Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Author: Sadjad Fakouri-Baygi [aut] ,
Dinesh Barupal [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>
Diff between IDSL.IPA versions 2.6 dated 2023-01-06 and 2.7 dated 2023-03-31
DESCRIPTION | 21 - LICENSE | 2 MD5 | 78 ++-- NAMESPACE | 3 R/IPA_GapFiller.R | 57 +-- R/IPA_IonPairing.R | 54 +++ R/IPA_PeakAlignment.R | 52 +-- R/IPA_PeakAnalyzer.R | 41 +- R/IPA_PeaklistAnnotation.R | 2 R/IPA_logRecorder.R | 7 R/IPA_message.R |only R/IPA_peak_alignment_folder_xlsxAnalyzer.R | 16 - R/IPA_spectraListAggregator.R | 8 R/IPA_targeted.R | 63 ++- R/IPA_targeted_xlsxAnalyzer.R | 85 ++--- R/IPA_workflow.R | 46 +- R/IPA_xlsxAnalyzer.R | 287 +++++++++--------- R/alignedPeakPropertyTableCorrelationListCalculator.R | 46 +- R/chromatographicPeakAnalysis.R | 4 R/gapFillingCore.R | 23 - R/global.R | 2 R/opendir.R | 3 R/peakAlignmentCore.R | 31 + R/peakGaussianityCalculator.R | 2 R/peakPropertyTableFreqCalculator.R | 21 - R/peakPropertyTableMedianCalculator.R | 21 - R/plot_mz_eic.R | 51 ++- R/plot_simple_tic.R | 47 ++ R/primaryXICdeconvoluter.R | 54 +++ R/recursiveMZpeaklistCorrector.R | 61 +++ build/partial.rdb |binary data/peak_spline.rda |binary data/segment.rda |binary inst/CITATION | 14 inst/extdata/IPA_parameters.xlsx |binary man/IPA_IonPairing.Rd | 5 man/IPA_logRecorder.Rd | 9 man/IPA_message.Rd |only man/IPA_workflow.Rd | 5 man/primaryXICdeconvoluter.Rd | 6 man/recursiveMZpeaklistCorrector.Rd | 5 41 files changed, 755 insertions(+), 477 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2022.9.16 dated 2022-09-19 and 2023.3.30 dated 2023-03-31
atime-2022.9.16/atime/inst/doc/PeakSegDisk.R |only atime-2022.9.16/atime/inst/doc/PeakSegDisk.Rmd |only atime-2022.9.16/atime/inst/doc/PeakSegDisk.html |only atime-2022.9.16/atime/inst/doc/binseg.R |only atime-2022.9.16/atime/inst/doc/binseg.Rmd |only atime-2022.9.16/atime/inst/doc/binseg.html |only atime-2022.9.16/atime/inst/doc/data.table.R |only atime-2022.9.16/atime/inst/doc/data.table.Rmd |only atime-2022.9.16/atime/inst/doc/data.table.html |only atime-2022.9.16/atime/inst/doc/git.R |only atime-2022.9.16/atime/inst/doc/git.Rmd |only atime-2022.9.16/atime/inst/doc/git.html |only atime-2022.9.16/atime/inst/doc/optseg.R |only atime-2022.9.16/atime/inst/doc/optseg.Rmd |only atime-2022.9.16/atime/inst/doc/optseg.html |only atime-2022.9.16/atime/vignettes/PeakSegDisk.Rmd |only atime-2022.9.16/atime/vignettes/binseg.Rmd |only atime-2022.9.16/atime/vignettes/data.table.Rmd |only atime-2022.9.16/atime/vignettes/git.Rmd |only atime-2022.9.16/atime/vignettes/optseg.Rmd |only atime-2023.3.30/atime/DESCRIPTION | 10 atime-2023.3.30/atime/MD5 | 76 - atime-2023.3.30/atime/NAMESPACE | 2 atime-2023.3.30/atime/NEWS | 13 atime-2023.3.30/atime/R/atime.R | 134 ++ atime-2023.3.30/atime/R/references.R | 107 + atime-2023.3.30/atime/R/versions.R | 264 ++++ atime-2023.3.30/atime/build/vignette.rds |binary atime-2023.3.30/atime/inst/doc/Custom_Plots.R |only atime-2023.3.30/atime/inst/doc/Custom_Plots.Rmd |only atime-2023.3.30/atime/inst/doc/Custom_Plots.html |only atime-2023.3.30/atime/inst/doc/Custom_References.R |only atime-2023.3.30/atime/inst/doc/Custom_References.Rmd |only atime-2023.3.30/atime/inst/doc/Custom_References.html |only atime-2023.3.30/atime/inst/doc/Custom_Units.R |only atime-2023.3.30/atime/inst/doc/Custom_Units.Rmd |only atime-2023.3.30/atime/inst/doc/Custom_Units.html |only atime-2023.3.30/atime/inst/doc/cum_median.R | 61 - atime-2023.3.30/atime/inst/doc/cum_median.Rmd | 74 - atime-2023.3.30/atime/inst/doc/cum_median.html | 542 +--------- atime-2023.3.30/atime/inst/doc/regex.R | 97 - atime-2023.3.30/atime/inst/doc/regex.Rmd | 111 -- atime-2023.3.30/atime/inst/doc/regex.html | 389 ++----- atime-2023.3.30/atime/man/atime.Rd | 90 - atime-2023.3.30/atime/man/atime_grid.Rd |only atime-2023.3.30/atime/man/atime_pkg.Rd |only atime-2023.3.30/atime/man/atime_versions.Rd | 3 atime-2023.3.30/atime/man/atime_versions_exprs.Rd | 3 atime-2023.3.30/atime/man/references_best.Rd | 77 - atime-2023.3.30/atime/tests/testthat/test-CRAN.R | 154 ++ atime-2023.3.30/atime/vignettes/Custom_Plots.Rmd |only atime-2023.3.30/atime/vignettes/Custom_References.Rmd |only atime-2023.3.30/atime/vignettes/Custom_Units.Rmd |only atime-2023.3.30/atime/vignettes/binseg.html |only atime-2023.3.30/atime/vignettes/compare-data.table-tidyverse.html |only atime-2023.3.30/atime/vignettes/cum_median.Rmd | 74 - atime-2023.3.30/atime/vignettes/regex.Rmd | 111 -- 57 files changed, 1080 insertions(+), 1312 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.1 dated 2023-03-28 and 0.0.2 dated 2023-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary tests/tinytest.R | 4 +++- 5 files changed, 14 insertions(+), 8 deletions(-)
Title: Cooperative Learning for Multi-View Analysis
Description: Cooperative learning combines the usual squared error loss of predictions with an agreement penalty to encourage the predictions from different data views to agree. By varying the weight of the agreement penalty, we get a continuum of solutions that include the well-known early and late fusion approaches. Cooperative learning chooses the degree of agreement (or fusion) in an adaptive manner, using a validation set or cross-validation to estimate test set prediction error. In the setting of cooperative regularized linear regression, the method combines the lasso penalty with the agreement penalty (Ding, D., Li, S., Narasimhan, B., Tibshirani, R. (2021) <doi:10.1073/pnas.2202113119>).
Author: Daisy Yi Ding [aut],
Robert J. Tibshirani [aut],
Balasubramanian Narasimhan [aut, cre],
Trevor Hastie [aut],
Kenneth Tay [aut],
James Yang [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between multiview versions 0.7 dated 2022-11-04 and 0.8 dated 2023-03-31
DESCRIPTION | 11 +- MD5 | 20 ++-- NEWS.md | 14 +-- R/multiview.R | 1 R/view.contribution.R | 200 ++++++++++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/multiview.Rmd | 2 inst/doc/multiview.pdf |binary man/view.contribution.Rd | 3 src/Makevars | 2 vignettes/multiview.Rmd | 2 11 files changed, 199 insertions(+), 56 deletions(-)
Title: Interface to the Comparative Legislators Database
Description: Facilitates access to the Comparative Legislators Database (CLD). The CLD includes political, sociodemographic, career, online presence, public attention, and visual information for over 67,000 contemporary and historical politicians from 16 countries.
Author: Sascha Goebel [aut, cre] ,
Simon Munzert [aut]
Maintainer: Sascha Goebel <sascha.goebel@soz.uni-frankfurt.de>
Diff between legislatoR versions 1.0 dated 2020-04-24 and 1.1.0 dated 2023-03-31
legislatoR-1.0/legislatoR/tests/testthat/test-get_.R |only legislatoR-1.1.0/legislatoR/DESCRIPTION | 17 legislatoR-1.1.0/legislatoR/MD5 | 63 legislatoR-1.1.0/legislatoR/NEWS.md |only legislatoR-1.1.0/legislatoR/R/cld_content.R | 23 legislatoR-1.1.0/legislatoR/R/get_core.R | 27 legislatoR-1.1.0/legislatoR/R/get_history.R | 20 legislatoR-1.1.0/legislatoR/R/get_ids.R | 19 legislatoR-1.1.0/legislatoR/R/get_office.R | 19 legislatoR-1.1.0/legislatoR/R/get_political.R | 23 legislatoR-1.1.0/legislatoR/R/get_portrait.R | 21 legislatoR-1.1.0/legislatoR/R/get_profession.R | 19 legislatoR-1.1.0/legislatoR/R/get_social.R | 19 legislatoR-1.1.0/legislatoR/R/get_traffic.R | 17 legislatoR-1.1.0/legislatoR/R/sysdata.rda |only legislatoR-1.1.0/legislatoR/build/vignette.rds |binary legislatoR-1.1.0/legislatoR/inst/doc/legislatoR.html | 716 +++++++--- legislatoR-1.1.0/legislatoR/man/get_core.Rd | 16 legislatoR-1.1.0/legislatoR/man/get_history.Rd | 8 legislatoR-1.1.0/legislatoR/man/get_ids.Rd | 8 legislatoR-1.1.0/legislatoR/man/get_office.Rd | 8 legislatoR-1.1.0/legislatoR/man/get_political.Rd | 12 legislatoR-1.1.0/legislatoR/man/get_portrait.Rd | 10 legislatoR-1.1.0/legislatoR/man/get_profession.Rd | 8 legislatoR-1.1.0/legislatoR/man/get_social.Rd | 8 legislatoR-1.1.0/legislatoR/man/get_traffic.Rd | 6 legislatoR-1.1.0/legislatoR/man/legislatoR.Rd | 1 legislatoR-1.1.0/legislatoR/tests/testthat.R | 13 legislatoR-1.1.0/legislatoR/tests/testthat/test-cld_content.R | 16 legislatoR-1.1.0/legislatoR/tests/testthat/test-errors.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_core.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_history.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_ids.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_office.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_political.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_portrait.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_profession.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_social.R |only legislatoR-1.1.0/legislatoR/tests/testthat/test-get_traffic.R |only 39 files changed, 756 insertions(+), 361 deletions(-)
Title: Interpolation Methods
Description: Bivariate data interpolation on regular and irregular
grids, either linear or using splines are the main part of this
package. It is intended to provide FOSS replacement functions for
the ACM licensed akima::interp and tripack::tri.mesh functions.
Linear interpolation is implemented in
interp::interp(..., method="linear"), this corresponds to the call
akima::interp(..., linear=TRUE) which is the default setting and
covers most of akima::interp use cases in depending packages.
A re-implementation of Akimas irregular grid spline
interpolation (akima::interp(..., linear=FALSE)) is now also
available via interp::interp(..., method="akima").
Estimators for partial derivatives are now also available in
interp::locpoly(), these are a prerequisite for the spline interpolation.
The basic part is a GPLed triangulation algorithm (sweep hull
algorithm by David Sinclair) providing the starting point for the
irregular grid interpolator. As side effect this algorithm is also
used to provide replacem [...truncated...]
Author: Albrecht Gebhardt [aut, cre, cph],
Roger Bivand [aut],
David Sinclair [aut, cph]
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between interp versions 1.1-3 dated 2022-07-13 and 1.1-4 dated 2023-03-31
DESCRIPTION | 10 +- MD5 | 70 ++++++++------ NAMESPACE | 3 R/RcppExports.R | 12 ++ R/bicubic.R | 2 R/bilinear.R | 36 +++++++ R/interp.R | 9 + R/locpoly.R | 2 R/print.triSht.R | 2 R/tri.mesh.R | 11 +- README | 5 - build/vignette.rds |binary inst/doc/interp.R |only inst/doc/interp.Rnw |only inst/doc/interp.pdf |only inst/doc/partDeriv.R | 82 ++++++++--------- inst/doc/partDeriv.Rnw | 110 ++++++++++++++--------- inst/doc/partDeriv.pdf |binary inst/doc/tri.R |only inst/doc/tri.Rnw |only inst/doc/tri.pdf |only man/bilinear.Rd | 8 + man/bilinear.grid.Rd | 9 + man/convex.hull.Rd | 7 + man/interp.Rd | 2 man/locpoly.Rd | 2 man/tri.mesh.Rd | 7 + src/BiLin.cpp |only src/RcppExports.cpp | 34 ++++++- src/aSpline.cpp | 2 src/convexHull.cpp |only src/init.c | 8 + src/interp.cpp | 49 +++++++--- src/interp.h | 4 src/s_hull_pro.cpp | 19 +++ src/s_hull_pro.h | 2 src/shullDeltri.cpp | 152 +++++++++++++++++++++++++++---- vignettes/interp.Rnw |only vignettes/lit.bib | 229 ++++++++++++++++++++++++++++++++++++++++++++++++ vignettes/partDeriv.Rnw | 110 ++++++++++++++--------- vignettes/tri.Rnw |only 41 files changed, 770 insertions(+), 228 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of
functions. With its progressive approach, we can construct display tables
with a cohesive set of table parts. Table values can be formatted using any
of the included formatting functions. Footnotes and cell styles can be
precisely added through a location targeting system. The way in which 'gt'
handles things for you means that you don't often have to worry about the
fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Ellis Hughes [aut] ,
Alexandra Lauer [aut] ,
JooYoung Seo [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between gt versions 0.8.0 dated 2022-11-16 and 0.9.0 dated 2023-03-31
gt-0.8.0/gt/tests/testthat/test-color_handling.R |only gt-0.8.0/gt/tests/testthat/test-cols_label.R |only gt-0.8.0/gt/tests/testthat/test-cols_width.R |only gt-0.8.0/gt/tests/testthat/test-escaping.R |only gt-0.8.0/gt/tests/testthat/test-fmt_date_time.R |only gt-0.8.0/gt/tests/testthat/test-h_md_html.R |only gt-0.8.0/gt/tests/testthat/test-info_tables.R |only gt-0.8.0/gt/tests/testthat/test-input_data_validation.R |only gt-0.8.0/gt/tests/testthat/test-opt_functions.R |only gt-0.8.0/gt/tests/testthat/test-rtf_column_widths.R |only gt-0.8.0/gt/tests/testthat/test-tab_style.R |only gt-0.8.0/gt/tests/testthat/test-text_transform.R |only gt-0.8.0/gt/tests/testthat/test-util_functions.R |only gt-0.8.0/gt/tests/testthat/test-utils.R |only gt-0.8.0/gt/tests/testthat/test-utils_formatters.R |only gt-0.8.0/gt/tests/testthat/test-utils_render_html.R |only gt-0.9.0/gt/DESCRIPTION | 60 gt-0.9.0/gt/LICENSE | 4 gt-0.9.0/gt/MD5 | 550 + gt-0.9.0/gt/NAMESPACE | 43 gt-0.9.0/gt/NEWS.md | 100 gt-0.9.0/gt/R/build_data.R | 2 gt-0.9.0/gt/R/compile_scss.R | 7 gt-0.9.0/gt/R/data_color.R | 1066 +++ gt-0.9.0/gt/R/datasets.R | 586 + gt-0.9.0/gt/R/dt_boxhead.R | 11 gt-0.9.0/gt/R/dt_cols_merge.R | 3 gt-0.9.0/gt/R/dt_data.R | 6 gt-0.9.0/gt/R/dt_groups_rows.R | 26 gt-0.9.0/gt/R/dt_options.R | 39 gt-0.9.0/gt/R/dt_spanners.R | 10 gt-0.9.0/gt/R/dt_summary.R | 323 - gt-0.9.0/gt/R/export.R | 310 - gt-0.9.0/gt/R/format_data.R | 4397 +++++++++++++-- gt-0.9.0/gt/R/format_vec.R | 644 +- gt-0.9.0/gt/R/gt.R | 25 gt-0.9.0/gt/R/gt_group.R |only gt-0.9.0/gt/R/gt_preview.R | 27 gt-0.9.0/gt/R/gt_split.R |only gt-0.9.0/gt/R/helpers.R | 1048 ++- gt-0.9.0/gt/R/image.R | 57 gt-0.9.0/gt/R/info_tables.R | 96 gt-0.9.0/gt/R/location_methods.R | 22 gt-0.9.0/gt/R/modify_columns.R | 1498 +++-- gt-0.9.0/gt/R/modify_rows.R | 14 gt-0.9.0/gt/R/opts.R | 1073 ++- gt-0.9.0/gt/R/print.R | 127 gt-0.9.0/gt/R/render_as_html.R | 60 gt-0.9.0/gt/R/render_as_i_html.R |only gt-0.9.0/gt/R/resolver.R | 54 gt-0.9.0/gt/R/shiny.R | 82 gt-0.9.0/gt/R/substitution.R | 405 + gt-0.9.0/gt/R/summary_rows.R | 920 ++- gt-0.9.0/gt/R/sysdata.rda |binary gt-0.9.0/gt/R/tab_create_modify.R | 647 +- gt-0.9.0/gt/R/tab_info.R | 19 gt-0.9.0/gt/R/tab_remove.R | 120 gt-0.9.0/gt/R/tab_style_body.R | 71 gt-0.9.0/gt/R/text_transform.R | 505 + gt-0.9.0/gt/R/utils.R | 519 + gt-0.9.0/gt/R/utils_formatters.R | 160 gt-0.9.0/gt/R/utils_general_str_formatting.R | 92 gt-0.9.0/gt/R/utils_quarto.R |only gt-0.9.0/gt/R/utils_render_common.R | 288 gt-0.9.0/gt/R/utils_render_html.R | 657 +- gt-0.9.0/gt/R/utils_render_latex.R | 422 + gt-0.9.0/gt/R/utils_render_rtf.R | 180 gt-0.9.0/gt/R/utils_render_xml.R | 1088 +++ gt-0.9.0/gt/R/z_utils_render_footnotes.R | 172 gt-0.9.0/gt/R/zzz.R | 27 gt-0.9.0/gt/data/countrypops.rda |binary gt-0.9.0/gt/data/exibble.rda |binary gt-0.9.0/gt/data/gtcars.rda |binary gt-0.9.0/gt/data/metro.rda |only gt-0.9.0/gt/data/pizzaplace.rda |binary gt-0.9.0/gt/data/rx_addv.rda |only gt-0.9.0/gt/data/rx_adsl.rda |only gt-0.9.0/gt/data/sp500.rda |binary gt-0.9.0/gt/data/sza.rda |binary gt-0.9.0/gt/data/towny.rda |only gt-0.9.0/gt/inst/css/gt_styles_default.scss | 63 gt-0.9.0/gt/inst/metro_svg |only gt-0.9.0/gt/man/adjust_luminance.Rd | 33 gt-0.9.0/gt/man/as_latex.Rd | 19 gt-0.9.0/gt/man/as_raw_html.Rd | 15 gt-0.9.0/gt/man/as_rtf.Rd | 37 gt-0.9.0/gt/man/as_word.Rd | 34 gt-0.9.0/gt/man/cell_borders.Rd | 29 gt-0.9.0/gt/man/cell_fill.Rd | 20 gt-0.9.0/gt/man/cell_text.Rd | 20 gt-0.9.0/gt/man/cells_body.Rd | 52 gt-0.9.0/gt/man/cells_column_labels.Rd | 38 gt-0.9.0/gt/man/cells_column_spanners.Rd | 25 gt-0.9.0/gt/man/cells_footnotes.Rd | 33 gt-0.9.0/gt/man/cells_grand_summary.Rd | 60 gt-0.9.0/gt/man/cells_group.Rd | 7 gt-0.9.0/gt/man/cells_row_groups.Rd | 40 gt-0.9.0/gt/man/cells_source_notes.Rd | 23 gt-0.9.0/gt/man/cells_stub.Rd | 27 gt-0.9.0/gt/man/cells_stub_grand_summary.Rd | 40 gt-0.9.0/gt/man/cells_stub_summary.Rd | 51 gt-0.9.0/gt/man/cells_stubhead.Rd | 27 gt-0.9.0/gt/man/cells_summary.Rd | 62 gt-0.9.0/gt/man/cells_title.Rd | 23 gt-0.9.0/gt/man/cols_align.Rd | 18 gt-0.9.0/gt/man/cols_align_decimal.Rd | 14 gt-0.9.0/gt/man/cols_hide.Rd | 30 gt-0.9.0/gt/man/cols_label.Rd | 137 gt-0.9.0/gt/man/cols_label_with.Rd |only gt-0.9.0/gt/man/cols_merge.Rd | 127 gt-0.9.0/gt/man/cols_merge_n_pct.Rd | 56 gt-0.9.0/gt/man/cols_merge_range.Rd | 43 gt-0.9.0/gt/man/cols_merge_uncert.Rd | 45 gt-0.9.0/gt/man/cols_move.Rd | 18 gt-0.9.0/gt/man/cols_move_to_end.Rd | 28 gt-0.9.0/gt/man/cols_move_to_start.Rd | 28 gt-0.9.0/gt/man/cols_unhide.Rd | 18 gt-0.9.0/gt/man/cols_width.Rd | 14 gt-0.9.0/gt/man/countrypops.Rd | 41 gt-0.9.0/gt/man/currency.Rd | 14 gt-0.9.0/gt/man/data_color.Rd | 622 +- gt-0.9.0/gt/man/default_fonts.Rd | 38 gt-0.9.0/gt/man/escape_latex.Rd | 16 gt-0.9.0/gt/man/exibble.Rd | 45 gt-0.9.0/gt/man/extract_cells.Rd | 9 gt-0.9.0/gt/man/extract_summary.Rd | 80 gt-0.9.0/gt/man/fmt.Rd | 68 gt-0.9.0/gt/man/fmt_auto.Rd |only gt-0.9.0/gt/man/fmt_bins.Rd |only gt-0.9.0/gt/man/fmt_bytes.Rd | 110 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gt-0.9.0/gt/man/vec_fmt_currency.Rd | 20 gt-0.9.0/gt/man/vec_fmt_date.Rd | 24 gt-0.9.0/gt/man/vec_fmt_datetime.Rd | 30 gt-0.9.0/gt/man/vec_fmt_duration.Rd | 20 gt-0.9.0/gt/man/vec_fmt_engineering.Rd | 56 gt-0.9.0/gt/man/vec_fmt_fraction.Rd | 20 gt-0.9.0/gt/man/vec_fmt_index.Rd |only gt-0.9.0/gt/man/vec_fmt_integer.Rd | 20 gt-0.9.0/gt/man/vec_fmt_markdown.Rd | 18 gt-0.9.0/gt/man/vec_fmt_number.Rd | 20 gt-0.9.0/gt/man/vec_fmt_partsper.Rd | 20 gt-0.9.0/gt/man/vec_fmt_percent.Rd | 20 gt-0.9.0/gt/man/vec_fmt_roman.Rd | 12 gt-0.9.0/gt/man/vec_fmt_scientific.Rd | 57 gt-0.9.0/gt/man/vec_fmt_spelled_num.Rd |only gt-0.9.0/gt/man/vec_fmt_time.Rd | 28 gt-0.9.0/gt/man/web_image.Rd | 20 gt-0.9.0/gt/tests/testthat/helper-gt_attr_expectations.R | 2 gt-0.9.0/gt/tests/testthat/test-cols_align.R | 4 gt-0.9.0/gt/tests/testthat/test-cols_move.R | 6 gt-0.9.0/gt/tests/testthat/test-conditional_fmt.R | 20 gt-0.9.0/gt/tests/testthat/test-gt_object.R | 140 gt-0.9.0/gt/tests/testthat/test-gt_preview.R | 2 gt-0.9.0/gt/tests/testthat/test-helper_functions.R | 16 gt-0.9.0/gt/tests/testthat/test-l_cols_align.R | 2 gt-0.9.0/gt/tests/testthat/test-l_cols_merge.R | 6 gt-0.9.0/gt/tests/testthat/test-l_cols_move.R | 6 gt-0.9.0/gt/tests/testthat/test-l_conditional_fmt.R | 20 gt-0.9.0/gt/tests/testthat/test-l_fmt_currency.R | 2 gt-0.9.0/gt/tests/testthat/test-l_fmt_date_time.R | 6 gt-0.9.0/gt/tests/testthat/test-l_fmt_engineering.R | 8 gt-0.9.0/gt/tests/testthat/test-l_fmt_integer.R | 4 gt-0.9.0/gt/tests/testthat/test-l_fmt_markdown.R | 30 gt-0.9.0/gt/tests/testthat/test-l_fmt_missing.R | 2 gt-0.9.0/gt/tests/testthat/test-l_fmt_number.R | 2 gt-0.9.0/gt/tests/testthat/test-l_fmt_passthrough.R | 2 gt-0.9.0/gt/tests/testthat/test-l_fmt_percent.R | 2 gt-0.9.0/gt/tests/testthat/test-l_fmt_scientific.R | 6 gt-0.9.0/gt/tests/testthat/test-l_row_group_order.R | 2 gt-0.9.0/gt/tests/testthat/test-l_tab_spanner_delim.R | 2 gt-0.9.0/gt/tests/testthat/test-r_table_parts.R | 2 gt-0.9.0/gt/tests/testthat/test-resolver.R | 6 gt-0.9.0/gt/tests/testthat/test-row_group_order.R | 6 gt-0.9.0/gt/tests/testthat/test-tab_caption.R | 2 283 files changed, 20476 insertions(+), 5912 deletions(-)
Title: Additional Families for Generalized Linear Models
Description: Creates family objects identical to stats
family but for new links.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between extendedFamily versions 0.2.1 dated 2021-06-16 and 0.2.2 dated 2023-03-31
DESCRIPTION | 13 ++++++------- MD5 | 12 ++++++------ NEWS | 3 +++ R/binomialEF.R | 17 +++++++++++++++-- README.md | 18 ++++++++++++------ man/binomialEF.Rd | 2 ++ tests/testthat/test_binomialEF.R | 32 ++++++++++++++++---------------- 7 files changed, 60 insertions(+), 37 deletions(-)
More information about extendedFamily at CRAN
Permanent link
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of categorical sequences, and more generally the mining of sequence data in the field of social sciences. Although this sequence analysis toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] ,
Nicolas Mueller [aut],
Reto Buergin [aut] ,
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.2-6 dated 2022-12-01 and 2.2-7 dated 2023-03-31
DESCRIPTION | 11 - MD5 | 47 ++++---- NAMESPACE | 10 + NEWS | 58 +++++++++- R/TraMineR-legend.R | 25 +++- R/TraMineR-logging_helpers.R | 2 R/TraMineR-weights.R | 5 R/dissrf.R | 17 ++- R/seqMD.R | 54 +++++---- R/seqdomassoc.R |only R/seqplot.R | 61 ++++++++-- R/seqplotMD.R | 195 +++++++++++++++++++++-------------- R/seqrf.R | 18 +-- R/stslist-methods.R | 28 +++-- inst/CITATION | 57 ++++++---- inst/NEWS.Rd | 56 +++++++++- inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 man/dissdomassoc.Rd | 3 man/dissmfacw.Rd | 13 ++ man/dissrf.Rd | 10 - man/seqMD.Rd | 63 +++++++---- man/seqdomassoc.Rd |only man/seqlength-align.Rd | 6 - man/seqplot.Rd | 57 ++++++---- man/seqplotMD.Rd |only 26 files changed, 544 insertions(+), 254 deletions(-)
Title: Interpolation of Data with Variable Spatial Support
Description: Data with irregular spatial support, such as runoff related data or data from administrative units, can with 'rtop' be interpolated to locations without observations with the top-kriging method. A description of the package is given by Skøien et al (2014) <doi:10.1016/j.cageo.2014.02.009>.
Author: Jon Olav Skoeien [aut, cre],
Qingyun Duan [ctb]
Maintainer: Jon Olav Skoeien <jon.skoien@gmail.com>
Diff between rtop versions 0.6-5 dated 2023-03-30 and 0.6-6 dated 2023-03-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- tests/rtop.R | 4 ++++ tests/rtop.rout.save | 4 ++++ tests/rtop_sf.R | 2 ++ tests/rtop_sf.Rout.save | 2 ++ 6 files changed, 21 insertions(+), 9 deletions(-)
Title: Tools for Plant Ecophysiology & Modeling
Description: Contains modeling and analytical tools for plant ecophysiology.
MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer,
Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and
Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that
parameters are properly specified and transformed before calculations.
Temperature response functions get automatically "baked" into all
parameters based on leaf temperature following Bernacchi et al. (2002)
<doi:10.1104/pp.008250>. The package includes boundary layer, cuticular,
stomatal, and mesophyll conductances to CO2, which each can vary on the
upper and lower portions of the leaf. Use straightforward functions to
simulate photosynthesis over environmental gradients such as Photosynthetic
Photon Flux Density (PPFD) and leaf temperature, or over trait gradients
such as CO2 conductance or photochemistry.
ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>)
and [...truncated...]
Author: Joseph Stinziano [aut] ,
Cassaundra Roback [aut],
Demi Sargent [aut],
Bridget Murphy [aut],
Patrick Hudson [aut, dtc],
Chris Muir [aut, cre]
Maintainer: Chris Muir <cdmuir@hawaii.edu>
Diff between photosynthesis versions 2.1.1 dated 2022-11-19 and 2.1.2 dated 2023-03-31
DESCRIPTION | 18 ++-- MD5 | 117 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 11 ++ R/FvCB.R | 54 ++++++------- R/bake-par.R | 2 R/bake.R | 36 ++++----- R/calculated-parameters.R | 2 R/conductance.R | 73 +++++++++--------- R/constants.R | 2 R/data.R | 4 - R/enviro-par.R | 2 R/fit_aq_response.R | 10 +- R/fit_photosynthesis.R | 20 ++--- R/fit_r_light.R | 7 + R/leaf-par.R | 11 +- R/make_parameters.R | 32 ++++---- R/models.R | 2 R/photosynthesis-package.R | 8 +- R/photosynthesis.R | 112 +++++++++++++++------------- R/simulate_error.R |only R/utils.R | 6 - build/vignette.rds |binary inst/CITATION | 16 ++-- inst/doc/co2-response.html | 4 - inst/doc/hydraulic-vulnerability.html | 4 - inst/doc/light-respiration.html | 4 - inst/doc/light-response.html | 14 ++- inst/doc/mesophyll-conductance.html | 4 - inst/doc/modeling-recommendations.html | 4 - inst/doc/photosynthesis-introduction.html | 4 - inst/doc/pressure-volume.html | 4 - inst/doc/sensitivity-analysis.html | 4 - inst/doc/stomatal-conductance.html | 4 - inst/doc/temperature-response.html | 40 +++++----- inst/extdata/photo-2d-parameters.csv |only inst/extdata/photo-parameters.csv | 8 +- man/A_supply.Rd | 4 - man/CO2_conductance.Rd | 50 +++++++----- man/FvCB.Rd | 16 ++-- man/aq_response.Rd | 4 - man/bake.Rd | 14 +-- man/baked-class.Rd | 2 man/constants.Rd | 2 man/enviro_par.Rd | 2 man/fit_PV_curve.Rd | 2 man/fit_aci_response.Rd | 2 man/fit_aq_response2.Rd | 14 +-- man/fit_hydra_vuln_curve.Rd | 6 - man/fit_photosynthesis.Rd | 16 ++-- man/fit_r_light.Rd | 4 - man/fit_r_light2.Rd | 14 +-- man/leaf_par.Rd | 2 man/make_parameters.Rd | 28 +++---- man/models.Rd | 6 - man/parameter_names.Rd | 2 man/photo_parameters.Rd | 20 ++--- man/photosynthesis.Rd | 18 ++-- man/required_variables.Rd | 6 - man/simulate_error.Rd |only tests/testthat/test-fit_aq_response2.R | 44 ++++++----- 61 files changed, 490 insertions(+), 433 deletions(-)
More information about photosynthesis at CRAN
Permanent link
Title: Statistics for Matrix Distributions
Description: Tools for phase-type distributions including the following variants:
continuous, discrete, multivariate, in-homogeneous, right-censored, and regression.
Methods for functional evaluation, simulation and estimation using the
expectation-maximization (EM) algorithm are provided for all models.
The methods of this package are based on the following references.
Asmussen, S., Nerman, O., & Olsson, M. (1996). Fitting phase-type distributions via the EM algorithm,
Olsson, M. (1996). Estimation of phase-type distributions from censored data,
Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>,
Albrecher, H., Bladt, M., & Yslas, J. (2022) <doi:10.1111/sjos.12505>,
Albrecher, H., Bladt, M., Bladt, M., & Yslas, J. (2022) <doi:10.1016/j.insmatheco.2022.08.001>,
Bladt, M., & Yslas, J. (2022) <doi:10.1080/03461238.2022.2097019>,
Bladt, M. (2022) <doi:10.1017/asb.2021.40>,
Bladt, M. (2023) <doi:10.1080/10920277.2023.2167833>,
Albrecher, [...truncated...]
Author: Martin Bladt [aut, cre],
Jorge Yslas [aut],
Alaric Mueller [ctb]
Maintainer: Martin Bladt <martinbladt@gmail.com>
Diff between matrixdist versions 1.1.6 dated 2022-10-16 and 1.1.7 dated 2023-03-31
DESCRIPTION | 24 +- MD5 | 385 ++++++++++++++++++++-------------------- NEWS.md |only R/0.generics.R | 45 ++-- R/1.ph.R | 103 +++++----- R/2.iph.R | 30 +-- R/2b.iph_regression.R | 8 R/3.mph.R | 61 +++--- R/3b.miph.MoE.R | 12 - R/3b.miph.R | 25 +- R/4.MPHstar.R | 46 +--- R/4b.bivph.R | 40 +--- R/4c.biviph.R | 13 - R/5.phMoE.R | 40 +++- R/6.sph.R | 21 +- R/7.dph.R | 72 +++---- R/8.bivdph.R | 32 +-- R/9.mdph.R | 51 ++--- README.md | 10 - man/EM_step_mPH_rc.Rd | 8 man/Fisher-sph-method.Rd | 4 man/Fisher.Rd | 2 man/LRT-ph-ph-method.Rd | 4 man/LRT.Rd | 3 man/MPHstar-class.Rd | 2 man/MPHstar.Rd | 4 man/MPHstar_data_aggregation.Rd | 2 man/MoE-bivdph-method.Rd | 4 man/MoE-dph-method.Rd | 6 man/MoE-mdph-method.Rd | 4 man/MoE-mph-method.Rd | 6 man/MoE-ph-method.Rd | 6 man/MoE.Rd | 2 man/Nfold-dph-method.Rd | 4 man/Nfold.Rd | 2 man/TVR-ph-method.Rd | 4 man/TVR.Rd | 2 man/biviph-class.Rd | 2 man/biviph.Rd | 4 man/cdf-dph-method.Rd | 6 man/cdf-iph-method.Rd | 6 man/cdf-miph-method.Rd | 7 man/cdf-mph-method.Rd | 6 man/cdf-ph-method.Rd | 6 man/cdf.Rd | 2 man/coef-dph-method.Rd | 4 man/coef-iph-method.Rd | 4 man/coef-ph-method.Rd | 4 man/coef-sph-method.Rd | 4 man/cor-MPHstar-method.Rd | 4 man/cor-bivdph-method.Rd | 4 man/cor-bivph-method.Rd | 4 man/cor-mdph-method.Rd | 4 man/cor-mph-method.Rd | 4 man/default_step_length.Rd | 2 man/dens-dph-method.Rd | 4 man/dens-iph-method.Rd | 4 man/dens-miph-method.Rd | 4 man/dens-mph-method.Rd | 4 man/dens-ph-method.Rd | 4 man/dens.Rd | 2 man/dph-class.Rd | 2 man/dph.Rd | 7 man/dph_pgf.Rd | 2 man/dphcdf.Rd | 4 man/dphdensity.Rd | 2 man/embedded_mc.Rd | 2 man/evaluate-sph-method.Rd | 4 man/evaluate.Rd | 2 man/find_weight.Rd | 2 man/fit-MPHstar-method.Rd | 4 man/fit-bivdph-method.Rd | 4 man/fit-bivph-method.Rd | 4 man/fit-dph-method.Rd | 4 man/fit-mdph-method.Rd | 4 man/fit-mph-method.Rd | 8 man/fit-ph-method.Rd | 6 man/fit.Rd | 2 man/haz-ph-method.Rd | 4 man/haz.Rd | 2 man/initial_state.Rd | 2 man/iph-class.Rd | 2 man/iph.Rd | 4 man/laplace-bivph-method.Rd | 4 man/laplace-mph-method.Rd | 4 man/laplace-ph-method.Rd | 6 man/laplace.Rd | 2 man/linCom-MPHstar-method.Rd | 4 man/linCom-bivph-method.Rd | 4 man/logLik-ph-method.Rd | 4 man/matrixdist-package.Rd | 24 +- man/maximum-dph-dph-method.Rd | 4 man/maximum-iph-iph-method.Rd | 4 man/maximum-ph-ph-method.Rd | 4 man/maximum.Rd | 2 man/mdph-class.Rd | 4 man/mdph.Rd | 4 man/mdphdensity.Rd | 2 man/mean-MPHstar-method.Rd | 4 man/mean-bivdph-method.Rd | 4 man/mean-dph-method.Rd | 4 man/mean-mdph-method.Rd | 4 man/mean-mph-method.Rd | 4 man/mean-ph-method.Rd | 6 man/mgevcdf.Rd | 2 man/mgevden.Rd | 2 man/mgf-bivph-method.Rd | 4 man/mgf-mph-method.Rd | 4 man/mgf-ph-method.Rd | 8 man/mgf.Rd | 4 man/mgompertzcdf.Rd | 2 man/mgompertzden.Rd | 2 man/minimum-dph-dph-method.Rd | 4 man/minimum-iph-iph-method.Rd | 4 man/minimum-ph-ph-method.Rd | 4 man/minimum.Rd | 2 man/miph-class.Rd | 2 man/miph.Rd | 4 man/mixture-dph-dph-method.Rd | 4 man/mixture-ph-ph-method.Rd | 4 man/mixture.Rd | 2 man/mloglogisticcdf.Rd | 2 man/mloglogisticden.Rd | 2 man/mlognormalcdf.Rd | 2 man/mlognormalden.Rd | 2 man/moment-dph-method.Rd | 4 man/moment-mdph-method.Rd | 4 man/moment-mph-method.Rd | 4 man/moment-ph-method.Rd | 6 man/moment.Rd | 2 man/mparetocdf.Rd | 2 man/mparetoden.Rd | 2 man/mph-class.Rd | 2 man/mph.Rd | 4 man/mweibullcdf.Rd | 2 man/mweibullden.Rd | 2 man/new_state.Rd | 2 man/pgf-bivdph-method.Rd | 6 man/pgf-dph-method.Rd | 2 man/pgf-mdph-method.Rd | 4 man/pgf.Rd | 4 man/ph-class.Rd | 2 man/ph.Rd | 7 man/ph_laplace.Rd | 2 man/phcdf.Rd | 4 man/phdensity.Rd | 2 man/plus-dph-dph-method.Rd | 4 man/plus-ph-ph-method.Rd | 4 man/quan-ph-method.Rd | 4 man/quan.Rd | 2 man/rMIPHstar.Rd | 2 man/rMPHstar.Rd | 2 man/random_reward.Rd | 2 man/random_structure.Rd | 4 man/random_structure_bivph.Rd | 2 man/reg-ph-method.Rd | 8 man/reg.Rd | 2 man/revers_data_trans.Rd | 4 man/riph.Rd | 2 man/rmatrixgev.Rd | 2 man/show-MPHstar-method.Rd | 4 man/show-biviph-method.Rd | 4 man/show-dph-method.Rd | 4 man/show-iph-method.Rd | 4 man/show-mdph-method.Rd | 4 man/show-miph-method.Rd | 4 man/show-mph-method.Rd | 4 man/show-ph-method.Rd | 4 man/show-sph-method.Rd | 4 man/sim-MPHstar-method.Rd | 4 man/sim-bivdph-method.Rd | 2 man/sim-biviph-method.Rd | 2 man/sim-bivph-method.Rd | 2 man/sim-dph-method.Rd | 6 man/sim-iph-method.Rd | 6 man/sim-mdph-method.Rd | 4 man/sim-miph-method.Rd | 8 man/sim-mph-method.Rd | 4 man/sim-ph-method.Rd | 4 man/sim.Rd | 2 man/sph-class.Rd | 2 man/sph.Rd | 6 man/sum_dph.Rd | 8 man/sum_ph.Rd | 8 man/var-MPHstar-method.Rd | 4 man/var-bivdph-method.Rd | 4 man/var-bivph-method.Rd | 4 man/var-dph-method.Rd | 4 man/var-mdph-method.Rd | 4 man/var-mph-method.Rd | 4 man/var-ph-method.Rd | 6 src/Makevars | 14 - src/Makevars.win | 14 - src/dph_EM_LL.cpp | 4 194 files changed, 843 insertions(+), 867 deletions(-)
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 80 classes of statistical models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Marcio Augusto Diniz [ctb] ,
Noah Greifer [ctb] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.11.0 dated 2023-03-10 and 0.11.1 dated 2023-03-31
DESCRIPTION | 49 +++++++------- MD5 | 114 +++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 29 ++++++++ R/comparisons.R | 17 +++-- R/datagrid.R | 94 ++++++++++++++++++++++++---- R/get_contrast_data_numeric.R | 15 +++- R/get_contrasts.R | 20 +++-- R/get_predict.R | 6 + R/get_se_delta.R | 26 +++++-- R/hypotheses.R | 4 - R/methods_glmmTMB.R | 6 - R/methods_nlme.R |only R/methods_ordinal.R | 6 - R/plot_comparisons.R | 39 +++++++++-- R/plot_predictions.R | 33 ++++++++- R/plot_slopes.R | 13 +++ R/predictions.R | 25 ++++++- R/sanitize_comparison.R | 10 +- R/sanitize_newdata.R | 8 +- R/sanitize_variables.R | 10 ++ R/sanity_dots.R | 3 R/sanity_model.R | 3 R/set_coef.R | 7 +- R/slopes.R | 2 README.md | 6 - inst/WORDLIST | 40 +++++++++-- inst/tinytest/test-aaa-warn_once.R | 1 inst/tinytest/test-bugfix.R | 34 ++++++++++ inst/tinytest/test-by.R | 25 +++++++ inst/tinytest/test-comparisons.R | 6 + inst/tinytest/test-contrast.R | 3 inst/tinytest/test-datagrid.R | 37 +++++++++++ inst/tinytest/test-pkg-MASS.R | 14 ++-- inst/tinytest/test-pkg-fixest.R | 25 ++++--- inst/tinytest/test-pkg-glmmTMB.R | 5 - inst/tinytest/test-pkg-mclogit.R | 6 + inst/tinytest/test-pkg-nlme.R | 15 ++++ inst/tinytest/test-pkg-ordinal.R | 67 +++++++++++++++++++ inst/tinytest/test-pkg-phylolm.R |only inst/tinytest/test-pkg-pscl.R | 4 - inst/tinytest/test-pkg-robustlmm.R | 2 inst/tinytest/test-plot_comparisons.R | 23 ++++++ inst/tinytest/test-plot_predictions.R | 25 +++++++ inst/tinytest/test-plot_slopes.R | 22 ++++++ inst/tinytest/test-variables.R | 7 ++ inst/tinytest/test-weights.R | 75 +++++++++++++++++++++- man/comparisons.Rd | 14 +--- man/datagrid.Rd | 17 ++--- man/get_predict.Rd | 2 man/plot_cap.Rd | 44 +++++++++++++ man/plot_cco.Rd | 44 +++++++++++++ man/plot_cme.Rd | 44 +++++++++++++ man/plot_comparisons.Rd | 48 ++++++++++++++ man/plot_predictions.Rd | 48 ++++++++++++++ man/plot_slopes.Rd | 47 +++++++++++++- man/predictions.Rd | 3 man/set_coef.Rd | 9 +- man/slopes.Rd | 2 59 files changed, 1091 insertions(+), 213 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Block Forests: Random Forests for Blocks of Clinical and Omics
Covariate Data
Description: A random forest variant 'block forest' ('BlockForest') tailored to the
prediction of binary, survival and continuous outcomes using block-structured
covariate data, for example, clinical covariates plus measurements of a certain
omics data type or multi-omics data, that is, data for which measurements of
different types of omics data and/or clinical data for each patient exist. Examples
of different omics data types include gene expression measurements, mutation data
and copy number variation measurements.
Block forest are presented in Hornung & Wright (2019). The package includes four
other random forest variants for multi-omics data: 'RandomBlock', 'BlockVarSel',
'VarProb', and 'SplitWeights'. These were also considered in Hornung & Wright (2019),
but performed worse than block forest in their comparison study based on 20 real
multi-omics data sets. Therefore, we recommend to use block forest ('BlockForest')
in applications. The other random forest variants can, however, be c [...truncated...]
Author: Roman Hornung, Marvin N. Wright
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between blockForest versions 0.2.5 dated 2022-10-20 and 0.2.6 dated 2023-03-31
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- build/partial.rdb |binary src/AAA_check_cpp11.cpp | 4 ++-- src/Makevars | 2 -- src/Makevars.win | 2 -- 6 files changed, 13 insertions(+), 16 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for a single non-normal variable, ANOVA (Dag and Ilk, 2017) <doi:10.1080/03610918.2016.1204458> and Linear Models via different estimation techniques: maximum likelihood estimation, least square estimation, goodness-of-fit tests (Asar et al., 2017) <doi:10.1080/03610918.2014.957839>, artificial covariate (Dag et al., 2014) <doi:10.1080/03610918.2012.744042>, meta analysis (Yilmaz and Dag, 2022) <doi:10.28979/jarnas.1037343>. It also performs graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut], Muhammed Ali Yilmaz [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 2.7 dated 2022-06-13 and 2.8 dated 2023-03-31
DESCRIPTION | 12 +++--- MD5 | 16 ++++---- R/boxcoxfr.R | 73 ++++++++++++++++++++++++++-------------- R/boxcoxlm.R | 26 +++++++++----- R/boxcoxmeta.R | 41 ++++++++++++---------- R/boxcoxnc.R | 69 +++++++++++++++++++++----------------- inst/citation | 101 +++++++++++++++++++++++++++++++------------------------- man/AID.Rd | 2 - man/boxcoxfr.Rd | 2 - 9 files changed, 200 insertions(+), 142 deletions(-)
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee
(2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert
and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>. For
models with up to eight features, the results are exact regarding the
selected background data. Otherwise, an almost exact hybrid algorithm
involving iterative sampling is used. The package plays well together
with meta-learning packages like 'tidymodels', 'caret' or 'mlr3'.
Visualizations can be done using the R package 'shapviz'.
Author: Michael Mayer [aut, cre],
David Watson [aut],
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.3.4 dated 2023-02-25 and 0.3.5 dated 2023-03-31
kernelshap-0.3.4/kernelshap/man/ks_extract.Rd |only kernelshap-0.3.5/kernelshap/DESCRIPTION | 17 kernelshap-0.3.5/kernelshap/MD5 | 37 kernelshap-0.3.5/kernelshap/NAMESPACE | 3 kernelshap-0.3.5/kernelshap/NEWS.md | 16 kernelshap-0.3.5/kernelshap/R/exact.R | 16 kernelshap-0.3.5/kernelshap/R/kernelshap.R | 12 kernelshap-0.3.5/kernelshap/R/methods.R | 60 kernelshap-0.3.5/kernelshap/R/sampling.R | 19 kernelshap-0.3.5/kernelshap/R/utils.R | 32 kernelshap-0.3.5/kernelshap/README.md | 35 kernelshap-0.3.5/kernelshap/man/figures/README-lm-dep.svg | 2236 ++++----- kernelshap-0.3.5/kernelshap/man/figures/README-nn-dep.svg | 2421 ++++------ kernelshap-0.3.5/kernelshap/man/figures/README-rf-dep.svg | 2328 ++++----- kernelshap-0.3.5/kernelshap/man/is.kernelshap.Rd | 2 kernelshap-0.3.5/kernelshap/man/kernelshap.Rd | 3 kernelshap-0.3.5/kernelshap/tests/testthat/test-kernelshap-multioutput.R | 25 kernelshap-0.3.5/kernelshap/tests/testthat/test-kernelshap.R | 145 kernelshap-0.3.5/kernelshap/tests/testthat/test-methods.R | 30 kernelshap-0.3.5/kernelshap/tests/testthat/test-utils_etc.R | 93 20 files changed, 3778 insertions(+), 3752 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 5.8 dated 2022-11-09 and 5.9 dated 2023-03-31
DESCRIPTION | 10 MD5 | 32 +- NAMESPACE | 2 NEWS | 12 R/HelpersMG-package.R | 4 R/MHalgoGen.R | 30 +- R/RandomFromHessianOrMCMC.R | 2 R/SEfromHessian.R | 171 ++++++------ R/Snbinom.R | 583 ++++++++++++++++++++++++++++++----------- R/sysdata.rda |binary R/universalmclapply.R | 3 inst/shiny/cutter/ui.R | 2 man/HelpersMG-package.Rd | 4 man/MHalgoGen.Rd | 6 man/RandomFromHessianOrMCMC.Rd | 2 man/Snbinom.Rd | 353 ++++++++++++++++++------ man/universalmclapply.Rd | 3 17 files changed, 861 insertions(+), 358 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic,
and programmer friendly through a flexible and robust API. Core functionality
includes a rich set of S3 generic grouped and weighted statistical functions
for vectors, matrices and data frames, which provide efficient low-level
vectorizations, OpenMP multithreading, and skip missing values by default.
These are integrated with fast grouping and ordering algorithms (also callable
from C), and efficient data manipulation functions. The package also provides
a flexible and rigorous approach to time series and panel data in R. It further
includes fast functions for common statistical procedures, detailed (grouped,
weighted) summary statistics, powerful tools to work with nested data, fast
data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated wit [...truncated...]
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [ [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.9.3 dated 2023-02-27 and 1.9.4 dated 2023-03-31
DESCRIPTION | 8 MD5 | 50 ++--- NEWS.md | 8 R/descr.R | 13 - R/list_functions.R | 117 +++++++++---- inst/doc/collapse_documentation.html | 4 man/unlist2d.Rd | 2 src/TRA.c | 287 ++++++++++++++++++++++------------ src/collapse_c.h | 13 + src/data.table_init.c | 14 - src/ffirst.c | 2 src/flast.c | 2 src/fmean.c | 96 ++++++----- src/fmin_fmax.c | 6 src/fmode.c | 12 - src/fndistinct.c | 18 -- src/fnobs.c | 11 - src/fnth_fmedian_fquantile.c | 8 src/fprod.c | 3 src/fsum.c | 72 ++++---- src/gsplit.c | 12 - src/handle_attributes.c | 3 src/programming.c | 116 +++++++------ src/small_helper.c | 17 +- tests/testthat/test-list-processing.R | 2 tests/testthat/test-misc.R | 1 26 files changed, 540 insertions(+), 357 deletions(-)
Title: Constrained Multivariate Least Squares
Description: Solves multivariate least squares (MLS) problems subject to constraints on the coefficients, e.g., non-negativity, orthogonality, equality, inequality, monotonicity, unimodality, smoothness, etc. Includes flexible functions for solving MLS problems subject to user-specified equality and/or inequality constraints, as well as a wrapper function that implements 24 common constraint options. Also does k-fold or generalized cross-validation to tune constraint options for MLS problems. See ten Berge (1993, ISBN:9789066950832) for an overview of MLS problems, and see Goldfarb and Idnani (1983) <doi:10.1007/BF02591962> for a discussion of the underlying quadratic programming algorithm.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between CMLS versions 1.0-0 dated 2018-06-10 and 1.0-1 dated 2023-03-31
ChangeLog |only DESCRIPTION | 8 +++---- MD5 | 29 ++++++++++++++----------- R/IsplineBasis.R | 4 +-- R/cmls.R | 58 ++++++++++++++++++++++++++++++++++----------------- R/cv.cmls.R | 9 ++++++- R/kcvmae.R | 2 - R/kcvmse.R | 2 - build/partial.rdb |binary man/CMLS-internal.Rd | 2 - man/CMLS-package.Rd | 4 +-- man/IsplineBasis.Rd |only man/MsplineBasis.Rd |only man/cmls.Rd | 9 ++++--- man/cv.cmls.Rd | 12 +++++----- man/mlsei.Rd | 4 +-- man/mlsun.Rd | 4 +-- 17 files changed, 87 insertions(+), 60 deletions(-)
Title: Two-Way Tests in Independent Groups Designs
Description: Performs two-way tests in independent groups designs. These are two-way ANOVA, two-way ANOVA under heteroscedasticity: parametric bootstrap based generalized test and generalized pivotal quantity based generalized test (Ananda et al., 2022) <doi:10.1080/03610926.2022.2059682>, two-way ANOVA for medians, trimmed means, M-estimators (Wilcox, 2011; ISBN:978-0-12-386983-8). The package performs descriptive statistics and graphical approaches. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots. All 'twowaytests' functions are designed for two-way layout.
Author: Osman Dag [aut, cre], Sam Weerahandi [aut], Malwane Ananda [aut], Muhammed Ali Yilmaz [aut], Merve Kasikci [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between twowaytests versions 1.2 dated 2023-02-23 and 1.3 dated 2023-03-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/paircompTwoWay.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database
from the downloaded images. All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 1.0.0 dated 2023-03-17 and 1.0.1 dated 2023-03-31
DESCRIPTION | 8 +-- MD5 | 83 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 7 +++ R/export_notes.R |only README.md | 16 ++++++ man/export_notes.Rd |only tests/covr.R | 5 +- tests/testthat/test-all_ids_mi2b2.R | 2 tests/testthat/test-convert_dia.R | 2 tests/testthat/test-convert_enc.R | 2 tests/testthat/test-convert_lab.R | 2 tests/testthat/test-convert_med.R | 2 tests/testthat/test-convert_notes.R | 2 tests/testthat/test-convert_phy.R | 2 tests/testthat/test-convert_prc.R | 2 tests/testthat/test-convert_rfv.R | 2 tests/testthat/test-create_img_db.R | 2 tests/testthat/test-export_notes.R |only tests/testthat/test-find_exam.R | 2 tests/testthat/test-load_all.R | 2 tests/testthat/test-load_all_data.R | 2 tests/testthat/test-load_bib.R | 2 tests/testthat/test-load_con.R | 2 tests/testthat/test-load_dem.R | 2 tests/testthat/test-load_dem_old.R | 2 tests/testthat/test-load_dia.R | 2 tests/testthat/test-load_enc.R | 2 tests/testthat/test-load_lab.R | 2 tests/testthat/test-load_lno.R | 2 tests/testthat/test-load_mcm.R | 2 tests/testthat/test-load_med.R | 2 tests/testthat/test-load_mic.R | 2 tests/testthat/test-load_mrn.R | 2 tests/testthat/test-load_notes.R | 2 tests/testthat/test-load_phy.R | 2 tests/testthat/test-load_prc.R | 2 tests/testthat/test-load_prv.R | 2 tests/testthat/test-load_ptd.R | 2 tests/testthat/test-load_rdt.R | 2 tests/testthat/test-load_rfv.R | 2 tests/testthat/test-load_trn.R | 2 tests/testthat/test-pretty_mrn.R | 2 tests/testthat/test-pretty_text.R | 2 44 files changed, 108 insertions(+), 82 deletions(-)
Title: Diallel Analysis with R
Description: Performs Diallel Analysis with R using Griffing's and Hayman's approaches. Four different Methods (1: Method-I (Parents + F1's + reciprocals); 2: Method-II (Parents and one set of F1's); 3: Method-III (One set of F1's and reciprocals); 4: Method-IV (One set of F1's only)) and two Models (1: Fixed Effects Model; 2: Random Effects Model) can be applied using Griffing's approach.
Author: Muhammad Yaseen [aut, cre, cph]
,
Kent M. Eskridge [ctb, aut],
Pedro A. M. Barbosa [ctb, aut],
Yuhang Guo [ctb, aut]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between DiallelAnalysisR versions 0.4.0 dated 2021-02-25 and 0.5.0 dated 2023-03-31
DESCRIPTION | 32 +++++---- MD5 | 10 +- NEWS.md | 43 +++++++----- R/Griffing.R | 66 +++++++++--------- README.md | 205 ++++++++++++++++++++++++++++------------------------------ inst/CITATION | 58 ++-------------- 6 files changed, 191 insertions(+), 223 deletions(-)
More information about DiallelAnalysisR at CRAN
Permanent link
Title: Bayesian Modeling of Spatio-Temporal Data with R
Description: Fits, validates and compares a number of Bayesian models for
spatial and space time point referenced and areal unit data. Model fitting
is done using several packages: 'rstan', 'INLA', 'spBayes', 'spTimer',
'spTDyn', 'CARBayes' and 'CARBayesST'. Model comparison is performed using
the DIC and WAIC, and K-fold cross-validation where the user is free
to select their own subset of data rows for validation. Sahu (2022)
<doi:10.1201/9780429318443> describes the methods in detail.
Author: Sujit K. Sahu [aut, cre] ,
Duncan P. Lee [aut],
K. Shuvo Bakar [aut]
Maintainer: Sujit K. Sahu <S.K.Sahu@soton.ac.uk>
Diff between bmstdr versions 0.3.0 dated 2022-07-14 and 0.4.1 dated 2023-03-31
DESCRIPTION | 39 ++-- MD5 | 32 ++- R/Bmoving_sptime.R | 36 +++- R/stanmodels.R | 56 +++--- R/utilities.R | 30 +-- build/partial.rdb |binary configure |only configure.win |only inst/doc/bmstdr-vig_bookdown.html | 300 +++++++++++++++++++----------------- inst/stan/ind_gpp_marginal.stan | 9 - man/Bmoving_sptime.Rd | 18 ++ src/Makevars | 3 src/Makevars.win | 3 src/stanExports_gp_marginal.cc | 2 src/stanExports_ind_gpp_marginal.cc | 2 src/stanExports_ind_gpp_marginal.h | 269 +++++++++++++++----------------- src/stanExports_normal.cc | 2 src/stanExports_spatial_model.cc | 2 18 files changed, 431 insertions(+), 372 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.1.0 dated 2023-02-11 and 3.1.1 dated 2023-03-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/lmbasic.R | 4 ++-- R/lmcovlatent.R | 4 ++-- inst/doc/vignetteLMest.html | 6 +++--- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: Analysis of the International Trade Network
Description: Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
Author: Matthew Smith
Maintainer: Matthew Smith <matt_smith.90@hotmail.co.uk>
Diff between ITNr versions 0.6.0 dated 2020-03-11 and 0.7.0 dated 2023-03-31
ITNr-0.6.0/ITNr/R/adjust_mat_function.R |only ITNr-0.6.0/ITNr/man/adjust_mat.Rd |only ITNr-0.7.0/ITNr/DESCRIPTION | 10 ITNr-0.7.0/ITNr/MD5 | 90 ++++--- ITNr-0.7.0/ITNr/NAMESPACE | 8 ITNr-0.7.0/ITNr/R/Comtradrclean_function.R | 58 +---- ITNr-0.7.0/ITNr/R/ITNadjust_function.R | 2 ITNr-0.7.0/ITNr/R/ITNcentrality_function.R | 89 +------ ITNr-0.7.0/ITNr/R/ITNproperties_base_function.R |only ITNr-0.7.0/ITNr/R/ITNproperties_function.R | 214 ++++++++++++------- ITNr-0.7.0/ITNr/R/WITSclean_function.R | 14 - ITNr-0.7.0/ITNr/R/abs_diff_mat_function.R |only ITNr-0.7.0/ITNr/R/core_periphery_weighted_function.R | 2 ITNr-0.7.0/ITNr/R/make_trade_network_function.R |only ITNr-0.7.0/ITNr/R/receiver_mat_function.R |only ITNr-0.7.0/ITNr/R/sender_mat_function.R |only ITNr-0.7.0/ITNr/man/Comtradrclean.Rd | 85 ++----- ITNr-0.7.0/ITNr/man/ELEnet16.Rd | 32 +- ITNr-0.7.0/ITNr/man/ELEnetList.Rd | 32 +- ITNr-0.7.0/ITNr/man/ITN_make_plot.Rd | 66 ++--- ITNr-0.7.0/ITNr/man/ITN_map_plot.Rd | 54 ++-- ITNr-0.7.0/ITNr/man/ITNadjust.Rd | 88 +++---- ITNr-0.7.0/ITNr/man/ITNblock_plot.Rd | 68 +++--- ITNr-0.7.0/ITNr/man/ITNblock_se.Rd | 64 ++--- ITNr-0.7.0/ITNr/man/ITNcentrality.Rd | 64 ++--- ITNr-0.7.0/ITNr/man/ITNcentrality_binary.Rd | 60 ++--- ITNr-0.7.0/ITNr/man/ITNcluster.Rd | 52 ++-- ITNr-0.7.0/ITNr/man/ITNcorr.Rd | 60 ++--- ITNr-0.7.0/ITNr/man/ITNdegdist.Rd | 54 ++-- ITNr-0.7.0/ITNr/man/ITNdynamic.Rd | 76 +++--- ITNr-0.7.0/ITNr/man/ITNhistdegdist.Rd | 58 ++--- ITNr-0.7.0/ITNr/man/ITNimvex.Rd | 68 +++--- ITNr-0.7.0/ITNr/man/ITNplotset.Rd | 58 ++--- ITNr-0.7.0/ITNr/man/ITNproperties.Rd | 62 ++--- ITNr-0.7.0/ITNr/man/ITNproperties_base.Rd |only ITNr-0.7.0/ITNr/man/WITSclean.Rd | 61 ++--- ITNr-0.7.0/ITNr/man/abs_diff_mat.Rd |only ITNr-0.7.0/ITNr/man/cap_lat_lon.Rd | 24 +- ITNr-0.7.0/ITNr/man/core_periphery_weighted.Rd | 78 +++--- ITNr-0.7.0/ITNr/man/ei_group.Rd | 68 +++--- ITNr-0.7.0/ITNr/man/ei_ind.Rd | 68 +++--- ITNr-0.7.0/ITNr/man/ei_network.Rd | 68 +++--- ITNr-0.7.0/ITNr/man/get.backbone.Rd | 74 +++--- ITNr-0.7.0/ITNr/man/isEmpty.Rd | 32 +- ITNr-0.7.0/ITNr/man/make_trade_network.Rd |only ITNr-0.7.0/ITNr/man/mixing_matrix_igraph.Rd | 66 ++--- ITNr-0.7.0/ITNr/man/plot_degree_distribution.Rd | 54 ++-- ITNr-0.7.0/ITNr/man/receiver_mat.Rd |only ITNr-0.7.0/ITNr/man/region_circle_plot.Rd | 52 ++-- ITNr-0.7.0/ITNr/man/reorder_df.Rd | 62 ++--- ITNr-0.7.0/ITNr/man/round_df.Rd | 58 ++--- ITNr-0.7.0/ITNr/man/sender_mat.Rd |only 52 files changed, 1154 insertions(+), 1199 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2022)
<doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple
measurements per individual, time-varying and time-invariant effects, and a
wide range of discrete and continuous distributions. Estimation of these
dynamic multivariate panel models is carried out via 'Stan'.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.1.1 dated 2023-02-03 and 1.3.1 dated 2023-03-31
dynamite-1.1.1/dynamite/R/default_priors.R |only dynamite-1.1.1/dynamite/R/exported_gets.R |only dynamite-1.1.1/dynamite/data/latent_factor_example.rda |only dynamite-1.1.1/dynamite/data/latent_factor_example_fit.rda |only dynamite-1.1.1/dynamite/man/latent_factor_example.Rd |only dynamite-1.1.1/dynamite/man/latent_factor_example_fit.Rd |only dynamite-1.3.1/dynamite/DESCRIPTION | 14 dynamite-1.3.1/dynamite/MD5 | 222 dynamite-1.3.1/dynamite/NAMESPACE | 4 dynamite-1.3.1/dynamite/NEWS.md | 157 dynamite-1.3.1/dynamite/R/as_data_frame.R | 55 dynamite-1.3.1/dynamite/R/as_data_table.R | 1235 +-- dynamite-1.3.1/dynamite/R/as_draws.R | 10 dynamite-1.3.1/dynamite/R/ci.R | 5 dynamite-1.3.1/dynamite/R/coef.R | 6 dynamite-1.3.1/dynamite/R/deterministic.R | 24 dynamite-1.3.1/dynamite/R/dynamite-package.R | 121 dynamite-1.3.1/dynamite/R/dynamite.R | 726 -- dynamite-1.3.1/dynamite/R/dynamiteformula.R | 1318 ++- dynamite-1.3.1/dynamite/R/families.R | 35 dynamite-1.3.1/dynamite/R/fitted.R | 6 dynamite-1.3.1/dynamite/R/getters.R |only dynamite-1.3.1/dynamite/R/lags.R | 384 + dynamite-1.3.1/dynamite/R/latent_factor.R | 171 dynamite-1.3.1/dynamite/R/lfo.R | 26 dynamite-1.3.1/dynamite/R/loo.R | 1 dynamite-1.3.1/dynamite/R/mcmc_diagnostics.R | 3 dynamite-1.3.1/dynamite/R/model_matrix.R | 67 dynamite-1.3.1/dynamite/R/ndraws.R | 1 dynamite-1.3.1/dynamite/R/nobs.R | 69 dynamite-1.3.1/dynamite/R/plot.R | 37 dynamite-1.3.1/dynamite/R/predict.R | 406 - dynamite-1.3.1/dynamite/R/predict_helpers.R | 2446 ++++-- dynamite-1.3.1/dynamite/R/prepare_stan_input.R | 2092 +++-- dynamite-1.3.1/dynamite/R/print.R | 15 dynamite-1.3.1/dynamite/R/priors.R |only dynamite-1.3.1/dynamite/R/random.R | 89 dynamite-1.3.1/dynamite/R/specials.R | 129 dynamite-1.3.1/dynamite/R/splines.R | 5 dynamite-1.3.1/dynamite/R/stan_utilities.R |only dynamite-1.3.1/dynamite/R/stanblocks.R | 727 +- dynamite-1.3.1/dynamite/R/stanblocks_families.R | 3512 ++++------ dynamite-1.3.1/dynamite/R/summary.R | 1 dynamite-1.3.1/dynamite/R/sysdata.rda |binary dynamite-1.3.1/dynamite/R/update.R | 21 dynamite-1.3.1/dynamite/R/utilities.R | 118 dynamite-1.3.1/dynamite/README.md | 27 dynamite-1.3.1/dynamite/build/vignette.rds |binary dynamite-1.3.1/dynamite/data/categorical_example_fit.rda |binary dynamite-1.3.1/dynamite/data/gaussian_example_fit.rda |binary dynamite-1.3.1/dynamite/data/gaussian_simulation_fit.rda |only dynamite-1.3.1/dynamite/data/multichannel_example_fit.rda |binary dynamite-1.3.1/dynamite/inst/CITATION | 34 dynamite-1.3.1/dynamite/inst/doc/dynamite.R | 332 dynamite-1.3.1/dynamite/inst/doc/dynamite.Rmd | 910 +- dynamite-1.3.1/dynamite/inst/doc/dynamite.html | 1316 +-- dynamite-1.3.1/dynamite/inst/doc/dynamite_priors.R |only dynamite-1.3.1/dynamite/inst/doc/dynamite_priors.Rmd |only dynamite-1.3.1/dynamite/inst/doc/dynamite_priors.html |only dynamite-1.3.1/dynamite/inst/doc/dynamite_simulation.R |only dynamite-1.3.1/dynamite/inst/doc/dynamite_simulation.Rmd |only dynamite-1.3.1/dynamite/inst/doc/dynamite_simulation.html |only dynamite-1.3.1/dynamite/man/as.data.frame.dynamitefit.Rd | 70 dynamite-1.3.1/dynamite/man/as.data.table.dynamitefit.Rd | 16 dynamite-1.3.1/dynamite/man/as_draws-dynamitefit.Rd | 25 dynamite-1.3.1/dynamite/man/categorical_example.Rd | 10 dynamite-1.3.1/dynamite/man/categorical_example_fit.Rd | 10 dynamite-1.3.1/dynamite/man/coef.dynamitefit.Rd | 16 dynamite-1.3.1/dynamite/man/confint.dynamitefit.Rd | 20 dynamite-1.3.1/dynamite/man/dynamite.Rd | 63 dynamite-1.3.1/dynamite/man/dynamiteformula.Rd | 39 dynamite-1.3.1/dynamite/man/figures/README-unnamed-chunk-10-1.png |binary dynamite-1.3.1/dynamite/man/fitted.dynamitefit.Rd | 10 dynamite-1.3.1/dynamite/man/gaussian_example.Rd | 10 dynamite-1.3.1/dynamite/man/gaussian_example_fit.Rd | 10 dynamite-1.3.1/dynamite/man/gaussian_simulation_fit.Rd |only dynamite-1.3.1/dynamite/man/get_code.Rd | 20 dynamite-1.3.1/dynamite/man/get_data.Rd | 18 dynamite-1.3.1/dynamite/man/get_parameter_dims.Rd |only dynamite-1.3.1/dynamite/man/get_parameter_names.Rd | 26 dynamite-1.3.1/dynamite/man/get_parameter_types.Rd | 18 dynamite-1.3.1/dynamite/man/get_priors.Rd | 21 dynamite-1.3.1/dynamite/man/lags.Rd | 9 dynamite-1.3.1/dynamite/man/lfactor.Rd | 49 dynamite-1.3.1/dynamite/man/lfo.Rd | 8 dynamite-1.3.1/dynamite/man/loo.dynamitefit.Rd | 6 dynamite-1.3.1/dynamite/man/mcmc_diagnostics.Rd | 6 dynamite-1.3.1/dynamite/man/multichannel_example.Rd | 10 dynamite-1.3.1/dynamite/man/multichannel_example_fit.Rd | 10 dynamite-1.3.1/dynamite/man/ndraws.dynamitefit.Rd | 16 dynamite-1.3.1/dynamite/man/nobs.dynamitefit.Rd | 18 dynamite-1.3.1/dynamite/man/plot.dynamitefit.Rd | 22 dynamite-1.3.1/dynamite/man/plot.lfo.Rd | 4 dynamite-1.3.1/dynamite/man/plot_betas.Rd | 9 dynamite-1.3.1/dynamite/man/plot_deltas.Rd | 9 dynamite-1.3.1/dynamite/man/plot_lambdas.Rd | 9 dynamite-1.3.1/dynamite/man/plot_nus.Rd | 9 dynamite-1.3.1/dynamite/man/plot_psis.Rd | 9 dynamite-1.3.1/dynamite/man/predict.dynamitefit.Rd | 20 dynamite-1.3.1/dynamite/man/print.lfo.Rd | 4 dynamite-1.3.1/dynamite/man/random_spec.Rd | 9 dynamite-1.3.1/dynamite/man/roxygen |only dynamite-1.3.1/dynamite/man/splines.Rd | 13 dynamite-1.3.1/dynamite/man/update.dynamitefit.Rd | 18 dynamite-1.3.1/dynamite/tests/README.md | 8 dynamite-1.3.1/dynamite/tests/testthat/grunfeld.rds |only dynamite-1.3.1/dynamite/tests/testthat/test-cmdstanr.R |only dynamite-1.3.1/dynamite/tests/testthat/test-edgecases.R | 1115 +-- dynamite-1.3.1/dynamite/tests/testthat/test-errors.R | 325 dynamite-1.3.1/dynamite/tests/testthat/test-extended.R |only dynamite-1.3.1/dynamite/tests/testthat/test-grunfeld.R | 46 dynamite-1.3.1/dynamite/tests/testthat/test-internals.R | 356 - dynamite-1.3.1/dynamite/tests/testthat/test-lfactor.R |only dynamite-1.3.1/dynamite/tests/testthat/test-output.R | 470 - dynamite-1.3.1/dynamite/tests/testthat/test-predict.R | 131 dynamite-1.3.1/dynamite/tests/testthat/test-priors.R | 108 dynamite-1.3.1/dynamite/tests/testthat/test-random.R |only dynamite-1.3.1/dynamite/tests/testthat/test-recovery.R | 97 dynamite-1.3.1/dynamite/tests/testthat/test-scaling.R | 10 dynamite-1.3.1/dynamite/tests/testthat/test-warnings.R | 475 - dynamite-1.3.1/dynamite/vignettes/dag.png |binary dynamite-1.3.1/dynamite/vignettes/dynamite.Rmd | 910 +- dynamite-1.3.1/dynamite/vignettes/dynamite.bib | 1021 +- dynamite-1.3.1/dynamite/vignettes/dynamite_priors.Rmd |only dynamite-1.3.1/dynamite/vignettes/dynamite_simulation.Rmd |only 125 files changed, 12459 insertions(+), 10159 deletions(-)
Title: Adaptive Trial Simulator
Description: Package that simulates adaptive (multi-arm, multi-stage) clinical
trials using adaptive stopping, adaptive arm dropping, and/or adaptive
randomisation. Developed as part of the INCEPT (Intensive Care Platform
Trial) project (<https://incept.dk/>), which is primarily supported by a
grant from Sygeforsikringen "danmark" (<https://www.sygeforsikring.dk/>).
Author: Anders Granholm [aut, cre] ,
Benjamin Skov Kaas-Hansen [aut]
,
Aksel Karl Georg Jensen [ctb] ,
Theis Lange [ctb]
Maintainer: Anders Granholm <andersgran@gmail.com>
Diff between adaptr versions 1.2.0 dated 2022-12-13 and 1.3.0 dated 2023-03-31
DESCRIPTION | 26 MD5 | 233 - NAMESPACE | 11 NEWS.md | 129 R/adaptr-package.R | 42 R/calibrate_trial.R |only R/check_performance.R | 246 - R/check_remaining_arms.R |only R/extract_results.R | 339 + R/get_ys_and_draws.R | 309 - R/gp_opt.R |only R/plot_convergence.R | 50 R/plot_history.R | 60 R/plot_metrics_ecdf.R |only R/plot_status.R | 18 R/print.R | 105 R/prob_funs.R | 8 R/run_trial.R | 62 R/run_trials.R | 179 - R/setup_cluster.R |only R/setup_trial.R | 289 - R/summary.R | 31 R/test_helpers.R | 7 R/update_saved_trials.R | 25 R/utils.R | 58 R/zzz.R | 15 README.md | 96 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 44 inst/doc/Advanced-example.R | 4 inst/doc/Advanced-example.Rmd | 31 inst/doc/Advanced-example.html | 59 inst/doc/Basic-examples.R | 1 inst/doc/Basic-examples.Rmd | 32 inst/doc/Basic-examples.html | 107 inst/doc/Overview.R | 6 inst/doc/Overview.Rmd | 93 inst/doc/Overview.html | 266 - inst/testdata/binom__results__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened__sparse.RData |binary inst/testdata/binom__setup__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__setup__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/norm__results__3_arms__common_control__fixed__all_arms_fixed.RData |binary inst/testdata/norm__setup__3_arms__common_control__fixed__all_arms_fixed.RData |binary inst/testdata/norm__setup__3_arms__common_control__matched__varying_probs.RData |binary man/adaptr-package.Rd | 36 man/calculate_idp.Rd | 2 man/calibrate_trial.Rd |only man/check_performance.Rd | 164 man/check_remaining_arms.Rd |only man/cov_mat.Rd |only man/dispatch_trial_runs.Rd | 31 man/equivalent_funs.Rd | 7 man/extract_results.Rd | 96 man/extract_results_batch.Rd |only man/extract_statuses.Rd | 9 man/figures/README-plot-1.png |binary man/figures/README-plot-2.png |binary man/get_draws_binom.Rd | 2 man/get_draws_generic.Rd | 2 man/get_draws_norm.Rd | 14 man/gp_opt.Rd |only man/make_x_scale.Rd | 5 man/make_y_scale.Rd | 4 man/plot_convergence.Rd | 103 man/plot_history.Rd | 41 man/plot_metrics_ecdf.Rd |only man/plot_status.Rd | 21 man/pow_abs_dist.Rd |only man/print.Rd | 92 man/prob_all_equi.Rd | 14 man/prob_better.Rd | 16 man/prog_breaks.Rd | 24 man/reallocate_probs.Rd | 21 man/run_trial.Rd | 56 man/run_trials.Rd | 61 man/setup_cluster.Rd |only man/setup_trial.Rd | 233 - man/setup_trial_binom.Rd | 141 man/setup_trial_norm.Rd | 135 man/summarise_dist.Rd | 4 man/summarise_num.Rd | 6 man/summary.Rd | 91 man/update_saved_trials.Rd | 21 man/validate_trial.Rd | 132 man/verify_int.Rd | 3 man/which_nearest.Rd |only tests/testthat/_snaps/calibrate_trial |only tests/testthat/_snaps/calibrate_trial.md |only tests/testthat/_snaps/check_performance.md | 630 +-- tests/testthat/_snaps/check_remaining_arms.md |only tests/testthat/_snaps/extract.md | 1732 +++++----- tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-2-splits.svg | 88 tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-prob-concl-prob-sup-idp.svg | 292 - tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-size-mean-rmse-selected.svg | 73 tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-size-mean-superior.svg | 35 tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-size-mean.svg | 45 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-followed-n-2-cores.svg |only tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-followed-n.svg | 46 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-total-n.svg | 46 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct.svg | 46 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-prob.svg | 46 tests/testthat/_snaps/plot_metrics_ecdf |only tests/testthat/_snaps/plot_status.md | 342 - tests/testthat/_snaps/plot_status/status-plot-across-arms-binomial.svg | 38 tests/testthat/_snaps/plot_status/status-plot-for-all-arms-binomial.svg | 126 tests/testthat/_snaps/plot_status/status-plot-for-arm-c-binom.svg | 42 tests/testthat/_snaps/run_trials.md | 975 +++-- tests/testthat/_snaps/setup_trial.md | 248 - tests/testthat/_snaps/summary-print.md | 742 ++-- tests/testthat/_snaps/utils.md | 24 tests/testthat/test-calibrate_trial.R |only tests/testthat/test-check_performance.R | 15 tests/testthat/test-check_remaining_arms.R |only tests/testthat/test-extract.R | 9 tests/testthat/test-gp_opt.R |only tests/testthat/test-plot_history.R | 5 tests/testthat/test-plot_metrics_ecdf.R |only tests/testthat/test-run_trials.R | 38 tests/testthat/test-setup_cluster.R |only tests/testthat/test-setup_trial.R | 11 tests/testthat/test-update_saved_trials.R | 8 tests/testthat/test-utils.R | 9 vignettes/Advanced-example.Rmd | 31 vignettes/Basic-examples.Rmd | 32 vignettes/Overview.Rmd | 93 128 files changed, 5879 insertions(+), 4556 deletions(-)
Title: Create Maps of Air Pollution Data
Description: Combine the air quality data analysis methods of 'openair'
with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library.
Functionality includes plotting site maps, "directional analysis"
figures such as polar plots, and air mass trajectories.
Author: Jack Davison [cre, aut],
David Carslaw [aut]
Maintainer: Jack Davison <davison.jack.jd@gmail.com>
Diff between openairmaps versions 0.7.0 dated 2023-02-09 and 0.8.0 dated 2023-03-31
DESCRIPTION | 13 - MD5 | 92 ++++--- NAMESPACE | 3 NEWS.md | 144 ++++++++---- R/addPolarMarkers.R | 37 +-- R/networkMap.R | 186 ++++++++++----- R/openairmaps-package.R | 3 R/polar_annulusMap.R | 38 ++- R/polar_diffMap.R | 69 ++++- R/polar_freqMap.R | 38 ++- R/polar_percentileMap.R | 37 ++- R/polar_polarMap.R | 65 +++-- R/polar_pollroseMap.R | 35 ++ R/polar_windroseMap.R | 37 ++- R/traj_trajLevelMap.R | 394 +++++++++++++++++++++++++++------ R/traj_trajMap.R | 197 +++++++++++++++- R/utils-map.R | 128 +++++++--- README.md | 8 man/annulusMap.Rd | 21 - man/annulusMapStatic.Rd | 7 man/diffMap.Rd | 23 + man/diffMapStatic.Rd | 7 man/figures/README-static-1.png |binary man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/freqMap.Rd | 21 - man/freqMapStatic.Rd | 7 man/networkMap.Rd | 11 man/percentileMap.Rd | 21 - man/percentileMapStatic.Rd | 7 man/polarMap.Rd | 21 - man/polarMapStatic.Rd | 7 man/pollroseMap.Rd | 21 - man/pollroseMapStatic.Rd | 7 man/trajLevelMap.Rd | 78 ++++-- man/trajLevelMapStatic.Rd |only man/trajMap.Rd | 16 - man/trajMapStatic.Rd |only man/windroseMap.Rd | 21 - man/windroseMapStatic.Rd | 7 tests |only 47 files changed, 1339 insertions(+), 488 deletions(-)
Title: Non-Negative and Sparse CCA
Description: Two implementations of canonical correlation analysis
(CCA) that are based on iterated regression. By choosing the
appropriate regression algorithm for each data domain, it is
possible to enforce sparsity, non-negativity or other kinds of
constraints on the projection vectors. Multiple canonical
variables are computed sequentially using a generalized
deflation scheme, where the additional correlation not
explained by previous variables is maximized. nscancor() is
used to analyze paired data from two domains, and has the same
interface as cancor() from the 'stats' package (plus some extra
parameters). mcancor() is appropriate for analyzing data from
three or more domains. See
<https://sigg-iten.ch/learningbits/2014/01/20/canonical-correlation-analysis-under-constraints/>
and Sigg et al. (2007) <doi:10.1109/MLSP.2007.4414315> for more
details.
Author: Christian Sigg [aut, cph, cre]
,
R Core team [cph, ctb] interface and documentation)
Maintainer: Christian Sigg <christian@sigg-iten.ch>
Diff between nscancor versions 0.6.1-25 dated 2018-02-15 and 0.7.0-6 dated 2023-03-31
nscancor-0.6.1-25/nscancor/man/cardinality.Rd |only nscancor-0.6.1-25/nscancor/tests/testthat/test_acor.R |only nscancor-0.6.1-25/nscancor/tests/testthat/test_macor.R |only nscancor-0.6.1-25/nscancor/tests/testthat/test_mcancor.R |only nscancor-0.6.1-25/nscancor/tests/testthat/test_nscancor.R |only nscancor-0.7.0-6/nscancor/DESCRIPTION | 38 +-- nscancor-0.7.0-6/nscancor/MD5 | 43 +-- nscancor-0.7.0-6/nscancor/NAMESPACE | 3 nscancor-0.7.0-6/nscancor/NEWS.md |only nscancor-0.7.0-6/nscancor/R/acor.R | 10 nscancor-0.7.0-6/nscancor/R/cardinality.R | 17 + nscancor-0.7.0-6/nscancor/R/macor.R | 9 nscancor-0.7.0-6/nscancor/R/mcancor.R | 8 nscancor-0.7.0-6/nscancor/R/nscancor-package.R | 3 nscancor-0.7.0-6/nscancor/R/nscancor.R | 18 - nscancor-0.7.0-6/nscancor/README.md | 4 nscancor-0.7.0-6/nscancor/inst/atexample/acor_examples.R |only nscancor-0.7.0-6/nscancor/inst/atexample/macor_examples.R |only nscancor-0.7.0-6/nscancor/inst/atexample/mcancor_examples.R | 74 +++--- nscancor-0.7.0-6/nscancor/inst/atexample/nscancor_examples.R | 95 ++++--- nscancor-0.7.0-6/nscancor/man/acor.Rd | 34 ++ nscancor-0.7.0-6/nscancor/man/colCardinalities.Rd |only nscancor-0.7.0-6/nscancor/man/macor.Rd | 14 + nscancor-0.7.0-6/nscancor/man/mcancor.Rd | 92 ++++--- nscancor-0.7.0-6/nscancor/man/nscancor.Rd | 134 ++++++----- nscancor-0.7.0-6/nscancor/tests/testthat/test-acor.R |only nscancor-0.7.0-6/nscancor/tests/testthat/test-macor.R |only nscancor-0.7.0-6/nscancor/tests/testthat/test-mcancor.R |only nscancor-0.7.0-6/nscancor/tests/testthat/test-nscancor.R |only 29 files changed, 363 insertions(+), 233 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut],
Jina Park [aut, cre],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Jina Park <pja0707@yonsei.ac.kr>
Diff between lsirm12pl versions 1.1.0 dated 2022-10-18 and 1.2.0 dated 2023-03-31
DESCRIPTION | 13 MD5 | 34 NAMESPACE | 14 R/RcppExports.R | 12 R/lsirm12pl-package.R | 9 R/lsirm1pl_normal.R |only R/lsirm2pl_normal.R |only R/plot.lsirm.R | 316 +++- R/print.summary.R |only R/print.summary.lsirm.R | 2 R/utilities.R | 286 ++++ data/BFPT.csv | 2990 ++++++++++++++++++++++++++++++--------------- data/TDRI.csv | 2154 ++++++++++++++++---------------- man/lsirm1pl_normal.Rd |only man/lsirm2pl_normal.Rd |only man/plot.lsirm.Rd | 15 man/print.summary.lsirm.Rd | 14 src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 45 src/lsirm2pl_mcar_ss.cpp | 148 +- src/utility_cpp.cpp |only 22 files changed, 3827 insertions(+), 2225 deletions(-)
Title: Tools for Create Emissions for Air Quality Models
Description: Processing tools to create emissions for use in numerical air
quality models. Emissions can be calculated both using emission factors
and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using
pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>.
Functions to process individual point emissions, line emissions and
area emissions of pollutants are available as well as methods to
incorporate alternative data for Spatial distribution of emissions
such as satellite images (Gavidia Calderon et. al, 2018)
<doi:10.1016/j.atmosenv.2018.09.026> or openstreetmap data
(Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
Author: Daniel Schuch [aut, cre] ,
Sergio Ibarra-Espinosa [aut]
Maintainer: Daniel Schuch <underschuch@gmail.com>
Diff between EmissV versions 0.665.6.3 dated 2022-06-01 and 0.665.6.6 dated 2023-03-31
EmissV-0.665.6.3/EmissV/inst/extdata/streets.osm.xz |only EmissV-0.665.6.6/EmissV/DESCRIPTION | 17 +++--- EmissV-0.665.6.6/EmissV/MD5 | 37 +++++++------- EmissV-0.665.6.6/EmissV/NAMESPACE | 1 EmissV-0.665.6.6/EmissV/NEWS.md | 5 + EmissV-0.665.6.6/EmissV/R/areaSouce.R | 13 +---- EmissV-0.665.6.6/EmissV/R/emission.R | 47 +++++++++++------- EmissV-0.665.6.6/EmissV/R/gridinfo.R | 20 ++++--- EmissV-0.665.6.6/EmissV/R/lineSource.R | 24 +++------ EmissV-0.665.6.6/EmissV/R/pointSource.R | 14 +++-- EmissV-0.665.6.6/EmissV/R/rasterSource.R | 2 EmissV-0.665.6.6/EmissV/R/read.R | 11 ++-- EmissV-0.665.6.6/EmissV/inst/CITATION | 52 ++++++++------------ EmissV-0.665.6.6/EmissV/inst/extdata/streets.dbf |only EmissV-0.665.6.6/EmissV/inst/extdata/streets.prj |only EmissV-0.665.6.6/EmissV/inst/extdata/streets.shp |only EmissV-0.665.6.6/EmissV/inst/extdata/streets.shx |only EmissV-0.665.6.6/EmissV/man/areaSource.Rd | 8 --- EmissV-0.665.6.6/EmissV/man/gridInfo.Rd | 9 +-- EmissV-0.665.6.6/EmissV/man/lineSource.Rd | 23 +++----- EmissV-0.665.6.6/EmissV/man/pointSource.Rd | 4 - EmissV-0.665.6.6/EmissV/man/read.Rd | 11 ++-- 22 files changed, 149 insertions(+), 149 deletions(-)
Title: Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics
Description: Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis. See Zyla et al (2019)
<doi:10.1093/bioinformatics/btz447>.
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tmod versions 0.50.11 dated 2022-09-26 and 0.50.13 dated 2023-03-31
DESCRIPTION | 10 MD5 | 39 - R/celltypes.R | 7 R/modmetabo.R | 7 R/multivariate.R | 5 R/statisticaltests.R | 7 R/visualizations.R | 9 README.md | 37 - build/vignette.rds |binary inst/CITATION |only inst/doc/tmod.R | 37 + inst/doc/tmod.Rmd | 94 ++ inst/doc/tmod.html | 1497 ++++++++++++++++++++++++++++++--------------- man/cell_signatures.Rd | 7 man/figures |only man/modmetabo.Rd | 7 man/tmodPCA.Rd | 5 vignettes/bibliography.bib | 12 vignettes/logo.png |binary vignettes/tmod.Rmd | 94 ++ 20 files changed, 1352 insertions(+), 522 deletions(-)
Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality
restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Yves Rosseel [ctb],
Rebecca Kuiper [aut],
Aleksandra Dacko [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>
Diff between restriktor versions 0.4-500 dated 2023-03-23 and 0.4-501 dated 2023-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/con_constraints.R | 6 ++++-- R/con_goric.R | 38 +++++++++++++++++++------------------- man/restriktor-package.rd | 4 ++-- 5 files changed, 32 insertions(+), 30 deletions(-)
Title: 'REDCap' Data Management
Description: Access and manage 'REDCap' data. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to programmatic access data and project meta data (such as the data dictionary) from the web. This package allows us to read 'REDCap' data, exported or using an API connection, identify missing or extreme values, identify missing 'REDCap' events in each observation, do a follow-up of the queries initially identified and it also facilitates the process of data management.
Author: Joao Carmezim [aut, cre],
Judith Penafiel [aut],
Pau Satorra [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <ubidi@idibell.cat>
Diff between REDCapDM versions 0.5.0 dated 2023-03-24 and 0.6.0 dated 2023-03-31
DESCRIPTION | 10 MD5 | 30 +- NEWS.md | 12 + R/rd_event.R | 2 R/rd_query.R | 12 - R/rd_transform.R | 32 +- R/utils-transform.R | 2 build/vignette.rds |binary inst/doc/REDCapDM.R | 8 inst/doc/REDCapDM.Rmd | 55 ++-- inst/doc/REDCapDM.html | 489 ++++++++++++++++++++++---------------------- man/REDCapDM.Rd | 56 ++--- man/checkbox_names.Rd | 40 +-- man/fill_data.Rd | 36 +-- man/transform_checkboxes.Rd | 2 vignettes/REDCapDM.Rmd | 55 ++-- 16 files changed, 433 insertions(+), 408 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Hege Boevelstad [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.5.0 dated 2022-08-30 and 0.6.0 dated 2023-03-31
GaussSuppression-0.5.0/GaussSuppression/R/NcontributorsRule.R |only GaussSuppression-0.5.0/GaussSuppression/man/NcontributorsRule.Rd |only GaussSuppression-0.6.0/GaussSuppression/DESCRIPTION | 26 GaussSuppression-0.6.0/GaussSuppression/MD5 | 63 +- GaussSuppression-0.6.0/GaussSuppression/NAMESPACE | 7 GaussSuppression-0.6.0/GaussSuppression/NEWS.md | 18 GaussSuppression-0.6.0/GaussSuppression/R/Candidates.R | 8 GaussSuppression-0.6.0/GaussSuppression/R/DominanceRule.R | 277 ++++++++-- GaussSuppression-0.6.0/GaussSuppression/R/GaussSuppressionFromData.R | 246 +++++++- GaussSuppression-0.6.0/GaussSuppression/R/NContributorsRule.R |only GaussSuppression-0.6.0/GaussSuppression/R/PackageSpecs.R |only GaussSuppression-0.6.0/GaussSuppression/R/Primary.R | 42 + GaussSuppression-0.6.0/GaussSuppression/R/PrimaryFromSuppressedData.R | 2 GaussSuppression-0.6.0/GaussSuppression/R/Singleton.R | 173 ++++++ GaussSuppression-0.6.0/GaussSuppression/R/SuppressDominantCells.R |only GaussSuppression-0.6.0/GaussSuppression/R/SuppressFewContributors.R |only GaussSuppression-0.6.0/GaussSuppression/R/SuppressKDisclosure.R | 183 +++--- GaussSuppression-0.6.0/GaussSuppression/R/SuppressSmallCounts.R |only GaussSuppression-0.6.0/GaussSuppression/R/X_from_mc.R | 16 GaussSuppression-0.6.0/GaussSuppression/build |only GaussSuppression-0.6.0/GaussSuppression/inst |only GaussSuppression-0.6.0/GaussSuppression/man/CandidatesDefault.Rd | 2 GaussSuppression-0.6.0/GaussSuppression/man/DominanceRule.Rd | 84 ++- GaussSuppression-0.6.0/GaussSuppression/man/FindDominantCells.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/GaussSuppressionFromData.Rd | 45 + GaussSuppression-0.6.0/GaussSuppression/man/KDisclosurePrimary.Rd | 21 GaussSuppression-0.6.0/GaussSuppression/man/NContributorsRule.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/NcontributorsRule_identical.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/PackageSpecs.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/SingletonDefault.Rd | 5 GaussSuppression-0.6.0/GaussSuppression/man/SingletonUniqueContributor.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/SuppressDominantCells.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/SuppressFewContributors.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/SuppressKDisclosure.Rd | 54 - GaussSuppression-0.6.0/GaussSuppression/man/SuppressSmallCounts.Rd |only GaussSuppression-0.6.0/GaussSuppression/man/X_from_mc.Rd | 6 GaussSuppression-0.6.0/GaussSuppression/tests/testthat/test-DominanceRule.R |only GaussSuppression-0.6.0/GaussSuppression/tests/testthat/test-GaussSuppressDec.R | 2 GaussSuppression-0.6.0/GaussSuppression/tests/testthat/test-GaussSuppressionFromData.R | 242 ++++++++ GaussSuppression-0.6.0/GaussSuppression/tests/testthat/test-GaussSuppressionTwoWay.R | 3 GaussSuppression-0.6.0/GaussSuppression/vignettes |only 41 files changed, 1263 insertions(+), 262 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Extinction Simulation in Ecological Networks
Description: Simulates the extinction of species in ecological networks and it analyzes
its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.
Author: Derek Corcoran [aut, cre] ,
M. Isidora Ávila-Thieme [aut] ,
Fernanda S. Valdovinos [aut],
Sergio A. Navarrete [aut],
Pablo A. Marquet [aut] ,
Erik Kusch [aut]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>
Diff between NetworkExtinction versions 1.0.2 dated 2022-12-07 and 1.0.3 dated 2023-03-31
NetworkExtinction-1.0.2/NetworkExtinction/README.md |only NetworkExtinction-1.0.2/NetworkExtinction/man/figures/README-pressure-1.png |only NetworkExtinction-1.0.2/NetworkExtinction/man/figures/README-unnamed-chunk-13-1.png |only NetworkExtinction-1.0.2/NetworkExtinction/man/figures/README-unnamed-chunk-18-1.png |only NetworkExtinction-1.0.2/NetworkExtinction/man/figures/README-unnamed-chunk-4-1.png |only NetworkExtinction-1.0.2/NetworkExtinction/man/figures/README-unnamed-chunk-7-1.png |only NetworkExtinction-1.0.3/NetworkExtinction/DESCRIPTION | 10 NetworkExtinction-1.0.3/NetworkExtinction/MD5 | 66 +- NetworkExtinction-1.0.3/NetworkExtinction/NAMESPACE | 12 NetworkExtinction-1.0.3/NetworkExtinction/R/Data.R | 9 NetworkExtinction-1.0.3/NetworkExtinction/R/Extintions.R | 299 ++++++++-- NetworkExtinction-1.0.3/NetworkExtinction/R/Plots.R | 10 NetworkExtinction-1.0.3/NetworkExtinction/R/Powerlaw.R | 163 +++-- NetworkExtinction-1.0.3/NetworkExtinction/build/vignette.rds |binary NetworkExtinction-1.0.3/NetworkExtinction/data/mutual.rda |only NetworkExtinction-1.0.3/NetworkExtinction/inst/doc/NetworkExtinction.html | 18 NetworkExtinction-1.0.3/NetworkExtinction/man/ExtinctionOrder.Rd | 7 NetworkExtinction-1.0.3/NetworkExtinction/man/RandomExtinctions.Rd | 17 NetworkExtinction-1.0.3/NetworkExtinction/man/SimulateExtinctions.Rd | 21 NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-mostconnected3-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-10-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-11-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-12-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-14-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-15-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-16-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-19-1.png |only NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-5-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-8-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/figures/README-unnamed-chunk-9-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/man/mutual.Rd |only NetworkExtinction-1.0.3/NetworkExtinction/tests/testthat/test-DataInit.R |only NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresmostconnected3-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-10-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-12-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-13-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-14-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-17-1.png |binary NetworkExtinction-1.0.3/NetworkExtinction/vignettes/vignettes/figuresunnamed-chunk-7-1.png |binary 39 files changed, 460 insertions(+), 172 deletions(-)
More information about NetworkExtinction at CRAN
Permanent link
Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of
Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
regression models, partially linear instrumental variable regression models,
interactive regression models and interactive instrumental variable
regression models. 'DoubleML' allows estimation of the nuisance parts in
these models by machine learning methods and computation of the Neyman
orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
the 'R6' package is very flexible.
Author: Philipp Bach [aut, cre],
Victor Chernozhukov [aut],
Malte S. Kurz [aut],
Martin Spindler [aut],
Klaassen Sven [aut]
Maintainer: Philipp Bach <philipp.bach@uni-hamburg.de>
Diff between DoubleML versions 0.5.2 dated 2022-11-23 and 0.5.3 dated 2023-03-31
DESCRIPTION | 14 ++++++------ LICENSE | 4 +-- MD5 | 20 ++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_DoubleML.html | 4 +-- inst/doc/getstarted.R | 12 +++++----- inst/doc/getstarted.Rmd | 17 +++++++------- inst/doc/getstarted.html | 38 ++++++++++++++++----------------- man/DoubleML.Rd | 11 ++++++++- vignettes/getstarted.Rmd | 17 +++++++------- 11 files changed, 75 insertions(+), 62 deletions(-)
Title: Access Victorian Spatial Data Through Web File Services (WFS)
Description: Easily interfaces R to spatial datasets available through
the Victorian Government's WFS (Web Feature Service): <https://services.land.vic.gov.au/catalogue/publicproxy/guest/dv_geoserver/wfs?request=getCapabilities>,
which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Author: Justin Cally [aut, cre] ,
Rachel Swain [ctb],
Andy Teucher [aut] ,
Sam Albers [aut] ,
Stephanie Hazlitt [aut] ,
Province of British Columbia [cph]
Maintainer: Justin Cally <justin.g.cally@gmail.com>
Diff between VicmapR versions 0.1.9 dated 2022-06-10 and 0.1.10 dated 2023-03-31
DESCRIPTION | 6 MD5 | 10 NEWS.md | 3 R/cql-translate.R | 2 inst/doc/beginner_vicmap.html | 422 ++++++++++++++++++++++++++++++++++++------ inst/doc/query_vicmap.html | 251 +++++++++++++++++++++++- 6 files changed, 618 insertions(+), 76 deletions(-)
Title: Functions for Set-Theoretic Multi-Method Research and Advanced
QCA
Description: Functions for performing set-theoretic multi-method research, QCA for clustered data, theory evaluation, Enhanced Standard Analysis, indirect calibration, radar visualisations. Additionally it includes data to replicate the examples in the books by Oana, I.E, C. Q. Schneider, and E. Thomann. Qualitative Comparative Analysis (QCA) using R: A Beginner's Guide. Cambridge University Press and C. Q. Schneider and C. Wagemann "Set Theoretic Methods for the Social Sciences", Cambridge University Press.
Author: Ioana-Elena Oana [aut, cre],
Juraj Medzihorsky [aut],
Mario Quaranta [aut],
Carsten Q. Schneider [aut]
Maintainer: Ioana-Elena Oana <ioana.oana@eui.eu>
Diff between SetMethods versions 3.0 dated 2021-11-03 and 4.0 dated 2023-03-31
DESCRIPTION | 8 MD5 | 43 +- NEWS | 4 R/cluster.R | 34 - R/cluster.plot.R | 6 R/helper_case_smmr.R | 170 +++++++-- R/helper_cluster.R | 16 R/helper_match_smmr.R | 791 +++++++++++++++++++++++++++++++++++----------- R/helper_nec_smmr.R |only R/helper_rob.R | 39 +- R/rob.calibrange.R | 16 R/rob.cases.R | 16 R/rob.corefit.R | 2 R/rob.fit.R | 6 R/rob.inclrange.R | 3 R/rob.ncutrange.R | 4 R/rob.xyplot.R | 4 R/smmr.R | 253 ++++++++++---- R/stargazerSol.R | 2 R/stargazerTT.R | 2 inst/CITATION | 3 man/SetMethods-package.Rd | 14 man/smmr.Rd | 46 ++ 23 files changed, 1074 insertions(+), 408 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between mongolite versions 2.7.1 dated 2023-01-07 and 2.7.2 dated 2023-03-31
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 4 ++++ R/pool.R | 2 +- inst/CITATION | 12 +++--------- src/kms/kms_crypto_apple.c | 4 ++-- 6 files changed, 18 insertions(+), 20 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo, as
described in Vehtari, Gelman, and Gabry (2017)
<doi:10.1007/s11222-016-9696-4>.
The approximation uses Pareto smoothed importance sampling (PSIS),
a new procedure for regularizing importance weights.
As a byproduct of the calculations, we also obtain approximate
standard errors for estimated predictive errors and for the comparison
of predictive errors between models. The package also provides methods
for using stacking and other model weighting techniques to average
Bayesian predictive distributions.
Author: Aki Vehtari [aut],
Jonah Gabry [cre, aut],
Mans Magnusson [aut],
Yuling Yao [aut],
Paul-Christian Buerkner [aut],
Topi Paananen [aut],
Andrew Gelman [aut],
Ben Goodrich [ctb],
Juho Piironen [ctb],
Bruno Nicenboim [ctb],
Leevi Lindgren [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 2.5.1 dated 2022-03-25 and 2.6.0 dated 2023-03-31
loo-2.5.1/loo/tests/testthat/function_method_stuff.R |only loo-2.5.1/loo/tests/testthat/loo_subsample_vignette.rda |only loo-2.5.1/loo/tests/testthat/normal_reg_waic_test_example.rda |only loo-2.5.1/loo/tests/testthat/normal_reg_waic_test_example2.rda |only loo-2.5.1/loo/tests/testthat/test_data_psis_approximate_posterior.rda |only loo-2.5.1/loo/tests/testthat/test_radon_laplace_loo.rda |only loo-2.6.0/loo/DESCRIPTION | 20 loo-2.6.0/loo/MD5 | 124 - loo-2.6.0/loo/NAMESPACE | 12 loo-2.6.0/loo/NEWS.md | 19 loo-2.6.0/loo/R/E_loo.R | 2 loo-2.6.0/loo/R/crps.R |only loo-2.6.0/loo/R/datasets.R | 10 loo-2.6.0/loo/R/effective_sample_sizes.R | 14 loo-2.6.0/loo/R/loo_compare.R | 3 loo-2.6.0/loo/R/loo_model_weights.R | 39 loo-2.6.0/loo/R/loo_predictive_metric.R |only loo-2.6.0/loo/R/loo_subsample.R | 17 loo-2.6.0/loo/R/psis.R | 6 loo-2.6.0/loo/build/partial.rdb |only loo-2.6.0/loo/build/vignette.rds |binary loo-2.6.0/loo/data/voice.rda |only loo-2.6.0/loo/data/voice_loo.rda |only loo-2.6.0/loo/inst/CITATION | 2 loo-2.6.0/loo/inst/doc/loo2-elpd.html | 580 +++++-- loo-2.6.0/loo/inst/doc/loo2-example.html | 570 +++++-- loo-2.6.0/loo/inst/doc/loo2-large-data.html | 581 +++++-- loo-2.6.0/loo/inst/doc/loo2-lfo.html | 814 +++++++--- loo-2.6.0/loo/inst/doc/loo2-mixis.R |only loo-2.6.0/loo/inst/doc/loo2-mixis.Rmd |only loo-2.6.0/loo/inst/doc/loo2-mixis.html |only loo-2.6.0/loo/inst/doc/loo2-moment-matching.html | 523 +++++- loo-2.6.0/loo/inst/doc/loo2-non-factorized.html | 753 +++++++-- loo-2.6.0/loo/inst/doc/loo2-weights.html | 615 ++++++- loo-2.6.0/loo/inst/doc/loo2-with-rstan.html | 455 ++++- loo-2.6.0/loo/man/ap_psis.Rd | 8 loo-2.6.0/loo/man/crps.Rd |only loo-2.6.0/loo/man/elpd.Rd | 6 loo-2.6.0/loo/man/figures/logo.svg |only loo-2.6.0/loo/man/loo-datasets.Rd | 9 loo-2.6.0/loo/man/loo.Rd | 14 loo-2.6.0/loo/man/loo_approximate_posterior.Rd | 14 loo-2.6.0/loo/man/loo_model_weights.Rd | 22 loo-2.6.0/loo/man/loo_moment_match.Rd | 4 loo-2.6.0/loo/man/loo_predictive_metric.Rd |only loo-2.6.0/loo/man/loo_subsample.Rd | 10 loo-2.6.0/loo/man/parallel_psis_list.Rd | 12 loo-2.6.0/loo/man/psis.Rd | 8 loo-2.6.0/loo/man/psis_approximate_posterior.Rd | 5 loo-2.6.0/loo/man/relative_eff.Rd | 18 loo-2.6.0/loo/man/sis.Rd | 8 loo-2.6.0/loo/man/tis.Rd | 8 loo-2.6.0/loo/man/update.psis_loo_ss.Rd | 12 loo-2.6.0/loo/man/waic.Rd | 14 loo-2.6.0/loo/tests/testthat/data-for-tests |only loo-2.6.0/loo/tests/testthat/reference-results/crps.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_crps.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_acc_mean.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_acc_quant.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_bacc_mean.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_bacc_quant.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_mae_mean.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_mae_quant.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_mse_mean.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_mse_quant.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_rmse_mean.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_predictive_metric_rmse_quant.rds |only loo-2.6.0/loo/tests/testthat/reference-results/loo_scrps.rds |only loo-2.6.0/loo/tests/testthat/reference-results/scrps.rds |only loo-2.6.0/loo/tests/testthat/test_crps.R |only loo-2.6.0/loo/tests/testthat/test_extract_log_lik.R | 2 loo-2.6.0/loo/tests/testthat/test_loo_and_waic.R | 2 loo-2.6.0/loo/tests/testthat/test_loo_predictive_metric.R |only loo-2.6.0/loo/tests/testthat/test_loo_subsampling.R | 26 loo-2.6.0/loo/tests/testthat/test_model_weighting.R | 18 loo-2.6.0/loo/tests/testthat/test_psis_approximate_posterior.R | 2 loo-2.6.0/loo/tests/testthat/test_relative_eff.R | 4 loo-2.6.0/loo/vignettes/loo2-mixis.Rmd |only 78 files changed, 4097 insertions(+), 1288 deletions(-)
Title: Dynamic Factor Models
Description: Efficient estimation of Dynamic Factor Models using the Expectation Maximization (EM) algorithm
or Two-Step (2S) estimation, supporting datasets with missing data. The estimation options follow advances in the
econometric literature: either running the Kalman Filter and Smoother once with initial values from PCA -
2S estimation as in Doz, Giannone and Reichlin (2011) <doi:10.1016/j.jeconom.2011.02.012> - or via iterated
Kalman Filtering and Smoothing until EM convergence - following Doz, Giannone and Reichlin (2012)
<doi:10.1162/REST_a_00225> - or using the adapted EM algorithm of Banbura and Modugno (2014) <doi:10.1002/jae.2306>,
allowing arbitrary patterns of missing data. The implementation makes heavy use of the 'Armadillo' 'C++' library and
the 'collapse' package, providing for particularly speedy estimation. A comprehensive set of methods supports
interpretation and visualization of the model as well as forecasting. Information criteria to choose the number
of f [...truncated...]
Author: Sebastian Krantz [aut, cre],
Rytis Bagdziunas [aut]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dfms versions 0.1.4 dated 2023-01-12 and 0.2.0 dated 2023-03-31
DESCRIPTION | 6 - MD5 | 40 +++--- NAMESPACE | 2 NEWS.md | 10 + R/DFM.R | 66 +++++------ R/EMBM.R | 31 ++--- R/EMBM_idio.R |only R/init_cond.R |only R/methods.R | 53 +++++--- R/utils.R | 20 ++- README.md | 22 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dynamic_factor_models.Rnw |only inst/doc/dynamic_factor_models.pdf |only inst/doc/introduction.R | 26 ++-- inst/doc/introduction.Rmd | 14 +- inst/doc/introduction.html | 178 +++++++++++------------------- man/DFM.Rd | 7 + man/residuals.dfm.Rd | 4 tests/testthat/test-SKFS.R | 6 - vignettes/dynamic_factor_models.Rnw |only vignettes/dynamic_factor_models_paper.pdf |only vignettes/introduction.Rmd | 14 +- 24 files changed, 258 insertions(+), 241 deletions(-)
Title: Alternating Optimization
Description: Alternating optimization of (high-dimensional) functions is an
iterative procedure for optimizing jointly over all parameters by
alternately optimizing parameter subsets.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 0.2.5 dated 2023-01-23 and 0.2.6 dated 2023-03-31
DESCRIPTION | 13 - MD5 | 34 +-- NEWS.md | 4 R/ao.R | 364 +++++++++++++++++++++--------------------- R/package.R | 68 +++---- R/utils.R | 48 ++--- README.md | 165 +++++++++---------- inst/doc/ao.R | 3 inst/doc/ao.Rmd | 165 +++++++++---------- inst/doc/ao.html | 24 +- man/ao.Rd | 1 man/figures/logo.png |binary man/is_number.Rd | 52 +++--- tests/testthat.R | 8 tests/testthat/test-ao.R | 218 ++++++++++++------------- tests/testthat/test-package.R | 8 tests/testthat/test-utils.R | 12 - vignettes/ao.Rmd | 165 +++++++++---------- 18 files changed, 679 insertions(+), 673 deletions(-)
Title: R Client for the 'Civis Platform API'
Description: A convenient interface for making
requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform/>.
Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.
Author: Peter Cooman [cre, ctb],
Patrick Miller [aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Stephen Hoover [ctb],
Danning Chen [ctb],
Elizabeth Sander [ctb],
Madison Hobbs [ctb],
Anna Bladey [...truncated...]
Maintainer: Peter Cooman <pcooman@civisanalytics.com>
Diff between civis versions 3.1.1 dated 2023-02-28 and 3.1.2 dated 2023-03-31
DESCRIPTION | 6 - MD5 | 53 ++++++------ NAMESPACE | 4 R/civis_future.R | 12 ++ R/generated_client.R | 125 ++++++++++++++++++++++++------ inst/doc/civis_scripts.html | 4 man/databases_list_groups.Rd |only man/databases_list_users.Rd |only man/enhancements_get_cass_ncoa.Rd | 2 man/enhancements_patch_cass_ncoa.Rd | 6 - man/enhancements_post_cass_ncoa.Rd | 6 - man/enhancements_put_cass_ncoa.Rd | 6 - man/enhancements_put_cass_ncoa_archive.Rd | 2 man/resolved.Rd |only man/scripts_get_custom.Rd | 1 man/scripts_list_custom.Rd | 1 man/scripts_patch_custom.Rd | 1 man/scripts_post_custom.Rd | 1 man/scripts_post_custom_clone.Rd | 1 man/scripts_put_custom.Rd | 1 man/scripts_put_custom_archive.Rd | 1 man/tables_get_enhancements_cass_ncoa.Rd | 2 man/tables_post_enhancements_cass_ncoa.Rd | 6 - man/users_delete_me_superadmin.Rd | 1 man/users_list_me.Rd | 1 man/users_list_me_favorites.Rd | 13 ++- man/users_patch_me.Rd | 2 man/users_post_me_favorites.Rd | 13 ++- man/users_post_me_superadmin.Rd | 1 29 files changed, 198 insertions(+), 74 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-07 1.0.2
2022-04-06 1.0.1
2022-02-14 0.1.2
2022-01-05 0.1.1
2021-08-10 0.1.0
Title: Topic Models
Description: Provides an interface to the C code for Latent Dirichlet
Allocation (LDA) models and Correlated Topics Models
(CTM) by David M. Blei and co-authors and the C++ code
for fitting LDA models using Gibbs sampling by Xuan-Hieu
Phan and co-authors.
Author: Bettina Gruen [aut, cre] ,
Kurt Hornik [aut] ,
David M Blei [ctb, cph] ,
John D Lafferty [ctb, cph] ,
Xuan-Hieu Phan [ctb, cph] ,
Makoto Matsumoto [ctb, cph] ,
Takuji Nishimura [ctb, cph] ,
Shawn Cokus [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between topicmodels versions 0.2-13 dated 2022-12-06 and 0.2-14 dated 2023-03-31
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary data/AssociatedPress.rda |binary inst/CITATION | 10 +++++----- inst/NEWS.Rd | 6 ++++++ inst/doc/topicmodels.pdf |binary 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Density Estimation via Bayesian Inference Engines
Description: Bayesian density estimates for univariate continuous random samples are provided using the Bayesian inference engine paradigm. The engine options are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field variational Bayes and slice sampling. The methodology is described in Wand and Yu (2020) <arXiv:2009.06182>.
Author: Matt P. Wand [aut, cre]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between densEstBayes versions 1.0-2.1 dated 2022-04-05 and 1.0-2.2 dated 2023-03-31
densEstBayes-1.0-2.1/densEstBayes/src/stan_files |only densEstBayes-1.0-2.2/densEstBayes/DESCRIPTION | 8 +-- densEstBayes-1.0-2.2/densEstBayes/MD5 | 23 ++++------ densEstBayes-1.0-2.2/densEstBayes/NAMESPACE | 4 - densEstBayes-1.0-2.2/densEstBayes/R/stanmodels.R | 2 densEstBayes-1.0-2.2/densEstBayes/build/vignette.rds |binary densEstBayes-1.0-2.2/densEstBayes/configure | 1 densEstBayes-1.0-2.2/densEstBayes/configure.win | 1 densEstBayes-1.0-2.2/densEstBayes/inst/doc/manual.pdf |binary densEstBayes-1.0-2.2/densEstBayes/src/Makevars | 22 +++------ densEstBayes-1.0-2.2/densEstBayes/src/Makevars.win | 18 ++----- densEstBayes-1.0-2.2/densEstBayes/src/RcppExports.cpp | 5 ++ densEstBayes-1.0-2.2/densEstBayes/src/stanExports_PoissonSimpleMixedModel.cc | 2 13 files changed, 40 insertions(+), 46 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-21 4.0
2020-09-16 3.0
2020-03-17 2.0
2020-02-13 1.1
2019-11-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-13 2.0.0
2018-04-14 1.0.0
2017-04-26 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-18 1.0
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2022-04-01 1.10.6
2021-06-25 1.10.3
2020-10-26 1.9.13
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2022-02-05 2.0
2022-01-15 1.0
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2021-05-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-28 1.1.0
2019-07-25 1.0.3
2019-07-18 1.0.2
2019-03-21 1.0.1
2018-09-12 1.0.0
2017-04-05 0.7.4
2016-12-30 0.7.1
2016-10-27 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-30 0.1.3
2021-02-23 0.1.2
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2019-04-07 1.3
2017-02-06 1.2
2015-07-15 1.1
2015-03-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-09 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-17 0.1.1
2022-08-31 0.1.0
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2023-02-12 0.3.1
2021-10-06 0.3.0
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2021-04-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-13 1.2-0
2018-08-20 1.1-0
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