Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre],
Silvia Grieder [aut],
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.4.4 dated 2023-01-06 and 0.4.5 dated 2024-12-22
DESCRIPTION | 8 MD5 | 28 R/OMEGA.R | 4 R/OMEGA_helper.R | 4 README.md | 88 - build/vignette.rds |binary inst/CITATION | 11 inst/doc/EFAtools.R | 2 inst/doc/EFAtools.html | 1918 +++++++++++++++---------------- inst/doc/Replicate_SPSS_psych.R | 2 inst/doc/Replicate_SPSS_psych.html | 992 ++++++++-------- man/OMEGA.Rd | 4 man/figures/README-unnamed-chunk-5-4.png |binary src/Makevars | 6 src/Makevars.win | 6 15 files changed, 1518 insertions(+), 1555 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@studenti.unipd.it>
Diff between XDNUTS versions 1.5.4 dated 2024-12-05 and 1.5.5 dated 2024-12-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/interface.R | 14 +++++++++----- build/partial.rdb |binary 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 0.1.2 dated 2024-12-10 and 1.0.0 dated 2024-12-22
DESCRIPTION | 10 +++--- MD5 | 77 ++++++++++++++++++++++++++++++++++++++++++------- NAMESPACE | 2 + NEWS.md | 9 ++--- R/biovizseq.R |only R/combi_plot.R | 68 +++++++++++++++++++++++++++++++++---------- R/gff_plot.R | 4 +- R/globalvariables.R | 10 +++++- R/motif_plot.R | 10 ------ R/plantcare_plot.R | 4 +- R/smart_plot.R | 1 README.md |only inst/extdata/target.fa |only inst/shinyapp |only man/biovizseq.Rd |only man/combi_p.Rd | 17 ++++++++++ man/figures |only man/globalVariables.Rd | 2 - 18 files changed, 160 insertions(+), 54 deletions(-)
Title: Design Patterns in R
Description: Build robust and maintainable software with object-oriented design
patterns in R. Design patterns abstract and present in neat, well-defined
components and interfaces the experience of many software designers and
architects over many years of solving similar problems. These are solutions
that have withstood the test of time with respect to re-usability,
flexibility, and maintainability. 'R6P' provides abstract base classes with
examples for a few known design patterns. The patterns were selected by
their applicability to analytic projects in R. Using these patterns in R
projects have proven effective in dealing with the complexity that
data-driven applications possess.
Author: Harel Lustiger [aut, cre] ,
Tidylab [cph, fnd]
Maintainer: Harel Lustiger <tidylab@gmail.com>
Diff between R6P versions 0.3.0 dated 2022-10-02 and 0.4.0 dated 2024-12-22
R6P-0.3.0/R6P/R/utils-pipes.R |only R6P-0.3.0/R6P/R/utils.R |only R6P-0.3.0/R6P/man/pipes.Rd |only R6P-0.4.0/R6P/DESCRIPTION | 49 +- R6P-0.4.0/R6P/MD5 | 39 - R6P-0.4.0/R6P/NAMESPACE | 4 R6P-0.4.0/R6P/NEWS.md | 6 R6P-0.4.0/R6P/R/R6P-helpers.R | 43 + R6P-0.4.0/R6P/R/R6P-package.R |only R6P-0.4.0/R6P/R/base-NullObject.R | 12 R6P-0.4.0/R6P/R/base-Singleton.R | 82 +-- R6P-0.4.0/R6P/R/base-ValueObject.R | 71 +-- R6P-0.4.0/R6P/R/object_relational-Repository.R | 63 +- R6P-0.4.0/R6P/R/zzz.R | 29 - R6P-0.4.0/R6P/README.md | 58 -- R6P-0.4.0/R6P/man/NullObject.Rd | 101 ---- R6P-0.4.0/R6P/man/R6P-package.Rd |only R6P-0.4.0/R6P/man/Repository.Rd | 89 +-- R6P-0.4.0/R6P/man/Singleton.Rd | 61 -- R6P-0.4.0/R6P/man/ValueObject.Rd | 229 ---------- R6P-0.4.0/R6P/tests/testthat/helpers-xyz.R | 23 - R6P-0.4.0/R6P/tests/testthat/test-base-Singleton.R | 64 +- R6P-0.4.0/R6P/tests/testthat/test-object_relational-Repository.R | 14 23 files changed, 329 insertions(+), 708 deletions(-)
Title: Explore Your Data with Interactive Figures
Description: A framework for creating interactive figures for data exploration.
All plots are automatically linked and support several kinds of interactive features,
including selection, zooming, panning, and parameter manipulation. The figures
can be interacted with either manually, using a mouse and a keyboard,
or by running code from inside an active R session.
Author: Adam Bartonicek [aut, cre, cph]
Maintainer: Adam Bartonicek <bartonicek@gmail.com>
Diff between plotscaper versions 0.2.4 dated 2024-11-20 and 0.2.5 dated 2024-12-22
DESCRIPTION | 6 +-- MD5 | 18 ++++----- NEWS.md | 2 + build/vignette.rds |binary inst/doc/algebra.html | 10 ++--- inst/doc/available-interactions.html | 62 ++++++++++++++++---------------- inst/doc/layout.html | 14 +++---- inst/doc/performance.html | 6 +-- inst/doc/plotscaper.html | 14 +++---- inst/htmlwidgets/plotscape/main.iife.js | 2 - 10 files changed, 68 insertions(+), 66 deletions(-)
Title: Phytosanitary Calculator for Inspection Plans Based on Risks
Description: A 'Shiny' application for calculating phytosanitary inspection plans based on risks. It generates a diagram of pallets in a lot, highlights the units to be sampled, and documents them based on the selected sampling method (simple random or systematic sampling).
Author: Gustavo Ramirez-Valverde [aut, cre],
Luis Gabriel Otero-Prevost [aut],
Pedro Macias-Canales [ctb],
Juan A. Villanueva-Jimenez [ctb],
Jorge Luis Leyva-Vazquez [ctb]
Maintainer: Gustavo Ramirez-Valverde <gustavoramirezvalverde@gmail.com>
Diff between PhytosanitaryCalculator versions 1.1.1 dated 2024-05-30 and 1.1.3 dated 2024-12-22
DESCRIPTION | 26 - MD5 | 9 NAMESPACE | 2 R/phitosanitarycalculator.R | 801 ++++++++++++++++++++++++++------- R/www |only man/PhytosanitaryCalculator-package.Rd | 75 +-- 6 files changed, 716 insertions(+), 197 deletions(-)
More information about PhytosanitaryCalculator at CRAN
Permanent link
Title: Group Factor Analysis
Description: Several group factor analysis algorithms are implemented, including Canonical Correlation-based Estimation by Choi et al. (2021) <doi:10.1016/j.jeconom.2021.09.008> , Generalised Canonical Correlation Estimation by Lin and Shin (2023) <doi:10.2139/ssrn.4295429>, Circularly Projected Estimation by Chen (2022) <doi:10.1080/07350015.2022.2051520>, and Aggregated projection method.
Author: Jiaqi Hu [cre, aut],
Ting Li [aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between GrFA versions 0.2 dated 2024-08-24 and 0.2.1 dated 2024-12-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- data/UShouseprice.rda |binary man/UShouseprice.Rd | 40 ++++++++++++++++++++++++++++++++++++++-- 4 files changed, 45 insertions(+), 9 deletions(-)
Title: Utilities for Fude Polygon
Description: Provides utilities to facilitate handling of Fude Polygon data
downloadable from the Ministry of Agriculture, Forestry and Fisheries
website <https://open.fude.maff.go.jp>.
Author: Takeshi Nishimura [aut, cph, cre]
Maintainer: Takeshi Nishimura <takenishi@gmail.com>
Diff between fude versions 0.3.6 dated 2024-05-18 and 0.3.7 dated 2024-12-22
fude-0.3.6/fude/R/zzz.R |only fude-0.3.6/fude/data/pref_table.rda |only fude-0.3.6/fude/man/figures/README-facet_wrap_gogoshima-1.png |only fude-0.3.6/fude/man/figures/README-facet_wrap_gogoshima_hist-1.png |only fude-0.3.6/fude/man/figures/README-gogoshima_with_minimap-1.png |only fude-0.3.6/fude/man/figures/README-matsuyama-1.png |only fude-0.3.6/fude/man/figures/README-sample-1.png |only fude-0.3.6/fude/man/figures/README-yawatahama-1.png |only fude-0.3.6/fude/man/figures/README-yusukawa-1.png |only fude-0.3.6/fude/man/pref_table.Rd |only fude-0.3.7/fude/DESCRIPTION | 14 fude-0.3.7/fude/MD5 | 63 - fude-0.3.7/fude/NAMESPACE | 3 fude-0.3.7/fude/NEWS.md | 6 fude-0.3.7/fude/R/bind_fude.R | 19 fude-0.3.7/fude/R/cite_fude.R |only fude-0.3.7/fude/R/combine_fude.R | 320 ++----- fude-0.3.7/fude/R/data.R | 36 fude-0.3.7/fude/R/extract_boundary.R |only fude-0.3.7/fude/R/extract_fude.R | 68 + fude-0.3.7/fude/R/get_boundary.R | 72 + fude-0.3.7/fude/R/ls_fude.R | 48 - fude-0.3.7/fude/R/read_fude.R | 170 +++- fude-0.3.7/fude/R/rename_fude.R | 8 fude-0.3.7/fude/R/shiny_fude.R |only fude-0.3.7/fude/README.md | 406 ++++------ fude-0.3.7/fude/data/community_code_table.rda |only fude-0.3.7/fude/data/pref_code_table.rda |only fude-0.3.7/fude/man/cite_fude.Rd |only fude-0.3.7/fude/man/combine_fude.Rd | 13 fude-0.3.7/fude/man/community_code_table.Rd |only fude-0.3.7/fude/man/extract_boundary.Rd |only fude-0.3.7/fude/man/extract_fude.Rd | 21 fude-0.3.7/fude/man/figures/README-gogoshima-1.png |binary fude-0.3.7/fude/man/figures/README-gogoshimafgb-1.png |only fude-0.3.7/fude/man/figures/README-nosplit_gogoshima-1.png |binary fude-0.3.7/fude/man/get_boundary.Rd | 18 fude-0.3.7/fude/man/lg_code_table.Rd | 10 fude-0.3.7/fude/man/ls_fude.Rd | 6 fude-0.3.7/fude/man/pref_code_table.Rd |only fude-0.3.7/fude/man/read_fude.Rd | 32 fude-0.3.7/fude/man/shiny_fude.Rd |only fude-0.3.7/fude/tests/testthat/test-extract_fude.R | 16 43 files changed, 684 insertions(+), 665 deletions(-)
Title: Building Networks of Hospitals Through Patients Transfers
Description: Set of tools to help interested researchers to build hospital networks
from data on hospitalized patients transferred between hospitals. Methods provided
have been used in Donker T, Wallinga J, Grundmann H. (2010) <doi:10.1371/journal.pcbi.1000715>,
and Nekkab N, Crépey P, Astagneau P, Opatowski L, Temime L. (2020) <doi:10.1038/s41598-020-71212-6>.
Author: Pascal Crepey [aut, cre, cph],
Tjibbe Donker [aut],
Clement Massonnaud [aut],
Michael Lydeamore [aut]
Maintainer: Pascal Crepey <pascal.crepey@ehesp.fr>
Diff between HospitalNetwork versions 0.9.3 dated 2023-02-27 and 0.9.4 dated 2024-12-21
DESCRIPTION | 8 - MD5 | 45 +++--- NEWS.md | 4 R/FakePatientsDB.R | 2 R/HospiNet.R | 40 ++--- R/NetworkAnalysis.R | 18 +- README.md | 4 build/vignette.rds |binary inst/doc/HospitalNetwork-Workflow.R | 11 + inst/doc/HospitalNetwork-Workflow.Rmd | 3 inst/doc/HospitalNetwork-Workflow.html | 134 ++++++++++---------- man/HospiNet.Rd | 6 man/get_hubs_bycluster.Rd | 4 man/get_hubs_global.Rd | 4 tests/testthat/_snaps/HospiNet/circclust500.svg |only tests/testthat/_snaps/HospiNet/clmat100.svg | 8 - tests/testthat/_snaps/HospiNet/clustdeg500.svg | 20 +- tests/testthat/_snaps/HospiNet/clustmatclust500.svg | 26 +-- tests/testthat/_snaps/HospiNet/deg100.svg | 20 +- tests/testthat/_snaps/HospiNet/mat100.svg | 26 +-- tests/testthat/_snaps/HospiNet/matclust500.svg | 18 +- tests/testthat/test-DataManagement.R | 13 - tests/testthat/test-HospiNet.R | 2 vignettes/HospitalNetwork-Workflow.Rmd | 3 24 files changed, 212 insertions(+), 207 deletions(-)
More information about HospitalNetwork at CRAN
Permanent link
Title: Predict with 'tidymodels' Workflows in Databases
Description: Turn 'tidymodels' workflows into objects containing the
sufficient sequential equations to perform predictions. These smaller
objects allow for low dependency prediction locally or directly in
databases.
Author: Emil Hvitfeldt [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between orbital versions 0.2.0 dated 2024-07-28 and 0.3.0 dated 2024-12-21
DESCRIPTION | 21 MD5 | 272 ++++++------ NAMESPACE | 6 NEWS.md | 14 R/aaa.R |only R/augment.R |only R/dt.R | 32 - R/inline.R | 38 - R/json.R | 93 ++-- R/last_fit.R | 7 R/model-glm.R |only R/model-partykit.R |only R/model-xgboost.R |only R/orbital.R | 129 +++-- R/parsnip.R | 138 +++++- R/predict.R | 22 R/r_fun.R | 53 +- R/recipes-utils.R | 91 ++-- R/recipes.R | 111 ++-- R/reexports.R |only R/sql.R | 26 - R/step_adasyn.R | 8 R/step_bin2factor.R | 21 R/step_boxcox.R | 24 - R/step_bsmote.R | 8 R/step_center.R | 20 R/step_corr.R | 2 R/step_discretize.R | 79 +-- R/step_downsample.R | 8 R/step_dummy.R | 26 - R/step_filter_missing.R | 2 R/step_impute_mean.R | 20 R/step_impute_median.R | 22 R/step_impute_mode.R | 20 R/step_indicate_na.R | 26 - R/step_intercept.R | 18 R/step_inverse.R | 32 - R/step_lag.R | 34 - R/step_lencode_bayes.R | 6 R/step_lencode_glm.R | 6 R/step_lencode_mixed.R | 6 R/step_lincomb.R | 2 R/step_log.R | 36 - R/step_mutate.R | 12 R/step_nearmiss.R | 8 R/step_normalize.R | 26 - R/step_novel.R | 34 - R/step_nzv.R | 2 R/step_other.R | 40 - R/step_pca.R | 6 R/step_pca_sparse.R | 6 R/step_pca_sparse_bayes.R | 6 R/step_pca_truncated.R | 6 R/step_range.R | 44 - R/step_ratio.R | 22 R/step_rename.R | 10 R/step_rm.R | 2 R/step_rose.R | 8 R/step_scale.R | 20 R/step_select.R | 2 R/step_smote.R | 8 R/step_smotenc.R | 8 R/step_sqrt.R | 20 R/step_tomek.R | 8 R/step_unknown.R | 20 R/step_upsample.R | 8 R/step_zv.R | 2 R/utils.R |only R/workflows.R | 42 + README.md | 7 build/vignette.rds |binary inst/doc/supported-models.R | 51 ++ inst/doc/supported-models.Rmd | 79 ++- inst/doc/supported-models.html | 633 ++++++++++++++++++++++------ man/augment.orbital_class.Rd |only man/figures |only man/orbital.Rd | 13 man/reexports.Rd |only tests/testthat/_snaps/parsnip.md | 58 ++ tests/testthat/_snaps/workflows.md |only tests/testthat/derby.log | 8 tests/testthat/helper-context.R | 148 +++--- tests/testthat/helper-initialize.R | 311 +++++++------ tests/testthat/helper-reporter.R | 257 +++++------ tests/testthat/helper-utils.R | 16 tests/testthat/test-augment.R |only tests/testthat/test-dt.R | 46 +- tests/testthat/test-inline.R | 30 - tests/testthat/test-json.R | 74 ++- tests/testthat/test-model-glm.R |only tests/testthat/test-model-partykit.R |only tests/testthat/test-model-xgboost.R |only tests/testthat/test-orbital.R | 295 ++++++------- tests/testthat/test-parsnip.R | 131 ++++- tests/testthat/test-predict.R | 30 - tests/testthat/test-recipes.R | 66 +- tests/testthat/test-sql.R | 48 +- tests/testthat/test-step_adasyn.R | 188 ++++---- tests/testthat/test-step_bin2factor.R | 167 +++---- tests/testthat/test-step_boxcox.R | 163 +++---- tests/testthat/test-step_bsmote.R | 187 ++++---- tests/testthat/test-step_center.R | 163 +++---- tests/testthat/test-step_corr.R | 56 +- tests/testthat/test-step_discretize.R | 253 +++++------ tests/testthat/test-step_downsample.R | 187 ++++---- tests/testthat/test-step_dummy.R | 225 ++++----- tests/testthat/test-step_filter_missing.R | 56 +- tests/testthat/test-step_impute_mean.R | 175 +++---- tests/testthat/test-step_impute_median.R | 177 +++---- tests/testthat/test-step_impute_mode.R | 207 ++++----- tests/testthat/test-step_indicate_na.R | 176 +++---- tests/testthat/test-step_intercept.R | 147 +++--- tests/testthat/test-step_inverse.R | 181 ++++---- tests/testthat/test-step_lag.R | 127 ++--- tests/testthat/test-step_lencode_bayes.R | 257 +++++------ tests/testthat/test-step_lencode_glm.R | 227 +++++----- tests/testthat/test-step_lencode_mixed.R | 257 +++++------ tests/testthat/test-step_lincomb.R | 56 +- tests/testthat/test-step_log.R | 181 ++++---- tests/testthat/test-step_mutate.R | 163 +++---- tests/testthat/test-step_nearmiss.R | 187 ++++---- tests/testthat/test-step_normalize.R | 163 +++---- tests/testthat/test-step_novel.R | 227 +++++----- tests/testthat/test-step_nzv.R | 56 +- tests/testthat/test-step_other.R | 263 +++++------ tests/testthat/test-step_pca.R | 221 ++++----- tests/testthat/test-step_pca_sparse.R | 275 ++++++------ tests/testthat/test-step_pca_sparse_bayes.R | 291 ++++++------ tests/testthat/test-step_pca_truncated.R | 271 ++++++----- tests/testthat/test-step_range.R | 193 ++++---- tests/testthat/test-step_ratio.R | 185 ++++---- tests/testthat/test-step_rename.R | 163 +++---- tests/testthat/test-step_rm.R | 56 +- tests/testthat/test-step_rose.R | 187 ++++---- tests/testthat/test-step_scale.R | 163 +++---- tests/testthat/test-step_select.R | 56 +- tests/testthat/test-step_smote.R | 187 ++++---- tests/testthat/test-step_smotenc.R | 187 ++++---- tests/testthat/test-step_sqrt.R | 163 +++---- tests/testthat/test-step_tomek.R | 187 ++++---- tests/testthat/test-step_unknown.R | 215 ++++----- tests/testthat/test-step_upsample.R | 199 ++++---- tests/testthat/test-step_zv.R | 54 +- tests/testthat/test-workflows.R |only vignettes/supported-models.Rmd | 79 ++- 145 files changed, 6665 insertions(+), 5689 deletions(-)
Title: OECD PISA Datasets from 2000-2022 in an Easy-to-Use Format
Description: The Programme for International Student Assessment (PISA) is a global study conducted by the Organization for Economic Cooperation and Development (OECD) in member and non-member countries to assess educational systems by assessing 15-year-old school students academic performance in mathematics, science, and reading. This datasets contains information on their scores and other socioeconomic characteristics, information about their school and its infrastructure, as well as the countries that are taking part in the program.
Author: Kevin Wang [aut, cre],
Paul Yacobellis [aut],
Erika Siregar [aut],
Sarah Romanes [aut],
Kim Fitter [aut],
Giulio Valentino Dalla Riva [aut],
Dianne Cook [aut],
Nick Tierney [aut],
Priya Dingorkar [aut],
Shabarish Sai Subramanian [aut],
Guan Ru Chen [ [...truncated...]
Maintainer: Kevin Wang <kevinwangstats@gmail.com>
Diff between learningtower versions 1.0.1 dated 2023-02-18 and 1.1.0 dated 2024-12-21
learningtower-1.0.1/learningtower/data/datalist |only learningtower-1.1.0/learningtower/DESCRIPTION | 22 - learningtower-1.1.0/learningtower/LICENSE | 2 learningtower-1.1.0/learningtower/MD5 | 65 +-- learningtower-1.1.0/learningtower/NEWS.md |only learningtower-1.1.0/learningtower/R/data.R | 47 +- learningtower-1.1.0/learningtower/R/load_student.R | 11 learningtower-1.1.0/learningtower/R/zzz.R | 11 learningtower-1.1.0/learningtower/README.md | 181 ++++----- learningtower-1.1.0/learningtower/build/vignette.rds |binary learningtower-1.1.0/learningtower/data/countrycode.rda |binary learningtower-1.1.0/learningtower/data/school.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2000.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2003.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2006.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2009.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2012.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2015.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2018.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2022.rda |only learningtower-1.1.0/learningtower/inst/CITATION |only learningtower-1.1.0/learningtower/inst/doc/learningtower_school.R | 47 +- learningtower-1.1.0/learningtower/inst/doc/learningtower_school.Rmd | 63 +-- learningtower-1.1.0/learningtower/inst/doc/learningtower_school.html | 118 +++--- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.R | 52 -- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.Rmd | 62 +-- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.html | 194 +++++----- learningtower-1.1.0/learningtower/man/figures/readme.png |only learningtower-1.1.0/learningtower/man/load_student.Rd | 6 learningtower-1.1.0/learningtower/man/school.Rd | 12 learningtower-1.1.0/learningtower/man/student.Rd | 31 - learningtower-1.1.0/learningtower/tests/testthat/test-countrycode-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-merge.R |only learningtower-1.1.0/learningtower/tests/testthat/test-school-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-student-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-test-load.R | 10 learningtower-1.1.0/learningtower/vignettes/learningtower_school.Rmd | 63 +-- learningtower-1.1.0/learningtower/vignettes/learningtower_student.Rmd | 62 +-- 38 files changed, 549 insertions(+), 510 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.2.1 dated 2024-12-07 and 1.3.0 dated 2024-12-21
SVEMnet-1.2.1/SVEMnet/inst/scripts |only SVEMnet-1.3.0/SVEMnet/DESCRIPTION | 10 SVEMnet-1.3.0/SVEMnet/MD5 | 36 SVEMnet-1.3.0/SVEMnet/NAMESPACE | 7 SVEMnet-1.3.0/SVEMnet/NEWS | 4 SVEMnet-1.3.0/SVEMnet/R/SVEMnet-package.R | 1 SVEMnet-1.3.0/SVEMnet/R/glmnet_with_cv.R |only SVEMnet-1.3.0/SVEMnet/R/svem_significance_test.R | 2 SVEMnet-1.3.0/SVEMnet/R/svem_significance_test_parallel.R | 27 SVEMnet-1.3.0/SVEMnet/R/svemnet_sim_mixture.R |only SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.R | 21 SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 37 SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.html | 847 ++++++++++- SVEMnet-1.3.0/SVEMnet/man/SVEMnet-package.Rd | 1 SVEMnet-1.3.0/SVEMnet/man/glmnet_with_cv.Rd |only SVEMnet-1.3.0/SVEMnet/man/predict_cv.Rd |only SVEMnet-1.3.0/SVEMnet/man/svem_significance_test.Rd | 2 SVEMnet-1.3.0/SVEMnet/man/svem_significance_test_parallel.Rd | 7 SVEMnet-1.3.0/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 37 SVEMnet-1.3.0/SVEMnet/vignettes/figures/mixture_v2.png |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim.R |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim_identity.R |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim_mixture_v2.R |only 23 files changed, 964 insertions(+), 75 deletions(-)
Title: Variable Table for Variable Documentation
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@seattleu.edu>
Diff between vtable versions 1.4.7 dated 2024-10-17 and 1.4.8 dated 2024-12-21
DESCRIPTION | 6 +- MD5 | 44 +++++++------- NEWS.md | 4 + R/dftotable.R | 2 R/helpers.R | 6 +- R/sumtable.R | 26 +++++++- R/vtable.R | 63 ++++++++++++++++----- build/vignette.rds |binary inst/doc/dftotable.R | 98 ++++++++++++++++---------------- inst/doc/dftotable.html | 4 - inst/doc/labeltable.R | 28 ++++----- inst/doc/labeltable.html | 4 - inst/doc/sumtable.R | 98 ++++++++++++++++---------------- inst/doc/sumtable.html | 4 - inst/doc/vtable.html | 4 - inst/doc/vtablefunction.R | 128 +++++++++++++++++++++---------------------- inst/doc/vtablefunction.html | 4 - inst/doc/vtablehelpers.R | 18 +++--- inst/doc/vtablehelpers.html | 10 +-- man/dftoLaTeX.Rd | 2 man/sumtable.Rd | 2 man/vtable.Rd | 6 +- man/weighted.sd.Rd | 2 23 files changed, 312 insertions(+), 251 deletions(-)
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.6 dated 2024-10-29 and 1.6.6.1 dated 2024-12-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ data/brcancer.rda |binary data/colon.rda |binary data/legendre.quadrature.rule.200.rda |binary data/popmort.rda |binary src/test-nmmin.cpp | 16 ++++++++-------- 7 files changed, 17 insertions(+), 17 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>.
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [ctb],
Stefanos Fafalios [aut],
Ioannis Tsamardinos [ctb],
Matteo Fasiolo [ctb],
Giorgos Borboudakis [ctb],
John Burkardt [ctb],
Changliang Zou [ctb],
Kleanthi Lakiotaki [ctb] [...truncated...]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.0 dated 2023-11-09 and 2.1.2 dated 2024-12-21
Rfast-2.1.0/Rfast/R/F-tests.R |only Rfast-2.1.0/Rfast/src/calc_qpois_regs.cpp |only Rfast-2.1.0/Rfast/src/calc_qpois_regs.h |only Rfast-2.1.0/Rfast/src/total_dista.cpp |only Rfast-2.1.0/Rfast/src/total_dists.cpp |only Rfast-2.1.2/Rfast/DESCRIPTION | 10 Rfast-2.1.2/Rfast/MD5 | 160 - Rfast-2.1.2/Rfast/NAMESPACE | 2 Rfast-2.1.2/Rfast/NEWS.md | 45 Rfast-2.1.2/Rfast/R/Dist.R | 28 Rfast-2.1.2/Rfast/R/anova_related.R | 70 Rfast-2.1.2/Rfast/R/as_integer.R | 4 Rfast-2.1.2/Rfast/R/dista.R | 21 Rfast-2.1.2/Rfast/R/distance_cov_cor.R | 2 Rfast-2.1.2/Rfast/R/group.R | 13 Rfast-2.1.2/Rfast/R/mad2.R | 7 Rfast-2.1.2/Rfast/R/random_values_simulation.R | 6 Rfast-2.1.2/Rfast/R/real_mle.R | 6 Rfast-2.1.2/Rfast/R/regression_models.R | 69 Rfast-2.1.2/Rfast/R/sort_unique.R | 5 Rfast-2.1.2/Rfast/R/system_and_package.R | 60 Rfast-2.1.2/Rfast/R/ttest_related_functions.R | 34 Rfast-2.1.2/Rfast/README.md | 12 Rfast-2.1.2/Rfast/build/partial.rdb |binary Rfast-2.1.2/Rfast/inst/include/Rfast/Set.h |only Rfast-2.1.2/Rfast/inst/include/Rfast/matrix.hpp | 50 Rfast-2.1.2/Rfast/inst/include/Rfast/parallel.h | 2 Rfast-2.1.2/Rfast/inst/include/Rfast/templates.h | 21 Rfast-2.1.2/Rfast/inst/include/Rfast/types.hpp | 75 Rfast-2.1.2/Rfast/inst/include/Rfast/vector.hpp | 25 Rfast-2.1.2/Rfast/man/AddToNamespace.Rd | 7 Rfast-2.1.2/Rfast/man/Dist.Rd | 58 Rfast-2.1.2/Rfast/man/Lgamma.Rd | 2 Rfast-2.1.2/Rfast/man/Median.Rd | 2 Rfast-2.1.2/Rfast/man/Order.Rd | 2 Rfast-2.1.2/Rfast/man/Stack.Rd | 2 Rfast-2.1.2/Rfast/man/Table.Rd | 2 Rfast-2.1.2/Rfast/man/checkNamespace.Rd | 16 Rfast-2.1.2/Rfast/man/coeff.Rd | 2 Rfast-2.1.2/Rfast/man/colnormal.mle.Rd | 2 Rfast-2.1.2/Rfast/man/colrange.Rd | 2 Rfast-2.1.2/Rfast/man/cor.fsreg.Rd | 2 Rfast-2.1.2/Rfast/man/dista.Rd | 39 Rfast-2.1.2/Rfast/man/env.copy.Rd | 2 Rfast-2.1.2/Rfast/man/ftest.Rd | 2 Rfast-2.1.2/Rfast/man/gchi2Test.Rd | 4 Rfast-2.1.2/Rfast/man/geom.regs.Rd | 2 Rfast-2.1.2/Rfast/man/group.Rd | 10 Rfast-2.1.2/Rfast/man/is_integer.Rd | 7 Rfast-2.1.2/Rfast/man/iterator.Rd | 2 Rfast-2.1.2/Rfast/man/knn.cv.Rd | 5 Rfast-2.1.2/Rfast/man/macros/system.Rd | 54 Rfast-2.1.2/Rfast/man/mat.mult.Rd | 2 Rfast-2.1.2/Rfast/man/multinom.regs.Rd | 2 Rfast-2.1.2/Rfast/man/read.directory.Rd | 23 Rfast-2.1.2/Rfast/man/rowMins.Rd | 2 Rfast-2.1.2/Rfast/man/rvmf.Rd | 5 Rfast-2.1.2/Rfast/man/sort_unique.Rd | 7 Rfast-2.1.2/Rfast/man/sourceR.Rd | 11 Rfast-2.1.2/Rfast/man/ttests.Rd | 3 Rfast-2.1.2/Rfast/src/Coeff.cpp | 12 Rfast-2.1.2/Rfast/src/Coeff.h | 5 Rfast-2.1.2/Rfast/src/Dist.h | 83 Rfast-2.1.2/Rfast/src/add_to_namespace.cpp | 12 Rfast-2.1.2/Rfast/src/as_integer.cpp | 51 Rfast-2.1.2/Rfast/src/check.cpp | 110 - Rfast-2.1.2/Rfast/src/col_row_utilities.cpp | 9 Rfast-2.1.2/Rfast/src/col_row_utilities_p.cpp | 676 +++--- Rfast-2.1.2/Rfast/src/dista.cpp | 1171 ++++++++++-- Rfast-2.1.2/Rfast/src/dists.cpp | 2228 ++++++++++------------- Rfast-2.1.2/Rfast/src/each.cpp | 742 +++---- Rfast-2.1.2/Rfast/src/energy.cpp | 16 Rfast-2.1.2/Rfast/src/group.cpp | 1065 ++++++---- Rfast-2.1.2/Rfast/src/init.c | 66 Rfast-2.1.2/Rfast/src/maha_ex.cpp | 3 Rfast-2.1.2/Rfast/src/mn.cpp | 6 Rfast-2.1.2/Rfast/src/mn.h | 2 Rfast-2.1.2/Rfast/src/qpois.cpp | 37 Rfast-2.1.2/Rfast/src/read.cpp | 120 - Rfast-2.1.2/Rfast/src/rvmf.cpp | 450 ++-- Rfast-2.1.2/Rfast/src/sort_unique.cpp | 285 +- Rfast-2.1.2/Rfast/src/system_files.cpp | 79 Rfast-2.1.2/Rfast/src/system_files.h | 27 Rfast-2.1.2/Rfast/src/utilities.cpp | 518 ++--- 84 files changed, 4974 insertions(+), 3807 deletions(-)
Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.5 dated 2024-09-23 and 1.0.6 dated 2024-12-21
DESCRIPTION | 10 MD5 | 200 +++++---- NAMESPACE | 1 NEWS.md | 13 R/data.R | 5 R/esci-package.R | 1 R/estimate_mdiff_2x2_mixed.R | 455 ++++++++++++++++++++-- R/jamovimdiff2x2.b.R | 7 R/jamovimdiff2x2.h.R | 8 R/plot_meta.R | 8 R/tools_jamovi.R | 4 README.md | 2 build/stage23.rdb |binary data/data_effronraj_fakenews.rda |binary man/data_altruism_happiness.Rd | 76 +-- man/data_anchor_estimate_ma.Rd | 86 ++-- man/data_basol_badnews.Rd | 96 ++-- man/data_bem_psychic.Rd | 96 ++-- man/data_bodywellf.Rd | 48 +- man/data_bodywellfm.Rd | 48 +- man/data_bodywellm.Rd | 48 +- man/data_campus_involvement.Rd | 66 +-- man/data_chap_8_paired_ex_8.18.Rd | 54 +- man/data_clean_moral.Rd | 78 +-- man/data_college_survey_1.Rd | 90 ++-- man/data_college_survey_2.Rd | 76 +-- man/data_damischrcj.Rd | 52 +- man/data_effronraj_fakenews.Rd | 6 man/data_emotion_heartrate.Rd | 64 +-- man/data_exam_scores.Rd | 58 +- man/data_flag_priming_ma.Rd | 76 +-- man/data_gender_math_iat.Rd | 78 +-- man/data_gender_math_iat_ma.Rd | 84 ++-- man/data_halagappa.Rd | 82 +-- man/data_home_prices.Rd | 66 +-- man/data_kardas_expt_3.Rd | 86 ++-- man/data_kardas_expt_4.Rd | 94 ++-- man/data_labels_flavor.Rd | 78 +-- man/data_latimier_3groups.Rd | 84 ++-- man/data_latimier_prequiz.Rd | 56 +- man/data_latimier_quiz.Rd | 56 +- man/data_latimier_quiz_prequiz.Rd | 56 +- man/data_latimier_reread.Rd | 56 +- man/data_latimier_reread_prequiz.Rd | 56 +- man/data_latimier_reread_quiz.Rd | 56 +- man/data_macnamara_r_ma.Rd | 86 ++-- man/data_mccabemichael_brain.Rd | 130 +++--- man/data_mccabemichael_brain2.Rd | 68 +-- man/data_meditationbrain.Rd | 92 ++-- man/data_organicmoral.Rd | 92 ++-- man/data_penlaptop1.Rd | 52 +- man/data_powerperformance_ma.Rd | 94 ++-- man/data_rattanmotivation.Rd | 82 +-- man/data_religionsharing.Rd | 72 +-- man/data_religious_belief.Rd | 54 +- man/data_selfexplain.Rd | 78 +-- man/data_simmonscredibility.Rd | 120 ++--- man/data_sleep_beauty.Rd | 58 +- man/data_smithrecall.Rd | 54 +- man/data_stickgold.Rd | 74 +-- man/data_studystrategies.Rd | 82 +-- man/data_thomason_1.Rd | 60 +- man/data_videogameaggression.Rd | 74 +-- man/estimate_mdiff_2x2_mixed.Rd | 5 man/estimate_r.Rd | 312 +++++++-------- tests/testthat/_snaps |only tests/testthat/test_CI_diamond_ratio.R | 1 tests/testthat/test_CI_smd_ind_contrast.R | 1 tests/testthat/test_estimate_magnitude.R | 22 - tests/testthat/test_estimate_mdiff_2x2between.R | 58 -- tests/testthat/test_estimate_mdiff_2x2mixed.R | 240 +++++++++-- tests/testthat/test_estimate_mdiff_ind_contrast.R | 39 - tests/testthat/test_estimate_mdiff_one.R | 6 tests/testthat/test_estimate_mdiff_paired.R | 40 - tests/testthat/test_estimate_mdiff_two.R | 38 - tests/testthat/test_estimate_meta_d1.R | 9 tests/testthat/test_estimate_meta_d2.R | 15 tests/testthat/test_estimate_meta_mdiff_two.R | 62 -- tests/testthat/test_estimate_meta_mean.R | 35 - tests/testthat/test_estimate_meta_pdiff_two.R | 3 tests/testthat/test_estimate_meta_r.R | 1 tests/testthat/test_estimate_pdiff_ind_contrast.R | 10 tests/testthat/test_estimate_pdiff_one.R | 8 tests/testthat/test_estimate_pdiff_paired.R | 8 tests/testthat/test_estimate_pdiff_two.R | 8 tests/testthat/test_estimate_proportion.R | 6 tests/testthat/test_estimate_r.R | 7 tests/testthat/test_estimate_rdiff_two.R | 9 tests/testthat/test_overview.R | 2 tests/testthat/test_overview_nominal.R | 2 90 files changed, 2887 insertions(+), 2302 deletions(-)
Title: Analyzing and Visualizing Multidimensional Plant Traits
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Author: Yan He [aut, cre]
Maintainer: Yan He <heyan@njfu.edu.cn>
Diff between MultiTraits versions 0.1.0 dated 2024-11-26 and 0.2.0 dated 2024-12-21
MultiTraits-0.1.0/MultiTraits/data/WH.rda |only MultiTraits-0.1.0/MultiTraits/man/WH.Rd |only MultiTraits-0.1.0/MultiTraits/man/figures/1.png |only MultiTraits-0.1.0/MultiTraits/man/figures/2.png |only MultiTraits-0.1.0/MultiTraits/man/figures/3.png |only MultiTraits-0.1.0/MultiTraits/man/figures/4.png |only MultiTraits-0.1.0/MultiTraits/man/figures/5.png |only MultiTraits-0.2.0/MultiTraits/DESCRIPTION | 8 MultiTraits-0.2.0/MultiTraits/MD5 | 51 MultiTraits-0.2.0/MultiTraits/NAMESPACE | 8 MultiTraits-0.2.0/MultiTraits/NEWS.md |only MultiTraits-0.2.0/MultiTraits/R/CSR.R | 105 - MultiTraits-0.2.0/MultiTraits/R/LHS.R | 40 MultiTraits-0.2.0/MultiTraits/R/NPT.R | 40 MultiTraits-0.2.0/MultiTraits/R/TN.R | 77 MultiTraits-0.2.0/MultiTraits/R/data.R | 63 MultiTraits-0.2.0/MultiTraits/README.md | 173 + MultiTraits-0.2.0/MultiTraits/build/vignette.rds |binary MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.R | 76 MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.Rmd | 167 + MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.html | 1005 +++++----- MultiTraits-0.2.0/MultiTraits/man/CSR_plot.Rd | 42 MultiTraits-0.2.0/MultiTraits/man/PFF.Rd | 8 MultiTraits-0.2.0/MultiTraits/man/TN.Rd | 15 MultiTraits-0.2.0/MultiTraits/man/TN_corr.Rd | 15 MultiTraits-0.2.0/MultiTraits/man/TN_metrics.Rd | 10 MultiTraits-0.2.0/MultiTraits/man/TN_plot.Rd | 21 MultiTraits-0.2.0/MultiTraits/man/figures/1.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/2.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/3.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/4.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/5.jpg |only MultiTraits-0.2.0/MultiTraits/vignettes/MultiTraits_tutorial.Rmd | 167 + 33 files changed, 1278 insertions(+), 813 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.6.0 dated 2024-09-29 and 0.7.0 dated 2024-12-21
vcfppR-0.6.0/vcfppR/src/htslib-1.18 |only vcfppR-0.6.0/vcfppR/src/htslib-1.19.1 |only vcfppR-0.7.0/vcfppR/DESCRIPTION | 6 vcfppR-0.7.0/vcfppR/MD5 | 659 +++------- vcfppR-0.7.0/vcfppR/NEWS.md | 6 vcfppR-0.7.0/vcfppR/R/common.R | 10 vcfppR-0.7.0/vcfppR/R/vcf-compare.R | 9 vcfppR-0.7.0/vcfppR/R/vcf-tables.R | 1 vcfppR-0.7.0/vcfppR/README.md | 12 vcfppR-0.7.0/vcfppR/build/vignette.rds |binary vcfppR-0.7.0/vcfppR/cleanup | 4 vcfppR-0.7.0/vcfppR/cleanup.win | 4 vcfppR-0.7.0/vcfppR/configure |only vcfppR-0.7.0/vcfppR/configure.win |only vcfppR-0.7.0/vcfppR/inst/doc/concordance-of-two-vcf-files.html | 209 +-- vcfppR-0.7.0/vcfppR/inst/include/vcfpp.h | 13 vcfppR-0.7.0/vcfppR/man/vcfcomp.Rd | 8 vcfppR-0.7.0/vcfppR/src/Makevars | 18 vcfppR-0.7.0/vcfppR/src/Makevars.win | 15 vcfppR-0.7.0/vcfppR/src/htslib-1.21 |only vcfppR-0.7.0/vcfppR/src/vcf-reader.cpp | 4 21 files changed, 370 insertions(+), 608 deletions(-)
Title: 'calendR' Fork with Additional Features (Backwards Compatible)
Description: Fork of 'calendR' R package to generate ready to print
calendars with 'ggplot2' (see <https://r-coder.com/calendar-plot-r/>)
with additional features (backwards compatible).
'calendRio' provides a 'calendR()' function that serves as a drop-in
replacement for the upstream version but allows for additional
parameters unlocking extra functionality.
Author: Jose Carlos Soage Gonzalez [aut, cph],
Natalia Perez Veiga [aut, cph],
Marcel Schilling [aut, cph, cre]
Maintainer: Marcel Schilling <foss@mschilli.com>
Diff between calendRio versions 0.2.0 dated 2022-03-10 and 0.2.1 dated 2024-12-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/calendRio.R | 16 ++++++++++------ 3 files changed, 16 insertions(+), 12 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity,
outliers and heavy-tailed distributions in the response variable. In addition,
it can flexibly model dynamic patterns of regression coefficients through
nonparametric varying coefficient functions. In this package, we have implemented
the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with
spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient
Bayesian shrinkage estimation, variable selection and statistical inference. In particular,
valid Bayesian inferences on sparse quantile varying coefficient functions can be validated
on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
and alternative models can be efficiently performed by using the package.
Author: Cen Wu [aut, cre],
Kun Fan [aut],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.2 dated 2023-09-14 and 1.0.3 dated 2024-12-21
DESCRIPTION | 35 +++-- MD5 | 38 +++--- R/NonRobust.R |only R/RcppExports.R | 8 + R/Robust.R |only R/pqrBayes-package.R | 14 +- R/pqrBayes.R | 264 +++------------------------------------------ R/predict.pqrBayes.R | 219 ++++++++++++++++++------------------- R/select.VC.R | 160 +++++++++++++++------------ README.md | 38 ++++-- build/partial.rdb |binary man/data.Rd | 90 +++++++-------- man/pqrBayes-package.Rd | 121 ++++++++++---------- man/pqrBayes.Rd | 206 ++++++++++++++++++----------------- man/predict.pqrBayes.Rd | 108 +++++++++--------- man/print.VCselect.Rd | 48 ++++---- man/print.pqrBayes.Rd | 48 ++++---- man/print.pqrBayes.pred.Rd | 48 ++++---- man/select.VC.Rd | 99 ++++++++++------ src/BGL-SS0.cpp |only src/BGL.cpp |only src/RcppExports.cpp | 59 ++++++++++ 22 files changed, 762 insertions(+), 841 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots, which include loaPlot(), loaMapPlot() and trianglePlot(), and use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins [aut, cre]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>
Diff between loa versions 0.3.0.1 dated 2024-12-13 and 0.3.1.1 dated 2024-12-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/specialist.panels.01.R | 21 +++++++++++++-------- R/specialist.panels.03.zcase.glyphs.R | 4 ++-- man/2.1.specialist.panels.Rd | 2 +- man/loa-package.Rd | 4 ++-- 7 files changed, 36 insertions(+), 23 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.1.1 dated 2024-11-21 and 1.2.0 dated 2024-12-20
DESCRIPTION | 6 ++-- MD5 | 21 ++++++++-------- NEWS.md | 4 +-- R/generate_setup_code.R | 27 +++++++++++---------- R/learn_allocation_rule.R | 2 - R/simulate_one_trial.R | 8 +++--- README.md | 38 +++++++++++++++--------------- inst/doc/RLoptimal.R | 34 +++++++++++++------------- inst/doc/RLoptimal.Rmd | 34 +++++++++++++------------- inst/doc/RLoptimal.html | 38 +++++++++++++++--------------- tests/testthat/test-generate_setup_code.R |only vignettes/RLoptimal.Rmd | 34 +++++++++++++------------- 12 files changed, 126 insertions(+), 120 deletions(-)
Title: Interactively Visualize Structural Equation Modeling Diagrams
Description: It allows users to perform interactive and reproducible visualizations of path diagrams for structural equation modeling (SEM) and small-to-medium sized networks using the 'ggplot2' engine. Its 'shiny' app provides an interface that allows extensive customization, and creates CSV outputs, which can then be used to recreate the figures either using the 'shiny' app or in a typical 'ggplot2' workflow.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.1.1 dated 2024-11-11 and 0.1.2 dated 2024-12-20
ggsem-0.1.1/ggsem/man/launch.Rd |only ggsem-0.1.2/ggsem/DESCRIPTION | 6 ggsem-0.1.2/ggsem/MD5 | 14 - ggsem-0.1.2/ggsem/NAMESPACE | 48 ++-- ggsem-0.1.2/ggsem/R/launch.R | 2 ggsem-0.1.2/ggsem/README.md | 2 ggsem-0.1.2/ggsem/inst/shiny/app.R | 115 +++++++--- ggsem-0.1.2/ggsem/inst/shiny/rsconnect/shinyapps.io/smin95/ggsem.dcf | 2 ggsem-0.1.2/ggsem/man/ggsem.Rd |only 9 files changed, 127 insertions(+), 62 deletions(-)
Title: Cellular Energetics Analysis Software
Description: Measuring cellular energetics is essential to understanding a
matrix’s (e.g. cell, tissue or biofluid) metabolic state. The Agilent
Seahorse machine is a common method to measure real-time cellular
energetics, but existing analysis tools are highly manual or lack
functionality. The Cellular Energetics Analysis Software (ceas) R package
fills this analytical gap by providing modular and automated Seahorse data
analysis and visualization using the methods described by Mookerjee et al.
(2017) <doi:10.1074/jbc.m116.774471>.
Author: Rachel House [aut, cre] ,
James P. Eapen [aut] ,
Hui Shen [fnd] ,
Carrie R. Graveel [fnd] ,
Matthew R. Steensma [fnd] ,
Van Andel Institute [cph]
Maintainer: Rachel House <rachel.house@vai.org>
Diff between ceas versions 1.0.0 dated 2024-05-07 and 1.3.0 dated 2024-12-20
DESCRIPTION | 38 -- MD5 | 60 +-- NAMESPACE | 14 NEWS.md | 102 +++++ R/atp_plot.R | 89 +++- R/bioscope_plot.R | 52 ++ R/energetics.R | 238 ++++++++++-- R/fit_lme.R |only R/globals.R |only R/normalize.R | 100 ++++- R/rate_plot.R | 239 +++++++++++- R/reader.R | 75 +++ README.md | 39 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/ceas.R | 145 ++++++- inst/doc/ceas.Rmd | 270 +++++++++++--- inst/doc/ceas.html | 738 +++++++++++++++++++++++++++------------ inst/extdata/well_norm.csv |only man/atp_plot.Rd | 53 ++ man/bioscope_plot.Rd | 29 + man/ceas-package.Rd | 8 man/energetics_lme_summary.Rd |only man/energetics_ols_summary.Rd |only man/fit_lme.Rd |only man/get_energetics.Rd | 7 man/get_energetics_summary.Rd | 40 +- man/get_rate_summary.Rd | 50 ++ man/normalize.Rd | 58 ++- man/rate_plot.Rd | 34 + man/rates_lme_summary.Rd |only man/read_data.Rd | 56 ++ tests/testthat/test-energetics.R | 16 vignettes/ceas.Rmd | 270 +++++++++++--- 35 files changed, 2247 insertions(+), 573 deletions(-)
Title: Map Layers and Spatial Utilities for British Columbia
Description: Various layers of B.C., including administrative boundaries,
natural resource management boundaries, census boundaries etc. All
layers are available in BC Albers
(<https://spatialreference.org/ref/epsg/3005/>) equal-area projection,
which is the B.C. government standard. The layers are sourced from the
British Columbia and Canadian government under open licenses,
including B.C. Data Catalogue (<https://data.gov.bc.ca>), the
Government of Canada Open Data Portal
(<https://open.canada.ca/en/using-open-data>), and Statistics Canada
(<https://www.statcan.gc.ca/en/reference/licence>).
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between bcmaps versions 2.2.0 dated 2024-01-24 and 2.2.1 dated 2024-12-20
DESCRIPTION | 24 +-- MD5 | 88 +++++------ NEWS.md | 271 ++++++++++++++++++++++------------- R/bc_bound.R | 2 R/cded.R | 8 - R/utm-convert.R | 21 +- README.md | 2 build/vignette.rds |binary inst/doc/add_points.html | 7 inst/doc/bcmaps.html | 13 - man/airzones.Rd | 2 man/bc_cities.Rd | 2 man/bec.Rd | 2 man/census_dissemination_area.Rd | 2 man/census_division.Rd | 2 man/census_economic.Rd | 2 man/census_metropolitan_area.Rd | 2 man/census_subdivision.Rd | 2 man/census_tract.Rd | 2 man/ecoprovinces.Rd | 2 man/ecoregions.Rd | 2 man/ecosections.Rd | 2 man/fsa.Rd | 2 man/gw_aquifers.Rd | 2 man/health_chsa.Rd | 2 man/health_ha.Rd | 2 man/health_hsda.Rd | 2 man/health_lha.Rd | 2 man/hydrozones.Rd | 2 man/mapsheets_250K.Rd | 2 man/mapsheets_50K.Rd | 2 man/municipalities.Rd | 2 man/nr_areas.Rd | 2 man/nr_districts.Rd | 2 man/nr_regions.Rd | 2 man/regional_districts.Rd | 2 man/tsa.Rd | 2 man/vrt_info.Rd | 2 man/water_districts.Rd | 2 man/water_precincts.Rd | 2 man/watercourses_15M.Rd | 2 man/watercourses_5M.Rd | 2 man/wsc_drainages.Rd | 2 tests/testthat/test-data_functions.R | 9 - tests/testthat/test-utm-convert.R | 88 +++++++++++ 45 files changed, 389 insertions(+), 210 deletions(-)
Title: 'fxl' Single Case Design Charting Package
Description: The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).
Author: Shawn Gilroy [aut, cre, cph]
Maintainer: Shawn Gilroy <sgilroy1@lsu.edu>
Diff between fxl versions 1.7.1 dated 2024-06-05 and 1.7.2 dated 2024-12-20
COPYING | 1352 DESCRIPTION | 6 MD5 | 324 NAMESPACE | 146 R/data.R | 406 R/element-anno-arrows-draw.R | 106 R/element-anno-arrows.R | 122 R/element-anno-brackets-draw.R | 128 R/element-anno-brackets.R | 116 R/element-anno-guide-line-draw.R | 176 R/element-anno-guide-line.R | 86 R/element-anno-rect-draw.R | 82 R/element-anno-rect.R | 72 R/element-axis-x.R | 186 R/element-axis-y.R | 137 R/element-criterion-draw.R | 174 R/element-criterion-line.R | 74 R/element-label-facet-draw.R | 114 R/element-label-facet.R | 110 R/element-label-phase-draw.R | 288 R/element-label-phase.R | 124 R/element-label-title.R | 80 R/element-label-xlabel.R | 98 R/element-label-ylabel.R | 98 R/element-legend-draw.R | 104 R/element-legend.R | 132 R/element-line-cumsum-line-draw.R | 116 R/element-line-cumsum-line.R | 84 R/element-line-draw.R | 140 R/element-line.R | 78 R/element-phasechange-draw.R | 214 R/element-phasechange-multiple.R | 54 R/element-phasechange-single.R | 74 R/element-point-cumsum-point-draw.R | 168 R/element-point-cumsum-point.R | 90 R/element-point-draw.R | 242 R/element-point.R | 112 R/element-support-bar-draw.R | 280 R/element-support-bar.R | 148 R/fxl-debugging.R | 488 R/fxl-map.R | 28 R/fxl-print-semilog.R | 1051 R/fxl-print.R | 1122 R/fxl-save.R | 116 R/fxl-utilities.R | 198 R/fxl.R | 392 README.md | 460 build/vignette.rds |binary demo/00Index | 46 demo/annotatedplot.R | 814 demo/atd_concurrentoperant.R | 320 demo/beezdemandInd.R | 158 demo/challenge_1.R | 602 demo/challenge_2.R | 680 demo/challenge_3.R | 644 demo/challenge_4.R | 1150 demo/changing_criterion.R | 386 demo/cigarettepolicy.R | 388 demo/concurrentplot.R | 498 demo/cumulativeplot.R | 570 demo/faplot.R | 210 demo/faplotintegrity.R | 414 demo/greyed_training.R | 632 demo/multiplebaselineplot.R | 302 demo/reports_academic.R | 386 demo/reports_academic_celeration_classes.R | 564 demo/reports_academic_celeration_classes_local_norms.R | 616 demo/reports_academic_rti.R | 536 demo/run_all_demos.R | 44 demo/run_coverage.R | 56 demo/semilogplot.R | 391 demo/silvermanplot.R | 338 inst/CITATION | 24 inst/doc/fxl.R | 4292 +-- inst/doc/fxl.Rmd | 5092 +-- inst/doc/fxl.html | 4206 +- man/Challenge1Data.Rd | 58 man/Challenge2Data.Rd | 46 man/Challenge4Data.Rd | 58 man/GelinoEtAl2022.Rd | 60 man/Gilroyetal2015.Rd | 54 man/Gilroyetal2019.Rd | 60 man/Gilroyetal2019Tx.Rd | 58 man/Gilroyetal2021.Rd | 56 man/KoffarnusEtAl2011.Rd | 48 man/LozyEtAl2020.Rd | 52 man/SimulatedAcademicFluency.Rd | 50 man/assert_input_type.Rd | 42 man/cnvrt_coords.Rd | 54 man/draw_arrows.Rd | 48 man/draw_bar_support.Rd | 52 man/draw_brackets.Rd | 48 man/draw_cumsum_lines.Rd | 48 man/draw_cumsum_points.Rd | 48 man/draw_guide_line.Rd | 48 man/draw_label_facet.Rd | 48 man/draw_label_phase.Rd | 48 man/draw_legend.Rd | 40 man/draw_lines.Rd | 48 man/draw_points.Rd | 52 man/draw_rect.Rd | 52 man/draw_scr_criterion.Rd | 48 man/draw_scr_plines.Rd | 48 man/figures/dragon-cairo.ps.xml | 8504 ++--- man/figures/like-cairo-mod.ps.xml | 614 man/figures/scorpion-cairo.ps.xml |12826 ++++----- man/figures/skinner-cairo.ps.xml |24178 ++++++++--------- man/figures/star-cairo-mod.ps.xml | 1138 man/isValidAXSCharacter.Rd | 38 man/isValidAestheticMapping.Rd | 38 man/isValidCharacterVector.Rd | 42 man/isValidDataFrame.Rd | 38 man/isValidLogicalVector.Rd | 42 man/isValidNumericVector.Rd | 42 man/print.fxl.Rd | 46 man/print.fxlsemilog.Rd | 46 man/scr_anno_arrows.Rd | 98 man/scr_anno_brackets.Rd | 92 man/scr_anno_guide_line.Rd | 74 man/scr_anno_rect.Rd | 52 man/scr_bar_support.Rd | 104 man/scr_criterion_lines.Rd | 68 man/scr_cumsum_lines.Rd | 56 man/scr_cumsum_points.Rd | 74 man/scr_label_facet.Rd | 86 man/scr_label_phase.Rd | 92 man/scr_legend.Rd | 140 man/scr_lines.Rd | 56 man/scr_plines.Rd | 56 man/scr_plines_mbd.Rd | 48 man/scr_plot.Rd | 140 man/scr_points.Rd | 86 man/scr_save.Rd | 80 man/scr_title.Rd | 60 man/scr_xlabel.Rd | 80 man/scr_xoverride.Rd | 98 man/scr_ylabel.Rd | 80 man/scr_yoverride.Rd | 77 man/var_map.Rd | 34 tests/testthat.R | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-demo-annotatedplot.R | 742 tests/testthat/test-demo-changingcriterion.R | 626 tests/testthat/test-demo-cigarettepolicy.R | 382 tests/testthat/test-demo-concurrentplot.R | 516 tests/testthat/test-demo-cumulativeplot.R | 536 tests/testthat/test-demo-cumulativeplot_single.R | 192 tests/testthat/test-demo-faplot.R | 156 tests/testthat/test-demo-faplotintegrity.R | 208 tests/testthat/test-demo-faplotintegrity_extra.R | 380 tests/testthat/test-demo-multiplebaseline_greyed.R | 1008 tests/testthat/test-demo-multiplebaselineplot.R | 256 tests/testthat/test-demo-semilogplot.R | 368 tests/testthat/test-demo-semilogplot_multi.R | 528 tests/testthat/test-demo-silvermanplot.R | 302 tests/testthat/test-element-bar.R | 390 tests/testthat/test-element-label-facet.R | 190 tests/testthat/test-element-label-phase.R | 190 tests/testthat/test-element-scr_arrows.R | 462 tests/testthat/test-element-scr_xoverride.R | 1252 tests/testthat/test-element-scr_yoverride.R | 640 tests/testthat/test-fxl.R | 800 vignettes/fxl.Rmd | 5092 +-- 163 files changed, 50447 insertions(+), 50429 deletions(-)
Title: Survey Analysis with Auxiliary Discretized Variables
Description: Probability surveys often use auxiliary continuous data from administrative records, but the utility of this data is diminished when it is discretized for confidentiality. We provide a set of survey estimators to make full use of information from the discretized variables. See Williams, S.Z., Zou, J., Liu, Y., Si, Y., Galea, S. and Chen, Q. (2024), Improving Survey Inference Using Administrative Records Without Releasing Individual-Level Continuous Data. Statistics in Medicine, 43: 5803-5813. <doi:10.1002/sim.10270> for details.
Author: Jungang Zou [aut, cre],
Yutao Liu [aut],
Sharifa Williams [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between AuxSurvey versions 0.9 dated 2024-12-09 and 1.0 dated 2024-12-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 6 +++++- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>. Functio [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian M Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.8-0 dated 2022-08-31 and 1.9-0 dated 2024-12-20
synthpop-1.8-0/synthpop/R/utility.tables.r |only synthpop-1.9-0/synthpop/DESCRIPTION | 48 synthpop-1.9-0/synthpop/MD5 | 162 - synthpop-1.9-0/synthpop/NAMESPACE | 42 synthpop-1.9-0/synthpop/NEWS | 1031 ++++---- synthpop-1.9-0/synthpop/R/IO.r | 984 ++++--- synthpop-1.9-0/synthpop/R/codebook.syn.r | 102 synthpop-1.9-0/synthpop/R/compare.syn.r | 1364 +++++----- synthpop-1.9-0/synthpop/R/disclosure.R |only synthpop-1.9-0/synthpop/R/functions.syn.r | 2583 ++++++++++---------- synthpop-1.9-0/synthpop/R/methods.syn.r | 1654 ++++++------- synthpop-1.9-0/synthpop/R/multi.compare.syn.r | 226 - synthpop-1.9-0/synthpop/R/multi.disclosure.R |only synthpop-1.9-0/synthpop/R/numtocat.syn.r | 286 +- synthpop-1.9-0/synthpop/R/padMis.syn.r | 250 - synthpop-1.9-0/synthpop/R/padModel.syn.r | 218 - synthpop-1.9-0/synthpop/R/sampler.syn.r | 675 ++--- synthpop-1.9-0/synthpop/R/syn.r | 2796 +++++++++++----------- synthpop-1.9-0/synthpop/R/syn.strata.r | 382 +-- synthpop-1.9-0/synthpop/R/synorig.compare.R |only synthpop-1.9-0/synthpop/R/utility.syn.r | 1724 ++++++------- synthpop-1.9-0/synthpop/R/utility.tables.R |only synthpop-1.9-0/synthpop/R/zzz.r | 10 synthpop-1.9-0/synthpop/build/partial.rdb |binary synthpop-1.9-0/synthpop/build/vignette.rds |binary synthpop-1.9-0/synthpop/inst/CITATION | 48 synthpop-1.9-0/synthpop/inst/doc/disclosure.R |only synthpop-1.9-0/synthpop/inst/doc/disclosure.Rnw |only synthpop-1.9-0/synthpop/inst/doc/disclosure.pdf |only synthpop-1.9-0/synthpop/inst/doc/inference.Rnw | 1494 +++++------ synthpop-1.9-0/synthpop/inst/doc/inference.pdf |binary synthpop-1.9-0/synthpop/inst/doc/synthpop.Rnw | 1328 +++++----- synthpop-1.9-0/synthpop/inst/doc/synthpop.pdf |binary synthpop-1.9-0/synthpop/inst/doc/utility.Rnw | 1100 ++++---- synthpop-1.9-0/synthpop/inst/doc/utility.pdf |binary synthpop-1.9-0/synthpop/inst/logo.png |only synthpop-1.9-0/synthpop/man/SD2011.Rd | 132 - synthpop-1.9-0/synthpop/man/codebook.syn.Rd | 68 synthpop-1.9-0/synthpop/man/compare.Rd | 64 synthpop-1.9-0/synthpop/man/compare.fit.synds.Rd | 300 +- synthpop-1.9-0/synthpop/man/compare.synds.Rd | 263 +- synthpop-1.9-0/synthpop/man/disclosure.Rd |only synthpop-1.9-0/synthpop/man/glm.synds.Rd | 166 - synthpop-1.9-0/synthpop/man/mergelevels.syn.Rd |only synthpop-1.9-0/synthpop/man/multi.compare.Rd | 128 - synthpop-1.9-0/synthpop/man/multi.disclosure.Rd |only synthpop-1.9-0/synthpop/man/multinom.synds.Rd | 130 - synthpop-1.9-0/synthpop/man/numtocat.syn.Rd | 108 synthpop-1.9-0/synthpop/man/polr.synds.Rd | 128 - synthpop-1.9-0/synthpop/man/read.obs.Rd | 62 synthpop-1.9-0/synthpop/man/replicated.uniques.Rd | 100 synthpop-1.9-0/synthpop/man/sdc.Rd | 118 synthpop-1.9-0/synthpop/man/summary.fit.synds.Rd | 250 - synthpop-1.9-0/synthpop/man/summary.synds.Rd | 106 synthpop-1.9-0/synthpop/man/syn.Rd | 768 +++--- synthpop-1.9-0/synthpop/man/syn.bag.Rd | 74 synthpop-1.9-0/synthpop/man/syn.cart.Rd | 158 - synthpop-1.9-0/synthpop/man/syn.catall.Rd | 193 - synthpop-1.9-0/synthpop/man/syn.ipf.Rd | 234 - synthpop-1.9-0/synthpop/man/syn.lognorm.Rd | 82 synthpop-1.9-0/synthpop/man/syn.logreg.Rd | 96 synthpop-1.9-0/synthpop/man/syn.nested.Rd | 72 synthpop-1.9-0/synthpop/man/syn.norm.Rd | 66 synthpop-1.9-0/synthpop/man/syn.normrank.Rd | 90 synthpop-1.9-0/synthpop/man/syn.passive.Rd | 166 - synthpop-1.9-0/synthpop/man/syn.pmm.Rd | 92 synthpop-1.9-0/synthpop/man/syn.polr.Rd | 118 synthpop-1.9-0/synthpop/man/syn.polyreg.Rd | 124 synthpop-1.9-0/synthpop/man/syn.ranger.Rd | 74 synthpop-1.9-0/synthpop/man/syn.rf.Rd | 76 synthpop-1.9-0/synthpop/man/syn.sample.Rd | 72 synthpop-1.9-0/synthpop/man/syn.satcat.Rd | 95 synthpop-1.9-0/synthpop/man/syn.smooth.Rd | 78 synthpop-1.9-0/synthpop/man/syn.survctree.Rd | 192 - synthpop-1.9-0/synthpop/man/synorig.compare.Rd |only synthpop-1.9-0/synthpop/man/synthpop-package.Rd | 89 synthpop-1.9-0/synthpop/man/utility.gen.Rd | 498 +-- synthpop-1.9-0/synthpop/man/utility.tab.Rd | 436 +-- synthpop-1.9-0/synthpop/man/utility.tables.Rd | 437 +-- synthpop-1.9-0/synthpop/man/write.syn.Rd | 99 synthpop-1.9-0/synthpop/vignettes/disclosure.Rnw |only synthpop-1.9-0/synthpop/vignettes/disclosure.bib |only synthpop-1.9-0/synthpop/vignettes/fig1dis.png |only synthpop-1.9-0/synthpop/vignettes/fig2dis.png |only synthpop-1.9-0/synthpop/vignettes/fig3dis.png |only synthpop-1.9-0/synthpop/vignettes/inference.Rnw | 1494 +++++------ synthpop-1.9-0/synthpop/vignettes/inference.bib | 152 - synthpop-1.9-0/synthpop/vignettes/synthpop.Rnw | 1328 +++++----- synthpop-1.9-0/synthpop/vignettes/synthpop.bib | 730 ++--- synthpop-1.9-0/synthpop/vignettes/utility.Rnw | 1100 ++++---- synthpop-1.9-0/synthpop/vignettes/utility.bib | 6 91 files changed, 15219 insertions(+), 14700 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.4 dated 2024-11-15 and 1.5.5 dated 2024-12-20
DESCRIPTION | 8 MD5 | 94 R/GPModel.R | 109 R/gpb.Booster.R | 12 R/gpb.cv.R | 80 R/gpboost.R | 2 configure | 8 configure.ac | 25 configure.win | 25 demo/GPBoost_algorithm.R | 8 man/GPModel.Rd | 39 man/GPModel_shared_params.Rd | 50 man/fit.GPModel.Rd | 14 man/fit.Rd | 14 man/fitGPModel.Rd | 45 man/gpb.cv.Rd | 17 man/gpb.grid.search.tune.parameters.Rd | 13 man/gpboost.Rd | 15 man/predict.GPModel.Rd | 40 man/set_optim_params.GPModel.Rd | 14 man/set_optim_params.Rd | 14 man/set_prediction_data.GPModel.Rd | 20 man/set_prediction_data.Rd | 20 src/CG_utils.cpp | 229 src/GP_utils.cpp | 2 src/Vecchia_utils.cpp | 11 src/c_api.cpp | 5 src/gpboost_R.cpp | 13 src/gpboost_R.h | 11 src/include/GPBoost/CG_utils.h | 140 src/include/GPBoost/GP_utils.h | 4 src/include/GPBoost/cov_fcts.h | 74 src/include/GPBoost/likelihoods.h | 1249 +++- src/include/GPBoost/re_comp.h | 42 src/include/GPBoost/re_model.h | 6 src/include/GPBoost/re_model_template.h | 808 ++- src/include/LightGBM/bin.h | 1 src/include/LightGBM/c_api.h | 2 src/include/LightGBM/dataset.h | 1 src/include/LightGBM/feature_group.h | 1 src/include/LightGBM/train_share_states.h | 1 src/include/LightGBM/tree.h | 1 src/include/LightGBM/utils/log.h | 7 src/io/json11.cpp | 1 src/re_model.cpp | 104 tests/testthat/_snaps |only tests/testthat/test_GPModel_gaussian_process.R | 264 tests/testthat/test_GPModel_non_Gaussian_data.R | 6440 ++++++++++++------------ tests/testthat/test_z_GPBoost_algorithm.R | 43 49 files changed, 5951 insertions(+), 4195 deletions(-)
Title: Constrained Ordinary Least Squares
Description: Constrained ordinary least squares is performed. One constraint is that all beta coefficients (including the constant) cannot be negative. They can be either 0 or strictly positive. Another constraint is that the sum of the beta coefficients equals a constant. References: Hansen, B. E. (2022). Econometrics, Princeton University Press. <ISBN:9780691235899>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cols versions 1.3 dated 2024-11-19 and 1.5 dated 2024-12-20
DESCRIPTION | 8 ++++---- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 2 +- R/int.cls.R | 9 +++++---- R/int.mcls.R |only R/mpcls.R | 8 ++++---- R/mpls.R | 8 ++++---- R/mvpls.R | 8 ++++---- R/pcls.R | 6 +++--- R/pls.R | 6 +++--- man/cls.Rd | 2 +- man/cols-package.Rd | 4 ++-- man/int.cls.Rd | 8 +++++--- man/mvpls.Rd | 3 ++- man/pcls.Rd | 3 ++- man/pls.Rd | 3 ++- 16 files changed, 57 insertions(+), 50 deletions(-)
Title: Working with ISO8601 Dates and Times
Description: Functions to parse strings with ISO8601 dates, times, and
date-times into R-objects. Additionally, there are functions to determine
the type of ISO8601 string and to standardise ISO8601 strings.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between iso8601 versions 0.1.1 dated 2024-12-18 and 0.1.2 dated 2024-12-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 7 +++++++ src/parsedatetime.cpp | 3 ++- 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Parametric and Non-Parametric Copula-Based Imputation Methods
Description: Copula-based imputation methods: parametric and non-parametric algorithms for missing multivariate data through conditional copulas.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Aurora Gatto [aut],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoImp versions 2.0.1 dated 2024-09-09 and 2.0.2 dated 2024-12-20
ChangeLog | 7 + DESCRIPTION | 8 +- MD5 | 12 +-- R/InternalFunction.R | 10 +- R/NPCoImp.R | 186 ++++++++++++++++++++++++++------------------------- man/NPCoImp-class.Rd | 4 - man/NPCoImp.Rd | 21 +++-- 7 files changed, 130 insertions(+), 118 deletions(-)
Title: Bayesian Post-Estimation on the Mean Scale
Description: Computes Bayesian posterior distributions of predictions, marginal effects, and differences of marginal effects for various generalized linear models. Importantly, the posteriors are on the mean (response) scale, allowing for more natural interpretation than summaries on the link scale. Also, predictions and marginal effects of the count probabilities for Poisson and negative binomial models can be computed.
Author: David M. Dalenberg [aut, cre]
Maintainer: David M. Dalenberg <dalenbe2@gmail.com>
Diff between bayesMeanScale versions 0.1.4 dated 2024-05-30 and 0.2.0 dated 2024-12-20
DESCRIPTION | 10 MD5 | 108 ++++--- NAMESPACE | 8 NEWS.md | 11 R/bayes-count-marg-effects.R | 66 +++- R/bayes-count-preds.R | 42 +-- R/bayes-marg-compare.R | 28 +- R/bayes-marg-effects.R | 63 +++- R/bayes-ordinal-marg-effects.R |only R/bayes-ordinal-preds.R |only R/bayes-preds.R | 42 +-- R/combo-check.R |only R/count-marg-table.R | 17 - R/count-mean-diff-continuous.R |only R/count-pred-table.R | 7 R/global-vars.R | 18 + R/levels-prep.R | 6 R/marg-compare-error-check.R | 4 R/marg-model-data-continuous.R |only R/marg-model-data.R | 46 ++- R/marg-table.R | 17 - R/mean-count-pred.R | 2 R/mean-diff-continuous.R |only R/mean-diff.R | 2 R/mean-pred-ordinal.R |only R/mean-pred.R | 2 R/new-value-continuous.R |only R/ordinal-marg-effects-error-check.R |only R/ordinal-marg-table.R |only R/ordinal-mean-diff-continuous.R |only R/ordinal-mean-diff.R |only R/ordinal-pred-table.R |only R/pred-table.R | 19 - R/preds-error-check.R | 10 R/preds-ordinal-error-check.R |only R/print.R | 6 R/sysdata.rda |only README.md | 4 build/vignette.rds |binary inst/doc/introduction.R | 47 ++- inst/doc/introduction.Rmd | 69 +++- inst/doc/introduction.html | 279 +++++++++----------- man/bayesCountMargEffF.Rd | 17 - man/bayesCountPredsF.Rd | 13 man/bayesMargCompareF.Rd | 2 man/bayesMargEffF.Rd | 17 - man/bayesOrdinalMargEffF.Rd |only man/bayesOrdinalPredsF.Rd |only man/bayesPredsF.Rd | 10 tests/testthat/test-bayes-count-marg-effects.R | 4 tests/testthat/test-bayes-count-preds.R | 25 - tests/testthat/test-bayes-ordinal-marg-effects.R |only tests/testthat/test-bayes-ordinal-preds.R |only tests/testthat/test-bayes-preds.R | 2 tests/testthat/test-count-marg-effect-error-check.R | 3 tests/testthat/test-count-preds-error-check.R | 1 tests/testthat/test-levels-prep.R | 4 tests/testthat/test-marg-compare-error-check.R | 4 tests/testthat/test-marg-compare.R | 18 + tests/testthat/test-marg-effects-error-check.R | 5 tests/testthat/test-marg-effects.R | 12 tests/testthat/test-new-value.R | 2 tests/testthat/test-preds-error-check.R | 5 tests/testthat/test-preds-ordinal-error-check.R |only vignettes/introduction.Rmd | 69 +++- 65 files changed, 700 insertions(+), 446 deletions(-)
More information about bayesMeanScale at CRAN
Permanent link
Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients,
regression coefficients (linear, logistic, gamma, and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogerio Boff Borges [aut, cre]
,
Guilherme Serpa Azambuja [aut]
,
Aline Castello Branco Mancuso [aut]
,
Vanessa Bielefeldt Leotti [aut]
,
Vania Naomi Hirakata [aut] ,
Suzi Alves Camey [aut] ,
Stela Maris de Jezus Castro [aut]
,
Gustavo Thomas [aut] , [...truncated...]
Maintainer: Rogerio Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 1.0.2 dated 2023-07-14 and 1.1.4 dated 2024-12-20
DESCRIPTION | 20 ++- MD5 | 28 ++-- NAMESPACE | 1 R/PSS_Health.R | 1 build/vignette.rds |binary inst/PSS.Health/R/modulo_1_media.R | 21 ++- inst/PSS.Health/R/modulo_2_medias_independentes.R | 3 inst/PSS.Health/R/modulo_medidas_repetidas.R | 90 ++++++++++++++- inst/PSS.Health/R/modulo_nao_inferioridade.R | 9 + inst/PSS.Health/R/modulo_regressao_linear.R | 126 +++++++++++----------- inst/PSS.Health/R/modulo_regressao_logistica.R | 2 inst/PSS.Health/global.R | 2 inst/PSS.Health/server.R | 15 +- inst/doc/Vignettes.R | 2 inst/doc/Vignettes.html | 14 +- 15 files changed, 215 insertions(+), 119 deletions(-)
Title: Ecological Niche Modeling using Presence-Absence Data
Description: A set of tools to perform Ecological Niche Modeling with
presence-absence data. It includes algorithms for data partitioning,
model fitting, calibration, evaluation, selection, and prediction.
Other functions help to explore signals of ecological niche using univariate
and multivariate analyses, and model features such as variable response
curves and variable importance. Unique characteristics of this package are
the ability to exclude models with concave quadratic responses, and the
option to clamp model predictions to specific variables. These tools are
implemented following principles proposed in
Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>,
Cobos et al., (2019) <doi:10.7717/peerj.6281>,
and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
Author: Luis F. Arias-Giraldo [aut, cre]
,
Marlon E. Cobos [aut] ,
A. Townsend Peterson [ctb]
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Diff between enmpa versions 0.1.8 dated 2024-06-19 and 0.1.9 dated 2024-12-20
DESCRIPTION | 10 - MD5 | 30 ++- NAMESPACE | 14 + NEWS.md | 12 + R/calibration_glm.R | 6 R/enmpa.R | 3 R/jackknife.R |only R/plot_jk.R |only R/resp2var.R |only README.md | 158 ++++++++++++------- man/enmpa.Rd | 3 man/figures/README-figures-jackk-1.png |binary man/figures/README-figures-jackk-2.png |binary man/figures/README-figures-jackk-3.png |binary man/figures/README-figures-jackk-4.png |binary man/figures/README-figures-prediction_selected-1.png |binary man/jackknife.Rd |only man/plot_jk.Rd |only man/resp2var.Rd |only 19 files changed, 160 insertions(+), 76 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.1 dated 2024-10-19 and 1.2.2 dated 2024-12-20
climate-1.2.1/climate/R/hydro_imgw_annual.R |only climate-1.2.1/climate/man/hydro_imgw_annual.Rd |only climate-1.2.2/climate/DESCRIPTION | 6 climate-1.2.2/climate/MD5 | 53 ++++---- climate-1.2.2/climate/NAMESPACE | 1 climate-1.2.2/climate/NEWS.md | 11 + climate-1.2.2/climate/R/clean_metadata_hydro.R | 17 -- climate-1.2.2/climate/R/hydro_imgw.R | 14 -- climate-1.2.2/climate/R/hydro_imgw_daily.R | 137 ++++++++++++---------- climate-1.2.2/climate/R/hydro_imgw_monthly.R | 19 +-- climate-1.2.2/climate/R/hydro_metadata_imgw.R | 8 - climate-1.2.2/climate/R/hydro_shortening_imgw.R | 3 climate-1.2.2/climate/R/imgw_read.R |only climate-1.2.2/climate/R/meteo_imgw_daily.R | 36 +---- climate-1.2.2/climate/R/meteo_imgw_datastore.R | 5 climate-1.2.2/climate/R/meteo_imgw_hourly.R | 24 +-- climate-1.2.2/climate/R/meteo_imgw_monthly.R | 17 -- climate-1.2.2/climate/R/meteo_shortening_imgw.R | 3 climate-1.2.2/climate/R/nearest_stations_imgw.R | 2 climate-1.2.2/climate/R/ogimet_daily.R | 8 - climate-1.2.2/climate/R/ogimet_hourly.R | 26 ++-- climate-1.2.2/climate/README.md | 53 +++----- climate-1.2.2/climate/data/imgw_hydro_abbrev.rda |binary climate-1.2.2/climate/inst/doc/getstarted.Rmd | 2 climate-1.2.2/climate/inst/doc/getstarted.html | 43 +++--- climate-1.2.2/climate/man/hydro_imgw.Rd | 3 climate-1.2.2/climate/man/meteo_imgw_datastore.Rd | 3 climate-1.2.2/climate/man/ogimet_hourly.Rd | 3 climate-1.2.2/climate/vignettes/getstarted.Rmd | 2 29 files changed, 231 insertions(+), 268 deletions(-)
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.3.7 dated 2024-08-26 and 0.3.8 dated 2024-12-20
DESCRIPTION | 12 MD5 | 26 - NEWS.md | 4 R/bde_check_access.R | 121 +++--- R/bde_tidy_palettes.R | 144 ++++---- R/catalogs.R | 772 +++++++++++++++++++++---------------------- R/indicators.R | 298 ++++++++-------- R/series.R | 872 ++++++++++++++++++++++++------------------------- R/superseded.R | 106 ++--- R/utils.R | 577 ++++++++++++++++---------------- README.md | 8 build/vignette.rds |binary inst/schemaorg.json | 4 man/tidyBdE-package.Rd | 2 14 files changed, 1476 insertions(+), 1470 deletions(-)
Title: Download Weather Station Data from GHCN
Description: The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.
Author: Emilio Berti [aut, cre]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between GHCNr versions 0.8.0 dated 2024-12-13 and 1.0.0 dated 2024-12-20
DESCRIPTION | 8 MD5 | 66 ++++--- NAMESPACE | 10 - R/annual.R | 18 +- R/coverage.R | 84 +++++++--- R/daily.R | 60 ++++--- R/data.R | 17 +- R/flags.R | 9 - R/get-country-shapefile.R | 34 +++- R/monthly.R | 1 R/plotting.R | 212 +++++++++++++------------ R/s3_classes.R | 10 - R/stations.R | 38 +++- R/utils.R | 25 ++- data/USC00010655.rda |only inst/doc/daily.R | 135 +++++++++------- inst/doc/daily.Rmd | 132 +++++++++------ inst/doc/daily.html | 298 ++++++++++++++++++++---------------- man/CA003076680.Rd | 4 man/USC00010655.Rd |only man/annual.Rd | 13 + man/annual_coverage.Rd | 7 man/as_daily.Rd | 2 man/coverage.Rd | 8 man/dot-api_error.Rd |only man/dot-missing_variables.Rd | 4 man/monthly_coverage.Rd | 9 - man/period_coverage.Rd | 11 - man/plot.ghcn_annual.Rd | 2 man/plot.ghcn_daily.Rd | 2 man/plot.ghcn_monthly.Rd | 2 man/remove_flagged.Rd | 5 man/stations.Rd | 13 + tests/testthat/test-flags.R |only tests/testthat/test-geoboundaries.R |only tests/testthat/test-inventory.R |only vignettes/daily.Rmd | 132 +++++++++------ 37 files changed, 822 insertions(+), 549 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. 'dsims' repeatedly generates
instances of a user defined population within a given survey region. It then
generates realisations of a survey design and simulates the detection process.
The data are then analysed so that the results can be compared for accuracy
and precision across all replications. This process allows users to optimise
survey designs for their specific set of survey conditions. The effects of
uncertainty in population distribution or parameters can be investigated
under a number of simulations so that users can be confident that they have
achieved a robust survey design before deploying vessels into the field. The
distance sampling designs used in this package from 'dssd' are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13:
978-0199225873). General distance sampling methods are detailed in Introduction
to Distance Sampling: Estimating Abundance of Biological Populations, Buckland
et. al. (2004 [...truncated...]
Author: Laura Marshall [aut, cre],
Thomas Len [ctb]
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between dsims versions 1.0.4 dated 2023-11-29 and 1.0.5 dated 2024-12-20
dsims-1.0.4/dsims/NEWS |only dsims-1.0.4/dsims/build |only dsims-1.0.4/dsims/inst |only dsims-1.0.4/dsims/vignettes |only dsims-1.0.5/dsims/DESCRIPTION | 17 - dsims-1.0.5/dsims/MD5 | 49 +-- dsims-1.0.5/dsims/NEWS.md |only dsims-1.0.5/dsims/R/ClassConstructors.R | 10 dsims-1.0.5/dsims/R/Simulation.R | 37 ++ dsims-1.0.5/dsims/R/Survey.LT.R | 2 dsims-1.0.5/dsims/R/Survey.PT.R | 2 dsims-1.0.5/dsims/R/calculate.scale.param.R | 2 dsims-1.0.5/dsims/R/dsims-package.R | 11 dsims-1.0.5/dsims/R/simulation.consistency.check.R |only dsims-1.0.5/dsims/README.md | 29 -- dsims-1.0.5/dsims/man/Survey.LT-class.Rd | 2 dsims-1.0.5/dsims/man/Survey.PT-class.Rd | 2 dsims-1.0.5/dsims/man/dsims-package.Rd | 11 dsims-1.0.5/dsims/man/make.density.Rd | 2 dsims-1.0.5/dsims/man/make.ds.analysis.Rd | 2 dsims-1.0.5/dsims/man/make.population.description.Rd | 2 dsims-1.0.5/dsims/man/make.simulation.Rd | 4 dsims-1.0.5/dsims/tests/testthat/test-ProblemCases.R | 41 +++ dsims-1.0.5/dsims/tests/testthat/test-check_Constructors.R | 124 ++++++++++ dsims-1.0.5/dsims/tests/testthat/test-check_ExtremeCases.R | 2 dsims-1.0.5/dsims/tests/testthat/test-check_IndividualCovariates.R | 52 ++++ 26 files changed, 313 insertions(+), 90 deletions(-)
Title: Calculate Ecological Information and Diatom Based Indices
Description: Calculate multiple biotic indices using diatoms from environmental samples. Diatom species are recognized by their species' name using a heuristic search, and their ecological data is retrieved from multiple sources.
It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices.
It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder.
- Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>).
- The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>),and the combined classification of guilds and size classes established by B-Béres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>).
- Current diatom-based biotic indices include the DES index by Descy (1979)
- EPID index by Dell'Uomo (1996, ISBN: 3950009002)
- [...truncated...]
Author: Maria Mercedes Nicolosi Gelis [aut]
,
Maria Belen Sathicq [aut] ,
Joaquin Cochero [cre]
Maintainer: Joaquin Cochero <jcochero@ilpla.edu.ar>
Diff between diathor versions 0.1.4 dated 2024-09-20 and 0.1.5 dated 2024-12-20
DESCRIPTION | 36 +++++- MD5 | 115 +++++++++++--------- NAMESPACE | 3 R/data.R | 52 +++++++-- R/diaThor.R | 16 ++ R/diat_cemfgs_rb.R | 196 +++++++++++++---------------------- R/diat_ddi.R |only R/diat_des.R | 14 -- R/diat_disp.R | 12 -- R/diat_diversity.R | 13 -- R/diat_edi.R |only R/diat_epid.R | 13 -- R/diat_getDiatBarcode.R | 7 - R/diat_guilds.R | 13 -- R/diat_idap.R | 13 -- R/diat_idch.R | 12 -- R/diat_idp.R | 12 -- R/diat_ilm.R | 12 -- R/diat_ips.R | 13 -- R/diat_loadData.R | 49 +++----- R/diat_lobo.R | 15 -- R/diat_morpho.R | 13 -- R/diat_pbidw.R | 13 -- R/diat_pdise.R |only R/diat_sla.R | 16 -- R/diat_spear.R | 12 -- R/diat_tdi.R | 13 -- R/diathorAll.R | 53 +++++++-- README.md |only data/ddi.rda |only data/edi.rda |only data/pdise.rda |only man/cemfgs_rb.Rd | 2 man/dbc_offline.Rd | 4 man/ddi.Rd |only man/diaThor.Rd | 252 +++++++++++++++++++++++---------------------- man/diaThorAll.Rd | 153 +++++++++++++-------------- man/diat_cemfgs_rb.Rd | 78 ++++++------- man/diat_checkName.Rd | 42 +++---- man/diat_ddi.Rd |only man/diat_disp.Rd | 88 +++++++-------- man/diat_diversity.Rd | 54 ++++----- man/diat_edi.Rd |only man/diat_getDiatBarcode.Rd | 38 +++--- man/diat_idch.Rd | 88 +++++++-------- man/diat_ips.Rd | 88 +++++++-------- man/diat_loadData.Rd | 10 + man/diat_pdise.Rd |only man/diat_sampleData.Rd | 2 man/diat_sla.Rd | 3 man/diat_spear.Rd | 88 +++++++-------- man/diat_taxaList.Rd | 32 ++--- man/diathor-package.Rd | 40 +++---- man/disp.Rd | 2 man/edi.Rd |only man/idch.Rd | 46 ++++---- man/idp.Rd | 46 ++++---- man/ilm.Rd | 46 ++++---- man/ips.Rd | 43 ++++--- man/lobo.Rd | 40 +++---- man/pbidw.Rd | 46 ++++---- man/pdise.Rd |only man/sla.Rd | 46 ++++---- man/spear.Rd | 2 man/tdi.Rd | 46 ++++---- 65 files changed, 1074 insertions(+), 1087 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.4 dated 2024-11-20 and 2.2.5 dated 2024-12-20
argparse-2.2.4/argparse/R/utils.R |only argparse-2.2.5/argparse/DESCRIPTION | 8 +- argparse-2.2.5/argparse/MD5 | 11 +-- argparse-2.2.5/argparse/NEWS.md | 5 + argparse-2.2.5/argparse/README.md | 2 argparse-2.2.5/argparse/inst/doc/argparse.html | 60 +++++++++++------ argparse-2.2.5/argparse/tests/testthat/test-argparse.R | 26 +++---- 7 files changed, 65 insertions(+), 47 deletions(-)
Title: Outcome Weights of Treatment Effect Estimators
Description: Many treatment effect estimators can be written as weighted outcomes.
These weights have established use cases like checking covariate balancing via packages like 'cobalt'.
This package takes the original estimator objects and outputs these outcome weights.
It builds on the general framework of Knaus (2024) <doi:10.48550/arXiv.2411.11559>.
This version is compatible with the 'grf' package and provides an internal implementation of Double Machine Learning.
Author: Michael C. Knaus [aut, cre] ,
Henri Pfleiderer [ctb]
Maintainer: Michael C. Knaus <michael.knaus@uni-tuebingen.de>
Diff between OutcomeWeights versions 0.1.0 dated 2024-11-21 and 0.1.1 dated 2024-12-20
DESCRIPTION | 6 +-- MD5 | 9 ++-- NEWS.md | 7 +++ R/NuPa_honest_forest.R | 6 +-- README.md | 48 ++++++++++++++++---------- tests/testthat/test-estimator_combinatorics.R |only 6 files changed, 49 insertions(+), 27 deletions(-)
More information about OutcomeWeights at CRAN
Permanent link
Title: Quantile-Frequency Analysis (QFA) of Time Series
Description: Quantile-frequency analysis (QFA) of time series based on trigonometric quantile regression.
References:
[1] Li, T.-H. (2012) "Quantile periodograms", Journal of the American Statistical
Association, 107, 765–776, <doi:10.1080/01621459.2012.682815>.
[2] Li, T.-H. (2014) Time Series with Mixed Spectra, CRC Press, <doi:10.1201/b15154>
[3] Li, T.-H. (2022) "Quantile Fourier transform, quantile series, and nonparametric
estimation of quantile spectra", <doi:10.48550/arXiv.2211.05844>.
[4] Li, T.-H. (2024) "Quantile crossing spectrum and spline autoregression
estimation," <doi:10.48550/arXiv.2412.02513>.
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl024@outlook.com>
Diff between qfa versions 2.1 dated 2023-08-21 and 3.1 dated 2024-12-20
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Title: Salary Analysis by the Swiss Federal Office for Gender Equality
Description: Implementation of the Swiss Confederation's standard analysis
model for salary analyses
<https://www.ebg.admin.ch/en/equal-pay-analysis-with-logib> in R. The
analysis is run at company-level and the model is intended for
medium-sized and large companies. It can technically be used with 50
or more employees (apprentices, trainees/interns and expats are not
included in the analysis). Employees with at least 100 employees are
required by the Gender Equality Act to conduct an equal pay analysis.
This package allows users to run the equal salary analysis in R,
providing additional transparency with respect to the methodology and
simple automation possibilities.
Author: Marc Stoeckli [aut, cre],
Jonathan Chassot [aut],
Jeremy Kolly [ctb],
Federal Office for Gender Equality of Switzerland [cph, fnd]
Maintainer: Marc Stoeckli <marc.stoeckli@ebg.admin.ch>
Diff between logib versions 0.1.2 dated 2021-11-21 and 0.2.0 dated 2024-12-20
logib-0.1.2/logib/R/sysdata.rda |only logib-0.1.2/logib/data/datalist_imprimerie.rda |only logib-0.1.2/logib/man/cleanup_errors.Rd |only logib-0.1.2/logib/man/datalist_imprimerie.Rd |only logib-0.1.2/logib/tests/testthat/test_analysis.R |only logib-0.2.0/logib/DESCRIPTION | 48 +- logib-0.2.0/logib/MD5 | 79 ++-- logib-0.2.0/logib/NAMESPACE | 15 logib-0.2.0/logib/NEWS.md | 16 logib-0.2.0/logib/R/analysis.R | 69 +--- logib-0.2.0/logib/R/data.R | 6 logib-0.2.0/logib/R/data_check.R | 158 +++++---- logib-0.2.0/logib/R/data_preparation.R | 166 +++++----- logib-0.2.0/logib/R/data_transformation.R | 21 - logib-0.2.0/logib/R/datalists.R | 73 +++- logib-0.2.0/logib/R/models.R | 17 - logib-0.2.0/logib/README.md | 15 logib-0.2.0/logib/data/all_column_names.rda |only logib-0.2.0/logib/data/datalist_example.rda |only logib-0.2.0/logib/man/all_column_names.Rd | 34 +- logib-0.2.0/logib/man/analysis.Rd | 43 +- logib-0.2.0/logib/man/build_custom_mapping.Rd | 72 ++-- logib-0.2.0/logib/man/build_errors.Rd | 60 +-- logib-0.2.0/logib/man/check_data.Rd | 48 +- logib-0.2.0/logib/man/compute_age.Rd | 54 +-- logib-0.2.0/logib/man/compute_years_of_service.Rd | 72 ++-- logib-0.2.0/logib/man/datalist_example.Rd |only logib-0.2.0/logib/man/download_datalist.Rd | 44 +- logib-0.2.0/logib/man/download_example_datalist.Rd |only logib-0.2.0/logib/man/feb29_between.Rd | 40 +- logib-0.2.0/logib/man/get_kennedy_estimator.Rd | 60 +-- logib-0.2.0/logib/man/prepare_data.Rd | 124 +++---- logib-0.2.0/logib/man/read_data.Rd | 86 ++--- logib-0.2.0/logib/man/read_official_excel.Rd | 38 +- logib-0.2.0/logib/man/run_standard_analysis_model.Rd | 64 +-- logib-0.2.0/logib/man/summary.analysis_model.Rd | 5 logib-0.2.0/logib/man/transform_data.Rd | 86 ++--- logib-0.2.0/logib/man/within_a_year.Rd | 40 +- logib-0.2.0/logib/man/yearfrac.Rd | 44 +- logib-0.2.0/logib/tests/testthat.R | 1 logib-0.2.0/logib/tests/testthat/Beispiel_Datenblatt_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_d.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_e.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_f.xlsx |only logib-0.2.0/logib/tests/testthat/Datalist_i.xlsx |only logib-0.2.0/logib/tests/testthat/Esempio_foglio_di_dati_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Example_data_sheet_M1.xlsx |only logib-0.2.0/logib/tests/testthat/Exemple_feuille_de_donnees_M1.xlsx |only logib-0.2.0/logib/tests/testthat/test-analysis.R |only logib-0.2.0/logib/tests/testthat/test-download.R |only 50 files changed, 921 insertions(+), 777 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 1.0.0 dated 2024-02-15 and 1.0.1 dated 2024-12-20
holiglm-1.0.0/holiglm/inst/doc/extending_holiglm.Rmd |only holiglm-1.0.0/holiglm/inst/doc/extending_holiglm.html |only holiglm-1.0.0/holiglm/vignettes/extending_holiglm.Rmd |only holiglm-1.0.1/holiglm/DESCRIPTION | 12 holiglm-1.0.1/holiglm/MD5 | 41 +-- holiglm-1.0.1/holiglm/NAMESPACE | 2 holiglm-1.0.1/holiglm/R/auxiliary.R | 6 holiglm-1.0.1/holiglm/R/hglm.R | 57 ++-- holiglm-1.0.1/holiglm/R/log-likelihood.R | 199 +++++++++++++++- holiglm-1.0.1/holiglm/R/simulate.R | 4 holiglm-1.0.1/holiglm/build/partial.rdb |binary holiglm-1.0.1/holiglm/build/vignette.rds |binary holiglm-1.0.1/holiglm/inst/doc/conic_representable.html | 130 +++++----- holiglm-1.0.1/holiglm/inst/doc/solver_installation.Rmd | 2 holiglm-1.0.1/holiglm/inst/doc/solver_installation.html | 34 ++ holiglm-1.0.1/holiglm/inst/tinytest/test_binomial.R | 5 holiglm-1.0.1/holiglm/inst/tinytest/test_gaussian.R | 5 holiglm-1.0.1/holiglm/inst/tinytest/test_poisson.R | 5 holiglm-1.0.1/holiglm/man/hglm.Rd | 12 holiglm-1.0.1/holiglm/man/hglm_fit.Rd | 5 holiglm-1.0.1/holiglm/man/hglm_model.Rd | 5 holiglm-1.0.1/holiglm/man/holiglm-package.Rd | 1 holiglm-1.0.1/holiglm/vignettes/solver_installation.Rmd | 2 23 files changed, 376 insertions(+), 151 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 0.3.3 dated 2024-04-22 and 1.0.0 dated 2024-12-20
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aifeducation-1.0.0/aifeducation/MD5 | 312 +++-- aifeducation-1.0.0/aifeducation/NAMESPACE | 83 - aifeducation-1.0.0/aifeducation/NEWS.md | 232 +++ aifeducation-1.0.0/aifeducation/R/AIFEBaseModel.R |only aifeducation-1.0.0/aifeducation/R/AIFETransformerMaker.R |only aifeducation-1.0.0/aifeducation/R/DataManager.R |only aifeducation-1.0.0/aifeducation/R/EmbeddedText.R |only aifeducation-1.0.0/aifeducation/R/FeatureExtractor.R |only aifeducation-1.0.0/aifeducation/R/LargeDataSetBase.R |only aifeducation-1.0.0/aifeducation/R/LargeDataSetForTextEmbeddings.R |only aifeducation-1.0.0/aifeducation/R/LargeDataSetForTexts.R |only aifeducation-1.0.0/aifeducation/R/RcppExports.R | 12 aifeducation-1.0.0/aifeducation/R/Studio.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_CCardModelArchitecture.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_Create.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_TCardBaseModel.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_TCardDataset.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_TCardTrainTuneSettings.R |only aifeducation-1.0.0/aifeducation/R/Studio_BaseModel_Train.R |only aifeducation-1.0.0/aifeducation/R/Studio_Classifier_Create.R |only aifeducation-1.0.0/aifeducation/R/Studio_Classifier_Use.R |only aifeducation-1.0.0/aifeducation/R/Studio_DocumentationPage.R |only aifeducation-1.0.0/aifeducation/R/Studio_ErrorModal_ProcessModal.R |only aifeducation-1.0.0/aifeducation/R/Studio_Error_Checks.R |only aifeducation-1.0.0/aifeducation/R/Studio_ExtendedTasks.R |only aifeducation-1.0.0/aifeducation/R/Studio_FeatureExtractor_Create.R |only aifeducation-1.0.0/aifeducation/R/Studio_FeatureExtractor_Use.R |only aifeducation-1.0.0/aifeducation/R/Studio_Home.R |only aifeducation-1.0.0/aifeducation/R/Studio_License.R |only aifeducation-1.0.0/aifeducation/R/Studio_ProgressModal.R |only aifeducation-1.0.0/aifeducation/R/Studio_SaveModal.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Classifier_Predict.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_DM_CreateTextDataSet.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_DM_DataSetEditor.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_DM_TableEditor.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Description.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Embed.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Fill_Mask.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Reliability.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_TokenizerEncodeDecode.R |only aifeducation-1.0.0/aifeducation/R/Studio_Tabs_Training.R |only aifeducation-1.0.0/aifeducation/R/Studio_TextEmbeddingModel_Create.R |only aifeducation-1.0.0/aifeducation/R/Studio_TextEmbeddingModel_Use.R |only aifeducation-1.0.0/aifeducation/R/TEClassifierProtoNet.R |only aifeducation-1.0.0/aifeducation/R/TEClassifierRegular.R |only aifeducation-1.0.0/aifeducation/R/TextEmbeddingModel.R |only aifeducation-1.0.0/aifeducation/R/data.R | 54 aifeducation-1.0.0/aifeducation/R/dotAIFEBaseTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFEBertTransfomer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFECustomTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFEDebertaTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFEFunnelTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFELongformerTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFEMpnetTransformer.R |only aifeducation-1.0.0/aifeducation/R/dotAIFERobertaTransformer.R |only aifeducation-1.0.0/aifeducation/R/install_and_config.R | 589 ++++----- aifeducation-1.0.0/aifeducation/R/onLoad.R | 101 - 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Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or 'scintigraphic' measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.6.2 dated 2024-12-04 and 0.7.0 dated 2024-12-20
DESCRIPTION | 16 +-- MD5 | 21 ++-- R/fitfuncs.r | 2 R/fitnlme.R | 7 + R/fitparams.R | 61 +++++++++++--- R/stan_gastempt.R | 16 +-- inst/doc/gastempt.html | 4 inst/shiny/server.R | 6 - man/simulate_gastempt.Rd | 182 +++++++++++++++++++++--------------------- man/stan_gastempt.Rd | 12 +- tests/testthat/_snaps |only tests/testthat/test-fitnlme.R | 7 + 12 files changed, 188 insertions(+), 146 deletions(-)
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.3.6 dated 2024-12-11 and 0.3.8 dated 2024-12-19
FuzzyImputationTest-0.3.6/FuzzyImputationTest/R/distanceNames.R |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/R/errorTypes.R |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/R/measuresTypes.R |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/R/setsNames.R |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/R/testsNames.R |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/man/distanceNames.Rd |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/man/errorTypes.Rd |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/man/measuresTypes.Rd |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/man/setsNames.Rd |only FuzzyImputationTest-0.3.6/FuzzyImputationTest/man/testsNames.Rd |only FuzzyImputationTest-0.3.8/FuzzyImputationTest/DESCRIPTION | 6 - FuzzyImputationTest-0.3.8/FuzzyImputationTest/MD5 | 32 ++++------ FuzzyImputationTest-0.3.8/FuzzyImputationTest/NAMESPACE | 7 -- FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/ImputationTests.R | 25 +++++-- FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/MethodsComparison.R | 17 +++-- FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/summary.impTest.R |only FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/summary.metComp.R |only FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/utils.R | 22 ++++++ FuzzyImputationTest-0.3.8/FuzzyImputationTest/man/ImputationTests.Rd | 10 ++- FuzzyImputationTest-0.3.8/FuzzyImputationTest/man/MethodsComparison.Rd | 9 ++ FuzzyImputationTest-0.3.8/FuzzyImputationTest/man/summary.impTest.Rd |only FuzzyImputationTest-0.3.8/FuzzyImputationTest/man/summary.metComp.Rd |only FuzzyImputationTest-0.3.8/FuzzyImputationTest/tests/testthat/_snaps/ImputationTests.md | 8 ++ FuzzyImputationTest-0.3.8/FuzzyImputationTest/tests/testthat/_snaps/MethodsComparison.md | 6 + 24 files changed, 97 insertions(+), 45 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: Creating Demographic Table
Description: Functions for creating demographic
table of simple summary statistics and
comparison(s) over one or more groups.
Returned value is printed via package
'flextable'.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.1.9 dated 2024-09-17 and 0.1.10 dated 2024-12-19
DemographicTable-0.1.10/DemographicTable/DESCRIPTION | 34 - DemographicTable-0.1.10/DemographicTable/MD5 | 37 - DemographicTable-0.1.10/DemographicTable/NAMESPACE | 36 - DemographicTable-0.1.10/DemographicTable/NEWS.md | 4 DemographicTable-0.1.10/DemographicTable/R/0PACKAGE.R | 2 DemographicTable-0.1.10/DemographicTable/R/DemographicTable.R | 312 +++------- DemographicTable-0.1.10/DemographicTable/R/as_flextable.R |only DemographicTable-0.1.10/DemographicTable/R/c.R |only DemographicTable-0.1.10/DemographicTable/R/pval_shapiro.R | 7 DemographicTable-0.1.10/DemographicTable/R/rmd_.DemographicTable.R | 31 DemographicTable-0.1.10/DemographicTable/R/sumstat.R |only DemographicTable-0.1.10/DemographicTable/inst/extR/toCRAN.R | 8 DemographicTable-0.1.10/DemographicTable/inst/xtable.R |only DemographicTable-0.1.10/DemographicTable/man/DemographicTable-package.Rd | 2 DemographicTable-0.1.10/DemographicTable/man/DemographicTable.Rd | 76 -- DemographicTable-0.1.10/DemographicTable/man/as_flextable.DemographicTable.Rd | 11 DemographicTable-0.1.10/DemographicTable/man/c.DemographicTable.Rd |only DemographicTable-0.1.10/DemographicTable/man/pval_shapiro.Rd | 2 DemographicTable-0.1.10/DemographicTable/man/rmd_.DemographicTable.Rd | 9 DemographicTable-0.1.10/DemographicTable/man/sumstat.Rd |only DemographicTable-0.1.9/DemographicTable/R/Sprintf.DemographicTable.R |only DemographicTable-0.1.9/DemographicTable/R/summaryText.R |only DemographicTable-0.1.9/DemographicTable/man/Sprintf.DemographicTable.Rd |only DemographicTable-0.1.9/DemographicTable/man/summaryText.Rd |only DemographicTable-0.1.9/DemographicTable/man/xtable.DemographicTable.Rd |only 25 files changed, 259 insertions(+), 312 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Robust Multi-Model Subset Selection
Description: Efficient algorithms for generating ensembles of robust, sparse and diverse models via robust
multi-model subset selection (RMSS). The robust ensembles are generated by minimizing the sum of
the least trimmed square loss of the models in the ensembles under constraints for the size of
the models and the sharing of the predictors. Tuning parameters for the robustness, sparsity and
diversity of the robust ensemble are selected by cross-validation.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RMSS versions 1.1.1 dated 2023-09-13 and 1.1.2 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 ++++- R/cv.RMSS.R | 11 +++++++---- README.md | 4 ++-- 5 files changed, 21 insertions(+), 15 deletions(-)
Title: Client for the 'KoboToolbox' API
Description: Suite of utilities for accessing and manipulating
data from the 'KoboToolbox' API. 'KoboToolbox' is a robust
platform designed for field data collection in various disciplines.
This package aims to simplify the process of fetching and handling
data from the API. Detailed documentation for the 'KoboToolbox' API
can be found at <https://support.kobotoolbox.org/api.html>.
Author: Ahmadou Dicko [aut, cre, cph],
Hisham Galal [ctb]
Maintainer: Ahmadou Dicko <mail@ahmadoudicko.com>
Diff between robotoolbox versions 1.3.2 dated 2023-06-09 and 1.4 dated 2024-12-19
DESCRIPTION | 13 MD5 | 108 +-- NAMESPACE | 14 R/kobo_asset.R | 4 R/kobo_audit.R | 54 + R/kobo_data.R | 143 ++++- R/kobo_file.R |only R/kobo_form.R | 7 R/kobo_setup.R | 3 R/utils.R | 218 ++++++- README.md | 45 + build/vignette.rds |binary data/asset_audit.rda |binary data/asset_ml.rda |binary data/asset_rg.rda |binary data/asset_sm_label.rda |binary data/asset_spatial.rda |binary data/data_audit.rda |binary data/data_ml_ar.rda |binary data/data_ml_default.rda |binary data/data_ml_en.rda |binary data/data_ml_fr.rda |binary data/data_ml_vlabel.rda |binary data/data_rg.rda |binary data/data_sm.rda |binary data/data_sm_label.rda |binary data/data_spatial.rda |binary inst/doc/audit-data.R | 28 inst/doc/audit-data.Rmd | 20 inst/doc/audit-data.html | 63 +- inst/doc/intro.R | 126 ++-- inst/doc/intro.Rmd | 22 inst/doc/intro.html | 95 +-- inst/doc/multilang-forms.R | 62 +- inst/doc/multilang-forms.Rmd | 6 inst/doc/multilang-forms.html | 106 +-- inst/doc/repeat-group-data.R | 36 - inst/doc/repeat-group-data.Rmd | 51 + inst/doc/repeat-group-data.html | 261 ++++++--- inst/doc/spatial-data.R | 34 - inst/doc/spatial-data.Rmd | 31 - inst/doc/spatial-data.html | 816 +++++++++++++++++++++-------- man/kobo_asset_file_list.Rd |only man/kobo_attachment_download.Rd |only man/kobo_audit.Rd | 5 man/kobo_data.Rd | 15 tests/testthat/_snaps/kobo_asset.md | 2 tests/testthat/_snaps/kobo_settings.md | 2 tests/testthat/test-kobo_asset_file_list.R |only tests/testthat/test-kobo_audit.R | 14 tests/testthat/test-kobo_data.R | 66 ++ tests/testthat/test-kobo_form.R | 18 vignettes/audit-data.Rmd | 20 vignettes/intro.Rmd | 22 vignettes/multilang-forms.Rmd | 6 vignettes/repeat-group-data.Rmd | 51 + vignettes/spatial-data.Rmd | 31 - 57 files changed, 1850 insertions(+), 768 deletions(-)
Title: Collect And Investigate Street Views For Urban Science
Description: A collection of functions to search and download street view imagery
('Mapilary' <https://www.mapillary.com/developer/api-documentation>) and
to extract, quantify, and visualize visual features. Moreover, there are
functions provided to generate Qualtrics survey in TXT format using
the collection of street views for various research purposes.
Author: Xiaohao Yang [aut, cre, cph],
Derek Van Berkel [aut],
Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Diff between streetscape versions 1.0.3 dated 2024-08-31 and 1.0.4 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Viewscape Analysis
Description: A collection of functions to make R a more effective viewscape analysis
tool for calculating viewscape metrics based on computing the viewable area for
given a point/multiple viewpoints and a digital elevation model.The method of calculating
viewscape metrics implemented in this package are based on the work of
Tabrizian et al. (2020) <doi:10.1016/j.landurbplan.2019.103704>. The algorithm of computing
viewshed is based on the work of
Franklin & Ray. (1994) <https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=555780f6f5d7e537eb1edb28862c86d1519af2be>.
Author: Xiaohao Yang [aut, cre, cph],
Nathan Fox [aut],
Derek Van Berkel [aut],
Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Diff between viewscape versions 2.0.1 dated 2024-11-10 and 2.0.2 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Analysis of Continuous Glucose Monitor Data
Description: Reads in continuous glucose monitor data of many different formats, calculates a host of glycemic variability metrics, and plots glucose over time.
Author: Evan Olawsky [aut, cre],
Yuan Zhang [ctb],
Lynn Eberly [ctb]
Maintainer: Evan Olawsky <evanolawsky@gmail.com>
Diff between rGV versions 0.0.4 dated 2023-01-16 and 0.0.5 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md | 4 ++-- R/metrics.R | 5 +---- inst |only 5 files changed, 11 insertions(+), 13 deletions(-)
Title: DSM and LiDAR downloader
Description: A collection of functions to search and donwload
DSM (Digital Surface Model) and LiDAR (Light Detection and Ranging) data via APIs,
including 'OpenTopography' <https://portal.opentopography.org/apidocs/> and
'TNMAccess' <https://apps.nationalmap.gov/tnmaccess/#/>.
Author: Xiaohao Yang [aut, cre, cph],
Nathan Fox [aut],
Derek Van Berkel [aut],
Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Diff between dsmSearch versions 1.0.2 dated 2024-08-20 and 1.1.0 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/get_dsm_30.R | 12 ++++++++---- R/utils.R | 43 ++++++++++++++++++++++++++----------------- man/get_dsm_30.Rd | 13 +++++++++---- 5 files changed, 51 insertions(+), 33 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.1.0 dated 2024-11-28 and 1.1.1 dated 2024-12-19
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++---------- NEWS.md | 5 ++++ R/rintcal.R | 53 +++++++++++++++++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rintcal.R | 4 ++- inst/doc/rintcal.Rmd | 4 ++- inst/doc/rintcal.html | 52 +++++++++++++++++++++++++------------------------ man/ccurve.Rd | 11 +++++++++- man/mix.ccurves.Rd | 1 vignettes/rintcal.Rmd | 4 ++- 12 files changed, 97 insertions(+), 65 deletions(-)
Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre, cph]
,
Henrik Singmann [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between gratia versions 0.9.2 dated 2024-06-25 and 0.10.0 dated 2024-12-19
DESCRIPTION | 14 MD5 | 456 ++-- NAMESPACE | 23 NEWS.md | 51 R/basis-funs.R | 9 R/conditional-values.R |only R/data-slice.R | 34 R/derivatives.R | 3 R/diagnose.R | 115 - R/distributional-models.R |only R/draw-gam.R | 16 R/draw-methods.R | 8 R/evenly.R | 7 R/family-utils.R | 13 R/fitted_values.R | 60 R/gjrm-methods.R | 2 R/penalty.R | 5 R/posterior-samples.R | 42 R/residuals.R | 4 R/samplers.R | 11 R/smooth-data.R | 27 R/smooth-estimates.R | 92 R/smooth-type.R | 2 R/subsetting.R | 12 R/utililties.R | 104 + README.md | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/data-slices.R | 8 inst/doc/data-slices.Rmd | 8 inst/doc/data-slices.html | 488 ++--- inst/doc/gratia.Rmd | 39 inst/doc/gratia.html | 100 - man/appraise.Rd | 29 man/basis.Rd | 15 man/conditional_values.Rd |only man/data_slice.Rd | 37 man/derivative_samples.Rd | 5 man/dispersion.Rd |only man/draw.conditional_values.Rd |only man/draw.gam.Rd | 8 man/draw.gamlss.Rd | 2 man/draw.smooth_estimates.Rd | 3 man/eval_smooth.Rd | 2 man/figures/README-draw-gam-figure-2d-1.png |binary man/lss_parameters.Rd | 2 man/model_constant.Rd | 18 man/n_eta.Rd |only man/penalty.Rd | 15 man/post_link_funs.Rd | 2 man/qq_plot.Rd | 45 man/smooth_type.Rd | 4 man/user_draws.Rd | 14 man/worm_plot.Rd | 23 tests/Examples/gratia-Ex.Rout.save | 113 + tests/testthat/_snaps/backward/response-derivatives.md | 20 tests/testthat/_snaps/bam-ar/draw-bam-ar-1-factor-by.svg | 20 tests/testthat/_snaps/basis/draw-basis-works-with-a-gam-multiple-smooths.svg | 60 tests/testthat/_snaps/by-variables/draw-gam-user-select-and-parametric-true.svg | 20 tests/testthat/_snaps/central/response-derivatives.md | 20 tests/testthat/_snaps/compare-smooths/compare-smooths-all-smooths.svg | 221 -- tests/testthat/_snaps/compare-smooths/compare-smooths-bottom-legend.svg | 221 -- tests/testthat/_snaps/compare-smooths/compare-smooths-set-nrow-ncol.svg | 223 -- tests/testthat/_snaps/conditional-values |only tests/testthat/_snaps/conditional-values.md |only tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-complex-factor-by.svg | 64 tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-factor-by.svg | 40 tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg | 62 tests/testthat/_snaps/derivatives/draw-issue-47-derivs-for-ordered-factor-by.svg | 64 tests/testthat/_snaps/derivatives/draw-issue-57-derivatives-for-factor-by.svg | 70 tests/testthat/_snaps/diagnostic-plots/appraise-diagnostic-plots.svg | 60 tests/testthat/_snaps/diagnostic-plots/appraise-lm.svg | 60 tests/testthat/_snaps/diagnostic-plots/appraise-worm-plot.svg | 60 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bam.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bivariate-gam-contours.svg | 30 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bivariate-gam.svg | 30 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-fixed-scales.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-inc-grp-means.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-ref-line.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-user-data.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam.svg | 40 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gamm.svg | 56 tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gamm4.svg | 40 tests/testthat/_snaps/draw-gam/draw-gam-dlnm-m.svg | 53 tests/testthat/_snaps/draw-gam/draw-gam-m-2-fac-parametric.svg | 80 tests/testthat/_snaps/draw-gam/draw-gam-m-2-fac.svg | 40 tests/testthat/_snaps/draw-gam/draw-gam-m-ar1-by.svg | 20 tests/testthat/_snaps/draw-gam/draw-gam-m-bam.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gam-constant-fun.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gam-constant.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gam-fun.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gam-rotated.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gam.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gamgcv.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gamm.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-gamm4.svg | 84 tests/testthat/_snaps/draw-gam/draw-gam-m-gaulss.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-m-para-sm-parametric.svg | 80 tests/testthat/_snaps/draw-gam/draw-gam-m-para-sm.svg | 20 tests/testthat/_snaps/draw-gam/draw-gam-m-scat.svg | 60 tests/testthat/_snaps/draw-gam/draw-gam-parametric-only-model-rotated-labels.svg | 80 tests/testthat/_snaps/draw-gam/draw-gam-quadvar-te.svg | 20 tests/testthat/_snaps/draw-gam/draw-gam-rm1.svg | 80 tests/testthat/_snaps/draw-gam/draw-gam-rm2.svg | 100 - 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tests/testthat/setup.R | 24 tests/testthat/test-basis.R | 7 tests/testthat/test-conditional-values.R |only tests/testthat/test-confint-methods.R | 6 tests/testthat/test-derivatives.R | 10 tests/testthat/test-draw-methods.R | 2 tests/testthat/test-hgam-paper.R | 8 tests/testthat/test-penalty.R | 7 tests/testthat/test-posterior-samples.R | 5 tests/testthat/test-utilities.R | 22 vignettes/data-slices.Rmd | 8 vignettes/getting-started.bib |only vignettes/gratia.Rmd | 39 234 files changed, 7117 insertions(+), 6473 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.4.2-1 dated 2023-05-03 and 1.5.0 dated 2024-12-19
DESCRIPTION | 12 MD5 | 52 +- NAMESPACE | 9 NEWS.md | 31 + R/MLR.R | 71 +-- R/NLR.R | 695 +++++++++++++++++++------------ R/difNLR-package.R | 12 R/difNLR.R | 1074 +++++++++++++++++++++++++++--------------------- R/difORD.R | 3 R/estimNLR.R | 951 +++++++++++++++++++++++++++++++++++------- R/formulaNLR.R | 396 +++++++++++------ R/private.R | 22 R/startNLR.R | 323 +++++++++----- README.md | 10 build/partial.rdb |binary man/NLR.Rd | 308 ++++++++----- man/coef.difNLR.Rd | 59 +- man/difNLR-package.Rd | 11 man/difNLR.Rd | 302 +++++++------ man/difORD.Rd | 3 man/estimNLR.Rd | 199 ++++++-- man/formulaNLR.Rd | 125 +++-- man/logLik.difNLR.Rd | 35 - man/plot.difNLR.Rd | 85 ++- man/predict.difNLR.Rd | 61 +- man/residuals.difNLR.Rd | 36 - man/startNLR.Rd | 128 +++-- 27 files changed, 3242 insertions(+), 1771 deletions(-)
Title: Embedding FusionCharts in R
Description: FusionCharts provides awesome and minimalist functions to make beautiful interactive charts <https://www.fusioncharts.com/>.
Author: Alex Yahiaoui Martinez [aut, cre]
Maintainer: Alex Yahiaoui Martinez <yahiaoui-martinez.alex@outlook.com>
Diff between fusionchartsR versions 1.0.0 dated 2024-11-09 and 1.1.0 dated 2024-12-19
DESCRIPTION | 8 MD5 | 91 ++-- NAMESPACE | 3 R/fusionAnchors.R | 115 ++--- R/fusionAxis.R | 119 ++--- R/fusionBackground.R | 199 ++++----- R/fusionCanvas.R | 162 +++---- R/fusionCaption.R | 106 ++--- R/fusionCustomAxis.R | 480 +++++++++++------------ R/fusionCustomBoxplot.R | 126 +++--- R/fusionCustomLegend.R | 238 +++++------ R/fusionDiv.R | 177 ++++---- R/fusionLegend.R | 117 ++--- R/fusionLogo.R | 80 +-- R/fusionMultiPlot.R | 424 ++++++++++---------- R/fusionPalette.R | 30 - R/fusionPlot.R | 458 ++++++++++------------ R/fusionSubcaption.R | 92 ++-- R/fusionTheme.R | 49 +- R/fusionTooltip.R | 85 ++-- R/fusionTrendline.R | 198 ++++----- R/ggfusionPlot.R |only R/runDemo.R | 149 +++---- README.md | 2 inst/htmlwidgets/fusionMultiPlot.js | 663 ++++++++++++++++---------------- inst/htmlwidgets/fusionPlot.js | 681 ++++++++++++++++----------------- man/figures/lifecycle-experimental.svg |only man/figures/logo.png |binary man/fusionAnchors.Rd | 8 man/fusionAxis.Rd | 10 man/fusionBackground.Rd | 8 man/fusionCanvas.Rd | 8 man/fusionCaption.Rd | 18 man/fusionCustomAxis.Rd | 13 man/fusionCustomBoxplot.Rd | 10 man/fusionCustomLegend.Rd | 8 man/fusionDiv.Rd | 10 man/fusionLegend.Rd | 8 man/fusionLogo.Rd | 8 man/fusionPalette.Rd | 8 man/fusionPlot.Rd | 2 man/fusionSubcaption.Rd | 18 man/fusionTheme.Rd | 7 man/fusionTooltip.Rd | 8 man/fusionTrendline.Rd | 8 man/ggfusionPlot.Rd |only man/pipe.Rd | 2 man/runDemo.Rd | 8 48 files changed, 2492 insertions(+), 2530 deletions(-)
Title: Analyse Eye Data
Description: Enables the automation of actions across the pipeline, including
initial steps of transforming binocular data and gap repair to event-based
processing such as fixations, saccades, and entry/duration in Areas of
Interest (AOIs). It also offers visualisation of eye movement and AOI
entries. These tools take relatively raw (trial, time, x, and y form) data
and can be used to return fixations, saccades, and AOI entries and time spent
in AOIs. As the tools rely on this basic data format, the functions can work
with data from any eye tracking device. Implements fixation and saccade
detection using methods proposed by Salvucci and Goldberg (2000)
<doi:10.1145/355017.355028>.
Author: Tom Beesley [aut, cre],
Matthew Ivory [aut]
Maintainer: Tom Beesley <t.beesley@lancaster.ac.uk>
Diff between eyetools versions 0.8.0 dated 2024-12-18 and 0.8.1 dated 2024-12-19
DESCRIPTION | 8 MD5 | 72 +++--- NAMESPACE | 1 NEWS.md | 8 R/AOI_seq.R | 10 R/AOI_time.R | 34 ++- R/compare_algorithms.R | 12 - R/create_AOI_df.R | 36 ++- R/fixation_VTI.R | 23 -- R/fixation_dispersion.R | 41 +-- R/plot_seq.R | 7 R/smoother.R | 2 README.md | 5 inst/doc/eyetools.R | 46 +--- inst/doc/eyetools.Rmd | 48 ++-- inst/doc/eyetools.html | 418 +++++++++++++++---------------------- man/AOI_seq.Rd | 10 man/AOI_time.Rd | 5 man/compare_algorithms.Rd | 6 man/create_AOI_df.Rd | 16 + man/figures/unnamed-chunk-10-1.png |binary man/figures/unnamed-chunk-18-1.png |binary man/figures/unnamed-chunk-25-1.png |binary man/figures/unnamed-chunk-26-1.png |binary man/figures/unnamed-chunk-26-2.png |binary man/figures/unnamed-chunk-27-1.png |binary man/figures/unnamed-chunk-28-1.png |binary man/figures/unnamed-chunk-28-2.png |binary man/figures/unnamed-chunk-28-3.png |binary man/figures/unnamed-chunk-29-1.png |binary man/figures/unnamed-chunk-30-1.png |binary man/figures/unnamed-chunk-30-2.png |binary man/figures/unnamed-chunk-30-3.png |binary man/figures/unnamed-chunk-9-1.png |binary man/fixation_VTI.Rd | 6 man/fixation_dispersion.Rd | 4 vignettes/eyetools.Rmd | 48 ++-- 37 files changed, 422 insertions(+), 444 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and
transparency in data processing. It provides functionality such as
automatic meta data creation and management, rudimentary quality
management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this
package to deliver everything what is needed to achieve full
reproducibility and transparency, but we believe that it supports
efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre] ,
Lavinia Baumstark [aut] ,
Stephen Wirth [aut] ,
Anastasis Giannousakis [aut],
Renato Rodrigues [aut] ,
Benjamin Leon Bodirsky [aut] ,
Debbora Leip [aut] ,
Ulrich Kreidenweis [aut],
David Klein [aut] ,
Pascal Sauer [a [...truncated...]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 3.6.4 dated 2023-08-23 and 3.15.6 dated 2024-12-19
DESCRIPTION | 59 +++++++---- MD5 | 158 ++++++++++++++++++-------------- NAMESPACE | 8 - R/cacheName.R | 15 ++- R/calcOutput.R | 89 +++++++----------- R/cleanComment.R |only R/compareMadratOutputs.R | 2 R/convertTau.R | 51 +++++----- R/downloadSource.R | 4 R/fingerprint.R | 114 ++++++++++++----------- R/fullEXAMPLE.R | 8 - R/functionCallString.R |only R/getConfig.R | 6 + R/getFromComment.R |only R/getLinkFunction.R |only R/getMadratGraph.R | 2 R/getMadratInfo.R | 8 - R/getSourceFolder.R |only R/initializeConfig.R | 27 +++-- R/installedMadratUniverse.R | 23 +++- R/isWrapperActive.R | 1 R/madrat-package.R | 3 R/prepComment.R |only R/prepExtendedComment.R |only R/prepFunctionName.R | 95 ++++++++++--------- R/pucAggregate.R | 15 ++- R/putMadratMessage.R | 2 R/readSource.R | 38 ++++--- R/redirect.R |only R/redirectSource.R |only R/redirectTau.R |only R/resetMadratMessages.R | 2 R/retrieveData.R | 40 ++++---- R/robustOrder.R | 4 R/setConfig.R | 5 - R/toolAggregate.R | 45 +++++---- R/toolGetMapping.R | 49 ++++++--- R/toolISOhistorical.R | 19 ++- R/toolTimeAverage.R | 54 ++++++---- R/toolstartmessage.R | 32 +----- R/visualizeDependencies.R | 32 ++++-- README.md | 15 +-- build/partial.rdb |only build/vignette.rds |binary inst/doc/madrat-caching.R | 20 ++-- inst/doc/madrat-caching.html | 38 +++---- inst/doc/madrat-puc.R | 14 +- inst/doc/madrat-puc.Rmd | 6 - inst/doc/madrat-puc.html | 14 +- inst/doc/madrat.R | 28 ++--- inst/doc/madrat.html | 36 +++---- inst/extdata/country2iso.csv | 7 + man/calcOutput.Rd | 6 + man/cleanComment.Rd |only man/compareMadratOutputs.Rd | 2 man/downloadSource.Rd | 2 man/fingerprint.Rd | 2 man/fullEXAMPLE.Rd | 10 -- man/functionCallString.Rd |only man/getFromComment.Rd |only man/getLinkFunction.Rd |only man/getSourceFolder.Rd |only man/initializeConfig.Rd | 5 - man/installedMadratUniverse.Rd | 16 +-- man/madrat-package.Rd | 26 +++++ man/prepComment.Rd |only man/prepExtendedComment.Rd |only man/prepFunctionName.Rd | 8 - man/readSource.Rd | 2 man/redirect.Rd |only man/redirectSource.Rd |only man/redirectTau.Rd |only man/retrieveData.Rd | 2 man/robustOrder.Rd | 2 man/setConfig.Rd | 6 + man/toolAggregate.Rd | 14 +- man/toolGetMapping.Rd | 2 man/toolTimeAverage.Rd | 4 man/toolstartmessage.Rd | 12 +- tests/testthat/setup.R | 1 tests/testthat/test-calcOutput.R | 49 +++++---- tests/testthat/test-fingerprint.R | 1 tests/testthat/test-puc.R | 40 ++++---- tests/testthat/test-readSource.R | 48 +++++++-- tests/testthat/test-redirectSource.R |only tests/testthat/test-toolAggregate.R | 18 +++ tests/testthat/test-toolCountryFill.R | 6 - tests/testthat/test-toolGetMapping.R | 10 +- tests/testthat/test-toolISOhistorical.R | 44 +++++--- tests/testthat/test-toolTimeAverage.R | 3 vignettes/madrat-puc.Rmd | 6 - 91 files changed, 868 insertions(+), 667 deletions(-)
Title: Just Another Latent Space Network Clustering Algorithm
Description: Fit and simulate latent space network cluster models using an expectation-maximization algorithm.
Enables flexible modeling of unweighted network data, supporting both directed and undirected networks,
with or without degree heterogeneity. Designed to handle large networks efficiently, it allows users to explore
network structure through latent space representations, identify clusters within network data, and simulate models
with varying clustering and connectivity patterns.
Author: Alan Arakkal [aut, cre, cph] ,
Daniel Sewell [aut]
Maintainer: Alan Arakkal <alan-arakkal@uiowa.edu>
Diff between JANE versions 0.1.1 dated 2024-11-14 and 0.2.1 dated 2024-12-19
DESCRIPTION | 6 - MD5 | 16 ++-- NAMESPACE | 2 NEWS.md | 13 +++- R/generics.R | 169 +++++++++++++++++++++++++++++++++++++++------------- R/imports.R | 2 R/plot_data.R | 155 +++++++++++++++++++++++++---------------------- man/plot.JANE.Rd | 12 +++ man/summary.JANE.Rd | 1 9 files changed, 253 insertions(+), 123 deletions(-)
Title: An 'Armadillo' Interface
Description: Provides function declarations and inline function definitions that
facilitate communication between R and the 'Armadillo' 'C++' library for
linear algebra and scientific computing. This implementation is detailed
in Vargas Sepulveda and Schneider Malamud (2024)
<doi:10.48550/arXiv.2408.11074>.
Author: Mauricio Vargas Sepulveda [aut, cre]
,
Jonathan Schneider Malamud [ctb],
Conrad Sanderson [aut] )
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between cpp11armadillo versions 0.4.0 dated 2024-12-13 and 0.4.1 dated 2024-12-19
DESCRIPTION | 10 +++--- MD5 | 17 ++++++---- NEWS.md | 8 ++++ R/cpp11armadillo-package.R | 17 ++++++++++ README.md | 75 +++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary configure | 31 ++++++++++++++---- inst/doc/data-types.R |only inst/doc/data-types.Rmd |only inst/doc/data-types.html |only man/check_cpp11.Rd |only vignettes/data-types.Rmd |only 12 files changed, 120 insertions(+), 38 deletions(-)
More information about cpp11armadillo at CRAN
Permanent link
Title: Spatial Empirical Dynamic Modeling
Description: Integrates empirical dynamic modeling (EDM) with geospatial cross-sectional data to analyze causality via geographical convergent cross mapping (GCCM) described in Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.0 dated 2024-12-16 and 1.1 dated 2024-12-19
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS.md | 4 + R/gccm.R | 12 +--- README.md | 4 - inst/doc/GCCM.Rmd | 132 ++++++++++++++++++++++++++-------------------------- inst/doc/GCCM.html | 134 ++++++++++++++++++++++++++--------------------------- man/gccm.Rd | 8 +-- vignettes/GCCM.Rmd | 132 ++++++++++++++++++++++++++-------------------------- 9 files changed, 226 insertions(+), 222 deletions(-)
Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Rebecca Kuiper [aut],
Yves Rosseel [ctb],
Aleksandra Dacko [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>
Diff between restriktor versions 0.5-90 dated 2024-09-11 and 0.6-10 dated 2024-12-19
DESCRIPTION | 6 MD5 | 74 ++- NAMESPACE | 11 R/conGLM.R | 4 R/conLM.R | 14 R/conMLM.R | 4 R/conRLM.R | 4 R/con_constraints.R | 59 +-- R/ext_ic_infer.R | 2 R/goric.R | 311 +++++++++++----- R/goric_benchmark.R | 68 ++- R/goric_benchmark_plot.R | 43 +- R/goric_benchmark_print.R | 50 +- R/goric_benchmark_utilities.R | 106 ----- R/goric_calculate_IC_weights.R | 31 - R/goric_evSyn.R | 583 +++++++----------------------- R/goric_evSyn_plot.R |only R/goric_evSyn_print.R |only R/goric_evSyn_summary.R |only R/goric_evSyn_utilities.R |only R/goric_penalty.R | 2 R/goric_print.R | 217 ++++++++--- R/goric_utilities.R | 103 +++++ R/gorica_est.R | 62 ++- R/gorica_est_summary.R | 2 R/restriktor_print.R | 2 R/restriktor_print_summary.R | 14 R/restriktor_summary.R | 16 R/utilities.R | 169 +++++++- inst/doc/Guidelines_GORIC-benchmarks.R | 2 inst/doc/Guidelines_GORIC-benchmarks.Rmd | 4 inst/doc/Guidelines_GORIC-benchmarks.html | 196 +++++----- inst/doc/Guidelines_GORIC_output.html | 407 +++++++++++--------- man/calculate_IC_weights.Rd | 10 man/evSyn.Rd | 105 ++++- man/goric.Rd | 49 +- man/goric_benchmark.Rd | 22 - man/myLLs.Rd | 4 man/restriktor-package.rd | 4 vignettes/Guidelines_GORIC-benchmarks.Rmd | 4 40 files changed, 1570 insertions(+), 1194 deletions(-)
Title: Interpolating Age-Specific Mortality Rates at All Ages
Description: Mortality rates are typically provided in an abridged format, i.e., by age groups 0, [1, 5], [5, 10]', '[10, 15]', and so on. Some applications necessitate a detailed (single) age description. Despite the large number of proposed approaches in the literature, only a few methods ensure great performance at both younger and higher ages. For example, the 6-term 'Lagrange' interpolation function is well suited to mortality interpolation at younger ages (with irregular intervals), but not at older ages. The 'Karup-King' method, on the other hand, performs well at older ages but is not suitable for younger ones. Interested readers can find a full discussion of the two stated methods in the book Shryock, Siegel, and Associates (1993).The Q2q package combines the two methods to allow for the interpolation of mortality rates across all age groups. It begins by implementing each method independently, and then the resulting curves are linked using a 5-age averaged error between the two partial cu [...truncated...]
Author: Farid FLICI [aut, cre]
Maintainer: Farid FLICI <farid.flici@cread.dz>
Diff between Q2q versions 0.1.1 dated 2024-11-07 and 0.1.2 dated 2024-12-19
DESCRIPTION | 10 +-- MD5 | 18 ++--- R/Q2q.R | 98 ++++++++++++++++++------------ README.md | 64 +++++++------------ man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-21-2.png |binary man/getqx.Rd | 18 ++--- man/getqxt.Rd | 22 +++--- 10 files changed, 121 insertions(+), 109 deletions(-)
Title: Graph the Relationship Between Functions in an R Package
Description: It is often useful when developing an R package to track the relationship between functions in order to appropriately test and track changes. This package generates a graph of the relationship between all R functions in a package. It can also be used on any directory containing .R files which can be very useful for 'shiny' apps or other non-package workflows.
Author: David Oliver [aut, cre, cph]
Maintainer: David Oliver <doliv071@gmail.com>
Diff between pkgGraphR versions 0.2.0 dated 2024-04-02 and 0.3.0 dated 2024-12-19
DESCRIPTION | 8 +-- MD5 | 20 ++++----- R/functions.r | 97 +++++++++++++++++++++++------------------------ README.md | 81 +++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/pkgGraphR.Rmd | 2 inst/doc/pkgGraphR.html | 42 ++++++++++---------- man/buildPackageGraph.Rd | 4 - man/collectFunNames.Rd | 2 man/plotPackageGraph.Rd | 12 ++--- vignettes/pkgGraphR.Rmd | 2 11 files changed, 165 insertions(+), 105 deletions(-)
Title: Access to the Global Inventory of Floras and Traits (GIFT)
Description: Retrieving regional plant checklists, species traits and
distributions, and environmental data from the Global Inventory of Floras and
Traits (GIFT). More information about the GIFT database can be found at
<https://gift.uni-goettingen.de/about> and the map of available floras can be
visualized at <https://gift.uni-goettingen.de/map>. The API and associated
queries can be accessed according the following scheme:
<https://gift.uni-goettingen.de/api/extended/index2.0.php?query=env_raster>.
Author: Pierre Denelle [aut, cre] ,
Patrick Weigelt [aut]
Maintainer: Pierre Denelle <pierre.denelle@gmail.com>
Diff between GIFT versions 1.3.2 dated 2024-02-27 and 1.3.3 dated 2024-12-19
GIFT-1.3.2/GIFT/inst/doc/GIFT_API.R |only GIFT-1.3.2/GIFT/inst/doc/GIFT_API.Rmd |only GIFT-1.3.2/GIFT/inst/doc/GIFT_API.html |only GIFT-1.3.2/GIFT/inst/doc/GIFT_advanced_users.R |only GIFT-1.3.2/GIFT/inst/doc/GIFT_advanced_users.Rmd |only GIFT-1.3.2/GIFT/inst/doc/GIFT_advanced_users.html |only GIFT-1.3.2/GIFT/vignettes/GIFT_API.Rmd |only GIFT-1.3.2/GIFT/vignettes/GIFT_advanced_users.Rmd |only GIFT-1.3.3/GIFT/DESCRIPTION | 8 GIFT-1.3.3/GIFT/MD5 | 43 GIFT-1.3.3/GIFT/NEWS.md | 12 GIFT-1.3.3/GIFT/R/GIFT_checklists.R | 9 GIFT-1.3.3/GIFT/R/GIFT_spatial.R | 9 GIFT-1.3.3/GIFT/R/GIFT_taxgroup.R | 2 GIFT-1.3.3/GIFT/README.md | 17 GIFT-1.3.3/GIFT/build/vignette.rds |binary GIFT-1.3.3/GIFT/inst/doc/GIFT.R | 872 ++++++------- GIFT-1.3.3/GIFT/inst/doc/GIFT.Rmd | 18 GIFT-1.3.3/GIFT/inst/doc/GIFT.html | 1012 +++++++++++++++- GIFT-1.3.3/GIFT/man/GIFT_checklists.Rd | 9 GIFT-1.3.3/GIFT/man/GIFT_spatial.Rd | 9 GIFT-1.3.3/GIFT/man/figures/GIFT_complete_floristic.svg | 136 +- GIFT-1.3.3/GIFT/man/figures/GIFT_complete_taxon.svg | 140 +- GIFT-1.3.3/GIFT/man/figures/anemone_map.png |binary GIFT-1.3.3/GIFT/man/figures/anemone_map2.png |binary GIFT-1.3.3/GIFT/man/figures/tenerife_phylogeny.png |only GIFT-1.3.3/GIFT/vignettes/GIFT.Rmd | 18 27 files changed, 1623 insertions(+), 691 deletions(-)
Title: Constrained B-Splines (Sparse Matrix Based)
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng [aut],
Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cobs versions 1.3-8 dated 2024-03-06 and 1.3-9 dated 2024-12-19
cobs-1.3-8/cobs/README |only cobs-1.3-9/cobs/ChangeLog | 22 ++++ cobs-1.3-9/cobs/DESCRIPTION | 19 ++-- cobs-1.3-9/cobs/MD5 | 40 ++++---- cobs-1.3-9/cobs/R/drqssbc.R | 16 ++- cobs-1.3-9/cobs/R/l1Design.R | 6 - cobs-1.3-9/cobs/R/looDesign.R | 6 - cobs-1.3-9/cobs/R/qbsks.R | 108 ++++++++++++----------- cobs-1.3-9/cobs/R/scobs.R | 63 ++++++------- cobs-1.3-9/cobs/README.md |only cobs-1.3-9/cobs/TODO | 5 + cobs-1.3-9/cobs/build/partial.rdb |binary cobs-1.3-9/cobs/man/cobs.Rd | 10 +- cobs-1.3-9/cobs/man/drqssbc.Rd | 4 cobs-1.3-9/cobs/man/qbsks.Rd | 28 +++--- cobs-1.3-9/cobs/tests/ex1.R | 5 - cobs-1.3-9/cobs/tests/ex2-long.R | 7 - cobs-1.3-9/cobs/tests/ex3.Rout.save | 13 +- cobs-1.3-9/cobs/tests/multi-constr.R | 44 +++++---- cobs-1.3-9/cobs/tests/multi-constr.Rout.save | 126 ++++++++++++++++++++------- cobs-1.3-9/cobs/tests/small-ex.Rout.save | 14 +-- cobs-1.3-9/cobs/tests/temp.Rout.save | 35 +++++-- 22 files changed, 361 insertions(+), 210 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.10 dated 2024-12-02 and 0.3.11 dated 2024-12-19
anytime-0.3.10/anytime/inst/tinytest/test_simple.R |only anytime-0.3.11/anytime/ChangeLog | 6 ++++++ anytime-0.3.11/anytime/DESCRIPTION | 8 ++++---- anytime-0.3.11/anytime/MD5 | 11 +++++------ anytime-0.3.11/anytime/build/partial.rdb |binary anytime-0.3.11/anytime/inst/NEWS.Rd | 6 ++++++ anytime-0.3.11/anytime/inst/doc/anytime-introduction.pdf |binary 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural point estimators, which are neural networks that map data to a point summary of the posterior distribution. These estimators are likelihood-free and amortised, in the sense that, after an initial setup cost, inference from observed data can be made in a fraction of the time required by conventional approaches; see Sainsbury-Dale, Zammit-Mangion, and Huser (2024) <doi:10.1080/00031305.2023.2249522> for further details and an accessible introduction. The package also enables the construction of neural networks that approximate the likelihood-to-evidence ratio in an amortised manner, allowing one to perform inference based on the likelihood function or the entire posterior distribution; see Zammit-Mangion, Sainsbury-Dale, and Huser (2024, Sec. 5.2) <doi:10.48550/arXiv.2404.12484>, and the references therein. The package accommodates any model for which [...truncated...]
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.1.1 dated 2024-11-03 and 0.1.2 dated 2024-12-19
DESCRIPTION | 6 ++-- MD5 | 24 +++++++++---------- R/core.R | 33 +++++++++++++++++---------- README.md | 6 +++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 50 +++++++++++++++++++++++++++++------------ inst/doc/NeuralEstimators.html | 2 - man/bootstrap.Rd | 17 +++++++++++++ man/estimate.Rd | 9 ++++--- man/loadstate.Rd | 2 - man/loadweights.Rd | 3 +- tests/testthat/test-core.R | 1 13 files changed, 103 insertions(+), 50 deletions(-)
More information about NeuralEstimators at CRAN
Permanent link
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],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.11 dated 2024-11-14 and 1.12 dated 2024-12-19
DESCRIPTION | 6 MD5 | 156 ++++----- NAMESPACE | 8 NEWS.md | 27 + R/RcppExports.R | 4 R/class-style_mgr.R | 34 +- R/class-workbook-utils.R | 26 + R/class-workbook-wrappers.R | 138 ++++++-- R/class-workbook.R | 425 +++++++++++++++++--------- R/class-worksheet.R | 24 + R/conditional_formatting.R | 2 R/get-named-regions.R | 3 R/helper-functions.R | 200 ++++++++++-- R/openxlsx2-package.R | 12 R/pivot_table.R | 2 R/read.R | 30 - R/utils.R | 13 R/wb_functions.R | 1 R/wb_load.R | 69 +++- R/wb_styles.R | 5 R/write.R | 91 +++-- inst/AUTHORS | 2 inst/WORDLIST | 4 inst/doc/Update-from-openxlsx.html | 5 inst/doc/conditional-formatting.html | 5 inst/doc/openxlsx2.html | 5 inst/doc/openxlsx2_charts_manual.html | 5 inst/doc/openxlsx2_formulas_manual.html | 5 inst/doc/openxlsx2_read_to_df.R | 2 inst/doc/openxlsx2_read_to_df.Rmd | 2 inst/doc/openxlsx2_read_to_df.html | 7 inst/doc/openxlsx2_style_manual.html | 5 man/create_cell_style.Rd | 4 man/create_sparklines.Rd | 32 + man/grouping-wb.Rd | 8 man/properties-wb.Rd | 5 man/waivers.Rd | 2 man/wbWorkbook.Rd | 55 +++ man/wb_add_cell_style.Rd | 4 man/wb_add_data_table.Rd | 3 man/wb_add_slicer.Rd | 3 man/wb_merge_cells.Rd | 11 man/wb_set_bookview.Rd | 38 ++ man/wb_set_header_footer.Rd | 23 + man/wb_workbook.Rd | 3 src/RcppExports.cpp | 34 +- src/helper_functions.cpp | 324 ++++++++++--------- src/load_workbook.cpp | 12 src/openxlsx2.h | 16 src/openxlsx2_types.h | 57 +-- src/pugi.cpp | 81 ++-- src/strings_xml.cpp | 2 src/styles_xml.cpp | 230 +++++++------- src/write_file.cpp | 8 src/xlsb.cpp | 141 ++++---- src/xlsb_funs.h | 194 ++++++----- tests/testthat/test-class-comment.R | 9 tests/testthat/test-class-hyperlink.R | 3 tests/testthat/test-class-workbook-wrappers.R | 12 tests/testthat/test-class-workbook.R | 62 +++ tests/testthat/test-class-worksheet.R | 80 ++++ tests/testthat/test-date_time_conversion.R | 3 tests/testthat/test-deleting_tables.R | 3 tests/testthat/test-fill_merged_cells.R | 12 tests/testthat/test-formulas.R | 12 tests/testthat/test-helper-functions.R | 195 +++++++++++ tests/testthat/test-loading_workbook.R | 23 + tests/testthat/test-loading_workbook_tables.R | 3 tests/testthat/test-outlines.R | 26 + tests/testthat/test-read_from_created_wb.R | 6 tests/testthat/test-read_sources.R | 38 ++ tests/testthat/test-save.R | 5 tests/testthat/test-styles_xml.R | 12 tests/testthat/test-tables.R | 2 tests/testthat/test-wb_functions.R | 22 + tests/testthat/test-wb_styles.R | 12 tests/testthat/test-write.R | 150 ++++++++- tests/testthat/test-writing_posixct.R | 6 vignettes/openxlsx2_read_to_df.Rmd | 2 79 files changed, 2306 insertions(+), 1005 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.8.0 dated 2024-12-09 and 0.8.1 dated 2024-12-19
DESCRIPTION | 6 MD5 | 24 NAMESPACE | 1 NEWS.md | 31 R/DrugUtilisation-package.R | 5 R/addIntersect.R | 98 R/summariseDrugRestart.R | 8 R/summariseDrugUtilisation.R | 10 R/summariseIntersect.R | 30 R/summariseProportionOfPatientsCovered.R | 6 inst/doc/create_cohorts.html | 54 inst/doc/drug_utilisation.html | 8713 +++++++++++++++++++++++++------ man/addIndication.Rd | 6 13 files changed, 7373 insertions(+), 1619 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 1.6.1 dated 2024-11-29 and 1.7.0 dated 2024-12-19
CDMConnector-1.6.1/CDMConnector/man/assert_tables.Rd |only CDMConnector-1.6.1/CDMConnector/man/cdmName.Rd |only CDMConnector-1.6.1/CDMConnector/man/cdm_from_con.Rd |only CDMConnector-1.6.1/CDMConnector/man/cdm_from_environment.Rd |only CDMConnector-1.6.1/CDMConnector/man/cdm_from_files.Rd |only CDMConnector-1.6.1/CDMConnector/man/cdm_select_tbl.Rd |only CDMConnector-1.6.1/CDMConnector/man/cohort_erafy.Rd |only CDMConnector-1.6.1/CDMConnector/man/cohort_union.Rd |only CDMConnector-1.6.1/CDMConnector/man/copy_cdm_to.Rd |only CDMConnector-1.6.1/CDMConnector/man/eunomia_is_available.Rd |only CDMConnector-1.6.1/CDMConnector/man/intersect_cohorts.Rd |only CDMConnector-1.6.1/CDMConnector/man/list_tables.Rd |only CDMConnector-1.6.1/CDMConnector/man/read_cohort_set.Rd |only CDMConnector-1.6.1/CDMConnector/man/recordCohortAttrition.Rd |only CDMConnector-1.6.1/CDMConnector/man/summarise_quantile.Rd |only CDMConnector-1.6.1/CDMConnector/man/tbl_group.Rd |only CDMConnector-1.6.1/CDMConnector/man/union_cohorts.Rd |only CDMConnector-1.6.1/CDMConnector/man/uniqueTableName.Rd |only CDMConnector-1.6.1/CDMConnector/man/validate_cdm.Rd |only CDMConnector-1.6.1/CDMConnector/tests/testthat/test-validate.R |only CDMConnector-1.7.0/CDMConnector/DESCRIPTION | 12 CDMConnector-1.7.0/CDMConnector/MD5 | 237 ++-- CDMConnector-1.7.0/CDMConnector/NAMESPACE | 7 CDMConnector-1.7.0/CDMConnector/NEWS.md | 13 CDMConnector-1.7.0/CDMConnector/R/Eunomia.R | 53 - CDMConnector-1.7.0/CDMConnector/R/benchmarkCDMConnector.R | 43 CDMConnector-1.7.0/CDMConnector/R/cdm.R | 497 ++++------ CDMConnector-1.7.0/CDMConnector/R/cdmSubset.R | 58 - CDMConnector-1.7.0/CDMConnector/R/cdm_from_environment.R | 38 CDMConnector-1.7.0/CDMConnector/R/cohortTransformations.R | 25 CDMConnector-1.7.0/CDMConnector/R/cohort_ddl.R | 14 CDMConnector-1.7.0/CDMConnector/R/compute.R | 42 CDMConnector-1.7.0/CDMConnector/R/copy_cdm_to.R | 14 CDMConnector-1.7.0/CDMConnector/R/dateadd.R | 7 CDMConnector-1.7.0/CDMConnector/R/dbSource.R | 13 CDMConnector-1.7.0/CDMConnector/R/generateCohortSet.R | 116 +- CDMConnector-1.7.0/CDMConnector/R/generateConceptCohortSet.R | 11 CDMConnector-1.7.0/CDMConnector/R/reexports-omopgenerics.R | 23 CDMConnector-1.7.0/CDMConnector/R/summariseQuantile.R | 33 CDMConnector-1.7.0/CDMConnector/R/utils.R | 101 +- CDMConnector-1.7.0/CDMConnector/R/validate.R | 71 - CDMConnector-1.7.0/CDMConnector/R/zzz-deprecated.R | 36 CDMConnector-1.7.0/CDMConnector/inst/cohortsNonUTF8 |only CDMConnector-1.7.0/CDMConnector/inst/doc/a01_getting-started.R | 16 CDMConnector-1.7.0/CDMConnector/inst/doc/a01_getting-started.html | 356 +++---- CDMConnector-1.7.0/CDMConnector/inst/doc/a02_cohorts.R | 4 CDMConnector-1.7.0/CDMConnector/inst/doc/a02_cohorts.html | 381 +++---- CDMConnector-1.7.0/CDMConnector/inst/doc/a04_DBI_connection_examples.R | 145 +- CDMConnector-1.7.0/CDMConnector/inst/doc/a04_DBI_connection_examples.Rmd | 59 - CDMConnector-1.7.0/CDMConnector/inst/doc/a04_DBI_connection_examples.html | 57 - CDMConnector-1.7.0/CDMConnector/inst/doc/a05_cdm_reference_backends.R | 106 +- CDMConnector-1.7.0/CDMConnector/inst/doc/a06_using_cdm_attributes.R | 28 CDMConnector-1.7.0/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 13 CDMConnector-1.7.0/CDMConnector/man/appendPermanent.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/assertTables.Rd |only CDMConnector-1.7.0/CDMConnector/man/assert_write_schema.Rd | 3 CDMConnector-1.7.0/CDMConnector/man/benchmarkCDMConnector.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/cdmCon.Rd | 8 CDMConnector-1.7.0/CDMConnector/man/cdmFlatten.Rd | 6 CDMConnector-1.7.0/CDMConnector/man/cdmFromCon.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmFromEnvironment.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmFromFiles.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmSample.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/cdmSelectTbl.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmSubset.Rd | 6 CDMConnector-1.7.0/CDMConnector/man/cdmSubsetCohort.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/cdmWriteSchema.Rd | 8 CDMConnector-1.7.0/CDMConnector/man/cdm_from_tables.Rd | 6 CDMConnector-1.7.0/CDMConnector/man/cdm_name.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortAttrition.Rd | 2 CDMConnector-1.7.0/CDMConnector/man/cohortErafy.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortSet.Rd | 2 CDMConnector-1.7.0/CDMConnector/man/cohortUnion.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohort_count.Rd | 8 CDMConnector-1.7.0/CDMConnector/man/computeQuery.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/copyCdmTo.Rd |only CDMConnector-1.7.0/CDMConnector/man/dbms.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/eunomiaDir.Rd | 16 CDMConnector-1.7.0/CDMConnector/man/eunomiaIsAvailable.Rd |only CDMConnector-1.7.0/CDMConnector/man/exampleDatasets.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/generateCohortSet.Rd | 9 CDMConnector-1.7.0/CDMConnector/man/intersectCohorts.Rd |only CDMConnector-1.7.0/CDMConnector/man/listTables.Rd |only CDMConnector-1.7.0/CDMConnector/man/new_generated_cohort_set.Rd | 10 CDMConnector-1.7.0/CDMConnector/man/readCohortSet.Rd |only CDMConnector-1.7.0/CDMConnector/man/record_cohort_attrition.Rd |only CDMConnector-1.7.0/CDMConnector/man/reexports.Rd | 6 CDMConnector-1.7.0/CDMConnector/man/requireEunomia.Rd | 2 CDMConnector-1.7.0/CDMConnector/man/snapshot.Rd | 4 CDMConnector-1.7.0/CDMConnector/man/stow.Rd | 6 CDMConnector-1.7.0/CDMConnector/man/summariseQuantile.Rd |only CDMConnector-1.7.0/CDMConnector/man/tblGroup.Rd |only CDMConnector-1.7.0/CDMConnector/man/unionCohorts.Rd |only CDMConnector-1.7.0/CDMConnector/man/unique_table_name.Rd |only CDMConnector-1.7.0/CDMConnector/man/validateCdm.Rd |only CDMConnector-1.7.0/CDMConnector/man/version.Rd | 4 CDMConnector-1.7.0/CDMConnector/tests/testthat/old_tests/test-02-db-cdm.R | 50 - CDMConnector-1.7.0/CDMConnector/tests/testthat/old_tests/test-cdm.R | 152 +-- CDMConnector-1.7.0/CDMConnector/tests/testthat/old_tests/test-db-omopgenerics.R | 4 CDMConnector-1.7.0/CDMConnector/tests/testthat/old_tests/test-summariseQuantile.R | 80 - CDMConnector-1.7.0/CDMConnector/tests/testthat/setup.R | 60 - CDMConnector-1.7.0/CDMConnector/tests/testthat/test-01-db-DBI.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-02-db-cdm.R | 57 - CDMConnector-1.7.0/CDMConnector/tests/testthat/test-03-db-generateCohortSet.R | 77 - CDMConnector-1.7.0/CDMConnector/tests/testthat/test-04-db-generateConceptCohortSet.R | 136 +- CDMConnector-1.7.0/CDMConnector/tests/testthat/test-05-db-cohort_ddl.R | 8 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-06-db-compute.R | 12 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-07-db-dateadd.R | 77 - CDMConnector-1.7.0/CDMConnector/tests/testthat/test-08-db-casing.R | 2 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-09-db-copy_cdm_to.R | 30 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-10-db-summariseQuantile.R | 18 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-11-cdm_tranformations.R | 10 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-12-db-dplyr.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-13-db-custom_cohort_creation.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-14-db-cohortTransformations.R | 18 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-15-db-benchmarkCDMConnector.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-16-db-dbSource.R | 23 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-17-db-generic-bind.R | 10 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-18-db-newGeneratedCohortSet.R | 28 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-Eunomia.R | 36 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-cohort-reconnect.R | 16 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-benchmarkCDMConnector.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-dplyr.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-example-analysis.R | 24 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-in_schema.R | 39 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-recordCohortAttrition.R | 16 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-sample.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-temp-tables.R | 8 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-utils.R | 24 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-write_schema_with_database.R | 2 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-deprecations.R | 4 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-local_cdm.R | 18 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-memory-issue.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-omopgenerics.R |only CDMConnector-1.7.0/CDMConnector/tests/testthat/test-pool.R | 8 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-readCohortSet.R | 6 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-write_prefix.r | 2 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-write_prefix_cohort_generation_snowflake.R | 12 CDMConnector-1.7.0/CDMConnector/tests/testthat/test-zzz-DBI.R | 6 CDMConnector-1.7.0/CDMConnector/vignettes/a04_DBI_connection_examples.Rmd | 59 - 140 files changed, 2198 insertions(+), 1745 deletions(-)
Title: Various Non-Additive Models for Genetic Associations
Description: The goal of 'gnonadd' is to simplify workflows in the analysis of non-additive effects of sequence variants. This includes variance effects (Ivarsdottir et. al (2017) <doi:10.1038/ng.3928>), correlation effects, interaction effects and dominance effects. The package also includes convenience functions for visualization.
Author: Audunn S. Snaebjarnarson [aut, cre, ctb],
Gudmundur Einarsson [aut, ctb],
Daniel F. Gudbjartsson [aut, ctb],
deCODE Genetics/AMGEN [cph, fnd]
Maintainer: Audunn S. Snaebjarnarson <audunn.snaebjarnarson@decode.is>
Diff between gnonadd versions 1.0.2 dated 2023-09-22 and 1.0.3 dated 2024-12-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/Variance_summary_stats.R | 2 +- R/variance_continuous_conditional.R | 4 ++-- README.md | 31 ++++++++++++++++++------------- 6 files changed, 35 insertions(+), 25 deletions(-)
Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in
'Tidy Eval' code that calculates the predictions. It works with
several databases back-ends because it leverages 'dplyr' and 'dbplyr'
for the final 'SQL' translation of the algorithm. It currently
supports lm(), glm(), randomForest(), ranger(), earth(),
xgb.Booster.complete(), cubist(), and ctree() models.
Author: Emil Hvitfeldt [aut, cre],
Edgar Ruiz [aut],
Max Kuhn [aut]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidypredict versions 0.5 dated 2023-01-18 and 0.5.1 dated 2024-12-19
tidypredict-0.5.1/tidypredict/DESCRIPTION | 32 tidypredict-0.5.1/tidypredict/MD5 | 161 +-- tidypredict-0.5.1/tidypredict/NAMESPACE | 2 tidypredict-0.5.1/tidypredict/NEWS.md | 6 tidypredict-0.5.1/tidypredict/R/acceptable.R | 9 tidypredict-0.5.1/tidypredict/R/as-parsed-model.R | 4 tidypredict-0.5.1/tidypredict/R/model-cubist.R | 4 tidypredict-0.5.1/tidypredict/R/model-earth.R | 97 +- tidypredict-0.5.1/tidypredict/R/model-glm.R |only tidypredict-0.5.1/tidypredict/R/model-lm.R | 33 tidypredict-0.5.1/tidypredict/R/model-partykit.R | 111 ++ tidypredict-0.5.1/tidypredict/R/model-ranger.R | 17 tidypredict-0.5.1/tidypredict/R/model-rf.R | 13 tidypredict-0.5.1/tidypredict/R/model-xgboost.R | 58 + tidypredict-0.5.1/tidypredict/R/predict-column.R | 2 tidypredict-0.5.1/tidypredict/R/predict-fit.R | 2 tidypredict-0.5.1/tidypredict/R/predict-interval.R | 4 tidypredict-0.5.1/tidypredict/R/tidymodels.R | 10 tidypredict-0.5.1/tidypredict/R/tidypredict-package.R |only tidypredict-0.5.1/tidypredict/R/tidypredict_test.R |only tidypredict-0.5.1/tidypredict/README.md | 84 - tidypredict-0.5.1/tidypredict/build/vignette.rds |binary tidypredict-0.5.1/tidypredict/inst/doc/cubist.R | 2 tidypredict-0.5.1/tidypredict/inst/doc/cubist.Rmd | 18 tidypredict-0.5.1/tidypredict/inst/doc/cubist.html | 182 +-- tidypredict-0.5.1/tidypredict/inst/doc/glm.R | 6 tidypredict-0.5.1/tidypredict/inst/doc/glm.Rmd | 6 tidypredict-0.5.1/tidypredict/inst/doc/glm.html | 106 +- tidypredict-0.5.1/tidypredict/inst/doc/lm.R | 6 tidypredict-0.5.1/tidypredict/inst/doc/lm.Rmd | 4 tidypredict-0.5.1/tidypredict/inst/doc/lm.html | 192 ++-- tidypredict-0.5.1/tidypredict/inst/doc/mars.R | 5 tidypredict-0.5.1/tidypredict/inst/doc/mars.Rmd | 21 tidypredict-0.5.1/tidypredict/inst/doc/mars.html | 241 ++--- tidypredict-0.5.1/tidypredict/inst/doc/non-r.R | 2 tidypredict-0.5.1/tidypredict/inst/doc/non-r.html | 178 +-- tidypredict-0.5.1/tidypredict/inst/doc/ranger.R | 4 tidypredict-0.5.1/tidypredict/inst/doc/ranger.Rmd | 4 tidypredict-0.5.1/tidypredict/inst/doc/ranger.html | 112 +- tidypredict-0.5.1/tidypredict/inst/doc/regression.R | 4 tidypredict-0.5.1/tidypredict/inst/doc/rf.R | 4 tidypredict-0.5.1/tidypredict/inst/doc/rf.Rmd | 4 tidypredict-0.5.1/tidypredict/inst/doc/rf.html | 114 +- tidypredict-0.5.1/tidypredict/inst/doc/save.R | 28 tidypredict-0.5.1/tidypredict/inst/doc/save.html | 136 +- tidypredict-0.5.1/tidypredict/inst/doc/sql.R | 36 tidypredict-0.5.1/tidypredict/inst/doc/sql.Rmd | 32 tidypredict-0.5.1/tidypredict/inst/doc/sql.html | 225 ++-- tidypredict-0.5.1/tidypredict/inst/doc/tree.R | 4 tidypredict-0.5.1/tidypredict/inst/doc/xgboost.R | 6 tidypredict-0.5.1/tidypredict/inst/doc/xgboost.Rmd | 20 tidypredict-0.5.1/tidypredict/inst/doc/xgboost.html | 468 +++++----- tidypredict-0.5.1/tidypredict/man/dot-extract_partykit_classprob.Rd |only tidypredict-0.5.1/tidypredict/man/dot-extract_xgb_trees.Rd |only tidypredict-0.5.1/tidypredict/man/figures/logo.png |binary tidypredict-0.5.1/tidypredict/man/knit_print.tidypredict_test.Rd | 2 tidypredict-0.5.1/tidypredict/man/print.tidypredict_test.Rd | 2 tidypredict-0.5.1/tidypredict/man/tidypredict-package.Rd | 5 tidypredict-0.5.1/tidypredict/man/tidypredict_test.Rd | 2 tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-cubist.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-earth.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-glm.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-lm.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-partykit.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-rf.md |only tidypredict-0.5.1/tidypredict/tests/testthat/_snaps/model-xgboost.md |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-cubist.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-earth.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-glm.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-lm.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-partykit.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-ranger.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-rf.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-model-xgboost.R |only tidypredict-0.5.1/tidypredict/tests/testthat/test-tidypredict_test.R |only tidypredict-0.5.1/tidypredict/vignettes/cubist.Rmd | 18 tidypredict-0.5.1/tidypredict/vignettes/glm.Rmd | 6 tidypredict-0.5.1/tidypredict/vignettes/lm.Rmd | 4 tidypredict-0.5.1/tidypredict/vignettes/mars.Rmd | 21 tidypredict-0.5.1/tidypredict/vignettes/ranger.Rmd | 4 tidypredict-0.5.1/tidypredict/vignettes/rf.Rmd | 4 tidypredict-0.5.1/tidypredict/vignettes/sql.Rmd | 32 tidypredict-0.5.1/tidypredict/vignettes/xgboost.Rmd | 20 tidypredict-0.5/tidypredict/R/test-predictions.R |only tidypredict-0.5/tidypredict/R/tidypredict.R |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/cubist.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/earth.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/glm.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/lm.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/party.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/rf.md |only tidypredict-0.5/tidypredict/tests/testthat/_snaps/xgboost.md |only tidypredict-0.5/tidypredict/tests/testthat/test-cubist.R |only tidypredict-0.5/tidypredict/tests/testthat/test-earth.R |only tidypredict-0.5/tidypredict/tests/testthat/test-party.R |only tidypredict-0.5/tidypredict/tests/testthat/test-ranger.R |only tidypredict-0.5/tidypredict/tests/testthat/test-rf.R |only tidypredict-0.5/tidypredict/tests/testthat/test-tester.R |only tidypredict-0.5/tidypredict/tests/testthat/test_glm.R |only tidypredict-0.5/tidypredict/tests/testthat/test_lm.R |only tidypredict-0.5/tidypredict/tests/testthat/test_xgboost.R |only 101 files changed, 1523 insertions(+), 1416 deletions(-)
Title: FaaS (Function as a Service) Package
Description: Allows users to create and deploy the workflow with multiple functions
in Function-as-a-Service (FaaS) cloud computing platforms.
The 'FaaSr' package makes it simpler for R developers to use FaaS platforms by providing the following functionality:
1) Parsing and validating a JSON-based payload compliant to 'FaaSr' schema supporting multiple FaaS platforms
2) Invoking user functions written in R in a Docker container (derived from rocker), using a list generated from
the parser as argument
3) Downloading/uploading of files from/to S3 buckets using simple primitives
4) Logging to files in S3 buckets
5) Triggering downstream actions supporting multiple FaaS platforms
6) Generating FaaS-specific API calls to simplify the registering of a user's workflow with a FaaS platform
Supported FaaS platforms:
Apache OpenWhisk <https://openwhisk.apache.org/>
GitHub Actions <https://github.com/features/actions>
Amazon Web Services (AWS) Lambda <https://aws.amazon.com/lambda/>
Support [...truncated...]
Author: Figueiredo Renato [aut, cre, ths, cph]
,
Park Sungjae [aut] ,
Mu Nan [ctb],
Ku Yun-Jung [ctb],
Daneshmand Vahid [ctb],
Thomas R. Quinn [aut],
Carey Cayelan [ctb]
Maintainer: Figueiredo Renato <renato.figueiredo@oregonstate.edu>
Diff between FaaSr versions 1.3.0 dated 2024-06-10 and 1.4.3 dated 2024-12-19
DESCRIPTION | 12 MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 6 R/faasr_abort_on_multiple_invocations.R | 12 R/faasr_check_workflow_cycle.R | 7 R/faasr_client_api_github-actions.R | 73 ++++-- R/faasr_client_tools.R | 16 - R/faasr_get_file.R | 3 R/faasr_init_log_folder.R | 2 R/faasr_lock.R | 2 R/faasr_put_file.R | 5 R/faasr_rank.R |only R/faasr_run_user_function.R | 4 R/faasr_s3_check.R | 35 +- R/faasr_test.R | 2 R/faasr_trigger.R | 387 +++++++++++++++++--------------- README.md | 2 inst/CITATION |only inst/WORDLIST | 2 man/faasr_rank.Rd |only man/faasr_s3_check.Rd | 2 22 files changed, 357 insertions(+), 255 deletions(-)
Title: Dose Response Models for Bayesian Model Averaging
Description: Fits dose-response models utilizing a Bayesian model
averaging approach as outlined in Gould (2019) <doi:10.1002/bimj.201700211>
for both continuous and binary responses. Longitudinal dose-response modeling
is also supported in a Bayesian model averaging framework as outlined in
Payne, Ray, and Thomann (2024)
<doi:10.1080/10543406.2023.2292214>. Functions
for plotting and calculating various posterior quantities
(e.g. posterior mean, quantiles, probability of minimum efficacious dose,
etc.) are also implemented. Copyright Eli Lilly and Company (2019).
Author: Richard Daniel Payne [aut, cre],
William Michael Landau [rev],
Mitch Thomann [rev],
Eli Lilly and Company [cph]
Maintainer: Richard Daniel Payne <paynestatistics@gmail.com>
Diff between dreamer versions 3.1.0 dated 2022-09-01 and 3.2.0 dated 2024-12-19
DESCRIPTION | 24 MD5 | 58 +- NAMESPACE | 122 ++++ NEWS.md | 6 R/assert.R | 30 + R/diagnostics.R | 8 R/dreamer.R | 65 -- R/dreamer_data.R | 2 R/dreamer_mean.R | 16 R/epll.R | 16 R/fit_model.R | 56 +- R/get_extreme.R | 6 R/get_jags_data.R | 28 - R/get_jags_model.R | 58 ++ R/plot.R | 81 +-- R/post_medx.R | 2 R/posterior.R | 10 R/pr_med.R | 4 R/pr_medx.R | 4 R/summary.R | 12 build/vignette.rds |binary inst/doc/dreamer.R | 6 inst/doc/dreamer.html | 963 ++++++++++++++++++++++++--------------- inst/doc/dreamer_method.R | 2 inst/doc/dreamer_method.html | 247 +++++++++- man/dreamerplot.Rd | 2 man/posterior.Rd | 2 tests/testthat/test-assertions.R | 3 tests/testthat/test-plots.R | 8 tests/testthat/test-print.R | 18 30 files changed, 1313 insertions(+), 546 deletions(-)
Title: Analyzing Animal's Rhythmicity
Description: Analyze and visualize the rhythmic behavior of animals using the
degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>),
compute and visualize harmonic power, actograms, average activity and diurnality
index.
Author: Hassan-Roland Nasser [aut, cre],
Marie Schneider [aut, ctb],
Joanna Stachowicz [aut, rev],
Christina Umstaetter [aut, ths]
Maintainer: Hassan-Roland Nasser <hassan.nasser@me.com>
Diff between digiRhythm versions 2.3 dated 2024-11-07 and 2.4 dated 2024-12-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/daily_average_activity.R | 8 +++++--- inst/doc/Actgram_diurnality_avg_activity.html | 6 +++--- inst/doc/DFC_and_HP_and_changing_plots.html | 4 ++-- inst/doc/Loading_and_preprocessing_data_in_DigiRhythm.html | 6 +++--- inst/doc/Visualisation.html | 4 ++-- 7 files changed, 24 insertions(+), 22 deletions(-)
Title: Statistical Methods for Psychologists
Description: Implements confidence interval and sample size methods that
are especially useful in psychological research. The methods can be
applied in 1-group, 2-group, paired-samples, and multiple-group designs
and to a variety of parameters including means, medians, proportions,
slopes, standardized mean differences, standardized linear contrasts
of means, plus several measures of correlation and association.
Confidence interval and sample size functions are given for single
parameters as well as differences, ratios, and linear contrasts of
parameters. The sample size functions can be used to approximate the
sample size needed to estimate a parameter or function of parameters
with desired confidence interval precision or to perform a variety of
hypothesis tests (directional two-sided, equivalence, superiority,
noninferiority) with desired power. For details see: Statistical Methods
for Psychologists, Volumes 1 – 4, <https://dgbonett.sites.ucsc.edu/>.
Author: Douglas G. Bonett [aut, cre],
Robert J. Calin-Jageman [ctb]
Maintainer: Douglas G. Bonett <dgbonett@ucsc.edu>
Diff between statpsych versions 1.6.0 dated 2024-07-08 and 1.7.0 dated 2024-12-18
DESCRIPTION | 27 + MD5 | 147 +++++----- NAMESPACE | 13 NEWS.md | 40 ++ R/statpsych1.R | 440 ++++++++++++++++++++---------- R/statpsych2.R | 488 ++++++++++++++++++++++++++++++---- R/statpsych3.R | 554 +++++++++++++++++++++++++++++++++------ build/partial.rdb |binary inst/REFERENCES.bib | 10 man/adj.se.Rd | 2 man/ci.2x2.mean.mixed.Rd | 16 - man/ci.2x2.median.bs.Rd | 2 man/ci.2x2.median.mixed.Rd | 26 - man/ci.2x2.median.ws.Rd | 24 - man/ci.2x2.stdmean.bs.Rd | 5 man/ci.2x2.stdmean.mixed.Rd | 36 +- man/ci.2x2.stdmean.ws.Rd | 1 man/ci.agree.Rd | 5 man/ci.bayes.cor.Rd |only man/ci.bayes.normal.Rd | 6 man/ci.bayes.prop.Rd | 8 man/ci.bayes.spcor.Rd |only man/ci.cor.Rd | 2 man/ci.cor2.gen.Rd | 4 man/ci.cramer.Rd | 7 man/ci.kappa.Rd | 8 man/ci.lc.gen.bs.Rd | 7 man/ci.lc.glm.Rd | 2 man/ci.lc.median.bs.Rd | 4 man/ci.median.Rd | 9 man/ci.median.ps.Rd | 15 - man/ci.median2.Rd | 11 man/ci.oddsratio.Rd | 4 man/ci.ratio.mad.ps.Rd | 2 man/ci.ratio.median.ps.Rd | 1 man/ci.ratio.median2.Rd | 3 man/ci.sign.Rd | 10 man/ci.tukey.Rd | 2 man/etasqr.adj.Rd | 2 man/etasqr.gen.2way.Rd | 2 man/expon.slope.Rd |only man/pi.cor.Rd | 33 +- man/pi.prop.Rd | 33 +- man/pi.var.Rd |only man/pi.var.upper.Rd | 3 man/power.cor2.Rd | 4 man/signal.Rd |only man/sim.ci.mean.Rd | 6 man/sim.ci.mean.ps.Rd | 2 man/sim.ci.mean2.Rd | 9 man/sim.ci.stdmean.ps.Rd | 2 man/size.ci.ancova2.Rd |only man/size.ci.biphi.Rd |only man/size.ci.cor.prior.Rd | 2 man/size.ci.mean.prior.Rd | 2 man/size.ci.mean2.Rd | 18 + man/size.ci.oddsratio.Rd |only man/size.ci.phi.Rd |only man/size.ci.prop2.Rd | 24 + man/size.ci.ratio.mean2.Rd | 8 man/size.ci.ratio.prop2.Rd | 22 + man/size.ci.slope.gen.Rd |only man/size.ci.stdmean2.Rd | 7 man/size.ci.yule.Rd |only man/size.test.ancova2.Rd |only man/size.test.cor2.Rd | 26 + man/size.test.lc.ancova.Rd | 2 man/size.test.lc.prop.bs.Rd | 10 man/size.test.mean2.Rd | 12 man/size.test.prop2.Rd | 15 - man/size.test.slope.gen.Rd |only man/test.cor.Rd | 5 man/test.cor2.Rd | 6 man/test.spear.Rd | 5 man/test.spear2.Rd | 5 tests/testthat/_snaps |only tests/testthat/test_statpsych1.R | 180 ++++++++++++ tests/testthat/test_statpsych2.R | 181 ++++++++++++ tests/testthat/test_statpsych3.R | 151 ++++++++++ tests/testthat/test_statpsych4.R | 14 80 files changed, 2174 insertions(+), 558 deletions(-)
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling
Algorithms for 'nimble'
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes two versions of Hamiltonian Monte Carlo (HMC) No-U-Turn (NUTS) sampling, and (under development) Langevin samplers. The `NUTS_classic` sampler implements the original HMC-NUTS algorithm as described in Hoffman and Gelman (2014) <doi:10.48550/arXiv.1111.4246>. The `NUTS` sampler is a modern version of HMC-NUTS sampling matching the HMC sampler available in version 2.32.2 of Stan (Stan Development Team, 2023). In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling.
Author: Daniel Turek [aut, cre],
Perry de Valpine [aut],
Christopher Paciorek [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleHMC versions 0.2.2 dated 2024-06-28 and 0.2.3 dated 2024-12-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/HMC_samplers.R | 12 ++++++++---- inst/NEWS.md | 4 ++++ 4 files changed, 20 insertions(+), 12 deletions(-)
Title: Processing and Analysing Animal Trajectories
Description: Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Author: Bart Kranstauber [aut, cre] ,
Kamran Safi [aut] ,
Anne K. Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move2 versions 0.4.0 dated 2024-12-09 and 0.4.2 dated 2024-12-18
DESCRIPTION | 6 MD5 | 46 - NEWS.md | 6 R/movebank_constants.R | 8 README.md | 11 inst/WORDLIST | 2 inst/doc/albatross.R | 20 inst/doc/albatross.Rmd | 18 inst/doc/albatross.html | 887 +++++++++++++++----------- inst/doc/convert.html | 248 ++++--- inst/doc/filtering_tracks.R | 2 inst/doc/filtering_tracks.Rmd | 2 inst/doc/filtering_tracks.html | 1095 ++++++++++++++++----------------- inst/doc/movebank.R | 42 - inst/doc/movebank.html | 1067 +++++++++++++++++--------------- inst/doc/programming_move2_object.html | 418 ++++++++---- inst/doc/trajectory_analysis.R | 19 inst/doc/trajectory_analysis.Rmd | 19 inst/doc/trajectory_analysis.html | 568 ++++++++--------- man/figures/README-deps-1.png |binary man/mt_filter_unique.Rd | 2 vignettes/albatross.Rmd | 18 vignettes/filtering_tracks.Rmd | 2 vignettes/trajectory_analysis.Rmd | 19 24 files changed, 2456 insertions(+), 2069 deletions(-)
Title: Miscellaneous Functions for the Analysis of Educational
Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive
analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep',
'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
The function for defining (weighted) contrasts in weighted effect coding refers to
te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
Functions for weighted statistics refer to
Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Karoline Sachse [aut],
Benjamin Becker [aut],
Nicole Mahler [aut],
Edna Grewers [ctb]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatTools versions 0.7.7 dated 2024-10-11 and 0.7.8 dated 2024-12-18
DESCRIPTION | 6 +++--- MD5 | 11 +++++++---- NAMESPACE | 4 ++++ NEWS.md | 6 +++++- R/cleanifyString.r |only man/cleanifyString.Rd |only tests/testthat/test_cleanifyString.R |only tests/testthat/test_remove_funs.R | 10 +++++----- 8 files changed, 24 insertions(+), 13 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.4.0 dated 2024-11-08 and 0.5.0 dated 2024-12-18
connectapi-0.4.0/connectapi/man/jobs.Rd |only connectapi-0.5.0/connectapi/DESCRIPTION | 6 connectapi-0.5.0/connectapi/MD5 | 141 +++--- connectapi-0.5.0/connectapi/NAMESPACE | 4 connectapi-0.5.0/connectapi/NEWS.md | 31 + connectapi-0.5.0/connectapi/R/audits.R | 2 connectapi-0.5.0/connectapi/R/connect.R | 33 + connectapi-0.5.0/connectapi/R/connectapi.R | 1 connectapi-0.5.0/connectapi/R/content.R | 148 ++++++ connectapi-0.5.0/connectapi/R/get.R | 226 ++++------ connectapi-0.5.0/connectapi/R/groups.R |only connectapi-0.5.0/connectapi/R/parse.R | 17 connectapi-0.5.0/connectapi/R/ptype.R | 43 + connectapi-0.5.0/connectapi/R/utils.R | 20 connectapi-0.5.0/connectapi/R/variant.R | 5 connectapi-0.5.0/connectapi/inst/doc/customize-http.html | 4 connectapi-0.5.0/connectapi/inst/doc/getting-started.html | 4 connectapi-0.5.0/connectapi/inst/scratch |only connectapi-0.5.0/connectapi/man/Content.Rd | 20 connectapi-0.5.0/connectapi/man/ContentTask.Rd | 1 connectapi-0.5.0/connectapi/man/EnvironmentR6.Rd | 1 connectapi-0.5.0/connectapi/man/PositConnect.Rd | 41 + connectapi-0.5.0/connectapi/man/Vanity.Rd | 1 connectapi-0.5.0/connectapi/man/VariantR6.Rd | 1 connectapi-0.5.0/connectapi/man/VariantSchedule.Rd | 1 connectapi-0.5.0/connectapi/man/VariantTask.Rd | 1 connectapi-0.5.0/connectapi/man/content_delete.Rd | 2 connectapi-0.5.0/connectapi/man/content_item.Rd | 2 connectapi-0.5.0/connectapi/man/content_title.Rd | 2 connectapi-0.5.0/connectapi/man/content_update.Rd | 2 connectapi-0.5.0/connectapi/man/create_random_name.Rd | 2 connectapi-0.5.0/connectapi/man/dashboard_url.Rd | 2 connectapi-0.5.0/connectapi/man/dashboard_url_chr.Rd | 2 connectapi-0.5.0/connectapi/man/delete_thumbnail.Rd | 2 connectapi-0.5.0/connectapi/man/delete_vanity_url.Rd | 2 connectapi-0.5.0/connectapi/man/deploy_repo.Rd | 2 connectapi-0.5.0/connectapi/man/environment.Rd | 2 connectapi-0.5.0/connectapi/man/get_bundles.Rd | 4 connectapi-0.5.0/connectapi/man/get_group_content.Rd |only connectapi-0.5.0/connectapi/man/get_group_members.Rd | 10 connectapi-0.5.0/connectapi/man/get_groups.Rd | 8 connectapi-0.5.0/connectapi/man/get_image.Rd | 2 connectapi-0.5.0/connectapi/man/get_job.Rd |only connectapi-0.5.0/connectapi/man/get_jobs.Rd |only connectapi-0.5.0/connectapi/man/get_oauth_content_credentials.Rd |only connectapi-0.5.0/connectapi/man/get_thumbnail.Rd | 2 connectapi-0.5.0/connectapi/man/get_users.Rd | 27 + connectapi-0.5.0/connectapi/man/get_vanity_url.Rd | 2 connectapi-0.5.0/connectapi/man/get_vanity_urls.Rd |only connectapi-0.5.0/connectapi/man/git.Rd | 2 connectapi-0.5.0/connectapi/man/has_thumbnail.Rd | 2 connectapi-0.5.0/connectapi/man/permissions.Rd | 2 connectapi-0.5.0/connectapi/man/set_image.Rd | 2 connectapi-0.5.0/connectapi/man/set_run_as.Rd | 2 connectapi-0.5.0/connectapi/man/set_thumbnail.Rd | 2 connectapi-0.5.0/connectapi/man/set_vanity_url.Rd | 2 connectapi-0.5.0/connectapi/man/swap_vanity_url.Rd | 2 connectapi-0.5.0/connectapi/man/terminate_jobs.Rd |only connectapi-0.5.0/connectapi/man/verify_content_name.Rd | 4 connectapi-0.5.0/connectapi/tests/integrated/test-content.R | 9 connectapi-0.5.0/connectapi/tests/integrated/test-get.R | 8 connectapi-0.5.0/connectapi/tests/testthat/2024.07.0 |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/01234567/jobs.json |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/8f37d6e0/jobs |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/8f37d6e0/jobs.json |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/experimental |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-f08930-POST.json |only connectapi-0.5.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-fe6213-POST.json | 2 connectapi-0.5.0/connectapi/tests/testthat/Rplots.pdf |only connectapi-0.5.0/connectapi/tests/testthat/_snaps/groups.md |only connectapi-0.5.0/connectapi/tests/testthat/test-content.R | 83 +++ connectapi-0.5.0/connectapi/tests/testthat/test-get.R | 53 ++ connectapi-0.5.0/connectapi/tests/testthat/test-groups.R | 19 connectapi-0.5.0/connectapi/tests/testthat/test-oauth.R | 44 + connectapi-0.5.0/connectapi/tests/testthat/test-utils.R | 4 75 files changed, 842 insertions(+), 229 deletions(-)
Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of assets,
funds, and trading strategies, based on the Sharpe ratio and overfit
of the same. Provides density, distribution, quantile and random generation
of the Sharpe ratio distribution based on normal returns, as well
as the optimal Sharpe ratio over multiple assets. Computes confidence intervals
on the Sharpe and provides a test of equality of Sharpe ratios based on
the Delta method. The statistical foundations of the Sharpe can be found in
the author's Short Sharpe Course <doi:10.2139/ssrn.3036276>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between SharpeR versions 1.3.0 dated 2021-08-18 and 1.4.0 dated 2024-12-18
ChangeLog | 7 ++ DESCRIPTION | 15 ++-- MD5 | 90 ++++++++++++++------------- NAMESPACE | 9 ++ R/SharpeR.r | 15 +++- R/data.r | 8 -- R/distributions.r | 4 - R/estimation.r | 128 +++++++++++++++++++++++++++++++++++++-- R/overoptimism.r |only R/sr.r | 7 +- R/sr_bias.r | 8 -- R/tests.r | 4 - R/unified.r | 4 - R/utils.r | 15 +++- README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 21 +++--- inst/doc/AsymptoticMarkowitz.pdf |binary inst/doc/SharpeR.pdf |binary inst/doc/SharpeRatio.pdf |binary man/NEWS.Rd | 10 +++ man/SharpeR.Rd | 12 +++ man/as.sr.Rd | 2 man/as.sropt.Rd | 4 - man/asnr_confint.Rd |only man/confint.Rd | 6 - man/dsr.Rd | 2 man/dsropt.Rd | 4 - man/inference.Rd | 9 ++ man/is.sr.Rd | 2 man/is.sropt.Rd | 4 - man/pco_sropt.Rd | 4 - man/plambdap.Rd | 2 man/power.sr_test.Rd | 2 man/power.sropt_test.Rd | 4 - man/predint.Rd | 2 man/print.Rd | 2 man/reannualize.Rd | 6 - man/se.Rd | 4 - man/sr_conditional_test.Rd |only man/sr_equality_test.Rd | 2 man/sr_max_test.Rd |only man/sr_test.Rd | 2 man/sr_unpaired_test.Rd | 2 man/sr_vcov.Rd | 2 man/sric.Rd | 1 man/summary.Rd | 4 - 48 files changed, 307 insertions(+), 128 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 3.0.0 dated 2024-12-05 and 3.0.1 dated 2024-12-18
DESCRIPTION | 8 - MD5 | 28 ++--- NEWS.md | 19 +++ R/Internal_Utilities.R | 157 +++++++++++++++++----------- R/Object_Utilities.R | 10 - R/Plotting_Seurat.R | 4 R/Plotting_Seurat_Iterative.R | 188 +++++++++++++++++++++++++++------- man/Iterate_Cluster_Highlight_Plot.Rd | 8 + man/Iterate_DimPlot_bySample.Rd | 6 + man/Iterate_FeaturePlot_scCustom.Rd | 6 + man/Iterate_Meta_Highlight_Plot.Rd | 8 + man/Iterate_Plot_Density_Custom.Rd | 6 + man/Iterate_Plot_Density_Joint.Rd | 6 + man/Iterate_VlnPlot_scCustom.Rd | 6 + man/Random_Cells_Downsample.Rd | 4 15 files changed, 336 insertions(+), 128 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
,
Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.40.1 dated 2024-12-04 and 1.41.0 dated 2024-12-18
DESCRIPTION | 6 MD5 | 27 + NEWS.md | 26 + R/availableCores.R | 248 ++++++++++-------- R/availableWorkers.R | 412 +++++++++++++++++------------- R/launchNodePSOCK.R | 2 R/serializedSize.R | 2 R/utils,cluster.R | 8 inst/doc/parallelly-20-limit-workers.html | 39 ++ inst/doc/parallelly-20-limit-workers.md | 52 +++ man/availableCores.Rd | 11 man/serializedSize.Rd | 2 src/calc-serialized-size.c | 6 tests/utils,cluster.R |only vignettes/parallelly-20-limit-workers.md | 52 +++ 15 files changed, 584 insertions(+), 309 deletions(-)
Title: Creating Groups from Data
Description: Methods for dividing data into groups.
Create balanced partitions and cross-validation folds.
Perform time series windowing and general grouping and splitting of data.
Balance existing groups with up- and downsampling or collapse them to fewer groups.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between groupdata2 versions 2.0.3 dated 2023-06-18 and 2.0.5 dated 2024-12-18
groupdata2-2.0.3/groupdata2/build/groupdata2.pdf |only groupdata2-2.0.3/groupdata2/man/groupdata2.Rd |only groupdata2-2.0.5/groupdata2/DESCRIPTION | 13 groupdata2-2.0.5/groupdata2/MD5 | 60 groupdata2-2.0.5/groupdata2/NEWS.md | 8 groupdata2-2.0.5/groupdata2/R/all_groups_identical.R | 36 groupdata2-2.0.5/groupdata2/R/package_info.R | 4 groupdata2-2.0.5/groupdata2/R/table_of_content_markdown.R | 9 groupdata2-2.0.5/groupdata2/README.md | 4 groupdata2-2.0.5/groupdata2/build/stage23.rdb |only groupdata2-2.0.5/groupdata2/build/vignette.rds |binary groupdata2-2.0.5/groupdata2/inst/doc/automatic_groups_with_groupdata2.html | 142 +- groupdata2-2.0.5/groupdata2/inst/doc/cross-validation_with_groupdata2.html | 444 +++--- groupdata2-2.0.5/groupdata2/inst/doc/description_of_groupdata2.R | 10 groupdata2-2.0.5/groupdata2/inst/doc/description_of_groupdata2.html | 692 +++++----- groupdata2-2.0.5/groupdata2/inst/doc/introduction_to_groupdata2.html | 4 groupdata2-2.0.5/groupdata2/inst/doc/time_series_with_groupdata2.html | 164 +- groupdata2-2.0.5/groupdata2/man/all_groups_identical.Rd | 4 groupdata2-2.0.5/groupdata2/man/collapse_groups.Rd | 2 groupdata2-2.0.5/groupdata2/man/collapse_groups_by.Rd | 2 groupdata2-2.0.5/groupdata2/man/differs_from_previous.Rd | 4 groupdata2-2.0.5/groupdata2/man/find_missing_starts.Rd | 4 groupdata2-2.0.5/groupdata2/man/find_starts.Rd | 4 groupdata2-2.0.5/groupdata2/man/fold.Rd | 4 groupdata2-2.0.5/groupdata2/man/grapes-primes-grapes.Rd | 4 groupdata2-2.0.5/groupdata2/man/grapes-staircase-grapes.Rd | 4 groupdata2-2.0.5/groupdata2/man/group.Rd | 2 groupdata2-2.0.5/groupdata2/man/group_factor.Rd | 2 groupdata2-2.0.5/groupdata2/man/groupdata2-package.Rd |only groupdata2-2.0.5/groupdata2/man/partition.Rd | 4 groupdata2-2.0.5/groupdata2/man/render_toc.Rd | 10 groupdata2-2.0.5/groupdata2/man/splt.Rd | 4 groupdata2-2.0.5/groupdata2/tests/testthat/test_all_groups_identical.R | 21 33 files changed, 841 insertions(+), 824 deletions(-)
Title: Table Monster
Description: Provides a user friendly interface to
generation of booktab style tables using 'xtable'.
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between TableMonster versions 1.7 dated 2018-04-26 and 1.7.5 dated 2024-12-18
DESCRIPTION | 12 ++- MD5 | 16 +++- NAMESPACE | 5 - R/TableMonster.R | 166 +++++++++++++++++++++++++++++---------------------- man/basic.tmPrint.Rd |only man/concat.Rd |only man/tmCtypes.Rd | 4 - man/tmDisplay.Rd |only man/tmDisplayAssn.Rd |only man/tmTotals.Rd | 2 man/tmTotalsAssn.Rd | 2 11 files changed, 120 insertions(+), 87 deletions(-)
Title: Estimate Vapnik-Chervonenkis Dimension and Sample Complexity
Description: We provide a suite of tools for estimating the sample complexity of a chosen model through theoretical bounds and simulation. The package incorporates methods for estimating the Vapnik-Chervonenkis dimension (VCD) of a chosen algorithm, which can be used to estimate its sample complexity. Alternatively, we provide simulation methods to estimate sample complexity directly. For more details, see Carter, P & Choi, D (2024). "Learning from Noise: Applying Sample Complexity for Political Science Research" <doi:10.31219/osf.io/evrcj>.
Author: Perry Carter [aut, cre] ,
Dahyun Choi [aut]
Maintainer: Perry Carter <pjc504@nyu.edu>
Diff between scR versions 0.2.0 dated 2024-12-16 and 0.3.0 dated 2024-12-18
DESCRIPTION | 6 LICENSE | 4 MD5 | 22 - R/data.R | 22 - R/datagen.R | 106 ++++---- R/globals.R | 2 R/scR.R | 380 +++++++++++++++---------------- R/simulations.R | 644 +++++++++++++++++++++++++++-------------------------- man/acc_sim.Rd | 46 +-- man/br.Rd | 44 +-- man/loss.Rd | 60 ++-- man/risk_bounds.Rd | 38 +-- 12 files changed, 694 insertions(+), 680 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.18.0 dated 2024-11-24 and 2.19.0 dated 2024-12-18
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Extremal Dependence Models
Description: A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <doi:10.48550/arXiv.1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
Author: Boris Beranger [aut],
Simone Padoan [cre, aut],
Giulia Marcon [aut],
Steven G. Johnson [ctb] ,
Rudolf Schuerer [ctb] ,
Brian Gough [ctb] ,
Alec G. Stephenson [ctb],
Anne Sabourin [ctb] ,
Philippe Naveau [ctb]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremalDep versions 0.0.4-3 dated 2024-12-12 and 0.0.4-4 dated 2024-12-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/fExtDepSpat.R | 3 ++- R/plot_ExpDep.np.R | 2 ++ 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Tidy Prediction and Plotting of Generalised Additive Models
Description: Provides functions that compute predictions from Generalised
Additive Models (GAMs) fitted with 'mgcv' and return them as a tibble.
These can be plotted with a generic plot()-method that uses 'ggplot2' or
plotted as any other data frame. The main function is predict_gam().
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between tidygam versions 0.2.2 dated 2024-12-07 and 1.0.0 dated 2024-12-18
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 19 ++ R/predict.R | 29 --- README.md | 7 inst/doc/get-started.R | 24 ++ inst/doc/get-started.Rmd | 31 ++- inst/doc/get-started.html | 430 +++++++++++++++++++++++++--------------------- vignettes/get-started.Rmd | 31 ++- 9 files changed, 349 insertions(+), 246 deletions(-)
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph]
,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.6 dated 2024-12-14 and 0.1.6.1 dated 2024-12-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ cleanup | 4 ++-- inst/doc/my-vignette.html | 4 ++-- inst/include/sundials/sundials_config.h | 4 ++-- src/scripts/sundials_download.sh | 6 ++++++ tools/cmake_call.sh | 12 +++++++++++- 7 files changed, 33 insertions(+), 17 deletions(-)
Title: NASA POWER API Client
Description: An API client for NASA POWER global meteorology, surface
solar energy and climatology data API. POWER (Prediction Of Worldwide
Energy Resources) data are freely available for download with varying
spatial resolutions dependent on the original data and with several
temporal resolutions depending on the POWER parameter and community.
This work is funded through the NASA Earth Science Directorate Applied
Science Program. For more on the data themselves, the methodologies
used in creating, a web- based data viewer and web access, please see
<https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] ,
Scott Chamberlain [rev] ,
Hazel Kavili [rev] ,
Alison Boyer [rev] ,
Fernando Miguez [ctb] ,
Maelle Salmon [ctb] ,
Phillip D. Alderman [ctb] ` must use `I` for literal data as of
vroom 1.5.0.', see
<https://github.com/ropen [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between nasapower versions 4.2.1 dated 2024-05-17 and 4.2.2 dated 2024-12-18
DESCRIPTION | 10 MD5 | 72 - NEWS.md | 18 R/get_power.R | 521 +++++++------- R/internal_functions.R | 77 +- R/print_POWER_Info.R | 36 R/query_groupings.R | 10 R/query_parameters.R | 25 R/query_surfaces.R | 2 R/sysdata.rda |binary README.md | 386 ++++++++++ build/vignette.rds |binary inst/CITATION | 9 inst/WORDLIST | 1 inst/doc/nasapower.Rmd | 132 +-- inst/doc/nasapower.html | 201 ++--- man/get_power.Rd | 33 man/query_groupings.Rd | 2 man/query_parameters.Rd | 16 tests/fixtures/adjusted_air_pressure.json | 2 tests/fixtures/adjusted_wind_elevation.json | 2 tests/fixtures/climatology_ag_point.json | 2 tests/fixtures/daily_ag_point.json | 2 tests/fixtures/daily_sb_point_LST.json | 2 tests/fixtures/daily_sb_point_UTC.json | 2 tests/fixtures/query_groupings.json | 2 tests/fixtures/query_groupings_global.json | 2 tests/fixtures/query_parameters_comm&temporal_api.json | 2 tests/fixtures/query_surfaces_all.json | 2 tests/fixtures/query_surfaces_seaice.json | 2 tests/spelling.R | 11 tests/testthat/test-get_power.R | 329 ++++----- tests/testthat/test-internal_functions.R | 615 +++++++++-------- tests/testthat/test-query_groupings.R | 4 tests/testthat/test-query_parameters.R | 36 tests/testthat/test-query_surfaces.R | 7 vignettes/nasapower.Rmd | 132 +-- 37 files changed, 1649 insertions(+), 1058 deletions(-)
Title: Working with ISO8601 Dates and Times
Description: Functions to parse strings with ISO8601 dates, times, and
date-times into R-objects. Additionally, there are functions to determine
the type of ISO8601 string and to standardise ISO8601 strings.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between iso8601 versions 0.1.0 dated 2024-12-16 and 0.1.1 dated 2024-12-18
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS |only src/utils.cpp | 4 ++-- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Draw Network with Data
Description: Extends the 'ggplot2' plotting system to support network visualization. Inspired by the 'Method 1' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'ggtangle' is designed to work with network associated data.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggtangle versions 0.0.5 dated 2024-11-29 and 0.0.6 dated 2024-12-18
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/graph-layout.R |only R/graph.r | 3 ++- build/partial.rdb |only inst/doc/ggtangle.R | 6 +++--- inst/doc/ggtangle.Rmd | 6 +++--- inst/doc/ggtangle.html | 26 +++++++++++++------------- man/ggtangle-package.Rd | 2 +- vignettes/ggtangle.Rmd | 6 +++--- 12 files changed, 49 insertions(+), 38 deletions(-)
Title: Spatial Data Processing for Decision Making
Description: Methods for processing spatial data for decision-making.
This package is an R implementation of methods provided by the open source software GeoFIS <https://www.geofis.org> (Leroux et al. 2018) <doi:10.3390/agriculture8060073>.
The main functionalities are the management zone delineation (Pedroso et al. 2010) <doi:10.1016/j.compag.2009.10.007> and data aggregation (Mora-Herrera et al. 2020) <doi:10.1016/j.compag.2020.105624>.
Author: Serge Guillaume [aut],
Jean-Luc Lablee [aut, cre],
INRAE [cph]
Maintainer: Jean-Luc Lablee <jean-luc.lablee@inrae.fr>
Diff between GeoFIS versions 1.1.0 dated 2024-09-03 and 1.1.1 dated 2024-12-18
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 52 ++++++++++++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/data-fusion.html | 2 - src/Makevars | 2 - src/util/address_equal.hpp | 13 +---------- 8 files changed, 42 insertions(+), 47 deletions(-)
Title: Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and
Destruction Rate Modelling
Description: Distributions that are typically used for exposure rating in
general insurance, in particular to price reinsurance contracts.
The vignette shows code snippets to fit the distribution to
empirical data. See, e.g., Bernegger (1997) <doi:10.2143/AST.27.1.563208>
freely available on-line.
Author: Christophe Dutang [aut, cre] ,
Giorgio Spedicato [aut] ,
Markus Gesmann [ctb]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between mbbefd versions 0.8.12 dated 2024-10-17 and 0.8.13 dated 2024-12-18
mbbefd-0.8.12/mbbefd/NEWS |only mbbefd-0.8.12/mbbefd/tests/check-formula-integral.R |only mbbefd-0.8.12/mbbefd/tests/check-formula-variance.R |only mbbefd-0.8.12/mbbefd/tests/test-mbbefd-1stparam.R |only mbbefd-0.8.12/mbbefd/tests/test-mbbefd-2ndparam.R |only mbbefd-0.8.13/mbbefd/DESCRIPTION | 6 mbbefd-0.8.13/mbbefd/MD5 | 29 +--- mbbefd-0.8.13/mbbefd/NAMESPACE | 12 - mbbefd-0.8.13/mbbefd/R/fitDR-output.R | 76 +++++++----- mbbefd-0.8.13/mbbefd/R/fitDR.R | 95 +++++++-------- mbbefd-0.8.13/mbbefd/R/util-loglikfunc.R | 41 +++++- mbbefd-0.8.13/mbbefd/README.md | 39 +++--- mbbefd-0.8.13/mbbefd/build/partial.rdb |binary mbbefd-0.8.13/mbbefd/build/vignette.rds |binary mbbefd-0.8.13/mbbefd/inst/NEWS.Rd | 36 +++-- mbbefd-0.8.13/mbbefd/inst/doc/Introduction_to_mbbefd.pdf |binary mbbefd-0.8.13/mbbefd/tests/test-fit-MBBEFDgb.R | 10 + mbbefd-0.8.13/mbbefd/tests/test-fit-mbbefd.R | 9 + 18 files changed, 218 insertions(+), 135 deletions(-)
Title: Simple Automatic Differentiation
Description: Handles both vector and matrices, using a flexible S4 class for automatic differentiation.
The method used is forward automatic differentiation. Many functions and methods have been defined,
so that in most cases, functions written without automatic differentiation in mind can be
used without change.
Author: Herve Perdry [aut, cre]
Maintainer: Herve Perdry <herve.perdry@universite-paris-saclay.fr>
Diff between salad versions 1.1 dated 2024-11-04 and 1.2 dated 2024-12-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/dual-math.r | 2 +- build/vignette.rds |binary inst/doc/salad.html | 6 +++--- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Compress local and online images using the 'reSmush.it' API
service <https://resmush.it/>.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 0.2.0 dated 2024-07-19 and 0.2.1 dated 2024-12-18
DESCRIPTION | 8 - MD5 | 16 +-- NEWS.md | 4 R/resmush_clean_dir.R | 2 R/sysdata.rda |binary R/utils.R | 210 +++++++++++++++++++++++++------------------------- README.md | 20 ++-- build/vignette.rds |binary inst/schemaorg.json | 4 9 files changed, 135 insertions(+), 129 deletions(-)
Title: Get Executing Script's Path
Description: Determine the path of the executing script. Compatible
with several popular GUIs: 'Rgui', 'RStudio', 'Positron',
'VSCode', 'Jupyter', 'Emacs', and 'Rscript' (shell). Compatible
with several functions and packages: 'source()',
'sys.source()', 'debugSource()' in 'RStudio',
'compiler::loadcmp()', 'utils::Sweave()', 'box::use()',
'knitr::knit()', 'plumber::plumb()', 'shiny::runApp()',
'package:targets', and 'testthat::source_file()'.
Author: Iris Simmons [aut, cre]
Maintainer: Iris Simmons <ikwsimmo@gmail.com>
Diff between this.path versions 2.5.0 dated 2024-06-29 and 2.6.0 dated 2024-12-18
this.path-2.5.0/this.path/R/pathfuns.R |only this.path-2.5.0/this.path/man/path.functions.Rd |only this.path-2.6.0/this.path/DESCRIPTION | 30 this.path-2.6.0/this.path/MD5 | 117 +- this.path-2.6.0/this.path/NAMESPACE | 30 this.path-2.6.0/this.path/NEWS | 29 this.path-2.6.0/this.path/R/backports.R | 4 this.path-2.6.0/this.path/R/defunct.R | 41 - this.path-2.6.0/this.path/R/enhances.R | 87 +- this.path-2.6.0/this.path/R/error.R | 34 this.path-2.6.0/this.path/R/files.R | 56 - this.path-2.6.0/this.path/R/lineno.R | 6 this.path-2.6.0/this.path/R/make_fix_funs.R |only this.path-2.6.0/this.path/R/promises.R | 40 - this.path-2.6.0/this.path/R/relpath.R | 34 this.path-2.6.0/this.path/R/rprojroot.R | 2 this.path-2.6.0/this.path/R/thispath.R | 554 ++++++++------ this.path-2.6.0/this.path/R/utils.R | 8 this.path-2.6.0/this.path/R/zzz.R | 45 - this.path-2.6.0/this.path/README.md | 113 +- this.path-2.6.0/this.path/build/stage23.rdb |binary this.path-2.6.0/this.path/build/this.path.pdf |binary this.path-2.6.0/this.path/inst/NEWS.in.Rd | 36 this.path-2.6.0/this.path/man/Enhances.Rd | 11 this.path-2.6.0/this.path/man/check.path.Rd | 6 this.path-2.6.0/this.path/man/ext.Rd | 4 this.path-2.6.0/this.path/man/macros/macros.Rd | 5 this.path-2.6.0/this.path/man/make_fix_funs.Rd |only this.path-2.6.0/this.path/man/set.gui.path.Rd | 14 this.path-2.6.0/this.path/man/set.sys.path.Rd | 10 this.path-2.6.0/this.path/man/this.path-package.Rd | 10 this.path-2.6.0/this.path/man/this.path.Rd | 31 this.path-2.6.0/this.path/src/0.c | 8 this.path-2.6.0/this.path/src/backports.c | 3 this.path-2.6.0/this.path/src/backports.h | 13 this.path-2.6.0/this.path/src/devel.h | 15 this.path-2.6.0/this.path/src/error.c | 359 +++++++-- this.path-2.6.0/this.path/src/error.h | 47 - this.path-2.6.0/this.path/src/files.c | 99 ++ this.path-2.6.0/this.path/src/ns-hooks.c | 174 +++- this.path-2.6.0/this.path/src/ns-hooks.h | 6 this.path-2.6.0/this.path/src/pathjoin.c | 8 this.path-2.6.0/this.path/src/pathsplit.c | 19 this.path-2.6.0/this.path/src/print.c | 41 - this.path-2.6.0/this.path/src/progargs.c | 5 this.path-2.6.0/this.path/src/promises.c | 10 this.path-2.6.0/this.path/src/rgui_path.c | 20 this.path-2.6.0/this.path/src/setsyspath.c | 6 this.path-2.6.0/this.path/src/startup.c | 3 this.path-2.6.0/this.path/src/symbols.h | 3 this.path-2.6.0/this.path/src/this.path.h | 6 this.path-2.6.0/this.path/src/thispath.c | 197 ++-- this.path-2.6.0/this.path/src/thispathdefn.c | 44 - this.path-2.6.0/this.path/src/thispathdefn.h | 65 - this.path-2.6.0/this.path/src/utils.c | 102 ++ this.path-2.6.0/this.path/tests/ext-tests.R | 8 this.path-2.6.0/this.path/tests/faster-subsequent-times.R | 2 this.path-2.6.0/this.path/tests/package-box-supp |only this.path-2.6.0/this.path/tests/package-box-tests.R |only this.path-2.6.0/this.path/tools/configure.R | 13 this.path-2.6.0/this.path/tools/this_path_reg_ptrs.c | 10 61 files changed, 1756 insertions(+), 887 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.2.1 dated 2024-06-05 and 1.3.0 dated 2024-12-18
DESCRIPTION | 8 MD5 | 84 +-- NAMESPACE | 1 NEWS.md | 13 R/A_nhdplusTools.R | 16 R/arcrest_tools.R | 11 R/discover_nhdplus.R | 15 R/downloading_tools.R | 15 R/geoserver_tools.R | 2 R/get_hydro.R | 7 R/get_nhdplushr.R | 689 ++++++++++++++-------------- R/get_nldi.R | 49 + R/get_oaproc.R | 56 ++ R/plot_nhdplus.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/get_3dhp_data.html | 24 inst/doc/get_data_overview.Rmd | 686 +++++++++++++-------------- inst/doc/get_data_overview.html | 57 +- inst/doc/indexing.html | 18 inst/doc/nhdplusTools.Rmd | 2 inst/doc/nhdplusTools.html | 150 +++--- inst/doc/nhdplushr.html | 18 inst/doc/plot_nhdplus.html | 60 +- inst/extdata/sample_data.R | 18 man/discover_nldi_characteristics.Rd | 11 man/download_nhdplushr.Rd | 10 man/get_3dhp.Rd | 6 man/get_huc.Rd | 2 man/get_nldi_characteristics.Rd | 14 man/get_split_catchment.Rd | 16 man/query_usgs_arcrest.Rd | 6 tests/testthat/helper.R | 11 tests/testthat/test_00_plot_local_nhdplus.R | 2 tests/testthat/test_00_plot_nhdplus.R | 434 ++++++++--------- tests/testthat/test_01_get_nldi.R | 641 +++++++++++++------------- tests/testthat/test_02_subset_extras.R | 6 tests/testthat/test_03_get_functions.R | 544 +++++++++++----------- tests/testthat/test_get_nhdplushr.R | 416 +++++++++------- tests/testthat/test_get_vaa.R | 7 tests/testthat/test_rescale_catchments.R | 12 vignettes/get_data_overview.Rmd | 686 +++++++++++++-------------- vignettes/nhdplusTools.Rmd | 2 43 files changed, 2548 insertions(+), 2281 deletions(-)
Title: Analyse Eye Data
Description: Enables the automation of actions across the pipeline, including
initial steps of transforming binocular data and gap repair to event-based
processing such as fixations, saccades, and entry/duration in Areas of
Interest (AOIs). It also offers visualisation of eye movement and AOI
entries. These tools take relatively raw (trial, time, x, and y form) data
and can be used to return fixations, saccades, and AOI entries and time spent
in AOIs. As the tools rely on this basic data format, the functions can work
with data from any eye tracking device. Implements fixation and saccade
detection using methods proposed by Salvucci and Goldberg (2000)
<doi:10.1145/355017.355028>.
Author: Tom Beesley [aut, cre],
Matthew Ivory [aut]
Maintainer: Tom Beesley <t.beesley@lancaster.ac.uk>
Diff between eyetools versions 0.7.2 dated 2024-10-28 and 0.8.0 dated 2024-12-18
eyetools-0.7.2/eyetools/R/hdf5_to_csv.R |only eyetools-0.7.2/eyetools/man/figures/unnamed-chunk-23-1.png |only eyetools-0.7.2/eyetools/man/figures/unnamed-chunk-24-1.png |only eyetools-0.7.2/eyetools/man/figures/unnamed-chunk-24-2.png |only eyetools-0.7.2/eyetools/man/figures/unnamed-chunk-26-3.png |only eyetools-0.7.2/eyetools/man/hdf5_to_csv.Rd |only eyetools-0.8.0/eyetools/DESCRIPTION | 22 eyetools-0.8.0/eyetools/MD5 | 88 + eyetools-0.8.0/eyetools/NAMESPACE | 10 eyetools-0.8.0/eyetools/NEWS.md | 25 eyetools-0.8.0/eyetools/R/AOI_seq.R | 135 +-- eyetools-0.8.0/eyetools/R/AOI_time.R | 25 eyetools-0.8.0/eyetools/R/AOI_time_binned.R |only eyetools-0.8.0/eyetools/R/check_ppt_n.R | 3 eyetools-0.8.0/eyetools/R/create_AOI_df.R |only eyetools-0.8.0/eyetools/R/estimate_sample_rate.R |only eyetools-0.8.0/eyetools/R/fixation_VTI.R | 13 eyetools-0.8.0/eyetools/R/fixation_dispersion.R | 20 eyetools-0.8.0/eyetools/R/hdf5_get_event.R |only eyetools-0.8.0/eyetools/R/hdf5_to_df.R |only eyetools-0.8.0/eyetools/R/interpolate.R | 43 eyetools-0.8.0/eyetools/R/plot_AOI_growth.R |only eyetools-0.8.0/eyetools/R/plot_heatmap.R |only eyetools-0.8.0/eyetools/R/plot_seq.R | 81 + eyetools-0.8.0/eyetools/R/plot_spatial.R | 84 + eyetools-0.8.0/eyetools/R/saccade_VTI.R | 9 eyetools-0.8.0/eyetools/R/smoother.R | 9 eyetools-0.8.0/eyetools/README.md | 41 eyetools-0.8.0/eyetools/data/HCL_AOIs.rda |binary eyetools-0.8.0/eyetools/inst/doc/eyetools.R | 52 - eyetools-0.8.0/eyetools/inst/doc/eyetools.Rmd | 79 + eyetools-0.8.0/eyetools/inst/doc/eyetools.html | 573 ++++++++----- eyetools-0.8.0/eyetools/man/AOI_seq.Rd | 17 eyetools-0.8.0/eyetools/man/AOI_time.Rd | 5 eyetools-0.8.0/eyetools/man/AOI_time_binned.Rd |only eyetools-0.8.0/eyetools/man/create_AOI_df.Rd |only eyetools-0.8.0/eyetools/man/eyetools-package.Rd | 4 eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-10-1.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-18-1.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-25-1.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-26-1.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-26-2.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-27-1.png |binary eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-28-1.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-28-2.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-28-3.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-29-1.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-30-1.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-30-2.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-30-3.png |only eyetools-0.8.0/eyetools/man/figures/unnamed-chunk-9-1.png |binary eyetools-0.8.0/eyetools/man/hdf5_get_event.Rd |only eyetools-0.8.0/eyetools/man/hdf5_to_df.Rd |only eyetools-0.8.0/eyetools/man/interpolate.Rd | 9 eyetools-0.8.0/eyetools/man/plot_AOI_growth.Rd |only eyetools-0.8.0/eyetools/man/plot_heatmap.Rd |only eyetools-0.8.0/eyetools/man/plot_spatial.Rd | 2 eyetools-0.8.0/eyetools/vignettes/eyetools.Rmd | 79 + 58 files changed, 879 insertions(+), 549 deletions(-)
Title: Degrees of Freedom Adjustment for Robust Standard Errors
Description: Computes small-sample degrees of freedom adjustment for
heteroskedasticity robust standard errors, and for clustered standard errors
in linear regression. See Imbens and Kolesár (2016)
<doi:10.1162/REST_a_00552> for a discussion of these adjustments.
Author: Michal Kolesar [aut, cre, cph]
,
Kranz Sebastian [ctb]
Maintainer: Michal Kolesar <kolesarmi@googlemail.com>
Diff between dfadjust versions 1.0.5 dated 2023-10-04 and 1.1.0 dated 2024-12-18
DESCRIPTION | 25 ++++--- MD5 | 26 +++---- NEWS.md | 12 +++ R/ols.R | 76 ++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/dfadjust.R | 6 - inst/doc/dfadjust.Rmd | 6 - inst/doc/dfadjust.pdf |binary man/dfadjustSE.Rd | 20 +++--- tests/testthat/test-hc2-check.R | 129 ++++++++++++++++++++++----------------- tests/testthat/test_clustervar.R | 47 ++++++++++++++ vignettes/dfadjust.Rmd | 6 - 14 files changed, 230 insertions(+), 124 deletions(-)
Title: Add Inset Panels to Maps
Description: Helper to add insets based on geom_sf() from 'ggplot2'.
This package gives you a drop-in replacement for geom_sf() that supports
adding a zoomed inset map without having to create and embed a separate plot.
Author: Carl Suster [aut, cre] ,
Western Sydney Local Health District, NSW Health [cph]
Maintainer: Carl Suster <Carl.Suster@health.nsw.gov.au>
Diff between ggmapinset versions 0.3.0 dated 2023-04-28 and 0.4.0 dated 2024-12-18
DESCRIPTION | 15 +- LICENSE | 2 MD5 | 62 +++++---- NAMESPACE | 19 ++ NEWS.md | 9 + R/configure_inset.R | 174 +++++++++++++++----------- R/data.R |only R/geom_inset_frame.R | 154 +++++++++-------------- R/geom_sf_inset.R | 87 ++++++++----- R/geom_sf_text_inset.R | 56 ++++---- R/ggmapinset-package.R | 1 R/inset.R | 28 ++-- R/inset_shape_circle.R |only R/inset_shape_rectangle.R |only R/inset_shape_sf.R |only R/layer_helpers.R | 53 ++++---- R/stat_sf_coordinates_inset.R | 45 +++--- R/stat_sf_inset.R | 22 --- R/transform_to_inset.R | 6 README.md | 83 ++++++++++-- build/vignette.rds |binary data |only inst/COPYRIGHTS |only inst/doc/ggmapinset.R | 143 +++++++++++++++++++-- inst/doc/ggmapinset.Rmd | 186 ++++++++++++++++++++++++++-- inst/doc/ggmapinset.html | 256 ++++++++++++++++++++++++++++++++------- man/build_sf_inset_layers.Rd | 83 +++--------- man/configure_inset.Rd | 36 ++--- man/figures/README-example-1.png |binary man/geom_inset_frame.Rd | 25 +++ man/geom_sf_inset.Rd | 65 +-------- man/mozzies_nsw2301.Rd |only man/shape_circle.Rd |only man/shape_rectangle.Rd |only man/shape_sf.Rd |only man/stat_sf_coordinates_inset.Rd | 66 +++++++--- vignettes/ggmapinset.Rmd | 186 ++++++++++++++++++++++++++-- 37 files changed, 1283 insertions(+), 579 deletions(-)
Title: Explore and Import 'Metopio' Health Atlas Data and Spatial
Layers
Description: Allows for painless use of the 'Metopio' health atlas APIs
<https://metopio.com/how-it-works/atlas/> to explore and import data.
'Metopio' health atlases store open public health data. See what topics
(or indicators) are available among specific populations, periods, and
geographic layers. Download relevant data along with geographic
boundaries or point datasets. Spatial datasets are returned as 'sf'
objects.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between healthatlas versions 0.1.0 dated 2024-09-13 and 0.1.1 dated 2024-12-17
DESCRIPTION | 10 MD5 | 51 ++-- NEWS.md | 9 R/ha_coverage.R | 43 +--- R/ha_data.R | 94 +++----- R/ha_getset.R | 3 R/ha_layer.R | 44 +--- R/ha_point_layer.R | 53 +--- R/ha_stratifications.R | 13 - R/ha_subcategories.R | 20 - R/ha_topics.R | 30 +- R/helpers.R | 55 +++-- README.md | 79 ++++--- inst/doc/typical_usage.R | 41 +++ inst/doc/typical_usage.Rmd | 71 +++++- inst/doc/typical_usage.html | 333 ++++++++++++++++++++++--------- man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |only man/ha_data.Rd | 15 - tests/testthat/helpers.R | 2 tests/testthat/test-ha_coverage.R | 12 - tests/testthat/test-ha_data.R | 43 ---- tests/testthat/test-ha_layer.R | 8 tests/testthat/test-ha_point_layer.R | 8 tests/testthat/test-ha_subcategories.R | 4 tests/testthat/test-ha_topics.R | 8 vignettes/typical_usage.Rmd | 71 +++++- 27 files changed, 647 insertions(+), 473 deletions(-)
Title: Extracts Phylogenetic Island Community Data from Phylogenetic
Trees
Description: Extracts colonisation and branching times of island
species to be used for analysis in the R package 'DAISIE'. It uses
phylogenetic and endemicity data to extract the separate island colonists
and store them.
Author: Joshua W. Lambert [aut, cre] ,
Luis Valente [aut] ,
Pedro Santos Neves [aut] ,
Lizzie Roeble [aut] ,
Theo Pannetier [aut]
Maintainer: Joshua W. Lambert <j.w.l.lambert@rug.nl>
Diff between DAISIEprep versions 0.4.0 dated 2024-04-02 and 1.0.0 dated 2024-12-17
DAISIEprep-0.4.0/DAISIEprep/inst/extdata/coccyzus_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/columbiformes_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/finches_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/mimus_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/myiarchus_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/progne_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/pyrocephalus_phylod.rds |only DAISIEprep-0.4.0/DAISIEprep/inst/extdata/setophaga_phylod.rds |only DAISIEprep-1.0.0/DAISIEprep/DESCRIPTION | 17 DAISIEprep-1.0.0/DAISIEprep/MD5 | 108 - DAISIEprep-1.0.0/DAISIEprep/NEWS.md | 65 DAISIEprep-1.0.0/DAISIEprep/R/add_asr_node_states.R | 9 DAISIEprep-1.0.0/DAISIEprep/R/add_island_colonist.R | 33 DAISIEprep-1.0.0/DAISIEprep/R/create_endemicity_status.R | 17 DAISIEprep-1.0.0/DAISIEprep/R/data.R |only DAISIEprep-1.0.0/DAISIEprep/R/default_params_doc.R | 34 DAISIEprep-1.0.0/DAISIEprep/R/extract_island_species.R | 51 DAISIEprep-1.0.0/DAISIEprep/R/extract_multi_tip_species.R | 2 DAISIEprep-1.0.0/DAISIEprep/R/extract_nonendemic.R | 24 DAISIEprep-1.0.0/DAISIEprep/R/is_multi_tip_species.R | 23 DAISIEprep-1.0.0/DAISIEprep/R/plot_phylod.R | 15 DAISIEprep-1.0.0/DAISIEprep/R/rm_duplicate_island_species.R |only DAISIEprep-1.0.0/DAISIEprep/R/rm_nonendemic_in_clade.R |only DAISIEprep-1.0.0/DAISIEprep/README.md | 2 DAISIEprep-1.0.0/DAISIEprep/build/vignette.rds |binary DAISIEprep-1.0.0/DAISIEprep/data |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Forcing_nonendemic_singleton.R |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Forcing_nonendemic_singleton.Rmd |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Forcing_nonendemic_singleton.html |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Multi_tip_extraction.R |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Multi_tip_extraction.Rmd |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Multi_tip_extraction.html |only DAISIEprep-1.0.0/DAISIEprep/inst/doc/Performance.html | 5 DAISIEprep-1.0.0/DAISIEprep/inst/doc/Sensitivity.html | 5 DAISIEprep-1.0.0/DAISIEprep/inst/doc/Tutorial.R | 109 - DAISIEprep-1.0.0/DAISIEprep/inst/doc/Tutorial.Rmd | 570 +---- DAISIEprep-1.0.0/DAISIEprep/inst/doc/Tutorial.html | 984 +++++----- DAISIEprep-1.0.0/DAISIEprep/inst/extdata/plant_phylo.rds |only DAISIEprep-1.0.0/DAISIEprep/man/GalapagosTrees.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/add_asr_node_states.Rd | 8 DAISIEprep-1.0.0/DAISIEprep/man/coccyzus_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/columbiformes_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/create_endemicity_status.Rd | 5 DAISIEprep-1.0.0/DAISIEprep/man/default_params_doc.Rd | 35 DAISIEprep-1.0.0/DAISIEprep/man/extract_island_species.Rd | 27 DAISIEprep-1.0.0/DAISIEprep/man/extract_nonendemic_forced.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/finches_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/is_multi_tip_species.Rd | 19 DAISIEprep-1.0.0/DAISIEprep/man/mimus_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/myiarchus_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/plant_phylo.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/progne_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/pyrocephalus_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/rm_duplicate_island_species.Rd |only DAISIEprep-1.0.0/DAISIEprep/man/setophaga_phylod.Rd |only DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-add_asr_node_states.R | 11 DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-as_daisie_datatable.R | 4 DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-bind_colonist_to_tbl.R | 4 DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-create_endemicity_status.R | 21 DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-extract_multi_tip_species.R | 12 DAISIEprep-1.0.0/DAISIEprep/tests/testthat/test-rm_duplicate_island_species.R |only DAISIEprep-1.0.0/DAISIEprep/vignettes/Forcing_nonendemic_singleton.Rmd |only DAISIEprep-1.0.0/DAISIEprep/vignettes/Multi_tip_extraction.Rmd |only DAISIEprep-1.0.0/DAISIEprep/vignettes/Tutorial.Rmd | 570 +---- 64 files changed, 1367 insertions(+), 1422 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between pillar versions 1.9.0 dated 2023-03-22 and 1.10.0 dated 2024-12-17
pillar-1.10.0/pillar/DESCRIPTION | 12 pillar-1.10.0/pillar/MD5 | 128 pillar-1.10.0/pillar/NAMESPACE | 9 pillar-1.10.0/pillar/NEWS.md | 31 pillar-1.10.0/pillar/R/ctl_new_pillar.R | 2 pillar-1.10.0/pillar/R/ctl_new_pillar_list.R | 2 pillar-1.10.0/pillar/R/extent.R | 8 pillar-1.10.0/pillar/R/ggplot2.R | 18 pillar-1.10.0/pillar/R/glimpse.R | 15 pillar-1.10.0/pillar/R/num.R | 2 pillar-1.10.0/pillar/R/options.R | 7 pillar-1.10.0/pillar/R/pillar-package.R | 2 pillar-1.10.0/pillar/R/pillar.R | 2 pillar-1.10.0/pillar/R/shaft-.R | 8 pillar-1.10.0/pillar/R/styles.R | 9 pillar-1.10.0/pillar/R/tbl-format-body.R | 2 pillar-1.10.0/pillar/R/tbl-format-footer.R | 4 pillar-1.10.0/pillar/R/tbl-format-header.R | 2 pillar-1.10.0/pillar/R/tbl-format-setup.R | 112 pillar-1.10.0/pillar/R/tbl-format.R | 79 pillar-1.10.0/pillar/R/type.R | 5 pillar-1.10.0/pillar/R/utils.R | 22 pillar-1.10.0/pillar/R/vctr.R | 2 pillar-1.10.0/pillar/R/zzz.R | 9 pillar-1.10.0/pillar/README.md | 175 pillar-1.10.0/pillar/build/vignette.rds |binary pillar-1.10.0/pillar/inst/doc/debugme.R | 16 pillar-1.10.0/pillar/inst/doc/debugme.html | 18 pillar-1.10.0/pillar/inst/doc/extending.R | 2 pillar-1.10.0/pillar/inst/doc/extending.html | 458 - pillar-1.10.0/pillar/inst/doc/numbers.R | 148 pillar-1.10.0/pillar/inst/doc/printing.R | 356 - pillar-1.10.0/pillar/inst/doc/printing.Rmd | 1 pillar-1.10.0/pillar/inst/doc/printing.html | 3050 ---------- pillar-1.10.0/pillar/man/ctl_new_pillar.Rd | 2 pillar-1.10.0/pillar/man/ctl_new_pillar_list.Rd | 2 pillar-1.10.0/pillar/man/glimpse.Rd | 2 pillar-1.10.0/pillar/man/new_tbl_format_setup.Rd | 26 pillar-1.10.0/pillar/man/pillar-package.Rd | 2 pillar-1.10.0/pillar/man/pillar_options.Rd | 6 pillar-1.10.0/pillar/man/scale_x_num.Rd | 23 pillar-1.10.0/pillar/man/tbl_format_body.Rd | 2 pillar-1.10.0/pillar/man/tbl_format_footer.Rd | 2 pillar-1.10.0/pillar/man/tbl_format_header.Rd | 2 pillar-1.10.0/pillar/man/tbl_format_setup.Rd | 30 pillar-1.10.0/pillar/man/tbl_nrow.Rd |only pillar-1.10.0/pillar/tests/testthat/_snaps/ggplot2/basic.svg | 20 pillar-1.10.0/pillar/tests/testthat/_snaps/ggplot2/log-scale.svg | 84 pillar-1.10.0/pillar/tests/testthat/_snaps/glimpse.md | 69 pillar-1.10.0/pillar/tests/testthat/_snaps/num.md | 5 pillar-1.10.0/pillar/tests/testthat/_snaps/shaft-.md | 9 pillar-1.10.0/pillar/tests/testthat/_snaps/tbl-format-setup.md | 6 pillar-1.10.0/pillar/tests/testthat/test-ggplot2.R | 4 pillar-1.10.0/pillar/tests/testthat/test-glimpse.R | 22 pillar-1.10.0/pillar/tests/testthat/test-num.R | 3 pillar-1.10.0/pillar/tests/testthat/test-shaft-.R | 7 pillar-1.10.0/pillar/vignettes/printing.Rmd | 1 pillar-1.9.0/pillar/tests/testthat/_snaps/ansi/format_multi.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/format_multi.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/format_multi_fuzz.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/format_multi_fuzz_2.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2-ansi |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2-unicode |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2/format_multi.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2/format_multi_fuzz.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2/format_multi_fuzz_2.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.2/zzx-format_character.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.3-unicode |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.3/format_multi.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.3/format_multi_fuzz.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.3/format_multi_fuzz_2.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/testthat_3.1.3/zzx-format_character.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/unicode/format_multi.md |only pillar-1.9.0/pillar/tests/testthat/_snaps/zzx-format_character.md |only 74 files changed, 1350 insertions(+), 3695 deletions(-)
Title: Phase Error Correction and Baseline Correction for One
Dimensional ('1D') 'NMR' Data
Description: There are three distinct approaches for phase error correction, they are: a single linear model with a choice of optimization functions, multiple linear models with optimization function choices and a shrinkage-based method. The methodology is based on our new algorithms and various references (Binczyk et al. (2015) <doi:10.1186/1475-925X-14-S2-S5>,Chen et al. (2002) <doi:10.1016/S1090-7807(02)00069-1>, de Brouwer (2009) <doi:10.1016/j.jmr.2009.09.017>, Džakula (2000) <doi:10.1006/jmre.2000.2123>, Ernst (1969) <doi:10.1016/0022-2364(69)90003-1>, Liland et al. (2010) <doi:10.1366/000370210792434350>).
Author: Aixiang Jiang [aut, cre, cph]
Maintainer: Aixiang Jiang <aijiang@bccrc.ca>
Diff between NMRphasing versions 1.0.5 dated 2024-10-12 and 1.0.6 dated 2024-12-17
DESCRIPTION | 14 MD5 | 21 NAMESPACE | 8 R/findLocalMaxWinSizeR.R |only R/getLocalMaximumCWTR.R |only R/localMaximumR.R |only R/localMaximumSlidingWindowR.R |only R/peakDetectionCWTR.R |only R/peakSearch.R | 5 build/vignette.rds |binary inst/doc/NMRphasing_vignette.R | 30 - inst/doc/NMRphasing_vignette.html | 860 ++++++++++++++++++++------------------ inst/doc/NMRphasing_vignette.rmd | 32 - vignettes/NMRphasing_vignette.rmd | 32 - 14 files changed, 541 insertions(+), 461 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace
Approximation, Monte Carlo Expectation Maximization, and some other tools.
The nimbleFunction system makes it easy to do things like implement new MCMC
samplers from R, customize the assignment of samplers to different parts of
a model from R, and compile the new samplers automatically via C++ alongside
the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language
by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think
of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models,
one can use 'NIMBLE' for writing arbitrary other kinds of model-generic
algorithms as well. A full User Manual [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodriguez [aut] ,
Duncan Temple Lang [aut] ,
Wei Zhang [aut] ,
[...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 1.2.1 dated 2024-07-30 and 1.3.0 dated 2024-12-17
nimble-1.2.1/nimble/man/model_macro_builder.Rd |only nimble-1.3.0/nimble/DESCRIPTION | 12 nimble-1.3.0/nimble/INSTALL | 6 nimble-1.3.0/nimble/MD5 | 120 nimble-1.3.0/nimble/NAMESPACE | 7 nimble-1.3.0/nimble/R/BNP_samplers.R | 36 nimble-1.3.0/nimble/R/BUGS_BUGSdecl.R | 8 nimble-1.3.0/nimble/R/BUGS_macros.R | 59 nimble-1.3.0/nimble/R/BUGS_modelDef.R | 31 nimble-1.3.0/nimble/R/BUGS_readBUGS.R | 2 nimble-1.3.0/nimble/R/Laplace.R | 836 ++--- nimble-1.3.0/nimble/R/MCMC_configuration.R | 14 nimble-1.3.0/nimble/R/MCMC_run.R | 8 nimble-1.3.0/nimble/R/MCMC_samplers.R | 429 ++ nimble-1.3.0/nimble/R/MCMC_utils.R | 86 nimble-1.3.0/nimble/R/RCfunction_core.R | 6 nimble-1.3.0/nimble/R/distributions_processInputList.R | 9 nimble-1.3.0/nimble/R/externalCalls.R | 2 nimble-1.3.0/nimble/R/genCpp_exprClass.R | 2 nimble-1.3.0/nimble/R/genCpp_sizeProcessing.R | 23 nimble-1.3.0/nimble/R/genCpp_toEigenize.R | 6 nimble-1.3.0/nimble/R/nimbleFunction_Rderivs.R | 2 nimble-1.3.0/nimble/R/nimbleFunction_Rexecution.R | 51 nimble-1.3.0/nimble/R/nimbleFunction_compile.R | 9 nimble-1.3.0/nimble/R/nimbleList_core.R | 6 nimble-1.3.0/nimble/R/options.R | 26 nimble-1.3.0/nimble/R/types_util.R | 8 nimble-1.3.0/nimble/inst/CppCode/Utils.cpp | 6 nimble-1.3.0/nimble/inst/CppCode/predefinedNimbleLists.cpp | 55 nimble-1.3.0/nimble/inst/NEWS.md | 76 nimble-1.3.0/nimble/inst/include/nimble/Utils.h | 5 nimble-1.3.0/nimble/inst/include/nimble/nimOptim.h | 2 nimble-1.3.0/nimble/inst/include/nimble/predefinedNimbleLists.h | 6 nimble-1.3.0/nimble/man/buildMacro.Rd |only nimble-1.3.0/nimble/man/deregisterDistributions.Rd | 8 nimble-1.3.0/nimble/man/getMacroParameters.Rd | 2 nimble-1.3.0/nimble/man/laplace.Rd | 75 nimble-1.3.0/nimble/man/nimDerivs.Rd | 2 nimble-1.3.0/nimble/man/nimOptim.Rd | 28 nimble-1.3.0/nimble/man/nimble-internal.Rd | 17 nimble-1.3.0/nimble/man/runLaplace.Rd | 5 nimble-1.3.0/nimble/man/runMCMC.Rd | 2 nimble-1.3.0/nimble/man/samplers.Rd | 57 nimble-1.3.0/nimble/man/summaryLaplace.Rd | 10 nimble-1.3.0/nimble/tests/testthat/Makevars |only nimble-1.3.0/nimble/tests/testthat/barkerTestLog.Rout |only nimble-1.3.0/nimble/tests/testthat/barkerTestLog_Correct.Rout |only nimble-1.3.0/nimble/tests/testthat/dynamicIndexingTestLog.Rout | 51 nimble-1.3.0/nimble/tests/testthat/dynamicIndexingTestLog_Correct.Rout | 110 nimble-1.3.0/nimble/tests/testthat/mcemTestLog.Rout | 1508 +++++++++- nimble-1.3.0/nimble/tests/testthat/test-ADaghq.R | 42 nimble-1.3.0/nimble/tests/testthat/test-ADlaplace.R | 105 nimble-1.3.0/nimble/tests/testthat/test-barker.R |only nimble-1.3.0/nimble/tests/testthat/test-bnp.R | 96 nimble-1.3.0/nimble/tests/testthat/test-dynamicIndexing.R | 28 nimble-1.3.0/nimble/tests/testthat/test-errors.R | 10 nimble-1.3.0/nimble/tests/testthat/test-externalCalls.R | 2 nimble-1.3.0/nimble/tests/testthat/test-macros.R | 217 + nimble-1.3.0/nimble/tests/testthat/test-mcmc.R | 7 nimble-1.3.0/nimble/tests/testthat/test-nimbleList.R | 22 nimble-1.3.0/nimble/tests/testthat/test-optim.R | 81 nimble-1.3.0/nimble/tests/testthat/test-setupMargNodes.R | 44 nimble-1.3.0/nimble/tests/testthat/test-user.R | 74 nimble-1.3.0/nimble/tests/testthat/truncTestLog_Correct.Rout | 522 +-- 64 files changed, 3844 insertions(+), 1235 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 11.0.0 dated 2024-11-22 and 11.1.0 dated 2024-12-17
ggblanket-11.0.0/ggblanket/R/utils-pipe.R |only ggblanket-11.0.0/ggblanket/man/aes_colour_darken.Rd |only ggblanket-11.0.0/ggblanket/man/pipe.Rd |only ggblanket-11.1.0/ggblanket/DESCRIPTION | 13 ggblanket-11.1.0/ggblanket/MD5 | 435 +-- ggblanket-11.1.0/ggblanket/NAMESPACE | 8 ggblanket-11.1.0/ggblanket/NEWS.md | 11 ggblanket-11.1.0/ggblanket/R/aes.R | 66 ggblanket-11.1.0/ggblanket/R/annotate_axis_line.R |only ggblanket-11.1.0/ggblanket/R/dark_mode.R | 12 ggblanket-11.1.0/ggblanket/R/flex_mode.R | 16 ggblanket-11.1.0/ggblanket/R/get_base.R | 16 ggblanket-11.1.0/ggblanket/R/gg_area.R | 4 ggblanket-11.1.0/ggblanket/R/gg_bar.R | 4 ggblanket-11.1.0/ggblanket/R/gg_bin_2d.R | 4 ggblanket-11.1.0/ggblanket/R/gg_blanket.R | 185 + ggblanket-11.1.0/ggblanket/R/gg_boxplot.R | 5 ggblanket-11.1.0/ggblanket/R/gg_col.R | 4 ggblanket-11.1.0/ggblanket/R/gg_contour.R | 4 ggblanket-11.1.0/ggblanket/R/gg_contour_filled.R | 4 ggblanket-11.1.0/ggblanket/R/gg_crossbar.R | 29 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Title: 'R6'-Based Flexible Framework for Permutation Tests
Description: Implements non-parametric tests from Higgins (2004, ISBN:0534387756), including tests for one sample, two samples, k samples, paired comparisons, blocked designs, trends and association. Built with 'Rcpp' for efficiency and 'R6' for flexible, object-oriented design, the package provides a unified framework for performing or creating custom permutation tests.
Author: Yan Du [aut, cre]
Maintainer: Yan Du <isduyan@outlook.com>
Diff between LearnNonparam versions 1.2.5 dated 2024-11-14 and 1.2.6 dated 2024-12-17
LearnNonparam-1.2.5/LearnNonparam/README.md |only LearnNonparam-1.2.5/LearnNonparam/inst/include/pmt/reorder.hpp |only LearnNonparam-1.2.5/LearnNonparam/man/figures/README |only LearnNonparam-1.2.5/LearnNonparam/man/references |only LearnNonparam-1.2.6/LearnNonparam/DESCRIPTION | 6 LearnNonparam-1.2.6/LearnNonparam/MD5 | 126 ++---- LearnNonparam-1.2.6/LearnNonparam/NEWS.md | 52 +- LearnNonparam-1.2.6/LearnNonparam/R/AnsariBradley.R | 2 LearnNonparam-1.2.6/LearnNonparam/R/Friedman.R | 2 LearnNonparam-1.2.6/LearnNonparam/R/KolmogorovSmirnov.R | 2 LearnNonparam-1.2.6/LearnNonparam/R/Page.R | 4 LearnNonparam-1.2.6/LearnNonparam/R/PermuTest.R | 20 - LearnNonparam-1.2.6/LearnNonparam/R/RCBDOneWay.R | 3 LearnNonparam-1.2.6/LearnNonparam/R/do_call.R | 33 + LearnNonparam-1.2.6/LearnNonparam/R/pmt.R | 67 ++- LearnNonparam-1.2.6/LearnNonparam/data/Table1.1.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table1.2.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table2.1.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table2.3.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table2.6.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table2.6.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table2.8.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table3.1.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table3.2.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table3.2.3.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table3.3.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table3.4.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table4.1.1.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table4.1.3.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table4.4.3.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table4.5.3.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table5.1.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table5.2.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/data/Table5.4.2.rda |binary LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_association_pmt.hpp | 27 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_ksample_pmt.hpp | 20 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_multcomp_pmt.hpp | 26 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_paired_pmt.hpp | 26 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_rcbd_pmt.hpp | 50 +- LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_table_pmt.hpp | 32 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/impl_twosample_pmt.hpp | 36 - LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/permutation.hpp |only LearnNonparam-1.2.6/LearnNonparam/inst/include/pmt/progress.hpp | 129 +++--- LearnNonparam-1.2.6/LearnNonparam/man/CDF.Rd | 144 +++---- LearnNonparam-1.2.6/LearnNonparam/man/KSampleTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/OneSampleTest.Rd | 86 ++-- LearnNonparam-1.2.6/LearnNonparam/man/OneWay.Rd | 122 +++--- LearnNonparam-1.2.6/LearnNonparam/man/Page.Rd | 2 LearnNonparam-1.2.6/LearnNonparam/man/PairedDifference.Rd | 188 +++++----- LearnNonparam-1.2.6/LearnNonparam/man/PermuTest.Rd | 4 LearnNonparam-1.2.6/LearnNonparam/man/RCBDOneWay.Rd | 118 +++--- LearnNonparam-1.2.6/LearnNonparam/man/RCBDTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/Studentized.Rd | 166 ++++---- LearnNonparam-1.2.6/LearnNonparam/man/TwoSampleAssociationTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/TwoSampleLocationTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/TwoSamplePairedTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/TwoSampleTest.Rd | 24 - LearnNonparam-1.2.6/LearnNonparam/man/pmt.Rd | 62 ++- LearnNonparam-1.2.6/LearnNonparam/src/pmt_interface.cpp | 68 ++- 59 files changed, 933 insertions(+), 834 deletions(-)
Title: Visualize Item Metrics of the Classical Test Theory Framework
Description: Visualizes results of item analysis such as item difficulty,
item discrimination, and coefficient alpha for ease of result communication.
Author: Tarid Wongvorachan [aut, cre, cph]
Maintainer: Tarid Wongvorachan <taridwongvorachan@gmail.com>
Diff between CTTvis versions 0.1.0 dated 2024-11-21 and 0.1.1 dated 2024-12-17
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 13 ++++++++++--- R/coefficient_alpha_plot.R | 18 ++++++++++++++---- R/difficulty_plot.R | 17 +++++++++++++---- R/point_biserial_plot.R | 15 ++++++++++++--- README.md | 22 ++++++++++++++++++---- build/vignette.rds |binary inst/doc/CTTvis.html | 6 +++--- 10 files changed, 83 insertions(+), 33 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.7-0 dated 2024-06-05 and 3.8-3 dated 2024-12-17
survival-3.7-0/survival/noweb/survexpm.Rnw |only survival-3.8-3/survival/DESCRIPTION | 8 survival-3.8-3/survival/MD5 | 223 - survival-3.8-3/survival/NAMESPACE | 2 survival-3.8-3/survival/R/aareg.R | 6 survival-3.8-3/survival/R/agsurv.R | 20 survival-3.8-3/survival/R/anova.coxphlist.R | 11 survival-3.8-3/survival/R/anova.coxphms.R |only survival-3.8-3/survival/R/concordance.R | 16 survival-3.8-3/survival/R/coxph.R | 44 survival-3.8-3/survival/R/coxph.control.R | 12 survival-3.8-3/survival/R/coxsurvfit.R | 96 survival-3.8-3/survival/R/model.frame.survreg.R | 3 survival-3.8-3/survival/R/parsecovar.R | 16 survival-3.8-3/survival/R/plot.cox.zph.R | 14 survival-3.8-3/survival/R/plot.survfit.R | 352 +-- survival-3.8-3/survival/R/predict.coxph.R | 38 survival-3.8-3/survival/R/predict.coxphms.R | 336 ++ survival-3.8-3/survival/R/residuals.survfit.R | 2 survival-3.8-3/survival/R/rsurvpart2.R | 4 survival-3.8-3/survival/R/summary.survfit.R | 2 survival-3.8-3/survival/R/survcheck.R | 12 survival-3.8-3/survival/R/survdiff.R | 15 survival-3.8-3/survival/R/survexpm.R | 52 survival-3.8-3/survival/R/survfit.R | 16 survival-3.8-3/survival/R/survfit.coxphms.R | 31 survival-3.8-3/survival/R/survfitAJ.R | 15 survival-3.8-3/survival/R/survreg.R | 30 survival-3.8-3/survival/R/survreg.fit.R | 3 survival-3.8-3/survival/R/timeline.R |only survival-3.8-3/survival/R/xtras.R | 80 survival-3.8-3/survival/data/nafld.rda |binary survival-3.8-3/survival/data/reliability.rda |binary survival-3.8-3/survival/inst/NEWS.Rd | 86 survival-3.8-3/survival/inst/doc/adjcurve.pdf |binary survival-3.8-3/survival/inst/doc/approximate.pdf |binary survival-3.8-3/survival/inst/doc/compete.pdf |binary survival-3.8-3/survival/inst/doc/concordance.pdf |binary survival-3.8-3/survival/inst/doc/matrix.pdf |binary survival-3.8-3/survival/inst/doc/methods.R | 39 survival-3.8-3/survival/inst/doc/methods.Rnw | 539 ++++ survival-3.8-3/survival/inst/doc/methods.pdf |binary survival-3.8-3/survival/inst/doc/multi.pdf |binary survival-3.8-3/survival/inst/doc/other.pdf |binary survival-3.8-3/survival/inst/doc/population.pdf |binary survival-3.8-3/survival/inst/doc/redistribute.pdf |binary survival-3.8-3/survival/inst/doc/splines.pdf |binary survival-3.8-3/survival/inst/doc/survival.R | 25 survival-3.8-3/survival/inst/doc/survival.Rnw | 27 survival-3.8-3/survival/inst/doc/survival.pdf |binary survival-3.8-3/survival/inst/doc/tiedtimes.pdf |binary survival-3.8-3/survival/inst/doc/timedep.Rnw | 8 survival-3.8-3/survival/inst/doc/timedep.pdf |binary survival-3.8-3/survival/inst/doc/validate.pdf |binary survival-3.8-3/survival/man/coxph.Rd | 65 survival-3.8-3/survival/man/kidney.Rd | 4 survival-3.8-3/survival/man/lines.survfit.Rd | 11 survival-3.8-3/survival/man/nafld.Rd | 1 survival-3.8-3/survival/man/plot.cox.zph.Rd | 5 survival-3.8-3/survival/man/plot.survfit.Rd | 20 survival-3.8-3/survival/man/predict.coxph.Rd | 14 survival-3.8-3/survival/man/pseudo.Rd | 54 survival-3.8-3/survival/man/reliability.Rd | 10 survival-3.8-3/survival/man/royston.Rd | 12 survival-3.8-3/survival/man/solder.Rd | 21 survival-3.8-3/survival/man/summary.survfit.Rd | 40 survival-3.8-3/survival/man/survcondense.Rd | 9 survival-3.8-3/survival/man/survdiff.Rd | 11 survival-3.8-3/survival/man/timeline.Rd |only survival-3.8-3/survival/noweb/Makefile | 12 survival-3.8-3/survival/noweb/code.nw | 1283 +---------- survival-3.8-3/survival/noweb/concordance.Rnw | 18 survival-3.8-3/survival/noweb/coxph.Rnw | 44 survival-3.8-3/survival/noweb/coxsurv2.Rnw | 2 survival-3.8-3/survival/noweb/coxsurv3.Rnw | 31 survival-3.8-3/survival/noweb/parse.Rnw | 33 survival-3.8-3/survival/noweb/plot.Rnw | 137 - survival-3.8-3/survival/noweb/predict.coxph.Rnw | 38 survival-3.8-3/survival/src/agsurv4.c | 7 survival-3.8-3/survival/src/agsurv5.c | 6 survival-3.8-3/survival/src/cdecomp.c | 1 survival-3.8-3/survival/src/survreg6.c | 100 survival-3.8-3/survival/tests/Examples/survival-Ex.Rout.save | 56 survival-3.8-3/survival/tests/coxsurv.R | 7 survival-3.8-3/survival/tests/coxsurv.Rout.save | 11 survival-3.8-3/survival/tests/coxsurv3.R | 26 survival-3.8-3/survival/tests/coxsurv3.Rout.save | 31 survival-3.8-3/survival/tests/coxsurv6.R | 19 survival-3.8-3/survival/tests/coxsurv6.Rout.save | 44 survival-3.8-3/survival/tests/doublecolon.R |only survival-3.8-3/survival/tests/doublecolon.Rout.save |only survival-3.8-3/survival/tests/ekm.R | 2 survival-3.8-3/survival/tests/ekm.Rout.save | 6 survival-3.8-3/survival/tests/jasa.R | 2 survival-3.8-3/survival/tests/jasa.Rout.save | 44 survival-3.8-3/survival/tests/mstate.R | 2 survival-3.8-3/survival/tests/mstate.Rout.save | 6 survival-3.8-3/survival/tests/multi2.R | 7 survival-3.8-3/survival/tests/multi2.Rout.save | 15 survival-3.8-3/survival/tests/multi3.R | 8 survival-3.8-3/survival/tests/multi3.Rout.save | 16 survival-3.8-3/survival/tests/multistate.R | 23 survival-3.8-3/survival/tests/multistate.Rout.save | 31 survival-3.8-3/survival/tests/r_lung.Rout.save | 10 survival-3.8-3/survival/tests/r_resid.Rout.save | 10 survival-3.8-3/survival/tests/residsfx.Rtemp |only survival-3.8-3/survival/tests/survexpm.R.later |only survival-3.8-3/survival/tests/survexpm.R.notyet |only survival-3.8-3/survival/tests/survreg1.Rout.save | 10 survival-3.8-3/survival/tests/survreg2.R | 38 survival-3.8-3/survival/tests/survreg2.Rout.save | 47 survival-3.8-3/survival/tests/testreg.Rout.save | 10 survival-3.8-3/survival/tests/zph.R | 4 survival-3.8-3/survival/tests/zph.Rout.save | 12 survival-3.8-3/survival/vignettes/methods.Rnw | 539 ++++ survival-3.8-3/survival/vignettes/survival.Rnw | 27 survival-3.8-3/survival/vignettes/timedep.Rnw | 8 117 files changed, 3204 insertions(+), 2039 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.24.0 dated 2024-11-14 and 3.1.0 dated 2024-12-17
DESCRIPTION | 15 +- MD5 | 53 +++++--- NAMESPACE | 5 NEWS.md | 11 + R/abfit.R | 177 +++++++++++++++++++++++++++++- R/amp_scaling.R | 129 ++++++++++++++++----- R/fit_display.R | 14 +- R/fit_svs.R |only R/mol_parameters.R | 159 +++++++------------------- R/mrs_data_display.R | 13 -- R/mrs_data_io.R | 51 ++++---- R/mrs_data_proc.R | 2 R/mrs_read_ima.R | 7 + R/qm_simulation.R | 70 +++++++++++ R/utils.R | 42 +++++++ inst/doc/abfit-baseline-opts.html | 14 +- inst/doc/spant-basis-simulation.html | 10 - inst/doc/spant-intro.html | 128 +++++++++++---------- inst/doc/spant-metabolite-simulation.html | 61 +++++----- inst/doc/spant-preprocessing.html | 16 +- inst/extdata/press_refocus.pta |only inst/rmd/dyn_svs_report.Rmd |only inst/rmd/svs_report.Rmd |only man/abfit_reg_opts.Rd |only man/fit_svs.Rd |only man/fit_svs_gui.Rd |only man/read_mrs.Rd | 11 + man/scale_amp_legacy.Rd |only man/scale_amp_molar.Rd | 3 man/sim_basis.Rd | 9 + man/spant-package.Rd | 1 man/sv_res_table.Rd |only 32 files changed, 660 insertions(+), 341 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using the 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre],
John Magnotti [ctb] ,
Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.2.9 dated 2024-06-27 and 0.3.0 dated 2024-12-17
DESCRIPTION | 10 MD5 | 48 NAMESPACE | 2 NEWS.md | 8 R/aaa.R | 2 R/apply.R | 3 R/language.R | 14 R/parallels-apply-script.R | 2 R/parallels-future.R | 255 R/shiny-progress.R | 19 R/shiny-syncInputs.R | 2 build/vignette.rds |binary inst/doc/r_expr_addons.R | 59 inst/doc/r_expr_addons.Rmd | 51 inst/doc/r_expr_addons.html | 81 inst/doc/shiny_customized_widgets.R | 68 inst/doc/shiny_customized_widgets.Rmd | 10 inst/doc/shiny_customized_widgets.html | 7985 ---------------------- inst/doc/utility_functions.R | 58 inst/doc/utility_functions.html | 72 inst/shiny-addons/dipsaus/dipsaus-dipterix-lib.js | 35 man/do_aggregate.Rd | 3 man/no_op.Rd | 14 vignettes/r_expr_addons.Rmd | 51 vignettes/shiny_customized_widgets.Rmd | 10 25 files changed, 505 insertions(+), 8357 deletions(-)
Title: Next Generation Clustered Heat Maps
Description: Next-Generation Clustered Heat Maps (NG-CHMs) allow for
dynamic exploration of heat map data in a web browser. 'NGCHM' allows
users to create both stand-alone HTML files containing a
Next-Generation Clustered Heat Map, and .ngchm files to view in the
NG-CHM viewer. See Ryan MC, Stucky M, et al (2020)
<doi:10.12688/f1000research.20590.2> for more details.
Author: Bradley M Broom [aut] ,
Mary A Rohrdanz [ctb, cre],
Chris Wakefield [ctb],
James M Melott [ctb],
MD Anderson Cancer Center [cph]
Maintainer: Mary A Rohrdanz <marohrdanz@mdanderson.org>
Diff between NGCHM versions 1.0.3 dated 2024-05-08 and 1.0.4 dated 2024-12-17
DESCRIPTION | 12 +- MD5 | 22 ++-- R/allClasses.R | 10 - R/functions.R | 115 ++++++++++++++------ R/internalFunctions.R | 126 +++++++++++++++++------ R/package.R | 2 R/zzz.R | 4 inst/base.config/conf.d/01-server-protocol-scl.R | 9 + man/NGCHM-package.Rd | 18 ++- man/chmAddUMAP.Rd | 2 man/chmExportToHTML-method.Rd | 4 tests/testthat/test-clustering.R |only tests/testthat/test-validateColor.R |only 13 files changed, 226 insertions(+), 98 deletions(-)
Title: Cronbach's Alpha
Description: Cronbach's alpha and various formulas for confidence intervals. The relevant paper is Tsagris M., Frangos C.C. and Frangos C.C. (2013). "Confidence intervals for Cronbach's reliability coefficient". Recent Techniques in Educational Science, 14-16 May, Athens, Greece.
Author: Michail Tsagris [aut, cre],
Constantinos Frangos [aut],
Christos Frangos [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Cronbach versions 0.1 dated 2020-11-18 and 0.2 dated 2024-12-17
DESCRIPTION | 11 +++++------ MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/cron.ci.R | 5 +++-- R/cronbach.R | 2 +- R/cronfree.ci.R | 7 ++++--- man/Cronbach-package.Rd | 22 ++++++++++++---------- man/cron.ci.Rd | 13 ++++++------- man/cronbach.Rd | 4 ++-- man/cronfree.ci.Rd | 14 +++++++------- 10 files changed, 51 insertions(+), 47 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided. As of release 1.84.0-0, the following Boost libraries are
included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'beast'
'bimap' 'bind' 'circular_buffer' 'compute' 'concept' 'config'
'container' 'date_time' 'detail' 'dynamic_bitset' 'exception'
'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap'
'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams'
'iterator' 'lambda2' 'math' 'move' 'mp11' 'mpl' 'multiprecision'
'numeric' 'pending' 'phoenix' 'polygon' 'preprocessor' 'process'
'propery_tree' 'qvm' 'rando [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
John W. Emerson [aut],
Michael J. Kane [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.84.0-0 dated 2024-01-10 and 1.87.0-1 dated 2024-12-17
BH-1.84.0-0/BH/inst/include/boost/asio/experimental/cancellation_condition.hpp |only BH-1.84.0-0/BH/inst/include/boost/asio/experimental/impl/parallel_group.hpp |only BH-1.84.0-0/BH/inst/include/boost/asio/experimental/parallel_group.hpp |only BH-1.84.0-0/BH/inst/include/boost/asio/io_service.hpp |only BH-1.84.0-0/BH/inst/include/boost/asio/io_service_strand.hpp |only BH-1.84.0-0/BH/inst/include/boost/asio/ssl/impl/rfc2818_verification.ipp |only BH-1.84.0-0/BH/inst/include/boost/asio/ssl/rfc2818_verification.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/bind_cc.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/bind_mf2_cc.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/bind_mf_cc.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/bind_template.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/detail/is_same.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/detail/requires_cxx11.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/mem_fn_cc.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/mem_fn_template.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/mem_fn_vw.hpp |only BH-1.84.0-0/BH/inst/include/boost/bind/storage.hpp |only BH-1.84.0-0/BH/inst/include/boost/coroutine |only BH-1.84.0-0/BH/inst/include/boost/filesystem/convenience.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/detail |only BH-1.84.0-0/BH/inst/include/boost/function/function10.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function4.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function5.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function6.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function7.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function8.hpp |only BH-1.84.0-0/BH/inst/include/boost/function/function9.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/algorithms/detail/overlay/cluster_exits.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/algorithms/detail/recalculate.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/algorithms/detail/within/within_no_turns.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/io/wkt/detail/wkt_multi.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/multi/io/wkt/detail |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/get_rescale_policy.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/no_rescale_policy.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/rescale_policy.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/rescale_policy_tags.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/robust_point_type.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/robust_type.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/policies/robustness/segment_ratio_type.hpp |only BH-1.84.0-0/BH/inst/include/boost/geometry/util/for_each_with_index.hpp |only BH-1.84.0-0/BH/inst/include/boost/interprocess/detail/in_place_interface.hpp |only BH-1.84.0-0/BH/inst/include/boost/interprocess/indexes/unordered_map_index.hpp |only BH-1.84.0-0/BH/inst/include/boost/json/memory_resource.hpp |only BH-1.84.0-0/BH/inst/include/boost/json/system_error.hpp |only BH-1.84.0-0/BH/inst/include/boost/optional/detail/old_optional_implementation.hpp |only BH-1.84.0-0/BH/inst/include/boost/process/detail |only BH-1.84.0-0/BH/inst/include/boost/process/v2/detail/impl |only BH-1.84.0-0/BH/inst/include/boost/process/v2/ext/detail/impl |only BH-1.84.0-0/BH/inst/include/boost/process/v2/ext/impl |only BH-1.84.0-0/BH/inst/include/boost/process/v2/impl |only BH-1.84.0-0/BH/inst/include/boost/process/v2/posix/detail/close_handles.ipp |only BH-1.84.0-0/BH/inst/include/boost/process/v2/src.hpp |only BH-1.84.0-0/BH/inst/include/boost/process/v2/windows/impl |only BH-1.84.0-0/BH/inst/include/boost/smart_ptr/detail/operator_bool.hpp |only BH-1.84.0-0/BH/inst/include/boost/smart_ptr/detail/requires_cxx11.hpp |only BH-1.84.0-0/BH/inst/include/boost/smart_ptr/detail/sp_forward.hpp |only BH-1.84.0-0/BH/inst/include/boost/smart_ptr/detail/sp_nullptr_t.hpp |only BH-1.84.0-0/BH/inst/include/boost/system/detail/requires_cxx11.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/decode.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/move_chars.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/normalize.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/over_allocator.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/path.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/pattern.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/pct_format.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/detail/print.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/rfc/detail/charsets.hpp |only BH-1.84.0-0/BH/inst/include/boost/url/rfc/detail/fragment_part_rule.hpp |only 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BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/detail/within/multi_point.hpp | 29 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/difference.hpp | 49 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/discrete_frechet_distance.hpp | 27 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/discrete_hausdorff_distance.hpp | 78 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/closest_points.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/disjoint.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/distance.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/for_each.hpp | 4 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/length.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/line_interpolate.hpp | 15 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/num_geometries.hpp | 7 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/num_points.hpp | 5 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/point_on_surface.hpp | 6 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/remove_spikes.hpp | 20 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/simplify.hpp | 32 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/sym_difference.hpp | 70 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/transform.hpp | 47 BH-1.87.0-1/BH/inst/include/boost/geometry/algorithms/union.hpp | 93 BH-1.87.0-1/BH/inst/include/boost/geometry/arithmetic/determinant.hpp | 4 BH-1.87.0-1/BH/inst/include/boost/geometry/core/access.hpp | 139 BH-1.87.0-1/BH/inst/include/boost/geometry/core/closure.hpp | 35 BH-1.87.0-1/BH/inst/include/boost/geometry/core/config.hpp | 22 BH-1.87.0-1/BH/inst/include/boost/geometry/core/coordinate_dimension.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/core/coordinate_system.hpp | 13 BH-1.87.0-1/BH/inst/include/boost/geometry/core/coordinate_type.hpp | 35 BH-1.87.0-1/BH/inst/include/boost/geometry/core/cs.hpp | 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BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/distance.hpp | 4 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/envelope.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/equals.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/for_each.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/intersection.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/length.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/num_geometries.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/num_interior_rings.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/num_points.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/perimeter.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/remove_spikes.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/reverse.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/simplify.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/transform.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/unique.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/algorithms/within.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/closure.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/geometry_id.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/interior_rings.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/is_areal.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/point_order.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/point_type.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/ring_type.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/tags.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/core/topological_dimension.hpp | 2 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BH-1.87.0-1/BH/inst/include/boost/geometry/multi/io/dsv/write.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/io/wkt/read.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/io/wkt/wkt.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/io/wkt/write.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/multi.hpp | 3 BH-1.87.0-1/BH/inst/include/boost/geometry/multi/strategies/cartesian/centroid_average.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/is_valid/failing_reason_policy.hpp | 7 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/relate/direction.hpp | 8 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/relate/intersection_points.hpp | 16 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/relate/intersection_policy.hpp | 13 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/relate/intersection_ratios.hpp | 11 BH-1.87.0-1/BH/inst/include/boost/geometry/policies/robustness/segment_ratio.hpp | 16 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BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/intersection_result.hpp | 17 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/intersection_strategies.hpp | 22 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/normalize.hpp | 21 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/relate.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/side_info.hpp | 8 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/area.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/closest_points_pt_seg.hpp | 30 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/disjoint_segment_box.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/distance_cross_track_box_box.hpp | 18 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/distance_cross_track_point_box.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/distance_haversine.hpp | 16 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/distance_segment_box.hpp | 5 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/envelope.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/envelope_box.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/envelope_multipoint.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/envelope_point.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/envelope_segment.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/expand_box.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/expand_point.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/expand_segment.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/intersection.hpp | 12 BH-1.87.0-1/BH/inst/include/boost/geometry/strategies/spherical/point_in_poly_winding.hpp | 13 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| 21 BH-1.87.0-1/BH/inst/include/boost/unordered/detail/foa/types_constructibility.hpp |only BH-1.87.0-1/BH/inst/include/boost/unordered/detail/implementation.hpp | 36 BH-1.87.0-1/BH/inst/include/boost/unordered/detail/map.hpp | 19 BH-1.87.0-1/BH/inst/include/boost/unordered/detail/set.hpp | 17 BH-1.87.0-1/BH/inst/include/boost/unordered/detail/throw_exception.hpp |only BH-1.87.0-1/BH/inst/include/boost/unordered/detail/type_traits.hpp | 43 BH-1.87.0-1/BH/inst/include/boost/unordered/hash_traits.hpp | 40 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_flat_map.hpp | 39 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_flat_map_fwd.hpp | 15 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_flat_set.hpp | 21 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_flat_set_fwd.hpp | 14 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_map.hpp | 41 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_map_fwd.hpp | 19 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_node_map.hpp | 106 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_node_map_fwd.hpp | 15 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_node_set.hpp | 78 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_node_set_fwd.hpp | 14 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_printers.hpp |only BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_set.hpp | 20 BH-1.87.0-1/BH/inst/include/boost/unordered/unordered_set_fwd.hpp | 17 BH-1.87.0-1/BH/inst/include/boost/url.hpp | 1 BH-1.87.0-1/BH/inst/include/boost/url/authority_view.hpp | 19 BH-1.87.0-1/BH/inst/include/boost/url/decode_view.hpp | 59 BH-1.87.0-1/BH/inst/include/boost/url/detail/config.hpp | 20 BH-1.87.0-1/BH/inst/include/boost/url/detail/encode.hpp | 136 BH-1.87.0-1/BH/inst/include/boost/url/detail/format_args.hpp | 8 BH-1.87.0-1/BH/inst/include/boost/url/detail/impl/format_args.hpp | 6 BH-1.87.0-1/BH/inst/include/boost/url/detail/url_impl.hpp | 3 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BH-1.87.0-1/BH/inst/include/boost/url/pct_string_view.hpp | 21 BH-1.87.0-1/BH/inst/include/boost/url/rfc/absolute_uri_rule.hpp | 36 BH-1.87.0-1/BH/inst/include/boost/url/rfc/authority_rule.hpp | 32 BH-1.87.0-1/BH/inst/include/boost/url/rfc/detail/path_rules.hpp | 10 BH-1.87.0-1/BH/inst/include/boost/url/rfc/impl/pct_encoded_rule.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/url/rfc/ipv4_address_rule.hpp | 39 BH-1.87.0-1/BH/inst/include/boost/url/rfc/ipv6_address_rule.hpp | 47 BH-1.87.0-1/BH/inst/include/boost/url/rfc/origin_form_rule.hpp | 31 BH-1.87.0-1/BH/inst/include/boost/url/rfc/pct_encoded_rule.hpp | 55 BH-1.87.0-1/BH/inst/include/boost/url/rfc/query_rule.hpp | 40 BH-1.87.0-1/BH/inst/include/boost/url/rfc/relative_ref_rule.hpp | 31 BH-1.87.0-1/BH/inst/include/boost/url/rfc/uri_reference_rule.hpp | 34 BH-1.87.0-1/BH/inst/include/boost/url/rfc/uri_rule.hpp | 31 BH-1.87.0-1/BH/inst/include/boost/url/segments_base.hpp | 20 BH-1.87.0-1/BH/inst/include/boost/url/segments_encoded_base.hpp | 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BH-1.87.0-1/BH/inst/include/boost/variant/recursive_wrapper_fwd.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/variant/variant.hpp | 82 BH-1.87.0-1/BH/inst/include/boost/variant/variant_fwd.hpp | 45 BH-1.87.0-1/BH/inst/include/boost/variant2/variant.hpp | 16 BH-1.87.0-1/BH/inst/include/boost/version.hpp | 4 BH-1.87.0-1/BH/inst/include/boost/winapi/get_proc_address.hpp | 13 BH-1.87.0-1/BH/inst/include/boost/xpressive/detail/utility/counted_base.hpp | 2 BH-1.87.0-1/BH/inst/include/boost/xpressive/detail/utility/tracking_ptr.hpp | 4 BH-1.87.0-1/BH/inst/include/boost/xpressive/xpressive_static.hpp | 2 2530 files changed, 51383 insertions(+), 54083 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9.5 dated 2024-12-16 and 10.9.6 dated 2024-12-17
DESCRIPTION | 6 MD5 | 16 - R/NNS_MC.R | 27 + R/NNS_meboot.R | 447 ++++++++++++++++----------------- README.md | 4 inst/doc/NNSvignette_Sampling.html | 2 man/NNS.MC.Rd | 2 man/NNS.meboot.Rd | 9 vignettes/images/NNSmc_1_tgt_drift.png |binary 9 files changed, 260 insertions(+), 253 deletions(-)
Title: Get Water Attributes Visually in R
Description: Provides methods to Get Water Attributes Visually in R ('gwavr'). This allows the user to point and click on areas within the United States and get back hydrological data, e.g. flowlines, catchments, basin boundaries, comids, etc.
Author: Joshua Erickson [aut, cre]
Maintainer: Joshua Erickson <joshualerickson@gmail.com>
Diff between gwavr versions 0.3.1 dated 2024-05-10 and 0.3.2 dated 2024-12-17
DESCRIPTION | 12 MD5 | 28 NAMESPACE | 4 NEWS.md | 12 R/globals.R | 16 R/modules.R | 3682 ++++++++++++++++---------------- R/noaatlas.R |only R/streamnetwork.R | 4 R/utils.R | 142 + README.md | 152 - inst/www/pf.png |only man/get_noaatlas.Rd |only man/get_noaatlas_interactively.Rd |only man/get_noaatlas_png.Rd |only man/get_stream_network_interactively.Rd | 4 man/noaatlasMod.Rd |only man/noaatlasModUI.Rd |only tests/testthat/test-nldi.R | 116 - tests/testthat/test-noaa.R |only 19 files changed, 2237 insertions(+), 1935 deletions(-)
Title: Biodiversity Data Cleaning
Description: It brings together several aspects of biodiversity
data-cleaning in one place. 'bdc' is organized in thematic modules
related to different biodiversity dimensions, including 1) Merge
datasets: standardization and integration of different datasets; 2)
Pre-filter: flagging and removal of invalid or non-interpretable
information, followed by data amendments; 3) Taxonomy: cleaning,
parsing, and harmonization of scientific names from several taxonomic
groups against taxonomic databases locally stored through the
application of exact and partial matching algorithms; 4) Space:
flagging of erroneous, suspect, and low-precision geographic
coordinates; and 5) Time: flagging and, whenever possible, correction
of inconsistent collection date. In addition, it contains
features to visualize, document, and report data quality – which is
essential for making data quality assessment transparent and
reproducible. The reference for the methodology is Bruno et al. (2022)
<doi:10.1111/2041-210X.13868> [...truncated...]
Author: Bruno Ribeiro [aut, cre] ,
Santiago Velazco [aut] ,
Karlo Guidoni-Martins [aut] ,
Geiziane Tessarolo [aut] ,
Lucas Jardim [aut] ,
Steven Bachman [ctb] ,
Rafael Loyola [ctb]
Maintainer: Bruno Ribeiro <ribeiro.brr@gmail.com>
Diff between bdc versions 1.1.4 dated 2023-03-13 and 1.1.5 dated 2024-12-17
bdc-1.1.4/bdc/build |only bdc-1.1.4/bdc/inst/doc |only bdc-1.1.4/bdc/vignettes |only bdc-1.1.5/bdc/DESCRIPTION | 25 bdc-1.1.5/bdc/MD5 | 267 bdc-1.1.5/bdc/NAMESPACE | 268 bdc-1.1.5/bdc/NEWS.md | 144 bdc-1.1.5/bdc/R/bdc_basisOfRecords_notStandard.R | 208 bdc-1.1.5/bdc/R/bdc_clean_duplicates.R | 150 bdc-1.1.5/bdc/R/bdc_clean_names.R | 1946 - bdc-1.1.5/bdc/R/bdc_coord_trans.R | 196 bdc-1.1.5/bdc/R/bdc_coordinates_country_inconsistent.R | 442 bdc-1.1.5/bdc/R/bdc_coordinates_empty.R | 143 bdc-1.1.5/bdc/R/bdc_coordinates_from_locality.R | 246 bdc-1.1.5/bdc/R/bdc_coordinates_outOfRange.R | 136 bdc-1.1.5/bdc/R/bdc_coordinates_precision.R | 166 bdc-1.1.5/bdc/R/bdc_coordinates_transposed.R | 438 bdc-1.1.5/bdc/R/bdc_correct_coordinates.R | 372 bdc-1.1.5/bdc/R/bdc_country_from_coordinates.R | 333 bdc-1.1.5/bdc/R/bdc_country_standardized.R | 196 bdc-1.1.5/bdc/R/bdc_create_dir.R | 48 bdc-1.1.5/bdc/R/bdc_create_figures.R | 1087 - bdc-1.1.5/bdc/R/bdc_create_report.R | 1066 bdc-1.1.5/bdc/R/bdc_eventDate_empty.R | 106 bdc-1.1.5/bdc/R/bdc_filter_name.R | 210 bdc-1.1.5/bdc/R/bdc_filter_out_flags.R | 118 bdc-1.1.5/bdc/R/bdc_filter_out_names.R | 212 bdc-1.1.5/bdc/R/bdc_get_world_map.R | 88 bdc-1.1.5/bdc/R/bdc_query_names_taxadb.R | 1244 - bdc-1.1.5/bdc/R/bdc_quickmap.R | 299 bdc-1.1.5/bdc/R/bdc_return_names.R | 92 bdc-1.1.5/bdc/R/bdc_scientificName_empty.R | 98 bdc-1.1.5/bdc/R/bdc_standardize_country.R | 316 bdc-1.1.5/bdc/R/bdc_standardize_datasets.R | 638 bdc-1.1.5/bdc/R/bdc_stdz_cntr.R | 231 bdc-1.1.5/bdc/R/bdc_suggest_names_taxadb.R | 307 bdc-1.1.5/bdc/R/bdc_summary_col.R | 132 bdc-1.1.5/bdc/R/bdc_year_from_eventDate.R | 98 bdc-1.1.5/bdc/R/bdc_year_outOfRange.R | 198 bdc-1.1.5/bdc/R/utils-pipe.R | 28 bdc-1.1.5/bdc/R/utils.R | 78 bdc-1.1.5/bdc/README.md | 401 bdc-1.1.5/bdc/inst/WORDLIST | 226 bdc-1.1.5/bdc/inst/extdata/Config/DatabaseInfo.csv | 20 bdc-1.1.5/bdc/inst/extdata/Config/DatabaseInfo_description.csv | 34 bdc-1.1.5/bdc/inst/extdata/countries_names/country_names.txt |10773 +++++----- bdc-1.1.5/bdc/inst/extdata/countries_names/reword-countries.csv | 26 bdc-1.1.5/bdc/inst/extdata/encoding-chars.txt | 10 bdc-1.1.5/bdc/inst/extdata/input_files/at_epiphytes.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/bien.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/dryflor.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/gbif.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/icmbio.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/idigbio.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/neotroptree.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/sibbr.csv | 42 bdc-1.1.5/bdc/inst/extdata/input_files/specieslink.csv | 42 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/00_merged_database.csv | 362 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/01_Report_Prefilter.csv | 16 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/01_prefilter_database.csv | 232 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/02_Report_taxonomy.csv | 18 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/02_taxonomy_database.csv | 232 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/03_Report_space.csv | 26 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/03_space_database.csv | 232 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/04_Report_time.csv | 14 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/04_time_database.csv | 232 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/05_cleaned_database.csv | 92 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/example_clean_names.csv | 232 bdc-1.1.5/bdc/inst/extdata/outpus_vignettes/example_query_names.csv | 232 bdc-1.1.5/bdc/man/bdc_basisOfRecords_notStandard.Rd | 134 bdc-1.1.5/bdc/man/bdc_clean_names.Rd | 133 bdc-1.1.5/bdc/man/bdc_coordinates_country_inconsistent.Rd | 174 bdc-1.1.5/bdc/man/bdc_coordinates_empty.Rd | 104 bdc-1.1.5/bdc/man/bdc_coordinates_from_locality.Rd | 142 bdc-1.1.5/bdc/man/bdc_coordinates_outOfRange.Rd | 110 bdc-1.1.5/bdc/man/bdc_coordinates_precision.Rd | 104 bdc-1.1.5/bdc/man/bdc_coordinates_transposed.Rd | 230 bdc-1.1.5/bdc/man/bdc_country_from_coordinates.Rd | 114 bdc-1.1.5/bdc/man/bdc_country_standardized.Rd | 104 bdc-1.1.5/bdc/man/bdc_create_figures.Rd | 143 bdc-1.1.5/bdc/man/bdc_create_report.Rd | 118 bdc-1.1.5/bdc/man/bdc_eventDate_empty.Rd | 82 bdc-1.1.5/bdc/man/bdc_filter_out_flags.Rd | 76 bdc-1.1.5/bdc/man/bdc_filter_out_names.Rd | 142 bdc-1.1.5/bdc/man/bdc_query_names_taxadb.Rd | 398 bdc-1.1.5/bdc/man/bdc_quickmap.Rd | 114 bdc-1.1.5/bdc/man/bdc_scientificName_empty.Rd | 82 bdc-1.1.5/bdc/man/bdc_standardize_datasets.Rd | 149 bdc-1.1.5/bdc/man/bdc_summary_col.Rd | 66 bdc-1.1.5/bdc/man/bdc_year_from_eventDate.Rd | 80 bdc-1.1.5/bdc/man/bdc_year_outOfRange.Rd | 110 bdc-1.1.5/bdc/man/pipe.Rd | 40 bdc-1.1.5/bdc/tests/testthat.R | 8 bdc-1.1.5/bdc/tests/testthat/test-bdc_basisOfRecords_notStandard.R | 106 bdc-1.1.5/bdc/tests/testthat/test-bdc_clean_duplicates.R | 132 bdc-1.1.5/bdc/tests/testthat/test-bdc_clean_names.R | 170 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_country_inconsistent.R | 145 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_empty.R | 106 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_from_locality.R | 22 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_outOfRange.R | 42 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_precision.R | 48 bdc-1.1.5/bdc/tests/testthat/test-bdc_coordinates_transposed.R | 237 bdc-1.1.5/bdc/tests/testthat/test-bdc_correct_coordinates.R | 86 bdc-1.1.5/bdc/tests/testthat/test-bdc_country_from_coordinates.R | 177 bdc-1.1.5/bdc/tests/testthat/test-bdc_create_dir.R | 24 bdc-1.1.5/bdc/tests/testthat/test-bdc_create_figures.R | 65 bdc-1.1.5/bdc/tests/testthat/test-bdc_create_report.R | 76 bdc-1.1.5/bdc/tests/testthat/test-bdc_eventDate_empty.R | 66 bdc-1.1.5/bdc/tests/testthat/test-bdc_filter_name.R | 78 bdc-1.1.5/bdc/tests/testthat/test-bdc_filter_out_flags.R | 34 bdc-1.1.5/bdc/tests/testthat/test-bdc_filter_out_names.R | 202 bdc-1.1.5/bdc/tests/testthat/test-bdc_get_world_map.R | 21 bdc-1.1.5/bdc/tests/testthat/test-bdc_query_names_taxadb.R | 323 bdc-1.1.5/bdc/tests/testthat/test-bdc_quickmap.R | 28 bdc-1.1.5/bdc/tests/testthat/test-bdc_return_names.R | 56 bdc-1.1.5/bdc/tests/testthat/test-bdc_scientificName_empty.R | 46 bdc-1.1.5/bdc/tests/testthat/test-bdc_standardize_country.R | 74 bdc-1.1.5/bdc/tests/testthat/test-bdc_standardize_datasets.R | 438 bdc-1.1.5/bdc/tests/testthat/test-bdc_suggest_names_taxadb.R | 465 bdc-1.1.5/bdc/tests/testthat/test-bdc_summary_col.R | 22 bdc-1.1.5/bdc/tests/testthat/test-bdc_year_from_eventDate.R | 38 bdc-1.1.5/bdc/tests/testthat/test-bdc_year_outOfRange.R | 44 122 files changed, 16419 insertions(+), 16067 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.2.3 dated 2024-06-17 and 0.2.4 dated 2024-12-17
DESCRIPTION | 10 ++++---- MD5 | 11 +++++---- NEWS.md | 5 ++++ build |only man/aplot-package.Rd | 58 +++++++++++++++++++++++++-------------------------- man/aplot_label.Rd | 54 +++++++++++++++++++++++------------------------ man/gglistGrob.Rd | 34 ++++++++++++++--------------- 7 files changed, 89 insertions(+), 83 deletions(-)
Title: Approximate Optimal Experimental Designs Using Generalised
Linear Mixed Models
Description: Optimal design analysis algorithms for any study design that can be represented or
modelled as a generalised linear mixed model including cluster randomised trials,
cohort studies, spatial and temporal epidemiological studies, and split-plot designs.
See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a
detailed manual on model specification. A detailed discussion of the methods in this
package can be found in Watson, Hemming, and Girling (2023) <doi:10.1177/09622802231202379>.
Author: Sam Watson [aut, cre],
Yi Pan [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrOptim versions 0.3.5 dated 2024-06-02 and 0.3.6 dated 2024-12-17
glmmrOptim-0.3.5/glmmrOptim/src/openmp_utils.cpp |only glmmrOptim-0.3.6/glmmrOptim/DESCRIPTION | 8 glmmrOptim-0.3.6/glmmrOptim/MD5 | 19 - glmmrOptim-0.3.6/glmmrOptim/R/R6designspace.R | 38 ++- glmmrOptim-0.3.6/glmmrOptim/R/RcppExports.R | 20 -- glmmrOptim-0.3.6/glmmrOptim/build/partial.rdb |binary glmmrOptim-0.3.6/glmmrOptim/inst/include/optim/optimclass.h | 2 glmmrOptim-0.3.6/glmmrOptim/inst/include/optim/optimderivatives.h | 4 glmmrOptim-0.3.6/glmmrOptim/man/apportion.Rd | 98 +++++----- glmmrOptim-0.3.6/glmmrOptim/src/RcppExports.cpp | 24 +- glmmrOptim-0.3.6/glmmrOptim/src/gd_search.cpp | 34 +++ 11 files changed, 141 insertions(+), 106 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, and push the image to
DockerHub.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.0 dated 2024-12-09 and 0.1.1 dated 2024-12-17
DESCRIPTION | 8 +-- MD5 | 20 ++++----- NEWS.md | 20 +++++++++ R/build.R | 4 - R/create.R | 53 +++++------------------ R/dockerfile.R |only R/utils.R |only README.md | 95 ++++++++++++++++++++++++++++++++----------- man/build.Rd | 4 - man/create.Rd | 22 ++++----- tests/testthat/test-build.R | 89 ++++++++++++++++++++++++++++++++++++++-- tests/testthat/test-create.R | 9 +++- 12 files changed, 226 insertions(+), 98 deletions(-)
Title: Statistical Evaluation of UMAP Dimensionality Reductions
Description: A metric expressing the quality of a UMAP layout. This is a
package that contains the Saturn_coefficient() function that reads an
input matrix, its dimensionality reduction produced by UMAP, and
evaluates the quality of this dimensionality reduction by producing a
real value in the [0; 1] interval. We call this real value Saturn
coefficient. A higher value means better dimensionality reduction; a
lower value means worse dimensionality reduction.
Reference: Davide Chicco et al. "The Saturn coefficient for evaluating
the quality of UMAP dimensionality reduction results" (2025, in preparation).
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between SaturnCoefficient versions 1.2 dated 2024-12-11 and 1.3 dated 2024-12-17
SaturnCoefficient-1.2/SaturnCoefficient/man/three_metrics.Rd |only SaturnCoefficient-1.3/SaturnCoefficient/DESCRIPTION | 12 +++++----- SaturnCoefficient-1.3/SaturnCoefficient/MD5 | 8 +++--- SaturnCoefficient-1.3/SaturnCoefficient/NAMESPACE | 2 - SaturnCoefficient-1.3/SaturnCoefficient/R/Saturn_coefficient.r | 5 ++-- SaturnCoefficient-1.3/SaturnCoefficient/man/calculatesSaturnContinuityTrustworthiness.Rd |only 6 files changed, 14 insertions(+), 13 deletions(-)
More information about SaturnCoefficient at CRAN
Permanent link
Title: Geospatial Data and Maps for New South Wales, Australia
Description: Geospatial data for creating maps of New South Wales (NSW),
Australia, and some helpers to work with common problems like normalising
postcodes. Registers its data with 'cartographer'.
Author: Carl Suster [aut, cre] ,
Western Sydney Local Health District, NSW Health [cph]
Maintainer: Carl Suster <Carl.Suster@health.nsw.gov.au>
Diff between nswgeo versions 0.4.0 dated 2024-01-29 and 0.5.0 dated 2024-12-17
DESCRIPTION | 10 ++++---- LICENSE | 2 - MD5 | 42 +++++++++++++++++----------------- NEWS.md | 6 ++++ R/data.R | 29 ++++++++++++++++++----- R/utils.R | 16 ++++++++---- R/zzz.R | 2 - README.md | 40 +++++++++++++++++++++++++++++--- data/act.rda |binary data/jbt.rda |binary data/lga_nsw.rda |binary data/lhi.rda |binary data/nsw.rda |binary data/poa_lhd_concordance.rda |binary data/poa_nsw.rda |binary man/crs_gda2020.Rd | 6 +++- man/figures/README-cartographer-1.png |binary man/figures/README-ggplot-1.png |binary man/lhd.Rd | 5 +++- man/nsw.Rd | 4 +-- man/nsw_admin.Rd | 17 +++++++++++-- man/poa_lhd_concordance.Rd | 7 +++++ 22 files changed, 136 insertions(+), 50 deletions(-)
Title: Geographical Ecology and Conservation Knowledge Online
Description: Includes a collection of geographical analysis functions aimed primarily at ecology and conservation science studies, allowing processing of both point and raster data. Now integrates SPECTRE (<https://biodiversityresearch.org/spectre/>), a dataset of global geospatial threat data, developed by the authors.
Author: Vasco V. Branco [cre, aut] ,
Pedro Cardoso [aut] ,
Luis Correia [ctb]
Maintainer: Vasco V. Branco <vasco.branco@helsinki.fi>
Diff between gecko versions 1.0.0 dated 2023-11-23 and 1.0.1 dated 2024-12-17
gecko-1.0.0/gecko/README.md |only gecko-1.0.1/gecko/DESCRIPTION | 11 ++++++----- gecko-1.0.1/gecko/MD5 | 8 ++++---- gecko-1.0.1/gecko/R/aux_fn.R | 10 ++++++++-- gecko-1.0.1/gecko/R/outlier_fn.R | 2 +- gecko-1.0.1/gecko/man/figures |only 6 files changed, 19 insertions(+), 12 deletions(-)
Title: Robust Analytical Methods for Evaluating Educational
Interventions using Randomised Controlled Trials Designs
Description: Analysing data from evaluations of educational interventions using a randomised controlled trial design. Various analytical tools to perform sensitivity analysis using different methods are supported (e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The included commands can be used for simple randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other intervention designs using Frequentist and Bayesian multilevel models.
Author: Germaine Uwimpuhwe [aut, cre],
Qing Zhang [aut],
Akansha Singh [aut],
Dimitris Vallis [aut],
Jochen Einbeck [aut],
Steve Higgins [aut],
ZhiMin Xiao [aut],
Ewoud De Troyer [aut],
Adetayo Kasim [aut]
Maintainer: Germaine Uwimpuhwe <germaine.uwimpuhwe@durham.ac.uk>
Diff between eefAnalytics versions 1.1.3 dated 2024-10-20 and 1.1.4 dated 2024-12-17
eefAnalytics-1.1.3/eefAnalytics/R/hello.R |only eefAnalytics-1.1.4/eefAnalytics/DESCRIPTION | 8 eefAnalytics-1.1.4/eefAnalytics/MD5 | 44 eefAnalytics-1.1.4/eefAnalytics/NAMESPACE | 158 - eefAnalytics-1.1.4/eefAnalytics/NEWS.md | 2 eefAnalytics-1.1.4/eefAnalytics/R/crtBayes.R | 442 +-- eefAnalytics-1.1.4/eefAnalytics/R/mstBayes.R | 493 +--- eefAnalytics-1.1.4/eefAnalytics/R/mstFREQ.R | 1222 +++++----- eefAnalytics-1.1.4/eefAnalytics/R/srtBayes.R | 289 +- eefAnalytics-1.1.4/eefAnalytics/build/vignette.rds |binary eefAnalytics-1.1.4/eefAnalytics/inst/doc/eefAnalytics.R | 2 eefAnalytics-1.1.4/eefAnalytics/inst/doc/eefAnalytics.Rmd | 87 eefAnalytics-1.1.4/eefAnalytics/inst/doc/eefAnalytics.html | 198 + eefAnalytics-1.1.4/eefAnalytics/inst/examples/crtBExample.R | 117 eefAnalytics-1.1.4/eefAnalytics/inst/examples/mstBExample.R | 24 eefAnalytics-1.1.4/eefAnalytics/inst/examples/srtBExample.R | 107 eefAnalytics-1.1.4/eefAnalytics/inst/jags/CRT.txt | 22 eefAnalytics-1.1.4/eefAnalytics/inst/jags/MLM_UNC.txt | 90 eefAnalytics-1.1.4/eefAnalytics/inst/jags/MST-DW-PF24GQEJ.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/MST.txt | 55 eefAnalytics-1.1.4/eefAnalytics/man/crtBayes.Rd | 226 - eefAnalytics-1.1.4/eefAnalytics/man/mstBayes.Rd | 60 eefAnalytics-1.1.4/eefAnalytics/man/srtBayes.Rd | 202 - eefAnalytics-1.1.4/eefAnalytics/vignettes/eefAnalytics.Rmd | 87 24 files changed, 1921 insertions(+), 2014 deletions(-)
Title: Make, Update, and Query Binary Causal Models
Description: Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality (<DOI:10.1017/CBO9780511803161>).
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut] ,
Till Tietz [aut, cre] ,
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut] ,
Julio Solis [ctb],
Georgiy Syunyaev [aut]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between CausalQueries versions 1.3.0 dated 2024-12-14 and 1.3.1 dated 2024-12-17
DESCRIPTION | 6 MD5 | 71 ++++----- NEWS.md | 7 R/query_model.R | 7 inst/doc/a-getting-started.Rmd | 169 +++++---------------- inst/doc/a-getting-started.html | 302 ++++++++++++++++++--------------------- inst/doc/b-plotting.Rmd | 2 inst/doc/b-plotting.html | 23 +- inst/doc/c-canonical-models.Rmd | 74 ++------- inst/doc/c-canonical-models.html | 148 ++++++++----------- inst/doc/d-front-door.Rmd | 16 +- inst/doc/d-front-door.html | 60 ++++--- inst/doc/e-posteriors.Rmd | 196 ++++++++++++------------- inst/doc/e-posteriors.html | 216 ++++++++++++++------------- vignettes/a-getting-started.Rmd | 169 +++++---------------- vignettes/b-plotting.Rmd | 2 vignettes/b-plotting.Rmd.orig | 2 vignettes/c-canonical-models.Rmd | 74 ++------- vignettes/d-front-door.Rmd | 16 +- vignettes/e-posteriors.Rmd | 196 ++++++++++++------------- vignettes/unnamed-chunk-10-1.png |binary vignettes/unnamed-chunk-11-1.png |binary vignettes/unnamed-chunk-12-1.png |binary vignettes/unnamed-chunk-13-1.png |only vignettes/unnamed-chunk-14-1.png |binary vignettes/unnamed-chunk-15-1.png |binary vignettes/unnamed-chunk-16-1.png |binary vignettes/unnamed-chunk-19-1.png |only vignettes/unnamed-chunk-2-1.png |binary vignettes/unnamed-chunk-21-1.png |binary vignettes/unnamed-chunk-23-1.png |only vignettes/unnamed-chunk-3-1.png |binary vignettes/unnamed-chunk-4-1.png |binary vignettes/unnamed-chunk-5-1.png |binary vignettes/unnamed-chunk-6-1.png |binary vignettes/unnamed-chunk-7-1.png |binary vignettes/unnamed-chunk-8-1.png |binary vignettes/unnamed-chunk-9-1.png |binary 38 files changed, 758 insertions(+), 998 deletions(-)
Title: Regression Toward the Mean
Description: In repeated measures studies with extreme large or small values it is common
that the subjects measurements on average are closer to the mean of the basic population.
Interpreting possible changes in the mean in such situations can lead to biased results
since the values were not randomly selected, they come from truncated sampling.
This method allows to estimate the range of means where treatment effects are likely to occur
when regression toward the mean is present.
Ostermann, T., Willich, Stefan N. & Luedtke, Rainer. (2008). Regression toward the mean - a detection method for unknown population mean based on Mee and Chua's algorithm. BMC Medical Research Methodology.<doi:10.1186/1471-2288-8-52>.
Acknowledgments: We would like to acknowledge "Lena Roth" and "Nico Steckhan" for the package's initial updates (Q3 2024) and continued supervision and guidance. Both have contributed to discussing and integrating these methods into the package, ensuring they are up-to-date and con [...truncated...]
Author: Daniela Recchia [aut, cre],
Thomas Ostermann [ctb],
Julian Stein [ctb]
Maintainer: Daniela Recchia <daniela.rodriguesrecchia@uni-wh.de>
Diff between regtomean versions 1.1 dated 2022-10-26 and 1.2 dated 2024-12-17
regtomean-1.1/regtomean/R/globals.R |only regtomean-1.2/regtomean/DESCRIPTION | 22 ++++--- regtomean-1.2/regtomean/LICENSE | 2 regtomean-1.2/regtomean/MD5 | 38 +++++++----- regtomean-1.2/regtomean/NAMESPACE | 36 ++++++----- regtomean-1.2/regtomean/R/cordata.R | 69 +++++++++++++--------- regtomean-1.2/regtomean/R/meechua_eff.CI.R | 80 ++++++++++++++++++++------ regtomean-1.2/regtomean/R/meechua_plot.R | 34 +++++++---- regtomean-1.2/regtomean/R/meechua_reg.R | 40 +++---------- regtomean-1.2/regtomean/R/plot_mu.R |only regtomean-1.2/regtomean/R/plot_t.R |only regtomean-1.2/regtomean/R/replicate_data.R | 36 +++-------- regtomean-1.2/regtomean/R/zzz.R |only regtomean-1.2/regtomean/README.md |only regtomean-1.2/regtomean/man/cordata.Rd | 14 ++-- regtomean-1.2/regtomean/man/language_test.Rd | 1 regtomean-1.2/regtomean/man/meechua_eff.CI.Rd | 35 +++++++---- regtomean-1.2/regtomean/man/meechua_plot.Rd | 34 ++++++++--- regtomean-1.2/regtomean/man/meechua_reg.Rd | 48 ++++++++++++--- regtomean-1.2/regtomean/man/plot_mu.Rd |only regtomean-1.2/regtomean/man/plot_t.Rd |only regtomean-1.2/regtomean/man/replicate_data.Rd | 61 ++++++++++++++----- regtomean-1.2/regtomean/tests |only 23 files changed, 346 insertions(+), 204 deletions(-)
Title: Feature Finder
Description: Finds features through a detailed analysis of model residuals using rpart classification and regression trees. Scans the residuals of a model across subsets of the data to identify areas where the model differs from the actual data.
Author: Richard Davis [aut, cre]
Maintainer: Richard Davis <davisconsulting@gmail.com>
Diff between featurefinder versions 1.1 dated 2018-12-03 and 1.2 dated 2024-12-17
featurefinder-1.1/featurefinder/data/examples.rda |only featurefinder-1.1/featurefinder/data/futuresdata.rda |only featurefinder-1.1/featurefinder/data/mpgdata.rda |only featurefinder-1.1/featurefinder/inst/doc/featurefinder.R |only featurefinder-1.1/featurefinder/inst/doc/featurefinder.Rmd |only featurefinder-1.1/featurefinder/inst/doc/featurefinder.html |only featurefinder-1.1/featurefinder/man/addFeatures.Rd |only featurefinder-1.1/featurefinder/man/dat.Rd |only featurefinder-1.1/featurefinder/man/dat0.Rd |only featurefinder-1.1/featurefinder/man/doAllFactors.Rd |only featurefinder-1.1/featurefinder/man/expr.Rd |only featurefinder-1.1/featurefinder/man/fileConn.Rd |only featurefinder-1.1/featurefinder/man/filename.Rd |only featurefinder-1.1/featurefinder/man/futuresdata.Rd |only featurefinder-1.1/featurefinder/man/i.Rd |only featurefinder-1.1/featurefinder/man/mainfaclevels.Rd |only featurefinder-1.1/featurefinder/man/maxFactorLevels.Rd |only featurefinder-1.1/featurefinder/man/mpgdata.Rd |only featurefinder-1.1/featurefinder/man/names.Rd |only featurefinder-1.1/featurefinder/man/pathterms.Rd |only featurefinder-1.1/featurefinder/man/runname.Rd |only featurefinder-1.1/featurefinder/man/splitlist.Rd |only featurefinder-1.1/featurefinder/man/t.Rd |only featurefinder-1.1/featurefinder/man/tree.Rd |only featurefinder-1.1/featurefinder/man/treeGenerationMinBucket.Rd |only featurefinder-1.1/featurefinder/man/treeSummaryMinBucket.Rd |only featurefinder-1.1/featurefinder/man/treeSummaryResidualMagnitudeThreshold.Rd |only featurefinder-1.1/featurefinder/man/treeSummaryResidualThreshold.Rd |only featurefinder-1.1/featurefinder/man/trees.Rd |only featurefinder-1.1/featurefinder/man/treesAll.Rd |only featurefinder-1.1/featurefinder/man/vars.Rd |only featurefinder-1.1/featurefinder/vignettes/featurefinder.Rmd |only featurefinder-1.1/featurefinder/vignettes/futuresdata.csv |only featurefinder-1.1/featurefinder/vignettes/mpgdata.csv |only featurefinder-1.1/featurefinder/vignettes/vignettefigures |only featurefinder-1.2/featurefinder/DESCRIPTION | 23 featurefinder-1.2/featurefinder/LICENSE | 4 featurefinder-1.2/featurefinder/MD5 | 72 featurefinder-1.2/featurefinder/NAMESPACE | 23 featurefinder-1.2/featurefinder/R/featurefinder.r | 1455 +++------- featurefinder-1.2/featurefinder/build/vignette.rds |binary featurefinder-1.2/featurefinder/data/mycsv.rda |only featurefinder-1.2/featurefinder/inst/doc/my-vignette.R | 5 featurefinder-1.2/featurefinder/inst/doc/my-vignette.Rmd | 5 featurefinder-1.2/featurefinder/inst/doc/my-vignette.html | 408 ++ featurefinder-1.2/featurefinder/inst/extdata/featurefinder.pdf |only featurefinder-1.2/featurefinder/inst/extdata/test |only featurefinder-1.2/featurefinder/man/data.Rd | 17 featurefinder-1.2/featurefinder/man/findFeatures.Rd | 166 - featurefinder-1.2/featurefinder/man/generateResidualCutoffCode.Rd | 12 featurefinder-1.2/featurefinder/man/generateTrees.Rd | 16 featurefinder-1.2/featurefinder/man/getVarAv.Rd | 6 featurefinder-1.2/featurefinder/man/parseSplits.Rd | 6 featurefinder-1.2/featurefinder/man/printResiduals.Rd | 22 featurefinder-1.2/featurefinder/man/saveTree.Rd | 21 featurefinder-1.2/featurefinder/vignettes/my-vignette.Rmd |only 56 files changed, 970 insertions(+), 1291 deletions(-)
Title: Deductive Rational Method
Description: Apply the Deductive Rational Method to a monthly series of flow or precipitation data to fill in missing data. The method is as described in: Campos, D.F., (1984, ISBN:9686194444).
Author: Alonso Arriagada [aut, cre]
Maintainer: Alonso Arriagada <alonso.arriagada@usach.cl>
Diff between DeductiveR versions 1.0.0 dated 2021-12-03 and 1.1.0 dated 2024-12-17
DESCRIPTION | 14 + MD5 | 31 ++-- NAMESPACE | 4 R/DR_SVC_package.R |only R/DR_boxplot_package.R |only R/DR_package.R | 3 R/DR_plot_package.R | 1 R/data.R |only build/vignette.rds |binary data |only inst/doc/DeductiveR.R | 2 inst/doc/DeductiveR.Rmd | 5 inst/doc/DeductiveR.html | 360 ++++++++++++++++++++++++++++++++++++++--------- man/DR.Rd | 34 ++-- man/DR_SVC.Rd |only man/DR_boxplot.Rd |only man/DR_plot.Rd | 2 man/DR_stats.Rd | 2 man/data.Rd |only vignettes/DeductiveR.Rmd | 5 20 files changed, 353 insertions(+), 110 deletions(-)
Title: Interface with 'Nominatim' API Service
Description: Lite interface for getting data from 'OSM' service
'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract
coordinates from addresses, find places near a set of coordinates and
return spatial objects on 'sf' format.
Author: Diego Hernangomez [aut, cre, cph]
,
Jindra Lacko [ctb, rev] ,
Alex White [ctb],
OpenStreetMap [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between nominatimlite versions 0.4.1 dated 2024-07-19 and 0.4.2 dated 2024-12-17
DESCRIPTION | 8 - MD5 | 26 ++-- NEWS.md | 4 R/nominatim_check_access.R | 208 ++++++++++++++++---------------- README.md | 25 ++- build/vignette.rds |binary data/osm_amenities.rda |binary inst/doc/nominatimlite.Rmd | 12 - inst/doc/nominatimlite.html | 21 +-- inst/schemaorg.json | 4 man/figures/README-line-object-1.png |binary man/figures/README-pizzahut-1.png |binary man/figures/README-statue_liberty-1.png |binary vignettes/nominatimlite.Rmd | 12 - 14 files changed, 162 insertions(+), 158 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.2.1 dated 2024-11-26 and 1.3.0 dated 2024-12-17
DESCRIPTION | 37 ++++++++------- MD5 | 34 ++++++++------ NAMESPACE | 2 NEWS.md | 6 ++ R/ArchiveAsyncTuningFrozen.R |only R/ObjectiveTuningAsync.R | 6 -- R/TunerBatchIrace.R | 10 ++-- R/TuningInstanceAsyncMulticrit.R | 9 ++- R/TuningInstanceAsyncSingleCrit.R | 10 ++-- R/TuningInstanceBatchMulticrit.R | 10 ++-- R/TuningInstanceBatchSingleCrit.R | 10 ++-- R/mlr_callbacks.R | 22 +++++++++ R/zzz.R | 1 man/ArchiveAsyncTuningFrozen.Rd |only man/mlr3tuning.async_freeze_archive.Rd |only man/mlr_tuners_irace.Rd | 4 + tests/testthat/test_ArchiveAsyncTuningFrozen.R |only tests/testthat/test_TunerBatchIrace.R | 47 ++++++++++++++------ tests/testthat/test_TuningInstanceBatchSingleCrit.R | 37 +++++++++++++++ tests/testthat/test_mlr_callbacks.R | 37 +++++++++++++++ 20 files changed, 207 insertions(+), 75 deletions(-)
Title: Convert Digital Images into 'SpatRaster' Objects
Description: Generate 'SpatRaster' objects, as defined by the 'terra'
package, from digital images, using a specified spatial object as a
geographical reference.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rasterpic versions 0.2.5 dated 2024-04-12 and 0.2.6 dated 2024-12-17
DESCRIPTION | 12 +- MD5 | 30 +++--- NEWS.md | 96 ++++++++++--------- R/asp_ratio.R | 2 R/test_helpers.R | 26 ++--- R/utils.R | 240 ++++++++++++++++++++++++------------------------ README.md | 20 ++-- build/vignette.rds |binary inst/CITATION | 12 +- inst/doc/rasterpic.Rmd | 204 ++++++++++++++++++++-------------------- inst/img/UK_flag.png |binary inst/img/vertical.jpeg |binary inst/img/vertical.jpg |binary inst/schemaorg.json | 6 - tests/testthat.R | 4 vignettes/rasterpic.Rmd | 204 ++++++++++++++++++++-------------------- 16 files changed, 432 insertions(+), 424 deletions(-)
Title: Univariate Outlier Detection
Description: Detect outliers in one-dimensional data.
Author: Mark van der Loo [cre, aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between extremevalues versions 2.3.4 dated 2024-02-13 and 2.4.1 dated 2024-12-17
extremevalues-2.3.4/extremevalues/R/evGui.r |only extremevalues-2.3.4/extremevalues/man/evGui.Rd |only extremevalues-2.4.1/extremevalues/DESCRIPTION | 14 +++++++++----- extremevalues-2.4.1/extremevalues/MD5 | 12 +++++------- extremevalues-2.4.1/extremevalues/NAMESPACE | 5 ++--- extremevalues-2.4.1/extremevalues/NEWS | 4 ++++ extremevalues-2.4.1/extremevalues/build/vignette.rds |binary extremevalues-2.4.1/extremevalues/inst/doc/SN201003.pdf |binary 8 files changed, 20 insertions(+), 15 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/> [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 0.8.2 dated 2022-09-11 and 1.0.0 dated 2024-12-17
DESCRIPTION | 14 MD5 | 101 +-- NAMESPACE | 3 NEWS.md | 25 R/frag.edges.weighting.R | 204 +++--- R/frag.get.layers.pair.R | 10 R/frag.get.parameters.R | 31 R/frag.graph.plot.R | 9 R/frag.graph.reduce.R |only R/frag.layers.admixture.R | 25 R/frag.layers.cohesion.R | 37 - R/frag.relations.by.layers.R | 37 - R/frag.simul.compare.R | 29 R/frag.simul.process.R | 13 R/frag.simul.summarise.R | 11 R/make_frag_object.R | 42 - R/utils.R | 4 TODO |only build/vignette.rds |binary data/BoutDesVergnes.RData |only data/Chauzeys.RData |only data/FontJuvenal.RData |only data/GrandeRivoire.RData |only data/LiangAbu.RData |binary data/Tai.RData |only inst/CITATION | 4 inst/doc/archeofrag-vignette.R | 28 inst/doc/archeofrag-vignette.Rmd | 4 inst/doc/archeofrag-vignette.html | 901 +++++++++++++++++----------- man/BoutDesVergnes.Rd |only man/Chauzeys.Rd |only man/FontJuvenal.Rd |only man/GrandeRivoire.Rd |only man/LiangAbu.Rd | 31 man/Tai.Rd |only man/archeofrag-package.Rd | 9 man/frag.edges.weighting.Rd | 13 man/frag.get.layers.Rd | 10 man/frag.get.layers.pair.Rd | 13 man/frag.get.parameters.Rd | 29 man/frag.graph.plot.Rd | 4 man/frag.graph.reduce.Rd |only man/frag.layers.admixture.Rd | 27 man/frag.layers.cohesion.Rd | 25 man/frag.observer.failure.Rd | 2 man/frag.relations.by.layers.Rd | 2 man/frag.simul.compare.Rd | 5 man/frag.simul.process.Rd | 32 man/frag.simul.summarise.Rd | 8 tests/testthat/test-frag.diameters.R | 4 tests/testthat/test-frag.edges.weighting.R | 59 + tests/testthat/test-frag.layers.admixture.R | 38 + tests/testthat/test-frag.layers.cohesion.R | 38 + tests/testthat/test-frag.simul.compare.R | 17 tests/testthat/test-frag.simul.process.R | 11 tests/testthat/test-frag.simul.summarise.R | 8 tests/testthat/test.frag.get.parameters.R | 21 vignettes/archeofrag-vignette.Rmd | 4 58 files changed, 1225 insertions(+), 717 deletions(-)
Title: Working with netCDF for Essential Biodiversity Variables
Description: The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>)
comes with a data structure based on the Network Common Data Form (netCDF).
The 'ebvcube' 'R' package provides functionality to easily create, access and
visualise this data. The EBV netCDFs can be downloaded from the EBV Data
Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
Author: Luise Quoss [aut, cre] ,
Nestor Fernandez [aut] ,
Christian Langer [aut] ,
Jose Valdez [aut] ,
Henrique Miguel Pereira [aut]
Maintainer: Luise Quoss <luise.quoss@idiv.de>
Diff between ebvcube versions 0.3.1 dated 2024-12-05 and 0.3.3 dated 2024-12-17
ebvcube-0.3.1/ebvcube/inst/docs/ebvcube_0.2.2.pdf |only ebvcube-0.3.1/ebvcube/inst/docs/ebvcube_0.3.1.pdf |only ebvcube-0.3.3/ebvcube/DESCRIPTION | 8 ebvcube-0.3.3/ebvcube/MD5 | 15 ebvcube-0.3.3/ebvcube/NEWS.md | 10 ebvcube-0.3.3/ebvcube/R/ebvcube-package.R | 30 - ebvcube-0.3.3/ebvcube/README.md | 18 ebvcube-0.3.3/ebvcube/inst/docs/ebvcube_0.3.3.pdf |only ebvcube-0.3.3/ebvcube/man/ebvcube.Rd | 2 ebvcube-0.3.3/ebvcube/tests/testthat/test-ebv_utils.R | 482 +++++++++--------- 10 files changed, 287 insertions(+), 278 deletions(-)
Title: Geocoding with the 'ArcGIS' REST API Service
Description: Lite interface for finding locations of addresses or
businesses around the world using the 'ArcGIS' REST API service
<https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Address text can be converted to location candidates and a location
can be converted into an address. No API key required.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between arcgeocoder versions 0.2.0 dated 2024-03-21 and 0.2.1 dated 2024-12-17
DESCRIPTION | 11 - MD5 | 42 +-- NEWS.md | 4 R/arc_geo.R | 398 ++++++++++++++++++------------------- R/arc_geo_categories.R | 6 R/arcgeocoder_check_access.R | 19 - R/utils.R | 313 ++++++++++++++--------------- README.md | 59 +++-- build/vignette.rds |binary data/arc_categories.rda |binary data/arc_spatial_references.rda |binary inst/CITATION | 16 - inst/doc/arcgeocoder.Rmd | 26 +- inst/doc/arcgeocoder.html | 60 ++--- inst/doc/featuretypes.Rmd | 78 ++----- inst/doc/featuretypes.html | 183 ++++++----------- inst/schemaorg.json | 6 man/figures/README-eiffel-1.png |binary man/figures/README-eiffel_sf-1.png |binary vignettes/arcgeocoder.Rmd | 26 +- vignettes/eiffel-1.png |binary vignettes/featuretypes.Rmd | 78 ++----- 22 files changed, 626 insertions(+), 699 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/ [...truncated...]
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang [...truncated...]
Maintainer: Xiaolei Liu <xll198708@gmail.com>
Diff between rMVP versions 1.1.1 dated 2024-08-31 and 1.3.0 dated 2024-12-17
DESCRIPTION | 13 MD5 | 68 ++-- NAMESPACE | 3 R/MVP.Data.r | 60 ++-- R/MVP.FarmCPU.r | 115 +++++-- R/MVP.GLM.r | 28 + R/MVP.K.VanRaden.r | 72 +--- R/MVP.MLM.r | 27 + R/MVP.PCA.r | 14 R/MVP.Report.r | 4 R/MVP.Utility.r | 13 R/MVP.r | 166 ++++++++--- R/RcppExports.R | 28 + R/exports.R | 6 inst/extdata/05_mvp/mvp.geno.bin |binary inst/extdata/05_mvp/mvp.geno.desc | 6 inst/extdata/06_mvp-impute/mvp.imp.geno.bin |binary inst/extdata/06_mvp-impute/mvp.imp.geno.desc | 6 man/MVP.Data.Kin.Rd | 3 man/MVP.Data.PC.Rd | 3 man/MVP.Data.Rd | 10 man/MVP.Data.impute.Rd | 3 man/MVP.FarmCPU.Rd | 14 man/MVP.GLM.Rd | 21 + man/MVP.K.VanRaden.Rd | 14 man/MVP.MLM.Rd | 17 - man/MVP.PCA.Rd | 14 man/MVP.Rd | 12 man/MVP.Version.Rd | 2 src/RcppExports.cpp | 75 +++-- src/assoc.cpp | 399 +++++++++++++++++++-------- src/data_converter.cpp | 71 ++-- src/impute.cpp | 206 ++++++++++--- src/kinship.cpp | 270 +++++++++++++++--- src/mvp_omp.h | 2 35 files changed, 1234 insertions(+), 531 deletions(-)
Title: Intergovernmental Organizations Database
Description: Tools to extract information from the Intergovernmental
Organizations ('IGO') Database , version 3, provided by the Correlates
of War Project <https://correlatesofwar.org/>. See also Pevehouse, J.
C. et al. (2020). Version 3 includes information from 1815 to 2014.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between igoR versions 0.2.0 dated 2024-02-05 and 0.2.1 dated 2024-12-17
DESCRIPTION | 16 - MD5 | 62 ++-- NEWS.md | 22 - R/data.R | 4 R/igo_dyadic.R | 574 ++++++++++++++++++++++---------------------- R/igo_members.R | 2 R/igo_search.R | 2 R/igo_search_states.R | 2 R/igo_state_membership.R | 2 R/sysdata.rda |binary README.md | 81 +++--- build/partial.rdb |binary build/vignette.rds |binary data/igo_year_format3.rda |binary data/state_year_format3.rda |binary data/states2016.rda |binary inst/CITATION | 72 ++--- inst/WORDLIST | 1 inst/doc/igoR.Rmd | 2 inst/doc/igoR.html | 23 - inst/doc/mapping.Rmd | 36 +- inst/doc/mapping.html | 67 ++--- inst/schemaorg.json | 6 man/igo_dyadic.Rd | 2 man/igo_members.Rd | 2 man/igo_search.Rd | 2 man/igo_state_membership.Rd | 2 vignettes/AustShared-1.png |binary vignettes/NAShared-1.png |binary vignettes/UNMaps-1.png |binary vignettes/igoR.Rmd | 2 vignettes/mapping.Rmd | 36 +- 32 files changed, 516 insertions(+), 504 deletions(-)
Title: Progress Bar for Parallel Tasks
Description: A simple interface in the form of R6 classes for executing tasks in
parallel, tracking their progress, and displaying accurate progress bars.
Author: Mihai Constantin [aut, cre]
Maintainer: Mihai Constantin <mihai@mihaiconstantin.com>
Diff between parabar versions 1.3.0 dated 2024-12-10 and 1.4.2 dated 2024-12-17
DESCRIPTION | 6 +++--- MD5 | 11 +++++++---- NEWS.md | 20 ++++++++++++++++++++ README.md | 2 +- build/vignette.rds |binary inst/doc/foreach.Rmd |only inst/doc/foreach.html |only vignettes/foreach.Rmd |only 8 files changed, 31 insertions(+), 8 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Jeremie Dubois-Lacoste [aut],
Leslie Perez Caceres [aut],
Thomas Stuetzle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 4.0 dated 2024-11-26 and 4.1 dated 2024-12-17
irace-4.0/irace/tests/testthat/test-bug-blocksize.R |only irace-4.1/irace/DESCRIPTION | 6 irace-4.1/irace/MD5 | 103 +- irace-4.1/irace/NEWS.md | 33 irace-4.1/irace/R/ablation.R | 61 - irace-4.1/irace/R/configurations.R | 2 irace-4.1/irace/R/generation.R | 2 irace-4.1/irace/R/irace.R | 33 irace-4.1/irace/R/model.R | 6 irace-4.1/irace/R/multi_irace.R | 12 irace-4.1/irace/R/parameters.R | 27 irace-4.1/irace/R/psRace.R | 114 +- irace-4.1/irace/R/race-wrapper.R | 16 irace-4.1/irace/R/race.R | 429 ++++----- irace-4.1/irace/R/race_state.R | 12 irace-4.1/irace/R/readParameters.R | 6 irace-4.1/irace/R/scenario.R | 4 irace-4.1/irace/R/testing.R | 5 irace-4.1/irace/R/utils.R | 24 irace-4.1/irace/R/version.R | 2 irace-4.1/irace/build/partial.rdb |binary irace-4.1/irace/inst/doc/irace-package.Rnw | 17 irace-4.1/irace/inst/doc/irace-package.pdf |binary irace-4.1/irace/inst/exdata/irace-acotsp.Rdata |binary irace-4.1/irace/inst/exdata/log-ablation.Rdata |binary irace-4.1/irace/inst/exdata/sann.rda |binary irace-4.1/irace/man/ablation.Rd | 14 irace-4.1/irace/man/ablation_cmdline.Rd | 8 irace-4.1/irace/man/checkParameters.Rd | 2 irace-4.1/irace/man/configurations_print_command.Rd | 2 irace-4.1/irace/man/multi_irace.Rd | 12 irace-4.1/irace/man/parameters.Rd | 14 irace-4.1/irace/man/printParameters.Rd | 2 irace-4.1/irace/man/readConfigurationsFile.Rd | 2 irace-4.1/irace/man/target_evaluator_default.Rd | 2 irace-4.1/irace/man/target_runner_default.Rd | 2 irace-4.1/irace/tests/testthat/helper-common.R | 34 irace-4.1/irace/tests/testthat/test-GenericWrapper4AC.R | 7 irace-4.1/irace/tests/testthat/test-ablation-cmdline.R | 4 irace-4.1/irace/tests/testthat/test-ablation.R |only irace-4.1/irace/tests/testthat/test-blocksize.R | 9 irace-4.1/irace/tests/testthat/test-bug-10.R | 38 irace-4.1/irace/tests/testthat/test-capping.R | 51 - irace-4.1/irace/tests/testthat/test-maxTime.R | 4 irace-4.1/irace/tests/testthat/test-multi_irace.R | 12 irace-4.1/irace/tests/testthat/test-raceconfs.R | 32 irace-4.1/irace/tests/testthat/test-readParameters.R | 17 irace-4.1/irace/tests/testthat/test-repair.R | 4 irace-4.1/irace/tests/testthat/test-sann-irace.R | 22 irace-4.1/irace/tests/testthat/test-targeteval.R | 8 irace-4.1/irace/vignettes/examples.Rdata |binary irace-4.1/irace/vignettes/irace-acotsp-stdout.txt | 695 ++++++---------- irace-4.1/irace/vignettes/irace-package.Rnw | 17 irace-4.1/irace/vignettes/section/irace-options.tex |only 54 files changed, 945 insertions(+), 983 deletions(-)
Title: Gower's Distance
Description: Compute Gower's distance (or similarity) coefficient between records. Compute
the top-n matches between records. Core algorithms are executed in parallel on systems
supporting OpenMP.
Author: Mark van der Loo [aut, cre],
David Turner [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between gower versions 1.0.1 dated 2022-12-22 and 1.0.2 dated 2024-12-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/gower-pkg.R | 2 +- R/gower.R | 2 +- build/vignette.rds |binary inst/doc/intro.pdf |binary inst/tinytest/test_gower.R | 5 +++++ man/gower-package.Rd | 18 ++++++++++++++++++ 9 files changed, 41 insertions(+), 14 deletions(-)
Title: Lightweight Modern & Responsive Card Component for 'shiny'
Description: Responsive and modern 'HTML' card essentials for 'shiny' applications and dashboards. This novel card component in 'Bootstrap' provides a flexible and extensible content container with multiple variants and options for building robust 'R' based apps e.g for graph build or machine learning projects. The features rely on a combination of 'JQuery' <https://jquery.com> and 'CSS' styles to improve the card functionality.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between card.pro versions 2.2.0 dated 2024-09-28 and 2.2.1 dated 2024-12-17
DESCRIPTION | 8 MD5 | 33 +- NEWS.md | 6 R/cards.R | 10 R/misc.R | 11 README.md | 36 +- inst/bundle/opt/bjquery-ui.min.js | 12 inst/bundle/req/app.config.js | 318 --------------------- inst/bundle/req/app.min.js | 2 inst/bundle/req/bootstrap.min.js | 15 inst/bundle/req/prod.min.css | 2 inst/bundle/req/rembox.js | 513 ---------------------------------- inst/bundle/req/tpunch.min.js | 2 inst/doc/introduction_to_cardpro.html | 4 inst/shiny-test/app1/app.R | 113 ++++--- inst/shiny-test/app1/rsconnect |only man/card.pro.Rd | 6 man/use.cardpro.Rd | 5 18 files changed, 166 insertions(+), 930 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.4.1 dated 2024-11-27 and 1.5.0 dated 2024-12-17
DESCRIPTION | 12 +++---- MD5 | 36 +++++++++++---------- NAMESPACE | 1 NEWS.md | 7 ++++ R/ArchiveAsync.R | 6 +-- R/ArchiveAsyncFrozen.R |only R/ArchiveBatch.R | 6 +-- R/Codomain.R | 19 +++++++---- R/OptimInstanceBatch.R | 8 ++-- R/OptimizerAsync.R | 3 - R/OptimizerBatchIrace.R | 4 +- R/mlr_callbacks.R | 24 ++++++++++++++ R/zzz.R | 1 man/ArchiveAsyncFrozen.Rd |only man/Codomain.Rd | 15 +++++--- man/bbotk.async_freeze_archive.Rd |only man/mlr_optimizers_irace.Rd | 4 +- tests/testthat/test_ArchiveAsyncFrozen.R |only tests/testthat/test_OptimInstanceBatchSingleCrit.R | 2 - tests/testthat/test_OptimizerIrace.R | 2 - tests/testthat/test_mlr_callbacks.R | 33 +++++++++++++++++++ 21 files changed, 133 insertions(+), 50 deletions(-)
Title: Creating Composite Plots using 'aplot'
Description: Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Chun-Hui Gao [ctb] ,
Shensuo Li [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplotExtra versions 0.0.2 dated 2023-08-25 and 0.0.3 dated 2024-12-17
DESCRIPTION | 16 +++++++++------- MD5 | 10 ++++++---- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/aplotExtra-package.R |only R/oncoplot.r | 30 ++++++++++-------------------- man/aplotExtra-package.Rd |only 7 files changed, 31 insertions(+), 31 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre, cph]
,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.4.2 dated 2024-12-02 and 0.4.3 dated 2024-12-17
DESCRIPTION | 6 MD5 | 47 ++-- NEWS.md | 14 + R/create_wrds_dummy_database.R | 26 +- R/download_data_constituents.R | 196 ++++++++++--------- R/download_data_factors.R | 32 +-- R/download_data_fred.R | 67 +++--- R/download_data_macro_predictors.R | 11 - R/download_data_osap.R | 33 +-- R/download_data_stock_prices.R | 15 - R/download_data_wrds_compustat.R | 14 - R/download_data_wrds_crsp.R | 14 - R/download_data_wrds_trace_enhanced.R | 14 - R/handle_download_error.R | 2 R/validate.R |only README.md | 2 inst/doc/dates-in-tidyfinance.html | 16 - man/create_wrds_dummy_database.Rd | 11 - tests/testthat/test-create_wrds_dummy_database.R | 18 + tests/testthat/test-download_data_constituents.R | 42 ++-- tests/testthat/test-download_data_factors.R | 22 +- tests/testthat/test-download_data_fred.R | 27 +- tests/testthat/test-download_data_macro_predictors.R | 17 + tests/testthat/test-download_data_osap.R | 14 + tests/testthat/test-estimate_betas.R | 2 25 files changed, 375 insertions(+), 287 deletions(-)
Title: Versatile R Server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of
linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client
is included in this package as well. In addition, it can
also act as a secure WebSockets and HTTP/HTTPS server.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-13 dated 2023-11-28 and 1.8-15 dated 2024-12-17
DESCRIPTION | 18 +++-- MD5 | 39 +++++------ NAMESPACE | 2 NEWS | 63 ++++++++++++++++++ R/conn.R | 9 ++ R/zzz.R | 4 - inst/java/REngine.jar |binary inst/java/Rserve.jar |binary man/Rserve.http.add.static.Rd |only man/run.Rserve.Rd | 19 +++++ src/Makevars.win | 6 + src/Rserv.c | 98 +++++++++++++++++++++++++++- src/Rsrv.h | 4 - src/client/cxx/Rconnection.cc | 5 + src/client/cxx/Rconnection.h | 17 +++-- src/client/cxx/Rsrv.h | 4 - src/client/java/Rserve/Rserve.jar |binary src/http.c | 129 ++++++++++++++++++++++++++++---------- src/http.h | 11 +++ src/proxy/forward.c | 15 ++-- src/standalone.c | 15 ++++ 21 files changed, 374 insertions(+), 84 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula
models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and
Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Thomas Nagler [aut, cre],
Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between VineCopula versions 2.5.1 dated 2024-08-19 and 2.6.0 dated 2024-12-16
DESCRIPTION | 6 +-- MD5 | 15 ++++--- NAMESPACE | 1 NEWS.md | 12 ++++++ R/RVineLogLik.R | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 4 +- build/partial.rdb |binary man/RVineCDF.Rd |only src/logderiv.c | 5 +- 9 files changed, 131 insertions(+), 14 deletions(-)
Title: An Alternative Advanced Normalization Tools ('ANTs')
Description: Provides portable access from 'R' to biomedical image processing toolbox
'ANTs' by Avants et al. (2009) <doi:10.54294/uvnhin> via seamless
integration with the 'Python' implementation 'ANTsPy'. Allows biomedical
images to be processed in 'Python' and analyzed in 'R', and vice versa
via shared memory. See 'citation("rpyANTs")' for more reference information.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between rpyANTs versions 0.0.3 dated 2023-12-21 and 0.0.4 dated 2024-12-16
DESCRIPTION | 8 MD5 | 34 ++- NAMESPACE | 2 NEWS.md | 19 + R/aaa.R | 5 R/correction.R |only R/templates.R | 52 +++++ README.md | 14 - inst/rpyants/debug.py |only inst/rpyants/rpyants/registration/__init__.py | 1 inst/rpyants/rpyants/registration/halpern.py | 10 - inst/rpyants/rpyants/registration/normalization.py |only inst/rpyants/rpyants/registration/yael.py |only inst/rpyants/rpyants/utils/internals.py |only inst/rpyants/rpyants/utils/paths.py | 142 ++++++++++++++ inst/rpyants/rpyants/utils/transforms.py |only man/correct_intensity.Rd |only man/ensure_template.Rd |only man/figures/README-load-image-into-r-1.png |binary man/install_ants.Rd | 5 tests/testthat.R | 4 tests/testthat/test-transform.R | 201 +++++++++++++++++++++ 22 files changed, 459 insertions(+), 38 deletions(-)
Title: Fetch Economic and Financial Time Series Data from Public
Sources
Description: Download economic and financial time series from public sources,
including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics,
the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank,
the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.
Author: Abiel Reinhart [aut, cre]
Maintainer: Abiel Reinhart <abielr@gmail.com>
Diff between pdfetch versions 0.3.2 dated 2024-09-29 and 0.3.3 dated 2024-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/pdfetch.R | 15 ++++++++------- 4 files changed, 19 insertions(+), 14 deletions(-)
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Description: Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and
PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically
access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types.
Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between PubChemR versions 2.1.1 dated 2024-10-01 and 2.1.3 dated 2024-12-16
DESCRIPTION | 6 MD5 | 12 R/get_pug_rest.R | 36 inst/doc/Enhancing_Chemical_Data_Access_with_PubChemR.html | 25 inst/doc/Exploring_Chemical_Data_with_PubChemR.html | 109 inst/doc/Working_with_PubChemR_to_Access_Chemical_Data.html | 1591 ++++++------ tests/testthat/test-get_substances.R | 1 7 files changed, 903 insertions(+), 877 deletions(-)
Title: High Performance Remote File System, Database and 'Geospatial'
Access Using 'duckdb'
Description: Provides friendly wrappers for creating 'duckdb'-backed connections
to tabular datasets ('csv', parquet, etc) on local or remote file systems.
This mimics the behaviour of "open_dataset" in the 'arrow' package,
but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Author: Carl Boettiger [aut, cre] ,
Michael D. Sumner [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between duckdbfs versions 0.0.8 dated 2024-12-09 and 0.0.9 dated 2024-12-16
DESCRIPTION | 6 +-- MD5 | 11 +++-- NEWS.md | 4 ++ R/duckdb_config.R | 65 ++++++++++++++++++++++++----------- README.md | 4 +- man/load_spatial.Rd | 5 ++ tests/testthat/test-load_extension.R |only 7 files changed, 65 insertions(+), 30 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre] ,
Matthieu Stigler [ctb] ,
Eric Persson [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.6-3 dated 2023-08-28 and 0.6-4 dated 2024-12-16
rsdmx-0.6-3/rsdmx/man/getNamespaces.Rd |only rsdmx-0.6-3/rsdmx/man/getStructureType-methods.Rd |only rsdmx-0.6-3/rsdmx/man/namespaces.SDMX.Rd |only rsdmx-0.6-3/rsdmx/man/setDSD.Rd |only rsdmx-0.6-4/rsdmx/DESCRIPTION | 10 rsdmx-0.6-4/rsdmx/MD5 | 235 +++---- rsdmx-0.6-4/rsdmx/NAMESPACE | 208 ++---- rsdmx-0.6-4/rsdmx/R/SDMX-methods.R | 26 rsdmx-0.6-4/rsdmx/R/SDMXAgency-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXAgencyScheme-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXAttribute-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXCode-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXCodelist-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXCodelists-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXCompactData-methods.R | 5 rsdmx-0.6-4/rsdmx/R/SDMXComponents-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXConcept-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXConceptScheme-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXConcepts-methods.R | 8 rsdmx-0.6-4/rsdmx/R/SDMXCrossSectionalData-methods.R | 5 rsdmx-0.6-4/rsdmx/R/SDMXData-methods.R | 19 rsdmx-0.6-4/rsdmx/R/SDMXDataFlow-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXDataFlows-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXDataStructure-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXDataStructureDefinition-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXDataStructures-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXDimension-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXDotStatRequestBuilder-methods.R | 7 rsdmx-0.6-4/rsdmx/R/SDMXFooter-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXFooterMessage-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXGenericData-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXHeader-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXMessageGroup-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXOrganisation-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXOrganisationSchemes-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXPrimaryMeasure-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXREST20RequestBuilder-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXREST21RequestBuilder-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXRequestBuilder-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXRequestParams-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXSchema-methods.R | 1 rsdmx-0.6-4/rsdmx/R/SDMXServiceProvider-methods.R | 89 +- rsdmx-0.6-4/rsdmx/R/SDMXServiceProviders-methods.R | 3 rsdmx-0.6-4/rsdmx/R/SDMXStructureSpecificData-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXStructureSpecificTimeSeriesData-methods.R | 4 rsdmx-0.6-4/rsdmx/R/SDMXStructureType-methods.R | 14 rsdmx-0.6-4/rsdmx/R/SDMXTimeDimension-methods.R | 2 rsdmx-0.6-4/rsdmx/R/SDMXType-methods.R | 2 rsdmx-0.6-4/rsdmx/R/SDMXUtilityData-methods.R | 3 rsdmx-0.6-4/rsdmx/R/readSDMX.R | 4 rsdmx-0.6-4/rsdmx/R/rsdmx.R | 10 rsdmx-0.6-4/rsdmx/R/rsdmx_logger.R | 6 rsdmx-0.6-4/rsdmx/R/saveSDMX.R | 5 rsdmx-0.6-4/rsdmx/README.md | 43 - rsdmx-0.6-4/rsdmx/build/vignette.rds |binary rsdmx-0.6-4/rsdmx/inst/doc/quickstart.R | 58 - rsdmx-0.6-4/rsdmx/inst/doc/quickstart.Rmd | 38 - rsdmx-0.6-4/rsdmx/inst/doc/quickstart.html | 319 ++++++--- rsdmx-0.6-4/rsdmx/man/SDMX-methods.Rd |only rsdmx-0.6-4/rsdmx/man/SDMX.Rd | 106 +-- rsdmx-0.6-4/rsdmx/man/SDMXAgency.Rd | 56 - rsdmx-0.6-4/rsdmx/man/SDMXAgencyScheme.Rd | 114 +-- rsdmx-0.6-4/rsdmx/man/SDMXAttribute.Rd | 160 ++-- rsdmx-0.6-4/rsdmx/man/SDMXCode.Rd | 108 +-- rsdmx-0.6-4/rsdmx/man/SDMXCodelist.Rd | 124 +-- rsdmx-0.6-4/rsdmx/man/SDMXCodelists.Rd | 82 +- rsdmx-0.6-4/rsdmx/man/SDMXCompactData.Rd | 58 - rsdmx-0.6-4/rsdmx/man/SDMXComponents.Rd | 96 +- rsdmx-0.6-4/rsdmx/man/SDMXConcept.Rd | 126 +-- rsdmx-0.6-4/rsdmx/man/SDMXConceptScheme.Rd | 128 +-- rsdmx-0.6-4/rsdmx/man/SDMXConcepts.Rd | 92 +- rsdmx-0.6-4/rsdmx/man/SDMXCrossSectionalData.Rd | 58 - rsdmx-0.6-4/rsdmx/man/SDMXData-method.Rd |only rsdmx-0.6-4/rsdmx/man/SDMXData.Rd | 82 +- rsdmx-0.6-4/rsdmx/man/SDMXDataFlow.Rd | 130 ++-- rsdmx-0.6-4/rsdmx/man/SDMXDataFlows.Rd | 86 +- rsdmx-0.6-4/rsdmx/man/SDMXDataStructure.Rd | 128 +-- rsdmx-0.6-4/rsdmx/man/SDMXDataStructureDefinition.Rd | 104 +-- rsdmx-0.6-4/rsdmx/man/SDMXDataStructures.Rd | 86 +- rsdmx-0.6-4/rsdmx/man/SDMXDimension.Rd | 152 ++-- rsdmx-0.6-4/rsdmx/man/SDMXDotStatRequestBuilder.Rd | 136 ++-- rsdmx-0.6-4/rsdmx/man/SDMXFooter.Rd | 100 +-- rsdmx-0.6-4/rsdmx/man/SDMXFooterMessage.Rd | 104 +-- rsdmx-0.6-4/rsdmx/man/SDMXGenericData.Rd | 70 +- rsdmx-0.6-4/rsdmx/man/SDMXHeader.Rd | 146 ++-- rsdmx-0.6-4/rsdmx/man/SDMXItemScheme.Rd | 40 - rsdmx-0.6-4/rsdmx/man/SDMXMessageGroup.Rd | 70 +- rsdmx-0.6-4/rsdmx/man/SDMXOrganisation.Rd | 98 +-- rsdmx-0.6-4/rsdmx/man/SDMXOrganisationScheme.Rd | 42 - rsdmx-0.6-4/rsdmx/man/SDMXOrganisationSchemes.Rd | 82 +- rsdmx-0.6-4/rsdmx/man/SDMXPrimaryMeasure.Rd | 110 +-- rsdmx-0.6-4/rsdmx/man/SDMXREST20RequestBuilder.Rd | 147 ++-- rsdmx-0.6-4/rsdmx/man/SDMXREST21RequestBuilder.Rd | 149 ++-- rsdmx-0.6-4/rsdmx/man/SDMXRequestBuilder.Rd | 237 +++---- rsdmx-0.6-4/rsdmx/man/SDMXRequestParams.Rd | 189 ++--- rsdmx-0.6-4/rsdmx/man/SDMXSchema.Rd | 80 +- rsdmx-0.6-4/rsdmx/man/SDMXServiceProvider.Rd | 128 +-- rsdmx-0.6-4/rsdmx/man/SDMXServiceProviders.Rd | 76 +- rsdmx-0.6-4/rsdmx/man/SDMXStructureSpecificData.Rd | 70 +- rsdmx-0.6-4/rsdmx/man/SDMXStructureSpecificTimeSeriesData.Rd | 70 +- rsdmx-0.6-4/rsdmx/man/SDMXStructureType-methods.Rd |only rsdmx-0.6-4/rsdmx/man/SDMXStructureType.Rd | 78 +- rsdmx-0.6-4/rsdmx/man/SDMXTimeDimension.Rd | 126 +-- rsdmx-0.6-4/rsdmx/man/SDMXType.Rd | 96 +- rsdmx-0.6-4/rsdmx/man/SDMXUtilityData.Rd | 70 +- rsdmx-0.6-4/rsdmx/man/addSDMXServiceProvider.Rd | 80 +- rsdmx-0.6-4/rsdmx/man/findNamespace.Rd | 68 +- rsdmx-0.6-4/rsdmx/man/findSDMXServiceProvider.Rd | 66 +- rsdmx-0.6-4/rsdmx/man/getRegistryInterfaceResult.Rd | 58 - rsdmx-0.6-4/rsdmx/man/getSDMXServiceProviders.Rd | 50 - rsdmx-0.6-4/rsdmx/man/getSoapRequestResult.Rd | 58 - rsdmx-0.6-4/rsdmx/man/isRegistryInterfaceEnvelope.Rd | 62 - rsdmx-0.6-4/rsdmx/man/isSoapRequestEnvelope.Rd | 62 - rsdmx-0.6-4/rsdmx/man/readSDMX.Rd | 324 +++++----- rsdmx-0.6-4/rsdmx/man/rsdmx.Rd | 43 - rsdmx-0.6-4/rsdmx/man/rsdmxLogger.Rd | 5 rsdmx-0.6-4/rsdmx/man/saveSDMX.Rd | 55 - rsdmx-0.6-4/rsdmx/man/setSDMXServiceProviders.Rd | 56 - rsdmx-0.6-4/rsdmx/tests/testthat/test_Concepts.R | 6 rsdmx-0.6-4/rsdmx/tests/testthat/test_Main.R | 28 rsdmx-0.6-4/rsdmx/tests/testthat/test_Main_Helpers.R | 89 +- rsdmx-0.6-4/rsdmx/vignettes/quickstart.Rmd | 38 - 122 files changed, 3538 insertions(+), 3416 deletions(-)
Title: Fast Machine Learning Model Training and Evaluation
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing
comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning.
It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.2.0 dated 2024-11-30 and 0.3.0 dated 2024-12-16
fastml-0.2.0/fastml/man/define_bagging_spec.Rd |only fastml-0.2.0/fastml/man/define_bayes_glm_spec.Rd |only fastml-0.2.0/fastml/man/define_c5_0_spec.Rd |only fastml-0.2.0/fastml/man/define_decision_tree_spec.Rd |only fastml-0.2.0/fastml/man/define_deep_learning_spec.Rd |only fastml-0.2.0/fastml/man/define_elastic_net_spec.Rd |only fastml-0.2.0/fastml/man/define_knn_spec.Rd |only fastml-0.2.0/fastml/man/define_lasso_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_lda_spec.Rd |only fastml-0.2.0/fastml/man/define_lightgbm_spec.Rd |only fastml-0.2.0/fastml/man/define_linear_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_logistic_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_naive_bayes_spec.Rd |only fastml-0.2.0/fastml/man/define_neural_network_spec.Rd |only fastml-0.2.0/fastml/man/define_penalized_logistic_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_pls_spec.Rd |only fastml-0.2.0/fastml/man/define_qda_spec.Rd |only fastml-0.2.0/fastml/man/define_random_forest_spec.Rd |only fastml-0.2.0/fastml/man/define_ranger_spec.Rd |only fastml-0.2.0/fastml/man/define_ridge_regression_spec.Rd |only fastml-0.2.0/fastml/man/define_svm_linear_spec.Rd |only fastml-0.2.0/fastml/man/define_svm_radial_spec.Rd |only fastml-0.2.0/fastml/man/define_xgboost_spec.Rd |only fastml-0.3.0/fastml/DESCRIPTION | 16 fastml-0.3.0/fastml/MD5 | 48 fastml-0.3.0/fastml/NAMESPACE | 41 fastml-0.3.0/fastml/R/evaluate_models.R | 15 fastml-0.3.0/fastml/R/explain.fastml_model.R |only fastml-0.3.0/fastml/R/fastml.R | 317 +--- fastml-0.3.0/fastml/R/models.R |only fastml-0.3.0/fastml/R/plot.fastml_model.R | 14 fastml-0.3.0/fastml/R/summary.fastml_model.R | 393 ++++- fastml-0.3.0/fastml/R/train_models.R | 756 +--------- fastml-0.3.0/fastml/man/evaluate_models.Rd | 6 fastml-0.3.0/fastml/man/explain.Rd |only fastml-0.3.0/fastml/man/fastml.Rd | 52 fastml-0.3.0/fastml/man/summary.fastml_model.Rd | 39 fastml-0.3.0/fastml/man/train_models.Rd | 16 38 files changed, 715 insertions(+), 998 deletions(-)
Title: Extended Two-Way Fixed Effects
Description: Convenience functions for implementing extended two-way
fixed effect regressions a la Wooldridge (2021, 2023)
<doi:10.2139/ssrn.3906345>, <doi:10.1093/ectj/utad016>.
Author: Grant McDermott [aut, cre] ,
Frederic Kluser [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between etwfe versions 0.4.0 dated 2024-02-26 and 0.5.0 dated 2024-12-16
DESCRIPTION | 19 MD5 | 32 NAMESPACE | 6 NEWS.md | 33 R/emfx.R | 205 + R/etwfe.R | 457 ++- R/plot.R |only README.md | 78 build/vignette.rds |binary inst/doc/etwfe.R | 180 - inst/doc/etwfe.Rmd | 254 +- inst/doc/etwfe.html | 5392 ++++++++++++++++------------------------------ inst/tinytest/test_emfx.R | 22 inst/tinytest/test_xvar.R | 3 man/emfx.Rd | 150 - man/etwfe.Rd | 76 man/plot.emfx.Rd |only vignettes/etwfe.Rmd | 254 +- 18 files changed, 3027 insertions(+), 4134 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the
'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but
with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] ,
Jim Hester [aut] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between super versions 0.0.3 dated 2024-11-22 and 0.0.4 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/super.Rmd | 2 +- inst/doc/super.html | 28 ++++++++++++++-------------- man/super-package.Rd | 1 + vignettes/super.Rmd | 2 +- 9 files changed, 28 insertions(+), 26 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.36 dated 2024-12-03 and 1.5.37 dated 2024-12-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/CDCabove.R | 4 ++-- R/CDCbelow.R | 4 ++-- R/RobustCDCabove.R | 4 ++-- R/RobustCDCbelow.R | 4 ++-- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 4.3.0 dated 2024-01-26 and 4.4.0 dated 2024-12-16
DESCRIPTION | 8 - MD5 | 125 +++++++++++++++------------ NAMESPACE | 6 + NEWS.md | 11 ++ R/char2factor.R |only R/get_session_string.R |only R/pause.R |only R/r.R | 2 R/relative_difference.R | 29 ++++-- R/rename_package.R | 1 R/rownames2col.R |only R/runsed.R |only R/sloboba.R | 8 - R/string2words.R |only R/test_helpers.R | 2 README.md | 11 ++ build/vignette.rds |binary inst/NEWS.rd | 13 ++ inst/doc/Not_an_Introduction_to_fritools.pdf |binary inst/tinytest/test_char2factor.R |only inst/tinytest/test_relative_difference.R |only inst/tinytest/test_rownames2col.R |only inst/tinytest/test_runsed.R |only inst/tinytest/test_string2words.R |only man/bulk_read_csv.Rd | 4 man/bulk_write_csv.Rd | 4 man/char2factor.Rd |only man/check_ascii_file.Rd | 4 man/clipboard_path.Rd | 1 man/compare_vectors.Rd | 1 man/delete_trailing_blank_lines.Rd | 1 man/delete_trailing_whitespace.Rd | 1 man/develop_test.Rd | 1 man/file_copy.Rd | 1 man/file_modified_last.Rd | 2 man/file_save.Rd | 1 man/find_files.Rd | 2 man/fritools-package.Rd | 12 ++ man/fromto.Rd | 1 man/get_lines_between_tags.Rd | 1 man/get_mtime.Rd | 1 man/get_package_version.Rd | 4 man/get_session_string.Rd |only man/get_unique_string.Rd | 1 man/golden_ratio.Rd | 4 man/grep_file.Rd | 2 man/is_difftime_less.Rd | 4 man/is_files_current.Rd | 1 man/is_path.Rd | 1 man/is_r_package_installed.Rd | 4 man/is_valid_primary_key.Rd | 4 man/is_version_sufficient.Rd | 4 man/load_internal_functions.Rd | 3 man/missing_docs.Rd | 1 man/paths.Rd | 1 man/pause.Rd |only man/r_cmd_install.Rd | 4 man/relative_difference.Rd | 7 + man/rename_package.Rd | 8 + man/rownames2col.Rd |only man/runsed.Rd |only man/search_files.Rd | 2 man/search_rows.Rd | 1 man/sloboda.Rd | 2 man/split_code_file.Rd | 1 man/str2num.Rd | 4 man/string2words.Rd |only man/strip_off_attributes.Rd | 4 man/summary.filesearch.Rd | 1 man/tapply.Rd | 4 man/throw.Rd | 4 man/touch.Rd | 1 72 files changed, 249 insertions(+), 82 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.1.9 dated 2024-11-08 and 0.2.0 dated 2024-12-16
DESCRIPTION | 6 - MD5 | 15 ++-- NAMESPACE | 1 NEWS.md | 4 + R/RcppExports.R | 4 + R/vcg.R | 89 ++++++++++++++++++++++++++++ man/vcg_raycaster.Rd |only src/RcppExports.cpp | 18 +++++ src/vcgCommon.cpp | 160 +++++++++++++++++++++++++++++++++++++++++++++++++++ 9 files changed, 287 insertions(+), 10 deletions(-)
Title: Tidy Plots for Scientific Papers
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Diff between tidyplots versions 0.1.2 dated 2024-11-08 and 0.2.0 dated 2024-12-16
DESCRIPTION | 12 MD5 | 139 ++++--- NAMESPACE | 2 NEWS.md | 19 R/add-general.R | 24 - R/add-heatmap.R | 2 R/add-misc.R | 12 R/add-points.R | 7 R/add-proportional.R | 8 R/adjust.R | 60 ++- R/helpers.R | 21 - R/labels.R | 16 R/plot.R | 15 R/remove.R | 4 R/themes.R | 12 R/tidycolor.R | 10 README.md | 4 inst/CITATION |only inst/doc/tidyplots.R | 3 inst/doc/tidyplots.Rmd | 13 inst/doc/tidyplots.html | 15 man/add_areastack_absolute.Rd | 2 man/add_barstack_absolute.Rd | 2 man/add_boxplot.Rd | 4 man/add_count_bar.Rd | 4 man/add_curve_fit.Rd | 12 man/add_data_points.Rd | 4 man/add_heatmap.Rd | 2 man/add_line.Rd | 4 man/add_mean_bar.Rd | 4 man/add_median_bar.Rd | 4 man/add_reference_lines.Rd | 4 man/add_sem_errorbar.Rd | 4 man/add_sem_ribbon.Rd | 14 man/add_sum_bar.Rd | 4 man/add_violin.Rd | 4 man/adjust_legend_title.Rd | 20 - man/adjust_theme_details.Rd |only man/adjust_title.Rd | 50 ++ man/adjust_x_axis.Rd | 4 man/as_tidyplot.Rd | 6 man/colors_discrete_friendly.Rd | 11 man/common_arguments.Rd | 4 man/figures/logo.svg | 194 +++------- man/flip_plot.Rd | 2 man/remove_x_axis.Rd | 4 man/remove_y_axis.Rd | 4 man/rename_x_axis_labels.Rd | 4 man/reorder_x_axis_labels.Rd | 4 man/reverse_x_axis_labels.Rd | 4 man/save_plot.Rd | 6 man/sort_x_axis_labels.Rd | 4 man/tidyplot.Rd | 6 tests/testthat/_snaps/add-general/add-error-bars-xy.svg | 128 +++--- tests/testthat/_snaps/add-general/add-error-bars-yx.svg | 128 +++--- tests/testthat/_snaps/add-general/add-error-ribbon-xy.svg | 78 ++-- tests/testthat/_snaps/add-general/add-error-ribbon-yx.svg | 78 ++-- tests/testthat/_snaps/add-general/add-grouped-error-bar-xy.svg | 128 +++--- tests/testthat/_snaps/add-general/add-grouped-error-ribbon-xy.svg | 96 ++-- tests/testthat/_snaps/add-general/no-discrete-axis-dodge-width-0-8.svg |only tests/testthat/_snaps/add-general/no-discrete-axis-dodge-width-0.svg |only tests/testthat/_snaps/add-general/no-discrete-axis-no-provided-dodge-width.svg |only tests/testthat/_snaps/add-general/no-discrete-axis-override.svg |only tests/testthat/_snaps/add-general/no-discrete-axis.svg |only tests/testthat/_snaps/add-general/one-discrete-axis-dodge-width-0-8.svg |only tests/testthat/_snaps/add-general/one-discrete-axis-dodge-width-0.svg |only tests/testthat/_snaps/add-general/one-discrete-axis-no-provided-dodge-width.svg |only tests/testthat/_snaps/add-general/one-discrete-axis-override.svg |only tests/testthat/_snaps/add-general/one-discrete-axis.svg |only tests/testthat/_snaps/adjust/adjust-axes-limits-3.svg | 8 tests/testthat/_snaps/adjust/caption-font.svg |only tests/testthat/_snaps/adjust/legend-title-font.svg |only tests/testthat/_snaps/adjust/plot-title-font.svg |only tests/testthat/_snaps/adjust/x-axis-title-font.svg |only tests/testthat/_snaps/adjust/y-axis-title-font.svg |only tests/testthat/test-add-general.R | 73 +++ tests/testthat/test-adjust.R | 29 + tests/testthat/test-helpers.R | 2 vignettes/tidyplots.Rmd | 13 79 files changed, 911 insertions(+), 647 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9.4 dated 2024-12-02 and 10.9.5 dated 2024-12-16
DESCRIPTION | 8 - MD5 | 22 ++--- R/NNS_MC.R | 4 R/NNS_meboot.R | 5 - R/Partial_Moments.R | 3 README.md | 9 -- inst/doc/NNSvignette_Partial_Moments.R | 12 ++ inst/doc/NNSvignette_Partial_Moments.Rmd | 12 ++ inst/doc/NNSvignette_Partial_Moments.html | 132 +++++++++++++++--------------- man/NNS.MC.Rd | 3 man/NNS.meboot.Rd | 3 vignettes/NNSvignette_Partial_Moments.Rmd | 12 ++ 12 files changed, 127 insertions(+), 98 deletions(-)
Title: (Restricted) [external] Multidimensional Unfolding
Description: Functions for performing (external) multidimensional unfolding.
Restrictions (fixed coordinates or model restrictions) are available for both row and column coordinates in all combinations.
Author: Frank Busing [aut, cre],
Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>
Diff between fmdu versions 0.1.1 dated 2024-03-07 and 0.2.1 dated 2024-12-16
fmdu-0.1.1/fmdu/src/nnls.c |only fmdu-0.1.1/fmdu/src/uhelp.c |only fmdu-0.1.1/fmdu/src/uhelp.h |only fmdu-0.2.1/fmdu/DESCRIPTION | 8 fmdu-0.2.1/fmdu/MD5 | 50 fmdu-0.2.1/fmdu/NAMESPACE | 2 fmdu-0.2.1/fmdu/R/fastmdu.R | 73 fmdu-0.2.1/fmdu/R/ultrafastmdu.R |only fmdu-0.2.1/fmdu/man/fastmdu.Rd | 9 fmdu-0.2.1/fmdu/man/ultrafastmdu.Rd |only fmdu-0.2.1/fmdu/src/bigmdu.c |only fmdu-0.2.1/fmdu/src/colresmdu.c | 8 fmdu-0.2.1/fmdu/src/colresmduneg.c | 10 fmdu-0.2.1/fmdu/src/colreswgtmdu.c | 12 fmdu-0.2.1/fmdu/src/colreswgtmduneg.c | 12 fmdu-0.2.1/fmdu/src/external.c | 34 fmdu-0.2.1/fmdu/src/flib.c | 4687 ++++++++++++++++++++++++---------- fmdu-0.2.1/fmdu/src/flib.h | 154 - fmdu-0.2.1/fmdu/src/fmdu.h | 11 fmdu-0.2.1/fmdu/src/init.c | 19 fmdu-0.2.1/fmdu/src/pencolresmdu.c |only fmdu-0.2.1/fmdu/src/penrowresmdu.c |only fmdu-0.2.1/fmdu/src/resmdu.c | 18 fmdu-0.2.1/fmdu/src/resmduneg.c | 20 fmdu-0.2.1/fmdu/src/reswgtmdu.c | 20 fmdu-0.2.1/fmdu/src/reswgtmduneg.c | 20 fmdu-0.2.1/fmdu/src/rowresmdu.c | 8 fmdu-0.2.1/fmdu/src/rowresmduneg.c | 12 fmdu-0.2.1/fmdu/src/rowreswgtmdu.c | 12 fmdu-0.2.1/fmdu/src/rowreswgtmduneg.c | 12 30 files changed, 3670 insertions(+), 1541 deletions(-)
Title: Simple Imputation
Description: Easy to use interfaces to a number of imputation methods
that fit in the not-a-pipe operator of the 'magrittr' package.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between simputation versions 0.2.8 dated 2022-06-16 and 0.2.9 dated 2024-12-16
simputation-0.2.8/simputation/man/simputation.Rd |only simputation-0.2.8/simputation/src |only simputation-0.2.9/simputation/DESCRIPTION | 10 simputation-0.2.9/simputation/MD5 | 41 simputation-0.2.9/simputation/NAMESPACE | 1 simputation-0.2.9/simputation/NEWS | 13 simputation-0.2.9/simputation/R/hotdeck.R | 141 ++- simputation-0.2.9/simputation/R/linearmodels.R | 71 - simputation-0.2.9/simputation/R/simputation-pkg.R | 5 simputation-0.2.9/simputation/R/treemodels.R | 99 +- simputation-0.2.9/simputation/R/utils.R | 36 simputation-0.2.9/simputation/build/vignette.rds |binary simputation-0.2.9/simputation/inst/doc/intro.R | 54 - simputation-0.2.9/simputation/inst/doc/intro.html | 411 ++++++---- simputation-0.2.9/simputation/inst/tinytest/test_gh_issue_20.R |only simputation-0.2.9/simputation/inst/tinytest/test_groups.R |only simputation-0.2.9/simputation/inst/tinytest/test_hd.R | 166 +++- simputation-0.2.9/simputation/inst/tinytest/test_lm.R | 16 simputation-0.2.9/simputation/inst/tinytest/test_tree.R | 23 simputation-0.2.9/simputation/man/impute_hotdeck.Rd | 8 simputation-0.2.9/simputation/man/impute_lm.Rd | 11 simputation-0.2.9/simputation/man/impute_tree.Rd | 10 simputation-0.2.9/simputation/man/simputation-package.Rd |only 23 files changed, 717 insertions(+), 399 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] ,
Arnaud Barras [aut] ,
Veronika Braunisch [aut] ,
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sdmtune@gmail.com>
Diff between SDMtune versions 1.3.1 dated 2023-07-03 and 1.3.2 dated 2024-12-16
DESCRIPTION | 12 LICENSE.note | 102 MD5 | 522 +-- NAMESPACE | 132 NEWS.md | 249 - R/ANN-class.R | 90 R/BRT-class.R | 102 R/Maxent-class.R | 114 R/Maxnet-class.R | 76 R/RF-class.R | 86 R/RcppExports.R | 14 R/SDMmodel-class.R | 136 R/SDMmodel2MaxEnt.R | 108 R/SDMmodelCV-class.R | 146 R/SDMtune-class.R | 234 - R/SDMtune-package.R | 12 R/SWD-class.R | 142 R/addSamplesToBg.R | 162 - R/aicc.R | 200 - R/auc.R | 292 - R/chart-utils.R | 314 +- R/checkMaxentInstallation.R | 118 R/combineCV.R | 138 R/confMatrix.R | 222 - R/convertFolds.R | 96 R/corVar.R | 174 - R/doJk.R | 464 +-- R/getTunableArgs.R | 120 R/gridSearch.R | 406 +- R/maxentTh.R | 108 R/maxentVarImp.R | 176 - R/mergeSWD.R | 240 - R/modelReport.R | 852 ++--- R/optimizeModel.R | 940 +++--- R/plotCor.R | 188 - R/plotJk.R | 258 - R/plotPA.R | 234 - R/plotPred.R | 158 - R/plotROC.R | 198 - R/plotResponse.R | 506 +-- R/plotVarImp.R | 148 R/predict-ANN.R | 66 R/predict-BRT.R | 74 R/predict-Maxent.R | 142 R/predict-Maxnet.R | 70 R/predict-RF.R | 66 R/predict-SDMmodel.R | 374 +- R/predict-SDMmodelCV.R | 506 +-- R/prepareSWD.R | 240 - R/randomFolds.R | 144 R/randomSearch.R | 206 - R/reduceVar.R | 598 +-- R/swd2csv.R | 138 R/thinData.R | 334 +- R/thresholds.R | 270 - R/train.R | 586 +-- R/trainANN.R | 54 R/trainBRT.R | 60 R/trainMaxent.R | 304 - R/trainMaxnet.R | 42 R/trainRF.R | 52 R/trainValTest.R | 380 +- R/tss.R | 260 - R/utils.R | 684 ++-- R/varImp.R | 334 +- R/varSel.R | 636 ++-- R/virtualSp.R | 46 R/zzz.R | 30 README.md | 472 +-- build/vignette.rds |binary inst/CITATION | 40 inst/WORDLIST | 250 - inst/doc/basic-use.R | 622 ++-- inst/doc/basic-use.Rmd | 1246 ++++---- inst/doc/basic-use.html | 2139 +++++++------- inst/doc/hyper-tuning.R | 362 +- inst/doc/hyper-tuning.Rmd | 556 +-- inst/doc/hyper-tuning.html | 1355 ++++---- inst/doc/presence-absence.R | 154 - inst/doc/presence-absence.Rmd | 244 - inst/doc/presence-absence.html | 979 +++--- inst/doc/var-selection.R | 402 +- inst/doc/var-selection.Rmd | 682 ++-- inst/doc/var-selection.html | 1473 ++++----- inst/lib/Chart.min.js | 20 inst/lib/jquery.min.js | 4 inst/lib/style.css | 30 inst/scripts/gridSearch.js | 294 - inst/scripts/optimizeModel.js | 462 +-- inst/scripts/varSelection.js | 400 +- inst/templates/chart_template.html | 48 inst/templates/modelReport.Rmd | 194 - inst/templates/report.css | 114 man/ANN-class.Rd | 76 man/BRT-class.Rd | 82 man/Maxent-class.Rd | 102 man/Maxnet-class.Rd | 64 man/RF-class.Rd | 74 man/SDMmodel-class.Rd | 60 man/SDMmodel2MaxEnt.Rd | 96 man/SDMmodelCV-class.Rd | 70 man/SDMtune-class.Rd | 176 - man/SDMtune-package.Rd | 71 man/SWD-class.Rd | 82 man/addSamplesToBg.Rd | 112 man/aicc.Rd | 126 man/auc.Rd | 202 - man/checkMaxentInstallation.Rd | 64 man/combineCV.Rd | 148 man/confMatrix.Rd | 148 man/corVar.Rd | 142 man/doJk.Rd | 244 - man/getTunableArgs.Rd | 94 man/gridSearch.Rd | 236 - man/maxentTh.Rd | 98 man/maxentVarImp.Rd | 116 man/mergeSWD.Rd | 150 man/modelReport.Rd | 210 - man/optimizeModel.Rd | 260 - man/plotCor.Rd | 126 man/plotJk.Rd | 148 man/plotPA.Rd | 136 man/plotPred.Rd | 86 man/plotROC.Rd | 120 man/plotResponse.Rd | 302 - man/plotVarImp.Rd | 116 man/predict-ANN-method.Rd | 58 man/predict-BRT-method.Rd | 64 man/predict-Maxent-method.Rd | 78 man/predict-Maxnet-method.Rd | 70 man/predict-RF-method.Rd | 58 man/predict-SDMmodel-method.Rd | 256 - man/predict-SDMmodelCV-method.Rd | 308 +- man/prepareSWD.Rd | 128 man/randomFolds.Rd | 106 man/randomSearch.Rd | 218 - man/reduceVar.Rd | 268 - man/swd2csv.Rd | 118 man/thinData.Rd | 200 - man/thresholds.Rd | 154 - man/train.Rd | 532 +-- man/trainValTest.Rd | 150 man/tss.Rd | 202 - man/varImp.Rd | 180 - man/varSel.Rd | 324 +- man/virtualSp.Rd | 70 tests/testthat.R | 8 tests/testthat/_snaps/ANN-class.md | 32 tests/testthat/_snaps/BRT-class.md | 34 tests/testthat/_snaps/Maxent-class.md | 30 tests/testthat/_snaps/Maxnet-class.md | 28 tests/testthat/_snaps/RF-class.md | 30 tests/testthat/_snaps/SDMmodel-class.md | 194 - tests/testthat/_snaps/SDMmodel2MaxEnt.md | 10 tests/testthat/_snaps/SDMmodelCV-class.md | 202 - tests/testthat/_snaps/SDMtune-class.md | 28 tests/testthat/_snaps/SWD-class.md | 104 tests/testthat/_snaps/addSamplesToBg.md | 10 tests/testthat/_snaps/aicc.md | 30 tests/testthat/_snaps/auc.md | 20 tests/testthat/_snaps/checkMaxentInstallation.md | 22 tests/testthat/_snaps/confMatrix.md | 20 tests/testthat/_snaps/convertFolds.md | 8 tests/testthat/_snaps/corVar.md | 10 tests/testthat/_snaps/doJk.md | 20 tests/testthat/_snaps/gridSearch.md | 20 tests/testthat/_snaps/maxentTh.md | 10 tests/testthat/_snaps/maxentVarImp.md | 10 tests/testthat/_snaps/mergeSWD.md | 24 tests/testthat/_snaps/modelReport.md | 146 tests/testthat/_snaps/optimizeModel.md | 74 tests/testthat/_snaps/plotJk.md | 8 tests/testthat/_snaps/plotPA.md | 28 tests/testthat/_snaps/plotPred.md | 20 tests/testthat/_snaps/predict-SDMmodel.md | 58 tests/testthat/_snaps/predict-SDMmodelCV.md | 58 tests/testthat/_snaps/prepareSWD.md | 36 tests/testthat/_snaps/randomFolds.md | 10 tests/testthat/_snaps/reduceVar.md | 28 tests/testthat/_snaps/swd2csv.md | 8 tests/testthat/_snaps/thinData.md | 21 tests/testthat/_snaps/trainMaxent.md | 10 tests/testthat/_snaps/trainValTest.md | 10 tests/testthat/_snaps/tss.md | 20 tests/testthat/_snaps/utils.md | 134 tests/testthat/_snaps/varSel.md | 28 tests/testthat/helper.R | 26 tests/testthat/setup.R | 4 tests/testthat/test-ANN-class.R | 20 tests/testthat/test-BRT-class.R | 22 tests/testthat/test-Maxent-class.R | 8 tests/testthat/test-Maxnet-class.R | 8 tests/testthat/test-RF-class.R | 22 tests/testthat/test-SDMmodel-class.R | 20 tests/testthat/test-SDMmodel2MaxEnt.R | 28 tests/testthat/test-SDMmodelCV-class.R | 20 tests/testthat/test-SDMtune-class.R | 86 tests/testthat/test-SWD-class.R | 16 tests/testthat/test-addSamplesToBg.R | 46 tests/testthat/test-aicc.R | 86 tests/testthat/test-auc.R | 52 tests/testthat/test-chart-utils.R | 136 tests/testthat/test-checkMaxentInstallation.R | 16 tests/testthat/test-clamp.R | 46 tests/testthat/test-combineCV.R | 12 tests/testthat/test-confMatrix.R | 78 tests/testthat/test-convertFolds.R | 254 - tests/testthat/test-corVar.R | 46 tests/testthat/test-doJk.R | 380 +- tests/testthat/test-getTunableArgs.R | 34 tests/testthat/test-gridSearch.R | 200 - tests/testthat/test-maxentTh.R | 16 tests/testthat/test-maxentVarImp.R | 70 tests/testthat/test-mergeSWD.R | 98 tests/testthat/test-modelReport.R | 168 - tests/testthat/test-optimizeModel.R | 310 +- tests/testthat/test-plotCor.R | 40 tests/testthat/test-plotJk.R | 88 tests/testthat/test-plotPA.R | 82 tests/testthat/test-plotPred.R | 54 tests/testthat/test-plotROC.R | 26 tests/testthat/test-plotResponse.R | 148 tests/testthat/test-plotVarImp.R | 28 tests/testthat/test-predct-Maxnet.R | 26 tests/testthat/test-predict-ANN.R | 30 tests/testthat/test-predict-BRT.R | 32 tests/testthat/test-predict-Maxent.R | 214 - tests/testthat/test-predict-RF.R | 28 tests/testthat/test-predict-SDMmodel.R | 196 - tests/testthat/test-predict-SDMmodelCV.R | 336 +- tests/testthat/test-prepareSWD.R | 158 - tests/testthat/test-randomFolds.R | 66 tests/testthat/test-randomSearch.R | 82 tests/testthat/test-reduceVar.R | 158 - tests/testthat/test-swd2csv.R | 66 tests/testthat/test-thinData.R | 182 - tests/testthat/test-thresholds.R | 60 tests/testthat/test-train.R | 100 tests/testthat/test-trainANN.R | 34 tests/testthat/test-trainBRT.R | 38 tests/testthat/test-trainMaxent.R | 308 +- tests/testthat/test-trainMaxnet.R | 28 tests/testthat/test-trainRF.R | 34 tests/testthat/test-trainValTest.R | 310 +- tests/testthat/test-tss.R | 44 tests/testthat/test-utils.R | 476 +-- tests/testthat/test-varImp.R | 84 tests/testthat/test-varSel.R | 154 - vignettes/SDMtune.bib | 366 +- vignettes/articles/evaluate-model.Rmd | 170 - vignettes/articles/evaluation-strategies.Rmd | 430 +- vignettes/articles/make-predictions.Rmd | 358 +- vignettes/articles/prepare-data.Rmd | 448 +- vignettes/articles/train-model.Rmd | 304 - vignettes/articles/train-tune-presence-absence-models.Rmd | 314 +- vignettes/articles/tune-hyperparameters.Rmd | 682 ++-- vignettes/articles/variable-importance.Rmd | 532 +-- vignettes/articles/variable-selection.Rmd | 434 +- vignettes/basic-use.Rmd | 1246 ++++---- vignettes/hyper-tuning.Rmd | 556 +-- vignettes/presence-absence.Rmd | 244 - vignettes/var-selection.Rmd | 682 ++-- 262 files changed, 25232 insertions(+), 25279 deletions(-)
Title: Robust Tuning and Training for Cross-Source Prediction
Description: Provides robust parameter tuning and model training for predictive models applied across data sources where the data distribution varies slightly from source to source. This package implements three primary tuning methods: cross-validation-based internal tuning, external tuning, and the 'RobustTuneC' method. External tuning includes a conservative option where parameters are tuned internally on the training data and validating on an external dataset, providing a slightly pessimistic estimate. It supports Lasso, Ridge, Random Forest, Boosting, and Support Vector Machine classifiers. Currently, only binary classification is supported. The response variable must be the first column of the dataset and a factor with exactly two levels. The tuning methods are based on the paper by Nicole Ellenbach, Anne-Laure Boulesteix, Bernd Bischl, Kristian Unger, and Roman Hornung (2021) "Improved Outcome Prediction Across Data Sources Through Robust Parameter Tuning" <doi:10.1007/s00357-020-09368-z&g [...truncated...]
Author: Yuting He [aut, cre],
Nicole Ellenbach [ctb],
Roman Hornung [ctb]
Maintainer: Yuting He <yutingh19@gmail.com>
Diff between RobustPrediction versions 0.1.4 dated 2024-11-14 and 0.1.7 dated 2024-12-16
DESCRIPTION | 12 +- MD5 | 68 +++++++------- NAMESPACE | 4 R/package.R | 18 ++- R/tuneandtrainExtBoost.R | 158 ++++++++++++++++++++------------ R/tuneandtrainExtLasso.R | 110 +++++++++++++--------- R/tuneandtrainExtRF.R | 151 ++++++++++++++++++++----------- R/tuneandtrainExtRidge.R | 141 +++++++++++++++++++---------- R/tuneandtrainExtSVM.R | 174 ++++++++++++++++++++++-------------- R/tuneandtrainIntBoost.R | 14 -- R/tuneandtrainIntLasso.R | 10 -- R/tuneandtrainIntRF.R | 14 -- R/tuneandtrainIntRidge.R | 16 --- R/tuneandtrainIntSVM.R | 12 -- R/tuneandtrainRobustTuneCBoost.R | 13 +- R/tuneandtrainRobustTuneCLasso.R | 16 +-- R/tuneandtrainRobustTuneCRF.R | 9 - R/tuneandtrainRobustTuneCRidge.R | 13 +- R/tuneandtrainRobustTuneCSVM.R | 10 -- man/RobustPrediction.Rd | 20 ++-- man/tuneandtrainExtBoost.Rd | 72 +++++++++----- man/tuneandtrainExtLasso.Rd | 55 ++++++++--- man/tuneandtrainExtRF.Rd | 47 ++++++--- man/tuneandtrainExtRidge.Rd | 52 +++++++--- man/tuneandtrainExtSVM.Rd | 48 ++++++--- man/tuneandtrainIntBoost.Rd | 5 - man/tuneandtrainIntLasso.Rd | 3 man/tuneandtrainIntRF.Rd | 5 - man/tuneandtrainIntRidge.Rd | 5 - man/tuneandtrainIntSVM.Rd | 4 man/tuneandtrainRobustTuneCBoost.Rd | 4 man/tuneandtrainRobustTuneCLasso.Rd | 4 man/tuneandtrainRobustTuneCRF.Rd | 4 man/tuneandtrainRobustTuneCRidge.Rd | 4 man/tuneandtrainRobustTuneCSVM.Rd | 4 35 files changed, 772 insertions(+), 527 deletions(-)
More information about RobustPrediction at CRAN
Permanent link
Title: Statistical Tools for Quantitative Genetic Analyses
Description: Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.
Author: Peter Soerensen [aut, cre],
Palle Duun Rohde [aut],
Izel Fourie Soerensen [aut]
Maintainer: Peter Soerensen <peter.sorensen@r-qgg.org>
Diff between qgg versions 1.1.3 dated 2024-12-11 and 1.1.6 dated 2024-12-16
DESCRIPTION | 8 MD5 | 24 R/RcppExports.R | 40 - R/genomic_bayes.R | 1318 +++++++++++++++++++++++++--------------------------- src/Makevars.win | 2 src/RcppExports.cpp | 144 +---- src/bedfunc.cpp | 118 ++-- src/gbayes.cpp | 640 +++++++++++-------------- src/mtgbayes.cpp | 1 src/qgg_init.c | 74 +- src/solvebed.cpp | 9 src/sparseld.cpp | 2 src/utility.cpp | 8 13 files changed, 1085 insertions(+), 1303 deletions(-)
Title: Continuous Time Mediation
Description: Calculates standard errors and confidence intervals for effects in continuous-time mediation models. This package extends the work of
Deboeck and Preacher (2015) <doi:10.1080/10705511.2014.973960> and
Ryan and Hamaker (2021) <doi:10.1007/s11336-021-09767-0>
by providing methods to generate standard errors and confidence intervals for the total, direct, and indirect effects in these models.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.2 dated 2024-11-26 and 1.0.3 dated 2024-12-16
cTMed-1.0.2/cTMed/R/cTMed-posterior-phi.R |only cTMed-1.0.2/cTMed/man/PosteriorPhi.Rd |only cTMed-1.0.3/cTMed/DESCRIPTION | 8 - cTMed-1.0.3/cTMed/MD5 | 72 +++++++-------- cTMed-1.0.3/cTMed/NAMESPACE | 1 cTMed-1.0.3/cTMed/NEWS.md | 6 + cTMed-1.0.3/cTMed/man/DeltaBeta.Rd | 1 cTMed-1.0.3/cTMed/man/DeltaBetaStd.Rd | 1 cTMed-1.0.3/cTMed/man/DeltaIndirectCentral.Rd | 1 cTMed-1.0.3/cTMed/man/DeltaMed.Rd | 1 cTMed-1.0.3/cTMed/man/DeltaMedStd.Rd | 1 cTMed-1.0.3/cTMed/man/DeltaTotalCentral.Rd | 1 cTMed-1.0.3/cTMed/man/Direct.Rd | 1 cTMed-1.0.3/cTMed/man/DirectStd.Rd | 1 cTMed-1.0.3/cTMed/man/ExpCov.Rd | 1 cTMed-1.0.3/cTMed/man/ExpMean.Rd | 1 cTMed-1.0.3/cTMed/man/Indirect.Rd | 1 cTMed-1.0.3/cTMed/man/IndirectCentral.Rd | 1 cTMed-1.0.3/cTMed/man/IndirectStd.Rd | 1 cTMed-1.0.3/cTMed/man/MCBeta.Rd | 1 cTMed-1.0.3/cTMed/man/MCBetaStd.Rd | 1 cTMed-1.0.3/cTMed/man/MCIndirectCentral.Rd | 1 cTMed-1.0.3/cTMed/man/MCMed.Rd | 1 cTMed-1.0.3/cTMed/man/MCMedStd.Rd | 1 cTMed-1.0.3/cTMed/man/MCPhi.Rd | 1 cTMed-1.0.3/cTMed/man/MCTotalCentral.Rd | 1 cTMed-1.0.3/cTMed/man/Med.Rd | 1 cTMed-1.0.3/cTMed/man/MedStd.Rd | 1 cTMed-1.0.3/cTMed/man/PosteriorBeta.Rd | 1 cTMed-1.0.3/cTMed/man/PosteriorIndirectCentral.Rd | 1 cTMed-1.0.3/cTMed/man/PosteriorMed.Rd | 1 cTMed-1.0.3/cTMed/man/PosteriorTotalCentral.Rd | 1 cTMed-1.0.3/cTMed/man/Total.Rd | 1 cTMed-1.0.3/cTMed/man/TotalCentral.Rd | 1 cTMed-1.0.3/cTMed/man/TotalStd.Rd | 1 cTMed-1.0.3/cTMed/man/Trajectory.Rd | 1 cTMed-1.0.3/cTMed/src/source.cpp | 2 cTMed-1.0.3/cTMed/tests/testthat/test-indirect-central.R | 20 ++++ 38 files changed, 66 insertions(+), 73 deletions(-)
Title: A New Format for Lossless and Lossy Image Compression
Description: Lossless webp images are 26% smaller in size compared to PNG. Lossy
webp images are 25-34% smaller in size compared to JPEG. This package reads
and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using
conventions from the 'jpeg' and 'png' packages.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between webp versions 1.2.1 dated 2024-10-04 and 1.3.0 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 21 ++++++++++++++------- 4 files changed, 23 insertions(+), 13 deletions(-)
Title: Honest Inference in Regression Discontinuity Designs
Description: Honest and nearly-optimal confidence intervals in fuzzy and sharp
regression discontinuity designs and for inference at a point based on local
linear regression. The implementation is based on Armstrong and Kolesár (2018)
<doi:10.3982/ECTA14434>, and Kolesár and Rothe (2018)
<doi:10.1257/aer.20160945>. Supports covariates, clustering, and weighting.
Author: Michal Kolesar [aut, cre, cph]
,
Tim Armstrong [ctb]
Maintainer: Michal Kolesar <kolesarmi@googlemail.com>
Diff between RDHonest versions 1.0.0 dated 2024-03-22 and 1.0.1 dated 2024-12-16
DESCRIPTION | 8 +++---- MD5 | 40 +++++++++++++++++++-------------------- NEWS.md | 8 +++++++ R/NPRfunctions.R | 32 ++++++++++++++++++++++++------- R/RDHonest.R | 15 +++++--------- R/checks.R | 13 ++++++++---- R/documentation.R | 4 +++ build/partial.rdb |binary build/vignette.rds |binary data/rcp.rda |binary inst/WORDLIST | 1 inst/doc/RDHonest.R | 18 +++++++++++++++-- inst/doc/RDHonest.Rmd | 32 +++++++++++++++++++++++++++---- inst/doc/RDHonest.pdf |binary man/RDHonest.Rd | 2 - man/rcp.Rd | 4 +++ tests/spelling.R | 3 +- tests/testthat/test_covariates.R | 27 ++++++++++++++++++++++++++ tests/testthat/test_interface.R | 6 +---- vignettes/RDHonest.Rmd | 32 +++++++++++++++++++++++++++---- vignettes/np-testing-library.bib | 1 21 files changed, 186 insertions(+), 60 deletions(-)
Title: Extensible Style-Sheet Language Transformations
Description: An extension for the 'xml2' package to transform XML documents
by applying an 'xslt' style-sheet.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between xslt versions 1.4.6 dated 2024-10-04 and 1.5.0 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/Makevars.win | 30 ++++++++++++++++++------------ tools/winlibs.R | 6 ++---- 5 files changed, 30 insertions(+), 23 deletions(-)
Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to 'libsodium' <https://doc.libsodium.org/>: a modern,
easy-to-use software library for encryption, decryption, signatures, password
hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman
function by Daniel Bernstein, which has become very popular after it was
discovered that the NSA had backdoored Dual EC DRBG.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between sodium versions 1.3.2 dated 2024-10-04 and 1.4.0 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 3 +++ build/vignette.rds |binary cleanup | 1 + inst/doc/crypto101.html | 14 +++++++------- inst/doc/intro.html | 12 ++++++------ src/Makevars.win | 19 +++++++++++++------ 8 files changed, 40 insertions(+), 29 deletions(-)
Title: R Bindings for 'ZeroMQ'
Description: Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).
Author: Whit Armstrong [aut],
Michael Schubert [ctb],
Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between rzmq versions 0.9.14 dated 2024-10-04 and 0.9.15 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 31 ++++++++++++++++++------------- 4 files changed, 27 insertions(+), 19 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.2.2 dated 2024-09-20 and 2.3.0 dated 2024-12-16
DESCRIPTION | 6 ++--- MD5 | 26 +++++++++++------------ NEWS | 3 ++ R/hash.R | 8 +++++-- build/vignette.rds |binary cleanup | 1 configure | 5 ---- inst/doc/bignum.html | 32 ++++++++++++++-------------- inst/doc/crypto_hashing.html | 8 +++---- inst/doc/keys.html | 48 +++++++++++++++++++++---------------------- inst/doc/secure_rng.html | 18 ++++++++-------- man/hash.Rd | 8 +++++-- src/Makevars.win | 24 +++++++++++++-------- src/ssl.c | 4 ++- 14 files changed, 102 insertions(+), 89 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via by modsem it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8 [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.4 dated 2024-11-15 and 1.0.5 dated 2024-12-16
DESCRIPTION | 6 MD5 | 56 +++--- NAMESPACE | 10 + R/calc_se_da.R | 73 +++++--- R/est_lms.R | 3 R/est_qml.R | 3 R/method_settings_da.R | 2 R/model_da.R | 6 R/model_parameters_da.R | 8 R/modsem.R | 2 R/modsem_da.R | 15 + R/modsem_pi.R | 48 ++--- R/plot_interaction.R | 326 ++++++++++++++++++++++++++++++++++++--- R/simulate_partable.R | 7 R/utils.R | 22 ++ R/utils_da.R | 7 inst/CITATION | 13 - inst/doc/plot_interactions.R | 32 +++ inst/doc/plot_interactions.Rmd | 50 +++++ inst/doc/plot_interactions.html | 54 ++++++ man/modsem.Rd | 2 man/modsem_da.Rd | 6 man/modsem_pi.Rd | 4 man/plot_interaction.Rd | 7 man/plot_jn.Rd |only tests/testthat/test_lav_models.R | 10 + tests/testthat/test_lms.R | 2 tests/testthat/test_missing.R |only tests/testthat/test_qml.R | 10 + vignettes/plot_interactions.Rmd | 50 +++++ 30 files changed, 692 insertions(+), 142 deletions(-)
Title: Client for 'jq', a 'JSON' Processor
Description: Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>),
written in C. 'jq' allows the following with 'JSON' data: index into, parse,
do calculations, cut up and filter, change key names and values, perform
conditionals and comparisons, and more.
Author: Rich FitzJohn [aut],
Jeroen Ooms [aut, cre],
Scott Chamberlain [aut],
Stefan Milton Bache [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jqr versions 1.3.5 dated 2024-10-04 and 1.4.0 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ src/Makevars.win | 22 +++++++++++++++------- 4 files changed, 26 insertions(+), 13 deletions(-)
Title: Call 'EPANET' Functions to Simulate Pipe Networks
Description: Enables simulation of water piping networks using 'EPANET'.
The package provides functions from the 'EPANET' programmer's toolkit as R
functions so that basic or customized simulations can be carried out from R.
The package uses 'EPANET' version 2.2 from Open Water Analytics
<https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.
Author: Ernesto Arandia [aut],
Bradley Eck [aut, cre],
Lew Rossman [aut],
Michael Tryby [ctb],
Sam Hatchett [ctb],
Feng Shang [ctb],
James Uber [ctb],
Tom Taxon [ctb],
Hyoungmin Woo [ctb],
Jinduan Chen [ctb],
Yunier Soad [ctb],
Mike Kane [ctb],
Demetrios Eli [...truncated...]
Maintainer: Bradley Eck <brad@bradeck.net>
Diff between epanet2toolkit versions 1.0.5 dated 2024-05-26 and 1.0.8 dated 2024-12-16
epanet2toolkit-1.0.5/epanet2toolkit/man/epanet2toolkit.Rd |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/Net1-getrules.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/Net1-ld.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/Net1-rt.bin |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/pattern-tests-cawd.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/pattern-tests-fqta.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/pattern-tests-iawb.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/pattern-tests-mluf.rpt |only epanet2toolkit-1.0.5/epanet2toolkit/tests/testthat/pattern-tests-szak.rpt |only epanet2toolkit-1.0.8/epanet2toolkit/DESCRIPTION | 10 epanet2toolkit-1.0.8/epanet2toolkit/MD5 | 62 +- epanet2toolkit-1.0.8/epanet2toolkit/NAMESPACE | 24 - epanet2toolkit-1.0.8/epanet2toolkit/R/Rtoolkit.R | 12 epanet2toolkit-1.0.8/epanet2toolkit/R/controls.r | 8 epanet2toolkit-1.0.8/epanet2toolkit/R/epanet2toolkit.r | 21 epanet2toolkit-1.0.8/epanet2toolkit/R/hydraulics.r | 63 +- epanet2toolkit-1.0.8/epanet2toolkit/R/links.r | 7 epanet2toolkit-1.0.8/epanet2toolkit/R/nodes.r | 7 epanet2toolkit-1.0.8/epanet2toolkit/R/patterns.r | 14 epanet2toolkit-1.0.8/epanet2toolkit/man/ENrunH.Rd | 2 epanet2toolkit-1.0.8/epanet2toolkit/man/epanet2toolkit-package.Rd |only epanet2toolkit-1.0.8/epanet2toolkit/src/Repanet2.c | 68 ++ epanet2toolkit-1.0.8/epanet2toolkit/src/Repanet2.h | 12 epanet2toolkit-1.0.8/epanet2toolkit/src/init.c | 24 - epanet2toolkit-1.0.8/epanet2toolkit/src/input2.c | 8 epanet2toolkit-1.0.8/epanet2toolkit/src/report.c | 4 epanet2toolkit-1.0.8/epanet2toolkit/src/toolkit.c | 235 ---------- epanet2toolkit-1.0.8/epanet2toolkit/src/toolkit.h | 12 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/Net1.rpt | 6 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/Net2.rpt | 6 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/Net3.bin |binary epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/Net3.rpt | 6 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/test_ENclose.r | 2 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/test_call.r | 18 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/test_patterns.r | 2 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/test_report.r | 1 epanet2toolkit-1.0.8/epanet2toolkit/tests/testthat/test_times.r | 2 37 files changed, 226 insertions(+), 410 deletions(-)
More information about epanet2toolkit at CRAN
Permanent link
Title: Maximum Likelihood Estimation of Various Univariate and
Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre],
Sofia Piperaki [aut],
Muhammad Imran [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.2 dated 2024-10-23 and 1.3 dated 2024-12-16
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 2 ++ R/disc.mle.R | 17 +++++++++++++++++ R/positive.mle.R | 20 ++++++++++++++++++++ man/MLE-package.Rd | 4 ++-- man/disc.mle.Rd | 11 ++++++++--- man/positive.mle.Rd | 4 +++- 8 files changed, 65 insertions(+), 19 deletions(-)
Title: Estimate Vapnik-Chervonenkis Dimension and Sample Complexity
Description: We provide a suite of tools for estimating the sample complexity of a chosen model through theoretical bounds and simulation. The package incorporates methods for estimating the Vapnik-Chervonenkis dimension (VCD) of a chosen algorithm, which can be used to estimate its sample complexity. Alternatively, we provide simulation methods to estimate sample complexity directly. For more details, see Carter, P & Choi, D (2024). "Learning from Noise: Applying Sample Complexity for Political Science Research" <doi:10.31219/osf.io/evrcj>.
Author: Perry Carter [aut, cre] ,
Dahyun Choi [aut]
Maintainer: Perry Carter <pjc504@nyu.edu>
Diff between scR versions 0.1.0 dated 2024-12-02 and 0.2.0 dated 2024-12-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/simulations.R | 19 +++++++++++++++---- man/estimate_accuracy.Rd | 9 +++++++++ 4 files changed, 30 insertions(+), 10 deletions(-)
Title: The COR for Optimal Subset Selection in Distributed Estimation
Description: An algorithm of optimal subset selection, related to Covariance matrices, observation matrices and Response vectors (COR) to select the optimal subsets in distributed estimation. The philosophy of the package is described in Guo G. (2024) <doi:10.1007/s11222-024-10471-z>.
Author: Guangbao Guo [aut, cre] ,
Haoyue Song [aut],
Lixing Zhu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between COR versions 0.1.0 dated 2024-11-18 and 0.2.0 dated 2024-12-16
DESCRIPTION | 12 +++++------- MD5 | 38 +++++++++++++++++++------------------- R/COR.R | 2 ++ R/LICbeta.R | 2 ++ R/LICnew.R | 3 ++- R/MSEbeta.R | 3 ++- R/MSEcom.R | 2 ++ R/MSEver.R | 2 ++ R/beta_AD.R | 2 ++ R/beta_LW.R | 2 ++ R/beta_cor.R | 2 ++ man/COR.Rd | 3 +++ man/LICbeta.Rd | 3 +++ man/LICnew.Rd | 3 +++ man/MSEbeta.Rd | 3 +++ man/MSEcom.Rd | 3 +++ man/MSEver.Rd | 3 +++ man/beta_AD.Rd | 3 +++ man/beta_LW.Rd | 3 +++ man/beta_cor.Rd | 3 +++ 20 files changed, 69 insertions(+), 28 deletions(-)
Title: Multicountry Term Structure of Interest Rates Models
Description: Estimation routines for several classes of affine term structure of interest rates models. All the models are based on the single-country unspanned macroeconomic risk framework from Joslin, Priebsch, and Singleton (2014, JF) <doi:10.1111/jofi.12131>. Multicountry extensions such as the ones of Jotikasthira, Le, and Lundblad (2015, JFE) <doi:10.1016/j.jfineco.2014.09.004>, Candelon and Moura (2023, EM) <doi:10.1016/j.econmod.2023.106453>, and Candelon and Moura (Forthcoming, JFEC) <doi:10.1093/jjfinec/nbae008> are also available.
Author: Rubens Moura [aut, cre]
Maintainer: Rubens Moura <rubens.gtmoura@gmail.com>
Diff between MultiATSM versions 1.0.0 dated 2024-10-15 and 1.1.0 dated 2024-12-16
MultiATSM-1.0.0/MultiATSM/R/f_with_vectorized_parameters.R |only MultiATSM-1.0.0/MultiATSM/R/getx.R |only MultiATSM-1.0.0/MultiATSM/man/FitgraphsJoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/FitgraphsSep.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFSep.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFSep_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFgraphsJLLOrtho.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFgraphsJoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFgraphsSep.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFjoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFjointOrthoJLL.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFjointOrthoJLL_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/GIRFjoint_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFgraphsJLLOrtho.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFgraphsJoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFgraphsSep.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFjoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFjointOrthoJLL.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFjointOrthoJLL_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFjoint_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFsep.Rd |only MultiATSM-1.0.0/MultiATSM/man/IRFsep_BS.Rd |only MultiATSM-1.0.0/MultiATSM/man/VarianceExplainedJoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/VarianceExplainedSep.Rd |only MultiATSM-1.0.0/MultiATSM/man/YieldsFitJoint.Rd |only MultiATSM-1.0.0/MultiATSM/man/YieldsFitsep.Rd |only MultiATSM-1.0.0/MultiATSM/man/aux2true.Rd |only MultiATSM-1.0.0/MultiATSM/man/f_with_vectorized_parameters.Rd |only MultiATSM-1.0.0/MultiATSM/man/getx.Rd |only MultiATSM-1.0.0/MultiATSM/man/killa.Rd |only MultiATSM-1.0.0/MultiATSM/man/true2aux.Rd |only MultiATSM-1.0.0/MultiATSM/man/update_para.Rd |only MultiATSM-1.1.0/MultiATSM/DESCRIPTION | 12 MultiATSM-1.1.0/MultiATSM/MD5 | 113 MultiATSM-1.1.0/MultiATSM/NAMESPACE | 2 MultiATSM-1.1.0/MultiATSM/R/Bootstrap.R | 6 MultiATSM-1.1.0/MultiATSM/R/Buildx_xvec.R |only MultiATSM-1.1.0/MultiATSM/R/ConfidenceBoundsBootstrap.R | 2 MultiATSM-1.1.0/MultiATSM/R/DatabasePrep.R | 2 MultiATSM-1.1.0/MultiATSM/R/ForecastYields.R | 6 MultiATSM-1.1.0/MultiATSM/R/Functionf_vectorized.R |only MultiATSM-1.1.0/MultiATSM/R/GVAR.R | 33 MultiATSM-1.1.0/MultiATSM/R/GraphicalOutputs.R | 1371 ++++------ MultiATSM-1.1.0/MultiATSM/R/InputsForOpt.R | 6 MultiATSM-1.1.0/MultiATSM/R/JLL.R | 10 MultiATSM-1.1.0/MultiATSM/R/MLEdensity.R | 24 MultiATSM-1.1.0/MultiATSM/R/MinorOptimizationFunctions.R | 5 MultiATSM-1.1.0/MultiATSM/R/NumOutputs.R | 1315 ++------- MultiATSM-1.1.0/MultiATSM/R/NumOutputsBootstrap.R | 840 ------ MultiATSM-1.1.0/MultiATSM/R/Optimization.R | 41 MultiATSM-1.1.0/MultiATSM/R/Reg_K1Q.R | 9 MultiATSM-1.1.0/MultiATSM/R/RiskFactorsPrep.R | 2 MultiATSM-1.1.0/MultiATSM/inst/doc/Guidelines.html | 4 MultiATSM-1.1.0/MultiATSM/inst/doc/Paper-Replications.html | 4 MultiATSM-1.1.0/MultiATSM/man/AdjustPathIRFs.Rd |only MultiATSM-1.1.0/MultiATSM/man/Adjust_Const_Type.Rd |only MultiATSM-1.1.0/MultiATSM/man/Aux_BlockDiag.Rd |only MultiATSM-1.1.0/MultiATSM/man/Aux_BoundDiag.Rd |only MultiATSM-1.1.0/MultiATSM/man/Aux_JLLstruct.Rd |only MultiATSM-1.1.0/MultiATSM/man/Aux_Jordan.Rd |only MultiATSM-1.1.0/MultiATSM/man/Aux_PSD.Rd |only MultiATSM-1.1.0/MultiATSM/man/BuildIRFlist.Rd |only MultiATSM-1.1.0/MultiATSM/man/Build_xvec.Rd |only MultiATSM-1.1.0/MultiATSM/man/ComputeGIRFs.Rd |only MultiATSM-1.1.0/MultiATSM/man/ComputeIRFs.Rd |only MultiATSM-1.1.0/MultiATSM/man/Fit_Subplot.Rd |only MultiATSM-1.1.0/MultiATSM/man/Fitgraphs.Rd |only MultiATSM-1.1.0/MultiATSM/man/FolderPrep_IRFs.Rd |only MultiATSM-1.1.0/MultiATSM/man/Functionf_vectorized.Rd |only MultiATSM-1.1.0/MultiATSM/man/GetAuxPara.Rd |only MultiATSM-1.1.0/MultiATSM/man/GetTruePara.Rd |only MultiATSM-1.1.0/MultiATSM/man/IRFandGIRF.Rd |only MultiATSM-1.1.0/MultiATSM/man/IRFandGIRF_BS.Rd |only MultiATSM-1.1.0/MultiATSM/man/IRFandGIRFgraphs.Rd |only MultiATSM-1.1.0/MultiATSM/man/IRFandGIRFs_Format_Fac.Rd |only MultiATSM-1.1.0/MultiATSM/man/IRFandGIRFs_Format_Yields.Rd |only MultiATSM-1.1.0/MultiATSM/man/ImposeStat_Aux.Rd |only MultiATSM-1.1.0/MultiATSM/man/ImposeStat_True.Rd |only MultiATSM-1.1.0/MultiATSM/man/Jordan_JLL.Rd |only MultiATSM-1.1.0/MultiATSM/man/Optimization_PE.Rd | 4 MultiATSM-1.1.0/MultiATSM/man/Remove_at.Rd |only MultiATSM-1.1.0/MultiATSM/man/True_BlockDiag.Rd |only MultiATSM-1.1.0/MultiATSM/man/True_BoundDiag.Rd |only MultiATSM-1.1.0/MultiATSM/man/True_JLLstruct.Rd |only MultiATSM-1.1.0/MultiATSM/man/True_Jordan.Rd |only MultiATSM-1.1.0/MultiATSM/man/True_PSD.Rd |only MultiATSM-1.1.0/MultiATSM/man/Update_ParaList.Rd |only MultiATSM-1.1.0/MultiATSM/man/VarianceExplained.Rd |only MultiATSM-1.1.0/MultiATSM/man/Wished_Graphs_IRFandGIRF.Rd |only MultiATSM-1.1.0/MultiATSM/man/Y_Fit.Rd |only MultiATSM-1.1.0/MultiATSM/man/Y_ModImp.Rd |only MultiATSM-1.1.0/MultiATSM/man/YieldsFit.Rd |only MultiATSM-1.1.0/MultiATSM/man/getpara.Rd | 10 93 files changed, 1242 insertions(+), 2579 deletions(-)
Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance
for Generalized Additive Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of gam()in 'mgcv' package, applying the algorithm in this paper: Lai(2024) <doi:10.1016/j.pld.2024.06.002>.
Author: Jiangshan Lai [aut, cre] ,
Jing Tang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between gam.hp versions 0.0-2 dated 2024-07-25 and 0.0-3 dated 2024-12-15
DESCRIPTION | 10 - MD5 | 11 +- R/gam.hp.r | 267 +++++++++++++++++++++++++++++++++++++++++++++-------- R/permu.gamhp.r | 120 +++++++++-------------- R/zzz.R |only man/gam.hp.Rd | 7 + man/permu.gamhp.Rd | 8 + 7 files changed, 302 insertions(+), 121 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results [...truncated...]
Author: Emmanuel Paradis [aut, cre, cph]
,
Simon Blomberg [aut, cph] ,
Ben Bolker [aut, cph] ,
Joseph Brown [aut, cph] ,
Santiago Claramunt [aut, cph] ,
Julien Claude [aut, cph] ,
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] [...truncated...]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.8 dated 2024-04-11 and 5.8-1 dated 2024-12-15
DESCRIPTION | 12 MD5 | 50 NAMESPACE | 1 NEWS | 4336 +++++++++++++++++++++++++++++++++++++++- R/ace.R | 9 R/cophenetic.phylo.R | 11 R/plot.phylo.R | 92 R/read.nexus.R | 24 R/scales.R | 151 - R/summary.phylo.R | 17 R/write.nexus.R | 8 R/write.phyloXML.R |only R/write.tree.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/carnivora.csv.gz |binary inst/doc/DrawingPhylogenies.pdf |binary inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.pdf |binary man/axisPhylo.Rd | 9 man/cophenetic.phylo.Rd | 6 man/getAnnotationsGenBank.Rd | 2 man/image.DNAbin.Rd | 2 man/kronoviz.Rd | 11 man/write.nexus.Rd | 6 man/write.phyloXML.Rd |only man/write.tree.Rd | 15 27 files changed, 4592 insertions(+), 174 deletions(-)
Title: Hacks for 'ggplot2'
Description: A 'ggplot2' extension that does a variety of little
helpful things. The package extends 'ggplot2' facets through
customisation, by setting individual scales per panel, resizing panels
and providing nested facets. Also allows multiple colour and fill
scales per plot. Also hosts a smaller collection of stats, geoms and axis
guides.
Author: Teun van den Brand [aut, cre]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between ggh4x versions 0.2.8 dated 2024-01-23 and 0.3.0 dated 2024-12-15
ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.R |only ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.Rmd |only ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.html |only ggh4x-0.2.8/ggh4x/tests/testthat/_snaps/guide_axis_manual |only ggh4x-0.2.8/ggh4x/tests/testthat/_snaps/guide_axis_manual.md |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_logticks.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_manual.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_minor.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_nested.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_scalebar.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_truncated.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-scale_dendrogram.R |only ggh4x-0.2.8/ggh4x/vignettes/PositionGuides.Rmd |only ggh4x-0.3.0/ggh4x/DESCRIPTION | 37 ggh4x-0.3.0/ggh4x/MD5 | 199 ++-- ggh4x-0.3.0/ggh4x/NAMESPACE | 6 ggh4x-0.3.0/ggh4x/NEWS.md | 41 ggh4x-0.3.0/ggh4x/R/at_panel.R |only ggh4x-0.3.0/ggh4x/R/coord_axes_inside.R | 59 - ggh4x-0.3.0/ggh4x/R/facet_grid2.R | 15 ggh4x-0.3.0/ggh4x/R/facet_manual.R | 6 ggh4x-0.3.0/ggh4x/R/facet_nested.R | 4 ggh4x-0.3.0/ggh4x/R/facet_nested_wrap.R | 4 ggh4x-0.3.0/ggh4x/R/facet_wrap2.R | 46 - ggh4x-0.3.0/ggh4x/R/geom_outline_point.R | 2 ggh4x-0.3.0/ggh4x/R/geom_text_aimed.R | 2 ggh4x-0.3.0/ggh4x/R/guide_axis_logticks.R | 28 ggh4x-0.3.0/ggh4x/R/guide_axis_manual.R | 18 ggh4x-0.3.0/ggh4x/R/guide_axis_minor.R | 21 ggh4x-0.3.0/ggh4x/R/guide_axis_nested.R | 25 ggh4x-0.3.0/ggh4x/R/guide_axis_scalebar.R | 16 ggh4x-0.3.0/ggh4x/R/guide_axis_truncated.R | 21 ggh4x-0.3.0/ggh4x/R/guide_axis_utils.R | 6 ggh4x-0.3.0/ggh4x/R/guide_dendrogram.R | 14 ggh4x-0.3.0/ggh4x/R/guide_stringlegend.R | 420 +--------- ggh4x-0.3.0/ggh4x/R/help_secondary.R | 20 ggh4x-0.3.0/ggh4x/R/scale_dendrogram.R | 22 ggh4x-0.3.0/ggh4x/R/stat_difference.R | 2 ggh4x-0.3.0/ggh4x/R/stat_theodensity.R | 2 ggh4x-0.3.0/ggh4x/R/strip_tag.R |only ggh4x-0.3.0/ggh4x/R/strip_vanilla.R | 30 ggh4x-0.3.0/ggh4x/R/themes.R | 35 ggh4x-0.3.0/ggh4x/R/utils.R | 42 - ggh4x-0.3.0/ggh4x/README.md | 22 ggh4x-0.3.0/ggh4x/build/vignette.rds |binary ggh4x-0.3.0/ggh4x/inst/doc/Facets.R | 34 ggh4x-0.3.0/ggh4x/inst/doc/Facets.Rmd | 14 ggh4x-0.3.0/ggh4x/inst/doc/Facets.html | 96 +- ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.R | 13 ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.Rmd | 16 ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.html | 190 ++-- ggh4x-0.3.0/ggh4x/inst/doc/Statistics.R | 2 ggh4x-0.3.0/ggh4x/inst/doc/Statistics.html | 56 - ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.R | 2 ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.Rmd | 4 ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.html | 10 ggh4x-0.3.0/ggh4x/man/at_panel.Rd |only ggh4x-0.3.0/ggh4x/man/coord_axes_inside.Rd | 9 ggh4x-0.3.0/ggh4x/man/facet_grid2.Rd | 15 ggh4x-0.3.0/ggh4x/man/facet_manual.Rd | 14 ggh4x-0.3.0/ggh4x/man/facet_nested.Rd | 2 ggh4x-0.3.0/ggh4x/man/facet_nested_wrap.Rd | 2 ggh4x-0.3.0/ggh4x/man/facet_wrap2.Rd | 16 ggh4x-0.3.0/ggh4x/man/figures/README-facets-1.png |binary ggh4x-0.3.0/ggh4x/man/figures/lifecycle-deprecated.svg | 22 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-experimental.svg | 22 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-stable.svg | 30 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-superseded.svg | 22 ggh4x-0.3.0/ggh4x/man/geom_box.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_outline_point.Rd | 83 + ggh4x-0.3.0/ggh4x/man/geom_pointpath.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_polygonraster.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_rectmargin.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_text_aimed.Rd | 82 + ggh4x-0.3.0/ggh4x/man/ggh4x_extensions.Rd | 9 ggh4x-0.3.0/ggh4x/man/guide_axis_logticks.Rd | 32 ggh4x-0.3.0/ggh4x/man/guide_axis_manual.Rd | 21 ggh4x-0.3.0/ggh4x/man/guide_axis_minor.Rd | 26 ggh4x-0.3.0/ggh4x/man/guide_axis_nested.Rd | 29 ggh4x-0.3.0/ggh4x/man/guide_axis_scalebar.Rd | 8 ggh4x-0.3.0/ggh4x/man/guide_axis_truncated.Rd | 21 ggh4x-0.3.0/ggh4x/man/guide_dendro.Rd | 11 ggh4x-0.3.0/ggh4x/man/guide_stringlegend.Rd | 79 - ggh4x-0.3.0/ggh4x/man/help_secondary.Rd | 6 ggh4x-0.3.0/ggh4x/man/scale_dendrogram.Rd | 14 ggh4x-0.3.0/ggh4x/man/scale_x_manual.Rd | 8 ggh4x-0.3.0/ggh4x/man/stat_difference.Rd | 67 + ggh4x-0.3.0/ggh4x/man/stat_funxy.Rd | 62 + ggh4x-0.3.0/ggh4x/man/stat_rle.Rd | 47 - ggh4x-0.3.0/ggh4x/man/stat_rollingkernel.Rd | 47 - ggh4x-0.3.0/ggh4x/man/stat_theodensity.Rd | 51 - ggh4x-0.3.0/ggh4x/man/strip_nested.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_split.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_tag.Rd |only ggh4x-0.3.0/ggh4x/man/strip_themed.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_vanilla.Rd | 1 ggh4x-0.3.0/ggh4x/man/theme_extensions.Rd | 35 ggh4x-0.3.0/ggh4x/tests/testthat/Rplots.pdf |binary ggh4x-0.3.0/ggh4x/tests/testthat/_snaps/facetted_pos_scales.md | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_grid2.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_nested.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_wrap2.R | 8 ggh4x-0.3.0/ggh4x/tests/testthat/test-guide_axis_deprecated.R |only ggh4x-0.3.0/ggh4x/tests/testthat/test-guide_stringlegend.R | 17 ggh4x-0.3.0/ggh4x/tests/testthat/test-stat_theodensity.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-strip_tag.R |only ggh4x-0.3.0/ggh4x/tests/testthat/test-utils.R | 6 ggh4x-0.3.0/ggh4x/vignettes/Facets.Rmd | 14 ggh4x-0.3.0/ggh4x/vignettes/Miscellaneous.Rmd | 16 ggh4x-0.3.0/ggh4x/vignettes/ggh4x.Rmd | 4 110 files changed, 1579 insertions(+), 1244 deletions(-)
Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off
values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
power for Pearson's r with known sample size; (4) conduct prior power analysis and plan the
sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared,
post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared;
(7) conduct prior power analysis and plan the sample size for one or a set of predictors in
regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size.
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2024.11.25 dated 2024-11-24 and 2024.12.15 dated 2024-12-15
DESCRIPTION | 32 +++-- MD5 | 67 ++++++----- NAMESPACE | 3 NEWS.md | 16 +- R/Scale.R | 119 ++++++++++---------- R/calc_PRE.R | 21 ++- R/compare_lm.R | 71 +++++++----- R/cut_r.R | 15 +- R/data.R | 2 R/plot.Keng_power.R |only R/power_lm.R | 230 +++++++++++++++++++++++++-------------- R/power_r.R |only R/print.Keng_power.R |only R/test_r.R | 147 ++++++++++++++++-------- README.md | 49 +++++--- inst/doc/PRE.html | 57 +++++---- inst/doc/PartialRegression.html | 38 +++--- inst/doc/PlanSampleSize.R | 19 +++ inst/doc/PlanSampleSize.Rmd | 76 +++++++----- inst/doc/PlanSampleSize.html | 127 +++++++++++++-------- man/Scale.Rd | 4 man/calc_PRE.Rd | 2 man/compare_lm.Rd | 55 +++++---- man/cut_r.Rd | 10 - man/depress.Rd | 2 man/plot.Keng_power.Rd |only man/power_lm.Rd | 88 +++++++++++--- man/power_r.Rd |only man/print.Keng_power.Rd |only man/test_r.Rd | 68 +++++++---- tests/testthat/test-Scale.R | 4 tests/testthat/test-calc_PRE.R | 19 +++ tests/testthat/test-compare_lm.R | 36 +++++- tests/testthat/test-cut_r.R | 4 tests/testthat/test-power_lm.R | 47 +++++++ tests/testthat/test-power_r.R |only tests/testthat/test-test_r.R | 10 + vignettes/PlanSampleSize.Rmd | 76 +++++++----- 38 files changed, 976 insertions(+), 538 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.9.2 dated 2024-08-26 and 0.10.0 dated 2024-12-15
DESCRIPTION | 21 + MD5 | 46 ++-- NEWS.md | 7 R/esp_get_comarca.R | 345 +++++++++++++++++--------------- R/esp_get_prov.R | 9 R/sysdata.rda |binary R/utils_siane.R | 4 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary data/esp_codelist.rda |binary data/esp_munic.sf.rda |binary data/esp_nuts.sf.rda |binary data/esp_tiles_providers.rda |binary data/leaflet.providersESP.df.rda |binary data/pobmun19.rda |binary inst/WORDLIST | 10 inst/schemaorg.json | 4 man/esp_get_comarca.Rd | 59 +++-- man/mapSpain-package.Rd | 2 tests/testthat/test-esp_getTiles.R | 4 tests/testthat/test-esp_get_comarca.R | 8 tests/testthat/test-esp_get_munic.R | 1 tests/testthat/test-esp_make_provider.R | 4 24 files changed, 309 insertions(+), 221 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.10.0 dated 2024-10-29 and 1.11.0 dated 2024-12-15
microeco-1.10.0/microeco/inst/extdata/Tax4Fun_0.3.1.tar.gz |only microeco-1.11.0/microeco/DESCRIPTION | 6 microeco-1.11.0/microeco/MD5 | 33 - microeco-1.11.0/microeco/R/microtable.R | 32 - microeco-1.11.0/microeco/R/trans_abund.R | 48 ++ microeco-1.11.0/microeco/R/trans_alpha.R | 35 + microeco-1.11.0/microeco/R/trans_diff.R | 51 ++ microeco-1.11.0/microeco/R/trans_env.R | 248 +++++-------- microeco-1.11.0/microeco/R/trans_func.R | 68 --- microeco-1.11.0/microeco/R/trans_network.R | 104 +++-- microeco-1.11.0/microeco/R/utility.R | 3 microeco-1.11.0/microeco/man/microtable.Rd | 6 microeco-1.11.0/microeco/man/trans_abund.Rd | 9 microeco-1.11.0/microeco/man/trans_alpha.Rd | 19 microeco-1.11.0/microeco/man/trans_diff.Rd | 8 microeco-1.11.0/microeco/man/trans_env.Rd | 28 - microeco-1.11.0/microeco/man/trans_func.Rd | 25 - microeco-1.11.0/microeco/man/trans_network.Rd | 6 18 files changed, 379 insertions(+), 350 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 3.0.2 dated 2024-10-30 and 3.0.3 dated 2024-12-15
DESCRIPTION | 6 MD5 | 133 ++++++++----- NAMESPACE | 29 ++ NEWS.md | 32 +++ R/build.R | 11 - R/d.R | 181 +++++++++++++++++- R/dfIni.R | 234 +++++++++++++----------- R/elu.R |only R/err-foceiBase.R | 10 - R/et.R | 66 +++--- R/gelu.R |only R/lrelu.R |only R/parseFuns.R | 107 ++++++----- R/prelu.R |only R/relu.R |only R/rudfui.R | 33 +++ R/rxode2_md5.R | 2 R/rxrandomui.R | 340 +++++++++++++---------------------- R/selu.R |only R/softplus.R |only R/swish.R |only R/symengine.R | 142 +++++++++++++- R/utils.R | 31 +++ build/partial.rdb |binary build/vignette.rds |binary data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/doc/rxode2-syntax.html | 26 +- inst/include/rxode2_model_shared.c | 59 ++++++ inst/include/rxode2_model_shared.h | 6 inst/include/rxode2parseHandleEvid.h | 5 inst/include/rxode2parseVer.h | 4 inst/include/rxode2ptr.h | 5 inst/tools/workaround.R | 25 +- man/ELU.Rd |only man/GELU.Rd |only man/PReLU.Rd |only man/ReLU.Rd |only man/SELU.Rd |only man/Swish.Rd |only man/dELU.Rd |only man/dGELU.Rd |only man/dPReLU.Rd |only man/dReLU.Rd |only man/dSELU.Rd |only man/dSwish.Rd |only man/dlReLU.Rd |only man/dot-uiArg.Rd |only man/dsoftplus.Rd |only man/lReLU.Rd |only man/linMod.Rd | 1 man/rxUdfUiControl.Rd |only man/rxUdfUiData.Rd | 1 man/rxUdfUiEst.Rd | 1 man/rxUdfUiIniLhs.Rd | 1 man/rxUdfUiMv.Rd | 1 man/rxUdfUiNum.Rd | 1 man/rxUdfUiParsing.Rd | 1 man/softplus.Rd |only src/Makevars.in | 2 src/codegen.c | 4 src/codegen2.h | 28 ++ src/genModelVars.h | 60 +++++- src/init.c | 69 ++++++- src/parseCmtProperties.h | 10 - src/parseDdt.h | 7 src/parseFuns.h | 7 src/parseFunsDosing.h | 59 ++++-- src/parseVars.h | 1 src/rx2api.c | 4 src/rx2api.h | 3 src/tran.c | 3 src/tran.h | 31 ++- src/utilc.c | 256 ++++++++++++++++++++++++++ tests/testthat/test-activation.R |only tests/testthat/test-dsl.R | 78 +++++++- tests/testthat/test-et.R | 17 + tests/testthat/test-logit.R | 33 +++ tests/testthat/test-tad.R | 56 +++++ tests/testthat/test-transit.R | 32 +++ 81 files changed, 1701 insertions(+), 553 deletions(-)
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph]
,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.5 dated 2024-11-11 and 0.1.6 dated 2024-12-14
sundialr-0.1.5/sundialr/inst/include/nvector/nvector_openmp.h |only sundialr-0.1.5/sundialr/inst/include/nvector/nvector_openmpdev.h |only sundialr-0.1.5/sundialr/inst/include/nvector/nvector_parallel.h |only sundialr-0.1.5/sundialr/inst/include/sundials/priv/sundials_mpi_errors_impl.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_config.in |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_cuda_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_hip_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_mpi_errors.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_nvector_senswrapper.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_sycl_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_xbraid.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_ginkgo.hpp |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_klu.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_lapackband.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_lapackdense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_magmadense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_onemkldense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_superludist.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_superlumt.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_cusparse.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_ginkgo.hpp |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_magmadense.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_onemkldense.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_slunrloc.h |only sundialr-0.1.5/sundialr/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h |only sundialr-0.1.5/sundialr/src/Makevars |only sundialr-0.1.5/sundialr/src/sortTimes.cpp |only sundialr-0.1.5/sundialr/src/sundials |only sundialr-0.1.6/sundialr/DESCRIPTION | 6 sundialr-0.1.6/sundialr/LICENSE | 3 sundialr-0.1.6/sundialr/MD5 | 224 +--- sundialr-0.1.6/sundialr/NEWS | 7 sundialr-0.1.6/sundialr/R/zzz.R | 8 sundialr-0.1.6/sundialr/README.md | 16 sundialr-0.1.6/sundialr/cleanup |only sundialr-0.1.6/sundialr/cleanup.win |only sundialr-0.1.6/sundialr/configure |only sundialr-0.1.6/sundialr/configure.ac |only sundialr-0.1.6/sundialr/configure.win |only sundialr-0.1.6/sundialr/inst/COPYRIGHTS | 4 sundialr-0.1.6/sundialr/inst/doc/my-vignette.html | 8 sundialr-0.1.6/sundialr/inst/include/arkode |only sundialr-0.1.6/sundialr/inst/include/cvode/cvode_bandpre.h | 2 sundialr-0.1.6/sundialr/inst/include/cvodes/cvodes_bandpre.h | 2 sundialr-0.1.6/sundialr/inst/include/nvector/nvector_manyvector.h |only sundialr-0.1.6/sundialr/inst/include/sunadaptcontroller |only sundialr-0.1.6/sundialr/inst/include/sundials/LICENSE |only sundialr-0.1.6/sundialr/inst/include/sundials/NOTICE |only sundialr-0.1.6/sundialr/inst/include/sundials/priv/sundials_errors_impl.h | 22 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_adaptcontroller.h | 39 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_base.hpp | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_config.h | 28 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_convertibleto.hpp | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_errors.h | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_export.h | 6 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_math.h | 40 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_memory.h | 4 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_nvector.h | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_stepper.h |only sundialr-0.1.6/sundialr/inst/include/sunmemory |only sundialr-0.1.6/sundialr/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 2 sundialr-0.1.6/sundialr/src/Makevars.in |only sundialr-0.1.6/sundialr/src/cvode.cpp | 12 sundialr-0.1.6/sundialr/src/cvodes.cpp | 40 sundialr-0.1.6/sundialr/src/cvsolve.cpp | 491 ++++------ sundialr-0.1.6/sundialr/src/scripts |only sundialr-0.1.6/sundialr/src/utils |only sundialr-0.1.6/sundialr/tools |only 71 files changed, 471 insertions(+), 501 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.12 dated 2024-11-21 and 2.0.13 dated 2024-12-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.in | 4 +--- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using either an expectation–maximization (EM) type algorithm or its accelerated version (Damped Anderson Acceleration with Epsilon Monotonicity, DAAREM), including some possibilities for modeling the within-subject dependence. Details can be found in Schumacher, Lachos and Matos (2021) <doi:10.1002/sim.8870>.
Author: Fernanda L. Schumacher [aut, cre]
,
Larissa A. Matos [aut] ,
Victor H. Lachos [aut] ,
Katherine A. L. Valeriano [aut]
,
Nicholas Henderson [ctb],
Ravi Varadhan [ctb]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between skewlmm versions 1.1.0 dated 2023-06-30 and 1.1.2 dated 2024-12-14
DESCRIPTION | 18 +++--- MD5 | 51 ++++++++++++------- NAMESPACE | 66 ++++++++++++++++++------- NEWS.md | 13 ++++ R/mainfunctions-sim.R | 16 +++--- R/mainfunctions.R | 99 +++++++++++++++++++++++++++++++++----- R/residuals.R | 83 +++++++++++++++++++------------ R/smnCens_prin.R | 2 README.md | 15 ++++- data |only man/UTIdata.Rd |only man/coef.Rd |only man/confint.Rd |only man/figures/README-example1-1.png |binary man/figures/README-example2-1.png |binary man/figures/README-example2-3.png |binary man/figures/skewlmm_hex.png |only man/fixef.Rd |only man/formula.Rd |only man/healy.plot.Rd | 6 +- man/lmmControl.Rd | 2 man/logLik.Rd |only man/miceweight.Rd |only man/nobs.Rd |only man/plot.Rd | 5 + man/plot.SMNCens.Rd | 4 - man/plot.acfresid.Rd | 5 + man/plot.mahalDist.Rd | 4 - man/plot.mahalDist.SMNCens.Rd | 4 - man/ranef.Rd | 10 +++ man/sigma.Rd |only man/weight_plot.Rd |only 32 files changed, 289 insertions(+), 114 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment trial data
using parametric and non-parametric methods. Parametric methods
includes Additive Main Effects and Multiplicative Interaction (AMMI)
analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence
by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot
analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric
adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method, power law residuals (POLAR) statistics by Doring et al.
(2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted ave [...truncated...]
Author: Tiago Olivoto [aut, cre, cph]
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.18.0 dated 2023-03-05 and 1.19.0 dated 2024-12-14
metan-1.18.0/metan/R/ammi_indexes.R |only metan-1.18.0/metan/R/fai_blup.R |only metan-1.18.0/metan/R/mtsi.R |only metan-1.18.0/metan/R/waasb.R |only metan-1.18.0/metan/build/metan.pdf |only metan-1.18.0/metan/man/metan-package.Rd |only metan-1.18.0/metan/vignettes/ammi.RData |only metan-1.18.0/metan/vignettes/cvali.RData |only metan-1.18.0/metan/vignettes/indexes.RData |only metan-1.18.0/metan/vignettes/metan.RData |only metan-1.18.0/metan/vignettes/plots_corr.RData |only metan-1.18.0/metan/vignettes/wratio.RData |only metan-1.19.0/metan/DESCRIPTION | 16 metan-1.19.0/metan/MD5 | 475 +++++------ metan-1.19.0/metan/NAMESPACE | 3 metan-1.19.0/metan/NEWS.md | 7 metan-1.19.0/metan/R/AMMI_indexes.R |only metan-1.19.0/metan/R/FAI_BLUP.R |only metan-1.19.0/metan/R/MTSI.R |only metan-1.19.0/metan/R/WAASB.R |only metan-1.19.0/metan/R/acv.R | 2 metan-1.19.0/metan/R/anova_ind.R | 13 metan-1.19.0/metan/R/anova_joint.R | 41 - metan-1.19.0/metan/R/blup_indexes.R | 2 metan-1.19.0/metan/R/clustering.R | 3 metan-1.19.0/metan/R/coincidence_index.R | 6 metan-1.19.0/metan/R/colindiag.R | 108 +- metan-1.19.0/metan/R/corr_ci.R | 2 metan-1.19.0/metan/R/corr_ss.R | 2 metan-1.19.0/metan/R/cv_ammi.R | 2 metan-1.19.0/metan/R/cv_blup.R | 2 metan-1.19.0/metan/R/gamem_met.R | 2 metan-1.19.0/metan/R/ge_plot.R | 42 - metan-1.19.0/metan/R/ge_stats.R | 4 metan-1.19.0/metan/R/get_model_data.R | 35 metan-1.19.0/metan/R/metan-package.r | 3 metan-1.19.0/metan/R/mgidi.R | 276 ++++-- metan-1.19.0/metan/R/mps.R | 5 metan-1.19.0/metan/R/mtmps.R | 4 metan-1.19.0/metan/R/non_collinear_vars.R | 15 metan-1.19.0/metan/R/path_coeff.R | 6 metan-1.19.0/metan/R/plaisted_peterson.R |only metan-1.19.0/metan/R/plot_scores.R | 2 metan-1.19.0/metan/R/utilities.R | 30 metan-1.19.0/metan/R/utils-tidy-eval.R | 214 ++--- metan-1.19.0/metan/R/utils_as.R | 2 metan-1.19.0/metan/R/venn_plot.R | 51 - metan-1.19.0/metan/R/waas.R | 4 metan-1.19.0/metan/R/waas_means.R | 2 metan-1.19.0/metan/R/wsmp.R | 4 metan-1.19.0/metan/R/zzz.R | 4 metan-1.19.0/metan/build/stage23.rdb |only metan-1.19.0/metan/build/vignette.rds |binary metan-1.19.0/metan/inst/doc/metan_start.R | 6 metan-1.19.0/metan/inst/doc/metan_start.Rmd | 2 metan-1.19.0/metan/inst/doc/metan_start.html | 662 ++++++++-------- metan-1.19.0/metan/man/Annicchiarico.Rd | 140 +-- metan-1.19.0/metan/man/Fox.Rd | 116 +- metan-1.19.0/metan/man/Huehn.Rd | 120 +- metan-1.19.0/metan/man/Schmildt.Rd | 150 +-- metan-1.19.0/metan/man/Select_helper.Rd | 214 ++--- metan-1.19.0/metan/man/Shukla.Rd | 136 +-- metan-1.19.0/metan/man/Smith_Hazel.Rd | 194 ++-- metan-1.19.0/metan/man/Thennarasu.Rd | 98 +- metan-1.19.0/metan/man/acv.Rd | 140 +-- metan-1.19.0/metan/man/ammi_indexes.Rd | 5 metan-1.19.0/metan/man/anova_ind.Rd | 199 ++-- metan-1.19.0/metan/man/anova_joint.Rd | 168 ++-- metan-1.19.0/metan/man/arrange_ggplot.Rd | 192 ++-- metan-1.19.0/metan/man/as.lpcor.Rd | 72 - metan-1.19.0/metan/man/barplots.Rd | 516 ++++++------ metan-1.19.0/metan/man/bind_cv.Rd | 116 +- metan-1.19.0/metan/man/blup_indexes.Rd | 216 ++--- metan-1.19.0/metan/man/can_corr.Rd | 222 ++--- metan-1.19.0/metan/man/clustering.Rd | 282 +++--- metan-1.19.0/metan/man/coincidence_index.Rd | 102 +- metan-1.19.0/metan/man/colindiag.Rd | 173 ++-- metan-1.19.0/metan/man/comb_vars.Rd | 96 +- metan-1.19.0/metan/man/corr_ci.Rd | 166 ++-- metan-1.19.0/metan/man/corr_coef.Rd | 194 ++-- metan-1.19.0/metan/man/corr_focus.Rd | 52 - metan-1.19.0/metan/man/corr_plot.Rd | 460 +++++------ metan-1.19.0/metan/man/corr_ss.Rd | 94 +- metan-1.19.0/metan/man/corr_stab_ind.Rd | 138 +-- metan-1.19.0/metan/man/correlated_vars.Rd | 112 +- metan-1.19.0/metan/man/covcor_design.Rd | 168 ++-- metan-1.19.0/metan/man/cv_ammi.Rd | 236 ++--- metan-1.19.0/metan/man/cv_ammif.Rd | 220 ++--- metan-1.19.0/metan/man/cv_blup.Rd | 280 +++--- metan-1.19.0/metan/man/data_alpha.Rd | 64 - metan-1.19.0/metan/man/data_g.Rd | 82 +- metan-1.19.0/metan/man/data_ge.Rd | 62 - metan-1.19.0/metan/man/data_ge2.Rd | 88 +- metan-1.19.0/metan/man/data_simula.Rd | 234 ++--- metan-1.19.0/metan/man/desc_stat.Rd | 340 ++++---- metan-1.19.0/metan/man/doo.Rd | 100 +- metan-1.19.0/metan/man/ecovalence.Rd | 106 +- metan-1.19.0/metan/man/env_dissimilarity.Rd | 160 +-- metan-1.19.0/metan/man/env_stratification.Rd | 166 ++-- metan-1.19.0/metan/man/fai_blup.Rd | 172 ++-- metan-1.19.0/metan/man/find_outliers.Rd | 114 +- metan-1.19.0/metan/man/gafem.Rd | 268 +++--- metan-1.19.0/metan/man/gai.Rd | 126 +-- metan-1.19.0/metan/man/gamem.Rd | 340 ++++---- metan-1.19.0/metan/man/gamem_met.Rd | 392 ++++----- metan-1.19.0/metan/man/ge_acv.Rd | 112 +- metan-1.19.0/metan/man/ge_cluster.Rd | 192 ++-- metan-1.19.0/metan/man/ge_details.Rd | 94 +- metan-1.19.0/metan/man/ge_effects.Rd | 102 +- metan-1.19.0/metan/man/ge_factanal.Rd | 150 +-- metan-1.19.0/metan/man/ge_means.Rd | 108 +- metan-1.19.0/metan/man/ge_plot.Rd | 175 ++-- metan-1.19.0/metan/man/ge_reg.Rd | 140 +-- metan-1.19.0/metan/man/ge_stats.Rd | 362 ++++---- metan-1.19.0/metan/man/ge_winners.Rd | 124 +-- metan-1.19.0/metan/man/get_corvars.Rd | 90 +- metan-1.19.0/metan/man/get_covmat.Rd | 74 - metan-1.19.0/metan/man/get_dist.Rd | 74 - metan-1.19.0/metan/man/get_model_data.Rd | 855 ++++++++++----------- metan-1.19.0/metan/man/gge.Rd | 224 ++--- metan-1.19.0/metan/man/gtb.Rd | 168 ++-- metan-1.19.0/metan/man/gytb.Rd | 234 ++--- metan-1.19.0/metan/man/impute_missing_val.Rd | 242 ++--- metan-1.19.0/metan/man/inspect.Rd | 116 +- metan-1.19.0/metan/man/int.effects.Rd | 26 metan-1.19.0/metan/man/is.lpcor.Rd | 64 - metan-1.19.0/metan/man/is_balanced_trial.Rd | 78 - metan-1.19.0/metan/man/lineplots.Rd | 306 +++---- metan-1.19.0/metan/man/lpcor.Rd | 130 +-- metan-1.19.0/metan/man/mahala.Rd | 102 +- metan-1.19.0/metan/man/mahala_design.Rd | 154 +-- metan-1.19.0/metan/man/make_long.Rd | 94 +- metan-1.19.0/metan/man/make_mat.Rd | 98 +- metan-1.19.0/metan/man/mantel_test.Rd | 102 +- metan-1.19.0/metan/man/meansGxE.Rd | 30 metan-1.19.0/metan/man/metan.Rd |only metan-1.19.0/metan/man/mgidi.Rd | 53 - metan-1.19.0/metan/man/mps.Rd | 406 ++++----- metan-1.19.0/metan/man/mtmps.Rd | 236 ++--- metan-1.19.0/metan/man/mtsi.Rd | 276 +++--- metan-1.19.0/metan/man/network_plot.Rd | 186 ++-- metan-1.19.0/metan/man/non_collinear_vars.Rd | 104 +- metan-1.19.0/metan/man/pairs_mantel.Rd | 280 +++--- metan-1.19.0/metan/man/path_coeff.Rd | 412 ++++------ metan-1.19.0/metan/man/performs_ammi.Rd | 218 ++--- metan-1.19.0/metan/man/pipe.Rd | 24 metan-1.19.0/metan/man/plaisted_peterson.Rd |only metan-1.19.0/metan/man/plot.anova_joint.Rd | 74 - metan-1.19.0/metan/man/plot.can_cor.Rd | 246 +++--- metan-1.19.0/metan/man/plot.clustering.Rd | 80 - metan-1.19.0/metan/man/plot.corr_coef.Rd | 208 ++--- metan-1.19.0/metan/man/plot.correlated_vars.Rd | 54 - metan-1.19.0/metan/man/plot.cvalidation.Rd | 234 ++--- metan-1.19.0/metan/man/plot.env_dissimilarity.Rd | 62 - metan-1.19.0/metan/man/plot.env_stratification.Rd | 80 - metan-1.19.0/metan/man/plot.fai_blup.Rd | 160 +-- metan-1.19.0/metan/man/plot.gafem.Rd | 76 - metan-1.19.0/metan/man/plot.gamem.Rd | 266 +++--- metan-1.19.0/metan/man/plot.ge_cluster.Rd | 46 - metan-1.19.0/metan/man/plot.ge_effects.Rd | 120 +- metan-1.19.0/metan/man/plot.ge_factanal.Rd | 274 +++--- metan-1.19.0/metan/man/plot.ge_reg.Rd | 166 ++-- metan-1.19.0/metan/man/plot.gge.Rd | 318 +++---- metan-1.19.0/metan/man/plot.mgidi.Rd | 215 ++--- metan-1.19.0/metan/man/plot.mtmps.Rd | 232 ++--- metan-1.19.0/metan/man/plot.mtsi.Rd | 217 ++--- metan-1.19.0/metan/man/plot.path_coeff.Rd | 122 +- metan-1.19.0/metan/man/plot.performs_ammi.Rd | 74 - metan-1.19.0/metan/man/plot.resp_surf.Rd | 122 +- metan-1.19.0/metan/man/plot.sh.Rd | 132 +-- metan-1.19.0/metan/man/plot.waas.Rd | 74 - metan-1.19.0/metan/man/plot.waasb.Rd | 304 +++---- metan-1.19.0/metan/man/plot.wsmp.Rd | 126 +-- metan-1.19.0/metan/man/plot_blup.Rd | 278 +++--- metan-1.19.0/metan/man/plot_ci.Rd | 216 ++--- metan-1.19.0/metan/man/plot_eigen.Rd | 190 ++-- metan-1.19.0/metan/man/plot_scores.Rd | 568 ++++++------- metan-1.19.0/metan/man/plot_waasby.Rd | 214 ++--- metan-1.19.0/metan/man/predict.gamem.Rd | 66 - metan-1.19.0/metan/man/predict.gge.Rd | 106 +- metan-1.19.0/metan/man/predict.performs_ammi.Rd | 110 +- metan-1.19.0/metan/man/predict.waas.Rd | 116 +- metan-1.19.0/metan/man/predict.waasb.Rd | 68 - metan-1.19.0/metan/man/print.Annicchiarico.Rd | 82 +- metan-1.19.0/metan/man/print.Fox.Rd | 74 - metan-1.19.0/metan/man/print.Huehn.Rd | 72 - metan-1.19.0/metan/man/print.Schmildt.Rd | 80 - metan-1.19.0/metan/man/print.Shukla.Rd | 82 +- metan-1.19.0/metan/man/print.Thennarasu.Rd | 72 - metan-1.19.0/metan/man/print.ammi_indexes.Rd | 2 metan-1.19.0/metan/man/print.anova_ind.Rd | 72 - metan-1.19.0/metan/man/print.anova_joint.Rd | 72 - metan-1.19.0/metan/man/print.can_cor.Rd | 78 - metan-1.19.0/metan/man/print.coincidence.Rd | 74 - metan-1.19.0/metan/man/print.colindiag.Rd | 72 - metan-1.19.0/metan/man/print.corr_coef.Rd | 72 - metan-1.19.0/metan/man/print.ecovalence.Rd | 80 - metan-1.19.0/metan/man/print.env_dissimilarity.Rd | 70 - metan-1.19.0/metan/man/print.env_stratification.Rd | 76 - metan-1.19.0/metan/man/print.gamem.Rd | 82 +- metan-1.19.0/metan/man/print.ge_factanal.Rd | 78 - metan-1.19.0/metan/man/print.ge_reg.Rd | 74 - metan-1.19.0/metan/man/print.ge_stats.Rd | 82 +- metan-1.19.0/metan/man/print.lpcor.Rd | 84 +- metan-1.19.0/metan/man/print.mgidi.Rd | 84 +- metan-1.19.0/metan/man/print.mtmps.Rd | 82 +- metan-1.19.0/metan/man/print.mtsi.Rd | 86 +- metan-1.19.0/metan/man/print.path_coeff.Rd | 92 +- metan-1.19.0/metan/man/print.performs_ammi.Rd | 72 - metan-1.19.0/metan/man/print.plaisted_peterson.Rd |only metan-1.19.0/metan/man/print.sh.Rd | 78 - metan-1.19.0/metan/man/print.superiority.Rd | 72 - metan-1.19.0/metan/man/print.waas.Rd | 80 - metan-1.19.0/metan/man/print.waas_means.Rd | 78 - metan-1.19.0/metan/man/print.waasb.Rd | 84 +- metan-1.19.0/metan/man/reexports.Rd | 60 - metan-1.19.0/metan/man/reorder_cormat.Rd | 66 - metan-1.19.0/metan/man/resca.Rd | 176 ++-- metan-1.19.0/metan/man/residual_plots.Rd | 226 ++--- metan-1.19.0/metan/man/resp_surf.Rd | 126 +-- metan-1.19.0/metan/man/select_pred.Rd | 100 +- metan-1.19.0/metan/man/solve_svd.Rd | 66 - metan-1.19.0/metan/man/split_factors.Rd | 124 +-- metan-1.19.0/metan/man/stars_pval.Rd | 76 - metan-1.19.0/metan/man/superiority.Rd | 116 +- metan-1.19.0/metan/man/themes.Rd | 108 +- metan-1.19.0/metan/man/tidyeval.Rd | 196 ++-- metan-1.19.0/metan/man/transpose_df.Rd | 72 - metan-1.19.0/metan/man/tukey_hsd.Rd | 90 +- metan-1.19.0/metan/man/utils_as.Rd | 178 ++-- metan-1.19.0/metan/man/utils_bind.Rd | 106 +- metan-1.19.0/metan/man/utils_class.Rd | 106 +- metan-1.19.0/metan/man/utils_data.Rd | 88 +- metan-1.19.0/metan/man/utils_data_org.Rd | 168 ++-- metan-1.19.0/metan/man/utils_mat.Rd | 152 +-- metan-1.19.0/metan/man/utils_na_zero.Rd | 296 +++---- metan-1.19.0/metan/man/utils_num_str.Rd | 390 ++++----- metan-1.19.0/metan/man/utils_progress.Rd | 220 ++--- metan-1.19.0/metan/man/utils_rows_cols.Rd | 606 +++++++------- metan-1.19.0/metan/man/utils_samples.Rd | 108 +- metan-1.19.0/metan/man/utils_sets.Rd | 134 +-- metan-1.19.0/metan/man/utils_stats.Rd | 580 +++++++------- metan-1.19.0/metan/man/utils_wd.Rd | 94 +- metan-1.19.0/metan/man/venn_plot.Rd | 215 ++--- metan-1.19.0/metan/man/waas.Rd | 402 ++++----- metan-1.19.0/metan/man/waas_means.Rd | 252 +++--- metan-1.19.0/metan/man/waasb.Rd | 544 ++++++------- metan-1.19.0/metan/man/wsmp.Rd | 204 ++--- metan-1.19.0/metan/vignettes/metan_start.Rmd | 2 249 files changed, 16358 insertions(+), 16116 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen [aut, cre],
Jari Oksanen [aut]
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
Diff between eHOF versions 1.15 dated 2024-01-29 and 1.16 dated 2024-12-14
DESCRIPTION | 18 +++++++--- MD5 | 50 ++++++++++++++------------- NAMESPACE | 40 +++++++++++----------- R/HOF.fun.r | 2 - R/HOF.r | 4 +- R/Para.deriv.r | 7 +-- R/Para.opt.r | 12 +++++- R/betaresp.r | 26 ++++++-------- R/coef.HOF.r | 3 - R/eHOF-package.R | 12 +++--- R/pick.model.r | 93 +++++++++++++++++++++++++++------------------------- R/plot.HOF.list.r | 23 +++++++----- R/plot.HOF.r | 30 ++++++++++------ R/print.HOF.list.r | 13 +------ R/print.HOF.r | 1 R/svHOF.r | 5 +- build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog | 4 ++ inst/doc/eHOF.R | 14 ++++--- inst/doc/eHOF.Rnw | 19 ++++++---- inst/doc/eHOF.pdf |binary man/HOF.Rd | 2 - man/eHOF-package.Rd | 12 ++---- man/eHOF.Rd |only man/plot.HOF.Rd | 12 +++++- vignettes/eHOF.Rnw | 19 ++++++---- 27 files changed, 232 insertions(+), 189 deletions(-)
Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process
Emulations
Description: Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process,
and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI).
The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and
Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and
Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package,
see <https://mingdeyu.github.io/dgpsi-R/>.
Author: Deyu Ming [aut, cre, cph],
Daniel Williamson [aut]
Maintainer: Deyu Ming <deyu.ming.16@ucl.ac.uk>
Diff between dgpsi versions 2.4.0 dated 2024-01-14 and 2.5.0 dated 2024-12-14
dgpsi-2.4.0/dgpsi/R/kernel.R |only dgpsi-2.4.0/dgpsi/R/likelihood.R |only dgpsi-2.4.0/dgpsi/R/pei.R |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.R |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.html |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.R |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.html |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.R |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.html |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.R |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.html |only dgpsi-2.4.0/dgpsi/man/Hetero.Rd |only dgpsi-2.4.0/dgpsi/man/NegBin.Rd |only dgpsi-2.4.0/dgpsi/man/Poisson.Rd |only dgpsi-2.4.0/dgpsi/man/kernel.Rd |only dgpsi-2.4.0/dgpsi/man/pei.Rd |only dgpsi-2.4.0/dgpsi/vignettes/images |only dgpsi-2.4.0/dgpsi/vignettes/linked_DGP.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/motorcycle.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/seq_design.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/seq_design_2.Rmd |only dgpsi-2.5.0/dgpsi/DESCRIPTION | 15 dgpsi-2.5.0/dgpsi/MD5 | 165 +-- dgpsi-2.5.0/dgpsi/NAMESPACE | 17 dgpsi-2.5.0/dgpsi/NEWS.md | 33 dgpsi-2.5.0/dgpsi/R/alm.R | 910 +++++++++++++---- dgpsi-2.5.0/dgpsi/R/design.R | 1442 +++++++++++++++++---------- dgpsi-2.5.0/dgpsi/R/dgp.R | 301 +++-- dgpsi-2.5.0/dgpsi/R/dgpsi-package.R |only dgpsi-2.5.0/dgpsi/R/draw.R | 275 +++-- dgpsi-2.5.0/dgpsi/R/gp.R | 178 ++- dgpsi-2.5.0/dgpsi/R/initi_py.R | 94 + dgpsi-2.5.0/dgpsi/R/lgp.R | 473 ++++++++ dgpsi-2.5.0/dgpsi/R/mice.R | 275 +++-- dgpsi-2.5.0/dgpsi/R/plot.R | 740 +++++++++---- dgpsi-2.5.0/dgpsi/R/prediction.R | 465 +++++++- dgpsi-2.5.0/dgpsi/R/serialization.R |only dgpsi-2.5.0/dgpsi/R/update.R | 86 + dgpsi-2.5.0/dgpsi/R/utils.R | 1410 ++++++++++++++++++++++++-- dgpsi-2.5.0/dgpsi/R/validation.R | 642 +++++++++--- dgpsi-2.5.0/dgpsi/R/vigf.R | 893 +++++++++++++--- dgpsi-2.5.0/dgpsi/README.md | 27 dgpsi-2.5.0/dgpsi/build/partial.rdb |only dgpsi-2.5.0/dgpsi/build/vignette.rds |binary dgpsi-2.5.0/dgpsi/inst/CITATION | 16 dgpsi-2.5.0/dgpsi/inst/WORDLIST | 14 dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.R | 116 +- dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.Rmd | 86 - dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.html | 237 ++-- dgpsi-2.5.0/dgpsi/man/alm.Rd | 137 +- dgpsi-2.5.0/dgpsi/man/combine.Rd | 26 dgpsi-2.5.0/dgpsi/man/continue.Rd | 29 dgpsi-2.5.0/dgpsi/man/deserialize.Rd |only dgpsi-2.5.0/dgpsi/man/design.Rd | 282 +++-- dgpsi-2.5.0/dgpsi/man/dgp.Rd | 145 +- dgpsi-2.5.0/dgpsi/man/dgpsi-package.Rd |only dgpsi-2.5.0/dgpsi/man/draw.Rd | 27 dgpsi-2.5.0/dgpsi/man/figures |only dgpsi-2.5.0/dgpsi/man/get_thread_num.Rd |only dgpsi-2.5.0/dgpsi/man/gp.Rd | 85 - dgpsi-2.5.0/dgpsi/man/init_py.Rd | 2 dgpsi-2.5.0/dgpsi/man/lgp.Rd | 104 + dgpsi-2.5.0/dgpsi/man/mice.Rd | 117 +- dgpsi-2.5.0/dgpsi/man/nllik.Rd | 23 dgpsi-2.5.0/dgpsi/man/pack.Rd | 25 dgpsi-2.5.0/dgpsi/man/plot.Rd | 58 - dgpsi-2.5.0/dgpsi/man/predict.Rd | 117 +- dgpsi-2.5.0/dgpsi/man/prune.Rd | 18 dgpsi-2.5.0/dgpsi/man/serialize.Rd |only dgpsi-2.5.0/dgpsi/man/set_id.Rd |only dgpsi-2.5.0/dgpsi/man/set_imp.Rd | 6 dgpsi-2.5.0/dgpsi/man/set_linked_idx.Rd | 8 dgpsi-2.5.0/dgpsi/man/set_thread_num.Rd |only dgpsi-2.5.0/dgpsi/man/set_vecchia.Rd |only dgpsi-2.5.0/dgpsi/man/summary.Rd | 28 dgpsi-2.5.0/dgpsi/man/trace_plot.Rd | 4 dgpsi-2.5.0/dgpsi/man/unpack.Rd | 4 dgpsi-2.5.0/dgpsi/man/update.Rd | 36 dgpsi-2.5.0/dgpsi/man/validate.Rd | 122 +- dgpsi-2.5.0/dgpsi/man/vigf.Rd | 124 +- dgpsi-2.5.0/dgpsi/man/window.Rd | 18 dgpsi-2.5.0/dgpsi/man/write.Rd | 10 dgpsi-2.5.0/dgpsi/vignettes/dgpsi |only dgpsi-2.5.0/dgpsi/vignettes/dgpsi.Rmd | 86 - dgpsi-2.5.0/dgpsi/vignettes/references.bib | 17 89 files changed, 7755 insertions(+), 2813 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets and
association rules). Also provides C implementations of the
association mining algorithms Apriori and Eclat. Hahsler, Gruen and
Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph] ,
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7-8 dated 2024-08-22 and 1.7-9 dated 2024-12-14
arules-1.7-8/arules/src/Makevars |only arules-1.7-9/arules/DESCRIPTION | 8 arules-1.7-9/arules/MD5 | 271 ++--- arules-1.7-9/arules/NEWS.md | 8 arules-1.7-9/arules/R/AAADefs.R | 109 +- arules-1.7-9/arules/R/Adult.R | 97 +- arules-1.7-9/arules/R/DATAFRAME.R | 84 + arules-1.7-9/arules/R/Epub.R | 18 arules-1.7-9/arules/R/Groceries.R | 14 arules-1.7-9/arules/R/Income.R | 88 + arules-1.7-9/arules/R/LIST.R | 52 - arules-1.7-9/arules/R/Matrix.R | 25 arules-1.7-9/arules/R/Mushroom.R | 14 arules-1.7-9/arules/R/SunBai.R | 12 arules-1.7-9/arules/R/abbreviate.R | 101 +- arules-1.7-9/arules/R/addComplement.R | 60 - arules-1.7-9/arules/R/appearance.R | 134 +- arules-1.7-9/arules/R/apriori.R | 71 - arules-1.7-9/arules/R/associations.R | 210 ++-- arules-1.7-9/arules/R/c.R | 126 +- arules-1.7-9/arules/R/check_installed.R | 36 arules-1.7-9/arules/R/confint.R | 334 +++---- arules-1.7-9/arules/R/control.R | 131 +- arules-1.7-9/arules/R/coverage.R | 43 arules-1.7-9/arules/R/crossTable.R | 45 arules-1.7-9/arules/R/discretize.R | 249 +++-- arules-1.7-9/arules/R/dissimilarity.R | 345 ++++--- arules-1.7-9/arules/R/duplicated.R | 40 arules-1.7-9/arules/R/eclat.R | 51 - arules-1.7-9/arules/R/extract.R | 210 ++-- arules-1.7-9/arules/R/fim4r.R | 279 +++--- arules-1.7-9/arules/R/hierarchy.R | 101 +- arules-1.7-9/arules/R/image.R | 47 - arules-1.7-9/arules/R/inspect.R | 337 ++++--- arules-1.7-9/arules/R/interestMeasures.R | 604 +++++++------ arules-1.7-9/arules/R/is.closed.R | 47 - arules-1.7-9/arules/R/is.generator.R | 49 - arules-1.7-9/arules/R/is.maximal.R | 47 - arules-1.7-9/arules/R/is.redundant.R | 112 +- arules-1.7-9/arules/R/is.significant.R | 64 - arules-1.7-9/arules/R/is.superset.R | 179 ++- arules-1.7-9/arules/R/itemCoding.R | 323 ++++-- arules-1.7-9/arules/R/itemFrequency.R | 334 ++++--- arules-1.7-9/arules/R/itemMatrix.R | 455 ++++++--- arules-1.7-9/arules/R/itemsets.R | 190 ++-- arules-1.7-9/arules/R/match.R | 150 ++- arules-1.7-9/arules/R/merge.R | 35 arules-1.7-9/arules/R/parameter.R | 274 +++-- arules-1.7-9/arules/R/plot.R | 4 arules-1.7-9/arules/R/pmml.R | 78 - arules-1.7-9/arules/R/predict.R | 43 arules-1.7-9/arules/R/random.transactions.R | 349 ++++--- arules-1.7-9/arules/R/read_write.R | 184 ++- arules-1.7-9/arules/R/ruleInduction.R | 332 ++++--- arules-1.7-9/arules/R/rules.R | 312 ++++-- arules-1.7-9/arules/R/sample.R | 56 - arules-1.7-9/arules/R/sets.R | 93 +- arules-1.7-9/arules/R/setsItemwise.R | 70 - arules-1.7-9/arules/R/size.R | 29 arules-1.7-9/arules/R/sort.R | 49 - arules-1.7-9/arules/R/subset.R | 102 +- arules-1.7-9/arules/R/support.R | 178 ++- arules-1.7-9/arules/R/supportingTransactions.R | 45 arules-1.7-9/arules/R/tidLists.R | 314 ++++-- arules-1.7-9/arules/R/transactions.R | 380 ++++---- arules-1.7-9/arules/R/unique.R | 37 arules-1.7-9/arules/R/warm.R | 94 +- arules-1.7-9/arules/README.md | 30 arules-1.7-9/arules/build/partial.rdb |binary arules-1.7-9/arules/build/vignette.rds |binary arules-1.7-9/arules/inst/doc/arules.pdf |binary arules-1.7-9/arules/man/APappearance-class.Rd | 18 arules-1.7-9/arules/man/Adult.Rd | 33 arules-1.7-9/arules/man/DATAFRAME.Rd | 11 arules-1.7-9/arules/man/Epub.Rd | 1 arules-1.7-9/arules/man/Income.Rd | 34 arules-1.7-9/arules/man/apriori.Rd | 19 arules-1.7-9/arules/man/c.Rd | 2 arules-1.7-9/arules/man/confint.Rd | 11 arules-1.7-9/arules/man/discretize.Rd | 73 - arules-1.7-9/arules/man/dissimilarity.Rd | 6 arules-1.7-9/arules/man/eclat.Rd | 3 arules-1.7-9/arules/man/extract.Rd | 2 arules-1.7-9/arules/man/fim4r.Rd | 58 - arules-1.7-9/arules/man/hierarchy.Rd | 3 arules-1.7-9/arules/man/inspect.Rd | 6 arules-1.7-9/arules/man/interestMeasure.Rd | 12 arules-1.7-9/arules/man/is.generator.Rd | 12 arules-1.7-9/arules/man/is.redundant.Rd | 26 arules-1.7-9/arules/man/is.superset.Rd | 4 arules-1.7-9/arules/man/itemCoding.Rd | 56 - arules-1.7-9/arules/man/itemFrequencyPlot.Rd | 14 arules-1.7-9/arules/man/itemMatrix-class.Rd | 34 arules-1.7-9/arules/man/itemsets-class.Rd | 6 arules-1.7-9/arules/man/match.Rd | 2 arules-1.7-9/arules/man/merge.Rd | 2 arules-1.7-9/arules/man/predict.Rd | 2 arules-1.7-9/arules/man/random.transactions.Rd | 14 arules-1.7-9/arules/man/read.Rd | 17 arules-1.7-9/arules/man/ruleInduction.Rd | 2 arules-1.7-9/arules/man/rules-class.Rd | 9 arules-1.7-9/arules/man/subset.Rd | 10 arules-1.7-9/arules/man/supportingTransactions.Rd | 22 arules-1.7-9/arules/man/tidLists-class.Rd | 26 arules-1.7-9/arules/man/transactions-class.Rd | 39 arules-1.7-9/arules/man/weclat.Rd | 28 arules-1.7-9/arules/man/write.Rd | 4 arules-1.7-9/arules/src/bitmat.c | 83 - arules-1.7-9/arules/src/bitmat.h | 6 arules-1.7-9/arules/src/istree.c | 126 -- arules-1.7-9/arules/src/istree.h | 27 arules-1.7-9/arules/src/reclat.c | 4 arules-1.7-9/arules/src/symtab.c | 37 arules-1.7-9/arules/src/symtab.h | 10 arules-1.7-9/arules/src/tract.c | 81 - arules-1.7-9/arules/src/tract.h | 32 arules-1.7-9/arules/tests/testthat/test-apriori.R | 14 arules-1.7-9/arules/tests/testthat/test-associations.R | 71 - arules-1.7-9/arules/tests/testthat/test-concise.R | 20 arules-1.7-9/arules/tests/testthat/test-confint.R | 27 arules-1.7-9/arules/tests/testthat/test-crossTable.R | 23 arules-1.7-9/arules/tests/testthat/test-discretize.R | 38 arules-1.7-9/arules/tests/testthat/test-eclat.R | 25 arules-1.7-9/arules/tests/testthat/test-extract.R | 4 arules-1.7-9/arules/tests/testthat/test-fim4r.R | 14 arules-1.7-9/arules/tests/testthat/test-interestMeasures.R | 159 +-- arules-1.7-9/arules/tests/testthat/test-itemCoding.R | 10 arules-1.7-9/arules/tests/testthat/test-itemMatrix.R | 82 + arules-1.7-9/arules/tests/testthat/test-matrix.R | 53 - arules-1.7-9/arules/tests/testthat/test-mine_concise.R | 4 arules-1.7-9/arules/tests/testthat/test-missing.R | 1 arules-1.7-9/arules/tests/testthat/test-read_write.R | 51 - arules-1.7-9/arules/tests/testthat/test-ruleInduction.R | 110 +- arules-1.7-9/arules/tests/testthat/test-sets.R | 52 - arules-1.7-9/arules/tests/testthat/test-tidLists.R | 29 arules-1.7-9/arules/tests/testthat/test-transactions.R | 59 - arules-1.7-9/arules/tests/testthat/test-warm.R | 45 137 files changed, 6346 insertions(+), 4964 deletions(-)
Title: Soil and Water Conservation
Description: Includes four functions: RFactor_calc(), RFactor_est(), KFactor() and SoilLoss(). The rainfall erosivity factors can be calculated or estimated, and soil erodibility will be estimated by the equation extracted from the monograph. Soil loss will be estimated by the product of five factors (rainfall erosivity, soil erodibility, length and steepness slope, cover-management factor and support practice factor. In the future, additional functions can be included. This efforts to advance research in soil and water conservation, with fast and accurate results.
Author: Dione Pereira Cardoso [aut, cre]
,
Paulo Cesar Ossani [aut] ,
Junior Cesar Avanzi [aut]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Diff between SoilConservation versions 1.0.0 dated 2024-05-03 and 1.0.1 dated 2024-12-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/RFactor_est.R | 2 +- man/SoilConservation.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
More information about SoilConservation at CRAN
Permanent link
Title: FDR Based Multiple Testing Procedures with Adaptation for
Discrete Tests
Description: Implementations of the multiple testing procedures for discrete
tests described in the paper Döhler, Durand and Roquain (2018) "New FDR
bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The
main procedures of the paper (HSU and HSD), their adaptive counterparts
(AHSU and AHSD), and the HBR variant are available and are coded to take as
input the results of a test procedure from package 'DiscreteTests', or a set
of observed p-values and their discrete support under their nulls. A
shortcut function to obtain such p-values and supports is also provided,
along with a wrapper allowing to apply discrete procedures directly to data.
Author: Sebastian Doehler [aut, ctb] ,
Florian Junge [aut, ctb, cre] ,
Guillermo Durand [aut, ctb] ,
Etienne Roquain [ctb],
Christina Kihn [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteFDR versions 2.0.1 dated 2024-10-24 and 2.1.0 dated 2024-12-14
DESCRIPTION | 33 ++++---- MD5 | 89 +++++++++++------------ NAMESPACE | 3 NEWS.md | 110 +++++++++++++++++----------- R/ADBH_fun.R | 17 ++-- R/Aux_fun.R | 8 -- R/DBH_fun.R | 28 ++++--- R/DBR_fun.R | 37 +++++---- R/DBY_fun.R |only R/DiscreteFDR-package.R | 7 + R/RcppExports.R | 54 ++------------ R/discreteBH_fun.R | 59 +++++++++------ R/discreteFDR_fun.R | 162 +++++++++++++++++++++++++++++++----------- R/fast_appli.R | 26 +++++- R/plot_funs.R | 15 ++- R/print_fun.R | 24 ++++-- R/summary_funs.R | 38 +++++---- R/support.R | 35 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DiscreteFDR.html | 36 ++++++--- inst/doc/furtheranalyses.html | 16 ++-- inst/doc/toyexample.html | 20 ++++- man/ADBH.Rd | 38 +++++---- man/DBH.Rd | 38 +++++---- man/DBR.Rd | 47 +++++------- man/DBY.Rd |only man/DiscreteFDR.Rd | 8 +- man/direct.discrete.BH.Rd | 10 +- man/discrete.BH.Rd | 61 ++++++++------- man/fast.Discrete.Rd | 21 +++-- man/fisher.pvalues.support.Rd | 18 ++-- man/generate.pvalues.Rd | 5 - man/hist.DiscreteFDR.Rd | 8 +- man/kernel.Rd | 54 +------------- man/match.pvals.Rd | 16 ---- man/print.DiscreteFDR.Rd | 7 + man/summary.DiscreteFDR.Rd | 3 src/RcppExports.cpp | 56 +++++++++++--- src/helper.cpp | 93 ------------------------ src/helper.h | 56 ++++++-------- src/kernel.h | 131 ++++++++++++++++++--------------- src/kernel_ADBH.cpp | 86 +++++++++++++++------- src/kernel_DBH.cpp | 72 ++++++++++++++---- src/kernel_DBR.cpp | 44 ++++++++--- src/kernel_DBY.cpp |only src/kernel_common.cpp | 60 ++++----------- 47 files changed, 953 insertions(+), 796 deletions(-)