Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.1.0 dated 2024-01-15 and 1.2.0 dated 2024-02-15
simStateSpace-1.1.0/simStateSpace/R/simStateSpace-sim-ssm-ou.R |only simStateSpace-1.1.0/simStateSpace/R/simStateSpace-sim-ssm-var.R |only simStateSpace-1.1.0/simStateSpace/R/simStateSpace-sim-ssm.R |only simStateSpace-1.1.0/simStateSpace/man/OU2SSM.Rd |only simStateSpace-1.1.0/simStateSpace/man/SimSSM.Rd |only simStateSpace-1.1.0/simStateSpace/man/SimSSMOU.Rd |only simStateSpace-1.1.0/simStateSpace/man/SimSSMVAR.Rd |only simStateSpace-1.1.0/simStateSpace/tests/testthat/test-simStateSpace-ou-2-ssm.R |only simStateSpace-1.1.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou.R |only simStateSpace-1.1.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var.R |only simStateSpace-1.1.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm.R |only simStateSpace-1.2.0/simStateSpace/DESCRIPTION | 10 simStateSpace-1.2.0/simStateSpace/MD5 | 89 simStateSpace-1.2.0/simStateSpace/NAMESPACE | 7 simStateSpace-1.2.0/simStateSpace/NEWS.md | 4 simStateSpace-1.2.0/simStateSpace/R/RcppExports.R | 305 - simStateSpace-1.2.0/simStateSpace/R/methods.R | 414 + simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-fixed.R | 435 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-i-vary.R | 367 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-lin-growth-i-vary.R | 301 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-lin-growth.R | 270 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-lin-sde-fixed.R |only simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-lin-sde-i-vary.R |only simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-ou-fixed.R | 406 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-ou-i-vary.R | 375 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-var-fixed.R | 291 - simStateSpace-1.2.0/simStateSpace/R/simStateSpace-sim-ssm-var-i-vary.R | 186 simStateSpace-1.2.0/simStateSpace/man/LinSDE2SSM.Rd |only simStateSpace-1.2.0/simStateSpace/man/SimSSMFixed.Rd | 303 - simStateSpace-1.2.0/simStateSpace/man/SimSSMIVary.Rd | 246 simStateSpace-1.2.0/simStateSpace/man/SimSSMLinGrowth.Rd | 176 simStateSpace-1.2.0/simStateSpace/man/SimSSMLinGrowthIVary.Rd | 194 simStateSpace-1.2.0/simStateSpace/man/SimSSMLinSDEFixed.Rd |only simStateSpace-1.2.0/simStateSpace/man/SimSSMLinSDEIVary.Rd |only simStateSpace-1.2.0/simStateSpace/man/SimSSMOUFixed.Rd | 345 - simStateSpace-1.2.0/simStateSpace/man/SimSSMOUIVary.Rd | 318 - simStateSpace-1.2.0/simStateSpace/man/SimSSMVARFixed.Rd | 289 - simStateSpace-1.2.0/simStateSpace/man/SimSSMVARIVary.Rd | 180 simStateSpace-1.2.0/simStateSpace/man/as.data.frame.simstatespace.Rd | 93 simStateSpace-1.2.0/simStateSpace/man/as.matrix.simstatespace.Rd | 93 simStateSpace-1.2.0/simStateSpace/man/plot.simstatespace.Rd | 95 simStateSpace-1.2.0/simStateSpace/man/print.simstatespace.Rd | 91 simStateSpace-1.2.0/simStateSpace/src/RcppExports.cpp | 615 -- simStateSpace-1.2.0/simStateSpace/src/source.cpp | 2623 ++-------- simStateSpace-1.2.0/simStateSpace/tests/testthat/session |only simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-fixed.R | 156 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-i-vary.R | 188 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth-i-vary.R | 140 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth.R | 112 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-fixed.R |only simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-i-vary.R |only simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-fixed.R | 174 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-i-vary.R | 208 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-fixed.R | 59 simStateSpace-1.2.0/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-i-vary.R | 81 55 files changed, 4779 insertions(+), 5460 deletions(-)
Title: Factor Importance Ranking and Selection using Total Indices
Description: A model-independent factor importance ranking and selection procedure that is based on total Sobol' indices. Please see Huang and Joseph (2024) <arXiv:2401.00800>. This research is supported by U.S. National Science Foundation grants DMS-2310637 and DMREF-1921873.
Author: Chaofan Huang [aut, cre],
V. Roshan Joseph [aut]
Maintainer: Chaofan Huang <chaofan.huang@gatech.edu>
Diff between first versions 1.0 dated 2024-01-10 and 1.1 dated 2024-02-15
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 2 R/first.R | 611 +++++++++++++++++++++++++++++--------------------- man/first.Rd | 49 ++-- man/totalsobol.knn.Rd | 28 +- 6 files changed, 411 insertions(+), 297 deletions(-)
Title: Isotope Origin Clustering and Assignment Tools
Description: This resource provides tools to create, compare, and post-process
spatial isotope assignment models of animal origin. It generates
probability-of-origin maps for individuals based on user-provided tissue and
environment isotope values (e.g., as generated by IsoMAP, Bowen et al. [2013]
<doi:10.1111/2041-210X.12147>) using the framework established in Bowen et al.
(2010) <doi:10.1146/annurev-earth-040809-152429>). The package 'isocat' can then
quantitatively compare and cluster these maps to group individuals by
similar origin. It also includes techniques for applying four approaches
(cumulative sum, odds ratio, quantile only, and quantile simulation) with
which users can summarize geographic origins and probable distance traveled
by individuals. Campbell et al. [2020] establishes several of the functions
included in this package <doi:10.1515/ami-2020-0004>.
Author: Caitlin Campbell [aut, cre]
Maintainer: Caitlin Campbell <caitjcampbell@gmail.com>
Diff between isocat versions 0.2.6 dated 2020-07-03 and 0.3.0 dated 2024-02-15
DESCRIPTION | 12 MD5 | 70 NAMESPACE | 4 NEWS.md | 9 R/CumSumSuite.R | 8 R/getPrecisionPar.R | 3 R/isotopeAssignmentModel.R | 17 R/makeMultiMonthIsoscape.R |only R/makeOddsSurface.R | 3 R/makeQuantileSimulationSurface.R | 5 R/makeQuantileSurface.R | 4 R/meanAggregateClusterProbability.R | 8 R/projectSummaryMaxSurface.R | 5 R/schoenersD.R | 16 R/simmatrixMaker.R | 3 README.md | 5 build/vignette.rds |binary inst/CITATION | 20 inst/doc/isocat.Rmd | 6 inst/doc/isocat.html | 742 +++++----- man/dot-assignmentMaker.Rd | 4 man/makeMultiMonthIsoscape.Rd |only man/schoenersD.Rd | 3 vignettes/isocat.Rmd | 6 vignettes/isocat_files/figure-html/Create_mean_aggregate_surfaces-1.png |binary vignettes/isocat_files/figure-html/clusterSimmatrix-1.png |binary vignettes/isocat_files/figure-html/cluster_cutting_code-1.png |binary vignettes/isocat_files/figure-html/eval_odds_ratio_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantile_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantsim_surface-1.png |binary vignettes/isocat_files/figure-html/example_surface-1.png |binary vignettes/isocat_files/figure-html/hclust_instead-1.png |binary vignettes/isocat_files/figure-html/plot_cumulative_sum_surface-1.png |binary vignettes/isocat_files/figure-html/plot_isoscape_data-1.png |binary vignettes/isocat_files/figure-html/prob_of_orgin_surface-1.png |binary vignettes/isocat_files/figure-html/quantsim_values-1.png |binary vignettes/isocat_files/figure-html/summary_surface-1.png |binary 37 files changed, 555 insertions(+), 398 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org'
archives (<https://vertnet.org/>). Functions allow searching by many
parameters, including 'taxonomic' names, places, and dates. In addition,
there is an interface for conducting spatially delimited searches, and
another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cph] ,
Chris Ray [ctb],
Vijay Barve [ctb],
Dave Slager [aut, cre, cph]
Maintainer: Dave Slager <slager@uw.edu>
Diff between rvertnet versions 0.8.3 dated 2024-02-13 and 0.8.4 dated 2024-02-15
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 59 +++++++++++++++++++++++--------------------- inst/doc/rvertnet.Rmd | 16 ++--------- inst/doc/rvertnet.html | 28 ++++++++------------ vignettes/rvertnet.Rmd | 16 ++--------- vignettes/rvertnet.Rmd.orig | 7 ----- 7 files changed, 58 insertions(+), 86 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Oliver Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.3 dated 2024-01-12 and 1.4 dated 2024-02-15
DESCRIPTION | 8 MD5 | 225 - NAMESPACE | 9 NEWS.md | 46 R/baseXML.R | 252 -- R/class-color.R | 12 R/class-comment.R | 6 R/class-style_mgr.R | 16 R/class-workbook-utils.R | 20 R/class-workbook-wrappers.R | 156 + R/class-workbook.R | 269 +- R/class-worksheet.R | 4 R/converters.R | 7 R/helper-functions.R | 843 ------ R/openxlsx2-package.R | 86 R/pivot_table.R |only R/pugixml.R | 2 R/read.R | 58 R/utils.R | 22 R/wb_functions.R | 6 R/wb_load.R | 6 R/wb_styles.R | 385 ++- R/write.R | 76 R/write_xlsx.R | 34 README.md | 2 inst/WORDLIST | 34 inst/doc/conditional-formatting.html | 26 inst/doc/openxlsx2_charts_manual.html | 12 inst/doc/openxlsx2_style_manual.html | 2 inst/extdata/colors.R |only inst/extdata/colors.rds |only inst/extdata/fontwidth/FontWidth.csv | 3216 ++++++++++++++++++++++++++ inst/extdata/panose |only inst/extdata/themes.R | 5 inst/extdata/themes.rds |binary man/base_font-wb.Rd | 26 man/col_widths-wb.Rd | 8 man/comment_internal.Rd | 11 man/create_border.Rd | 10 man/create_cell_style.Rd | 15 man/create_colors_xml.Rd |only man/create_dxfs_style.Rd | 14 man/create_fill.Rd | 14 man/create_font.Rd | 18 man/create_hyperlink.Rd | 14 man/create_numfmt.Rd | 14 man/create_sparklines.Rd | 68 man/create_tablestyle.Rd | 80 man/creators-wb.Rd | 3 man/filter-wb.Rd | 4 man/grouping-wb.Rd | 12 man/named_region-wb.Rd | 2 man/openxlsx2-package.Rd | 91 man/row_heights-wb.Rd | 5 man/styles_on_sheet.Rd | 4 man/wbWorkbook.Rd | 140 + man/wb_add_chartsheet.Rd | 3 man/wb_add_comment.Rd | 11 man/wb_add_conditional_formatting.Rd | 2 man/wb_add_data.Rd | 24 man/wb_add_data_table.Rd | 31 man/wb_add_dxfs_style.Rd | 3 man/wb_add_font.Rd | 4 man/wb_add_formula.Rd | 5 man/wb_add_pivot_table.Rd | 9 man/wb_add_slicer.Rd | 5 man/wb_add_style.Rd | 3 man/wb_add_thread.Rd | 2 man/wb_add_worksheet.Rd | 3 man/wb_base_colors.Rd |only man/wb_clone_worksheet.Rd | 3 man/wb_color.Rd | 9 man/wb_copy_cells.Rd | 3 man/wb_data.Rd | 17 man/wb_freeze_pane.Rd | 5 man/wb_merge_cells.Rd | 5 man/wb_order.Rd | 14 man/wb_page_setup.Rd | 6 man/wb_save.Rd | 3 man/wb_set_last_modified_by.Rd | 3 man/wb_workbook.Rd | 6 man/write_datatable.Rd | 30 src/RcppExports.cpp | 4 src/helper_functions.cpp | 24 src/openxlsx2_types.h | 1 src/strings_xml.cpp | 10 tests/testthat/helper.R | 6 tests/testthat/test-base_font.R | 109 tests/testthat/test-class-color.R | 2 tests/testthat/test-class-comment.R | 61 tests/testthat/test-class-workbook-wrappers.R | 18 tests/testthat/test-class-workbook.R | 179 + tests/testthat/test-cloneWorksheet.R | 24 tests/testthat/test-conditional_formatting.R | 8 tests/testthat/test-converters.R | 41 tests/testthat/test-deleting_tables.R | 28 tests/testthat/test-formulas.R | 4 tests/testthat/test-helper-functions.R | 54 tests/testthat/test-loading_workbook.R | 11 tests/testthat/test-named_regions.R | 134 - tests/testthat/test-outlines.R | 26 tests/testthat/test-page_setup.R | 16 tests/testthat/test-protect-workbook.R | 4 tests/testthat/test-pugi_cpp.R | 26 tests/testthat/test-pugixml.R | 117 tests/testthat/test-read_from_created_wb.R | 60 tests/testthat/test-read_sources.R | 32 tests/testthat/test-remove_worksheets.R | 30 tests/testthat/test-save.R | 57 tests/testthat/test-strings_xml.R | 102 tests/testthat/test-tables.R | 117 tests/testthat/test-utils.R | 36 tests/testthat/test-wb_functions.R | 64 tests/testthat/test-wb_styles.R | 51 tests/testthat/test-write.R | 145 - tests/testthat/test-writing_posixct.R | 8 116 files changed, 6287 insertions(+), 1929 deletions(-)
Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.4.2 dated 2023-07-05 and 1.5.3 dated 2024-02-15
nebula-1.4.2/nebula/data/sample_data.RData |only nebula-1.5.3/nebula/DESCRIPTION | 25 + nebula-1.5.3/nebula/MD5 | 39 +-- nebula-1.5.3/nebula/NAMESPACE | 9 nebula-1.5.3/nebula/R/group_cell.R | 2 nebula-1.5.3/nebula/R/nbresidual.R | 31 +- nebula-1.5.3/nebula/R/nebula.R | 64 +++-- nebula-1.5.3/nebula/R/scToNeb.R |only nebula-1.5.3/nebula/R/utils.R | 34 +- nebula-1.5.3/nebula/README.md |only nebula-1.5.3/nebula/build/partial.rdb |binary nebula-1.5.3/nebula/build/vignette.rds |binary nebula-1.5.3/nebula/data/sample_data.rda |only nebula-1.5.3/nebula/data/sample_seurat.rda |only nebula-1.5.3/nebula/inst/doc/nebula_example.R | 26 +- nebula-1.5.3/nebula/inst/doc/nebula_example.Rmd | 41 ++- nebula-1.5.3/nebula/inst/doc/nebula_example.html | 288 +++++++++++++---------- nebula-1.5.3/nebula/man/sample_data.Rd | 44 +-- nebula-1.5.3/nebula/man/sample_seurat.Rd |only nebula-1.5.3/nebula/man/scToNeb.Rd |only nebula-1.5.3/nebula/src/RcppExports.cpp | 24 - nebula-1.5.3/nebula/src/optimization.cpp | 45 ++- nebula-1.5.3/nebula/vignettes/nebula_example.Rmd | 41 ++- nebula-1.5.3/nebula/vignettes/references.bib | 7 24 files changed, 433 insertions(+), 287 deletions(-)
Title: Estimate Incidence and Prevalence using the OMOP Common Data
Model
Description: Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
Author: Edward Burn [aut, cre] ,
Berta Raventos [aut] ,
Marti Catala [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Ger Inberg [ctb] ,
Kim Lopez [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between IncidencePrevalence versions 0.6.1 dated 2024-02-09 and 0.7.0 dated 2024-02-15
DESCRIPTION | 12 MD5 | 83 NAMESPACE | 6 R/benchmarkIncidencePrevalence.R | 627 - R/estimateIncidence.R | 978 +- R/estimatePrevalence.R | 1100 +- R/generateDenominatorCohortSet.R | 108 R/getDenominatorCohorts.R | 30 R/getIncidence.R | 807 - R/inputValidation.R | 711 - R/reexport-omopgenerics.R |only R/utils.R | 6 README.md | 60 inst/doc/a01_Introduction_to_IncidencePrevalence.html | 2 inst/doc/a02_Creating_denominator_populations.R | 8 inst/doc/a02_Creating_denominator_populations.Rmd | 8 inst/doc/a02_Creating_denominator_populations.html | 460 - inst/doc/a03_Creating_target_denominator_populations.R | 5 inst/doc/a03_Creating_target_denominator_populations.Rmd | 341 inst/doc/a03_Creating_target_denominator_populations.html | 67 inst/doc/a04_Calculating_prevalence.R | 19 inst/doc/a04_Calculating_prevalence.Rmd | 581 - inst/doc/a04_Calculating_prevalence.html | 513 - inst/doc/a05_Calculating_incidence.R | 19 inst/doc/a05_Calculating_incidence.Rmd | 569 - inst/doc/a05_Calculating_incidence.html | 379 man/estimateIncidence.Rd | 4 man/estimatePeriodPrevalence.Rd | 4 man/estimatePointPrevalence.Rd | 4 man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/generateDenominatorCohortSet.Rd | 5 man/generateTargetDenominatorCohortSet.Rd | 5 tests/manual/test-dbms.R | 106 tests/testthat/test-estimateIncidence.R | 6431 +++++++------- tests/testthat/test-estimatePrevalence.R | 2908 +++--- tests/testthat/test-generateDenominatorCohortSet.R | 3394 +++---- tests/testthat/test-plotting.R | 324 vignettes/a02_Creating_denominator_populations.Rmd | 8 vignettes/a03_Creating_target_denominator_populations.Rmd | 341 vignettes/a04_Calculating_prevalence.Rmd | 581 - vignettes/a05_Calculating_incidence.Rmd | 569 - 43 files changed, 11030 insertions(+), 11153 deletions(-)
More information about IncidencePrevalence at CRAN
Permanent link
Title: Bayesian Models for Dissolution Testing
Description: Fits Bayesian models (amongst others) to dissolution data sets that can be used for dissolution testing. The package was originally constructed to include only the Bayesian models outlined in Pourmohamad et al. (2022) <doi:10.1111/rssc.12535>. However, additional Bayesian and non-Bayesian models (based on bootstrapping and generalized pivotal quanties) have also been added. More models may be added over time.
Author: Tony Pourmohamad [aut, cre],
Steven Novick [ctb]
Maintainer: Tony Pourmohamad <tpourmohamad@gmail.com>
Diff between BayesDissolution versions 0.1.0 dated 2022-09-21 and 0.2.0 dated 2024-02-15
BayesDissolution-0.1.0/BayesDissolution/inst/logo |only BayesDissolution-0.1.0/BayesDissolution/man/figures |only BayesDissolution-0.2.0/BayesDissolution/ChangeLog | 10 ++ BayesDissolution-0.2.0/BayesDissolution/DESCRIPTION | 22 ++-- BayesDissolution-0.2.0/BayesDissolution/MD5 | 45 +++++++--- BayesDissolution-0.2.0/BayesDissolution/NAMESPACE | 9 ++ BayesDissolution-0.2.0/BayesDissolution/R/bmn.R | 23 ++--- BayesDissolution-0.2.0/BayesDissolution/R/dissplot.R | 6 + BayesDissolution-0.2.0/BayesDissolution/R/f2bayes.R |only BayesDissolution-0.2.0/BayesDissolution/R/f2bca.R |only BayesDissolution-0.2.0/BayesDissolution/R/f2boot.R |only BayesDissolution-0.2.0/BayesDissolution/R/f2calc.R | 36 +++----- BayesDissolution-0.2.0/BayesDissolution/R/f2gpq.R |only BayesDissolution-0.2.0/BayesDissolution/R/f2pbs.R |only BayesDissolution-0.2.0/BayesDissolution/R/ggdissplot.R |only BayesDissolution-0.2.0/BayesDissolution/R/hgp.R | 7 + BayesDissolution-0.2.0/BayesDissolution/R/make_dis_data.R |only BayesDissolution-0.2.0/BayesDissolution/R/process_results.R |only BayesDissolution-0.2.0/BayesDissolution/R/runExample.R |only BayesDissolution-0.2.0/BayesDissolution/inst/extdata |only BayesDissolution-0.2.0/BayesDissolution/inst/shiny-examples |only BayesDissolution-0.2.0/BayesDissolution/man/bmn.Rd | 3 BayesDissolution-0.2.0/BayesDissolution/man/dissplot.Rd | 3 BayesDissolution-0.2.0/BayesDissolution/man/f2bayes.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/f2bca.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/f2boot.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/f2calc.Rd | 5 - BayesDissolution-0.2.0/BayesDissolution/man/f2gpq.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/f2pbs.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/ggdissplot.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/hgp.Rd | 3 BayesDissolution-0.2.0/BayesDissolution/man/make_dis_data.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/process_results.Rd |only BayesDissolution-0.2.0/BayesDissolution/man/runExample.Rd |only 34 files changed, 107 insertions(+), 65 deletions(-)
More information about BayesDissolution at CRAN
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Title: Semi-Supervised Bayesian Mixture Models Incorporating Batch
Correction
Description: Semi-supervised and unsupervised Bayesian mixture models that
simultaneously infer the cluster/class structure and a batch correction.
Densities available are the multivariate normal and the multivariate t.
The model sampler is implemented in C++. This package is aimed at analysis of
low-dimensional data generated across several batches. See Coleman et al.
(2022) <doi:10.1101/2022.01.14.476352> for details of the model.
Author: Stephen Coleman [aut, cre],
Paul Kirk [aut],
Chris Wallace [aut]
Maintainer: Stephen Coleman <stcolema@tcd.ie>
Diff between batchmix versions 2.0.0 dated 2023-05-16 and 2.0.1 dated 2024-02-15
DESCRIPTION | 6 MD5 | 176 ++--- NAMESPACE | 108 +-- R/RcppExports.R | 710 ++++++++++----------- R/batchSemiSupervisedMixtureModel.R | 704 ++++++++++----------- R/batchmix-package.R | 116 +-- R/calcAllocProb.R | 144 ++-- R/catch-routine-registration.R | 22 R/checkDataGenerationInputs.R | 328 +++++----- R/checkProposalWindows.R | 122 +-- R/collectAcceptanceRates.R | 158 ++-- R/continueChain.R | 616 +++++++++--------- R/continueChains.R | 172 ++--- R/generateBatchData.R | 380 +++++------ R/generateBatchDataLogPoisson.R | 212 +++--- R/generateBatchDataMVT.R | 244 +++---- R/generateBatchDataVaryingRepresentation.R | 278 ++++---- R/generateGroupIDsInSimulator.R | 110 +-- R/generateInitialLabels.R | 112 +-- R/getLikelihood.R | 108 +-- R/getSampledBatchScale.R | 136 ++-- R/getSampledBatchShift.R | 142 ++-- R/getSampledClusterMeans.R | 136 ++-- R/plotAcceptanceRates.R | 138 ++-- R/plotLikelihoods.R | 158 ++-- R/plotSampledBatchMeans.R | 142 ++-- R/plotSampledBatchScales.R | 136 ++-- R/plotSampledClusterMeans.R | 142 ++-- R/plotSampledParameter.R | 122 +-- R/predictClass.R | 112 +-- R/predictFromMultipleChains.R | 394 ++++++------ R/prepareInitialParameters.R | 316 ++++----- R/processMCMCChain.R | 534 ++++++++-------- R/processMCMCChains.R | 168 ++--- R/rStickBreakingPrior.R | 42 - R/runBatchMix.R | 418 ++++++------ R/runMCMCChains.R | 298 ++++----- R/samplePriorLabels.R | 28 README.md | 70 +- build/vignette.rds |binary inst/doc/batchmix_workflow.R | 282 ++++---- inst/doc/batchmix_workflow.Rmd | 406 ++++++------ inst/doc/batchmix_workflow.html | 847 ++++++++++++++++---------- man/batchSemiSupervisedMixtureModel.Rd | 354 +++++----- man/batchmix-package.Rd | 118 +-- man/calcAllocProb.Rd | 112 +-- man/checkDataGenerationInputs.Rd | 188 ++--- man/checkProposalWindows.Rd | 98 +-- man/collectAcceptanceRates.Rd | 98 +-- man/continueChain.Rd | 152 ++-- man/continueChains.Rd | 156 ++-- man/createSimilarityMat.Rd | 42 - man/gammaLogLikelihood.Rd | 46 - man/generateBatchData.Rd | 188 ++--- man/generateBatchDataLogPoisson.Rd | 112 +-- man/generateBatchDataMVT.Rd | 152 ++-- man/generateBatchDataVaryingRepresentation.Rd | 158 ++-- man/generateGroupIDsInSimulator.Rd | 108 +-- man/generateInitialLabels.Rd | 102 +-- man/getLikelihood.Rd | 80 +- man/getSampledBatchScale.Rd | 106 +-- man/getSampledBatchShift.Rd | 112 +-- man/getSampledClusterMeans.Rd | 106 +-- man/invGammaLogLikelihood.Rd | 46 - man/invWishartLogLikelihood.Rd | 50 - man/plotAcceptanceRates.Rd | 110 +-- man/plotLikelihoods.Rd | 120 +-- man/plotSampledBatchMeans.Rd | 82 +- man/plotSampledBatchScales.Rd | 78 +- man/plotSampledClusterMeans.Rd | 82 +- man/plotSampledParameter.Rd | 90 +- man/predictClass.Rd | 126 +-- man/predictFromMultipleChains.Rd | 220 +++--- man/prepareInitialParameters.Rd | 98 +-- man/processMCMCChain.Rd | 180 ++--- man/processMCMCChains.Rd | 182 ++--- man/rStickBreakingPrior.Rd | 44 - man/runBatchMix.Rd | 368 +++++------ man/runMCMCChains.Rd | 298 ++++----- man/sampleMVN.Rd | 212 +++--- man/sampleMVT.Rd | 238 +++---- man/samplePriorLabels.Rd | 48 - man/sampleSemisupervisedMVN.Rd | 220 +++--- man/sampleSemisupervisedMVT.Rd | 230 +++---- man/wishartLogLikelihood.Rd | 50 - src/mvnSampler.cpp | 4 tests/testthat/test-cpp.R | 2 tests/testthat/test-pdfs.R | 130 +-- vignettes/batchmix_workflow.Rmd | 406 ++++++------ 89 files changed, 8260 insertions(+), 8035 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb],
Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 2.3.0 dated 2024-01-09 and 2.3.1 dated 2024-02-15
DESCRIPTION | 9 MD5 | 52 +-- NEWS.md | 6 R/datasets.R | 60 +++- README.md | 562 +++++++++++++++++++++-------------------- data/advantage_details.rda |binary data/advantage_movement.rda |binary data/auction_details.rda |binary data/boot_mapping.rda |binary data/castaway_details.rda |binary data/castaways.rda |binary data/challenge_description.rda |binary data/challenge_results.rda |binary data/confessionals.rda |binary data/episodes.rda |binary data/jury_votes.rda |binary data/season_palettes.rda |binary data/season_summary.rda |binary data/survivor_auction.rda |binary data/tribe_colours.rda |binary data/tribe_mapping.rda |binary data/viewers.rda |binary data/vote_history.rda |binary man/castaway_details.Rd | 15 - man/challenge_description.Rd | 40 ++ man/season_summary.Rd | 1 tests |only 27 files changed, 437 insertions(+), 308 deletions(-)
Title: Geographic Tools for Studying Gerrymandering
Description: A compilation of tools to complete common tasks for studying gerrymandering.
This focuses on the geographic tool side of common problems, such as linking
different levels of spatial units or estimating how to break up units. Functions
exist for creating redistricting-focused data for the US.
Author: Christopher T. Kenny [aut, cre]
,
Cory McCartan [ctb]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Diff between geomander versions 2.2.1 dated 2023-04-16 and 2.3.0 dated 2024-02-15
DESCRIPTION | 23 ++- MD5 | 48 +++--- NAMESPACE | 2 NEWS.md | 7 R/adjacency.R | 81 +++++++++-- R/baf_to_vtd.R | 46 ++++++ R/contiguity.R | 14 + R/dra_vtd.R | 2 R/lewis.R |only R/regionalize.R | 39 +++-- R/rpvnearme.R |only README.md | 20 +- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/Merging_Election_Data.R | 8 - inst/doc/Merging_Election_Data.html | 68 ++++----- inst/doc/Redistricting_School_Districts.R | 10 - inst/doc/Redistricting_School_Districts.html | 195 +++++++++++++-------------- man/add_edge.Rd | 21 ++ man/baf_to_vtd.Rd | 4 man/check_contiguity.Rd | 20 ++ man/get_lewis.Rd |only man/get_rpvnearme.Rd |only man/subtract_edge.Rd | 21 ++ src/moran.cpp | 2 tests/spelling.R |only tests/testthat/test-adjacency.R | 12 + 28 files changed, 415 insertions(+), 228 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.6.3 dated 2023-11-18 and 1.6.4 dated 2024-02-15
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NEWS.md | 10 +++++- R/Misc_fun.R | 43 ++++++++++++++++++++++++----- R/RCM2MOM.R | 27 ++++++++++++++++++ R/RCM_int.R | 64 +++++++++++++++++++++++++++++++++----------- R/RCM_rmd.R | 1 R/define_S4_class_RCModel.R | 22 +++++++++++++-- R/report_auxiliary.R | 4 +- R/rmd_report.R | 8 ++--- build/partial.rdb |binary 11 files changed, 160 insertions(+), 47 deletions(-)
Title: Download and Analyze Crash Data
Description: Download crash data from the National Highway Traffic Safety Administration and prepare it for research.
Author: Steve Jackson [aut, cre]
Maintainer: Steve Jackson <steve.jackson@toxcel.com>
Diff between rfars versions 0.3.0 dated 2023-05-05 and 1.1.0 dated 2024-02-15
rfars-0.3.0/rfars/inst/doc/Crash_sequences.R |only rfars-0.3.0/rfars/inst/doc/Crash_sequences.Rmd |only rfars-0.3.0/rfars/inst/doc/Crash_sequences.html |only rfars-0.3.0/rfars/inst/doc/Rural_roads.R |only rfars-0.3.0/rfars/inst/doc/Rural_roads.Rmd |only rfars-0.3.0/rfars/inst/doc/Rural_roads.html |only rfars-0.3.0/rfars/vignettes/Crash-Sequences.R |only rfars-0.3.0/rfars/vignettes/Crash-Sequences.html |only rfars-0.3.0/rfars/vignettes/Crash_sequences.Rmd |only rfars-0.3.0/rfars/vignettes/Rural_roads.Rmd |only rfars-1.1.0/rfars/DESCRIPTION | 13 rfars-1.1.0/rfars/MD5 | 81 rfars-1.1.0/rfars/NEWS.md | 11 rfars-1.1.0/rfars/R/compare_counts.R | 20 rfars-1.1.0/rfars/R/counts.R | 12 rfars-1.1.0/rfars/R/data.R | 4 rfars-1.1.0/rfars/R/download_fars.R | 10 rfars-1.1.0/rfars/R/download_gescrss.R | 4 rfars-1.1.0/rfars/R/get_fars.R | 11 rfars-1.1.0/rfars/R/get_gescrss.R | 10 rfars-1.1.0/rfars/R/prep_fars.R | 27 rfars-1.1.0/rfars/R/prep_gescrss.R | 17 rfars-1.1.0/rfars/R/read_basic_sas.R | 1 rfars-1.1.0/rfars/R/use_gescrss.R | 8 rfars-1.1.0/rfars/README.md | 2045 ++++-------- rfars-1.1.0/rfars/build/vignette.rds |binary rfars-1.1.0/rfars/data/fars_codebook.rda |binary rfars-1.1.0/rfars/data/geo_relations.rda |binary rfars-1.1.0/rfars/data/gescrss_codebook.rda |binary rfars-1.1.0/rfars/inst/doc/Counts.R |only rfars-1.1.0/rfars/inst/doc/Counts.Rmd |only rfars-1.1.0/rfars/inst/doc/Counts.html |only rfars-1.1.0/rfars/inst/doc/Crash_sequence_of_events.R |only rfars-1.1.0/rfars/inst/doc/Crash_sequence_of_events.Rmd |only rfars-1.1.0/rfars/inst/doc/Crash_sequence_of_events.html |only rfars-1.1.0/rfars/inst/doc/Searchable_Codebooks.R |only rfars-1.1.0/rfars/inst/doc/Searchable_Codebooks.Rmd |only rfars-1.1.0/rfars/inst/doc/Searchable_Codebooks.html |only rfars-1.1.0/rfars/man/compare_counts.Rd | 19 rfars-1.1.0/rfars/man/counts.Rd | 11 rfars-1.1.0/rfars/man/fars_codebook.Rd | 2 rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-13-1.png |binary rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-14-1.png |binary rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-15-1.png |binary rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-16-1.png |only rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-18-1.png |only rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-27-1.png |binary rfars-1.1.0/rfars/man/figures/README-unnamed-chunk-29-1.png |only rfars-1.1.0/rfars/man/gescrss_codebook.Rd | 2 rfars-1.1.0/rfars/man/get_fars.Rd | 10 rfars-1.1.0/rfars/man/get_gescrss.Rd | 10 rfars-1.1.0/rfars/vignettes/Counts.Rmd |only rfars-1.1.0/rfars/vignettes/Crash_sequence_of_events.Rmd |only rfars-1.1.0/rfars/vignettes/Searchable_Codebooks.Rmd |only 54 files changed, 913 insertions(+), 1415 deletions(-)
Title: Additional Operators for Image Models
Description: Implements additional operators for computer vision models, including
operators necessary for image segmentation and object detection deep learning
models.
Author: Daniel Falbel [aut, cre],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvisionlib versions 0.4.0 dated 2023-05-30 and 0.5.0 dated 2024-02-15
DESCRIPTION | 9 ++++++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 12 insertions(+), 5 deletions(-)
More information about torchvisionlib at CRAN
Permanent link
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 0.1.4 dated 2024-01-12 and 0.1.5 dated 2024-02-15
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ inst/doc/Multiwave-Object.Rmd | 2 +- inst/doc/Multiwave-Object.html | 2 +- inst/doc/optimall-vignette.html | 2 +- tests/testthat/test-optimall_shiny.R | 1 + vignettes/Multiwave-Object.Rmd | 2 +- 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Generative Artificial Intelligence
Description: Utilizing Generative Artificial Intelligence models like 'GPT-4' and 'Gemini Pro' as coding and writing assistants for 'R' users. Through these models, 'GenAI' offers a variety of functions, encompassing text generation, code optimization, natural language processing, chat, and image interpretation. The goal is to aid 'R' users in streamlining laborious coding and language processing tasks.
Author: Li Yuan [aut, cre]
Maintainer: Li Yuan <lyuan@gd.edu.kg>
Diff between GenAI versions 0.1.15 dated 2024-01-18 and 0.2.0 dated 2024-02-15
GenAI-0.1.15/GenAI/R/GenAI_utils.R |only GenAI-0.1.15/GenAI/R/chat.convert.R |only GenAI-0.1.15/GenAI/R/chat.recent.R |only GenAI-0.1.15/GenAI/R/chat.save.R |only GenAI-0.1.15/GenAI/R/chat.setup.R |only GenAI-0.1.15/GenAI/R/connect.genai.R |only GenAI-0.1.15/GenAI/R/txt.explain.code.R |only GenAI-0.1.15/GenAI/R/txt.fix.grammar.R |only GenAI-0.1.15/GenAI/R/txt.optimize.code.R |only GenAI-0.1.15/GenAI/man/chat.convert.Rd |only GenAI-0.1.15/GenAI/man/chat.recent.Rd |only GenAI-0.1.15/GenAI/man/chat.save.Rd |only GenAI-0.1.15/GenAI/man/chat.setup.Rd |only GenAI-0.1.15/GenAI/man/connect.genai.Rd |only GenAI-0.1.15/GenAI/man/txt.explain.code.Rd |only GenAI-0.1.15/GenAI/man/txt.fix.grammar.Rd |only GenAI-0.1.15/GenAI/man/txt.optimize.code.Rd |only GenAI-0.2.0/GenAI/DESCRIPTION | 12 GenAI-0.2.0/GenAI/MD5 | 99 ++- GenAI-0.2.0/GenAI/NAMESPACE | 25 GenAI-0.2.0/GenAI/R/available.models.R | 23 GenAI-0.2.0/GenAI/R/chat.R | 377 ++++++------ GenAI-0.2.0/GenAI/R/chat.edit.R | 407 +++++++------- GenAI-0.2.0/GenAI/R/chat.history.convert.R |only GenAI-0.2.0/GenAI/R/chat.history.export.R |only GenAI-0.2.0/GenAI/R/chat.history.import.R |only GenAI-0.2.0/GenAI/R/chat.history.print.R |only GenAI-0.2.0/GenAI/R/chat.history.reset.R |only GenAI-0.2.0/GenAI/R/chat.history.save.R |only GenAI-0.2.0/GenAI/R/genai.google.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.edit.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.convert.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.export.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.import.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.print.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.reset.R |only GenAI-0.2.0/GenAI/R/genai.google.chat.history.save.R |only GenAI-0.2.0/GenAI/R/genai.google.class.R |only GenAI-0.2.0/GenAI/R/genai.google.txt.R |only GenAI-0.2.0/GenAI/R/genai.google.txt.image.R |only GenAI-0.2.0/GenAI/R/genai.google.utils.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.edit.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.convert.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.export.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.import.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.print.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.reset.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.chat.history.save.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.class.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.txt.R |only GenAI-0.2.0/GenAI/R/genai.moonshot.utils.R |only GenAI-0.2.0/GenAI/R/genai.openai.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.edit.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.convert.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.export.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.import.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.print.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.reset.R |only GenAI-0.2.0/GenAI/R/genai.openai.chat.history.save.R |only GenAI-0.2.0/GenAI/R/genai.openai.class.R |only GenAI-0.2.0/GenAI/R/genai.openai.img.R |only GenAI-0.2.0/GenAI/R/genai.openai.txt.R |only GenAI-0.2.0/GenAI/R/genai.openai.txt.image.R |only GenAI-0.2.0/GenAI/R/genai.openai.utils.R |only GenAI-0.2.0/GenAI/R/genai.utils.R |only GenAI-0.2.0/GenAI/R/img.R |only GenAI-0.2.0/GenAI/R/imports.R |only GenAI-0.2.0/GenAI/R/txt.R | 326 ++++++----- GenAI-0.2.0/GenAI/R/txt.image.R | 339 ++++++----- GenAI-0.2.0/GenAI/man/available.models.Rd | 19 GenAI-0.2.0/GenAI/man/chat.Rd | 267 ++++++--- GenAI-0.2.0/GenAI/man/chat.edit.Rd | 297 ++++++---- GenAI-0.2.0/GenAI/man/chat.history.convert.Rd |only GenAI-0.2.0/GenAI/man/chat.history.export.Rd |only GenAI-0.2.0/GenAI/man/chat.history.import.Rd |only GenAI-0.2.0/GenAI/man/chat.history.print.Rd |only GenAI-0.2.0/GenAI/man/chat.history.reset.Rd |only GenAI-0.2.0/GenAI/man/chat.history.save.Rd |only GenAI-0.2.0/GenAI/man/genai.google.Rd |only GenAI-0.2.0/GenAI/man/genai.moonshot.Rd |only GenAI-0.2.0/GenAI/man/genai.openai.Rd |only GenAI-0.2.0/GenAI/man/img.Rd |only GenAI-0.2.0/GenAI/man/txt.Rd | 234 ++++++-- GenAI-0.2.0/GenAI/man/txt.image.Rd | 221 +++++-- 88 files changed, 1646 insertions(+), 1000 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
Description: A collection of functions allowing to derive the posterior distribution of the model parameters in random-effects meta-analysis or meta-regression, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.; For more details, see also Roever C (2020) <doi:10.18637/jss.v093.i06>, or Roever C and Friede T (2022) <doi:10.1016/j.cmpb.2022.107303>.
Author: Christian Roever [aut, cre] ,
Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 3.3 dated 2023-06-27 and 3.4 dated 2024-02-15
DESCRIPTION | 8 - MD5 | 30 ++-- R/bayesmeta.R | 63 +++++--- R/bmr.R | 34 +++- build/partial.rdb |binary build/vignette.rds |binary data/Rubin1981.R | 7 inst/doc/Roever2020-bayesmeta.pdf |binary inst/doc/RoeverFriede2023-UsingBayesmetaForMetaRegression.pdf |binary inst/doc/bayesmeta.R | 12 - inst/doc/bayesmeta.html | 26 +-- man/Rubin1981.Rd | 1 man/bayesmeta-package.Rd | 4 man/bayesmeta.Rd | 73 ++++++++-- man/bmr.Rd | 2 man/traceplot.bayesmeta.Rd | 5 16 files changed, 173 insertions(+), 92 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.5.1 dated 2023-11-28 and 1.6.0 dated 2024-02-15
RNifti-1.5.1/RNifti/inst/include/zlib |only RNifti-1.6.0/RNifti/DESCRIPTION | 8 RNifti-1.6.0/RNifti/MD5 | 89 RNifti-1.6.0/RNifti/NEWS | 32 RNifti-1.6.0/RNifti/R/nifti.R | 9 RNifti-1.6.0/RNifti/README.md | 6 RNifti-1.6.0/RNifti/cleanup | 3 RNifti-1.6.0/RNifti/configure | 49 RNifti-1.6.0/RNifti/configure.ac | 15 RNifti-1.6.0/RNifti/inst/include/RNifti.h | 2 RNifti-1.6.0/RNifti/inst/include/RNifti/NiftiImage.h | 67 RNifti-1.6.0/RNifti/inst/include/znzlib/znzlib.h | 2 RNifti-1.6.0/RNifti/man/niftiHeader.Rd | 6 RNifti-1.6.0/RNifti/src/Makevars.in | 12 RNifti-1.6.0/RNifti/src/Makevars.win | 3 RNifti-1.6.0/RNifti/src/main.cpp | 114 RNifti-1.6.0/RNifti/src/niftilib/nifti1_io.c | 1 RNifti-1.6.0/RNifti/src/zlib/Makefile.in |only RNifti-1.6.0/RNifti/src/zlib/adler32.c | 39 RNifti-1.6.0/RNifti/src/zlib/compress.c | 65 RNifti-1.6.0/RNifti/src/zlib/configure |only RNifti-1.6.0/RNifti/src/zlib/crc32.c | 1244 +- RNifti-1.6.0/RNifti/src/zlib/crc32.h | 9877 ++++++++++++++++++- RNifti-1.6.0/RNifti/src/zlib/deflate.c | 1591 +-- RNifti-1.6.0/RNifti/src/zlib/deflate.h | 76 RNifti-1.6.0/RNifti/src/zlib/gzclose.c | 4 RNifti-1.6.0/RNifti/src/zlib/gzguts.h | 49 RNifti-1.6.0/RNifti/src/zlib/gzlib.c | 134 RNifti-1.6.0/RNifti/src/zlib/gzread.c | 224 RNifti-1.6.0/RNifti/src/zlib/gzwrite.c | 406 RNifti-1.6.0/RNifti/src/zlib/infback.c | 52 RNifti-1.6.0/RNifti/src/zlib/inffast.c | 116 RNifti-1.6.0/RNifti/src/zlib/inffast.h | 2 RNifti-1.6.0/RNifti/src/zlib/inflate.c | 277 RNifti-1.6.0/RNifti/src/zlib/inflate.h | 14 RNifti-1.6.0/RNifti/src/zlib/inftrees.c | 37 RNifti-1.6.0/RNifti/src/zlib/inftrees.h | 8 RNifti-1.6.0/RNifti/src/zlib/trees.c | 733 - RNifti-1.6.0/RNifti/src/zlib/uncompr.c | 100 RNifti-1.6.0/RNifti/src/zlib/win32 |only RNifti-1.6.0/RNifti/src/zlib/zconf.h |only RNifti-1.6.0/RNifti/src/zlib/zconf.h.in |only RNifti-1.6.0/RNifti/src/zlib/zlib.h |only RNifti-1.6.0/RNifti/src/zlib/zlib.pc.in |only RNifti-1.6.0/RNifti/src/zlib/zutil.c | 115 RNifti-1.6.0/RNifti/src/zlib/zutil.h | 92 RNifti-1.6.0/RNifti/tests/testthat/test-05-nifti.R | 3 47 files changed, 12761 insertions(+), 2915 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-products
matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). The related 'candisc' package
provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Georges Monette [aut] ,
Phil Chalmers [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.6.0 dated 2023-09-05 and 1.6.2 dated 2024-02-15
DESCRIPTION | 18 +++---- MD5 | 57 +++++++++++++----------- NAMESPACE | 6 ++ NEWS.md | 13 +++++ R/coefplot.mlm.R | 2 R/datasets.R | 70 ++++++++++++++++++++++++++++++ R/ellipse.axes.R |only R/ellipse.box.R |only R/ellipse3d.axes.R | 24 ++++++---- R/heplot.R | 20 ++++---- R/heplots-package.R | 17 ++++--- R/interpPlot.R | 6 +- R/label.ellipse.R | 10 +++- R/robmlm.R | 2 R/utility-car.R | 9 +++ build/partial.rdb |binary build/vignette.rds |binary data/peng.RData |only inst/WORDLIST | 3 - inst/doc/HE_manova.R | 62 +++++++++++++------------- inst/doc/HE_manova.html | 8 +-- inst/doc/HE_mmra.R | 62 +++++++++++++------------- inst/doc/HE_mmra.html | 8 +-- man/df.terms.Rd |only man/ellipse.axes.Rd |only man/ellipse.box.Rd |only man/ellipse3d.axes.Rd | 10 ++-- man/figures/README-iris4-1.png |binary man/heplot.Rd | 20 ++++---- man/heplots-package.Rd | 19 ++++---- man/peng.Rd |only vignettes/fig/manova-jury-can1-1.png |binary vignettes/fig/mmra-grades-can-class-1.png |binary 33 files changed, 290 insertions(+), 156 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, and regularized discriminant analysis. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress <snodg031@umn.edu>
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.1-1 dated 2024-02-03 and 1.1-2 dated 2024-02-15
DESCRIPTION | 12 ++--- MD5 | 22 ++++----- R/kcv.rda.R | 6 -- R/predict.cpfa.R | 43 ++++++++++--------- R/tune.cpfa.R | 25 ++++++++--- inst/ChangeLog.txt | 24 ++++++++++ man/cpfa.Rd | 96 +++++++++++++++++++++++++++++++++++++++---- man/cpm.Rd | 6 +- man/cpm.all.Rd | 14 +++--- man/predict.cpfa.Rd | 116 ++++++++++++++++++++++++++++++++++++++++++++++++++-- man/print.cpfa.Rd | 10 ++-- man/tune.cpfa.Rd | 95 +++++++++++++++++++++++++++++++++++++++--- 12 files changed, 394 insertions(+), 75 deletions(-)
Title: 'Toggl.com' Api for 'Rstudio'
Description: Use the <https://toggl.com> time tracker api through R.
Author: Vincent Guyader [aut, cre],
ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between togglr versions 0.1.99 dated 2022-07-11 and 0.2 dated 2024-02-15
togglr-0.1.99/togglr/man/get_project_task_detail.Rd |only togglr-0.2/togglr/DESCRIPTION | 14 togglr-0.2/togglr/MD5 | 16 togglr-0.2/togglr/NAMESPACE | 176 ++++----- togglr-0.2/togglr/R/get_dashboard.R | 37 +- togglr-0.2/togglr/R/get_detailled_report.R | 274 ++++++++------- togglr-0.2/togglr/R/onAttach.R | 6 togglr-0.2/togglr/inst/doc/togglr.html | 161 ++++---- togglr-0.2/togglr/man/get_current_project_task_detail.Rd |only togglr-0.2/togglr/man/get_detailled_report_paged.Rd | 19 - 10 files changed, 385 insertions(+), 318 deletions(-)
Title: Graph of Daily and Cumulative Downloads of your Packages
Description: Plot the daily and cumulative number of downloads of your packages.
It is designed to be slightly more convenient than the several similar programs. If you want to run this each morning,
you do not need to keep typing in the names of your packages. Also, this combines the daily and cumulative counts in one
run, you do not need to run separate programs to get both types of information.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between myCRAN versions 1.0 dated 2023-04-20 and 1.1 dated 2024-02-15
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/myCRAN.R | 40 ++++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/myCRAN.Rmd | 2 +- inst/doc/myCRAN.html | 4 ++-- man/myCRAN.Rd | 25 +++++++++++++++++++++---- vignettes/myCRAN.Rmd | 2 +- 8 files changed, 71 insertions(+), 26 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507> and
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Alessandra Menafoglio [aut],
Biagio Palumbo [aut],
Simone Vantini [aut]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.3.2 dated 2023-09-05 and 1.4.0 dated 2024-02-15
funcharts-1.3.2/funcharts/R/funcharts.R |only funcharts-1.3.2/funcharts/man/funcharts.Rd |only funcharts-1.4.0/funcharts/DESCRIPTION | 13 funcharts-1.4.0/funcharts/MD5 | 54 - funcharts-1.4.0/funcharts/NAMESPACE | 112 --- funcharts-1.4.0/funcharts/NEWS.md | 12 funcharts-1.4.0/funcharts/R/00_mfd.R | 396 ++++++----- funcharts-1.4.0/funcharts/R/01_pca.mfd.R | 57 - funcharts-1.4.0/funcharts/R/02_fof_pc.R | 42 - funcharts-1.4.0/funcharts/R/02_sof_pc.R | 29 funcharts-1.4.0/funcharts/R/03_phaseI_training.R | 62 - funcharts-1.4.0/funcharts/R/04_phaseII.R | 278 ++++---- funcharts-1.4.0/funcharts/R/05_fault_detection.R | 146 ++-- funcharts-1.4.0/funcharts/R/funcharts-package.R | 4 funcharts-1.4.0/funcharts/R/real_time_00_mfd.R | 96 +- funcharts-1.4.0/funcharts/R/real_time_01_pca.mfd.R | 22 funcharts-1.4.0/funcharts/R/real_time_02_fof_pc.R | 32 funcharts-1.4.0/funcharts/R/real_time_02_sof_pc.R | 28 funcharts-1.4.0/funcharts/R/real_time_04_phaseII.R | 580 ++++++++--------- funcharts-1.4.0/funcharts/R/rmfcc.R |only funcharts-1.4.0/funcharts/R/simulate.R | 24 funcharts-1.4.0/funcharts/build/partial.rdb |binary funcharts-1.4.0/funcharts/build/vignette.rds |binary funcharts-1.4.0/funcharts/inst/CITATION |only funcharts-1.4.0/funcharts/man/RoMFCC_PhaseI.Rd |only funcharts-1.4.0/funcharts/man/RoMFCC_PhaseII.Rd |only funcharts-1.4.0/funcharts/man/RoMFDI.Rd |only funcharts-1.4.0/funcharts/man/control_charts_sof_pc.Rd | 2 funcharts-1.4.0/funcharts/man/funcharts-package.Rd | 2 funcharts-1.4.0/funcharts/man/functional_filter.Rd |only funcharts-1.4.0/funcharts/man/rpca_mfd.Rd |only funcharts-1.4.0/funcharts/tests/testthat/test_mfd.R | 1 funcharts-1.4.0/funcharts/tests/testthat/test_romfcc.R |only 33 files changed, 994 insertions(+), 998 deletions(-)
Title: Dependency Logo
Description: Plots dependency logos from a set of aligned input sequences.
Author: Jan Grau [aut, cre],
Jens Keilwagen [aut],
Martin Nettling [aut]
Maintainer: Jan Grau <grau@informatik.uni-halle.de>
Diff between DepLogo versions 1.2 dated 2021-04-16 and 1.2.1 dated 2024-02-15
DESCRIPTION | 9 MD5 | 30 - NAMESPACE | 1 R/DepLogoR.R | 42 +- R/seqLogo.R | 2 build/vignette.rds |binary inst/doc/DepLogo.R | 70 +-- inst/doc/DepLogo.html | 938 +++++++++++++++++++++++++++++++++++++++----------- man/getDeps.Rd | 8 man/getPWM.Rd | 3 man/partition.Rd | 11 man/plotBlocks.Rd | 20 + man/plotDeplogo.Rd | 23 + man/replaceColors.Rd | 3 man/revcom.Rd | 3 man/suggestColors.Rd | 3 16 files changed, 899 insertions(+), 267 deletions(-)
Title: Holistic Generalized Linear Models
Description: Holistic generalized linear models (HGLMs) extend generalized linear models (GLMs) by enabling the possibility to add further constraints to the model. The 'holiglm' package simplifies estimating HGLMs using convex optimization. Additional information about the package can be found in the reference manual, the 'README' and the accompanying paper <doi:10.18637/jss.v108.i07>.
Author: Benjamin Schwendinger [aut, cre],
Florian Schwendinger [aut],
Laura Vana [aut]
Maintainer: Benjamin Schwendinger <benjaminschwe@gmail.com>
Diff between holiglm versions 0.2.6 dated 2023-06-27 and 1.0.0 dated 2024-02-15
DESCRIPTION | 9 -- MD5 | 31 +++---- R/hglm.R | 8 - R/holiglm-package.R | 4 R/log-likelihood.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/conic_representable.html | 96 +++++++++------------- inst/doc/extending_holiglm.Rmd | 53 +++++------- inst/doc/extending_holiglm.html | 159 +++++++++++++++++++------------------- inst/doc/solver_installation.R | 12 +- inst/doc/solver_installation.html | 18 +++- man/hglm.Rd | 6 - man/holiglm-package.Rd | 4 vignettes/extending_holiglm.Rmd | 53 +++++------- vignettes/holiglm.bib | 2 17 files changed, 221 insertions(+), 237 deletions(-)
Title: Comprehensive Analysis of Nucleotide Conversion Sequencing Data
Description: Nucleotide conversion sequencing experiments have been
developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such
experiments require specialized tools for primary processing such as GRAND-SLAM,
(see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for
downstream analyses. 'grandR' provides a comprehensive toolbox for quality control,
kinetic modeling, differential gene expression analysis and visualization of such data.
Author: Florian Erhard [aut, cre] ,
Teresa Rummel [ctb],
Lygeri Sakellaridi [ctb],
Kevin Berg [ctb]
Maintainer: Florian Erhard <Florian.Erhard@informatik.uni-regensburg.de>
Diff between grandR versions 0.2.2 dated 2023-04-20 and 0.2.5 dated 2024-02-15
DESCRIPTION | 24 - MD5 | 78 +-- NAMESPACE | 5 NEWS.md | 37 + R/diagnostics.R | 12 R/diffexp.R | 167 +++++-- R/dropout.R | 59 +- R/grandR.R | 91 ++- R/load.R | 221 ++++++++- R/modeling.R | 12 R/paramest.R | 19 R/plot.R | 108 +++- R/processing.R | 149 ++++++ R/seurat.R | 44 + R/shiny.R | 808 +++++++++++++++++++++++------------ R/utils.R | 25 - inst/doc/getting-started.html | 4 man/Analyses.Rd | 11 man/ApplyContrasts.Rd | 3 man/ComputeColumnStatistics.Rd |only man/CreateConvolutionTable.Rd |only man/CreatePseudobulkTable.Rd |only man/Defer.Rd | 4 man/EstimateRegulation.Rd | 2 man/FitKineticsSnapshot.Rd | 2 man/FormatCorrelation.Rd | 10 man/GetPairContrasts.Rd |only man/LFC.Rd | 11 man/LikelihoodRatioTest.Rd | 2 man/Normalize.Rd | 5 man/Pairwise.Rd | 8 man/PairwiseDESeq2.Rd | 8 man/PlotGeneProgressiveTimecourse.Rd | 2 man/PlotScatter.Rd | 18 man/PlotSimulation.Rd | 11 man/Plots.Rd | 8 man/PoolColumns.Rd |only man/ReadFeatureCounts.Rd |only man/ServeGrandR.Rd | 27 + man/ToIndex.Rd | 4 man/dropout.Rd | 7 man/grandR.Rd | 2 src/fastsparsemat.c | 54 ++ 43 files changed, 1560 insertions(+), 502 deletions(-)
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. More information available in the
publication in the Journal of Statistical Software: <doi:10.18637/jss.v108.i03>.
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 0.5.3 dated 2023-03-31 and 1.0.0 dated 2024-02-15
DESCRIPTION | 11 +-- MD5 | 48 +++++++------- R/datasets.R | 4 - R/double_ml.R | 6 - R/double_ml_pliv.R | 2 R/double_ml_plr.R | 2 R/helper.R | 4 - README.md | 108 +++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 42 +++++++----- inst/doc/Introduction_to_DoubleML.Rmd | 4 - inst/doc/Introduction_to_DoubleML.html | 14 ++-- inst/doc/getstarted.R | 4 - inst/doc/getstarted.html | 30 ++++----- inst/doc/install.R | 8 +- man/DoubleML.Rd | 2 man/DoubleMLIIVM.Rd | 4 - man/DoubleMLIRM.Rd | 4 - man/DoubleMLPLIV.Rd | 6 - man/DoubleMLPLR.Rd | 6 - man/fetch_bonus.Rd | 2 man/figures/logo.png |binary man/make_plr_turrell2018.Rd | 2 vignettes/Introduction_to_DoubleML.Rmd | 4 - 25 files changed, 168 insertions(+), 149 deletions(-)
Title: Control Polygon Reduction
Description: Implementation of the Control Polygon Reduction and Control Net
Reduction methods for finding parsimonious B-spline regression models.
Author: Peter DeWitt [aut, cre] ,
Samantha MaWhinney [ths],
Nichole Carlson [ths]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between cpr versions 0.3.0 dated 2023-11-29 and 0.4.0 dated 2024-02-15
cpr-0.3.0/cpr/R/cnr_diagnostics.R |only cpr-0.3.0/cpr/R/cp_diagnostics.R |only cpr-0.3.0/cpr/R/cpr_diagnostics.R |only cpr-0.3.0/cpr/R/extract_cpr_bsplines.R |only cpr-0.3.0/cpr/R/influence_of.R |only cpr-0.3.0/cpr/R/influence_weights.R |only cpr-0.3.0/cpr/R/spdg.R |only cpr-0.3.0/cpr/R/theta.R |only cpr-0.3.0/cpr/inst/doc/cpr-pkg.R |only cpr-0.3.0/cpr/inst/doc/cpr-pkg.Rmd |only cpr-0.3.0/cpr/inst/doc/cpr-pkg.html |only cpr-0.3.0/cpr/man/boehm.Rd |only cpr-0.3.0/cpr/man/cnr_diagnostics.Rd |only cpr-0.3.0/cpr/man/cp_diagnostics.Rd |only cpr-0.3.0/cpr/man/cpr_diagnostics.Rd |only cpr-0.3.0/cpr/man/extract_cpr_bsplines.Rd |only cpr-0.3.0/cpr/man/influence_of.Rd |only cpr-0.3.0/cpr/man/influence_weights.Rd |only cpr-0.3.0/cpr/man/plot.cpr_influence_of.Rd |only cpr-0.3.0/cpr/man/theta.Rd |only cpr-0.3.0/cpr/src/boehm.cpp |only cpr-0.3.0/cpr/src/diag_only.cpp |only cpr-0.3.0/cpr/tests/test-influence_of.R |only cpr-0.3.0/cpr/tests/test-recover-know-spline.R |only cpr-0.3.0/cpr/vignettes/cpr-pkg.Rmd |only cpr-0.4.0/cpr/DESCRIPTION | 18 - cpr-0.4.0/cpr/MD5 | 236 ++++++++----- cpr-0.4.0/cpr/NAMESPACE | 36 +- cpr-0.4.0/cpr/NEWS.md | 50 ++ cpr-0.4.0/cpr/R/RcppExports.R | 95 +---- cpr-0.4.0/cpr/R/bsplineD.R |only cpr-0.4.0/cpr/R/bsplines.R | 244 +++----------- cpr-0.4.0/cpr/R/btensor.R | 30 - cpr-0.4.0/cpr/R/build_tensor.R | 58 ++- cpr-0.4.0/cpr/R/cn.R | 126 +++---- cpr-0.4.0/cpr/R/cnr.R | 109 +++--- cpr-0.4.0/cpr/R/coef_vcov.R |only cpr-0.4.0/cpr/R/cp.R | 241 +++---------- cpr-0.4.0/cpr/R/cp_diff.R |only cpr-0.4.0/cpr/R/cp_value.R |only cpr-0.4.0/cpr/R/cpr-defunct.R |only cpr-0.4.0/cpr/R/cpr-package.R | 13 cpr-0.4.0/cpr/R/cpr.R | 156 ++++---- cpr-0.4.0/cpr/R/datasets.R |only cpr-0.4.0/cpr/R/generate_cp_formula_data.R | 145 +++++--- cpr-0.4.0/cpr/R/get_spline.R | 181 ++++------ cpr-0.4.0/cpr/R/get_surface.R |only cpr-0.4.0/cpr/R/iknots_or_df.R |only cpr-0.4.0/cpr/R/influence_of_iknots.R |only cpr-0.4.0/cpr/R/insert_a_knot.R |only cpr-0.4.0/cpr/R/knot_expr.R | 19 + cpr-0.4.0/cpr/R/loglikelihood.R | 27 - cpr-0.4.0/cpr/R/newknots.R |only cpr-0.4.0/cpr/R/order_statistics.R |only cpr-0.4.0/cpr/R/plot.cpr_bs.R |only cpr-0.4.0/cpr/R/plot.cpr_cn.R | 22 + cpr-0.4.0/cpr/R/plot.cpr_cnr.R |only cpr-0.4.0/cpr/R/plot.cpr_cp.R |only cpr-0.4.0/cpr/R/plot.cpr_cpr.R |only cpr-0.4.0/cpr/R/plot.cpr_summary_cpr_cpr.R |only cpr-0.4.0/cpr/R/predict.R | 78 ++-- cpr-0.4.0/cpr/R/summary.cpr_cn.R |only cpr-0.4.0/cpr/R/summary.cpr_cnr.R |only cpr-0.4.0/cpr/R/summary.cpr_cp.R |only cpr-0.4.0/cpr/R/summary.cpr_cpr.R |only cpr-0.4.0/cpr/R/trimmed_quantile.R | 3 cpr-0.4.0/cpr/R/update_bsplines.R | 99 ++--- cpr-0.4.0/cpr/R/wiggle.R | 100 +++++ cpr-0.4.0/cpr/README.md |only cpr-0.4.0/cpr/build/vignette.rds |binary cpr-0.4.0/cpr/data/spdg.rda |binary cpr-0.4.0/cpr/data/us_covid_cases.rda |only cpr-0.4.0/cpr/inst/WORDLIST | 52 ++ cpr-0.4.0/cpr/inst/doc/cnr.R |only cpr-0.4.0/cpr/inst/doc/cnr.Rmd |only cpr-0.4.0/cpr/inst/doc/cnr.html |only cpr-0.4.0/cpr/inst/doc/cpr.R |only cpr-0.4.0/cpr/inst/doc/cpr.Rmd |only cpr-0.4.0/cpr/inst/doc/cpr.html |only cpr-0.4.0/cpr/inst/local_support.R |only cpr-0.4.0/cpr/inst/test_statistic_simulation.R |only cpr-0.4.0/cpr/man/bsplineD.Rd | 84 ++++ cpr-0.4.0/cpr/man/bsplines.Rd | 44 +- cpr-0.4.0/cpr/man/btensor.Rd | 20 - 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cpr-0.4.0/cpr/man/print.cpr_bs.Rd | 3 cpr-0.4.0/cpr/man/sign_changes.Rd |only cpr-0.4.0/cpr/man/spdg.Rd | 2 cpr-0.4.0/cpr/man/summary.cpr_cn.Rd |only cpr-0.4.0/cpr/man/summary.cpr_cnr.Rd |only cpr-0.4.0/cpr/man/summary.cpr_cp.Rd |only cpr-0.4.0/cpr/man/summary.cpr_cpr.Rd |only cpr-0.4.0/cpr/man/trimmed_quantile.Rd | 6 cpr-0.4.0/cpr/man/update_bsplines.Rd | 33 + cpr-0.4.0/cpr/man/us_covid_cases.Rd |only cpr-0.4.0/cpr/man/wiggle.Rd | 33 + cpr-0.4.0/cpr/src/Makevars | 1 cpr-0.4.0/cpr/src/Makevars.win | 3 cpr-0.4.0/cpr/src/RcppExports.cpp | 152 ++++---- cpr-0.4.0/cpr/src/bsplines.cpp | 169 ++++++--- cpr-0.4.0/cpr/src/cpr.cpp | 191 +++++++---- cpr-0.4.0/cpr/src/cpr.h | 153 +++++++- cpr-0.4.0/cpr/src/tensors.cpp | 3 cpr-0.4.0/cpr/tests/tensorAB.rds |only cpr-0.4.0/cpr/tests/tensorABA.rds |only cpr-0.4.0/cpr/tests/tensorABAA.rds |only cpr-0.4.0/cpr/tests/tensorBA.rds |only cpr-0.4.0/cpr/tests/test-bsplineD.R |only cpr-0.4.0/cpr/tests/test-bsplines.R | 347 ++++++++++++++------ cpr-0.4.0/cpr/tests/test-btensor.R | 296 +++++++++++++---- cpr-0.4.0/cpr/tests/test-build_tensor.R |only cpr-0.4.0/cpr/tests/test-cn.R |only cpr-0.4.0/cpr/tests/test-cnr.R | 120 ------ cpr-0.4.0/cpr/tests/test-coef_vcov.R |only cpr-0.4.0/cpr/tests/test-cp.R |only cpr-0.4.0/cpr/tests/test-cp_diff.R |only cpr-0.4.0/cpr/tests/test-cp_value.R |only cpr-0.4.0/cpr/tests/test-cpr.R | 262 +++------------ cpr-0.4.0/cpr/tests/test-datasets.R |only cpr-0.4.0/cpr/tests/test-generate_cp_formula_data.R |only cpr-0.4.0/cpr/tests/test-get_spline.R |only cpr-0.4.0/cpr/tests/test-get_surface.R |only cpr-0.4.0/cpr/tests/test-iknots_or_df.R |only cpr-0.4.0/cpr/tests/test-influence_of_iknots.R |only cpr-0.4.0/cpr/tests/test-insert_a_knot.R |only cpr-0.4.0/cpr/tests/test-knot_expr.R | 57 +++ cpr-0.4.0/cpr/tests/test-loglikelihood.R |only cpr-0.4.0/cpr/tests/test-matrix_rank.R | 9 cpr-0.4.0/cpr/tests/test-modify-formula-and-data.R |only cpr-0.4.0/cpr/tests/test-newknots.R |only cpr-0.4.0/cpr/tests/test-order_statistics.R |only cpr-0.4.0/cpr/tests/test-plot.cpr_bs.R |only cpr-0.4.0/cpr/tests/test-plot.cpr_cn.R |only cpr-0.4.0/cpr/tests/test-plot.cpr_cnr.R |only cpr-0.4.0/cpr/tests/test-plot.cpr_cp.R |only cpr-0.4.0/cpr/tests/test-plot.cpr_cpr.R |only cpr-0.4.0/cpr/tests/test-predict.R |only cpr-0.4.0/cpr/tests/test-recover-known-spline.R |only cpr-0.4.0/cpr/tests/test-summary.cpr_cn.R |only cpr-0.4.0/cpr/tests/test-summary.cpr_cnr.R |only cpr-0.4.0/cpr/tests/test-summary.cpr_cp.R |only cpr-0.4.0/cpr/tests/test-summary.cpr_cpr.R |only cpr-0.4.0/cpr/tests/test-trimmed_quantile.R | 5 cpr-0.4.0/cpr/tests/test-update_bsplines.R |only cpr-0.4.0/cpr/tests/test-wiggle.R |only cpr-0.4.0/cpr/vignettes/cnr.Rmd |only cpr-0.4.0/cpr/vignettes/cpr.Rmd |only cpr-0.4.0/cpr/vignettes/references.bib | 6 175 files changed, 2683 insertions(+), 1973 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between V8 versions 4.4.1 dated 2023-12-04 and 4.4.2 dated 2024-02-15
V8-4.4.1/V8/inst/js/underscore.js |only V8-4.4.2/V8/DESCRIPTION | 6 +++--- V8-4.4.2/V8/MD5 | 13 ++++++------- V8-4.4.2/V8/NEWS | 5 +++++ V8-4.4.2/V8/build/partial.rdb |binary V8-4.4.2/V8/configure | 4 ++-- V8-4.4.2/V8/inst/doc/npm.html | 4 ++-- V8-4.4.2/V8/inst/doc/v8_intro.html | 6 +++--- 8 files changed, 21 insertions(+), 17 deletions(-)
Title: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses
Description: An implementation of a phylogenetic comparative method. It can fit univariate among-species Ornstein-Uhlenbeck models of phenotypic trait evolution, where the trait evolves towards a primary optimum. The optimum can be modelled as a single parameter, as multiple discrete regimes on the phylogenetic tree, and/or with continuous covariates. See also Hansen (1997) <doi:10.2307/2411186>, Butler & King (2004) <doi:10.1086/426002>, Hansen et al. (2008) <doi:10.1111/j.1558-5646.2008.00412.x>.
Author: Bjoern Tore Kopperud [aut, cre],
Jason Pienaar [aut],
Kjetil Lysne Voje [aut],
Steven Hecht Orzack [aut],
Thomas F. Hansen [aut],
Mark Grabowski [ctb]
Maintainer: Bjoern Tore Kopperud <kopperud@protonmail.com>
Diff between slouch versions 2.1.4 dated 2020-02-21 and 2.1.5 dated 2024-02-15
DESCRIPTION | 14 +- MD5 | 44 +++---- NEWS.md | 8 + R/fit.R | 28 ++++ R/interface.R | 10 + R/methods.R | 3 R/reg.R | 51 +++++++- R/seed.R | 14 +- R/weightmatrix.R | 61 ++++++++-- build/partial.rdb |only build/vignette.rds |binary inst/doc/examples.R | 42 +++---- inst/doc/examples.html | 237 ++++++++++++++++------------------------ man/artiodactyla.Rd | 4 man/brown.fit.Rd | 6 + man/hillclimbplot.Rd | 4 man/neocortex.Rd | 4 man/plot.slouch.Rd | 13 -- man/regimeplot.Rd | 4 man/slouch-package.Rd | 6 - man/slouch.fit.Rd | 6 + tests/testthat/test_anticrash.R | 2 tests/testthat/test_simmap.R |only tests/testthat/test_weights.R | 4 24 files changed, 321 insertions(+), 244 deletions(-)
Title: Latent Class Discriminant Analysis
Description: Providing a method for Local Discrimination via Latent Class Models. The approach is described in <https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Bucker.pdf>.
Author: Michael Buecker
Maintainer: Michael Buecker <michael.buecker@fh-muenster.de>
Diff between lcda versions 0.3.1 dated 2022-03-11 and 0.3.2 dated 2024-02-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/cclcda2.default.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-12 2.2.2
2021-02-17 1.4.2.2
2021-02-16 1.4.2
2020-09-04 1.4.1.1
2020-05-25 1.4.1
Title: Weighted Cumulative Exposure Models
Description: A flexible method for modeling cumulative effects of time-varying exposures, weighted according to their relative proximity in time, and represented by time-dependent covariates. The current implementation estimates the weight function in the Cox proportional hazards model. The function that assigns weights to doses taken in the past is estimated using cubic regression splines.
Author: Marie-Pierre Sylvestre [aut, cre]
,
Marie-Eve Beauchamp [ctb],
Ryan Patrick Kyle [ctb],
Michal Abrahamowicz [ctb]
Maintainer: Marie-Pierre Sylvestre <marie-pierre.sylvestre@umontreal.ca>
Diff between WCE versions 1.0.2 dated 2018-08-08 and 1.0.3 dated 2024-02-15
WCE-1.0.2/WCE/NEWS |only WCE-1.0.2/WCE/R/WCE-internal.R |only WCE-1.0.2/WCE/R/WCE.cox.R |only WCE-1.0.2/WCE/R/WCE.default.R |only WCE-1.0.2/WCE/build |only WCE-1.0.2/WCE/data/drugdata.RData |only WCE-1.0.2/WCE/inst |only WCE-1.0.2/WCE/man/wce-package.Rd |only WCE-1.0.2/WCE/vignettes |only WCE-1.0.3/WCE/DESCRIPTION | 27 +- WCE-1.0.3/WCE/MD5 | 73 +++-- WCE-1.0.3/WCE/NAMESPACE | 43 ++- WCE-1.0.3/WCE/R/EstimateSplineConstrainedC.R |only WCE-1.0.3/WCE/R/EstimateSplineConstrainedCC.R |only WCE-1.0.3/WCE/R/EstimateSplineConstrainedNCC.R |only WCE-1.0.3/WCE/R/EstimateSplineUnconstrainedC.R |only WCE-1.0.3/WCE/R/EstimateSplineUnconstrainedCC.R |only WCE-1.0.3/WCE/R/EstimateSplineUnconstrainedNCC.R |only WCE-1.0.3/WCE/R/HR.WCE.R | 33 ++ WCE-1.0.3/WCE/R/WCE.R | 220 +++++++++++++++++ WCE-1.0.3/WCE/R/WCE_data_frame.R |only WCE-1.0.3/WCE/R/WCEpackage.R |only WCE-1.0.3/WCE/R/add.R |only WCE-1.0.3/WCE/R/augm_knots.R |only WCE-1.0.3/WCE/R/checkWCE.R | 71 ++++- WCE-1.0.3/WCE/R/coef.WCE.R | 30 ++ WCE-1.0.3/WCE/R/drugdata.R |only WCE-1.0.3/WCE/R/gap.R |only WCE-1.0.3/WCE/R/gapi.R |only WCE-1.0.3/WCE/R/get_interior.R |only WCE-1.0.3/WCE/R/knotsWCE.R | 21 + WCE-1.0.3/WCE/R/knotsequi.R |only WCE-1.0.3/WCE/R/maxfu.R |only WCE-1.0.3/WCE/R/my_bic_c.R |only WCE-1.0.3/WCE/R/nicer.R |only WCE-1.0.3/WCE/R/plot.WCE.R | 70 +++-- WCE-1.0.3/WCE/R/print.WCE.R | 45 +-- WCE-1.0.3/WCE/R/sumWCEall.R |only WCE-1.0.3/WCE/R/sumWCEbest.R |only WCE-1.0.3/WCE/R/summary.WCE.R | 35 ++ WCE-1.0.3/WCE/R/vcov.WCE.R | 26 +- WCE-1.0.3/WCE/R/wcecalc.R |only WCE-1.0.3/WCE/data/drugdata.rda |only WCE-1.0.3/WCE/man/HR.WCE.Rd | 82 ++---- WCE-1.0.3/WCE/man/WCE-package.Rd |only WCE-1.0.3/WCE/man/WCE.Rd | 292 ++++++++++++----------- WCE-1.0.3/WCE/man/checkWCE.Rd | 68 ++--- WCE-1.0.3/WCE/man/coef.WCE.Rd | 73 ++--- WCE-1.0.3/WCE/man/drugdata.Rd | 65 ++--- WCE-1.0.3/WCE/man/knotsWCE.Rd | 61 ++-- WCE-1.0.3/WCE/man/plot.WCE.Rd | 55 ++-- WCE-1.0.3/WCE/man/summary.WCE.Rd | 64 ++--- WCE-1.0.3/WCE/man/vcov.WCE.Rd | 39 +-- 53 files changed, 965 insertions(+), 528 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Mathilde Hagens [ctb],
Andreas Hofmann [ctb],
Jens-Daniel Mueller [ctb],
Aurelien Proye [ctb],
James Rae [ctb],
Karline Soe [...truncated...]
Maintainer: Jean-Pierre Gattuso <jean-pierre.gattuso@imev-mer.fr>
Diff between seacarb versions 3.3.2 dated 2023-05-21 and 3.3.3 dated 2024-02-15
ChangeLog | 10 +++++++- DESCRIPTION | 8 +++---- MD5 | 62 ++++++++++++++++++++++++++++++------------------------- NAMESPACE | 1 R/K1.R | 32 +++++++++++++++++++++++++--- R/K2.R | 30 +++++++++++++++++++++++--- R/errors.R | 4 +-- R/fH.R |only R/pHnbs2sws.R |only R/pHsws2nbs.R |only man/K1.Rd | 6 ++++- man/K2.Rd | 8 +++++-- man/Om.Rd | 4 ++- man/SIR.Rd | 7 ++++-- man/SIR_b.Rd | 5 +++- man/SIR_full.Rd | 6 ++++- man/buffer.Rd | 7 ++++-- man/buffergen.Rd | 4 ++- man/buffesm.Rd | 6 ++++- man/carb.Rd | 40 ++++++++++++++++++++++++++++------- man/carbb.Rd | 6 ++++- man/carbfull.Rd | 6 ++++- man/derivnum.Rd | 4 ++- man/errors.Rd | 16 +++++++------- man/fH.Rd |only man/oa.Rd | 6 ++++- man/pCa.Rd | 8 +++++-- man/pHinsi.Rd | 6 ++++- man/pHnbs2sws.Rd |only man/pHsws2nbs.Rd |only man/pTA.Rd | 6 ++++- man/pgas.Rd | 8 +++++-- man/pmix.Rd | 8 +++++-- man/ppH.Rd | 8 +++++-- man/psi.Rd | 6 ++++- 35 files changed, 244 insertions(+), 84 deletions(-)
Title: Multivariate Difference Between Two Groups
Description: Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Lönnqvist & Ilmarinen (2021) <doi:10.1007/s11109-021-09681-2> and Ilmarinen et al. (2023) <doi:10.1177/08902070221088155>.
Includes tools that help in understanding difference score reliability, predictions of difference score variables, conditional intra-class correlations, and heterogeneity of variance estimates. Package development was supported by the Academy of Finland research grant 338891.
Author: Ville-Juhani Ilmarinen [aut, cre]
Maintainer: Ville-Juhani Ilmarinen <vj.ilmarinen@gmail.com>
Diff between multid versions 0.9.0 dated 2024-01-16 and 1.0.0 dated 2024-02-15
multid-0.9.0/multid/man/D_regularized_fold.Rd |only multid-0.9.0/multid/man/D_regularized_fold_out.Rd |only multid-0.9.0/multid/man/D_regularized_out.Rd |only multid-0.9.0/multid/man/D_regularized_vanilla.Rd |only multid-0.9.0/multid/man/colwise_pool.Rd |only multid-1.0.0/multid/DESCRIPTION | 11 multid-1.0.0/multid/MD5 | 50 - multid-1.0.0/multid/NAMESPACE | 5 multid-1.0.0/multid/NEWS.md | 10 multid-1.0.0/multid/R/D_regularized.R | 17 multid-1.0.0/multid/R/D_regularized_fold.R | 39 - multid-1.0.0/multid/R/D_regularized_fold_out.R | 45 - multid-1.0.0/multid/R/D_regularized_out.R | 36 - multid-1.0.0/multid/R/D_regularized_vanilla.R | 25 multid-1.0.0/multid/R/boot_ddsc_ml_fixef.R |only multid-1.0.0/multid/R/ci_to_ddsc_ml.R |only multid-1.0.0/multid/R/colwise_pool.R | 12 multid-1.0.0/multid/R/ddsc_ml.R | 301 ++++++---- multid-1.0.0/multid/R/ddsc_sem.R | 96 ++- multid-1.0.0/multid/R/ml_dadas.R | 1 multid-1.0.0/multid/R/pcc.R | 3 multid-1.0.0/multid/R/plot_ddsc.R |only multid-1.0.0/multid/R/sem_dadas.R | 2 multid-1.0.0/multid/README.md | 126 ++-- multid-1.0.0/multid/build/partial.rdb |only multid-1.0.0/multid/inst/doc/multivariate_sex_differences_in_personality.html | 12 multid-1.0.0/multid/man/D_regularized.Rd | 18 multid-1.0.0/multid/man/ddsc_ml.Rd | 7 multid-1.0.0/multid/man/ddsc_sem.Rd | 15 multid-1.0.0/multid/man/pcc.Rd | 3 multid-1.0.0/multid/man/plot_ddsc.Rd |only 31 files changed, 447 insertions(+), 387 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.5.5 dated 2024-02-08 and 5.5.6 dated 2024-02-15
DESCRIPTION | 6 ++-- MD5 | 23 ++++++++-------- NEWS.md | 8 +++++ R/aaa-utils.R | 4 ++ inst/doc/design-principles.html | 6 ++-- inst/doc/huxreg.html | 36 +++++++++++++------------- inst/doc/huxtable.pdf |binary inst/doc/themes.html | 30 ++++++++++----------- man/dplyr-verbs.Rd | 2 - man/huxtable-news.Rd | 6 ++++ tests/testthat/404.html |only tests/testthat/quarto-test-tex-labels-out.pdf |binary tests/testthat/table-tester-2.log | 8 ++--- 13 files changed, 74 insertions(+), 55 deletions(-)
Title: Stochastic Volatility Models with or without Leverage
Description: The efficient Markov chain Monte Carlo estimation of stochastic volatility models with and without leverage (asymmetric and symmetric stochastic volatility models). Further, it computes the logarithm of the likelihood given parameters using particle filters.
Author: Yasuhiro Omori [aut, cre],
Ryuji Hashimoto [ctr]
Maintainer: Yasuhiro Omori <omori.yasuhiro@gmail.com>
Diff between ASV versions 1.1.2 dated 2024-01-19 and 1.1.4 dated 2024-02-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary src/asv.cpp | 41 +++++++++++++++++++++-------------------- 5 files changed, 33 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-08 0.4.6
2023-08-21 0.4.5
2022-11-20 0.4.4
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.25 dated 2023-11-29 and 2.3.27 dated 2024-02-15
DESCRIPTION | 7 +++-- MD5 | 17 ++++++------- NEWS.md | 8 ++++++ R/matrix.R | 1 R/tgstat-package.R | 2 - R/utils.R | 21 +++++++++------- build/vignette.rds |binary inst/doc/manual.R | 2 - inst/doc/manual.html | 66 ++++++++++++++++++++++++++++++++------------------- src/Makevars |only 10 files changed, 76 insertions(+), 48 deletions(-)
Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al. 2020 <doi:10.1007/s11634-019-00375-6>). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between palasso versions 0.0.8 dated 2021-04-19 and 0.0.9 dated 2024-02-15
DESCRIPTION | 11 MD5 | 50 NAMESPACE | 36 NEWS.md | 56 - R/function.R | 1490 +++++++++++++-------------- R/hidden.R | 2052 +++++++++++++++++++------------------- R/methods.R | 646 +++++------ README.md | 110 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/doc/article.Rmd | 40 inst/doc/article.html | 543 +++++----- inst/doc/script.R | 1980 ++++++++++++++++++------------------ inst/doc/script.Rmd | 2090 +++++++++++++++++++------------------- inst/doc/script.html | 2643 ++++++++++++++++++++++++------------------------- inst/doc/vignette.R | 94 - inst/doc/vignette.Rmd | 220 ++-- inst/doc/vignette.html | 823 +++++++-------- man/dot-args.Rd | 46 man/other.Rd | 2 tests/testthat.R | 8 tests/testthat/test.R | 432 ++++---- vignettes/article.Rmd | 40 vignettes/script.Rmd | 2090 +++++++++++++++++++------------------- vignettes/vignette.Rmd | 220 ++-- 26 files changed, 7886 insertions(+), 7866 deletions(-)
Title: Statistical Functions for the Design of Studies with Composite
Endpoints
Description: It has been designed to calculate the required sample size in randomized clinical trials with composite endpoints. It also calculates the expected effect and the probability of observing the composite endpoint, among others. The methodology can be found in Bofill & Gómez (2019) <doi:10.1002/sim.8092> and Gómez & Lagakos (2013) <doi:10.1002/sim.5547>.
Author: Marta Bofill Roig [aut, cre], Jordi Cortes Martinez [aut], Guadalupe Gomez Melis [ctb]
Maintainer: Marta Bofill Roig <marta.bofillroig@meduniwien.ac.at>
Diff between CompAREdesign versions 2.2 dated 2022-10-02 and 2.3.1 dated 2024-02-15
DESCRIPTION | 8 ++++---- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 1 + R/ARE_tte.R | 6 +----- R/CopulaSelection.R | 2 +- R/effectsize_tte.R | 6 +----- R/get_prob1.R | 17 +++++++++++++++++ R/plot_tte.R | 6 +----- R/simula_tte.R | 6 +----- R/surv_tte.R | 6 +----- man/ARE_tte.Rd | 6 +----- man/CompAREdesign-package.Rd | 2 +- man/CopulaSelection.Rd | 2 +- man/effectsize_tte.Rd | 6 +----- man/get_prob1.Rd |only man/plot_tte.Rd | 6 +----- man/samplesize_tte.Rd | 6 +----- man/simula_tte.Rd | 6 +----- man/surv_tte.Rd | 6 +----- 19 files changed, 54 insertions(+), 79 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.4.1 dated 2024-01-09 and 1.5.1 dated 2024-02-15
targets-1.4.1/targets/inst/names |only targets-1.4.1/targets/man/tar_random_name.Rd |only targets-1.4.1/targets/man/use_targets_scheduler.Rd |only targets-1.5.1/targets/DESCRIPTION | 40 - targets-1.5.1/targets/MD5 | 275 ++++++------- targets-1.5.1/targets/NAMESPACE | 11 targets-1.5.1/targets/NEWS.md | 26 + targets-1.5.1/targets/R/class_active.R | 15 targets-1.5.1/targets/R/class_crew.R | 43 +- targets-1.5.1/targets/R/class_feather.R | 4 targets-1.5.1/targets/R/class_glimpse.R | 2 targets-1.5.1/targets/R/class_inspection.R | 2 targets-1.5.1/targets/R/class_parquet.R | 4 targets-1.5.1/targets/R/class_process.R | 54 ++ targets-1.5.1/targets/R/class_store.R | 1 targets-1.5.1/targets/R/tar_config_get.R | 2 targets-1.5.1/targets/R/tar_config_set.R | 17 targets-1.5.1/targets/R/tar_debug_instructions.R | 31 - targets-1.5.1/targets/R/tar_make.R | 64 ++- targets-1.5.1/targets/R/tar_package.R | 7 targets-1.5.1/targets/R/tar_seed_create.R | 48 -- targets-1.5.1/targets/R/tar_seed_get.R | 11 targets-1.5.1/targets/R/tar_seed_set.R | 11 targets-1.5.1/targets/R/tar_source.R | 4 targets-1.5.1/targets/R/tar_target.R | 16 targets-1.5.1/targets/R/tar_target_raw.R | 16 targets-1.5.1/targets/R/use_targets.R | 238 +---------- targets-1.5.1/targets/R/utils_assert.R | 30 - targets-1.5.1/targets/R/utils_callr.R | 2 targets-1.5.1/targets/R/utils_cli.R | 2 targets-1.5.1/targets/R/utils_condition.R | 13 targets-1.5.1/targets/R/utils_data.R | 26 - targets-1.5.1/targets/R/utils_digest.R | 12 targets-1.5.1/targets/R/utils_time.R | 8 targets-1.5.1/targets/inst/WORDLIST | 5 targets-1.5.1/targets/inst/doc/overview.html | 155 +------ targets-1.5.1/targets/inst/pipelines/use_targets.R | 37 - targets-1.5.1/targets/man/tar_active.Rd | 4 targets-1.5.1/targets/man/tar_assert.Rd | 5 targets-1.5.1/targets/man/tar_backoff.Rd | 4 targets-1.5.1/targets/man/tar_branch_index.Rd | 2 targets-1.5.1/targets/man/tar_branches.Rd | 2 targets-1.5.1/targets/man/tar_call.Rd | 4 targets-1.5.1/targets/man/tar_cancel.Rd | 4 targets-1.5.1/targets/man/tar_canceled.Rd | 6 targets-1.5.1/targets/man/tar_completed.Rd | 6 targets-1.5.1/targets/man/tar_condition.Rd | 3 targets-1.5.1/targets/man/tar_config_set.Rd | 7 targets-1.5.1/targets/man/tar_crew.Rd | 6 targets-1.5.1/targets/man/tar_cue.Rd | 4 targets-1.5.1/targets/man/tar_definition.Rd | 4 targets-1.5.1/targets/man/tar_delete.Rd | 2 targets-1.5.1/targets/man/tar_destroy.Rd | 2 targets-1.5.1/targets/man/tar_dispatched.Rd | 6 targets-1.5.1/targets/man/tar_edit.Rd | 2 targets-1.5.1/targets/man/tar_envir.Rd | 4 targets-1.5.1/targets/man/tar_errored.Rd | 6 targets-1.5.1/targets/man/tar_format.Rd | 4 targets-1.5.1/targets/man/tar_github_actions.Rd | 2 targets-1.5.1/targets/man/tar_group.Rd | 4 targets-1.5.1/targets/man/tar_invalidate.Rd | 2 targets-1.5.1/targets/man/tar_load.Rd | 4 targets-1.5.1/targets/man/tar_load_everything.Rd | 6 targets-1.5.1/targets/man/tar_load_globals.Rd | 4 targets-1.5.1/targets/man/tar_load_raw.Rd | 6 targets-1.5.1/targets/man/tar_make.Rd | 8 targets-1.5.1/targets/man/tar_make_clustermq.Rd | 4 targets-1.5.1/targets/man/tar_make_future.Rd | 4 targets-1.5.1/targets/man/tar_manifest.Rd | 2 targets-1.5.1/targets/man/tar_meta_delete.Rd | 4 targets-1.5.1/targets/man/tar_meta_download.Rd | 4 targets-1.5.1/targets/man/tar_meta_sync.Rd | 4 targets-1.5.1/targets/man/tar_meta_upload.Rd | 4 targets-1.5.1/targets/man/tar_name.Rd | 4 targets-1.5.1/targets/man/tar_network.Rd | 2 targets-1.5.1/targets/man/tar_newer.Rd | 4 targets-1.5.1/targets/man/tar_objects.Rd | 6 targets-1.5.1/targets/man/tar_older.Rd | 4 targets-1.5.1/targets/man/tar_option_set.Rd | 16 targets-1.5.1/targets/man/tar_outdated.Rd | 2 targets-1.5.1/targets/man/tar_path.Rd | 2 targets-1.5.1/targets/man/tar_path_script.Rd | 2 targets-1.5.1/targets/man/tar_path_script_support.Rd | 2 targets-1.5.1/targets/man/tar_path_store.Rd | 4 targets-1.5.1/targets/man/tar_path_target.Rd | 4 targets-1.5.1/targets/man/tar_pattern.Rd | 2 targets-1.5.1/targets/man/tar_pid.Rd | 6 targets-1.5.1/targets/man/tar_poll.Rd | 6 targets-1.5.1/targets/man/tar_process.Rd | 6 targets-1.5.1/targets/man/tar_progress.Rd | 4 targets-1.5.1/targets/man/tar_progress_branches.Rd | 6 targets-1.5.1/targets/man/tar_progress_summary.Rd | 6 targets-1.5.1/targets/man/tar_read.Rd | 2 targets-1.5.1/targets/man/tar_read_raw.Rd | 2 targets-1.5.1/targets/man/tar_renv.Rd | 2 targets-1.5.1/targets/man/tar_reprex.Rd | 4 targets-1.5.1/targets/man/tar_resources_aws.Rd | 4 targets-1.5.1/targets/man/tar_resources_clustermq.Rd | 4 targets-1.5.1/targets/man/tar_resources_crew.Rd | 4 targets-1.5.1/targets/man/tar_resources_feather.Rd | 4 targets-1.5.1/targets/man/tar_resources_fst.Rd | 4 targets-1.5.1/targets/man/tar_resources_future.Rd | 4 targets-1.5.1/targets/man/tar_resources_gcp.Rd | 4 targets-1.5.1/targets/man/tar_resources_network.Rd | 4 targets-1.5.1/targets/man/tar_resources_parquet.Rd | 4 targets-1.5.1/targets/man/tar_resources_qs.Rd | 4 targets-1.5.1/targets/man/tar_resources_url.Rd | 4 targets-1.5.1/targets/man/tar_script.Rd | 2 targets-1.5.1/targets/man/tar_seed_create.Rd | 34 - targets-1.5.1/targets/man/tar_seed_get.Rd | 34 - targets-1.5.1/targets/man/tar_seed_set.Rd | 34 - targets-1.5.1/targets/man/tar_sitrep.Rd | 2 targets-1.5.1/targets/man/tar_skipped.Rd | 6 targets-1.5.1/targets/man/tar_source.Rd | 4 targets-1.5.1/targets/man/tar_store.Rd | 4 targets-1.5.1/targets/man/tar_target.Rd | 16 targets-1.5.1/targets/man/tar_target_raw.Rd | 16 targets-1.5.1/targets/man/tar_traceback.Rd | 4 targets-1.5.1/targets/man/tar_unversion.Rd | 4 targets-1.5.1/targets/man/tar_validate.Rd | 2 targets-1.5.1/targets/man/tar_watch.Rd | 2 targets-1.5.1/targets/man/tar_watch_server.Rd | 6 targets-1.5.1/targets/man/tar_watch_ui.Rd | 6 targets-1.5.1/targets/man/targets-package.Rd | 5 targets-1.5.1/targets/man/use_targets.Rd | 85 ---- targets-1.5.1/targets/tests/hpc/test-crew_local.R | 117 +++++ targets-1.5.1/targets/tests/hpc/test-crew_sge.R |only targets-1.5.1/targets/tests/interactive/test-job.R |only targets-1.5.1/targets/tests/interactive/test-process.R |only targets-1.5.1/targets/tests/interactive/test-use_targets.R | 2 targets-1.5.1/targets/tests/testthat/test-class_crew.R | 12 targets-1.5.1/targets/tests/testthat/test-class_feather.R | 4 targets-1.5.1/targets/tests/testthat/test-class_parquet.R | 4 targets-1.5.1/targets/tests/testthat/test-tar_config_set.R | 15 targets-1.5.1/targets/tests/testthat/test-tar_make.R | 2 targets-1.5.1/targets/tests/testthat/test-tar_process.R | 2 targets-1.5.1/targets/tests/testthat/test-tar_source.R | 4 targets-1.5.1/targets/tests/testthat/test-tar_target.R | 2 targets-1.5.1/targets/tests/testthat/test-use_targets.R | 105 ---- targets-1.5.1/targets/tests/testthat/test-utils_assert.R | 21 targets-1.5.1/targets/tests/testthat/test-utils_time.R | 5 141 files changed, 1013 insertions(+), 1071 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.3.8 dated 2023-08-22 and 0.4.3 dated 2024-02-15
ProTrackR-0.3.8/ProTrackR/NEWS |only ProTrackR-0.4.3/ProTrackR/DESCRIPTION | 19 ProTrackR-0.4.3/ProTrackR/MD5 | 176 +- ProTrackR-0.4.3/ProTrackR/NEWS.md |only ProTrackR-0.4.3/ProTrackR/R/01supporting_functions.r | 146 +- ProTrackR-0.4.3/ProTrackR/R/02PTCell.r | 270 ++-- ProTrackR-0.4.3/ProTrackR/R/03PTTrack.r | 24 ProTrackR-0.4.3/ProTrackR/R/04PTPattern.r | 26 ProTrackR-0.4.3/ProTrackR/R/05PTSample.r | 454 +++---- ProTrackR-0.4.3/ProTrackR/R/06PTModule.r | 351 ++--- ProTrackR-0.4.3/ProTrackR/R/07PTBlock.r | 88 - ProTrackR-0.4.3/ProTrackR/R/08coercion.r | 258 ++-- ProTrackR-0.4.3/ProTrackR/R/09playing_routines.r | 174 +- ProTrackR-0.4.3/ProTrackR/R/10ModArchiveHelpers.r | 96 - ProTrackR-0.4.3/ProTrackR/R/11MODPlugHelpers.r | 40 ProTrackR-0.4.3/ProTrackR/R/12ModLandHelpers.r | 46 ProTrackR-0.4.3/ProTrackR/R/ProTrackR-package.r | 156 +- ProTrackR-0.4.3/ProTrackR/R/data.r | 52 ProTrackR-0.4.3/ProTrackR/README.md |only ProTrackR-0.4.3/ProTrackR/man/MODPlugToPTPattern.Rd | 274 ++-- ProTrackR-0.4.3/ProTrackR/man/PTBlock.Rd | 148 +- ProTrackR-0.4.3/ProTrackR/man/PTCell-class.Rd | 176 +- ProTrackR-0.4.3/ProTrackR/man/PTCell-method.Rd | 244 +-- ProTrackR-0.4.3/ProTrackR/man/PTModule-class.Rd | 210 +-- ProTrackR-0.4.3/ProTrackR/man/PTPattern-class.Rd | 128 +- ProTrackR-0.4.3/ProTrackR/man/PTPattern-method.Rd | 196 +-- ProTrackR-0.4.3/ProTrackR/man/PTPatternToMODPlug.Rd | 154 +- ProTrackR-0.4.3/ProTrackR/man/PTSample-class.Rd | 50 ProTrackR-0.4.3/ProTrackR/man/PTSample-method.Rd | 6 ProTrackR-0.4.3/ProTrackR/man/PTTrack-class.Rd | 126 - ProTrackR-0.4.3/ProTrackR/man/PTTrack-method.Rd | 206 +-- ProTrackR-0.4.3/ProTrackR/man/ProTrackR-package.Rd | 375 ++--- ProTrackR-0.4.3/ProTrackR/man/appendPattern.Rd | 186 +- ProTrackR-0.4.3/ProTrackR/man/as.character.Rd | 154 +- ProTrackR-0.4.3/ProTrackR/man/as.raw.Rd | 242 +-- ProTrackR-0.4.3/ProTrackR/man/clearSamples.Rd | 110 - ProTrackR-0.4.3/ProTrackR/man/clearSong.Rd | 112 - ProTrackR-0.4.3/ProTrackR/man/deletePattern.Rd | 176 +- ProTrackR-0.4.3/ProTrackR/man/effect.Rd | 148 +- ProTrackR-0.4.3/ProTrackR/man/figures/README-power_cyberride-1.png |only ProTrackR-0.4.3/ProTrackR/man/fineTune.Rd | 140 +- ProTrackR-0.4.3/ProTrackR/man/fix.PTModule.Rd | 170 +- ProTrackR-0.4.3/ProTrackR/man/funk_table.Rd | 48 ProTrackR-0.4.3/ProTrackR/man/loopLength.Rd | 172 +- ProTrackR-0.4.3/ProTrackR/man/loopSample.Rd | 144 +- ProTrackR-0.4.3/ProTrackR/man/loopStart.Rd | 170 +- ProTrackR-0.4.3/ProTrackR/man/loopState.Rd | 128 +- ProTrackR-0.4.3/ProTrackR/man/mod.intro.Rd | 76 - ProTrackR-0.4.3/ProTrackR/man/modArchive.Rd | 631 ++++------ ProTrackR-0.4.3/ProTrackR/man/modLand.Rd | 197 +-- ProTrackR-0.4.3/ProTrackR/man/modToWave.Rd | 22 ProTrackR-0.4.3/ProTrackR/man/moduleSize.Rd | 142 +- ProTrackR-0.4.3/ProTrackR/man/name.Rd | 188 +- ProTrackR-0.4.3/ProTrackR/man/note.Rd | 202 +-- ProTrackR-0.4.3/ProTrackR/man/noteManipulation.Rd | 224 +-- ProTrackR-0.4.3/ProTrackR/man/noteToPeriod.Rd | 118 - ProTrackR-0.4.3/ProTrackR/man/nybble.Rd | 162 +- ProTrackR-0.4.3/ProTrackR/man/nybbleToSignedInt.Rd | 148 +- ProTrackR-0.4.3/ProTrackR/man/octave.Rd | 176 +- ProTrackR-0.4.3/ProTrackR/man/pasteBlock.Rd | 168 +- ProTrackR-0.4.3/ProTrackR/man/patternLength.Rd | 136 +- ProTrackR-0.4.3/ProTrackR/man/patternOrder.Rd | 284 ++-- ProTrackR-0.4.3/ProTrackR/man/patternOrderLength.Rd | 184 +- ProTrackR-0.4.3/ProTrackR/man/paula_clock.Rd | 62 ProTrackR-0.4.3/ProTrackR/man/periodToChar.Rd | 116 - ProTrackR-0.4.3/ProTrackR/man/period_table.Rd | 78 - ProTrackR-0.4.3/ProTrackR/man/playMod.Rd | 4 ProTrackR-0.4.3/ProTrackR/man/playSample.Rd | 222 +-- ProTrackR-0.4.3/ProTrackR/man/playWave.Rd | 12 ProTrackR-0.4.3/ProTrackR/man/playingtable.Rd | 256 ++-- ProTrackR-0.4.3/ProTrackR/man/plot.Rd | 98 - ProTrackR-0.4.3/ProTrackR/man/print.Rd | 98 - ProTrackR-0.4.3/ProTrackR/man/proTrackerVibrato.Rd | 74 - ProTrackR-0.4.3/ProTrackR/man/rawToCharNull.Rd | 118 - ProTrackR-0.4.3/ProTrackR/man/rawToPTModule.Rd | 162 +- ProTrackR-0.4.3/ProTrackR/man/rawToSignedInt.Rd | 112 - ProTrackR-0.4.3/ProTrackR/man/rawToUnsignedInt.Rd | 120 - ProTrackR-0.4.3/ProTrackR/man/read.module.Rd | 208 +-- ProTrackR-0.4.3/ProTrackR/man/read.sample.Rd | 164 +- ProTrackR-0.4.3/ProTrackR/man/resample.Rd | 88 - ProTrackR-0.4.3/ProTrackR/man/sampleLength.Rd | 104 - ProTrackR-0.4.3/ProTrackR/man/sampleNumber.Rd | 124 - ProTrackR-0.4.3/ProTrackR/man/sampleRate.Rd | 168 +- ProTrackR-0.4.3/ProTrackR/man/signedIntToNybble.Rd | 152 +- ProTrackR-0.4.3/ProTrackR/man/signedIntToRaw.Rd | 116 - ProTrackR-0.4.3/ProTrackR/man/trackerFlag.Rd | 170 +- ProTrackR-0.4.3/ProTrackR/man/unsignedIntToRaw.Rd | 134 +- ProTrackR-0.4.3/ProTrackR/man/volume.Rd | 138 +- ProTrackR-0.4.3/ProTrackR/man/waveform.Rd | 8 ProTrackR-0.4.3/ProTrackR/man/write.module.Rd | 160 +- ProTrackR-0.4.3/ProTrackR/man/write.sample.Rd | 152 +- 91 files changed, 6608 insertions(+), 6637 deletions(-)
Title: Genetic Algorithm Optimization
Description: Genetic algorithm are a class of optimization
algorithms inspired by the process of natural selection and genetics.
This package is for learning purposes and allows users to optimize
various functions or parameters by mimicking biological evolution
processes such as selection, crossover, and mutation. Ideal for tasks
like machine learning parameter tuning, mathematical function
optimization, and solving combinatorial problems.
Author: Dany Mukesha [aut, cre]
Maintainer: Dany Mukesha <danymukesha@gmail.com>
Diff between genetic.algo.optimizeR versions 0.2.5 dated 2024-02-14 and 0.2.6 dated 2024-02-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/introduction.html | 10 +++++----- tests/testthat/test-test_crossover.R | 7 ------- 4 files changed, 11 insertions(+), 18 deletions(-)
More information about genetic.algo.optimizeR at CRAN
Permanent link
Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces.
Playing surfaces are drawn pursuant to rule-book specifications.
This package should be used as a baseline plot for displaying any type of
tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>
Diff between sportyR versions 2.2.1 dated 2023-06-15 and 2.2.2 dated 2024-02-15
DESCRIPTION | 15 +-- MD5 | 46 +++++----- NEWS.md | 7 + R/features-basketball.R | 8 - R/features-football.R | 4 R/features-hockey.R | 2 R/features-lacrosse.R | 7 - R/geom-curling.R | 14 +-- R/geom-hockey.R | 66 +++++++++------ R/plot-helpers.R | 4 inst/doc/animating-tracking-data.html | 78 ++++++++--------- inst/doc/customize-plot.html | 132 +++++++++++++++--------------- inst/doc/plotting-tracking-data.html | 132 +++++++++++++++--------------- inst/doc/sportyR.html | 38 ++++---- man/basketball_center_circle_fill.Rd | 2 man/basketball_free_throw_circle_dash.Rd | 2 man/basketball_painted_area.Rd | 4 man/curling_features_set_colors.Rd | 22 ++--- man/football_field_border.Rd | 4 man/football_field_border_outline.Rd | 4 man/hockey_features_set_colors.Rd | 76 +++++++++++------ man/hockey_goaltenders_restricted_area.Rd | 2 man/lacrosse_off_field_officials_box.Rd | 6 - man/lacrosse_penalty_box_outline.Rd | 6 - 24 files changed, 366 insertions(+), 315 deletions(-)
Title: Random-Effects Stochastic Reaction Networks
Description: A random-effects stochastic model that allows quick detection of
clonal dominance events from clonal tracking data collected in gene therapy studies. Starting from the Ito-type equation describing the dynamics of cells duplication, death and differentiation at clonal level, we first considered its local linear approximation as the base model.
The parameters of the base model, which are inferred using a maximum likelihood approach,
are assumed to be shared across the clones. Although this assumption makes inference easier,
in some cases it can be too restrictive and does not take into account possible scenarios of clonal dominance.
Therefore we extended the base model by introducing random effects for the clones.
In this extended formulation the dynamic parameters are estimated using a tailor-made
expectation maximization algorithm. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.05.31.494100>.
Author: Luca Del Core [aut, cre, cph] ,
Marco Grzegorczyk [aut, ths] ,
Ernst Wit [aut, ths]
Maintainer: Luca Del Core <l.del.core@rug.nl>
Diff between RestoreNet versions 1.0 dated 2022-09-20 and 1.0.1 dated 2024-02-15
DESCRIPTION | 8 +- MD5 | 22 +++--- R/functions.R | 153 ++++++++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/RestoreNet.pdf |binary man/compile.h.Rd | 2 man/dmvNorm.Rd | 2 man/fit.null.Rd | 32 +++++----- man/fit.re.Rd | 47 +++++++++----- man/get.V.Rd | 2 man/nullModelFitting.Rd | 34 ++++++---- man/rndEffModelStats.Rd | 35 ++++++---- 12 files changed, 199 insertions(+), 138 deletions(-)
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Francisco
Martinez et al. (2022) <doi:10.1016/j.neucom.2021.12.028>. When the forecasting
horizon is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.4 dated 2023-03-24 and 1.0.5 dated 2024-02-15
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 4 R/forecasting.R | 5 build/vignette.rds |binary inst/doc/tsfgrnn.R | 24 ++-- inst/doc/tsfgrnn.html | 288 +++++++++++++++++++++++++------------------------- 7 files changed, 173 insertions(+), 166 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Description: Diff, patch and merge for data frames. Document changes in data
sets and use them to apply patches. Changes to data can be made visible by using
render_diff(). The 'V8' package is used to wrap the 'daff.js' 'JavaScript' library
which is included in the package.
Author: Paul Fitzpatrick [aut] ,
Edwin de Jonge [aut, cre] ,
Gregory R. Warnes [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between daff versions 1.0.1 dated 2023-10-08 and 1.1.1 dated 2024-02-15
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NEWS.md | 4 ++++ R/context.R | 2 +- README.md | 2 +- inst/js/underscore.js |only man/figures |only 7 files changed, 15 insertions(+), 9 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), used in the computation of
marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.8.6 dated 2023-01-13 and 0.8.7 dated 2024-02-15
modelbased-0.8.6/modelbased/tests/testthat/helper.R |only modelbased-0.8.6/modelbased/tests/testthat/test-get_marginalmeans.R |only modelbased-0.8.7/modelbased/DESCRIPTION | 17 modelbased-0.8.7/modelbased/MD5 | 108 +- modelbased-0.8.7/modelbased/NAMESPACE | 1 modelbased-0.8.7/modelbased/NEWS.md | 2 modelbased-0.8.7/modelbased/R/describe_nonlinear.R | 18 modelbased-0.8.7/modelbased/R/estimate_contrasts.R | 20 modelbased-0.8.7/modelbased/R/estimate_grouplevel.R | 2 modelbased-0.8.7/modelbased/R/estimate_means.R | 74 - modelbased-0.8.7/modelbased/R/estimate_predicted.R | 44 - modelbased-0.8.7/modelbased/R/estimate_slopes.R | 77 +- modelbased-0.8.7/modelbased/R/get_emmeans.R | 86 +- modelbased-0.8.7/modelbased/R/get_marginaleffects.R | 6 modelbased-0.8.7/modelbased/R/get_marginalmeans.R | 92 +- modelbased-0.8.7/modelbased/R/print_md.R | 7 modelbased-0.8.7/modelbased/R/reexports.R | 4 modelbased-0.8.7/modelbased/R/smoothing.R | 26 modelbased-0.8.7/modelbased/R/visualisation_matrix.R | 2 modelbased-0.8.7/modelbased/R/visualisation_recipe.estimate_means.R | 79 -- modelbased-0.8.7/modelbased/R/visualisation_recipe.estimate_predicted.R | 30 modelbased-0.8.7/modelbased/R/visualisation_recipe.estimate_slopes.R | 2 modelbased-0.8.7/modelbased/README.md | 6 modelbased-0.8.7/modelbased/build/vignette.rds |binary modelbased-0.8.7/modelbased/inst/WORDLIST | 18 modelbased-0.8.7/modelbased/man/describe_nonlinear.Rd | 8 modelbased-0.8.7/modelbased/man/estimate_contrasts.Rd | 9 modelbased-0.8.7/modelbased/man/estimate_means.Rd | 29 modelbased-0.8.7/modelbased/man/estimate_slopes.Rd | 64 - modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-10-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-12-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-14-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-15-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-16-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-17-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-3-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-4-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-6-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-8-1.png |binary modelbased-0.8.7/modelbased/man/figures/unnamed-chunk-9-1.png |binary modelbased-0.8.7/modelbased/man/modelbased-package.Rd | 1 modelbased-0.8.7/modelbased/man/reexports.Rd | 4 modelbased-0.8.7/modelbased/man/visualisation_recipe.estimate_predicted.Rd | 84 +- modelbased-0.8.7/modelbased/tests/testthat/test-attributes_visualisation.R | 59 - modelbased-0.8.7/modelbased/tests/testthat/test-brms.R | 49 - modelbased-0.8.7/modelbased/tests/testthat/test-describe_nonlinear.R | 88 +- modelbased-0.8.7/modelbased/tests/testthat/test-estimate_contrasts.R | 379 +++++----- modelbased-0.8.7/modelbased/tests/testthat/test-estimate_expectation.R | 124 +-- modelbased-0.8.7/modelbased/tests/testthat/test-estimate_grouplevel.R | 75 - modelbased-0.8.7/modelbased/tests/testthat/test-estimate_means.R | 346 +++++---- modelbased-0.8.7/modelbased/tests/testthat/test-estimate_predicted.R | 306 ++++---- modelbased-0.8.7/modelbased/tests/testthat/test-estimate_slopes.R | 42 - modelbased-0.8.7/modelbased/tests/testthat/test-get_marginaleffects.R | 15 modelbased-0.8.7/modelbased/tests/testthat/test-glmmTMB.R | 122 +-- modelbased-0.8.7/modelbased/tests/testthat/test-mgcv.R | 127 +-- modelbased-0.8.7/modelbased/tests/testthat/test-signal.R | 16 56 files changed, 1425 insertions(+), 1243 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-01 2024.1.31
2023-08-31 2023.8.24
2023-05-01 2023.5.1
2020-08-10 2020.8.6
2020-05-14 2020.5.13
2020-03-25 2020.3.23
2020-03-04 2020.2.27
2020-01-31 2020.1.16
2019-10-28 2019.10.19
2019-09-23 2019.9.16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-02 2.9.6
2022-09-29 2.9.5
2021-10-19 2.9.4
2017-04-27 2.9.3
2016-01-29 2.8
2015-07-14 2.7
2014-11-14 2.6
2014-02-20 2.5
2013-10-29 2.4
2013-10-24 2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-01 0.2.3
Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test
and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko_k@gmx.de>
Diff between fbst versions 2.1 dated 2022-11-10 and 2.2 dated 2024-02-15
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/fbst.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/twodimfbst.html | 45 +++++++++++++++++++++------------------------ 6 files changed, 32 insertions(+), 35 deletions(-)
Title: Bayesian MMRMs using 'brms'
Description: The mixed model for repeated measures (MMRM) is a popular
model for longitudinal clinical trial data with continuous endpoints,
and 'brms' is a powerful and versatile package for fitting Bayesian
regression models. The 'brms.mmrm' R package leverages 'brms' to run
MMRMs, and it supports a simplified interfaced to reduce difficulty
and align with the best practices of the life sciences. References:
Bürkner (2017) <doi:10.18637/jss.v080.i01>, Mallinckrodt (2008)
<doi:10.1177/009286150804200402>.
Author: William Michael Landau [aut, cre]
,
Kevin Kunzmann [aut] ,
Yoni Sidi [aut],
Christian Stock [aut] ,
Eli Lilly and Company [cph, fnd],
Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between brms.mmrm versions 0.0.2 dated 2023-08-18 and 0.1.0 dated 2024-02-15
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Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Author: Paulo Justiniano Ribeiro Jr [aut, cre] <paulojus@ufpr.br>,
Peter Diggle [aut, cre] <p.diggle@lancaster.ac.uk>,
Ole Christensen [ctb],
Martin Schlather [ctb],
Roger Bivand [ctb],
Brian Ripley [ctb]
Maintainer: Paulo Justiniano Ribeiro Jr <paulojus@ufpr.br>
Diff between geoR versions 1.9-3 dated 2023-12-11 and 1.9-4 dated 2024-02-15
geoR-1.9-3/geoR/tests |only geoR-1.9-4/geoR/DESCRIPTION | 8 ++++---- geoR-1.9-4/geoR/MD5 | 15 +++++++-------- geoR-1.9-4/geoR/R/geobayes.R | 5 ----- geoR-1.9-4/geoR/R/likGRF.R | 29 +++++++++++++---------------- geoR-1.9-4/geoR/R/profiles.R | 6 ++---- geoR-1.9-4/geoR/R/variofit.R | 10 +++------- geoR-1.9-4/geoR/R/xvalid.R | 16 +++------------- geoR-1.9-4/geoR/inst/doc/CHANGES | 8 ++++++++ 9 files changed, 40 insertions(+), 57 deletions(-)
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics,
prior and posterior predictive checks, and other visualizations
to support the applied Bayesian workflow advocated in
Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
The package is designed not only to provide convenient functionality
for users, but also a common set of functions that can be easily used by
developers working on a variety of R packages for Bayesian modeling,
particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut],
Paul-Christian Buerkner [ctb],
Martin Modrak [ctb],
Malcolm Barrett [ctb],
Frank Weber [ctb],
Eduardo Coronado Sroka [ctb],
Teemu Sailynoja [ctb],
Aki Vehtari [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between bayesplot versions 1.11.0 dated 2024-01-30 and 1.11.1 dated 2024-02-15
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 4 +- R/helpers-ppc.R | 2 - R/ppc-distributions.R | 57 +++++++++++++++++----------------- inst/doc/graphical-ppcs.html | 4 +- inst/doc/plotting-mcmc-draws.html | 4 +- inst/doc/visual-mcmc-diagnostics.html | 4 +- man/MCMC-traces.Rd | 11 +++--- man/PPC-distributions.Rd | 36 +++++++++++---------- 10 files changed, 78 insertions(+), 70 deletions(-)