0.3.1/fastbeta/tests/fastbeta.R | 2 fastbeta-0.3.1/fastbeta/tests/ptpi.R | 2 fastbeta-0.3.1/fastbeta/tests/seir.R | 8 33 files changed, 609 insertions(+), 234 deletions(-)
Title: Easy Access to High-Resolution Daily Climate Data for Europe
Description: Get high-resolution (1 km) daily climate data (precipitation,
minimum and maximum temperatures) for points and polygons within
Europe.
Author: Veronica Cruz-Alonso [aut, cre, cph]
,
Francisco Rodriguez-Sanchez [aut, cph]
,
Christoph Pucher [aut] ,
Paloma Ruiz-Benito [aut] ,
Julen Astigarraga [aut] ,
Mathias Neumann [aut] ,
Sophia Ratcliffe [aut]
Maintainer: Veronica Cruz-Alonso <veronica.cral@gmail.com>
Diff between easyclimate versions 0.2.1 dated 2023-07-11 and 0.2.2 dated 2024-11-22
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 4 R/build_url.R | 104 ++--- R/get_daily_climate.R | 2 R/get_daily_climate_single.R | 660 +++++++++++++++++------------------ README.md | 32 + man/easyclimate-package.Rd | 4 man/get_daily_climate.Rd | 2 tests/testthat/test-build_url.R | 50 +- tests/testthat/test-period_to_days.R | 87 ++-- 11 files changed, 495 insertions(+), 478 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.0.1 dated 2024-09-24 and 4.0.2 dated 2024-11-22
OlinkAnalyze-4.0.1/OlinkAnalyze/tests/data |only OlinkAnalyze-4.0.2/OlinkAnalyze/DESCRIPTION | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/MD5 | 94 +++--- OlinkAnalyze-4.0.2/OlinkAnalyze/NEWS.md | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/R/olink_normalization_utils.R | 52 ++- OlinkAnalyze-4.0.2/OlinkAnalyze/R/read_npx_parquet.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/R/sysdata.rda |binary OlinkAnalyze-4.0.2/OlinkAnalyze/build/vignette.rds |binary OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/LOD.html | 8 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/OutlierExclusion.html | 30 +- OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/Vignett.html | 28 +- OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.Rmd | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.html | 26 - OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/bridging_introduction.html | 22 - OlinkAnalyze-4.0.2/OlinkAnalyze/inst/doc/plate_randomizer.html | 16 - OlinkAnalyze-4.0.2/OlinkAnalyze/man/olink_norm_input_assay_overlap.Rd | 11 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 - OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/_snaps/npxProcessing.md | 130 ++++----- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/data |only OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/helper-get_example_olink_data.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_anova.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_boxplot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_bridgeselector.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_heatmap.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_one_non_parametric.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_ordinalRegression.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_plate_randomizer.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Olink_ttest.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-Volcano_plot.R | 5 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-dist_plot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-linear_mixed_model.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-npxProcessing.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_Pathway_Enrichment.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 86 +++++- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_n.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 99 ++++--- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 136 ++++++---- OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-olink_qc_plot.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-pca_plot.R | 6 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test-umap_plot.R | 2 OlinkAnalyze-4.0.2/OlinkAnalyze/tests/testthat/test_Olink_wilcox.R | 4 OlinkAnalyze-4.0.2/OlinkAnalyze/vignettes/bridging_E3072toEHT.Rmd | 4 43 files changed, 521 insertions(+), 342 deletions(-)
Title: Implementation of LT-FH++
Description: Implementation of LT-FH++, an extension of
the liability threshold family history (LT-FH) model.
LT-FH++ uses a Gibbs sampler for sampling from the truncated
multivariate normal distribution and allows for
flexible family structures. LT-FH++ was first described in
Pedersen, Emil M., et al. (2022)
<doi:10.1016/j.ajhg.2022.01.009>
as an extension to LT-FH with more flexible family structures,
and again as the age-dependent liability threshold (ADuLT) model
Pedersen, Emil M., et al. (2023)
<doi:10.1038/s41467-023-41210-z>
as an alternative to traditional time-to-event genome-wide
association studies, where family history was not considered.
Author: Emil Michael Pedersen [aut, cre],
Florian Prive [aut, ths],
Bjarni Johann Vilhjalmsson [ths],
Esben Agerbo [ths],
Jette Steinbach [aut],
Lucas Rasmussen [ctb]
Maintainer: Emil Michael Pedersen <emp@ph.au.dk>
Diff between LTFHPlus versions 2.1.1 dated 2024-02-12 and 2.1.2 dated 2024-11-22
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NEWS.md | 14 +++++++++----- R/Simulate_under_LTM.R | 12 ++++++------ R/tmp.R |only R/tmp2.R |only man/LTFHPlus-package.Rd | 2 +- man/simulate_under_LTM.Rd | 2 +- man/simulate_under_LTM_multi.Rd | 6 +++--- 9 files changed, 35 insertions(+), 29 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Offers a suite of helper functions to simplify various data science techniques for non-experts. This package aims to enable individuals with only a minimal level of coding knowledge to become acquainted with these techniques in an accessible manner. Inspired by an ancient Persian idiom, we liken this process to "eating the liver of data science," suggesting a deep and intimate engagement with the field of data science. This package includes functions for tasks such as data partitioning for out-of-sample testing, calculating Mean Squared Error (MSE) to assess prediction accuracy, and data transformations (z-score and min-max). In addition to these helper functions, the 'liver' package also features several intriguing datasets valuable for multivariate analysis.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.17 dated 2024-10-28 and 1.18 dated 2024-11-22
liver-1.17/liver/R/transform.R |only liver-1.17/liver/man/transform.Rd |only liver-1.18/liver/DESCRIPTION | 6 liver-1.18/liver/MD5 | 34 ++-- liver-1.18/liver/NAMESPACE | 2 liver-1.18/liver/NEWS.md | 8 + liver-1.18/liver/R/kNN.R | 12 - liver-1.18/liver/R/kNN.plot.R | 216 +++++++++++++-------------- liver-1.18/liver/R/partition.R | 28 +-- liver-1.18/liver/R/scaler.R |only liver-1.18/liver/inst/doc/liver-example.R | 60 +++---- liver-1.18/liver/inst/doc/liver-example.Rmd | 68 ++++---- liver-1.18/liver/inst/doc/liver-example.html | 54 +++--- liver-1.18/liver/man/kNN.Rd | 8 - liver-1.18/liver/man/kNN.plot.Rd | 20 +- liver-1.18/liver/man/minmax.Rd | 6 liver-1.18/liver/man/partition.Rd | 7 liver-1.18/liver/man/scaler.Rd |only liver-1.18/liver/man/zscore.Rd | 6 liver-1.18/liver/vignettes/liver-example.Rmd | 68 ++++---- 20 files changed, 305 insertions(+), 298 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables <doi:10.18637/jss.v111.i02>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <madslindskou@gmail.com>
Diff between sparta versions 0.8.4 dated 2022-04-12 and 1.0.1 dated 2024-11-22
DESCRIPTION | 13 - MD5 | 29 +-- NAMESPACE | 1 NEWS.md | 5 R/api_converters.R | 2 R/api_sparta.R | 2 R/helpers_sparta.R | 1 build/vignette.rds |binary inst/CITATION |only inst/doc/using_sparta.R | 2 inst/doc/using_sparta.html | 341 ++++++++++++++++++++++++++------------------- man/as_sparta.Rd | 3 man/merge.Rd | 3 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 16 files changed, 245 insertions(+), 166 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.15.0 dated 2024-10-29 and 0.15.1 dated 2024-11-22
DESCRIPTION | 9 +++++---- MD5 | 18 +++++++++--------- NEWS.md | 11 ++++++++++- R/handler_notifier.R | 1 - R/handler_ntfy.R | 6 ++---- R/handler_rpushbullet.R | 8 ++++---- build/vignette.rds |binary man/handler_notifier.Rd | 1 - man/handler_ntfy.Rd | 8 +++----- man/handler_rpushbullet.Rd | 11 ++++++++--- 10 files changed, 41 insertions(+), 32 deletions(-)
Title: Download and Import Open Street Map Data Extracts
Description: Match, download, convert and import Open Street Map data extracts
obtained from several providers.
Author: Andrea Gilardi [aut, cre] ,
Robin Lovelace [aut] ,
Barry Rowlingson [ctb] ,
Salva Fernandez [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/395>),
Nicholas Potter [rev] for
rOpenSci, see
<https://github.com/ropensci/soft [...truncated...]
Maintainer: Andrea Gilardi <andrea.gilardi@polimi.it>
Diff between osmextract versions 0.5.1 dated 2024-04-30 and 0.5.2 dated 2024-11-22
DESCRIPTION | 12 - MD5 | 68 +++--- NEWS.md | 314 +++++++++++++++--------------- R/data.R | 2 R/download.R | 2 R/get-key-values.R | 2 R/get-network.R | 78 ++----- R/get.R | 64 ++---- R/vectortranslate.R | 23 +- inst/WORDLIST | 1 inst/doc/osmextract.R | 310 +++++++++++++++-------------- inst/doc/osmextract.Rmd | 36 +-- inst/doc/osmextract.html | 151 +++++++------- inst/doc/providers.R | 8 inst/doc/providers.html | 7 inst/doc/providers_comparisons.R | 8 inst/doc/providers_comparisons.html | 24 +- inst/osmconf.ini | 9 man/figures/README-iow1-1.png |binary man/figures/README-points-lines-iow-1.png |binary man/figures/README-points-lines-iow-2.png |binary man/oe_download.Rd | 13 - man/oe_find.Rd | 14 - man/oe_get.Rd | 64 ++---- man/oe_get_boundary.Rd | 8 man/oe_get_keys.Rd | 6 man/oe_get_network.Rd | 23 +- man/oe_match.Rd | 34 +-- man/oe_read.Rd | 27 +- man/oe_vectortranslate.Rd | 18 - man/openstreetmap_fr_zones.Rd | 2 tests/testthat/_snaps/get-keys.md | 60 ++--- tests/testthat/test-get-keys.R | 2 tests/testthat/test-get-network.R | 35 +++ vignettes/osmextract.Rmd | 36 +-- 35 files changed, 750 insertions(+), 711 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.4.0 dated 2024-11-21 and 0.4.1 dated 2024-11-22
DESCRIPTION | 6 MD5 | 20 +-- NEWS.md | 8 + R/MaestroPipeline.R | 16 ++ R/MaestroPipelineList.R | 32 ++++- inst/doc/maestro-4-advanced-scheduling.html | 14 +- inst/doc/maestro-5-directed-acyclic-graphs.html | 24 +-- man/MaestroPipeline.Rd | 42 ++++++ man/MaestroPipelineList.Rd | 4 tests/testthat/_snaps/dags.md | 28 ++++ tests/testthat/test-dags.R | 148 ++++++++++++++++++++++++ 11 files changed, 302 insertions(+), 40 deletions(-)
Title: Ternary Plots
Description: Ternary plots made simple. This package allows to create
ternary plots using 'graphics'. It provides functions to display the
data in the ternary space, to add or tune graphical elements and to
display statistical summaries. It also includes common ternary
diagrams which are useful for the archaeologist (e.g. soil texture
charts, ceramic phase diagram).
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 isopleuros versions 1.2.0 dated 2024-01-08 and 1.3.0 dated 2024-11-22
DESCRIPTION | 29 +- MD5 | 108 +++++---- NAMESPACE | 1 NEWS.md | 8 R/AllGenerics.R | 70 ++++-- R/coordinates.R | 2 R/isopleuros-internal.R | 18 + R/isopleuros-package.R | 2 R/ternary_arrows.R | 2 R/ternary_axes.R | 2 R/ternary_box.R | 2 R/ternary_contour.R | 15 - R/ternary_crosshairs.R | 7 R/ternary_density.R | 19 - R/ternary_ellipse.R | 8 R/ternary_grid.R | 6 R/ternary_hull.R | 15 - R/ternary_image.R |only R/ternary_labels.R | 255 +++++++++++++++------- R/ternary_lines.R | 7 R/ternary_mean.R | 8 R/ternary_pca.R | 7 R/ternary_plot.R | 34 -- R/ternary_polygon.R | 6 R/ternary_segments.R | 2 R/ternary_text.R | 16 - R/ternary_title.R | 2 R/ternary_window.R |only R/triangle_phase.R | 4 R/triangle_soil.R | 4 README.md | 38 +-- build/partial.rdb |binary inst/examples/ex-image.R |only inst/examples/ex-plot.R | 9 inst/tinytest/_tinysnapshot/image_density.svg |only inst/tinytest/_tinysnapshot/image_interpolate.svg |only inst/tinytest/_tinysnapshot/image_rgb.svg |only inst/tinytest/_tinysnapshot/zoom_x.svg | 78 +++--- inst/tinytest/_tinysnapshot/zoom_y.svg | 78 +++--- inst/tinytest/_tinysnapshot/zoom_z.svg | 63 ++--- inst/tinytest/test_plot.R | 8 inst/tinytest/test_scale.R | 12 + inst/tinytest/test_statistics.R | 56 ++-- inst/tinytest/test_tiles.R |only man/coordinates_cartesian.Rd | 8 man/coordinates_ternary.Rd | 5 man/isopleuros-package.Rd | 3 man/ternary_arrows.Rd | 1 man/ternary_crosshairs.Rd | 1 man/ternary_density.Rd | 5 man/ternary_hull.Rd | 10 man/ternary_image.Rd |only man/ternary_labels.Rd | 24 +- man/ternary_lines.Rd | 1 man/ternary_plot.Rd | 15 - man/ternary_points.Rd | 7 man/ternary_polygon.Rd | 1 man/ternary_segments.Rd | 1 man/ternary_text.Rd | 19 + 59 files changed, 673 insertions(+), 429 deletions(-)
Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] ,
Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>
Diff between hyperbolicDEA versions 1.0.1 dated 2024-11-19 and 1.0.2 dated 2024-11-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/check_arguments.R | 4 +--- 3 files changed, 6 insertions(+), 8 deletions(-)
Title: Three-Way / Multigroup Data Analysis Through Densities
Description: The data consist of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides tools to create or manage such data and functional methods (principal component analysis, multidimensional scaling, cluster analysis, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza [aut],
Pierre Santagostini [aut, cre],
Smail Yousfi [aut],
Gilles Hunault [ctb],
Julie Bourbeillon [ctb],
Besnik Pumo [ctb],
Sabine Demotes-Mainard [aut]
Maintainer: Pierre Santagostini <pierre.santagostini@agrocampus-ouest.fr>
Diff between dad versions 4.1.2 dated 2023-08-30 and 4.1.5 dated 2024-11-22
DESCRIPTION | 40 ++++++++++-- MD5 | 52 +++++++-------- build/vignette.rds |binary inst/doc/dad-intro.Rmd | 2 inst/doc/dad-intro.html | 8 +- inst/doc/mds-discrete-distributions.Rmd | 2 inst/doc/mds-discrete-distributions.html | 14 ++-- man/associations.Rd | 2 man/associations.folder.Rd | 2 man/castles.dated.Rd | 2 man/castles.nondated.Rd | 2 man/departments.Rd | 10 +-- man/dspg.Rd | 26 +++---- man/dspgd2015.Rd | 26 +++---- man/dstatis.inter.Rd | 5 - man/kurtosis.folder.Rd | 6 - man/mdsdd.Rd | 2 man/mtgplant1.Rd | 2 man/mtgplant2.Rd | 2 man/plotframes.Rd | 94 ++++++++++++++-------------- man/roseflowers.Rd | 2 man/roseleaves.Rd | 2 man/roses.Rd | 36 +++++----- man/skewness.folder.Rd | 102 +++++++++++++++---------------- man/varietyleaves.Rd | 2 vignettes/dad-intro.Rmd | 2 vignettes/mds-discrete-distributions.Rmd | 2 27 files changed, 238 insertions(+), 209 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre],
Muhammed Ali Yilmaz [aut],
Ozgur Asar [ctb],
Ozlem Ilk [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 2.9 dated 2023-09-13 and 3.0 dated 2024-11-22
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- R/confInt.R | 2 +- man/boxcoxmeta.Rd | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Implementation of the SVM-Maj Algorithm
Description: Implements the SVM-Maj algorithm to train data with support vector machine
<doi:10.1007/s11634-008-0020-9>.
This algorithm uses two efficient updates, one for linear kernel and one
for the nonlinear kernel.
Author: Hoksan Yip [aut, cre],
Patrick J.F. Groenen [aut],
Georgi Nalbantov [aut]
Maintainer: Hoksan Yip <hoksan@gmail.com>
Diff between SVMMaj versions 0.2.9.2 dated 2024-08-19 and 0.2.9.3 dated 2024-11-22
DESCRIPTION | 10 MD5 | 72 ++-- R/classification.R | 44 +- R/data.R | 102 +++--- R/hinge.R | 217 ++++++------- R/ispline.R | 167 +++++----- R/normalize.R | 169 +++++----- R/plotsvmmaj.R | 175 +++++------ R/predict.R | 140 ++++---- R/printsvmmaj.R | 213 +++++++------ R/roccurve.R | 79 ++--- R/svmmaj.R | 515 +++++++++++++++++--------------- R/svmmajcrossval.R | 551 ++++++++++++++++++----------------- R/update.R | 142 ++++----- build/vignette.rds |binary inst/doc/paper.R | 131 ++++---- inst/doc/paper.Rnw | 133 ++++---- inst/doc/paper.pdf |binary man/auc.Rd | 2 man/classification.Rd | 12 man/diabetes.Rd | 14 man/getHinge.Rd | 24 - man/isb.Rd | 24 - man/normalize.Rd | 6 man/plot.hinge.Rd | 4 man/plot.svmmajcrossval.Rd | 6 man/predict.svmmaj.Rd | 4 man/print.svmmaj.Rd | 34 +- man/print.svmmajcrossval.Rd | 2 man/svmmaj.Rd | 48 +-- man/svmmajcrossval.Rd | 8 man/transformdata.Rd | 6 man/voting.Rd | 30 - tests/test_all.R | 2 tests/testthat/test_svmmaj.R | 178 +++++------ tests/testthat/test_svmmajcrossval.R | 53 ++- vignettes/paper.Rnw | 133 ++++---- 37 files changed, 1791 insertions(+), 1659 deletions(-)
Title: Utilities Dealing with Solar Time Such as Sun Position and Time
of Sunrise
Description: Provide utilities to work with solar time,
i.e. where noon is exactly when sun culminates.
Provides functions for computing sun position and times of sunrise and sunset.
Author: Thomas Wutzler [aut, cre]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between solartime versions 0.0.2 dated 2021-04-22 and 0.0.4 dated 2024-11-22
DESCRIPTION | 16 MD5 | 51 +-- NAMESPACE | 1 NEWS.md | 10 R/utilSolarTime.R | 47 ++ build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/overview.Rmd | 16 inst/doc/overview.html | 471 ++++++++++++++++++++++------- man/computeDayLength.Rd | 38 +- man/computeDayLengthDoy.Rd | 52 +-- man/computeIsDayByHour.Rd | 48 +- man/computeIsDayByLocation.Rd | 82 ++--- man/computeSolarToLocalTimeDifference.Rd | 74 ++-- man/computeSunPosition.Rd | 38 +- man/computeSunPositionDoyHour.Rd | 88 ++--- man/computeSunriseHour.Rd | 50 +-- man/computeSunriseHourDoy.Rd | 84 ++--- man/computeSunsetHour.Rd | 50 +-- man/computeSunsetHourDoy.Rd | 80 ++-- man/getFractionalHours.Rd | 34 +- man/getHoursAheadOfUTC.Rd | 36 +- man/getSolarTimeHour.Rd | 36 +- man/setLocalTimeZone.Rd |only tests/spelling.R |only tests/testthat/test_compute_sun_position.R |only tools/README-eccentricityPlot-1.png |binary vignettes/overview.Rmd | 16 28 files changed, 870 insertions(+), 552 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models for conditional quantile functions:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press,
<doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression,
CRC Press, <doi:10.1201/9781315120256>.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] ,
Pin Tian Ng [ctb] ,
Blaise Melly [ctb] ,
Achim Zeileis [ctb] ,
Philip Grosjean [ctb] ,
Cleve Moler [ctb] ,
Yousef Saad [ctb] ,
Victor Chernozhukov [ctb] ,
Ivan Fernandez-Val [ctb] ,
Martin Maechler [c [...truncated...]
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.99 dated 2024-10-22 and 5.99.1 dated 2024-11-22
DESCRIPTION | 10 ++- MD5 | 22 ++++---- R/sfn.R | 123 +++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/ChangeLog | 8 +++ inst/doc/rq.pdf |binary man/akj.Rd | 2 man/sfn.control.Rd | 51 +++++++++----------- src/chlfct.f | 5 + src/quantreg_init.c | 2 src/srqfn.f | 74 +++++++++++++++-------------- src/srqfnc.f | 132 +++++++++++++++++++++++++++------------------------- 12 files changed, 227 insertions(+), 202 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.3.1 dated 2024-09-21 and 0.4.0 dated 2024-11-22
omopgenerics-0.3.1/omopgenerics/R/methodParticipants.R |only omopgenerics-0.3.1/omopgenerics/man/participants.Rd |only omopgenerics-0.3.1/omopgenerics/tests/testthat/test-methodParticipants.R |only omopgenerics-0.4.0/omopgenerics/DESCRIPTION | 15 omopgenerics-0.4.0/omopgenerics/MD5 | 233 omopgenerics-0.4.0/omopgenerics/NAMESPACE | 23 omopgenerics-0.4.0/omopgenerics/R/addSettings.R |only omopgenerics-0.4.0/omopgenerics/R/assert.R | 136 omopgenerics-0.4.0/omopgenerics/R/casting.R | 21 omopgenerics-0.4.0/omopgenerics/R/cdmFromTables.R | 5 omopgenerics-0.4.0/omopgenerics/R/classAchillesTable.R | 5 omopgenerics-0.4.0/omopgenerics/R/classCdmReference.R | 155 omopgenerics-0.4.0/omopgenerics/R/classCdmSource.R | 10 omopgenerics-0.4.0/omopgenerics/R/classCdmTable.R | 23 omopgenerics-0.4.0/omopgenerics/R/classCodelist.R | 32 omopgenerics-0.4.0/omopgenerics/R/classCodelistWithDetails.R | 35 omopgenerics-0.4.0/omopgenerics/R/classCohortTable.R | 109 omopgenerics-0.4.0/omopgenerics/R/classConceptSetExpression.R | 59 omopgenerics-0.4.0/omopgenerics/R/classOmopTable.R | 23 omopgenerics-0.4.0/omopgenerics/R/classSummarisedResult.R | 532 - omopgenerics-0.4.0/omopgenerics/R/columns.R |only omopgenerics-0.4.0/omopgenerics/R/combineStrata.R | 4 omopgenerics-0.4.0/omopgenerics/R/compute.R | 57 omopgenerics-0.4.0/omopgenerics/R/exportCodelist.R | 79 omopgenerics-0.4.0/omopgenerics/R/exportConceptSetExpression.R | 85 omopgenerics-0.4.0/omopgenerics/R/exportSummarisedResult.R | 19 omopgenerics-0.4.0/omopgenerics/R/filter.R |only omopgenerics-0.4.0/omopgenerics/R/importCodelist.R | 40 omopgenerics-0.4.0/omopgenerics/R/importConceptSetExpression.R | 84 omopgenerics-0.4.0/omopgenerics/R/importSummarisedResult.R | 77 omopgenerics-0.4.0/omopgenerics/R/methodBind.R | 17 omopgenerics-0.4.0/omopgenerics/R/methodDropTable.R | 2 omopgenerics-0.4.0/omopgenerics/R/methodInsertTable.R | 2 omopgenerics-0.4.0/omopgenerics/R/methodSettings.R | 1 omopgenerics-0.4.0/omopgenerics/R/methodSuppress.R | 88 omopgenerics-0.4.0/omopgenerics/R/methodTidy.R |only omopgenerics-0.4.0/omopgenerics/R/overwriteClasses.R | 2 omopgenerics-0.4.0/omopgenerics/R/pivot.R |only omopgenerics-0.4.0/omopgenerics/R/recordCohortAttrition.R | 2 omopgenerics-0.4.0/omopgenerics/R/split.R |only omopgenerics-0.4.0/omopgenerics/R/summary.R | 18 omopgenerics-0.4.0/omopgenerics/R/sysdata.rda |binary omopgenerics-0.4.0/omopgenerics/R/unite.R |only omopgenerics-0.4.0/omopgenerics/R/utilities.R | 26 omopgenerics-0.4.0/omopgenerics/R/validate.R | 270 omopgenerics-0.4.0/omopgenerics/README.md | 37 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.R | 19 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.Rmd | 19 omopgenerics-0.4.0/omopgenerics/inst/doc/codelists.html | 47 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.R | 48 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.Rmd | 48 omopgenerics-0.4.0/omopgenerics/inst/doc/cohorts.html | 233 omopgenerics-0.4.0/omopgenerics/inst/doc/reexport.Rmd | 10 omopgenerics-0.4.0/omopgenerics/inst/doc/reexport.html | 7 omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.R | 283 omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.Rmd | 497 + omopgenerics-0.4.0/omopgenerics/inst/doc/summarised_result.html | 4130 +++++++++- omopgenerics-0.4.0/omopgenerics/man/addSettings.Rd |only omopgenerics-0.4.0/omopgenerics/man/additionalColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/cdmName.Rd | 1 omopgenerics-0.4.0/omopgenerics/man/compute.cdm_table.Rd | 11 omopgenerics-0.4.0/omopgenerics/man/emptyAchillesTable.Rd | 2 omopgenerics-0.4.0/omopgenerics/man/exportCodelist.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/exportConceptSetExpression.Rd | 5 omopgenerics-0.4.0/omopgenerics/man/filterAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterSettings.Rd |only omopgenerics-0.4.0/omopgenerics/man/filterStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/groupColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/importCodelist.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/importConceptSetExpression.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/newSummarisedResult.Rd | 44 omopgenerics-0.4.0/omopgenerics/man/omopColumns.Rd | 9 omopgenerics-0.4.0/omopgenerics/man/omopgenerics-package.Rd | 3 omopgenerics-0.4.0/omopgenerics/man/pivotEstimates.Rd |only omopgenerics-0.4.0/omopgenerics/man/print.codelist_with_details.Rd | 6 omopgenerics-0.4.0/omopgenerics/man/print.conceptSetExpression.Rd | 26 omopgenerics-0.4.0/omopgenerics/man/reexports.Rd | 5 omopgenerics-0.4.0/omopgenerics/man/settingsColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitAll.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/splitStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/strataColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/summary.summarised_result.Rd | 2 omopgenerics-0.4.0/omopgenerics/man/suppress.summarised_result.Rd | 26 omopgenerics-0.4.0/omopgenerics/man/tidy.summarised_result.Rd |only omopgenerics-0.4.0/omopgenerics/man/tidyColumns.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteAdditional.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteGroup.Rd |only omopgenerics-0.4.0/omopgenerics/man/uniteStrata.Rd |only omopgenerics-0.4.0/omopgenerics/man/validateCohortArgument.Rd | 4 omopgenerics-0.4.0/omopgenerics/man/validateCohortIdArgument.Rd | 10 omopgenerics-0.4.0/omopgenerics/man/validateNewColumn.Rd |only omopgenerics-0.4.0/omopgenerics/man/validateResultArgument.Rd | 22 omopgenerics-0.4.0/omopgenerics/tests/testthat/_snaps/utilities.md | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/setup.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-addSettings.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-assert.R | 33 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCdmReference.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCodelist.R | 49 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCodelistWithDetails.R | 38 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classCohortTable.R | 104 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classConceptSetExpression.R | 233 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-classSummarisedResult.R | 70 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-cohortCodelist.R | 113 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-columns.R | 41 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-combineStrata.R | 23 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-emptyObjects.R | 23 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportCodelist.R | 54 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportConceptSetExpression.R | 75 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-exportSummarisedResult.R | 21 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-filter.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importCodelist.R | 36 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importConceptSetExpression.R | 132 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-importSummarisedResult.R | 147 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodBind.R | 82 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodComputeTable.R | 13 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodDropSourceTable.R | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodInsertTable.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodReadSourceTable.R | 2 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodSummary.R | 7 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodSuppress.R | 52 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-methodTidy.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-overwriteClasses.R | 9 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-pivot.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-prefix.R | 6 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-recordCohortAttrition.R | 1 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-split.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-unite.R |only omopgenerics-0.4.0/omopgenerics/tests/testthat/test-utilities.R | 63 omopgenerics-0.4.0/omopgenerics/tests/testthat/test-validate.R | 200 omopgenerics-0.4.0/omopgenerics/vignettes/codelists.Rmd | 19 omopgenerics-0.4.0/omopgenerics/vignettes/cohorts.Rmd | 48 omopgenerics-0.4.0/omopgenerics/vignettes/reexport.Rmd | 10 omopgenerics-0.4.0/omopgenerics/vignettes/summarised_result.Rmd | 497 + 136 files changed, 7965 insertions(+), 2094 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.2.4 dated 2024-11-13 and 2.2.5 dated 2024-11-22
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/MVar.pt-package.Rd | 6 +++--- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Multivariate Analysis
Description: Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.2.4 dated 2024-11-13 and 2.2.5 dated 2024-11-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/MVar-package.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Easily Handling Data from the ‘m-Path’ Platform
Description: Provides tools for importing and cleaning Experience Sampling
Method (ESM) data collected via the 'm-Path' platform. The goal is
to provide with a few utility functions to be able to read and perform
some common operations in ESM data collected through the 'm-Path'
platform (<https://m-path.io/landing/>). Functions include raw data
handling, format standardization, and basic data checks, as well as to
calculate the response rate in data from ESM studies.
Author: Merijn Mestdagh [aut, cre] ,
Lara Navarrete [aut],
Koen Niemeijer [aut] ,
m-Path Software [cph]
Maintainer: Merijn Mestdagh <merijn.mestdagh@m-path.io>
Diff between mpathr versions 1.0.1 dated 2024-10-21 and 1.0.2 dated 2024-11-22
mpathr-1.0.1/mpathr/man/figures/README-pressure-1.png |only mpathr-1.0.1/mpathr/man/figures/logo2.png |only mpathr-1.0.1/mpathr/man/figures/logo2.svg |only mpathr-1.0.2/mpathr/DESCRIPTION | 6 +-- mpathr-1.0.2/mpathr/MD5 | 17 ++++----- mpathr-1.0.2/mpathr/NEWS.md | 18 ++++++++++ mpathr-1.0.2/mpathr/R/cast_vec.R | 15 ++++++++ mpathr-1.0.2/mpathr/R/read_mpath.R | 19 ++++++++--- mpathr-1.0.2/mpathr/README.md | 12 +++++- mpathr-1.0.2/mpathr/build/vignette.rds |binary mpathr-1.0.2/mpathr/tests/testthat/test-cast_vec.R | 31 ++++++++++++++++++ 11 files changed, 98 insertions(+), 20 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 10.0.0 dated 2024-07-26 and 11.0.0 dated 2024-11-22
ggblanket-10.0.0/ggblanket/R/unexported.R |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_c.Rd |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_d.Rd |only ggblanket-10.0.0/ggblanket/man/weave_col_palette_o.Rd |only ggblanket-11.0.0/ggblanket/DESCRIPTION | 10 ggblanket-11.0.0/ggblanket/MD5 | 303 +- ggblanket-11.0.0/ggblanket/NAMESPACE | 5 ggblanket-11.0.0/ggblanket/NEWS.md | 10 ggblanket-11.0.0/ggblanket/R/aes.R | 8 ggblanket-11.0.0/ggblanket/R/flex_mode.R | 56 ggblanket-11.0.0/ggblanket/R/gg_blanket.R | 15 ggblanket-11.0.0/ggblanket/R/gg_qq.R | 28 ggblanket-11.0.0/ggblanket/R/gg_ribbon.R | 25 ggblanket-11.0.0/ggblanket/R/gg_smooth.R | 1 ggblanket-11.0.0/ggblanket/R/label_every_nth.R |only ggblanket-11.0.0/ggblanket/R/set_blanket.R | 158 - ggblanket-11.0.0/ggblanket/R/weave.R | 268 +- ggblanket-11.0.0/ggblanket/inst/WORDLIST | 2 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.R | 23 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.Rmd | 32 ggblanket-11.0.0/ggblanket/inst/doc/ggblanket.html | 163 - 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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 1.2.0 dated 2024-09-23 and 1.3.1 dated 2024-11-22
cvasi-1.2.0/cvasi/R/class-Algae.R |only cvasi-1.2.0/cvasi/R/class-Deb.R |only cvasi-1.2.0/cvasi/R/class-GutsRed.R |only cvasi-1.2.0/cvasi/R/class-Lemna.R |only cvasi-1.2.0/cvasi/R/class-Myriophyllum.R |only cvasi-1.2.0/cvasi/R/class-parameter_set.R |only cvasi-1.2.0/cvasi/R/import.R |only cvasi-1.2.0/cvasi/R/morse.R |only cvasi-1.2.0/cvasi/man/import_exposure_text.Rd |only cvasi-1.2.0/cvasi/man/morse.Rd |only cvasi-1.2.0/cvasi/src/algae_TKTD.c |only cvasi-1.2.0/cvasi/tests/testthat/test-simulate_Lemna.R |only cvasi-1.3.1/cvasi/DESCRIPTION | 32 cvasi-1.3.1/cvasi/MD5 | 229 cvasi-1.3.1/cvasi/NAMESPACE | 15 cvasi-1.3.1/cvasi/NEWS.md | 28 cvasi-1.3.1/cvasi/R/calibrate.R | 9 cvasi-1.3.1/cvasi/R/class-EffectScenario.R | 3 cvasi-1.3.1/cvasi/R/class-ParameterSet.R |only cvasi-1.3.1/cvasi/R/class-ScenarioSequence.R | 6 cvasi-1.3.1/cvasi/R/class-Transferable.R | 2 cvasi-1.3.1/cvasi/R/data.R | 4 cvasi-1.3.1/cvasi/R/dose_response.R | 93 cvasi-1.3.1/cvasi/R/effect.R | 15 cvasi-1.3.1/cvasi/R/fx.R | 82 cvasi-1.3.1/cvasi/R/get.R | 8 cvasi-1.3.1/cvasi/R/globals.R | 13 cvasi-1.3.1/cvasi/R/has.R | 6 cvasi-1.3.1/cvasi/R/import_morse.R |only cvasi-1.3.1/cvasi/R/import_toxswa.R | 398 - cvasi-1.3.1/cvasi/R/is.R | 2 cvasi-1.3.1/cvasi/R/man-deb.R |only cvasi-1.3.1/cvasi/R/man-lemna.R |only cvasi-1.3.1/cvasi/R/man-macrophytes.R |only cvasi-1.3.1/cvasi/R/model-algae.R |only cvasi-1.3.1/cvasi/R/model-deb_abj.R |only cvasi-1.3.1/cvasi/R/model-debtox.R | 37 cvasi-1.3.1/cvasi/R/model-guts_red.R |only cvasi-1.3.1/cvasi/R/model-lemna_schmitt.R |only cvasi-1.3.1/cvasi/R/model-lemna_setac.R |only cvasi-1.3.1/cvasi/R/model-myriophyllum.R |only cvasi-1.3.1/cvasi/R/plot.R |only cvasi-1.3.1/cvasi/R/plotting.r | 39 cvasi-1.3.1/cvasi/R/set.R | 12 cvasi-1.3.1/cvasi/R/set_exposure.R | 22 cvasi-1.3.1/cvasi/R/set_param.R | 10 cvasi-1.3.1/cvasi/R/simulate.R | 95 cvasi-1.3.1/cvasi/R/solver.R | 505 - cvasi-1.3.1/cvasi/R/survival.R | 6 cvasi-1.3.1/cvasi/README.md |only cvasi-1.3.1/cvasi/data/Rsubcapitata.rda |binary cvasi-1.3.1/cvasi/data/americamysis.rda |binary cvasi-1.3.1/cvasi/data/focusd1.rda |binary cvasi-1.3.1/cvasi/data/minnow_it.rda |binary cvasi-1.3.1/cvasi/data/minnow_sd.rda |binary cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.R | 14 cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.Rmd | 11 cvasi-1.3.1/cvasi/inst/doc/cvasi-1-manual.html | 17 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.R | 18 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.Rmd | 20 cvasi-1.3.1/cvasi/inst/doc/cvasi-2-howto.html | 24 cvasi-1.3.1/cvasi/man/Algae-models.Rd | 12 cvasi-1.3.1/cvasi/man/Algae_Simple.Rd | 30 cvasi-1.3.1/cvasi/man/Algae_TKTD.Rd | 30 cvasi-1.3.1/cvasi/man/Algae_Weber.Rd | 30 cvasi-1.3.1/cvasi/man/DEB-models.Rd | 12 cvasi-1.3.1/cvasi/man/DEB_abj.Rd | 21 cvasi-1.3.1/cvasi/man/DEBtox.Rd | 30 cvasi-1.3.1/cvasi/man/GUTS-RED-models.Rd | 10 cvasi-1.3.1/cvasi/man/GUTS_RED_IT.Rd | 2 cvasi-1.3.1/cvasi/man/GUTS_RED_SD.Rd | 2 cvasi-1.3.1/cvasi/man/Lemna-models.Rd | 10 cvasi-1.3.1/cvasi/man/Lemna_SETAC.Rd | 62 cvasi-1.3.1/cvasi/man/Lemna_Schmitt.Rd | 58 cvasi-1.3.1/cvasi/man/Macrophyte-models.Rd | 10 cvasi-1.3.1/cvasi/man/Myrio.Rd | 43 cvasi-1.3.1/cvasi/man/Myrio_log.Rd | 43 cvasi-1.3.1/cvasi/man/Myriophyllum-models.Rd | 10 cvasi-1.3.1/cvasi/man/Rsubcapitata.Rd | 2 cvasi-1.3.1/cvasi/man/Scenarios.Rd | 10 cvasi-1.3.1/cvasi/man/Transferable.Rd | 10 cvasi-1.3.1/cvasi/man/dose_response.Rd | 10 cvasi-1.3.1/cvasi/man/figures |only cvasi-1.3.1/cvasi/man/focusd1.Rd | 2 cvasi-1.3.1/cvasi/man/fx.Rd | 19 cvasi-1.3.1/cvasi/man/get_model.Rd | 2 cvasi-1.3.1/cvasi/man/get_tag.Rd | 2 cvasi-1.3.1/cvasi/man/import_morse.Rd |only cvasi-1.3.1/cvasi/man/import_swash.Rd | 6 cvasi-1.3.1/cvasi/man/import_toxswa.Rd | 63 cvasi-1.3.1/cvasi/man/minnow_it.Rd | 2 cvasi-1.3.1/cvasi/man/minnow_sd.Rd | 2 cvasi-1.3.1/cvasi/man/parameter_set.Rd | 5 cvasi-1.3.1/cvasi/man/plot.Rd |only cvasi-1.3.1/cvasi/man/plot_epx.Rd | 2 cvasi-1.3.1/cvasi/man/plot_ppc.Rd | 3 cvasi-1.3.1/cvasi/man/plot_ppc_combi.Rd | 6 cvasi-1.3.1/cvasi/man/plot_scenario.Rd | 10 cvasi-1.3.1/cvasi/man/plot_sd.Rd | 3 cvasi-1.3.1/cvasi/man/set_mode_of_action.Rd | 7 cvasi-1.3.1/cvasi/man/set_param.Rd | 96 cvasi-1.3.1/cvasi/man/set_times.Rd | 2 cvasi-1.3.1/cvasi/man/simulate_batch.Rd | 35 cvasi-1.3.1/cvasi/man/solver.Rd | 81 cvasi-1.3.1/cvasi/man/survival.Rd | 6 cvasi-1.3.1/cvasi/src/algae_simple.c | 11 cvasi-1.3.1/cvasi/src/algae_tktd.c |only cvasi-1.3.1/cvasi/src/algae_weber.c | 13 cvasi-1.3.1/cvasi/src/deb_abj.c | 18 cvasi-1.3.1/cvasi/src/lemna_schmitt.c | 50 cvasi-1.3.1/cvasi/src/lemna_setac.c |only cvasi-1.3.1/cvasi/src/myriophyllum.c | 31 cvasi-1.3.1/cvasi/tests/data/TOXSWA/testonil.out | 3531 ---------- cvasi-1.3.1/cvasi/tests/data/morse |only cvasi-1.3.1/cvasi/tests/testthat/_snaps/verify_guts.md | 12 cvasi-1.3.1/cvasi/tests/testthat/lemna_helpers.R |only cvasi-1.3.1/cvasi/tests/testthat/morse_guts-red.R | 8 cvasi-1.3.1/cvasi/tests/testthat/test-calibrate.R | 2 cvasi-1.3.1/cvasi/tests/testthat/test-epx.R | 11 cvasi-1.3.1/cvasi/tests/testthat/test-get.R | 4 cvasi-1.3.1/cvasi/tests/testthat/test-import_morse.R |only cvasi-1.3.1/cvasi/tests/testthat/test-import_toxswa.R | 167 cvasi-1.3.1/cvasi/tests/testthat/test-plot.R |only cvasi-1.3.1/cvasi/tests/testthat/test-set.R | 84 cvasi-1.3.1/cvasi/tests/testthat/test-set_exposure.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_batch.R | 28 cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_schmitt.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_setac.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_sequence.R | 2 cvasi-1.3.1/cvasi/vignettes/cvasi-1-manual.Rmd | 11 cvasi-1.3.1/cvasi/vignettes/cvasi-2-howto.Rmd | 20 131 files changed, 1302 insertions(+), 5277 deletions(-)
Title: Carbon-Related Assessment of Silvicultural Concepts
Description: A simulation model and accompanying functions that support
assessing silvicultural concepts on the forest estate level with a focus on
the CO2 uptake by wood growth and CO2 emissions by forest operations. For
achieving this, a virtual forest estate area is split into the areas covered
by typical phases of the silvicultural concept of interest. Given initial
area shares of these phases, the dynamics of these areas is simulated. The
typical carbon stocks and flows which are known for all phases are
attributed post-hoc to the areas and upscaled to the estate level. CO2
emissions by forest operations are estimated based on the amounts and
dimensions of the harvested timber. Probabilities of damage events are taken
into account.
Author: Peter Biber [aut, cre, cph] ,
Stefano Grigolato [ctb] ,
Julia Schmucker [ctb] ,
Enno Uhl [ctb] ,
Hans Pretzsch [ctb]
Maintainer: Peter Biber <p.biber@tum.de>
Diff between care4cmodel versions 1.0.2 dated 2024-06-04 and 1.0.3 dated 2024-11-22
DESCRIPTION | 10 MD5 | 20 - NEWS.md | 18 R/co2_evaluation.R | 6 R/plot_c4c_co2_result.R | 14 R/setup_simulation.R | 4 README.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started-with-care4cmodel.html | 498 ++++++++++++------------- man/setup_statevars.Rd | 4 11 files changed, 292 insertions(+), 285 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 24.10.3 dated 2024-10-03 and 24.11.2 dated 2024-11-22
REDCapCAST-24.10.3/REDCapCAST/R/create_instrument_meta.R |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.R |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.Rmd |only REDCapCAST-24.10.3/REDCapCAST/inst/doc/Introduction.html |only REDCapCAST-24.10.3/REDCapCAST/man/server_factory.Rd |only REDCapCAST-24.10.3/REDCapCAST/man/ui_factory.Rd |only REDCapCAST-24.10.3/REDCapCAST/vignettes/Introduction.Rmd |only REDCapCAST-24.11.2/REDCapCAST/DESCRIPTION | 32 REDCapCAST-24.11.2/REDCapCAST/MD5 | 79 REDCapCAST-24.11.2/REDCapCAST/NAMESPACE | 27 REDCapCAST-24.11.2/REDCapCAST/NEWS.md | 34 REDCapCAST-24.11.2/REDCapCAST/R/as_factor.R |only REDCapCAST-24.11.2/REDCapCAST/R/ds2dd_detailed.R | 439 +++-- REDCapCAST-24.11.2/REDCapCAST/R/export_redcap_instrument.R |only REDCapCAST-24.11.2/REDCapCAST/R/redcapcast_data.R | 3 REDCapCAST-24.11.2/REDCapCAST/R/shiny_cast.R | 268 ++- REDCapCAST-24.11.2/REDCapCAST/README.md | 51 REDCapCAST-24.11.2/REDCapCAST/build/vignette.rds |binary REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_data.csv |only REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_data.rda |binary REDCapCAST-24.11.2/REDCapCAST/data/redcapcast_meta.rda |binary REDCapCAST-24.11.2/REDCapCAST/inst/WORDLIST | 26 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.R | 54 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.Rmd | 2 REDCapCAST-24.11.2/REDCapCAST/inst/doc/Database-creation.html | 859 ---------- REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.R |only REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.Rmd |only REDCapCAST-24.11.2/REDCapCAST/inst/doc/REDCapCAST.html |only REDCapCAST-24.11.2/REDCapCAST/inst/shiny-examples |only REDCapCAST-24.11.2/REDCapCAST/man/REDCapCAST-package.Rd | 4 REDCapCAST-24.11.2/REDCapCAST/man/all_na.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/as_factor.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/cast_data_overview.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/cast_meta_overview.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/compact_vec.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/create_instrument_meta.Rd | 25 REDCapCAST-24.11.2/REDCapCAST/man/ds2dd_detailed.Rd | 35 REDCapCAST-24.11.2/REDCapCAST/man/export_redcap_instrument.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/fct2num.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/file_extension.Rd | 6 REDCapCAST-24.11.2/REDCapCAST/man/get_attr.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/guess_time_only.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/haven_all_levels.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/named_levels.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/nav_bar_page.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/numchar2fct.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/parse_data.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/possibly_roman.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/redcapcast_data.Rd | 3 REDCapCAST-24.11.2/REDCapCAST/man/set_attr.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/shiny_cast.Rd | 7 REDCapCAST-24.11.2/REDCapCAST/man/var2fct.Rd |only REDCapCAST-24.11.2/REDCapCAST/man/vec2choice.Rd |only REDCapCAST-24.11.2/REDCapCAST/tests/testthat/test-ds2dd.R |only REDCapCAST-24.11.2/REDCapCAST/vignettes/Database-creation.Rmd | 2 REDCapCAST-24.11.2/REDCapCAST/vignettes/REDCapCAST.Rmd |only 56 files changed, 864 insertions(+), 1092 deletions(-)
Title: Neutrosophic Statistics
Description: Analyzes data involving imprecise and vague information. Provides summary statistics and describes the characteristics of neutrosophic data, as defined by Florentin Smarandache (2013).<ISBN:9781599732749>.
Author: Zahid Khan [aut],
Zsolt T. Kosztyan [aut, cre]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between neutrostat versions 0.0.1 dated 2024-10-11 and 0.0.2 dated 2024-11-22
DESCRIPTION | 7 ++++--- MD5 | 18 ++++++++++++++++-- NAMESPACE | 40 ++++++++++++++++++++++++++++++++++++++++ R/nexp.R |only R/ngam.R |only R/nlap.R |only R/nnorm.R |only R/nray.R |only R/nwbl.R |only inst |only man/nexp.Rd |only man/ngam.Rd |only man/nlap.Rd |only man/nnorm.Rd |only man/nray.Rd |only man/nwbl.Rd |only 16 files changed, 60 insertions(+), 5 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.0.9 dated 2024-09-25 and 1.0.10 dated 2024-11-22
DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/DESCRIPTION | 9 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/MD5 | 205 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/NAMESPACE | 1 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/NEWS.md | 5 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDaysSupply.R | 117 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugDose.R | 104 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugExposureDuration.R | 33 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugQuantity.R | 28 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugRoutes.R | 47 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugSig.R | 40 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugSourceConcepts.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugType.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkDrugsMissing.R | 72 + DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/checkVerbatimEndDate.R | 38 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/executeChecks.R | 181 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/getDrugRecords.R | 18 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/getDrugStrength.R | 21 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/ingredientDescendantsInDb.R | 103 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/mockDrugExposure.R | 423 +++++----- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/obscureCounts.R | 13 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/runBenchmark.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/shiny.R | 1 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/summariseChecks.R | 128 +-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/R/utils.R | 59 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/README.md | 166 ++- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/build/vignette.rds |binary DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DaysSupply.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDose.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugDuration.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSig.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.html | 122 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/DrugTypes.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 180 ++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Missingness.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Quantity.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/Routes.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.R | 10 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.html | 126 ++ DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data/eunomia.zip |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/dataPlotPanel.R | 235 +++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/global.R | 17 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/metaDataPanel.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/mock.zip |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/plots.R | 93 +- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/server.R | 165 ++- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/tests/testthat/test-shinytest2.R | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/ui.R | 21 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/utils.R | 57 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/executeChecks.Rd | 3 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/executeChecksSingleIngredient.Rd | 2 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/runBenchmarkExecuteSingleIngredient.Rd |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/man/writeResultToDisk.Rd | 3 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-CheckDrugSig.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-CheckVerbatimEndDate.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-GetDrugRecords.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-MockDrugExposure.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-ObscureCounts.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-SummariseChecks.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 17 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDaysSupply.R | 58 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugDose.R | 84 + DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugExposureDuration.R | 49 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugMissings.R | 56 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugQuantity.R | 27 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugRoutes.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugSourceConcepts.R | 48 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-checkDrugTypes.R | 52 - DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-executeChecks.R | 266 ++++-- DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-runBenchmark.R |only DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/tests/testthat/test-utils.R | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DaysSupply.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugDuration.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugSig.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugSourceConcepts.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/DrugTypes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 42 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Missingness.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Quantity.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/Routes.Rmd | 8 DrugExposureDiagnostics-1.0.10/DrugExposureDiagnostics/vignettes/VerbatimEndDate.Rmd | 8 DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data/mock.zip |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-checkDrugSig.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-checkVerbatimEndDate.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-getDrugRecords.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-mockDrugExposure.R |only DrugExposureDiagnostics-1.0.9/DrugExposureDiagnostics/tests/testthat/test-summariseChecks.R |only 112 files changed, 3242 insertions(+), 2025 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Document a Universe of Packages
Description: Creates a data frame containing the metadata associated with
the documentation of a collection of R packages. It allows for linking
topic names to their corresponding documentation online. If you
maintain a universe meta-package, it helps create a comprehensive
reference for its website.
Author: Mauro Lepore [aut, cre, cph]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between dverse versions 0.0.1 dated 2024-11-05 and 0.1.0 dated 2024-11-22
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS.md | 26 ++++++- R/document_universe.R | 103 ++++++++++------------------ R/s3_strip_class.R | 3 R/search_documentation.R | 13 +-- README.md | 104 +++++++++++++++++++++-------- inst/WORDLIST | 11 +-- man/document_universe.Rd | 6 + tests/testthat/test-document_universe.R | 38 ++++++++-- tests/testthat/test-search_documentation.R | 12 --- 11 files changed, 201 insertions(+), 143 deletions(-)
Title: Bootstrapping in Different One-Way and Two-Way ANOVA
Description: To address the violation of the assumption of normally distributed variables, researchers frequently employ bootstrapping. Building upon established packages for R (Sigmann et al. (2024) <doi:10.32614/CRAN.package.afex>, Lenth (2024) <doi:10.32614/CRAN.package.emmeans>), we provide bootstrapping functions to approximate a normal distribution of the parameter estimates for between-subject, within-subject, and mixed one-way and two-way ANOVA.
Author: Lisa-Marie Segbert [aut],
Christian Bloetner [aut, cre]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between AOboot versions 0.1.0 dated 2024-09-03 and 0.1.1 dated 2024-11-22
DESCRIPTION | 8 MD5 | 8 R/AObootMixed.R | 1338 ++++++++++++++++++++++++++-------------------------- man/AObootMixed.Rd | 4 man/AObootWithin.Rd | 4 5 files changed, 685 insertions(+), 677 deletions(-)
Title: Matching Adjusted Indirect Comparison
Description: Facilitates performing matching adjusted indirect comparison
(MAIC) analysis where the endpoint of interest is either time-to-event
(e.g. overall survival) or binary (e.g. objective tumor response). The method
is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.
Author: Gregory Chen [aut],
Michael Seo [aut],
Isaac Gravestock [aut, cre],
Miranta Antoniou [ctb],
Chrysostomos Kalyvas [ctb],
MSD, Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between maicplus versions 0.1.0 dated 2024-11-10 and 0.1.1 dated 2024-11-22
maicplus-0.1.0/maicplus/tests/testthat/Rplots.pdf |only maicplus-0.1.1/maicplus/DESCRIPTION | 10 +- maicplus-0.1.1/maicplus/MD5 | 37 ++++------ maicplus-0.1.1/maicplus/NEWS.md | 4 + maicplus-0.1.1/maicplus/R/maic_anchored.R | 24 +++--- maicplus-0.1.1/maicplus/R/maic_unanchored.R | 4 - maicplus-0.1.1/maicplus/inst/doc/anchored_binary.R | 2 maicplus-0.1.1/maicplus/inst/doc/anchored_binary.Rmd | 2 maicplus-0.1.1/maicplus/inst/doc/anchored_binary.html | 12 +-- maicplus-0.1.1/maicplus/inst/doc/anchored_survival.html | 4 - maicplus-0.1.1/maicplus/inst/doc/calculating_weights.html | 6 - maicplus-0.1.1/maicplus/inst/doc/introduction.html | 4 - maicplus-0.1.1/maicplus/inst/doc/kaplan_meier_plots.html | 16 ++-- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.R | 10 +- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.Rmd | 10 +- maicplus-0.1.1/maicplus/inst/doc/unanchored_binary.html | 4 - maicplus-0.1.1/maicplus/inst/doc/unanchored_survival.html | 4 - maicplus-0.1.1/maicplus/tests/testthat/_snaps/maic_anchored.md | 16 ++-- maicplus-0.1.1/maicplus/vignettes/anchored_binary.Rmd | 2 maicplus-0.1.1/maicplus/vignettes/unanchored_binary.Rmd | 10 +- 20 files changed, 95 insertions(+), 86 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.16 dated 2024-08-19 and 1.0.17 dated 2024-11-22
DESCRIPTION | 8 ++-- MD5 | 52 ++++++++++++++--------------- NEWS.md | 5 ++ R/data.R | 4 ++ build/vignette.rds |binary data/municipality_key.rda |binary data/municipality_key_2013.rda |binary data/municipality_key_2014.rda |binary data/municipality_key_2015.rda |binary data/municipality_key_2016.rda |binary data/municipality_key_2017.rda |binary data/municipality_key_2018.rda |binary data/municipality_key_2019.rda |binary data/municipality_key_2020.rda |binary data/municipality_key_2021.rda |binary data/municipality_key_2022.rda |binary data/municipality_key_2023.rda |binary data/municipality_key_2024.rda |binary inst/doc/geofi_datasets.R | 10 ++--- inst/doc/geofi_datasets.html | 30 ++++++++-------- inst/doc/geofi_joining_attribute_data.R | 10 ++--- inst/doc/geofi_joining_attribute_data.html | 4 +- inst/doc/geofi_making_maps.R | 10 ++--- inst/doc/geofi_making_maps.html | 32 ++++++++--------- inst/doc/geofi_spatial_analysis.R | 10 ++--- inst/doc/geofi_spatial_analysis.html | 18 +++++----- man/municipality_key_2024.Rd | 4 ++ 27 files changed, 105 insertions(+), 92 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.4.2 dated 2024-09-20 and 3.4.3 dated 2024-11-22
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/bsroc.R | 1 + R/plot.metadiag.R | 4 +++- R/plotcompare.R | 3 ++- R/plotcredibility.R | 3 ++- 7 files changed, 32 insertions(+), 13 deletions(-)
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] ,
Thibaut Jombart [ctb]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 2.5.0 dated 2024-10-06 and 2.6.0 dated 2024-11-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 29 +++++++++++++++++++++++++++++ R/incidence.R | 24 +++++++++++++++--------- R/plot.R | 6 +++++- R/utils.R | 2 ++ build/vignette.rds |binary inst/doc/incidence2.html | 34 +++++++++++++++++----------------- 8 files changed, 79 insertions(+), 38 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 2.0.0 dated 2024-09-12 and 2.0.1 dated 2024-11-22
vDiveR-2.0.0/vDiveR/R/plot_conservationLevel.R |only vDiveR-2.0.0/vDiveR/R/plot_worldmap.R |only vDiveR-2.0.0/vDiveR/man/plot_conservationLevel.Rd |only vDiveR-2.0.0/vDiveR/man/plot_worldmap.Rd |only vDiveR-2.0.1/vDiveR/DESCRIPTION | 14 vDiveR-2.0.1/vDiveR/MD5 | 50 vDiveR-2.0.1/vDiveR/NAMESPACE | 11 vDiveR-2.0.1/vDiveR/NEWS.md | 5 vDiveR-2.0.1/vDiveR/R/json2csv.R | 3 vDiveR-2.0.1/vDiveR/R/metadata_extraction.R | 2 vDiveR-2.0.1/vDiveR/R/plot_conservation_level.R |only vDiveR-2.0.1/vDiveR/R/plot_correlation.R | 2 vDiveR-2.0.1/vDiveR/R/plot_dynamics_protein.R | 68 vDiveR-2.0.1/vDiveR/R/plot_dynamics_proteome.R | 116 vDiveR-2.0.1/vDiveR/R/plot_entropy.R | 31 vDiveR-2.0.1/vDiveR/R/plot_time.R | 2 vDiveR-2.0.1/vDiveR/R/plot_world_map.R |only vDiveR-2.0.1/vDiveR/R/sample_data.R | 2 vDiveR-2.0.1/vDiveR/data/metadata.rda |binary vDiveR-2.0.1/vDiveR/data/protein_2hosts.rda |binary vDiveR-2.0.1/vDiveR/inst/extdata/city_mapper.csv |87098 ++++++++++----------- vDiveR-2.0.1/vDiveR/man/metadata.Rd | 2 vDiveR-2.0.1/vDiveR/man/metadata_extraction.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_conservation_level.Rd |only vDiveR-2.0.1/vDiveR/man/plot_dynamics_protein.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_dynamics_proteome.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_entropy.Rd | 4 vDiveR-2.0.1/vDiveR/man/plot_time.Rd | 2 vDiveR-2.0.1/vDiveR/man/plot_world_map.Rd |only vDiveR-2.0.1/vDiveR/tests/testthat/test-json2csv.R | 4 30 files changed, 42621 insertions(+), 44801 deletions(-)
Title: Robust Score Testing in GLMs, by Sign-Flip Contributions
Description: Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Author: Livio Finos [cre, aut] ,
Jelle J. Goeman [ctb],
Jesse Hemerik [ctb],
Riccardo De Santis [ctb]
Maintainer: Livio Finos <livio.finos@unipd.it>
Diff between flipscores versions 1.2.0 dated 2022-08-15 and 1.3.1 dated 2024-11-22
DESCRIPTION | 22 +++- MD5 | 31 ++++-- NAMESPACE | 37 ++++---- R/anova_flipscores.R | 7 - R/compute_flips.R |only R/compute_scores.R | 201 +++++++++++++++++++++++++++++---------------- R/flipscores-package.R |only R/flipscores.R | 107 +++++++++++++++++------ R/flipscores_package.R | 6 - R/make_flips.R |only R/utility_functions.R | 23 +++-- R/utiliy_score_functions.R | 119 +++++++++++++------------- build |only man/anova.flipscores.Rd | 84 +++++++++--------- man/compute_scores.Rd | 4 man/flipscores-method.Rd | 50 +++++------ man/flipscores-package.Rd | 20 +++- man/flipscores.Rd | 40 +++++--- man/make_flips.Rd |only 19 files changed, 459 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-22 2.4.6
2022-04-28 2.4.5
2021-03-20 2.4.4
2020-12-10 2.4.3
2020-10-01 2.4.2
2020-07-27 2.4.1
2020-07-09 2.4.0
2019-11-15 2.3.0
2019-01-31 2.2.0
2018-12-05 2.1.3
2018-10-17 2.1.2
2018-08-17 2.1.1
2018-03-14 2.1.0
2017-05-23 2.0.8
2017-02-11 2.0.4
2016-12-01 2.0.2
2015-09-16 1.0.1
2015-08-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-15 1.6.6
2022-04-10 1.6.5
2022-03-29 1.6.4
2021-10-07 1.6.3
2021-03-22 1.6.2
2020-10-01 1.6.0
2019-10-22 1.5.2
2019-08-06 1.5.1
2019-06-05 1.5.0
2018-09-19 1.4.9
2018-05-07 1.4.8
2017-07-08 1.4.6
2017-06-09 1.4.5
2017-03-12 1.4.3
2017-02-11 1.4.1
2016-12-19 1.3.9
2016-11-30 1.3.8
2016-04-20 1.0.7-1
2016-01-06 1.0.7
2015-07-21 1.0.5
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.11.4 dated 2023-12-10 and 0.11.5 dated 2024-11-22
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- inst/doc/networkDynamic.R | 2 +- inst/doc/networkDynamic.Rnw | 2 +- inst/doc/networkDynamic.pdf |binary man/Newcomb.Rd | 4 ++-- man/add.active.Rd | 12 ++++++------ man/age.at.Rd | 2 +- man/as.networkDynamic.Rd | 4 ++-- man/is.active.Rd | 4 ++-- man/network.extensions.Rd | 2 +- man/persistent_ids.Rd | 2 +- man/print.networkDynamic.Rd | 2 +- man/tea_functions.Rd | 2 +- vignettes/networkDynamic.Rnw | 2 +- 16 files changed, 41 insertions(+), 39 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-29 0.1.0
2020-01-15 0.0.2
2018-08-16 0.0.1
Title: Prioritize Variables with Joint Variable Importance Plot in
Observational Study Design
Description: In the observational study design stage, matching/weighting methods are
conducted. However, when many background variables are present, the decision as to
which variables to prioritize for matching/weighting is not trivial. Thus, the
joint treatment-outcome variable importance plots are created to guide variable
selection. The joint variable importance plots enhance variable comparisons via
unadjusted bias curves derived under the omitted variable bias framework. The
plots translate variable importance into recommended values for tuning parameters
in existing methods. Post-matching and/or weighting plots can also be used to
visualize and assess the quality of the observational study design. The method
motivation and derivation is presented in "Prioritizing Variables for Observational
Study Design using the Joint Variable Importance Plot" by Liao et al. (2024)
<doi:10.1080/00031305.2024.2303419>. See the package paper by Liao and Pimentel
(2024) <doi:10.21105/joss.06093> for [...truncated...]
Author: Lauren D. Liao [aut, cre] ,
Samuel D. Pimentel [aut]
Maintainer: Lauren D. Liao <ldliao@berkeley.edu>
Diff between jointVIP versions 0.1.2 dated 2023-03-08 and 1.0.0 dated 2024-11-21
jointVIP-0.1.2/jointVIP/R/general.R |only jointVIP-0.1.2/jointVIP/R/measures.R |only jointVIP-1.0.0/jointVIP/DESCRIPTION | 26 jointVIP-1.0.0/jointVIP/LICENSE | 2 jointVIP-1.0.0/jointVIP/MD5 | 92 +- jointVIP-1.0.0/jointVIP/NEWS.md | 16 jointVIP-1.0.0/jointVIP/R/check_measures.R |only jointVIP-1.0.0/jointVIP/R/create_jointVIP.R |only jointVIP-1.0.0/jointVIP/R/create_post_jointVIP.R |only jointVIP-1.0.0/jointVIP/R/data.R |only jointVIP-1.0.0/jointVIP/R/get_boot_measures.R |only jointVIP-1.0.0/jointVIP/R/get_measures.R |only jointVIP-1.0.0/jointVIP/R/get_post_measures.R |only jointVIP-1.0.0/jointVIP/R/plot.R |only jointVIP-1.0.0/jointVIP/R/print.R |only jointVIP-1.0.0/jointVIP/R/summary.R |only jointVIP-1.0.0/jointVIP/R/support.R |only jointVIP-1.0.0/jointVIP/README.md | 51 + jointVIP-1.0.0/jointVIP/build/vignette.rds |binary jointVIP-1.0.0/jointVIP/data |only jointVIP-1.0.0/jointVIP/inst/CITATION | 21 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.R | 2 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.Rmd | 1 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.html | 305 ++++---- jointVIP-1.0.0/jointVIP/inst/doc/jointVIP.R | 2 jointVIP-1.0.0/jointVIP/inst/doc/jointVIP.html | 380 +++++----- jointVIP-1.0.0/jointVIP/man/add_bias_curves.Rd | 2 jointVIP-1.0.0/jointVIP/man/add_variable_labels.Rd | 2 jointVIP-1.0.0/jointVIP/man/bootstrap.plot.Rd | 4 jointVIP-1.0.0/jointVIP/man/brfss.Rd |only jointVIP-1.0.0/jointVIP/man/ceiling_dec.Rd | 2 jointVIP-1.0.0/jointVIP/man/check_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/create_jointVIP.Rd | 12 jointVIP-1.0.0/jointVIP/man/create_post_jointVIP.Rd | 8 jointVIP-1.0.0/jointVIP/man/figures/README-plot-1.png |binary jointVIP-1.0.0/jointVIP/man/floor_dec.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_boot_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_post_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/one_hot.Rd |only jointVIP-1.0.0/jointVIP/man/plot.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/plot.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/man/print.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/print.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/man/summary.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/summary.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/tests/testthat.R | 5 jointVIP-1.0.0/jointVIP/tests/testthat/test-create_jointVIP.R | 118 +++ jointVIP-1.0.0/jointVIP/tests/testthat/test-create_post_jointVIP.R |only jointVIP-1.0.0/jointVIP/tests/testthat/test-get_measures.R |only jointVIP-1.0.0/jointVIP/tests/testthat/test-plot.R | 311 +++++++- jointVIP-1.0.0/jointVIP/tests/testthat/test-post.R | 21 jointVIP-1.0.0/jointVIP/tests/testthat/test-print.R | 52 + jointVIP-1.0.0/jointVIP/tests/testthat/test-summary.R | 57 + jointVIP-1.0.0/jointVIP/vignettes/additional_options.Rmd | 1 jointVIP-1.0.0/jointVIP/vignettes/ref.bib | 2 56 files changed, 1059 insertions(+), 476 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@insitro.com>
Diff between AllelicSeries versions 0.1.0.2 dated 2024-10-22 and 0.1.1.1 dated 2024-11-21
AllelicSeries-0.1.0.2/AllelicSeries/R/allelic_series_test.R |only AllelicSeries-0.1.1.1/AllelicSeries/DESCRIPTION | 13 AllelicSeries-0.1.1.1/AllelicSeries/MD5 | 100 +-- AllelicSeries-0.1.1.1/AllelicSeries/NEWS.md | 13 AllelicSeries-0.1.1.1/AllelicSeries/R/RcppExports.R | 46 + AllelicSeries-0.1.1.1/AllelicSeries/R/allelic_series.R |only AllelicSeries-0.1.1.1/AllelicSeries/R/allelic_series_sumstats.R | 149 +++-- AllelicSeries-0.1.1.1/AllelicSeries/R/class.R | 15 AllelicSeries-0.1.1.1/AllelicSeries/R/generate_data.R | 125 ++-- AllelicSeries-0.1.1.1/AllelicSeries/R/generate_sumstats.R | 33 - AllelicSeries-0.1.1.1/AllelicSeries/R/input_checks.R | 60 +- AllelicSeries-0.1.1.1/AllelicSeries/R/utilities.R | 54 + AllelicSeries-0.1.1.1/AllelicSeries/build/vignette.rds |binary AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.R | 27 AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.Rmd | 43 + AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.html | 284 ++++++---- AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.R |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.html |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.R |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.html |only AllelicSeries-0.1.1.1/AllelicSeries/man/ASBT.Rd | 17 AllelicSeries-0.1.1.1/AllelicSeries/man/ASBTSS.Rd | 29 - AllelicSeries-0.1.1.1/AllelicSeries/man/ASKAT.Rd | 10 AllelicSeries-0.1.1.1/AllelicSeries/man/ASKATSS.Rd | 23 AllelicSeries-0.1.1.1/AllelicSeries/man/Aggregator.Rd | 22 AllelicSeries-0.1.1.1/AllelicSeries/man/AllelicSeries-package.Rd | 8 AllelicSeries-0.1.1.1/AllelicSeries/man/BaselineSS.Rd | 13 AllelicSeries-0.1.1.1/AllelicSeries/man/COAST-class.Rd | 2 AllelicSeries-0.1.1.1/AllelicSeries/man/COAST.Rd | 17 AllelicSeries-0.1.1.1/AllelicSeries/man/COASTSS.Rd | 28 AllelicSeries-0.1.1.1/AllelicSeries/man/CalcRegParam.Rd | 4 AllelicSeries-0.1.1.1/AllelicSeries/man/CalcSumstats.Rd | 16 AllelicSeries-0.1.1.1/AllelicSeries/man/CheckInputs.Rd | 2 AllelicSeries-0.1.1.1/AllelicSeries/man/CheckInputsSS.Rd | 6 AllelicSeries-0.1.1.1/AllelicSeries/man/Counts.Rd | 7 AllelicSeries-0.1.1.1/AllelicSeries/man/DGP.Rd | 40 - AllelicSeries-0.1.1.1/AllelicSeries/man/GenAnno.Rd | 12 AllelicSeries-0.1.1.1/AllelicSeries/man/GenGeno.Rd | 10 AllelicSeries-0.1.1.1/AllelicSeries/man/GenGenoMat.Rd | 5 AllelicSeries-0.1.1.1/AllelicSeries/man/GenPheno.Rd | 26 AllelicSeries-0.1.1.1/AllelicSeries/man/SumCountSS.Rd | 14 AllelicSeries-0.1.1.1/AllelicSeries/src/RcppExports.cpp | 37 - AllelicSeries-0.1.1.1/AllelicSeries/src/counting.cpp | 17 AllelicSeries-0.1.1.1/AllelicSeries/src/skat.cpp | 13 AllelicSeries-0.1.1.1/AllelicSeries/src/sumstats.cpp | 73 ++ AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-allelic_series.R | 219 +++++++ AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-allelic_series_sumstats.R | 217 ++++++- AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-binary.R | 40 - AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-counts.R | 45 + AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-data_generation.R | 220 ++++++- AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-score_test.R | 6 AllelicSeries-0.1.1.1/AllelicSeries/vignettes/coast.Rmd | 43 + AllelicSeries-0.1.1.1/AllelicSeries/vignettes/coast_ss.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/vignettes/data_generation.Rmd |only 56 files changed, 1653 insertions(+), 550 deletions(-)
Title: VPC Percentiles and Prediction Intervals
Description: Perform a Visual Predictive Check (VPC), while accounting for
stratification, censoring, and prediction correction. Using piping from
'magrittr', the intuitive syntax gives users a flexible and powerful method
to generate VPCs using both traditional binning and a new binless approach
Jamsen et al. (2018) <doi:10.1002/psp4.12319> with Additive Quantile
Regression (AQR) and Locally Estimated Scatterplot Smoothing (LOESS)
prediction correction.
Author: Olivier Barriere [aut],
Benjamin Rich [aut],
James Craig [aut, cre] ,
Samer Mouksassi [aut],
Bill Denney [ctb] ,
Michael Tomashevskiy [ctb],
Kris Jamsen [ctb],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between tidyvpc versions 1.5.1 dated 2024-01-18 and 1.5.2 dated 2024-11-21
tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.html |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.html |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.html |only tidyvpc-1.5.2/tidyvpc/DESCRIPTION | 17 tidyvpc-1.5.2/tidyvpc/LICENSE | 2 tidyvpc-1.5.2/tidyvpc/MD5 | 64 tidyvpc-1.5.2/tidyvpc/NEWS.md | 11 tidyvpc-1.5.2/tidyvpc/R/binless.R | 15 tidyvpc-1.5.2/tidyvpc/R/npde.R | 117 - tidyvpc-1.5.2/tidyvpc/R/plot.R | 22 tidyvpc-1.5.2/tidyvpc/R/vpcstats.R | 179 + tidyvpc-1.5.2/tidyvpc/R/vpcstats_fun.R | 27 tidyvpc-1.5.2/tidyvpc/README.md | 2 tidyvpc-1.5.2/tidyvpc/build/vignette.rds |binary tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cat.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cat.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cont.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cont.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_nlmixr2.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_nlmixr2.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/extdata/NPDE/npdeobs.csv | 1102 +++++----- tidyvpc-1.5.2/tidyvpc/man/npde.Rd | 2 tidyvpc-1.5.2/tidyvpc/man/observed.Rd | 16 tidyvpc-1.5.2/tidyvpc/man/predcorrect.Rd | 38 tidyvpc-1.5.2/tidyvpc/man/simulated.Rd | 7 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-aql.svg | 212 + tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-bql-aql.svg | 286 +- tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-bql.svg | 214 + tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/one-sided-strat-formula-with-facet-wrap.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/single-value-group.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/two-sided-strat-formula-with-facet-grid.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/test-vpcstats.R | 92 tidyvpc-1.5.2/tidyvpc/tests/testthat/test_npde.R | 56 tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_cat.pdf.asis |only tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_cont.pdf.asis |only tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_nlmixr2.pdf.asis |only 42 files changed, 1514 insertions(+), 1123 deletions(-)
Title: Assessing and Visualizing Fragility of Clinical Results with
Binary Outcomes
Description: A collection of user-friendly functions for assessing and visualizing fragility of individual studies (Walsh et al., 2014 <doi:10.1016/j.jclinepi.2013.10.019>; Lin, 2021 <doi:10.1111/jep.13428>), conventional pairwise meta-analyses (Atal et al., 2019 <doi:10.1016/j.jclinepi.2019.03.012>), and network meta-analyses of multiple treatments with binary outcomes (Xing et al., 2020 <doi:10.1016/j.jclinepi.2020.07.003>). The included functions are designed to: 1) calculate the fragility index (i.e., the minimal event status modifications that can alter the significance or non-significance of the original result) and fragility quotient (i.e., fragility index divided by sample size) at a specific significance level; 2) give the cases of event status modifications for altering the result's significance or non-significance and visualize these cases; 3) visualize the trend of statistical significance as event status is modified; 4) efficiently derive fragility indexes and f [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between fragility versions 1.5 dated 2024-08-18 and 1.6 dated 2024-11-21
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 4 +++- R/frag.nma.R | 8 ++++---- R/frag.nma.alpha.R | 8 ++++---- build/partial.rdb |binary 6 files changed, 23 insertions(+), 20 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.11 dated 2023-03-17 and 2.0.12 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ inst/CITATION | 3 +-- inst/tools/workaround.R | 26 ++++++++++++++++---------- 5 files changed, 30 insertions(+), 20 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.1.0 dated 2024-11-03 and 1.1.1 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 17 ++++++++++------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/allocation_rule.R | 9 +-------- R/utils.R | 29 ++++++++++++++++++++++++++--- README.md | 2 +- inst/doc/RLoptimal.html | 4 ++-- inst/extdata |only tests/testthat/test-allocation_rule.R |only 10 files changed, 49 insertions(+), 25 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.2.0 dated 2024-11-08 and 1.3.0 dated 2024-11-21
DESCRIPTION | 6 MD5 | 73 +- NAMESPACE | 2 NEWS.md | 340 ++++++------ R/cluster_cloud.R | 2 R/correct_radii.R | 7 R/export_mat.R | 2 R/export_mesh.R | 4 R/plot_qsm.R | 36 - R/qsm_summary.R | 157 ++++- R/rTwig-package.R | 23 R/standardize_qsm.R | 4 R/tools.R | 31 + R/tree_metrics.R | 229 +++++++- R/update_cylinders.R | 9 README.md | 2 build/partial.rdb |binary inst/doc/Box-Dimension.R | 8 inst/doc/Box-Dimension.Rmd | 2 inst/doc/Box-Dimension.html | 14 inst/doc/Metrics.R | 850 ++++++++++++++++---------------- inst/doc/Metrics.html | 4 inst/doc/Overview.R | 118 ++-- inst/doc/Twigs.R | 8 inst/doc/Validation.R | 88 +++ inst/doc/Validation.Rmd | 106 +++- inst/doc/Validation.html | 1128 +++++++++++++++++++++++++++++-------------- inst/extdata/validation2.csv |only man/cluster_cloud.Rd | 2 man/correct_radii.Rd | 7 man/export_mat.Rd | 2 man/export_mesh.Rd | 4 man/plot_qsm.Rd | 8 man/standardize_qsm.Rd | 4 man/tree_metrics.Rd | 16 src/colors.cpp | 2 vignettes/Box-Dimension.Rmd | 2 vignettes/Validation.Rmd | 106 +++- 38 files changed, 2203 insertions(+), 1203 deletions(-)
Title: Calculates the Percentage CV for Mass Spectrometry-Based
Proteomics Data
Description: Calculates the percentage coefficient of variation (CV) for mass spectrometry-based proteomic data. The CV can be calculated with the traditional formula for raw (non log transformed) intensity data, or log transformed data.
Author: Alejandro Brenes [aut, cre]
Maintainer: Alejandro Brenes <abrenes@ed.ac.uk>
Diff between proteomicsCV versions 0.3.0 dated 2024-08-16 and 0.4.0 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/proteomicsCV.R | 2 +- man/proteomicsCV.Rd | 7 ++++--- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.7 dated 2024-11-15 and 0.2.8 dated 2024-11-21
DESCRIPTION | 6 +-- MD5 | 37 +++++++++++----------- NAMESPACE | 1 NEWS.md | 7 +++- R/OptimizerADBO.R | 41 +++++++++++++----------- R/OptimizerAsyncMbo.R | 43 ++++++++++++++------------ R/TunerADBO.R | 35 ++++++++++++--------- R/TunerAsyncMbo.R | 37 ++++++++++++---------- R/helper.R | 27 ++++++++++++++++ man/mlr_optimizers_adbo.Rd | 41 +++++++++++++----------- man/mlr_optimizers_async_mbo.Rd | 43 ++++++++++++++------------ man/mlr_tuners_adbo.Rd | 34 +++++++++++--------- man/mlr_tuners_async_mbo.Rd | 37 ++++++++++++---------- man/redis_available.Rd |only tests/testthat/test_AcqFunctionStochasticCB.R | 5 +++ tests/testthat/test_AcqFunctionStochasticEI.R | 3 + tests/testthat/test_OptimizerADBO.R | 1 tests/testthat/test_OptimizerAsyncMbo.R | 2 + tests/testthat/test_TunerADBO.R | 1 tests/testthat/test_TunerAsyncMbo.R | 1 20 files changed, 244 insertions(+), 158 deletions(-)
Title: Discontinuous Regression and Image Processing
Description: A collection of functions that perform jump regression
and image analysis such as denoising, deblurring and
jump detection. The implemented methods are based on
the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>,
Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>,
Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>,
Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>,
Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>,
Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>,
Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.
Author: Yicheng Kang [aut, cre],
Peihua Qiu [aut, ctb]
Maintainer: Yicheng Kang <kangyicheng0527@gmail.com>
Diff between DRIP versions 2.2 dated 2024-11-18 and 2.3 dated 2024-11-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/JPLLK_surface.R | 5 +++++ tests/testthat/test-JPLLK_surface.R | 6 +++++- 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Parametrized Active Bindings
Description: Provides a simple interface for creating active bindings where the
bound function accepts additional arguments.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between bindr versions 0.1.1 dated 2018-03-13 and 0.1.2 dated 2024-11-21
DESCRIPTION | 17 +++----- MD5 | 12 ++--- NEWS.md | 12 +++++ R/populate.R | 4 - README.md | 106 ++++++++++++++++++++++++++++++++++++++------------- man/bindr-package.Rd | 9 +--- man/create_env.Rd | 3 - 7 files changed, 112 insertions(+), 51 deletions(-)
Title: Annual Regional Database of the European Commission (ARDECO)
Description: A set of functions to access the 'ARDECO' (Annual Regional Database
of the European Commission) data directly from the official ARDECO public
repository through the exploitation of the 'ARDECO' APIs.
The APIs are completely transparent to the user and the provided functions
provide a direct access to the 'ARDECO' data.
The 'ARDECO' database is a collection of variables related to demography,
employment, labour market, domestic product, capital formation.
Each variable can be exposed in one or more units of measure as well as
refers to total values plus additional dimensions like economic sectors, gender,
age classes. Data can be also aggregated at country level according
to the tercet classes as defined by EUROSTAT.
The description of the 'ARDECO' database can be found at the following URL
<https://urban.jrc.ec.europa.eu/ardeco>.
Author: Carmelo Attardo [cre],
Giuseppe Bucciarelli [aut],
European Commission, JRC [cph]
Maintainer: Carmelo Attardo <carmelo.attardo@ec.europa.eu>
Diff between ARDECO versions 2.0.0 dated 2024-08-27 and 2.1.0 dated 2024-11-21
DESCRIPTION | 12 ++++---- MD5 | 21 ++++++++------ NAMESPACE | 2 - NEWS | 2 + R/get_dataset_data.R | 71 +++++++++++++++++++++++++++++++++++++++++++----- R/get_dataset_list.R | 3 -- R/get_tercet_list.R |only R/get_variable_list.R | 31 +------------------- R/get_variable_props.R |only README.md | 7 +--- man/ardeco.Rd | 7 ++++ man/get_dataset_data.Rd | 15 ++++++++-- man/get_tercet_list.Rd |only 13 files changed, 110 insertions(+), 61 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), Programme for International Student Assessment (PISA), and others.
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.0.0 dated 2024-11-08 and 1.2.5 dated 2024-11-21
DESCRIPTION | 13 + MD5 | 88 +++++++++++-- NAMESPACE | 4 NEWS.md | 29 +++- R/ILSAdownload.R | 9 - R/ILSAfile.info.R | 27 +--- R/ILSAmerge.R | 246 +++++++++++++++++++++++++++---------- R/ILSArename.R |only R/addSchools.R |only R/availableILSA.R |only R/combineStudents.R |only R/justload.R | 84 ++++++++++-- R/readILSA.R |only R/spss.syntax.R | 36 ++--- R/uID.R |only README.md | 325 +++---------------------------------------------- build |only inst |only man/ILSAdownload.Rd | 5 man/ILSAfile.info.Rd | 9 - man/ILSAmerge.Rd | 25 ++- man/ILSArename.Rd |only man/addSchools.Rd |only man/availableILSA.Rd |only man/combineStudents.Rd |only man/justload.Rd | 30 +++- man/spss.syntax.Rd | 19 +- vignettes |only 28 files changed, 466 insertions(+), 483 deletions(-)
Title: Quickly Get Datetime Data Ready for Analysis
Description: Transforms datetime data into a format ready for analysis.
It offers two core functionalities; aggregating data to a higher level interval
(thicken) and imputing records where observations were absent (pad).
Author: Edwin Thoen [aut, cre]
Maintainer: Edwin Thoen <edwinthoen@gmail.com>
Diff between padr versions 0.6.2 dated 2022-11-23 and 0.6.3 dated 2024-11-21
DESCRIPTION | 18 ++-- MD5 | 18 ++-- NEWS.md | 4 + R/create_emrgency.R | 1 README.md | 10 +- inst/doc/padr.html | 142 +++++++++++++++++++------------------- inst/doc/padr_custom.html | 72 +++++++++---------- inst/doc/padr_implementation.html | 28 +++---- man/emergency.Rd | 3 tests/testthat/test_thicken.R | 3 10 files changed, 150 insertions(+), 149 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.3.0 dated 2024-09-23 and 0.4.0 dated 2024-11-21
maestro-0.3.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs.R |only maestro-0.4.0/maestro/DESCRIPTION | 10 maestro-0.4.0/maestro/MD5 | 107 +++--- maestro-0.4.0/maestro/NAMESPACE | 14 maestro-0.4.0/maestro/NEWS.md | 22 + maestro-0.4.0/maestro/R/MaestroPipeline.R | 114 ++++-- maestro-0.4.0/maestro/R/MaestroPipelineList.R | 161 +++++++++ maestro-0.4.0/maestro/R/MaestroSchedule.R | 49 ++ maestro-0.4.0/maestro/R/build_schedule.R | 3 maestro-0.4.0/maestro/R/build_schedule_entry.R | 40 ++ maestro-0.4.0/maestro/R/create_pipeline.R | 26 + maestro-0.4.0/maestro/R/maestro_tags.R | 3 maestro-0.4.0/maestro/R/roxy_maestro.R | 122 +++---- maestro-0.4.0/maestro/R/show_network.R |only maestro-0.4.0/maestro/R/suggest_orch_frequency.R | 5 maestro-0.4.0/maestro/R/utils.R | 51 ++ maestro-0.4.0/maestro/README.md | 17 maestro-0.4.0/maestro/build/vignette.rds |binary maestro-0.4.0/maestro/inst/doc/maestro-1-quick-start.R | 32 - maestro-0.4.0/maestro/inst/doc/maestro-1-quick-start.html | 2 maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.R | 44 +- maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.Rmd | 4 maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.html | 19 - maestro-0.4.0/maestro/inst/doc/maestro-3-use-cases.R | 172 +++++----- maestro-0.4.0/maestro/inst/doc/maestro-3-use-cases.html | 2 maestro-0.4.0/maestro/inst/doc/maestro-4-advanced-scheduling.R | 102 ++--- maestro-0.4.0/maestro/inst/doc/maestro-4-advanced-scheduling.html | 14 maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.R |only maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.Rmd |only maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.html |only maestro-0.4.0/maestro/inst/pipeline_template | 3 maestro-0.4.0/maestro/man/MaestroPipeline.Rd | 55 +++ maestro-0.4.0/maestro/man/MaestroPipelineList.Rd | 63 +++ maestro-0.4.0/maestro/man/MaestroSchedule.Rd | 37 +- maestro-0.4.0/maestro/man/create_pipeline.Rd | 11 maestro-0.4.0/maestro/man/figures/README-/unnamed-chunk-3-dark.svg | 2 maestro-0.4.0/maestro/man/figures/README-/unnamed-chunk-3.svg | 2 maestro-0.4.0/maestro/man/is_valid_dag.Rd |only maestro-0.4.0/maestro/man/maestro_tags.Rd | 3 maestro-0.4.0/maestro/man/show_network.Rd |only maestro-0.4.0/maestro/tests/testthat/_snaps/MaestroSchedule.md |only maestro-0.4.0/maestro/tests/testthat/_snaps/dags.md |only maestro-0.4.0/maestro/tests/testthat/_snaps/get_schedule.md | 21 + maestro-0.4.0/maestro/tests/testthat/test-MaestroPipeline.R | 2 maestro-0.4.0/maestro/tests/testthat/test-MaestroPipelineList.R | 5 maestro-0.4.0/maestro/tests/testthat/test-MaestroSchedule.R | 1 maestro-0.4.0/maestro/tests/testthat/test-build_schedule_entry.R | 21 + maestro-0.4.0/maestro/tests/testthat/test-dags.R |only maestro-0.4.0/maestro/tests/testthat/test-get_schedule.R | 6 maestro-0.4.0/maestro/tests/testthat/test-roclets.R | 40 ++ maestro-0.4.0/maestro/tests/testthat/test-show_network.R |only maestro-0.4.0/maestro/tests/testthat/test-suggest_orch_frequency.R | 5 maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs_bad.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs_good.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_maestro.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_outputs_bad.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_outputs_good.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_dags_good/dags.R | 60 +++ maestro-0.4.0/maestro/tests/testthat/test_pipelines_dags_run_bad |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags.R | 3 maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags_self_reference_inputs.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags_self_reference_outputs.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_good/dags.R |only maestro-0.4.0/maestro/vignettes/maestro-2-motivation-concepts.Rmd | 4 maestro-0.4.0/maestro/vignettes/maestro-5-directed-acyclic-graphs.Rmd |only 65 files changed, 1064 insertions(+), 415 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.11.1 dated 2024-07-01 and 2.12.0 dated 2024-11-21
inlabru-2.11.1/inlabru/R/bru.integration.R |only inlabru-2.11.1/inlabru/R/bru.spatial.R |only inlabru-2.11.1/inlabru/R/data.seals.R |only inlabru-2.11.1/inlabru/R/integration.R |only inlabru-2.11.1/inlabru/R/mesh.R |only inlabru-2.11.1/inlabru/data/gorillas.rda |only inlabru-2.11.1/inlabru/data/mexdolphin.rda |only inlabru-2.11.1/inlabru/data/seals_sp.rda |only inlabru-2.11.1/inlabru/inst/examples/gg.inla.mesh.R |only inlabru-2.11.1/inlabru/inst/examples/gg.spatial.R |only inlabru-2.11.1/inlabru/inst/examples/like.R |only inlabru-2.11.1/inlabru/man/bru_int_polygon.Rd |only inlabru-2.11.1/inlabru/man/component.Rd |only inlabru-2.11.1/inlabru/man/component_eval.Rd |only inlabru-2.11.1/inlabru/man/component_list.Rd |only inlabru-2.11.1/inlabru/man/evaluate_comp_simple_list_subsetting.Rd |only inlabru-2.11.1/inlabru/man/gm.Rd |only inlabru-2.11.1/inlabru/man/gmap.Rd |only inlabru-2.11.1/inlabru/man/like.Rd |only inlabru-2.11.1/inlabru/man/row_kron.Rd |only inlabru-2.11.1/inlabru/man/seals.Rd |only inlabru-2.12.0/inlabru/DESCRIPTION | 36 inlabru-2.12.0/inlabru/MD5 | 439 +- inlabru-2.12.0/inlabru/NAMESPACE | 187 - inlabru-2.12.0/inlabru/NEWS.md | 64 inlabru-2.12.0/inlabru/R/bru.gof.R | 105 inlabru-2.12.0/inlabru/R/bru.inference.R | 1726 +++++----- inlabru-2.12.0/inlabru/R/bru_sp.R |only inlabru-2.12.0/inlabru/R/data.Poisson1_1D.R | 12 inlabru-2.12.0/inlabru/R/data.Poisson2_1D.R | 11 inlabru-2.12.0/inlabru/R/data.Poisson3_1D.R | 28 inlabru-2.12.0/inlabru/R/data.gorillas.R | 190 - inlabru-2.12.0/inlabru/R/data.mexdolphin.R | 170 inlabru-2.12.0/inlabru/R/data.mrsea.R | 21 inlabru-2.12.0/inlabru/R/data.robins_subset.R | 9 inlabru-2.12.0/inlabru/R/data.shrimp.R | 22 inlabru-2.12.0/inlabru/R/data.toygroups.R | 9 inlabru-2.12.0/inlabru/R/data.toypoints.R | 3 inlabru-2.12.0/inlabru/R/deltaIC.R | 9 inlabru-2.12.0/inlabru/R/deprecated.R | 4 inlabru-2.12.0/inlabru/R/effect.R | 721 ++-- inlabru-2.12.0/inlabru/R/environment.R | 117 inlabru-2.12.0/inlabru/R/fmesher.R | 120 inlabru-2.12.0/inlabru/R/ggplot.R | 537 +-- inlabru-2.12.0/inlabru/R/inla.R | 92 inlabru-2.12.0/inlabru/R/inlabru-package.R | 21 inlabru-2.12.0/inlabru/R/local_testthat.R | 78 inlabru-2.12.0/inlabru/R/mapper_repeat.R |only inlabru-2.12.0/inlabru/R/mappers.R | 555 +-- inlabru-2.12.0/inlabru/R/model.R | 175 - inlabru-2.12.0/inlabru/R/nlinla.R | 124 inlabru-2.12.0/inlabru/R/plotsample.R | 127 inlabru-2.12.0/inlabru/R/rgl.R | 90 inlabru-2.12.0/inlabru/R/sampling.R | 205 - inlabru-2.12.0/inlabru/R/spatstat.R | 32 inlabru-2.12.0/inlabru/R/spde.R | 71 inlabru-2.12.0/inlabru/R/stack.R | 6 inlabru-2.12.0/inlabru/R/track_plotting.R | 36 inlabru-2.12.0/inlabru/R/transformation.R | 14 inlabru-2.12.0/inlabru/R/used.R |only inlabru-2.12.0/inlabru/R/utils.R | 132 inlabru-2.12.0/inlabru/README.md | 67 inlabru-2.12.0/inlabru/build/vignette.rds |binary inlabru-2.12.0/inlabru/data/gorillas_sf.rda |binary inlabru-2.12.0/inlabru/data/mrsea.rda |binary 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inlabru-2.12.0/inlabru/inst/examples/predict.bru.R | 8 inlabru-2.12.0/inlabru/inst/examples/prediction.bru.R | 2 inlabru-2.12.0/inlabru/inst/examples/rgl.R | 2 inlabru-2.12.0/inlabru/inst/examples/spde.posterior.R | 2 inlabru-2.12.0/inlabru/inst/extdata/gorillas_cov.tif |binary inlabru-2.12.0/inlabru/inst/figures |only inlabru-2.12.0/inlabru/inst/misc/2d_lgcp_residuals_functions.R | 34 inlabru-2.12.0/inlabru/inst/misc/2d_lgcp_residuals_functions_sf.R |only inlabru-2.12.0/inlabru/man/Poisson1_1D.Rd | 12 inlabru-2.12.0/inlabru/man/Poisson2_1D.Rd | 11 inlabru-2.12.0/inlabru/man/Poisson3_1D.Rd | 28 inlabru-2.12.0/inlabru/man/add_mappers.Rd | 4 inlabru-2.12.0/inlabru/man/bincount.Rd | 16 inlabru-2.12.0/inlabru/man/bru.Rd | 62 inlabru-2.12.0/inlabru/man/bru_call_options.Rd | 1 inlabru-2.12.0/inlabru/man/bru_component.Rd |only inlabru-2.12.0/inlabru/man/bru_component_eval.Rd |only inlabru-2.12.0/inlabru/man/bru_component_list.Rd |only inlabru-2.12.0/inlabru/man/bru_compute_linearisation.Rd | 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inlabru-2.12.0/inlabru/man/bru_mapper_const.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_factor.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_1d.Rd | 36 inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_2d.Rd | 17 inlabru-2.12.0/inlabru/man/bru_mapper_fmesher.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_generics.Rd | 22 inlabru-2.12.0/inlabru/man/bru_mapper_harmonics.Rd | 12 inlabru-2.12.0/inlabru/man/bru_mapper_index.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_linear.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_logsumexp.Rd | 49 inlabru-2.12.0/inlabru/man/bru_mapper_marginal.Rd | 23 inlabru-2.12.0/inlabru/man/bru_mapper_matrix.Rd | 7 inlabru-2.12.0/inlabru/man/bru_mapper_mesh_B.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_multi.Rd | 19 inlabru-2.12.0/inlabru/man/bru_mapper_pipe.Rd | 14 inlabru-2.12.0/inlabru/man/bru_mapper_repeat.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_scale.Rd | 10 inlabru-2.12.0/inlabru/man/bru_mapper_shift.Rd | 10 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inlabru-2.12.0/inlabru/man/gg.fm_mesh_1d.Rd | 11 inlabru-2.12.0/inlabru/man/gg.fm_mesh_2d.Rd | 37 inlabru-2.12.0/inlabru/man/gg.matrix.Rd | 6 inlabru-2.12.0/inlabru/man/gg.sf.Rd | 58 inlabru-2.12.0/inlabru/man/globe.Rd | 2 inlabru-2.12.0/inlabru/man/glplot.Rd | 26 inlabru-2.12.0/inlabru/man/gorillas.Rd | 86 inlabru-2.12.0/inlabru/man/gorillas_sf.Rd | 71 inlabru-2.12.0/inlabru/man/iinla.Rd | 2 inlabru-2.12.0/inlabru/man/inlabru-deprecated.Rd | 205 - inlabru-2.12.0/inlabru/man/inlabru-package.Rd | 17 inlabru-2.12.0/inlabru/man/input_eval.Rd | 84 inlabru-2.12.0/inlabru/man/lgcp.Rd | 61 inlabru-2.12.0/inlabru/man/local_testthat.Rd | 17 inlabru-2.12.0/inlabru/man/materncov.bands.Rd | 15 inlabru-2.12.0/inlabru/man/mexdolphin.Rd | 77 inlabru-2.12.0/inlabru/man/mexdolphin_sf.Rd | 76 inlabru-2.12.0/inlabru/man/mrsea.Rd | 21 inlabru-2.12.0/inlabru/man/multiplot.Rd | 26 inlabru-2.12.0/inlabru/man/plot.bru_prediction.Rd | 6 inlabru-2.12.0/inlabru/man/plotsample.Rd | 40 inlabru-2.12.0/inlabru/man/point2count.Rd | 18 inlabru-2.12.0/inlabru/man/predict.bru.Rd | 14 inlabru-2.12.0/inlabru/man/reexports.Rd | 62 inlabru-2.12.0/inlabru/man/robins_subset.Rd | 9 inlabru-2.12.0/inlabru/man/sample.lgcp.Rd | 84 inlabru-2.12.0/inlabru/man/shrimp.Rd | 22 inlabru-2.12.0/inlabru/man/sline.Rd | 48 inlabru-2.12.0/inlabru/man/spatial.to.ppp.Rd | 20 inlabru-2.12.0/inlabru/man/spde.posterior.Rd | 17 inlabru-2.12.0/inlabru/man/spoly.Rd | 42 inlabru-2.12.0/inlabru/man/summary.bru.Rd | 30 inlabru-2.12.0/inlabru/man/summary.component.Rd | 39 inlabru-2.12.0/inlabru/man/toygroups.Rd | 9 inlabru-2.12.0/inlabru/man/toypoints.Rd | 3 inlabru-2.12.0/inlabru/tests/testthat/_snaps/01_lgcp_2d.md | 4 inlabru-2.12.0/inlabru/tests/testthat/_snaps/lgcp_2d_plotsample.md | 2 inlabru-2.12.0/inlabru/tests/testthat/test-01_lgcp_2d.R | 10 inlabru-2.12.0/inlabru/tests/testthat/test-aggregate.R | 22 inlabru-2.12.0/inlabru/tests/testthat/test-bru_sf.R | 52 inlabru-2.12.0/inlabru/tests/testthat/test-component.R | 98 inlabru-2.12.0/inlabru/tests/testthat/test-copy.R | 38 inlabru-2.12.0/inlabru/tests/testthat/test-data.R | 62 inlabru-2.12.0/inlabru/tests/testthat/test-eval_spatial.R | 39 inlabru-2.12.0/inlabru/tests/testthat/test-fmesher_pixels.R | 3 inlabru-2.12.0/inlabru/tests/testthat/test-globe_mesh.R | 21 inlabru-2.12.0/inlabru/tests/testthat/test-latent_fixed_effects.R | 10 inlabru-2.12.0/inlabru/tests/testthat/test-latent_rw2.R | 5 inlabru-2.12.0/inlabru/tests/testthat/test-latent_spde_2d.R | 13 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_1d.R | 32 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_1d_nonlinear.R | 34 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_2d_covars.R | 5 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_2d_plotsample.R | 7 inlabru-2.12.0/inlabru/tests/testthat/test-linearisation.R | 17 inlabru-2.12.0/inlabru/tests/testthat/test-mapper.R | 125 inlabru-2.12.0/inlabru/tests/testthat/test-mdata.R | 38 inlabru-2.12.0/inlabru/tests/testthat/test-multi_like.R | 53 inlabru-2.12.0/inlabru/tests/testthat/test-offset.R | 22 inlabru-2.12.0/inlabru/tests/testthat/test-response_size.R |only inlabru-2.12.0/inlabru/tests/testthat/test-utils.R | 8 inlabru-2.12.0/inlabru/vignettes/bru_mapper.Rmd | 33 inlabru-2.12.0/inlabru/vignettes/component.Rmd | 4 inlabru-2.12.0/inlabru/vignettes/linearapprox.Rmd | 28 241 files changed, 5950 insertions(+), 4366 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.1.2 dated 2024-10-30 and 1.1.3 dated 2024-11-21
duckdb-1.1.2/duckdb/src/Makevars.duckdb |only duckdb-1.1.2/duckdb/src/duckdb |only duckdb-1.1.3/duckdb/DESCRIPTION | 6 duckdb-1.1.3/duckdb/MD5 | 3071 ---------------- duckdb-1.1.3/duckdb/NEWS.md | 23 duckdb-1.1.3/duckdb/R/cpp11.R | 20 duckdb-1.1.3/duckdb/R/relational.R | 46 duckdb-1.1.3/duckdb/R/rethrow-gen.R | 26 duckdb-1.1.3/duckdb/cleanup |only duckdb-1.1.3/duckdb/cleanup.win |only duckdb-1.1.3/duckdb/src/cpp11.cpp | 38 duckdb-1.1.3/duckdb/src/duckdb.tar.xz |only duckdb-1.1.3/duckdb/src/include/rapi.hpp | 3 duckdb-1.1.3/duckdb/src/relational.cpp | 25 duckdb-1.1.3/duckdb/src/reltoaltrep.cpp | 51 duckdb-1.1.3/duckdb/src/utils.cpp | 6 duckdb-1.1.3/duckdb/tests/testthat/_snaps/relational.md |only duckdb-1.1.3/duckdb/tests/testthat/test-DBItest.R | 19 duckdb-1.1.3/duckdb/tests/testthat/test-list.R | 1 duckdb-1.1.3/duckdb/tests/testthat/test-register.R | 2 duckdb-1.1.3/duckdb/tests/testthat/test-rel_api.R | 8 duckdb-1.1.3/duckdb/tests/testthat/test-relational.R | 119 22 files changed, 294 insertions(+), 3170 deletions(-)
Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis [cre, aut] ,
John Alroy [aut] ,
Carl J. Reddin [aut] ,
Wolfgang Kiessling [aut] ,
Deutsche Forschungsgemeinschaft [fnd],
FAU GeoZentrum Nordbayern [fnd]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between divDyn versions 0.8.2 dated 2022-09-05 and 0.8.3 dated 2024-11-21
divDyn-0.8.2/divDyn/inst/NEWS |only divDyn-0.8.2/divDyn/inst/doc/handout.R |only divDyn-0.8.2/divDyn/inst/doc/handout.Rmd |only divDyn-0.8.2/divDyn/inst/doc/handout.pdf |only divDyn-0.8.2/divDyn/vignettes/handout.Rmd |only divDyn-0.8.3/divDyn/DESCRIPTION | 26 + divDyn-0.8.3/divDyn/MD5 | 79 +++-- divDyn-0.8.3/divDyn/NEWS.md |only divDyn-0.8.3/divDyn/R/RcppExports.R | 4 divDyn-0.8.3/divDyn/R/affinity.R | 95 +++++-- divDyn-0.8.3/divDyn/R/data.R | 15 - divDyn-0.8.3/divDyn/R/diversityDynamics.r | 10 divDyn-0.8.3/divDyn/R/fadLad.R | 2 divDyn-0.8.3/divDyn/R/georange.R | 2 divDyn-0.8.3/divDyn/R/slice.R | 2 divDyn-0.8.3/divDyn/R/subsample.R | 19 + divDyn-0.8.3/divDyn/R/subtrials.R | 20 + divDyn-0.8.3/divDyn/R/tabinate.R | 2 divDyn-0.8.3/divDyn/R/zzz.R | 2 divDyn-0.8.3/divDyn/README.md | 343 -------------------------- divDyn-0.8.3/divDyn/build/vignette.rds |binary divDyn-0.8.3/divDyn/data/corals.RData |binary divDyn-0.8.3/divDyn/data/keys.RData |binary divDyn-0.8.3/divDyn/data/stages.RData |binary divDyn-0.8.3/divDyn/data/stages2018.RData |binary divDyn-0.8.3/divDyn/data/stratkeys.RData |binary divDyn-0.8.3/divDyn/data/tens.RData |binary divDyn-0.8.3/divDyn/inst/CITATION | 7 divDyn-0.8.3/divDyn/inst/doc/handout_pdf.R |only divDyn-0.8.3/divDyn/inst/doc/handout_pdf.Rmd |only divDyn-0.8.3/divDyn/inst/doc/handout_pdf.pdf |only divDyn-0.8.3/divDyn/man/affinity.Rd | 12 divDyn-0.8.3/divDyn/man/corals.Rd | 2 divDyn-0.8.3/divDyn/man/divDyn.Rd | 8 divDyn-0.8.3/divDyn/man/fadlad.Rd | 2 divDyn-0.8.3/divDyn/man/figures |only divDyn-0.8.3/divDyn/man/keys.Rd | 4 divDyn-0.8.3/divDyn/man/slice.Rd | 2 divDyn-0.8.3/divDyn/man/stratkeys.Rd | 4 divDyn-0.8.3/divDyn/man/subsample.Rd | 2 divDyn-0.8.3/divDyn/man/tabinate.Rd | 2 divDyn-0.8.3/divDyn/man/tens.Rd | 5 divDyn-0.8.3/divDyn/src/Engine.cpp | 9 divDyn-0.8.3/divDyn/src/RcppExports.cpp | 7 divDyn-0.8.3/divDyn/src/init.c | 4 divDyn-0.8.3/divDyn/vignettes/handout_pdf.Rmd |only 46 files changed, 233 insertions(+), 458 deletions(-)
More information about roxy.shinylive at CRAN
Permanent link
Title: Estimate Brain Networks and Connectivity with ICA and Empirical
Priors
Description: Implements the template ICA (independent components analysis) model
proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the
spatial template ICA model proposed in proposed in Mejia et al. (2022)
<doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level
brain as deviations from known population-level networks, which are
estimated using standard ICA algorithms. Both models employ an
expectation-maximization algorithm for estimation of the latent brain
networks and unknown model parameters. Includes direct support for 'CIFTI',
'GIFTI', and 'NIFTI' neuroimaging file formats.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Daniel Spencer [ctb] ,
Mary Beth Nebel [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between templateICAr versions 0.8.8 dated 2024-10-14 and 0.9.1 dated 2024-11-21
templateICAr-0.8.8/templateICAr/R/EM_FCtemplateICA.R |only templateICAr-0.8.8/templateICAr/R/RcppExports.R |only templateICAr-0.8.8/templateICAr/R/templateICAr-package.R |only templateICAr-0.8.8/templateICAr/build |only templateICAr-0.8.8/templateICAr/man/EM_FCtemplateICA.Rd |only templateICAr-0.8.8/templateICAr/man/Gibbs_AS_posteriorCPP.Rd |only templateICAr-0.8.8/templateICAr/man/UpdateTheta_FCtemplateICA.Rd |only templateICAr-0.8.8/templateICAr/man/UpdateTheta_FCtemplateICAcpp.Rd |only templateICAr-0.8.8/templateICAr/man/compute_LL_FC.Rd |only templateICAr-0.8.8/templateICAr/man/templateICAr-package.Rd |only templateICAr-0.8.8/templateICAr/src |only templateICAr-0.9.1/templateICAr/DESCRIPTION | 18 +++--- templateICAr-0.9.1/templateICAr/MD5 | 26 ++-------- templateICAr-0.9.1/templateICAr/NAMESPACE | 8 --- templateICAr-0.9.1/templateICAr/NEWS.md | 5 + templateICAr-0.9.1/templateICAr/R/VB_FCtemplateICA.R | 3 - templateICAr-0.9.1/templateICAr/R/activations.R | 12 +++- templateICAr-0.9.1/templateICAr/R/dual_reg2.R | 2 templateICAr-0.9.1/templateICAr/R/make_mesh.R | 9 +-- 19 files changed, 38 insertions(+), 45 deletions(-)
Title: A 'shiny' App to Compare Two Data Frames
Description: A tool developed with the 'Golem' framework which provides
an easier way to check cells differences between two data
frames. The user provides two data frames for comparison,
selects IDs variables identifying each row of input data,
then clicks a button to perform the comparison. Several
'R' package functions are used to describe the data
and perform the comparison in the server of the
application. The main ones are comparedf() from 'arsenal'
and skim() from 'skimr'. For more details see the
description of comparedf() from the 'arsenal' package and
that of skim() from the 'skimr' package.
Author: Sergio Ewane Ebouele [aut, cre]
Maintainer: Sergio Ewane Ebouele <info@dataforknow.com>
Diff between dataCompare versions 1.0.3 dated 2024-11-14 and 1.0.4 dated 2024-11-21
DESCRIPTION | 14 +++--- MD5 | 35 ++++++++------- NAMESPACE | 9 ++-- NEWS.md | 11 ++++ R/apex_libraries.R | 6 -- R/app_server.R | 2 R/dataCompare-package.R | 8 +-- R/mod_comp_desc.R | 24 ++++++++-- R/mod_comp_details.R | 8 ++- R/mod_comp_report.R | 6 ++ R/mod_comp_report_fct_display.R | 47 +++++++++++++++++++++ R/mod_intro.R | 3 - R/mod_load_data.R | 43 +++++++++++++------ README.md | 9 +++- inst/doc/dataCompare.R | 10 ++++ inst/doc/dataCompare.Rmd | 13 +++++ inst/doc/dataCompare.html | 71 ++++++++++++++++++-------------- man/compare_data_frame_object_report.Rd |only vignettes/dataCompare.Rmd | 13 +++++ 19 files changed, 242 insertions(+), 90 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.7 dated 2024-01-22 and 1.3.8 dated 2024-11-21
DESCRIPTION | 11 MD5 | 24 R/VolcanoPlotW.R | 38 - R/imageW.R | 166 ++++-- R/plotPCAw.R | 8 R/vioplotW.R | 72 +- build/vignette.rds |binary inst/doc/wrGraphVignette1.R | 45 + inst/doc/wrGraphVignette1.Rmd | 109 ++-- inst/doc/wrGraphVignette1.html | 999 ++++++++++++++--------------------------- man/imageW.Rd | 38 - man/vioplotW.Rd | 5 vignettes/wrGraphVignette1.Rmd | 109 ++-- 13 files changed, 744 insertions(+), 880 deletions(-)
Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>)
databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running
'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam'
core and provides functions to open/close a database (redatam_open()/redatam_close()),
list entities and variables from the database (redatam_entities(), redatam_variables())
and execute a 'SPC' program and gets the results as data frames
(redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] ,
CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>
Diff between redatamx versions 1.0.0 dated 2024-10-29 and 1.0.1 dated 2024-11-21
redatamx-1.0.0/redatamx/src/dependencies.txt |only redatamx-1.0.1/redatamx/DESCRIPTION | 11 redatamx-1.0.1/redatamx/MD5 | 43 +-- redatamx-1.0.1/redatamx/NAMESPACE | 4 redatamx-1.0.1/redatamx/NEWS.md | 13 - redatamx-1.0.1/redatamx/R/output-env.R | 8 redatamx-1.0.1/redatamx/R/redatam-api.R | 33 +- redatamx-1.0.1/redatamx/R/redatam-query.R | 205 +++++++++--------- redatamx-1.0.1/redatamx/R/redatam-run.R | 1 redatamx-1.0.1/redatamx/README.md | 52 ++++ redatamx-1.0.1/redatamx/man/outputs.Rd | 6 redatamx-1.0.1/redatamx/man/redatam_close.Rd | 5 redatamx-1.0.1/redatamx/man/redatam_destroy_.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_entities.Rd | 2 redatamx-1.0.1/redatamx/man/redatam_init_.Rd | 3 redatamx-1.0.1/redatamx/man/redatam_internal_query.Rd | 3 redatamx-1.0.1/redatamx/man/redatam_internal_run.Rd | 7 redatamx-1.0.1/redatamx/man/redatam_open.Rd | 2 redatamx-1.0.1/redatamx/man/redatam_query.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_run.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_save.Rd | 4 redatamx-1.0.1/redatamx/man/redatam_variables.Rd | 2 redatamx-1.0.1/redatamx/man/redatamx-package.Rd | 9 23 files changed, 237 insertions(+), 179 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.7-3 dated 2024-01-08 and 1.7-4 dated 2024-11-21
DESCRIPTION | 17 MD5 | 125 - NAMESPACE | 1 NEWS.md | 23 R/RBesT-package.R | 1 R/dlink.R | 1 R/integrate_logit_log.R | 32 R/mix.R | 40 R/mixcombine.R | 10 R/mixess.R | 62 R/mixplot.R | 4 R/mixstanvar.R | 35 R/plot_gMAP.R | 2 R/predict_gMAP.R | 36 R/sysdata.rda |binary R/zzz.R | 1 build/vignette.rds |binary configure | 1 data/AS.rda |binary data/colitis.rda |binary data/crohn.rda |binary data/transplant.rda |binary demo/robustMAP.R | 24 inst/doc/RBesT.pdf |binary inst/doc/introduction.R | 20 inst/doc/introduction.Rmd | 16 inst/doc/introduction.html | 394 ++--- inst/examples |only inst/sbc/calibration.md5 | 6 inst/sbc/make_reference_rankhist.R | 17 inst/sbc/sbc_report.html | 976 ++++++------- inst/sbc/sbc_tools.R | 75 - inst/stan/gMAP.stan | 32 man/RBesT-package.Rd | 1 man/ess.Rd | 8 man/integrate_density_log.Rd | 2 man/mixbeta.Rd | 4 man/mixcombine.Rd | 5 man/mixgamma.Rd | 4 man/mixmvnorm.Rd | 4 man/mixnorm.Rd | 4 man/mixplot.Rd | 6 man/oc1S.Rd | 2 man/oc2S.Rd | 2 man/plot.gMAP.Rd | 2 man/pos1S.Rd | 2 man/pos2S.Rd | 2 man/predict.gMAP.Rd | 1 src/stanExports_gMAP.h | 2770 ++++++++++++++++++------------------- tests/testthat/helper-utils.R |only tests/testthat/test-EM.R | 36 tests/testthat/test-gMAP.R | 47 tests/testthat/test-mixdiff.R | 29 tests/testthat/test-mixdist.R | 65 tests/testthat/test-mixstanvar.R | 73 tests/testthat/test-oc1S.R | 39 tests/testthat/test-oc2S.R | 52 tests/testthat/test-pos1S.R | 11 tests/testthat/test-pos2S.R | 38 tests/testthat/test-postmix.R | 1 tests/testthat/test-preddist.R | 13 tests/testthat/test-utils.R | 74 vignettes/introduction.Rmd | 16 63 files changed, 2665 insertions(+), 2599 deletions(-)
Title: Grab Longitudinal Employer-Household Dynamics (LEHD) Flat Files
Description: Designed to query Longitudinal Employer-Household Dynamics (LEHD)
workplace/residential association and origin-destination flat files and
optionally aggregate Census block-level data to block group, tract, county,
or state. Data comes from the LODES FTP server <https://lehd.ces.census.gov/data/lodes/LODES8/>.
Author: Jamaal Green [cre, aut],
Liming Wang [aut],
Dillon Mahmoudi [aut],
Matthew Rogers [ctb],
Kyle Walker [ctb]
Maintainer: Jamaal Green <jamaal.green@gmail.com>
Diff between lehdr versions 1.1.3 dated 2023-11-27 and 1.1.4 dated 2024-11-21
DESCRIPTION | 8 LICENSE | 2 MD5 | 30 - NAMESPACE | 32 - R/grab_crosswalk.R | 212 ++++---- R/lehdr.R | 568 +++++++++++----------- README.md | 274 +++++----- build/vignette.rds |binary inst/doc/getting_started.R | 224 ++++---- inst/doc/getting_started.Rmd | 342 ++++++------- inst/doc/getting_started.html | 1066 +++++++++++++++++++++--------------------- man/grab_crosswalk.Rd | 66 +- man/grab_lodes.Rd | 196 +++---- tests/testthat.R | 10 tests/testthat/test-lehdr.R | 268 +++++----- vignettes/getting_started.Rmd | 342 ++++++------- 16 files changed, 1820 insertions(+), 1820 deletions(-)
Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.2.0 dated 2024-10-04 and 0.3.0 dated 2024-11-21
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 64 +- R/StratPal-package.R | 12 R/apply_niche.R | 174 ++++---- R/apply_taphonomy.R | 112 ++--- R/ornstein_uhlenbeck_sl.R | 2 R/plot.pre_paleoTS.R |only R/random_walk_sl.R | 104 ++-- README.md | 206 ++++----- inst/CITATION | 16 inst/WORDLIST | 5 inst/doc/event_data.Rmd | 672 +++++++++++++++---------------- inst/doc/paleoTS_functionality.R | 4 inst/doc/paleoTS_functionality.Rmd | 6 inst/doc/paleoTS_functionality.html | 16 inst/doc/phenotypic_evolution.html | 8 man/ornstein_uhlenbeck_sl.Rd | 2 man/plot.pre_paleoTS.Rd |only man/random_walk_sl.Rd | 2 tests/testthat/test_ornstein_uhlenbeck.R | 34 - tests/testthat/test_p3.R | 42 - tests/testthat/test_p3_var_rate.R | 42 - vignettes/event_data.Rmd | 672 +++++++++++++++---------------- vignettes/paleoTS_functionality.Rmd | 6 26 files changed, 1134 insertions(+), 1122 deletions(-)
Title: Ceteris Paribus Profiles
Description: Ceteris Paribus Profiles (What-If Plots) are designed to present model
responses around selected points in a feature space.
For example around a single prediction for an interesting observation.
Plots are designed to work in a model-agnostic fashion, they are working
for any predictive Machine Learning model and allow for model comparisons.
Ceteris Paribus Plots supplement the Break Down Plots from 'breakDown' package.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ceterisParibus versions 0.4.2 dated 2020-03-27 and 0.6 dated 2024-11-21
ceterisParibus-0.4.2/ceterisParibus/R/plot_interactive_what_if.R |only ceterisParibus-0.4.2/ceterisParibus/README.md |only ceterisParibus-0.4.2/ceterisParibus/man/plot_interactive.Rd |only ceterisParibus-0.4.2/ceterisParibus/tests/testthat/test_plot_interactive_what_if.R |only ceterisParibus-0.6/ceterisParibus/DESCRIPTION | 11 +-- ceterisParibus-0.6/ceterisParibus/MD5 | 36 ++++------ ceterisParibus-0.6/ceterisParibus/NAMESPACE | 4 - ceterisParibus-0.6/ceterisParibus/NEWS.md | 23 +++--- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles.R | 12 ++- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles_lce.R | 1 ceterisParibus-0.6/ceterisParibus/R/ceteris_paribus.R | 5 - ceterisParibus-0.6/ceterisParibus/R/coral_plots.R | 4 - ceterisParibus-0.6/ceterisParibus/R/plot_ceteris_paribus.R | 2 ceterisParibus-0.6/ceterisParibus/R/plot_coral_plots.R | 2 ceterisParibus-0.6/ceterisParibus/R/select_neighbours.R | 4 - ceterisParibus-0.6/ceterisParibus/R/select_samples.R | 2 ceterisParibus-0.6/ceterisParibus/man/calculate_variable_splits.Rd | 9 ++ ceterisParibus-0.6/ceterisParibus/man/ceteris_paribus.Rd | 3 ceterisParibus-0.6/ceterisParibus/man/local_fit.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_neighbours.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_sample.Rd | 2 21 files changed, 72 insertions(+), 56 deletions(-)
More information about ceterisParibus at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 0.2.0
2023-03-31 0.1.0
Title: Read and Write '.gltf' and '.glb' Files
Description: The 'glTF' file format is used to describe 3D models. This package
provides read and write functions to work with it.
Author: Duncan Murdoch [aut, cre],
Morten S. Mikkelsen [cph]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl2gltf versions 1.0.5 dated 2024-09-24 and 1.0.7 dated 2024-11-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/gltfWidget.R | 19 +++++++++---------- inst/doc/shininess.html | 12 ++++++------ 5 files changed, 26 insertions(+), 23 deletions(-)
Title: Power and Sample Size Tools
Description: Power and sample size calculations for a variety of study designs and
outcomes. Methods include t tests, ANOVA (including tests for interactions,
simple effects and contrasts), proportions, categorical data (chi-square tests
and proportional odds), linear, logistic and Poisson regression, alternative
and coprimary endpoints, power for confidence intervals, correlation
coefficient tests, cluster randomized trials, individually randomized group
treatment trials, multisite trials, treatment-by-covariate interaction effects
and nonparametric tests of location. Utilities are provided for
computing various effect sizes. Companion package to the book
"Power and Sample Size in R", Crespi (2025, ISBN:9781138591622).
Author: Catherine M. Crespi [aut, cre],
Zichen Liu [aut],
Kristen M. McGreevy [ctb]
Maintainer: Catherine M. Crespi <ccrespi@ucla.edu>
Diff between powertools versions 0.1.0 dated 2024-11-14 and 0.1.2 dated 2024-11-21
DESCRIPTION | 6 +- MD5 | 20 ++++---- R/check.param.R | 2 R/chisq.gof.R | 2 man/chisq.gof.Rd | 2 man/ttest.1samp.Rd | 88 ++++++++++++++++++------------------ man/ttest.2samp.Rd | 126 ++++++++++++++++++++++++++-------------------------- man/ttest.paired.Rd | 94 +++++++++++++++++++------------------- man/ztest.1samp.Rd | 90 ++++++++++++++++++------------------- man/ztest.2samp.Rd | 114 +++++++++++++++++++++++------------------------ man/ztest.paired.Rd | 98 ++++++++++++++++++++-------------------- 11 files changed, 321 insertions(+), 321 deletions(-)
Title: Circle Packing
Description: Algorithms to find arrangements of non-overlapping circles.
Author: Michael Bedward [aut, cre],
David Eppstein [aut] ,
Peter Menzel [aut]
Maintainer: Michael Bedward <michael.bedward@gmail.com>
Diff between packcircles versions 0.3.6 dated 2023-09-08 and 0.3.7 dated 2024-11-21
DESCRIPTION | 12 +- MD5 | 44 ++++----- NEWS.md | 7 + R/circleGraphLayout.R | 5 + R/circleRemoveOverlaps.R | 19 +++- R/circleRepelLayout.R | 56 ++++++++---- R/circleVertices.R | 112 ++++++++++++++++++------- README.md | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/graph_packing.R | 78 ++++++++--------- inst/doc/graph_packing.html | 10 +- inst/doc/intro.R | 6 - inst/doc/intro.html | 14 +-- inst/doc/progressive_packing.R | 2 inst/doc/progressive_packing.Rmd | 2 inst/doc/progressive_packing.html | 53 ++++++++--- man/circleLayoutVertices.Rd | 170 +++++++++++++++++++------------------- man/circlePlotData.Rd | 64 +++++++------- man/circleRemoveOverlaps.Rd | 156 +++++++++++++++++----------------- man/circleRepelLayout.Rd | 161 +++++++++++++++++------------------ man/circleVertices.Rd | 58 ++++++------ vignettes/progressive_packing.Rmd | 2 23 files changed, 582 insertions(+), 458 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:
FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Sturges (1926) <doi:10.1080/01621459.1926.10502161> formula.
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 [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.6 dated 2024-11-13 and 0.1.7 dated 2024-11-21
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 7 - R/FishPar.R | 204 +++++++++++++++++++++++++++++---------------- R/FrequencyTable.R | 73 +++++++++------- inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 14 +-- inst/doc/Introduction.html | 132 +++++++++++++++-------------- man/FrequencyTable.Rd | 26 ++--- vignettes/Introduction.Rmd | 14 +-- 10 files changed, 287 insertions(+), 209 deletions(-)
More information about OutcomeWeights at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-16 1.0.0
2019-02-04 0.1.1
Title: Synthetic Microdata Generator
Description: This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
Author: Hang J. Kim [aut, cre],
Juhee Lee [aut],
Young-Min Kim [aut],
Jared Murray [aut]
Maintainer: Hang J. Kim <hangkim0@gmail.com>
Diff between synMicrodata versions 2.0.0 dated 2024-04-07 and 2.1.0 dated 2024-11-21
DESCRIPTION | 8 +- MD5 | 13 +-- NAMESPACE | 2 R/R_functions.R | 163 ++++++++++++++++++++++++++++++++--------- man/Rcpp_modelobject-class.Rd | 6 + man/plot.synMicro_object.Rd | 9 ++ man/readData.Rd | 9 ++ man/summary.synMicro_object.Rd |only 8 files changed, 165 insertions(+), 45 deletions(-)
Title: Analysis of Korean National Forest Inventory Database
Description: Understanding the current status of forest resources is essential for monitoring changes
in forest ecosystems and generating related statistics. In South Korea, the National Forest
Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items,
including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI
as the primary data for research, such as biomass estimation or analyzing the importance value of
each species over time and space, depending on the research purpose. However, the large volume
of accumulated forest survey data from across the country can make it challenging to manage and
utilize such a vast dataset. To address this issue, we developed an R package that efficiently
handles large-scale NFI data across time and space. The package offers a comprehensive
workflow for NFI data analysis. It starts with data processing, where read_nfi() function
reconstructs NFI data according to the researcher's needs while [...truncated...]
Author: Sinyoung Park [aut, cre] ,
Wonhee Cho [aut, ctb] ,
Inyoo Kim [aut, ctb] ,
Wontaek Lim [aut, ctb] ,
Dongwook W. Ko [aut, ths]
Maintainer: Sinyoung Park <youngsin0306@kookmin.ac.kr>
Diff between knfi versions 1.0.0 dated 2024-10-14 and 1.0.1 dated 2024-11-20
knfi-1.0.0/knfi/R/summary_NFI.R |only knfi-1.0.0/knfi/data/col_name.rda |only knfi-1.0.0/knfi/man/col_name.Rd |only knfi-1.0.1/knfi/DESCRIPTION | 8 knfi-1.0.1/knfi/MD5 | 60 +-- knfi-1.0.1/knfi/NAMESPACE | 6 knfi-1.0.1/knfi/NEWS.md | 15 knfi-1.0.1/knfi/R/biomass_nfi.R | 92 +++--- knfi-1.0.1/knfi/R/cwd_biomass_nfi.R | 35 +- knfi-1.0.1/knfi/R/diversity_nfi.R | 68 ++++ knfi-1.0.1/knfi/R/filter_nfi.R | 161 +++++----- knfi-1.0.1/knfi/R/globalvars.R | 6 knfi-1.0.1/knfi/R/info_nfi.R | 6 knfi-1.0.1/knfi/R/iv_nfi.R | 112 ++++--- knfi-1.0.1/knfi/R/read_nfi.R | 93 +++--- knfi-1.0.1/knfi/R/summary_nfi.R |only knfi-1.0.1/knfi/R/switchcol_nfi.R | 14 knfi-1.0.1/knfi/R/sysdata.rda |binary knfi-1.0.1/knfi/R/tsvis_nfi.R | 505 +++++++++++++++++++-------------- knfi-1.0.1/knfi/README.md | 1 knfi-1.0.1/knfi/data/nfi_col.rda |only knfi-1.0.1/knfi/inst/doc/knfi.R | 23 - knfi-1.0.1/knfi/inst/doc/knfi.Rmd | 23 - knfi-1.0.1/knfi/inst/doc/knfi.html | 61 ++- knfi-1.0.1/knfi/man/biomass_nfi.Rd | 7 knfi-1.0.1/knfi/man/cwd_biomass_nfi.Rd | 7 knfi-1.0.1/knfi/man/diversity_nfi.Rd | 13 knfi-1.0.1/knfi/man/iv_nfi.Rd | 11 knfi-1.0.1/knfi/man/nfi_col.Rd |only knfi-1.0.1/knfi/man/read_nfi.Rd | 17 - knfi-1.0.1/knfi/man/summary_nfi.Rd | 14 knfi-1.0.1/knfi/man/switchcol_nfi.Rd | 2 knfi-1.0.1/knfi/man/tsvis_nfi.Rd | 37 ++ knfi-1.0.1/knfi/vignettes/knfi.Rmd | 23 - 34 files changed, 875 insertions(+), 545 deletions(-)
Title: Play Minesweeper
Description: Play and record games of minesweeper using a graphics device that supports event handling.
Replay recorded games and save GIF animations of them. Based on classic minesweeper as detailed by
Crow P. (1997) <https://minesweepergame.com/math/a-mathematical-introduction-to-the-game-of-minesweeper-1997.pdf>.
Author: Harry Thompson [aut, cre, cph]
Maintainer: Harry Thompson <harry@mayesfield.uk>
Diff between minesweeper versions 1.0.0 dated 2024-08-30 and 1.0.1 dated 2024-11-20
DESCRIPTION | 8 MD5 | 93 +++++------ NEWS.md | 2 R/cell2grob.R | 24 +- R/chord.R | 22 +- R/count2str.R | 14 - R/create_viewports.R | 128 +++++++-------- R/draw_cell.R | 6 R/draw_count.R | 32 +-- R/draw_raster.R | 10 - R/flag_cell.R | 18 +- R/get_extdata.R | 6 R/hide_cells.R | 16 - R/in_smiley.R | 6 R/interpolate.R | 6 R/minesweeper-package.R | 12 - R/ndc2cell.R | 18 +- R/neighbors.R | 14 - R/new_board.R | 10 - R/new_mineplot.R | 20 +- R/new_mines.R | 12 - R/no_play.R | 6 R/on_board.R | 6 R/on_mouse_down.R | 26 +-- R/on_mouse_up.R | 32 +-- R/peek_cell.R | 8 R/peek_neighbors.R | 8 R/play_minesweeper.R | 362 +++++++++++++++++++++++--------------------- R/print.R | 10 - R/refresh_board.R | 8 R/replay.R | 98 +++++------ R/replay_minesweeper.R | 32 +-- R/reveal.R | 34 ++-- R/reveal_surrounding.R | 12 - R/save_minesweeper_gif.R | 88 +++++----- R/set_board.R | 24 +- R/update_cell.R | 12 - R/update_cells.R | 18 +- R/update_minecount.R | 10 - R/update_neighbors.R | 10 - R/update_smiley.R | 10 - R/update_timer.R | 10 - R/wind.R | 20 +- README.md | 72 ++++---- man/figures |only man/play_minesweeper.Rd | 20 ++ man/replay_minesweeper.Rd | 4 man/save_minesweeper_gif.Rd | 4 48 files changed, 730 insertions(+), 691 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen [aut, cre],
Caitlin K. Frankish [aut]
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.3 dated 2024-06-28 and 1.2.4 dated 2024-11-20
DESCRIPTION | 20 +++++-- MD5 | 19 +++--- NAMESPACE | 2 R/a-misc.R | 2 R/dyn-methods.R | 89 +++++++++++++++++++++++++++++++- R/track-methods.R | 25 ++++++++ build/partial.rdb |binary man/DEPONS2R.Rd | 2 man/as.data.frame-DeponsDyn-method.Rd |only man/as.data.frame-DeponsTrack-method.Rd |only man/make.DeponsDyn.Rd |only man/read.DeponsDyn.Rd | 3 - 12 files changed, 144 insertions(+), 18 deletions(-)
Title: Gaussian Location-Scale Regression
Description: The Gaussian location-scale regression model is a multi-predictor
model with explanatory variables for the mean (= location) and the standard
deviation (= scale) of a response variable. This package implements maximum
likelihood and Markov chain Monte Carlo (MCMC) inference (using algorithms
from Girolami and Calderhead (2011) <doi:10.1111/j.1467-9868.2010.00765.x>
and Nesterov (2009) <doi:10.1007/s10107-007-0149-x>), a parametric
bootstrap algorithm, and diagnostic plots for the model class.
Author: Hannes Riebl [aut, cre]
Maintainer: Hannes Riebl <hriebl@posteo.de>
Diff between lmls versions 0.1.0 dated 2022-01-18 and 0.1.1 dated 2024-11-20
DESCRIPTION | 15 ++++++++------- LICENSE | 2 +- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/testthat-helpers.R | 2 +- README.md | 36 ++++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lmls.R | 34 +++++++++++++++++----------------- inst/doc/lmls.Rmd | 18 +++++++----------- inst/doc/lmls.pdf |binary man/figures/README-abdom-plot-1.png |binary vignettes/lmls.Rmd | 18 +++++++----------- 13 files changed, 79 insertions(+), 76 deletions(-)
Title: Latent Class Capture-Recapture Models
Description: Estimation of latent class models with individual covariates for capture-recapture data. See Bartolucci, F. and Forcina, A. (2022), Estimating the size of a closed population by modeling latent and observed heterogeneity, Biometrics, 80(2), ujae017.
Author: Francesco Bartolucci [aut, cre],
Antonio Forcina [aut]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LCCR versions 1.3 dated 2021-12-04 and 2.0 dated 2024-11-20
DESCRIPTION | 12 +- MD5 | 63 ++++++------ NAMESPACE | 4 R/aggr_data.R | 11 +- R/confint.estLCCR.R | 119 ++++++++++++++++------- R/confint.estLCCRcon.R |only R/design_matrix_logit.R | 49 +++++---- R/design_matrix_loglin.R | 30 +++-- R/estLCCR.R | 162 ++++++++++++++++++------------- R/estLCCRcon.R | 234 +++++++++++++++++++++++++++++----------------- R/freq_data.R | 10 + R/lkLCCR.R | 40 +++---- R/lkLCCRcon.R | 29 ++--- R/matrix_logit.R | 11 +- R/plot.confLCCR.R | 4 R/plot.confLCCRcon.R |only R/print.confLCCR.R | 4 R/print.confLCCRcon.R |only R/print.estLCCR.R | 6 - R/print.estLCCRcon.R | 8 - R/simLCCR.R | 35 +++--- R/sq.R | 7 - R/summary.confLCCR.R | 4 R/summary.confLCCRcon.R |only R/summary.estLCCR.R | 18 +-- R/summary.estLCCRcon.R | 20 +-- build/partial.rdb |binary man/confint.estLCCR.Rd | 17 ++- man/confint.estLCCRcon.Rd |only man/estLCCR.Rd | 18 +-- man/estLCCRcon.Rd | 20 ++- man/freq_data.Rd | 5 man/plot.Rd | 1 man/print.Rd | 1 man/simLCCR.Rd | 17 +-- 35 files changed, 582 insertions(+), 377 deletions(-)
Title: 'shiny' Application for Adverse Event Analysis of 'OnCore' Data
Description: An application for analysis of Adverse Events, as described in Chen, et al., (2023) <doi:10.3390/cancers15092521>.
The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data.
The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results
for the association of adverse event biomarkers and overall survival and progression free survival.
The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events.
Plots and tables of results are downloadable.
Author: Z Thompson [aut, cre],
A Obermayer [aut],
DT Chen [aut]
Maintainer: Z Thompson <zachary.thompson@moffitt.org>
Diff between AdverseEvents versions 0.0.3 dated 2024-11-04 and 0.0.4 dated 2024-11-20
DESCRIPTION | 7 +- MD5 | 11 ++-- README.md |only inst/app/server.R | 111 ++++++++++++++++++++++++++++++++++++++------ inst/doc/AdverseEvents.html | 4 - vignettes/correlations.PNG |binary vignettes/responsetests.PNG |binary 7 files changed, 110 insertions(+), 23 deletions(-)
Title: Calculate Sun Position, Sunrise, Sunset, Solar Noon and Twilight
Description: Provides a set of convenient functions for calculating sun-related information, including the sun's position (elevation and azimuth), and the times of sunrise, sunset, solar noon, and twilight for any given geographical location on Earth. These calculations are based on equations provided by the National Oceanic & Atmospheric Administration (NOAA) <https://gml.noaa.gov/grad/solcalc/calcdetails.html> as described in "Astronomical Algorithms" by Jean Meeus (1991, ISBN: 978-0-943396-35-4).
Author: Roger Bivand [aut] ,
Adriaan M. Dokter [ctb, cre] ,
Pieter Huybrechts [ctb] ,
Sebastian Luque [aut],
Greg Pelletier [ctb],
Alexander Tedeschi [ctb]
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Diff between suntools versions 1.0.0 dated 2023-07-06 and 1.0.1 dated 2024-11-20
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/crepuscule.R | 2 +- R/solarnoon.R | 2 +- R/sunriset.R | 2 +- man/crepuscule.Rd | 2 +- man/solarnoon.Rd | 2 +- man/sunriset.Rd | 2 +- man/suntools-package.Rd | 2 +- tests/testthat/test-sun-methods.R | 12 ++++++------ 11 files changed, 36 insertions(+), 30 deletions(-)
Title: Interface for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 0.1.0 dated 2024-11-10 and 0.2.0 dated 2024-11-20
DESCRIPTION | 21 MD5 | 58 NAMESPACE | 6 R/Artifact.R | 18 R/Instance.R | 125 + R/InstanceAPI.R | 43 R/Record.R | 116 + R/Registry.R | 204 + R/connect.R | 26 R/core_loaders.R |only R/laminr-package.R | 6 R/settings_load.R | 11 R/utils.R | 39 README.md | 20 build/vignette.rds |binary inst/doc/architecture.R | 103 inst/doc/architecture.html | 2490 ++++++++++++++++++++++- inst/doc/architecture.qmd | 105 inst/doc/development.html | 288 ++ inst/doc/development.qmd | 38 man/Instance.Rd | 74 man/Record.Rd | 21 man/Registry.Rd | 118 + man/laminr-package.Rd | 8 tests/testthat/helper-setup_lamindata_instance.R | 2 tests/testthat/test-Artifact.R |only tests/testthat/test-core_loaders.R |only vignettes/architecture.qmd | 105 vignettes/cellxgene_basic.html |only vignettes/development.qmd | 38 vignettes/example_workflow.Rmd |only vignettes/example_workflow.html |only vignettes/laminr.Rmd | 10 33 files changed, 3673 insertions(+), 420 deletions(-)
More information about cellularautomata at CRAN
Permanent link
More information about sampledatasets at CRAN
Permanent link
Title: Growth Models
Description: A model for the growth of self-limiting populations using three, four, or five parameter
functions, which have wide applications in a variety of fields.
The dependent variable in a dynamical modeling could be the population size at time x,
where x is the independent variable. In the analysis of quantitative polymerase chain reaction
(qPCR), the dependent variable would be the fluorescence intensity and the independent variable
the cycle number. This package then would calculate the TWW cycle threshold.
Author: Mohammad Tabatabai [aut],
Derek Wilus [aut, cre]
Maintainer: Derek Wilus <dwilus@mmc.edu>
Diff between TWW versions 0.0.1 dated 2024-09-02 and 0.1.0 dated 2024-11-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/tww.R | 23 +++++++++++++++++------ man/tww.Rd | 15 +++++++++++---- 4 files changed, 34 insertions(+), 16 deletions(-)
Title: Exploration and Graphics for RivEr Trends
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut] ,
Laura DeCicco [aut, cre] ,
Tim Cohn [ctb],
David Watkins [ctb],
Lindsay Carr [ctb],
Jennifer Murphy [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 3.0.9 dated 2023-04-18 and 3.0.10 dated 2024-11-20
EGRET-3.0.10/EGRET/DESCRIPTION | 8 EGRET-3.0.10/EGRET/MD5 | 146 - EGRET-3.0.10/EGRET/NAMESPACE | 23 EGRET-3.0.10/EGRET/NEWS | 9 EGRET-3.0.10/EGRET/R/EGRET.R | 37 EGRET-3.0.10/EGRET/R/blankTime.R | 35 EGRET-3.0.10/EGRET/R/boxConcMonth.R | 4 EGRET-3.0.10/EGRET/R/boxConcThree.R | 4 EGRET-3.0.10/EGRET/R/boxQTwice.R | 4 EGRET-3.0.10/EGRET/R/boxResidMonth.R | 6 EGRET-3.0.10/EGRET/R/calculateMonthlyResults.R | 20 EGRET-3.0.10/EGRET/R/compressData.r | 29 EGRET-3.0.10/EGRET/R/cumQdate.R | 4 EGRET-3.0.10/EGRET/R/errorStats.R | 2 EGRET-3.0.10/EGRET/R/estSurfaces.R | 2 EGRET-3.0.10/EGRET/R/genericEGRETplot.R | 6 EGRET-3.0.10/EGRET/R/kalman_functions.R | 4 EGRET-3.0.10/EGRET/R/makeAnnualSeries.R | 8 EGRET-3.0.10/EGRET/R/plot1of15.R | 2 EGRET-3.0.10/EGRET/R/plotConcQSmooth.R | 6 EGRET-3.0.10/EGRET/R/plotConcTimeSmooth.R | 6 EGRET-3.0.10/EGRET/R/plotContours.R | 24 EGRET-3.0.10/EGRET/R/plotDiffContours.R | 22 EGRET-3.0.10/EGRET/R/plotMonthTrend.R | 4 EGRET-3.0.10/EGRET/R/plotSDLogQ.R | 2 EGRET-3.0.10/EGRET/R/populateDaily.r | 2 EGRET-3.0.10/EGRET/R/populateSampleColumns.r | 7 EGRET-3.0.10/EGRET/R/printSeries.R | 2 EGRET-3.0.10/EGRET/R/processQWData.r | 9 EGRET-3.0.10/EGRET/R/readDataFromFile.r | 2 EGRET-3.0.10/EGRET/R/readMetaData.r | 4 EGRET-3.0.10/EGRET/R/readNWISSample.R |only EGRET-3.0.10/EGRET/R/readUserSample.r | 6 EGRET-3.0.10/EGRET/R/readWQPSample.R | 83 - EGRET-3.0.10/EGRET/R/runGroups.R | 2 EGRET-3.0.10/EGRET/R/runPairs.R | 4 EGRET-3.0.10/EGRET/R/runSurvReg.R | 10 EGRET-3.0.10/EGRET/R/setupYears.R | 4 EGRET-3.0.10/EGRET/R/stitch.R | 4 EGRET-3.0.10/EGRET/R/tableResults.R | 2 EGRET-3.0.10/EGRET/README.md | 143 - EGRET-3.0.10/EGRET/build/partial.rdb |binary EGRET-3.0.10/EGRET/build/vignette.rds |binary EGRET-3.0.10/EGRET/inst/CITATION | 4 EGRET-3.0.10/EGRET/inst/doc/EGRET.R | 540 +++---- EGRET-3.0.10/EGRET/inst/doc/EGRET.Rmd | 7 EGRET-3.0.10/EGRET/inst/doc/EGRET.html | 896 ++++++------ EGRET-3.0.10/EGRET/inst/doc/Overview.Rmd | 62 EGRET-3.0.10/EGRET/inst/doc/Overview.html | 247 +-- EGRET-3.0.10/EGRET/inst/doc/parallel.R | 78 - EGRET-3.0.10/EGRET/inst/doc/parallel.html | 80 - EGRET-3.0.10/EGRET/inst/doc/units.html | 130 - EGRET-3.0.10/EGRET/man/Constants.Rd | 8 EGRET-3.0.10/EGRET/man/EGRET-package.Rd | 14 EGRET-3.0.10/EGRET/man/blankTime.Rd | 10 EGRET-3.0.10/EGRET/man/boxConcMonth.Rd | 2 EGRET-3.0.10/EGRET/man/boxQTwice.Rd | 2 EGRET-3.0.10/EGRET/man/boxResidMonth.Rd | 2 EGRET-3.0.10/EGRET/man/cumQdate.Rd | 2 EGRET-3.0.10/EGRET/man/figures/README-plotFours-1.png |binary EGRET-3.0.10/EGRET/man/figures/README-plotFours-2.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-1.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-2.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-3.png |binary EGRET-3.0.10/EGRET/man/plotContours.Rd | 7 EGRET-3.0.10/EGRET/man/plotDiffContours.Rd | 6 EGRET-3.0.10/EGRET/man/processQWData.Rd | 4 EGRET-3.0.10/EGRET/man/readNWISSample.Rd | 7 EGRET-3.0.10/EGRET/man/readUserSample.Rd | 128 - EGRET-3.0.10/EGRET/tests/testthat/Rplots.pdf |binary EGRET-3.0.10/EGRET/tests/testthat/tests_imports.R | 35 EGRET-3.0.10/EGRET/tests/testthat/tests_utils.R | 6 EGRET-3.0.10/EGRET/vignettes/EGRET.Rmd | 7 EGRET-3.0.10/EGRET/vignettes/Overview.Rmd | 62 EGRET-3.0.9/EGRET/R/readNWISSample.r |only 75 files changed, 1510 insertions(+), 1537 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.11.0 dated 2023-10-07 and 0.12.0 dated 2024-11-20
DESCRIPTION | 12 MD5 | 97 ++-- NAMESPACE | 6 NEWS | 10 R/cfda-package.R | 11 R/check.R | 64 ++- R/dataPlot.R | 27 - R/datasets.R | 6 R/encoding.R | 52 +- R/estimation.R | 10 R/fmca.print.R | 8 R/generateData.R | 18 R/plotEncoding.R | 44 -- R/predict.R | 11 R/pretreatment.R | 62 +- R/reconstructData.R |only R/stat.R | 66 +-- R/zzz.R | 5 build/vignette.rds |binary inst/doc/cfda.R | 20 inst/doc/cfda.Rmd | 45 +- inst/doc/cfda.html | 506 ++++++++++++++---------- man/boxplot.timeSpent.Rd | 2 man/cfda-package.Rd | 21 man/compute_duration.Rd | 2 man/compute_number_jumps.Rd | 2 man/compute_optimal_encoding.Rd | 6 man/compute_time_spent.Rd | 2 man/convertToCfd.Rd | 20 man/estimate_Markov.Rd | 2 man/estimate_pt.Rd | 6 man/flours.Rd | 6 man/hist.duration.Rd | 2 man/hist.njump.Rd | 2 man/matrixToCfd.Rd | 13 man/plot.fmca.Rd | 2 man/plot.pt.Rd | 2 man/plotComponent.Rd | 1 man/plotEigenvalues.Rd | 1 man/plotIndicatorsReconstruction.Rd |only man/predict.fmca.Rd | 2 man/print.fmca.Rd | 2 man/reconstructIndicators.Rd |only man/summary.fmca.Rd | 2 tests/testthat/test.bootstrap.R | 3 tests/testthat/test.check.R | 74 +++ tests/testthat/test.encoding.R | 66 +-- tests/testthat/test.encoding0columnManagement.R | 2 tests/testthat/test.generate.R | 16 tests/testthat/test.stat.R | 56 +- vignettes/cfda.Rmd | 45 +- 51 files changed, 937 insertions(+), 503 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.2.5 dated 2024-09-29 and 4.2.6 dated 2024-11-20
ChangeLog | 4 DESCRIPTION | 6 MD5 | 10 inst/doc/browseMovebank.html | 753 ++++++++----- inst/doc/move.html | 1418 ++++++++++++++++---------- tests/testthat/test.getDuplicatedTimestamps.R | 2 6 files changed, 1361 insertions(+), 832 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.1.3 dated 2024-11-05 and 0.1.4 dated 2024-11-20
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/diceplot.R | 63 ++++++++++++++++++++++++++------------- man/dice_plot.Rd | 11 ++++++ tests/factor_df_test.R |only tests/test_diceplots.R | 3 + tests/test_reordering_diceplot.R |only 7 files changed, 63 insertions(+), 30 deletions(-)
Title: A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Description: S3 classes and methods to create and work
with year-quarter, year-month and year-isoweek vectors. Basic
arithmetic operations (such as adding and subtracting) are supported,
as well as formatting and converting to and from standard R date
types.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between dint versions 2.1.4 dated 2022-10-17 and 2.1.5 dated 2024-11-20
DESCRIPTION | 8 MD5 | 102 ++-- NAMESPACE | 13 NEWS.md | 8 R/arithmetic.R | 5 R/format.R | 1 R/increment.R | 11 R/scale_date_xx.R | 132 ++++-- R/zoo-compat.R | 6 README.md | 6 build/vignette.rds |binary inst/doc/dint.R | 4 inst/doc/dint.html | 529 ++++++++++++------------- man/Ops.date_xx.Rd | 54 +- man/Summary.date_xx.Rd | 50 +- man/as.Date.date_xx.Rd | 130 +++--- man/as_yearqtr.Rd | 126 ++--- man/c.date_xx.Rd | 52 +- man/date_xx.Rd | 98 ++-- man/date_xx_arithmetic.Rd | 76 +-- man/date_xx_arithmetic_disabled.Rd | 76 +-- man/date_xx_breaks.Rd | 64 +-- man/date_xx_sequences.Rd | 60 +- man/date_y.Rd | 86 ++-- man/date_ym.Rd | 96 ++-- man/date_yq.Rd | 96 ++-- man/date_yw.Rd | 96 ++-- man/day_of_isoweek.Rd | 102 ++-- man/day_of_isoyear.Rd | 80 +-- man/day_of_month.Rd | 110 ++--- man/day_of_quarter.Rd | 62 +- man/day_of_year.Rd | 94 ++-- man/dint-package.Rd | 49 +- man/extract_date_xx.Rd | 183 ++++---- man/first_of_yq.Rd | 88 ++-- man/format_date_xx.Rd | 212 +++++----- man/format_ym.Rd | 122 ++--- man/format_yq.Rd | 122 ++--- man/format_yw.Rd | 119 ++--- man/getters.Rd | 130 +++--- man/increment.Rd |only man/period_bounds.Rd | 98 ++-- man/print.date_xx.Rd | 36 - man/rep.date_xx.Rd | 36 - man/round_date_xx.Rd | 80 +-- man/scale_date_xx.Rd | 269 ++++++------ man/y-plus.Rd | 98 ++-- man/year.Rd | 92 ++-- man/yq.Rd | 78 +-- tests/testthat/manual_tests/ggplot_scales.html |only tests/testthat/test_date_xx.R | 6 tests/testthat/test_first_of.R | 12 tests/testthat/test_scale_date_xx.R | 5 53 files changed, 2170 insertions(+), 2098 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.4 dated 2024-09-04 and 0.15.5 dated 2024-11-20
DESCRIPTION | 12 +- MD5 | 34 +++---- NEWS.md | 6 + R/data.R | 194 +++++++++++++++++++++---------------------- R/sysdata.rda |binary inst/doc/eq5d.R | 2 inst/doc/eq5d.html | 59 +++++-------- man/CW.Rd | 16 +-- man/DSU3L.Rd | 4 man/DSU5L.Rd | 4 man/TTO.Rd | 63 +++++++------ man/VAS.Rd | 8 - man/VT.Rd | 85 +++++++++--------- man/Y3L.Rd | 20 ++-- man/eq5d-package.Rd | 2 tests/testthat/test-eq5d3l.R | 8 + tests/testthat/test-eq5d5l.R | 10 ++ tests/testthat/test-eq5dcw.R | 11 ++ 18 files changed, 287 insertions(+), 251 deletions(-)
Title: Comparing Two Diagnostic Tests with Dichotomous Results using
Paired Data
Description: Provides a method for comparing the results of two binary diagnostic tests using paired data.
Users can rapidly perform descriptive and inferential statistics in a single function call. Options permit users to select which parameters they are interested in comparing and methods for correction for multiple comparisons.
Confidence intervals are calculated using the methods with the best coverage. Hypothesis tests use the methods with the best asymptotic performance. A summary of the methods is available in Roldán-Nofuentes (2020) <doi:10.1186/s12874-020-00988-y>.
This package is targeted at clinical researchers who want to rapidly and effectively compare results from binary diagnostic tests.
Author: Kyle J. Wilson [cre, aut] ,
Marc Henrion [aut] ,
Jose Antonio Roldan Nofuentes [aut]
Maintainer: Kyle J. Wilson <kyle.jordan.wilson@googlemail.com>
Diff between testCompareR versions 1.1.0 dated 2024-10-02 and 1.1.1 dated 2024-11-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 8 ++++++++ R/compareR.R | 7 +++++++ README.md | 4 +++- inst/CITATION |only man/compareR.Rd | 4 ++++ 7 files changed, 31 insertions(+), 9 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Koslik [aut, cre]
Maintainer: Jan-Ole Koslik <jan-ole.koslik@uni-bielefeld.de>
Diff between LaMa versions 2.0.1 dated 2024-11-13 and 2.0.2 dated 2024-11-20
LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.RData |only LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.rdb |only LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.rdx |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.RData |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.rdb |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.rdx |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.RData |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.rdb |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.rdx |only LaMa-2.0.2/LaMa/DESCRIPTION | 6 - LaMa-2.0.2/LaMa/MD5 | 46 +++++----- LaMa-2.0.2/LaMa/R/decoding_functions.R | 32 ++++-- LaMa-2.0.2/LaMa/README.md | 6 - LaMa-2.0.2/LaMa/inst/doc/Continuous_time_HMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/HSMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Inhomogeneous_HMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Intro_to_LaMa.html | 2 LaMa-2.0.2/LaMa/inst/doc/Longitudinal_data.html | 6 - LaMa-2.0.2/LaMa/inst/doc/MMMPPs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Penalised_splines.html | 6 - LaMa-2.0.2/LaMa/inst/doc/Periodic_HMMs.html | 2 LaMa-2.0.2/LaMa/inst/doc/State_space_models.Rmd | 2 LaMa-2.0.2/LaMa/inst/doc/State_space_models.html | 12 +- LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.RData |only LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.rdb |only LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.rdx |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.RData |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.rdb |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.rdx |only LaMa-2.0.2/LaMa/vignettes/State_space_models.Rmd | 2 LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.RData |only LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.rdb |only LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.rdx |only 33 files changed, 75 insertions(+), 63 deletions(-)
Title: Geographical Detectors for Assessing Spatial Factors
Description: Geographical detectors for measuring spatial stratified heterogeneity,
as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and
Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the
optimal discretization of continuous data, four primary functions of
geographical detectors, comparison of size effects of spatial unit and
the visualizations of results. To use the package and to refer the
descriptions of the package, methods and case datasets, please cite
Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>. The model has
been applied in factor exploration of road performance and multi-scale
spatial segmentation for network data, as described in
Yongze Song (2018) <doi:10.3390/rs10111696> and
Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.
Author: Yongze Song [aut, cph] ,
Wenbo Lv [aut, cre]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between GD versions 10.6 dated 2024-10-30 and 10.8 dated 2024-11-20
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 18 ++- R/zzz.R | 2 README.md | 6 - build/vignette.rds |binary inst/doc/GD.R | 244 ++++++++++++++++++++++++++--------------------------- inst/doc/GD.html | 6 - 8 files changed, 151 insertions(+), 147 deletions(-)
Title: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Description: Programmatic interface to the 'SNOTEL' snow data
(<https://www.nrcs.usda.gov/programs-initiatives/sswsf-snow-survey-and-water-supply-forecasting-program>). Provides easy downloads of snow
data into your R work space or a local directory. Additional post-processing
routines to extract snow season indexes are provided.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between snotelr versions 1.5.1 dated 2024-10-02 and 1.5.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/snotel_download.r | 9 +++++++-- R/snotel_metric.r | 3 +++ build/vignette.rds |binary inst/doc/snotelr-vignette.html | 4 ++-- man/snotel_download.Rd | 11 ++++++++++- 7 files changed, 32 insertions(+), 15 deletions(-)
Title: Permanent Random Number Sampling
Description: Survey sampling using permanent random numbers (PRN's). A solution
to the problem of unknown overlap between survey samples, which leads to a
low precision in estimates when the survey is repeated or combined with
other surveys. The PRN solution is to supply the U(0, 1) random numbers to
the sampling procedure, instead of having the sampling procedure generate
them. In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited
papers, it is shown how this is carried out and how it improves the
estimates. This package supports two common fixed-size sampling procedures
(simple random sampling and probability-proportional-to-size sampling) and
includes a function for transforming the PRN's in order to control the
sample overlap.
Author: Kira Coder Gylling [aut, cre]
Maintainer: Kira Coder Gylling <kira.gylling@gmail.com>
Diff between prnsamplr versions 0.3.0 dated 2023-03-08 and 1.0.0 dated 2024-11-20
prnsamplr-0.3.0/prnsamplr/NEWS.md |only prnsamplr-0.3.0/prnsamplr/R/transf.R |only prnsamplr-0.3.0/prnsamplr/README.md |only prnsamplr-0.3.0/prnsamplr/build |only prnsamplr-0.3.0/prnsamplr/data/ExampleData.RData |only prnsamplr-1.0.0/prnsamplr/DESCRIPTION | 42 ++-- prnsamplr-1.0.0/prnsamplr/LICENSE | 2 prnsamplr-1.0.0/prnsamplr/MD5 | 38 ++-- prnsamplr-1.0.0/prnsamplr/NAMESPACE | 25 +- prnsamplr-1.0.0/prnsamplr/R/data.R |only prnsamplr-1.0.0/prnsamplr/R/pps.R | 198 +++++++++++++-------- prnsamplr-1.0.0/prnsamplr/R/prnsamplr-package.R |only prnsamplr-1.0.0/prnsamplr/R/samp.R | 58 ++++-- prnsamplr-1.0.0/prnsamplr/R/srs.R | 131 +++++++++---- prnsamplr-1.0.0/prnsamplr/R/transformprn.R |only prnsamplr-1.0.0/prnsamplr/data/ExampleData.rda |only prnsamplr-1.0.0/prnsamplr/man/ExampleData.Rd | 40 ++-- prnsamplr-1.0.0/prnsamplr/man/pps.Rd | 60 +++--- prnsamplr-1.0.0/prnsamplr/man/prnsamplr-package.Rd | 110 +++++++---- prnsamplr-1.0.0/prnsamplr/man/samp.Rd | 91 +++++---- prnsamplr-1.0.0/prnsamplr/man/srs.Rd | 52 ++--- prnsamplr-1.0.0/prnsamplr/man/transformprn.Rd | 60 +++--- prnsamplr-1.0.0/prnsamplr/tests |only 23 files changed, 563 insertions(+), 344 deletions(-)
Title: Year-Based Time Scales
Description: Provides a consistent representation of year-based time scales as a
numeric vector with an associated 'era'. There are built-in era definitions
for many year numbering systems used in contemporary and historic calendars
(e.g. Common Era, Islamic 'Hijri' years); year-based time scales used in
archaeology, astronomy, geology, and other palaeosciences (e.g.
Before Present, SI-prefixed 'annus'); and support for arbitrary user-defined
eras. Years can converted from any one era to another using a generalised
transformation function. Methods are also provided for robust casting and
coercion between years and other numeric types, type-stable arithmetic with
years, and pretty-printing in tables.
Author: Joe Roe [aut, cre]
Maintainer: Joe Roe <joe@joeroe.io>
Diff between era versions 0.4.1 dated 2022-11-17 and 0.5.0 dated 2024-11-20
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 4 NEWS.md | 5 R/yr_sort_range.R |only README.md | 20 +- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/era.R | 2 inst/doc/era.html | 294 ++++++++++++++++++------------------ man/era.Rd | 4 man/era_parameters.Rd | 6 man/era_year.Rd | 4 man/era_year_parameters.Rd | 4 man/is_era.Rd | 4 man/is_era_year.Rd | 4 man/is_yr.Rd | 6 man/this_year.Rd | 6 man/yr_era.Rd | 4 man/yr_extremes.Rd |only man/yr_sort.Rd |only man/yr_transform.Rd | 4 tests/testthat/test-yr_sort_range.R |only 23 files changed, 218 insertions(+), 205 deletions(-)
Title: Vaccines Pharmacometrics
Description: Estimate vaccine efficacy (VE) using immunogenicity data.
The inclusion of immunogenicity data in regression models can increase precision in VE.
The methods are described in the publications "Elucidating vaccine efficacy using a correlate of protection, demographics, and logistic regression" and "Improving precision of vaccine efficacy evaluation using immune correlate data in time-to-event models" by Julie Dudasova, Zdenek Valenta, and Jeffrey R. Sachs (2024).
Author: Julie Dudasova [aut, cre]
Maintainer: Julie Dudasova (MSD) <julie.dudasova@merck.com>
Diff between vaxpmx versions 0.0.3 dated 2024-02-28 and 0.0.6 dated 2024-11-20
DESCRIPTION | 14 +++--- LICENSE.note | 3 - MD5 | 31 +++++++------- NAMESPACE | 1 NEWS.md | 11 +++-- R/data.R | 1 R/ve.R | 85 +++++++++++++++++++++++++++++++++++---- README.md | 17 ++++++- data/data_temp.rda |binary inst/extdata/vaxpmx_mockupData.R | 5 +- man/EfficacyCI.Rd | 2 man/coxphParametricSampling.Rd |only man/data_temp.Rd | 1 man/glmParametricSampling.Rd | 2 man/ve.Rd | 14 +++++- tests/testthat.R | 1 tests/testthat/testve.R | 24 ++++++++++- 17 files changed, 169 insertions(+), 43 deletions(-)
More information about Certara.RsNLME at CRAN
Permanent link
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.2.2 dated 2024-08-29 and 1.3.0 dated 2024-11-20
grates-1.2.2/grates/R/defunct.R |only grates-1.2.2/grates/man/grates-defunct.Rd |only grates-1.3.0/grates/DESCRIPTION | 6 grates-1.3.0/grates/MD5 | 31 ++-- grates-1.3.0/grates/NAMESPACE | 33 ++++ grates-1.3.0/grates/NEWS.md | 6 grates-1.3.0/grates/R/accessors.R | 7 grates-1.3.0/grates/R/int_period.R |only grates-1.3.0/grates/R/month.R | 4 grates-1.3.0/grates/R/scale-int_period.R |only grates-1.3.0/grates/build/vignette.rds |binary grates-1.3.0/grates/inst/doc/grates.html | 74 +++------- grates-1.3.0/grates/man/as_int_period.Rd |only grates-1.3.0/grates/man/grouped_date_accessors.Rd | 3 grates-1.3.0/grates/man/new_int_period.Rd |only grates-1.3.0/grates/man/print.grates_int_period.Rd |only grates-1.3.0/grates/man/scale_x_grates_int_period.Rd |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_breaks.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_breaks_centred.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_one.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_two.png |only grates-1.3.0/grates/tests/testthat/test-int_period.R |only grates-1.3.0/grates/tests/testthat/test-plots.R | 60 +++++++- 23 files changed, 152 insertions(+), 72 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.3 dated 2024-04-09 and 2.2.4 dated 2024-11-20
DESCRIPTION | 17 +++++++++-------- MD5 | 15 ++++++++------- NEWS.md | 5 +++++ R/argparse.R | 23 ++++++++++++----------- R/utils.R |only build/vignette.rds |binary inst/doc/argparse.html | 38 +++++++++++++++++++------------------- man/ArgumentParser.Rd | 22 +++++++++++----------- tests/testthat/test-argparse.R | 11 +++++++++++ 9 files changed, 75 insertions(+), 56 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.8.0 dated 2024-10-02 and 1.9.0 dated 2024-11-20
targets-1.8.0/targets/R/class_memory.R |only targets-1.8.0/targets/R/class_pedigree.R |only targets-1.8.0/targets/tests/testthat/test-class_memory.R |only targets-1.8.0/targets/tests/testthat/test-class_pedigree.R |only targets-1.9.0/targets/DESCRIPTION | 34 targets-1.9.0/targets/LICENSE.note |only targets-1.9.0/targets/MD5 | 424 +++++----- targets-1.9.0/targets/NAMESPACE | 15 targets-1.9.0/targets/NEWS.md | 30 targets-1.9.0/targets/R/class_active.R | 19 targets-1.9.0/targets/R/class_auto.R | 4 targets-1.9.0/targets/R/class_aws.R | 46 - targets-1.9.0/targets/R/class_aws_file.R | 22 targets-1.9.0/targets/R/class_branch.R | 94 +- targets-1.9.0/targets/R/class_bud.R | 59 - targets-1.9.0/targets/R/class_build.R | 7 targets-1.9.0/targets/R/class_builder.R | 173 ++-- targets-1.9.0/targets/R/class_cloud.R | 23 targets-1.9.0/targets/R/class_clustermq.R | 14 targets-1.9.0/targets/R/class_command.R | 44 - targets-1.9.0/targets/R/class_counter.R | 15 targets-1.9.0/targets/R/class_crew.R | 14 targets-1.9.0/targets/R/class_cue.R | 31 targets-1.9.0/targets/R/class_database.R | 40 targets-1.9.0/targets/R/class_database_aws.R | 4 targets-1.9.0/targets/R/class_database_gcp.R | 4 targets-1.9.0/targets/R/class_database_local.R | 4 targets-1.9.0/targets/R/class_external.R | 4 targets-1.9.0/targets/R/class_feather.R | 4 targets-1.9.0/targets/R/class_file.R | 27 targets-1.9.0/targets/R/class_frames.R | 27 targets-1.9.0/targets/R/class_fst.R | 4 targets-1.9.0/targets/R/class_fst_dt.R | 4 targets-1.9.0/targets/R/class_fst_tbl.R | 4 targets-1.9.0/targets/R/class_future.R | 27 targets-1.9.0/targets/R/class_gcp.R | 46 - targets-1.9.0/targets/R/class_gcp_file.R | 22 targets-1.9.0/targets/R/class_group.R | 6 targets-1.9.0/targets/R/class_imports.R | 4 targets-1.9.0/targets/R/class_inspection.R | 12 targets-1.9.0/targets/R/class_inventory.R | 18 targets-1.9.0/targets/R/class_inventory_aws.R | 16 targets-1.9.0/targets/R/class_inventory_gcp.R | 16 targets-1.9.0/targets/R/class_junction.R | 60 - targets-1.9.0/targets/R/class_keras.R | 4 targets-1.9.0/targets/R/class_list.R | 6 targets-1.9.0/targets/R/class_local.R | 6 targets-1.9.0/targets/R/class_lookup.R |only targets-1.9.0/targets/R/class_meta.R | 40 targets-1.9.0/targets/R/class_metrics.R | 27 targets-1.9.0/targets/R/class_null.R | 4 targets-1.9.0/targets/R/class_options.R | 13 targets-1.9.0/targets/R/class_outdated.R | 3 targets-1.9.0/targets/R/class_parquet.R | 4 targets-1.9.0/targets/R/class_passive.R | 2 targets-1.9.0/targets/R/class_pattern.R | 139 ++- targets-1.9.0/targets/R/class_patternview.R | 10 targets-1.9.0/targets/R/class_pipeline.R | 122 ++ targets-1.9.0/targets/R/class_prelocal.R | 4 targets-1.9.0/targets/R/class_process.R | 10 targets-1.9.0/targets/R/class_progress.R | 58 - 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targets-1.9.0/targets/tests/testthat/test-class_counter.R | 9 targets-1.9.0/targets/tests/testthat/test-class_crew.R | 63 - targets-1.9.0/targets/tests/testthat/test-class_cue.R | 10 targets-1.9.0/targets/tests/testthat/test-class_database.R | 22 targets-1.9.0/targets/tests/testthat/test-class_feather.R | 12 targets-1.9.0/targets/tests/testthat/test-class_frames.R | 56 - targets-1.9.0/targets/tests/testthat/test-class_fst.R | 12 targets-1.9.0/targets/tests/testthat/test-class_fst_dt.R | 12 targets-1.9.0/targets/tests/testthat/test-class_fst_tbl.R | 14 targets-1.9.0/targets/tests/testthat/test-class_future.R | 2 targets-1.9.0/targets/tests/testthat/test-class_gcp.R | 10 targets-1.9.0/targets/tests/testthat/test-class_gcp_file.R | 10 targets-1.9.0/targets/tests/testthat/test-class_imports.R | 6 targets-1.9.0/targets/tests/testthat/test-class_junction.R | 62 - targets-1.9.0/targets/tests/testthat/test-class_keras.R | 8 targets-1.9.0/targets/tests/testthat/test-class_lookup.R |only targets-1.9.0/targets/tests/testthat/test-class_meta.R | 6 targets-1.9.0/targets/tests/testthat/test-class_options.R | 29 targets-1.9.0/targets/tests/testthat/test-class_parquet.R | 12 targets-1.9.0/targets/tests/testthat/test-class_pattern.R | 2 targets-1.9.0/targets/tests/testthat/test-class_pipeline.R | 83 + targets-1.9.0/targets/tests/testthat/test-class_progress.R | 26 targets-1.9.0/targets/tests/testthat/test-class_qs.R | 46 - 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Title: Explore Your Data with Interactive Figures
Description: A framework for creating interactive figures for data exploration.
All plots are automatically linked and support several kinds of interactive features,
including selection, zooming, panning, and parameter manipulation. The figures
can be interacted with either manually, using a mouse and a keyboard,
or by running code from inside an active R session.
Author: Adam Bartonicek [aut, cre, cph]
Maintainer: Adam Bartonicek <bartonicek@gmail.com>
Diff between plotscaper versions 0.2.3 dated 2024-10-18 and 0.2.4 dated 2024-11-20
DESCRIPTION | 10 +- MD5 | 34 +++---- NEWS.md | 4 R/message_senders.R | 11 +- inst/doc/algebra.html | 12 +- inst/doc/available-interactions.R | 6 + inst/doc/available-interactions.Rmd | 9 + inst/doc/available-interactions.html | 124 ++++++++++++++------------- inst/doc/layout.html | 16 +-- inst/doc/performance.html | 8 - inst/doc/plotscaper.R | 3 inst/doc/plotscaper.Rmd | 3 inst/doc/plotscaper.html | 39 ++++---- inst/htmlwidgets/plotscape/main.iife.js | 4 man/figures/readme1.pngunnamed-chunk-3-1.png |binary man/set_scale.Rd | 3 vignettes/available-interactions.Rmd | 9 + vignettes/plotscaper.Rmd | 3 18 files changed, 177 insertions(+), 121 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.3-1 dated 2024-11-13 and 0.3-2 dated 2024-11-20
DESCRIPTION | 6 +-- MD5 | 6 +-- R/language.R | 86 ++++++++++++++++++++++++++++---------------------------- man/language.Rd | 4 +- 4 files changed, 53 insertions(+), 49 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-15 1.0.1
2020-12-09 1.0.0
2020-11-25 0.0.1
Title: Tide Heights
Description: Calculates tide heights based on tide station harmonics. It
includes the harmonics data for 637 US stations. The harmonics data
was converted from
<https://github.com/poissonconsulting/rtide/blob/main/data-raw/harmonics-dwf-20151227-free.tar.bz2>,
NOAA web site data processed by David Flater for 'XTide'. The code to
calculate tide heights from the harmonics is based on 'XTide'.
Author: Joe Thorley [aut] ,
Luke Miller [aut, cre],
Abram Fleishman [aut],
Poisson Consulting [cph]
Maintainer: Luke Miller <contact@lukemiller.org>
Diff between rtide versions 0.0.10 dated 2024-08-19 and 0.0.11 dated 2024-11-20
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/tide-height.R | 2 +- README.md | 28 +++++++++++----------------- man/rtide-package.Rd | 5 ++--- man/tide_datetimes.Rd | 2 +- tests/testthat/test-tide-height.R | 14 +++++++------- 8 files changed, 40 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-14 0.2.4
2023-03-17 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-18 0.4.3
2023-08-08 0.4.2
2022-02-24 0.4.1
2020-09-10 0.3.0
2020-03-02 0.2.7
2020-02-15 0.2.6
2019-10-08 0.2.4
2019-07-25 0.2.3
2019-07-23 0.2.2
Title: S-Core Graph Decomposition
Description: S-Core Graph Decomposition algorithm for graphs. This is a method
for decomposition of a weighted graph, as proposed by Eidsaa and
Almaas (2013) <doi:10.1103/PhysRevE.88.062819>. The high speed and the low
memory usage make it suitable for large graphs.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between scoredec versions 0.1.1 dated 2024-10-20 and 0.1.2 dated 2024-11-20
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 6 ++++++ README.md | 7 ++++--- build/partial.rdb |binary build/vignette.rds |binary 6 files changed, 22 insertions(+), 15 deletions(-)
Title: 'Shiny' Application for Olympic Data
Description: 'Shiny' Application to visualize Olympic Data. From 1896 to
2016. Even Winter Olympics events are included. Data is from Kaggle at
<https://www.kaggle.com/heesoo37/120-years-of-olympic-history-athletes-and-results>.
Author: Amalan Mahendran [cre, aut]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between OlympicRshiny versions 1.0.1 dated 2024-02-06 and 1.0.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/app_server.R | 13 ++++++++----- 3 files changed, 14 insertions(+), 11 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.5.3 dated 2024-10-10 and 1.5.4 dated 2024-11-20
DESCRIPTION | 6 MD5 | 251 ++++++++++++++++---------------- R/AddBin.R | 164 ++++++++------------ R/BMD_ABD.R | 3 R/Beta.R | 69 ++------ R/BetaCorrBin.R | 102 +++++-------- R/COMPBin.R | 34 +--- R/CorrBin.R | 48 +----- R/Data.R | 150 +++++++++---------- R/GHGbeta.R | 70 ++------ R/Gamma.R | 128 ++++------------ R/Gbeta1.R | 101 +++--------- R/Kumaraswamy.R | 83 ++-------- R/LMultiBin.R | 41 +---- R/MultiBin.R | 32 ---- R/Overdispersion.R | 6 R/SimulateBOD.R | 19 ++ R/Triangle.R | 112 ++++++-------- R/Uniform.R | 56 +------ R/ml.R | 1 build/partial.rdb |binary man/figures/Table-1.png |binary man/fitBin.Rd | 4 tests/testthat/test-AIC.R | 32 +--- tests/testthat/test-Alcohol_data.R | 25 ++- tests/testthat/test-BODextract.R | 23 +- tests/testthat/test-Chromosome_data.R | 20 +- tests/testthat/test-Course_data.R | 20 +- tests/testthat/test-Epidemic_Cold.R | 38 +--- tests/testthat/test-EstMGFBetaBin.R | 45 +---- tests/testthat/test-EstMLEAddBin.R | 38 ---- tests/testthat/test-EstMLEBetaBin.R | 30 +-- tests/testthat/test-EstMLEBetaCorrBin.R | 29 +-- tests/testthat/test-EstMLECOMPBin.R | 29 +-- tests/testthat/test-EstMLECorrBin.R | 26 +-- tests/testthat/test-EstMLEGHGBB.R | 31 +-- tests/testthat/test-EstMLEGammaBin.R | 29 +-- tests/testthat/test-EstMLEGrasiaIIBin.R | 29 +-- tests/testthat/test-EstMLELMBin.R | 29 +-- tests/testthat/test-EstMLEMcGBB.R | 29 +-- tests/testthat/test-EstMLEMultiBin.R | 29 +-- tests/testthat/test-EstMLETriBin.R | 46 ++--- tests/testthat/test-Exam_data.R | 20 +- tests/testthat/test-GenerateBOD.R |only tests/testthat/test-Male_Children.R | 12 + tests/testthat/test-NegLLAddBin.R | 71 +-------- tests/testthat/test-NegLLBetaBin.R | 55 ++----- tests/testthat/test-NegLLBetaCorrBin.R | 63 ++------ tests/testthat/test-NegLLCOMPBin.R | 54 ++---- tests/testthat/test-NegLLCorrBin.R | 74 ++------- tests/testthat/test-NegLLGHGBB.R | 61 ++----- tests/testthat/test-NegLLGammaBin.R | 55 ++----- tests/testthat/test-NegLLGrassiaIIBin.R | 53 +----- tests/testthat/test-NegLLKumBin.R | 64 ++------ tests/testthat/test-NegLLLMBin.R | 59 ++----- tests/testthat/test-NegLLMcGBB.R | 59 ++----- tests/testthat/test-NegLLMultiBin.R | 59 ++----- tests/testthat/test-NegLLTriBin.R | 55 ++----- tests/testthat/test-Overdispersion.R | 93 ----------- tests/testthat/test-Plant_DiseaseData.R | 20 +- tests/testthat/test-Terror_data_ARG.R | 20 +- tests/testthat/test-Terror_data_USA.R | 20 +- tests/testthat/test-dAddBin.R | 71 ++------- tests/testthat/test-dBETA.R | 45 +---- tests/testthat/test-dBetaBin.R | 51 ++---- tests/testthat/test-dBetaCorrBin.R | 54 ++---- tests/testthat/test-dCOMPBin.R | 53 ++---- tests/testthat/test-dCorrBin.R | 66 ++------ tests/testthat/test-dGAMMA.R | 48 ++---- tests/testthat/test-dGBeta1.R | 52 ++---- tests/testthat/test-dGHGBB.R | 58 ++----- tests/testthat/test-dGHGBeta.R | 56 ++----- tests/testthat/test-dGammaBin.R | 55 ++----- tests/testthat/test-dGrassiaIIBin.R | 55 ++----- tests/testthat/test-dKUM.R | 48 ++---- tests/testthat/test-dKumBin.R | 61 ++----- tests/testthat/test-dLMBin.R | 35 ++-- tests/testthat/test-dMcGBB.R | 58 ++----- tests/testthat/test-dMultiBin.R | 61 ++----- tests/testthat/test-dTRI.R | 46 ++--- tests/testthat/test-dTriBin.R | 54 ++---- tests/testthat/test-dUNI.R | 36 +--- tests/testthat/test-dUniBin.R | 42 ++--- tests/testthat/test-fitAddBin.R | 45 ++--- tests/testthat/test-fitBetaBin.R | 45 ++--- tests/testthat/test-fitBetaCorrBin.R | 45 ++--- tests/testthat/test-fitBin.R | 43 ++--- tests/testthat/test-fitCOMPBin.R | 45 ++--- tests/testthat/test-fitCorrBin.R | 45 ++--- tests/testthat/test-fitGHGBB.R | 43 +---- tests/testthat/test-fitGammaBin.R | 45 ++--- tests/testthat/test-fitGrassiaIIBin.R | 45 ++--- tests/testthat/test-fitKumBin.R | 45 ++--- tests/testthat/test-fitLMBin.R | 45 ++--- tests/testthat/test-fitMcGBB.R | 45 ++--- tests/testthat/test-fitMultiBin.R | 45 ++--- tests/testthat/test-fitTriBin.R | 45 ++--- tests/testthat/test-fitted.R | 24 --- tests/testthat/test-mazBETA.R | 39 +--- tests/testthat/test-mazGAMMA.R | 39 +--- tests/testthat/test-mazGBeta1.R | 42 +---- tests/testthat/test-mazGHGBeta.R | 51 ++---- tests/testthat/test-mazKUM.R | 39 +--- tests/testthat/test-mazTRI.R | 39 +--- tests/testthat/test-mazUNI.R | 27 +-- tests/testthat/test-pAddBin.R | 34 ++-- tests/testthat/test-pBETA.R | 49 ++---- tests/testthat/test-pBetaBin.R | 30 ++- tests/testthat/test-pBetaCorrBin.R | 35 +++- tests/testthat/test-pCOMPBin.R | 35 +++- tests/testthat/test-pCorrBin.R | 38 +++- tests/testthat/test-pGAMMA.R | 50 ++---- tests/testthat/test-pGBeta1.R | 52 ++---- tests/testthat/test-pGHGBB.R | 34 ++-- tests/testthat/test-pGHGBeta.R | 58 ++----- tests/testthat/test-pGammaBin.R | 35 +++- tests/testthat/test-pGrassiaIIBin.R | 34 ++-- tests/testthat/test-pKUM.R | 48 ++---- tests/testthat/test-pKumBin.R | 38 +++- tests/testthat/test-pLMBin.R | 34 ++-- tests/testthat/test-pMcGBB.R | 34 ++-- tests/testthat/test-pMultiBin.R | 38 +++- tests/testthat/test-pTRI.R | 48 ++---- tests/testthat/test-pTriBin.R | 34 ++-- tests/testthat/test-pUNI.R | 36 +--- tests/testthat/test-pUniBin.R | 30 ++- tests/testthat/test-residuals.R | 2 127 files changed, 2285 insertions(+), 3596 deletions(-)
Title: Corbae-Ouliaris Frequency Domain Filtering
Description: Corbae-Ouliaris frequency domain filtering. According to
Corbae and Ouliaris (2006) <doi:10.1017/CBO9781139164863.008>,
this is a solution for extracting cycles from time series, like
business cycles etc. when filtering. This method is valid for both
stationary and non-stationary time series.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between corbouli versions 0.1.2 dated 2024-10-04 and 0.1.3 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ README.md | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 4 ++-- inst/doc/Introduction.html | 5 ++--- man/corbae_ouliaris.Rd | 2 +- man/figures/figure2.png |binary vignettes/Introduction.Rmd | 4 ++-- vignettes/figure2.png |binary 12 files changed, 32 insertions(+), 27 deletions(-)
Title: Sound Waves Onto Morphometric Data
Description: Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Author: Pedro Rocha [aut, cre]
Maintainer: Pedro Rocha <p.rocha1990@gmail.com>
Diff between SoundShape versions 1.3.1 dated 2024-10-02 and 1.3.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/eigensound.R | 4 ++-- R/hypo.surf.R | 10 +++++----- R/threeDspectro.R | 18 +++++++++--------- build/vignette.rds |binary inst/doc/Getting-started.html | 4 ++-- man/eigensound.Rd | 4 ++-- man/hypo.surf.Rd | 10 +++++----- man/threeDspectro.Rd | 18 +++++++++--------- 10 files changed, 47 insertions(+), 47 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.2-1 dated 2024-09-22 and 3.3-0 dated 2024-11-19
DESCRIPTION | 16 ++++---- MD5 | 32 ++++++++--------- NEWS | 8 ++++ build/vignette.rds |binary inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 + inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 16 ++++---- inst/doc/updates.Rnw | 82 ++++++++++++++++++++++++++++++++++++++++----- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 + man/spatstat-package.Rd | 6 +++ vignettes/updates.Rnw | 82 ++++++++++++++++++++++++++++++++++++++++----- 17 files changed, 199 insertions(+), 47 deletions(-)
Title: Genetic Analysis of Pooled Samples
Description: Analyzing genetic data obtained from pooled samples.
This package can read in Fragment Analysis output files, process the data,
and score peaks, as well as facilitate various analyses, including cluster
analysis, calculation of genetic distances and diversity indices,
as well as bootstrap resampling for statistical inference. Specifically
tailored to handle genetic data efficiently, researchers can explore
population structure, genetic differentiation, and genetic relatedness
among samples. We updated some functions from Covarrubias-Pazaran et al.
(2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats
and referenced the following to write our genetic analysis functions:
Long et al. (2022) <doi:10.1038/s41598-022-04776-0>, Jost (2008)
<doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973)
<doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006)
<doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008)
<doi:10.1111/j.1541-0420.2008.01010 [...truncated...]
Author: Kathleen Kuesters [aut, cre, cph]
,
Jeffrey Long [aut],
Jessica Blanton [aut],
Walter Blank [ctb],
Jeffrey Kovach [ctb],
Ronald Blanton [ctb]
Maintainer: Kathleen Kuesters <kathleen.kuesters@gmail.com>
Diff between pooledpeaks versions 1.0.6 dated 2024-09-12 and 1.0.7 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ R/Pop_Gen_setup.R | 21 ++++++++++++++++++--- build/partial.rdb |binary 5 files changed, 27 insertions(+), 10 deletions(-)
Title: 'REST' API Client for Accessing Data on 'WEkEO HDA V2'
Description: Provides seamless access to the WEkEO Harmonised Data Access (HDA) API, enabling
users to query, download, and process data efficiently from the HDA platform.
With 'hdar', researchers and data scientists can integrate the extensive HDA
datasets into their R workflows, enhancing their data analysis capabilities.
Comprehensive information on the API functionality and usage is available
at <https://gateway.prod.wekeo2.eu/hda-broker/docs>.
Author: Matteo Mattiuzzi [aut, cre]
Maintainer: Matteo Mattiuzzi <matteo.mattiuzzi@eea.europa.eu>
Diff between hdar versions 1.0.2 dated 2024-09-28 and 1.0.4 dated 2024-11-19
DESCRIPTION | 6 MD5 | 18 - R/client.R | 2 R/paginator.R | 20 - R/search_results.R | 51 ++-- inst/doc/hdar.R | 598 +++++++++++++++++++++++++-------------------------- inst/doc/hdar.Rmd | 2 inst/doc/hdar.html | 2 man/SearchResults.Rd | 5 vignettes/hdar.Rmd | 2 10 files changed, 360 insertions(+), 346 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.5.4 dated 2024-09-06 and 0.5.5 dated 2024-11-19
DESCRIPTION | 6 +- MD5 | 50 ++++++++++++---- NAMESPACE | 1 NEWS.md | 5 + R/check_query.R | 33 ----------- R/collaboration_area.R | 2 R/create_bar.R | 13 +--- R/create_dist.R | 13 +--- R/create_fizz.R | 15 ++--- R/create_line.R | 2 R/create_lorenz.R | 15 ++++- R/create_stacked.R | 8 +- R/xicor.R |only man/create_lorenz.Rd | 83 ++++++++++++++++------------ man/xicor.Rd |only tests/testthat/test_create_IV.R | 4 + tests/testthat/test_create_bar.R |only tests/testthat/test_create_bar_asis.R |only tests/testthat/test_create_boxplot.R |only tests/testthat/test_create_bubble.R |only tests/testthat/test_create_density.R |only tests/testthat/test_create_dist.R |only tests/testthat/test_create_dt.R |only tests/testthat/test_create_fizz.R |only tests/testthat/test_create_hist.R |only tests/testthat/test_create_inc.R |only tests/testthat/test_create_line.R |only tests/testthat/test_create_line_asis.R |only tests/testthat/test_create_lorenz.R |only tests/testthat/test_create_period_scatter.R |only tests/testthat/test_create_rank.R |only tests/testthat/test_create_sankey.R |only tests/testthat/test_create_scatter.R |only tests/testthat/test_create_stacked.R |only tests/testthat/test_create_tracking.R |only tests/testthat/test_create_trend.R |only tests/testthat/test_network_p2p.R | 4 + 37 files changed, 137 insertions(+), 117 deletions(-)
Title: A Robust Boosting Algorithm
Description: An implementation of robust boosting algorithms for regression in R. This includes the RRBoost method proposed in the paper "Robust Boosting for Regression Problems" (Ju X and Salibian-Barrera M. 2020) <doi:10.1016/j.csda.2020.107065>. It also implements previously proposed boosting algorithms in the simulation section of the paper: L2Boost, LADBoost, MBoost (Friedman, J. H. (2001) <doi:10.1214/aos/1013203451>) and Robloss (Lutz et al. (2008) <doi:10.1016/j.csda.2007.11.006>).
Author: Xiaomeng Ju [aut, cre],
Matias Salibian-Barrera [aut]
Maintainer: Xiaomeng Ju <xiaomeng.ju@stat.ubc.ca>
Diff between RRBoost versions 0.1 dated 2020-10-13 and 0.2 dated 2024-11-19
DESCRIPTION | 18 +++++++++------- MD5 | 16 ++++++++------- R/Boost.R | 51 ++++++++++++++++++++++++------------------------ man/Boost.Rd | 9 ++++---- man/Boost.control.Rd | 6 ++--- man/Boost.validation.Rd | 6 ++--- man/cal_imp_func.Rd | 6 ++--- man/cal_predict.Rd | 6 ++--- tests |only 9 files changed, 62 insertions(+), 56 deletions(-)
Title: Find the Pole of Inaccessibility (Visual Center) of a Polygon
Description: A wrapper around the C++ library 'polylabel' from 'Mapbox',
providing an efficient routine for finding the approximate pole of
inaccessibility of a polygon, which usually serves as an excellent candidate
for labeling of a polygon.
Author: Johan Larsson [aut, cre] ,
Kent Johnson [ctb],
Mapbox [cph]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between polylabelr versions 0.2.0 dated 2020-04-19 and 0.3.0 dated 2024-11-19
DESCRIPTION | 19 ++--- MD5 | 68 +++++++++++---------- NAMESPACE | 2 NEWS.md | 20 ++++-- R/poi.R | 15 ++-- R/poi_multi.R |only R/poi_sf.R | 22 ++---- R/utils.R |only README.md | 25 ++----- build |only inst/CITATION | 2 inst/WORDLIST | 5 - inst/include/mapbox/feature.hpp |only inst/include/mapbox/geometry.hpp | 1 inst/include/mapbox/geometry/box.hpp | 6 + inst/include/mapbox/geometry/empty.hpp |only inst/include/mapbox/geometry/envelope.hpp | 4 - inst/include/mapbox/geometry/for_each_point.hpp | 18 +++-- inst/include/mapbox/geometry/geometry.hpp | 32 ++++----- inst/include/mapbox/geometry/line_string.hpp | 6 + inst/include/mapbox/geometry/multi_line_string.hpp | 4 - inst/include/mapbox/geometry/multi_point.hpp | 4 - inst/include/mapbox/geometry/multi_polygon.hpp | 4 - inst/include/mapbox/geometry/point.hpp | 6 + inst/include/mapbox/geometry/polygon.hpp | 8 +- inst/include/mapbox/geometry_io.hpp |only inst/include/mapbox/polylabel.hpp | 16 +--- man/figures/README-unnamed-chunk-1-1.png |binary man/poi.Rd | 6 - man/poi_multi.Rd |only man/polylabelr-package.Rd | 7 -- src/Makevars | 1 src/RcppExports.cpp | 5 + src/poi.cpp | 24 ++++--- tests/testthat/helper_point_in_polygon.R | 5 - tests/testthat/test-assertions.R | 2 tests/testthat/test-poi-multi.R |only tests/testthat/test-poi-sf.R | 55 ++++++++-------- tests/testthat/test-poi.R | 2 39 files changed, 210 insertions(+), 184 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.2 dated 2024-08-23 and 6.3 dated 2024-11-19
DESCRIPTION | 8 MD5 | 22 +- NAMESPACE | 2 NEWS | 13 + R/HelpersMG-package.R | 4 R/MHalgoGen.R | 13 + R/as.parameters.R | 3 R/plot.mcmcComposite.R | 386 ++++++++++++++++++++++++++++++---------------- inst/shiny/cutter/ui.R | 2 man/HelpersMG-package.Rd | 4 man/MHalgoGen.Rd | 7 man/plot.mcmcComposite.Rd | 53 ++++-- 12 files changed, 340 insertions(+), 177 deletions(-)
Title: Wildlife Mortality Estimator for Low Fatality Rates and
Imperfect Detection
Description: Evidence of Absence software (EoA) is a user-friendly application for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The models are applicable even when zero carcasses have been found in searches, following Huso et al. (2015) <doi:10.1890/14-0764.1>, Dalthorp et al. (2017) <doi:10.3133/ds1055>, and Dalthorp and Huso (2015) <doi:10.3133/ofr20151227>.
Author: Daniel Dalthorp [aut, cre]
Maintainer: Daniel Dalthorp <ddalthorp@protonmail.com>
Diff between eoa3 versions 1.0.0.1 dated 2023-07-04 and 1.0.0.2 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/eoa.r | 4 ++-- man/eoa3.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: SDTM Datacut
Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM),
as part of the analysis of specific points in time of the data, normally as part of
investigation into clinical trials. The functions support different approaches of
cutting to the different domains of SDTM normally observed.
Author: Tim Barnett [cph, aut, cre],
Nathan Rees [aut],
Alana Harris [aut],
Cara Andrews [aut]
Maintainer: Tim Barnett <timothy.barnett@roche.com>
Diff between datacutr versions 0.1.0 dated 2023-03-31 and 0.2.0 dated 2024-11-19
DESCRIPTION | 26 + MD5 | 96 +++--- NAMESPACE | 3 NEWS.md | 34 ++ R/create_dcut.R | 14 R/datcutr-package.R | 2 R/date_cut.R | 19 - R/global.R | 3 R/impute_dcutdtc.R | 9 R/process_cut.R | 157 +++++++--- R/read_out.R |only R/special_dm_cut.R | 15 - README.md | 14 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/contribution_model.html | 232 +++++++++++++++- inst/doc/datacutr.Rmd | 2 inst/doc/datacutr.html | 304 +++++++++++++++++++-- inst/doc/examplemodular.R | 7 inst/doc/examplemodular.Rmd | 5 inst/doc/examplemodular.html | 504 ++++++++++++++++++++++++----------- inst/doc/examplewrapped.R | 7 inst/doc/examplewrapped.Rmd | 5 inst/doc/examplewrapped.html | 432 ++++++++++++++++++++++-------- inst/doc/modular.R | 33 +- inst/doc/modular.Rmd | 5 inst/doc/modular.html | 479 ++++++++++++++++++++++++--------- inst/doc/variable_cut.R | 19 - inst/doc/variable_cut.Rmd | 9 inst/doc/variable_cut.html | 427 ++++++++++++++++++++++------- inst/doc/wrapper.R | 15 - inst/doc/wrapper.Rmd | 5 inst/doc/wrapper.html | 419 ++++++++++++++++++++++------- inst/read-out |only man/create_dcut.Rd | 2 man/datacutr-package.Rd | 10 man/impute_dcutdtc.Rd | 2 man/process_cut.Rd | 23 + man/read_out.Rd |only tests/testthat/test-create_dcut.R | 36 ++ tests/testthat/test-date_cut.R | 46 +++ tests/testthat/test-impute_dcutdtc.R | 26 - tests/testthat/test-process_cut.R | 53 +++ tests/testthat/test-read_out.R |only tests/testthat/test-special_dm_cut.R | 50 +++ vignettes/datacutr.Rmd | 2 vignettes/examplemodular.Rmd | 5 vignettes/examplewrapped.Rmd | 5 vignettes/modular.Rmd | 5 vignettes/variable_cut.Rmd | 9 vignettes/wrapper.Rmd | 5 51 files changed, 2720 insertions(+), 861 deletions(-)
Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions.
The random sampling scheme of the package offers two sampling
algorithms that are based of the results of Sablica, Hornik and Leydold (2022)
<https://research.wu.ac.at/en/publications/random-sampling-from-the-watson-distribution>.
What is more, the package offers a smart tool to combine these two methods,
and based on the selected parameters, it approximates the relative sampling
speed for both methods and picks the faster one. In addition, the package
offers a fitting function for the mixtures of Watson distribution, that
uses the expectation-maximization (EM) algorithm. Special features are
the possibility to use multiple variants of the E-step and M-step,
sparse matrices for the data representation and state of the art methods
for numerical evaluation of needed special functions using the results of
Sablica and Hornik (2022) <https://www.ams.org/journals/mcom/2022-91-334/S0025-5718-2021-03690-X/>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Josef Leydold [aut] ,
Gerard Jungman [ctb, cph] ,
Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between watson versions 0.4 dated 2023-06-01 and 0.5 dated 2024-11-19
watson-0.4/watson/R/sysdata.rda |only watson-0.5/watson/DESCRIPTION | 12 ++++--- watson-0.5/watson/MD5 | 13 ++++--- watson-0.5/watson/NAMESPACE | 5 ++ watson-0.5/watson/NEWS.md | 6 +++ watson-0.5/watson/R/watson.R | 68 ++++++++++++++++++++++++++++++++++++++++ watson-0.5/watson/man/id.Rd |only watson-0.5/watson/tests |only 8 files changed, 94 insertions(+), 10 deletions(-)
Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] ,
Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>
Diff between hyperbolicDEA versions 1.0.0 dated 2024-03-18 and 1.0.1 dated 2024-11-19
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 1 R/check_arguments.R | 26 ++++- R/costDEA.R | 3 R/hyperbolicDEA.R | 20 ++-- R/lprofitDEA.R | 2 R/nlprofitDEA.R | 2 R/wrDEA.R | 75 ++++++++++++++- man/costDEA.Rd | 87 +++++++++--------- man/hyperbolicDEA.Rd | 5 + man/lprofitDEA.Rd | 95 ++++++++++--------- man/nlprofitDEA.Rd | 91 +++++++++---------- man/wrDEA.Rd | 172 +++++++++++++++++++----------------- tests/testthat/test-hyperbolicDEA.R | 53 +++++++++-- 15 files changed, 410 insertions(+), 258 deletions(-)
Title: Constrained Ordinary Least Squares
Description: Constrained ordinary least squares is performed. One constraint is that all beta coefficients (including the constant) cannot be negative. They can be either 0 or strictly positive. Another constraint is that the sum of the beta coefficients equals a constant. References: Hansen, B. E. (2022). Econometrics, Princeton University Press. <ISBN:9780691235899>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cols versions 1.2 dated 2024-10-16 and 1.3 dated 2024-11-19
cols-1.2/cols/R/mcls.R |only cols-1.3/cols/DESCRIPTION | 8 ++++---- cols-1.3/cols/MD5 | 12 +++++++----- cols-1.3/cols/NAMESPACE | 2 +- cols-1.3/cols/R/int.cls.R |only cols-1.3/cols/R/mvcls.R |only cols-1.3/cols/man/cls.Rd | 8 ++++---- cols-1.3/cols/man/cols-package.Rd | 4 ++-- cols-1.3/cols/man/int.cls.Rd |only 9 files changed, 18 insertions(+), 16 deletions(-)
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.1 dated 2024-10-13 and 0.1.2 dated 2024-11-19
CDsampling-0.1.1/CDsampling/R/constrained_uniform.R |only CDsampling-0.1.1/CDsampling/man/constrained_uniform.Rd |only CDsampling-0.1.2/CDsampling/DESCRIPTION | 6 CDsampling-0.1.2/CDsampling/MD5 | 46 - CDsampling-0.1.2/CDsampling/NAMESPACE | 5 CDsampling-0.1.2/CDsampling/R/F_func_GLM.R | 9 CDsampling-0.1.2/CDsampling/R/F_func_MLM.R | 3 CDsampling-0.1.2/CDsampling/R/Fi_func_MLM.R | 12 CDsampling-0.1.2/CDsampling/R/W_func_GLM.R | 1 CDsampling-0.1.2/CDsampling/R/approxtoexact_constrained_func.R | 6 CDsampling-0.1.2/CDsampling/R/approxtoexact_func.R | 5 CDsampling-0.1.2/CDsampling/R/bounded_uniform.R |only CDsampling-0.1.2/CDsampling/R/liftone_GLM.R | 14 CDsampling-0.1.2/CDsampling/R/liftone_MLM.R | 16 CDsampling-0.1.2/CDsampling/R/liftone_constrained_GLM.R | 22 CDsampling-0.1.2/CDsampling/R/liftone_constrained_MLM.R | 18 CDsampling-0.1.2/CDsampling/R/print.list_output.R |only CDsampling-0.1.2/CDsampling/R/print.matrix_list.R |only CDsampling-0.1.2/CDsampling/R/print.matrix_output.R |only CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.R | 18 CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.Rmd | 18 CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.html | 310 ++++++---- CDsampling-0.1.2/CDsampling/man/F_func_GLM.Rd | 6 CDsampling-0.1.2/CDsampling/man/bounded_uniform.Rd |only CDsampling-0.1.2/CDsampling/man/liftone_MLM.Rd | 2 CDsampling-0.1.2/CDsampling/man/print.list_output.Rd |only CDsampling-0.1.2/CDsampling/man/print.matrix_list.Rd |only CDsampling-0.1.2/CDsampling/man/print.matrix_output.Rd |only CDsampling-0.1.2/CDsampling/vignettes/Intro_to_CDsampling.Rmd | 18 29 files changed, 323 insertions(+), 212 deletions(-)
Title: Synthesise and Correlate Likert Scale and Related Rating-Scale
Data
Description: Synthesise Likert scale and related rating-scale data with
predefined first and second moments (mean and standard deviation),
and, optionally, correlate multiple vectors using a predefined
correlation matrix. Additionally, generate synthetic rating-scale
items with a predefined Cronbach's Alpha, or create rating-scale items
based on a predefined summated scale.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 0.3.0 dated 2024-05-19 and 0.4.0 dated 2024-11-19
LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_1.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_2.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_4.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_hex.png |only LikertMakeR-0.4.0/LikertMakeR/DESCRIPTION | 22 LikertMakeR-0.4.0/LikertMakeR/MD5 | 38 LikertMakeR-0.4.0/LikertMakeR/NAMESPACE | 2 LikertMakeR-0.4.0/LikertMakeR/NEWS.md | 10 LikertMakeR-0.4.0/LikertMakeR/R/lexact.R | 1 LikertMakeR-0.4.0/LikertMakeR/R/lfast.R | 7 LikertMakeR-0.4.0/LikertMakeR/R/makeItems.R | 3 LikertMakeR-0.4.0/LikertMakeR/R/makeItemsScale.R | 322 +- LikertMakeR-0.4.0/LikertMakeR/README.md | 225 + LikertMakeR-0.4.0/LikertMakeR/build/vignette.rds |binary LikertMakeR-0.4.0/LikertMakeR/inst/CITATION | 2 LikertMakeR-0.4.0/LikertMakeR/inst/WORDLIST |only LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.R | 287 +- LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.Rmd | 442 ++- LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.html | 1263 ++++++---- LikertMakeR-0.4.0/LikertMakeR/man/figures/logo.png |binary LikertMakeR-0.4.0/LikertMakeR/man/makeItemsScale.Rd | 194 + LikertMakeR-0.4.0/LikertMakeR/vignettes/LikertMakeR_vignette.Rmd | 442 ++- LikertMakeR-0.4.0/LikertMakeR/vignettes/skew_chart.png |only 23 files changed, 2230 insertions(+), 1030 deletions(-)
Title: Gaussian Process Laboratory
Description: Gaussian process regression with an emphasis on kernels.
Quantitative and qualitative inputs are accepted. Some pre-defined
kernels are available, such as radial or tensor-sum for
quantitative inputs, and compound symmetry, low rank, group kernel
for qualitative inputs. The user can define new kernels and
composite kernels through a formula mechanism. Useful methods
include parameter estimation by maximum likelihood, simulation,
prediction and leave-one-out validation.
Author: Yves Deville [aut] ,
David Ginsbourger [aut] ,
Olivier Roustant [aut, cre],
Nicolas Durrande [ctb]
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>
Diff between kergp versions 0.5.7 dated 2024-02-05 and 0.5.8 dated 2024-11-19
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 18 +++++++++--------- build/partial.rdb |binary inst/doc/OptimMLE.pdf |binary inst/doc/beam.pdf |binary inst/doc/groupKernel.pdf |binary man/gp.Rd | 8 +++++--- man/influence.gp.Rd | 2 +- man/kergp-package.Rd | 25 ++++++++++++++----------- man/simulate.covAll.Rd | 4 ++-- 10 files changed, 49 insertions(+), 32 deletions(-)
Title: Hidden Markov Models for Reliability and Maintenance
Description: Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.
Author: M.L. Gamiz [aut, cre, cph],
N. Limnios [aut, cph],
M.C. Segovia-Garcia [aut, cph]
Maintainer: M.L. Gamiz <mgamiz@ugr.es>
Diff between HMMRel versions 0.1.0 dated 2024-11-15 and 0.1.1 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md |only man/HMMRel-package.Rd | 2 +- man/cost.cspc.Rd | 4 ++-- man/cost.wspc.Rd | 9 ++++----- man/def.hmmR.Rd | 6 +++--- man/fit.hmmR.Rd | 4 ++-- 8 files changed, 23 insertions(+), 23 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.8.10 dated 2024-05-17 and 0.8.11 dated 2024-11-19
ggiraph-0.8.10/ggiraph/inst/tinytest/test-ggiraph.R |only ggiraph-0.8.11/ggiraph/DESCRIPTION | 10 ggiraph-0.8.11/ggiraph/MD5 | 221 ++++----- ggiraph-0.8.11/ggiraph/NAMESPACE | 9 ggiraph-0.8.11/ggiraph/NEWS.md | 11 ggiraph-0.8.11/ggiraph/R/annotate_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/annotation_raster_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/element_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/facet_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_abline_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_bar_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/geom_bin_2d_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_boxplot_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_contour_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_count_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_crossbar_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_density_2d_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_density_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_dotplot_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_errorbarh_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_hex_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_histogram_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_jitter_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_map_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_path_interactive.R | 31 + ggiraph-0.8.11/ggiraph/R/geom_point_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_polygon_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_quantile_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_raster_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_rect_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_ribbon_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_segment_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_sf_interactive.R | 7 ggiraph-0.8.11/ggiraph/R/geom_smooth_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_spoke_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_text_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_violin_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/ggiraph.R | 106 ---- ggiraph-0.8.11/ggiraph/R/guide_bins_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_colourbar_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_coloursteps_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_legend_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/ipar.R | 4 ggiraph-0.8.11/ggiraph/R/labeller_interactive.R | 10 ggiraph-0.8.11/ggiraph/R/scale_alpha_interactive.R | 14 ggiraph-0.8.11/ggiraph/R/scale_brewer_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_colour_interactive.R | 28 - ggiraph-0.8.11/ggiraph/R/scale_gradient_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_linetype_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/scale_manual_interactive.R | 14 ggiraph-0.8.11/ggiraph/R/scale_shape_interactive.R | 10 ggiraph-0.8.11/ggiraph/R/scale_size_interactive.R | 20 ggiraph-0.8.11/ggiraph/R/scale_steps_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_viridis_interactive.R | 16 ggiraph-0.8.11/ggiraph/R/utils_ggplot2.R | 240 ++++++++++ ggiraph-0.8.11/ggiraph/build/vignette.rds |binary ggiraph-0.8.11/ggiraph/inst/examples/rmd/flexdashboard/flexdashboard.Rmd | 2 ggiraph-0.8.11/ggiraph/man/annotate_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/annotation_raster_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/element_interactive.Rd | 8 ggiraph-0.8.11/ggiraph/man/facet_grid_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/facet_wrap_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/geom_abline_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_bar_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_bin_2d_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_boxplot_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/geom_contour_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_count_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_crossbar_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_density_2d_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_density_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_dotplot_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_errorbarh_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_hex_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_histogram_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_jitter_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_map_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_path_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_point_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_polygon_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_quantile_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_raster_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_rect_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_ribbon_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_segment_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_sf_interactive.Rd | 7 ggiraph-0.8.11/ggiraph/man/geom_smooth_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_spoke_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_text_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_text_repel_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/geom_violin_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/ggiraph.Rd | 62 -- ggiraph-0.8.11/ggiraph/man/ggiraphOutput.Rd | 22 ggiraph-0.8.11/ggiraph/man/guide_bins_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_colourbar_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_coloursteps_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_legend_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/interactive_parameters.Rd | 4 ggiraph-0.8.11/ggiraph/man/label_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/labeller_interactive.Rd | 10 ggiraph-0.8.11/ggiraph/man/renderggiraph.Rd | 18 ggiraph-0.8.11/ggiraph/man/scale_alpha_interactive.Rd | 14 ggiraph-0.8.11/ggiraph/man/scale_colour_brewer_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_colour_interactive.Rd | 28 - ggiraph-0.8.11/ggiraph/man/scale_colour_steps_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_gradient_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_linetype_interactive.Rd | 8 ggiraph-0.8.11/ggiraph/man/scale_manual_interactive.Rd | 14 ggiraph-0.8.11/ggiraph/man/scale_shape_interactive.Rd | 10 ggiraph-0.8.11/ggiraph/man/scale_size_interactive.Rd | 20 ggiraph-0.8.11/ggiraph/man/scale_viridis_interactive.Rd | 16 ggiraph-0.8.11/ggiraph/src/tinyxml2.cpp | 8 112 files changed, 719 insertions(+), 601 deletions(-)
Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between file2meco versions 0.9.0 dated 2024-10-31 and 0.9.1 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/qiime2meco.R | 15 ++++++++++----- 3 files changed, 15 insertions(+), 10 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.1-2 dated 2024-10-04 and 1.2-0 dated 2024-11-19
tram-1.1-2/tram/src |only tram-1.1-2/tram/vignettes/mtram-rendered.pdf |only tram-1.2-0/tram/DESCRIPTION | 18 tram-1.2-0/tram/MD5 | 62 tram-1.2-0/tram/NAMESPACE | 2 tram-1.2-0/tram/R/mtram.R | 195 +- tram-1.2-0/tram/build/partial.rdb |binary tram-1.2-0/tram/build/vignette.rds |binary tram-1.2-0/tram/demo/00Index | 13 tram-1.2-0/tram/demo/hcc.R | 2 tram-1.2-0/tram/demo/mnc.R |only tram-1.2-0/tram/demo/mtram.R | 75 tram-1.2-0/tram/demo/npb.R |only tram-1.2-0/tram/demo/stram.R | 4 tram-1.2-0/tram/demo/survtram.R | 115 - tram-1.2-0/tram/demo/tram.R |only tram-1.2-0/tram/inst/NEWS.Rd | 11 tram-1.2-0/tram/inst/doc/mtram.R |only tram-1.2-0/tram/inst/doc/mtram.Rnw | 2001 ++++++++++++++++++++++- tram-1.2-0/tram/inst/doc/mtram.pdf |binary tram-1.2-0/tram/inst/doc/tram.R | 21 tram-1.2-0/tram/inst/doc/tram.Rnw | 7 tram-1.2-0/tram/inst/doc/tram.pdf |binary tram-1.2-0/tram/inst/simulations/mtram_sim.R | 10 tram-1.2-0/tram/inst/simulations/sim2d.R | 6 tram-1.2-0/tram/inst/simulations/sim2d.Rout.save |only tram-1.2-0/tram/inst/simulations/sim2d.pdf.save |only tram-1.2-0/tram/inst/simulations/sim5d.R | 19 tram-1.2-0/tram/inst/simulations/sim5d.Rout.save |only tram-1.2-0/tram/inst/simulations/sim5d.pdf.save |only tram-1.2-0/tram/man/Coxph.Rd | 8 tram-1.2-0/tram/man/mtram.Rd | 38 tram-1.2-0/tram/tests/bugfixes.R | 6 tram-1.2-0/tram/tests/mtram-Ex.R |only tram-1.2-0/tram/tests/mtram-Ex.Rout.save |only tram-1.2-0/tram/vignettes/mtram.Rnw | 2001 ++++++++++++++++++++++- tram-1.2-0/tram/vignettes/tram.Rnw | 7 37 files changed, 4357 insertions(+), 264 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister [aut, cre],
Markus Janczyk [aut]
Maintainer: Roland Pfister <mail@roland-pfister.net>
Diff between schoRsch versions 1.10 dated 2022-11-01 and 1.11 dated 2024-11-19
DESCRIPTION | 18 +++++++++++++----- MD5 | 14 ++++++++------ R/bimod_coef.R |only R/cor_out.R | 25 +++++++++++++++++++------ R/t_out.R | 1 + man/bimod_coef.Rd |only man/clear_all_but.Rd | 3 ++- man/cor_out.Rd | 3 ++- man/schoRsch.Rd | 12 ++++++++---- 9 files changed, 53 insertions(+), 23 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-9 dated 2024-09-20 and 1.1-10 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.R | 2 +- inst/doc/mlt.Rnw | 2 +- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 2 +- 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.2-2 dated 2024-09-20 and 3.2-3 dated 2024-11-19
DESCRIPTION | 16 ++++++++-------- MD5 | 13 +++++++------ NEWS | 13 +++++++++++++ R/shortestpath.R |only inst/doc/packagesizes.txt | 2 +- inst/info/packagesizes.txt | 2 +- man/pairdist.lpp.Rd | 1 + man/plot.linim.Rd | 3 ++- 8 files changed, 33 insertions(+), 17 deletions(-)
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