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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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 RcppAlgos-2.7.1/RcppAlgos/inst/include/CppConvert |only RcppAlgos-2.7.1/RcppAlgos/inst/include/CppConvert.h |only RcppAlgos-2.7.1/RcppAlgos/inst/include/FunAssign.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/GetCombPerm.h | 9 RcppAlgos-2.7.1/RcppAlgos/inst/include/GetCombPermApply.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/NthResult.h | 11 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/Eratosthenes.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/EulerPhiSieve.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/MotleyStartIndex.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PhiTinyLookup.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PollardRhoDepends.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PollardRhoUtils.h | 18 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimeFactorizeSieve.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimesPolRho.h | 63 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 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NextPermSectionRep.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NextPermutation.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NthPermutation.h | 10 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationResults.h | 32 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsDistinct.h | 57 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsMultiset.h | 67 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsRep.h | 25 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteCount.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteDistinctApply.h | 10 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteHelper.h | 7 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteManager.h | 5 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteMultisetApply.h | 10 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteOptimized.h | 8 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(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-21 0.1.0
Title: Convolution-Type Smoothed Quantile Regression
Description: Estimation and inference for conditional linear quantile regression models using a convolution smoothed approach. In the low-dimensional setting, efficient gradient-based methods are employed for fitting both a single model and a regression process over a quantile range. Normal-based and (multiplier) bootstrap confidence intervals for all slope coefficients are constructed. In high dimensions, the conquer method is complemented with flexible types of penalties (Lasso, elastic-net, group lasso, sparse group lasso, scad and mcp) to deal with complex low-dimensional structures.
Author: Xuming He [aut],
Xiaoou Pan [aut, cre],
Kean Ming Tan [aut],
Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between conquer versions 1.3.1 dated 2022-09-13 and 1.3.2 dated 2023-02-05
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/smqr.R | 32 +++++++++++++++++++++++++++++++- README.md | 23 ++++++++++++++++------- src/Makevars | 2 +- src/Makevars.win | 2 +- src/highdGauss.cpp | 6 ++++++ src/highdLogistic.cpp | 6 ++++++ src/highdPara.cpp | 6 ++++++ src/highdTrian.cpp | 6 ++++++ src/highdUnif.cpp | 6 ++++++ 11 files changed, 94 insertions(+), 25 deletions(-)
Title: Sunburst 'Htmlwidget'
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] ,
Kerry Rodden [aut, cph] ,
Kevin Warne [aut, cph] ,
Kent Russell [aut, cre] ,
Florian Breitwieser [ctb] ,
CJ Yetman [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 2.1.6 dated 2021-09-19 and 2.1.8 dated 2023-02-05
DESCRIPTION | 10 MD5 | 14 NEWS.md | 12 R/converters.R | 4 R/sunburst.R | 34 README.md | 47 inst/doc/sunburst-2-0-0.html |12110 ++++++++++++++++++++++++++++++++++++++++++- inst/htmlwidgets/sund2b.js | 2 8 files changed, 12082 insertions(+), 151 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.9.4 dated 2023-01-07 and 0.9.5 dated 2023-02-05
sasLM-0.9.4/sasLM/inst/doc/Report-Different-Simplest2301071812.pdf |only sasLM-0.9.4/sasLM/inst/doc/Report-NOT-OKs2301071813.pdf |only sasLM-0.9.4/sasLM/inst/doc/Validation-Report-GLM-2301071814.pdf |only sasLM-0.9.5/sasLM/DESCRIPTION | 6 sasLM-0.9.5/sasLM/MD5 | 44 +++--- sasLM-0.9.5/sasLM/R/GLM.R | 14 +- sasLM-0.9.5/sasLM/R/LSM.R | 19 +- sasLM-0.9.5/sasLM/R/RDmn.R | 4 sasLM-0.9.5/sasLM/R/REG.R | 28 +++- sasLM-0.9.5/sasLM/R/T3test.R | 67 +++++++--- sasLM-0.9.5/sasLM/R/aov1.R | 28 +++- sasLM-0.9.5/sasLM/R/aov2.R | 28 +++- sasLM-0.9.5/sasLM/R/aov3.R | 28 +++- sasLM-0.9.5/sasLM/inst/NEWS.Rd | 10 + sasLM-0.9.5/sasLM/inst/doc/Report-Different-Simplest2301290914.pdf |only sasLM-0.9.5/sasLM/inst/doc/Report-NOT-OKs2301290915.pdf |only sasLM-0.9.5/sasLM/inst/doc/Validation-Report-GLM-2301290915.pdf |only sasLM-0.9.5/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.9.5/sasLM/man/GLM.Rd | 8 + sasLM-0.9.5/sasLM/man/LSM.Rd | 7 - sasLM-0.9.5/sasLM/man/REG.Rd | 16 +- sasLM-0.9.5/sasLM/man/T3test.Rd | 4 sasLM-0.9.5/sasLM/man/aov1.Rd | 12 + sasLM-0.9.5/sasLM/man/aov2.Rd | 12 + sasLM-0.9.5/sasLM/man/aov3.Rd | 12 + sasLM-0.9.5/sasLM/man/est.Rd | 2 26 files changed, 265 insertions(+), 84 deletions(-)
Title: Read and Write 'Matlab' Files
Description: Read and write 'Matlab' MAT files from R. The 'rmatio'
package supports reading MAT version 4, MAT version 5 and MAT
compressed version 5. The 'rmatio' package can write version 5 MAT
files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] ,
Christopher Hulbert [aut]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between rmatio versions 0.17.0 dated 2023-01-25 and 0.18.0 dated 2023-02-05
rmatio-0.17.0/rmatio/R/have_lib.R |only rmatio-0.17.0/rmatio/R/have_lib.R.in |only rmatio-0.18.0/rmatio/DESCRIPTION | 8 rmatio-0.18.0/rmatio/MD5 | 53 rmatio-0.18.0/rmatio/NEWS.md | 61 rmatio-0.18.0/rmatio/R/read_mat.R | 26 rmatio-0.18.0/rmatio/R/rmatio.R | 16 rmatio-0.18.0/rmatio/R/write_mat.R | 177 rmatio-0.18.0/rmatio/configure | 4378 +++++++++-------------- rmatio-0.18.0/rmatio/configure.ac | 2505 +++++++------ rmatio-0.18.0/rmatio/man/read.mat.Rd | 18 rmatio-0.18.0/rmatio/man/rmatio.Rd | 14 rmatio-0.18.0/rmatio/man/write.mat-methods.Rd | 79 rmatio-0.18.0/rmatio/src/matio/config.h | 2 rmatio-0.18.0/rmatio/src/matio/config.h.in | 2 rmatio-0.18.0/rmatio/tests/arguments.R | 53 rmatio-0.18.0/rmatio/tests/array.R | 212 - rmatio-0.18.0/rmatio/tests/cell.R | 981 ++--- rmatio-0.18.0/rmatio/tests/complex.R | 30 rmatio-0.18.0/rmatio/tests/dgCMatrix.R | 77 rmatio-0.18.0/rmatio/tests/lists.R | 14 rmatio-0.18.0/rmatio/tests/logical.R | 63 rmatio-0.18.0/rmatio/tests/matio_test_datasets.R | 1204 +++--- rmatio-0.18.0/rmatio/tests/matrix.R | 60 rmatio-0.18.0/rmatio/tests/one_only.R | 6 rmatio-0.18.0/rmatio/tests/string.R | 120 rmatio-0.18.0/rmatio/tests/structure.R | 1048 ++--- rmatio-0.18.0/rmatio/tests/vector.R | 98 rmatio-0.18.0/rmatio/tools/pkg.m4 |only 29 files changed, 5617 insertions(+), 5688 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect
sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes
(d) for AB/BA cross-over repeated-measures experimental designs), data
presentation functions (e.g., density curve overlaid on histogram),
and the data sets analyzed in different research papers in software
engineering (e.g., related to software defect prediction or multi-site
experiment concerning the extent to which structured abstracts were
clearer and more complete than conventional abstracts) to streamline
reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] ,
Barbara Kitchenham [ctb] ,
Tomasz Lewowski [ctb] ,
Marian Jureczko [ctb] ,
David Budgen [ctb] ,
Pearl Brereton [ctb] ,
Jacky Keung [ctb] ,
Stuart Charters [ctb] ,
Shirley Gibbs [ctb] ,
Amnart Pohthong [ctb] ,
Giuseppe [...truncated...]
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.5.0 dated 2023-01-16 and 0.5.1 dated 2023-02-05
DESCRIPTION | 8 - MD5 | 20 ++-- NEWS.md | 10 +- R/NPSimulation.R | 123 ++++++++++++++++++--------- R/reproducer.R | 10 +- inst/CITATION | 91 ++++++++++++------- man/MetaAnalysisSimulations.Rd | 2 man/RandomExperimentSimulations.Rd | 2 man/RandomizedBlocksExperimentSimulations.Rd | 2 man/calculate2GMdMRE.Rd | 38 ++++---- man/calculate4GMdMRE.Rd | 16 +++ 11 files changed, 211 insertions(+), 111 deletions(-)
Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with
large-than-RAM datasets. Aims to lower the barrier-to-entry for
manipulating large datasets by adhering closely to popular and
familiar data manipulation paradigms like 'dplyr' verbs and
'data.table' syntax.
Author: Dai ZJ [aut, cre],
Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>
Diff between disk.frame versions 0.7.2 dated 2022-03-07 and 0.8.0 dated 2023-02-05
disk.frame-0.7.2/disk.frame/man/sub-.disk.frame.Rd |only disk.frame-0.8.0/disk.frame/DESCRIPTION | 12 disk.frame-0.8.0/disk.frame/MD5 | 28 - disk.frame-0.8.0/disk.frame/NAMESPACE | 1 disk.frame-0.8.0/disk.frame/NEWS.md | 7 disk.frame-0.8.0/disk.frame/R/anti_join.r | 4 disk.frame-0.8.0/disk.frame/R/as.data.frame.r | 2 disk.frame-0.8.0/disk.frame/R/collect.summarized_disk.frame.r | 52 ++- disk.frame-0.8.0/disk.frame/R/data.table.r | 27 + disk.frame-0.8.0/disk.frame/R/inner_join.r | 4 disk.frame-0.8.0/disk.frame/R/left_join.r | 4 disk.frame-0.8.0/disk.frame/R/semi_join.r | 4 disk.frame-0.8.0/disk.frame/README.md | 145 +++------- disk.frame-0.8.0/disk.frame/man/as.data.frame.disk.frame.Rd | 54 +-- disk.frame-0.8.0/disk.frame/man/disk.frame_to_parquet.Rd | 32 +- disk.frame-0.8.0/disk.frame/man/sub-sub-.disk.frame.Rd |only 16 files changed, 179 insertions(+), 197 deletions(-)
Title: 'd3.js' Utilities for R
Description: Provides a suite of functions to help ease the use of 'd3.js' in R.
These helpers include 'htmltools::htmlDependency' functions, hierarchy
builders, and conversion tools for 'partykit', 'igraph,' 'table',
and 'data.frame' R objects into the 'JSON' that 'd3.js' expects.
Author: Mike Bostock [aut, cph] ,
Kent Russell [aut, cre, cph] ,
Gregor Aisch [aut, cph] ,
Adam Pearce [aut] ,
Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 1.0.0 dated 2021-08-15 and 1.0.1 dated 2023-02-05
DESCRIPTION | 10 MD5 | 22 NEWS.md | 5 R/dependencies.R | 4 R/igraph.R | 2 README.md | 23 inst/www/d3/v7/API.md | 1390 +++++++++++++++++++++--------------------- inst/www/d3/v7/CHANGES.md | 4 inst/www/d3/v7/LICENSE | 2 inst/www/d3/v7/README.md | 20 inst/www/d3/v7/dist/d3.min.js | 4 tests/testthat/test_deps.R | 1 12 files changed, 761 insertions(+), 726 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between av versions 0.8.2 dated 2022-10-06 and 0.8.3 dated 2023-02-05
av-0.8.2/av/src/Makevars.ucrt |only av-0.8.3/av/DESCRIPTION | 9 ++++----- av-0.8.3/av/MD5 | 11 +++++------ av-0.8.3/av/NEWS | 4 ++++ av-0.8.3/av/src/Makevars.in | 1 - av-0.8.3/av/src/Makevars.win | 11 +++++++++-- av-0.8.3/av/src/fft.c | 4 ++-- 7 files changed, 24 insertions(+), 16 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 3.0.6 dated 2022-03-03 and 3.0.7 dated 2023-02-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/json_extractors.R | 2 +- R/parsers.R | 1 + R/url_to_json.R | 5 ++++- 6 files changed, 19 insertions(+), 11 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: Mediation Analysis Using Joint Significance
Description: A set of helper functions to conduct joint-significance tests
for mediation analysis, as recommended by Yzerbyt, Muller, Batailler,
& Judd. (2018) <doi:10.1037/pspa0000132>.
Author: Cedric Batailler [aut, cre] ,
Dominique Muller [aut] ,
Vincent Yzerbyt [aut],
Charles Judd [aut],
Yoann Julliard [ctb] ,
Arnold Ho [dtc],
Nour Kteily [dtc],
Jacqueline Chen [dtc],
Simone Dohle [dtc],
Michael Siegrist [dtc]
Maintainer: Cedric Batailler <cedric.batailler@gmail.com>
Diff between JSmediation versions 0.2.0 dated 2021-09-02 and 0.2.1 dated 2023-02-05
JSmediation-0.2.0/JSmediation/R/JSmediation.R |only JSmediation-0.2.1/JSmediation/DESCRIPTION | 14 JSmediation-0.2.1/JSmediation/LICENSE | 4 JSmediation-0.2.1/JSmediation/MD5 | 180 JSmediation-0.2.1/JSmediation/NAMESPACE | 112 JSmediation-0.2.1/JSmediation/NEWS.md | 96 JSmediation-0.2.1/JSmediation/R/JSmediation-package.R |only JSmediation-0.2.1/JSmediation/R/add_index.R | 48 JSmediation-0.2.1/JSmediation/R/apastylr.R | 118 JSmediation-0.2.1/JSmediation/R/build_contrast.R | 112 JSmediation-0.2.1/JSmediation/R/check_assumptions.R | 188 JSmediation-0.2.1/JSmediation/R/check_variables.R | 100 JSmediation-0.2.1/JSmediation/R/compute_indirect_effect_for.R | 314 JSmediation-0.2.1/JSmediation/R/create_path.R | 48 JSmediation-0.2.1/JSmediation/R/display_models.R | 74 JSmediation-0.2.1/JSmediation/R/dohle_siegrist.R | 58 JSmediation-0.2.1/JSmediation/R/dohle_siegrist_w.R | 58 JSmediation-0.2.1/JSmediation/R/extract_models.R | 250 JSmediation-0.2.1/JSmediation/R/ho_et_al.R | 70 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JSmediation-0.2.1/JSmediation/build/vignette.rds |binary JSmediation-0.2.1/JSmediation/inst/apa.csl | 3832 +++---- JSmediation-0.2.1/JSmediation/inst/doc/jsmediation.R | 94 JSmediation-0.2.1/JSmediation/inst/doc/jsmediation.Rmd | 498 JSmediation-0.2.1/JSmediation/inst/doc/jsmediation.html | 1121 +- JSmediation-0.2.1/JSmediation/inst/doc/moderated-mediation.R | 108 JSmediation-0.2.1/JSmediation/inst/doc/moderated-mediation.Rmd | 312 JSmediation-0.2.1/JSmediation/inst/doc/moderated-mediation.html | 1151 +- JSmediation-0.2.1/JSmediation/inst/references.bib | 214 JSmediation-0.2.1/JSmediation/man/JSmediation-package.Rd | 127 JSmediation-0.2.1/JSmediation/man/add_index.Rd | 64 JSmediation-0.2.1/JSmediation/man/add_index.moderated_mediation.Rd | 128 JSmediation-0.2.1/JSmediation/man/add_index.simple_mediation.Rd | 92 JSmediation-0.2.1/JSmediation/man/add_index.within_participant_mediation.Rd | 92 JSmediation-0.2.1/JSmediation/man/apastylr.Rd | 54 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Title: Air Quality Data Analysis
Description: Utilities for working with hourly air quality monitoring data
with a focus on small particulates (PM2.5). A compact data model is
structured as a list with two dataframes. A 'meta' dataframe contains
spatial and measuring device metadata associated with deployments at known
locations. A 'data' dataframe contains a 'datetime' column followed by
columns of measurements associated with each "device-deployment".
Algorithms to calculate NowCast and the associated Air Quality Index (AQI)
are defined at the US Environmental Projection Agency AirNow program:
<https://www.airnow.gov/sites/default/files/2020-05/aqi-technical-assistance-document-sept2018.pdf>.
Author: Jonathan Callahan [aut, cre],
Spencer Pease [ctb],
Hans Martin [ctb],
Rex Thompson [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between AirMonitor versions 0.2.2 dated 2022-03-31 and 0.3.9 dated 2023-02-05
DESCRIPTION | 16 MD5 | 132 NAMESPACE | 3 NEWS.md | 69 R/AirMonitor.R | 3 R/airnow_loadAnnual.R | 2 R/airsis_loadAnnual.R | 31 R/airsis_loadDaily.R | 28 R/airsis_loadLatest.R | 28 R/data.R | 27 R/epa_aqs_loadAnnual.R |only R/monitor_collapse.R | 20 R/monitor_combine.R | 47 R/monitor_filterDate.R | 13 R/monitor_filterDatetime.R | 14 R/monitor_fromPWFSLSmoke.R | 69 R/monitor_getCurrentStatus.R | 2 R/monitor_getDistance.R | 4 R/monitor_leaflet.R | 2 R/monitor_load.R | 8 R/monitor_loadAnnual.R | 114 R/monitor_nowcast.R | 6 R/monitor_selectWhere.R |only R/monitor_timeseriesPlot.R | 11 R/monitor_toPWFSLSmoke.R | 9 R/utils-QC.R |only R/utils-monitor.R | 2 R/wrcc_loadAnnual.R | 28 R/wrcc_loadDaily.R | 28 R/wrcc_loadLatest.R | 28 README.md | 1 build/vignette.rds |binary data/Camp_Fire.rda |binary data/Carmel_Valley.rda |binary data/NW_Megafires.rda |binary inst/doc/AirMonitor.R | 35 inst/doc/AirMonitor.Rmd | 83 inst/doc/AirMonitor.html | 331 + inst/doc/Data_Model.R | 77 inst/doc/Data_Model.Rmd | 163 inst/doc/Data_Model.html | 5393 ++++++++++++++++++++++++++- inst/doc/Developer_Style_Guide.Rmd | 25 inst/doc/Developer_Style_Guide.html | 97 man/Camp_Fire.Rd | 4 man/Carmel_Valley.Rd | 6 man/NW_Megafires.Rd | 11 man/QC_invalidateConsecutiveSuspectValues.Rd |only man/airsis_loadAnnual.Rd | 15 man/airsis_loadDaily.Rd | 15 man/airsis_loadLatest.Rd | 15 man/epa_aqs_loadAnnual.Rd |only man/monitor_check.Rd | 2 man/monitor_collapse.Rd | 20 man/monitor_combine.Rd | 42 man/monitor_filterDate.Rd | 3 man/monitor_filterDatetime.Rd | 3 man/monitor_getCurrentStatus.Rd | 2 man/monitor_getDistance.Rd | 4 man/monitor_load.Rd | 6 man/monitor_loadAnnual.Rd | 14 man/monitor_selectWhere.Rd |only man/wrcc_loadAnnual.Rd | 15 man/wrcc_loadDaily.Rd | 15 man/wrcc_loadLatest.Rd | 15 vignettes/AirMonitor.Rmd | 83 vignettes/Data_Model.Rmd | 163 vignettes/Developer_Style_Guide.Rmd | 25 vignettes/articles/Citations.Rmd | 2 vignettes/articles/NowCast.Rmd | 207 - vignettes/articles/Save_Data_as_CSV.Rmd | 49 70 files changed, 6798 insertions(+), 887 deletions(-)
Title: Client for the 'DataCite' API
Description: Client for the web service methods provided by 'DataCite'
(<https://www.datacite.org/>), including functions to interface with
their 'RESTful' search API. The API is backed by 'Elasticsearch',
allowing expressive queries, including faceting.
Author: Scott Chamberlain [aut] ,
Bianca Kramer [cre]
Maintainer: Bianca Kramer <bianca.kramer@gmail.com>
Diff between rdatacite versions 0.5.2 dated 2020-03-04 and 0.5.4 dated 2023-02-05
rdatacite-0.5.2/rdatacite/README.md |only rdatacite-0.5.4/rdatacite/DESCRIPTION | 40 - rdatacite-0.5.4/rdatacite/LICENSE | 4 rdatacite-0.5.4/rdatacite/MD5 | 92 ++-- rdatacite-0.5.4/rdatacite/NAMESPACE | 29 - rdatacite-0.5.4/rdatacite/NEWS.md | 130 +++-- rdatacite-0.5.4/rdatacite/R/dc_activities.R | 56 +- rdatacite-0.5.4/rdatacite/R/dc_client_prefixes.R | 62 +- rdatacite-0.5.4/rdatacite/R/dc_clients.R | 66 +- rdatacite-0.5.4/rdatacite/R/dc_cn.R |only rdatacite-0.5.4/rdatacite/R/dc_dois.R | 180 +++---- rdatacite-0.5.4/rdatacite/R/dc_events.R | 134 ++--- rdatacite-0.5.4/rdatacite/R/dc_prefixes.R | 50 +- rdatacite-0.5.4/rdatacite/R/dc_provider_prefixes.R | 50 +- rdatacite-0.5.4/rdatacite/R/dc_providers.R | 84 +-- rdatacite-0.5.4/rdatacite/R/dc_reports.R | 98 ++-- rdatacite-0.5.4/rdatacite/R/dc_status.R | 50 +- rdatacite-0.5.4/rdatacite/R/print_dc.R | 50 +- rdatacite-0.5.4/rdatacite/R/rdatacite-package.R | 121 ++--- rdatacite-0.5.4/rdatacite/R/rest_helpers.R | 89 ++- rdatacite-0.5.4/rdatacite/R/zzz.r | 74 +-- rdatacite-0.5.4/rdatacite/inst/ignore/dc_person.R | 32 - rdatacite-0.5.4/rdatacite/man/dc_activities.Rd | 92 ++-- rdatacite-0.5.4/rdatacite/man/dc_check.Rd | 30 - rdatacite-0.5.4/rdatacite/man/dc_client_prefixes.Rd | 104 ++-- rdatacite-0.5.4/rdatacite/man/dc_clients.Rd | 108 ++-- rdatacite-0.5.4/rdatacite/man/dc_cn.Rd |only rdatacite-0.5.4/rdatacite/man/dc_dois.Rd | 230 +++++----- rdatacite-0.5.4/rdatacite/man/dc_events.Rd | 186 ++++---- rdatacite-0.5.4/rdatacite/man/dc_prefixes.Rd | 60 +- rdatacite-0.5.4/rdatacite/man/dc_provider_prefixes.Rd | 60 +- rdatacite-0.5.4/rdatacite/man/dc_providers.Rd | 110 ++-- rdatacite-0.5.4/rdatacite/man/dc_reports.Rd | 122 ++--- rdatacite-0.5.4/rdatacite/man/dc_status.Rd | 40 - rdatacite-0.5.4/rdatacite/man/rdatacite-package.Rd | 158 +++--- rdatacite-0.5.4/rdatacite/tests/fixtures/dc_activities.yml | 78 +-- rdatacite-0.5.4/rdatacite/tests/fixtures/dc_client_prefixes.yml | 80 +-- rdatacite-0.5.4/rdatacite/tests/fixtures/dc_clients.yml | 80 +-- rdatacite-0.5.4/rdatacite/tests/fixtures/dc_cn.yml |only rdatacite-0.5.4/rdatacite/tests/fixtures/dc_cn_fail.yml |only rdatacite-0.5.4/rdatacite/tests/fixtures/dc_dois.yml | 78 +-- rdatacite-0.5.4/rdatacite/tests/fixtures/dc_events.yml | 78 +-- rdatacite-0.5.4/rdatacite/tests/test-all.R | 4 rdatacite-0.5.4/rdatacite/tests/testthat/helper-rdatacite.R | 6 rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_activities.R | 44 - rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_client_prefixes.R | 44 - rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_clients.R | 44 - rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_cn.R |only rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_dois.R | 44 - rdatacite-0.5.4/rdatacite/tests/testthat/test-dc_events.R | 46 +- 50 files changed, 1729 insertions(+), 1688 deletions(-)
Title: Automated Reporting of Results and Statistical Models
Description: The aim of the 'report' package is to bridge the gap between
R’s output and the formatted results contained in your manuscript.
This package converts statistical models and data frames into textual
reports suited for publication, ensuring standardization and quality
in results reporting.
Author: Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut, cre] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Rudolf Siegel [ctb]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between report versions 0.5.5 dated 2022-08-22 and 0.5.6 dated 2023-02-05
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report-0.5.6/report/man/report_sample.Rd | 5 report-0.5.6/report/man/report_statistics.Rd | 21 report-0.5.6/report/man/report_table.Rd | 41 report-0.5.6/report/man/report_text.Rd | 28 report-0.5.6/report/tests/testthat.R | 54 - report-0.5.6/report/tests/testthat/_snaps/windows/report.aov.md | 86 +- report-0.5.6/report/tests/testthat/_snaps/windows/report.brmsfit.md |only report-0.5.6/report/tests/testthat/_snaps/windows/report.data.frame.md | 2 report-0.5.6/report/tests/testthat/_snaps/windows/report.htest-chi2.md |only report-0.5.6/report/tests/testthat/_snaps/windows/report.htest-correlation.md | 74 - report-0.5.6/report/tests/testthat/_snaps/windows/report.htest-t-test.md | 362 +++++--- report-0.5.6/report/tests/testthat/_snaps/windows/report.htest-wilcox.md |only report-0.5.6/report/tests/testthat/_snaps/windows/report.ivreg.md | 88 -- report-0.5.6/report/tests/testthat/_snaps/windows/report.lavaan.md | 150 +-- report-0.5.6/report/tests/testthat/_snaps/windows/report.lm.md | 48 - report-0.5.6/report/tests/testthat/_snaps/windows/report.lmer.md | 96 +- report-0.5.6/report/tests/testthat/_snaps/windows/report.stanreg.md | 114 +- report-0.5.6/report/tests/testthat/_snaps/windows/report.survreg.md | 77 - 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report-0.5.6/report/tests/testthat/test-report.stanreg.R | 62 - report-0.5.6/report/tests/testthat/test-report.survreg.R | 24 report-0.5.6/report/tests/testthat/test-report_intercept.R | 95 +- report-0.5.6/report/tests/testthat/test-report_participants.R | 86 +- report-0.5.6/report/tests/testthat/test-report_performance.R | 197 +++- report-0.5.6/report/tests/testthat/test-report_sample.R |only report-0.5.6/report/vignettes/cite_packages.Rmd | 1 report-0.5.6/report/vignettes/report.Rmd | 16 report-0.5.6/report/vignettes/report_table.Rmd |only 127 files changed, 2921 insertions(+), 2566 deletions(-)
Title: Estimation of Life Years Lost
Description: Estimation of life expectancy and
Life Years Lost (LYL, or lillies for short) for a given population, for
example those with a given disease or condition. In addition, the package
can be used to compare estimates from different populations, or to estimate
confidence intervals. Technical details of the method are available in
Plana-Ripoll et al. (2020) <doi:10.1371/journal.pone.0228073> and Andersen
(2017) <doi:10.1002/sim.7357>.
Author: Oleguer Plana-Ripoll [aut, cre]
Maintainer: Oleguer Plana-Ripoll <opr@clin.au.dk>
Diff between lillies versions 0.2.9 dated 2021-02-16 and 0.2.10 dated 2023-02-05
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- R/lyl.R | 3 ++- R/lyl_aggregated_range.R | 2 +- R/lyl_aux.R | 18 ++++++++++++------ R/lyl_ci.R | 19 ++++++++++++------- R/lyl_diff.R | 28 ++++++++++++++++++---------- R/lyl_diff_aux.R | 6 ++++-- R/lyl_diff_ref.R | 28 ++++++++++++++++++---------- R/lyl_plot.R | 14 +++++++++----- R/lyl_range.R | 3 ++- R/lyl_summary.R | 12 ++++++------ man/lyl.Rd | 3 ++- man/lyl_ci.Rd | 4 ++-- man/lyl_diff.Rd | 4 ++-- man/lyl_range.Rd | 3 ++- man/summary.lyl_ci.Rd | 6 +++--- 17 files changed, 118 insertions(+), 81 deletions(-)
Title: Calculate How many Imputations are Needed for Multiple
Imputation
Description: When performing multiple imputations, while 5-10 imputations are
sufficient for obtaining point estimates, a larger number of
imputations are needed for proper standard error estimates.
This package allows you to calculate how many imputations are
needed, following the work of von Hippel (2020)
<doi:10.1177/0049124117747303>.
Author: Josh Errickson [aut, cre]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between howManyImputations versions 0.2.3 dated 2022-05-31 and 0.2.4 dated 2023-02-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 +++++- inst/CITATION | 38 ++++++++++++++++++-------------------- 4 files changed, 30 insertions(+), 28 deletions(-)
More information about howManyImputations at CRAN
Permanent link
Title: Various Andrews Curves
Description: Visualisation of multidimensional data through different Andrews curves:
Andrews, D. F. (1972) Plots of High-Dimensional Data. Biometrics, 28(1), 125-136. <doi:10.2307/2528964>.
Author: Jaroslav Myslivec [aut],
Sigbert Klinke [cre, ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between andrews versions 1.1.0 dated 2023-01-08 and 1.1.1 dated 2023-02-05
DESCRIPTION | 13 ++++--- MD5 | 18 +++++----- NAMESPACE | 5 ++ R/andrews.R | 85 +++++++++----------------------------------------- R/normalize.R | 35 ++++++++++++++------ R/outlyingness.R |only README.md | 5 +- inst/doc/andrews.html | 6 +-- man/andrews.Rd | 14 ++++---- man/normalize.Rd | 11 +++++- man/outlyingness.Rd |only 11 files changed, 85 insertions(+), 107 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] ,
Kurt Hornik [aut] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-10 dated 2022-12-14 and 0.7-11 dated 2023-02-05
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- inst/CITATION | 12 +++++++++--- inst/NEWS.Rd | 9 ++++++++- inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/acq.Rd | 2 +- man/crude.Rd | 2 +- man/readDOC.Rd | 13 ++++++++----- man/readReut21578XML.Rd | 2 +- 10 files changed, 42 insertions(+), 26 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Description: The main purpose of this package is to perform simulation-based
estimation of stochastic actor-oriented models for longitudinal network
data collected as panel data. Dependent variables can be single or
multivariate networks, which can be directed, non-directed, or two-mode;
and associated actor variables.
There are also functions for testing parameters and checking goodness of fit.
An overview of these models is given in Tom A.B. Snijders (2017), Stochastic
Actor-Oriented Models for Network Dynamics, Annual Review of Statistics and
Its Application, 4, 343-363 <doi: 10.1146/annurev-statistics-060116-054035>.
An extensive manual, scripts, and much further information is at the Siena
website <http://www.stats.ox.ac.uk/~snijders/siena/>.
Author: Tom A.B. Snijders [cre, aut] ,
Ruth Ripley [aut],
Krists Boitmanis [aut, ctb],
Christian Steglich [aut, ctb] ,
Johan Koskinen [aut, ctb] ,
Nynke Niezink [aut, ctb] ,
Viviana Amati [aut, ctb] ,
Christoph Stadtfeld [ctb] ,
James Hollway [ctb] ,
Per Blo [...truncated...]
Maintainer: Tom A.B. Snijders <tom.snijders@nuffield.ox.ac.uk>
Diff between RSiena versions 1.3.14 dated 2022-11-04 and 1.3.14.1 dated 2023-02-05
DESCRIPTION | 8 ++--- MD5 | 4 +- src/siena07internals.cpp | 75 +++++++++++++++++++++++------------------------ 3 files changed, 44 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-12 0.2.5
2022-04-19 0.2.3
2022-04-17 0.2.2
2022-04-04 0.1.3
2022-03-31 0.1.1
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between tree versions 1.0-42 dated 2022-05-29 and 1.0-43 dated 2023-02-05
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/prune.tree.Rd | 5 +++-- tests/Examples/tree-Ex.Rout.save | 11 ++++++----- 5 files changed, 25 insertions(+), 15 deletions(-)
Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing,
to use separately or with the book "Visual Statistics. Use R!":
Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Dr Alexey Shipunov died in December 2022.
Most useful functions:
Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering;
Recode() which does multiple recoding in a fast, simple and flexible way;
Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which measures group separation on any projection;
Biarrows() which converts any scatterplot into biplot;
and Pleiad() which is fast and flexible correlogram.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Cor [...truncated...]
Maintainer: ORPHANED
Diff between shipunov versions 1.17 dated 2022-02-26 and 1.17.1 dated 2023-02-05
DESCRIPTION | 13 ++++++++----- MD5 | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-)
Title: Convenience Functions for Package 'lavaan'
Description: Affords an alternative, vector-based syntax to 'lavaan', as well as other
convenience functions such as naming paths and defining indirect
links automatically, in addition to convenience formatting optimized
for a publication and script sharing workflow.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between lavaanExtra versions 0.1.3 dated 2022-10-04 and 0.1.4 dated 2023-02-04
lavaanExtra-0.1.3/lavaanExtra/R/save_as_x.R |only lavaanExtra-0.1.3/lavaanExtra/man/save_as_x.Rd |only lavaanExtra-0.1.3/lavaanExtra/tests/testthat/test-save_as_x.R |only lavaanExtra-0.1.4/lavaanExtra/DESCRIPTION | 14 lavaanExtra-0.1.4/lavaanExtra/MD5 | 114 - lavaanExtra-0.1.4/lavaanExtra/NAMESPACE | 26 lavaanExtra-0.1.4/lavaanExtra/NEWS.md | 17 lavaanExtra-0.1.4/lavaanExtra/R/cfa_fit_plot.R | 160 +- lavaanExtra-0.1.4/lavaanExtra/R/lavaan_cov.R | 96 - lavaanExtra-0.1.4/lavaanExtra/R/lavaan_ind.R | 106 - lavaanExtra-0.1.4/lavaanExtra/R/lavaan_reg.R | 86 - lavaanExtra-0.1.4/lavaanExtra/R/nice_fit.R | 96 - lavaanExtra-0.1.4/lavaanExtra/R/nice_lavaanPlot.R | 104 - lavaanExtra-0.1.4/lavaanExtra/R/nice_tidySEM.R | 267 +-- lavaanExtra-0.1.4/lavaanExtra/R/write_lavaan.R | 316 ++-- lavaanExtra-0.1.4/lavaanExtra/R/zzz.R | 18 lavaanExtra-0.1.4/lavaanExtra/README.md | 719 +++++---- lavaanExtra-0.1.4/lavaanExtra/build/vignette.rds |binary lavaanExtra-0.1.4/lavaanExtra/inst/CITATION |only lavaanExtra-0.1.4/lavaanExtra/inst/doc/example.Rmd | 760 +++++----- lavaanExtra-0.1.4/lavaanExtra/inst/doc/example.html | 129 - lavaanExtra-0.1.4/lavaanExtra/inst/doc/fullworkflow.R | 16 lavaanExtra-0.1.4/lavaanExtra/inst/doc/fullworkflow.Rmd | 17 lavaanExtra-0.1.4/lavaanExtra/inst/doc/fullworkflow.html | 534 +++---- lavaanExtra-0.1.4/lavaanExtra/inst/doc/indirect.Rmd | 672 ++++---- lavaanExtra-0.1.4/lavaanExtra/inst/doc/indirect.html | 159 +- lavaanExtra-0.1.4/lavaanExtra/inst/doc/regression.Rmd | 74 lavaanExtra-0.1.4/lavaanExtra/inst/doc/regression.html | 165 +- lavaanExtra-0.1.4/lavaanExtra/inst/doc/special.Rmd | 64 lavaanExtra-0.1.4/lavaanExtra/inst/doc/special.html | 111 - lavaanExtra-0.1.4/lavaanExtra/inst/doc/test.Rmd | 48 lavaanExtra-0.1.4/lavaanExtra/inst/doc/test.html | 115 - lavaanExtra-0.1.4/lavaanExtra/man/cfa_fit_plot.Rd | 156 +- lavaanExtra-0.1.4/lavaanExtra/man/figures/README-cfa2-1.png |binary lavaanExtra-0.1.4/lavaanExtra/man/figures/README-indirect2-1.png |binary lavaanExtra-0.1.4/lavaanExtra/man/figures/README-path2-1.png |binary lavaanExtra-0.1.4/lavaanExtra/man/figures/semplot2.png |only lavaanExtra-0.1.4/lavaanExtra/man/lavaan_cov.Rd | 110 - lavaanExtra-0.1.4/lavaanExtra/man/lavaan_ind.Rd | 119 - lavaanExtra-0.1.4/lavaanExtra/man/lavaan_reg.Rd | 100 - lavaanExtra-0.1.4/lavaanExtra/man/nice_fit.Rd | 113 - lavaanExtra-0.1.4/lavaanExtra/man/nice_lavaanPlot.Rd | 138 - lavaanExtra-0.1.4/lavaanExtra/man/nice_tidySEM.Rd | 204 +- lavaanExtra-0.1.4/lavaanExtra/man/write_lavaan.Rd | 172 +- lavaanExtra-0.1.4/lavaanExtra/tests/testthat.R | 24 lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-cfa_fit_plot.R | 109 - lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-lavaan_cov.R | 60 lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-lavaan_ind.R | 62 lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-lavaan_reg.R | 62 lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-nice_fit.R | 45 lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-nice_lavaanPlot.R | 130 - lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-nice_tidySEM.R | 234 +-- lavaanExtra-0.1.4/lavaanExtra/tests/testthat/test-write_lavaan.R | 592 +++---- lavaanExtra-0.1.4/lavaanExtra/tests/testthat/testthat-problems.rds |only lavaanExtra-0.1.4/lavaanExtra/vignettes/example.Rmd | 760 +++++----- lavaanExtra-0.1.4/lavaanExtra/vignettes/fullworkflow.Rmd | 17 lavaanExtra-0.1.4/lavaanExtra/vignettes/images/fullworkflow/holzinger_model.png |binary lavaanExtra-0.1.4/lavaanExtra/vignettes/indirect.Rmd | 672 ++++---- lavaanExtra-0.1.4/lavaanExtra/vignettes/regression.Rmd | 74 lavaanExtra-0.1.4/lavaanExtra/vignettes/special.Rmd | 64 lavaanExtra-0.1.4/lavaanExtra/vignettes/test.Rmd | 48 61 files changed, 4605 insertions(+), 4463 deletions(-)
Title: Estimation and Simulation of Drifting Semi-Markov Models
Description: Performs parametric and non-parametric estimation and simulation of
drifting semi-Markov processes. The definition of parametric and non-parametric
model specifications is also possible. Furthermore, three different types of
drifting semi-Markov models are considered. These models differ in the number
of transition matrices and sojourn time distributions used for the computation
of a number of semi-Markov kernels, which in turn characterize the drifting
semi-Markov kernel. For the parametric model estimation and specification,
several discrete distributions are considered for the sojourn times: Uniform,
Poisson, Geometric, Discrete Weibull and Negative Binomial. The non-parametric
model specification makes no assumptions about the shape of the sojourn time
distributions. Semi-Markov models are described in:
Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>.
Drifting Markov models are described in:
Vergne, N. (2008) <doi:10.2202/1544-6115.1326>.
Reliability ind [...truncated...]
Author: Vlad Stefan Barbu [aut] ,
Ioannis Mavrogiannis [aut, cre],
Nicolas Vergne [aut]
Maintainer: Ioannis Mavrogiannis <mavrogiannis.ioa@gmail.com>
Diff between dsmmR versions 0.0.96 dated 2022-11-16 and 1.0.1 dated 2023-02-04
DESCRIPTION | 18 ++-- MD5 | 33 ++++---- NEWS.md |only R/dsmmR-package.R | 86 ++++++++++++---------- R/fitmodel.R | 145 ++++++++++++++++++++----------------- R/generic_functions.R | 156 +++++++++++++++++++++------------------- R/nonparametric.R | 28 +++---- R/parametric.R | 30 +++---- R/parametric_estimation.R | 6 - R/utils.R | 37 ++++----- README.md | 178 ++++++++++++++++++++++++++++++++++++++++++++-- man/create_sequence.Rd | 4 - man/dsmmR-package.Rd | 84 ++++++++++++--------- man/fit_dsmm.Rd | 82 +++++++++++---------- man/get_kernel.Rd | 38 ++++----- man/nonparametric_dsmm.Rd | 28 +++---- man/parametric_dsmm.Rd | 28 +++---- man/simulate.dsmm.Rd | 19 ++-- 18 files changed, 612 insertions(+), 388 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information see Sparapani, Spanbauer and McCulloch <doi:10.18637/jss.v097.i01>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Charles Spanbauer [aut],
Robert Gramacy [aut],
Matthew Pratola [aut],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.9 dated 2021-01-05 and 2.9.3 dated 2023-02-04
BART-2.9.3/BART/DESCRIPTION | 8 +-- BART-2.9.3/BART/MD5 | 48 ++++++++----------- BART-2.9.3/BART/NEWS | 12 ++++ BART-2.9.3/BART/R/recur.pwbart.R | 2 BART-2.9.3/BART/R/surv.pre.bart.R | 60 +++++++++++++++++++----- BART-2.9.3/BART/build/vignette.rds |binary BART-2.9.3/BART/data/ACTG175.rda |binary BART-2.9.3/BART/data/alligator.rda |binary BART-2.9.3/BART/data/arq.rda |binary BART-2.9.3/BART/data/bladder.rda |binary BART-2.9.3/BART/data/leukemia.rda |binary BART-2.9.3/BART/data/lung.rda |binary BART-2.9.3/BART/data/transplant.rda |binary BART-2.9.3/BART/data/xdm20.test.rda |binary BART-2.9.3/BART/data/xdm20.train.rda |binary BART-2.9.3/BART/data/ydm20.test.rda |binary BART-2.9.3/BART/data/ydm20.train.rda |binary BART-2.9.3/BART/demo/leuk.R | 9 ++- BART-2.9.3/BART/inst/doc/the-BART-R-package.pdf |binary BART-2.9.3/BART/src/Makevars.in | 8 --- BART-2.9.3/BART/src/Makevars.win | 3 - BART-2.9.3/BART/src/init.c | 2 BART-2.9.3/BART/src/mc_cores_openmp.cpp | 4 - BART-2.9/BART/vignettes/article.pdf |only BART-2.9/BART/vignettes/article.tex |only BART-2.9/BART/vignettes/bart.pdf |only BART-2.9/BART/vignettes/bart.tex |only 27 files changed, 100 insertions(+), 56 deletions(-)
Title: Transforms Institutional Data into Text Files for IPEDS
Automated Import/Upload
Description: Starting from user-supplied institutional data, these scripts
transform, aggregate, and reshape the information to produce
key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System)
through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes.
Final files are saved locally to a location of the user's choice.
User-friendly readable files can also be produced for purposes of data review and validation.
Author: Alison Lanski [aut, cre],
Shiloh Fling [aut]
Maintainer: Alison Lanski <alanski@nd.edu>
Diff between IPEDSuploadables versions 2.6.5 dated 2022-12-07 and 2.7.5 dated 2023-02-04
DESCRIPTION | 8 +- MD5 | 84 +++++++++++++-------------- NAMESPACE | 1 NEWS.md | 8 ++ R/create_dummy_data_ef1.R | 15 ++++ R/ef1_students.R | 5 - R/make_ef1_part_H.R |only R/make_gr_part_E.R | 15 +++- R/prep_hr_data_frame.R | 8 ++ R/produce_com_report.R | 3 R/produce_e1d_report.R | 6 - R/produce_ef1_report.R | 21 +++++- R/produce_gr_report.R | 4 - R/produce_hr_report.R | 4 - R/specs_EF1.R | 2 R/zzz.R | 2 build/vignette.rds |binary data/ef1_retention.rda |binary data/ef1_students.rda |binary data/part_outputs.rda |binary data/specs_EF1.rda |binary inst/doc/howto_overall_ipedsuploadables.Rmd | 2 inst/doc/howto_overall_ipedsuploadables.html | 22 ++++--- inst/doc/howto_use_autoformat.html | 19 ++++-- inst/doc/setup_for_fallenrollment.R | 5 - inst/doc/setup_for_fallenrollment.Rmd | 5 - inst/doc/setup_for_fallenrollment.html | 11 +++ inst/doc/setup_for_hr.Rmd | 3 inst/doc/setup_for_hr.html | 9 ++ man/create_dummy_data_ef1.Rd | 4 - man/ef1_students.Rd | 7 +- man/make_ef1_part_H.Rd |only man/produce_com_report.Rd | 3 man/produce_e1d_report.Rd | 4 - man/produce_ef1_report.Rd | 12 +++ man/produce_gr_report.Rd | 4 - man/produce_hr_report.Rd | 4 - man/set_report_path.Rd | 28 ++++----- man/specs_EF1.Rd | 2 man/specs_HR.Rd | 32 +++++----- tests/testthat/test-part-outputs.R | 1 vignettes/howto_overall_ipedsuploadables.Rmd | 2 vignettes/setup_for_fallenrollment.Rmd | 5 - vignettes/setup_for_hr.Rmd | 3 44 files changed, 241 insertions(+), 132 deletions(-)
More information about IPEDSuploadables at CRAN
Permanent link
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between gaselect versions 1.0.11 dated 2022-04-06 and 1.0.21 dated 2023-02-04
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++-------- configure | 27 ++++++++++++++++----------- configure.ac | 11 ++++++++--- src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/ShuffledSet.h | 20 +++++++++++++------- src/autoconfig.win.h | 4 ++-- src/config.h | 11 ++++++++--- 9 files changed, 62 insertions(+), 42 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for
density clustering. For that, this package provides an R interface for the
efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria,
David L. Millman, Vincent Rouvreau.
Maintainer: Jisu Kim <jisu.kim@inria.fr>
Diff between TDA versions 1.8.8 dated 2022-10-30 and 1.9 dated 2023-02-04
DESCRIPTION | 12 MD5 | 22 NEWS | 6 inst/doc/article.pdf |binary man/TDA-package.Rd | 4 src/CGAL/GMP/Gmpfr_type.h | 15 src/Makevars | 12 src/boost/container/detail/copy_move_algo.hpp | 827 +++++++++++++++++++++++--- src/boost/container/detail/flat_tree.hpp | 46 - src/boost/container/flat_map.hpp | 31 src/boost/container/vector.hpp | 385 +----------- src/utilities/circular_list.h | 8 12 files changed, 905 insertions(+), 463 deletions(-)
Title: A Tool for Creating Custom Neural Networks in C++ and using Them
in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <vnikolaidis@us.uop.gr>
Diff between nnlib2Rcpp versions 0.1.9 dated 2022-05-26 and 0.1.10 dated 2023-02-04
DESCRIPTION | 6 LICENSE | 4 MD5 | 32 ++-- NAMESPACE | 8 - R/NNClasses.R | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/manual.pdf |binary man/NN-class.Rd | 49 +++++- src/Rcpp_NN_module.cpp | 288 +++++++++++++++++++++++++++++++-------- src/additional_parts.h | 4 src/connection_set.h | 9 - src/layer.h | 358 +++++++++++++++++++++++++++++-------------------- src/nn.cpp | 47 ++++++ src/nn.h | 6 src/nnlib2.h | 4 src/pe.cpp | 2 17 files changed, 572 insertions(+), 253 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.7.1 dated 2022-09-02 and 0.7.2 dated 2023-02-04
DESCRIPTION | 12 +- MD5 | 89 +++++++-------- NEWS | 18 +++ R/MCMCsim.R | 51 ++++++-- R/MatrixUtils.R | 39 ++---- R/RcppExports.R | 28 +++- R/TMVN_sampler.R | 229 ++++++++++++--------------------------- R/aux_closures.R | 19 +-- R/cholesky.R | 125 +++++++-------------- R/mc_block.R | 7 + R/mc_gen.R | 62 ++++++++-- R/mc_mec.R | 2 R/mc_reg.R | 5 R/modelmatrix.R | 2 R/models.R | 76 +++++-------- R/parallel.R | 5 R/prediction.R | 58 ++++++--- R/samplers.R | 19 +-- build/vignette.rds |binary inst/doc/area_level.html | 195 ++++++++++++++++----------------- inst/doc/linear_weighting.Rmd | 1 inst/doc/linear_weighting.html | 142 ++++++++++++++---------- inst/doc/unit_level.html | 129 ++++++++++------------ man/MCMC-object-conversion.Rd | 13 +- man/MCMCsim.Rd | 8 - man/Matrix-methods.Rd | 3 man/computeDesignMatrix.Rd | 9 - man/correlation.Rd | 5 man/create_TMVN_sampler.Rd | 12 +- man/create_sampler.Rd | 2 man/predict.mcdraws.Rd | 5 src/Makevars | 3 src/Makevars.win | 5 src/RcppExports.cpp | 98 +++++++++++----- src/TN.cpp | 239 +++++++++++++++++++++++++++++++++++++++-- src/c_export.cpp | 6 - src/chMatrix.c | 63 ---------- src/mcmcsae_init.c | 153 +++++++++++++------------- src/speed_ups.cpp | 44 ++++--- src/tabMatrix.cpp | 36 +++--- tests/testthat/test_Cholesky.R | 12 -- tests/testthat/test_Poisson.R | 2 tests/testthat/test_TMVN.R | 45 ++++--- tests/testthat/test_linalg.R | 8 + tests/testthat/test_predict.R |only vignettes/linear_weighting.Rmd | 1 46 files changed, 1149 insertions(+), 936 deletions(-)
Title: R Markdown Templates for Journal of Data Science
Description: Customized R Markdown templates for authoring articles
for Journal of Data Science.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between jds.rmd versions 0.3.1 dated 2022-07-05 and 0.3.2 dated 2023-02-04
DESCRIPTION | 8 +-- MD5 | 10 +-- NEWS.md | 7 ++ R/draft.R | 20 +++++-- inst/rmarkdown/templates/pdf_article/resources/jdsart.cls | 26 ++++++++-- inst/rmarkdown/templates/pdf_article/resources/template-jdsart.cls.tex | 2 6 files changed, 51 insertions(+), 22 deletions(-)
Title: Meta Analysis of Factor Analysis Based on CO-Occurrence Matrices
Description: Provide a series of functions to conduct a meta analysis of
factor analysis based on co-occurrence matrices. The tool can be used to
solve the factor structure (i.e. inner structure of a construct, or scale)
debate in several disciplines, such as psychology, psychiatry, management,
education so on. References: Shafer (2005) <doi:10.1037/1040-3590.17.3.324>;
Shafer (2006) <doi:10.1002/jclp.20213>; Loeber and Schmaling (1985) <doi:10.1007/BF00910652>.
Author: Xijian Zheng [aut, cre],
Huiyong Fan [aut]
Maintainer: Xijian Zheng <psydreammer@foxmail.com>
Diff between coefa versions 1.0.2 dated 2022-11-18 and 1.0.3 dated 2023-02-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 2 +- inst/doc/Introduction.html | 8 ++++---- vignettes/Introduction.Rmd | 2 +- 8 files changed, 21 insertions(+), 17 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-06 0.1.4
2021-03-18 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-06 1.2
2021-06-14 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-17 0.3.1
2022-01-21 0.2.0
2021-09-27 0.1.2
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>.
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Philipp Otto [ctb],
Jan Linnenbrink [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 0.7.0 dated 2022-08-24 and 0.7.1 dated 2023-02-04
DESCRIPTION | 16 +- MD5 | 60 +++++----- NAMESPACE | 1 NEWS.md | 11 + R/CreateSpacetimeFolds.R | 2 R/aoa.R | 66 +++++------ R/calibrate_aoa.R | 36 ++++-- R/clustered_sample.R |only R/ffs.R | 14 +- R/nndm.R | 113 +++++++++++++------ R/plot_geodist.R | 72 +++++++++--- R/trainDI.R | 107 ++++++++++++++---- README.md | 16 +- build/partial.rdb |binary inst/doc/cast01-CAST-intro.html | 123 ++++++++++---------- inst/doc/cast02-AOA-tutorial.html | 137 +++++++++++------------ inst/doc/cast03-AOA-parallel.R | 7 - inst/doc/cast03-AOA-parallel.Rmd | 20 --- inst/doc/cast03-AOA-parallel.html | 224 ++++++++++++++++---------------------- inst/doc/cast04-plotgeodist.R | 54 ++------- inst/doc/cast04-plotgeodist.Rmd | 55 ++------- inst/doc/cast04-plotgeodist.html | 169 ++++++++++++++-------------- man/CreateSpacetimeFolds.Rd | 2 man/aoa.Rd | 20 +-- man/calibrate_aoa.Rd | 6 + man/clustered_sample.Rd |only man/ffs.Rd | 4 man/nndm.Rd | 91 +++++++++++---- man/plot_geodist.Rd | 16 +- man/trainDI.Rd | 11 + vignettes/cast03-AOA-parallel.Rmd | 20 --- vignettes/cast04-plotgeodist.Rmd | 55 ++------- 32 files changed, 808 insertions(+), 720 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between tidybayes versions 3.0.2 dated 2022-01-05 and 3.0.3 dated 2023-02-04
tidybayes-3.0.2/tidybayes/tests/testthat/fontconfig-helper.R |only tidybayes-3.0.3/tidybayes/DESCRIPTION | 13 tidybayes-3.0.3/tidybayes/MD5 | 105 tidybayes-3.0.3/tidybayes/NAMESPACE | 2 tidybayes-3.0.3/tidybayes/NEWS.md | 10 tidybayes-3.0.3/tidybayes/R/compare_levels.R | 2 tidybayes-3.0.3/tidybayes/R/deprecated.R | 24 tidybayes-3.0.3/tidybayes/R/predicted_draws.R | 55 tidybayes-3.0.3/tidybayes/R/predicted_rvars.R | 36 tidybayes-3.0.3/tidybayes/R/spread_draws.R | 16 tidybayes-3.0.3/tidybayes/R/spread_rvars.R | 2 tidybayes-3.0.3/tidybayes/R/tidy_draws.R | 9 tidybayes-3.0.3/tidybayes/R/ungather_draws.R | 2 tidybayes-3.0.3/tidybayes/R/unspread_draws.R | 8 tidybayes-3.0.3/tidybayes/build/partial.rdb |binary tidybayes-3.0.3/tidybayes/build/vignette.rds |binary tidybayes-3.0.3/tidybayes/inst/doc/tidy-brms.R | 27 tidybayes-3.0.3/tidybayes/inst/doc/tidy-brms.Rmd | 35 tidybayes-3.0.3/tidybayes/inst/doc/tidy-brms.html | 1107 ++++-- tidybayes-3.0.3/tidybayes/inst/doc/tidy-posterior.R | 60 tidybayes-3.0.3/tidybayes/inst/doc/tidy-posterior.Rmd | 86 tidybayes-3.0.3/tidybayes/inst/doc/tidy-posterior.html | 1059 ++++-- tidybayes-3.0.3/tidybayes/inst/doc/tidy-rstanarm.R | 6 tidybayes-3.0.3/tidybayes/inst/doc/tidy-rstanarm.Rmd | 8 tidybayes-3.0.3/tidybayes/inst/doc/tidy-rstanarm.html | 954 ++++- tidybayes-3.0.3/tidybayes/inst/doc/tidybayes-residuals.R | 22 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes-residuals.Rmd | 24 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes-residuals.html | 632 ++- tidybayes-3.0.3/tidybayes/inst/doc/tidybayes.R | 5 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes.Rmd | 9 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes.html | 1705 +++++++--- tidybayes-3.0.3/tidybayes/man/add_predicted_draws.Rd | 72 tidybayes-3.0.3/tidybayes/man/add_predicted_rvars.Rd | 73 tidybayes-3.0.3/tidybayes/man/reexports.Rd | 2 tidybayes-3.0.3/tidybayes/man/spread_draws.Rd | 6 tidybayes-3.0.3/tidybayes/tests/testthat/_snaps/test.geom_dotsinterval/stat-dotsh-with-a-group-with-1-dot.svg | 80 tidybayes-3.0.3/tidybayes/tests/testthat/_snaps/test.geom_dotsinterval/vanilla-geom-dotsh.svg | 80 tidybayes-3.0.3/tidybayes/tests/testthat/_snaps/test.stat_eye/two-parameter-factor-horizontal-eye-fill.svg | 4 tidybayes-3.0.3/tidybayes/tests/testthat/test.add_draws.R | 2 tidybayes-3.0.3/tidybayes/tests/testthat/test.emmeans_comparison.R | 1 tidybayes-3.0.3/tidybayes/tests/testthat/test.epred_draws.R | 23 tidybayes-3.0.3/tidybayes/tests/testthat/test.epred_rvars.R | 2 tidybayes-3.0.3/tidybayes/tests/testthat/test.gather_emmeans_draws.R | 2 tidybayes-3.0.3/tidybayes/tests/testthat/test.linpred_draws.R | 8 tidybayes-3.0.3/tidybayes/tests/testthat/test.linpred_rvars.R | 2 tidybayes-3.0.3/tidybayes/tests/testthat/test.predicted_draws.R | 12 tidybayes-3.0.3/tidybayes/tests/testthat/test.predicted_rvars.R | 5 tidybayes-3.0.3/tidybayes/tests/testthat/test.residual_draws.R | 2 tidybayes-3.0.3/tidybayes/tests/testthat/test.spread_draws.R | 8 tidybayes-3.0.3/tidybayes/vignettes/tidy-brms.Rmd | 35 tidybayes-3.0.3/tidybayes/vignettes/tidy-posterior.Rmd | 86 tidybayes-3.0.3/tidybayes/vignettes/tidy-rstanarm.Rmd | 8 tidybayes-3.0.3/tidybayes/vignettes/tidybayes-residuals.Rmd | 24 tidybayes-3.0.3/tidybayes/vignettes/tidybayes.Rmd | 9 54 files changed, 4678 insertions(+), 1891 deletions(-)
Title: Fuzzy Measure Tools
Description: Various tools for handling fuzzy measures, calculating Shapley value and interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using 'lpsolve' package, whose source in C adapted to the R environment
is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package. Please refer to the following:
[1] <https://personal-sites.deakin.edu.au/~gleb/fmtools.html>
[2] G. Beliakov, H. Bustince, T. Calvo, 'A Practical Guide to Averaging', Springer, (2016, ISBN: 978-3-319-24753-3).
[3] G. Beliakov, S. James, J-Z. Wu, 'Discrete Fuzzy Measures', Springer, (2020, ISBN: 978-3-030-15305-2).
Author: Gleb Beliakov [aut, cre],
Quan Vu [ctb],
Andrei Kelarev [ctb],
Michel Berkelaar [ctb],
Kjell Eikland [ctb],
Samuel E. Buttrey [ctb],
Stefan I. Larimore [ctb],
Timothy A. Davis [ctb],
John Gilbert [ctb],
Esmond Ng [ctb],
Peter Notebaert [ctb],
Richard [...truncated...]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>
Diff between Rfmtool versions 4.1.9 dated 2022-11-30 and 4.1.10 dated 2023-02-04
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- inst/doc/Rfmtool_manual.pdf |binary src/Makevars | 2 +- src/Makevars.win | 2 +- src/fuzzymeasurefit.cpp | 10 ++++++---- src/fuzzymeasurefit3.cpp | 26 +++++++++++++------------- src/lp_MPS.c | 11 +++++++++++ src/lp_lib.c | 9 ++++++++- src/lp_params.c | 9 +++++++++ src/lp_presolve.c | 9 +++++++++ src/lusol.c | 11 +++++++++++ src/mmio.c | 9 +++++++++ src/yacc_read.c | 10 ++++++++++ 14 files changed, 105 insertions(+), 37 deletions(-)
Title: Evidential Regression
Description: An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.36227/techrxiv.21791831.v1>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).
Author: Thierry Denoeux [aut, cre]
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evreg versions 1.0.0 dated 2023-01-17 and 1.0.1 dated 2023-02-04
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS |only R/ENNreg.R | 4 +--- R/ENNreg_cv.R | 10 +++++++--- R/pl_contour.R | 2 +- R/predict.ENNreg.R | 5 +++-- inst/doc/Introduction.html | 16 ++++++++-------- man/ENNreg.Rd | 4 +--- man/ENNreg_cv.Rd | 2 +- man/pl_contour.Rd | 2 +- 11 files changed, 37 insertions(+), 35 deletions(-)
Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional
data (e.g. portions of substances) and positive numbers (e.g. concentrations)
in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart <boogaart@hzdr.de>,
Raimon Tolosana-Delgado, Matevz Bren
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between compositions versions 2.0-4 dated 2022-01-05 and 2.0-5 dated 2023-02-04
ChangeLog | 4 DESCRIPTION | 10 MD5 | 82 +- R/3d.R | 4 R/Geostat.R | 2 R/PrincipalBalances.R | 4 R/compositions.R | 4 build/partial.rdb |binary inst/doc/UsingCompositions.pdf |binary inst/doc/UsingCompositions.rnw | 2 inst/doc/compositions_v2.html | 1149 +++++++++++++++++++++------------------- man/HouseholdExp.Rd | 6 man/acomp.Rd | 4 man/acomparith.Rd | 4 man/acompmargin.Rd | 2 man/alr.Rd | 2 man/arrows3d.Rd | 2 man/axis3d.Rd | 2 man/balancebase.Rd | 4 man/biplot3d.Rd | 2 man/codadendrogram.Rd | 2 man/compositions.Rd | 4 man/gsigetbalstruct.Rd | 2 man/gsimerge2signary.Rd | 2 man/gsivarwithlosts.Rd | 2 man/ilr.Rd | 2 man/ilrBase.Rd | 2 man/mix2compositions.Rd | 2 man/mixRead.Rd | 4 man/pairwisePlot.Rd | 6 man/plot.Rd | 4 man/plot3d.Rd | 2 man/plot3dacomp.Rd | 2 man/plot3daplus.Rd | 2 man/plot3drmult.Rd | 2 man/plot3drplus.Rd | 2 man/princompacomp.Rd | 4 man/pwlr.Rd | 2 man/pwlrPlot.Rd | 6 man/rDirichlet.Rd | 2 man/zeroreplace.Rd | 4 vignettes/UsingCompositions.rnw | 2 42 files changed, 715 insertions(+), 636 deletions(-)
Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Description: Produces ANOVA tables in the format used by Judd, McClelland,
and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook,
Data Analysis. This includes proportional reduction in error and
formatting to improve ease the transition between the book and R.
Author: Adam Blake [cre, aut] ,
Jeff Chrabaszcz [aut],
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adamblake@g.ucla.edu>
Diff between supernova versions 2.5.3 dated 2022-07-11 and 2.5.5 dated 2023-02-04
supernova-2.5.3/supernova/R/data.R |only supernova-2.5.3/supernova/data |only supernova-2.5.3/supernova/man/Fingers.Rd |only supernova-2.5.3/supernova/man/Fingers.messy.Rd |only supernova-2.5.3/supernova/man/Servers.Rd |only supernova-2.5.3/supernova/man/Survey.Rd |only supernova-2.5.3/supernova/man/Tables.Rd |only supernova-2.5.3/supernova/man/TipExperiment.Rd |only supernova-2.5.3/supernova/man/class_data.Rd |only supernova-2.5.3/supernova/tests/testthat/test-print.supernova.R |only supernova-2.5.5/supernova/DESCRIPTION | 9 supernova-2.5.5/supernova/MD5 | 35 - supernova-2.5.5/supernova/NEWS.md | 101 +-- supernova-2.5.5/supernova/R/generate_models.R | 2 supernova-2.5.5/supernova/R/supernova.R | 3 supernova-2.5.5/supernova/README.md | 298 +++++----- supernova-2.5.5/supernova/tests/testthat/_snaps/generate_models.md | 72 +- supernova-2.5.5/supernova/tests/testthat/_snaps/supernova.lmerMod.md |only supernova-2.5.5/supernova/tests/testthat/_snaps/supernova.md | 104 ++- supernova-2.5.5/supernova/tests/testthat/test-supernova.lmerMod.R | 26 supernova-2.5.5/supernova/tests/testthat/test-supernova.r | 36 - 21 files changed, 381 insertions(+), 305 deletions(-)
Title: Choice Models with Economic Foundation
Description: Implements choice models based on economic theory, including estimation using Markov chain Monte Carlo (MCMC), prediction, and more. Its usability is inspired by ideas from 'tidyverse'. Models include versions of the Hierarchical Multinomial Logit and Multiple Discrete-Continous (Volumetric) models with and without screening. The foundations of these models are described in Allenby, Hardt and Rossi (2019) <doi:10.1016/bs.hem.2019.04.002>. Models with conjunctive screening are described in Kim, Hardt, Kim and Allenby (2022) <doi:10.1016/j.ijresmar.2022.04.001>. Models with set-size variation are described in Hardt and Kurz (2020) <doi:10.2139/ssrn.3418383>.
Author: Nino Hardt [aut, cre]
Maintainer: Nino Hardt <me@ninohardt.com>
Diff between echoice2 versions 0.2.0 dated 2023-02-02 and 0.2.1 dated 2023-02-04
DESCRIPTION | 20 ++-- MD5 | 5 - src/echoice2.cpp | 252 ++++++++++++++++++++----------------------------------- src/myomp.h |only 4 files changed, 106 insertions(+), 171 deletions(-)
Title: Quantile Least Mahalanobis Distance Estimator for Tukey g-&-h
Mixture
Description: Functions for simulation, estimation, and model selection of finite
mixtures of Tukey's g-and-h distributions.
Author: Tingting Zhan [aut, cre, cph],
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <Tingting.Zhan@jefferson.edu>
Diff between QuantileGH versions 0.1.2 dated 2022-05-05 and 0.1.3 dated 2023-02-04
QuantileGH-0.1.2/QuantileGH/R/0setS4_QuantileGH.R |only QuantileGH-0.1.2/QuantileGH/R/CvM_test.R |only QuantileGH-0.1.2/QuantileGH/R/KL_dist.R |only QuantileGH-0.1.2/QuantileGH/R/LikRatio.R |only QuantileGH-0.1.2/QuantileGH/R/QLMDinit.R |only QuantileGH-0.1.2/QuantileGH/R/StepK_fmx.R |only QuantileGH-0.1.2/QuantileGH/R/Step_fmx.R |only QuantileGH-0.1.2/QuantileGH/R/autoplot.fmx.R |only QuantileGH-0.1.2/QuantileGH/R/ks_test.R |only QuantileGH-0.1.2/QuantileGH/man/CvM_test.Rd |only QuantileGH-0.1.2/QuantileGH/man/K.fmx.Rd |only QuantileGH-0.1.2/QuantileGH/man/KL_dist.Rd |only QuantileGH-0.1.2/QuantileGH/man/LikRatio.Rd |only QuantileGH-0.1.2/QuantileGH/man/QLMDinit.Rd |only QuantileGH-0.1.2/QuantileGH/man/S3_fmx_QLMDe.Rd |only QuantileGH-0.1.2/QuantileGH/man/StepK_fmx.Rd |only QuantileGH-0.1.2/QuantileGH/man/Step_fmx.Rd |only QuantileGH-0.1.2/QuantileGH/man/autoplot.fitdist.Rd |only QuantileGH-0.1.2/QuantileGH/man/autoplot_fmx.Rd |only QuantileGH-0.1.2/QuantileGH/man/fmx_QLMDe-class.Rd |only QuantileGH-0.1.2/QuantileGH/man/ks_test.Rd |only QuantileGH-0.1.3/QuantileGH/DESCRIPTION | 35 QuantileGH-0.1.3/QuantileGH/MD5 | 153 +- QuantileGH-0.1.3/QuantileGH/NAMESPACE | 97 + QuantileGH-0.1.3/QuantileGH/NEWS.md | 5 QuantileGH-0.1.3/QuantileGH/R/0Int_base_stats.R | 31 QuantileGH-0.1.3/QuantileGH/R/0S4_fmx.R |only QuantileGH-0.1.3/QuantileGH/R/Kolmogorov_dist_vanilla.R |only QuantileGH-0.1.3/QuantileGH/R/QLMDe.R | 543 +--------- QuantileGH-0.1.3/QuantileGH/R/QLMDe_stepK.R |only QuantileGH-0.1.3/QuantileGH/R/QLMDp.R | 18 QuantileGH-0.1.3/QuantileGH/R/QuantileGH_info.R | 49 QuantileGH-0.1.3/QuantileGH/R/TukeyGH.R | 42 QuantileGH-0.1.3/QuantileGH/R/as.fmx.R |only QuantileGH-0.1.3/QuantileGH/R/distribution_ext.R |only QuantileGH-0.1.3/QuantileGH/R/drop1.fmx.R |only QuantileGH-0.1.3/QuantileGH/R/fitdist_ext.R | 122 -- QuantileGH-0.1.3/QuantileGH/R/fmx.R | 481 ++++---- QuantileGH-0.1.3/QuantileGH/R/fmx_constraint.R | 202 ++- QuantileGH-0.1.3/QuantileGH/R/fmx_diagnosis.R |only QuantileGH-0.1.3/QuantileGH/R/fmx_init.R |only QuantileGH-0.1.3/QuantileGH/R/fmx_repar.R |only QuantileGH-0.1.3/QuantileGH/R/letterValue.R | 35 QuantileGH-0.1.3/QuantileGH/R/methods_fmx.R |only QuantileGH-0.1.3/QuantileGH/R/mixsmsn_dpqr.R |only QuantileGH-0.1.3/QuantileGH/R/mixsmsn_ext.R |only QuantileGH-0.1.3/QuantileGH/R/mixtools_ext.R |only QuantileGH-0.1.3/QuantileGH/R/mlogis.R | 16 QuantileGH-0.1.3/QuantileGH/R/quantile_ext.R |only QuantileGH-0.1.3/QuantileGH/R/reAssign.R | 9 QuantileGH-0.1.3/QuantileGH/R/step_fmx.R |only QuantileGH-0.1.3/QuantileGH/R/vuniroot2.R | 16 QuantileGH-0.1.3/QuantileGH/build/partial.rdb |binary QuantileGH-0.1.3/QuantileGH/build/vignette.rds |only QuantileGH-0.1.3/QuantileGH/data |only QuantileGH-0.1.3/QuantileGH/inst |only QuantileGH-0.1.3/QuantileGH/man/CK5.Rd |only QuantileGH-0.1.3/QuantileGH/man/CycD1.Rd |only QuantileGH-0.1.3/QuantileGH/man/Kolmogorov_dist.Rd |only QuantileGH-0.1.3/QuantileGH/man/QLMDe.Rd | 75 - QuantileGH-0.1.3/QuantileGH/man/QLMDe_stepK.Rd |only QuantileGH-0.1.3/QuantileGH/man/QLMDp.Rd | 22 QuantileGH-0.1.3/QuantileGH/man/QuantileGH-package.Rd | 10 QuantileGH-0.1.3/QuantileGH/man/TukeyGH.Rd | 26 QuantileGH-0.1.3/QuantileGH/man/approxdens.Rd |only QuantileGH-0.1.3/QuantileGH/man/as.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/as.fmx.fitdist.Rd |only QuantileGH-0.1.3/QuantileGH/man/as.fmx.mixEM.Rd |only QuantileGH-0.1.3/QuantileGH/man/as_fmx_mixsmsn.Rd |only QuantileGH-0.1.3/QuantileGH/man/autolayer_fmx_continuous.Rd |only QuantileGH-0.1.3/QuantileGH/man/autolayer_fmx_discrete.Rd |only QuantileGH-0.1.3/QuantileGH/man/autoplot.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/clusterList.Rd |only QuantileGH-0.1.3/QuantileGH/man/coef.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/confint.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/constraint_TeX.Rd |only QuantileGH-0.1.3/QuantileGH/man/crossprod_inv.Rd | 2 QuantileGH-0.1.3/QuantileGH/man/dbl2fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/dfmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/distArgs.Rd |only QuantileGH-0.1.3/QuantileGH/man/distType.Rd |only QuantileGH-0.1.3/QuantileGH/man/dist_logtrans.Rd |only QuantileGH-0.1.3/QuantileGH/man/drop1_fmx.Rd | 65 - QuantileGH-0.1.3/QuantileGH/man/fmx-class.Rd | 30 QuantileGH-0.1.3/QuantileGH/man/fmx.Rd | 132 -- QuantileGH-0.1.3/QuantileGH/man/fmx2dbl.Rd |only QuantileGH-0.1.3/QuantileGH/man/fmx_cluster.Rd |only QuantileGH-0.1.3/QuantileGH/man/fmx_constraint.Rd | 56 - QuantileGH-0.1.3/QuantileGH/man/fmx_diagnosis.Rd |only QuantileGH-0.1.3/QuantileGH/man/fmx_hybrid.Rd |only QuantileGH-0.1.3/QuantileGH/man/fmx_normix.Rd |only QuantileGH-0.1.3/QuantileGH/man/letterValue.Rd | 37 QuantileGH-0.1.3/QuantileGH/man/logLik.fitdist.Rd |only QuantileGH-0.1.3/QuantileGH/man/logLik.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/logLik.mixEM.Rd |only QuantileGH-0.1.3/QuantileGH/man/mahalanobis_int.Rd | 4 QuantileGH-0.1.3/QuantileGH/man/mixEM_pars.Rd |only QuantileGH-0.1.3/QuantileGH/man/mixsmsn_skewNormal.Rd |only QuantileGH-0.1.3/QuantileGH/man/mixsmsn_skewT.Rd |only QuantileGH-0.1.3/QuantileGH/man/mlogis.Rd | 20 QuantileGH-0.1.3/QuantileGH/man/nobs.fitdist.Rd |only QuantileGH-0.1.3/QuantileGH/man/nobs.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/npar.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/outer_allequal.Rd | 14 QuantileGH-0.1.3/QuantileGH/man/print.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/quantile_vcov.Rd | 16 QuantileGH-0.1.3/QuantileGH/man/reAssign.Rd | 9 QuantileGH-0.1.3/QuantileGH/man/show-fmx-method.Rd | 8 QuantileGH-0.1.3/QuantileGH/man/sort.mixEM.Rd |only QuantileGH-0.1.3/QuantileGH/man/sort_mixsmsn.Rd |only QuantileGH-0.1.3/QuantileGH/man/step_fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/sub-fmx-ANY-ANY-ANY-method.Rd | 31 QuantileGH-0.1.3/QuantileGH/man/ud_allequal.Rd | 8 QuantileGH-0.1.3/QuantileGH/man/user_constraint.Rd |only QuantileGH-0.1.3/QuantileGH/man/vcov.fmx.Rd |only QuantileGH-0.1.3/QuantileGH/man/vuniroot2.Rd | 14 QuantileGH-0.1.3/QuantileGH/vignettes |only 117 files changed, 1039 insertions(+), 1394 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-19 2.1.10
2022-06-15 2.1.9
Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre],
Mark Fredrickson [aut],
Ben Hansen [aut],
Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.3-1 dated 2022-08-10 and 0.3-2 dated 2023-02-03
DESCRIPTION | 8 ++--- MD5 | 13 ++++---- NEWS.md | 8 +++++ R/Design.R | 5 ++- R/plot.balancetest.R | 23 ++++++++------- inst/CITATION | 64 ++++++++++++++++++++----------------------- man/scale.DesignOptions.Rd |only tests/testthat/test.Design.R | 30 -------------------- 8 files changed, 65 insertions(+), 86 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 11. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.2.6 dated 2023-01-23 and 0.2.7 dated 2023-02-03
UKFE-0.2.6/UKFE/man/BivarSim.Rd |only UKFE-0.2.7/UKFE/DESCRIPTION | 6 - UKFE-0.2.7/UKFE/MD5 | 11 +-- UKFE-0.2.7/UKFE/R/All.R | 133 +------------------------------------- UKFE-0.2.7/UKFE/R/ThamesPQ.R | 2 UKFE-0.2.7/UKFE/data/ThamesPQ.rda |binary UKFE-0.2.7/UKFE/man/ThamesPQ.Rd | 2 7 files changed, 14 insertions(+), 140 deletions(-)
Title: Pedigree/Family-Based Genetic Association Tests Analysis and
Power
Description: This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Author: Thomas Hoffmann <tjhoffm@gmail.com>, with contributions from Christoph Lange <clange@hsph.harvard.edu>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between pbatR versions 2.2-13 dated 2018-04-19 and 2.2-15 dated 2023-02-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/pbat.R | 3 ++- R/pbatGUI.R | 12 ++++++++---- src/data.cpp | 3 ++- src/pbatR_init.c | 6 ++++-- 6 files changed, 26 insertions(+), 18 deletions(-)
Title: An Implementation of Ordinal Pattern Analysis
Description: Quantifies hypothesis to data fit for repeated measures
and longitudinal data, as described by Thorngate (1987)
<doi:10.1016/S0166-4115(08)60083-7> and Grice et al., (2015)
<doi:10.1177/2158244015604192>. Hypothesis and data are encoded as
pairwise relative orderings which are then compared to determine the
percentage of orderings in the data that are matched by the hypothesis.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>
Diff between opa versions 0.6 dated 2023-01-06 and 0.7.1 dated 2023-02-03
opa-0.6/opa/R/calculate_cvalues.R |only opa-0.7.1/opa/DESCRIPTION | 8 - opa-0.7.1/opa/MD5 | 27 +++--- opa-0.7.1/opa/R/RcppExports.R | 20 ++-- opa-0.7.1/opa/R/calculate_pccs.R | 31 ------- opa-0.7.1/opa/R/condition_comparison.R | 14 +-- opa-0.7.1/opa/R/fitopa.R | 44 +--------- opa-0.7.1/opa/R/utility.R | 14 --- opa-0.7.1/opa/README.md | 10 +- opa-0.7.1/opa/man/compare_conditions.Rd | 9 -- opa-0.7.1/opa/man/opa.Rd | 17 ---- opa-0.7.1/opa/src/RcppExports.cpp | 63 +++++++++------ opa-0.7.1/opa/src/cpp11.cpp | 20 ++-- opa-0.7.1/opa/src/cpp_functions.cpp | 119 +++++++++++++++++------------ opa-0.7.1/opa/tests/testthat/test-fitopa.R | 18 ---- 15 files changed, 181 insertions(+), 233 deletions(-)
Title: Alluvial Plots in 'ggplot2'
Description: Alluvial plots use variable-width ribbons and stacked bar plots to
represent multi-dimensional or repeated-measures data with categorical or
ordinal variables; see Riehmann, Hanfler, and Froehlich (2005)
<doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010)
<doi:10.1371/journal.pone.0008694>.
Alluvial plots are statistical graphics in the sense of Wilkinson (2006)
<doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and
parallel sets plots but are uniquely determined from the data and a small
set of parameters. This package extends Wickham's (2010)
<doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate
alluvial plots from tidy data.
Author: Jason Cory Brunson [aut, cre],
Quentin D. Read [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ggalluvial versions 0.12.3 dated 2020-12-05 and 0.12.4 dated 2023-02-03
ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_alluvium.jpg |only ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_empty_area.jpg |only ggalluvial-0.12.3/ggalluvial/vignettes/img/hover_stratum.jpg |only ggalluvial-0.12.4/ggalluvial/DESCRIPTION | 12 ggalluvial-0.12.4/ggalluvial/MD5 | 149 + ggalluvial-0.12.4/ggalluvial/NAMESPACE | 17 ggalluvial-0.12.4/ggalluvial/NEWS.md | 33 ggalluvial-0.12.4/ggalluvial/R/alluvial-data.r | 60 ggalluvial-0.12.4/ggalluvial/R/geom-alluvium.r | 193 +- ggalluvial-0.12.4/ggalluvial/R/geom-flow.r | 112 - ggalluvial-0.12.4/ggalluvial/R/geom-lode.r | 4 ggalluvial-0.12.4/ggalluvial/R/geom-stratum.r | 2 ggalluvial-0.12.4/ggalluvial/R/ggalluvial-package.r | 5 ggalluvial-0.12.4/ggalluvial/R/lode-guidance-functions.r | 7 ggalluvial-0.12.4/ggalluvial/R/self-adjoin.r | 5 ggalluvial-0.12.4/ggalluvial/R/stat-alluvium.r | 13 ggalluvial-0.12.4/ggalluvial/R/stat-flow.r | 27 ggalluvial-0.12.4/ggalluvial/R/stat-stratum.r | 8 ggalluvial-0.12.4/ggalluvial/R/stat-utils.r | 11 ggalluvial-0.12.4/ggalluvial/R/utils.r | 2 ggalluvial-0.12.4/ggalluvial/README.md | 41 ggalluvial-0.12.4/ggalluvial/build/partial.rdb |only ggalluvial-0.12.4/ggalluvial/build/vignette.rds |binary ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.R | 20 ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.html | 834 ++++++-- ggalluvial-0.12.4/ggalluvial/inst/doc/ggalluvial.rmd | 66 ggalluvial-0.12.4/ggalluvial/inst/doc/labels.html | 542 ++++- ggalluvial-0.12.4/ggalluvial/inst/doc/labels.rmd | 16 ggalluvial-0.12.4/ggalluvial/inst/doc/order-rectangles.html | 864 +++++++-- ggalluvial-0.12.4/ggalluvial/inst/doc/order-rectangles.rmd | 20 ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.R | 455 +--- ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.Rmd | 580 ++---- ggalluvial-0.12.4/ggalluvial/inst/doc/shiny.html | 934 +++++----- ggalluvial-0.12.4/ggalluvial/inst/examples/ex-geom-alluvium.r | 2 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-geom-flow.r | 2 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-shiny-long-data |only ggalluvial-0.12.4/ggalluvial/inst/examples/ex-shiny-wide-data |only ggalluvial-0.12.4/ggalluvial/inst/examples/ex-stat-alluvium.r | 17 ggalluvial-0.12.4/ggalluvial/inst/examples/ex-stat-flow.r | 4 ggalluvial-0.12.4/ggalluvial/man/alluvial-data.Rd | 4 ggalluvial-0.12.4/ggalluvial/man/figures/README-unnamed-chunk-6-1.png |binary ggalluvial-0.12.4/ggalluvial/man/figures/README-unnamed-chunk-7-1.png |binary ggalluvial-0.12.4/ggalluvial/man/geom_alluvium.Rd | 41 ggalluvial-0.12.4/ggalluvial/man/geom_flow.Rd | 54 ggalluvial-0.12.4/ggalluvial/man/geom_lode.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/geom_stratum.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/ggalluvial-ggproto.Rd | 6 ggalluvial-0.12.4/ggalluvial/man/ggalluvial-package.Rd | 14 ggalluvial-0.12.4/ggalluvial/man/lode-guidance-functions.Rd | 5 ggalluvial-0.12.4/ggalluvial/man/stat_alluvium.Rd | 37 ggalluvial-0.12.4/ggalluvial/man/stat_flow.Rd | 24 ggalluvial-0.12.4/ggalluvial/man/stat_stratum.Rd | 14 ggalluvial-0.12.4/ggalluvial/tests/testthat/_snaps |only ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-alluvium.r | 38 ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-flow.r | 18 ggalluvial-0.12.4/ggalluvial/tests/testthat/test-geom-lode.r | 4 ggalluvial-0.12.4/ggalluvial/vignettes/ggalluvial.rmd | 66 ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_alluvium.png |only ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_empty_area.png |only ggalluvial-0.12.4/ggalluvial/vignettes/img/hover_stratum.png |only ggalluvial-0.12.4/ggalluvial/vignettes/labels.rmd | 16 ggalluvial-0.12.4/ggalluvial/vignettes/order-rectangles.rmd | 20 ggalluvial-0.12.4/ggalluvial/vignettes/shiny.Rmd | 580 ++---- 63 files changed, 3493 insertions(+), 2533 deletions(-)
Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org>
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2D, 3D, 4D, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this.
Author: Jean-Romain Roussel [cph, ctb] ,
C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Pavlo Mozharovskyi [cph, aut],
David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.4.6.1 dated 2022-07-04 and 0.4.7 dated 2023-02-03
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 1 + NEWS | 40 ++++++++++++++++++++++++++++++++++++++++ R/convhulln.R | 10 +++++----- R/delaunayn.R | 43 +++++++++++++++++++++++++++++++++++++++---- R/qhull-options.R | 6 ++++-- R/surf.tri.R | 16 ++++++++-------- R/tetramesh.R | 8 ++++---- build/vignette.rds |binary inst/doc/qhull-eg.pdf |binary man/convhulln.Rd | 8 ++++---- man/delaunayn.Rd | 13 ++++++++----- man/surf.tri.Rd | 16 ++++++++-------- man/tetramesh.Rd | 4 ++-- src/Rgeometry.c | 2 +- src/global_r.c | 8 ++++---- src/rboxlib_r.c | 2 +- 18 files changed, 151 insertions(+), 70 deletions(-)
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-5 dated 2022-02-12 and 1.0-7 dated 2023-02-03
DESCRIPTION | 9 - MD5 | 38 ++--- src/RExportGen.cpp | 4 src/cgFbat.cpp | 344 ++++++++++++++++++++++++++--------------------------- src/datamatrix.cpp | 16 +- src/datamatrix.h | 10 - src/defines.h | 2 src/fbatdist.cpp | 18 +- src/fbatge.cpp | 24 +-- src/fbati_init.c | 28 ++-- src/fbatmeev.cpp | 16 +- src/fbatmeev.h | 2 src/joint.cpp | 12 - src/joint.h | 2 src/nuclify.cpp | 24 +-- src/nuclify.h | 8 - src/rmatrix.cpp | 10 - src/rmatrix.h | 2 src/rvector.cpp | 8 - src/rvector.h | 2 20 files changed, 296 insertions(+), 283 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-011-0040-5>. Subnational probabilistic projections are also supported.
Author: Hana Sevcikova , Leontine Alkema , Peiran Liu , Adrian Raftery , Bailey Fosdick , Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 7.2-2 dated 2022-12-12 and 7.3-0 dated 2023-02-03
ChangeLog | 11 ++ DESCRIPTION | 12 +- MD5 | 32 +++---- NAMESPACE | 3 R/get_outputs.R | 6 - R/plot_functions.R | 191 ++++++++++++++++++++++++++++++++++------------ R/predict_tfr.R | 19 +++- R/tfr_median_set_new.R | 54 +++++++------ R/wpp_data.R | 6 - build/partial.rdb |binary data/iso3166.rda |binary inst/CITATION | 11 -- man/tfr.map.Rd | 37 ++++++-- man/tfr.median.set.Rd | 17 ++-- man/tfr.median.set.all.Rd | 6 - tests/run_tests.R | 25 +++--- tests/test_functions.R | 148 ++++++++++++++++++++++++----------- 17 files changed, 391 insertions(+), 187 deletions(-)
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] ,
Chao Cheng [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between SASmarkdown versions 0.8.0 dated 2022-09-20 and 0.8.1 dated 2023-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sas_collectcode.r | 4 +++- man/find_sas.Rd | 2 +- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark
shapes, including Procrustes analysis, graphical displays, principal
components analysis, permutation and bootstrap tests, thin-plate
spline transformation grids and comparing covariance matrices.
See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis,
with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>
Diff between shapes versions 1.2.6 dated 2021-03-31 and 1.2.7 dated 2023-02-03
DESCRIPTION | 8 MD5 | 78 +- NEWS.md | 158 ++-- R/shapes.R | 1576 ++++++++++++++++++++++++++------------------- README.md |only data/apes.rda |binary data/brains.rda |binary data/cortical.rda |binary data/digit3.dat.rda |binary data/dna.dat.rda |binary data/gels.rda |binary data/gorf.dat.rda |binary data/gorm.dat.rda |binary data/humanmove.rda |binary data/macaques.rda |binary data/macf.dat.rda |binary data/macm.dat.rda |binary data/mice.rda |binary data/nsa.rda |binary data/panf.dat.rda |binary data/panm.dat.rda |binary data/pongof.dat.rda |binary data/pongom.dat.rda |binary data/protein.rda |binary data/qcet2.dat.rda |binary data/qlet2.dat.rda |binary data/qset2.dat.rda |binary data/rats.rda |binary data/sand.rda |binary data/schizophrenia.dat.rda |binary data/schizophrenia.rda |binary data/shells.rda |binary data/sooty.dat.rda |binary data/sooty.rda |binary data/steroids.rda |binary man/backfit.Rd |only man/pns.Rd | 11 man/pns4pc.Rd | 2 man/pnss3d.Rd | 22 man/shapes-internal.Rd | 4 man/shapes.cva.Rd | 3 41 files changed, 1102 insertions(+), 760 deletions(-)
Title: Sieve Analysis Methods for Proportional Hazards Models
Description: Implements semiparametric estimation and testing procedures for a continuous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an event of interest in a randomized treatment efficacy trial with a time-to-event endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 69(2):328 337 <doi:10.1111/biom.12016>, and in Juraska M and Gilbert PB (2016), Mark-specific hazard ratio model with missing multivariate marks. Lifetime Data Analysis 22(4): 606-25 <doi:10.1007/s10985-015-9353-9>. The former considers continuous multivariate marks fully observed in all subjects who experience the event of interest, whereas the latter extends the previous work to allow multivariate marks that are subject to missingness-at-random. For models with missing marks, two estimators are implemented based on (i) inverse probability weighting (IPW) of complete case [...truncated...]
Author: Michal Juraska [aut, cre],
Stephanie Wu [ctb],
Li Li [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between sievePH versions 1.0.3 dated 2022-08-16 and 1.0.4 dated 2023-02-03
sievePH-1.0.3/sievePH/inst |only sievePH-1.0.4/sievePH/DESCRIPTION | 14 ++++++++------ sievePH-1.0.4/sievePH/MD5 | 9 +++++---- sievePH-1.0.4/sievePH/NAMESPACE | 4 ++++ sievePH-1.0.4/sievePH/NEWS |binary sievePH-1.0.4/sievePH/R/ggplot_sieve.R |only sievePH-1.0.4/sievePH/man/ggplot_sieve.Rd |only 7 files changed, 17 insertions(+), 10 deletions(-)
Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments
that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut] ,
Benjamin D. Schalet [ctb],
Aaron J. Kaat [ctb],
David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between PROsetta versions 0.3.5 dated 2022-01-03 and 0.4.1 dated 2023-02-03
PROsetta-0.3.5/PROsetta/R/configPROsetta.R |only PROsetta-0.3.5/PROsetta/inst/shiny/app.R |only PROsetta-0.3.5/PROsetta/tests/testthat/test_runCalibration.R |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.rdb |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha_4e7587a89a24fad71d6ecf02728fb351.rdx |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib2_5978dfb0cb71fc7d2170190dbc80afb9.RData |only PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/calib2_5978dfb0cb71fc7d2170190dbc80afb9.rdb |only 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PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/sl_1beed426aa05dccb0e770ab845b4aeda.rdx |only PROsetta-0.4.1/PROsetta/DESCRIPTION | 24 PROsetta-0.4.1/PROsetta/MD5 | 200 PROsetta-0.4.1/PROsetta/NAMESPACE | 6 PROsetta-0.4.1/PROsetta/NEWS.md | 16 PROsetta-0.4.1/PROsetta/R/RcppExports.R |only PROsetta-0.4.1/PROsetta/R/core_functions.R | 351 - PROsetta-0.4.1/PROsetta/R/datasets.R | 12 PROsetta-0.4.1/PROsetta/R/helper_functions.R | 60 PROsetta-0.4.1/PROsetta/R/import.R | 3 PROsetta-0.4.1/PROsetta/R/linking_functions.R | 140 PROsetta-0.4.1/PROsetta/R/loading_functions.R |only PROsetta-0.4.1/PROsetta/R/plot_functions.R | 127 PROsetta-0.4.1/PROsetta/R/post_functions.R | 112 PROsetta-0.4.1/PROsetta/R/preanalysis_functions.r |only PROsetta-0.4.1/PROsetta/R/runshiny.R | 9 PROsetta-0.4.1/PROsetta/build/vignette.rds |binary PROsetta-0.4.1/PROsetta/data/anchor_asq.rda |binary PROsetta-0.4.1/PROsetta/data/anchor_dep.rda |binary PROsetta-0.4.1/PROsetta/data/data_asq.rda |binary PROsetta-0.4.1/PROsetta/data/data_dep.rda |binary PROsetta-0.4.1/PROsetta/data/itemmap_asq.rda |binary PROsetta-0.4.1/PROsetta/data/itemmap_dep.rda |binary PROsetta-0.4.1/PROsetta/data/response_asq.rda |binary PROsetta-0.4.1/PROsetta/data/response_dep.rda |binary PROsetta-0.4.1/PROsetta/inst/CITATION | 6 PROsetta-0.4.1/PROsetta/inst/data-raw/anchor_AxMASQ.csv | 60 PROsetta-0.4.1/PROsetta/inst/data-raw/anchor_DeCESD.csv | 58 PROsetta-0.4.1/PROsetta/inst/doc/PROsetta.Rmd | 1 PROsetta-0.4.1/PROsetta/inst/doc/PROsetta.html | 2254 ++++++++-- PROsetta-0.4.1/PROsetta/inst/shiny/global.r |only PROsetta-0.4.1/PROsetta/inst/shiny/server.r |only PROsetta-0.4.1/PROsetta/inst/shiny/styles.css | 7 PROsetta-0.4.1/PROsetta/inst/shiny/ui.r |only PROsetta-0.4.1/PROsetta/man/PROsetta.Rd | 5 PROsetta-0.4.1/PROsetta/man/checkFrequency.Rd | 17 PROsetta-0.4.1/PROsetta/man/compareScores.Rd | 11 PROsetta-0.4.1/PROsetta/man/computeResponseProbability.Rd |only PROsetta-0.4.1/PROsetta/man/dataset_asq.Rd | 5 PROsetta-0.4.1/PROsetta/man/dataset_dep.Rd | 5 PROsetta-0.4.1/PROsetta/man/detectParameterization.Rd |only PROsetta-0.4.1/PROsetta/man/getCompleteData.Rd | 11 PROsetta-0.4.1/PROsetta/man/getEscore.Rd | 2 PROsetta-0.4.1/PROsetta/man/getItemNames.Rd | 8 PROsetta-0.4.1/PROsetta/man/getRSSS.Rd | 30 PROsetta-0.4.1/PROsetta/man/getResponse.Rd | 2 PROsetta-0.4.1/PROsetta/man/getScaleSum.Rd | 9 PROsetta-0.4.1/PROsetta/man/getTheta.Rd | 33 PROsetta-0.4.1/PROsetta/man/loadData.Rd | 5 PROsetta-0.4.1/PROsetta/man/makeCalibrationModel.Rd |only PROsetta-0.4.1/PROsetta/man/plot-methods.Rd | 22 PROsetta-0.4.1/PROsetta/man/plotInfo-methods.Rd | 14 PROsetta-0.4.1/PROsetta/man/runCFA.Rd | 11 PROsetta-0.4.1/PROsetta/man/runCalibration.Rd | 8 PROsetta-0.4.1/PROsetta/man/runClassical.Rd | 6 PROsetta-0.4.1/PROsetta/man/runDescriptive.Rd | 4 PROsetta-0.4.1/PROsetta/man/runEquateObserved.Rd | 3 PROsetta-0.4.1/PROsetta/man/runFrequency.Rd | 6 PROsetta-0.4.1/PROsetta/man/runLinking.Rd | 16 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Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust
results, without the need of repetitive coding or extensive R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.1.4 dated 2022-09-08 and 5.2.0 dated 2023-02-03
lares-5.1.4/lares/man/fb_post.Rd |only lares-5.1.4/lares/man/fb_posts.Rd |only lares-5.2.0/lares/DESCRIPTION | 8 lares-5.2.0/lares/MD5 | 254 ++++--- lares-5.2.0/lares/NAMESPACE | 4 lares-5.2.0/lares/R/audio.R | 5 lares-5.2.0/lares/R/cache.R | 2 lares-5.2.0/lares/R/checks.R | 8 lares-5.2.0/lares/R/clusters.R | 28 lares-5.2.0/lares/R/colour_palettes.R | 1 lares-5.2.0/lares/R/correlations.R | 84 +- lares-5.2.0/lares/R/cran.R | 37 - lares-5.2.0/lares/R/crosstab.R | 2 lares-5.2.0/lares/R/currency.R | 2 lares-5.2.0/lares/R/dim_reduction.R | 3 lares-5.2.0/lares/R/distribution.R | 21 lares-5.2.0/lares/R/dropbox.R | 4 lares-5.2.0/lares/R/facebook.R | 769 +++++++++--------------- lares-5.2.0/lares/R/forecasting.R | 5 lares-5.2.0/lares/R/frequencies.R | 11 lares-5.2.0/lares/R/google_sheets.R | 6 lares-5.2.0/lares/R/google_trends.R | 8 lares-5.2.0/lares/R/hubspot.R | 4 lares-5.2.0/lares/R/lares.R | 2 lares-5.2.0/lares/R/lasso.R | 2 lares-5.2.0/lares/R/linkedin.R | 3 lares-5.2.0/lares/R/logo.R |only lares-5.2.0/lares/R/mails.R | 3 lares-5.2.0/lares/R/model_functions.R | 31 lares-5.2.0/lares/R/model_metrics.R | 9 lares-5.2.0/lares/R/model_plots.R | 84 +- lares-5.2.0/lares/R/model_predict.R | 10 lares-5.2.0/lares/R/model_preprocessing.R | 28 lares-5.2.0/lares/R/object_detection.R | 2 lares-5.2.0/lares/R/onehotencoding.R | 18 lares-5.2.0/lares/R/other_functions.R | 893 ---------------------------- lares-5.2.0/lares/R/other_plots.R | 3 lares-5.2.0/lares/R/outliers.R | 2 lares-5.2.0/lares/R/scrabble.R | 17 lares-5.2.0/lares/R/shapley.R | 1 lares-5.2.0/lares/R/statusbar.R | 15 lares-5.2.0/lares/R/stocks.R | 85 +- lares-5.2.0/lares/R/text_mining.R | 24 lares-5.2.0/lares/R/theme_lares.R | 9 lares-5.2.0/lares/R/tictoc.R | 5 lares-5.2.0/lares/R/wordle.R | 25 lares-5.2.0/lares/R/wrangling.R |only lares-5.2.0/lares/R/x2y.R | 25 lares-5.2.0/lares/README.md | 2 lares-5.2.0/lares/build/vignette.rds |binary lares-5.2.0/lares/inst/doc/h2o_automl.html | 541 ++++++++-------- lares-5.2.0/lares/man/autoline.Rd | 15 lares-5.2.0/lares/man/balance_data.Rd | 11 lares-5.2.0/lares/man/bind_files.Rd | 15 lares-5.2.0/lares/man/bring_api.Rd | 18 lares-5.2.0/lares/man/categ_reducer.Rd | 11 lares-5.2.0/lares/man/clean_text.Rd | 9 lares-5.2.0/lares/man/cran_logs.Rd | 3 lares-5.2.0/lares/man/date_cuts.Rd | 11 lares-5.2.0/lares/man/date_feats.Rd | 9 lares-5.2.0/lares/man/db_download.Rd | 15 lares-5.2.0/lares/man/db_upload.Rd | 15 lares-5.2.0/lares/man/dist2d.Rd | 2 lares-5.2.0/lares/man/export_plot.Rd | 15 lares-5.2.0/lares/man/export_results.Rd | 15 lares-5.2.0/lares/man/fb_accounts.Rd | 21 lares-5.2.0/lares/man/fb_ads.Rd | 33 - 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131 files changed, 2096 insertions(+), 2502 deletions(-)
Title: Modeling and Forecasting Visitor Counts Using Social Media
Description: Performs modeling and forecasting of park visitor counts
using social media data and (partial) on-site visitor counts.
Specifically, the model is built based on an automatic decomposition
of the trend and seasonal components of the social media-based park visitor counts,
from which short-term forecasts of the visitor counts and percent changes
in the visitor counts can be made. A reference for generating social media-based
visitor counts can be found at
Wood, Guerry, Silver, and Lacayo (2013) <doi:10.1038/srep02976>.
Author: Russell Goebel [aut],
Robert Bowen [aut, cre],
Beth Ann Brackett [ctb],
Kimihiro Noguchi [aut],
Dylan Way [aut]
Maintainer: Robert Bowen <robertbowen.bham@gmail.com>
Diff between VisitorCounts versions 1.0.1 dated 2022-04-21 and 1.0.2 dated 2023-02-03
VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.R |only VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.Rmd |only VisitorCounts-1.0.1/VisitorCounts/inst/doc/VisitorCounts_Analysis.pdf |only VisitorCounts-1.0.1/VisitorCounts/vignettes/VisitorCounts_Analysis.Rmd |only VisitorCounts-1.0.2/VisitorCounts/DESCRIPTION | 12 VisitorCounts-1.0.2/VisitorCounts/MD5 | 67 - VisitorCounts-1.0.2/VisitorCounts/NAMESPACE | 2 VisitorCounts-1.0.2/VisitorCounts/NEWS.md | 9 VisitorCounts-1.0.2/VisitorCounts/R/classes.R | 33 VisitorCounts-1.0.2/VisitorCounts/R/data.R | 26 VisitorCounts-1.0.2/VisitorCounts/R/function_visitation_model.R | 447 ++++++++-- VisitorCounts-1.0.2/VisitorCounts/R/helpers_visitation_model.R | 65 + VisitorCounts-1.0.2/VisitorCounts/R/methods_plot.R | 2 VisitorCounts-1.0.2/VisitorCounts/R/methods_predict.R | 51 - VisitorCounts-1.0.2/VisitorCounts/R/methods_print.R | 12 VisitorCounts-1.0.2/VisitorCounts/R/methods_summary.R | 24 VisitorCounts-1.0.2/VisitorCounts/build/vignette.rds |binary VisitorCounts-1.0.2/VisitorCounts/data/forest_visitation.rda |only VisitorCounts-1.0.2/VisitorCounts/inst/doc/VisitorCounts.Rmd | 2 VisitorCounts-1.0.2/VisitorCounts/inst/doc/VisitorCounts.html | 329 ++++++- VisitorCounts-1.0.2/VisitorCounts/man/check_arguments.Rd | 5 VisitorCounts-1.0.2/VisitorCounts/man/decompose_proxy.Rd | 8 VisitorCounts-1.0.2/VisitorCounts/man/estimate_parameters.Rd | 9 VisitorCounts-1.0.2/VisitorCounts/man/fit_model.Rd | 5 VisitorCounts-1.0.2/VisitorCounts/man/forest_visitation.Rd |only VisitorCounts-1.0.2/VisitorCounts/man/imputation.Rd |only VisitorCounts-1.0.2/VisitorCounts/man/new_visitation_forecast.Rd | 7 VisitorCounts-1.0.2/VisitorCounts/man/new_visitation_model.Rd | 10 VisitorCounts-1.0.2/VisitorCounts/man/predict.decomposition.Rd | 2 VisitorCounts-1.0.2/VisitorCounts/man/predict.visitation_model.Rd | 3 VisitorCounts-1.0.2/VisitorCounts/man/print.visitation_forecast.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/print.visitation_model.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/summary.decomposition.Rd | 2 VisitorCounts-1.0.2/VisitorCounts/man/summary.visitation_model.Rd | 1 VisitorCounts-1.0.2/VisitorCounts/man/visitation_model.Rd | 31 VisitorCounts-1.0.2/VisitorCounts/man/yearsToMonths.Rd |only VisitorCounts-1.0.2/VisitorCounts/tests/testthat/test_predict.R | 6 VisitorCounts-1.0.2/VisitorCounts/vignettes/VisitorCounts.Rmd | 2 VisitorCounts-1.0.2/VisitorCounts/vignettes/VisitorCounts_Analysis.pdf |only 39 files changed, 946 insertions(+), 228 deletions(-)
Title: Quick Table Generation & Exploratory Analyses on ADaM-Ish
Datasets
Description: Provides users a quick exploratory dive into common
visualizations without writing a single line of code given the users
data follows the Analysis Data Model (ADaM) standards put forth by the
Clinical Data Interchange Standards Consortium (CDISC)
<https://www.cdisc.org>. Prominent modules/ features of the
application are the Table Generator, Population Explorer, and the
Individual Explorer. The Table Generator allows users to drag and drop
variables and desired statistics (frequencies, means, ANOVA, t-test,
and other summary statistics) into bins that automagically create
stunning tables with validated information. The Population Explorer
offers various plots to visualize general trends in the population
from various vantage points. Plot modules currently include scatter
plot, spaghetti plot, box plot, histogram, means plot, and bar plot.
Each plot type allows the user to plot uploaded variables against one
another, and dissect the population by filtering out certain subjects.
La [...truncated...]
Author: Aaron Clark [aut, cre] ,
Jeff Thompson [aut],
Teresa Wilson [aut],
Nate Mockler [ccp, led],
Maya Gans [aut],
Robert Krajcik [ctb],
Marly Gotti [ctb],
Biogen Inc [cph]
Maintainer: Aaron Clark <clark.aaronchris@gmail.com>
Diff between tidyCDISC versions 0.1.0 dated 2022-08-30 and 0.2.0 dated 2023-02-03
tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_dark2lite.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_dark2lite_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_lite2dark_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_lite2dark_aura_cropped.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_solid_blue.png |only tidyCDISC-0.1.0/tidyCDISC/man/figures/demo_tidyCDISC_button_solid_blue_aura.PNG |only tidyCDISC-0.1.0/tidyCDISC/man/gather_rules.Rd |only tidyCDISC-0.2.0/tidyCDISC/DESCRIPTION | 57 +- tidyCDISC-0.2.0/tidyCDISC/MD5 | 77 +- tidyCDISC-0.2.0/tidyCDISC/NAMESPACE | 2 tidyCDISC-0.2.0/tidyCDISC/NEWS.md | 55 +- tidyCDISC-0.2.0/tidyCDISC/R/data-phuse_TDF_ADaM.R | 5 tidyCDISC-0.2.0/tidyCDISC/R/golem_utils_ui.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_dataComplyRules_fct_helpers.R | 2 tidyCDISC-0.2.0/tidyCDISC/R/mod_dataUpload.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExpPatEvents.R | 4 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_fct_buildEvents.R | 8 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_srv.R | 8 tidyCDISC-0.2.0/tidyCDISC/R/mod_indvExp_ui.R | 1 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp.R | 48 + tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_line.R | 6 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_scatter.R | 2 tidyCDISC-0.2.0/tidyCDISC/R/mod_popExp_ui.R | 1 tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen.R | 267 +++++++--- tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_fct_methods.R | 116 ++-- tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_ui.R | 7 tidyCDISC-0.2.0/tidyCDISC/R/mod_tableGen_utils.R | 175 +++++- tidyCDISC-0.2.0/tidyCDISC/R/utils_helpers.R | 6 tidyCDISC-0.2.0/tidyCDISC/README.md | 91 +-- tidyCDISC-0.2.0/tidyCDISC/build/vignette.rds |binary tidyCDISC-0.2.0/tidyCDISC/data/example_dat1.rda |binary tidyCDISC-0.2.0/tidyCDISC/data/example_dat2.rda |binary tidyCDISC-0.2.0/tidyCDISC/inst/WORDLIST | 6 tidyCDISC-0.2.0/tidyCDISC/inst/app/www/recipe.js | 242 +++------ tidyCDISC-0.2.0/tidyCDISC/inst/app/www/script.js | 80 +- tidyCDISC-0.2.0/tidyCDISC/inst/app/www/styles.css | 17 tidyCDISC-0.2.0/tidyCDISC/inst/doc/getting_started.html | 16 tidyCDISC-0.2.0/tidyCDISC/man/app_methods.Rd | 28 - tidyCDISC-0.2.0/tidyCDISC/man/data_to_filter.Rd | 12 tidyCDISC-0.2.0/tidyCDISC/man/data_to_use_str.Rd | 20 tidyCDISC-0.2.0/tidyCDISC/man/prep_adae.Rd | 12 tidyCDISC-0.2.0/tidyCDISC/man/prep_bds.Rd | 10 tidyCDISC-0.2.0/tidyCDISC/man/std_footnote.Rd |only tidyCDISC-0.2.0/tidyCDISC/man/tg_gt.Rd |only 44 files changed, 858 insertions(+), 537 deletions(-)
Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre],
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>
Diff between logrx versions 0.2.0 dated 2023-01-18 and 0.2.1 dated 2023-02-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/get.R | 18 ++++++++++++++++-- tests/testthat/test-get.R | 20 ++++++++++++++++++++ 6 files changed, 49 insertions(+), 10 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb],
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.5.0 dated 2022-12-05 and 0.5.1 dated 2023-02-03
DESCRIPTION | 18 MD5 | 61 +- NEWS.md | 17 R/compute-npc.r | 51 +- R/geom-grob.R | 4 R/geom-label-linked.r | 4 R/geom-margin-point.r | 8 R/geom-plot.R | 2 R/geom-point-linked.r | 8 R/geom-table.R | 2 R/geom-text-linked.r | 10 R/stat-dens1d-filter.r | 169 +++++-- R/stat-dens1d-labels.r | 279 +++++++++--- R/stat-dens2d-filter.r | 214 ++++++--- R/stat-dens2d-labels.r | 372 +++++++++++++--- README.md | 4 inst/doc/grammar-extensions.R | 77 ++- inst/doc/grammar-extensions.Rmd | 305 +++++++++---- inst/doc/grammar-extensions.html | 861 ++++++++++++++++++++++----------------- inst/doc/nudge-examples.R | 20 inst/doc/nudge-examples.Rmd | 26 + inst/doc/nudge-examples.html | 288 ++++++------- man/compute_npcx.Rd | 44 + man/ggpp-package.Rd | 2 man/keep_these2logical.Rd |only man/stat_dens1d_filter.Rd | 89 +++- man/stat_dens1d_labels.Rd | 115 ++++- man/stat_dens2d_filter.Rd | 96 +++- man/stat_dens2d_labels.Rd | 90 +++- man/stat_panel_counts.Rd | 506 +++++++++++----------- vignettes/grammar-extensions.Rmd | 305 +++++++++---- vignettes/nudge-examples.Rmd | 26 + 32 files changed, 2751 insertions(+), 1322 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative
divide in social science research. It uses a Boolean minimization
algorithm, resulting in a minimal causal configuration associated
with a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] ,
Ciprian Paduraru [ctb] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
lp_solve [cph] ,
Vasil Dinkov [ctb, cph] ,
Dmitry Baranovskiy [ctb, cph] ,
Emmanuel Quentin [ctb, cph] ,
Jimmy Breck-McKye [ctb, cph] ,
[...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.17 dated 2022-10-03 and 3.18 dated 2023-02-03
DESCRIPTION | 8 MD5 | 220 +++++++++++++------------- R/XYplot.R | 2 R/Xplot.R | 2 R/allExpressions.R | 2 R/calibrate.R | 2 R/causalChain.R | 2 R/combint.R | 2 R/complexity.R | 2 R/createMatrix.R | 2 R/dimnames.R | 2 R/findRows.R | 2 R/findSubsets.R | 2 R/findSupersets.R | 2 R/findTh.R | 2 R/findmin.R | 2 R/fuzzyand.R | 2 R/fuzzyor.R | 2 R/generate.R | 2 R/getRow.R | 2 R/getSolution.R | 2 R/makeChart.R | 2 R/minimize.R | 2 R/modelFit.R | 2 R/onAttach.R | 2 R/onUnload.R | 2 R/panel.R | 2 R/pof.R | 2 R/pofind.R | 2 R/print.R | 2 R/removeRedundants.R | 2 R/replaceCategories.R | 8 R/retention.R | 2 R/rowDominance.R | 2 R/runGUI.R | 2 R/solveChart.R | 2 R/sortMatrix.R | 2 R/sortVector.R | 2 R/string.R | 2 R/superSubset.R | 2 R/truthTable.R | 9 - R/verifyQCA.R | 41 ++-- R/writeSolution.R | 2 build/partial.rdb |binary data/HarKem.RData |binary data/d.HK.RData |binary data/d.partybans.RData |binary inst/CITATION | 9 - inst/ChangeLog | 6 inst/gui/server.R | 7 inst/gui/www/js/maincode.js | 4 inst/gui/www/js/utils.js | 2 inst/staticdocs/CV.html | 4 inst/staticdocs/LegacyDatasets.html | 4 inst/staticdocs/Lipset.html | 4 inst/staticdocs/QCA_package.html | 8 inst/staticdocs/RS.html | 4 inst/staticdocs/SOPexpressions.html | 4 inst/staticdocs/XYplot.html | 4 inst/staticdocs/Xplot.html | 4 inst/staticdocs/calibrate.html | 4 inst/staticdocs/causalChain.html | 4 inst/staticdocs/chartFunctions.html | 4 inst/staticdocs/export.html | 4 inst/staticdocs/factorize.html | 4 inst/staticdocs/findRows.html | 4 inst/staticdocs/findTh.html | 4 inst/staticdocs/fuzzyops.html | 4 inst/staticdocs/generate.html | 4 inst/staticdocs/implicantMatrixFunctions.html | 4 inst/staticdocs/index.html | 4 inst/staticdocs/intersection.html | 4 inst/staticdocs/minimize.html | 4 inst/staticdocs/modelFit.html | 4 inst/staticdocs/negate.html | 4 inst/staticdocs/pof.html | 4 inst/staticdocs/retention.html | 4 inst/staticdocs/runGUI.html | 4 inst/staticdocs/subsetsAndSupersets.html | 4 inst/staticdocs/truthTable.html | 4 man/QCA_package.Rd | 4 src/CCubes.c | 2 src/QCA.c | 2 src/consistency.c | 2 src/consistent_solution.c | 2 src/find_consistent_models.c | 2 src/find_min.c | 2 src/find_models.c | 2 src/generate_matrix.c | 2 src/lp_MPS.c | 20 +- src/lp_lib.c | 12 - src/lp_matrix.c | 3 src/lp_mipbb.c | 2 src/lp_params.c | 6 src/lp_presolve.c | 26 +-- src/lp_report.c | 1 src/lp_report.h | 1 src/lp_rlp.c | 6 src/lp_rlp.h | 9 - src/lp_types.h | 1 src/lp_utils.c | 1 src/lusol.c | 2 src/registerDynamicSymbol.c | 2 src/row_dominance.c | 2 src/sort_cols.c | 2 src/sort_matrix.c | 2 src/super_rows.c | 2 src/truthTable.c | 2 src/utils.c | 2 src/yacc_read.c | 32 +-- src/yacc_read.h | 4 111 files changed, 337 insertions(+), 329 deletions(-)
Title: Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain
Cost Conditions
Description: Functions for cost-sensitive multi-criteria ensemble selection (CSMES) (as described in De bock et al. (2020) <doi:10.1016/j.ejor.2020.01.052>) for cost-sensitive learning under unknown cost conditions.
Author: Koen W. De Bock, Kristof Coussement and Stefan Lessmann
Maintainer: Koen W. De Bock <kdebock@audencia.com>
Diff between CSMES versions 1.0.0 dated 2020-02-22 and 1.0.1 dated 2023-02-03
DESCRIPTION | 8 +++---- MD5 | 19 +++++++++-------- NAMESPACE | 48 ++++++++++++++++++++++----------------------- R/brierCurve.R | 3 +- R/globals.R |only R/plotBrierCurve.R | 2 - man/BFP.Rd | 5 ++-- man/CSMES.ensNomCurve.Rd | 5 ++-- man/CSMES.ensSel.Rd | 8 ++----- man/CSMES.predict.Rd | 5 ++-- man/CSMES.predictPareto.Rd | 6 ++--- 11 files changed, 56 insertions(+), 53 deletions(-)
Title: Add Logging to Functions
Description: Decorate functions to make them return enhanced output. The enhanced output consists in an object of type
'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function
was run, what were its inputs, what were the errors (if the function failed to run) and other useful information.
Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.
Author: Bruno Rodrigues [aut, cre, cph]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between chronicler versions 0.2.0 dated 2022-05-17 and 0.2.1 dated 2023-02-03
DESCRIPTION | 10 MD5 | 78 +- NAMESPACE | 82 +- NEWS.md | 21 R/chronicle.R | 1202 +++++++++++++++---------------- R/data.R | 12 R/zzz.R | 2 README.md | 940 ++++++++++++------------ build/vignette.rds |binary inst/doc/advanced-topics.R | 438 +++++------ inst/doc/advanced-topics.Rmd | 850 ++++++++++----------- inst/doc/advanced-topics.html | 1196 +++++++++++++++++++----------- inst/doc/maybe-monad.R | 68 - inst/doc/maybe-monad.Rmd | 154 +-- inst/doc/maybe-monad.html | 645 +++++++++++----- inst/doc/real-world-example.R | 131 +-- inst/doc/real-world-example.Rmd | 227 ++--- inst/doc/real-world-example.html | 792 +++++++++++++------- man/as_chronicle.Rd | 44 - man/bind_record.Rd | 52 - man/check_diff.Rd | 60 - man/check_g.Rd | 58 - man/flatten_record.Rd | 48 - man/fmap_record.Rd | 48 - man/grapes-greater-than-equals-grapes.Rd | 48 - man/is_chronicle.Rd | 34 man/make_log_df.Rd | 86 +- man/pick.Rd | 48 - man/print.chronicle.Rd | 64 - man/purely.Rd | 56 - man/read_log.Rd | 44 - man/record.Rd | 74 - man/record_many.Rd | 82 +- tests/testthat.R | 8 tests/testthat/test-run_time.R | 32 tests/testthat/test-test_chronicler.R | 218 ++--- tests/testthat/test-test_purely.R | 168 ++-- vignettes/advanced-topics.Rmd | 850 ++++++++++----------- vignettes/maybe-monad.Rmd | 154 +-- vignettes/real-world-example.Rmd | 227 ++--- 40 files changed, 5059 insertions(+), 4292 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-5 dated 2023-01-23 and 0.0-6 dated 2023-02-03
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/lme4_functions.R | 2 +- src/Makevars.in | 2 +- src/Makevars.win | 2 +- src/include/stan/math/prim/fun/acosh.hpp | 2 +- src/include/stan/math/prim/fun/asinh.hpp | 2 +- src/include/stan/math/prim/fun/pow.hpp | 2 +- src/stan_files/continuous.hpp | 4 ++-- src/stan_sampler_includes.hpp | 10 ++++++++++ tests/testthat/test-01-continuous.R | 1 + 11 files changed, 33 insertions(+), 22 deletions(-)
Title: Read 'Excel' Binary (.xlsb) Workbooks
Description: Import data from 'Excel' binary (.xlsb) workbooks into R.
Author: Michael Allen [aut, cre]
Maintainer: Michael Allen <michael@velofrog.com>
Diff between readxlsb versions 0.1.4 dated 2020-09-29 and 0.1.5 dated 2023-02-03
DESCRIPTION | 10 - MD5 | 18 +- build/vignette.rds |binary inst/doc/read-xlsb-workbook.html | 261 +++++++++++++++++++++++---------------- src/BinaryReader.h | 1 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 src/RecordNames.h | 1 src/StreamReader.h | 1 10 files changed, 180 insertions(+), 121 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between Luminescence versions 0.9.20 dated 2022-07-16 and 0.9.21 dated 2023-02-03
DESCRIPTION | 28 +- MD5 | 309 +++++++++++++++--------------- NEWS.md | 104 +++------- R/Risoe.BINfileData-class.R | 2 R/analyse_SAR.CWOSL.R | 1 R/analyse_portableOSL.R | 107 +++++++--- R/apply_CosmicRayRemoval.R | 6 R/calc_OSLLxTxRatio.R | 2 R/combine_De_Dr.R | 14 - R/convert_PSL2CSV.R | 75 ++++++- R/convert_Wavelength2Energy.R | 2 R/fit_LMCurve.R | 101 ++++----- R/github.R | 4 R/internals_RLum.R | 2 R/plot_RadialPlot.R | 43 +--- R/read_BIN2R.R | 25 +- R/read_PSL2R.R | 6 R/write_RLum2CSV.R | 16 - README.md | 83 +++----- inst/CITATION | 3 man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/GitHub-API.Rd | 4 man/PSL2Risoe.BINfileData.Rd | 2 man/RLum-class.Rd | 6 man/RLum.Analysis-class.Rd | 18 - man/RLum.Data.Curve-class.Rd | 18 - man/RLum.Data.Image-class.Rd | 12 - man/RLum.Data.Spectrum-class.Rd | 14 - man/RLum.Results-class.Rd | 14 - man/Risoe.BINfileData-class.Rd | 10 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 2 man/analyse_Al2O3C_ITC.Rd | 2 man/analyse_Al2O3C_Measurement.Rd | 2 man/analyse_FadingMeasurement.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 3 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 2 man/analyse_pIRIRSequence.Rd | 2 man/analyse_portableOSL.Rd | 44 ++-- man/apply_CosmicRayRemoval.Rd | 8 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CobbleDoseRate.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Kars2008.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxDecomposed.Rd | 2 man/calc_OSLLxTxRatio.Rd | 4 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/calc_gSGC_feldspar.Rd | 2 man/combine_De_Dr.Rd | 2 man/convert_Activity2Concentration.Rd | 2 man/convert_BIN2CSV.Rd | 2 man/convert_Concentration2DoseRate.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 20 + man/convert_RLum2Risoe.BINfileData.Rd | 2 man/convert_SG2MG.Rd | 2 man/convert_Wavelength2Energy.Rd | 4 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/extract_ROI.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_EmissionSpectra.Rd | 2 man/fit_LMCurve.Rd | 4 man/fit_OSLLifeTimes.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/fit_ThermalQuenching.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 8 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/names_RLum.Rd | 6 man/plot_AbanicoPlot.Rd | 2 man/plot_DRCSummary.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_NRt.Rd | 2 man/plot_OSLAgeSummary.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_ROI.Rd | 2 man/plot_RadialPlot.Rd | 4 man/plot_Risoe.BINfileData.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 4 man/read_Daybreak2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_RF2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_TIFF2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/scale_GammaDose.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 6 man/structure_RLum.Rd | 6 man/template_DRAC.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/write_R2BIN.Rd | 2 man/write_R2TIFF.Rd | 2 man/write_RLum2CSV.Rd | 6 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_analyse_portableOSL.R | 19 + tests/testthat/test_combine_De_Dr.R | 4 tests/testthat/test_convert_PSL2CSV.R | 13 + tests/testthat/test_fit_CWCurve.R | 19 + tests/testthat/test_fit_LMCurve.R | 19 + tests/testthat/test_plot_RadialPlot.R |only tests/testthat/test_read_BIN2R.R | 19 + 156 files changed, 817 insertions(+), 646 deletions(-)
Title: Melt Curve Fitting and Melt Shift Analysis
Description: Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment.
McCracken (2022) <doi:10.1101/2022.12.30.522131>.
Author: Neil McCracken [aut],
Hao Liu [ctb],
Amber Mosley [cre]
Maintainer: Amber Mosley <almosley@iu.edu>
Diff between InflectSSP versions 1.4.5 dated 2022-10-03 and 1.5 dated 2023-02-03
InflectSSP-1.4.5/InflectSSP/R/ReportPANTHER.R |only InflectSSP-1.4.5/InflectSSP/man/ReportPANTHER.Rd |only InflectSSP-1.5/InflectSSP/DESCRIPTION | 10 InflectSSP-1.5/InflectSSP/MD5 | 26 -- InflectSSP-1.5/InflectSSP/NAMESPACE | 8 InflectSSP-1.5/InflectSSP/R/InflectSSP.R | 17 - InflectSSP-1.5/InflectSSP/R/MeltCalc.R | 8 InflectSSP-1.5/InflectSSP/R/ReportDataMelts.R | 2 InflectSSP-1.5/InflectSSP/R/ReportSTRING.R | 60 +++- InflectSSP-1.5/InflectSSP/inst/doc/InflectSSPVignette.Rmd | 19 - InflectSSP-1.5/InflectSSP/inst/doc/InflectSSPVignette.html | 169 +++++-------- InflectSSP-1.5/InflectSSP/man/InflectSSP.Rd | 14 - InflectSSP-1.5/InflectSSP/man/ReportDataMelts.Rd | 2 InflectSSP-1.5/InflectSSP/man/ReportSTRING.Rd | 6 InflectSSP-1.5/InflectSSP/vignettes/InflectSSPVignette.Rmd | 19 - 15 files changed, 169 insertions(+), 191 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/eq-5d-instruments/eq-5d-3l-about/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>)
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 scores. 29 TTO and 11 VAS EQ-5D-3L
value [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.13.0 dated 2022-11-11 and 0.14.0 dated 2023-02-03
DESCRIPTION | 12 MD5 | 82 + NAMESPACE | 5 NEWS.md | 187 ++-- R/data.R | 6 R/eq5d.R | 2 R/eq5dcf.R | 49 - R/eq5dlfs.R | 6 R/eq5dlss.R | 5 R/eq5dy.R | 19 R/eqhpg.R |only R/eqhsdi.R |only R/eqpchc.R | 42 R/eqps.R |only R/eqshannon.R |only R/helpers.R | 8 R/imports.R | 1 R/sysdata.rda |binary README.md | 236 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/eq5d.R | 116 ++ inst/doc/eq5d.Rmd | 143 ++- inst/doc/eq5d.html | 930 ++++++++++----------- inst/extdata/eq5d3l_example.csv |only inst/extdata/eq5d3l_five_digit_example.csv |only inst/extdata/eq5d5l_example.csv |only inst/shiny/server.R | 157 +++ inst/shiny/ui.R | 11 man/VT.Rd | 6 man/Y.Rd | 4 man/eq5d-package.Rd | 2 man/eq5dcf.Rd | 14 man/figures/README-hpg-1.png |only man/figures/README-hsdi-1.png |only man/hpg.Rd |only man/hsdi.Rd |only man/lfs.Rd | 7 man/lss.Rd | 6 man/pchc.Rd | 19 man/ps.Rd |only man/shannon.Rd |only tests/testdata/hpg_3l_uk_tto_no_problems_false.csv |only tests/testthat/test-eq5d5l.R | 30 tests/testthat/test-eq5dy.R | 14 tests/testthat/test-eqhpg.R |only tests/testthat/test-eqhsdi.R |only tests/testthat/test-eqpchc.R | 7 tests/testthat/test-eqps.R |only tests/testthat/test-eqshannon.R |only vignettes/eq5d.Rmd | 143 ++- 51 files changed, 1565 insertions(+), 704 deletions(-)
Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in King, Tomz, and Wittenberg (2000) <doi:10.2307/2669316>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] ,
Steven Worthington [aut] ,
Stefano Iacus [aut] ,
Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between clarify versions 0.1.0 dated 2023-01-25 and 0.1.1 dated 2023-02-03
DESCRIPTION | 8 MD5 | 38 ++-- NEWS.md | 8 R/checks.R | 35 +++ R/clarify_predict.R | 5 R/sim_adrf.R | 4 R/sim_ame.R | 4 R/sim_setx.R | 4 R/summary.clarify_est.R | 21 -- README.md | 283 ++++++++++++++++--------------- build/vignette.rds |binary inst/doc/Zelig.Rmd | 2 inst/doc/clarify.R | 6 inst/doc/clarify.Rmd | 24 +- inst/doc/clarify.html | 185 ++++++++++++-------- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/summary.clarify_est.Rd | 7 vignettes/Zelig.Rmd | 2 vignettes/clarify.Rmd | 24 +- 21 files changed, 378 insertions(+), 282 deletions(-)
Title: Distribution of the 'BayesX' C++ Sources
Description: 'BayesX' performs Bayesian inference in structured additive regression (STAR) models.
The R package BayesXsrc provides the 'BayesX' command line tool for easy installation.
A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre] ,
Daniel Adler [aut],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesXsrc versions 3.0-3 dated 2022-11-03 and 3.0-4 dated 2023-02-03
DESCRIPTION | 16 ++--- MD5 | 46 ++++++++--------- inst/CITATION | 78 ++++++++++++++++------------- src/Makefile | 7 ++ src/Makefile.inner.win | 7 ++ src/Makefile.win | 5 + src/bayesxsrc/andrea/baseline.cpp | 4 - src/bayesxsrc/bib/Random.cpp | 12 ++-- src/bayesxsrc/bib/adminparse.h | 2 src/bayesxsrc/bib/bayesreg.cpp | 5 + src/bayesxsrc/bib/model.h | 2 src/bayesxsrc/bib/realvar.cpp | 2 src/bayesxsrc/bib/sparsemat.h | 2 src/bayesxsrc/bib/tarray.h | 2 src/bayesxsrc/bib/tpremat.cpp | 9 ++- src/bayesxsrc/bib/tsearcht.h | 2 src/bayesxsrc/bib/vectorn.h | 2 src/bayesxsrc/mcmc/mcmc_const.cpp | 10 +-- src/bayesxsrc/structadd/design_kriging.cpp | 2 src/dev-Makefile | 7 ++ src/dev-Makefile.inner.win | 7 ++ src/dev-Makefile.win | 5 + src/rel-Makefile | 7 ++ src/rel-Makefile.win | 7 ++ 24 files changed, 155 insertions(+), 93 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Sta [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut],
Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.2.1 dated 2022-11-04 and 1.2.2 dated 2023-02-03
BayesMallows-1.2.1/BayesMallows/man/plot_alpha_posterior.Rd |only BayesMallows-1.2.1/BayesMallows/man/plot_rho_posterior.Rd |only BayesMallows-1.2.2/BayesMallows/DESCRIPTION | 8 BayesMallows-1.2.2/BayesMallows/MD5 | 115 +-- BayesMallows-1.2.2/BayesMallows/NAMESPACE | 1 BayesMallows-1.2.2/BayesMallows/NEWS.md | 8 BayesMallows-1.2.2/BayesMallows/R/RcppExports.R | 42 - BayesMallows-1.2.2/BayesMallows/R/all_topological_sorts.R | 1 BayesMallows-1.2.2/BayesMallows/R/get_mallows_loglik.R | 2 BayesMallows-1.2.2/BayesMallows/R/plot.SMCMallows.R |only BayesMallows-1.2.2/BayesMallows/R/smc_mallows_deprecated.R | 39 - BayesMallows-1.2.2/BayesMallows/R/smc_post_processing_functions.R | 97 -- BayesMallows-1.2.2/BayesMallows/build/partial.rdb |binary BayesMallows-1.2.2/BayesMallows/build/vignette.rds |binary BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.R | 33 BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.Rmd | 68 - BayesMallows-1.2.2/BayesMallows/inst/doc/SMC-Mallows.html | 343 ++++------ BayesMallows-1.2.2/BayesMallows/inst/examples/metropolis_hastings_alpha_example.R | 16 BayesMallows-1.2.2/BayesMallows/inst/examples/plot.SMCMallows_example.R |only BayesMallows-1.2.2/BayesMallows/man/calculate_backward_probability.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/calculate_forward_probability.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/compute_posterior_intervals_alpha.Rd | 3 BayesMallows-1.2.2/BayesMallows/man/compute_posterior_intervals_rho.Rd | 3 BayesMallows-1.2.2/BayesMallows/man/compute_rho_consensus.Rd | 5 BayesMallows-1.2.2/BayesMallows/man/correction_kernel_pseudo.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/get_exponent_sum.Rd | 2 BayesMallows-1.2.2/BayesMallows/man/get_sample_probabilities.Rd | 8 BayesMallows-1.2.2/BayesMallows/man/leap_and_shift_probs.Rd | 12 BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_alpha.Rd | 40 - BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_aug_ranking.Rd | 8 BayesMallows-1.2.2/BayesMallows/man/metropolis_hastings_rho.Rd | 13 BayesMallows-1.2.2/BayesMallows/man/plot.SMCMallows.Rd |only BayesMallows-1.2.2/BayesMallows/man/smc_mallows_new_item_rank.Rd | 28 BayesMallows-1.2.2/BayesMallows/man/smc_mallows_new_users.Rd | 28 BayesMallows-1.2.2/BayesMallows/src/Makevars | 2 BayesMallows-1.2.2/BayesMallows/src/Makevars.win | 2 BayesMallows-1.2.2/BayesMallows/src/RcppExports.cpp | 62 - BayesMallows-1.2.2/BayesMallows/src/parameterupdates.cpp | 2 BayesMallows-1.2.2/BayesMallows/src/smc.h | 8 BayesMallows-1.2.2/BayesMallows/src/smc_calculate_probability.cpp | 14 BayesMallows-1.2.2/BayesMallows/src/smc_correction_kernel_pseudo.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_get_exponent_sum.cpp | 2 BayesMallows-1.2.2/BayesMallows/src/smc_get_sample_probabilities.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_leap_and_shift_probs.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_item_rank.cpp | 61 - BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users.cpp | 40 - BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users.h | 9 BayesMallows-1.2.2/BayesMallows/src/smc_mallows_new_users_funs.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_alpha.cpp | 8 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_aug_ranking.cpp | 4 BayesMallows-1.2.2/BayesMallows/src/smc_metropolis_hastings_rho.cpp | 4 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-assess_convergence.R | 1 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-bulletproofing.R | 32 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-compute_mallows.R | 2 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-get_mallows_loglik.R | 4 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_individual_functions.R | 29 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_mallows_new_item_rank.R | 29 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_mallows_partial_rankings.R | 22 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_pseudolikelihood.R | 10 BayesMallows-1.2.2/BayesMallows/tests/testthat/test-smc_updated_new_item_rank.R | 8 BayesMallows-1.2.2/BayesMallows/vignettes/SMC-Mallows.Rmd | 68 - 61 files changed, 595 insertions(+), 781 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>),
'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>),
'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.15 dated 2021-01-11 and 0.9.16 dated 2023-02-03
DESCRIPTION | 8 MD5 | 30 NEWS.md | 9 R/Export.R | 2 R/Registry.R | 4 R/Worker.R | 4 R/addExperiments.R | 30 R/clusterFunctionsSlurm.R | 14 R/waitForFiles.R | 2 build/vignette.rds |binary inst/CITATION | 8 inst/doc/batchtools.html | 1774 +++++++++++++++++++---------------- man/addExperiments.Rd | 5 man/makeExperimentRegistry.Rd | 4 man/makeRegistry.Rd | 4 tests/testthat/test_addExperiments.R | 1 16 files changed, 1090 insertions(+), 809 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut],
Duncan Murdoch [ctb]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan3d versions 1.1-2 dated 2018-10-25 and 1.2-0 dated 2023-02-03
DESCRIPTION | 14 ++++++++------ MD5 | 30 +++++++++++++++--------------- R/ordirgl.R | 26 +++++++++++++------------- R/orditree3d.R | 12 ++++++------ R/orglpoints.R | 2 +- R/orglsegments.R | 2 +- R/orglspantree.R | 4 ++-- R/orglspider.R | 4 ++-- R/orgltext.R | 2 +- R/rgl.isomap.R | 2 +- R/rgl.renyiaccum.R | 24 ++++++++++++------------ build/partial.rdb |binary inst/NEWS.md | 7 +++++++ man/ordirgl.Rd | 14 +++++++------- man/orditree3d.Rd | 2 +- man/vegan3d-package.Rd | 2 +- 16 files changed, 78 insertions(+), 69 deletions(-)
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', and 'kernelshap'
are added for convenience. By separating visualization and
computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.4.1 dated 2023-01-11 and 0.5.0 dated 2023-02-03
DESCRIPTION | 28 +-- MD5 | 62 ++++---- NAMESPACE | 6 NEWS.md | 28 +++ R/bee.R | 10 - R/collapse_shap.R | 67 ++++++-- R/shapviz-package.R | 2 R/shapviz.R | 98 ++++++++++--- R/shapviz_methods.R | 41 ++++- R/sv_dependence.R | 112 ++++++++++---- R/sv_force.R | 4 R/sv_importance.R | 144 ++++++++----------- R/sv_interaction.R |only R/sv_waterfall.R | 6 README.md | 35 ++++ inst/doc/shapviz.R | 11 + inst/doc/shapviz.Rmd | 32 +++- inst/doc/shapviz.html | 269 +++++++++++++++++++----------------- man/collapse_shap.Rd | 26 +-- man/extractors.Rd | 112 ++++++++------ man/figures/README-dep2.png |only man/figures/README-interactions.png |only man/potential_interactions.Rd | 17 +- man/shapviz-package.Rd | 2 man/shapviz.Rd | 25 ++- man/sv_dependence.Rd | 40 +++-- man/sv_force.Rd | 2 man/sv_importance.Rd | 14 - man/sv_interaction.Rd |only man/sv_waterfall.Rd | 2 tests/testthat/test-collapse_shap.R | 45 ++++++ tests/testthat/test-interface.R | 44 +++++ tests/testthat/test-plots.R | 56 ++++++- vignettes/shapviz.Rmd | 32 +++- 34 files changed, 899 insertions(+), 473 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2022)
<doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple
measurements per individual, time-varying and time-invariant effects, and a
wide range of discrete and continuous distributions. Estimation of these
dynamic multivariate panel models is carried out via 'Stan'.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.0.1 dated 2022-12-23 and 1.1.1 dated 2023-02-03
dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-11-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-4-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-5-1.png |only dynamite-1.0.1/dynamite/man/figures/README-unnamed-chunk-6-1.png |only dynamite-1.0.1/dynamite/man/random.Rd |only dynamite-1.0.1/dynamite/tests/testthat/Rplots.pdf |only dynamite-1.1.1/dynamite/DESCRIPTION | 12 dynamite-1.1.1/dynamite/MD5 | 177 dynamite-1.1.1/dynamite/NAMESPACE | 7 dynamite-1.1.1/dynamite/NEWS.md | 163 dynamite-1.1.1/dynamite/R/as_data_frame.R | 37 dynamite-1.1.1/dynamite/R/as_data_table.R | 102 dynamite-1.1.1/dynamite/R/as_draws.R | 21 dynamite-1.1.1/dynamite/R/ci.R | 4 dynamite-1.1.1/dynamite/R/coef.R | 49 dynamite-1.1.1/dynamite/R/default_priors.R | 46 dynamite-1.1.1/dynamite/R/deterministic.R | 81 dynamite-1.1.1/dynamite/R/dynamite-package.R | 50 dynamite-1.1.1/dynamite/R/dynamite.R | 330 - dynamite-1.1.1/dynamite/R/dynamiteformula.R | 1166 +++-- dynamite-1.1.1/dynamite/R/exported_gets.R | 401 +- dynamite-1.1.1/dynamite/R/fitted.R | 162 dynamite-1.1.1/dynamite/R/lags.R | 25 dynamite-1.1.1/dynamite/R/latent_factor.R | 183 dynamite-1.1.1/dynamite/R/lfo.R | 621 +-- dynamite-1.1.1/dynamite/R/loo.R | 159 dynamite-1.1.1/dynamite/R/mcmc_diagnostics.R | 67 dynamite-1.1.1/dynamite/R/model_matrix.R | 75 dynamite-1.1.1/dynamite/R/plot.R | 901 ++-- dynamite-1.1.1/dynamite/R/predict.R | 1343 +++--- dynamite-1.1.1/dynamite/R/predict_helpers.R | 1995 +++++----- dynamite-1.1.1/dynamite/R/prepare_stan_input.R | 157 dynamite-1.1.1/dynamite/R/print.R | 9 dynamite-1.1.1/dynamite/R/random.R | 98 dynamite-1.1.1/dynamite/R/specials.R | 42 dynamite-1.1.1/dynamite/R/stanblocks.R | 182 dynamite-1.1.1/dynamite/R/stanblocks_families.R | 796 ++- dynamite-1.1.1/dynamite/R/summary.R | 12 dynamite-1.1.1/dynamite/R/sysdata.rda |binary dynamite-1.1.1/dynamite/R/update.R | 2 dynamite-1.1.1/dynamite/R/utilities.R | 687 +-- dynamite-1.1.1/dynamite/README.md | 92 dynamite-1.1.1/dynamite/data/categorical_example_fit.rda |binary dynamite-1.1.1/dynamite/data/gaussian_example_fit.rda |binary dynamite-1.1.1/dynamite/data/latent_factor_example_fit.rda |binary dynamite-1.1.1/dynamite/data/multichannel_example_fit.rda |binary dynamite-1.1.1/dynamite/inst/doc/dynamite.R | 42 dynamite-1.1.1/dynamite/inst/doc/dynamite.Rmd | 1122 ++--- dynamite-1.1.1/dynamite/inst/doc/dynamite.html | 453 +- dynamite-1.1.1/dynamite/man/as.data.frame.dynamitefit.Rd | 35 dynamite-1.1.1/dynamite/man/as.data.table.dynamitefit.Rd | 22 dynamite-1.1.1/dynamite/man/as_draws-dynamitefit.Rd | 29 dynamite-1.1.1/dynamite/man/categorical_example_fit.Rd | 11 dynamite-1.1.1/dynamite/man/coef.dynamitefit.Rd | 26 dynamite-1.1.1/dynamite/man/confint.dynamitefit.Rd | 2 dynamite-1.1.1/dynamite/man/dynamite.Rd | 66 dynamite-1.1.1/dynamite/man/dynamiteformula.Rd | 28 dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-10-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-7-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-8-1.png |binary dynamite-1.1.1/dynamite/man/figures/README-unnamed-chunk-9-1.png |binary dynamite-1.1.1/dynamite/man/figures/logo.png |only dynamite-1.1.1/dynamite/man/fitted.dynamitefit.Rd | 16 dynamite-1.1.1/dynamite/man/gaussian_example_fit.Rd | 20 dynamite-1.1.1/dynamite/man/get_code.Rd | 17 dynamite-1.1.1/dynamite/man/get_data.Rd | 12 dynamite-1.1.1/dynamite/man/get_parameter_names.Rd |only dynamite-1.1.1/dynamite/man/get_parameter_types.Rd |only dynamite-1.1.1/dynamite/man/get_priors.Rd | 12 dynamite-1.1.1/dynamite/man/lags.Rd | 2 dynamite-1.1.1/dynamite/man/latent_factor_example_fit.Rd | 2 dynamite-1.1.1/dynamite/man/lfactor.Rd | 12 dynamite-1.1.1/dynamite/man/lfo.Rd | 5 dynamite-1.1.1/dynamite/man/loo.dynamitefit.Rd | 5 dynamite-1.1.1/dynamite/man/mcmc_diagnostics.Rd | 4 dynamite-1.1.1/dynamite/man/multichannel_example_fit.Rd | 16 dynamite-1.1.1/dynamite/man/plot.dynamitefit.Rd | 42 dynamite-1.1.1/dynamite/man/plot_betas.Rd | 12 dynamite-1.1.1/dynamite/man/plot_deltas.Rd | 5 dynamite-1.1.1/dynamite/man/plot_nus.Rd | 14 dynamite-1.1.1/dynamite/man/predict.dynamitefit.Rd | 41 dynamite-1.1.1/dynamite/man/random_spec.Rd |only dynamite-1.1.1/dynamite/tests/testthat/test-edgecases.R | 193 dynamite-1.1.1/dynamite/tests/testthat/test-errors.R | 320 + dynamite-1.1.1/dynamite/tests/testthat/test-grunfeld.R | 17 dynamite-1.1.1/dynamite/tests/testthat/test-internals.R | 114 dynamite-1.1.1/dynamite/tests/testthat/test-output.R | 33 dynamite-1.1.1/dynamite/tests/testthat/test-predict.R | 891 ++-- dynamite-1.1.1/dynamite/tests/testthat/test-priors.R | 5 dynamite-1.1.1/dynamite/tests/testthat/test-recovery.R | 188 dynamite-1.1.1/dynamite/tests/testthat/test-scaling.R | 53 dynamite-1.1.1/dynamite/tests/testthat/test-warnings.R | 368 - dynamite-1.1.1/dynamite/tests/testthat/testmodel.stan |only dynamite-1.1.1/dynamite/vignettes/dynamite.Rmd | 1122 ++--- dynamite-1.1.1/dynamite/vignettes/dynamite.bib | 23 95 files changed, 8636 insertions(+), 7018 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 1.0.1 dated 2022-11-04 and 2.0.0 dated 2023-02-03
dsfa-1.0.1/dsfa/R/OwenT.R |only dsfa-1.0.1/dsfa/R/chainrule.R |only dsfa-1.0.1/dsfa/R/check_arguments.R |only dsfa-1.0.1/dsfa/R/comperr.R |only dsfa-1.0.1/dsfa/R/comperr_mv.R |only dsfa-1.0.1/dsfa/R/comperr_mv_mgcv.R |only dsfa-1.0.1/dsfa/R/cop.R |only dsfa-1.0.1/dsfa/R/cop_mgcv.R |only dsfa-1.0.1/dsfa/R/dsfa.R |only dsfa-1.0.1/dsfa/R/erf.R |only dsfa-1.0.1/dsfa/R/normexp.R |only dsfa-1.0.1/dsfa/R/normexp_mgcv.R |only dsfa-1.0.1/dsfa/R/normhnorm.R |only dsfa-1.0.1/dsfa/R/normhnorm_mgcv.R |only dsfa-1.0.1/dsfa/R/reparametrize.R |only dsfa-1.0.1/dsfa/R/rsp.R |only dsfa-1.0.1/dsfa/R/utility_functions.R |only dsfa-1.0.1/dsfa/R/zeta.R |only dsfa-1.0.1/dsfa/README.md |only dsfa-1.0.1/dsfa/man/OwenT.Rd |only dsfa-1.0.1/dsfa/man/check_arguments.Rd |only dsfa-1.0.1/dsfa/man/comperr_mv.Rd |only dsfa-1.0.1/dsfa/man/dcomperr.Rd |only dsfa-1.0.1/dsfa/man/dcomperr_mv.Rd |only dsfa-1.0.1/dsfa/man/erf.Rd |only dsfa-1.0.1/dsfa/man/normexp.Rd |only dsfa-1.0.1/dsfa/man/normhnorm.Rd |only dsfa-1.0.1/dsfa/man/pos_eigen.Rd |only dsfa-1.0.1/dsfa/man/reparametrize.Rd |only dsfa-1.0.1/dsfa/man/rsp.Rd |only dsfa-1.0.1/dsfa/man/zeta.Rd |only dsfa-2.0.0/dsfa/DESCRIPTION | 19 +++-- dsfa-2.0.0/dsfa/MD5 | 112 ++++++++++++++++++------------- dsfa-2.0.0/dsfa/NAMESPACE | 55 +++++++-------- dsfa-2.0.0/dsfa/NEWS.md | 16 +++- dsfa-2.0.0/dsfa/R/RcppExports.R |only dsfa-2.0.0/dsfa/R/cdf2quantile.R |only dsfa-2.0.0/dsfa/R/dcomper.R |only dsfa-2.0.0/dsfa/R/dcomper_mv.R |only dsfa-2.0.0/dsfa/R/dcop.R |only dsfa-2.0.0/dsfa/R/delta_bounds.R |only dsfa-2.0.0/dsfa/R/dnormexp.R |only dsfa-2.0.0/dsfa/R/dnormhnorm.R |only dsfa-2.0.0/dsfa/R/dsfa-package.R |only dsfa-2.0.0/dsfa/R/efficiency.R | 115 ++++++++++++++++---------------- dsfa-2.0.0/dsfa/R/elasticity.R | 81 +++++++++------------- dsfa-2.0.0/dsfa/R/manuf.R |only dsfa-2.0.0/dsfa/R/mgcv_comper.R |only dsfa-2.0.0/dsfa/R/mgcv_comper_mv.R |only dsfa-2.0.0/dsfa/R/mgcv_cop.R |only dsfa-2.0.0/dsfa/R/mom2par.R |only dsfa-2.0.0/dsfa/R/par2mom.R |only dsfa-2.0.0/dsfa/build/partial.rdb |binary dsfa-2.0.0/dsfa/data |only dsfa-2.0.0/dsfa/inst/REFERENCES.bib | 8 ++ dsfa-2.0.0/dsfa/man/cdf2quantile.Rd |only dsfa-2.0.0/dsfa/man/chainrule.Rd | 56 ++++++++------- dsfa-2.0.0/dsfa/man/comper.Rd |only dsfa-2.0.0/dsfa/man/comper_mv.Rd |only dsfa-2.0.0/dsfa/man/cop.Rd | 89 ++++++++++++++++-------- dsfa-2.0.0/dsfa/man/dcomper.Rd |only dsfa-2.0.0/dsfa/man/dcomper_mv.Rd |only dsfa-2.0.0/dsfa/man/dcop.Rd | 60 +++++++++------- dsfa-2.0.0/dsfa/man/delta_bounds.Rd |only dsfa-2.0.0/dsfa/man/derivs_transform.Rd |only dsfa-2.0.0/dsfa/man/differencerule.Rd |only dsfa-2.0.0/dsfa/man/dnormexp.Rd | 86 +++++++++++------------ dsfa-2.0.0/dsfa/man/dnormhnorm.Rd | 73 +++++++++----------- dsfa-2.0.0/dsfa/man/dsfa.Rd | 115 +++++++++++++++++++++++--------- dsfa-2.0.0/dsfa/man/efficiency.Rd | 14 +-- dsfa-2.0.0/dsfa/man/elasticity.Rd | 8 -- dsfa-2.0.0/dsfa/man/ind2joint.Rd |only dsfa-2.0.0/dsfa/man/list2derivs.Rd |only dsfa-2.0.0/dsfa/man/manuf.Rd |only dsfa-2.0.0/dsfa/man/mom2par.Rd |only dsfa-2.0.0/dsfa/man/par2mom.Rd |only dsfa-2.0.0/dsfa/man/productrule.Rd |only dsfa-2.0.0/dsfa/man/quotientrule.Rd |only dsfa-2.0.0/dsfa/man/sumrule.Rd |only dsfa-2.0.0/dsfa/man/transform.Rd |only dsfa-2.0.0/dsfa/man/trind.Rd |only dsfa-2.0.0/dsfa/man/trind_generator.Rd |only dsfa-2.0.0/dsfa/src |only 83 files changed, 509 insertions(+), 398 deletions(-)
Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the
'bbotk' package. 'miesmuschel' offers both ready-to-use optimization
algorithms, as well as their fundamental building blocks that can be used to
manually construct specialized optimization loops. The Mixed Integer Evolution
Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be
implemented, as well as the multi-objective optimization algorithms NSGA-II
by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre],
Lennart Schneider [ctb] ,
Susanne Dandl [ctb] ,
Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between miesmuschel versions 0.0.2 dated 2022-11-16 and 0.0.3 dated 2023-02-03
DESCRIPTION | 12 MD5 | 33 + NAMESPACE | 3 NEWS.md | 6 R/OptimizerMies.R | 2 R/TerminatorGenerationPerfReached.R |only R/TerminatorGenerationStagnation.R |only R/bibentries.R | 8 R/mies_methods.R | 306 +++++++++++++++++- R/utils_mo.R | 32 + R/zzz.R | 2 inst/tinytest/test_TerminatorGenerationPerfReached.R |only inst/tinytest/test_TerminatorGenerationStagnation.R |only inst/tinytest/test_mies_aggregate_single_generation.R |only inst/tinytest/test_mies_generation_apply.R |only man/OptimizerMies.Rd | 2 man/domhv.Rd |only man/mies_aggregate_generations.Rd | 8 man/mies_aggregate_single_generation.Rd |only man/mies_generation_apply.Rd |only man/mies_get_generation_results.Rd | 6 man/mlr_terminators_genperfreached.Rd |only man/mlr_terminators_genstag.Rd |only 23 files changed, 391 insertions(+), 29 deletions(-)
Title: Simulates Dice Rolls and Coin Flips
Description: Utils for basic statistical experiments, that can be used for teaching
introductory statistics. Each experiment generates a tibble.
Dice rolls and coin flips are simulated using sample().
The properties of the dice can be changed, like the number of sides.
A coin flip is simulated using a two sided dice.
Experiments can be combined with the pipe-operator.
Author: Roland Krasser [aut, cre],
Giovanni Marco Dall'Olio [aut]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between tidydice versions 0.1.1 dated 2021-04-19 and 1.0.0 dated 2023-02-03
tidydice-0.1.1/tidydice/R/plot_dice.R |only tidydice-0.1.1/tidydice/R/tidydice.R |only tidydice-1.0.0/tidydice/DESCRIPTION | 21 tidydice-1.0.0/tidydice/MD5 | 52 tidydice-1.0.0/tidydice/NAMESPACE | 8 tidydice-1.0.0/tidydice/NEWS.md | 11 tidydice-1.0.0/tidydice/R/binom.R | 16 tidydice-1.0.0/tidydice/R/coin-plot.R |only tidydice-1.0.0/tidydice/R/coin.R |only tidydice-1.0.0/tidydice/R/dice-formula.R |only tidydice-1.0.0/tidydice/R/dice-plot.R |only tidydice-1.0.0/tidydice/R/dice.R |only tidydice-1.0.0/tidydice/README.md | 123 + tidydice-1.0.0/tidydice/build/vignette.rds |binary tidydice-1.0.0/tidydice/inst/doc/tidydice.R | 43 tidydice-1.0.0/tidydice/inst/doc/tidydice.Rmd | 68 tidydice-1.0.0/tidydice/inst/doc/tidydice.html | 699 +++++++--- tidydice-1.0.0/tidydice/man/circle_points.Rd | 2 tidydice-1.0.0/tidydice/man/figures/tidydice-binom-dice-60.png |only tidydice-1.0.0/tidydice/man/figures/tidydice-roll-dice-60.png |only tidydice-1.0.0/tidydice/man/flip_coin.Rd | 2 tidydice-1.0.0/tidydice/man/force_coin.Rd | 2 tidydice-1.0.0/tidydice/man/force_dice.Rd | 2 tidydice-1.0.0/tidydice/man/parse_dice_formula.Rd |only tidydice-1.0.0/tidydice/man/parse_dice_formula_part.Rd |only tidydice-1.0.0/tidydice/man/plot_binom.Rd | 4 tidydice-1.0.0/tidydice/man/plot_coin.Rd |only tidydice-1.0.0/tidydice/man/plot_dice.Rd | 4 tidydice-1.0.0/tidydice/man/plot_single_coin.Rd |only tidydice-1.0.0/tidydice/man/plot_single_dice.Rd | 4 tidydice-1.0.0/tidydice/man/roll_dice.Rd | 2 tidydice-1.0.0/tidydice/man/roll_dice_formula.Rd |only tidydice-1.0.0/tidydice/man/top_n_dice.Rd |only tidydice-1.0.0/tidydice/tests/testthat/test_dice_formula.R |only tidydice-1.0.0/tidydice/vignettes/tidydice.Rmd | 68 35 files changed, 876 insertions(+), 255 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.2.0 dated 2022-10-13 and 3.3.0 dated 2023-02-03
DESCRIPTION | 6 ++-- MD5 | 47 ++++++++++++++++----------------- NAMESPACE | 1 R/opal.table.R | 51 ++++++++++++++++++++++++++++++++++++ inst/doc/datashield-admin.html | 4 +- inst/doc/opal-files.html | 4 +- inst/doc/opal-projects.html | 4 +- inst/doc/opal-rsession.html | 4 +- man/opal.resource_view_create.Rd | 3 +- man/opal.resource_view_reconnect.Rd | 3 +- man/opal.table_create.Rd | 3 +- man/opal.table_delete.Rd | 3 +- man/opal.table_dictionary_get.Rd | 3 +- man/opal.table_dictionary_update.Rd | 3 +- man/opal.table_exists.Rd | 3 +- man/opal.table_export.Rd | 3 +- man/opal.table_get.Rd | 3 +- man/opal.table_import.Rd | 3 +- man/opal.table_perm.Rd | 3 +- man/opal.table_perm_add.Rd | 3 +- man/opal.table_perm_delete.Rd | 3 +- man/opal.table_save.Rd | 3 +- man/opal.table_truncate.Rd | 3 +- man/opal.table_view_create.Rd | 3 +- man/opal.table_view_update.Rd |only 25 files changed, 119 insertions(+), 50 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 1.9.19 dated 2022-11-06 and 2.0.1 dated 2023-02-03
DESCRIPTION | 15 ++-- MD5 | 22 +++--- NAMESPACE | 6 - NEWS.md | 14 +++ R/HFDutils.R | 11 +-- R/HMDutils.R | 174 +++++++++++++++++++++++++++++++++++++------------ R/readHFD.R | 2 R/readHMD.R | 123 ++++++++++++++++++++++------------ inst/CITATION | 7 + man/getHFDitemavail.Rd | 2 man/getHMDitemavail.Rd | 10 -- man/readHMDweb.Rd | 8 -- 12 files changed, 263 insertions(+), 131 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.3-1 dated 2022-11-19 and 1.4-0 dated 2023-02-03
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NAMESPACE | 8 +++-- R/all_style.R |only R/line_length_style.R | 2 - R/nomagic_style.R | 77 ++++++++++++++++++++++++++++++++++++-------------- inst/NEWS.Rd | 19 ++++++++++++ man/all_style.Rd |only man/nomagic_style.Rd | 2 + tests/style-tests.R | 54 +++++++++++++++++++++++++++++++++-- 10 files changed, 147 insertions(+), 39 deletions(-)
Title: Automatically Position Non-Overlapping Text Labels with
'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid
overlapping text labels. Labels repel away from each other and away from the
data points.
Author: Kamil Slowikowski [aut, cre] ,
Alicia Schep [ctb] ,
Sean Hughes [ctb] ,
Trung Kien Dang [ctb] ,
Saulius Lukauskas [ctb],
Jean-Olivier Irisson [ctb] ,
Zhian N Kamvar [ctb] ,
Thompson Ryan [ctb] ,
Dervieux Christophe [ctb] ,
Yutani Hiroaki [ctb],
Pierr [...truncated...]
Maintainer: Kamil Slowikowski <kslowikowski@gmail.com>
Diff between ggrepel versions 0.9.2 dated 2022-11-06 and 0.9.3 dated 2023-02-03
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 12 ++++++++++++ R/geom-label-repel.R | 8 ++++---- R/geom-text-repel.R | 10 +++++----- R/utilities.R | 8 ++++++++ inst/doc/ggrepel.html | 6 +++--- tests/testthat/test-just-with-angle.R | 19 +++++++++++-------- 8 files changed, 56 insertions(+), 32 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.3.4 dated 2023-01-06 and 0.3.5 dated 2023-02-03
GE-0.3.4/GE/R/gemIntertemporalStochastic_Bank_3Periods.R |only GE-0.3.4/GE/R/gemIntertemporal_Stochastic_2_2.R |only GE-0.3.4/GE/man/gemIntertemporalStochastic_Bank_3Periods.Rd |only GE-0.3.4/GE/man/gemIntertemporal_Stochastic_2_2.Rd |only GE-0.3.5/GE/DESCRIPTION | 8 GE-0.3.5/GE/MD5 | 48 +++-- GE-0.3.5/GE/NAMESPACE | 6 GE-0.3.5/GE/R/demCreditPolicy.R | 81 +++++++++- GE-0.3.5/GE/R/gemDualLinearProgramming.R | 40 +--- GE-0.3.5/GE/R/gemInputOutputTable_8_8.R | 2 GE-0.3.5/GE/R/gemIntertemporalStochastic_Bank_ThreePeriods.R |only GE-0.3.5/GE/R/gemIntertemporalStochastic_ThreePeriods_2_2.R |only GE-0.3.5/GE/R/gemIntertemporalStochastic_TwoPeriods.R |only GE-0.3.5/GE/R/gemIntertemporal_2_2.R | 3 GE-0.3.5/GE/R/gemMoney_3_2.R | 2 GE-0.3.5/GE/R/gemResearchDevelopmentIntensity.R |only GE-0.3.5/GE/R/gem_3_4.R | 30 +++ GE-0.3.5/GE/R/output.R | 9 + GE-0.3.5/GE/R/policyMarketClearingPrice.R | 7 GE-0.3.5/GE/man/demCreditPolicy.Rd | 81 +++++++++- GE-0.3.5/GE/man/gemDualLinearProgramming.Rd | 40 +--- GE-0.3.5/GE/man/gemInputOutputTable_8_8.Rd | 2 GE-0.3.5/GE/man/gemIntertemporalStochastic_Bank_ThreePeriods.Rd |only GE-0.3.5/GE/man/gemIntertemporalStochastic_ThreePeriods_2_2.Rd |only GE-0.3.5/GE/man/gemIntertemporalStochastic_TwoPeriods.Rd |only GE-0.3.5/GE/man/gemIntertemporal_2_2.Rd | 3 GE-0.3.5/GE/man/gemMoney_3_2.Rd | 2 GE-0.3.5/GE/man/gemResearchDevelopmentIntensity.Rd |only GE-0.3.5/GE/man/gem_3_4.Rd | 30 +++ GE-0.3.5/GE/man/output.Rd | 9 + GE-0.3.5/GE/man/policyMarketClearingPrice.Rd | 5 31 files changed, 299 insertions(+), 109 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 0.4.0 dated 2022-09-30 and 0.5.0 dated 2023-02-02
DESCRIPTION | 8 MD5 | 238 ++++----- NAMESPACE | 1 NEWS.md | 49 + R/compilation.R | 87 ++- R/geometry.R | 24 R/interface.R | 193 +++++-- R/print.R | 2 R/tree-sequences.R | 93 ++- R/utils.R | 21 R/visualization.R | 29 - R/zzz.R | 49 + README.md | 23 build/vignette.rds |binary inst/doc/vignette-00-installation.Rmd | 10 inst/doc/vignette-00-installation.html | 41 - inst/doc/vignette-01-tutorial.R | 21 inst/doc/vignette-01-tutorial.Rmd | 39 - inst/doc/vignette-01-tutorial.html | 293 ++++++----- inst/doc/vignette-02-grid-model.R | 87 +++ inst/doc/vignette-02-grid-model.Rmd | 112 ++++ inst/doc/vignette-02-grid-model.html | 397 +++++++++++----- inst/doc/vignette-03-interactions.R | 4 inst/doc/vignette-03-interactions.Rmd | 4 inst/doc/vignette-03-interactions.html | 80 +-- inst/doc/vignette-04-nonspatial-models.R | 6 inst/doc/vignette-04-nonspatial-models.Rmd | 6 inst/doc/vignette-04-nonspatial-models.html | 66 +- inst/doc/vignette-05-tree-sequences.R | 13 inst/doc/vignette-05-tree-sequences.Rmd | 22 inst/doc/vignette-05-tree-sequences.html | 524 ++++++++++----------- inst/doc/vignette-06-locations.R | 131 +++-- inst/doc/vignette-06-locations.Rmd | 151 +++--- inst/doc/vignette-06-locations.html | 544 ++++++++++------------ inst/doc/vignette-07-backends.R | 8 inst/doc/vignette-07-backends.Rmd | 8 inst/doc/vignette-07-backends.html | 18 inst/doc/vignette-08-nonslendr-tskit.R | 4 inst/doc/vignette-08-nonslendr-tskit.Rmd | 4 inst/doc/vignette-08-nonslendr-tskit.html | 42 - inst/doc/vignette-09-paper.R | 205 ++++++-- inst/doc/vignette-09-paper.Rmd | 256 +++++++--- inst/doc/vignette-09-paper.html | 321 ++++++------ inst/extdata/models/introgression.trees |binary inst/extdata/models/introgression/checksums.tsv | 8 inst/extdata/models/introgression/populations.tsv | 2 inst/extdata/models/introgression/ranges.rds |binary inst/extdata/models/introgression/script.py | 68 +- inst/extdata/models/introgression/script.slim | 24 inst/extdata/models/msprime.trees |binary inst/scripts/__pycache__/script.cpython-311.pyc |only inst/scripts/__pycache__/script.cpython-38.pyc |binary inst/scripts/script.py | 56 +- inst/scripts/script.slim | 22 man/check_env.Rd | 5 man/compile_model.Rd | 2 man/init_env.Rd |only man/msprime.Rd | 2 man/plot_model.Rd | 2 man/population.Rd | 6 man/read_model.Rd | 2 man/schedule_sampling.Rd | 2 man/slim.Rd | 2 man/ts_afs.Rd | 2 man/ts_ancestors.Rd | 2 man/ts_coalesced.Rd | 2 man/ts_descendants.Rd | 2 man/ts_divergence.Rd | 2 man/ts_diversity.Rd | 2 man/ts_draw.Rd | 2 man/ts_edges.Rd | 2 man/ts_f4ratio.Rd | 2 man/ts_fst.Rd | 2 man/ts_genotypes.Rd | 2 man/ts_load.Rd | 2 man/ts_metadata.Rd | 2 man/ts_mutate.Rd | 2 man/ts_nodes.Rd | 2 man/ts_phylo.Rd | 2 man/ts_recapitate.Rd | 2 man/ts_samples.Rd | 2 man/ts_save.Rd | 2 man/ts_segregating.Rd | 2 man/ts_simplify.Rd | 2 man/ts_tajima.Rd | 2 man/ts_tree.Rd | 2 tests/testthat/map.rds |binary tests/testthat/test-compilation.R | 51 +- tests/testthat/test-coordinate-conversions.R | 2 tests/testthat/test-geneflow.R | 12 tests/testthat/test-geometrical-operations.R | 10 tests/testthat/test-interaction-changes.R | 2 tests/testthat/test-manual-ts.R | 2 tests/testthat/test-msprime-geneflow.R | 4 tests/testthat/test-msprime-metadata.R | 2 tests/testthat/test-msprime.R | 4 tests/testthat/test-nonserialized.R | 4 tests/testthat/test-pure-msprime-vs-slendr.R | 4 tests/testthat/test-pure-slim-vs-slendr.R | 4 tests/testthat/test-resizes-locked.R | 2 tests/testthat/test-resizes.R | 2 tests/testthat/test-runners.R | 4 tests/testthat/test-sampling.R | 4 tests/testthat/test-serialization.R | 4 tests/testthat/test-simulation-runs.R | 2 tests/testthat/test-time-direction.R | 6 tests/testthat/test-trees.R | 2 tests/testthat/test-ts-ancestors-descendants.R | 2 tests/testthat/test-ts-pure-nonspatial.R | 4 tests/testthat/test-ts-pure-spatial.R | 2 tests/testthat/test-ts.R | 2 vignettes/vignette-00-installation.Rmd | 10 vignettes/vignette-01-tutorial.Rmd | 39 - vignettes/vignette-02-grid-model.Rmd | 112 ++++ vignettes/vignette-03-interactions.Rmd | 4 vignettes/vignette-04-nonspatial-models.Rmd | 6 vignettes/vignette-05-tree-sequences.Rmd | 22 vignettes/vignette-06-locations.Rmd | 151 +++--- vignettes/vignette-07-backends.Rmd | 8 vignettes/vignette-08-nonslendr-tskit.Rmd | 4 vignettes/vignette-09-paper.Rmd | 256 +++++++--- 121 files changed, 3206 insertions(+), 2026 deletions(-)
Title: R for High-Dimensional Omic Data
Description: Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.
Author: Sean Hackett [aut, cre] ,
Calico Life Sciences LLC [cph, fnd]
Maintainer: Sean Hackett <sean@calicolabs.com>
Diff between romic versions 1.0.0 dated 2021-07-20 and 1.1.1 dated 2023-02-02
romic-1.0.0/romic/R/app_scatter.R |only romic-1.0.0/romic/man/add_pca_loadings.Rd |only romic-1.0.0/romic/man/app_scatter.Rd |only romic-1.1.1/romic/DESCRIPTION | 13 romic-1.1.1/romic/MD5 | 149 romic-1.1.1/romic/NAMESPACE | 5 romic-1.1.1/romic/NEWS.md |only romic-1.1.1/romic/R/app_heatmap.R | 363 +- romic-1.1.1/romic/R/app_pcs.R |only romic-1.1.1/romic/R/data.R | 1 romic-1.1.1/romic/R/data_classes.R | 132 romic-1.1.1/romic/R/design.R | 1 romic-1.1.1/romic/R/dim_reduction.R | 201 + romic-1.1.1/romic/R/export.R | 68 romic-1.1.1/romic/R/filters.R | 14 romic-1.1.1/romic/R/module_filter.R | 1 romic-1.1.1/romic/R/module_ggbiv.R | 125 romic-1.1.1/romic/R/module_ggplot.R | 14 romic-1.1.1/romic/R/module_gguniv.R | 24 romic-1.1.1/romic/R/module_lasso.R | 7 romic-1.1.1/romic/R/module_organize.R | 22 romic-1.1.1/romic/R/module_plotsaver.R | 84 romic-1.1.1/romic/R/module_sort.R | 2 romic-1.1.1/romic/R/mutates.R | 88 romic-1.1.1/romic/R/romic.R | 4 romic-1.1.1/romic/R/utils.R | 42 romic-1.1.1/romic/README.md | 19 romic-1.1.1/romic/build/vignette.rds |binary romic-1.1.1/romic/inst/doc/romic.R | 14 romic-1.1.1/romic/inst/doc/romic.Rmd | 14 romic-1.1.1/romic/inst/doc/romic.html | 1561 +++++++++- romic-1.1.1/romic/man/add_pcs.Rd |only romic-1.1.1/romic/man/app_heatmap.Rd | 6 romic-1.1.1/romic/man/app_pcs.Rd |only romic-1.1.1/romic/man/center_tomic.Rd | 1 romic-1.1.1/romic/man/check_tidy_omic.Rd | 3 romic-1.1.1/romic/man/check_tomic.Rd | 1 romic-1.1.1/romic/man/check_triple_omic.Rd | 3 romic-1.1.1/romic/man/convert_wide_to_tidy_omic.Rd | 1 romic-1.1.1/romic/man/create_tidy_omic.Rd | 1 romic-1.1.1/romic/man/create_triple_omic.Rd | 1 romic-1.1.1/romic/man/downsample_heatmap.Rd |only romic-1.1.1/romic/man/export_tomic_as_tidy.Rd | 2 romic-1.1.1/romic/man/export_tomic_as_triple.Rd | 4 romic-1.1.1/romic/man/export_tomic_as_wide.Rd | 4 romic-1.1.1/romic/man/filter_tomic.Rd | 1 romic-1.1.1/romic/man/format_names_for_plotting.Rd | 6 romic-1.1.1/romic/man/get_design_tbl.Rd | 1 romic-1.1.1/romic/man/ggplotOutput.Rd | 10 romic-1.1.1/romic/man/hclust_order.Rd | 3 romic-1.1.1/romic/man/impute_missing_values.Rd |only romic-1.1.1/romic/man/lassoServer.Rd | 2 romic-1.1.1/romic/man/plot_bivariate.Rd | 21 romic-1.1.1/romic/man/plot_heatmap.Rd | 10 romic-1.1.1/romic/man/plot_univariate.Rd | 3 romic-1.1.1/romic/man/plotsaverInput.Rd | 8 romic-1.1.1/romic/man/plotsaverServer.Rd | 5 romic-1.1.1/romic/man/shiny_filter_test.Rd | 1 romic-1.1.1/romic/man/shiny_ggbiv_test.Rd | 3 romic-1.1.1/romic/man/shiny_ggplot_test.Rd | 3 romic-1.1.1/romic/man/shiny_gguniv_test.Rd | 3 romic-1.1.1/romic/man/shiny_lasso_test.Rd | 1 romic-1.1.1/romic/man/shiny_lasso_test_reactval.Rd | 1 romic-1.1.1/romic/man/shiny_organize_test.Rd | 1 romic-1.1.1/romic/man/shiny_plotsaver_test.Rd | 1 romic-1.1.1/romic/man/shiny_sort_test.Rd | 1 romic-1.1.1/romic/man/sort_tomic.Rd | 1 romic-1.1.1/romic/man/tidy_to_triple.Rd | 1 romic-1.1.1/romic/man/tomic_sort_status.Rd | 1 romic-1.1.1/romic/man/tomic_to.Rd | 1 romic-1.1.1/romic/man/triple_to_tidy.Rd | 1 romic-1.1.1/romic/man/update_tidy_omic.Rd | 1 romic-1.1.1/romic/man/update_tomic.Rd | 1 romic-1.1.1/romic/man/var_partial_match.Rd |only romic-1.1.1/romic/tests/testthat/test-coerce_to_classes.R |only romic-1.1.1/romic/tests/testthat/test-dim_reduction.R | 30 romic-1.1.1/romic/tests/testthat/test-downsampling.R |only romic-1.1.1/romic/tests/testthat/test-factor_pks.R |only romic-1.1.1/romic/tests/testthat/test-hclust.R | 17 romic-1.1.1/romic/tests/testthat/test-import_export.R |only romic-1.1.1/romic/tests/testthat/test-test-variable_partial_string_matching.R |only romic-1.1.1/romic/tests/testthat/test-triple_omic.R | 4 romic-1.1.1/romic/vignettes/romic.Rmd | 14 83 files changed, 2458 insertions(+), 694 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230202.1600 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.1-1 dated 2022-05-19 and 1.2-0 dated 2023-02-02
DESCRIPTION | 12 - MD5 | 86 +++++---- NAMESPACE | 8 NEWS.md | 22 ++ R/addDictionaryEntry.R | 1 R/countAnnotations.R | 6 R/countMatchingAnnotations.R |only R/formatTranscript.R |only R/getAnnotations.R | 6 R/getFragmentAnnotations.R |only R/getFragments.R | 30 ++- R/getMatchAlignments.R | 2 R/getMatchLabels.R | 2 R/getMatches.R | 165 +++++++++++------- R/getMatchingAnnotations.R |only R/getMedia.R | 92 +++++++--- R/getMediaUrl.R |only R/getTranscriptIds.R | 6 R/getTranscriptIdsInCorpus.R | 6 R/getTranscriptIdsWithParticipant.R | 6 R/nzilbb.labbcat.R | 4 R/praatScriptIntensity.R | 4 R/praatScriptPitch.R | 5 build/partial.rdb |binary man/addDictionaryEntry.Rd | 2 man/countAnnotations.Rd | 6 man/countMatchingAnnotations.Rd |only man/formatTranscript.Rd |only man/getAnnotations.Rd | 5 man/getFragmentAnnotations.Rd |only man/getFragments.Rd | 5 man/getMatches.Rd | 118 ++++++++---- man/getMatchingAnnotations.Rd |only man/getMedia.Rd | 35 ++- man/getMediaUrl.Rd |only man/nzilbb.labbcat.Rd | 2 man/praatScriptIntensity.Rd | 4 man/praatScriptPitch.Rd | 5 man/removeDictionaryEntry.Rd | 2 tests/testthat/test-countAnnotations.R | 12 + tests/testthat/test-countMatchingAnnotations.R |only tests/testthat/test-formatTranscript.R |only tests/testthat/test-getAnnotations.R | 19 +- tests/testthat/test-getFragmentAnnotations.R |only tests/testthat/test-getMatchAlignments.R | 14 - tests/testthat/test-getMatchLabels.R | 8 tests/testthat/test-getMatches.R | 14 + tests/testthat/test-getMatchingAnnotations.R |only tests/testthat/test-getMedia.R | 23 ++ tests/testthat/test-getTranscriptIdsInCorpus.R | 8 tests/testthat/test-getTranscriptIdsWithParticipant.R | 8 51 files changed, 525 insertions(+), 228 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre],
Krisztian Sebestyen [aut],
Han Sunwoo [aut],
Jason Becker [ctb],
Bendix Carstensen [ctb],
Daryl Morris [ctb],
Josh Pasek [ctb],
Dennis Chao [ctb],
Andri Signorell [ctb],
Sue Li [ctb],
Jonathan Bartlett [ctb],
Christophe Dutang [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between kyotil versions 2022.12-20 dated 2022-12-20 and 2023.2-2 dated 2023-02-02
ChangeLog | 10 ++++++---- DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/CITATION | 4 +--- inst/doc/kyotil-vignette.pdf |binary man/predictCompetingRisk2.Rd | 4 ++-- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between imager versions 0.42.16 dated 2022-12-19 and 0.42.18 dated 2023-02-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ inst/doc/gettingstarted.html | 6 +++--- inst/doc/pixsets.R | 12 ++++++------ inst/doc/pixsets.Rmd | 12 ++++++------ inst/doc/pixsets.html | 16 ++++++++-------- vignettes/pixsets.Rmd | 12 ++++++------ 7 files changed, 40 insertions(+), 40 deletions(-)
Title: 'Shiny' Extension of 'video.js'
Description: Video interactivity within 'shiny' applications using 'video.js'. Enables
the status of the video to be sent from the UI to the server, and allows events
such as playing and pausing the video to be triggered from the server.
Author: Ashley Baldry [aut, cre],
Steve Heffernan [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Diff between video versions 0.1.0 dated 2022-07-21 and 0.1.1 dated 2023-02-02
video-0.1.0/video/R/data.R |only video-0.1.0/video/man/video_formats.Rd |only video-0.1.1/video/DESCRIPTION | 10 +- video-0.1.1/video/MD5 | 16 +-- video-0.1.1/video/NEWS.md | 6 + video-0.1.1/video/R/server-side.R | 2 video-0.1.1/video/R/sysdata.rda |binary video-0.1.1/video/build/vignette.rds |binary video-0.1.1/video/inst/doc/video.html | 124 +++++++++++++++-------------- video-0.1.1/video/man/video-server.Rd | 140 ++++++++++++++++----------------- 10 files changed, 154 insertions(+), 144 deletions(-)
Title: 'Apple App Store' and 'iTunes' Data Extraction
Description: Using 'Apple App Store' <https://www.apple.com/app-store/> web scraping and 'iTunes' API
<https://performance-partners.apple.com/search-api>
to extract content information, app ratings and reviews.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Diff between appler versions 0.1.4 dated 2022-10-06 and 0.2.0 dated 2023-02-02
DESCRIPTION | 22 ++-- MD5 | 42 +++++--- NAMESPACE | 14 +- NEWS.md | 9 + R/data.R | 128 ++++++++++++++------------ R/data_internal.R |only R/info.R | 7 + R/ratings.R | 16 ++- R/reviews.R | 103 ++++++++++++++------- R/top.R | 31 ++++-- README.md | 197 +++++++++++++---------------------------- build |only data |only inst/doc |only inst/scripts |only man/apple_apps.Rd |only man/figures |only man/get_apple_chart_postion.Rd | 27 ++++- man/get_apple_rating_split.Rd | 13 ++ man/get_apple_reviews.Rd | 53 +++++++++-- man/itunes_artists.Rd |only man/lookup_apple.Rd | 5 - man/search_apple.Rd | 2 tests/testthat/test-review.R | 49 +++++++--- vignettes |only 25 files changed, 416 insertions(+), 302 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.0.1 dated 2023-01-17 and 1.0.2 dated 2023-02-02
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/f1st.R | 2 +- R/f3st.R | 17 ++++++++++------- data/abcq.rda |binary data/boston.rda |binary data/leukemia.rda |binary data/mel_temp.rda |binary data/redwine.rda |binary data/snspt.rda |binary 10 files changed, 24 insertions(+), 21 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 0.2.5 dated 2021-07-20 and 0.2.6 dated 2023-02-02
DESCRIPTION | 12 MD5 | 12 NEWS.md | 8 R/plot.sivs.R | 9 R/sivs.R | 97 ++++-- build/vignette.rds |binary inst/doc/vignette_simple_usage.html | 523 ++++++++++++++++++++---------------- 7 files changed, 376 insertions(+), 285 deletions(-)
Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>.
OTP is an open source platform for multi-modal and multi-agency
journey planning written in 'Java'. The package allows you to manage a local version or
connect to remote OTP server to find walking, cycling, driving, or transit routes.
This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] ,
Marcus Young [aut] ,
Robin Lovelace [aut] ,
Layik Hama [ctb]
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>
Diff between opentripplanner versions 0.5 dated 2023-01-06 and 0.5.1 dated 2023-02-02
opentripplanner-0.5.1/opentripplanner/DESCRIPTION | 10 opentripplanner-0.5.1/opentripplanner/MD5 | 23 - opentripplanner-0.5.1/opentripplanner/NEWS.md | 6 opentripplanner-0.5.1/opentripplanner/R/otp-plan.R | 2 opentripplanner-0.5.1/opentripplanner/build/vignette.rds |binary opentripplanner-0.5.1/opentripplanner/inst/CITATION | 7 opentripplanner-0.5.1/opentripplanner/inst/doc/Analyst.html | 124 +++++---- opentripplanner-0.5.1/opentripplanner/inst/doc/OTPv2.html | 124 +++++---- opentripplanner-0.5.1/opentripplanner/inst/doc/advanced_features.html | 128 +++++----- opentripplanner-0.5.1/opentripplanner/inst/doc/known_issues.html | 18 - opentripplanner-0.5.1/opentripplanner/inst/doc/opentripplanner.html | 128 +++++----- opentripplanner-0.5.1/opentripplanner/inst/doc/prerequisites.html | 18 - opentripplanner-0.5/opentripplanner/vignettes/centroids.gpkg |only 13 files changed, 308 insertions(+), 280 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>
Diff between omu versions 1.0.7 dated 2022-08-27 and 1.0.9 dated 2023-02-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/PCA_plot.R | 5 ++++- R/check_zeros.R | 3 ++- R/omu_summary.R | 2 ++ inst/CITATION | 4 +--- inst/doc/Omu_vignette.html | 22 +++++++++++----------- 7 files changed, 29 insertions(+), 25 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
Author: Felicien Le Louedec [aut, cre]
,
Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <felicienlelouedec@proton.me>
Diff between mapbayr versions 0.8.0 dated 2022-09-29 and 0.9.0 dated 2023-02-02
mapbayr-0.8.0/mapbayr/R/mrgmod.R |only mapbayr-0.8.0/mapbayr/tests/testthat/test-mbrest.R |only mapbayr-0.9.0/mapbayr/DESCRIPTION | 14 mapbayr-0.9.0/mapbayr/MD5 | 101 - mapbayr-0.9.0/mapbayr/NAMESPACE | 16 mapbayr-0.9.0/mapbayr/NEWS.md | 438 +++-- mapbayr-0.9.0/mapbayr/R/data_helpers.R |only mapbayr-0.9.0/mapbayr/R/deprecations.R |only mapbayr-0.9.0/mapbayr/R/eta.R | 48 mapbayr-0.9.0/mapbayr/R/get.R | 553 +++--- mapbayr-0.9.0/mapbayr/R/mapbayest.R | 26 mapbayr-0.9.0/mapbayr/R/mapbayest_check_and_preprocess.R | 817 +++++----- mapbayr-0.9.0/mapbayr/R/mapbayest_ofv_computation.R | 20 mapbayr-0.9.0/mapbayr/R/mapbayest_optimization.R | 13 mapbayr-0.9.0/mapbayr/R/mapbayest_postprocess.R | 185 +- mapbayr-0.9.0/mapbayr/R/mapbayests.R | 777 +++++---- mapbayr-0.9.0/mapbayr/R/use_posterior.R | 10 mapbayr-0.9.0/mapbayr/R/vs_nonmem.R | 358 ++-- mapbayr-0.9.0/mapbayr/R/zzz_utils.R | 139 - mapbayr-0.9.0/mapbayr/README.md | 207 +- mapbayr-0.9.0/mapbayr/inst/WORDLIST | 154 - mapbayr-0.9.0/mapbayr/inst/run20eta.phi |only mapbayr-0.9.0/mapbayr/man/add_covariates.Rd |only mapbayr-0.9.0/mapbayr/man/adm_rows.Rd |only mapbayr-0.9.0/mapbayr/man/compute_ofv.Rd | 7 mapbayr-0.9.0/mapbayr/man/data_helpers.Rd | 86 - mapbayr-0.9.0/mapbayr/man/deprecations.Rd |only mapbayr-0.9.0/mapbayr/man/filter.mrgmod.Rd |only mapbayr-0.9.0/mapbayr/man/get_x.Rd | 3 mapbayr-0.9.0/mapbayr/man/hist.mapbayests.Rd | 16 mapbayr-0.9.0/mapbayr/man/mapbayest.Rd | 17 mapbayr-0.9.0/mapbayr/man/obs_rows.Rd |only mapbayr-0.9.0/mapbayr/man/parse_datehour.Rd |only mapbayr-0.9.0/mapbayr/man/preprocess.ofv.Rd | 7 mapbayr-0.9.0/mapbayr/man/preprocess.optim.Rd | 3 mapbayr-0.9.0/mapbayr/man/reexports.Rd |only mapbayr-0.9.0/mapbayr/tests/testthat/test-add_covariates.R | 56 mapbayr-0.9.0/mapbayr/tests/testthat/test-adm_lines.R | 110 - mapbayr-0.9.0/mapbayr/tests/testthat/test-blq.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_data.R | 59 mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_model.R | 6 mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_modeldata.R | 112 - mapbayr-0.9.0/mapbayr/tests/testthat/test-compute_ofv.R | 24 mapbayr-0.9.0/mapbayr/tests/testthat/test-data_helpers.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-deprecations.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-eta.R | 15 mapbayr-0.9.0/mapbayr/tests/testthat/test-fill_eta.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-get_data.R | 9 mapbayr-0.9.0/mapbayr/tests/testthat/test-get_phi.R | 10 mapbayr-0.9.0/mapbayr/tests/testthat/test-hist.R | 83 - mapbayr-0.9.0/mapbayr/tests/testthat/test-newini2.R | 3 mapbayr-0.9.0/mapbayr/tests/testthat/test-obs_lines.R | 106 + mapbayr-0.9.0/mapbayr/tests/testthat/test-parse_datehour.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-preprocess.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-preprocess.optim.R | 6 mapbayr-0.9.0/mapbayr/tests/testthat/test-progress.R | 38 mapbayr-0.9.0/mapbayr/tests/testthat/test-read_mrgsolve_model.R | 3 mapbayr-0.9.0/mapbayr/tests/testthat/test-reset-conditions.R | 16 mapbayr-0.9.0/mapbayr/tests/testthat/test-select_eta.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-use_posterior.R | 10 mapbayr-0.9.0/mapbayr/tests/testthat/test-vs_nonmem.R | 21 61 files changed, 2683 insertions(+), 2019 deletions(-)
Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column
names; provide quick counts of variable combinations (i.e., frequency
tables and crosstabs); and explore duplicate records. Other janitor functions
nicely format the tabulation results. These tabulate-and-report functions
approximate popular features of SPSS and Microsoft Excel. This package
follows the principles of the "tidyverse" and works well with the pipe function
%>%. janitor was built with beginning-to-intermediate R users in mind and is
optimized for user-friendliness.
Author: Sam Firke [aut, cre],
Bill Denney [ctb],
Chris Haid [ctb],
Ryan Knight [ctb],
Malte Grosser [ctb],
Jonathan Zadra [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>
Diff between janitor versions 2.1.0 dated 2021-01-04 and 2.2.0 dated 2023-02-02
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Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre] ,
Henrik Singmann [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between gratia versions 0.7.3 dated 2022-05-10 and 0.8.1 dated 2023-02-02
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Title: Load 'CDRC' Data
Description: A wrapper for the 'CDRC' 'API' that returns data frames or 'sf' of 'CDRC' data. The 'API' web reference is:<https://api.cdrc.ac.uk/swagger/index.html>.
Author: Alessia Calafiore [aut, cre]
Maintainer: Alessia Calafiore <aelissa3388@gmail.com>
Diff between cdrcR versions 0.0.1 dated 2021-11-19 and 0.1.0 dated 2023-02-02
DESCRIPTION | 13 +++++++------ MD5 | 7 ++++--- NEWS.md |only R/getCDRC.R | 6 +++--- README.md | 10 ++++++++-- 5 files changed, 22 insertions(+), 14 deletions(-)
Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode
Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new
algorithm, extricate, that performs EEMD in seconds, a linear interpolation
algorithm using the greatest rational common divisor of depth or time,
different algorithms to compute instantaneous amplitude, frequency and
ratios of frequencies, and functions to verify and visualise the outputs.
The functions were developed during the CRASH project (Checking the
Reproducibility of Astrochronology in the Hauterivian). When using for
publication please cite Wouters, S., Crucifix, M., Sinnesael, M., Da Silva,
A.C., Zeeden, C., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2022,
"A decomposition approach to cyclostratigraphic signal processing".
Earth-Science Reviews 225 (103894).
<doi:10.1016/j.earscirev.2021.103894>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <wouterseb@gmail.com>
Diff between DecomposeR versions 1.0.5 dated 2022-12-02 and 1.0.6 dated 2023-02-02
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/DecomposeR.R | 15 +++++++-------- R/check.emd.R | 4 ++-- R/extremist.R | 4 ++-- R/extricate.R | 2 +- inst/CITATION | 47 ++++++++++++++++------------------------------- man/DecomposeR.Rd | 15 +++++++-------- 9 files changed, 58 insertions(+), 70 deletions(-)
Title: Interface to 'ChatGPT' from R
Description: 'OpenAI's 'ChatGPT' <https://chat.openai.com/> coding assistant for 'RStudio'. A set
of functions and 'RStudio' addins that aim to help the R developer in tedious coding tasks.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Diff between chatgpt versions 0.1.4 dated 2023-01-16 and 0.1.5 dated 2023-02-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++---- NAMESPACE | 2 ++ R/addins.R | 2 ++ R/ask_chatgpt.R |only R/create_unit_tests.R |only inst/rstudio/addins.dcf | 5 +++++ man/ask_chatgpt.Rd |only man/create_unit_tests.Rd |only 9 files changed, 22 insertions(+), 9 deletions(-)
Title: Present Data with Style
Description: Consists of custom wrapper functions using packages
'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames.
These viewer friendly outputs are intended to match expectations of professional looking presentations
in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data
frame to have certain properties in order to take advantage of the automated formatting.
Author: Harrison Tietze [aut, cre]
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Diff between presenter versions 0.1.1 dated 2021-11-18 and 0.1.2 dated 2023-02-02
DESCRIPTION | 12 LICENSE | 4 MD5 | 112 +- NAMESPACE | 36 NEWS.md | 2 R/flextable_helpers.R | 270 +++--- R/formatters.R | 275 +++---- R/get_piped_name.R | 304 +++---- R/globals.R | 6 R/make_excel.R | 822 ++++++++++----------- R/make_flextable.R | 462 +++++------ R/make_pivot_table.R | 702 +++++++++--------- R/make_powerpoint.R | 142 +-- R/make_simple_excel.R | 88 +- R/pivot_summary.R | 106 +- R/utils-pipe.R | 22 README.md | 148 +-- build/vignette.rds |binary inst/doc/exportToExcel.R | 68 - inst/doc/exportToExcel.Rmd | 180 ++-- inst/doc/exportToExcel.html | 676 +++++++++++------ inst/doc/flextableAndPowerpoint.R | 88 +- inst/doc/flextableAndPowerpoint.Rmd | 128 +-- inst/doc/flextableAndPowerpoint.html | 954 +++++++++++++++--------- inst/doc/flextableThemes.R | 98 +- inst/doc/flextableThemes.Rmd | 166 ++-- inst/doc/flextableThemes.html | 1358 ++++++++++++++++++++--------------- inst/doc/formattedFlextable.R | 92 +- inst/doc/formattedFlextable.Rmd | 140 +-- inst/doc/formattedFlextable.html | 970 +++++++++++++++---------- inst/doc/pivotSummary.R | 94 +- inst/doc/pivotSummary.Rmd | 192 ++-- inst/doc/pivotSummary.html | 712 +++++++++++------- man/charvec_to_formula.Rd | 36 man/finish_excel_wb.Rd | 38 man/flex_create_headers.Rd | 40 - man/flex_mergev1.Rd | 40 - man/flex_mergev1_formula.Rd | 36 man/flex_set_headers.Rd | 44 - man/format_number.Rd | 130 +-- man/format_red.Rd | 44 - man/get_piped_name.Rd | 98 +- man/is_percentage.Rd | 47 - man/make_excel.Rd | 62 - man/make_excel_wb.Rd | 68 - man/make_flextable.Rd | 70 - man/make_pivot_table.Rd | 85 +- man/make_powerpoint.Rd | 66 - man/make_simple_excel.Rd | 38 man/pipe.Rd | 24 man/pivot_summary.Rd | 50 - man/style_header_sequence.Rd | 52 - vignettes/exportToExcel.Rmd | 180 ++-- vignettes/flextableAndPowerpoint.Rmd | 128 +-- vignettes/flextableThemes.Rmd | 166 ++-- vignettes/formattedFlextable.Rmd | 140 +-- vignettes/pivotSummary.Rmd | 192 ++-- 57 files changed, 6211 insertions(+), 5092 deletions(-)
More information about SampleSizeMeans at CRAN
Permanent link
Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7].
Main references:
[1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>,
[2] Mualem (1976) <doi:10.1029/WR012i003p00513>,
[3] Peters (2013) <doi:10.1002/wrcr.20548>,
[4] Iden and Durner (2013) <doi:10.1002/2014WR015937>,
[5] Peters (2014) <doi:10.1002/2014WR015937>,
[6] Wind G. P. (1966),
[7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and
[8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre],
Felix Andrews [ctb] which is not on r-cran
. The SCEoptim function is
adapted, and substantially revised from Brecht Donckels MATLAB code
which is in turn adopted from Qingyun Duans MATLAB code),
Brecht Donckels [ctb] ,
[...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Diff between SoilHyP versions 0.1.6 dated 2022-05-25 and 0.1.7 dated 2023-02-02
DESCRIPTION | 8 - MD5 | 6 - R/Ku.R | 328 ++++++++++++++++++++++++++++++------------------------------ R/SWC.R | 287 ++++++++++++++++++++++++++-------------------------- 4 files changed, 315 insertions(+), 314 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
and 'lbfgsb_cpp' is a 'C++' wrapper by Colin Fang around 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Pascal Have [aut],
Yann Richet [aut, cre] ,
Yves Deville [aut],
Conrad Sanderson [ctb],
Colin Fang [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.7-4.1 dated 2023-01-17 and 0.7-4.2 dated 2023-02-02
rlibkriging-0.7-4.1/rlibkriging/tools/libKriging_CMakeLists.txt |only rlibkriging-0.7-4.2/rlibkriging/DESCRIPTION | 8 - rlibkriging-0.7-4.2/rlibkriging/MD5 | 9 - rlibkriging-0.7-4.2/rlibkriging/src/libK/CMakeLists.txt | 48 +++++----- rlibkriging-0.7-4.2/rlibkriging/src/libK/src/lib/CMakeLists.txt | 4 rlibkriging-0.7-4.2/rlibkriging/tools/setup.sh | 16 +++ 6 files changed, 49 insertions(+), 36 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 0.5.1 dated 2022-12-15 and 0.6.0 dated 2023-02-02
DESCRIPTION | 7 +- MD5 | 64 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 20 +++++++ R/OCN_to_SSN.R | 40 +++++++++++++-- R/aggregate_OCN.R | 100 +++++++++++++++++++++++++------------- R/create_OCN.R | 32 ++++++------ R/create_general_contour_OCN.R |only R/draw_contour_OCN.R | 8 +-- R/draw_elev2D_OCN.R | 30 +++++++++-- R/draw_elev3D_OCN.R | 27 +++++++--- R/draw_elev3Drgl_OCN.R | 67 ++++++++++++++++++------- R/draw_simple_OCN.R | 6 +- R/draw_subcatchments_OCN.R | 45 ++++++++++++++--- R/draw_thematic_OCN.R | 89 ++++++++++++++++++++------------- R/landscape_OCN.R | 2 R/paths_OCN.R | 3 + data/flowDir.rda |only inst/CITATION | 28 ++++------ inst/doc/OCNet.html | 3 - man/OCN_to_SSN.Rd | 39 +++++++++++--- man/OCNet-package.Rd | 4 + man/aggregate_OCN.Rd | 19 ++++++- man/continue_OCN.Rd | 6 +- man/create_OCN.Rd | 25 ++++----- man/create_general_contour_OCN.Rd |only man/draw_contour_OCN.Rd | 2 man/draw_elev3D_OCN.Rd | 2 man/draw_elev3Drgl_OCN.Rd | 2 man/draw_simple_OCN.Rd | 2 man/draw_subcatchments_OCN.Rd | 7 ++ man/draw_thematic_OCN.Rd | 26 ++++++--- man/flowDir.Rd |only man/landscape_OCN.Rd | 3 - man/paths_OCN.Rd | 10 +-- 35 files changed, 489 insertions(+), 230 deletions(-)
Title: Steve's R Markdown Templates
Description: These are my collection of 'R Markdown' templates, mostly for compilation to PDF.
These are useful for all things academic and professional, if you are using 'R Markdown'
for things like your CV or your articles and manuscripts.
Author: Steven V. Miller
Maintainer: Steven V. Miller <steven.v.miller@gmail.com>
Diff between stevetemplates versions 0.8.0 dated 2022-09-29 and 0.9.0 dated 2023-02-02
DESCRIPTION | 6 +-- MD5 | 24 ++++++------ NEWS.md | 7 +++ R/beamer.R | 1 inst/rmarkdown/templates/anonms/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/article/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/article2/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/beamer/resources/template.tex | 9 +++- inst/rmarkdown/templates/cover_letter/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/cv/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/html_article/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/statement/skeleton/skeleton.Rmd | 4 +- inst/rmarkdown/templates/syllabus/skeleton/skeleton.Rmd | 4 +- 13 files changed, 39 insertions(+), 28 deletions(-)
More information about stevetemplates at CRAN
Permanent link
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.5.4 dated 2023-01-11 and 0.5.5 dated 2023-02-02
DESCRIPTION | 6 - MD5 | 9 +- NEWS.md | 3 R/credential_providers.R | 160 +++++++++++++++++++++++++++----------- tests/testthat/data_sso_ini |only tests/testthat/test_config.R | 179 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 304 insertions(+), 53 deletions(-)
Title: Convert Images to Usable Color Schemes
Description: A fast and adaptable tool to convert photos and images into usable colour schemes for data visualisation. Contains functionality to extract colour palettes from images, as well for the conversion of images between colour spaces.
Author: Stuart Morrison [aut, cre]
Maintainer: Stuart Morrison <smorrison@ucdavis.edu>
Diff between schemr versions 0.1.0 dated 2021-03-10 and 0.2.0 dated 2023-02-02
DESCRIPTION | 17 ++++++++--------- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++-- R/color-spaces.R | 6 ++++-- R/extract-colours.R | 50 +++++++++++++++++++++++++------------------------- README.md | 17 +++++++++++------ 7 files changed, 57 insertions(+), 50 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data
structures and functions that facilitate the plotting of missing values and
examination of imputations. This allows missing data dependencies to be
explored with minimal deviation from the common work patterns of 'ggplot2'
and tidy data. The work is fully discussed at Tierney & Cook (2023)
<doi:10.18637/jss.v105.i07>.
Author: Nicholas Tierney [aut, cre] ,
Di Cook [aut] ,
Miles McBain [aut] ,
Colin Fay [aut] ,
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb],
Andrew Heiss [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.6.1 dated 2021-05-14 and 1.0.0 dated 2023-02-02
naniar-0.6.1/naniar/man/group_by_fun.Rd |only naniar-0.6.1/naniar/man/label_shadow.Rd |only naniar-0.6.1/naniar/man/new_shade.Rd |only naniar-0.6.1/naniar/man/shadow_expand_relevel.Rd |only naniar-0.6.1/naniar/man/test_if_dataframe.Rd |only naniar-0.6.1/naniar/man/test_if_missing.Rd |only naniar-0.6.1/naniar/man/test_if_null.Rd |only naniar-0.6.1/naniar/man/update_shadow.Rd |only naniar-0.6.1/naniar/man/what_levels.Rd |only naniar-0.6.1/naniar/tests/testthat/fontconfig-helper.R |only naniar-1.0.0/naniar/DESCRIPTION | 33 naniar-1.0.0/naniar/MD5 | 273 ++-- naniar-1.0.0/naniar/NAMESPACE | 5 naniar-1.0.0/naniar/NEWS.md | 30 naniar-1.0.0/naniar/R/add-cols.R | 2 naniar-1.0.0/naniar/R/add-n-prop-miss.R | 2 naniar-1.0.0/naniar/R/data-common-na-strings.R | 1 naniar-1.0.0/naniar/R/data-pedestrian.R | 4 naniar-1.0.0/naniar/R/geom2plotly.R | 2 naniar-1.0.0/naniar/R/gg-miss-case-cumsum.R | 2 naniar-1.0.0/naniar/R/gg-miss-case.R | 4 naniar-1.0.0/naniar/R/gg-miss-fct.R | 8 naniar-1.0.0/naniar/R/gg-miss-span.R | 12 naniar-1.0.0/naniar/R/gg-miss-var-cumsum.R | 2 naniar-1.0.0/naniar/R/gg-miss-var.R | 9 naniar-1.0.0/naniar/R/mcar-test.R | 4 naniar-1.0.0/naniar/R/miss-scan-count.R | 10 naniar-1.0.0/naniar/R/miss-x-cumsum.R | 5 naniar-1.0.0/naniar/R/naniar-package.R | 3 naniar-1.0.0/naniar/R/set-n-prop-miss.R |only naniar-1.0.0/naniar/R/shade.R | 16 naniar-1.0.0/naniar/R/shadow-recode.R | 18 naniar-1.0.0/naniar/R/shadows.R | 45 naniar-1.0.0/naniar/R/utils.R | 45 naniar-1.0.0/naniar/README.md | 134 + naniar-1.0.0/naniar/build/partial.rdb |binary naniar-1.0.0/naniar/build/vignette.rds |binary naniar-1.0.0/naniar/data/common_na_strings.rda |binary naniar-1.0.0/naniar/inst/CITATION |only naniar-1.0.0/naniar/inst/WORDLIST | 5 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.R | 7 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.Rmd | 7 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.html | 437 ++++-- naniar-1.0.0/naniar/inst/doc/getting-started-w-naniar.Rmd | 2 naniar-1.0.0/naniar/inst/doc/getting-started-w-naniar.html | 681 +++++++--- naniar-1.0.0/naniar/inst/doc/naniar-visualisation.html | 465 +++++- naniar-1.0.0/naniar/inst/doc/replace-with-na.R | 5 naniar-1.0.0/naniar/inst/doc/replace-with-na.Rmd | 7 naniar-1.0.0/naniar/inst/doc/replace-with-na.html | 526 +++++-- naniar-1.0.0/naniar/inst/doc/special-missing-values.Rmd | 2 naniar-1.0.0/naniar/inst/doc/special-missing-values.html | 495 +++++-- naniar-1.0.0/naniar/man/add_prop_miss.Rd | 2 naniar-1.0.0/naniar/man/common_na_strings.Rd | 3 naniar-1.0.0/naniar/man/figures/README-facet-by-month-1.png |binary naniar-1.0.0/naniar/man/figures/README-geom-miss-point-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-span-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-upset-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-var-1.png |binary naniar-1.0.0/naniar/man/figures/README-regular-geom-point-1.png |binary naniar-1.0.0/naniar/man/figures/README-shadow-impute-1.png |binary naniar-1.0.0/naniar/man/figures/README-shadow-w-ggplot-1.png |binary naniar-1.0.0/naniar/man/mcar_test.Rd | 4 naniar-1.0.0/naniar/man/naniar.Rd | 3 naniar-1.0.0/naniar/man/pedestrian.Rd | 4 naniar-1.0.0/naniar/man/plotly_helpers.Rd | 1 naniar-1.0.0/naniar/man/recode_shadow.Rd | 6 naniar-1.0.0/naniar/man/set-prop-n-miss.Rd |only naniar-1.0.0/naniar/tests/testthat.R | 8 naniar-1.0.0/naniar/tests/testthat/_snaps |only naniar-1.0.0/naniar/tests/testthat/test-add-any-miss.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-label-missings.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-label-shadow.R | 5 naniar-1.0.0/naniar/tests/testthat/test-add-n-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-add-prop-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-add-shadow-shift.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-all-na.R | 2 naniar-1.0.0/naniar/tests/testthat/test-as-shadow.R | 18 naniar-1.0.0/naniar/tests/testthat/test-as_shadow_upset.R | 2 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow-shift-label.R | 5 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow-shift.R | 4 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-defunct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gather-shadow.R | 6 naniar-1.0.0/naniar/tests/testthat/test-geom-miss-point.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-case-cumsum.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-case.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-fct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-span.R | 3 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-var-cumsum.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-var-plot.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-which.R | 2 naniar-1.0.0/naniar/tests/testthat/test-impute-below-at.R | 4 naniar-1.0.0/naniar/tests/testthat/test-impute-below.R | 11 naniar-1.0.0/naniar/tests/testthat/test-impute-median.R | 2 naniar-1.0.0/naniar/tests/testthat/test-impute_mean.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-miss-1d.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-miss-2d.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-mcar-test.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-case-summary.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-case-table.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-prop-summary.R | 4 naniar-1.0.0/naniar/tests/testthat/test-miss-scan-count.R | 5 naniar-1.0.0/naniar/tests/testthat/test-miss-summary.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-run.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-span.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-summary.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-var-table.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-var-which.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-x-pct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-n-complete.R | 2 naniar-1.0.0/naniar/tests/testthat/test-n-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-nabular.R | 6 naniar-1.0.0/naniar/tests/testthat/test-prop-complete.R | 2 naniar-1.0.0/naniar/tests/testthat/test-prop-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-prop_row.R | 2 naniar-1.0.0/naniar/tests/testthat/test-replace-with-na-scoped-var.R | 2 naniar-1.0.0/naniar/tests/testthat/test-replace-with-na.R | 2 naniar-1.0.0/naniar/tests/testthat/test-set-n-prop-miss.R |only naniar-1.0.0/naniar/tests/testthat/test-shade-verifiers.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shade.R | 21 naniar-1.0.0/naniar/tests/testthat/test-shadow-expand-relevel.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-identifiers.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-long.R | 8 naniar-1.0.0/naniar/tests/testthat/test-shadow-shift-inf.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-shift.R | 2 naniar-1.0.0/naniar/tests/testthat/test-special-missing-values.R | 28 naniar-1.0.0/naniar/tests/testthat/test-test-any-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-unbind.R | 4 naniar-1.0.0/naniar/vignettes/exploring-imputed-values.Rmd | 7 naniar-1.0.0/naniar/vignettes/getting-started-w-naniar.Rmd | 2 naniar-1.0.0/naniar/vignettes/replace-with-na.Rmd | 7 naniar-1.0.0/naniar/vignettes/special-missing-values.Rmd | 2 134 files changed, 2550 insertions(+), 1057 deletions(-)
Title: Filter Methods for Parameter Estimation in Linear and Non Linear
Regression Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. Parameters of logistic regression models are also estimated using an evolutionary particle filter method.
Author: Christian Llano Robayo [aut, cre],
Nazrul Shaikh [aut],
Pegu Nilutpal [aut]
Maintainer: Christian Llano Robayo <info@cecareus.com>
Diff between LMfilteR versions 0.1.3 dated 2020-10-12 and 0.1.3.1 dated 2023-02-02
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/EPF_L_compl.R | 2 +- R/EPF_logist_compl.R | 2 +- 5 files changed, 20 insertions(+), 15 deletions(-)
Title: Exponential Multivariate Hawkes Model
Description: Simulate and fitting exponential multivariate Hawkes model.
This package simulates a multivariate Hawkes model, introduced by Hawkes (1971) <doi:10.2307/2334319>, with an exponential kernel and fits the parameters from the data.
Models with the constant parameters, as well as complex dependent structures, can also be simulated and estimated.
The estimation is based on the maximum likelihood method, introduced by introduced by Ozaki (1979) <doi:10.1007/BF02480272>, with 'maxLik' package.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>
Diff between emhawkes versions 0.9.5 dated 2021-02-16 and 0.9.7 dated 2023-02-02
emhawkes-0.9.5/emhawkes/man/logLik-hspec-method.Rd |only emhawkes-0.9.7/emhawkes/DESCRIPTION | 13 emhawkes-0.9.7/emhawkes/MD5 | 48 emhawkes-0.9.7/emhawkes/NAMESPACE | 2 emhawkes-0.9.7/emhawkes/NEWS.md |only emhawkes-0.9.7/emhawkes/R/harrival.R | 2 emhawkes-0.9.7/emhawkes/R/hfit.R | 131 - emhawkes-0.9.7/emhawkes/R/hgfit.R | 179 - emhawkes-0.9.7/emhawkes/R/hllf.R | 129 - emhawkes-0.9.7/emhawkes/R/hmoment.R | 251 ++ emhawkes-0.9.7/emhawkes/R/hreal.R | 63 emhawkes-0.9.7/emhawkes/R/hsim.R | 128 - emhawkes-0.9.7/emhawkes/R/hspec.R | 244 +- emhawkes-0.9.7/emhawkes/R/utilities.R | 9 emhawkes-0.9.7/emhawkes/build/vignette.rds |binary emhawkes-0.9.7/emhawkes/inst/doc/example.R | 357 +++ emhawkes-0.9.7/emhawkes/inst/doc/example.Rmd | 793 ++++++- emhawkes-0.9.7/emhawkes/inst/doc/example.html | 2306 ++++++++++++++++----- emhawkes-0.9.7/emhawkes/man/hfit.Rd | 47 emhawkes-0.9.7/emhawkes/man/hreal.Rd | 34 emhawkes-0.9.7/emhawkes/man/hsim.Rd | 93 emhawkes-0.9.7/emhawkes/man/hspec-class.Rd | 33 emhawkes-0.9.7/emhawkes/man/hvol.Rd |only emhawkes-0.9.7/emhawkes/man/infer_lambda.Rd | 24 emhawkes-0.9.7/emhawkes/man/logLik.Rd |only emhawkes-0.9.7/emhawkes/man/residual_process.Rd | 39 emhawkes-0.9.7/emhawkes/vignettes/example.Rmd | 793 ++++++- 27 files changed, 4567 insertions(+), 1151 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2022) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.1 dated 2022-10-19 and 1.1.1 dated 2023-02-02
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS.md | 8 +++++- R/CheckDiemFormat.r | 2 - R/diem.r | 5 +--- inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 +-- man/CheckDiemFormat.Rd | 2 - 7 files changed, 22 insertions(+), 17 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-06 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-23 0.2.7
2021-01-07 0.2.6
2020-01-27 0.2.3
2019-03-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-02 0.10.2
2019-12-14 0.10.1
2017-02-17 0.10
2015-07-01 0.8
2014-11-04 0.3
2013-03-21 0.2
2013-02-21 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-04 1.1-11
2022-10-31 1.1-10
2022-06-17 1.1-8
2022-06-01 1.1-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-03 0.1.3.3
2019-03-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-14 2.1.34
2021-06-02 2.1.33
2021-01-06 2.1.31
2020-12-15 2.1.30
2020-11-18 2.1.26
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-04 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-09 0.1-1
2014-11-18 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-21 0.1.9
2017-12-18 0.1.8
2017-06-30 0.1.7
2017-06-01 0.1.6
2017-05-20 0.1.5
2017-03-15 0.1.3
2017-03-05 0.1.2
2017-02-12 0.1.1
2016-12-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-29 2.0.1
2019-07-28 2.0.0
2018-12-25 1.0.0
Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire
dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] ,
Sean Hughes [rev] ,
Mara Averick [rev] ,
Stuart Lee [ctb],
Earo Wang [ctb],
Nic Crane [ctb],
Christophe Regouby [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between visdat versions 0.5.3 dated 2019-02-15 and 0.6.0 dated 2023-02-01
visdat-0.5.3/visdat/man/add_vis_dat_pal.Rd |only visdat-0.5.3/visdat/man/all_numeric.Rd |only visdat-0.5.3/visdat/man/compare_print.Rd |only visdat-0.5.3/visdat/man/expect_frame.Rd |only visdat-0.5.3/visdat/man/expect_guide_label.Rd |only visdat-0.5.3/visdat/man/fingerprint.Rd |only visdat-0.5.3/visdat/man/gather_cor.Rd |only visdat-0.5.3/visdat/man/guess_type.Rd |only visdat-0.5.3/visdat/man/label_col_missing_pct.Rd |only visdat-0.5.3/visdat/man/miss_guide_label.Rd |only visdat-0.5.3/visdat/man/test_if_dataframe.Rd |only visdat-0.5.3/visdat/man/vis_create_.Rd |only visdat-0.5.3/visdat/man/vis_extract_value_.Rd |only visdat-0.5.3/visdat/man/vis_gather_.Rd |only visdat-0.5.3/visdat/tests/figs |only visdat-0.5.3/visdat/tests/testthat/fontconfig-helper.R |only visdat-0.6.0/visdat/DESCRIPTION | 24 visdat-0.6.0/visdat/MD5 | 211 ++- visdat-0.6.0/visdat/NAMESPACE | 17 visdat-0.6.0/visdat/NEWS.md | 30 visdat-0.6.0/visdat/R/abbreviate.R |only visdat-0.6.0/visdat/R/data-binary-data.R |only visdat-0.6.0/visdat/R/data-vis-cor.R |only visdat-0.6.0/visdat/R/data-vis-dat.R |only visdat-0.6.0/visdat/R/data-vis-miss.R |only visdat-0.6.0/visdat/R/internals.R | 350 ++++-- visdat-0.6.0/visdat/R/utils-pipe.R |only visdat-0.6.0/visdat/R/vis-binary.R |only visdat-0.6.0/visdat/R/vis-compare.R | 26 visdat-0.6.0/visdat/R/vis-cor.R | 101 - visdat-0.6.0/visdat/R/vis-dat.R | 60 - visdat-0.6.0/visdat/R/vis-expect.R | 38 visdat-0.6.0/visdat/R/vis-guess.R | 9 visdat-0.6.0/visdat/R/vis-miss.R | 195 +-- visdat-0.6.0/visdat/R/vis-value.R |only visdat-0.6.0/visdat/R/visdat-package.r | 7 visdat-0.6.0/visdat/README.md | 173 ++- visdat-0.6.0/visdat/build/vignette.rds |binary visdat-0.6.0/visdat/data/dat_bin.rda |only visdat-0.6.0/visdat/inst/WORDLIST | 68 - visdat-0.6.0/visdat/inst/doc/customising-colour-palettes.R |only visdat-0.6.0/visdat/inst/doc/customising-colour-palettes.Rmd |only visdat-0.6.0/visdat/inst/doc/customising-colour-palettes.html |only visdat-0.6.0/visdat/inst/doc/using_visdat.R | 67 - visdat-0.6.0/visdat/inst/doc/using_visdat.Rmd | 53 visdat-0.6.0/visdat/inst/doc/using_visdat.html | 574 ++++++---- visdat-0.6.0/visdat/man/abbreviate_vars.Rd |only visdat-0.6.0/visdat/man/dat_bin.Rd |only visdat-0.6.0/visdat/man/data-vis-cor.Rd |only visdat-0.6.0/visdat/man/data-vis-dat.Rd |only visdat-0.6.0/visdat/man/data-vis-miss.Rd |only visdat-0.6.0/visdat/man/figures/README-iris-error-fix-1.png |only visdat-0.6.0/visdat/man/figures/README-vis-bin-1.png |only visdat-0.6.0/visdat/man/figures/README-vis-compare-iris-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-cor-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-dat-aq-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-dat-month-1.png |only visdat-0.6.0/visdat/man/figures/README-vis-expect-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-guess-messy-df-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-guess-messy-df-2.png |binary visdat-0.6.0/visdat/man/figures/README-vis-miss-aq-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-miss-aq-cluster-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-miss-aq-sort-miss-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-miss-mtcars-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-miss-test-1.png |binary visdat-0.6.0/visdat/man/figures/README-vis-value-1.png |only visdat-0.6.0/visdat/man/figures/visdat-logo.svg |only visdat-0.6.0/visdat/man/pipe.Rd |only visdat-0.6.0/visdat/man/typical_data.Rd | 6 visdat-0.6.0/visdat/man/typical_data_large.Rd | 6 visdat-0.6.0/visdat/man/vis_binary.Rd |only visdat-0.6.0/visdat/man/vis_compare.Rd | 2 visdat-0.6.0/visdat/man/vis_cor.Rd | 17 visdat-0.6.0/visdat/man/vis_dat.Rd | 25 visdat-0.6.0/visdat/man/vis_expect.Rd | 14 visdat-0.6.0/visdat/man/vis_miss.Rd | 46 visdat-0.6.0/visdat/man/vis_value.Rd |only visdat-0.6.0/visdat/man/visdat.Rd | 17 visdat-0.6.0/visdat/tests/testthat/_snaps |only visdat-0.6.0/visdat/tests/testthat/test-gather_funs.R |only visdat-0.6.0/visdat/tests/testthat/test-guess-type.R | 17 visdat-0.6.0/visdat/tests/testthat/test-test-vis-miss-one-col.R | 5 visdat-0.6.0/visdat/tests/testthat/test-vis-binary.R |only visdat-0.6.0/visdat/tests/testthat/test-vis-compare.R | 24 visdat-0.6.0/visdat/tests/testthat/test-vis-cor.R | 38 visdat-0.6.0/visdat/tests/testthat/test-vis-dat.R | 45 visdat-0.6.0/visdat/tests/testthat/test-vis-expect.R | 10 visdat-0.6.0/visdat/tests/testthat/test-vis-guess.R | 22 visdat-0.6.0/visdat/tests/testthat/test-vis-large.R | 13 visdat-0.6.0/visdat/tests/testthat/test-vis-miss.R | 59 - visdat-0.6.0/visdat/tests/testthat/test-vis-value.R |only visdat-0.6.0/visdat/tests/testthat/test-visdat-internals.R | 34 visdat-0.6.0/visdat/tests/testthat/test-vismiss-legend.R | 7 visdat-0.6.0/visdat/tests/testthat/test_variable_spaces.R | 6 visdat-0.6.0/visdat/vignettes/customising-colour-palettes.Rmd |only visdat-0.6.0/visdat/vignettes/using_visdat.Rmd | 53 96 files changed, 1637 insertions(+), 832 deletions(-)
Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based
spatial relative risk functions that are estimated using the 'sparr' package.
Details about the 'sparr' package methods can be found in the tutorial: Davies
et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation
can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More
information about relative risk functions using kernel density estimation can
be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Derek W. Brown [aut, cph] ,
Mitchell J. Machiela [ctb] ,
Timothy A. Myers [ctb],
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between sparrpowR versions 0.2.6 dated 2022-12-02 and 0.2.7 dated 2023-02-01
DESCRIPTION | 19 MD5 | 64 - NAMESPACE | 92 +- NEWS.md | 182 ++--- R/globals.R | 2 R/jitter_power.R | 606 +++++++++--------- R/package.R | 106 +-- R/pval_correct.R | 116 +-- R/spatial_data.R | 558 ++++++++--------- R/spatial_plots.R | 478 +++++++------- R/spatial_power.R | 968 ++++++++++++++--------------- R/utils.R | 36 - R/zzz.R | 6 README.md | 412 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 48 - inst/doc/vignette.html | 1012 ++++++++++++++++++++----------- inst/doc/vignette.html.asis | 6 man/jitter_power.Rd | 198 +++--- man/pval_correct.Rd | 72 +- man/sparrpowR-package.Rd | 83 +- man/spatial_data.Rd | 228 +++--- man/spatial_plots.Rd | 162 ++-- man/spatial_power.Rd | 316 ++++----- tests/spelling.R | 6 tests/testthat.R | 20 tests/testthat/test-jitter_power.R | 152 ++-- tests/testthat/test-test-spatial_data.R | 276 ++++---- tests/testthat/test-test-spatial_plots.R | 134 ++-- tests/testthat/test-test-spatial_power.R | 440 ++++++------- vignettes/vignette.Rmd | 477 +++++++------- vignettes/vignette.html.asis | 6 33 files changed, 3802 insertions(+), 3479 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Table and
Figure
Description: Create production-ready Rich Text Format (RTF) table and figure
with flexible format.
Author: Yilong Zhang [aut, cre],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [ctb],
Daniel Woodie [c [...truncated...]
Maintainer: Yilong Zhang <elong0527@gmail.com>
Diff between r2rtf versions 1.0.0 dated 2023-01-11 and 1.0.1 dated 2023-02-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 ++++++- R/dictionary.R | 6 +++--- R/rtf_convert_format.R | 2 +- tests/testthat/test-independent-testing-content_create.R | 8 ++++---- 6 files changed, 22 insertions(+), 17 deletions(-)
Title: Environmental Interpolation using Spatial Kernel Density
Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel
density-based estimation methods. For a single species with presence and absence data,
the 'envi' package uses the spatial relative risk function that is estimated using the
'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
relative risk functions using kernel density estimation can be found in J. F. Bithell
(1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Lance A. Waller [ctb, ths] ,
Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between envi versions 0.1.15 dated 2022-08-30 and 0.1.17 dated 2023-02-01
DESCRIPTION | 18 MD5 | 84 - NAMESPACE | 130 +- NEWS.md | 149 +-- R/div_plot.R | 204 ++-- R/globals.R | 2 R/lrren.R | 722 +++++++------- R/package.R | 117 +- R/perlrren.R | 550 +++++------ R/plot_cv.R | 226 ++-- R/plot_obs.R | 344 +++---- R/plot_perturb.R | 595 ++++++------ R/plot_predict.R | 389 +++----- R/pval_correct.R | 116 +- R/seq_plot.R | 139 +- R/utils.R | 117 +- R/zzz.R | 6 README.md | 620 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 inst/doc/vignette.html | 1798 ++++++++++++++++++------------------- inst/doc/vignette.html.asis | 6 man/div_plot.Rd | 86 - man/envi-package.Rd | 90 - man/lrren.Rd | 306 +++--- man/perlrren.Rd | 258 ++--- man/plot_cv.Rd | 134 +- man/plot_obs.Rd | 170 +-- man/plot_perturb.Rd | 190 +-- man/plot_predict.Rd | 189 +-- man/pval_correct.Rd | 72 - man/seq_plot.Rd | 64 - tests/spelling.R | 6 tests/testthat.R | 20 tests/testthat/test-lrren.R | 674 ++++++------- tests/testthat/test-perlrren.R | 339 +++--- tests/testthat/test-plot_cv.R | 273 ++--- tests/testthat/test-plot_obs.R | 211 ++-- tests/testthat/test-plot_perturb.R | 213 ++-- tests/testthat/test-plot_predict.R | 311 +++--- vignettes/vignette.Rmd | 843 ++++++++--------- vignettes/vignette.html.asis | 6 43 files changed, 5433 insertions(+), 5392 deletions(-)
Title: Narrowest-Over-Threshold Change-Point Detection
Description: Provides efficient implementation of the Narrowest-Over-Threshold methodology for detecting an unknown number of change-points occurring at unknown locations in one-dimensional data following 'deterministic signal + noise' model. Currently implemented scenarios are: piecewise-constant signal, piecewise-constant signal with a heavy-tailed noise, piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal and with piecewise-constant variance of the noise. For details, see Baranowski, Chen and Fryzlewicz (2019) <doi:10.1111/rssb.12322>.
Author: Rafal Baranowski, Yining Chen, Piotr Fryzlewicz
Maintainer: Yining Chen <Y.Chen101@lse.ac.uk>
Diff between not versions 1.4 dated 2022-10-06 and 1.5 dated 2023-02-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/contrasts.c | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] ,
Elena Hsieh [ctb] ,
Debashis Ghosh [ctb] ,
Lance A. Waller [ctb] ,
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between gateR versions 0.1.12 dated 2022-12-01 and 0.1.13 dated 2023-02-01
DESCRIPTION | 14 MD5 | 68 - NAMESPACE | 77 - NEWS.md | 137 +-- R/gating.R | 582 +++++++-------- R/lotrrs.R | 646 ++++++++-------- R/lrr_plot.R | 210 ++--- R/package.R | 94 +- R/pval_correct.R | 296 +++---- R/pval_plot.R | 68 - R/randCyto.R | 38 R/rrs.R | 486 ++++++------ R/utils.R | 4 R/zzz.R | 6 README.md | 532 ++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 inst/doc/vignette.html | 1657 +++++++++++++++++++++---------------------- inst/doc/vignette.html.asis | 6 man/gateR-package.Rd | 78 +- man/gating.Rd | 234 +++--- man/lotrrs.Rd | 192 ++-- man/lrr_plot.Rd | 86 +- man/pval_correct.Rd | 86 +- man/pval_plot.Rd | 52 - man/randCyto.Rd | 64 - man/rrs.Rd | 174 ++-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-gating.R | 344 ++++---- tests/testthat/test-lotrrs.R | 148 +-- tests/testthat/test-rrs.R | 104 +- vignettes/vignette.Rmd | 804 ++++++++++---------- vignettes/vignette.html.asis | 6 35 files changed, 3680 insertions(+), 3665 deletions(-)
Title: Schedule R Scripts and Processes with the Windows Task Scheduler
Description: Schedule R scripts/processes with the Windows task scheduler. This
allows R users to automate R processes on specific time points from R itself.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Oliver Belmans [cph, aut]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between taskscheduleR versions 1.6 dated 2022-03-16 and 1.7 dated 2023-02-01
DESCRIPTION | 8 - MD5 | 14 +-- R/taskscheduleR.R | 4 README.md | 5 - inst/NEWS | 3 inst/doc/taskscheduleR.html | 129 +++++++++++++++-------------- man/taskscheduler_create.Rd | 3 tests/testthat/test-taskscheduler_create.R | 6 - 8 files changed, 96 insertions(+), 76 deletions(-)
Title: Call 'EPANET' Functions to Simulate Pipe Networks
Description: Enables simulation of water piping networks using 'EPANET'.
The package provides functions from the 'EPANET' programmer's toolkit as R
functions so that basic or customized simulations can be carried out from R.
The package uses 'EPANET' version 2.2 from Open Water Analytics
<https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.
Author: Ernesto Arandia [aut],
Bradley Eck [aut, cre],
Lew Rossman [aut],
Michael Tryby [ctb],
Sam Hatchett [ctb],
Feng Shang [ctb],
James Uber [ctb],
Tom Taxon [ctb],
Hyoungmin Woo [ctb],
Jinduan Chen [ctb],
Yunier Soad [ctb],
Mike Kane [ctb],
Demetrios Eli [...truncated...]
Maintainer: Bradley Eck <brad@bradeck.net>
Diff between epanet2toolkit versions 0.5.1 dated 2021-04-22 and 0.6.2 dated 2023-02-01
epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/Net1-ld.rpt |only epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/Net1.rpt |only epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/Net2.rpt |only epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/Net3.bin |only epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/n3.rpt |only epanet2toolkit-0.5.1/epanet2toolkit/tests/testthat/net3.rpt |only epanet2toolkit-0.6.2/epanet2toolkit/DESCRIPTION | 8 epanet2toolkit-0.6.2/epanet2toolkit/MD5 | 48 +- epanet2toolkit-0.6.2/epanet2toolkit/README.md | 19 - epanet2toolkit-0.6.2/epanet2toolkit/src/Repanet2.c | 12 epanet2toolkit-0.6.2/epanet2toolkit/src/epanet.c | 12 epanet2toolkit-0.6.2/epanet2toolkit/src/epanet2.c | 26 - epanet2toolkit-0.6.2/epanet2toolkit/src/epanet2.h | 22 - epanet2toolkit-0.6.2/epanet2toolkit/src/filemanager.c | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/filemanager.h | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/hash.c | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/hydsolver.c | 8 epanet2toolkit-0.6.2/epanet2toolkit/src/inpfile.c | 42 +- epanet2toolkit-0.6.2/epanet2toolkit/src/input1.c | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/input2.c | 8 epanet2toolkit-0.6.2/epanet2toolkit/src/mempool.c | 4 epanet2toolkit-0.6.2/epanet2toolkit/src/mempool.h | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/project.c | 2 epanet2toolkit-0.6.2/epanet2toolkit/src/report.c | 178 +++++----- epanet2toolkit-0.6.2/epanet2toolkit/src/rules.c | 21 - epanet2toolkit-0.6.2/epanet2toolkit/src/toolkit.c | 16 epanet2toolkit-0.6.2/epanet2toolkit/src/toolkit.h | 16 epanet2toolkit-0.6.2/epanet2toolkit/tests/testthat/test_links.r | 31 + 28 files changed, 264 insertions(+), 219 deletions(-)
More information about epanet2toolkit at CRAN
Permanent link
Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy
data frames describing node and edge data respectively. 'tidygraph'
provides an approach to manipulate these two virtual data frames using the
API defined in the 'dplyr' package, as well as provides tidy interfaces to
a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tidygraph versions 1.2.2 dated 2022-08-22 and 1.2.3 dated 2023-02-01
DESCRIPTION | 11 +++++------ MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/centrality.R | 7 +++---- README.md | 24 ++++++++++++------------ man/bind_graphs.Rd | 2 +- man/centrality.Rd | 5 +---- man/graph_join.Rd | 41 ++++++++++++++++++++++++++--------------- man/reexports.Rd | 2 +- tests/testthat/test-group.R | 2 +- 10 files changed, 63 insertions(+), 53 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.7.1 dated 2022-11-09 and 0.7.2 dated 2023-02-01
DESCRIPTION | 10 +++--- MD5 | 57 ++++++++++++++++++------------------- NEWS.md | 12 +++++++ R/emmeans_test.R | 18 ++++++++++- man/anova_test.Rd | 6 +-- man/binom_test.Rd | 8 ++--- man/chisq_test.Rd | 18 +++++------ man/cor_mat.Rd | 8 ++--- man/cor_reshape.Rd | 6 +-- man/cor_test.Rd | 4 +- man/df_label_value.Rd | 6 +-- man/df_unite.Rd | 8 ++--- man/emmeans_test.Rd | 4 +- man/eta_squared.Rd | 6 +-- man/factors.Rd | 8 ++--- man/fisher_test.Rd | 8 ++--- man/get_pvalue_position.Rd | 10 +++--- man/get_test_label.Rd | 12 +++---- man/mcnemar_test.Rd | 6 +-- man/outliers.Rd | 8 ++--- man/p_value.Rd | 14 ++++----- man/prop_test.Rd | 8 ++--- man/pull_triangle.Rd | 8 ++--- man/replace_triangle.Rd | 8 ++--- man/shapiro_test.Rd | 6 +-- man/sign_test.Rd | 6 +-- man/t_test.Rd | 6 +-- man/tukey_hsd.Rd | 8 ++--- man/wilcox_test.Rd | 6 +-- tests/testthat/test-emmeans_test.R |only 30 files changed, 160 insertions(+), 133 deletions(-)
Title: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Description: Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
Author: Antonio Profico [aut, cre],
Luca Bondioli [aut],
Pasquale Raia [aut],
Julien Claude [ctb],
Paul O'Higgins [aut],
Damiano Marchi [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>
Diff between morphomap versions 1.3 dated 2020-12-16 and 1.4 dated 2023-02-01
DESCRIPTION | 10 +++++----- MD5 | 23 +++++++++++++++++------ NAMESPACE | 7 ++++++- R/Ex_mpShapeList.R |only R/morphomap.R | 4 ++-- R/morphomap2Dmap.R | 1 + R/morphomapCheck.R | 2 +- R/morphomapExport.R |only R/morphomapImport.R |only R/morphomapPCA.R |only R/morphomapVariations.R |only data/Ex_mpShapeList.rda |only data/datalist | 1 + man/Ex_mpShapeList.Rd |only man/morphomapExport.Rd |only man/morphomapImport.Rd |only man/morphomapPCA.Rd |only man/morphomapVariations.Rd |only 18 files changed, 33 insertions(+), 15 deletions(-)
Title: Handling an Inconsistently Coded Categorical Variable in a
Longitudinal Dataset
Description: Unifying an inconsistently coded categorical variable between two different time points in accordance with a mapping table.
The main rule is to replicate the observation if it could be assigned to a few categories.
Then using frequencies or statistical methods to approximate the probabilities of being assigned to each of them.
This procedure was invented and implemented in the paper by Nasinski, Majchrowska, and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between cat2cat versions 0.4.5 dated 2022-09-25 and 0.4.6 dated 2023-02-01
cat2cat-0.4.5/cat2cat/tests/testthat/test-utils.R |only cat2cat-0.4.6/cat2cat/DESCRIPTION | 27 cat2cat-0.4.6/cat2cat/LICENSE |only cat2cat-0.4.6/cat2cat/MD5 | 49 cat2cat-0.4.6/cat2cat/NEWS.md | 10 cat2cat-0.4.6/cat2cat/R/cat2cat.R | 10 cat2cat-0.4.6/cat2cat/R/cat2cat_agg.R | 73 - cat2cat-0.4.6/cat2cat/R/data.R | 15 cat2cat-0.4.6/cat2cat/R/mapping.R | 4 cat2cat-0.4.6/cat2cat/R/plot_cat2cat.R | 8 cat2cat-0.4.6/cat2cat/inst/doc/cat2cat.R | 141 +- cat2cat-0.4.6/cat2cat/inst/doc/cat2cat.Rmd | 145 +- cat2cat-0.4.6/cat2cat/inst/doc/cat2cat.html | 670 +++++----- cat2cat-0.4.6/cat2cat/man/cat2cat.Rd | 7 cat2cat-0.4.6/cat2cat/man/cat2cat_agg.Rd | 27 cat2cat-0.4.6/cat2cat/man/get_freqs.Rd | 4 cat2cat-0.4.6/cat2cat/man/verticals2.Rd | 15 cat2cat-0.4.6/cat2cat/tests/testthat.R | 10 cat2cat-0.4.6/cat2cat/tests/testthat/Rplots.pdf |binary cat2cat-0.4.6/cat2cat/tests/testthat/setup.R |only cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat-internal-utils.R |only cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat-utils.R |only cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat.R | 455 +++--- cat2cat-0.4.6/cat2cat/tests/testthat/test-cat2cat_agg.R | 95 + cat2cat-0.4.6/cat2cat/tests/testthat/test-lms.R | 61 cat2cat-0.4.6/cat2cat/tests/testthat/test-multi-cat2cat.R | 7 cat2cat-0.4.6/cat2cat/tests/testthat/test-plot.R | 17 cat2cat-0.4.6/cat2cat/vignettes/cat2cat.Rmd | 145 +- 28 files changed, 1170 insertions(+), 825 deletions(-)
Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique
for dimension reduction. The algorithm was described by McInnes and
Healy (2018) in <arXiv:1802.03426>. This package provides an interface
for two implementations. One is written from scratch, including components
for nearest-neighbor search and for embedding. The second implementation
is a wrapper for 'python' package 'umap-learn' (requires separate
installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between umap versions 0.2.9.0 dated 2022-08-25 and 0.2.10.0 dated 2023-02-01
DESCRIPTION | 6 - MD5 | 36 ++++---- R/umap.R | 14 +-- R/umap_checks.R | 10 +- R/umap_learn.R | 5 - R/umap_naive.R | 3 inst/doc/umap.R | 9 +- inst/doc/umap.Rmd | 193 ++++++++++++++++++++++++++++++++----------- inst/doc/umap.html | 49 +++++----- inst/doc/umap_learn.Rmd | 70 +++++++++++---- inst/doc/umap_learn.html | 8 - tests/testthat/test_checks.R | 50 +++++------ tests/testthat/test_config.R | 13 +- tests/testthat/test_knn.R | 4 tests/testthat/test_naive.R | 15 +++ tests/testthat/test_python.R | 17 +++ tests/testthat/test_rcpp.R | 2 vignettes/umap.Rmd | 193 ++++++++++++++++++++++++++++++++----------- vignettes/umap_learn.Rmd | 70 +++++++++++---- 19 files changed, 534 insertions(+), 233 deletions(-)