Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 4.0.2 dated 2022-11-10 and 4.0.4 dated 2023-02-06
DESCRIPTION | 10 ++-- MD5 | 34 +++++++------- NEWS.md | 10 ++++ R/CCAMLRGIS.R | 2 R/DensifyData.R | 103 +++++++++++++++++++++++++++++++++++++----- R/Pies.R | 61 ++++++++++++++++++------- R/add_Cscale.R | 23 ++++++--- R/cGrid.r | 7 +- R/cLines.R | 2 R/cPolys.R | 2 R/create.R | 13 ++--- README.md | 116 ++++++++++++++++++++++++------------------------ data/SmallBathy.RData |binary inst/doc/CCAMLRGIS.html | 18 +++---- man/add_Cscale.Rd | 15 ++++++ man/add_PieLegend.Rd | 7 ++ man/create_Lines.Rd | 6 +- man/create_Polys.Rd | 7 +- 18 files changed, 290 insertions(+), 146 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss size and
frequency: 23 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities. Main reference: <doi:10.18637/jss.v025.i07>.
Implementation of the Feller-Pareto family of distributions:
<doi:10.18637/jss.v103.i06>.
Author: Vincent Goulet [cre, aut],
Sebastien Auclair [ctb],
Christophe Dutang [aut],
Walter Garcia-Fontes [ctb],
Nicholas Langevin [ctb],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Alexandre Parent [ctb],
Mathieu Pigeon [aut],
Louis-Philippe Pouliot [ctb],
J [...truncated...]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 3.3-1 dated 2022-10-27 and 3.3-2 dated 2023-02-06
actuar-3.3-1/actuar/vignettes/auto |only actuar-3.3-2/actuar/DESCRIPTION | 8 actuar-3.3-2/actuar/MD5 | 130 ++-- actuar-3.3-2/actuar/R/adjCoef.R | 27 actuar-3.3-2/actuar/R/aggregateDist.R | 18 actuar-3.3-2/actuar/R/bayes.R | 36 - actuar-3.3-2/actuar/R/bstraub.R | 3 actuar-3.3-2/actuar/R/cm.R | 3 actuar-3.3-2/actuar/R/coverage.R | 2 actuar-3.3-2/actuar/R/discretize.R | 9 actuar-3.3-2/actuar/R/emm.R | 4 actuar-3.3-2/actuar/R/grouped.data.R | 9 actuar-3.3-2/actuar/R/hist.grouped.data.R | 3 actuar-3.3-2/actuar/R/mde.R | 16 actuar-3.3-2/actuar/R/ogive.R | 3 actuar-3.3-2/actuar/R/panjer.R | 19 actuar-3.3-2/actuar/R/rcompound.R | 34 - actuar-3.3-2/actuar/R/rmixture.R | 9 actuar-3.3-2/actuar/R/ruin.R | 60 +- actuar-3.3-2/actuar/R/simul.summaries.R | 2 actuar-3.3-2/actuar/R/unroll.R | 2 actuar-3.3-2/actuar/build/partial.rdb |binary actuar-3.3-2/actuar/inst/CITATION | 4 actuar-3.3-2/actuar/inst/NEWS.Rd | 18 actuar-3.3-2/actuar/inst/doc/actuar.R | 4 actuar-3.3-2/actuar/inst/doc/actuar.Rnw | 60 -- actuar-3.3-2/actuar/inst/doc/actuar.pdf |binary actuar-3.3-2/actuar/inst/doc/coverage.R | 24 actuar-3.3-2/actuar/inst/doc/coverage.Rnw | 43 - actuar-3.3-2/actuar/inst/doc/coverage.pdf |binary actuar-3.3-2/actuar/inst/doc/credibility.R | 28 actuar-3.3-2/actuar/inst/doc/credibility.Rnw | 66 -- actuar-3.3-2/actuar/inst/doc/credibility.pdf |binary actuar-3.3-2/actuar/inst/doc/distributions.Rnw | 123 ---- actuar-3.3-2/actuar/inst/doc/distributions.pdf |binary actuar-3.3-2/actuar/inst/doc/modeling.R | 127 ++-- actuar-3.3-2/actuar/inst/doc/modeling.Rnw | 136 +--- actuar-3.3-2/actuar/inst/doc/modeling.pdf |binary actuar-3.3-2/actuar/inst/doc/risk.R | 79 +- actuar-3.3-2/actuar/inst/doc/risk.Rnw | 107 --- actuar-3.3-2/actuar/inst/doc/risk.pdf |binary actuar-3.3-2/actuar/inst/doc/simulation.R | 38 - actuar-3.3-2/actuar/inst/doc/simulation.Rnw | 73 -- actuar-3.3-2/actuar/inst/doc/simulation.pdf |binary actuar-3.3-2/actuar/inst/po/en@quot/LC_MESSAGES/R-actuar.mo |binary actuar-3.3-2/actuar/inst/po/en@quot/LC_MESSAGES/actuar.mo |binary actuar-3.3-2/actuar/inst/po/fr/LC_MESSAGES/R-actuar.mo |binary actuar-3.3-2/actuar/inst/po/it/LC_MESSAGES/R-actuar.mo |binary actuar-3.3-2/actuar/man/rcompound.Rd | 2 actuar-3.3-2/actuar/man/rmixture.Rd | 32 + actuar-3.3-2/actuar/po/R-actuar.pot | 204 ++++-- actuar-3.3-2/actuar/po/R-fr.po | 354 ++++++------ actuar-3.3-2/actuar/po/R-it.po | 351 +++++++---- actuar-3.3-2/actuar/po/actuar.pot | 4 actuar-3.3-2/actuar/tests/rcompound-tests.R |only actuar-3.3-2/actuar/tests/rmixture-tests.R | 87 ++ actuar-3.3-2/actuar/vignettes/Makefile |only actuar-3.3-2/actuar/vignettes/actuar.Rnw | 60 -- actuar-3.3-2/actuar/vignettes/coverage.Rnw | 43 - actuar-3.3-2/actuar/vignettes/credibility.Rnw | 66 -- actuar-3.3-2/actuar/vignettes/distributions.Rnw | 123 ---- actuar-3.3-2/actuar/vignettes/modeling.Rnw | 136 +--- actuar-3.3-2/actuar/vignettes/risk.Rnw | 107 --- actuar-3.3-2/actuar/vignettes/share |only actuar-3.3-2/actuar/vignettes/simulation.Rnw | 73 -- 65 files changed, 1226 insertions(+), 1743 deletions(-)
Title: Implementing Methods for Spatial Fuzzy Unsupervised
Classification
Description: Provides functions to apply spatial fuzzy unsupervised classification, visualize and interpret results. This method is well suited when the user wants to analyze data with a fuzzy clustering algorithm and to account for the spatial dimension of the dataset. In addition, indexes for estimating the spatial consistency and classification quality are proposed.
The methods were originally proposed in the field of brain imagery (seed Cai and al. 2007 <doi:10.1016/j.patcog.2006.07.011> and Zaho and al. 2013 <doi:10.1016/j.dsp.2012.09.016>) and recently applied in geography (see Gelb and Apparicio <doi:10.4000/cybergeo.36414>).
Author: Jeremy Gelb [aut, cre],
Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>
Diff between geocmeans versions 0.3.2 dated 2023-01-08 and 0.3.3 dated 2023-02-06
DESCRIPTION | 10 - MD5 | 40 ++--- NEWS.md | 5 R/raster_support.R | 2 R/shinyapp.R | 81 ++++++++++- README.md | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 +- inst/doc/FCMres.html | 134 ++++++++++--------- inst/doc/adjustinconsistency.html | 150 +++++++++++----------- inst/doc/introduction.html | 176 +++++++++++++------------- inst/doc/rasters.R | 2 inst/doc/rasters.Rmd | 2 inst/doc/rasters.html | 169 +++++++++++++----------- inst/extdata/results_vignette_intro.rda |binary inst/extdata/results_vignette_raster.rda |binary inst/shiny-examples/cluster_explorer/server.R | 15 +- src/Makevars | 6 src/Makevars.win | 6 vignettes/rasters.Rmd | 2 21 files changed, 469 insertions(+), 359 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.56 dated 2023-01-15 and 2.0.57 dated 2023-02-06
DESCRIPTION | 10 MD5 | 24 NEWS | 17 R/epi.2by2.R | 178 ++-- R/epi.kappa.R | 4 R/epi.prcc.R | 10 inst/doc/epiR_descriptive.html | 880 ++++++++------------ inst/doc/epiR_measures_of_association.html | 1248 ++++++++++++----------------- inst/doc/epiR_sample_size.html | 345 ++------ inst/doc/epiR_surveillance.html | 1063 ++++++++---------------- man/epi.about.Rd | 6 man/epi.directadj.Rd | 15 man/epi.prcc.Rd | 2 13 files changed, 1516 insertions(+), 2286 deletions(-)
Title: Quality Control and Analysis of Massachusetts Water Quality Data
Description: Methods for quality control and exploratory analysis of surface
water quality data collected in Massachusetts, USA. Functions are developed
to facilitate data formatting for the Water Quality Exchange Network
<https://www.epa.gov/waterdata/water-quality-data-upload-wqx> and reporting
of data quality objectives to state agencies. Quality control methods are
from Massachusetts Department of Environmental Protection (2020)
<https://www.mass.gov/orgs/massachusetts-department-of-environmental-protection>.
Author: Marcus Beck [aut, cre] ,
Jill Carr [aut],
Ben Wetherill [aut] ,
Pam DiBona [aut]
Maintainer: Marcus Beck <mbeck@tbep.org>
Diff between MassWateR versions 2.0.0 dated 2023-01-20 and 2.0.1 dated 2023-02-06
DESCRIPTION | 6 MD5 | 53 ++--- NEWS.md |only R/formMWRacc.R | 14 - R/formMWRfrecom.R | 7 R/formMWRresults.R | 14 - R/formMWRwqx.R | 7 R/qcMWRacc.R | 120 +++++++----- R/qcMWRcom.R | 6 R/qcMWRfre.R | 6 R/tabMWRfre.R | 6 R/tabMWRwqx.R | 161 +++++++++-------- R/utilMWRfilter.R | 8 R/utilMWRlimits.R | 14 - R/utilMWRyscale.R | 14 - README.md | 1 inst/extdata/WQX_Phys-Chem_Template_for_MassWateR.xlsx |binary man/checkMWRacc.Rd | 86 ++++----- man/checkMWRfrecom.Rd | 92 ++++----- man/checkMWRsites.Rd | 80 ++++---- man/readMWRacc.Rd | 60 +++--- man/readMWRfrecom.Rd | 62 +++--- man/readMWRsites.Rd | 56 ++--- man/utilMWRconfint.Rd | 94 ++++----- man/utilMWRfiltersurface.Rd | 60 +++--- man/utilMWRoutlier.Rd | 52 ++--- tests/testthat.R | 8 tests/testthat/test-utilMWRfilter.R | 84 ++++---- 28 files changed, 607 insertions(+), 564 deletions(-)
Title: Exact Multinomial Test: Goodness-of-Fit Test for Discrete
Multivariate Data
Description: Goodness-of-fit tests for discrete multivariate data. It is
tested if a given observation is likely to have occurred under
the assumption of an ab-initio model. Monte Carlo methods are provided to
make the package capable of solving high-dimensional problems.
Author: Uwe Menzel
Maintainer: Uwe Menzel <uwemenzel@gmail.com>
Diff between EMT versions 1.2 dated 2021-11-02 and 1.3 dated 2023-02-06
DESCRIPTION | 8 MD5 | 12 - R/EMT.R | 453 ++++++++++++++++++++++++++---------------------- man/EMT-internal.Rd | 5 man/EMT-package.Rd | 4 man/multinomial.test.Rd | 234 ++++++++++++------------ man/plotMultinom.Rd | 3 7 files changed, 383 insertions(+), 336 deletions(-)
Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values.
Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith,
and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>.
Other palettes available in this library have been derived from
'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and
'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between colourvalues versions 0.3.7 dated 2020-12-07 and 0.3.8 dated 2023-02-06
DESCRIPTION | 17 +++---- MD5 | 20 ++++----- NEWS.md | 5 ++ README.md | 66 +++++++++++++++--------------- inst/include/colourvalues/scale/scale.hpp | 17 +++++-- man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 ++ tests/testthat/test-colour_values_hex.R | 4 - 11 files changed, 76 insertions(+), 62 deletions(-)
Title: R Access to LEMON Graph Algorithms
Description: Allows easy access to the LEMON Graph Library set of algorithms, written in C++.
See the LEMON project page at <https://lemon.cs.elte.hu/trac/lemon>.
Current LEMON version is 1.3.1.
Author: Arav Agarwal [aut],
Aditya Tewari [aut],
Josh Errickson [cre, aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between rlemon versions 0.2.0 dated 2022-04-15 and 0.2.1 dated 2023-02-06
rlemon-0.2.0/rlemon/tests/testthat/test-Approximation.R |only rlemon-0.2.0/rlemon/tests/testthat/test-Connectivity.R |only rlemon-0.2.0/rlemon/tests/testthat/test-GraphSearch.R |only rlemon-0.2.0/rlemon/tests/testthat/test-MaxFlow.R |only rlemon-0.2.0/rlemon/tests/testthat/test-MinCostFlow.R |only rlemon-0.2.0/rlemon/tests/testthat/test-MinCut.R |only rlemon-0.2.0/rlemon/tests/testthat/test-MinMeanCycle.R |only rlemon-0.2.0/rlemon/tests/testthat/test-MinSpanningTree.R |only rlemon-0.2.0/rlemon/tests/testthat/test-ShortestPath.R |only rlemon-0.2.0/rlemon/tests/testthat/test-TravelingSalesperson.R |only rlemon-0.2.1/rlemon/DESCRIPTION | 8 rlemon-0.2.1/rlemon/MD5 | 118 +- rlemon-0.2.1/rlemon/NEWS.md | 11 rlemon-0.2.1/rlemon/R/approximation.R | 13 rlemon-0.2.1/rlemon/R/connectivity.R | 39 rlemon-0.2.1/rlemon/R/graphsearch.R | 48 rlemon-0.2.1/rlemon/R/maxflow.R | 43 rlemon-0.2.1/rlemon/R/maxmatching.R | 64 - rlemon-0.2.1/rlemon/R/mincostflow.R | 37 rlemon-0.2.1/rlemon/R/mincut.R | 49 rlemon-0.2.1/rlemon/R/minimummeancycle.R | 23 rlemon-0.2.1/rlemon/R/minimumspanningtree.R | 48 rlemon-0.2.1/rlemon/R/planarityembedding.R | 52 rlemon-0.2.1/rlemon/R/runners.R | 8 rlemon-0.2.1/rlemon/R/shortestpath.R | 42 rlemon-0.2.1/rlemon/R/travellingsalespersonproblem.R | 31 rlemon-0.2.1/rlemon/inst/lemon/bits/array_map.h | 571 +++++----- rlemon-0.2.1/rlemon/inst/lemon/maps.h | 19 rlemon-0.2.1/rlemon/man/AllPairsMinCut.Rd | 8 rlemon-0.2.1/rlemon/man/FindBiEdgeConnectedCutEdges.Rd | 4 rlemon-0.2.1/rlemon/man/FindStronglyConnectedCutArcs.Rd | 4 rlemon-0.2.1/rlemon/man/GetAndCheckTopologicalSort.Rd | 9 rlemon-0.2.1/rlemon/man/GetBipartitePartitions.Rd | 6 rlemon-0.2.1/rlemon/man/GraphSearch.Rd | 7 rlemon-0.2.1/rlemon/man/MaxCardinalityMatching.Rd | 4 rlemon-0.2.1/rlemon/man/MaxCardinalitySearch.Rd | 5 rlemon-0.2.1/rlemon/man/MaxClique.Rd | 4 rlemon-0.2.1/rlemon/man/MaxFlow.Rd | 7 rlemon-0.2.1/rlemon/man/MaxMatching.Rd | 4 rlemon-0.2.1/rlemon/man/MinCostArborescence.Rd | 8 rlemon-0.2.1/rlemon/man/MinCostFlow.Rd | 11 rlemon-0.2.1/rlemon/man/MinCut.Rd | 14 rlemon-0.2.1/rlemon/man/MinMeanCycle.Rd | 5 rlemon-0.2.1/rlemon/man/MinSpanningTree.Rd | 13 rlemon-0.2.1/rlemon/man/NetworkCirculation.Rd | 5 rlemon-0.2.1/rlemon/man/PlanarColoring.Rd | 7 rlemon-0.2.1/rlemon/man/PlanarDrawing.Rd | 6 rlemon-0.2.1/rlemon/man/PlanarEmbedding.Rd | 10 rlemon-0.2.1/rlemon/man/ShortestPath.Rd | 9 rlemon-0.2.1/rlemon/man/ShortestPathFromSource.Rd | 5 rlemon-0.2.1/rlemon/man/TravelingSalesperson.Rd | 4 rlemon-0.2.1/rlemon/man/lemon_runners.Rd | 8 rlemon-0.2.1/rlemon/tests/testthat/test-AllPairsMinCut.R | 7 rlemon-0.2.1/rlemon/tests/testthat/test-MaxCardinalityMatching.R | 9 rlemon-0.2.1/rlemon/tests/testthat/test-MaxCardinalitySearch.R | 1 rlemon-0.2.1/rlemon/tests/testthat/test-MaxMatching.R | 13 rlemon-0.2.1/rlemon/tests/testthat/test-MinCostArboresence.R | 12 rlemon-0.2.1/rlemon/tests/testthat/test-NetworkCirculation.R | 1 rlemon-0.2.1/rlemon/tests/testthat/test-Planarity.R | 19 rlemon-0.2.1/rlemon/tests/testthat/test-ShortestPathFromSource.R | 9 rlemon-0.2.1/rlemon/tests/testthat/test-approximation.R |only rlemon-0.2.1/rlemon/tests/testthat/test-connectivity.R |only rlemon-0.2.1/rlemon/tests/testthat/test-graphsearch.R |only rlemon-0.2.1/rlemon/tests/testthat/test-maxflow.R |only rlemon-0.2.1/rlemon/tests/testthat/test-mincostflow.R |only rlemon-0.2.1/rlemon/tests/testthat/test-mincut.R |only rlemon-0.2.1/rlemon/tests/testthat/test-minmeancycle.R |only rlemon-0.2.1/rlemon/tests/testthat/test-minspanningtree.R |only rlemon-0.2.1/rlemon/tests/testthat/test-shortestPath.R |only rlemon-0.2.1/rlemon/tests/testthat/test-travelingsalesperson.R |only 70 files changed, 768 insertions(+), 694 deletions(-)
Title: Bayesian Variable Selection Methods for Multivariate Data
Description: Bayesian variable selection methods for data with multivariate responses and multiple covariates. The package contains implementations of multivariate Bayesian variable selection methods for continuous data (Lee et al., Biometrics, 2017 <doi:10.1111/biom.12557>) and zero-inflated count data (Lee et al., Biostatistics, 2020 <doi:10.1093/biostatistics/kxy067>).
Author: Kyu Ha Lee, Mahlet G. Tadesse, Brent A. Coull, Jacqueline R. Starr
Maintainer: Kyu Ha Lee <klee15239@gmail.com>
Diff between mBvs versions 1.5 dated 2021-06-17 and 1.6 dated 2023-02-06
DESCRIPTION | 10 MD5 | 34 +- R/methods.R | 231 ++++------------ R/mvnBvs.R | 220 +++++++-------- R/mzipBvs.R | 581 ++++++++++++++++++++--------------------- man/mBvs-package.Rd | 4 man/mvnBvs.Rd | 19 - man/mzipBvs.Rd | 15 - src/MBVSfa.c | 13 src/MBVSfa_Updates.c | 3 src/MBVSus.c | 13 src/MBVSus_Updates.c | 3 src/mzipBVS_general.c | 2 src/mzipBVS_general_Updates.c | 10 src/mzip_restricted1.c | 3 src/mzip_restricted1_Updates.c | 7 src/mzip_restricted2.c | 2 src/mzip_restricted2_Updates.c | 10 18 files changed, 525 insertions(+), 655 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built
on top of the 'libuv' C library.
Author: Jim Hester [aut],
Hadley Wickham [aut],
Gabor Csardi [aut, cre],
libuv project contributors [cph] ,
Joyent, Inc. and other Node contributors [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between fs versions 1.6.0 dated 2023-01-23 and 1.6.1 dated 2023-02-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/Makevars | 2 +- src/Makevars.win | 4 +--- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bia [...truncated...]
Author: Ioannis Kosmidis [aut, cre] ,
Euloge Clovis Kenne Pagui [aut],
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.8.2 dated 2021-11-21 and 0.9 dated 2023-02-06
brglm2-0.8.2/brglm2/man/ordinal_superiority.Rd |only brglm2-0.8.2/brglm2/man/print.summary.brnb.Rd |only brglm2-0.9/brglm2/DESCRIPTION | 10 brglm2-0.9/brglm2/MD5 | 149 +++--- brglm2-0.9/brglm2/NAMESPACE | 5 brglm2-0.9/brglm2/NEWS.md | 20 brglm2-0.9/brglm2/R/bracl.R | 80 +-- brglm2-0.9/brglm2/R/brglm2-defunct.R | 23 brglm2-0.9/brglm2/R/brglm2-package.R | 103 +--- brglm2-0.9/brglm2/R/brglmControl.R | 178 +++---- brglm2-0.9/brglm2/R/brglmFit.R | 495 ++++++++------------- brglm2-0.9/brglm2/R/brmultinom.R | 172 +++---- brglm2-0.9/brglm2/R/brnb.R | 276 +++++------ brglm2-0.9/brglm2/R/data.R | 151 +++--- brglm2-0.9/brglm2/R/expo.R |only brglm2-0.9/brglm2/R/mis-link.R | 18 brglm2-0.9/brglm2/R/ordinal_superiority.R | 62 ++ brglm2-0.9/brglm2/R/utils.R | 10 brglm2-0.9/brglm2/R/warnings.R | 2 brglm2-0.9/brglm2/R/zzz_conventions.R | 2 brglm2-0.9/brglm2/README.md | 112 +++- brglm2-0.9/brglm2/build/partial.rdb |binary brglm2-0.9/brglm2/build/vignette.rds |binary brglm2-0.9/brglm2/data/aids.rda |only brglm2-0.9/brglm2/inst/CITATION | 4 brglm2-0.9/brglm2/inst/WORDLIST | 18 brglm2-0.9/brglm2/inst/doc/adjacent.html | 234 ++++++--- brglm2-0.9/brglm2/inst/doc/expo.R |only brglm2-0.9/brglm2/inst/doc/expo.Rmd |only brglm2-0.9/brglm2/inst/doc/expo.html |only brglm2-0.9/brglm2/inst/doc/iteration.Rmd | 2 brglm2-0.9/brglm2/inst/doc/iteration.html | 380 +++++++++++----- brglm2-0.9/brglm2/inst/doc/multinomial.html | 257 ++++++---- brglm2-0.9/brglm2/inst/doc/negativeBinomial.Rmd | 2 brglm2-0.9/brglm2/inst/doc/negativeBinomial.html | 235 ++++++--- brglm2-0.9/brglm2/inst/tinytest |only brglm2-0.9/brglm2/man/aids.Rd |only brglm2-0.9/brglm2/man/alligators.Rd | 27 - brglm2-0.9/brglm2/man/bracl.Rd | 48 +- brglm2-0.9/brglm2/man/brglm2-defunct.Rd | 25 - brglm2-0.9/brglm2/man/brglm2.Rd | 63 +- brglm2-0.9/brglm2/man/brglmControl.Rd | 150 +++--- brglm2-0.9/brglm2/man/brglmFit.Rd | 196 +++----- brglm2-0.9/brglm2/man/brmultinom.Rd | 80 +-- brglm2-0.9/brglm2/man/brnb.Rd | 98 +--- brglm2-0.9/brglm2/man/coalition.Rd | 26 - brglm2-0.9/brglm2/man/coef.brglmFit.Rd | 10 brglm2-0.9/brglm2/man/coef.brglmFit_expo.Rd |only brglm2-0.9/brglm2/man/coef.brnb.Rd | 10 brglm2-0.9/brglm2/man/confint.brglmFit.Rd | 4 brglm2-0.9/brglm2/man/confint.brmultinom.Rd | 4 brglm2-0.9/brglm2/man/confint.brnb.Rd | 4 brglm2-0.9/brglm2/man/endometrial.Rd | 42 - brglm2-0.9/brglm2/man/expo.brglmFit.Rd |only brglm2-0.9/brglm2/man/lizards.Rd | 40 - brglm2-0.9/brglm2/man/mis.Rd | 16 brglm2-0.9/brglm2/man/ordinal_superiority.bracl.Rd |only brglm2-0.9/brglm2/man/predict.bracl.Rd | 19 brglm2-0.9/brglm2/man/predict.brmultinom.Rd | 22 brglm2-0.9/brglm2/man/residuals.brmultinom.Rd | 12 brglm2-0.9/brglm2/man/simulate.brmultinom.Rd | 24 - brglm2-0.9/brglm2/man/simulate.brnb.Rd | 11 brglm2-0.9/brglm2/man/stemcell.Rd | 26 - brglm2-0.9/brglm2/man/summary.brglmFit.Rd | 21 brglm2-0.9/brglm2/man/summary.brnb.Rd | 32 - brglm2-0.9/brglm2/man/vcov.brglmFit.Rd | 14 brglm2-0.9/brglm2/man/vcov.brnb.Rd | 19 brglm2-0.9/brglm2/vignettes/brglm2.bib | 13 brglm2-0.9/brglm2/vignettes/expo.Rmd |only brglm2-0.9/brglm2/vignettes/iteration.Rmd | 2 brglm2-0.9/brglm2/vignettes/negativeBinomial.Rmd | 2 71 files changed, 2193 insertions(+), 1867 deletions(-)
Title: Adversarial Random Forests
Description: Adversarial random forests (ARFs) recursively partition data into
fully factorized leaves, where features are jointly independent. The
procedure is iterative, with alternating rounds of generation and
discrimination. Data becomes increasingly realistic at each round, until
original and synthetic samples can no longer be reliably distinguished.
This is useful for several unsupervised learning tasks, such as density
estimation and data synthesis. Methods for both are implemented in this
package. ARFs naturally handle unstructured data with mixed continuous and
categorical covariates. They inherit many of the benefits of random forests,
including speed, flexibility, and solid performance with default parameters.
For details, see Watson et al. (2022) <arXiv:2205.09435>.
Author: Marvin N. Wright [aut, cre] ,
David S. Watson [aut]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between arf versions 0.1.2 dated 2022-12-16 and 0.1.3 dated 2023-02-06
DESCRIPTION | 10 MD5 | 30 + NEWS.md |only R/adversarial_rf.R | 107 +++--- R/forde.R | 140 ++++++-- R/forge.R | 9 R/lik.R | 24 - R/utils.R |only README.md | 46 +- inst/doc/vignette.R | 46 ++ inst/doc/vignette.Rmd | 79 +++- inst/doc/vignette.html | 610 +++++++++++++++++++++---------------- man/adversarial_rf.Rd | 8 man/col_rename.Rd |only man/figures |only man/forde.Rd | 25 - tests/testthat/test-return_types.R | 8 vignettes/vignette.Rmd | 79 +++- 18 files changed, 773 insertions(+), 448 deletions(-)
Title: The Acute COPD Exacerbation Prediction Tool (ACCEPT)
Description: Allows clinicians to predict the rate and severity of future acute exacerbation in Chronic Obstructive Pulmonary Disease (COPD) patients, based on the clinical prediction models published in Adibi et al. (2020) <doi:10.1016/S2213-2600(19)30397-2> and Safari et al. (2022) <doi:10.1016/j.eclinm.2022.101574>.
Author: Amin Adibi [aut, cre],
Mohsen Sadatsafavi [aut, cph],
Abdollah Safari [aut],
Ainsleigh Hill [aut]
Maintainer: Amin Adibi <adibi@alumni.ubc.ca>
Diff between accept versions 0.9.1 dated 2022-07-15 and 1.0.0 dated 2023-02-06
DESCRIPTION | 13 +- MD5 | 22 ++--- NAMESPACE | 1 NEWS.md | 7 + R/charts.R | 5 - R/predict.R | 206 ++++++++++++++++++++++++++++++++++++++++------- R/sysdata.rda |only README.md | 14 ++- man/accept.Rd | 26 ++--- man/accept1.Rd |only man/plotExacerbations.Rd | 2 man/plotHeatMap.Rd | 2 man/predictCountProb.Rd | 2 13 files changed, 227 insertions(+), 73 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.1-6 dated 2017-02-20 and 0.1-7 dated 2023-02-06
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- man/w3c_markup_validate.Rd | 4 ++-- man/w3c_markup_validate_baseurl.Rd | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of
information and tables optionally based on search words from
PDF (Portable Document Format) files and enables the visualization
of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Diff between PDE versions 1.4.2 dated 2022-12-12 and 1.4.3 dated 2023-02-06
DESCRIPTION | 6 MD5 | 20 NEWS.md | 8 R/PDE.R | 600 +++++----- README.md | 7 inst/doc/PDE.Rmd | 7 inst/doc/PDE.html | 126 +- inst/examples/tsvs/PDE_parameters_v1.4_all_files+-0.tsv | 1 vignettes/PDE.Rmd | 7 vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_MTX_example.png |binary vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_empty.png |binary 11 files changed, 439 insertions(+), 343 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut, cre],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb],
Jordan Mark Barbone [ctb]
Maintainer: Philipp Schauberger <philipp@schauberger.co.at>
Diff between openxlsx versions 4.2.5.1 dated 2022-10-24 and 4.2.5.2 dated 2023-02-06
DESCRIPTION | 8 MD5 | 18 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/Formatting.R | 556 ++++++++--------- inst/doc/Formatting.html | 1115 +++++++++++++++++++++-------------- inst/doc/Introduction.R | 842 +++++++++++++------------- inst/doc/Introduction.html | 1413 +++++++++++++++++++++++++-------------------- src/read_workbook.cpp | 6 src/write_data.cpp | 2 10 files changed, 2184 insertions(+), 1776 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-08 2.4.2
Title: R Interface to 'pytorch''s 'torchaudio'
Description: Provides access to datasets, models and processing
facilities for deep learning in audio.
Author: Sigrid Keydana [aut, cre],
Athos Damiani [aut],
Daniel Falbel [aut]
Maintainer: Sigrid Keydana <sigrid@posit.co>
Diff between torchaudio versions 0.2.2 dated 2023-01-23 and 0.3.0 dated 2023-02-06
torchaudio-0.2.2/torchaudio/R/RcppExports.R |only torchaudio-0.2.2/torchaudio/R/backend-audiofile.R |only torchaudio-0.2.2/torchaudio/R/backend-tuneR_backend.R |only torchaudio-0.2.2/torchaudio/R/temp.R |only torchaudio-0.2.2/torchaudio/R/tranforms.R |only torchaudio-0.2.2/torchaudio/man/audiofile_loader.Rd |only torchaudio-0.2.2/torchaudio/man/backend_utils_list_audio_backends.Rd |only torchaudio-0.2.2/torchaudio/man/info.Rd |only torchaudio-0.2.2/torchaudio/man/mp3_info.Rd |only torchaudio-0.2.2/torchaudio/man/set_audio_backend.Rd |only torchaudio-0.2.2/torchaudio/man/torchaudio_loader.Rd |only torchaudio-0.2.2/torchaudio/man/wav_info.Rd |only torchaudio-0.2.2/torchaudio/src |only torchaudio-0.2.2/torchaudio/tests/testthat/test-backend-audiofile.R |only torchaudio-0.2.2/torchaudio/tests/testthat/test-backend-av_backend.R |only torchaudio-0.2.2/torchaudio/tests/testthat/test-backend-no_backend.R |only torchaudio-0.2.2/torchaudio/tests/testthat/test-backend-tuneR_backend.R |only torchaudio-0.3.0/torchaudio/DESCRIPTION | 13 torchaudio-0.3.0/torchaudio/MD5 | 103 +-- torchaudio-0.3.0/torchaudio/NAMESPACE | 14 torchaudio-0.3.0/torchaudio/NEWS.md | 30 torchaudio-0.3.0/torchaudio/R/backend-av.R | 73 -- torchaudio-0.3.0/torchaudio/R/backend-common.R | 332 ++-------- torchaudio-0.3.0/torchaudio/R/backend-tuneR.R |only torchaudio-0.3.0/torchaudio/R/backend-utils.R | 15 torchaudio-0.3.0/torchaudio/R/dataset-cmuarctic.R | 3 torchaudio-0.3.0/torchaudio/R/dataset-speechcommands.R | 3 torchaudio-0.3.0/torchaudio/R/dataset-yesno.R | 3 torchaudio-0.3.0/torchaudio/R/torchaudio-package.R | 12 torchaudio-0.3.0/torchaudio/R/transforms.R |only torchaudio-0.3.0/torchaudio/build/vignette.rds |binary torchaudio-0.3.0/torchaudio/inst/doc/audio_preprocessing_tutorial.html | 13 torchaudio-0.3.0/torchaudio/man/av_loader.Rd | 14 torchaudio-0.3.0/torchaudio/man/list_audio_backends.Rd |only torchaudio-0.3.0/torchaudio/man/torchaudio_info.Rd |only torchaudio-0.3.0/torchaudio/man/torchaudio_load.Rd | 58 - torchaudio-0.3.0/torchaudio/man/transform__axismasking.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_amplitude_to_db.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_complex_norm.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_compute_deltas.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_fade.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_frequencymasking.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_inverse_mel_scale.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_mel_scale.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_mel_spectrogram.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_mfcc.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_mu_law_decoding.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_mu_law_encoding.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_resample.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_sliding_window_cmn.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_spectrogram.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_time_stretch.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_timemasking.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_to_tensor.Rd | 18 torchaudio-0.3.0/torchaudio/man/transform_vad.Rd | 2 torchaudio-0.3.0/torchaudio/man/transform_vol.Rd | 2 torchaudio-0.3.0/torchaudio/man/tuneR_loader.Rd | 16 torchaudio-0.3.0/torchaudio/tests/testthat/test-backend-av.R |only torchaudio-0.3.0/torchaudio/tests/testthat/test-backend-common.R | 141 ---- torchaudio-0.3.0/torchaudio/tests/testthat/test-backend-tuneR.R |only torchaudio-0.3.0/torchaudio/tests/testthat/test-dataset-speechcommands.R | 7 torchaudio-0.3.0/torchaudio/tools |only 62 files changed, 268 insertions(+), 638 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray <stephane.dray@univ-lyon1.fr>, Anne-Beatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sebastien Ollier, D [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-20 dated 2022-11-01 and 1.7-22 dated 2023-02-06
ChangeLog | 177 + DESCRIPTION | 10 MD5 | 69 NAMESPACE | 17 R/RV.randtest.R |only R/RVintra.randtest.R |only R/RcppExports.R |only R/dist.ktab.R | 6366 ++++++++++++++++++++---------------------- R/kdisteuclid.R | 3 R/mantel.randtest.R | 7 R/procuste.R | 2 R/procuste.randtest.R | 24 R/randtest.between.R | 5 R/randtest.coinertia.R | 9 R/randtest.discrimin.R | 2 R/s.label.R | 2 inst/include |only inst/pictures/atyacarto.pnm |binary inst/pictures/atyadigi.pnm |binary inst/pictures/avijonseau.pnm |binary inst/pictures/avijonsrou.pnm |binary inst/pictures/avijonsveg.pnm |binary inst/pictures/avijonsvil.pnm |binary inst/pictures/butterfly.pnm |binary inst/pictures/capitales.pnm |binary inst/pictures/fatala.pnm |binary inst/pictures/france_sm00.pnm |binary inst/pictures/ireland.pnm |binary inst/pictures/paris.pnm |binary inst/pictures/sarcelles.pnm |binary inst/pictures/tintoodiel.pnm |binary man/RV.randtest.Rd |only man/RVintra.randtest.Rd |only man/ade4-internal.Rd | 11 man/presid2002.Rd | 2 src/Makevars | 4 src/RcppExports.cpp |only src/ade4libCpp.cpp |only src/init.c | 31 src/testsCpp.cpp |only 40 files changed, 3500 insertions(+), 3241 deletions(-)
Title: Inference Tool for Antibody Haplotype
Description: Infers V-D-J haplotypes and gene deletions from AIRR-seq data for Ig and TR chains,
based on J, D, or V genes as anchor, by adapting a Bayesian framework.
It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene.
Citation:
Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>.
Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.
Author: Ayelet Peres [aut, cre],
Moriah Gidoni [aut],
Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <peresay@biu.ac.il>
Diff between rabhit versions 0.2.4 dated 2022-09-22 and 0.2.5 dated 2023-02-06
rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_a08e7ca6b9a86629fe0e849373707843.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_a08e7ca6b9a86629fe0e849373707843.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_a08e7ca6b9a86629fe0e849373707843.rdx |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_746cf0fdfdaba4ed6f84309289262c31.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_746cf0fdfdaba4ed6f84309289262c31.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_746cf0fdfdaba4ed6f84309289262c31.rdx |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_338a6b89bd12f96ba6702114d25f1edb.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_338a6b89bd12f96ba6702114d25f1edb.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_338a6b89bd12f96ba6702114d25f1edb.rdx |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_966f6a75bf1e076ada86879e7de41f02.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_966f6a75bf1e076ada86879e7de41f02.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_966f6a75bf1e076ada86879e7de41f02.rdx |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_ea80b68e88a1759c962086f6dd09a22e.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_ea80b68e88a1759c962086f6dd09a22e.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_ea80b68e88a1759c962086f6dd09a22e.rdx |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_069d08e4135a5eda4e99b097c6da8af2.RData |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_069d08e4135a5eda4e99b097c6da8af2.rdb |only rabhit-0.2.4/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_069d08e4135a5eda4e99b097c6da8af2.rdx |only rabhit-0.2.5/rabhit/DESCRIPTION | 8 - rabhit-0.2.5/rabhit/MD5 | 64 +++++----- rabhit-0.2.5/rabhit/NAMESPACE | 10 - rabhit-0.2.5/rabhit/NEWS.md | 7 + rabhit-0.2.5/rabhit/R/graphic_functions.R | 53 ++++---- rabhit-0.2.5/rabhit/R/internal_functions.R | 2 rabhit-0.2.5/rabhit/R/rabhit.R | 12 - rabhit-0.2.5/rabhit/build/vignette.rds |binary rabhit-0.2.5/rabhit/inst/doc/RAbHIT-vignette.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_28d3f4207ffb92882179bdf5836f4383.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_28d3f4207ffb92882179bdf5836f4383.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-10_28d3f4207ffb92882179bdf5836f4383.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_699273935e0a29d7fc47f3c881cb47f5.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_699273935e0a29d7fc47f3c881cb47f5.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-13_699273935e0a29d7fc47f3c881cb47f5.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_0da31ed1bac7aca3aa0b4d6841e3d57d.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_0da31ed1bac7aca3aa0b4d6841e3d57d.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-14_0da31ed1bac7aca3aa0b4d6841e3d57d.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_8c3a53c4f1d985d05f5872318669df3f.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_8c3a53c4f1d985d05f5872318669df3f.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-20_8c3a53c4f1d985d05f5872318669df3f.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_65c82eb0877685fc44935d31fd0d3e06.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_65c82eb0877685fc44935d31fd0d3e06.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-21_65c82eb0877685fc44935d31fd0d3e06.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_653a8eea7cef350e23462297a7da38a3.RData |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_653a8eea7cef350e23462297a7da38a3.rdb |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_cache/latex/unnamed-chunk-9_653a8eea7cef350e23462297a7da38a3.rdx |only rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-10-1.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-12-1.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-19-1.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-21-1.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-4-1.pdf |binary rabhit-0.2.5/rabhit/vignettes/RAbHIT-vignette_files/figure-latex/unnamed-chunk-8-1.pdf |binary 51 files changed, 77 insertions(+), 79 deletions(-)
Title: Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Description: Helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich <https://fgcz.ch>. We use this package
mainly for prototyping, teaching, and having fun with proteomics data.
But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] ,
Jonas Grossmann [aut] ,
Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
Diff between protViz versions 0.7.3 dated 2022-04-04 and 0.7.7 dated 2023-02-06
.Rinstignore | 1 DESCRIPTION | 6 MD5 | 40 +++--- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 +-- inst/doc/ADP-Ribosylated-peptides.pdf |binary inst/doc/PTM_MarkerFinder.pdf |binary inst/doc/poster.pdf |binary inst/doc/protViz.R | 225 +++++++++++++++++++--------------- inst/doc/protViz.Rnw | 198 +++++++++++++++++------------ inst/doc/protViz.pdf |binary man/AA.Rd | 6 man/ADPR.Rd | 4 man/peakplot.Rd | 18 +- src/aa2mass.cpp | 5 src/base/ms/deisotoper.h | 6 src/computeFragmentIons.c | 24 +-- src/computeParentIonMass.c | 2 src/fasta.cpp | 3 vignettes/protViz.Rnw | 198 +++++++++++++++++------------ 22 files changed, 429 insertions(+), 329 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52,
<https://journals.sagepub.com/doi/full/10.1177/1094428115584005>).
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates [...truncated...]
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 3.2.1 dated 2022-09-15 and 3.3.0 dated 2023-02-06
DESCRIPTION | 8 - MD5 | 40 ++--- NAMESPACE | 6 R/nca.R | 22 +- R/nca_outliers.R | 384 ++++++++++++++++++++++++++++++++++++------------- R/nca_output.R | 6 R/nca_plotly.R | 20 ++ R/nca_tests.R | 12 - R/p_bottleneck.R | 4 R/p_bottleneck_table.R | 11 - R/p_constants.R | 1 R/p_loop_data.R | 8 - R/p_nca_c_lp.R | 2 R/p_nca_sfa.R | 5 R/p_scope.R | 16 +- R/p_utils.R | 228 ++++++++++++++++------------- R/p_validate.R | 25 +-- man/NCA-package.Rd | 4 man/nca_analysis.Rd | 2 man/nca_outliers.Rd | 32 +++- man/nca_output.Rd | 4 21 files changed, 546 insertions(+), 294 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.3.4 dated 2022-12-14 and 1.3.6 dated 2023-02-06
jsmodule-1.3.4/jsmodule/man/jsRepeatedGadjet.Rd |only jsmodule-1.3.6/jsmodule/DESCRIPTION | 12 +- jsmodule-1.3.6/jsmodule/MD5 | 20 ++-- jsmodule-1.3.6/jsmodule/NAMESPACE | 2 jsmodule-1.3.6/jsmodule/NEWS.md | 16 +++ jsmodule-1.3.6/jsmodule/R/jsRepeatedGadget.R | 18 +-- jsmodule-1.3.6/jsmodule/R/kaplan.R | 2 jsmodule-1.3.6/jsmodule/R/roc.R | 52 +++++----- jsmodule-1.3.6/jsmodule/build/vignette.rds |binary jsmodule-1.3.6/jsmodule/inst/doc/jsmodule.html | 115 +++++++++++------------- jsmodule-1.3.6/jsmodule/man/jsRepeatedAddin.Rd | 8 - jsmodule-1.3.6/jsmodule/man/jsRepeatedGadget.Rd |only 12 files changed, 132 insertions(+), 113 deletions(-)
Title: Generation of Code Names for Organizations, People, Projects,
and Whatever Else
Description: This creates code names that a user can consider for their organizations, their projects, themselves, people
in their organizations or projects, or whatever else. The user can also supply a numeric seed (and even a character seed)
for maximum reproducibility. Use is simple and the code names produced come in various types too, contingent on what the
user may be desiring as a code name or nickname.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between codename versions 0.4.0 dated 2021-09-07 and 0.5.0 dated 2023-02-06
DESCRIPTION | 8 +-- MD5 | 24 ++++----- NEWS.md | 21 ++++---- R/codename.R | 74 ++++++++++++++++++++++++---- R/codename_message.R | 5 + R/data.R | 16 ++++++ R/variety_pack.R | 4 - R/zzz.R | 2 README.md | 125 +++++++++++++++++++++++++++++++----------------- data/nicka_blocks.rda |only man/codename.Rd | 43 ++++++++++++++-- man/codename_message.Rd | 3 - man/nicka_blocks.Rd |only man/variety_pack.Rd | 2 14 files changed, 240 insertions(+), 87 deletions(-)
Title: Spatial and Environmental Blocking for K-Fold and LOO
Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre],
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 2.1.4 dated 2021-06-17 and 3.0-0 dated 2023-02-06
blockCV-2.1.4/blockCV/NEWS.md |only blockCV-2.1.4/blockCV/R/helper_functions.R |only blockCV-2.1.4/blockCV/README.md |only blockCV-2.1.4/blockCV/inst/doc/BlockCV_for_SDM.R |only blockCV-2.1.4/blockCV/inst/doc/BlockCV_for_SDM.Rmd |only blockCV-2.1.4/blockCV/inst/doc/BlockCV_for_SDM.html |only blockCV-2.1.4/blockCV/inst/extdata/PA.csv |only blockCV-2.1.4/blockCV/inst/extdata/PB.csv |only blockCV-2.1.4/blockCV/inst/extdata/awt.grd |only blockCV-2.1.4/blockCV/inst/extdata/awt.gri |only blockCV-2.1.4/blockCV/man/figures/logo.png |only blockCV-2.1.4/blockCV/man/figures/variogram.jpeg |only blockCV-2.1.4/blockCV/tests/testthat/testBuffering.R |only blockCV-2.1.4/blockCV/tests/testthat/testData.R |only blockCV-2.1.4/blockCV/tests/testthat/testEnvBlock.R |only blockCV-2.1.4/blockCV/tests/testthat/testHelper_function.R |only blockCV-2.1.4/blockCV/tests/testthat/testSpatialAutoRange.R |only blockCV-2.1.4/blockCV/tests/testthat/testSpatialBlock.R |only blockCV-2.1.4/blockCV/vignettes/BlockCV_for_SDM.Rmd |only blockCV-3.0-0/blockCV/DESCRIPTION | 33 blockCV-3.0-0/blockCV/MD5 | 98 +- blockCV-3.0-0/blockCV/NAMESPACE | 28 blockCV-3.0-0/blockCV/R/RcppExports.R |only blockCV-3.0-0/blockCV/R/blockCV-package.R |only blockCV-3.0-0/blockCV/R/blockCV.R | 25 blockCV-3.0-0/blockCV/R/blocking.R | 314 +++++-- blockCV-3.0-0/blockCV/R/buffering.R | 197 ---- blockCV-3.0-0/blockCV/R/checks.R |only blockCV-3.0-0/blockCV/R/cv_buffer.R |only blockCV-3.0-0/blockCV/R/cv_cluster.R |only blockCV-3.0-0/blockCV/R/cv_explorer.R |only blockCV-3.0-0/blockCV/R/cv_nndm.R |only blockCV-3.0-0/blockCV/R/cv_plot.R |only blockCV-3.0-0/blockCV/R/cv_similarity.R |only blockCV-3.0-0/blockCV/R/cv_spatial.R |only blockCV-3.0-0/blockCV/R/cv_spatial_autocor.R |only blockCV-3.0-0/blockCV/R/environBlock.R | 207 +---- blockCV-3.0-0/blockCV/R/explorer.R | 410 ---------- blockCV-3.0-0/blockCV/R/spatialAutoRange.R | 298 +------ blockCV-3.0-0/blockCV/R/zzz.R |only blockCV-3.0-0/blockCV/build/vignette.rds |binary blockCV-3.0-0/blockCV/inst/CITATION | 15 blockCV-3.0-0/blockCV/inst/doc/tutorial_1.R |only blockCV-3.0-0/blockCV/inst/doc/tutorial_1.Rmd |only blockCV-3.0-0/blockCV/inst/doc/tutorial_1.html |only blockCV-3.0-0/blockCV/inst/extdata/au |only blockCV-3.0-0/blockCV/inst/extdata/species.csv |only blockCV-3.0-0/blockCV/man/blockCV.Rd | 23 blockCV-3.0-0/blockCV/man/buffering.Rd | 70 - blockCV-3.0-0/blockCV/man/cv_block_size.Rd |only blockCV-3.0-0/blockCV/man/cv_buffer.Rd |only blockCV-3.0-0/blockCV/man/cv_cluster.Rd |only blockCV-3.0-0/blockCV/man/cv_nndm.Rd |only blockCV-3.0-0/blockCV/man/cv_plot.Rd |only blockCV-3.0-0/blockCV/man/cv_similarity.Rd |only blockCV-3.0-0/blockCV/man/cv_spatial.Rd |only blockCV-3.0-0/blockCV/man/cv_spatial_autocor.Rd |only blockCV-3.0-0/blockCV/man/envBlock.Rd | 65 - blockCV-3.0-0/blockCV/man/figures/roc_rf.csv |only blockCV-3.0-0/blockCV/man/figures/rocpr.jpeg |binary blockCV-3.0-0/blockCV/man/foldExplorer.Rd | 59 - blockCV-3.0-0/blockCV/man/rangeExplorer.Rd | 52 - blockCV-3.0-0/blockCV/man/spatialAutoRange.Rd | 76 - blockCV-3.0-0/blockCV/man/spatialBlock.Rd | 103 -- blockCV-3.0-0/blockCV/src |only blockCV-3.0-0/blockCV/tests/testthat.R | 8 blockCV-3.0-0/blockCV/tests/testthat/test-cv_buffer.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_cluster.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_nndm.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_plot.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_similarity.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_spatial.R |only blockCV-3.0-0/blockCV/tests/testthat/test-cv_spatial_autocor.R |only blockCV-3.0-0/blockCV/tests/testthat/test-data.R |only blockCV-3.0-0/blockCV/tests/testthat/test-v2-functions.R |only blockCV-3.0-0/blockCV/vignettes/tutorial_1.Rmd |only 76 files changed, 558 insertions(+), 1523 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre],
Jack Davison [aut],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.14 dated 2023-01-25 and 2.15 dated 2023-02-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 ++++++-- R/importUKAQ.R | 2 +- R/polarPlot.R | 12 ++++++------ inst/CITATION | 42 +++++++++++++++++++++--------------------- 6 files changed, 43 insertions(+), 39 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database.
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.6 dated 2022-10-05 and 0.9.7 dated 2023-02-06
worldmet-0.9.6/worldmet/man/figures/map.png |only worldmet-0.9.6/worldmet/man/figures/windRose-1.png |only worldmet-0.9.6/worldmet/man/worldmet.Rd |only worldmet-0.9.7/worldmet/DESCRIPTION | 22 worldmet-0.9.7/worldmet/MD5 | 39 - worldmet-0.9.7/worldmet/NAMESPACE | 19 worldmet-0.9.7/worldmet/R/exportADMS.R | 79 +- worldmet-0.9.7/worldmet/R/getMeta.R | 332 +++++---- worldmet-0.9.7/worldmet/R/metNOAA.R | 511 +++++++------- worldmet-0.9.7/worldmet/R/weatherCodes.R | 25 worldmet-0.9.7/worldmet/R/worldmet-package.R | 51 - worldmet-0.9.7/worldmet/README.md | 122 +-- worldmet-0.9.7/worldmet/build |only worldmet-0.9.7/worldmet/data/weatherCodes.rda |binary worldmet-0.9.7/worldmet/inst |only worldmet-0.9.7/worldmet/man/exportADMS.Rd | 16 worldmet-0.9.7/worldmet/man/figures/README-map.png |only worldmet-0.9.7/worldmet/man/figures/README-windRose-1.png |only worldmet-0.9.7/worldmet/man/getMeta.Rd | 75 +- worldmet-0.9.7/worldmet/man/getMetaLive.Rd | 4 worldmet-0.9.7/worldmet/man/importNOAA.Rd | 59 - worldmet-0.9.7/worldmet/man/weatherCodes.Rd | 7 worldmet-0.9.7/worldmet/man/worldmet-package.Rd |only worldmet-0.9.7/worldmet/vignettes |only 24 files changed, 717 insertions(+), 644 deletions(-)
Title: Stable Iterative Variable Selection
Description: An iterative feature selection method (manuscript submitted) that
internally utilizes various Machine Learning methods that have embedded
feature reduction in order to shrink down the feature space into a small
and yet robust set.
Author: Mehrad Mahmoudian [aut, cre] ,
Mikko Venaelaeinen [aut, rev] ,
Riku Klen [aut, ths] ,
Laura Elo [aut, ths, fnd]
Maintainer: Mehrad Mahmoudian <mehrad.mahmoudian@utu.fi>
Diff between sivs versions 0.2.6 dated 2023-02-02 and 0.2.7 dated 2023-02-06
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 5 + R/plot.sivs.R | 6 - R/sivs.R | 3 R/suggest.R | 22 +++- inst/doc/vignette_simple_usage.html | 177 ------------------------------------ man/suggest.Rd | 2 8 files changed, 37 insertions(+), 200 deletions(-)
Title: Convenience Functions for Psychology
Description: Make your workflow faster and easier. Easily customizable
plots (via 'ggplot2'), nice APA tables (following the style of the
*American Psychological Association*) exportable to Word (via
'flextable'), easily run statistical tests or check assumptions, and
automatize various other tasks.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between rempsyc versions 0.1.0 dated 2022-11-01 and 0.1.1 dated 2023-02-06
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rempsyc-0.1.1/rempsyc/inst/doc/circles.html | 120 rempsyc-0.1.1/rempsyc/inst/doc/contrasts.R | 253 + rempsyc-0.1.1/rempsyc/inst/doc/contrasts.Rmd | 699 ++-- rempsyc-0.1.1/rempsyc/inst/doc/contrasts.html | 331 +- rempsyc-0.1.1/rempsyc/inst/doc/moderation.R | 20 rempsyc-0.1.1/rempsyc/inst/doc/moderation.Rmd | 406 +- rempsyc-0.1.1/rempsyc/inst/doc/moderation.html | 619 +-- rempsyc-0.1.1/rempsyc/inst/doc/randomize.R | 2 rempsyc-0.1.1/rempsyc/inst/doc/randomize.Rmd | 322 +- rempsyc-0.1.1/rempsyc/inst/doc/randomize.html | 173 - rempsyc-0.1.1/rempsyc/inst/doc/scatter.html | 115 rempsyc-0.1.1/rempsyc/inst/doc/t-test.R | 11 rempsyc-0.1.1/rempsyc/inst/doc/t-test.Rmd | 333 +- rempsyc-0.1.1/rempsyc/inst/doc/t-test.html | 546 +-- rempsyc-0.1.1/rempsyc/inst/doc/table.R | 31 rempsyc-0.1.1/rempsyc/inst/doc/table.Rmd | 701 ++-- rempsyc-0.1.1/rempsyc/inst/doc/table.html | 1229 +++---- rempsyc-0.1.1/rempsyc/inst/doc/violin.html | 143 rempsyc-0.1.1/rempsyc/man/best_duplicate.Rd | 68 rempsyc-0.1.1/rempsyc/man/extract_duplicates.Rd | 83 rempsyc-0.1.1/rempsyc/man/figures/README-nice_contrasts-1.png |binary rempsyc-0.1.1/rempsyc/man/figures/README-nice_lm-1.png |only rempsyc-0.1.1/rempsyc/man/figures/README-nice_lm_slopes-1.png |only rempsyc-0.1.1/rempsyc/man/figures/README-nice_mod-1.png |binary rempsyc-0.1.1/rempsyc/man/figures/README-nice_normality-1.png |binary rempsyc-0.1.1/rempsyc/man/figures/README-nice_slopes-1.png |binary rempsyc-0.1.1/rempsyc/man/figures/README-nice_violin-1.png |binary rempsyc-0.1.1/rempsyc/man/figures/README-plot_outliers-1.png |only rempsyc-0.1.1/rempsyc/man/figures/README-plot_outliers-2.png |only rempsyc-0.1.1/rempsyc/man/figures/logo-image.png |only rempsyc-0.1.1/rempsyc/man/figures/logo.png |binary rempsyc-0.1.1/rempsyc/man/find_mad.Rd | 123 rempsyc-0.1.1/rempsyc/man/nice_assumptions.Rd | 96 rempsyc-0.1.1/rempsyc/man/nice_contrasts.Rd | 23 rempsyc-0.1.1/rempsyc/man/nice_density.Rd | 3 rempsyc-0.1.1/rempsyc/man/nice_lm.Rd | 21 rempsyc-0.1.1/rempsyc/man/nice_lm_contrasts.Rd |only rempsyc-0.1.1/rempsyc/man/nice_lm_slopes.Rd | 27 rempsyc-0.1.1/rempsyc/man/nice_mod.Rd | 18 rempsyc-0.1.1/rempsyc/man/nice_na.Rd | 182 - 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Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible combinatorial iterators
implemented in C++ for solving problems in combinatorics and
computational mathematics. Utilizes the RMatrix class from 'RcppParallel'
for thread safety. There are combination/permutation functions with
constraint parameters that allow for generation of all results of a vector
meeting specific criteria (e.g. generating integer partitions/compositions
or finding all combinations such that the sum is between two bounds).
Capable of generating specific combinations/permutations (e.g. retrieve
only the nth lexicographical result) which sets up nicely for
parallelization as well as random sampling. Gmp support permits exploration
where the total number of results is large (e.g. comboSample(10000, 500,
n = 4)). Additionally, there are several high performance number theoretic
functions that are useful for problems common in computational mathematics.
Some of these functions make use of the fast integer division library
'libdiv [...truncated...]
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.6.0 dated 2022-08-15 and 2.7.1 dated 2023-02-06
RcppAlgos-2.6.0/RcppAlgos/inst/include/CleanConvert.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/Cpp14MakeUnique.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/ImportExportMPZ.h |only RcppAlgos-2.6.0/RcppAlgos/src/CleanConvert.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/ImportExportMPZ.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/PollardRho.cpp |only RcppAlgos-2.7.1/RcppAlgos/DESCRIPTION | 19 RcppAlgos-2.7.1/RcppAlgos/MD5 | 475 ++-- RcppAlgos-2.7.1/RcppAlgos/NEWS.md | 12 RcppAlgos-2.7.1/RcppAlgos/README.md | 2 RcppAlgos-2.7.1/RcppAlgos/inst/NEWS.Rd | 18 RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombPermConstraints.Rmd | 243 +- RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombPermConstraints.html | 385 ++-- RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombinatorialSampling.Rmd | 189 - RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombinatorialSampling.html | 394 ++-- RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombinatoricsIterators.Rmd | 434 ++-- RcppAlgos-2.7.1/RcppAlgos/inst/doc/CombinatoricsIterators.html | 953 +++++----- RcppAlgos-2.7.1/RcppAlgos/inst/doc/ComputationalMathematics.Rmd | 205 +- RcppAlgos-2.7.1/RcppAlgos/inst/doc/ComputationalMathematics.html | 480 ++--- RcppAlgos-2.7.1/RcppAlgos/inst/doc/GeneralCombinatorics.Rmd | 146 - RcppAlgos-2.7.1/RcppAlgos/inst/doc/GeneralCombinatorics.html | 575 +++--- RcppAlgos-2.7.1/RcppAlgos/inst/doc/HighPerformanceBenchmarks.Rmd | 249 +- RcppAlgos-2.7.1/RcppAlgos/inst/doc/HighPerformanceBenchmarks.html | 363 +-- RcppAlgos-2.7.1/RcppAlgos/inst/doc/OtherCombinatorics.Rmd | 138 - RcppAlgos-2.7.1/RcppAlgos/inst/doc/OtherCombinatorics.html | 305 +-- RcppAlgos-2.7.1/RcppAlgos/inst/doc/SubsetSum.Rmd | 174 + RcppAlgos-2.7.1/RcppAlgos/inst/doc/SubsetSum.html | 608 +++--- RcppAlgos-2.7.1/RcppAlgos/inst/include/CheckReturn.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ClassUtils.h | 41 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboApplyClass.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboClass.h | 13 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboResClass.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/GetPrevCombPerm.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/GetPrevCombPermApply.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/NextCombinatorics.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/PrevCombinatorics.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/BigComboCount.h | 13 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationResults.h | 30 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsDistinct.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsMultiset.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsRep.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboCount.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboDistinctApply.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboManager.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboMultisetApply.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboRepApply.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboResGlue.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboResMain.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/NextComboSection.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/NthCombination.h | 16 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/RankCombination.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ThreadSafeComb.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/CombinatoricsResGlue.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComboCartesian.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComboGroupsUtils.h | 12 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComputedCount.h | 13 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/CnstrntsSpecialClass.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/CnstrntsToRClass.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsClass.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsDistinct.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsGeneral.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsMultiset.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsRep.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsSpecial.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsTypes.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/ConstraintsUtils.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/GetContraints.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/PartitionsEsqueDistinct.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/PartitionsEsqueMultiset.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/PartitionsEsqueRep.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/UserConstraintFuns.h | 5 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RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimesSegSieve.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/Wheel.h | 493 ++--- RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/libdivide.h | 377 ++- RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/BigPartsCountDistinct.h | 30 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/BigPartsCountRep.h | 24 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/BigPartsCountSection.h | 11 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/CompositionsRep.h | 16 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/NextComposition.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/NextPartition.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/NthPartition.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsClass.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsCount.h | 35 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsCountDistinct.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsCountMultiset.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsCountRep.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsCountSection.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsDesign.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsDistinct.h | 41 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsManager.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsMultiset.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsRep.h | 29 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsTypes.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsUtils.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/RankPartition.h | 8 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/ThreadSafeParts.h | 15 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/BigPermuteCount.h | 13 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RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteRepApply.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteResGlue.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteResMain.h | 10 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/RankPermutation.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/ThreadSafePerm.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/PopulateVec.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/RMatrix.h | 374 +-- RcppAlgos-2.7.1/RcppAlgos/inst/include/RankResult.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/RankUtils.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Sample/SampCombPermStd.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Sample/SampleApply.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/Sample/SamplePartitions.h | 8 RcppAlgos-2.7.1/RcppAlgos/inst/include/SetUpUtils.h | 36 RcppAlgos-2.7.1/RcppAlgos/man/comboGroups.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/divisorsRcpp.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/divisorsSieve.Rd | 6 RcppAlgos-2.7.1/RcppAlgos/man/eulerPhiSieve.Rd | 7 RcppAlgos-2.7.1/RcppAlgos/man/isPrimeRcpp.Rd | 4 RcppAlgos-2.7.1/RcppAlgos/man/numDivisorSieve.Rd | 4 RcppAlgos-2.7.1/RcppAlgos/man/partitionsCount.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/partitionsGeneral.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/partitionsIterator.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/partitionsRank.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/partitionsSample.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/primeCount.Rd | 4 RcppAlgos-2.7.1/RcppAlgos/man/primeFactorize.Rd | 2 RcppAlgos-2.7.1/RcppAlgos/man/primeFactorizeSieve.Rd | 6 RcppAlgos-2.7.1/RcppAlgos/man/primeSieve.Rd | 3 RcppAlgos-2.7.1/RcppAlgos/src/BigComboCount.cpp | 99 - RcppAlgos-2.7.1/RcppAlgos/src/BigPartsCountDistinct.cpp | 153 - RcppAlgos-2.7.1/RcppAlgos/src/BigPartsCountRep.cpp | 137 - RcppAlgos-2.7.1/RcppAlgos/src/BigPartsCountSection.cpp | 43 RcppAlgos-2.7.1/RcppAlgos/src/BigPermuteCount.cpp | 80 RcppAlgos-2.7.1/RcppAlgos/src/CartesianContainer.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/src/CheckReturn.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/src/ClassUtils.cpp | 102 - RcppAlgos-2.7.1/RcppAlgos/src/CnstrntsSpecialClass.cpp | 4 RcppAlgos-2.7.1/RcppAlgos/src/CnstrntsToRClass.cpp | 4 RcppAlgos-2.7.1/RcppAlgos/src/CombinationResults.cpp | 144 - RcppAlgos-2.7.1/RcppAlgos/src/CombinatoricsApply.cpp | 29 RcppAlgos-2.7.1/RcppAlgos/src/CombinatoricsCount.cpp | 31 RcppAlgos-2.7.1/RcppAlgos/src/CombinatoricsMain.cpp | 29 RcppAlgos-2.7.1/RcppAlgos/src/ComboApplyClass.cpp | 75 RcppAlgos-2.7.1/RcppAlgos/src/ComboCartesian.cpp | 57 RcppAlgos-2.7.1/RcppAlgos/src/ComboClass.cpp | 102 - RcppAlgos-2.7.1/RcppAlgos/src/ComboCount.cpp | 15 RcppAlgos-2.7.1/RcppAlgos/src/ComboGroups.cpp | 200 +- RcppAlgos-2.7.1/RcppAlgos/src/ComboGroupsUtils.cpp | 63 RcppAlgos-2.7.1/RcppAlgos/src/ComboResClass.cpp | 58 RcppAlgos-2.7.1/RcppAlgos/src/ComboResMain.cpp | 10 RcppAlgos-2.7.1/RcppAlgos/src/CompositionsRep.cpp | 67 RcppAlgos-2.7.1/RcppAlgos/src/ComputedCount.cpp | 6 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsClass.cpp | 13 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsMain.cpp | 45 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsSpecial.cpp | 6 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsUtils.cpp | 15 RcppAlgos-2.7.1/RcppAlgos/src/ConvertUtils.cpp |only RcppAlgos-2.7.1/RcppAlgos/src/DivNumSieve.cpp | 110 - RcppAlgos-2.7.1/RcppAlgos/src/ExposeClass.cpp | 38 RcppAlgos-2.7.1/RcppAlgos/src/FunAssign.cpp | 33 RcppAlgos-2.7.1/RcppAlgos/src/GetClassVals.cpp | 30 RcppAlgos-2.7.1/RcppAlgos/src/GetCombPerm.cpp | 4 RcppAlgos-2.7.1/RcppAlgos/src/GetCombPermApply.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/src/GetConstraints.cpp | 46 RcppAlgos-2.7.1/RcppAlgos/src/GetPrevCombPerm.cpp | 15 RcppAlgos-2.7.1/RcppAlgos/src/GmpConvert.cpp |only RcppAlgos-2.7.1/RcppAlgos/src/Makevars | 2 RcppAlgos-2.7.1/RcppAlgos/src/MotleyPrimes.cpp | 173 - RcppAlgos-2.7.1/RcppAlgos/src/NextPartition.cpp | 5 RcppAlgos-2.7.1/RcppAlgos/src/NthCombination.cpp | 80 RcppAlgos-2.7.1/RcppAlgos/src/NthPartition.cpp | 199 -- RcppAlgos-2.7.1/RcppAlgos/src/NthPermutation.cpp | 112 - RcppAlgos-2.7.1/RcppAlgos/src/NthResult.cpp | 8 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsClass.cpp | 96 - RcppAlgos-2.7.1/RcppAlgos/src/PartitionsCount.cpp | 120 - RcppAlgos-2.7.1/RcppAlgos/src/PartitionsCountDistinct.cpp | 1 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsCountMultiset.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsCountRep.cpp | 1 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsDesign.cpp | 4 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsDistinct.cpp | 153 - RcppAlgos-2.7.1/RcppAlgos/src/PartitionsMultiset.cpp | 10 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsRep.cpp | 72 RcppAlgos-2.7.1/RcppAlgos/src/PartitionsUtils.cpp | 1 RcppAlgos-2.7.1/RcppAlgos/src/PermuteCount.cpp | 12 RcppAlgos-2.7.1/RcppAlgos/src/PermuteOptimized.cpp | 92 RcppAlgos-2.7.1/RcppAlgos/src/PermuteResMain.cpp | 15 RcppAlgos-2.7.1/RcppAlgos/src/PermuteResults.cpp | 163 - RcppAlgos-2.7.1/RcppAlgos/src/PollardRhoContainer.cpp |only RcppAlgos-2.7.1/RcppAlgos/src/PollardRhoDepends.cpp | 13 RcppAlgos-2.7.1/RcppAlgos/src/PollardRhoUtils.cpp | 119 - RcppAlgos-2.7.1/RcppAlgos/src/PopulateVec.cpp | 14 RcppAlgos-2.7.1/RcppAlgos/src/PrimeCount.cpp | 10 RcppAlgos-2.7.1/RcppAlgos/src/PrimeSieve.cpp | 12 RcppAlgos-2.7.1/RcppAlgos/src/RankCombPermMain.cpp | 33 RcppAlgos-2.7.1/RcppAlgos/src/RankCombination.cpp | 59 RcppAlgos-2.7.1/RcppAlgos/src/RankPartition.cpp | 134 - RcppAlgos-2.7.1/RcppAlgos/src/RankPartitionMain.cpp | 28 RcppAlgos-2.7.1/RcppAlgos/src/RankPermutation.cpp | 62 RcppAlgos-2.7.1/RcppAlgos/src/RankResult.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/src/RankUtils.cpp | 14 RcppAlgos-2.7.1/RcppAlgos/src/SampCombPermStd.cpp | 65 RcppAlgos-2.7.1/RcppAlgos/src/SampleApply.cpp | 30 RcppAlgos-2.7.1/RcppAlgos/src/SampleCombPerm.cpp | 28 RcppAlgos-2.7.1/RcppAlgos/src/SamplePartitions.cpp | 86 RcppAlgos-2.7.1/RcppAlgos/src/SetUpUtils.cpp | 214 -- RcppAlgos-2.7.1/RcppAlgos/src/StdConvert.cpp |only RcppAlgos-2.7.1/RcppAlgos/src/ThreadSafeComb.cpp | 8 RcppAlgos-2.7.1/RcppAlgos/src/ThreadSafeParts.cpp | 21 RcppAlgos-2.7.1/RcppAlgos/src/ThreadSafePerm.cpp | 25 RcppAlgos-2.7.1/RcppAlgos/src/cpp11.cpp | 2 RcppAlgos-2.7.1/RcppAlgos/tests/testthat/testComboClass.R | 19 RcppAlgos-2.7.1/RcppAlgos/vignettes/CombPermConstraints.Rmd | 243 +- RcppAlgos-2.7.1/RcppAlgos/vignettes/CombinatorialSampling.Rmd | 189 - RcppAlgos-2.7.1/RcppAlgos/vignettes/CombinatoricsIterators.Rmd | 434 ++-- RcppAlgos-2.7.1/RcppAlgos/vignettes/ComputationalMathematics.Rmd | 205 +- RcppAlgos-2.7.1/RcppAlgos/vignettes/GeneralCombinatorics.Rmd | 146 - RcppAlgos-2.7.1/RcppAlgos/vignettes/HighPerformanceBenchmarks.Rmd | 249 +- RcppAlgos-2.7.1/RcppAlgos/vignettes/OtherCombinatorics.Rmd | 138 - RcppAlgos-2.7.1/RcppAlgos/vignettes/SubsetSum.Rmd | 174 + 243 files changed, 7263 insertions(+), 7541 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.7.1 dated 2022-11-24 and 0.7.2 dated 2023-02-06
DESCRIPTION | 8 LICENSE | 2 MD5 | 49 NEWS.md | 8 R/api_get.R | 73 R/caching.R | 14 R/coords.R | 27 R/dates.R | 204 R/finbif_collections.R | 46 R/finbif_occurrence.R | 19 R/finbif_occurrence_load.R | 6 R/finbif_records.R | 14 R/finbif_taxa.R | 27 R/map-utils.R | 25 R/sysdata.rda |binary R/utils.R | 6 README.md | 6 inst/CITATION | 32 inst/NEWS.Rd | 9 tests/testthat/_snaps/finbif_occurrence/fungi.svg | 2194 +++++----- tests/testthat/test-finbif_api_get.R | 28 tests/testthat/test-finbif_dates.R | 144 tests/testthat/test-local-finbif_coords.R | 4 tests/testthat/test-local-finbif_occurrence_load.R | 8 tests/testthat/test-utils.R | 7 tests/write-files/finbif_cache_file_1571d33d6deb0431188fc3d56cdc8bbd |only 26 files changed, 1608 insertions(+), 1352 deletions(-)
Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://debruine.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre] ,
Anna Krystalli [ctb] ,
Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>
Diff between faux versions 1.1.0 dated 2021-09-13 and 1.2.0 dated 2023-02-06
DESCRIPTION | 12 MD5 | 106 ++-- NAMESPACE | 11 NEWS.md | 29 + R/add_ranef.R | 26 R/check_design.R | 1 R/codebook.R | 1 R/codebook_interactive.R | 1 R/distribution_convertors.R | 168 +++++- R/get_coefs.R |only R/long2wide.R | 8 R/nested_list.R | 1 R/norta.R |only R/rnorm_multi.R | 8 R/sim_df.R | 32 + R/utils-pipe.R | 7 R/wide2long.R | 3 README.md | 34 - build/vignette.rds |binary inst/CITATION | 9 inst/doc/codebook.html | 622 ++++++++++++++++------- inst/doc/continuous.R | 2 inst/doc/continuous.Rmd | 2 inst/doc/continuous.html | 388 +++++++++++--- inst/doc/contrasts.Rmd | 14 inst/doc/contrasts.html | 949 +++++++++++++++++++++++++++++------- inst/doc/norta.R |only inst/doc/norta.Rmd |only inst/doc/norta.html |only inst/doc/rnorm_multi.html | 377 +++++++++++--- inst/doc/sim_design.html | 492 ++++++++++++++---- inst/doc/sim_df.html | 372 +++++++++++--- man/OR.Rd | 7 man/add_random.Rd | 6 man/codebook_interactive.Rd | 1 man/convert_r.Rd |only man/distfuncs.Rd |only man/dlikert.Rd |only man/fh_bounds.Rd |only man/get_coefs.Rd |only man/long2wide.Rd | 11 man/norm2likert.Rd | 4 man/norm2norm.Rd |only man/norm2trunc.Rd | 14 man/plikert.Rd |only man/plot_design.Rd | 8 man/print.design.Rd | 1 man/print.nested_list.Rd | 1 man/print.psychds_codebook.Rd | 1 man/qlikert.Rd |only man/rlikert.Rd |only man/rmulti.Rd |only man/sim_df.Rd | 19 tests/testthat/Rplots.pdf |binary tests/testthat/test-add_ranef.R | 37 + tests/testthat/test-distributions.R | 87 +++ tests/testthat/test-get_coefs.R |only tests/testthat/test-norta.R |only tests/testthat/test-rnorm_multi.R | 10 tests/testthat/test-sim_df.R | 37 + vignettes/continuous.Rmd | 2 vignettes/contrasts.Rmd | 14 vignettes/norta.Rmd |only 63 files changed, 3084 insertions(+), 851 deletions(-)
Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] ,
Thanh Wang [ctb]
Maintainer: Miao YU <yufreecas@gmail.com>
Diff between enviGCMS versions 0.6.6 dated 2020-06-04 and 0.7.1 dated 2023-02-06
enviGCMS-0.6.6/enviGCMS/R/msmsanno.R |only enviGCMS-0.6.6/enviGCMS/inst/shinyapps/MDPlot |only enviGCMS-0.6.6/enviGCMS/man/getoverlapmass.Rd |only enviGCMS-0.6.6/enviGCMS/man/getoverlaprt.Rd |only enviGCMS-0.7.1/enviGCMS/DESCRIPTION | 14 enviGCMS-0.7.1/enviGCMS/MD5 | 163 ++--- enviGCMS-0.7.1/enviGCMS/NAMESPACE | 28 enviGCMS-0.7.1/enviGCMS/NEWS.md | 46 + enviGCMS-0.7.1/enviGCMS/R/anno.R |only enviGCMS-0.7.1/enviGCMS/R/deprecated.R | 40 - enviGCMS-0.7.1/enviGCMS/R/general.R | 104 +-- enviGCMS-0.7.1/enviGCMS/R/getdata.R | 14 enviGCMS-0.7.1/enviGCMS/R/getmzrt.R | 579 +++++++++++++------ enviGCMS-0.7.1/enviGCMS/R/io.R | 342 ++++++++--- enviGCMS-0.7.1/enviGCMS/R/mda.R | 139 +++- enviGCMS-0.7.1/enviGCMS/R/peaks.R | 64 +- enviGCMS-0.7.1/enviGCMS/R/plotmzrt.R | 173 +++-- enviGCMS-0.7.1/enviGCMS/R/sccp.R | 50 - enviGCMS-0.7.1/enviGCMS/R/shiny.R | 4 enviGCMS-0.7.1/enviGCMS/README.md | 6 enviGCMS-0.7.1/enviGCMS/build/vignette.rds |binary enviGCMS-0.7.1/enviGCMS/inst/CITATION | 33 - enviGCMS-0.7.1/enviGCMS/inst/doc/GCMSDA.Rmd | 32 - enviGCMS-0.7.1/enviGCMS/inst/doc/GCMSDA.html | 203 +++++- enviGCMS-0.7.1/enviGCMS/inst/doc/PooledQC.R | 2 enviGCMS-0.7.1/enviGCMS/inst/doc/PooledQC.Rmd | 2 enviGCMS-0.7.1/enviGCMS/inst/doc/PooledQC.html | 271 +++++--- enviGCMS-0.7.1/enviGCMS/inst/shinyapps/csvdemo.png |only enviGCMS-0.7.1/enviGCMS/inst/shinyapps/mdplot.Rmd |only enviGCMS-0.7.1/enviGCMS/inst/shinyapps/sccp/server.R | 20 enviGCMS-0.7.1/enviGCMS/man/GetIntegration.Rd | 16 enviGCMS-0.7.1/enviGCMS/man/Integration.Rd | 10 enviGCMS-0.7.1/enviGCMS/man/dotpanno.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/findline.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/findohc.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/findpfc.Rd |only enviGCMS-0.7.1/enviGCMS/man/getalign.Rd |only enviGCMS-0.7.1/enviGCMS/man/getalign2.Rd |only enviGCMS-0.7.1/enviGCMS/man/getarea.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/getcompare.Rd |only enviGCMS-0.7.1/enviGCMS/man/getcsv.Rd | 6 enviGCMS-0.7.1/enviGCMS/man/getdata.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getdata2.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getdoe.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getdwtus.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getfilter.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/getformula.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/getmd.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getmr.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getms1anno.Rd |only enviGCMS-0.7.1/enviGCMS/man/getmzrt.Rd | 6 enviGCMS-0.7.1/enviGCMS/man/getmzrt2.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getmzrtcsv.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getoverlappeak.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/getpn.Rd |only enviGCMS-0.7.1/enviGCMS/man/getretcor.Rd |only enviGCMS-0.7.1/enviGCMS/man/getsccp.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/getupload.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/gifmr.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/ma.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotanno.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plotcc.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotden.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotgroup.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plothist.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plothm.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotint.Rd | 8 enviGCMS-0.7.1/enviGCMS/man/plotintslope.Rd | 6 enviGCMS-0.7.1/enviGCMS/man/plotmrc.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plotms.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotmsrt.Rd | 6 enviGCMS-0.7.1/enviGCMS/man/plotpca.Rd | 8 enviGCMS-0.7.1/enviGCMS/man/plotridges.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plotrla.Rd | 8 enviGCMS-0.7.1/enviGCMS/man/plotrsd.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plotrtms.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/plotsub.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plott.Rd | 4 enviGCMS-0.7.1/enviGCMS/man/plottic.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/sccp.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/svabatch.Rd | 6 enviGCMS-0.7.1/enviGCMS/man/svadata.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/svapca.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/svaupload.Rd | 2 enviGCMS-0.7.1/enviGCMS/man/writeMSP.Rd | 20 enviGCMS-0.7.1/enviGCMS/man/xrankanno.Rd | 4 enviGCMS-0.7.1/enviGCMS/vignettes/GCMSDA.Rmd | 32 - enviGCMS-0.7.1/enviGCMS/vignettes/PooledQC.Rmd | 2 88 files changed, 1613 insertions(+), 954 deletions(-)
Title: Exploration of Dental Surface Topography
Description: Tools for exploring the topography of 3d triangle meshes.
The functions were developed with dental surfaces in mind, but could be
applied to any triangle mesh of class 'mesh3d'. More specifically, 'doolkit'
allows to isolate the border of a mesh, or a subpart of the mesh using the
polygon networks method; crop a mesh; compute basic descriptors (elevation,
orientation, footprint area); compute slope, angularity and relief index
(Ungar and Williamson (2000) <https://palaeo-electronica.org/2000_1/gorilla/issue1_00.htm>;
Boyer (2008) <doi:10.1016/j.jhevol.2008.08.002>), inclination and occlusal
relief index or gamma (Guy et al. (2013) <doi:10.1371/journal.pone.0066142>),
OPC (Evans et al. (2007) <doi:10.1038/nature05433>), OPCR (Wilson et al.
(2012) <doi:10.1038/nature10880>), DNE (Bunn et al. (2011) <doi:10.1002/ajpa.21489>;
Pampush et al. (2016) <doi:10.1007/s10914-016-9326-0>), form factor (Horton
(1932) <doi:10.1029/TR013i001p00350>), bas [...truncated...]
Author: Ghislain Thiery [aut, cre],
Franck Guy [aut],
Vincent Lazzari [aut]
Maintainer: Ghislain Thiery <ghislain.thiery@ntymail.com>
Diff between doolkit versions 1.42.1 dated 2022-05-14 and 1.42.2 dated 2023-02-06
DESCRIPTION | 10 +++--- MD5 | 34 ++++++++++---------- NAMESPACE | 14 +++++++- R/doolkit.R | 15 ++++++++- R/polygon.networks.R | 13 ++----- R/topography.R | 84 ++++++++++++++++++++++++++++++++------------------- R/utility.R | 18 ++++++---- build/partial.rdb |binary data/dkmodel.rda |binary data/dkpongo.rda |binary man/arc.Rd | 4 +- man/area2d.Rd | 10 ++++++ man/dkborder.Rd | 4 +- man/dksetview.Rd | 3 + man/dne.Rd | 11 ++++++ man/opcr.Rd | 8 ++-- man/poly.network.Rd | 10 ------ man/rfi.Rd | 9 ++++- 18 files changed, 158 insertions(+), 89 deletions(-)