Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.27 dated 2022-02-23 and 1.1.28 dated 2022-12-09
warbleR-1.1.27/warbleR/R/boxw_wrblr_int.R |only warbleR-1.1.27/warbleR/R/duration_wavs.R |only warbleR-1.1.27/warbleR/R/fade_env_wrblr_int.R |only warbleR-1.1.27/warbleR/R/filled_contour_color_wrblr_int.R |only warbleR-1.1.27/warbleR/R/filled_contour_wrblr_int.R |only warbleR-1.1.27/warbleR/R/fix_cntr_wrblr_int.R |only warbleR-1.1.27/warbleR/R/frd_plot_wrblr_int.R |only warbleR-1.1.27/warbleR/R/frd_wrblr_int.R |only warbleR-1.1.27/warbleR/R/img_wrblr_int.R |only warbleR-1.1.27/warbleR/R/pblapply_wrblr_int.R |only warbleR-1.1.27/warbleR/R/rectw_wrblr_int.R |only warbleR-1.1.27/warbleR/R/resample_est_waves.R |only warbleR-1.1.27/warbleR/R/specprop_wrblr_int.R |only warbleR-1.1.27/warbleR/R/spectro_wrblr_int.R |only warbleR-1.1.27/warbleR/R/spectro_wrblr_int2.R |only warbleR-1.1.27/warbleR/R/stft_wrblr_int.R |only warbleR-1.1.27/warbleR/R/wpd_feature_wrblr_int.R |only warbleR-1.1.28/warbleR/DESCRIPTION | 11 warbleR-1.1.28/warbleR/MD5 | 206 - warbleR-1.1.28/warbleR/NAMESPACE | 2 warbleR-1.1.28/warbleR/NEWS.md | 12 warbleR-1.1.28/warbleR/R/auto_detec.R | 67 warbleR-1.1.28/warbleR/R/by_element_est.R |only warbleR-1.1.28/warbleR/R/catalog.R | 122 warbleR-1.1.28/warbleR/R/catalog2pdf.R | 6 warbleR-1.1.28/warbleR/R/check_sels.R | 28 warbleR-1.1.28/warbleR/R/check_sound_files.R | 35 warbleR-1.1.28/warbleR/R/compare_methods.R | 2 warbleR-1.1.28/warbleR/R/consolidate.R | 15 warbleR-1.1.28/warbleR/R/cross_correlation.R | 53 warbleR-1.1.28/warbleR/R/cut_sels.R | 22 warbleR-1.1.28/warbleR/R/deprec_funs.R | 2 warbleR-1.1.28/warbleR/R/duration_sound_files.R |only warbleR-1.1.28/warbleR/R/filter_sels.R | 16 warbleR-1.1.28/warbleR/R/find_clipping.R | 12 warbleR-1.1.28/warbleR/R/find_peaks.R | 4 warbleR-1.1.28/warbleR/R/fix_wavs.R | 32 warbleR-1.1.28/warbleR/R/freq_DTW.R | 2 warbleR-1.1.28/warbleR/R/freq_range.R | 2 warbleR-1.1.28/warbleR/R/freq_ts.R | 9 warbleR-1.1.28/warbleR/R/full_spectrogram2pdf.R | 6 warbleR-1.1.28/warbleR/R/image_to_wave.R | 8 warbleR-1.1.28/warbleR/R/inflections.R | 4 warbleR-1.1.28/warbleR/R/info_sound_files.R | 11 warbleR-1.1.28/warbleR/R/internal_functions.R |only warbleR-1.1.28/warbleR/R/lbh_selec_table2-data.R | 2 warbleR-1.1.28/warbleR/R/mfcc_stats.R | 34 warbleR-1.1.28/warbleR/R/move_imgs.R | 6 warbleR-1.1.28/warbleR/R/mp32wav.R | 75 warbleR-1.1.28/warbleR/R/multi_DTW.R | 16 warbleR-1.1.28/warbleR/R/open_wd.R | 2 warbleR-1.1.28/warbleR/R/optimize_auto_detec.R | 14 warbleR-1.1.28/warbleR/R/overlapping_sels.R | 14 warbleR-1.1.28/warbleR/R/phylo_spectro.R | 24 warbleR-1.1.28/warbleR/R/plot_coordination.R | 28 warbleR-1.1.28/warbleR/R/query_xc.R | 12 warbleR-1.1.28/warbleR/R/read_sound_file.R | 26 warbleR-1.1.28/warbleR/R/read_wave.R | 2 warbleR-1.1.28/warbleR/R/remove_channels.R | 6 warbleR-1.1.28/warbleR/R/remove_silence.R | 377 +- warbleR-1.1.28/warbleR/R/rename_est_waves.R | 12 warbleR-1.1.28/warbleR/R/resample_est.R |only warbleR-1.1.28/warbleR/R/selection_table.R | 92 warbleR-1.1.28/warbleR/R/sig2noise.R | 20 warbleR-1.1.28/warbleR/R/simulate_songs.R | 468 ++- warbleR-1.1.28/warbleR/R/snr_spectrograms.R | 22 warbleR-1.1.28/warbleR/R/song_analysis.R | 28 warbleR-1.1.28/warbleR/R/sound_pressure_level.R | 203 + warbleR-1.1.28/warbleR/R/spectro_analysis.R | 48 warbleR-1.1.28/warbleR/R/spectrograms.R | 9 warbleR-1.1.28/warbleR/R/split_sound_files.R | 26 warbleR-1.1.28/warbleR/R/tailor_sels.R | 38 warbleR-1.1.28/warbleR/R/test_coordination.R | 26 warbleR-1.1.28/warbleR/R/track_freq_contour.R | 42 warbleR-1.1.28/warbleR/R/tweak_spectro.R | 6 warbleR-1.1.28/warbleR/R/warbleR_options.R | 6 warbleR-1.1.28/warbleR/R/wav_2_flac.R | 8 warbleR-1.1.28/warbleR/R/wpd_features.R | 18 warbleR-1.1.28/warbleR/R/xc_maps.R | 12 warbleR-1.1.28/warbleR/README.md | 106 warbleR-1.1.28/warbleR/inst/doc/Intro_to_warbleR.html | 1770 +++++++++++++ warbleR-1.1.28/warbleR/inst/doc/warbleR_workflow_01.html | 1701 ++++++++++++- warbleR-1.1.28/warbleR/inst/doc/warbleR_workflow_02.html | 1573 +++++++++++- warbleR-1.1.28/warbleR/inst/doc/warbleR_workflow_03.R | 4 warbleR-1.1.28/warbleR/inst/doc/warbleR_workflow_03.Rmd | 6 warbleR-1.1.28/warbleR/inst/doc/warbleR_workflow_03.html | 1772 +++++++++++++- warbleR-1.1.28/warbleR/man/by_element_est.Rd |only warbleR-1.1.28/warbleR/man/catalog.Rd | 13 warbleR-1.1.28/warbleR/man/cross_correlation.Rd | 2 warbleR-1.1.28/warbleR/man/duration_sound_files.Rd | 11 warbleR-1.1.28/warbleR/man/duration_wavs.Rd | 9 warbleR-1.1.28/warbleR/man/fix_wavs.Rd | 10 warbleR-1.1.28/warbleR/man/freq_DTW.Rd | 2 warbleR-1.1.28/warbleR/man/image_to_wave.Rd | 2 warbleR-1.1.28/warbleR/man/info_sound_files.Rd | 7 warbleR-1.1.28/warbleR/man/info_wavs.Rd | 8 warbleR-1.1.28/warbleR/man/lbh_selec_table2.Rd | 2 warbleR-1.1.28/warbleR/man/make.selection.table.Rd | 2 warbleR-1.1.28/warbleR/man/mp32wav.Rd | 2 warbleR-1.1.28/warbleR/man/phylo_spectro.Rd | 16 warbleR-1.1.28/warbleR/man/rename_est_waves.Rd | 5 warbleR-1.1.28/warbleR/man/resample_est.Rd |only warbleR-1.1.28/warbleR/man/resample_est_waves.Rd | 66 warbleR-1.1.28/warbleR/man/selection_table.Rd | 11 warbleR-1.1.28/warbleR/man/sim_songs.Rd | 3 warbleR-1.1.28/warbleR/man/simulate_songs.Rd | 51 warbleR-1.1.28/warbleR/man/sound_pressure_level.Rd | 37 warbleR-1.1.28/warbleR/man/specreator.Rd | 2 warbleR-1.1.28/warbleR/man/spectro_analysis.Rd | 46 warbleR-1.1.28/warbleR/man/spectrograms.Rd | 7 warbleR-1.1.28/warbleR/man/wav_dur.Rd | 9 warbleR-1.1.28/warbleR/man/wav_info.Rd | 8 warbleR-1.1.28/warbleR/man/wavdur.Rd | 9 warbleR-1.1.28/warbleR/vignettes/warbleR_sticker_v2.png |only warbleR-1.1.28/warbleR/vignettes/warbleR_sticker_v3.png |only warbleR-1.1.28/warbleR/vignettes/warbleR_sticker_v4.png |only warbleR-1.1.28/warbleR/vignettes/warbleR_workflow_03.Rmd | 6 117 files changed, 8092 insertions(+), 1597 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.1.5 dated 2022-10-08 and 3.1.6 dated 2022-12-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/custom-expectation.html | 2 +- inst/doc/skipping.html | 2 +- inst/doc/third-edition.html | 2 +- inst/include/testthat/vendor/catch.h | 24 +++++++----------------- 7 files changed, 23 insertions(+), 29 deletions(-)
Title: The Exterior Calculus
Description: Provides functionality for working with tensors, alternating
forms, wedge products, Stokes's theorem, and related concepts
from the exterior calculus. Uses 'disordR' discipline
(Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). The
canonical reference would be M. Spivak
(1965, ISBN:0-8053-9021-9) "Calculus on Manifolds". To cite
the package in publications please use Hankin (2022)
<doi:10.48550/ARXIV.2210.17008>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between stokes versions 1.1-3 dated 2022-06-14 and 1.1-6 dated 2022-12-09
stokes-1.1-3/stokes/man/cross.Rd |only stokes-1.1-6/stokes/DESCRIPTION | 19 stokes-1.1-6/stokes/MD5 | 142 ++--- stokes-1.1-6/stokes/NAMESPACE | 8 stokes-1.1-6/stokes/NEWS.md | 15 stokes-1.1-6/stokes/R/mult.R | 69 ++ stokes-1.1-6/stokes/R/ops.R | 4 stokes-1.1-6/stokes/README.md | 31 - stokes-1.1-6/stokes/build/partial.rdb |binary stokes-1.1-6/stokes/build/stokes.pdf |binary stokes-1.1-6/stokes/build/vignette.rds |binary stokes-1.1-6/stokes/data/dx.rda |binary stokes-1.1-6/stokes/inst/CITATION |only stokes-1.1-6/stokes/inst/doc/Alt.R | 9 stokes-1.1-6/stokes/inst/doc/Alt.Rmd | 68 +- stokes-1.1-6/stokes/inst/doc/Alt.html | 265 ++++++--- stokes-1.1-6/stokes/inst/doc/contract.R | 2 stokes-1.1-6/stokes/inst/doc/contract.Rmd | 4 stokes-1.1-6/stokes/inst/doc/contract.html | 169 +++--- stokes-1.1-6/stokes/inst/doc/dovs.R | 5 stokes-1.1-6/stokes/inst/doc/dovs.Rmd | 44 - stokes-1.1-6/stokes/inst/doc/dovs.html | 140 +++-- stokes-1.1-6/stokes/inst/doc/dx.Rmd | 2 stokes-1.1-6/stokes/inst/doc/dx.html | 114 ++-- stokes-1.1-6/stokes/inst/doc/hodge.R | 13 stokes-1.1-6/stokes/inst/doc/hodge.Rmd | 32 - stokes-1.1-6/stokes/inst/doc/hodge.html | 155 ++++- stokes-1.1-6/stokes/inst/doc/inner.R | 22 stokes-1.1-6/stokes/inst/doc/inner.Rmd | 85 ++- stokes-1.1-6/stokes/inst/doc/inner.html | 164 ++++- stokes-1.1-6/stokes/inst/doc/kinner.R | 3 stokes-1.1-6/stokes/inst/doc/kinner.Rmd | 5 stokes-1.1-6/stokes/inst/doc/kinner.pdf |binary stokes-1.1-6/stokes/inst/doc/stokes.R | 26 stokes-1.1-6/stokes/inst/doc/stokes.Rmd | 36 - stokes-1.1-6/stokes/inst/doc/stokes.html | 473 +++++++++-------- stokes-1.1-6/stokes/inst/doc/vector_cross_product.Rmd | 67 +- stokes-1.1-6/stokes/inst/doc/vector_cross_product.html | 152 +++-- stokes-1.1-6/stokes/inst/doc/volume.R |only stokes-1.1-6/stokes/inst/doc/volume.Rmd |only stokes-1.1-6/stokes/inst/doc/volume.html |only stokes-1.1-6/stokes/inst/doc/wedge.R | 2 stokes-1.1-6/stokes/inst/doc/wedge.Rmd | 36 - stokes-1.1-6/stokes/inst/doc/wedge.html | 145 +++-- stokes-1.1-6/stokes/inst/stokes.bib |only stokes-1.1-6/stokes/inst/stokes_arxiv.Rnw |only stokes-1.1-6/stokes/man/Alt.Rd | 8 stokes-1.1-6/stokes/man/Ops.Rd | 48 - stokes-1.1-6/stokes/man/dovs.Rd | 6 stokes-1.1-6/stokes/man/dx.Rd | 14 stokes-1.1-6/stokes/man/issmall.Rd | 6 stokes-1.1-6/stokes/man/ktensor.Rd | 4 stokes-1.1-6/stokes/man/print.Rd | 51 + stokes-1.1-6/stokes/man/scalar.Rd | 40 + stokes-1.1-6/stokes/man/stokes-package.Rd | 2 stokes-1.1-6/stokes/man/summary.Rd |only stokes-1.1-6/stokes/man/symbolic.Rd | 6 stokes-1.1-6/stokes/man/tensorprod.Rd |only stokes-1.1-6/stokes/man/transform.Rd | 2 stokes-1.1-6/stokes/man/volume.Rd | 5 stokes-1.1-6/stokes/man/zero.Rd | 7 stokes-1.1-6/stokes/tests/testthat/test_cross.R | 14 stokes-1.1-6/stokes/tests/testthat/test_misc.R | 3 stokes-1.1-6/stokes/tests/testthat/test_mult.R | 6 stokes-1.1-6/stokes/tests/testthat/test_print.R | 34 + stokes-1.1-6/stokes/tests/testthat/test_wedge.R | 4 stokes-1.1-6/stokes/vignettes/Alt.Rmd | 68 +- stokes-1.1-6/stokes/vignettes/contract.Rmd | 4 stokes-1.1-6/stokes/vignettes/dovs.Rmd | 44 - stokes-1.1-6/stokes/vignettes/dx.Rmd | 2 stokes-1.1-6/stokes/vignettes/hodge.Rmd | 32 - stokes-1.1-6/stokes/vignettes/inner.Rmd | 85 ++- stokes-1.1-6/stokes/vignettes/kinner.Rmd | 5 stokes-1.1-6/stokes/vignettes/stokes.Rmd | 36 - stokes-1.1-6/stokes/vignettes/vector_cross_product.Rmd | 67 +- stokes-1.1-6/stokes/vignettes/volume.Rmd |only stokes-1.1-6/stokes/vignettes/wedge.Rmd | 36 - 77 files changed, 2044 insertions(+), 1121 deletions(-)
Title: A Soil Survey Toolkit
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: Dylan Beaudette [cre, aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 1.11 dated 2022-10-04 and 1.12 dated 2022-12-09
sharpshootR-1.11/sharpshootR/R/sampleRasterStackByMU2.R |only sharpshootR-1.12/sharpshootR/DESCRIPTION | 8 +- sharpshootR-1.12/sharpshootR/MD5 | 23 ++---- sharpshootR-1.12/sharpshootR/NEWS.md | 3 sharpshootR-1.12/sharpshootR/R/dueling.dendrograms.R | 38 ---------- sharpshootR-1.12/sharpshootR/R/huePositionPlot.R | 2 sharpshootR-1.12/sharpshootR/R/plotWB.R | 2 sharpshootR-1.12/sharpshootR/R/sample.by.poly.R | 20 ++++- sharpshootR-1.12/sharpshootR/man/dueling.dendrograms.Rd | 38 ---------- sharpshootR-1.12/sharpshootR/man/huePositionPlot.Rd | 2 sharpshootR-1.12/sharpshootR/man/sampleRasterStackByMU.Rd | 17 ---- sharpshootR-1.12/sharpshootR/tests/testthat/Rplots.pdf |binary sharpshootR-1.12/sharpshootR/tests/testthat/test-plotProfileDendrogram.R | 4 - 13 files changed, 42 insertions(+), 115 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured by the negative log-likelihood under the null hypothesis that all selection probabilities are identical (B Bodinier et al (2021) <arXiv:2106.02521>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <b.bodinier@imperial.ac.uk>
Diff between sharp versions 1.2.0 dated 2022-08-15 and 1.2.1 dated 2022-12-09
sharp-1.2.0/sharp/man/CheckInputRegression.Rd |only sharp-1.2.0/sharp/man/PlotROC.Rd |only sharp-1.2.0/sharp/man/ROC.Rd |only sharp-1.2.0/sharp/man/Rates.Rd |only sharp-1.2.0/sharp/tests |only sharp-1.2.1/sharp/DESCRIPTION | 20 sharp-1.2.1/sharp/MD5 | 109 - sharp-1.2.1/sharp/NAMESPACE | 5 sharp-1.2.1/sharp/NEWS.md | 8 sharp-1.2.1/sharp/R/algorithms.R | 2 sharp-1.2.1/sharp/R/bi_selection.R | 16 sharp-1.2.1/sharp/R/calibration.R | 925 ++++++------ sharp-1.2.1/sharp/R/check.R | 211 +- sharp-1.2.1/sharp/R/dimensionality_reduction.R | 15 sharp-1.2.1/sharp/R/ensemble.R | 12 sharp-1.2.1/sharp/R/explanatory_performance.R | 493 ++---- sharp-1.2.1/sharp/R/graphical_model.R | 15 sharp-1.2.1/sharp/R/igraph_object.R | 6 sharp-1.2.1/sharp/R/lambda_grid.R | 17 sharp-1.2.1/sharp/R/parallelisation.R | 122 - sharp-1.2.1/sharp/R/penalised_models.R | 4 sharp-1.2.1/sharp/R/s3_classes.R | 155 +- sharp-1.2.1/sharp/R/selection_performance.R | 4 sharp-1.2.1/sharp/R/sharp-package.R | 38 sharp-1.2.1/sharp/R/variable_selection.R | 56 sharp-1.2.1/sharp/README.md | 471 ------ sharp-1.2.1/sharp/build/partial.rdb |binary sharp-1.2.1/sharp/inst/REFERENCES.bib | 49 sharp-1.2.1/sharp/inst/WORDLIST | 9 sharp-1.2.1/sharp/man/Adjacency.Rd | 3 sharp-1.2.1/sharp/man/AggregatedEffects.Rd | 4 sharp-1.2.1/sharp/man/BiSelection.Rd | 15 sharp-1.2.1/sharp/man/CalibrationCurve.Rd |only sharp-1.2.1/sharp/man/CalibrationPlot.Rd | 8 sharp-1.2.1/sharp/man/CheckDataRegression.Rd |only sharp-1.2.1/sharp/man/CheckParamRegression.Rd |only sharp-1.2.1/sharp/man/Combine.Rd | 6 sharp-1.2.1/sharp/man/EnsemblePredictions.Rd | 4 sharp-1.2.1/sharp/man/ExplanatoryPerformance.Rd | 39 sharp-1.2.1/sharp/man/GraphicalModel.Rd | 9 sharp-1.2.1/sharp/man/GroupPLS.Rd | 2 sharp-1.2.1/sharp/man/Incremental.Rd | 26 sharp-1.2.1/sharp/man/PLS.Rd | 2 sharp-1.2.1/sharp/man/PlotIncremental.Rd | 26 sharp-1.2.1/sharp/man/Refit.Rd | 38 sharp-1.2.1/sharp/man/SelectionAlgo.Rd | 2 sharp-1.2.1/sharp/man/SelectionPerformance.Rd | 2 sharp-1.2.1/sharp/man/SelectionPerformanceGraph.Rd | 2 sharp-1.2.1/sharp/man/SparseGroupPLS.Rd | 2 sharp-1.2.1/sharp/man/SparsePLS.Rd | 4 sharp-1.2.1/sharp/man/VariableSelection.Rd | 39 sharp-1.2.1/sharp/man/figures/README-unnamed-chunk-24-1.png |binary sharp-1.2.1/sharp/man/figures/README-unnamed-chunk-7-1.png |binary sharp-1.2.1/sharp/man/figures/logo.png |only sharp-1.2.1/sharp/man/plot.roc_band.Rd |only sharp-1.2.1/sharp/man/sharp-package.Rd | 38 56 files changed, 1424 insertions(+), 1609 deletions(-)
Title: Comprehensive GO Terms Comparison Between Species
Description: Supports the assessment of functional enrichment analyses obtained for several lists of genes and provides a workflow to analyze them between two species via weighted graphs. Methods are described in Sosa et al. (2023) <doi:10.1016/j.ygeno.2022.110528>.
Author: Chrystian Camilo Sosa [aut, cre, cph]
,
Diana Carolina Clavijo-Buritica [aut],
Mauricio Alberto Quimbaya [aut],
Maria Victoria Diaz [ctb],
Camila Riccio Rengifo [ctb],
Nicolas Lopez-Rozo [ctb],
Victor Hugo Garcia Merchan [aut, ctb],
Arlen James Mosqu [...truncated...]
Maintainer: Chrystian Camilo Sosa <ccsosaa@javerianacali.edu.co>
Diff between GOCompare versions 1.0.2 dated 2022-11-08 and 1.0.2.1 dated 2022-12-09
DESCRIPTION | 17 +- MD5 | 16 +- R/GOCompare-package.R | 4 R/compareGOspecies.R | 155 +++++++++++++++-------- R/graph_GOspecies.R | 88 ++++++------- R/graph_two_GOspecies.R | 314 +++++++++++++++++++++++------------------------ build/GOCompare.pdf |binary man/GOCompare-package.Rd | 4 man/compareGOspecies.Rd | 7 + 9 files changed, 335 insertions(+), 270 deletions(-)
Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams
using numerical optimization. An Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Diagrams may be fit with ellipses and circles via
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre] ,
A. Jonathan R. Godfrey [ctb],
Peter Gustafsson [ctb],
David H. Eberly [ctb] ,
Emanuel Huber [ctb] ,
Florian Prive [ctb]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between eulerr versions 6.1.1 dated 2021-09-06 and 7.0.0 dated 2022-12-09
eulerr-6.1.1/eulerr/src/areas.h |only eulerr-6.1.1/eulerr/src/label-repel.cpp |only eulerr-6.1.1/eulerr/src/solver.h |only eulerr-7.0.0/eulerr/DESCRIPTION | 12 eulerr-7.0.0/eulerr/MD5 | 118 ++-- eulerr-7.0.0/eulerr/NEWS.md | 17 eulerr-7.0.0/eulerr/R/RcppExports.R | 66 -- eulerr-7.0.0/eulerr/R/data.R | 3 eulerr-7.0.0/eulerr/R/euler.R | 70 +- eulerr-7.0.0/eulerr/R/fit_diagram.R | 172 +++-- eulerr-7.0.0/eulerr/R/plot.euler.R | 10 eulerr-7.0.0/eulerr/R/setup_grobs.R | 2 eulerr-7.0.0/eulerr/R/tag-grobs.R | 54 - eulerr-7.0.0/eulerr/R/utils.R | 93 +-- eulerr-7.0.0/eulerr/README.md | 66 +- eulerr-7.0.0/eulerr/build/partial.rdb |binary eulerr-7.0.0/eulerr/build/vignette.rds |binary eulerr-7.0.0/eulerr/inst/doc/gallery.R | 7 eulerr-7.0.0/eulerr/inst/doc/gallery.Rmd | 11 eulerr-7.0.0/eulerr/inst/doc/gallery.html | 404 +++----------- eulerr-7.0.0/eulerr/inst/doc/introduction.html | 375 +++--------- eulerr-7.0.0/eulerr/inst/doc/loss-functions.R |only eulerr-7.0.0/eulerr/inst/doc/loss-functions.Rmd |only eulerr-7.0.0/eulerr/inst/doc/loss-functions.html |only eulerr-7.0.0/eulerr/inst/doc/under-the-hood.html | 277 +-------- eulerr-7.0.0/eulerr/inst/doc/venn-diagrams.html | 271 +-------- eulerr-7.0.0/eulerr/inst/doc/visualization.html | 285 +-------- eulerr-7.0.0/eulerr/man/euler.Rd | 36 - eulerr-7.0.0/eulerr/man/eulerr-package.Rd | 7 eulerr-7.0.0/eulerr/man/pain.Rd | 3 eulerr-7.0.0/eulerr/man/setup_grobs.Rd | 11 eulerr-7.0.0/eulerr/man/venn.Rd | 12 eulerr-7.0.0/eulerr/src/Makevars | 2 eulerr-7.0.0/eulerr/src/Makevars.win | 2 eulerr-7.0.0/eulerr/src/RcppExports.cpp | 32 - eulerr-7.0.0/eulerr/src/compute-areas.cpp |only eulerr-7.0.0/eulerr/src/compute-areas.h |only eulerr-7.0.0/eulerr/src/conic.cpp |only eulerr-7.0.0/eulerr/src/conic.h | 44 - eulerr-7.0.0/eulerr/src/constants.h | 7 eulerr-7.0.0/eulerr/src/ellipse.cpp |only eulerr-7.0.0/eulerr/src/ellipse.h | 30 - eulerr-7.0.0/eulerr/src/geometry.h | 38 - eulerr-7.0.0/eulerr/src/helpers.cpp |only eulerr-7.0.0/eulerr/src/helpers.h | 127 +--- eulerr-7.0.0/eulerr/src/intersections.cpp |only eulerr-7.0.0/eulerr/src/intersections.h | 125 ---- eulerr-7.0.0/eulerr/src/loss.cpp |only eulerr-7.0.0/eulerr/src/loss.h |only eulerr-7.0.0/eulerr/src/optim_final.cpp | 75 +- eulerr-7.0.0/eulerr/src/optim_init.cpp | 44 - eulerr-7.0.0/eulerr/src/point.cpp |only eulerr-7.0.0/eulerr/src/point.h | 38 - eulerr-7.0.0/eulerr/src/solve_cubic.cpp |only eulerr-7.0.0/eulerr/src/solve_cubic.h |only eulerr-7.0.0/eulerr/src/transformations.h | 38 - eulerr-7.0.0/eulerr/src/utils.cpp | 41 - eulerr-7.0.0/eulerr/tests/testthat/test-accuracy.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-assertions.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-geometry.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-inputs.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-methods.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-montecarlo.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-plotting.R | 16 eulerr-7.0.0/eulerr/tests/testthat/test-printing.R | 2 eulerr-7.0.0/eulerr/tests/testthat/test-reproducibility.R | 212 +++++-- eulerr-7.0.0/eulerr/tests/testthat/test-utils.R | 2 eulerr-7.0.0/eulerr/vignettes/gallery.Rmd | 11 eulerr-7.0.0/eulerr/vignettes/loss-functions.Rmd |only 69 files changed, 1091 insertions(+), 2189 deletions(-)
Title: Providing Fast and Flexible Functions for Distance Correlation
Analysis
Description: Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <arXiv:1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Author: Dominic Edelmann [aut, cre],
Jochen Fiedler [aut]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Diff between dcortools versions 0.1.5 dated 2022-12-07 and 0.1.6 dated 2022-12-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ build/partial.rdb |binary inst/include/dcortools_types.h | 3 +++ 5 files changed, 19 insertions(+), 7 deletions(-)
Title: Read 'IPUMS' Extract Files
Description: An easy way to import census, survey and geographic data provided by 'IPUMS'
into R plus tools to help use the associated metadata to make analysis easier. 'IPUMS'
data describing 1.4 billion individuals drawn from over 750 censuses and surveys is
available free of charge from our website <https://www.ipums.org>.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Finn Roberts [ctb],
Dan Ehrlich [ctb],
Renae Rodgers [ctb],
Minnesota Population Center [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between ipumsr versions 0.5.1 dated 2022-09-30 and 0.5.2 dated 2022-12-09
DESCRIPTION | 6 MD5 | 108 - NEWS.md | 265 +-- R/api.R | 149 - R/bind_rows.r | 114 - R/callbacks.r | 376 ++-- R/compat_friendly_type.R | 118 - R/ddi_print.r | 52 R/ddi_read.r | 1132 +++++++------- R/examples.r | 70 R/import.r | 202 +- R/ipums_info.r | 442 ++--- R/ipumsr.r | 6 R/list_files.r | 154 - R/micro_read_chunked.r | 490 +++--- R/micro_read_helpers.r | 272 +-- R/micro_read_yield.r | 454 ++--- R/proj_config.r | 204 +- R/shape_join.r | 688 ++++---- R/shape_read.r | 690 ++++---- R/web_url.r | 280 +-- build/vignette.rds |binary inst/doc/ipums-api.R | 308 +-- inst/doc/ipums-api.html | 1327 ++++++++--------- inst/doc/ipums-bigdata.R | 536 +++--- inst/doc/ipums-bigdata.html | 2707 +++++++++++++++++------------------ inst/doc/ipums-cps.R | 406 ++--- inst/doc/ipums-cps.Rmd | 704 ++++----- inst/doc/ipums-cps.html | 1511 +++++++++---------- inst/doc/ipums-geography.R | 480 +++--- inst/doc/ipums-geography.Rmd | 1102 +++++++------- inst/doc/ipums-geography.html | 1753 +++++++++++----------- inst/doc/ipums-nhgis.R | 322 ++-- inst/doc/ipums-nhgis.Rmd | 642 ++++---- inst/doc/ipums-nhgis.html | 1487 +++++++++---------- inst/doc/ipums-terra.R | 244 +-- inst/doc/ipums-terra.Rmd | 642 ++++---- inst/doc/ipums-terra.html | 1272 +++++++--------- inst/doc/ipums.R | 256 +-- inst/doc/ipums.html | 1509 +++++++++---------- inst/doc/value-labels.R | 256 +-- inst/doc/value-labels.Rmd | 680 ++++---- inst/doc/value-labels.html | 1692 ++++++++++----------- man/add_to_extract.Rd | 5 man/ipumsr-package.Rd | 2 man/remove_from_extract.Rd | 19 tests/fixtures/ready-cps-extract.yml | 90 - tests/fixtures/ready-usa-extract.yml | 90 - tests/testthat/test_api.R | 50 tests/testthat/test_viewer.r | 96 - vignettes/ipums-cps.Rmd | 704 ++++----- vignettes/ipums-geography.Rmd | 1102 +++++++------- vignettes/ipums-nhgis.Rmd | 642 ++++---- vignettes/ipums-terra.Rmd | 642 ++++---- vignettes/value-labels.Rmd | 680 ++++---- 55 files changed, 15063 insertions(+), 15167 deletions(-)
Title: Lightweight Well-Known Geometry Parsing
Description: Provides a minimal R and C++ API for parsing
well-known binary and well-known text representation of
geometries to and from R-native formats.
Well-known binary is compact
and fast to parse; well-known text is human-readable
and is useful for writing tests. These formats are
useful in R only if the information they contain can be
accessed in R, for which high-performance functions
are provided here.
Author: Dewey Dunnington [aut, cre] ,
Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between wk versions 0.7.0 dated 2022-10-12 and 0.7.1 dated 2022-12-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/wk-vctr.R | 2 +- man/wk-package.Rd | 2 +- src/void-handler.c | 10 +++------- tests/testthat/Rplots.pdf |binary 7 files changed, 21 insertions(+), 20 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.2.3 dated 2022-09-16 and 1.3 dated 2022-12-09
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 6 ++++++ R/acs.R | 32 ++++++++++++-------------------- R/census.R | 15 +++++---------- R/estimates.R | 11 ++--------- R/flows.R | 8 ++------ R/helpers.R | 23 +++++++++++++++++++++++ R/load_data.R | 2 +- R/pums.R | 14 +++----------- R/search_variables.R | 13 ++++++++----- R/utils.R | 4 ++-- R/zzz.r | 2 +- data/pums_variables.rda |binary man/get_acs.Rd | 10 +++------- man/get_decennial.Rd | 5 +++-- man/get_pums.Rd | 2 +- man/load_variables.Rd | 13 +++++++------ man/pums_variables.Rd | 2 +- 19 files changed, 103 insertions(+), 105 deletions(-)
Title: Regression Models with Break-Points / Change-Points (with
Possibly Random Effects) Estimation
Description: Given a regression model, segmented `updates' it by adding one or more segmented
(i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in
in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 1.6-1 dated 2022-11-08 and 1.6-2 dated 2022-12-09
DESCRIPTION | 8 MD5 | 14 NEWS | 785 +++++++++++++++++++++++------------------------ R/selgmented.r | 368 +++++++++++++--------- R/slope.R | 32 + man/segmented-package.Rd | 162 ++++----- man/selgmented.Rd | 220 +++++++------ man/slope.Rd | 2 8 files changed, 872 insertions(+), 719 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis functions
of the geographical information system (GIS) 'SAGA' (System for Automated
Geoscientific Analyses) from within R by running the command line version of
SAGA. This package furthermore provides several R functions for handling ASCII
grids, including a flexible framework for applying local functions (including
predict methods of fitted models) and focal functions to multiple grids. SAGA
GIS is available under GPL-2 / LGPL-2 licences from
<https://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] ,
Donovan Bangs [aut],
Marc Becker [aut],
Patrick Schratz [ctb] ,
Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 1.3.0 dated 2018-11-12 and 1.4.0 dated 2022-12-09
DESCRIPTION | 20 - MD5 | 114 +++---- R/RSAGA-core.R | 29 - R/RSAGA-modules.R | 421 +++++---------------------- R/RSAGA-package.R | 62 ++-- R/gridtools.R | 14 R/landslides.R | 11 build/vignette.rds |binary inst/doc/RSAGA.R | 36 +- inst/doc/RSAGA.Rmd | 16 - inst/doc/RSAGA.html | 501 +++++++++++++++++++++++---------- man/RSAGA-package.Rd | 4 man/create.variable.name.Rd | 3 man/focal.function.Rd | 47 ++- man/grid.predict.Rd | 16 - man/grid.to.xyz.Rd | 3 man/landslides.Rd | 9 man/match.arg.ext.Rd | 10 man/multi.focal.function.Rd | 72 +++- man/pick.from.points.Rd | 101 +++++- man/read.ascii.grid.Rd | 60 ++- man/rsaga.add.grid.values.to.points.Rd | 12 man/rsaga.close.gaps.Rd | 2 man/rsaga.contour.Rd | 12 man/rsaga.env.Rd | 29 + man/rsaga.esri.to.sgrd.Rd | 8 man/rsaga.esri.wrapper.Rd | 19 - man/rsaga.fill.sinks.Rd | 11 man/rsaga.filter.gauss.Rd | 10 man/rsaga.filter.simple.Rd | 12 man/rsaga.geoprocessor.Rd | 28 + man/rsaga.get.modules.Rd | 19 - man/rsaga.get.modules.path.Rd | 3 man/rsaga.grid.calculus.Rd | 12 man/rsaga.grid.to.points.Rd | 15 man/rsaga.hillshade.Rd | 11 man/rsaga.html.help.Rd | 9 man/rsaga.import.gdal.Rd | 214 -------------- man/rsaga.insolation.Rd | 36 +- man/rsaga.intersect.polygons.Rd | 65 +--- man/rsaga.inverse.distance.Rd | 56 ++- man/rsaga.local.morphometry.Rd | 58 +++ man/rsaga.parallel.processing.Rd | 22 + man/rsaga.pisr.Rd | 51 ++- man/rsaga.pisr2.Rd | 44 ++ man/rsaga.set.env.Rd | 15 man/rsaga.sgrd.to.esri.Rd | 11 man/rsaga.slope.asp.curv.Rd | 31 +- man/rsaga.solar.radiation.Rd | 27 + man/rsaga.target.Rd | 12 man/rsaga.topdown.processing.Rd | 27 + man/rsaga.union.polygons.Rd | 58 +-- man/rsaga.wetness.index.Rd | 21 + man/wind.shelter.Rd | 4 tests/testthat.R | 1 tests/testthat/test-core.R | 75 ++++ tests/testthat/test-modules.R | 179 ++++++++--- vignettes/RSAGA.Rmd | 16 - 58 files changed, 1550 insertions(+), 1234 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre],
Giulio Costantini [aut],
Jonas Haslbeck [aut],
Adela Isvoranu [aut],
Angelique O. J. Cramer [ctb],
Lourens J. Waldorp [ctb],
Verena D. Schmittmann [ctb],
Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.9.2 dated 2022-03-04 and 1.9.3 dated 2022-12-09
COPYRIGHTS | 20 DESCRIPTION | 8 MD5 | 188 NAMESPACE | 292 - NEWS | 1213 +++-- R/00PolyShapes.R | 426 +- R/Cent2EdgeNode.R | 180 R/DrawArrow.R | 162 R/EBICgraph.R | 72 R/FDRnetwork.R | 40 R/Fade.R | 44 R/IntInNode.r | 184 R/PLOT.R | 2640 ++++++------- R/RcppExports.R | 14 R/SelfLoop.R | 176 R/VARglm.R | 128 R/XKCD.R | 20 R/addTitle.R | 8 R/addTrans.R | 40 R/as_ggraph.R | 124 R/averageLayout.R | 80 R/centralityFunctions.R | 712 +-- R/centralityPlot.R | 210 - R/centralityTable.R | 240 - R/clusteringPlot.R | 220 - R/clusteringTable.R | 410 +- R/cor_auto.R | 272 - R/drawEdge.R | 184 R/drawNode.R | 584 +- R/fixnames.R | 16 R/flow.R | 246 - R/getArgs.R | 22 R/getWmat.R | 474 +- R/ggmFit.R | 572 +- R/ggmModSelect.R | 354 - R/glasso_methods.R | 482 +- R/glasso_tests.R | 434 +- R/igraphConversion.R | 106 R/isColor.R | 10 R/layout.R | 182 R/logGaus.R | 66 R/makeBW.R | 122 R/mapusr2in.R | 134 R/mixCols.R | 22 R/mixGraphs.R | 122 R/mutualInformation.R | 112 R/palettes.R | 76 R/pathways.R | 108 R/pie2.R | 138 R/printplotsummary.R | 26 R/qgraph.R | 6268 +++++++++++++++---------------- R/qgraph.rack.R | 254 - R/qgraphAnnotate.R | 154 R/qgraphD3.R | 206 - R/qgraphGUI.R | 472 +- R/qgraph_growth.R | 614 +-- R/qgraph_loadings.R | 642 +-- R/qgraph_mixed.R | 148 R/scale2.R | 14 R/smallworldIndex.R | 82 R/toJSONarray.R | 40 R/vein.R | 290 - README | 8 inst/CITATION | 44 man/CentAndClusfuns.Rd | 142 man/EBICglasso.Rd | 234 - man/FDRnetwork.Rd | 176 man/VARglm.Rd | 82 man/as.igraph.Rd | 56 man/averageLayout.Rd | 70 man/big5.Rd | 46 man/big5groups.Rd | 50 man/centrality.Rd | 152 man/centrality_auto.Rd | 122 man/clustcoef_auto.Rd | 182 man/cor_auto.Rd | 156 man/flow.Rd | 134 man/getWmat.Rd | 96 man/ggmFit.Rd | 138 man/ggmModSelect.Rd | 198 man/makeBW.Rd | 106 man/mat2vec.Rd | 54 man/mutualInformation.Rd | 62 man/pathways.Rd | 118 man/plot.qgraph.Rd | 64 man/print.qgraph.Rd | 58 man/qgraph.Rd | 1202 ++--- man/qgraph.animate.Rd | 328 - man/qgraph.layout.fruchtermanreingold.Rd | 208 - man/qgraphMixed.Rd | 104 man/qgraph_loadings.Rd | 122 man/smallworldIndex.Rd | 50 man/smallworldness.Rd | 166 man/summary.qgraph.Rd | 58 man/wi2net.Rd | 54 95 files changed, 13379 insertions(+), 13360 deletions(-)
Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Author: Herve Perdry [cre, aut, cph],
Claire Dandine-Roulland [aut, cph],
Deepak Bandyopadhyay [cph] ,
Lutz Kettner [cph]
Maintainer: Herve Perdry <herve.perdry@universite-paris-saclay.fr>
Diff between gaston versions 1.5.7 dated 2020-09-24 and 1.5.8 dated 2022-12-09
gaston-1.5.7/gaston/NEWS |only gaston-1.5.8/gaston/DESCRIPTION | 12 ++-- gaston-1.5.8/gaston/MD5 | 37 +++++++------ gaston-1.5.8/gaston/NAMESPACE | 1 gaston-1.5.8/gaston/NEWS.md |only gaston-1.5.8/gaston/R/bm_stats.r | 4 - gaston-1.5.8/gaston/R/ld_clump.r |only gaston-1.5.8/gaston/R/ld_thin.r | 3 - gaston-1.5.8/gaston/R/snp_duplicated.r | 5 + gaston-1.5.8/gaston/R/snp_match.r | 6 +- gaston-1.5.8/gaston/R/snp_rm_duplicates.r | 2 gaston-1.5.8/gaston/TODO | 27 +++++++++ gaston-1.5.8/gaston/build/vignette.rds |binary gaston-1.5.8/gaston/inst/doc/gaston-faq.pdf |binary gaston-1.5.8/gaston/inst/doc/gaston.pdf |binary gaston-1.5.8/gaston/inst/include/gaston/ai-reml-nk-covar.h | 2 gaston-1.5.8/gaston/inst/include/gaston/ai-reml-nk.h | 1 gaston-1.5.8/gaston/inst/include/gaston/m4_ld.h | 1 gaston-1.5.8/gaston/man/LD.clump.Rd |only gaston-1.5.8/gaston/src/export-aireml-nk.cpp | 1 gaston-1.5.8/gaston/src/gaston_init.c | 2 gaston-1.5.8/gaston/src/ld_clump.cpp |only 22 files changed, 71 insertions(+), 33 deletions(-)
Title: Elastic Analysis of Sparse, Dense and Irregular Curves
Description: Provides functions to align curves and to compute mean curves based on the
elastic distance defined in the square-root-velocity framework. For more details on
this framework see Srivastava and Klassen (2016, <doi:10.1007/978-1-4939-4020-2>).
For more theoretical details on our methods and algorithms see
Steyer et al. (2021, <arXiv:2104.11039>).
Author: Lisa Steyer <lisa.steyer@hu-berlin.de>
Maintainer: Lisa Steyer <lisa.steyer@hu-berlin.de>
Diff between elasdics versions 0.2.0 dated 2022-04-08 and 1.1.1 dated 2022-12-09
DESCRIPTION | 8 +-- MD5 | 66 +++++++++++++++------------ NAMESPACE | 6 ++ R/align_curves.R | 33 ++++++------- R/compute_elastic_mean.R | 6 +- R/find_optimal_t.R | 45 +++++++++++++----- R/find_optimal_t_discrete.R | 14 ++--- R/find_optimal_t_discrete_closed.R | 14 ++--- R/fit_elastic_regression.R |only R/fit_mean.R | 2 R/fit_mean_closed.R | 3 - R/get_srv_from_points.R | 26 +++++----- R/helper_fun_closed_reg.R |only R/helper_functions.R | 4 - R/plot_aligned_curves.R | 4 - R/plot_elastic_mean.R | 3 - R/plot_elastic_reg_model.R |only R/predict_elastic_reg_model.R |only man/align_curves.Rd | 14 ++--- man/compute_elastic_mean.Rd | 6 +- man/find_optimal_t.Rd | 4 - man/find_optimal_t_discrete.Rd | 4 - man/find_optimal_t_discrete_closed.Rd | 4 - man/fit_elastic_regression.Rd |only man/fit_mean.Rd | 2 man/fit_mean_closed.Rd | 2 man/get_srv_from_points.Rd | 24 ++++----- man/optimise_one_coord_analytic.Rd | 6 +- man/optimise_one_coord_analytic_closed.Rd | 6 +- man/plot.aligned_curves.Rd | 4 - man/plot.elastic_reg_model.Rd |only man/predict.elastic_reg_model.Rd |only man/project_curve_on_closed.Rd |only man/srvf_to_curve.Rd | 6 +- tests/testthat/Rplots.pdf |binary tests/testthat/test_align_curves.R | 6 +- tests/testthat/test_find_optimal_t.R | 4 + tests/testthat/test_fit_elastic_regression.R |only tests/testthat/test_plot_elastic_reg_model.R |only 39 files changed, 182 insertions(+), 144 deletions(-)
Title: Violin Plot
Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Author: Daniel Adler [aut, cph],
S. Thomas Kelly [aut, cre],
Tom M. Elliott [aut, ctb],
Jordan Adamson [aut, ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between vioplot versions 0.3.7 dated 2021-07-27 and 0.4.0 dated 2022-12-09
vioplot-0.3.7/vioplot/tests/testthat/Rplots.pdf |only vioplot-0.4.0/vioplot/DESCRIPTION | 16 - vioplot-0.4.0/vioplot/MD5 | 43 +++- vioplot-0.4.0/vioplot/NAMESPACE | 6 vioplot-0.4.0/vioplot/NEWS.md | 27 ++ vioplot-0.4.0/vioplot/R/histoplot.R |only vioplot-0.4.0/vioplot/R/vioplot.R | 30 ++- vioplot-0.4.0/vioplot/build/vignette.rds |binary vioplot-0.4.0/vioplot/inst/CITATION | 8 vioplot-0.4.0/vioplot/inst/COPYRIGHT | 62 +++--- vioplot-0.4.0/vioplot/inst/doc/histogram_customisation.R |only vioplot-0.4.0/vioplot/inst/doc/histogram_customisation.Rmd |only vioplot-0.4.0/vioplot/inst/doc/histogram_customisation.html |only vioplot-0.4.0/vioplot/inst/doc/histogram_formulae.R |only vioplot-0.4.0/vioplot/inst/doc/histogram_formulae.Rmd |only vioplot-0.4.0/vioplot/inst/doc/histogram_formulae.html |only vioplot-0.4.0/vioplot/inst/doc/overlaying_annotations.R |only vioplot-0.4.0/vioplot/inst/doc/overlaying_annotations.Rmd |only vioplot-0.4.0/vioplot/inst/doc/overlaying_annotations.html |only vioplot-0.4.0/vioplot/inst/doc/violin_area.html | 91 ++++------ vioplot-0.4.0/vioplot/inst/doc/violin_customisation.html | 5 vioplot-0.4.0/vioplot/inst/doc/violin_formulae.html | 5 vioplot-0.4.0/vioplot/inst/doc/violin_split.html | 73 +++++--- vioplot-0.4.0/vioplot/inst/doc/violin_ylog.html | 23 +- vioplot-0.4.0/vioplot/man/histoplot.Rd |only vioplot-0.4.0/vioplot/man/vioplot.Rd | 2 vioplot-0.4.0/vioplot/tests/testthat/test_histoplot_customisation.R |only vioplot-0.4.0/vioplot/tests/testthat/test_histoplot_formula.R |only vioplot-0.4.0/vioplot/vignettes/histogram_customisation.Rmd |only vioplot-0.4.0/vioplot/vignettes/histogram_formulae.Rmd |only vioplot-0.4.0/vioplot/vignettes/overlaying_annotations.Rmd |only 31 files changed, 239 insertions(+), 152 deletions(-)
Title: Perform Inference on Algorithm-Agnostic Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).
Author: Brian D. Williamson [aut, cre]
,
Jean Feng [ctb],
Noah Simon [ths] ,
Marco Carone [ths]
Maintainer: Brian D. Williamson <brian.d.williamson@kp.org>
Diff between vimp versions 2.3.0 dated 2022-11-14 and 2.3.1 dated 2022-12-09
DESCRIPTION | 6 MD5 | 112 +++--- NEWS.md | 10 R/cv_vim.R | 134 +++++-- R/est_predictiveness_cv.R | 341 +++++++++--------- R/measure_accuracy.R | 2 R/measure_anova.R | 2 R/measure_auc.R | 2 R/measure_deviance.R | 2 R/measure_r_squared.R | 2 R/sp_vim.R | 133 +++++-- R/utils.R | 37 -- R/vim.R | 162 ++++++-- R/vimp_accuracy.R | 116 +++--- R/vimp_anova.R | 158 ++++---- R/vimp_auc.R | 4 R/vimp_ci.R | 4 R/vimp_deviance.R | 4 R/vimp_rsquared.R | 4 build/partial.rdb |binary inst/doc/introduction-to-vimp.R | 8 inst/doc/introduction-to-vimp.Rmd | 8 inst/doc/introduction-to-vimp.html | 313 ++++++++--------- inst/doc/ipcw-vim.html | 70 ++- inst/doc/precomputed-regressions.R | 82 ++-- inst/doc/precomputed-regressions.Rmd | 470 +++++++++++++------------- inst/doc/precomputed-regressions.html | 198 +++++----- inst/doc/types-of-vims.html | 56 +-- man/bootstrap_se.Rd | 8 man/cv_vim.Rd | 36 + man/est_predictiveness_cv.Rd | 44 +- man/estimate_nuisances.Rd | 2 man/measure_accuracy.Rd | 2 man/measure_anova.Rd | 2 man/measure_auc.Rd | 2 man/measure_deviance.Rd | 2 man/measure_r_squared.Rd | 2 man/sp_vim.Rd | 17 man/vim.Rd | 51 +- man/vimp_accuracy.Rd | 23 - man/vimp_anova.Rd | 16 man/vimp_auc.Rd | 23 - man/vimp_deviance.Rd | 23 - man/vimp_regression.Rd | 14 man/vimp_rsquared.Rd | 23 - tests/testthat/test-average_vim.R | 2 tests/testthat/test-avg_value.R | 18 tests/testthat/test-binary_outcomes.R | 55 +-- tests/testthat/test-bootstrap.R | 2 tests/testthat/test-continuous_outcomes.R | 2 tests/testthat/test-cv_vim.R | 167 +++++---- tests/testthat/test-ipcw.R | 17 tests/testthat/test-merge_vim.R | 166 ++++----- tests/testthat/test-predictiveness_measures.R | 10 tests/testthat/test-vim.R | 255 +++++++------- vignettes/introduction-to-vimp.Rmd | 8 vignettes/precomputed-regressions.Rmd | 470 +++++++++++++------------- 57 files changed, 2163 insertions(+), 1739 deletions(-)
Title: Evolutionary Minimizer for R
Description: A C++ implementation of the following evolutionary
algorithms: Bat Algorithm (Yang, 2010 <doi:10.1007/978-3-642-12538-6_6>),
Cuckoo Search (Yang, 2009 <doi:10.1109/nabic.2009.5393690>),
Genetic Algorithms (Holland, 1992, ISBN:978-0262581110),
Gravitational Search Algorithm (Rashedi et al., 2009 <doi:10.1016/j.ins.2009.03.004>),
Grey Wolf Optimization (Mirjalili et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>),
Harmony Search (Geem et al., 2001 <doi:10.1177/003754970107600201>),
Improved Harmony Search (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>),
Moth-flame Optimization (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>),
Particle Swarm Optimization (Kennedy et al., 2001 ISBN:1558605959),
Simulated Annealing (Kirkpatrick et al., 1983 <doi:10.1126/science.220.4598.671>),
Whale Optimization Algorithm (Mirjalili and Lewis, 2016 <doi:10.1016/j.advengsoft.2016.01.008>).
'EmiR' can be used not only for unconstrained optimiz [...truncated...]
Author: Davide Pagano [aut],
Lorenzo Sostero [aut, cre]
Maintainer: Lorenzo Sostero <l.sostero@studenti.unibs.it>
Diff between EmiR versions 1.0.3 dated 2022-04-21 and 1.0.4 dated 2022-12-09
EmiR-1.0.3/EmiR/R/AAA_CREATE_MAKEVARS.R |only EmiR-1.0.3/EmiR/R/catch-routine-registration.R |only EmiR-1.0.3/EmiR/src/test-example.cpp |only EmiR-1.0.3/EmiR/src/test-runner.cpp |only EmiR-1.0.3/EmiR/tests |only EmiR-1.0.4/EmiR/DESCRIPTION | 14 EmiR-1.0.4/EmiR/MD5 | 138 ++-- EmiR-1.0.4/EmiR/NAMESPACE | 84 +- EmiR-1.0.4/EmiR/R/ALGO__ABC.R | 146 ++-- EmiR-1.0.4/EmiR/R/ALGO__BAT.R | 198 +++--- EmiR-1.0.4/EmiR/R/ALGO__CS.R | 150 ++-- EmiR-1.0.4/EmiR/R/ALGO__GA.R | 154 ++--- EmiR-1.0.4/EmiR/R/ALGO__GSA.R | 150 ++-- EmiR-1.0.4/EmiR/R/ALGO__GWO.R | 122 +-- EmiR-1.0.4/EmiR/R/ALGO__HS.R | 164 ++--- EmiR-1.0.4/EmiR/R/ALGO__IHS.R | 184 +++--- EmiR-1.0.4/EmiR/R/ALGO__MFO.R | 122 +-- EmiR-1.0.4/EmiR/R/ALGO__PS.R | 188 +++--- EmiR-1.0.4/EmiR/R/ALGO__SA.R | 198 +++--- EmiR-1.0.4/EmiR/R/ALGO__WOA.R | 122 +-- EmiR-1.0.4/EmiR/R/CLASS__ConstrainedFunction.R | 62 +- EmiR-1.0.4/EmiR/R/CLASS__Constraint.R | 62 +- EmiR-1.0.4/EmiR/R/CLASS__MinimizationResult.R | 206 +++--- EmiR-1.0.4/EmiR/R/CLASS__MinimizerOpts.R | 236 +++---- EmiR-1.0.4/EmiR/R/CLASS__Parameter.R | 94 +-- EmiR-1.0.4/EmiR/R/CONFIG_ALGO.R | 176 ++--- EmiR-1.0.4/EmiR/R/CONFIG__ABC.R | 106 +-- EmiR-1.0.4/EmiR/R/CONFIG__BAT.R | 130 ++-- EmiR-1.0.4/EmiR/R/CONFIG__CS.R | 106 +-- EmiR-1.0.4/EmiR/R/CONFIG__GA.R | 106 +-- EmiR-1.0.4/EmiR/R/CONFIG__GSA.R | 106 +-- EmiR-1.0.4/EmiR/R/CONFIG__GWO.R | 94 +-- EmiR-1.0.4/EmiR/R/CONFIG__HS.R | 112 +-- EmiR-1.0.4/EmiR/R/CONFIG__IHS.R | 124 ++-- EmiR-1.0.4/EmiR/R/CONFIG__MFO.R | 94 +-- EmiR-1.0.4/EmiR/R/CONFIG__PS.R | 124 ++-- EmiR-1.0.4/EmiR/R/CONFIG__SA.R | 136 ++-- EmiR-1.0.4/EmiR/R/CONFIG__WOA.R | 94 +-- EmiR-1.0.4/EmiR/R/CheckOptions.R | 366 +++++------ EmiR-1.0.4/EmiR/R/DATASETS.R | 50 - EmiR-1.0.4/EmiR/R/EmiR.R | 12 EmiR-1.0.4/EmiR/R/FUNC__Ackley.R | 98 +-- EmiR-1.0.4/EmiR/R/FUNC__Bohachevsky.R | 86 +- EmiR-1.0.4/EmiR/R/FUNC__Colville.R | 102 +-- EmiR-1.0.4/EmiR/R/FUNC__Freudenstein.R | 86 +- EmiR-1.0.4/EmiR/R/FUNC__Griewank.R | 88 +- EmiR-1.0.4/EmiR/R/FUNC__Miele.R | 90 +- EmiR-1.0.4/EmiR/R/FUNC__Rastrigin.R | 80 +- EmiR-1.0.4/EmiR/R/FUNC__Rosenbrock.R | 84 +- EmiR-1.0.4/EmiR/R/FUNC__Schwefel.R | 84 +- EmiR-1.0.4/EmiR/R/FUNC__Styblinski-Tang.R | 86 +- EmiR-1.0.4/EmiR/R/INTERFACE__ConstrainedFunction.R | 56 - EmiR-1.0.4/EmiR/R/INTERFACE__Constraint.R | 68 +- EmiR-1.0.4/EmiR/R/INTERFACE__Parameter.R | 144 ++-- EmiR-1.0.4/EmiR/R/METHOD__Minimize.R | 296 ++++----- EmiR-1.0.4/EmiR/R/METHOD__Plot_history.R | 422 ++++++------- EmiR-1.0.4/EmiR/R/METHOD__Population.R | 72 +- EmiR-1.0.4/EmiR/R/RcppExports.R | 102 +-- EmiR-1.0.4/EmiR/README.md | 93 +-- EmiR-1.0.4/EmiR/build/EmiR.pdf |binary EmiR-1.0.4/EmiR/build/partial.rdb |binary EmiR-1.0.4/EmiR/demo/00Index | 6 EmiR-1.0.4/EmiR/demo/G06_constr_benchmark.R | 82 +- EmiR-1.0.4/EmiR/demo/Integer_unconst.R | 80 +- EmiR-1.0.4/EmiR/demo/Pressure_vessel_design_constr.R | 106 +-- EmiR-1.0.4/EmiR/inst/REFERENCES.bib | 580 +++++++++---------- EmiR-1.0.4/EmiR/src/Makevars | 4 EmiR-1.0.4/EmiR/src/RcppExports.cpp | 3 68 files changed, 3857 insertions(+), 3871 deletions(-)
Title: Download Stats of R Packages
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages.
Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>.
'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between dlstats versions 0.1.5 dated 2022-04-13 and 0.1.6 dated 2022-12-09
DESCRIPTION | 8 +- MD5 | 11 ++- NAMESPACE | 1 R/cran_stats.R | 19 ++++++ build/vignette.rds |binary inst/doc/dlstats.html | 128 +++++++++++++++++++++++---------------------- man/set_cran_start_year.Rd |only 7 files changed, 98 insertions(+), 69 deletions(-)
Title: Chaos Game
Description: The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.
Author: Thimo Kasper <thimo.kasper@plus.ac.at>,
Florian Griessenberger <florian.griessenberger@plus.ac.at>,
Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Johannes Bartel <>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Marco Tschimpke <marco.tschimpke@plus.ac.at>
Diff between ChaosGame versions 1.3 dated 2022-07-05 and 1.4 dated 2022-12-09
DESCRIPTION | 23 +++++++++-------------- MD5 | 2 +- 2 files changed, 10 insertions(+), 15 deletions(-)
Title: Statistics of Extremes
Description: Conducts inference in statistical models for extreme values (de Carvalho et al (2012), <doi:10.1080/03610926.2012.709905>; de Carvalho and Davison (2014), <doi:10.1080/01621459.2013.872651>; Einmahl et al (2016), <doi:10.1111/rssb.12099>).
Author: Miguel de Carvalho [aut, cre],
Rodrigo Rubio [aut],
Vianey Palacios [aut]
Maintainer: Miguel de Carvalho <miguel.decarvalho@ed.ac.uk>
Diff between extremis versions 1.2 dated 2020-11-26 and 1.2.1 dated 2022-12-09
extremis-1.2.1/extremis/DESCRIPTION | 21 +++----- extremis-1.2.1/extremis/MD5 | 23 ++------- extremis-1.2.1/extremis/NAMESPACE | 7 +- extremis-1.2.1/extremis/R/cdensity.R | 37 ++------------- extremis-1.2.1/extremis/R/kgvar.R | 3 - extremis-1.2.1/extremis/R/khetmeans.R | 3 - extremis-1.2.1/extremis/man/cdensity.Rd | 59 +++++++------------------ extremis-1.2/extremis/R/cPTdensity.R |only extremis-1.2/extremis/man/cPTdensity.Rd |only extremis-1.2/extremis/src/PTudensitybetapmh.f |only extremis-1.2/extremis/src/ToolsCDF.f |only extremis-1.2/extremis/src/ToolsCdflib.f |only extremis-1.2/extremis/src/ToolsDistributions.f |only extremis-1.2/extremis/src/ToolsRandlib.f |only extremis-1.2/extremis/src/ToolsRfun.c |only extremis-1.2/extremis/src/ToolsRnumbers.f |only extremis-1.2/extremis/src/ToolsStat.f |only extremis-1.2/extremis/src/init.c |only 18 files changed, 48 insertions(+), 105 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.3.2 dated 2022-11-02 and 1.3.4 dated 2022-12-09
DESCRIPTION | 10 LICENSE | 2 MD5 | 346 +- NAMESPACE | 320 +- NEWS.md | 704 ++--- R/AlphaSimR.R | 58 R/Class-HybridPop.R | 256 +- R/Class-LociMap.R | 752 +++--- R/Class-Pop.R | 1998 ++++++++-------- R/Class-RRsol.R | 54 R/Class-SimParam.R | 4682 +++++++++++++++++++-------------------- R/GS.R | 3036 ++++++++++++------------- R/RcppExports.R | 718 ++--- R/crossing.R | 1786 +++++++------- R/founderPop.R | 1166 ++++----- R/hybrids.R | 854 +++---- R/importData.R | 563 ++-- R/mergePops.R | 296 +- R/misc.R | 1577 ++++++------- R/phenotypes.R | 522 ++-- R/polyploids.R | 608 ++--- R/popSummary.R | 1248 +++++----- R/pullGeno.R | 2218 +++++++++--------- R/selection.R | 922 +++---- R/writePlink.R | 276 +- R/writeRecords.R | 214 - README.md | 64 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 32 inst/REFERENCES.bib | 340 +- inst/doc/intro.R | 100 inst/doc/intro.Rmd | 264 +- inst/doc/intro.html | 1188 ++++----- inst/doc/traits.Rmd | 372 +-- inst/doc/traits.pdf |binary man/AlphaSimR-package.Rd | 96 man/HybridPop-class.Rd | 122 - man/LociMap-class.Rd | 42 man/MapPop-class.Rd | 102 man/MegaPop-class.Rd | 102 man/NamedMapPop-class.Rd | 96 man/Pop-class.Rd | 148 - man/RRBLUP.Rd | 130 - man/RRBLUP2.Rd | 222 - man/RRBLUPMemUse.Rd | 56 man/RRBLUP_D.Rd | 132 - man/RRBLUP_D2.Rd | 176 - man/RRBLUP_GCA.Rd | 134 - man/RRBLUP_GCA2.Rd | 174 - man/RRBLUP_SCA.Rd | 132 - man/RRBLUP_SCA2.Rd | 182 - man/RRsol-class.Rd | 52 man/RawPop-class.Rd | 122 - man/SimParam.Rd | 3414 ++++++++++++++-------------- man/TraitA-class.Rd | 36 man/TraitA2-class.Rd | 34 man/TraitA2D-class.Rd | 32 man/TraitAD-class.Rd | 32 man/TraitADE-class.Rd | 32 man/TraitADEG-class.Rd | 40 man/TraitADG-class.Rd | 40 man/TraitAE-class.Rd | 32 man/TraitAEG-class.Rd | 40 man/TraitAG-class.Rd | 40 man/aa.Rd | 62 man/addSegSite.Rd | 80 man/attrition.Rd | 72 man/bv.Rd | 60 man/cChr.Rd | 54 man/calcGCA.Rd | 72 man/dd.Rd | 60 man/dot-newPop.Rd | 108 man/doubleGenome.Rd | 78 man/ebv.Rd | 58 man/editGenome.Rd | 96 man/editGenomeTopQtl.Rd | 88 man/fastRRBLUP.Rd | 154 - man/genParam.Rd | 128 - man/genicVarA.Rd | 60 man/genicVarAA.Rd | 62 man/genicVarD.Rd | 60 man/genicVarG.Rd | 60 man/getGenMap.Rd | 80 man/getMisc.Rd | 112 man/getNumThreads.Rd | 38 man/getPed.Rd | 66 man/getQtlMap.Rd | 86 man/getSnpMap.Rd | 88 man/gv.Rd | 56 man/hybridCross.Rd | 100 man/importGenMap.Rd | 64 man/importHaplo.Rd | 117 man/importInbredGeno.Rd | 115 man/isFemale.Rd | 76 man/isPop.Rd | 56 man/makeCross.Rd | 82 man/makeCross2.Rd | 86 man/makeDH.Rd | 84 man/meanG.Rd | 56 man/meanP.Rd | 56 man/mergeGenome.Rd | 84 man/mergePops.Rd | 64 man/mutate.Rd | 92 man/nInd.Rd | 56 man/newEmptyPop.Rd | 68 man/newMapPop.Rd | 106 man/newMegaPop.Rd | 68 man/newPop.Rd | 78 man/pedigreeCross.Rd | 158 - man/pheno.Rd | 56 man/popVar.Rd | 40 man/pullIbdHaplo.Rd | 80 man/pullMarkerGeno.Rd | 88 man/pullMarkerHaplo.Rd | 98 man/pullQtlGeno.Rd | 82 man/pullQtlHaplo.Rd | 104 man/pullSegSiteGeno.Rd | 80 man/pullSegSiteHaplo.Rd | 100 man/pullSnpGeno.Rd | 82 man/pullSnpHaplo.Rd | 104 man/quickHaplo.Rd | 70 man/randCross.Rd | 106 man/randCross2.Rd | 124 - man/reduceGenome.Rd | 108 man/resetPop.Rd | 72 man/runMacs.Rd | 158 - man/runMacs2.Rd | 162 - man/sampleHaplo.Rd | 66 man/selIndex.Rd | 90 man/selInt.Rd | 36 man/selectCross.Rd | 174 - man/selectFam.Rd | 164 - man/selectInd.Rd | 148 - man/selectOP.Rd | 154 - man/selectWithinFam.Rd | 166 - man/self.Rd | 82 man/setEBV.Rd | 132 - man/setMarkerHaplo.Rd | 100 man/setMisc.Rd | 114 man/setPheno.Rd | 220 - man/setPhenoGCA.Rd | 164 - man/setPhenoProgTest.Rd | 182 - man/smithHazel.Rd | 60 man/solveMKM.Rd | 48 man/solveMVM.Rd | 48 man/solveRRBLUP.Rd | 36 man/solveRRBLUPMK.Rd | 40 man/solveRRBLUPMV.Rd | 44 man/solveRRBLUP_EM.Rd | 60 man/solveRRBLUP_EM2.Rd | 68 man/solveRRBLUP_EM3.Rd | 76 man/solveUVM.Rd | 40 man/transMat.Rd | 97 man/usefulness.Rd | 122 - man/varA.Rd | 60 man/varAA.Rd | 62 man/varD.Rd | 60 man/varG.Rd | 56 man/varP.Rd | 56 man/writePlink.Rd | 138 - man/writeRecords.Rd | 80 src/alphaSuite.cpp | 4 src/calcGenParam.cpp | 28 tests/testthat.R | 8 tests/testthat/test-addTrait.R | 212 - tests/testthat/test-crossing.R | 256 +- tests/testthat/test-editGenome.R | 30 tests/testthat/test-hybrids.R | 128 - tests/testthat/test-importData.R | 94 tests/testthat/test-statistics.R | 60 vignettes/AlphaSimR.bib | 288 +- vignettes/intro.Rmd | 264 +- vignettes/traits.Rmd | 372 +-- 174 files changed, 21958 insertions(+), 21885 deletions(-)
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction
from noisy and high-dimensional data. It facilitates identification of patterns representing underlying
groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA.
(2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014)
Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Author: Stefano Cacciatore [aut, trl, cre]
,
Leonardo Tenori [aut]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 2.2 dated 2022-09-01 and 2.3 dated 2022-12-09
KODAMA-2.2/KODAMA/man/KODAMA.Rd |only KODAMA-2.3/KODAMA/DESCRIPTION | 10 - KODAMA-2.3/KODAMA/MD5 | 39 +++--- KODAMA-2.3/KODAMA/NAMESPACE | 4 KODAMA-2.3/KODAMA/R/KOD.R | 116 ++++++++++-------- KODAMA-2.3/KODAMA/inst/doc/KODAMA.R | 3 KODAMA-2.3/KODAMA/inst/doc/KODAMA.Rmd | 129 +++++++++----------- KODAMA-2.3/KODAMA/inst/doc/KODAMA.pdf |binary KODAMA-2.3/KODAMA/man/KODAMA.matrix.Rd |only KODAMA-2.3/KODAMA/man/KODAMA.visualization.Rd |only KODAMA-2.3/KODAMA/man/MetRef.Rd | 5 KODAMA-2.3/KODAMA/man/USA.Rd | 5 KODAMA-2.3/KODAMA/man/core_cpp.Rd | 2 KODAMA-2.3/KODAMA/man/k.test.Rd | 8 - KODAMA-2.3/KODAMA/man/knn.kodama.Rd | 164 +++++++++++++------------- KODAMA-2.3/KODAMA/man/loads.Rd | 86 ++++++------- KODAMA-2.3/KODAMA/man/lymphoma.Rd | 6 KODAMA-2.3/KODAMA/man/mcplot.Rd | 72 +++++------ KODAMA-2.3/KODAMA/man/pls.kodama.Rd | 136 ++++++++++----------- KODAMA-2.3/KODAMA/src/RcppExports.cpp | 2 KODAMA-2.3/KODAMA/src/prova.cpp | 29 +--- KODAMA-2.3/KODAMA/vignettes/KODAMA.Rmd | 129 +++++++++----------- 22 files changed, 478 insertions(+), 467 deletions(-)
Title: Hypothesis Testing Tree
Description: A novel decision tree algorithm in the hypothesis testing framework. The algorithm examines the distribution difference between two child nodes over all possible binary partitions. The test statistic of the hypothesis testing is equivalent to the generalized energy distance, which enables the algorithm to be more powerful in detecting the complex structure, not only the mean difference. It is applicable for numeric, nominal, ordinal explanatory variables and the response in general metric space of strong negative type. The algorithm has superior performance compared to other tree models in type I error, power, prediction accuracy, and complexity.
Author: Jiaqi Hu [cre, aut],
Zhe Gao [aut],
Bo Zhang [aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between HTT versions 0.1.0 dated 2022-12-01 and 0.1.1 dated 2022-12-09
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- NEWS.md | 5 +++ inst/doc/Intro.html | 68 ++++++++++++++++++++++++++++++++++++++++++---------- man/HTT.Rd | 1 src/Splits.cpp | 3 -- src/TreeGrow.cpp | 4 +-- 7 files changed, 73 insertions(+), 28 deletions(-)
Title: Flexible Data Simulation Using the Multivariate Normal
Distribution
Description: This R package can be used to generate artificial data conditionally on pre-specified (simulated or user-defined) relationships between the variables and/or observations. Each observation is drawn from a multivariate Normal distribution where the mean vector and covariance matrix reflect the desired relationships. Outputs can be used to evaluate the performances of variable selection, graphical modelling, or clustering approaches by comparing the true and estimated structures (B Bodinier et al (2021) <arXiv:2106.02521>).
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <b.bodinier@imperial.ac.uk>
Diff between fake versions 1.0.0 dated 2022-08-09 and 1.3.0 dated 2022-12-09
fake-1.0.0/fake/man/TuneExplainedVarianceReg.Rd |only fake-1.3.0/fake/DESCRIPTION | 9 fake-1.3.0/fake/MD5 | 58 - fake-1.3.0/fake/NAMESPACE | 9 fake-1.3.0/fake/NEWS.md | 8 fake-1.3.0/fake/R/goodness_of_fit.R |only fake-1.3.0/fake/R/internal.R |only fake-1.3.0/fake/R/s3_classes.R | 105 ++ fake-1.3.0/fake/R/simulations.R | 1151 ++++++++++++++++-------- fake-1.3.0/fake/R/tools.R | 553 ++++------- fake-1.3.0/fake/R/visualisation.R | 8 fake-1.3.0/fake/README.md | 101 +- fake-1.3.0/fake/build/partial.rdb |binary fake-1.3.0/fake/inst/REFERENCES.bib | 20 fake-1.3.0/fake/inst/WORDLIST | 11 fake-1.3.0/fake/man/Concordance.Rd |only fake-1.3.0/fake/man/ExpectedCommunities.Rd |only fake-1.3.0/fake/man/ExpectedConcordance.Rd |only fake-1.3.0/fake/man/Heatmap.Rd | 6 fake-1.3.0/fake/man/MaxContrast.Rd | 2 fake-1.3.0/fake/man/MinWithinProba.Rd |only fake-1.3.0/fake/man/ROC.Rd |only fake-1.3.0/fake/man/Rates.Rd |only fake-1.3.0/fake/man/SamplePredictors.Rd | 2 fake-1.3.0/fake/man/SimulateAdjacency.Rd | 33 fake-1.3.0/fake/man/SimulateClustering.Rd |only fake-1.3.0/fake/man/SimulateComponents.Rd | 35 fake-1.3.0/fake/man/SimulateCorrelation.Rd |only fake-1.3.0/fake/man/SimulateGraphical.Rd | 59 - fake-1.3.0/fake/man/SimulatePrecision.Rd | 19 fake-1.3.0/fake/man/SimulateRegression.Rd | 325 ++---- fake-1.3.0/fake/man/SimulateSymmetricMatrix.Rd | 2 fake-1.3.0/fake/man/TuneCStatisticLogit.Rd |only fake-1.3.0/fake/man/TuneExplainedVarianceCor.Rd | 16 fake-1.3.0/fake/man/TuneExplainedVarianceCov.Rd | 16 fake-1.3.0/fake/man/figures |only fake-1.3.0/fake/man/plot.roc_curve.Rd |only 37 files changed, 1496 insertions(+), 1052 deletions(-)
Title: Japanese Utility Functions and Data
Description: Some data treated by the Japanese R user require
unique operations and processing. These are caused by address, Kanji,
and traditional year representations. 'zipangu' transforms specific
to Japan into something more general one.
Author: Shinya Uryu [aut, cre] ,
Hiroaki Yutani [ctb] ,
Kazuhiro Maeda [ctb],
Mao Kobayashi [ctb],
Akiru Kato [ctb]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between zipangu versions 0.3.1 dated 2022-08-31 and 0.3.2 dated 2022-12-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 2 ++ R/kansuji.R | 6 +++--- R/label-kansuji.R | 5 +++-- README.md | 9 ++------- build/zipangu.pdf |binary man/label_kansuji.Rd | 3 ++- 8 files changed, 23 insertions(+), 24 deletions(-)
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
and dependence 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 0.3.0 dated 2022-11-26 and 0.4.0 dated 2022-12-09
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NEWS.md | 20 ++++++++++++++++++++ R/bee.R |only R/sv_importance.R | 20 ++++++++++++++++---- README.md | 2 +- inst/doc/shapviz.R | 2 +- inst/doc/shapviz.Rmd | 2 +- inst/doc/shapviz.html | 6 +++--- man/sv_importance.Rd | 12 +++++++++--- tests/testthat/test-interface.R | 2 +- vignettes/shapviz.Rmd | 2 +- 12 files changed, 69 insertions(+), 30 deletions(-)
Title: Helper Package to Install Packages for R
Description: Helper function to install packages for R using an external
'requirements.txt' or a string containing diverse packages from
several resources like Github or CRAN.
Author: Jonathan M. Mang [aut, cre] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between requiRements versions 0.0.1 dated 2021-06-18 and 0.0.2 dated 2022-12-09
DESCRIPTION | 26 +++++++++++--------------- MD5 | 4 ++-- README.md | 11 ++++++----- 3 files changed, 19 insertions(+), 22 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-19 0.8.1
2020-04-29 0.7.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-21 2.0
2014-07-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-07 2020.1.6
2020-09-28 2020.1.5