Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@gradcenter.cuny.edu>
Diff between wallace versions 1.1.0 dated 2021-05-24 and 1.1.2 dated 2022-02-12
DESCRIPTION | 18 +++++++++--------- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/wallace-package.R | 6 +++--- README.md | 6 +++--- inst/shiny/Rmd/text_intro.Rmd | 2 +- inst/shiny/Rmd/text_intro_tab.Rmd | 2 +- inst/shiny/Rmd/userReport.Rmd | 2 +- inst/shiny/modules/mod_c3_userEnvs.R | 3 ++- man/wallace-package.Rd | 6 +++--- 10 files changed, 38 insertions(+), 31 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (www.jamovi.org)
aims to make statistical analyses easy and intuitive. 'jamovi' produces
syntax that can directly be used in R (in connection with the R-package 'jmv').
Having import / export routines for the data files 'jamovi' produces ('.omv')
permits an easy transfer of analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre]
(<https://orcid.org/0000-0003-2576-5432>)
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.2.4 dated 2022-01-20 and 0.3.0 dated 2022-02-12
DESCRIPTION | 10 - MD5 | 74 +++++++--- NAMESPACE | 6 NEWS.md | 17 ++ R/convert_to_omv.R |only R/data.R | 58 +++++++- R/globals.R | 139 ++++++++++++++++++- R/long2wide_omv.R |only R/merge_cols_omv.R |only R/merge_rows_omv.R |only R/read_omv.R | 303 ++++++++++++++++++++++++++++++++++--------- R/sort_omv.R |only R/wide2long_omv.R |only R/write_omv.R | 143 +++++++++++--------- README.md | 122 ++++++++++++----- data/AlbumSales.rda |binary data/ToothGrowth.rda |binary data/bfi_sample.rda |binary data/bfi_sample2.rda |binary data/bfi_sample3.rda |only inst/WORDLIST | 26 +++ inst/doc/jmvReadWrite.R | 41 +++-- inst/doc/jmvReadWrite.Rmd | 104 ++++++++++---- inst/doc/jmvReadWrite.html | 148 +++++++++++---------- inst/extdata/ToothGrowth.omv |binary inst/extdata/bfi_sample.omv |binary inst/extdata/bfi_sample2.omv |binary inst/extdata/bfi_sample3.omv |only man/ToothGrowth.Rd | 8 - man/bfi_sample2.Rd | 3 man/bfi_sample3.Rd |only man/convert_to_omv.Rd |only man/long2wide_omv.Rd |only man/merge_cols_omv.Rd |only man/merge_rows_omv.Rd |only man/read_omv.Rd | 24 +-- man/sort_omv.Rd |only man/wide2long_omv.Rd |only man/write_omv.Rd | 37 ++--- tests |only vignettes/jmvReadWrite.Rmd | 104 ++++++++++---- 41 files changed, 991 insertions(+), 376 deletions(-)
Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for
visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as
frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as
bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include
but are not limited to: points with multiple uncertainty intervals,
eye plots (Spiegelhalter D., 1999) <doi:10.1111/1467-985X.00120>,
density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>,
quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>,
complementary cumulative distribution function
barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>,
and fit curves with multiple uncertainty ribbons.
Author: Matthew Kay [aut, cre],
Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ggdist versions 3.0.1 dated 2021-11-30 and 3.1.0 dated 2022-02-12
ggdist-3.0.1/ggdist/R/stat_dist_slabinterval.R |only ggdist-3.0.1/ggdist/R/stat_sample_slabinterval.R |only ggdist-3.0.1/ggdist/man/stat_dist_slabinterval.Rd |only ggdist-3.0.1/ggdist/man/stat_sample_slabinterval.Rd |only ggdist-3.0.1/ggdist/tests/testthat/_snaps/test.position_dodgejust/halfeye-w-point-and-rect-refs.svg |only ggdist-3.0.1/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/vanilla-stat-slabinterval.svg |only ggdist-3.0.1/ggdist/tests/testthat/test.geom.R |only ggdist-3.1.0/ggdist/DESCRIPTION | 42 ggdist-3.1.0/ggdist/MD5 | 322 +-- ggdist-3.1.0/ggdist/NAMESPACE | 46 ggdist-3.1.0/ggdist/NEWS.md | 81 ggdist-3.1.0/ggdist/R/abstract_geom.R |only ggdist-3.1.0/ggdist/R/abstract_stat.R |only ggdist-3.1.0/ggdist/R/abstract_stat_slabinterval.R |only ggdist-3.1.0/ggdist/R/binning_methods.R | 70 ggdist-3.1.0/ggdist/R/curve_interval.R | 94 ggdist-3.1.0/ggdist/R/cut_cdf_qi.R | 22 ggdist-3.1.0/ggdist/R/deprecated.R |only ggdist-3.1.0/ggdist/R/distributions.R | 116 - ggdist-3.1.0/ggdist/R/geom.R | 253 -- ggdist-3.1.0/ggdist/R/geom_dotsinterval.R | 222 -- ggdist-3.1.0/ggdist/R/geom_interval.R | 86 ggdist-3.1.0/ggdist/R/geom_lineribbon.R | 120 - ggdist-3.1.0/ggdist/R/geom_pointinterval.R | 88 ggdist-3.1.0/ggdist/R/geom_slab.R |only ggdist-3.1.0/ggdist/R/geom_slabinterval.R | 453 +--- ggdist-3.1.0/ggdist/R/ggdist-package.R | 10 ggdist-3.1.0/ggdist/R/lkjcorr_marginal.R | 8 ggdist-3.1.0/ggdist/R/parse_dist.R | 17 ggdist-3.1.0/ggdist/R/point_interval.R | 225 +- ggdist-3.1.0/ggdist/R/position_dodgejust.R | 113 - ggdist-3.1.0/ggdist/R/rd.R |only ggdist-3.1.0/ggdist/R/rd_lineribbon.R |only ggdist-3.1.0/ggdist/R/rd_slabinterval.R |only ggdist-3.1.0/ggdist/R/scale_.R | 4 ggdist-3.1.0/ggdist/R/scale_colour_ramp.R | 16 ggdist-3.1.0/ggdist/R/stat.R | 20 ggdist-3.1.0/ggdist/R/stat_dotsinterval.R | 293 -- ggdist-3.1.0/ggdist/R/stat_interval.R | 105 - ggdist-3.1.0/ggdist/R/stat_lineribbon.R | 193 - ggdist-3.1.0/ggdist/R/stat_pointinterval.R | 110 - ggdist-3.1.0/ggdist/R/stat_slabinterval.R | 1034 ++++++---- ggdist-3.1.0/ggdist/R/student_t.R | 4 ggdist-3.1.0/ggdist/R/testthat.R | 15 ggdist-3.1.0/ggdist/R/theme_ggdist.R | 2 ggdist-3.1.0/ggdist/R/tidy_format_translators.R | 6 ggdist-3.1.0/ggdist/R/util.R | 83 ggdist-3.1.0/ggdist/build/partial.rdb |binary ggdist-3.1.0/ggdist/build/vignette.rds |binary ggdist-3.1.0/ggdist/inst/doc/dotsinterval.R |only ggdist-3.1.0/ggdist/inst/doc/dotsinterval.Rmd |only ggdist-3.1.0/ggdist/inst/doc/dotsinterval.html |only ggdist-3.1.0/ggdist/inst/doc/freq-uncertainty-vis.R | 28 ggdist-3.1.0/ggdist/inst/doc/freq-uncertainty-vis.Rmd | 44 ggdist-3.1.0/ggdist/inst/doc/freq-uncertainty-vis.html | 48 ggdist-3.1.0/ggdist/inst/doc/lineribbon.R | 6 ggdist-3.1.0/ggdist/inst/doc/lineribbon.Rmd | 17 ggdist-3.1.0/ggdist/inst/doc/lineribbon.html | 21 ggdist-3.1.0/ggdist/inst/doc/slabinterval.R | 492 +++- ggdist-3.1.0/ggdist/inst/doc/slabinterval.Rmd | 754 ++++--- ggdist-3.1.0/ggdist/inst/doc/slabinterval.html | 867 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ggdist-3.1.0/ggdist/man/scales.Rd | 4 ggdist-3.1.0/ggdist/man/stat_ccdfinterval.Rd |only ggdist-3.1.0/ggdist/man/stat_cdfinterval.Rd |only ggdist-3.1.0/ggdist/man/stat_eye.Rd |only ggdist-3.1.0/ggdist/man/stat_gradientinterval.Rd |only ggdist-3.1.0/ggdist/man/stat_halfeye.Rd |only ggdist-3.1.0/ggdist/man/stat_histinterval.Rd |only ggdist-3.1.0/ggdist/man/stat_interval.Rd | 348 +-- ggdist-3.1.0/ggdist/man/stat_lineribbon.Rd | 256 +- ggdist-3.1.0/ggdist/man/stat_pointinterval.Rd | 362 +-- ggdist-3.1.0/ggdist/man/stat_ribbon.Rd |only ggdist-3.1.0/ggdist/man/stat_slab.Rd |only ggdist-3.1.0/ggdist/man/stat_slabinterval.Rd | 500 +++- ggdist-3.1.0/ggdist/man/student_t.Rd | 4 ggdist-3.1.0/ggdist/man/theme_ggdist.Rd | 2 ggdist-3.1.0/ggdist/man/tidy-format-translators.Rd | 6 ggdist-3.1.0/ggdist/tests/testthat/_snaps/test.curve_interval/conditional-curve-interval-with-mhd.svg |only ggdist-3.1.0/ggdist/tests/testthat/_snaps/test.geom_dotsinterval/dots-with-no-slab-from-na-removal.svg |only 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Title: Data to Support Fish Stock Assessment ('FSA') Package
Description: The datasets to support the Fish Stock Assessment ('FSA') package.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSAdata versions 0.3.8 dated 2019-05-18 and 0.3.9 dated 2022-02-12
DESCRIPTION | 10 - MD5 | 336 +++++++++++++++++++++++----------------------- man/AHerringChile.Rd | 78 +++++----- man/AfricanRivers.Rd | 74 +++++----- man/AlewifeLH.Rd | 80 +++++----- man/AnchovetaChile.Rd | 82 +++++------ man/BGHRfish.Rd | 86 ++++++----- man/BGHRsample.Rd | 82 +++++------ man/BSkateGB.Rd | 96 ++++++------- man/BassFL.Rd | 116 ++++++++------- man/BlackDrum2001.Rd | 96 ++++++------- man/BloaterLH.Rd | 80 +++++----- man/BlueCatfish.Rd | 72 +++++---- man/BlueCrab.Rd | 86 ++++++----- man/BluefishAge.Rd | 76 +++++----- man/BluegillIL.Rd | 82 +++++------ man/BluegillLM.Rd | 94 ++++++------ man/BluntnoseIL1.Rd | 86 ++++++----- man/Bonito.Rd | 80 +++++----- man/BrookTroutNC.Rd | 78 +++++----- man/BrookTroutNEWP.Rd | 92 ++++++------ man/BrookTroutNEWP1.Rd | 118 ++++++++-------- man/BrookTroutOnt.Rd | 88 ++++++------ man/BrownTroutVC1.Rd | 86 ++++++----- man/BullTroutRML1.Rd | 86 ++++++----- man/BullTroutRML2.Rd | 92 ++++++------ man/BullTroutTC.Rd | 72 +++++---- man/CCatfishNB.Rd | 86 ++++++----- man/Cabezon.Rd | 100 ++++++------- man/Casselman1990.Rd | 88 ++++++------ man/ChinookKR.Rd | 80 +++++----- man/CiscoTL.Rd | 92 ++++++------ man/CrappieARMS.Rd | 84 +++++------ man/CreekChub.Rd | 86 ++++++----- man/CreelMN.Rd | 114 +++++++-------- man/Croaker1.Rd | 80 +++++----- man/Croaker2.Rd | 80 +++++----- man/CutthroatALf.Rd | 92 ++++++------ man/DarterMahon.Rd | 96 ++++++------- man/DarterOnt.Rd | 86 ++++++----- man/Deckeretal1999.Rd | 96 ++++++------- man/EuroPerchTJ.Rd | 80 +++++----- man/FHCatfish.Rd | 82 +++++------ man/FHCatfishATL.Rd | 82 +++++------ man/FSAdata.Rd | 95 ++++++------- man/FWDrumLE1.Rd | 78 +++++----- man/FWDrumLE2.Rd | 78 +++++----- man/Ghats.Rd | 68 ++++----- man/GreensCreekMine.Rd | 98 ++++++------- man/Hake.Rd | 80 +++++----- man/HalibutPAC.Rd | 84 +++++------ man/Herman.Rd | 96 ++++++------- man/HerringBWE.Rd | 80 +++++----- man/HerringISS.Rd | 84 +++++------ man/HumpbackWFCR.Rd | 90 ++++++------ man/InchLake1.Rd | 104 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man/Pathfinder.Rd | 90 ++++++------ man/PikeHL.Rd | 94 ++++++------ man/PikeIL.Rd | 88 ++++++------ man/PikeNYPartial2.Rd | 94 ++++++------ man/PikeWindermere.Rd | 96 ++++++------- man/PygmyWFBC.Rd | 110 +++++++-------- man/RBSmeltErie.Rd | 74 +++++----- man/RBSmeltLM.Rd | 70 ++++----- man/RBTroutKenai.Rd | 78 +++++----- man/RBTroutUNSP.Rd | 86 ++++++----- man/RWhitefishAI.Rd | 72 +++++---- man/RWhitefishIR.Rd | 72 +++++---- man/RedDrum.Rd | 72 +++++---- man/Riffleshell.Rd | 94 ++++++------ man/RockBassCL.Rd | 72 +++++---- man/RockBassLO1.Rd | 78 +++++----- man/RockBassLO2.Rd | 84 +++++------ man/RuffeSLRH92.Rd | 128 ++++++++--------- man/RuffeTL89.Rd | 70 ++++----- man/SLampreyGL.Rd | 72 +++++---- man/SalmonADP.Rd | 78 +++++----- man/SalmonidsMCCA.Rd | 92 ++++++------ man/SardineChile.Rd | 84 +++++------ man/SardineLK.Rd | 72 +++++---- man/SardinesPacific.Rd | 80 +++++----- man/SculpinALTER.Rd | 102 +++++++------ man/ShadCR.Rd | 108 +++++++------- man/ShrimpGuam.Rd | 116 ++++++++------- man/SimonsonLyons.Rd | 90 ++++++------ man/SiscowetMI2004.Rd | 100 ++++++------- man/Snapper.Rd | 70 ++++----- man/SnapperHG1.Rd | 96 ++++++------- man/SnapperHG2.Rd | 88 ++++++------ man/SockeyeKL.Rd | 80 +++++----- man/SockeyeSR.Rd | 88 ++++++------ man/SpotVA2.Rd | 88 ++++++------ man/SpottedSucker1.Rd | 72 +++++---- man/StripedBass1.Rd | 80 +++++----- man/StripedBass2.Rd | 78 +++++----- man/StripedBass3.Rd | 82 +++++------ man/StripedBass4.Rd | 86 ++++++----- man/StripedBass5.Rd | 86 ++++++----- man/StripedBass6.Rd | 86 ++++++----- man/SturgeonBL.Rd | 88 ++++++------ man/SturgeonGB.Rd | 74 +++++----- man/SunfishIN.Rd | 86 ++++++----- man/SunfishLP.Rd | 72 +++++---- man/TPrawnsEG.Rd | 86 ++++++----- man/TroutADP.Rd | 80 +++++----- man/TroutBR.Rd | 80 +++++----- man/TroutperchLM1.Rd | 80 +++++----- man/TroutperchLM2.Rd | 70 ++++----- man/TroutperchLM3.Rd | 78 +++++----- man/VendaceLP.Rd | 80 +++++----- man/VendaceLP2.Rd | 78 +++++----- man/WShrimpGA.Rd | 88 ++++++------ man/WalleyeConsumption.Rd | 66 ++++----- man/WalleyeEL.Rd | 84 +++++------ man/WalleyeErie.Rd | 66 ++++----- man/WalleyeErie2.Rd | 112 +++++++-------- man/WalleyeKS.Rd | 98 ++++++------- man/WalleyeML.Rd | 90 ++++++------ man/WalleyeMN06a.Rd | 84 +++++------ man/WalleyeMN06b.Rd | 90 ++++++------ man/WalleyePL.Rd | 92 ++++++------ man/WalleyePS.Rd | 102 +++++++------ man/WalleyeRL.Rd | 98 ++++++------- man/WalleyeWad.Rd | 88 ++++++------ man/WalleyeWyrlng.Rd | 88 ++++++------ man/WhiteGrunt1.Rd | 72 +++++---- man/WhiteGrunt2.Rd | 80 +++++----- man/WhitefishGSL.Rd | 112 +++++++-------- man/WhitefishLS.Rd | 70 ++++----- man/WhitefishMB.Rd | 90 ++++++------ man/WhitefishTB.Rd | 84 +++++------ man/YERockfish.Rd | 100 ++++++------- man/YPerchCB1.Rd | 154 ++++++++++----------- man/YPerchCB2.Rd | 80 +++++----- man/YPerchGB.Rd | 68 ++++----- man/YPerchGL.Rd | 80 +++++----- man/YPerchRL.Rd | 68 ++++----- man/YPerchSB.Rd | 80 +++++----- man/YPerchSB1.Rd | 82 +++++------ man/YPerchTL.Rd | 90 ++++++------ man/YTFlounder.Rd | 88 ++++++------ 169 files changed, 7540 insertions(+), 7207 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering several procedures), functions to compute
the multivariate skewness, kurtosis, Mahalanobis distance (checking the positive
defineteness) and the Wilson-Hilferty transformation of chi squared variables. Furthermore,
the package provides interfaces to C code callable by another C code from other R packages.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.3-8196 dated 2021-10-18 and 0.4 dated 2022-02-12
fastmatrix-0.3-8196/fastmatrix/src/equilibrate.f |only fastmatrix-0.4/fastmatrix/ChangeLog | 9 + fastmatrix-0.4/fastmatrix/DESCRIPTION | 10 +- fastmatrix-0.4/fastmatrix/MD5 | 47 +++++----- fastmatrix-0.4/fastmatrix/NAMESPACE | 21 ++-- fastmatrix-0.4/fastmatrix/R/bezier.R |only fastmatrix-0.4/fastmatrix/R/chol.R |only fastmatrix-0.4/fastmatrix/R/equilibrate.R | 46 +++++++-- fastmatrix-0.4/fastmatrix/R/ridge.R | 27 ++++- fastmatrix-0.4/fastmatrix/R/sweep.R | 2 fastmatrix-0.4/fastmatrix/inst/CITATION | 8 - fastmatrix-0.4/fastmatrix/inst/include/fastmatrix.h | 4 fastmatrix-0.4/fastmatrix/inst/include/fastmatrix_API.h | 16 +++ fastmatrix-0.4/fastmatrix/man/bezier.Rd |only fastmatrix-0.4/fastmatrix/man/cg.Rd | 2 fastmatrix-0.4/fastmatrix/man/cholupdate.Rd |only fastmatrix-0.4/fastmatrix/man/equilibrate.Rd | 19 ++-- fastmatrix-0.4/fastmatrix/man/jacobi.Rd | 2 fastmatrix-0.4/fastmatrix/man/ridge.Rd | 16 ++- fastmatrix-0.4/fastmatrix/man/seidel.Rd | 2 fastmatrix-0.4/fastmatrix/src/R_init_fastmatrix.c | 11 +- fastmatrix-0.4/fastmatrix/src/bezier.c |only fastmatrix-0.4/fastmatrix/src/blas_1.c | 62 +++++++++++++ fastmatrix-0.4/fastmatrix/src/cholesky.c | 30 ++++++ fastmatrix-0.4/fastmatrix/src/decasteljau.f |only fastmatrix-0.4/fastmatrix/src/equilibrate.c |only fastmatrix-0.4/fastmatrix/src/equilibrate_cols.f |only fastmatrix-0.4/fastmatrix/src/fastmatrix.h | 32 +++++- fastmatrix-0.4/fastmatrix/src/ridge.c | 75 ++++++++++++++-- 29 files changed, 351 insertions(+), 90 deletions(-)
Title: Flexible 'Tidyverse'-Friendly Simulations
Description: A general, 'tidyverse'-friendly framework
for simulation studies, design analysis, and power analysis.
Specify data generation, define varying parameters, generate data,
fit models, and tidy model results in a single pipeline, without
needing loops or custom functions.
Author: Ethan Brown [aut, cre] (<https://orcid.org/0000-0003-3419-7465>),
Jeffrey Bye [ctb]
Maintainer: Ethan Brown <ecbrown@umn.edu>
Diff between simpr versions 0.2.1 dated 2022-01-12 and 0.2.2 dated 2022-02-12
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md |only R/tidyverse_verb_methods.R | 22 ++++++++++++++++------ README.md | 4 ++-- inst/doc/optimization.html | 24 ++++++++++++------------ inst/doc/simpr.html | 2 +- inst/doc/simulation-errors.html | 28 ++++++++++++++-------------- man/tidyverse_verbs.Rd | 16 ++++++++++++++++ 9 files changed, 73 insertions(+), 46 deletions(-)
Title: Data Version Control for the Targets Package
Description: In computationally demanding data analysis pipelines,
the 'targets' R package (2021, <doi:10.21105/joss.02959>) maintains
an up-to-date set of results while skipping tasks that do not need to rerun.
This process increases speed and increases trust in the final end product.
However, it also overwrites old output with new output, and past
results disappear by default. To preserve historical output, the 'gittargets'
package captures version-controlled snapshots of the data store,
and each snapshot links to the underlying commit of the source code.
That way, when the user rolls back the code to a previous branch or commit,
'gittargets' can recover the data contemporaneous with that commit so that
all targets remain up to date.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Saras Windecker [rev],
David Neuzerling [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between gittargets versions 0.0.1 dated 2022-01-13 and 0.0.3 dated 2022-02-12
DESCRIPTION | 35 +++++++++++++-------------------- MD5 | 26 ++++++++++++------------ NEWS.md | 10 ++++++++- R/tar_git_checkout.R | 2 + R/tar_git_ok.R | 2 + R/tar_package.R | 29 +++++++++++---------------- R/utils_git.R | 10 +++++++++ build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/git.html | 25 ++++++++++++----------- man/gittargets-package.Rd | 29 +++++++++++---------------- man/tar_git_ok.Rd | 2 + tests/testthat/test-tar_git_checkout.R | 13 ++++++++++++ tests/testthat/test-utils_git.R | 14 +++++++++++++ 14 files changed, 117 insertions(+), 81 deletions(-)
Title: Analyses of Text using Natural Language Processing and Machine
Learning
Description: Transforms text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] (<https://orcid.org/0000-0002-2728-6278>),
Salvatore Giorgi [aut] (<https://orcid.org/0000-0001-7381-6295>),
Andrew Schwartz [aut] (<https://orcid.org/0000-0002-6383-3339>)
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 0.9.10 dated 2020-12-14 and 0.9.50 dated 2022-02-12
text-0.9.10/text/R/4_1_textPlot.R |only text-0.9.10/text/data/wordembeddings4.rda |only text-0.9.10/text/man/wordembeddings4.Rd |only text-0.9.50/text/DESCRIPTION | 18 text-0.9.50/text/MD5 | 139 + text-0.9.50/text/NAMESPACE | 24 text-0.9.50/text/NEWS.md | 64 text-0.9.50/text/R/0_0_1_text_initialize.R |only text-0.9.50/text/R/0_0_text_install.R |only text-0.9.50/text/R/0_1_globals.R | 17 text-0.9.50/text/R/0_2_privateFunctions.R | 60 text-0.9.50/text/R/1_1_textEmbed.R | 246 ++- text-0.9.50/text/R/1_2_textEmbedStatic.R | 96 - text-0.9.50/text/R/2_1_textTrain.R | 218 ++ text-0.9.50/text/R/2_2_textTrainRegression.R | 452 ++--- text-0.9.50/text/R/2_3_textTrainRandomForest.R | 423 ++--- text-0.9.50/text/R/3_1_textSimilarity.R | 14 text-0.9.50/text/R/3_2_textSimilarityTest.R | 16 text-0.9.50/text/R/4_0_textPlot.R |only text-0.9.50/text/R/4_1_textPlotCentrality.R |only text-0.9.50/text/R/4_2_textPlotPCA.R |only text-0.9.50/text/R/4_3_textPlotProjection.R |only text-0.9.50/text/R/4_4_textPlotWordPrediction.R |only text-0.9.50/text/R/ExampleDataDescription.R | 6 text-0.9.50/text/R/zzz.R | 25 text-0.9.50/text/README.md | 108 - text-0.9.50/text/build/vignette.rds |binary text-0.9.50/text/data/DP_projections_HILS_SWLS_100.rda |binary text-0.9.50/text/data/Language_based_assessment_data_8.rda |binary text-0.9.50/text/data/word_embeddings_4.rda |only text-0.9.50/text/inst/doc/Computer_Capacity.html | 606 ------- text-0.9.50/text/inst/doc/Extended_Installation_Guide.R | 86 + text-0.9.50/text/inst/doc/Extended_Installation_Guide.Rmd | 122 + text-0.9.50/text/inst/doc/Extended_Installation_Guide.html | 510 ++---- text-0.9.50/text/inst/doc/Pre-registration.html | 577 ------- text-0.9.50/text/inst/doc/Removing_Cache_Files.html | 577 ------- text-0.9.50/text/inst/doc/Word_embeddings.R | 6 text-0.9.50/text/inst/doc/Word_embeddings.Rmd | 6 text-0.9.50/text/inst/doc/Word_embeddings.html | 681 -------- text-0.9.50/text/inst/doc/text.R | 10 text-0.9.50/text/inst/doc/text.Rmd | 12 text-0.9.50/text/inst/doc/text.html | 768 +--------- text-0.9.50/text/inst/python/huggingface_Interface3.py | 85 - text-0.9.50/text/man/figures/README-DPP_plot-1.png |binary text-0.9.50/text/man/find_textrpp.Rd |only text-0.9.50/text/man/find_textrpp_env.Rd |only text-0.9.50/text/man/textCentrality.Rd | 16 text-0.9.50/text/man/textCentralityPlot.Rd | 6 text-0.9.50/text/man/textEmbed.Rd | 54 text-0.9.50/text/man/textEmbedLayerAggregation.Rd | 7 text-0.9.50/text/man/textEmbedLayersOutput.Rd | 26 text-0.9.50/text/man/textEmbedStatic.Rd | 8 text-0.9.50/text/man/textPCA.Rd | 10 text-0.9.50/text/man/textPCAPlot.Rd | 8 text-0.9.50/text/man/textPlot.Rd |only text-0.9.50/text/man/textPredict.Rd | 6 text-0.9.50/text/man/textPredictTest.Rd |only text-0.9.50/text/man/textProjection.Rd | 26 text-0.9.50/text/man/textProjectionPlot.Rd | 92 - text-0.9.50/text/man/textSimilarity.Rd | 4 text-0.9.50/text/man/textSimilarityNorm.Rd | 8 text-0.9.50/text/man/textSimilarityTest.Rd | 6 text-0.9.50/text/man/textTrain.Rd | 22 text-0.9.50/text/man/textTrainLists.Rd | 27 text-0.9.50/text/man/textTrainRandomForest.Rd | 61 text-0.9.50/text/man/textTrainRegression.Rd | 38 text-0.9.50/text/man/textWordPrediction.Rd |only text-0.9.50/text/man/textrpp_initialize.Rd |only text-0.9.50/text/man/textrpp_install.Rd |only text-0.9.50/text/man/textrpp_uninstall.Rd |only text-0.9.50/text/man/word_embeddings_4.Rd |only text-0.9.50/text/tests/testthat.R | 4 text-0.9.50/text/tests/testthat/test_0_install_test.R |only text-0.9.50/text/tests/testthat/test_1_Analyses_flow.R | 8 text-0.9.50/text/tests/testthat/test_2_textTrain.R | 198 +- text-0.9.50/text/tests/testthat/test_3_textSimilarityAndtextDiff.R | 27 text-0.9.50/text/tests/testthat/test_4_textPlot.R | 53 text-0.9.50/text/tests/testthat/test_99_textEmbed.R | 42 text-0.9.50/text/vignettes/Extended_Installation_Guide.Rmd | 122 + text-0.9.50/text/vignettes/Word_embeddings.Rmd | 6 text-0.9.50/text/vignettes/text.Rmd | 12 81 files changed, 2375 insertions(+), 4494 deletions(-)
Title: Simulation-Based Random Variable Objects
Description: Implements a simulation-based random variable class and a suite of
methods for extracting parts of random vectors, calculating extremes of random
vectors, and generating random vectors under a variety of distributions
following Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>.
Author: Jouni Kerman [aut],
Jemma Stachelek [ctb, cre]
Maintainer: Jemma Stachelek <stachel2@msu.edu>
Diff between rv versions 2.3.4 dated 2020-02-03 and 2.3.5 dated 2022-02-12
DESCRIPTION | 14 - MD5 | 20 - NEWS.md | 51 ++- R/as.rv.stanfit.R | 2 README.md | 8 build/vignette.rds |binary inst/CITATION | 4 inst/doc/rv-doc.Rmd | 2 inst/doc/rv-doc.html | 670 ++++++++++++++++++++------------------------------- man/as.rv.stanfit.Rd | 2 vignettes/rv-doc.Rmd | 2 11 files changed, 321 insertions(+), 454 deletions(-)
Title: Average Bioequivalence with Expanding Limits (ABEL)
Description: Performs comparative bioavailability calculations for Average Bioequivalence with
Expanding Limits (ABEL). Implemented are 'Method A' and 'Method B' and the detection of outliers.
If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to
control the consumer risk.
Average Bioequivalence - optionally with a tighter (narrow therapeutic index drugs) or wider
acceptance range (Gulf Cooperation Council, South Africa: Cmax) - is implemented as well.
Author: Helmut Schütz [aut, cre] (<https://orcid.org/0000-0002-1167-7880>),
Michael Tomashevskiy [ctb],
Detlew Labes [ctb] (<https://orcid.org/0000-0003-2169-426X>)
Maintainer: Helmut Schütz <helmut.schuetz@bebac.at>
Diff between replicateBE versions 1.1.0 dated 2021-06-21 and 1.1.1 dated 2022-02-12
DESCRIPTION | 17 - MD5 | 30 +- NEWS.md | 92 +++--- R/ABE.R | 6 R/method.B.R | 2 README.md | 319 +++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette.R | 29 -- inst/doc/vignette.Rmd | 139 +++++----- inst/doc/vignette.html | 668 ++++++++++++++++++++++--------------------------- man/ABE.Rd | 4 man/method.A.Rd | 21 - man/method.B.Rd | 37 +- vignettes/figure1.png |binary vignettes/vignette.Rmd | 139 +++++----- 16 files changed, 705 insertions(+), 798 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 1.0-4 dated 2020-07-07 and 1.0-5 dated 2022-02-12
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- src/cgFbat.cpp | 4 ++-- src/fbatdist.cpp | 2 +- src/fbatge.cpp | 2 +- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between ecespa versions 1.1-13 dated 2021-03-14 and 1.1-14 dated 2022-02-12
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 4 +++- build/partial.rdb |binary man/Kci.Rd | 2 +- man/rIPCP.Rd | 10 +++++----- man/sim.poissonc.rd | 4 ++-- 7 files changed, 22 insertions(+), 20 deletions(-)
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 methods complemented with l_1-penalization and iteratively reweighted l_1-penalization are used to fit sparse models.
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 1.2.1 dated 2021-11-01 and 1.2.2 dated 2022-02-12
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 1 - R/generate_ns.R | 1 - R/smqr.R | 2 +- README.md |only src/RcppExports.cpp | 5 +++++ 7 files changed, 17 insertions(+), 13 deletions(-)
Title: Tools for Clinical Research
Description: Every research team have their own script for data management, statistics and
most importantly hemodynamic indices. The purpose is to standardize scripts
utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe,
and add both periods of interest (trigger-periods), and delete artifacts with deleter-files.
Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and
Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.
Author: Markus Harboe Olsen [cre, aut],
Christian Riberholt [ctb],
Ronan Berg [ctb],
Kirsten Moeller [ctb],
Janus Christian Jakobsen [ctb],
Aksel Karl Georg Jensen [ctb]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Diff between clintools versions 0.9.2 dated 2022-01-20 and 0.9.3 dated 2022-02-12
DESCRIPTION | 22 +++-- MD5 | 14 +-- NAMESPACE | 1 NEWS.md | 5 + R/rrGcomp.R | 19 ++-- R/sRCT.R | 223 +++++++++++++++++++++------------------------------------ man/rrGcomp.Rd | 2 man/sRCT.Rd | 29 ++----- 8 files changed, 129 insertions(+), 186 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 0.9.9 dated 2022-01-08 and 0.9.12 dated 2022-02-12
DESCRIPTION | 6 - MD5 | 58 +++++++------- NEWS.md | 6 + R/datasets.R | 26 +++--- R/helpers.R | 9 +- README.md | 157 +++++++++++++++++++--------------------- data/castaway_details.rda |binary data/castaways.rda |binary data/challenge_description.rda |binary data/challenge_results.rda |binary data/confessionals.rda |binary data/hidden-idols.rda |binary data/jury-votes.rda |binary data/season-palettes.rda |binary data/season-summary.rda |binary data/tribe-colours.rda |binary data/tribe-mapping.rda |binary data/viewers.rda |binary data/vote-history.rda |binary man/castaway_details.Rd | 3 man/castaways.Rd | 9 +- man/challenges.Rd | 2 man/clean_votes.Rd | 6 - man/confessionals.Rd | 2 man/hidden_idols.Rd | 2 man/jury_votes.Rd | 2 man/tribe_mapping.Rd | 2 man/viewers.Rd | 1 man/vote_history.Rd | 4 - tests/testthat/test-castaways.R | 10 +- 30 files changed, 159 insertions(+), 146 deletions(-)
Title: Power Analyses for Common Designs (Power to the People)
Description: Statistical power analysis for designs including t-tests, correlations,
multiple regression, ANOVA, mediation, and logistic regression. Functions accompany
Aberson (2019) <doi:10.4324/9781315171500>.
Author: Chris Aberson
Maintainer: Chris Aberson <cla18@humboldt.edu>
Diff between pwr2ppl versions 0.2.0 dated 2021-04-04 and 0.3.0 dated 2022-02-12
DESCRIPTION | 11 ++++++----- MD5 | 10 ++++++---- NAMESPACE | 1 + R/Assumptions.R |only R/MRC_all.R | 2 +- README.md | 3 +-- man/Assumptions.Rd |only 7 files changed, 15 insertions(+), 12 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Jason Doll [aut],
Powell Wheeler [aut],
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.9.1 dated 2021-07-17 and 0.9.2 dated 2022-02-12
FSA-0.9.1/FSA/R/deprecated-residPlot.R |only FSA-0.9.1/FSA/R/deprecated_fitPlot.R |only FSA-0.9.1/FSA/man/filterD.Rd |only FSA-0.9.1/FSA/man/fitPlot.Rd |only FSA-0.9.1/FSA/man/fsaNews.Rd |only FSA-0.9.1/FSA/man/residPlot.Rd |only FSA-0.9.2/FSA/DESCRIPTION | 10 ++-- FSA-0.9.2/FSA/MD5 | 30 ++++-------- FSA-0.9.2/FSA/NAMESPACE | 18 ------- FSA-0.9.2/FSA/NEWS.md | 13 +++++ FSA-0.9.2/FSA/R/FSA-defunct.R | 24 +++++++++ FSA-0.9.2/FSA/R/FSAUtils.R | 82 --------------------------------- FSA-0.9.2/FSA/R/psdAdd.R | 3 - FSA-0.9.2/FSA/R/psdVal.R | 3 - FSA-0.9.2/FSA/R/wrAdd.R | 4 - FSA-0.9.2/FSA/R/wsVal.R | 3 - FSA-0.9.2/FSA/data/PSDlit.rdata |binary FSA-0.9.2/FSA/data/WSlit.rdata |binary FSA-0.9.2/FSA/man/FSA-defunct.Rd | 12 ++++ 19 files changed, 71 insertions(+), 131 deletions(-)
Title: Select Point Pattern Models Based on Minimum Contrast, AIC and
Goodness of Fit
Description: Fit and selects point pattern models based on minimum contrast, AIC and and goodness of fit.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between selectspm versions 0.3 dated 2021-03-14 and 0.4 dated 2022-02-12
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 9 ++++++--- 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Individual Diversity-Area Relationships
Description: Computes and tests individual (species, phylogenetic and functional) diversity-area relationships, i.e., how species-, phylogenetic- and functional-diversity varies with spatial scale around the individuals of some species in a community. See applications of these methods in Wiegand et al. (2007) <doi:10.1073/pnas.0705621104> or Chacon-Labella et al. (2016) <doi:10.1007/s00442-016-3547-z>.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between idar versions 1.2 dated 2021-03-14 and 1.3 dated 2022-02-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 3 ++- man/ipsim.Rd | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between fsbrain versions 0.5.2 dated 2021-11-10 and 0.5.3 dated 2022-02-12
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 117 ++++++++++++++++---------------- NAMESPACE | 1 R/atlas.R | 2 R/cbar.R | 32 ++++++++ R/fsdir_abstraction_group.R | 48 ++++++++++++- R/fsdir_abstraction_subject.R | 14 +-- R/helpers.R | 122 ++++++++++++++++++++++++---------- R/morph_agg.R | 4 - R/morph_atlas_agg.R | 22 +++--- R/morph_concat.R | 8 +- R/vis.R | 20 ++--- R/vis_meshes.R | 2 R/vis_volume_3d.R | 6 - R/volume.R | 4 - build/vignette.rds |binary man/check.subjects.files.Rd |only man/check.subjectslist.Rd | 3 man/get.atlas.region.names.Rd | 10 +- man/group.agg.atlas.native.Rd | 2 man/group.annot.Rd | 2 man/group.concat.measures.native.Rd | 2 man/group.concat.measures.standard.Rd | 2 man/group.label.Rd | 2 man/group.morph.agg.native.Rd | 2 man/group.morph.native.Rd | 2 man/group.multimorph.agg.native.Rd | 2 man/group.surface.Rd | 2 man/label.border.fast.Rd |only man/mask.from.labeldata.for.hemi.Rd | 2 man/rglvoxels.Rd | 2 man/spread.values.over.annot.Rd | 2 man/spread.values.over.hemi.Rd | 2 man/spread.values.over.subject.Rd | 2 man/subject.annot.Rd | 2 man/subject.atlas.agg.Rd | 2 man/subject.label.Rd | 2 man/subject.mask.Rd | 2 man/subject.morph.native.Rd | 2 man/subject.morph.standard.Rd | 2 man/subject.surface.Rd | 2 man/subject.volume.Rd | 2 man/submesh.vertex.Rd | 21 ++++- man/vis.color.on.subject.Rd | 2 man/vis.coloredmeshes.Rd | 2 man/vis.colortable.legend.Rd | 2 man/vis.data.on.subject.Rd | 2 man/vis.labeldata.on.subject.Rd | 2 man/vis.mask.on.subject.Rd | 2 man/vis.region.values.on.subject.Rd | 2 man/vis.seg.legend.Rd |only man/vis.subject.annot.Rd | 2 man/vis.subject.label.Rd | 2 man/vis.subject.morph.native.Rd | 2 man/vis.subject.morph.standard.Rd | 2 man/vis.symmetric.data.on.subject.Rd | 2 man/volvis.contour.Rd | 2 man/volvis.voxels.Rd | 2 man/write.region.values.Rd | 2 tests/testthat/test-atlas.R | 40 +++++------ 61 files changed, 353 insertions(+), 207 deletions(-)
Title: Nearest Neighbour Contingency Table Analysis
Description: Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.
Author: Marcelino de la Cruz Rot and Philip M. Dixon
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between dixon versions 0.0-7 dated 2021-03-14 and 0.0-8 dated 2022-02-12
DESCRIPTION | 9 ++-- MD5 | 4 +- R/p2colasr.R | 109 +++++++++++++++++++++++++++++++---------------------------- 3 files changed, 66 insertions(+), 56 deletions(-)
Title: Calculates the Minimum Sample Size Required for Developing a
Multivariable Prediction Model
Description: Computes the minimum sample size required for the development of a new multivariable prediction model using the criteria proposed by Riley et al. (2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate the minimum sample size for the development of models with continuous, binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi: 10.1002/sim.7992> lay out a series of criteria the sample size should meet. These aim to minimise the overfitting and to ensure precise estimation of key parameters in the prediction model.
Author: Joie Ensor [aut, cre],
Emma C. Martin [aut],
Richard D. Riley [aut]
Maintainer: Joie Ensor <j.ensor@keele.ac.uk>
Diff between pmsampsize versions 1.1.1 dated 2021-11-22 and 1.1.2 dated 2022-02-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/pmsampsize_bin.R | 2 +- R/pmsampsize_cont.R | 52 ++++++++++++++++++++++++++-------------------------- R/pmsampsize_surv.R | 2 +- 6 files changed, 42 insertions(+), 37 deletions(-)
Title: A Tool for Calculation and Optimization of the Expected Gain
from Multi-Stage Selection
Description: Multi-stage selection is practiced in numerous fields of life
and social sciences and particularly in breeding. A special characteristic of
multi-stage selection is that candidates are evaluated in successive stages
with increasing intensity and effort, and only a fraction of the superior
candidates is selected and promoted to the next stage. For the optimum design
of such selection programs, the selection gain plays a crucial role. It can be
calculated by integration of a truncated multivariate normal (MVN) distribution.
While mathematical formulas for calculating the selection gain and the variance
among selected candidates were developed long time ago, solutions for numerical
calculation were not available. This package can also be used for optimizing
multi-stage selection programs for a given total budget and different costs of
evaluating the candidates in each stage.
Author: Xuefei Mi, Jose Marulanda, H. Friedrich Utz, Albrecht E. Melchinger
(Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi <mi_xue_fei@hotmail.com>
Diff between selectiongain versions 2.0.591 dated 2016-10-09 and 2.0.707 dated 2022-02-12
DESCRIPTION | 26 MD5 | 40 NAMESPACE | 1 R/SDselectiongain.R |only R/multistagecor.R | 1433 +++++++++++++++++++++++++++++----- R/multistagegain.R | 4 R/multistagegain.each.R | 10 R/multistageoptimum.grid.R | 467 ++++++----- R/multistageoptimum.nlm.R | 2 R/multistageoptimum.search.R | 115 +- R/multistageoptimum.searchIndexT.R |only R/multistageoptimum.searchThreeS.R | 63 + R/multistagetp.R | 17 R/multistagevariance.R | 5 man/SDselectiongain.Rd |only man/multistagecor.Rd | 68 + man/multistagegain.Rd | 2 man/multistagegain.each.Rd | 22 man/multistageoptimum.grid.Rd | 4 man/multistageoptimum.search.Rd | 7 man/multistageoptimum.searchIndexT.Rd |only man/multistageoptimum.searchThreeS.Rd | 38 man/multistagevariance.Rd | 32 23 files changed, 1772 insertions(+), 584 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.7 dated 2022-01-12 and 5.5.8 dated 2022-02-12
DESCRIPTION | 8 MD5 | 17 R/CLUSTERING-compare-clusterings.R | 2 build/partial.rdb |binary inst/NEWS.Rd | 6 inst/doc/dtwclust.pdf |binary inst/doc/parallelization-considerations.html | 140 ++++++- inst/doc/timing-experiments.html | 484 ++++++++++++++++++++++----- tests/testthat/Rplots.pdf |only tests/testthat/system/comparisons.R | 30 + 10 files changed, 550 insertions(+), 137 deletions(-)
Title: Statistical Process Control for Stochastic Textured Surfaces
Description: Provides statistical process control tools for stochastic
textured surfaces. The current version supports the following tools:
(1) generic modeling of stochastic textured surfaces.
(2) local defect monitoring and diagnostics in stochastic
textured surfaces, which was proposed by Bui and Apley (2018a)
<doi:10.1080/00401706.2017.1302362>.
(3) global change monitoring in the nature of stochastic
textured surfaces, which was proposed by Bui and Apley (2018b)
<doi:10.1080/00224065.2018.1507559>.
(4) computation of dissimilarity matrix of stochastic textured
surface images, which was proposed by Bui and Apley (2019b)
<doi:10.1016/j.csda.2019.01.019>.
Author: Anh Tuan Bui [aut, cre] and Daniel W. Apley [ths]
Maintainer: Anh Bui <atbui@u.northwestern.edu>
Diff between spc4sts versions 0.5.4 dated 2021-07-02 and 0.5.5 dated 2022-02-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/CITATION | 30 +++++++++++++++++++----------- 3 files changed, 24 insertions(+), 16 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes
(simple sequential inhibition, Matern inhibition models, Matern cluster process,
Neyman-Scott cluster processes, log-Gaussian Cox processes, product shot noise cluster processes)
and simulation of Gibbs point processes (Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler). Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Kasper Klitgaard Berthelsen [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 2.0-0 dated 2022-01-06 and 2.1-0 dated 2022-02-12
DESCRIPTION | 10 - MD5 | 20 +- NAMESPACE | 6 NEWS | 16 + R/clusterinfo.R | 383 ++++++++++++++++++++++++---------------- R/indefinteg.R |only R/randomNS.R | 7 inst/doc/packagesizes.txt | 1 man/default.expand.Rd | 2 man/indefinteg.Rd |only man/spatstat.random-internal.Rd | 2 man/spatstat.random-package.Rd | 75 ++++--- 12 files changed, 326 insertions(+), 196 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Sebastian Meyer [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 2.3-1 dated 2021-12-10 and 2.3-2 dated 2022-02-12
spatstat.geom-2.3-1/spatstat.geom/man/WindowOnly.Rd |only spatstat.geom-2.3-2/spatstat.geom/DESCRIPTION | 12 - spatstat.geom-2.3-2/spatstat.geom/MD5 | 96 +++++----- spatstat.geom-2.3-2/spatstat.geom/NEWS | 9 spatstat.geom-2.3-2/spatstat.geom/R/applynbd.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/as.im.R | 32 ++- spatstat.geom-2.3-2/spatstat.geom/R/centroid.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/clickpoly.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/colourtools.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/cut.ppp.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/deltametric.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/distancemetrics.R | 4 spatstat.geom-2.3-2/spatstat.geom/R/distances.psp.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/headtail.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/layered.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/nncross.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/nnutils.R | 6 spatstat.geom-2.3-2/spatstat.geom/R/plot.anylist.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/ppp.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/psp.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/randomseg.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/simplepanel.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/summary.im.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/terse.R | 2 spatstat.geom-2.3-2/spatstat.geom/R/unnormdensity.R | 2 spatstat.geom-2.3-2/spatstat.geom/inst/doc/packagesizes.txt | 1 spatstat.geom-2.3-2/spatstat.geom/man/Window.quad.Rd |only spatstat.geom-2.3-2/spatstat.geom/man/as.owin.Rd | 37 +++ spatstat.geom-2.3-2/spatstat.geom/man/bufftess.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/domain.Rd | 12 - spatstat.geom-2.3-2/spatstat.geom/man/macros/defns.Rd | 4 spatstat.geom-2.3-2/spatstat.geom/man/matchingdist.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/metric.object.Rd | 1 spatstat.geom-2.3-2/spatstat.geom/man/pointsOnLines.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/polartess.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/ppp.object.Rd | 16 - spatstat.geom-2.3-2/spatstat.geom/man/pppdist.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/pppmatching.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/pppmatching.object.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/quadratcount.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/quadrats.Rd | 4 spatstat.geom-2.3-2/spatstat.geom/man/rlinegrid.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/rsyst.Rd | 4 spatstat.geom-2.3-2/spatstat.geom/man/runifrect.Rd | 10 - spatstat.geom-2.3-2/spatstat.geom/man/spatstat.geom-deprecated.Rd | 7 spatstat.geom-2.3-2/spatstat.geom/man/spatstat.geom-internal.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/spatstat.options.Rd | 14 - spatstat.geom-2.3-2/spatstat.geom/man/summary.ppp.Rd | 2 spatstat.geom-2.3-2/spatstat.geom/man/tess.Rd | 4 spatstat.geom-2.3-2/spatstat.geom/man/venn.tess.Rd | 2 50 files changed, 195 insertions(+), 138 deletions(-)
Title: Access to Aquo domaintables from R (Dutch)
Description: The Aquo Standard is the Dutch Standard for the exchange of
data in water management. With *aquodom* (short for aquo domaintables)
it is easy to exploit the API (<https://www.aquo.nl/index.php/Hoofdpagina>) to download domaintables
of the Aquo Standard and use them in R.
Author: Johan van Tent [aut, cre]
Maintainer: Johan van Tent <tentvanjohan@hotmail.com>
Diff between aquodom versions 0.1.0 dated 2021-05-05 and 0.1.1 dated 2022-02-12
DESCRIPTION | 8 - LICENSE | 4 MD5 | 40 ++++----- NEWS.md | 21 +++-- R/dom.R | 12 +- R/dom_helpers.R | 2 R/dom_overzicht.R | 16 ++- R/dom_save.R | 148 ++++++++++++++++++------------------ R/zz_globals.R | 38 ++++----- R/zz_imports.R | 8 - R/zzz.R | 14 +-- README.md | 6 - man/dom.Rd | 92 +++++++++++----------- man/dom_guid.Rd | 48 +++++------ man/dom_kolommen.Rd | 48 +++++------ man/dom_save.Rd | 114 +++++++++++++-------------- man/is_domeintabel.Rd | 50 ++++++------ tests/testthat.R | 8 - tests/testthat/test-dom.R | 44 +++++----- tests/testthat/test-dom_helpers.R | 48 +++++------ tests/testthat/test-dom_overzicht.R | 4 21 files changed, 398 insertions(+), 375 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-11 0.0.101
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-17 3.0.0
2019-05-25 2.0.0
2017-03-12 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-09 0.2.1