Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.2.1 dated 2025-01-20 and 1.2.2 dated 2025-04-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/register_font.R | 15 ++++++++++++--- man/add_fonts.Rd | 2 +- src/Makevars.in | 2 +- 6 files changed, 28 insertions(+), 13 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 1.2.1 dated 2025-03-20 and 2.0.0 dated 2025-04-04
cucumber-1.2.1/cucumber/inst/examples/box_support/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/comments/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/covr_support |only cucumber-1.2.1/cucumber/inst/examples/custom_parameters/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/custom_steps_loader |only cucumber-1.2.1/cucumber/inst/examples/custom_test_dir/tests/acceptance/guess_the_word.feature |only cucumber-1.2.1/cucumber/inst/examples/custom_test_dir/tests/acceptance/steps |only cucumber-1.2.1/cucumber/inst/examples/custom_test_dir/tests/acceptance/test-cucumber.R |only cucumber-1.2.1/cucumber/inst/examples/custom_test_dir/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/docstring/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/hooks/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/hooks_after_error/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/long_scenario/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/multiple_features/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/one_feature/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/scenario_outline/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/shinytest2/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/snapshot_test/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/table/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/testthat_setup_files/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/with_testthat_failure/tests/testthat |only cucumber-1.2.1/cucumber/inst/examples/with_testthat_success/tests/testthat |only cucumber-1.2.1/cucumber/tests/testthat/_snaps/examples.md |only cucumber-2.0.0/cucumber/DESCRIPTION | 6 cucumber-2.0.0/cucumber/MD5 | 193 ++++------ cucumber-2.0.0/cucumber/NAMESPACE | 11 cucumber-2.0.0/cucumber/NEWS.md | 6 cucumber-2.0.0/cucumber/R/doc-opts.R | 6 cucumber-2.0.0/cucumber/R/hooks.R | 18 cucumber-2.0.0/cucumber/R/parse_token.R | 31 - cucumber-2.0.0/cucumber/R/run.R | 3 cucumber-2.0.0/cucumber/R/step.R | 4 cucumber-2.0.0/cucumber/R/test.R | 169 +++++--- cucumber-2.0.0/cucumber/R/tokenize.R | 2 cucumber-2.0.0/cucumber/README.md | 144 +++---- cucumber-2.0.0/cucumber/build/vignette.rds |binary cucumber-2.0.0/cucumber/inst/doc/bdd.R | 11 cucumber-2.0.0/cucumber/inst/doc/bdd.html | 49 +- cucumber-2.0.0/cucumber/inst/doc/bdd.qmd | 19 cucumber-2.0.0/cucumber/inst/doc/how-it-works.html | 6 cucumber-2.0.0/cucumber/inst/doc/how-it-works.qmd | 6 cucumber-2.0.0/cucumber/inst/doc/migration-to-2-0-0.html |only cucumber-2.0.0/cucumber/inst/doc/migration-to-2-0-0.qmd |only cucumber-2.0.0/cucumber/inst/doc/reference-gherkin.html | 2 cucumber-2.0.0/cucumber/inst/doc/reference-gherkin.qmd | 2 cucumber-2.0.0/cucumber/inst/examples/box_support/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/comments/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/custom_loading |only cucumber-2.0.0/cucumber/inst/examples/custom_parameters/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/custom_test_dir/tests/acceptance/test-dummy.R |only cucumber-2.0.0/cucumber/inst/examples/custom_test_dir/tests/e2e |only cucumber-2.0.0/cucumber/inst/examples/docstring/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/hooks/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/hooks_after_error/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/long_scenario/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/multiple_features/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/one_feature/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/scenario_outline/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/shinytest2/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/snapshot_test/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/table/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/testthat_setup_files/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/with_test_files |only cucumber-2.0.0/cucumber/inst/examples/with_testthat_failure/tests/acceptance |only cucumber-2.0.0/cucumber/inst/examples/with_testthat_filtering |only cucumber-2.0.0/cucumber/inst/examples/with_testthat_success/tests/acceptance |only cucumber-2.0.0/cucumber/man/hook.Rd | 21 - cucumber-2.0.0/cucumber/man/opts.Rd | 5 cucumber-2.0.0/cucumber/man/step.Rd | 4 cucumber-2.0.0/cucumber/man/test.Rd | 71 ++- cucumber-2.0.0/cucumber/tests/testthat/_snaps/local |only cucumber-2.0.0/cucumber/tests/testthat/test-examples.R | 144 ++++--- cucumber-2.0.0/cucumber/vignettes/bdd.qmd | 19 cucumber-2.0.0/cucumber/vignettes/how-it-works.qmd | 6 cucumber-2.0.0/cucumber/vignettes/migration-to-2-0-0.qmd |only cucumber-2.0.0/cucumber/vignettes/reference-gherkin.qmd | 2 76 files changed, 522 insertions(+), 438 deletions(-)
Title: Convert, Validate, Format and Print Geographic Coordinates and
Waypoints
Description: Convert, validate, format and elegantly print geographic coordinates and waypoints
(paired latitude and longitude values) in decimal degrees, degrees and minutes, and degrees,
minutes and seconds using high performance C++ code to enable rapid conversion and formatting
of large coordinate and waypoint datasets.
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark.eisler@bristol.ac.uk>
Diff between Waypoint versions 1.1.0 dated 2025-03-19 and 1.1.1 dated 2025-04-04
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/CoordBase.R | 40 +++++++++++++++++++++++++++++++--------- R/RcppExports.R | 8 ++++---- README.md | 16 +++++++++++++--- build/partial.rdb |binary man/coords.Rd | 2 +- man/format.Rd | 8 ++++++++ man/validate.Rd | 14 ++++++++++++-- man/waypoints.Rd | 4 ++-- src/CoordBase.cpp | 43 ++++++++++++++++++++++++++++--------------- src/RcppExports.cpp | 18 ++++++++++-------- 13 files changed, 134 insertions(+), 60 deletions(-)
Title: Synthesise and Correlate Likert Scale and Rating-Scale Data
Based on Summary Statistics Only
Description: Generate and correlate synthetic Likert and rating-scale data
with predefined means, standard deviations, _Cronbach's Alpha_,
_Factor Loading table_, and other summary statistics.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 0.4.0 dated 2024-11-19 and 1.0.0 dated 2025-04-04
DESCRIPTION | 22 MD5 | 54 - NAMESPACE | 4 NEWS.md | 29 R/correlateScales.R | 5 R/lcor.R | 6 R/lexact.R | 9 R/lfast.R | 29 R/makeCorrAlpha.R | 25 R/makeCorrLoadings.R |only R/makeItems.R | 22 R/makeItemsScale.R | 54 - R/makePaired.R |only README.md | 277 +++++++-- build/vignette.rds |binary inst/CITATION | 8 inst/doc/LikertMakeR_vignette.R | 55 + inst/doc/LikertMakeR_vignette.Rmd | 173 ++++- inst/doc/LikertMakeR_vignette.html | 997 +++++++++++++++++++-------------- man/correlateScales.Rd | 5 man/lcor.Rd | 3 man/lexact.Rd | 6 man/lfast.Rd | 18 man/makeCorrAlpha.Rd | 12 man/makeCorrLoadings.Rd |only man/makeItems.Rd | 8 man/makeItemsScale.Rd | 52 - man/makePaired.Rd |only tests/testthat/test-makeCorrLoadings.R |only tests/testthat/test-makePaired.R |only vignettes/LikertMakeR_vignette.Rmd | 173 ++++- 31 files changed, 1362 insertions(+), 684 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] ,
Jari Oksanen [aut],
Martin Maechler [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.17-7 dated 2024-09-21 and 0.18.0 dated 2025-04-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS | 19 +++++++++++++------ inst/doc/analogue_methods.pdf |binary tests/Examples/analogue-Ex.Rout.save | 7 +++---- 6 files changed, 25 insertions(+), 19 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 0.99.1 dated 2024-12-13 and 0.99.3 dated 2025-04-04
DESCRIPTION | 7 - MD5 | 21 ++-- NAMESPACE | 1 NEWS.md | 16 ++- R/calculator_f.R | 34 +++++++ R/run_sim_parallel.R | 4 README.md | 10 +- inst/doc/example_ssd.R | 4 inst/doc/example_ssd.Rmd | 4 inst/doc/example_ssd.html | 216 +++++++++++++++++++++++----------------------- man/qgamma_mse.Rd |only vignettes/example_ssd.Rmd | 4 12 files changed, 184 insertions(+), 137 deletions(-)
Title: Co-Correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Gavin L. Simpson [aut, cre, trl] ,
Cajo J.F. ter Braak [aut] ,
Andre P Schaffers [aut] ,
Ron Wehrens [aut] ),
Bjorn-Helge Mevik [aut] )
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between cocorresp versions 0.4-5 dated 2024-10-06 and 0.4-6 dated 2025-04-04
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++------------- build/vignette.rds |binary inst/ChangeLog | 5 +++++ inst/doc/cocorresp-intro.html | 9 +++++---- man/bryophyte.Rd | 2 +- man/coca.Rd | 6 +++--- man/coinertiaI.Rd | 2 +- man/crossval.Rd | 4 ++-- man/envfit.coca.Rd | 4 ++-- man/rescale.Rd | 2 +- man/resid.symcoca.Rd | 2 +- man/weights.Rd | 2 +- tests/Examples/cocorresp-Ex.Rout.save | 7 +++---- 14 files changed, 43 insertions(+), 37 deletions(-)
Title: Annual Regional Database of the European Commission (ARDECO)
Description: A set of functions to access the 'ARDECO' (Annual Regional Database
of the European Commission) data directly from the official ARDECO public
repository through the exploitation of the 'ARDECO' APIs.
The APIs are completely transparent to the user and the provided functions
provide a direct access to the 'ARDECO' data.
The 'ARDECO' database is a collection of variables related to demography,
employment, labour market, domestic product, capital formation.
Each variable can be exposed in one or more units of measure as well as
refers to total values plus additional dimensions like economic sectors, gender,
age classes. Data can be also aggregated at country level according
to the tercet classes as defined by EUROSTAT.
The description of the 'ARDECO' database can be found at the following URL
<https://urban.jrc.ec.europa.eu/ardeco>.
Author: Carmelo Attardo [cre],
Giuseppe Bucciarelli [aut],
European Commission, JRC [cph]
Maintainer: Carmelo Attardo <carmelo.attardo@ec.europa.eu>
Diff between ARDECO versions 2.1.0 dated 2024-11-21 and 2.2.0 dated 2025-04-04
DESCRIPTION | 10 - MD5 | 22 +- NAMESPACE | 5 NEWS | 5 R/ardeco.R |only R/get_dataset_data.R | 357 ++++++++++++++++++++++++++++++++++++++++-------- R/get_dataset_list.R | 9 - R/get_tercet_list.R | 11 + build |only inst |only man/ardeco.Rd | 9 - man/get_dataset_data.Rd | 31 ++-- vignettes |only 13 files changed, 370 insertions(+), 89 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.9 dated 2025-03-05 and 1.3.11 dated 2025-04-04
DESCRIPTION | 14 - MD5 | 57 ++-- NAMESPACE | 2 NEWS.md | 7 R/cox2.R | 132 ++++++++++- R/coxme.R | 84 ++++++- R/forestcox.R | 260 +++++++++++++++------- R/gee.R | 64 ++++- R/glmshow.R | 134 ++++++++++- R/lmer.R | 104 +++++++- R/svyCreateTableOneJS.R | 164 +++++++++++--- R/svycox.R | 74 +++++- R/svyglm.R | 151 +++++++++++- build/vignette.rds |binary inst/doc/jstable.html | 68 ++--- inst/doc/jstable_competing_risk_analysis.html | 4 inst/doc/jstable_options.html | 304 ++++++++++++-------------- man/ChangeSvyTable.Rd |only man/cox2.display.Rd | 4 man/coxme.display.Rd | 4 man/geeglm.display.Rd | 4 man/glmshow.display.Rd | 4 man/lmer.display.Rd | 4 man/svyCreateTableOne2.Rd | 5 man/svyCreateTableOneJS.Rd | 5 man/svycox.display.Rd | 4 man/svyglm.display.Rd | 4 tests/testthat/test-forestcox.R | 57 ++-- tests/testthat/test-regtable.R | 11 tests/testthat/test-svyCreateTableOne.R | 60 ++++- 30 files changed, 1342 insertions(+), 447 deletions(-)
Title: Ensemble-Based Data Assimilation with GR Hydrological Models
Description: Add-on to the 'airGR' package which provides the tools to assimilate observed discharges in daily GR hydrological models. The package consists in two functions allowing to perform the assimilation of observed discharges via the Ensemble Kalman filter or the Particle filter as described in Piazzi et al. (2021) <doi:10.1029/2020WR028390>.
Author: Gaia Piazzi [aut] ,
Olivier Delaigue [aut, cre] ,
Guillaume Thirel [ctb] ,
Maxime Logez [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRdatassim versions 0.1.3 dated 2021-02-11 and 0.1.4 dated 2025-04-04
airGRdatassim-0.1.3/airGRdatassim/man/airGRdatassim.Rd |only airGRdatassim-0.1.4/airGRdatassim/DESCRIPTION | 10 airGRdatassim-0.1.4/airGRdatassim/MD5 | 43 airGRdatassim-0.1.4/airGRdatassim/NAMESPACE | 54 airGRdatassim-0.1.4/airGRdatassim/NEWS.md |only airGRdatassim-0.1.4/airGRdatassim/R/CreateInputsPert.R | 374 +-- airGRdatassim-0.1.4/airGRdatassim/R/DA_EnKF.R | 256 +- airGRdatassim-0.1.4/airGRdatassim/R/DA_PF.R | 370 +-- airGRdatassim-0.1.4/airGRdatassim/R/RunModel_DA.R | 758 +++--- airGRdatassim-0.1.4/airGRdatassim/R/Utils.R | 48 airGRdatassim-0.1.4/airGRdatassim/R/plot.InputsPert.R | 142 - airGRdatassim-0.1.4/airGRdatassim/R/plot.OutputsModelDA.R | 128 - airGRdatassim-0.1.4/airGRdatassim/README.md | 135 - airGRdatassim-0.1.4/airGRdatassim/build/partial.rdb |binary airGRdatassim-0.1.4/airGRdatassim/build/vignette.rds |binary airGRdatassim-0.1.4/airGRdatassim/inst/CITATION | 80 airGRdatassim-0.1.4/airGRdatassim/inst/doc/get_started.R | 266 +- airGRdatassim-0.1.4/airGRdatassim/inst/doc/get_started.Rmd | 610 ++--- airGRdatassim-0.1.4/airGRdatassim/inst/doc/get_started.html | 1133 ++++++---- airGRdatassim-0.1.4/airGRdatassim/man/CreateInputsPert.Rd | 295 +- airGRdatassim-0.1.4/airGRdatassim/man/RunModel_DA.Rd | 371 +-- airGRdatassim-0.1.4/airGRdatassim/man/airGRdatassim-package.Rd |only airGRdatassim-0.1.4/airGRdatassim/vignettes/airgrdatassim_use.bib | 136 - airGRdatassim-0.1.4/airGRdatassim/vignettes/get_started.Rmd | 610 ++--- 24 files changed, 3098 insertions(+), 2721 deletions(-)
Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstIO' package
provides basic functionalities to read and write KST data from/to
files to be used together with the 'kst', 'kstMatrix', 'CDSS', 'pks', or
'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstIO versions 0.4-1 dated 2025-01-20 and 0.4-2 dated 2025-04-04
Changelog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/write_kbase.R | 1 + R/write_kdata.R | 1 + R/write_kspace.R | 1 + R/write_kstructure.R | 1 + build/vignette.rds |binary inst/doc/kstIO.pdf |binary 9 files changed, 19 insertions(+), 12 deletions(-)
Title: Shortest Paths Between Points in Grids
Description: Shortest paths between points in grids. Optional barriers and custom transition functions. Applications regarding planet Earth, as well as
generally spheres and planes. Optimized for computational performance, customizability, and user friendliness. Graph-theoretical implementation tailored
to gridded data. Currently focused on Dijkstra's (1959) <doi:10.1007/BF01386390> algorithm. Future updates broaden the scope to other least cost path
algorithms and to centrality measures.
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Diff between spaths versions 1.1.3 dated 2024-07-11 and 1.2.0 dated 2025-04-04
spaths-1.1.3/spaths/src/coordinates.cpp |only spaths-1.1.3/spaths/src/distances_multiple_calls_woweights.cpp |only spaths-1.1.3/spaths/src/distances_multiple_calls_wweights.cpp |only spaths-1.1.3/spaths/src/distances_one_call_woweights.cpp |only spaths-1.1.3/spaths/src/distances_one_call_wweights.cpp |only spaths-1.1.3/spaths/src/distances_woweights.cpp |only spaths-1.1.3/spaths/src/distances_wweights.cpp |only spaths-1.1.3/spaths/src/pair_types.h |only spaths-1.1.3/spaths/src/paths_multiple_calls_woweights.cpp |only spaths-1.1.3/spaths/src/paths_multiple_calls_wweights.cpp |only spaths-1.1.3/spaths/src/paths_one_call_woweights.cpp |only spaths-1.1.3/spaths/src/paths_one_call_wweights.cpp |only spaths-1.1.3/spaths/src/paths_woweights.cpp |only spaths-1.1.3/spaths/src/paths_wweights.cpp |only spaths-1.1.3/spaths/src/repeat_distances.cpp |only spaths-1.1.3/spaths/src/stat_target_distances.cpp |only spaths-1.1.3/spaths/src/stat_target_paths.cpp |only spaths-1.1.3/spaths/src/upd_affected_paths.cpp |only spaths-1.1.3/spaths/src/upd_distances_woweights.cpp |only spaths-1.1.3/spaths/src/upd_distances_wweights.cpp |only spaths-1.1.3/spaths/src/upd_paths_woweights.cpp |only spaths-1.1.3/spaths/src/upd_paths_wweights.cpp |only spaths-1.1.3/spaths/src/upd_starts_targets.cpp |only spaths-1.1.3/spaths/src/upd_starts_targets_map.cpp |only spaths-1.1.3/spaths/src/upd_target_distances.cpp |only spaths-1.1.3/spaths/src/upd_target_paths.cpp |only spaths-1.1.3/spaths/src/visited.cpp |only spaths-1.2.0/spaths/DESCRIPTION | 8 spaths-1.2.0/spaths/MD5 | 156 - spaths-1.2.0/spaths/NAMESPACE | 19 spaths-1.2.0/spaths/NEWS.md | 54 spaths-1.2.0/spaths/R/RcppExports.R | 136 - spaths-1.2.0/spaths/R/max_edges.R |only spaths-1.2.0/spaths/R/rnd_locations.R | 108 spaths-1.2.0/spaths/R/shortest_paths.R | 474 ++-- spaths-1.2.0/spaths/R/utils.R | 297 +- spaths-1.2.0/spaths/build/vignette.rds |binary spaths-1.2.0/spaths/inst/doc/spaths_introduction.R | 426 +-- spaths-1.2.0/spaths/inst/doc/spaths_introduction.Rmd | 33 spaths-1.2.0/spaths/inst/doc/spaths_introduction.html | 475 +--- spaths-1.2.0/spaths/inst/doc/transition_functions.R |only spaths-1.2.0/spaths/inst/doc/transition_functions.Rmd |only spaths-1.2.0/spaths/inst/doc/transition_functions.html |only spaths-1.2.0/spaths/inst/include |only spaths-1.2.0/spaths/man/max_edges.Rd |only spaths-1.2.0/spaths/man/rnd_locations.Rd | 3 spaths-1.2.0/spaths/man/shortest_paths.Rd | 248 +- spaths-1.2.0/spaths/src/RcppExports.cpp | 439 +++ spaths-1.2.0/spaths/src/convert_upd_rst.cpp | 22 spaths-1.2.0/spaths/src/coordinates.h | 169 + spaths-1.2.0/spaths/src/distances_multiple_calls_woweights.h | 185 - spaths-1.2.0/spaths/src/distances_multiple_calls_wweights.h | 158 - spaths-1.2.0/spaths/src/distances_one_call_woweights.h | 130 - spaths-1.2.0/spaths/src/distances_one_call_wweights.h | 105 spaths-1.2.0/spaths/src/distances_woweights.h | 117 - spaths-1.2.0/spaths/src/distances_wweights.h | 140 - spaths-1.2.0/spaths/src/from_to.cpp |only spaths-1.2.0/spaths/src/from_to.h |only spaths-1.2.0/spaths/src/graph_to.cpp | 67 spaths-1.2.0/spaths/src/graph_to.h | 5 spaths-1.2.0/spaths/src/graph_weights.cpp | 1158 ---------- spaths-1.2.0/spaths/src/graph_weights.h | 9 spaths-1.2.0/spaths/src/individual_distances.h | 10 spaths-1.2.0/spaths/src/paths_multiple_calls_woweights.h | 217 + spaths-1.2.0/spaths/src/paths_multiple_calls_wweights.h | 192 - spaths-1.2.0/spaths/src/paths_one_call_woweights.h | 156 + spaths-1.2.0/spaths/src/paths_one_call_wweights.h | 129 - spaths-1.2.0/spaths/src/paths_woweights.h | 97 spaths-1.2.0/spaths/src/paths_wweights.h | 114 spaths-1.2.0/spaths/src/r_distances_woweights.cpp | 28 spaths-1.2.0/spaths/src/r_distances_wweights.cpp | 44 spaths-1.2.0/spaths/src/r_paths_woweights.cpp | 27 spaths-1.2.0/spaths/src/r_paths_wweights.cpp | 42 spaths-1.2.0/spaths/src/r_tr_fun_args.cpp |only spaths-1.2.0/spaths/src/r_tr_fun_weights.cpp |only spaths-1.2.0/spaths/src/r_upd_distances_woweights.cpp | 30 spaths-1.2.0/spaths/src/r_upd_distances_wweights.cpp | 36 spaths-1.2.0/spaths/src/r_upd_paths_woweights.cpp | 26 spaths-1.2.0/spaths/src/r_upd_paths_wweights.cpp | 42 spaths-1.2.0/spaths/src/repeat_distances.h | 16 spaths-1.2.0/spaths/src/stat_target_distances.h | 77 spaths-1.2.0/spaths/src/stat_target_paths.h | 181 + spaths-1.2.0/spaths/src/structs.h |only spaths-1.2.0/spaths/src/target_distances.h | 155 - spaths-1.2.0/spaths/src/target_paths.h | 144 - spaths-1.2.0/spaths/src/targets_set.h | 46 spaths-1.2.0/spaths/src/upd_affected_paths.h | 61 spaths-1.2.0/spaths/src/upd_distances_woweights.h | 174 + spaths-1.2.0/spaths/src/upd_distances_wweights.h | 174 + spaths-1.2.0/spaths/src/upd_paths_woweights.h | 158 + spaths-1.2.0/spaths/src/upd_paths_wweights.h | 155 - spaths-1.2.0/spaths/src/upd_starts_targets.h | 133 - spaths-1.2.0/spaths/src/upd_starts_targets_map.h | 56 spaths-1.2.0/spaths/src/upd_target_distances.h | 46 spaths-1.2.0/spaths/src/upd_target_paths.h | 64 spaths-1.2.0/spaths/src/visited.h | 14 spaths-1.2.0/spaths/tests/testthat/test-max_edges.R |only spaths-1.2.0/spaths/vignettes/spaths_introduction.Rmd | 33 spaths-1.2.0/spaths/vignettes/transition_functions.Rmd |only 99 files changed, 4547 insertions(+), 3471 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-2 dated 2025-04-02 and 1.9-3 dated 2025-04-04
ChangeLog | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/qp.c | 8 ++++---- src/sparse.c | 4 ++-- 5 files changed, 18 insertions(+), 13 deletions(-)
Title: Lightweight Access to the 'Geospatial Data Abstraction Library'
('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.10.0 dated 2024-06-14 and 0.11.0 dated 2025-04-04
vapour-0.10.0/vapour/src/warpscratch.cpp |only vapour-0.11.0/vapour/DESCRIPTION | 13 vapour-0.11.0/vapour/MD5 | 69 vapour-0.11.0/vapour/NEWS.md | 4 vapour-0.11.0/vapour/R/RcppExports.R | 4 vapour-0.11.0/vapour/R/raster-info.R | 4 vapour-0.11.0/vapour/R/raster-input.R | 8 vapour-0.11.0/vapour/R/read_stream_internal.R | 109 vapour-0.11.0/vapour/R/vapour-gdal-library.R | 6 vapour-0.11.0/vapour/R/vapour-package.R | 6 vapour-0.11.0/vapour/R/vapour_input_attributes.R | 2 vapour-0.11.0/vapour/R/vapour_vrt.R | 2 vapour-0.11.0/vapour/R/vapour_vsi_list.R | 2 vapour-0.11.0/vapour/README.md | 12 vapour-0.11.0/vapour/build/vignette.rds |binary vapour-0.11.0/vapour/configure | 2700 ++++------ vapour-0.11.0/vapour/configure.ac | 9 vapour-0.11.0/vapour/inst/WORDLIST | 2 vapour-0.11.0/vapour/inst/doc/feature-access.html | 2 vapour-0.11.0/vapour/inst/doc/vapour.Rmd | 4 vapour-0.11.0/vapour/inst/doc/vapour.html | 618 +- vapour-0.11.0/vapour/inst/include/gdalarrowstream/gdalvectorstream.h | 652 +- vapour-0.11.0/vapour/man/vapour-package.Rd | 4 vapour-0.11.0/vapour/man/vapour_geolocation.Rd | 2 vapour-0.11.0/vapour/man/vapour_geom_summary.Rd | 2 vapour-0.11.0/vapour/man/vapour_raster_info.Rd | 2 vapour-0.11.0/vapour/man/vapour_report_fields.Rd | 2 vapour-0.11.0/vapour/man/vapour_set_config.Rd | 2 vapour-0.11.0/vapour/man/vapour_srs_wkt.Rd | 2 vapour-0.11.0/vapour/man/vapour_vrt.Rd | 2 vapour-0.11.0/vapour/man/vapour_vsi_list.Rd | 2 vapour-0.11.0/vapour/man/vapour_warp_raster.Rd | 8 vapour-0.11.0/vapour/src/000-stream.cpp | 32 vapour-0.11.0/vapour/src/RcppExports.cpp | 22 vapour-0.11.0/vapour/tests/testthat/test-crs-less-warp.R | 5 vapour-0.11.0/vapour/vignettes/vapour.Rmd | 4 36 files changed, 2126 insertions(+), 2193 deletions(-)
Title: Heterogeneous Treatment Effects in Regression Discontinuity
Designs
Description: Understanding heterogeneous causal effects based on pretreatment covariates is a crucial step in modern empirical work in data science. Building on the recent developments in Calonico et al (2025) <https://rdpackages.github.io/references/Calonico-Cattaneo-Farrell-Palomba-Titiunik_2025_HTERD.pdf>, this package provides tools for estimation and inference of heterogeneous treatment effects in Regression Discontinuity (RD) Designs. The package includes two main commands: 'rdhte' to conduct estimation and robust bias-corrected inference for conditional RD treatment effects (given choice of bandwidth parameter); and 'rdbwhte', which implements automatic bandwidth selection methods.
Author: Sebastian Calonico [aut, cre],
Matias D. Cattaneo [aut],
Max H. Farrell [aut],
Filippo Palomba [aut],
Rocio Titiunik [aut]
Maintainer: Sebastian Calonico <scalonico@ucdavis.edu>
Diff between rdhte versions 0.0.1 dated 2025-03-25 and 0.0.2 dated 2025-04-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rdbwhte.R | 2 +- R/rdhte-package.R | 2 +- R/rdhte.R | 6 +++--- man/rdbwhte.Rd | 2 +- man/rdhte-package.Rd | 2 +- man/rdhte.Rd | 2 +- 8 files changed, 18 insertions(+), 18 deletions(-)
Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers
using a non-scientific format optimized for human readers. Vectors of
numbers are rounded using significant digits, aligned at the decimal
point, and all zeros trailing the decimal point are dropped. See:
Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point
Numbers. In JSM Proceedings, Statistical Computing Section.
Alexandria, VA: American Statistical Association. 2270-2279.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between lucid versions 1.8 dated 2021-04-16 and 1.9 dated 2025-04-03
lucid-1.8/lucid/tests/testthat/test_lucid.R |only lucid-1.8/lucid/tests/testthat/test_vc.R |only lucid-1.9/lucid/DESCRIPTION | 36 - lucid-1.9/lucid/LICENSE |only lucid-1.9/lucid/MD5 | 29 - lucid-1.9/lucid/NEWS.md | 41 + lucid-1.9/lucid/R/lucid.R | 2 lucid-1.9/lucid/build/vignette.rds |binary lucid-1.9/lucid/inst/doc/lucid_examples.R | 69 +- lucid-1.9/lucid/inst/doc/lucid_examples.Rmd | 23 lucid-1.9/lucid/inst/doc/lucid_examples.html | 735 ++++++++++++++++++++------- lucid-1.9/lucid/man/antibiotic.Rd | 160 ++--- lucid-1.9/lucid/man/lucid.Rd | 186 +++--- lucid-1.9/lucid/man/vc.Rd | 168 +++--- lucid-1.9/lucid/tests/testthat/test_lucid.r |only lucid-1.9/lucid/tests/testthat/test_vc.r |only lucid-1.9/lucid/vignettes/lucid.bib | 2 lucid-1.9/lucid/vignettes/lucid_examples.Rmd | 23 18 files changed, 919 insertions(+), 555 deletions(-)
Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data,
including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre] ,
Ian C. Marschner [ths] ,
Alexandra C. Gillett [ctb] ,
The R Core Team [cph]
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>
Diff between logbin versions 2.0.5 dated 2021-08-09 and 2.0.6 dated 2025-04-03
logbin-2.0.5/logbin/R/contr.isotonic.rev.r |only logbin-2.0.5/logbin/man/contr.isotonic.rev.Rd |only logbin-2.0.5/logbin/man/interpret.logbin.smooth.Rd |only logbin-2.0.6/logbin/DESCRIPTION | 17 ++++-- logbin-2.0.6/logbin/MD5 | 37 ++++++++------ logbin-2.0.6/logbin/NAMESPACE | 4 - logbin-2.0.6/logbin/NEWS.md | 13 ++++- logbin-2.0.6/logbin/R/anova.logbin.r | 21 ++++++++ logbin-2.0.6/logbin/R/anova.logbinlist.r | 21 ++++++++ logbin-2.0.6/logbin/R/nplbin.r | 2 logbin-2.0.6/logbin/R/predict.logbin.r | 22 ++++++++ logbin-2.0.6/logbin/R/predict.logbin.smooth.r | 2 logbin-2.0.6/logbin/R/summary.logbin.r | 53 ++++++++++++++------- logbin-2.0.6/logbin/inst/CITATION | 37 +++++++------- logbin-2.0.6/logbin/man/anova.logbin.Rd | 4 - logbin-2.0.6/logbin/man/logbin-package.Rd | 6 +- logbin-2.0.6/logbin/man/logbin.smooth.Rd | 2 logbin-2.0.6/logbin/tests |only 18 files changed, 172 insertions(+), 69 deletions(-)
Title: Conditional Akaike Information Criterion for 'lme4' and 'nlme'
Description: Provides functions for the estimation of the conditional Akaike
information in generalized mixed-effect models fitted with (g)lmer()
from 'lme4', lme() from 'nlme' and gamm() from 'mgcv'.
For a manual on how to use 'cAIC4', see Saefken et al. (2021) <doi:10.18637/jss.v099.i08>.
Author: Benjamin Saefken [aut],
David Ruegamer [aut, cre],
Philipp Baumann [aut],
Rene-Marcel Kruse [aut],
Sonja Greven [aut],
Thomas Kneib [aut]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between cAIC4 versions 1.0 dated 2021-09-22 and 1.1 dated 2025-04-03
DESCRIPTION | 27 ++++++-- MD5 | 30 +++++---- NAMESPACE | 4 + R/bcMer.R | 122 +++++++++++++++++++-------------------- R/biasCorrectionBernoulli.R | 2 R/biasCorrectionGaussian.R | 62 +++++++++---------- R/cAIC.R | 5 - R/deleteZeroComponents.R | 4 - R/getModelComponents.R | 26 ++++++++ R/helperfuns_lme.R | 8 +- R/helperfuns_stepcAIC.R | 5 - build/partial.rdb |binary man/cAIC.Rd | 2 man/deleteZeroComponents.Rd | 4 - man/family.lme.Rd |only man/getModelComponents.Rd |only man/getModelComponents.lme.Rd |only man/getModelComponents.merMod.Rd |only 18 files changed, 176 insertions(+), 125 deletions(-)
Title: Causal Moderated Mediation Analysis
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
Author: Xu Qin [aut, cre, cph],
Lijuan Wang [ctb]
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between moderate.mediation versions 0.0.10 dated 2024-05-23 and 0.0.11 dated 2025-04-03
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/moderate.mediation.R | 10 ++++++++++ 3 files changed, 17 insertions(+), 7 deletions(-)
More information about moderate.mediation at CRAN
Permanent link
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 0.9.9 dated 2017-12-05 and 1.0.0 dated 2025-04-03
TriMatch-0.9.9/TriMatch/NEWS |only TriMatch-1.0.0/TriMatch/DESCRIPTION | 36 +++-- TriMatch-1.0.0/TriMatch/MD5 | 106 ++++++++-------- TriMatch-1.0.0/TriMatch/NEWS.md |only TriMatch-1.0.0/TriMatch/R/TriMatch-package.R | 3 TriMatch-1.0.0/TriMatch/R/as.data.frame.list.R | 2 TriMatch-1.0.0/TriMatch/R/covariateBalance.R | 4 TriMatch-1.0.0/TriMatch/R/merge.triangle.matches.R | 2 TriMatch-1.0.0/TriMatch/R/merge.triangle.psa.R | 4 TriMatch-1.0.0/TriMatch/R/plot.balance.R | 20 +-- TriMatch-1.0.0/TriMatch/R/plot.boxdiff.R | 2 TriMatch-1.0.0/TriMatch/R/plot.distances.R | 2 TriMatch-1.0.0/TriMatch/R/plot.loess.R | 14 +- TriMatch-1.0.0/TriMatch/R/plot.multibalance.R | 10 - TriMatch-1.0.0/TriMatch/R/plot.parallel.R | 2 TriMatch-1.0.0/TriMatch/R/plot.triangle.matches.R | 20 +-- TriMatch-1.0.0/TriMatch/R/plot.triangle.psa.R | 8 - TriMatch-1.0.0/TriMatch/R/summary.triangle.matches.R | 13 - TriMatch-1.0.0/TriMatch/R/summary.triangle.psa.R | 4 TriMatch-1.0.0/TriMatch/R/triangle.match.R | 16 +- TriMatch-1.0.0/TriMatch/R/triangle.psa.R | 2 TriMatch-1.0.0/TriMatch/R/unmatched.R | 12 - TriMatch-1.0.0/TriMatch/build |only TriMatch-1.0.0/TriMatch/inst |only TriMatch-1.0.0/TriMatch/man/OneToN.Rd | 2 TriMatch-1.0.0/TriMatch/man/as.data.frame.list.Rd | 2 TriMatch-1.0.0/TriMatch/man/balance.plot.Rd | 25 ++- TriMatch-1.0.0/TriMatch/man/boxdiff.plot.Rd | 11 + TriMatch-1.0.0/TriMatch/man/covariateBalance.Rd | 26 +++ TriMatch-1.0.0/TriMatch/man/data.frame.to.list.Rd | 30 ++++ TriMatch-1.0.0/TriMatch/man/distances.plot.Rd | 2 TriMatch-1.0.0/TriMatch/man/figures |only TriMatch-1.0.0/TriMatch/man/loess3.plot.Rd | 31 +++- TriMatch-1.0.0/TriMatch/man/maximumTreat.Rd | 2 TriMatch-1.0.0/TriMatch/man/merge.triangle.matches.Rd | 2 TriMatch-1.0.0/TriMatch/man/merge.triangle.psa.Rd | 4 TriMatch-1.0.0/TriMatch/man/multibalance.plot.Rd | 6 TriMatch-1.0.0/TriMatch/man/nmes.Rd | 4 TriMatch-1.0.0/TriMatch/man/parallel.plot.Rd | 2 TriMatch-1.0.0/TriMatch/man/plot.balance.plots.Rd | 5 TriMatch-1.0.0/TriMatch/man/plot.triangle.matches.Rd | 34 +++-- TriMatch-1.0.0/TriMatch/man/plot.triangle.psa.Rd | 20 ++- TriMatch-1.0.0/TriMatch/man/print.balance.plots.Rd | 10 - TriMatch-1.0.0/TriMatch/man/print.triangle.plot.Rd | 10 - TriMatch-1.0.0/TriMatch/man/print.trimatch.summary.Rd | 8 - TriMatch-1.0.0/TriMatch/man/summary.balance.plots.Rd | 4 TriMatch-1.0.0/TriMatch/man/summary.triangle.matches.Rd | 8 - TriMatch-1.0.0/TriMatch/man/summary.triangle.psa.Rd | 4 TriMatch-1.0.0/TriMatch/man/summary.unmatched.Rd | 2 TriMatch-1.0.0/TriMatch/man/trimatch.Rd | 23 ++- TriMatch-1.0.0/TriMatch/man/trimatch.apply2.Rd | 2 TriMatch-1.0.0/TriMatch/man/trips.Rd | 13 + TriMatch-1.0.0/TriMatch/man/tutoring.Rd | 4 TriMatch-1.0.0/TriMatch/man/unmatched.Rd | 10 - TriMatch-1.0.0/TriMatch/vignettes |only 55 files changed, 350 insertions(+), 238 deletions(-)
Title: Simple Framework for Simple Automation
Description: Build a project framework for users with
access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>
Diff between strata versions 1.4.3 dated 2025-03-05 and 1.4.5 dated 2025-04-03
DESCRIPTION | 6 MD5 | 37 ++-- NEWS.md | 4 R/build-core.R | 24 +- R/build-quick.R | 7 R/log-core.R | 42 ++-- R/main-utils.R | 112 ++++-------- R/survey-core.R | 1 R/survey-utils.R | 6 R/toml-io.R | 18 - R/toml-utils.R | 7 README.md | 346 +++++++++++++++++++------------------- man/format_timestamp.Rd |only tests/testthat/test-adhoc-core.R | 16 - tests/testthat/test-build-core.R | 12 - tests/testthat/test-build-quick.R | 10 - tests/testthat/test-main-core.R | 9 tests/testthat/test-main-utils.R | 58 +++++- tests/testthat/test-survey-core.R | 3 tests/testthat/test-toml-utils.R | 2 20 files changed, 386 insertions(+), 334 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts
[Anhoej, Olesen (2014) <doi:10.1371/journal.pone.0113825>] and basic
Shewhart control charts [Mohammed, Worthington, Woodall (2008)
<doi:10.1136/qshc.2004.012047>] for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.5.8 dated 2021-04-20 and 0.5.10 dated 2025-04-03
DESCRIPTION | 8 MD5 | 14 NEWS | 8 R/trc.R | 8 build/vignette.rds |binary inst/doc/controlcharts.html | 1059 ++++++++++++++++++++++++++++++-------------- inst/doc/runcharts.html | 576 +++++++++++++++++------ man/trc.Rd | 8 8 files changed, 1175 insertions(+), 506 deletions(-)
Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Author: Paolo Frumento [aut, cre]
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between qrcm versions 3.1 dated 2024-02-13 and 3.2 dated 2025-04-03
DESCRIPTION | 14 +++++++++----- MD5 | 12 ++++++------ NEWS.md | 9 +++------ R/iqr1_fit.R | 6 ++++-- man/iqr.Rd | 3 +-- man/qrcm-package.Rd | 8 ++++---- man/test.fit.iqr.Rd | 6 +++--- 7 files changed, 30 insertions(+), 28 deletions(-)
Title: Inference for Panel Partially Observed Markov Processes
Description: Data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Breto, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" <doi:10.1080/01621459.2019.1604367>.
Author: Carles Breto [aut] ,
Edward L. Ionides [aut] ,
Aaron A. King [aut] ,
Jesse Wheeler [aut, cre] ,
Aaron Abkemeier [ctb]
Maintainer: Jesse Wheeler <jeswheel@umich.edu>
Diff between panelPomp versions 1.5.0.0 dated 2024-12-08 and 1.6.0.0 dated 2025-04-03
panelPomp-1.5.0.0/panelPomp/man/unitlogLik-deprecated.Rd |only panelPomp-1.5.0.0/panelPomp/man/unitlogLik-pfilterd.ppomp-method.Rd |only panelPomp-1.6.0.0/panelPomp/DESCRIPTION | 10 +- panelPomp-1.6.0.0/panelPomp/MD5 | 34 +++++---- panelPomp-1.6.0.0/panelPomp/NAMESPACE | 3 panelPomp-1.6.0.0/panelPomp/R/generics.R | 35 ---------- panelPomp-1.6.0.0/panelPomp/R/mif2.R | 28 +++++++- panelPomp-1.6.0.0/panelPomp/R/panelMeasles.R | 3 panelPomp-1.6.0.0/panelPomp/R/panelPomp-package.R | 13 +-- panelPomp-1.6.0.0/panelPomp/R/pfilter_methods.R | 25 ------- panelPomp-1.6.0.0/panelPomp/build/partial.rdb |binary panelPomp-1.6.0.0/panelPomp/build/vignette.rds |binary panelPomp-1.6.0.0/panelPomp/inst/NEWS | 12 +++ panelPomp-1.6.0.0/panelPomp/inst/NEWS.Rd | 7 ++ panelPomp-1.6.0.0/panelPomp/man/dot-modifyOther.Rd |only panelPomp-1.6.0.0/panelPomp/man/dot-modifySelf.Rd |only panelPomp-1.6.0.0/panelPomp/src |only panelPomp-1.6.0.0/panelPomp/tests/pfilter_methods.R | 2 panelPomp-1.6.0.0/panelPomp/tests/pfilter_methods.Rout.save | 15 ---- panelPomp-1.6.0.0/panelPomp/tests/pparamArrayMods.R |only panelPomp-1.6.0.0/panelPomp/tests/pparamArrayMods.Rout.save |only 21 files changed, 78 insertions(+), 109 deletions(-)
Title: Finding Recurrent DNA Copy Number Alterations and Differences
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
can be found at <doi: 10.1093/bioinformatics/ [...truncated...]
Author: Vonn Walter [aut, cre] ,
Hyo Young Choi [aut] ,
Xiaobei Zhao [aut] ,
Yan Gao [aut] ,
David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between DiNAMIC.Duo versions 1.0.2 dated 2023-03-02 and 1.0.3 dated 2025-04-03
DESCRIPTION | 10 +- MD5 | 18 ++-- NAMESPACE | 2 NEWS.md | 11 ++- R/dataPrep.R | 142 +++++++++++++++++++++------------------ R/findNull.R |only build/vignette.rds |binary data/DiNAMIC.Duo.RData |binary inst/doc/DiNAMICDuo_vignette.pdf |binary man/dataPrep.Rd | 12 ++- man/findNull.Rd |only 11 files changed, 115 insertions(+), 80 deletions(-)
Title: Fast and Memory Efficient Fitting of Linear Models with
High-Dimensional Fixed Effects
Description: Fast and user-friendly estimation of generalized linear models with
multiple fixed effects and cluster the standard errors. The method to obtain
the estimated fixed-effects coefficients is based on Stammann (2018)
<doi:10.48550/arXiv.1707.01815> and Gaure (2013)
<doi:10.1016/j.csda.2013.03.024>.
Author: Mauricio Vargas Sepulveda [aut, cre]
,
Yoto Yotov [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between capybara versions 0.9.1 dated 2025-03-25 and 0.9.3 dated 2025-04-03
DESCRIPTION | 15 +++-- MD5 | 52 +++++++++--------- NAMESPACE | 2 NEWS.md | 11 +++ R/apes.R | 4 - R/autoplot.R | 4 - R/bias_corr.R | 4 - R/cpp11.R | 4 - R/feglm_control.R | 14 ++++ R/feglm_helpers.R | 2 R/felm_helpers.R | 2 R/generics_coef.R | 8 +- R/generics_confint.R | 2 R/generics_glance.R | 2 R/generics_print.R | 14 ++++ R/generics_summary.R | 44 +++++++-------- R/generics_tidy.R | 2 R/summary_table.R |only README.md | 67 +++++++++++++++-------- man/capybara-package.Rd | 5 + man/feglm_control.Rd | 5 + man/summary_table.Rd |only src/00_main.h | 2 src/02_center_variables.cpp | 93 +++++++++++++++++++++++++------- src/03_lm_fit.cpp | 17 ++--- src/04_glm_fit.cpp | 127 +++++++++++++++++++++----------------------- src/05_glm_offset_fit.cpp | 5 + src/cpp11.cpp | 8 +- 28 files changed, 323 insertions(+), 192 deletions(-)
Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.4 dated 2024-09-24 and 0.1.5 dated 2025-04-03
DESCRIPTION | 6 MD5 | 52 ++-- NEWS.md | 10 configure | 2 configure.ac | 2 inst/doc/speakeasyR.html | 20 - src/se2/CMakeLists.txt | 6 src/se2/include/speak_easy_2.h | 52 ++-- src/se2/src/speakeasy2/se2_core.c | 361 +++++++++++++--------------- src/se2/src/speakeasy2/se2_error_handling.h | 114 ++++---- src/se2/src/speakeasy2/se2_knn_graph.c | 58 ++-- src/se2/src/speakeasy2/se2_label.c | 130 +++++----- src/se2/src/speakeasy2/se2_label.h | 32 +- src/se2/src/speakeasy2/se2_modes.c | 170 ++++++------- src/se2/src/speakeasy2/se2_modes.h | 26 +- src/se2/src/speakeasy2/se2_neighborlist.c | 52 ++-- src/se2/src/speakeasy2/se2_neighborlist.h | 13 - src/se2/src/speakeasy2/se2_order_nodes.c | 22 - src/se2/src/speakeasy2/se2_partitions.c | 240 ++++++++++-------- src/se2/src/speakeasy2/se2_partitions.h | 106 +++----- src/se2/src/speakeasy2/se2_random.c | 15 - src/se2/src/speakeasy2/se2_random.h | 8 src/se2/src/speakeasy2/se2_reweigh_graph.c | 79 ++---- src/se2/src/speakeasy2/se2_reweigh_graph.h | 2 src/se2/src/speakeasy2/se2_seeding.c | 9 src/se2/src/speakeasy2/se2_seeding.h | 5 src/se2/vendor/CMakeLists.txt | 39 +-- 27 files changed, 831 insertions(+), 800 deletions(-)
Title: Import and Manipulate 'ForestGEO' Data
Description: To help you access, transform, analyze, and visualize
'ForestGEO' data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to easily import, filter, and modify 'ForestGEO' data. To
learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] ,
Richard Condit [aut],
Suzanne Lao [aut],
Anudeep Singh [aut],
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.tool versions 1.2.9 dated 2024-01-27 and 1.2.10 dated 2025-04-03
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/read_fgeo.R | 2 +- R/utils-tidy-eval.R | 2 +- README.md | 2 +- man/tidyeval.Rd | 2 +- man/type_vft.Rd | 2 +- 8 files changed, 20 insertions(+), 16 deletions(-)
Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara [aut, cre] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between BIOdry versions 0.9 dated 2022-05-02 and 0.9.1 dated 2025-04-03
DESCRIPTION | 22 +++-- MD5 | 66 +++++++-------- NEWS | 152 ++++++++++++++++------------------- R/anova.modelFrame.R | 16 +-- R/frametoLme.R | 14 +-- R/lmeForm.R | 2 R/modelFrame.R | 8 - R/muleMan.R | 15 +-- R/ringApply.R | 2 R/shiftFrame.R | 6 - R/summary.modelFrame.R | 2 build/partial.rdb |binary man/amod.Rd | 109 ++++++++++++------------- man/anova.modelFrame.Rd | 158 ++++++++++++++++++------------------ man/arguSelect.Rd | 145 +++++++++++++++++---------------- man/cClass.Rd | 66 +++++++-------- man/frametoLme.Rd | 188 ++++++++++++++++++++++--------------------- man/levexp.Rd | 62 +++++++------- man/lmeForm.Rd | 108 ++++++++++++------------- man/mUnits.Rd | 69 ++++++++-------- man/modelFrame.Rd | 197 +++++++++++++++++++++++----------------------- man/moveYr.Rd | 86 ++++++++++---------- man/muleMan.Rd | 152 +++++++++++++++++------------------ man/plot.modelFrame.Rd | 80 +++++++++--------- man/plot.muleMan.Rd | 114 +++++++++++++------------- man/plot.wlai.Rd | 88 ++++++++++---------- man/ringApply.Rd | 179 +++++++++++++++++++++-------------------- man/rtimes.Rd | 70 ++++++++-------- man/scacum.Rd | 73 ++++++++--------- man/shiftFrame.Rd | 117 +++++++++++++-------------- man/slitFrame.Rd | 77 +++++++++-------- man/summary.modelFrame.Rd | 83 +++++++++---------- man/tdForm.Rd | 108 ++++++++++++------------- man/wlai.Rd | 94 ++++++++++----------- 34 files changed, 1376 insertions(+), 1352 deletions(-)
Title: Analyze ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to implement analyses of plot species distributions,
topography, demography, and biomass. It also includes a torus
translation test to determine habitat associations of tree species as
described by Zuleta et al. (2018) <doi:10.1007/s11104-018-3878-0>. To
learn more about ForestGEO visit <https://forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] ,
Gabriel Arellano [aut, rev],
Richard Condit [aut],
Matteo Detto [aut],
Kyle Harms [aut],
Suzanne Lao [aut, rev],
KangMin Ngo [rev],
Haley Overstreet [rev],
Sabrina Russo [aut, rev],
Daniel Zuleta [aut, rev],
CTFS-Forest [...truncated...]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.analyze versions 1.1.14 dated 2020-12-05 and 1.1.15 dated 2025-04-03
DESCRIPTION | 9 - MD5 | 21 +-- NEWS.md | 8 + R/abundance.R | 6 R/as_tibble.R | 2 R/tt_test.R | 4 README.md | 283 ++++++++++++++++++++++++++++++++++++-------- build |only man/abundance.Rd | 6 man/fgeo.analyze-package.Rd | 11 - man/reexports.Rd | 2 man/tt_test.Rd | 4 12 files changed, 273 insertions(+), 83 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 0.3.0 dated 2024-12-17 and 0.3.1 dated 2025-04-03
DESCRIPTION | 8 +++--- MD5 | 44 ++++++++++++++++----------------- NEWS.md | 10 +++++++ R/parallels-future.R | 8 +++--- R/parallels.R | 8 +++--- R/shiny-actionbutton-styled.R | 5 +++ R/shiny-compoundInput2.R | 6 +++- R/shiny-fancyFileInput.R | 11 ++++---- R/shiny-setInputs.R | 3 +- R/shiny-swal-alert.R | 3 -- R/shortcuts.R | 2 - R/systems.R | 5 +++ R/zzz-finalizers.R | 21 +++++++++------ R/zzz.R | 2 - build/vignette.rds |binary inst/doc/r_expr_addons.html | 8 +++--- inst/doc/shiny_customized_widgets.html | 2 - inst/doc/utility_functions.html | 8 +++--- inst/shiny-addons/dipsaus/dipsaus.css | 2 - man/shared_finalizer.Rd | 8 +++--- man/shiny_alert2.Rd | 2 - src/utils.cpp | 36 ++++++++++++++++++--------- tests/testthat/test.finalizers.R | 2 - 23 files changed, 122 insertions(+), 82 deletions(-)
Title: Rule- And Instance-Based Regression Modeling
Description: Regression modeling using rules with added instance-based
corrections.
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Chris Keefer [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] ,
Rulequest Research Pty Ltd. [cph]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between Cubist versions 0.4.4 dated 2024-07-01 and 0.5.0 dated 2025-04-03
DESCRIPTION | 8 MD5 | 54 ++--- NEWS.md | 4 build/vignette.rds |binary inst/doc/cubist.R | 10 - inst/doc/cubist.html | 484 +++++++------------------------------------------- src/construct.c | 18 - src/contin.c | 4 src/defns.h | 8 src/discr.c | 2 src/formrules.c | 6 src/formtree.c | 12 - src/getdata.c | 18 - src/getnames.c | 8 src/global.c | 4 src/implicitatt.c | 38 +-- src/instance.c | 16 - src/modelfiles.c | 12 - src/predict.c | 4 src/prunetree.c | 8 src/rcubist.c | 4 src/regress.c | 24 +- src/rsample.c | 4 src/rulebasedmodels.c | 14 - src/rules.c | 26 +- src/sample.c | 4 src/trees.c | 6 src/utility.c | 24 +- 28 files changed, 246 insertions(+), 578 deletions(-)
Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>)
databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running
'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam'
core and provides functions to open/close a database (redatam_open()/redatam_close()),
list entities and variables from the database (redatam_entities(), redatam_variables())
and execute a 'SPC' program and gets the results as data frames
(redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] ,
CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>
Diff between redatamx versions 1.1.0 dated 2024-12-22 and 1.1.1 dated 2025-04-03
DESCRIPTION | 6 ++-- MD5 | 27 ++++++++++-------- NAMESPACE | 1 NEWS.md | 8 +++++ R/cpp11.R | 2 - R/redatam-api.R | 2 - R/redatam-plugins.R |only R/zzz.R | 4 +- README.md | 64 +++++++++++++++++++++++++++++++++++++++++++++ configure | 12 +++----- configure.win | 17 ++++------- man/redatam_load_plugin.Rd |only src/cpp11.cpp | 9 ++++++ src/red_initialize.cpp | 17 +++++++---- src/red_plugins.cpp |only src/redengine_c.h | 3 ++ 16 files changed, 128 insertions(+), 44 deletions(-)
Title: Tutorials for "R for Data Science"
Description: When assigned "R for Data Science" (Wickham, Çetinkaya-Rundel,
and Grolemund (2023, ISBN: 1492097402)), students should read the book and
type in all the associated R commands themselves. Sadly, that never happens.
These tutorials allow students to demonstrate (and their instructors
to be sure) that all work has been completed. See Kane (2023)
<https://ppbds.github.io/tutorial.helpers/articles/instructions.html> from
the 'tutorial.helpers' package for a background discussion.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between r4ds.tutorials versions 0.3.0 dated 2024-07-03 and 0.3.1 dated 2025-04-03
r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/02-rstudio-and-code |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/06-terminal/images/pwd.png |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/28-quarto-websites |only r4ds.tutorials-0.3.1/r4ds.tutorials/DESCRIPTION | 10 r4ds.tutorials-0.3.1/r4ds.tutorials/MD5 | 186 - r4ds.tutorials-0.3.1/r4ds.tutorials/NEWS.md | 4 r4ds.tutorials-0.3.1/r4ds.tutorials/README.md | 5 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/00-introduction/images/base.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/00-introduction/tutorial.Rmd | 981 ++++- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/01-data-visualization/images/EDA-boxplot.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/01-data-visualization/images/tidy-data.png |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/01-data-visualization/tutorial.Rmd | 1740 ++------- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/02a-rstudio-and-code |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/02b-rstudio-and-quarto |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/04a-rstudio-and-github-introduction |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/04b-rstudio-and-github-advanced |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/05-data-tidying/tutorial.Rmd | 599 --- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/06-terminal/images/download.png |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/06-terminal/tutorial.Rmd | 1177 +++++- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/07-data-import/tutorial.Rmd | 177 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/08-getting-help/tutorial.Rmd | 30 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/11-communication/tutorial.Rmd | 5 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/13-numbers/tutorial.Rmd | 1773 ++++------ r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/14-strings/tutorial.Rmd | 2 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/15-regular-expressions/tutorial.Rmd | 734 +++- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/16-factors/tutorial.Rmd | 303 + r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/17-dates-and-times/tutorial.Rmd | 1511 +++++++- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/18-missing-values/tutorial.Rmd | 385 +- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/anti.png |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/closest.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/cross.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/full.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/gte.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/inner-both.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/inner.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/left.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/lt.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/match-types.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/photo1.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/relational.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/right.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/semi.png |only r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/setup2.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/images/venn.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/19-joins/tutorial.Rmd | 1245 +++++-- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/20-spreadsheets/tutorial.Rmd | 12 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/21-databases/tutorial.Rmd | 134 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/22-arrow/tutorial.Rmd | 120 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/23-hierarchical-data/images/View-1-min.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/23-hierarchical-data/images/View-2-min.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/23-hierarchical-data/images/View-3-min.png |binary r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/23-hierarchical-data/tutorial.Rmd | 175 r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/24-web-scraping/tutorial.Rmd | 370 +- r4ds.tutorials-0.3.1/r4ds.tutorials/inst/tutorials/25-functions/tutorial.Rmd | 257 - 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More information about r4ds.tutorials at CRAN
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Title: R Markdown Output Formats for Storytelling
Description: R Markdown output formats based on JavaScript libraries such as
'Scrollama' (<https://github.com/russellsamora/scrollama>) for storytelling.
Author: Yihui Xie [aut, cre] ,
Siqi Zhang [ctb],
Russell Goldenberg [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rolldown versions 0.1 dated 2019-07-14 and 0.2 dated 2025-04-03
DESCRIPTION | 18 - LICENSE | 2 MD5 | 25 +- NEWS.md |only R/scrollama.R | 11 README.md | 35 ++ build/vignette.rds |binary inst/doc/scrollama-basic.R | 12 - inst/doc/scrollama-basic.Rmd | 2 inst/doc/scrollama-basic.html | 470 ++++++---------------------------------- inst/doc/scrollama-sidebar.R | 4 inst/doc/scrollama-sidebar.html | 162 +++++++------ man/scrollama.Rd | 15 - vignettes/scrollama-basic.Rmd | 2 14 files changed, 234 insertions(+), 524 deletions(-)
Title: Analysis of Chronological Patterns from Archaeological Count
Data
Description: A toolkit for absolute and relative dating and analysis of
chronological patterns. This package includes functions for
chronological modeling and dating of archaeological assemblages from
count data. It provides methods for matrix seriation. It also allows
to compute time point estimates and density estimates of the
occupation and duration of an archaeological site.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kairos versions 2.2.0 dated 2024-12-10 and 2.2.1 dated 2025-04-03
kairos-2.2.0/kairos/R/reexport.R |only kairos-2.2.0/kairos/man/reexports.Rd |only kairos-2.2.1/kairos/DESCRIPTION | 47 +-- kairos-2.2.1/kairos/MD5 | 90 +++--- kairos-2.2.1/kairos/NAMESPACE | 31 -- kairos-2.2.1/kairos/NEWS.md | 5 kairos-2.2.1/kairos/R/AllGenerics.R | 20 - kairos-2.2.1/kairos/R/aoristic.R | 6 kairos-2.2.1/kairos/R/coerce.R | 4 kairos-2.2.1/kairos/R/event_date.R | 10 kairos-2.2.1/kairos/R/event_model.R | 8 kairos-2.2.1/kairos/R/event_plot.R | 2 kairos-2.2.1/kairos/R/event_resample.R | 4 kairos-2.2.1/kairos/R/fit.R | 2 kairos-2.2.1/kairos/R/kairos-package.R | 5 kairos-2.2.1/kairos/R/mcd.R | 8 kairos-2.2.1/kairos/R/plot_time.R | 4 kairos-2.2.1/kairos/R/show.R | 2 kairos-2.2.1/kairos/R/zzz.R | 3 kairos-2.2.1/kairos/README.md | 16 - kairos-2.2.1/kairos/build/partial.rdb |binary kairos-2.2.1/kairos/build/vignette.rds |binary kairos-2.2.1/kairos/inst/CITATION | 2 kairos-2.2.1/kairos/inst/doc/event.Rmd | 3 kairos-2.2.1/kairos/inst/doc/event.html | 240 +++++++---------- kairos-2.2.1/kairos/inst/doc/seriation.Rmd | 1 kairos-2.2.1/kairos/inst/doc/seriation.html | 234 +++++++--------- kairos-2.2.1/kairos/inst/po/fr/LC_MESSAGES/R-kairos.mo |binary kairos-2.2.1/kairos/man/aoristic.Rd | 2 kairos-2.2.1/kairos/man/data.frame.Rd | 6 kairos-2.2.1/kairos/man/event.Rd | 2 kairos-2.2.1/kairos/man/fit.Rd | 2 kairos-2.2.1/kairos/man/kairos-package.Rd | 9 kairos-2.2.1/kairos/man/mcd.Rd | 2 kairos-2.2.1/kairos/man/plot_aoristic.Rd | 8 kairos-2.2.1/kairos/man/plot_event.Rd | 2 kairos-2.2.1/kairos/man/plot_fit.Rd | 4 kairos-2.2.1/kairos/man/plot_mcd.Rd | 6 kairos-2.2.1/kairos/man/plot_time.Rd | 6 kairos-2.2.1/kairos/man/predict_event.Rd | 22 - kairos-2.2.1/kairos/man/refine.Rd | 4 kairos-2.2.1/kairos/man/resample_event.Rd | 4 kairos-2.2.1/kairos/man/resample_mcd.Rd | 6 kairos-2.2.1/kairos/po/R-fr.po | 25 - kairos-2.2.1/kairos/vignettes/bibliography.bib | 62 ++-- kairos-2.2.1/kairos/vignettes/event.Rmd | 3 kairos-2.2.1/kairos/vignettes/seriation.Rmd | 1 47 files changed, 412 insertions(+), 511 deletions(-)
Title: Flexibly Format Dates and Times to a Given Locale
Description: Format dates and times flexibly and to whichever locales
make sense. Parses dates, times, and date-times in various formats
(including string-based ISO 8601 constructions). The formatting syntax gives
the user many options for formatting the date and time output in a precise
manner. Time zones in the input can be expressed in multiple ways and there
are many options for formatting time zones in the output as well. Several of
the provided helper functions allow for automatic generation of locale-aware
formatting patterns based on date/time skeleton formats and standardized
date/time formats with varying specificity.
Author: Richard Iannone [aut, cre] ,
Olivier Roy [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between bigD versions 0.3.0 dated 2024-11-08 and 0.3.1 dated 2025-04-03
bigD-0.3.0/bigD/tests/testthat/test-dates_times.R |only bigD-0.3.0/bigD/tests/testthat/test-time_zones.R |only bigD-0.3.1/bigD/DESCRIPTION | 16 bigD-0.3.1/bigD/MD5 | 21 bigD-0.3.1/bigD/NEWS.md | 7 bigD-0.3.1/bigD/R/dt_formatters.R | 1310 ---------------------- bigD-0.3.1/bigD/R/dt_replace.R |only bigD-0.3.1/bigD/R/fdt.R | 315 ----- bigD-0.3.1/bigD/R/fdt_locales.R | 4 bigD-0.3.1/bigD/R/utils-date_time_parse.R | 118 - bigD-0.3.1/bigD/R/utils.R | 8 bigD-0.3.1/bigD/R/zzz.R | 13 bigD-0.3.1/bigD/man/fdt_locales_vec.Rd | 4 13 files changed, 142 insertions(+), 1674 deletions(-)
Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
<http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaBase versions 3.2.9 dated 2019-08-24 and 3.2.10 dated 2025-04-03
DESCRIPTION | 18 +++++++++++------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/oompa.pdf |binary man/z02-colorSchemes.Rd | 10 +++++----- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: LaTeX Wrappers for R Users
Description: Provides the functionality to write LaTeX code from within R
without having to learn LaTeX. Functionality also exists to create HTML
and Markdown code. While the functionality still exists to write
complete documents with lazyWeave, it is generally easier to do so with
with markdown and knitr. lazyWeave's main strength now is the ability
to design custom and complex tables for reporting results.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between lazyWeave versions 3.0.2 dated 2018-01-25 and 3.0.3 dated 2025-04-03
lazyWeave-3.0.2/lazyWeave/data/Scout.RData |only lazyWeave-3.0.2/lazyWeave/man/Scout.rd |only lazyWeave-3.0.3/lazyWeave/DESCRIPTION | 8 lazyWeave-3.0.3/lazyWeave/MD5 | 162 - lazyWeave-3.0.3/lazyWeave/NAMESPACE | 74 lazyWeave-3.0.3/lazyWeave/NEWS | 118 - lazyWeave-3.0.3/lazyWeave/R/catconttable.R | 404 ++-- lazyWeave-3.0.3/lazyWeave/R/cattable.R | 458 ++-- lazyWeave-3.0.3/lazyWeave/R/conttable.R | 400 ++-- lazyWeave-3.0.3/lazyWeave/R/is.significant.R | 74 lazyWeave-3.0.3/lazyWeave/R/lazy.build.R | 286 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.citation.R | 116 - lazyWeave-3.0.3/lazyWeave/R/lazy.counter.R | 276 +- lazyWeave-3.0.3/lazyWeave/R/lazy.figure.R | 324 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.file.end.R | 44 lazyWeave-3.0.3/lazyWeave/R/lazy.file.start.R | 262 +- lazyWeave-3.0.3/lazyWeave/R/lazy.footnote.R | 154 - lazyWeave-3.0.3/lazyWeave/R/lazy.insert.code.R | 80 lazyWeave-3.0.3/lazyWeave/R/lazy.label.R | 54 lazyWeave-3.0.3/lazyWeave/R/lazy.landscape.R | 70 lazyWeave-3.0.3/lazyWeave/R/lazy.link.R | 118 - lazyWeave-3.0.3/lazyWeave/R/lazy.list.R | 344 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.matrix.R | 282 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.page.break.R | 68 lazyWeave-3.0.3/lazyWeave/R/lazy.page.number.R | 70 lazyWeave-3.0.3/lazyWeave/R/lazy.ref.R | 108 - lazyWeave-3.0.3/lazyWeave/R/lazy.section.R | 352 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.table.R | 924 +++++----- lazyWeave-3.0.3/lazyWeave/R/lazy.text.R | 298 +-- lazyWeave-3.0.3/lazyWeave/R/lazy.text.format.R | 126 - lazyWeave-3.0.3/lazyWeave/R/lazy.toc.R | 152 - lazyWeave-3.0.3/lazyWeave/R/lazy.verbatim.end.R | 28 lazyWeave-3.0.3/lazyWeave/R/lazy.verbatim.start.R | 78 lazyWeave-3.0.3/lazyWeave/R/lazy.write.R | 148 - lazyWeave-3.0.3/lazyWeave/R/lazyWeave.R | 79 lazyWeave-3.0.3/lazyWeave/R/mantel.test.R | 294 +-- lazyWeave-3.0.3/lazyWeave/R/map.size.R | 114 - lazyWeave-3.0.3/lazyWeave/R/print.ctable.R | 242 +- lazyWeave-3.0.3/lazyWeave/R/pvalString.R | 166 - lazyWeave-3.0.3/lazyWeave/R/setHtmlOptions.R | 114 - lazyWeave-3.0.3/lazyWeave/R/split_ctable.R | 56 lazyWeave-3.0.3/lazyWeave/R/univ.R | 346 +-- lazyWeave-3.0.3/lazyWeave/R/write.ctable.r | 678 +++---- lazyWeave-3.0.3/lazyWeave/R/write.univ.R | 224 +- lazyWeave-3.0.3/lazyWeave/R/zzz.R | 36 lazyWeave-3.0.3/lazyWeave/README.md | 52 lazyWeave-3.0.3/lazyWeave/man/ComparisonTable.Rd | 441 ++-- lazyWeave-3.0.3/lazyWeave/man/Delivery.rd | 68 lazyWeave-3.0.3/lazyWeave/man/WritePrintCtable.Rd | 262 +- lazyWeave-3.0.3/lazyWeave/man/is_significant.Rd | 76 lazyWeave-3.0.3/lazyWeave/man/lazy.build.Rd | 96 - lazyWeave-3.0.3/lazyWeave/man/lazy.citation.Rd | 92 lazyWeave-3.0.3/lazyWeave/man/lazy.counter.Rd | 156 - lazyWeave-3.0.3/lazyWeave/man/lazy.figure.Rd | 186 +- lazyWeave-3.0.3/lazyWeave/man/lazy.file.end.Rd | 36 lazyWeave-3.0.3/lazyWeave/man/lazy.file.start.Rd | 167 - lazyWeave-3.0.3/lazyWeave/man/lazy.footnote.Rd | 107 - lazyWeave-3.0.3/lazyWeave/man/lazy.insert.code.Rd | 70 lazyWeave-3.0.3/lazyWeave/man/lazy.landscape.Rd | 60 lazyWeave-3.0.3/lazyWeave/man/lazy.link.Rd | 68 lazyWeave-3.0.3/lazyWeave/man/lazy.list.Rd | 157 - lazyWeave-3.0.3/lazyWeave/man/lazy.matrix.Rd | 183 + lazyWeave-3.0.3/lazyWeave/man/lazy.page.break.Rd | 62 lazyWeave-3.0.3/lazyWeave/man/lazy.page.number.Rd | 58 lazyWeave-3.0.3/lazyWeave/man/lazy.ref.Rd | 74 lazyWeave-3.0.3/lazyWeave/man/lazy.section.Rd | 167 - lazyWeave-3.0.3/lazyWeave/man/lazy.table.Rd | 388 ++-- lazyWeave-3.0.3/lazyWeave/man/lazy.text.Rd | 184 + lazyWeave-3.0.3/lazyWeave/man/lazy.text.format.Rd | 99 - lazyWeave-3.0.3/lazyWeave/man/lazy.toc.Rd | 108 - lazyWeave-3.0.3/lazyWeave/man/lazy.verbatim.start.Rd | 72 lazyWeave-3.0.3/lazyWeave/man/lazy.write.Rd | 69 lazyWeave-3.0.3/lazyWeave/man/lazyWeave.Rd | 90 lazyWeave-3.0.3/lazyWeave/man/mantel.test.Rd | 128 - lazyWeave-3.0.3/lazyWeave/man/map.size.Rd | 80 lazyWeave-3.0.3/lazyWeave/man/pvalString.Rd | 100 - lazyWeave-3.0.3/lazyWeave/man/setHtmlOptions.Rd | 128 - lazyWeave-3.0.3/lazyWeave/man/univ.Rd | 196 +- lazyWeave-3.0.3/lazyWeave/man/write.univ.Rd | 248 +- lazyWeave-3.0.3/lazyWeave/tests/testthat.R | 6 lazyWeave-3.0.3/lazyWeave/tests/testthat/test-is.significant.R | 28 lazyWeave-3.0.3/lazyWeave/tests/testthat/test-lazy.citation.R | 48 lazyWeave-3.0.3/lazyWeave/tests/testthat/test-lazy.counter.R | 4 83 files changed, 6818 insertions(+), 6605 deletions(-)
Title: Association Rule Classification
Description: Implements the Classification-based on
Association Rules (CBA) algorithm for association rule classification.
The package, also described in Hahsler et al. (2019) <doi:10.32614/RJ-2019-048>,
contains several convenience methods that allow to automatically
set CBA parameters (minimum confidence, minimum support) and it also natively
handles numeric attributes by integrating a pre-discretization step.
The rule generation phase is handled by the 'arules' package.
To further decrease the size of the CBA models produced by the 'arc' package, postprocessing by the
'qCBA' package is suggested.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>
Diff between arc versions 1.4 dated 2023-08-17 and 1.4.2 dated 2025-04-03
arc-1.4.2/arc/DESCRIPTION | 20 ++++++++++++-------- arc-1.4.2/arc/MD5 | 21 +++++++++++---------- arc-1.4.2/arc/NEWS | 13 +++++++++++++ arc-1.4.2/arc/R/cba.R | 27 +++++++++++++++++++-------- arc-1.4.2/arc/R/m1prune.R | 2 +- arc-1.4.2/arc/R/mdlp2.R | 8 ++++---- arc-1.4.2/arc/data/humtemp.csv.gz |only arc-1.4.2/arc/data/humtemp.rda |only arc-1.4.2/arc/man/cba.Rd | 4 ++-- arc-1.4.2/arc/man/cba_manual.Rd | 4 ++-- arc-1.4.2/arc/man/discrNumeric.Rd | 4 ++-- arc-1.4.2/arc/man/prune.Rd | 2 +- arc-1.4/arc/data/humtemp.csv |only 13 files changed, 67 insertions(+), 38 deletions(-)
Title: Simulation-Based Inference Methods for Infectious Disease Models
Description: Provides some code to run simulations of state-space models, and then
use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC)
algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle
filter based particle Markov chain Monte Carlo (PMCMC) algorithm
(Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>).
Also provides functions to plot and summarise the outputs.
Author: Trevelyan J. McKinley [aut, cre],
Stefan Widgren [aut] ,
Pavol Bauer [cph] ,
Robin Eriksson [cph] ,
Stefan Engblom [cph]
Maintainer: Trevelyan J. McKinley <t.mckinley@exeter.ac.uk>
Diff between SimBIID versions 0.2.1 dated 2021-02-04 and 0.2.2 dated 2025-04-03
SimBIID-0.2.1/SimBIID/man/SimBIID-package.Rd |only SimBIID-0.2.2/SimBIID/DESCRIPTION | 8 ++-- SimBIID-0.2.2/SimBIID/MD5 | 54 +++++++++++++-------------- SimBIID-0.2.2/SimBIID/NEWS.md | 7 +++ SimBIID-0.2.2/SimBIID/R/ABCSMC.R | 4 -- SimBIID-0.2.2/SimBIID/R/PMCMC.R | 27 ++++++------- SimBIID-0.2.2/SimBIID/R/SimBIID-package.R | 5 +- SimBIID-0.2.2/SimBIID/R/bootStates.R | 2 - SimBIID-0.2.2/SimBIID/R/compileRcpp.R | 2 - SimBIID-0.2.2/SimBIID/R/mparseRcpp.R | 2 - SimBIID-0.2.2/SimBIID/R/plotABC.R | 2 - SimBIID-0.2.2/SimBIID/R/plotPMCMC.R | 2 - SimBIID-0.2.2/SimBIID/R/plotSimBIID_runs.R | 4 +- SimBIID-0.2.2/SimBIID/R/predictPMCMC.R | 4 +- SimBIID-0.2.2/SimBIID/R/printABC.R | 2 - SimBIID-0.2.2/SimBIID/R/printPMCMC.R | 2 - SimBIID-0.2.2/SimBIID/R/run.R | 4 -- SimBIID-0.2.2/SimBIID/R/summaryABC.R | 2 - SimBIID-0.2.2/SimBIID/R/summaryPMCMC.R | 2 - SimBIID-0.2.2/SimBIID/R/windowPMCMC.R | 4 +- SimBIID-0.2.2/SimBIID/man/ABCSMC.Rd | 2 - SimBIID-0.2.2/SimBIID/man/PMCMC.Rd | 19 ++++----- SimBIID-0.2.2/SimBIID/man/SimBIID.Rd |only SimBIID-0.2.2/SimBIID/man/mparseRcpp.Rd | 2 - SimBIID-0.2.2/SimBIID/man/run.Rd | 2 - SimBIID-0.2.2/SimBIID/man/window.PMCMC.Rd | 2 - SimBIID-0.2.2/SimBIID/src/Makevars | 4 +- SimBIID-0.2.2/SimBIID/src/Makevars.win | 4 +- SimBIID-0.2.2/SimBIID/src/RcppExports.cpp | 5 ++ 29 files changed, 88 insertions(+), 91 deletions(-)
Title: R Markdown Format for 'reveal.js' Presentations
Description: R Markdown format for 'reveal.js' presentations, a framework
for easily creating beautiful presentations using HTML.
Author: Christophe Dervieux [cre],
JJ Allaire [aut],
Hakim El Hattab [aut, cph] ,
Asvin Goel [ctb, cph] ,
Greg Denehy [ctb, cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Christophe Dervieux <cderv@posit.co>
Diff between revealjs versions 0.9 dated 2017-03-13 and 0.10.0 dated 2025-04-03
revealjs-0.10.0/revealjs/DESCRIPTION | 45 revealjs-0.10.0/revealjs/LICENSE | 4 revealjs-0.10.0/revealjs/MD5 | 236 - revealjs-0.10.0/revealjs/NAMESPACE | 8 revealjs-0.10.0/revealjs/NEWS.md |only revealjs-0.10.0/revealjs/R/revealjs.R | 6 revealjs-0.10.0/revealjs/R/revealjs_presentation.R | 663 ++-- revealjs-0.10.0/revealjs/R/utils.R |only revealjs-0.10.0/revealjs/inst/NOTICE | 858 ++--- revealjs-0.10.0/revealjs/inst/reveal.js-4.2.1 |only revealjs-0.10.0/revealjs/inst/rmarkdown/templates/revealjs_presentation/resources/default.html | 1434 ++++------ revealjs-0.10.0/revealjs/inst/rmarkdown/templates/revealjs_presentation/skeleton/skeleton.Rmd | 240 + revealjs-0.10.0/revealjs/inst/rmarkdown/templates/revealjs_presentation/template.yaml | 8 revealjs-0.10.0/revealjs/man/revealjs_presentation.Rd | 378 +- revealjs-0.10.0/revealjs/tests/testthat.R | 8 revealjs-0.10.0/revealjs/tests/testthat/helpers.R |only revealjs-0.10.0/revealjs/tests/testthat/test-revealjs_presentation.R |only revealjs-0.10.0/revealjs/tests/testthat/test-themes.R |only revealjs-0.10.0/revealjs/tests/testthat/test-utils.R |only revealjs-0.9/revealjs/inst/COPYING |only revealjs-0.9/revealjs/inst/NEWS |only revealjs-0.9/revealjs/inst/reveal.js-3.3.0.1 |only revealjs-0.9/revealjs/tests/testthat/test_themes.R |only 23 files changed, 2057 insertions(+), 1831 deletions(-)
Title: Response-Adaptive Randomization in Clinical Trials
Description: Some response-adaptive randomization methods commonly found in literature are included in this package. These methods include the randomized play-the-winner rule for binary endpoint (Wei and Durham (1978) <doi:10.2307/2286290>), the doubly adaptive biased coin design with minimal variance strategy for binary endpoint (Atkinson and Biswas (2013) <doi:10.1201/b16101>, Rosenberger and Lachin (2015) <doi:10.1002/9781118742112>) and maximal power strategy targeting Neyman allocation for binary endpoint (Tymofyeyev, Rosenberger, and Hu (2007) <doi:10.1198/016214506000000906>) and RSIHR allocation with each letter representing the first character of the names of the individuals who first proposed this rule (Youngsook and Hu (2010) <doi:10.1198/sbr.2009.0056>, Bello and Sabo (2016) <doi:10.1080/00949655.2015.1114116>), A-optimal Allocation for continuous endpoint (Sverdlov and Rosenberger (2013) <doi:10.1080/15598608.2013.783726>), Aa-optimal Allocatio [...truncated...]
Author: Chuyao Xu [aut, cre],
Thomas Lumley [aut, ths],
Alain Vandal [aut, ths],
Sofia S. Villar [cph],
Kyle J. Wathen [cph]
Maintainer: Chuyao Xu <cxu870@aucklanduni.ac.nz>
Diff between RARtrials versions 0.0.1 dated 2024-06-04 and 0.0.2 dated 2025-04-03
DESCRIPTION | 6 +- MD5 | 98 +++++++++++++++++++------------------- R/brar_select_au_binary.r | 6 +- R/brar_select_au_known_var.r | 4 - R/brar_select_au_unknown_var.r | 8 +-- R/convert_chisq_to_gamma.r | 6 +- R/convert_gamma_to_chisq.r | 6 +- R/dabcd_max_power.r | 4 + R/flgi_cut_off_binary.r | 1 R/flgi_cut_off_known_var.r | 2 R/flgi_cut_off_unknown_var.r | 2 R/pgreater_NIX.r | 9 +-- R/pgreater_beta.r | 8 +-- R/pgreater_normal.r | 12 ++-- R/pmax_NIX.r | 8 +-- R/pmax_beta.r | 4 - R/pmax_normal.r | 6 +- R/sim_brar_binary.r | 4 - R/sim_brar_known_var.r | 4 - R/sim_dabcd_max_power.r | 3 + R/sim_flgi_known_var.r | 2 R/sim_flgi_unknown_var.r | 2 R/update_par_nichisq.r | 6 +- README.md | 6 +- build/partial.rdb |binary inst/doc/RARtrials.R | 14 ++--- inst/doc/RARtrials.Rmd | 18 +++--- inst/doc/RARtrials.pdf |binary man/brar_select_au_binary.Rd | 6 +- man/brar_select_au_known_var.Rd | 4 - man/brar_select_au_unknown_var.Rd | 8 +-- man/convert_chisq_to_gamma.Rd | 6 +- man/convert_gamma_to_chisq.Rd | 6 +- man/dabcd_max_power.Rd | 3 + man/flgi_cut_off_binary.Rd | 1 man/flgi_cut_off_known_var.Rd | 2 man/flgi_cut_off_unknown_var.Rd | 2 man/pgreater_NIX.Rd | 9 +-- man/pgreater_beta.Rd | 8 +-- man/pgreater_normal.Rd | 12 ++-- man/pmax_NIX.Rd | 8 +-- man/pmax_beta.Rd | 4 - man/pmax_normal.Rd | 6 +- man/sim_brar_binary.Rd | 4 - man/sim_brar_known_var.Rd | 4 - man/sim_dabcd_max_power.Rd | 3 + man/sim_flgi_known_var.Rd | 2 man/sim_flgi_unknown_var.Rd | 2 man/update_par_nichisq.Rd | 6 +- vignettes/RARtrials.Rmd | 18 +++--- 50 files changed, 195 insertions(+), 178 deletions(-)
Title: Postprocessing of Rule Classification Models Learnt on Quantized
Data
Description: Implements the Quantitative Classification-based on
Association Rules (QCBA) algorithm (<doi:10.1007/s10489-022-04370-x>).
QCBA postprocesses rule classification models making them typically smaller and in some cases more accurate.
Supported are 'CBA' implementations from 'rCBA', 'arulesCBA' and 'arc' packages, and 'CPAR', 'CMAR', 'FOIL2' and 'PRM' implementations
from 'arulesCBA' package and 'SBRL' implementation from the 'sbrl' package. The result of the post-processing is an ordered CBA-like rule list.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>
Diff between qCBA versions 1.0 dated 2024-08-28 and 1.0.2 dated 2025-04-03
DESCRIPTION | 8 ++-- MD5 | 18 +++++------ NAMESPACE | 2 + NEWS | 8 ++++ R/rMARC.R | 63 ++++++++++++++++++++++++++------------- man/benchmarkQCBA.Rd | 3 + man/qCBARuleModel-class.Rd | 12 ++++++- man/qcbaIris.Rd | 2 + man/qcbaIris2.Rd | 2 + man/sbrlModel2arcCBARuleModel.Rd | 2 - 10 files changed, 85 insertions(+), 35 deletions(-)
Title: Augmented Backward Elimination
Description: Performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model. More details can be found in Dunkler et al. (2014) <doi:10.1371/journal.pone.0113677>.
Author: Rok Blagus [aut, cre],
Sladana Babic [ctb],
Daniela Dunkler [ctb],
Georg Heinze [ctb],
Gregor Steiner [ctb]
Maintainer: Rok Blagus <rok.blagus@mf.uni-lj.si>
Diff between abe versions 3.0.1 dated 2017-10-30 and 5.1.2 dated 2025-04-03
DESCRIPTION | 31 MD5 | 45 NAMESPACE | 26 R/abe-package.R |only R/abe.R | 4344 ++++++++++++++++++++++++++++++++++++++------------ README.md |only build |only man/abe-package.Rd |only man/abe.Rd | 131 - man/abe.boot.Rd | 101 - man/abe.fact1.Rd | 18 man/abe.fact1.boot.Rd | 18 man/abe.fact2.Rd | 18 man/abe.fact2.boot.Rd | 18 man/abe.num.Rd | 20 man/abe.num.boot.Rd | 18 man/abe.resampling.Rd |only man/my_grep.Rd | 2 man/my_grepl.Rd | 2 man/my_update.Rd | 2 man/my_update2.Rd | 2 man/my_update_boot.Rd | 2 man/pie.abe.Rd |only man/plot.abe.Rd | 76 man/print.abe.Rd |only man/summary.abe.Rd | 51 tests |only 27 files changed, 3696 insertions(+), 1229 deletions(-)
Title: An Integrated Framework for Textual Sentiment Time Series
Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2021) <doi:10.18637/jss.v099.i02>.
Author: Samuel Borms [aut, cre] ,
David Ardia [aut] ,
Keven Bluteau [aut] ,
Kris Boudt [aut] ,
Jeroen Van Pelt [ctb],
Andres Algaba [ctb]
Maintainer: Samuel Borms <borms_sam@hotmail.com>
Diff between sentometrics versions 1.0.0 dated 2021-08-18 and 1.0.1 dated 2025-04-03
DESCRIPTION | 10 ++-- MD5 | 48 ++++++++++----------- NEWS.md | 4 + R/attribution.R | 2 R/sentomeasures_methods.R | 4 - R/sentometrics.R | 10 ++-- R/sentomodel.R | 10 ++-- README.md | 6 +- build/partial.rdb |binary man/as.data.table.sento_measures.Rd | 82 ++++++++++++++++++------------------ man/list_lexicons.Rd | 8 +-- man/plot.attributions.Rd | 2 man/plot.sento_measures.Rd | 2 man/plot.sento_modelIter.Rd | 2 man/predict.sento_model.Rd | 8 +-- man/sentometrics-package.Rd | 2 man/usnews.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 5 ++ src/SentimentScorerBigrams.h | 1 src/SentimentScorerClusters.h | 1 src/SentimentScorerOnegrams.h | 1 src/SentimentScorerSentences.h | 1 src/utils.h | 49 --------------------- 25 files changed, 108 insertions(+), 154 deletions(-)
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],
Rafail Vargiakakis [aut],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.4 dated 2025-02-17 and 1.5 dated 2025-04-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 -- R/coldisc.mle.R | 4 ++-- R/disc.mle.R | 25 ++++++++++++++++++++++++- man/MLE-package.Rd | 4 ++-- 6 files changed, 38 insertions(+), 17 deletions(-)
Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0)
"Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences".
This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting
functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between HDANOVA versions 0.8.2 dated 2025-01-21 and 0.8.3 dated 2025-04-03
HDANOVA-0.8.2/HDANOVA/R/asca_fit.R |only HDANOVA-0.8.2/HDANOVA/man/asca_fit.Rd |only HDANOVA-0.8.3/HDANOVA/DESCRIPTION | 8 HDANOVA-0.8.3/HDANOVA/MD5 | 78 +- HDANOVA-0.8.3/HDANOVA/NAMESPACE | 17 HDANOVA-0.8.3/HDANOVA/NEWS | 9 HDANOVA-0.8.3/HDANOVA/R/HDANOVA-package.R | 5 HDANOVA-0.8.3/HDANOVA/R/apca.R | 21 HDANOVA-0.8.3/HDANOVA/R/asca.R | 21 HDANOVA-0.8.3/HDANOVA/R/asca_plots.R | 6 HDANOVA-0.8.3/HDANOVA/R/asca_results.R | 19 HDANOVA-0.8.3/HDANOVA/R/biplot.asca.R |only HDANOVA-0.8.3/HDANOVA/R/extract_estimates.R |only HDANOVA-0.8.3/HDANOVA/R/hdanova.R |only HDANOVA-0.8.3/HDANOVA/R/limmpca.R | 25 HDANOVA-0.8.3/HDANOVA/R/msca.R | 21 HDANOVA-0.8.3/HDANOVA/R/pcanova.R | 8 HDANOVA-0.8.3/HDANOVA/R/pcanova_plots.R | 2 HDANOVA-0.8.3/HDANOVA/R/pcanova_results.R | 2 HDANOVA-0.8.3/HDANOVA/R/permutation.R |only HDANOVA-0.8.3/HDANOVA/R/sca.R |only HDANOVA-0.8.3/HDANOVA/R/signflip.R |only HDANOVA-0.8.3/HDANOVA/R/utilities.R | 4 HDANOVA-0.8.3/HDANOVA/R/wrappers.R | 2 HDANOVA-0.8.3/HDANOVA/inst/doc/vignette_C_ASCA.R | 24 HDANOVA-0.8.3/HDANOVA/inst/doc/vignette_C_ASCA.Rmd | 50 + HDANOVA-0.8.3/HDANOVA/inst/doc/vignette_C_ASCA.html | 557 ++++++++++--------- HDANOVA-0.8.3/HDANOVA/man/HDANOVA.Rd | 98 ++- HDANOVA-0.8.3/HDANOVA/man/apca.Rd | 18 HDANOVA-0.8.3/HDANOVA/man/asca.Rd | 17 HDANOVA-0.8.3/HDANOVA/man/asca_plots.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/asca_results.Rd | 11 HDANOVA-0.8.3/HDANOVA/man/biplot.asca.Rd |only HDANOVA-0.8.3/HDANOVA/man/block.data.frame.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/extended.model.frame.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/extract_estimates.Rd |only HDANOVA-0.8.3/HDANOVA/man/limmpca.Rd | 10 HDANOVA-0.8.3/HDANOVA/man/msca.Rd | 17 HDANOVA-0.8.3/HDANOVA/man/pcanova.Rd | 4 HDANOVA-0.8.3/HDANOVA/man/pcanova_plots.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/pcanova_results.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/permutation.Rd |only HDANOVA-0.8.3/HDANOVA/man/prc.Rd | 2 HDANOVA-0.8.3/HDANOVA/man/sca.Rd |only HDANOVA-0.8.3/HDANOVA/man/signflip.Rd |only HDANOVA-0.8.3/HDANOVA/vignettes/vignette_B_ANOVA.tex |only HDANOVA-0.8.3/HDANOVA/vignettes/vignette_C_ASCA.Rmd | 50 + 47 files changed, 720 insertions(+), 396 deletions(-)
Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars, charts and markdown WYSIWYG editor with 'TOAST UI' <https://ui.toast.com/> libraries to
integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between toastui versions 0.3.4 dated 2024-09-18 and 0.4.0 dated 2025-04-03
DESCRIPTION | 8 MD5 | 50 +- NAMESPACE | 8 NEWS.md | 150 +++--- R/chart.R | 178 +++---- R/editor-proxy.R |only R/editor.R |only R/grid-editor.R | 422 ++++++++-------- R/grid-filters.R | 168 +++--- R/onLoad.R | 122 ++-- R/shiny.R | 286 ++++++----- README.md | 162 +++--- build/vignette.rds |binary inst/doc/toastui.R | 20 inst/doc/toastui.Rmd | 12 inst/doc/toastui.html | 796 ++++++++++++++++---------------- inst/examples/calendar-edit-schedules.R | 284 +++++------ inst/examples/calendar-popup-shiny.R | 234 ++++----- inst/htmlwidgets/datagrid.js | 2 inst/htmlwidgets/editor.js |only inst/htmlwidgets/editor.js.LICENSE.txt |only man/cal_proxy_toggle.Rd | 4 man/datagrid-shiny.Rd | 1 man/editor-proxy-show-hide.Rd |only man/editor-shiny.Rd |only man/editor.Rd |only man/editor_proxy.Rd |only man/editor_proxy_change_preview.Rd |only man/editor_proxy_insert.Rd |only man/figures/editor.png |only vignettes/figures/editor.png |only vignettes/toastui.Rmd | 12 32 files changed, 1508 insertions(+), 1411 deletions(-)
Title: Import and Export Data
Description: Import and export data from the most common statistical formats by using
R functions that guarantee the least loss of the data information, giving special
attention to the date variables and the labelled ones.
Author: Roger Pros [aut],
Isaac Subirana [aut, cre],
Joan Vila [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between ImportExport versions 1.3 dated 2020-09-21 and 1.3.1 dated 2025-04-03
DESCRIPTION | 15 ++++++++++----- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/access_export.R | 3 ++- R/excel_export.R | 3 ++- R/spss_export.R | 3 ++- R/spss_import.R | 15 ++++++++++----- build/partial.rdb |binary man/excel_export.Rd | 5 ++++- 9 files changed, 43 insertions(+), 22 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.2.2 dated 2025-02-11 and 2.3.0 dated 2025-04-03
GitStats-2.2.2/GitStats/inst/package_usage_workflow.R |only GitStats-2.2.2/GitStats/inst/roche/roche_get_package_usage.R |only GitStats-2.2.2/GitStats/man/get_R_package_usage.Rd |only GitStats-2.2.2/GitStats/tests/testthat/_snaps/get_usage_R_package.md |only GitStats-2.2.2/GitStats/tests/testthat/test-get_usage_R_package.R |only GitStats-2.3.0/GitStats/DESCRIPTION | 6 GitStats-2.3.0/GitStats/MD5 | 171 +-- GitStats-2.3.0/GitStats/NAMESPACE | 5 GitStats-2.3.0/GitStats/NEWS.md | 20 GitStats-2.3.0/GitStats/R/EngineGraphQL.R | 54 + GitStats-2.3.0/GitStats/R/EngineGraphQLGitHub.R | 233 +++- GitStats-2.3.0/GitStats/R/EngineGraphQLGitLab.R | 225 +++- GitStats-2.3.0/GitStats/R/EngineRest.R | 35 GitStats-2.3.0/GitStats/R/EngineRestGitHub.R | 229 +--- GitStats-2.3.0/GitStats/R/EngineRestGitLab.R | 291 +---- GitStats-2.3.0/GitStats/R/GQLQueryGitHub.R | 153 +-- GitStats-2.3.0/GitStats/R/GQLQueryGitLab.R | 100 + GitStats-2.3.0/GitStats/R/GitHost.R | 510 ++++++---- GitStats-2.3.0/GitStats/R/GitHostGitHub.R | 28 GitStats-2.3.0/GitStats/R/GitHostGitLab.R | 32 GitStats-2.3.0/GitStats/R/GitStats.R | 388 +++++-- GitStats-2.3.0/GitStats/R/get_commits.R | 31 GitStats-2.3.0/GitStats/R/get_files.R | 9 GitStats-2.3.0/GitStats/R/get_issues.R |only GitStats-2.3.0/GitStats/R/get_orgs.R |only GitStats-2.3.0/GitStats/R/get_release_logs.R |only GitStats-2.3.0/GitStats/R/get_repos.R | 123 +- GitStats-2.3.0/GitStats/R/get_users.R |only GitStats-2.3.0/GitStats/R/gitstats_functions.R | 117 -- GitStats-2.3.0/GitStats/R/global.R | 2 GitStats-2.3.0/GitStats/R/message_handler.R | 4 GitStats-2.3.0/GitStats/R/test_helpers.R | 14 GitStats-2.3.0/GitStats/README.md | 112 +- GitStats-2.3.0/GitStats/inst/cache_workflow.R | 10 GitStats-2.3.0/GitStats/inst/doc/get_repos_with_code.R | 54 - GitStats-2.3.0/GitStats/inst/doc/get_repos_with_code.Rmd | 2 GitStats-2.3.0/GitStats/inst/doc/get_repos_with_code.html | 2 GitStats-2.3.0/GitStats/inst/doc/set_hosts.R | 82 - GitStats-2.3.0/GitStats/inst/get_issues_workflow.R |only GitStats-2.3.0/GitStats/inst/get_orgs_workflow.R |only GitStats-2.3.0/GitStats/inst/get_repos_with_R_packages.R |only GitStats-2.3.0/GitStats/inst/roche/roche_api.R |only GitStats-2.3.0/GitStats/inst/roche/roche_get_files_workflow.R | 28 GitStats-2.3.0/GitStats/inst/roche/roche_get_orgs.R |only GitStats-2.3.0/GitStats/inst/roche/roche_get_repos_with_R_package.R |only GitStats-2.3.0/GitStats/inst/roche/roche_get_repos_workflow.R | 46 GitStats-2.3.0/GitStats/man/get_commits.Rd | 4 GitStats-2.3.0/GitStats/man/get_commits_stats.Rd | 2 GitStats-2.3.0/GitStats/man/get_issues.Rd |only GitStats-2.3.0/GitStats/man/get_issues_stats.Rd |only GitStats-2.3.0/GitStats/man/get_orgs.Rd |only GitStats-2.3.0/GitStats/man/get_release_logs.Rd | 4 GitStats-2.3.0/GitStats/man/get_repos_with_R_packages.Rd |only GitStats-2.3.0/GitStats/man/get_users.Rd | 2 GitStats-2.3.0/GitStats/tests/testthat/_snaps/00-get_orgs-GitHub.md |only GitStats-2.3.0/GitStats/tests/testthat/_snaps/00-get_orgs-GitLab.md |only GitStats-2.3.0/GitStats/tests/testthat/_snaps/00-get_orgs-GitStats.md |only GitStats-2.3.0/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 53 - 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Title: Easily Send HTML Email Messages
Description: Compose and send out responsive HTML email messages that render
perfectly across a range of email clients and device sizes. Helper functions
let the user insert embedded images, web link buttons, and 'ggplot2' plot
objects into the message body. Messages can be sent through an 'SMTP'
server, through the 'Posit Connect' service, or through the 'Mailgun' API
service <https://www.mailgun.com/>.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Jeroen Ooms [ctb] ,
Ted Goas [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between blastula versions 0.3.5 dated 2024-02-24 and 0.3.6 dated 2025-04-03
blastula-0.3.5/blastula/tests/testthat/test-add_readable_time.R |only blastula-0.3.5/blastula/tests/testthat/test-credentials.R |only blastula-0.3.5/blastula/tests/testthat/test-html_manip.R |only blastula-0.3.5/blastula/tests/testthat/test-mime.R |only blastula-0.3.5/blastula/tests/testthat/test-utils.R |only blastula-0.3.5/blastula/tests/testthat/test-utils.Rmd |only blastula-0.3.6/blastula/DESCRIPTION | 10 +- blastula-0.3.6/blastula/MD5 | 36 ++++------ blastula-0.3.6/blastula/NAMESPACE | 4 + blastula-0.3.6/blastula/NEWS.md | 8 ++ blastula-0.3.6/blastula/R/block_articles.R | 5 + blastula-0.3.6/blastula/R/connect_email.R | 12 +-- blastula-0.3.6/blastula/R/mime.R | 8 +- blastula-0.3.6/blastula/R/prepare_rsc_example_files.R | 6 - blastula-0.3.6/blastula/R/render_email.R | 2 blastula-0.3.6/blastula/inst/examples/connect-example-main.Rmd | 4 - blastula-0.3.6/blastula/inst/examples/connect-example-text-only.Rmd | 4 - blastula-0.3.6/blastula/man/attach_connect_email.Rd | 6 - blastula-0.3.6/blastula/man/prepare_rsc_example_files.Rd | 6 - blastula-0.3.6/blastula/man/render_email.Rd | 2 blastula-0.3.6/blastula/man/suppress_scheduled_email.Rd | 2 blastula-0.3.6/blastula/tests/testthat/test-connect_emailing.R | 2 22 files changed, 66 insertions(+), 51 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern
recognition that extend the work of Quinlan (1993,
ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Mark Culp [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] ,
RuleQuest Research [cph] ,
Rulequest Research Pty Ltd. [cph]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between C50 versions 0.1.8 dated 2023-02-08 and 0.2.0 dated 2025-04-03
DESCRIPTION | 10 MD5 | 70 ++--- NEWS.md | 4 build/vignette.rds |binary inst/doc/C5.0.html | 416 +++------------------------------- inst/doc/Class_Probability_Calcs.R | 2 inst/doc/Class_Probability_Calcs.html | 398 ++------------------------------ src/attwinnow.c | 27 +- src/classify.c | 61 ++-- src/confmat.c | 6 src/construct.c | 17 - src/contin.c | 8 src/defns.h | 14 - src/discr.c | 6 src/formrules.c | 8 src/formtree.c | 83 +++--- src/getdata.c | 24 - src/getnames.c | 15 - src/global.c | 2 src/implicitatt.c | 69 ++--- src/info.c | 8 src/modelfiles.c | 30 +- src/p-thresh.c | 9 src/prune.c | 21 - src/rc50.c | 8 src/rsample.c | 8 src/rulebasedmodels.c | 31 +- src/rules.c | 26 +- src/ruletree.c | 10 src/siftrules.c | 32 +- src/strbuf.h | 12 src/subset.c | 14 - src/text.h | 2 src/trees.c | 10 src/utility.c | 146 +++++------ src/xval.c | 4 36 files changed, 468 insertions(+), 1143 deletions(-)
Title: 'Amber' Electronic Data Capture Client
Description: 'Amber' is a server application for capturing electronic data records.
Rich forms are used to collect data. This 'Amber' client allows
to perform data extraction for reporting or data transfer at persistent location
purposes.
Author: Yannick Marcon [aut, cre] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between amberr versions 1.1.0 dated 2024-07-05 and 1.2.0 dated 2025-04-03
DESCRIPTION | 12 +- MD5 | 52 ++++++----- NAMESPACE | 11 ++ R/amber.interviews.R | 155 ++++++++++++++++++++++++++++++++++- R/amber.tasks.R |only README.md | 2 man/amber.campaign.Rd | 3 man/amber.campaigns.Rd | 3 man/amber.case_report_export.Rd | 3 man/amber.case_report_form.Rd | 3 man/amber.case_report_forms.Rd | 3 man/amber.case_reports.Rd | 3 man/amber.form.Rd | 3 man/amber.form_revision.Rd | 3 man/amber.form_revisions.Rd | 3 man/amber.forms.Rd | 3 man/amber.interview_design.Rd | 3 man/amber.interview_designs.Rd | 3 man/amber.interview_export.Rd | 3 man/amber.interviews.Rd | 6 + man/amber.interviews_step_actions.Rd |only man/amber.interviews_step_data.Rd |only man/amber.interviews_steps.Rd |only man/amber.participant.Rd | 3 man/amber.participants.Rd | 3 man/amber.studies.Rd | 3 man/amber.study.Rd | 3 man/amber.task.Rd |only man/amber.task_logs.Rd |only man/amber.tasks.Rd |only man/amber.tasks_logs.Rd |only 31 files changed, 258 insertions(+), 31 deletions(-)
Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian
finite mixture modeling by including: density estimation for data with
bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal
clustering using MEM (Modal EM) algorithm for Gaussian mixtures
(Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via
Gaussian mixture modeling (Robin & Scrucca, 2023
<doi:10.1016/j.csda.2022.107582>); Gaussian mixtures modeling of
financial log-returns (Scrucca, 2024 <doi:10.3390/e26110907>).
Author: Luca Scrucca [aut, cre, cph]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between mclustAddons versions 0.9.1 dated 2024-11-13 and 0.9.2 dated 2025-04-03
DESCRIPTION | 12 ++++----- MD5 | 22 ++++++++--------- NEWS.md | 6 ++++ R/GMM_finance.R | 3 -- R/MclustBounded.R | 20 ++++----------- R/ModalEM.R | 4 +-- R/densityMclustBounded.R | 58 ++++++++++++++++++++++++++++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mclustAddons.html | 42 ++++++++++++++++---------------- man/MclustBounded.Rd | 6 ++-- man/rangepowerTransform.Rd | 4 +-- 12 files changed, 95 insertions(+), 82 deletions(-)
Title: Delayed Read for 'GDAL' Vector Data Sources
Description: Lazy read for drawings. A 'dplyr' back end for data sources supported by
'GDAL' vector drivers, that allows working with local or remote sources as if they
are in-memory data frames. Basic features works with any drawing format ('GDAL vector
data source') supported by the 'sf' package.
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between lazysf versions 0.1.0 dated 2020-11-14 and 0.2.0 dated 2025-04-03
DESCRIPTION | 14 - MD5 | 44 ++-- NEWS.md | 6 R/SFSQLConnection.R | 13 + R/SFSQLDriver.R | 6 R/SFSQLResult.R | 4 R/connect.R | 2 R/lazysf-package.R | 1 R/lazysf.R | 2 README.md | 158 +++++++++-------- build/vignette.rds |binary inst/doc/GDALSQL.R | 2 inst/doc/GDALSQL.Rmd | 12 - inst/doc/GDALSQL.html | 337 +++++++++++++++++-------------------- inst/misc/SFSQL_PGDriver.R | 4 man/SFSQL.Rd | 2 man/SFSQLConnection-class.Rd | 2 man/SFSQLDriver-class.Rd | 6 man/SFSQLResult-class.Rd | 4 man/figures/README-sf-action-1.png |binary man/lazysf-package.Rd | 11 - man/lazysf.Rd | 2 vignettes/GDALSQL.Rmd | 12 - 23 files changed, 326 insertions(+), 318 deletions(-)
Title: Helper Tools for Managing Data, Dates, Missing Values, and Text
Description: An assortment of helper functions for managing data (e.g.,
rotating values in matrices by a user-defined angle, switching from
row- to column-indexing), dates (e.g., intuiting year from messy date
strings), handling missing values (e.g., removing elements/rows across
multiple vectors or matrices if any have an NA), text (e.g.,
flushing reports to the console in real-time); and combining data frames
with different schema (copying, filling, or concatenating columns or
applying functions before combining).
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between omnibus versions 1.2.14 dated 2024-09-17 and 1.2.15 dated 2025-04-03
omnibus-1.2.14/omnibus/R/ellipseNames.r |only omnibus-1.2.14/omnibus/man/ellipseNames.Rd |only omnibus-1.2.15/omnibus/DESCRIPTION | 13 - omnibus-1.2.15/omnibus/MD5 | 99 +++++------ omnibus-1.2.15/omnibus/NAMESPACE | 2 omnibus-1.2.15/omnibus/NEWS.md | 7 omnibus-1.2.15/omnibus/R/cull.r | 4 omnibus-1.2.15/omnibus/R/memUse.r | 14 - omnibus-1.2.15/omnibus/R/omnibus.r | 2 omnibus-1.2.15/omnibus/R/runifMatrix.r |only omnibus-1.2.15/omnibus/R/screenRes.r |only omnibus-1.2.15/omnibus/README.md | 28 +-- omnibus-1.2.15/omnibus/man/bracket.Rd | 96 +++++----- omnibus-1.2.15/omnibus/man/capIt.Rd | 48 ++--- omnibus-1.2.15/omnibus/man/combineDf.Rd | 170 +++++++++--------- omnibus-1.2.15/omnibus/man/corner.Rd | 64 +++---- omnibus-1.2.15/omnibus/man/countDecDigits.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/cull.Rd | 52 ++--- omnibus-1.2.15/omnibus/man/dirCreate.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/domLeap.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/domNonLeap.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/doyLeap.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/doyNonLeap.Rd | 40 ++-- omnibus-1.2.15/omnibus/man/eps.Rd | 34 +-- omnibus-1.2.15/omnibus/man/figures |only omnibus-1.2.15/omnibus/man/insert.Rd | 72 ++++---- omnibus-1.2.15/omnibus/man/insertCol.Rd | 104 +++++------ omnibus-1.2.15/omnibus/man/isLeapYear.Rd | 42 ++-- omnibus-1.2.15/omnibus/man/isTRUENA.Rd | 82 ++++----- omnibus-1.2.15/omnibus/man/listFiles.Rd | 54 +++--- omnibus-1.2.15/omnibus/man/longRun.Rd | 64 +++---- omnibus-1.2.15/omnibus/man/maxRuns.Rd | 100 +++++------ omnibus-1.2.15/omnibus/man/memUse.Rd | 68 +++---- omnibus-1.2.15/omnibus/man/mergeLists.Rd | 66 +++---- omnibus-1.2.15/omnibus/man/mirror.Rd | 74 ++++---- omnibus-1.2.15/omnibus/man/mmode.Rd | 50 ++--- omnibus-1.2.15/omnibus/man/naCompare.Rd | 160 ++++++++--------- omnibus-1.2.15/omnibus/man/naOmitMulti.Rd | 52 ++--- omnibus-1.2.15/omnibus/man/naRows.Rd | 50 ++--- omnibus-1.2.15/omnibus/man/omnibus.Rd | 215 ++++++++++++----------- omnibus-1.2.15/omnibus/man/pairDist.Rd | 64 +++---- omnibus-1.2.15/omnibus/man/prefix.Rd | 52 ++--- omnibus-1.2.15/omnibus/man/quadArea.Rd | 56 +++--- omnibus-1.2.15/omnibus/man/renumSeq.Rd | 64 +++---- omnibus-1.2.15/omnibus/man/rotateMatrix.Rd | 62 +++--- omnibus-1.2.15/omnibus/man/roundTo.Rd | 60 +++--- omnibus-1.2.15/omnibus/man/roundedSigDigits.Rd | 194 ++++++++++----------- omnibus-1.2.15/omnibus/man/rowColIndexing.Rd | 76 ++++---- omnibus-1.2.15/omnibus/man/runifMatrix.Rd |only omnibus-1.2.15/omnibus/man/say.Rd | 98 +++++----- omnibus-1.2.15/omnibus/man/screenRes.Rd |only omnibus-1.2.15/omnibus/man/stretchMinMax.Rd | 98 +++++----- omnibus-1.2.15/omnibus/man/which.pmax.Rd | 90 +++++----- omnibus-1.2.15/omnibus/man/yearFromDate.Rd | 224 ++++++++++++------------- 54 files changed, 1636 insertions(+), 1628 deletions(-)
Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference
using a spectral analysis of Gaussian process priors.
Gaussian processes are represented with a Fourier series
based on cosine basis functions. Currently the package
includes parametric linear models, partial linear additive
models with/without shape restrictions, generalized linear
additive models with/without shape restrictions, and
density estimation model. To maximize computational
efficiency, the actual Markov chain Monte Carlo sampling
for each model is done using codes written in FORTRAN 90.
This software has been developed using funding supported by
Basic Science Research Program through the National Research
Foundation of Korea (NRF) funded by the Ministry of Education
(no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut],
Taeryon Choi [aut],
Beomjo Park [aut, cre],
Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjop@gmail.com>
Diff between bsamGP versions 1.2.5 dated 2024-03-18 and 1.2.6 dated 2025-04-02
DESCRIPTION | 30 +++++++++++++++------ MD5 | 4 +- README.md | 82 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 64 insertions(+), 52 deletions(-)
Title: Tools for 'Box Geometry Model' (BGM) Files and Topology for the
Atlantis Ecosystem Model
Description: Facilities for working with Atlantis box-geometry model (BGM)
files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model.
Functions are provided to read from BGM files directly, preserving their
internal topology, as well as helper functions to generate spatial data from these
mesh forms. This functionality aims to simplify the creation and modification of box
and geometry as well as the ability to integrate with other data sources.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between rbgm versions 0.1.0 dated 2020-04-12 and 0.2.0 dated 2025-04-02
DESCRIPTION | 8 - MD5 | 26 +-- NEWS.md | 4 R/Spatial.R | 10 - R/rbgm.R | 9 - R/to_ll_hack.R | 1 README.md | 50 ------ build/vignette.rds |binary inst/doc/BGM_Spatial.R | 2 inst/doc/BGM_Spatial.html | 299 ++++++++++++++++++++++++----------------- inst/doc/BGM_examplefiles.R | 36 ++-- inst/doc/BGM_examplefiles.html | 233 +++++++++++++++++++------------ inst/doc/BGMfiles.html | 246 ++++++++++++++++++++------------- man/rbgm-package.Rd | 19 ++ 14 files changed, 538 insertions(+), 405 deletions(-)
Title: Generic Coordinate System Transformations Using 'PROJ'
Description: A wrapper around the generic coordinate transformation software 'PROJ'
that transforms coordinates from one coordinate reference system ('CRS')
to another. This includes cartographic projections as well as geodetic transformations. The intention is for this
package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5
pathways be provided by the 'proj4' package.
Author: Michael D. Sumner [aut, cre] ,
Jeroen Ooms [ctb] ,
Simon Urbanek [cph, ctb] ,
Dewey Dunnington [ctb] ,
Anthony North [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between PROJ versions 0.5.0 dated 2024-06-12 and 0.6.0 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/vignette.rds |binary configure | 5 ++--- configure.ac | 4 ++-- inst/doc/PROJ.html | 2 +- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 3.1.10 dated 2025-01-12 and 3.1.11 dated 2025-04-02
growthPheno-3.1.10/growthPheno/data/cart.dat.rda |only growthPheno-3.1.10/growthPheno/tests/testthat/testLongiPrime.r |only growthPheno-3.1.10/growthPheno/tests/testthat/testthat-problems.rds |only growthPheno-3.1.11/growthPheno/DESCRIPTION | 8 growthPheno-3.1.11/growthPheno/MD5 | 68 ++--- growthPheno-3.1.11/growthPheno/R/dataLongi_v10.r | 85 ++++-- growthPheno-3.1.11/growthPheno/R/traitSmooth.r | 1 growthPheno-3.1.11/growthPheno/build/partial.rdb |binary growthPheno-3.1.11/growthPheno/data/RicePrepped.dat.rda |binary growthPheno-3.1.11/growthPheno/data/RiceRaw.dat.rda |binary growthPheno-3.1.11/growthPheno/data/datalist | 3 growthPheno-3.1.11/growthPheno/data/exampleData.rda |binary growthPheno-3.1.11/growthPheno/data/tomato.dat.rda |binary growthPheno-3.1.11/growthPheno/inst/News.Rd | 10 growthPheno-3.1.11/growthPheno/inst/doc/Rice.pdf |binary growthPheno-3.1.11/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-3.1.11/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-3.1.11/growthPheno/man/RicePrepped.dat.Rd | 10 growthPheno-3.1.11/growthPheno/man/RiceRaw.dat.Rd | 2 growthPheno-3.1.11/growthPheno/man/calcTimes.Rd | 2 growthPheno-3.1.11/growthPheno/man/designFactors.Rd | 4 growthPheno-3.1.11/growthPheno/man/exampleData.Rd | 6 growthPheno-3.1.11/growthPheno/man/growthPheno-pkg.Rd | 2 growthPheno-3.1.11/growthPheno/man/importExcel.Rd | 19 - growthPheno-3.1.11/growthPheno/man/plotImagetimes.Rd | 6 growthPheno-3.1.11/growthPheno/man/prepImageData.Rd | 56 +++- growthPheno-3.1.11/growthPheno/tests/testthat/data/area.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/cart.dat.rda |only growthPheno-3.1.11/growthPheno/tests/testthat/data/chkpeadat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/dat1.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.19.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.RGB.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/raw.fluo.dat.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/data/testSpline.rda |binary growthPheno-3.1.11/growthPheno/tests/testthat/testContGRdiff.r | 30 +- growthPheno-3.1.11/growthPheno/tests/testthat/testImportXL.r | 14 - growthPheno-3.1.11/growthPheno/tests/testthat/testprepImageData.r | 130 +++++++--- 37 files changed, 286 insertions(+), 170 deletions(-)
Title: Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Description: Tools for detecting and summarize influential cases that
can affect exploratory and confirmatory factor analysis models as well as
structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>;
Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <doi:10.3389/fpsyg.2012.00055>).
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between faoutlier versions 0.7.6 dated 2021-01-10 and 0.7.7 dated 2025-04-02
DESCRIPTION | 9 +++---- MD5 | 38 +++++++++++++++--------------- NEWS.md | 6 ++-- R/GOF.R | 8 +++--- R/LD.R | 8 +++--- R/faoutlier.R | 20 +++++++-------- R/forward.search.R | 4 +-- R/gCD.R | 58 ++++++++++++++++++++++++++++++---------------- R/obs.resid.R | 4 +-- R/robustMD.R | 10 +++---- README.md | 2 - build/partial.rdb |binary inst/CITATION | 6 ++-- man/faoutlier.Rd | 8 +++--- man/gCD.Rd | 12 +++++++-- man/holzinger.Rd | 6 ++-- man/holzinger.outlier.Rd | 6 ++-- man/robustMD.Rd | 8 +++--- tests/testthat/test-GOF.R | 7 ++--- tests/testthat/test-gCD.R | 15 +++++++---- 20 files changed, 131 insertions(+), 104 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.10 dated 2024-09-26 and 1.1.11 dated 2025-04-02
glmmTMB-1.1.10/glmmTMB/inst/Matrix-version |only glmmTMB-1.1.10/glmmTMB/inst/TMB-version |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.R |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.csv |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/sherman.rda |only glmmTMB-1.1.10/glmmTMB/inst/vignette_data/tmbstan_traceplot.png |only glmmTMB-1.1.10/glmmTMB/vignettes/covstruct_files |only glmmTMB-1.1.10/glmmTMB/vignettes/lineno.sty |only glmmTMB-1.1.11/glmmTMB/DESCRIPTION | 13 glmmTMB-1.1.11/glmmTMB/MD5 | 152 ++-- glmmTMB-1.1.11/glmmTMB/NAMESPACE | 1 glmmTMB-1.1.11/glmmTMB/R/VarCorr.R | 2 glmmTMB-1.1.11/glmmTMB/R/diagnose.R | 4 glmmTMB-1.1.11/glmmTMB/R/enum.R | 4 glmmTMB-1.1.11/glmmTMB/R/family.R | 40 - glmmTMB-1.1.11/glmmTMB/R/glmmTMB.R | 141 ++-- glmmTMB-1.1.11/glmmTMB/R/methods.R | 51 + glmmTMB-1.1.11/glmmTMB/R/predict.R | 38 - glmmTMB-1.1.11/glmmTMB/R/profile.R | 2 glmmTMB-1.1.11/glmmTMB/R/utils.R | 100 +- glmmTMB-1.1.11/glmmTMB/build/partial.rdb |binary glmmTMB-1.1.11/glmmTMB/build/vignette.rds |binary glmmTMB-1.1.11/glmmTMB/inst/CITATION | 36 - glmmTMB-1.1.11/glmmTMB/inst/NEWS.Rd | 50 + glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.R | 352 +++++----- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.html | 96 +- glmmTMB-1.1.11/glmmTMB/inst/doc/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.R | 92 +- glmmTMB-1.1.11/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.R | 48 - glmmTMB-1.1.11/glmmTMB/inst/doc/hacking.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.R | 251 ++++--- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.html | 270 ++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/inst/doc/miscEx.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.R | 30 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/inst/doc/model_evaluation.pdf |binary glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.R | 58 - glmmTMB-1.1.11/glmmTMB/inst/doc/parallel.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.R | 26 glmmTMB-1.1.11/glmmTMB/inst/doc/priors.html | 4 glmmTMB-1.1.11/glmmTMB/inst/doc/sim.html | 6 glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.R | 154 ++-- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.html | 320 ++++++++- glmmTMB-1.1.11/glmmTMB/inst/doc/troubleshooting.rmd | 83 +- glmmTMB-1.1.11/glmmTMB/inst/test_data/models.rda |binary glmmTMB-1.1.11/glmmTMB/inst/test_data/sim_ar1.rds |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.R | 79 +- glmmTMB-1.1.11/glmmTMB/inst/vignette_data/mcmc.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_bounds_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/sleepstudy_traceplot_theta3.png |only glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.R | 8 glmmTMB-1.1.11/glmmTMB/inst/vignette_data/troubleshooting.rda |binary glmmTMB-1.1.11/glmmTMB/inst/vignette_data/volcano_data.png |binary glmmTMB-1.1.11/glmmTMB/man/dot-checkRankX.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/get_autopar.Rd |only glmmTMB-1.1.11/glmmTMB/man/get_cor.Rd | 22 glmmTMB-1.1.11/glmmTMB/man/glmmTMB.Rd | 5 glmmTMB-1.1.11/glmmTMB/man/glmmTMBControl.Rd | 2 glmmTMB-1.1.11/glmmTMB/man/mkTMBStruc.Rd | 1 glmmTMB-1.1.11/glmmTMB/man/nbinom2.Rd | 14 glmmTMB-1.1.11/glmmTMB/man/predict.glmmTMB.Rd | 20 glmmTMB-1.1.11/glmmTMB/man/simulate_new.Rd | 42 - glmmTMB-1.1.11/glmmTMB/src/glmmTMB.cpp | 127 ++- glmmTMB-1.1.11/glmmTMB/tests/testthat/test-basics.R | 23 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-control.R | 30 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-diagnose.R | 13 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-downstream.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-families.R | 38 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-mapequal.R | 2 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-methods.R | 46 + glmmTMB-1.1.11/glmmTMB/tests/testthat/test-predict.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-priors.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-propto.R | 17 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-rr.R | 35 glmmTMB-1.1.11/glmmTMB/tests/testthat/test-varstruc.R | 77 +- glmmTMB-1.1.11/glmmTMB/vignettes/covstruct.rmd | 49 - glmmTMB-1.1.11/glmmTMB/vignettes/glmmTMB.bib | 6 glmmTMB-1.1.11/glmmTMB/vignettes/mcmc.rmd | 162 +++- glmmTMB-1.1.11/glmmTMB/vignettes/model_evaluation.Rnw | 2 glmmTMB-1.1.11/glmmTMB/vignettes/troubleshooting.rmd | 83 +- 83 files changed, 2477 insertions(+), 1113 deletions(-)
Title: Estimating Dynamic Correlation
Description: Implementations for two different Bayesian models of differential co-expression. scdeco.cop() fits the bivariate Gaussian copula model from Zichen Ma, Shannon W. Davis, Yen-Yi Ho (2023) <doi:10.1111/biom.13701>, while scdeco.pg() fits the bivariate Poisson-Gamma model from Zhen Yang, Yen-Yi Ho (2022) <doi:10.1111/biom.13457>.
Author: Anderson Bussing [aut, cre],
Yen-Yi Ho [aut, ths],
Zichen Ma [aut],
Zhen Yang [aut]
Maintainer: Anderson Bussing <abussing@email.sc.edu>
Diff between scDECO versions 0.1.0 dated 2024-06-04 and 0.1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 13 +++--- NEWS.md |only R/scdeco.cop.R | 70 +++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/scDECO-Copula.html | 28 +++++++------- inst/doc/scDECO-Poisson-Gamma.html | 22 +++++------ man/scdeco.cop.Rd | 16 +++++++- 8 files changed, 110 insertions(+), 47 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see Garrison et al. (2024) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.3 dated 2025-02-19 and 1.3.5 dated 2025-04-02
BGmisc-1.3.3/BGmisc/man/compute_transpose.Rd |only BGmisc-1.3.3/BGmisc/tests/testthat/Rplots.pdf |only BGmisc-1.3.5/BGmisc/DESCRIPTION | 14 BGmisc-1.3.5/BGmisc/MD5 | 109 +- BGmisc-1.3.5/BGmisc/NAMESPACE | 5 BGmisc-1.3.5/BGmisc/NEWS.md | 17 BGmisc-1.3.5/BGmisc/R/calculateFamilySize.R | 3 BGmisc-1.3.5/BGmisc/R/checkPedigree.R |only BGmisc-1.3.5/BGmisc/R/checkSex.R | 20 BGmisc-1.3.5/BGmisc/R/computeRelatedness.R | 2 BGmisc-1.3.5/BGmisc/R/convertPedigree.R | 430 +++++++--- BGmisc-1.3.5/BGmisc/R/documentData.R | 49 + BGmisc-1.3.5/BGmisc/R/makeLinks.R |only BGmisc-1.3.5/BGmisc/R/plotPedigree.R | 55 - BGmisc-1.3.5/BGmisc/R/readPedigree.R | 272 +++++- BGmisc-1.3.5/BGmisc/R/summarizePedigree.R | 24 BGmisc-1.3.5/BGmisc/README.md | 10 BGmisc-1.3.5/BGmisc/build/vignette.rds |binary BGmisc-1.3.5/BGmisc/data/ASOIAF.rda |only BGmisc-1.3.5/BGmisc/data/royal92.rda |only BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.R | 8 BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/inst/doc/analyticrelatedness.html | 118 +- BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/inst/doc/modelingrelatedness.html | 12 BGmisc-1.3.5/BGmisc/inst/doc/partial.R |only BGmisc-1.3.5/BGmisc/inst/doc/partial.Rmd |only BGmisc-1.3.5/BGmisc/inst/doc/partial.html |only BGmisc-1.3.5/BGmisc/inst/doc/pedigree.html | 225 ----- BGmisc-1.3.5/BGmisc/inst/doc/validation.R | 21 BGmisc-1.3.5/BGmisc/inst/doc/validation.Rmd | 45 - BGmisc-1.3.5/BGmisc/inst/doc/validation.html | 148 +-- BGmisc-1.3.5/BGmisc/man/ASOIAF.Rd |only BGmisc-1.3.5/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.3.5/BGmisc/man/assignParentIDs.Rd | 4 BGmisc-1.3.5/BGmisc/man/checkPedigreeNetwork.Rd |only BGmisc-1.3.5/BGmisc/man/com2links.Rd |only BGmisc-1.3.5/BGmisc/man/compute_parent_adjacency.Rd |only BGmisc-1.3.5/BGmisc/man/createFamilyToParentsMapping.Rd | 2 BGmisc-1.3.5/BGmisc/man/dot-computeTranspose.Rd |only BGmisc-1.3.5/BGmisc/man/extractSummaryText.Rd |only BGmisc-1.3.5/BGmisc/man/inferRelatedness.Rd | 2 BGmisc-1.3.5/BGmisc/man/makeLongTree.Rd |only BGmisc-1.3.5/BGmisc/man/matchMembers.Rd |only BGmisc-1.3.5/BGmisc/man/parseRelationships.Rd |only BGmisc-1.3.5/BGmisc/man/parseTree.Rd |only BGmisc-1.3.5/BGmisc/man/ped2add.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2cn.Rd | 3 BGmisc-1.3.5/BGmisc/man/ped2com.Rd | 8 BGmisc-1.3.5/BGmisc/man/ped2mit.Rd | 5 BGmisc-1.3.5/BGmisc/man/processParents.Rd | 2 BGmisc-1.3.5/BGmisc/man/readWikifamilytree.Rd |only BGmisc-1.3.5/BGmisc/man/repairSex.Rd | 4 BGmisc-1.3.5/BGmisc/man/royal92.Rd |only BGmisc-1.3.5/BGmisc/man/summarizePedigrees.Rd | 3 BGmisc-1.3.5/BGmisc/tests/testthat/test-calculateFamilySize.R | 22 BGmisc-1.3.5/BGmisc/tests/testthat/test-checkPedigreeNetwork.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-checkSex.R | 27 BGmisc-1.3.5/BGmisc/tests/testthat/test-convertPedigree.R | 209 ++++ BGmisc-1.3.5/BGmisc/tests/testthat/test-makeLinks.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-plotPedigree.R |only BGmisc-1.3.5/BGmisc/tests/testthat/test-readPedigrees.R | 33 BGmisc-1.3.5/BGmisc/tests/testthat/test-simulatePedigree.R | 29 BGmisc-1.3.5/BGmisc/tests/testthat/test-tweakPedigree.R | 12 BGmisc-1.3.5/BGmisc/vignettes/analyticrelatedness.Rmd | 46 - BGmisc-1.3.5/BGmisc/vignettes/modelingrelatedness.Rmd | 3 BGmisc-1.3.5/BGmisc/vignettes/partial.Rmd |only BGmisc-1.3.5/BGmisc/vignettes/validation.Rmd | 45 - 68 files changed, 1413 insertions(+), 687 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types
of resampling objects (e.g. bootstrap, cross-validation).
Author: Hannah Frick [aut, cre] ,
Fanny Chow [aut],
Max Kuhn [aut],
Michael Mahoney [aut] ,
Julia Silge [aut] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between rsample versions 1.2.1 dated 2024-03-25 and 1.3.0 dated 2025-04-02
rsample-1.2.1/rsample/R/nest.R |only rsample-1.2.1/rsample/tests/testthat/_snaps/initial.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/nesting.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/strata.md |only rsample-1.2.1/rsample/tests/testthat/_snaps/validation.md |only rsample-1.2.1/rsample/tests/testthat/test-for-pred.R |only rsample-1.2.1/rsample/tests/testthat/test-initial.R |only rsample-1.2.1/rsample/tests/testthat/test-make-splits.R |only rsample-1.2.1/rsample/tests/testthat/test-names.R |only rsample-1.2.1/rsample/tests/testthat/test-nesting.R |only rsample-1.2.1/rsample/tests/testthat/test-rolling.R |only rsample-1.2.1/rsample/tests/testthat/test-strata.R |only rsample-1.2.1/rsample/tests/testthat/test-validation.R |only rsample-1.3.0/rsample/DESCRIPTION | 12 rsample-1.3.0/rsample/MD5 | 213 +- rsample-1.3.0/rsample/NAMESPACE | 32 rsample-1.3.0/rsample/NEWS.md | 65 rsample-1.3.0/rsample/R/apparent.R | 5 rsample-1.3.0/rsample/R/boot.R | 8 rsample-1.3.0/rsample/R/bootci.R | 272 ++- rsample-1.3.0/rsample/R/caret.R | 33 rsample-1.3.0/rsample/R/clustering.R | 4 rsample-1.3.0/rsample/R/compat-vctrs-helpers.R | 53 rsample-1.3.0/rsample/R/complement.R | 9 rsample-1.3.0/rsample/R/fingerprint.R |only rsample-1.3.0/rsample/R/form_pred.R | 2 rsample-1.3.0/rsample/R/import-standalone-obj-type.R |only rsample-1.3.0/rsample/R/import-standalone-types-check.R |only rsample-1.3.0/rsample/R/initial_split.R | 52 rsample-1.3.0/rsample/R/initial_validation_split.R | 41 rsample-1.3.0/rsample/R/inner_split.R |only rsample-1.3.0/rsample/R/labels.R | 19 rsample-1.3.0/rsample/R/loo.R | 2 rsample-1.3.0/rsample/R/make_groups.R | 27 rsample-1.3.0/rsample/R/make_strata.R | 36 rsample-1.3.0/rsample/R/mc.R | 12 rsample-1.3.0/rsample/R/misc.R | 248 --- rsample-1.3.0/rsample/R/nested_cv.R |only rsample-1.3.0/rsample/R/permutations.R | 15 rsample-1.3.0/rsample/R/printing.R | 6 rsample-1.3.0/rsample/R/reg_intervals.R | 16 rsample-1.3.0/rsample/R/reshuffle_rset.R |only rsample-1.3.0/rsample/R/reverse_splits.R |only rsample-1.3.0/rsample/R/rolling_origin.R | 16 rsample-1.3.0/rsample/R/rsample-package.R | 11 rsample-1.3.0/rsample/R/rset.R | 14 rsample-1.3.0/rsample/R/rsplit.R | 37 rsample-1.3.0/rsample/R/slide.R | 46 rsample-1.3.0/rsample/R/tidy.R | 16 rsample-1.3.0/rsample/R/validation_set.R | 33 rsample-1.3.0/rsample/R/validation_split.R | 11 rsample-1.3.0/rsample/R/vfold.R | 81 - rsample-1.3.0/rsample/build/vignette.rds |binary rsample-1.3.0/rsample/inst/doc/Common_Patterns.R | 2 rsample-1.3.0/rsample/inst/doc/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/inst/doc/Common_Patterns.html | 16 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.Rmd | 9 rsample-1.3.0/rsample/inst/doc/Working_with_rsets.html | 734 ++-------- rsample-1.3.0/rsample/inst/doc/rsample.html | 422 ----- rsample-1.3.0/rsample/man/add_resample_id.Rd | 2 rsample-1.3.0/rsample/man/as.data.frame.rsplit.Rd | 6 rsample-1.3.0/rsample/man/bootstraps.Rd | 2 rsample-1.3.0/rsample/man/dot-get_split_args.Rd |only rsample-1.3.0/rsample/man/form_pred.Rd | 2 rsample-1.3.0/rsample/man/get_fingerprint.Rd | 4 rsample-1.3.0/rsample/man/group_bootstraps.Rd | 2 rsample-1.3.0/rsample/man/initial_split.Rd | 11 rsample-1.3.0/rsample/man/initial_validation_split.Rd | 7 rsample-1.3.0/rsample/man/inner_split.Rd |only rsample-1.3.0/rsample/man/int_pctl.Rd | 56 rsample-1.3.0/rsample/man/labels.rset.Rd | 5 rsample-1.3.0/rsample/man/make_groups.Rd | 2 rsample-1.3.0/rsample/man/make_strata.Rd | 1 rsample-1.3.0/rsample/man/nested_cv.Rd | 24 rsample-1.3.0/rsample/man/permutations.Rd | 4 rsample-1.3.0/rsample/man/reg_intervals.Rd | 12 rsample-1.3.0/rsample/man/reshuffle_rset.Rd | 2 rsample-1.3.0/rsample/man/reverse_splits.Rd | 2 rsample-1.3.0/rsample/man/rolling_origin.Rd | 7 rsample-1.3.0/rsample/man/rsample2caret.Rd | 8 rsample-1.3.0/rsample/man/tidy.rsplit.Rd | 12 rsample-1.3.0/rsample/man/validation_set.Rd | 2 rsample-1.3.0/rsample/tests/testthat/_snaps/boot.md | 17 rsample-1.3.0/rsample/tests/testthat/_snaps/bootci.md | 224 ++- rsample-1.3.0/rsample/tests/testthat/_snaps/clustering.md | 48 rsample-1.3.0/rsample/tests/testthat/_snaps/form_pred.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/initial_validation_split.md | 4 rsample-1.3.0/rsample/tests/testthat/_snaps/labels.md | 34 rsample-1.3.0/rsample/tests/testthat/_snaps/make_strata.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/mc.md | 87 + rsample-1.3.0/rsample/tests/testthat/_snaps/misc.md | 163 -- rsample-1.3.0/rsample/tests/testthat/_snaps/nested_cv.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/permutations.md | 39 rsample-1.3.0/rsample/tests/testthat/_snaps/reg_intervals.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reshuffle_rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/reverse_splits.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rolling_origin.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rset.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/rsplit.md | 70 rsample-1.3.0/rsample/tests/testthat/_snaps/slide.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/validation_set.md | 1 rsample-1.3.0/rsample/tests/testthat/_snaps/validation_split.md |only rsample-1.3.0/rsample/tests/testthat/_snaps/vfold.md | 202 ++ rsample-1.3.0/rsample/tests/testthat/test-boot.R | 8 rsample-1.3.0/rsample/tests/testthat/test-bootci.R | 312 ++-- rsample-1.3.0/rsample/tests/testthat/test-caret.R | 405 +++-- rsample-1.3.0/rsample/tests/testthat/test-clustering.R | 31 rsample-1.3.0/rsample/tests/testthat/test-form_pred.R |only rsample-1.3.0/rsample/tests/testthat/test-initial_split.R |only rsample-1.3.0/rsample/tests/testthat/test-inner_split.R |only rsample-1.3.0/rsample/tests/testthat/test-labels.R | 16 rsample-1.3.0/rsample/tests/testthat/test-make_strata.R |only rsample-1.3.0/rsample/tests/testthat/test-mc.R | 44 rsample-1.3.0/rsample/tests/testthat/test-misc.R | 195 -- rsample-1.3.0/rsample/tests/testthat/test-nested_cv.R |only rsample-1.3.0/rsample/tests/testthat/test-permutations.R | 16 rsample-1.3.0/rsample/tests/testthat/test-reg_intervals.R |only rsample-1.3.0/rsample/tests/testthat/test-reshuffle_rset.R |only rsample-1.3.0/rsample/tests/testthat/test-reverse_splits.R |only rsample-1.3.0/rsample/tests/testthat/test-rolling_origin.R |only rsample-1.3.0/rsample/tests/testthat/test-rset.R | 31 rsample-1.3.0/rsample/tests/testthat/test-rsplit.R | 42 rsample-1.3.0/rsample/tests/testthat/test-slide.R | 72 rsample-1.3.0/rsample/tests/testthat/test-validation_split.R |only rsample-1.3.0/rsample/tests/testthat/test-vfold.R | 144 + rsample-1.3.0/rsample/vignettes/Applications/Intervals.Rmd | 2 rsample-1.3.0/rsample/vignettes/Common_Patterns.Rmd | 6 rsample-1.3.0/rsample/vignettes/Working_with_rsets.Rmd | 9 129 files changed, 2657 insertions(+), 2374 deletions(-)
Title: Friendly Input-Output Analysis
Description: Simplifies the process of importing and managing input-output
matrices from 'Microsoft Excel' into R, and provides a suite of functions for
analysis. It leverages the 'R6' class for clean, memory-efficient
object-oriented programming. Furthermore, all linear algebra computations are
implemented in 'Rust' to achieve highly optimized performance.
Author: Alberson da Silva Miranda [aut, cre, cph]
,
Celso Bissoli Sessa [dtc]
Maintainer: Alberson da Silva Miranda <albersonmiranda@hotmail.com>
Diff between fio versions 0.1.2 dated 2024-08-27 and 0.1.5 dated 2025-04-02
fio-0.1.2/fio/src/Makevars |only fio-0.1.2/fio/src/Makevars.ucrt |only fio-0.1.2/fio/src/Makevars.win |only fio-0.1.5/fio/DESCRIPTION | 14 fio-0.1.5/fio/MD5 | 52 +- fio-0.1.5/fio/NEWS.md | 16 fio-0.1.5/fio/R/extendr-wrappers.R | 1 fio-0.1.5/fio/R/import_iom.R | 2 fio-0.1.5/fio/R/r6.R | 91 ++-- fio-0.1.5/fio/README.md | 13 fio-0.1.5/fio/build/partial.rdb |binary fio-0.1.5/fio/build/vignette.rds |binary fio-0.1.5/fio/configure | 2 fio-0.1.5/fio/configure.win | 2 fio-0.1.5/fio/data/br_2020.rda |binary fio-0.1.5/fio/inst/doc/getting_started.html | 40 +- fio-0.1.5/fio/inst/extdata/iom/br/2020.xlsx |binary fio-0.1.5/fio/man/figures/example_leontief_inverse.png |binary fio-0.1.5/fio/man/import_element.Rd | 2 fio-0.1.5/fio/man/iom.Rd | 104 +++-- fio-0.1.5/fio/src/Makevars.in |only fio-0.1.5/fio/src/Makevars.win.in |only fio-0.1.5/fio/src/rust/Cargo.lock | 319 ++++++++++------- fio-0.1.5/fio/src/rust/Cargo.toml | 8 fio-0.1.5/fio/src/rust/src/lib.rs | 3 fio-0.1.5/fio/src/rust/vendor-config.toml | 5 fio-0.1.5/fio/src/rust/vendor.tar.xz |binary fio-0.1.5/fio/tests/testthat/test-computations.R | 13 fio-0.1.5/fio/tools/config.R |only fio-0.1.5/fio/tools/msrv.R | 4 30 files changed, 395 insertions(+), 296 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between AllelicSeries versions 0.1.1.2 dated 2024-11-23 and 0.1.1.5 dated 2025-04-02
DESCRIPTION | 10 - MD5 | 46 +++--- NAMESPACE | 2 NEWS.md | 3 R/allelic_series.R | 13 + R/generate_data.R | 17 ++ R/generate_sumstats.R | 15 +- R/input_checks.R | 1 R/utilities.R | 107 +++++++++++++++ build/vignette.rds |binary inst/doc/coast.R | 33 ++++ inst/doc/coast.Rmd | 48 ++++++ inst/doc/coast.html | 240 +++++++++++++++++++++------------- inst/doc/covariate_inference.R |only inst/doc/covariate_inference.Rmd |only inst/doc/covariate_inference.html |only man/AllelicSeries-package.Rd | 2 man/COAST.Rd | 4 man/CalcSumstats.Rd | 4 man/CollapseGeno.Rd |only man/ContainsInt.Rd |only man/DGP.Rd | 7 tests/testthat/test-allelic_series.R | 78 ++++++++++- tests/testthat/test-data_generation.R | 28 +++ tests/testthat/test-utils.R | 97 +++++++++++++ vignettes/coast.Rmd | 48 ++++++ vignettes/covariate_inference.Rmd |only 27 files changed, 675 insertions(+), 128 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.51 dated 2025-02-19 and 0.52 dated 2025-04-02
xfun-0.51/xfun/man/attr.Rd |only xfun-0.52/xfun/DESCRIPTION | 11 +-- xfun-0.52/xfun/MD5 | 64 ++++++++++---------- xfun-0.52/xfun/NAMESPACE | 3 xfun-0.52/xfun/NEWS.md | 18 +++++ xfun-0.52/xfun/R/algorithm.R |only xfun-0.52/xfun/R/cache.R | 13 +++- xfun-0.52/xfun/R/citation.R | 15 ++++ xfun-0.52/xfun/R/command.R | 11 --- xfun-0.52/xfun/R/data-structure.R | 2 xfun-0.52/xfun/R/image.R | 14 ---- xfun-0.52/xfun/R/io.R | 32 +++++++++- xfun-0.52/xfun/R/knitr.R | 17 ++++- xfun-0.52/xfun/R/markdown.R | 4 - xfun-0.52/xfun/R/packages.R | 2 xfun-0.52/xfun/R/record.R | 6 - xfun-0.52/xfun/R/utils.R | 14 +++- xfun-0.52/xfun/R/yaml.R | 17 +++-- xfun-0.52/xfun/build/vignette.rds |binary xfun-0.52/xfun/inst/doc/xfun.R | 6 - xfun-0.52/xfun/inst/doc/xfun.Rmd | 66 +------------------- xfun-0.52/xfun/inst/doc/xfun.html | 89 ++++++---------------------- xfun-0.52/xfun/man/attr2.Rd |only xfun-0.52/xfun/man/cache_exec.Rd | 4 + xfun-0.52/xfun/man/cache_rds.Rd | 11 +++ xfun-0.52/xfun/man/divide_chunk.Rd | 8 ++ xfun-0.52/xfun/man/pkg_bib.Rd | 10 ++- xfun-0.52/xfun/man/rand_unit.Rd |only xfun-0.52/xfun/man/upload_ftp.Rd | 6 - xfun-0.52/xfun/man/upload_imgur.Rd | 2 xfun-0.52/xfun/man/url_destination.Rd |only xfun-0.52/xfun/src/init.c | 2 xfun-0.52/xfun/src/rand_lcg.c |only xfun-0.52/xfun/tests/test-cran/test-utils.R | 6 - xfun-0.52/xfun/tests/test-cran/test-yaml.R | 4 + xfun-0.52/xfun/vignettes/xfun.Rmd | 66 +------------------- 36 files changed, 230 insertions(+), 293 deletions(-)
Title: Sample Size Calculation for Propensity Score Analysis
Description: Sample size calculations in causal inference with observational data are increasingly desired. This package is a tool to calculate sample size under prespecified power with minimal summary quantities needed.
Author: Bo Liu [aut, cre],
Xiaoxiao Zhou [ctb],
Fan Li [ctb]
Maintainer: Bo Liu <bl226@duke.edu>
Diff between PSpower versions 0.1.0 dated 2025-01-15 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 10 +- R/PSpower.R | 229 +++++++++++++++++++++++++--------------------------- R/util.R | 23 +---- man/PSpower.Rd | 29 ++---- man/plot.PSpower.Rd | 3 6 files changed, 143 insertions(+), 157 deletions(-)
Title: Tools for Summarising and Analysing Soundscape Data
Description: A variety of tools relevant to the analysis
of marine soundscape data. There are tools for downloading AIS (automatic identification system)
data from Marine Cadastre <https://hub.marinecadastre.gov>,
connecting AIS data to GPS coordinates, plotting summaries of various soundscape
measurements, and downloading relevant environmental variables (wind, swell height) from the
National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>.
Most tools were developed to work well with output from 'Triton' software, but can be adapted
to work with any similar measurements.
Author: Taiki Sakai [aut, cre],
Anne Simonis [ctb],
Shannon Rankin [ctb],
Megan McKenna [ctb],
Kaitlin Palmer [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMscapes versions 0.10.0 dated 2025-01-29 and 0.11.3 dated 2025-04-02
DESCRIPTION | 12 +- MD5 | 42 +++++---- NAMESPACE | 39 +++++++++ NEWS.md | 37 ++++++++ R/createOctaveLevel.R | 169 ++++++++++++--------------------------- R/evaluateDeployment.R |only R/evaluateRecordings.R |only R/formatEffort.R | 40 +++++++-- R/loadDetectionData.R | 128 ++++++++++++++++------------- R/loadMantaNc.R | 52 +++++++----- R/loadMultiscapeData.R | 13 +-- R/loadSoundscapeData.R | 109 ++++++++++++++++++++----- R/plotDetectionBoxplot.R | 6 + R/plotQAQC.R |only R/runQAQCReview.R |only R/utils.R | 13 ++- man/createOctaveLevel.Rd | 30 +++--- man/evaluateDeployment.Rd |only man/evaluateRecordings.Rd |only man/loadDetectionData.Rd | 11 +- man/loadMultiscapeData.Rd | 12 +- man/loadSoundscapeData.Rd | 7 + man/plotQAQC.Rd |only man/runQAQCReview.Rd |only tests/testthat/test-detection.R | 9 ++ tests/testthat/test-soundscape.R | 28 +++--- 26 files changed, 472 insertions(+), 285 deletions(-)
Title: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)
Description: This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tut [...truncated...]
Author: Matthew Mule [aut, cre] ,
Andrew Martins [aut] ,
John Tsang [pdr]
Maintainer: Matthew Mule <mattmule@gmail.com>
Diff between dsb versions 1.0.4 dated 2024-06-15 and 2.0.0 dated 2025-04-02
DESCRIPTION | 8 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 4 R/ModelNegativeADTnorm.r | 63 ++- R/dsb.r | 143 ++++---- README.md | 284 +++++++++------- build/vignette.rds |binary inst/doc/additional_topics.R | 22 - inst/doc/additional_topics.html | 356 ++++++++++----------- inst/doc/end_to_end_workflow.R | 36 +- inst/doc/end_to_end_workflow.html | 622 ++++++++++++++++++------------------- inst/doc/fastkm.R |only inst/doc/fastkm.Rmd |only inst/doc/fastkm.html |only inst/doc/no_empty_drops.R | 17 - inst/doc/no_empty_drops.Rmd | 12 inst/doc/no_empty_drops.html | 195 +++++------ inst/doc/understanding_dsb.R | 18 - inst/doc/understanding_dsb.html | 408 ++++++++++++------------ man/DSBNormalizeProtein.Rd | 47 +- man/ModelNegativeADTnorm.Rd | 11 man/figures/dsb_arguments.png |only man/figures/timingsfig2.png |only man/figures/vignette/compare.png |only man/figures/vignette/corr.png |only tests/testthat/test_dsb_function.R | 61 ++- vignettes/fastkm.Rmd |only vignettes/no_empty_drops.Rmd | 12 29 files changed, 1238 insertions(+), 1130 deletions(-)
Title: Parallel Numerical Derivatives, Gradients, Jacobians, and
Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations
can be calculated using the 'pnd' package with parallel capabilities and
optimal step-size selection to improve accuracy. These functions facilitate
efficient computation of derivatives, gradients, Jacobians, and Hessians,
allowing for more evaluations to reduce the mathematical and machine errors.
Designed for compatibility with the 'numDeriv' package,
which has not received updates in several years, it introduces advanced features
such as computing derivatives of arbitrary order, improving
the accuracy of Hessian approximations by avoiding repeated differencing,
and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between pnd versions 0.0.9 dated 2025-03-11 and 0.0.10 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 42 +++++----- NEWS.md | 1 R/gradient.R | 99 +++++++++++++------------ R/step-select.R | 118 +++++++++++++++--------------- R/zzz.R | 2 build/partial.rdb |binary inst/CITATION | 28 +++---- inst/doc/compatibility-with-numDeriv.html | 15 ++- inst/doc/fast-and-accurate.html | 7 + inst/doc/step-size-selection.html | 7 + man/GenD.Rd | 14 +++ man/Grad.Rd | 24 ++++-- man/Jacobian.Rd | 14 +++ man/checkDimensions.Rd | 6 + man/step.DV.Rd | 21 ++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-Grad.R | 14 +++ tests/testthat/test-Jacobian.R | 12 +++ tests/testthat/test-gradstep.R | 4 - tests/testthat/test-step.CR.R | 2 tests/testthat/test-step.DV.R | 9 +- 22 files changed, 262 insertions(+), 183 deletions(-)
Title: Methods for Penetrance Estimation in Family-Based Studies
Description: Implements statistical methods for estimating disease penetrance in
family-based studies. Penetrance refers to the probability of disease§
manifestation in individuals carrying specific genetic variants. The package
provides tools for age-specific penetrance estimation, handling missing data,
and accounting for ascertainment bias in family studies.
Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.
Author: Nicolas Kubista [aut, cre],
BayesMendel Lab [aut]
Maintainer: Nicolas Kubista <bmendel@jimmy.harvard.edu>
Diff between penetrance versions 0.1.0 dated 2025-03-03 and 0.1.1 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 14 +- R/helpers.R | 8 - R/mhChain.R | 187 ++++++++++++++++++++++++++--------- R/mhLoglikehood.r | 6 - R/penetranceMain.R | 277 ++++++++++++++++++++++++++++++++++++++++++----------- man/mhChain.Rd | 28 ++--- man/penetrance.Rd | 33 +++--- 8 files changed, 411 insertions(+), 148 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of
implementation can be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.2 dated 2024-12-07 and 3.0.3 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++++++-------- NAMESPACE | 4 ---- R/core_functions.R | 12 ------------ R/csi.R |only R/far.R |only R/nse.R |only R/pod.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/case_study.html | 4 ++-- inst/doc/introduction.html | 4 ++-- man/csi.Rd |only man/far.Rd |only man/nse.Rd |only man/pod.Rd |only man/reexports.Rd | 6 +----- 17 files changed, 24 insertions(+), 36 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.0 dated 2025-01-17 and 1.1 dated 2025-04-02
DESCRIPTION | 7 ++-- MD5 | 13 ++++--- NAMESPACE | 6 ++- R/diabetes.R |only R/main.R | 74 +++++++++++++++++++++++++++++++++++++-------- data |only man/create_kernel_plot.Rd | 14 ++++++-- man/diabetes.Rd |only tests/testthat/test-main.R | 27 +++++++++++++--- 9 files changed, 110 insertions(+), 31 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert
et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.
Author: Miika Ahdesmaki [aut, cre],
Konstantinos Fokianos [aut],
Korbinian Strimmer [aut]
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>
Diff between GeneCycle versions 1.1.5 dated 2021-01-05 and 1.1.6 dated 2025-04-02
CHANGES | 3 +++ DESCRIPTION | 26 ++++++++++++++++++++------ MD5 | 16 ++++++++-------- man/avpg.Rd | 2 +- man/dominant.freqs.Rd | 2 +- man/fisher.g.test.Rd | 2 +- man/is.constant.Rd | 2 +- man/periodogram.Rd | 2 +- man/robust.g.test.Rd | 2 +- 9 files changed, 37 insertions(+), 20 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-30 dated 2024-12-03 and 0.9-32 dated 2025-04-02
dbarts-0.9-30/dbarts/tests/testthat |only dbarts-0.9-30/dbarts/tests/testthat.R |only dbarts-0.9-32/dbarts/DESCRIPTION | 10 dbarts-0.9-32/dbarts/MD5 | 139 - dbarts-0.9-32/dbarts/R/A_class.R | 267 +- dbarts-0.9-32/dbarts/R/bart.R | 48 dbarts-0.9-32/dbarts/R/dbarts.R | 1333 +++++----- dbarts-0.9-32/dbarts/R/generics.R | 5 dbarts-0.9-32/dbarts/R/multipleAssignment.R | 1 dbarts-0.9-32/dbarts/R/partialDependence.R | 7 dbarts-0.9-32/dbarts/R/rbart.R | 14 dbarts-0.9-32/dbarts/build/vignette.rds |binary dbarts-0.9-32/dbarts/configure.ac | 2 dbarts-0.9-32/dbarts/inst/NEWS.Rd | 31 dbarts-0.9-32/dbarts/inst/doc/gibbs_sampler_mixture_model.pdf |binary dbarts-0.9-32/dbarts/inst/doc/working_with_saved_trees.pdf |binary dbarts-0.9-32/dbarts/inst/include/dbarts/R_C_interface.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/bartFit.hpp | 10 dbarts-0.9-32/dbarts/inst/include/dbarts/control.hpp | 99 dbarts-0.9-32/dbarts/inst/tinytest |only dbarts-0.9-32/dbarts/man/bart.Rd | 4 dbarts-0.9-32/dbarts/man/dbartsSampler-class.Rd | 20 dbarts-0.9-32/dbarts/src/R_C_interface.cpp | 31 dbarts-0.9-32/dbarts/src/R_interface.cpp | 12 dbarts-0.9-32/dbarts/src/R_interface_common.cpp | 2 dbarts-0.9-32/dbarts/src/R_interface_sampler.cpp | 50 dbarts-0.9-32/dbarts/src/R_interface_sampler.hpp | 8 dbarts-0.9-32/dbarts/src/crossvalidate.cpp | 4 dbarts-0.9-32/dbarts/src/dbarts/bartFit.cpp | 339 +- dbarts-0.9-32/dbarts/src/dbarts/tree.cpp | 14 dbarts-0.9-32/dbarts/src/dbarts/tree.hpp | 4 dbarts-0.9-32/dbarts/src/external/randomBase.c | 10 dbarts-0.9-32/dbarts/src/include/external/random.h | 2 dbarts-0.9-32/dbarts/src/include/misc/thread.h | 3 dbarts-0.9-32/dbarts/src/misc/hierarchicalThreadManager.c | 4 dbarts-0.9-32/dbarts/src/misc/partition_body.c | 79 dbarts-0.9-32/dbarts/src/misc/partition_neon.c | 39 dbarts-0.9-32/dbarts/src/rc/bounds.c | 71 dbarts-0.9-32/dbarts/tests/tinytest.R |only 39 files changed, 1653 insertions(+), 1019 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Data sets of the Spanish National Forest Inventory <https://www.miteco.gob.es/es/biodiversidad/servicios/banco-datos-naturaleza/informacion-disponible.html> are processed to compute tree metrics and statistics. Function metrics2Vol() controls most of the routines.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.4 dated 2021-09-20 and 0.4.1 dated 2025-04-02
DESCRIPTION | 30 ++++++++++++++++++++++++------ MD5 | 22 +++++++++++----------- NEWS | 14 +++++++++++++- R/nfiMetrics.R | 2 +- R/readNFI.R | 6 +++--- R/urlToTemp.R | 2 +- man/dbhMetric.Rd | 2 +- man/dendroMetrics.Rd | 16 ++++++++-------- man/metrics2Vol.Rd | 2 +- man/nfiMetrics.Rd | 4 ++-- man/readNFI.Rd | 20 ++++++++++---------- man/urlToTemp.Rd | 4 ++-- 12 files changed, 77 insertions(+), 47 deletions(-)
Title: 'shiny' App for National Accounts
Description: Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
Author: Muhammad Yaseen [aut, cre, cph]
,
Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakNAcc versions 0.1.0 dated 2024-11-11 and 0.3.0 dated 2025-04-02
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 6 ++++ README.md | 17 +++++++++-- inst/shinyapp/GNIConstant.RDS |binary inst/shinyapp/GNICurrent.RDS |binary inst/shinyapp/NAConstant.RDS |binary inst/shinyapp/NACurrent.RDS |binary inst/shinyapp/rsconnect/shinyapps.io/myaseen208/PakNAcc.dcf | 2 - inst/shinyapp/ui.R | 8 ++--- 10 files changed, 37 insertions(+), 20 deletions(-)
Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working with vector space models of semantics/distributional semantic models/word embeddings.
Originally built for LSA models (hence the name), but can be used for all such vector-based models.
For actually building a vector semantic space, use the package 'lsa' or other specialized software.
Downloadable semantic spaces can be found at <https://sites.google.com/site/fritzgntr/software-resources>.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>
Diff between LSAfun versions 0.7.1 dated 2023-11-17 and 0.8.1 dated 2025-04-02
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 2 ++ R/Predication.r | 13 +++++++------ R/centroid_analysis.r |only man/centroid_analysis.Rd |only 7 files changed, 28 insertions(+), 15 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.32 dated 2025-02-05 and 0.1.35 dated 2025-04-02
DESCRIPTION | 6 - MD5 | 8 + build/vignette.rds |binary src/core/isomorphism/foo.c |only src/core/isomorphism/lad.c | 136 ++++++++++++++++---------------- src/core/isomorphism/lad.c.org.20250205 |only 6 files changed, 76 insertions(+), 74 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both there 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [ctb]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>
Diff between dndR versions 2.0.0 dated 2024-04-26 and 3.0.0 dated 2025-04-02
DESCRIPTION | 27 +-- MD5 | 164 ++++++++++++---------- NEWS.md | 15 ++ R/ability_scores.R | 121 ++++++++-------- R/class_block.R | 120 ++++++++++------ R/cr_convert.R | 16 -- R/creature_list.R | 89 ++++++------ R/creature_text.R | 16 +- R/data-doc_creatures.R | 2 R/data-doc_monster-table.R | 2 R/data-doc_spells.R | 2 R/encounter_creator.R | 254 ++++++++++++++++++++++------------ R/mod_calc.R | 10 - R/monster_creator.R | 100 ++++++------- R/monster_stats.R | 21 +- R/npc_creator.R | 20 +- R/party_diagram.R | 131 +++++++++-------- R/pc_creator.R | 76 ++++++---- R/pc_level_calc.R | 18 -- R/probability_plot.R | 18 +- R/race_mods.R | 278 +++++++++++++++++++++++++------------- R/reference_functions.R | 6 R/reroll.R | 4 R/roll.R | 36 +++- R/spell_list.R | 19 +- R/spell_text.R | 16 +- R/xp_cost.R | 66 +++++---- R/xp_pool.R | 147 +++++++++++++------- README.md | 108 +------------- build/vignette.rds |binary data/creatures.rda |binary data/spells.rda |binary inst/doc/dndr_00_dice.html | 18 +- inst/doc/dndr_01_characters.html | 39 ++--- inst/doc/dndr_02_creatures.html | 50 ++++-- inst/doc/dndr_03_spells.html | 24 ++- inst/doc/dndr_04_encounters.R | 20 +- inst/doc/dndr_04_encounters.Rmd | 57 +++++-- inst/doc/dndr_04_encounters.html | 163 ++++++++++++++-------- inst/doc/dndr_05_visuals.html | 10 - inst/doc/dndr_99_dmg-vs-dndr.R | 5 inst/doc/dndr_99_dmg-vs-dndr.Rmd | 7 inst/doc/dndr_99_dmg-vs-dndr.html | 14 - man/ability_scores.Rd | 8 - man/class_block.Rd | 19 +- man/creature_list.Rd | 10 - man/creature_text.Rd | 8 - man/creatures.Rd | 2 man/dndR-package.Rd | 6 man/dnd_classes.Rd | 2 man/dnd_damage_types.Rd | 2 man/dnd_races.Rd | 2 man/encounter_creator.Rd | 26 +++ man/mod_calc.Rd | 2 man/monster_creator.Rd | 4 man/monster_stats.Rd | 8 + man/monster_table.Rd | 2 man/npc_creator.Rd | 2 man/party_diagram.Rd | 4 man/pc_creator.Rd | 23 +-- man/pc_level_calc.Rd | 2 man/probability_plot.Rd | 2 man/race_mods.Rd | 4 man/reroll.Rd | 4 man/roll.Rd | 6 man/spell_list.Rd | 9 - man/spell_text.Rd | 8 - man/spells.Rd | 2 man/xp_cost.Rd | 13 + man/xp_pool.Rd | 15 +- tests |only vignettes/dndr_04_encounters.Rmd | 57 +++++-- vignettes/dndr_99_dmg-vs-dndr.Rmd | 7 73 files changed, 1516 insertions(+), 1052 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.1.1 dated 2025-02-03 and 4.2.0 dated 2025-04-02
smooth-4.1.1/smooth/man/auto.ces.Rd |only smooth-4.1.1/smooth/man/auto.gum.Rd |only smooth-4.2.0/smooth/DESCRIPTION | 8 smooth-4.2.0/smooth/MD5 | 116 +++--- smooth-4.2.0/smooth/NAMESPACE | 2 smooth-4.2.0/smooth/NEWS | 11 smooth-4.2.0/smooth/R/RcppExports.R | 4 smooth-4.2.0/smooth/R/adam-ces.R |only smooth-4.2.0/smooth/R/adam-gum.R |only smooth-4.2.0/smooth/R/adam-sma.R | 2 smooth-4.2.0/smooth/R/adam.R | 383 +++++++++++++++------- smooth-4.2.0/smooth/R/adamGeneral.R | 43 ++ smooth-4.2.0/smooth/R/autoces.R | 283 +++++++--------- smooth-4.2.0/smooth/R/autogum.R | 288 +++++++--------- smooth-4.2.0/smooth/R/automsarima.R | 1 smooth-4.2.0/smooth/R/ces.R | 145 +------- smooth-4.2.0/smooth/R/es.R | 6 smooth-4.2.0/smooth/R/gum.R | 181 +--------- smooth-4.2.0/smooth/R/methods.R | 14 smooth-4.2.0/smooth/R/oes.R | 48 +- smooth-4.2.0/smooth/R/oesg.R | 79 ++-- smooth-4.2.0/smooth/R/smooth-package.R | 12 smooth-4.2.0/smooth/README.md | 2 smooth-4.2.0/smooth/build/partial.rdb |binary smooth-4.2.0/smooth/build/vignette.rds |binary smooth-4.2.0/smooth/inst/doc/adam.R | 6 smooth-4.2.0/smooth/inst/doc/adam.html | 228 ++++++------- smooth-4.2.0/smooth/inst/doc/ces.R | 11 smooth-4.2.0/smooth/inst/doc/ces.Rmd | 25 - smooth-4.2.0/smooth/inst/doc/ces.html | 137 +++---- smooth-4.2.0/smooth/inst/doc/es.R | 2 smooth-4.2.0/smooth/inst/doc/es.html | 18 - smooth-4.2.0/smooth/inst/doc/gum.R | 2 smooth-4.2.0/smooth/inst/doc/gum.Rmd | 2 smooth-4.2.0/smooth/inst/doc/gum.html | 137 ++----- smooth-4.2.0/smooth/inst/doc/oes.R | 7 smooth-4.2.0/smooth/inst/doc/oes.Rmd | 5 smooth-4.2.0/smooth/inst/doc/oes.html | 129 +++---- smooth-4.2.0/smooth/inst/doc/simulate.R | 2 smooth-4.2.0/smooth/inst/doc/simulate.Rmd | 4 smooth-4.2.0/smooth/inst/doc/simulate.html | 80 ++-- smooth-4.2.0/smooth/inst/doc/sma.html | 18 - smooth-4.2.0/smooth/inst/doc/smooth.html | 4 smooth-4.2.0/smooth/inst/doc/ssarima.R | 2 smooth-4.2.0/smooth/inst/doc/ssarima.html | 46 +- smooth-4.2.0/smooth/man/adam.Rd | 4 smooth-4.2.0/smooth/man/ces.Rd | 351 +++++++++----------- smooth-4.2.0/smooth/man/forecast.smooth.Rd | 7 smooth-4.2.0/smooth/man/gum.Rd | 352 ++++++++------------ smooth-4.2.0/smooth/man/msarima.Rd | 1 smooth-4.2.0/smooth/man/sim.ces.Rd | 8 smooth-4.2.0/smooth/man/smooth.Rd | 20 - smooth-4.2.0/smooth/src/RcppExports.cpp | 7 smooth-4.2.0/smooth/src/adamGeneral.cpp | 10 smooth-4.2.0/smooth/tests/testthat/test_ces.R | 30 - smooth-4.2.0/smooth/tests/testthat/test_gum.R | 28 - smooth-4.2.0/smooth/tests/testthat/test_ssarima.R | 2 smooth-4.2.0/smooth/vignettes/ces.Rmd | 25 - smooth-4.2.0/smooth/vignettes/gum.Rmd | 2 smooth-4.2.0/smooth/vignettes/oes.Rmd | 5 smooth-4.2.0/smooth/vignettes/simulate.Rmd | 4 61 files changed, 1563 insertions(+), 1786 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 2.20.4 dated 2025-03-15 and 2.21.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Consensus Clustering of Omic Data
Description: Procedures to perform consensus clustering starting from a dissimilarity matrix or a data matrix. It's allowed to select if the subsampling has to be by samples or features. In case of computational heavy load, the procedures can run in parallel.
Author: Stefano Maria Pagnotta [aut, cre, cph]
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>
Diff between yaConsensus versions 1.0 dated 2021-07-01 and 1.1 dated 2025-04-02
DESCRIPTION | 8 ++-- MD5 | 19 ++++++---- NAMESPACE | 7 ++- R/cut_k_leaves.R |only R/get_ecdf.R |only R/monti.R |only R/plot.yaConsensus.R | 78 +++++++++++++++++++++++++++++++++++-------- R/print.yaConsensus.R | 29 ++++++++------- R/reduce_dist.R |only R/summary.yaConsensus_plot.R | 6 +++ man/monti.Rd |only man/plot.yaConsensus.Rd | 15 ++++++-- man/yaConsensus.Rd | 2 - 13 files changed, 118 insertions(+), 46 deletions(-)
Title: Terrestrial Water Cycle
Description: An open-access tool/framework that constitutes the core functions
to analyze terrestrial water cycle data across various spatio-temporal scales.
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between twc versions 0.0.1 dated 2024-12-02 and 0.0.2 dated 2025-04-02
twc-0.0.1/twc/R/csi.R |only twc-0.0.1/twc/R/far.R |only twc-0.0.1/twc/R/pod.R |only twc-0.0.1/twc/man/csi.Rd |only twc-0.0.1/twc/man/far.Rd |only twc-0.0.1/twc/man/pod.Rd |only twc-0.0.2/twc/DESCRIPTION | 8 ++++---- twc-0.0.2/twc/MD5 | 18 +++++++----------- twc-0.0.2/twc/NAMESPACE | 8 +++++--- twc-0.0.2/twc/R/fldmean.R | 8 ++++++-- twc-0.0.2/twc/R/globals.R | 8 +++++--- twc-0.0.2/twc/R/rank_repres.R |only twc-0.0.2/twc/README.md | 2 +- twc-0.0.2/twc/man/rank_repres.Rd |only 14 files changed, 28 insertions(+), 24 deletions(-)
Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based
on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre, cph]
,
Frank Harrell [ctb]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between tbrf versions 0.1.5 dated 2020-04-09 and 0.1.6 dated 2025-04-02
tbrf-0.1.5/tbrf/tests/spelling.R |only tbrf-0.1.6/tbrf/DESCRIPTION | 18 tbrf-0.1.6/tbrf/MD5 | 40 tbrf-0.1.6/tbrf/NEWS.md | 8 tbrf-0.1.6/tbrf/R/tbr_binom.R | 2 tbrf-0.1.6/tbrf/R/tbr_gmean.R | 33 tbrf-0.1.6/tbrf/R/tbr_mean.R | 14 tbrf-0.1.6/tbrf/R/tbr_median.R | 14 tbrf-0.1.6/tbrf/R/tbr_sd.R | 2 tbrf-0.1.6/tbrf/R/tbr_sum.R | 2 tbrf-0.1.6/tbrf/README.md | 149 +-- tbrf-0.1.6/tbrf/build/vignette.rds |binary tbrf-0.1.6/tbrf/inst/CITATION |only tbrf-0.1.6/tbrf/inst/WORDLIST | 4 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.R | 2 tbrf-0.1.6/tbrf/inst/doc/intro_to_tbrf.html | 526 ++++++----- tbrf-0.1.6/tbrf/man/figures/README-tbr_hour-1.png |binary tbrf-0.1.6/tbrf/man/figures/README-tbr_threehour-1.png |binary tbrf-0.1.6/tbrf/man/gm_mean_ci.Rd | 16 tbrf-0.1.6/tbrf/man/mean_ci.Rd | 12 tbrf-0.1.6/tbrf/man/median_ci.Rd | 12 tbrf-0.1.6/tbrf/tests/testthat/test-internalStatsFunctions.R | 28 22 files changed, 510 insertions(+), 372 deletions(-)
Title: Access the City of Toronto Open Data Portal
Description: Access data from the "City of Toronto
Open Data Portal" (<https://open.toronto.ca>) directly from R.
Author: Sharla Gelfand [aut, cre],
City of Toronto [cph, fnd]
Maintainer: Sharla Gelfand <sharla.gelfand@gmail.com>
Diff between opendatatoronto versions 0.1.5 dated 2022-04-13 and 0.1.6 dated 2025-04-02
opendatatoronto-0.1.5/opendatatoronto/vignettes/articles/multiple_resources_purrr.Rmd |only opendatatoronto-0.1.6/opendatatoronto/DESCRIPTION | 8 opendatatoronto-0.1.6/opendatatoronto/LICENSE | 2 opendatatoronto-0.1.6/opendatatoronto/MD5 | 29 - opendatatoronto-0.1.6/opendatatoronto/NEWS.md | 4 opendatatoronto-0.1.6/opendatatoronto/R/utils.R | 2 opendatatoronto-0.1.6/opendatatoronto/README.md | 140 +++--- opendatatoronto-0.1.6/opendatatoronto/build/vignette.rds |binary opendatatoronto-0.1.6/opendatatoronto/inst/doc/intro-opendatatoronto.html | 216 +++++++++- opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-browse.R | 15 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-get_resource.R | 16 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-list_package_resources.R | 20 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-packages.R | 21 opendatatoronto-0.1.6/opendatatoronto/tests/testthat/test-utils.R | 7 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/opendatatoronto.Rmd | 4 opendatatoronto-0.1.6/opendatatoronto/vignettes/articles/spatial_data.Rmd | 87 ---- 16 files changed, 355 insertions(+), 216 deletions(-)
More information about opendatatoronto at CRAN
Permanent link
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-6 dated 2024-03-20 and 0.22-7 dated 2025-04-02
lattice-0.22-6/lattice/man/foo |only lattice-0.22-7/lattice/ChangeLog | 76 ++++++++++ lattice-0.22-7/lattice/DESCRIPTION | 8 - lattice-0.22-7/lattice/MD5 | 47 +++--- lattice-0.22-7/lattice/build/vignette.rds |binary lattice-0.22-7/lattice/data/barley.rda |binary lattice-0.22-7/lattice/data/environmental.rda |binary lattice-0.22-7/lattice/data/ethanol.rda |binary lattice-0.22-7/lattice/data/melanoma.rda |binary lattice-0.22-7/lattice/data/singer.rda |binary lattice-0.22-7/lattice/inst/doc/grid.pdf |binary lattice-0.22-7/lattice/inst/po/de/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary lattice-0.22-7/lattice/po/R-de.po | 30 ++- lattice-0.22-7/lattice/po/R-fr.po | 13 + lattice-0.22-7/lattice/po/R-it.po | 13 + lattice-0.22-7/lattice/po/R-ko.po | 13 + lattice-0.22-7/lattice/po/R-lattice.pot | 13 + lattice-0.22-7/lattice/po/R-pl.po | 17 +- lattice-0.22-7/lattice/tests/MASSch04.R | 6 lattice-0.22-7/lattice/tests/call.R | 2 lattice-0.22-7/lattice/tests/dataframe-methods.R | 2 lattice-0.22-7/lattice/tests/scales.R | 2 lattice-0.22-7/lattice/tests/temp.R | 6 lattice-0.22-7/lattice/tests/test.R | 12 - 25 files changed, 179 insertions(+), 81 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Camille Thabard [ctb] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.12.0 dated 2025-02-25 and 0.13.0 dated 2025-04-02
dimensio-0.12.0/dimensio/inst/examples/ex-envelopes.R |only dimensio-0.12.0/dimensio/inst/examples/ex-wrap.R |only dimensio-0.12.0/dimensio/man/viz_biplot.Rd |only dimensio-0.12.0/dimensio/man/wrap.Rd |only dimensio-0.13.0/dimensio/DESCRIPTION | 9 dimensio-0.13.0/dimensio/MD5 | 107 ++-- dimensio-0.13.0/dimensio/NEWS.md | 11 dimensio-0.13.0/dimensio/R/AllGenerics.R | 144 +++-- dimensio-0.13.0/dimensio/R/biplot.R | 55 +- dimensio-0.13.0/dimensio/R/ca.R | 19 dimensio-0.13.0/dimensio/R/dimensio-package.R | 2 dimensio-0.13.0/dimensio/R/export.R | 29 + dimensio-0.13.0/dimensio/R/pca.R | 4 dimensio-0.13.0/dimensio/R/pcoa.R | 8 dimensio-0.13.0/dimensio/R/plot.R | 33 + dimensio-0.13.0/dimensio/R/viz_ellipse.R | 80 +++ dimensio-0.13.0/dimensio/R/viz_hull.R | 75 ++- dimensio-0.13.0/dimensio/R/wrap_ellipses.R | 90 +++ dimensio-0.13.0/dimensio/R/wrap_hull.R | 38 + dimensio-0.13.0/dimensio/README.md | 4 dimensio-0.13.0/dimensio/inst/doc/pca.R | 20 dimensio-0.13.0/dimensio/inst/doc/pca.Rmd | 21 dimensio-0.13.0/dimensio/inst/doc/pca.html | 247 ++++------ dimensio-0.13.0/dimensio/inst/examples/ex-confidence.R |only dimensio-0.13.0/dimensio/inst/examples/ex-ellipses.R |only dimensio-0.13.0/dimensio/inst/examples/ex-hull.R |only dimensio-0.13.0/dimensio/inst/examples/ex-pcoa.R | 14 dimensio-0.13.0/dimensio/inst/examples/ex-plot.R | 2 dimensio-0.13.0/dimensio/inst/examples/ex-tolerance.R |only dimensio-0.13.0/dimensio/inst/tinytest/_snaps/pca_correlations.rds |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_contrib.svg | 200 ++++---- dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/CA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_col.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_biplot_sup_row.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_confidence.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_eig.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_hull.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quali.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_quanti.svg |only dimensio-0.13.0/dimensio/inst/tinytest/_tinysnapshot/PCOA_tolerance.svg |only dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_ca.R | 26 - dimensio-0.13.0/dimensio/inst/tinytest/test_biplot_pca.R | 18 dimensio-0.13.0/dimensio/inst/tinytest/test_ca.R | 1 dimensio-0.13.0/dimensio/inst/tinytest/test_pca.R | 4 dimensio-0.13.0/dimensio/inst/tinytest/test_pcoa.R | 34 + dimensio-0.13.0/dimensio/inst/tinytest/test_plot_ca.R | 2 dimensio-0.13.0/dimensio/inst/tinytest/test_plot_pca.R | 30 - dimensio-0.13.0/dimensio/man/PCOA-class.Rd | 14 dimensio-0.13.0/dimensio/man/biplot.Rd | 39 - dimensio-0.13.0/dimensio/man/ca.Rd | 12 dimensio-0.13.0/dimensio/man/dimensio-package.Rd | 2 dimensio-0.13.0/dimensio/man/export.Rd | 3 dimensio-0.13.0/dimensio/man/pcoa.Rd | 14 dimensio-0.13.0/dimensio/man/plot.Rd | 19 dimensio-0.13.0/dimensio/man/screeplot.Rd | 4 dimensio-0.13.0/dimensio/man/viz_confidence.Rd |only dimensio-0.13.0/dimensio/man/viz_contributions.Rd | 4 dimensio-0.13.0/dimensio/man/viz_ellipses.Rd | 115 ---- dimensio-0.13.0/dimensio/man/viz_hull.Rd |only dimensio-0.13.0/dimensio/man/viz_individuals.Rd | 6 dimensio-0.13.0/dimensio/man/viz_tolerance.Rd |only dimensio-0.13.0/dimensio/man/viz_variables.Rd | 6 dimensio-0.13.0/dimensio/vignettes/pca.Rmd | 21 67 files changed, 984 insertions(+), 602 deletions(-)
Title: Timing, Anatomical, Therapeutic and Chemical Based Medication
Clustering
Description: Agglomerative hierarchical clustering with a bespoke distance
measure based on medication similarities in the Anatomical Therapeutic
Chemical Classification System, medication timing and
medication amount or dosage. Tools for summarizing, illustrating and
manipulating the cluster objects are also available.
Author: Anna Laksafoss [aut, cre]
Maintainer: Anna Laksafoss <adls@ssi.dk>
Diff between tame versions 0.0.1 dated 2023-02-23 and 0.2.0 dated 2025-04-02
tame-0.0.1/tame/R/is.medic.R |only tame-0.0.1/tame/R/medic_helpers.R |only tame-0.0.1/tame/R/summary_helpers.R |only tame-0.0.1/tame/man/amounts.Rd |only tame-0.0.1/tame/man/frequencies.Rd |only tame-0.0.1/tame/man/interactions.Rd |only tame-0.0.1/tame/man/medications.Rd |only tame-0.0.1/tame/man/trajectories.Rd |only tame-0.0.1/tame/tests/testthat/test-medic_helpers.R |only tame-0.0.1/tame/tests/testthat/test-summary_helpers.R |only tame-0.2.0/tame/DESCRIPTION | 16 tame-0.2.0/tame/LICENSE | 4 tame-0.2.0/tame/MD5 | 84 - tame-0.2.0/tame/NAMESPACE | 70 + tame-0.2.0/tame/R/crop.R |only tame-0.2.0/tame/R/documenting_data.R | 6 tame-0.2.0/tame/R/employ.R | 202 ++-- tame-0.2.0/tame/R/enrich.R | 5 tame-0.2.0/tame/R/extractors.R | 37 tame-0.2.0/tame/R/medic-utils.R |only tame-0.2.0/tame/R/medic.R | 223 ++-- tame-0.2.0/tame/R/plot-utils.R |only tame-0.2.0/tame/R/plot.R |only tame-0.2.0/tame/R/summary-utils.R |only tame-0.2.0/tame/R/summary.R | 905 +++++++++++++++--- tame-0.2.0/tame/R/tame_package.R | 6 tame-0.2.0/tame/README.md | 23 tame-0.2.0/tame/man/cluster_frequency.Rd |only tame-0.2.0/tame/man/cluster_selector.Rd | 8 tame-0.2.0/tame/man/comedication_count.Rd |only tame-0.2.0/tame/man/construct_color_scales.Rd |only tame-0.2.0/tame/man/construct_plot_data.Rd |only tame-0.2.0/tame/man/construct_time_scale.Rd |only tame-0.2.0/tame/man/default_atc_groups.Rd |only tame-0.2.0/tame/man/employ.Rd | 2 tame-0.2.0/tame/man/enrich.Rd | 4 tame-0.2.0/tame/man/flatten_trajctories.Rd |only tame-0.2.0/tame/man/is.medic.Rd | 2 tame-0.2.0/tame/man/medic.Rd | 12 tame-0.2.0/tame/man/medication_frequency.Rd |only tame-0.2.0/tame/man/method_selector.Rd | 8 tame-0.2.0/tame/man/parameters_constructor.Rd | 6 tame-0.2.0/tame/man/plot_cluster_frequency.Rd |only tame-0.2.0/tame/man/plot_comedication_count.Rd |only tame-0.2.0/tame/man/plot_medication_frequency.Rd |only tame-0.2.0/tame/man/plot_summary.Rd |only tame-0.2.0/tame/man/plot_timing_atc_group.Rd |only tame-0.2.0/tame/man/plot_timing_trajectory.Rd |only tame-0.2.0/tame/man/print.summary.medic.Rd |only tame-0.2.0/tame/man/str.summary.medic.Rd |only tame-0.2.0/tame/man/summary.medic.Rd | 60 - tame-0.2.0/tame/man/summary_crop.Rd |only tame-0.2.0/tame/man/timing_atc_group.Rd |only tame-0.2.0/tame/man/timing_trajectory.Rd |only tame-0.2.0/tame/tests/testthat/test-RcppExports.R | 30 tame-0.2.0/tame/tests/testthat/test-enrich.R | 6 tame-0.2.0/tame/tests/testthat/test-extractors.R | 18 tame-0.2.0/tame/tests/testthat/test-ismedic.R | 6 tame-0.2.0/tame/tests/testthat/test-medic-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary-utils.R |only tame-0.2.0/tame/tests/testthat/test-summary.R | 6 61 files changed, 1261 insertions(+), 488 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.4.0 dated 2025-01-14 and 1.4.2 dated 2025-04-02
DESCRIPTION | 9 - MD5 | 36 ++-- NEWS.md | 10 + R/formantplot.R | 50 ++++- R/intensityplot.R | 45 ++++- R/pitchplot.R | 90 +++++++--- R/praatpicture.R | 44 +++- R/specplot.R | 74 ++++++-- R/tgplot.R | 55 +++++- R/waveplot.R | 34 ++- inst/shiny/shiny_praatpicture/rsconnect/shinyapps.io/rpuggaardrode/praatpicture.dcf | 2 inst/shiny/shiny_praatpicture/server.R | 18 +- inst/shiny/shiny_praatpicture/ui.R | 3 man/formantplot.Rd | 3 man/intensityplot.Rd | 3 man/pitchplot.Rd | 3 man/praatpicture.Rd | 25 ++ man/tgplot.Rd | 13 + man/waveplot.Rd | 3 19 files changed, 399 insertions(+), 121 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-1 dated 2023-12-20 and 1.9-2 dated 2025-04-02
ChangeLog | 81 + DESCRIPTION | 14 MD5 | 98 - NAMESPACE | 14 R/bam.r | 692 ++++++++----- R/efam.r | 854 ++++++++++++++-- R/fast-REML.r | 372 +++++-- R/gam.fit3.r | 55 - R/gam.fit4.r | 76 - R/gamlss.r | 207 ++-- R/mgcv.r | 488 ++++++--- R/misc.r | 87 + R/mvam.r | 8 R/plots.r | 24 R/smooth.r | 158 ++- build/partial.rdb |binary inst/CITATION | 18 man/NCV.Rd | 36 man/Sl.setup.Rd | 7 man/XWXd.Rd | 16 man/bam.Rd | 11 man/clog.Rd |only man/cpois.Rd |only man/family.mgcv.Rd | 9 man/gam.Rd | 2 man/gam.side.Rd | 2 man/gammals.Rd | 2 man/gevlss.Rd | 11 man/ldetS.Rd | 12 man/lp.Rd |only man/mchol.Rd |only man/mgcv-package.Rd | 2 man/mgcv-parallel.Rd | 6 man/mroot.Rd | 12 man/pcls.Rd | 3 man/predict.gam.Rd | 22 man/slanczos.Rd | 2 man/smooth.construct.gp.smooth.spec.Rd | 2 man/twlss.Rd | 12 src/Makevars | 3 src/discrete.c | 1697 +++++++++++++++++++++++++++++++-- src/gdi.c | 58 - src/init.c | 13 src/magic.c | 6 src/mat.c | 286 ++++- src/matrix.c | 201 --- src/mgcv.c | 153 -- src/mgcv.h | 59 - src/ncv.c | 16 src/qp.c | 125 ++ src/sparse.c | 1 src/tprs.c | 5 52 files changed, 4611 insertions(+), 1427 deletions(-)
Title: Estimation and Testing for a Lognormal-Pareto Mixture
Description: Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>
Diff between LNPar versions 1.1.0 dated 2025-03-24 and 1.1.1 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/dpareto.r | 42 +++++++++++++++++++++--------------------- build/partial.rdb |binary man/dpareto.Rd | 2 +- 6 files changed, 33 insertions(+), 33 deletions(-)
Title: Boltzmann Entropy for Spatial Data
Description: Calculates several entropy metrics for spatial data
inspired by Boltzmann's entropy formula.
It includes metrics introduced by Cushman for landscape mosaics
(Cushman (2015) <doi:10.1007/s10980-015-0305-2>),
and landscape gradients and point patterns
(Cushman (2021) <doi:10.3390/e23121616>); by Zhao and Zhang for
landscape mosaics (Zhao and Zhang (2019) <doi:10.1007/s10980-019-00876-x>);
and by Gao et al. for landscape gradients
(Gao et al. (2018) <doi:10.1111/tgis.12315>; Gao and Li (2019) <doi:10.1007/s10980-019-00854-3>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between bespatial versions 0.1.2 dated 2024-06-07 and 0.1.3 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/get_distance.R | 2 +- README.md | 12 +++++++----- build/partial.rdb |binary man/figures/README-unnamed-chunk-3-1.png |binary 6 files changed, 17 insertions(+), 15 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 3.5-0 dated 2024-11-07 and 3.6-0 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/java/SDMX.jar |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.0 dated 2025-03-19 and 1.0.1 dated 2025-04-02
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 84 R/estimateSurvival.R | 3356 +++++++++++++-------------- R/tableSurvival.R | 843 +++--- README.md | 2 inst/doc/a01_Single_event_of_interest.R | 12 inst/doc/a01_Single_event_of_interest.Rmd | 649 ++--- inst/doc/a01_Single_event_of_interest.html | 1436 +++++------ inst/doc/a02_Competing_risk_survival.html | 220 - inst/doc/a03_Further_survival_analyses.html | 22 man/CohortSurvival-package.Rd | 2 tests/testthat/test-reexports-omopgenerics.R | 32 tests/testthat/test-tableSurvival.R | 237 + vignettes/a01_Single_event_of_interest.Rmd | 649 ++--- 15 files changed, 3871 insertions(+), 3715 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Description: Tools designed to perform and evaluate cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
A test for seed sample heterogeneity is now available. Mantel's permutation test can be found in this package.
A new approach for calculating its power is implemented. biotools also contains tests for genetic covariance components.
Heuristic approaches for performing non-parametric spatial predictions of generic response variables and
spatial gene diversity are implemented.
Author: Anderson Rodrigo da Silva [aut, cre]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between biotools versions 4.2 dated 2021-08-07 and 4.3 dated 2025-04-02
DESCRIPTION | 11 MD5 | 55 +- NEWS | 11 README.md |only build/vignette.rds |binary inst/CITATION | 41 -- inst/doc/overview.R | 30 - inst/doc/overview.html | 946 ++++++++++++++++++++++++++++-------------------- man/D2.disc.Rd | 10 man/D2.dist.Rd | 2 man/aer.Rd | 2 man/biotools-package.Rd | 26 - man/confusionmatrix.Rd | 2 man/cov2pcov.Rd | 6 man/distClust.Rd | 2 man/findSubsample.Rd | 4 man/fitplotsize.Rd | 6 man/gencovtest.Rd | 38 - man/mantelPower.Rd | 8 man/mantelTest.Rd | 14 man/multcor.test.Rd | 8 man/mvpaircomp.Rd | 14 man/optimumplotsize.Rd | 6 man/raise.matrix.rd | 2 man/sHe.Rd | 22 - man/samplesize.Rd | 24 - man/singh.Rd | 2 man/spatialpred.Rd | 10 man/tocher.Rd | 18 29 files changed, 750 insertions(+), 570 deletions(-)
Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between BigDataPE versions 0.0.95 dated 2025-02-17 and 0.0.96 dated 2025-04-02
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only R/BigDataPE.R | 47 ++++++++++++++++++++++++++--------------------- README.md | 2 +- man/bdpe_fetch_chunks.Rd | 10 +++++----- man/bdpe_fetch_data.Rd | 12 ++++++------ 7 files changed, 48 insertions(+), 42 deletions(-)
Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut],
Patrick Miller [aut],
Alexander M. Schoemann [aut] ,
Terrence D. Jorgensen [aut, cre]
,
Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between simsem versions 0.5-16 dated 2021-03-28 and 0.5-17 dated 2025-04-02
DESCRIPTION | 18 +- MD5 | 63 ++++----- NAMESPACE | 4 R/analyze.R | 79 ++++++----- R/anova-methods.R | 312 ++++++++++++++++++++++++++--------------------- R/bind.R | 2 R/drawParam.R | 6 R/find.R | 158 ++++++++++++----------- R/generate.R | 6 R/getPowerCoverage.R | 83 ++++++------ R/imposeMissing.R | 4 R/miss.R | 88 +++++++------ R/model.R | 31 +++- R/openMx.R | 4 R/sim.R | 89 +++++++++---- R/summarySimResult.R | 15 +- inst/CITATION |only man/SimDataDist-class.Rd | 116 ++++++++--------- man/SimMissing-class.Rd | 114 ++++++++--------- man/SimResult-class.Rd | 244 ++++++++++++++++++------------------ man/analyze.Rd | 24 +-- man/createData.Rd | 208 +++++++++++++++---------------- man/exportData.Rd | 60 ++++----- man/findPower.Rd | 10 - man/getExtraOutput.Rd | 8 - man/likRatioFit.Rd | 4 man/miss.Rd | 26 +-- man/model.Rd | 54 ++++---- man/modelLavaan.Rd | 4 man/pValue.Rd | 2 man/pValueNested.Rd | 4 man/pValueNonNested.Rd | 4 man/sim.Rd | 24 +-- 33 files changed, 989 insertions(+), 879 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] ,
Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.11 dated 2025-01-10 and 0.3.12 dated 2025-04-02
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/nanotime.R | 2 +- build/vignette.rds |binary inst/doc/nanotime-introduction.pdf |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 1.1-0 dated 2025-01-26 and 1.2-0 dated 2025-04-02
Changelog | 6 + DESCRIPTION | 9 -- MD5 | 38 ++++---- NAMESPACE | 2 R/kmSRdiagram.R |only R/kmbasisdiagram.R | 4 R/kmhasse.R | 4 R/kmsrvalidate.R |only R/kmsurmisefunction.R | 3 R/kmvalidate.R | 2 R/xpl.R | 11 +- build/vignette.rds |binary data/xpl.rda |binary inst/doc/kstMatrix.html | 210 +++++++++++++++++++----------------------------- man/kmSRdiagram.Rd |only man/kmSRvalidate.Rd |only man/kmbasisdiagram.Rd | 5 - man/kmdist.Rd | 1 man/kmhasse.Rd | 5 - man/kmvalidate.Rd | 3 man/xpl.Rd | 11 +- src/basis.c | 2 22 files changed, 144 insertions(+), 172 deletions(-)
Title: Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to
apply generalized additive models to bivariate dependence structures and
non-simplified vine copulas.
Author: Thomas Nagler [aut],
Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>
Diff between gamCopula versions 0.0-7 dated 2020-02-05 and 0.0-8 dated 2025-04-02
DESCRIPTION | 11 - MD5 | 87 ++++---- NEWS.md | 40 ++- R/AllClasses.R | 7 R/gamBiCop.R | 22 +- R/gamBiCopCDF.R | 2 R/gamBiCopFit.R | 6 R/gamBiCopPDF.R | 2 R/gamBiCopPredict.R | 6 R/gamBiCopSelect.R | 8 R/gamBiCopSimulate.R | 2 R/gamCopula-package.R |only R/gamVine.R | 19 - R/gamVineCopSelect.R | 4 R/gamVinePDF.R | 2 R/gamVineSeqFit.R | 2 R/gamVineStructureSelect.R | 2 R/utilsFamilies.R | 3 R/utilsPrivate.R | 4 R/utilsPublic.R | 11 - README.md | 110 +++++----- man/BiCopEta2Par.Rd | 5 man/BiCopPar2Eta.Rd | 6 man/EDF.gamBiCop-methods.Rd | 2 man/RVM2GVC.Rd | 6 man/formula.gamBiCop-methods.Rd | 6 man/gamBiCop-class.Rd | 4 man/gamBiCop.Rd | 4 man/gamBiCopCDF.Rd | 2 man/gamBiCopFit.Rd | 6 man/gamBiCopPDF.Rd | 2 man/gamBiCopPredict.Rd | 6 man/gamBiCopSelect.Rd | 6 man/gamBiCopSimulate.Rd | 2 man/gamCopula-package.Rd | 409 ++++++++++++++++++++-------------------- man/gamVine-class.Rd | 3 man/gamVine.Rd | 2 man/gamVineCopSelect.Rd | 4 man/gamVinePDF.Rd | 2 man/gamVineSeqFit.Rd | 2 man/gamVineStructureSelect.Rd | 2 man/plot.gamBiCop-methods.Rd | 6 man/plot.gamVine-methods.Rd | 6 man/summary.gamBiCop-methods.Rd | 4 man/summary.gamVine-methods.Rd | 4 45 files changed, 433 insertions(+), 418 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut],
Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.4 dated 2025-02-15 and 0.1.41 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/TDAvec_vignette.html | 7 ++++--- man/computePersistenceLandscape.Rd | 14 ++++++++------ src/PersistenceLandscape.cpp | 30 ++++++++++++++++-------------- 6 files changed, 36 insertions(+), 31 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.2.0 dated 2025-01-10 and 3.2.1 dated 2025-04-02
DESCRIPTION | 35 ++-- MD5 | 44 ++--- NEWS.md | 4 R/AllGenerics.R | 28 ++- R/tabula-package.R | 2 README.md | 13 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/alpha.Rmd | 1 inst/doc/alpha.html | 282 ++++++++++++++++------------------- inst/doc/beta.Rmd | 1 inst/doc/beta.html | 225 ++++++++++++--------------- inst/tinytest/test_index.R | 14 - man/figures/README-sample-size-1.png |binary man/figures/README-sample-size-2.png |binary man/index_bray.Rd | 2 man/index_jaccard.Rd | 4 man/index_sorenson.Rd | 8 man/similarity.Rd | 18 +- man/tabula-package.Rd | 6 vignettes/alpha.Rmd | 1 vignettes/beta.Rmd | 1 23 files changed, 328 insertions(+), 363 deletions(-)
Title: Conditional Process Analysis (CPA) via SEM Approach
Description: Utilizes the Reliability-Adjusted Product Indicator (RAPI) method to
estimate effects among latent variables, thus allowing for more precise definition and analysis of
mediation and moderation models. Our simulation studies reveal that while 'silp' may exhibit
instability with smaller sample sizes and lower reliability scores (e.g., N = 100, 'omega' = 0.7),
implementing nearest positive definite matrix correction and bootstrap confidence interval
estimation can significantly ameliorate this volatility. When these adjustments are applied,
'silp' achieves estimations akin in quality to those derived from LMS. In conclusion, the 'silp'
package is a valuable tool for researchers seeking to explore complex relational structures between
variables without resorting to commercial software.
Cheung et al.(2021)<doi:10.1007/s10869-020-09717-0>
Hsiao et al.(2018)<doi:10.1177/0013164416679877>.
Author: Yi-Hsuan Tseng [aut, cre],
Po-Hsien Huang [aut]
Maintainer: Yi-Hsuan Tseng <r12227115@g.ntu.edu.tw>
Diff between silp versions 1.0.1 dated 2025-03-11 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ R/resilp.R | 2 ++ R/silp.R | 5 ++--- R/utility.R | 4 ++-- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
,
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 2.1.0 dated 2024-01-15 and 2.1.2 dated 2025-04-02
DESCRIPTION | 8 MD5 | 276 ++++---- NAMESPACE | 190 ++--- NEWS | 153 ++-- R/LawTable.R | 220 +++--- R/LifeTable.R | 1162 +++++++++++++++++------------------ R/MortalityLaw_S3.R | 342 +++++----- R/MortalityLaw_check.R | 98 +- R/MortalityLaw_main.R | 824 ++++++++++++------------ R/MortalityLaw_models.R | 1094 ++++++++++++++++---------------- R/MortalityLaws-data.R | 92 +- R/MortalityLaws-package.R | 48 - R/availableHMD.R | 155 ++-- R/availableLF.R | 120 +-- R/availableLaws.R | 428 ++++++------ R/convertFx.R | 172 ++--- R/graphics.R | 336 +++++----- R/readAHMD.R | 393 +++++------ R/readCHMD.R | 502 +++++++-------- R/readHMD.R | 800 ++++++++++++------------ R/readJMD.R | 550 ++++++++-------- R/utils.R | 98 +- R/zzz.R | 18 README.md | 98 +- THANKS | 28 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Installation.R | 24 inst/doc/Installation.Rmd | 122 +-- inst/doc/Installation.pdf |binary inst/doc/Intro.R | 236 +++---- inst/doc/Intro.Rmd | 486 +++++++------- inst/doc/Intro.pdf |binary man/AHMD_sample.Rd | 42 - man/AIC.MortalityLaw.Rd | 36 - man/AUSregions.Rd | 30 man/CANregions.Rd | 30 man/CHMD_sample.Rd | 42 - man/HMD_sample.Rd | 42 - man/HMDcountries.Rd | 30 man/HMDindices.Rd | 30 man/HP.Rd | 48 - man/HP2.Rd | 48 - man/HP3.Rd | 48 - man/HP4.Rd | 48 - man/JMD_sample.Rd | 42 - man/JPNregions.Rd | 30 man/LawTable.Rd | 234 +++---- man/LifeTable.check.Rd | 36 - man/LifeTable.core.Rd | 92 +- man/MortalityLaw.Rd | 314 ++++----- man/MortalityLaws.Rd | 62 - man/ReadAHMD.Rd | 249 +++---- man/ReadCHMD.Rd | 250 +++---- man/ReadHMD.Rd | 274 ++++---- man/ReadHMD.core.Rd | 114 +-- man/ReadJMD.Rd | 262 +++---- man/addDetails.Rd | 58 - man/ageMsg.Rd | 36 - man/ahmd.Rd | 62 - man/availableHMD.Rd | 60 - man/availableLF.Rd | 52 - man/availableLaws.Rd | 227 +++--- man/beard.Rd | 48 - man/beard_makeham.Rd | 48 - man/bring_parameters.Rd | 46 - man/carriere1.Rd | 48 - man/carriere2.Rd | 48 - man/check.MortalityLaw.Rd | 36 - man/check_input_ReadAHMD.Rd | 36 - man/check_input_ReadCHMD.Rd | 36 - man/check_input_ReadHMD.Rd | 36 - man/check_input_ReadJMD.Rd | 36 - man/choose_optim.Rd | 36 - man/coale.demeny.ax.Rd | 70 +- man/compute.ax.Rd | 46 - man/convertFx.Rd | 126 +-- man/data_format.Rd | 30 man/deviance.MortalityLaw.Rd | 36 - man/df.residual.MortalityLaw.Rd | 36 - man/dx_lx.Rd | 40 - man/find.my.case.Rd | 62 - man/ggompertz.Rd | 48 - man/gompertz.Rd | 48 - man/gompertz0.Rd | 48 - man/head_tail.Rd | 60 - man/invgompertz.Rd | 50 - man/invweibull.Rd | 54 - man/kannisto.Rd | 48 - man/kannisto_makeham.Rd | 48 - man/kostaki.Rd | 48 - man/logLik.MortalityLaw.Rd | 36 - man/make_http_request.Rd | 36 - man/makeham.Rd | 48 - man/makeham0.Rd | 48 - man/martinelle.Rd | 48 - man/mx_qx.Rd | 50 - man/objective_fun.Rd | 82 +- man/opperman.Rd | 48 - man/perks.Rd | 48 - man/plot.MortalityLaw.Rd | 58 - man/predict.MortalityLaw.Rd | 76 +- man/print.MortalityLaw.Rd | 40 - man/print.ReadAHMD.Rd | 40 - man/print.ReadCHMD.Rd | 40 - man/print.ReadHMD.Rd | 40 - man/print.ReadJMD.Rd | 40 - man/print.availableLF.Rd | 40 - man/print.availableLaws.Rd | 40 - man/print.summary.MortalityLaw.Rd | 40 - man/quadratic.Rd | 48 - man/rogersplanck.Rd | 48 - man/saveMsg.Rd | 30 man/saveOutput.Rd | 42 - man/scale_x.Rd | 36 - man/siler.Rd | 48 - man/strehler_mildvan.Rd | 48 - man/substrRight.Rd | 40 - man/summary.MortalityLaw.Rd | 44 - man/thiele.Rd | 48 - man/uxAbove100.Rd | 54 - man/vandermaen.Rd | 48 - man/vandermaen2.Rd | 48 - man/weibull.Rd | 56 - man/wittstein.Rd | 48 - tests/testthat.R | 20 tests/testthat/test_LawTable.R | 64 - tests/testthat/test_LifeTable.R | 402 ++++++------ tests/testthat/test_MortalityLaws.R | 338 +++++----- tests/testthat/test_MortalityLaws2.R | 478 +++++++------- tests/testthat/test_ReadAHMD.R | 100 +-- tests/testthat/test_ReadCHMD.R | 100 +-- tests/testthat/test_ReadHMD.R | 186 ++--- tests/testthat/test_ReadJMD.R | 108 +-- tests/testthat/test_availableX.R | 56 - tests/testthat/test_convertFx.R | 124 +-- vignettes/Installation.Rmd | 122 +-- vignettes/Intro.Rmd | 486 +++++++------- vignettes/Mlaw_Refrences.bib | 420 ++++++------ 139 files changed, 8974 insertions(+), 8967 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] ,
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between clustvarsel versions 2.3.4 dated 2020-12-16 and 2.3.5 dated 2025-04-02
DESCRIPTION | 14 MD5 | 29 - NEWS.md | 5 R/clvarselgrbkw.R | 12 R/clvarselgrfwd.R | 42 + R/clvarselhlfwd.R | 16 README.md | 4 build/vignette.rds |binary inst/CITATION | 34 - inst/doc/clustvarsel.R | 422 +++++++++---------- inst/doc/clustvarsel.Rmd | 2 inst/doc/clustvarsel.html | 959 +++++++++++++++++++++++++++++---------------- man/clustvarsel.Rd | 6 vignettes/clustvarsel.Rmd | 2 vignettes/vignette.css | 39 - vignettes/vignette_old.css |only 16 files changed, 958 insertions(+), 628 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb],
Roger Bivand [ctb] ,
Andrew Brown [ctb],
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-29 dated 2025-02-26 and 1.8-42 dated 2025-04-02
terra-1.8-29/terra/R/plot_legend.R |only terra-1.8-29/terra/src/Makevars.win |only terra-1.8-42/terra/DESCRIPTION | 10 terra-1.8-42/terra/MD5 | 891 ++--- terra-1.8-42/terra/NAMESPACE | 2 terra-1.8-42/terra/NEWS.md | 44 terra-1.8-42/terra/R/Aclasses.R | 315 - terra-1.8-42/terra/R/Agenerics.R | 6 terra-1.8-42/terra/R/Arith_generics.R | 1534 ++++---- terra-1.8-42/terra/R/RGB.R | 458 +- terra-1.8-42/terra/R/RcppExports.R | 4 terra-1.8-42/terra/R/SpatRasterDataset.R | 871 ++-- terra-1.8-42/terra/R/SpatVectorCollection.R | 336 - terra-1.8-42/terra/R/Zdeprecated.R | 138 terra-1.8-42/terra/R/aggregate.R | 654 +-- terra-1.8-42/terra/R/animate.R | 64 terra-1.8-42/terra/R/app.R | 688 +-- terra-1.8-42/terra/R/approximate.R | 126 terra-1.8-42/terra/R/arith.R | 74 terra-1.8-42/terra/R/autocor.R | 408 +- terra-1.8-42/terra/R/cells.R | 194 - terra-1.8-42/terra/R/clean.R | 140 terra-1.8-42/terra/R/click.R | 318 - terra-1.8-42/terra/R/clip.R | 84 terra-1.8-42/terra/R/coerce.R | 1529 ++++---- terra-1.8-42/terra/R/colors.R | 194 - terra-1.8-42/terra/R/connect.R | 162 terra-1.8-42/terra/R/crosstab.R | 168 terra-1.8-42/terra/R/crs.R | 784 ++-- terra-1.8-42/terra/R/dimensions.R | 414 +- terra-1.8-42/terra/R/distance.R | 607 +-- terra-1.8-42/terra/R/draw.R | 176 - terra-1.8-42/terra/R/expand.R | 126 terra-1.8-42/terra/R/extent.R | 746 ++-- terra-1.8-42/terra/R/extract.R | 1195 +++--- terra-1.8-42/terra/R/extract_single.R | 612 +-- terra-1.8-42/terra/R/focal.R | 1714 ++++----- terra-1.8-42/terra/R/focalMat.R | 148 terra-1.8-42/terra/R/gcp.R | 90 terra-1.8-42/terra/R/gdal.R | 362 +- terra-1.8-42/terra/R/generics.R | 2621 +++++++-------- terra-1.8-42/terra/R/geocolors.R | 22 terra-1.8-42/terra/R/geom.R | 1625 ++++----- terra-1.8-42/terra/R/graticule.R | 452 +- terra-1.8-42/terra/R/hist.R | 212 - terra-1.8-42/terra/R/ifelse.R | 102 terra-1.8-42/terra/R/image.R | 54 terra-1.8-42/terra/R/init.R | 84 terra-1.8-42/terra/R/inset.R | 252 - terra-1.8-42/terra/R/interpolate.R | 154 terra-1.8-42/terra/R/k_means.R | 126 terra-1.8-42/terra/R/lapp.R | 650 +-- terra-1.8-42/terra/R/layerCor.R | 396 +- terra-1.8-42/terra/R/levels.R | 1015 ++--- terra-1.8-42/terra/R/lines.R | 322 - terra-1.8-42/terra/R/makeVRT.R | 244 - terra-1.8-42/terra/R/match.R | 126 terra-1.8-42/terra/R/math.R | 240 - terra-1.8-42/terra/R/merge.R | 154 terra-1.8-42/terra/R/mergeTime.R | 208 - terra-1.8-42/terra/R/messages.R | 156 terra-1.8-42/terra/R/names.R | 548 +-- terra-1.8-42/terra/R/ncdf.R | 1214 +++--- terra-1.8-42/terra/R/options.R | 433 +- terra-1.8-42/terra/R/panel.R | 222 - terra-1.8-42/terra/R/plotExtent.R | 76 terra-1.8-42/terra/R/plotRGB.R | 146 terra-1.8-42/terra/R/plot_2rasters.R | 404 +- terra-1.8-42/terra/R/plot_add.R |only terra-1.8-42/terra/R/plot_axes.R | 396 +- terra-1.8-42/terra/R/plot_cartogram.R | 44 terra-1.8-42/terra/R/plot_helper.R |only terra-1.8-42/terra/R/plot_legend_classes.R |only terra-1.8-42/terra/R/plot_legend_continuous.R |only terra-1.8-42/terra/R/plot_let.R | 16 terra-1.8-42/terra/R/plot_raster.R | 1907 ++++------ terra-1.8-42/terra/R/plot_scale.R | 562 +-- terra-1.8-42/terra/R/plot_vector.R | 1626 ++++----- terra-1.8-42/terra/R/predict.R | 541 +-- terra-1.8-42/terra/R/princomp.R | 88 terra-1.8-42/terra/R/rapp.R | 152 terra-1.8-42/terra/R/rast.R | 1203 +++--- terra-1.8-42/terra/R/rasterize.R | 731 ++-- terra-1.8-42/terra/R/rasterizeWin.R | 734 ++-- terra-1.8-42/terra/R/readsvg.R | 152 terra-1.8-42/terra/R/regress.R | 350 +- terra-1.8-42/terra/R/relate.R | 830 ++-- terra-1.8-42/terra/R/replace.R | 606 +-- terra-1.8-42/terra/R/replace_layer.R | 264 - terra-1.8-42/terra/R/replace_values.R | 732 ++-- terra-1.8-42/terra/R/roll.R | 148 terra-1.8-42/terra/R/rowSums.R | 186 - terra-1.8-42/terra/R/sample.R | 2010 +++++------ terra-1.8-42/terra/R/select.R | 92 terra-1.8-42/terra/R/selectHigh.R | 24 terra-1.8-42/terra/R/show.R | 29 terra-1.8-42/terra/R/spatDF.R | 194 - terra-1.8-42/terra/R/subset.R | 614 +-- terra-1.8-42/terra/R/tags.R | 448 +- terra-1.8-42/terra/R/tapp.R | 380 +- terra-1.8-42/terra/R/tempfiles.R | 138 terra-1.8-42/terra/R/tiles.R | 282 - terra-1.8-42/terra/R/time.R | 774 ++-- terra-1.8-42/terra/R/twoClasses.R | 152 terra-1.8-42/terra/R/update.R | 22 terra-1.8-42/terra/R/values.R | 1172 +++--- terra-1.8-42/terra/R/vect.R | 1066 +++--- terra-1.8-42/terra/R/watershed.R | 88 terra-1.8-42/terra/R/window.R | 68 terra-1.8-42/terra/R/wrap.R | 1038 ++--- terra-1.8-42/terra/R/write.R | 378 +- terra-1.8-42/terra/R/xapp.R | 144 terra-1.8-42/terra/R/xyRowColCell.R | 468 +- terra-1.8-42/terra/R/zonal.R | 1150 +++--- terra-1.8-42/terra/R/zoom.R | 100 terra-1.8-42/terra/R/zzz.R | 121 terra-1.8-42/terra/build/partial.rdb |binary terra-1.8-42/terra/configure | 693 ++- terra-1.8-42/terra/configure.ac | 80 terra-1.8-42/terra/inst/ex/test.grd | 52 terra-1.8-42/terra/inst/tinytest/test_aggregate.R | 26 terra-1.8-42/terra/inst/tinytest/test_arith.R | 14 terra-1.8-42/terra/inst/tinytest/test_cats.R | 118 terra-1.8-42/terra/inst/tinytest/test_classify.R | 48 terra-1.8-42/terra/inst/tinytest/test_crds.R | 14 terra-1.8-42/terra/inst/tinytest/test_crop.R | 58 terra-1.8-42/terra/inst/tinytest/test_equal.R | 32 terra-1.8-42/terra/inst/tinytest/test_extent.R | 6 terra-1.8-42/terra/inst/tinytest/test_extract.R | 470 +- terra-1.8-42/terra/inst/tinytest/test_flowAccumulation.R | 68 terra-1.8-42/terra/inst/tinytest/test_focal.R | 164 terra-1.8-42/terra/inst/tinytest/test_geom.R | 44 terra-1.8-42/terra/inst/tinytest/test_global.R | 22 terra-1.8-42/terra/inst/tinytest/test_matrix-input.R | 102 terra-1.8-42/terra/inst/tinytest/test_merge.R | 46 terra-1.8-42/terra/inst/tinytest/test_multivariate.R | 24 terra-1.8-42/terra/inst/tinytest/test_patches.R | 66 terra-1.8-42/terra/inst/tinytest/test_pitfinder.R | 104 terra-1.8-42/terra/inst/tinytest/test_plot.R | 10 terra-1.8-42/terra/inst/tinytest/test_raster-vector.R | 124 terra-1.8-42/terra/inst/tinytest/test_rasterize.R | 16 terra-1.8-42/terra/inst/tinytest/test_rds.R | 18 terra-1.8-42/terra/inst/tinytest/test_replace.R | 50 terra-1.8-42/terra/inst/tinytest/test_tags.R |only terra-1.8-42/terra/inst/tinytest/test_time.R | 8 terra-1.8-42/terra/inst/tinytest/test_vect-geom.R | 28 terra-1.8-42/terra/inst/tinytest/test_vector-subset.R | 34 terra-1.8-42/terra/inst/tinytest/test_weighted-mean.R | 32 terra-1.8-42/terra/inst/tinytest/test_window.R | 64 terra-1.8-42/terra/inst/tinytest/test_wkt_grd.R | 34 terra-1.8-42/terra/inst/tinytest/test_zonal.R | 48 terra-1.8-42/terra/inst/tinytest/tinytest.R | 8 terra-1.8-42/terra/man/NAflag.Rd | 92 terra-1.8-42/terra/man/NIPD.Rd | 196 - terra-1.8-42/terra/man/RGB.Rd | 168 terra-1.8-42/terra/man/SpatExtent-class.Rd | 70 terra-1.8-42/terra/man/SpatRaster-class.Rd | 90 terra-1.8-42/terra/man/SpatVector-class.Rd | 60 terra-1.8-42/terra/man/activeCat.Rd | 100 terra-1.8-42/terra/man/add.Rd | 86 terra-1.8-42/terra/man/add_mtext.Rd | 72 terra-1.8-42/terra/man/aggregate.Rd | 158 terra-1.8-42/terra/man/align.Rd | 92 terra-1.8-42/terra/man/all.equal.Rd | 114 terra-1.8-42/terra/man/animate.Rd | 88 terra-1.8-42/terra/man/app.Rd | 184 - terra-1.8-42/terra/man/approximate.Rd | 124 terra-1.8-42/terra/man/arith-generic.Rd | 156 terra-1.8-42/terra/man/as.character.Rd | 78 terra-1.8-42/terra/man/as.data.frame.Rd | 96 terra-1.8-42/terra/man/as.lines.Rd | 130 terra-1.8-42/terra/man/as.list.Rd | 102 terra-1.8-42/terra/man/as.points.Rd | 112 terra-1.8-42/terra/man/as.polygons.Rd | 114 terra-1.8-42/terra/man/as.raster.Rd | 76 terra-1.8-42/terra/man/atan2.Rd | 84 terra-1.8-42/terra/man/autocor.Rd | 156 terra-1.8-42/terra/man/barplot.Rd | 92 terra-1.8-42/terra/man/bestMatch.Rd | 132 terra-1.8-42/terra/man/boundaries.Rd | 88 terra-1.8-42/terra/man/box.Rd | 60 terra-1.8-42/terra/man/boxplot.Rd | 126 terra-1.8-42/terra/man/buffer.Rd | 134 terra-1.8-42/terra/man/c.Rd | 130 terra-1.8-42/terra/man/cartogram.Rd | 84 terra-1.8-42/terra/man/catalyze.Rd | 108 terra-1.8-42/terra/man/cellSize.Rd | 120 terra-1.8-42/terra/man/cells.Rd | 154 terra-1.8-42/terra/man/centroids.Rd | 66 terra-1.8-42/terra/man/clamp.Rd | 88 terra-1.8-42/terra/man/clamp_ts.Rd | 96 terra-1.8-42/terra/man/classify.Rd | 196 - terra-1.8-42/terra/man/click.Rd | 120 terra-1.8-42/terra/man/coerce.Rd | 136 terra-1.8-42/terra/man/collapse.Rd | 78 terra-1.8-42/terra/man/colors.Rd | 118 terra-1.8-42/terra/man/compare-generics.Rd | 200 - terra-1.8-42/terra/man/compareGeom.Rd | 126 terra-1.8-42/terra/man/concats.Rd | 104 terra-1.8-42/terra/man/contour.Rd | 140 terra-1.8-42/terra/man/convhull.Rd | 118 terra-1.8-42/terra/man/costDist.Rd | 116 terra-1.8-42/terra/man/cover.Rd | 134 terra-1.8-42/terra/man/crds.Rd | 120 terra-1.8-42/terra/man/crop.Rd | 168 terra-1.8-42/terra/man/crosstab.Rd | 104 terra-1.8-42/terra/man/crs.Rd | 164 terra-1.8-42/terra/man/datatype.Rd | 160 terra-1.8-42/terra/man/deepcopy.Rd | 88 terra-1.8-42/terra/man/densify.Rd | 124 terra-1.8-42/terra/man/density.Rd | 70 terra-1.8-42/terra/man/deprecated.Rd | 44 terra-1.8-42/terra/man/depth.Rd | 101 terra-1.8-42/terra/man/describe.Rd | 86 terra-1.8-42/terra/man/diff.Rd | 70 terra-1.8-42/terra/man/dimensions.Rd | 302 - terra-1.8-42/terra/man/direction.Rd | 94 terra-1.8-42/terra/man/disaggregate.Rd | 106 terra-1.8-42/terra/man/distance.Rd | 10 terra-1.8-42/terra/man/divide.Rd | 118 terra-1.8-42/terra/man/dots.Rd | 94 terra-1.8-42/terra/man/draw.Rd | 76 terra-1.8-42/terra/man/erase.Rd | 156 terra-1.8-42/terra/man/expanse.Rd | 190 - terra-1.8-42/terra/man/ext.Rd | 4 terra-1.8-42/terra/man/extract.Rd | 259 - terra-1.8-42/terra/man/extractAlong.Rd | 88 terra-1.8-42/terra/man/extractRange.Rd | 92 terra-1.8-42/terra/man/factors.Rd | 247 - terra-1.8-42/terra/man/fill.Rd | 96 terra-1.8-42/terra/man/fillTime.Rd | 96 terra-1.8-42/terra/man/flip.Rd | 108 terra-1.8-42/terra/man/flowAccumulation.Rd | 214 - terra-1.8-42/terra/man/focal.Rd | 232 - terra-1.8-42/terra/man/focal3D.Rd | 120 terra-1.8-42/terra/man/focalCpp.Rd | 202 - terra-1.8-42/terra/man/focalMat.Rd | 78 terra-1.8-42/terra/man/focalPairs.Rd | 128 terra-1.8-42/terra/man/focalReg.Rd | 100 terra-1.8-42/terra/man/focalValues.Rd | 76 terra-1.8-42/terra/man/forceCCW.Rd | 66 terra-1.8-42/terra/man/freq.Rd | 108 terra-1.8-42/terra/man/gaps.Rd | 84 terra-1.8-42/terra/man/gdal.Rd | 110 terra-1.8-42/terra/man/geometry.Rd | 132 terra-1.8-42/terra/man/geomtype.Rd | 108 terra-1.8-42/terra/man/global.Rd | 102 terra-1.8-42/terra/man/graticule.Rd | 90 terra-1.8-42/terra/man/grid.Rd | 68 terra-1.8-42/terra/man/gridDist.Rd | 120 terra-1.8-42/terra/man/halo.Rd | 82 terra-1.8-42/terra/man/headtail.Rd | 94 terra-1.8-42/terra/man/hist.Rd | 112 terra-1.8-42/terra/man/identical.Rd | 84 terra-1.8-42/terra/man/ifelse.Rd | 112 terra-1.8-42/terra/man/image.Rd | 78 terra-1.8-42/terra/man/impose.Rd | 76 terra-1.8-42/terra/man/init.Rd | 79 terra-1.8-42/terra/man/inplace.Rd | 226 - terra-1.8-42/terra/man/inset.Rd | 194 - terra-1.8-42/terra/man/interpIDW.Rd | 126 terra-1.8-42/terra/man/interpNear.Rd | 124 terra-1.8-42/terra/man/interpolate.Rd | 304 - terra-1.8-42/terra/man/intersect.Rd | 180 - terra-1.8-42/terra/man/is.bool.Rd | 168 terra-1.8-42/terra/man/is.empty.Rd | 80 terra-1.8-42/terra/man/is.flipped.Rd | 82 terra-1.8-42/terra/man/is.lonlat.Rd | 100 terra-1.8-42/terra/man/is.rotated.Rd | 84 terra-1.8-42/terra/man/is.valid.Rd | 112 terra-1.8-42/terra/man/k_means.Rd | 86 terra-1.8-42/terra/man/lapp.Rd | 202 - terra-1.8-42/terra/man/layerCor.Rd | 146 terra-1.8-42/terra/man/legend.Rd | 72 terra-1.8-42/terra/man/linearUnits.Rd | 102 terra-1.8-42/terra/man/lines.Rd | 172 terra-1.8-42/terra/man/makeTiles.Rd | 136 terra-1.8-42/terra/man/makeVRT.Rd | 94 terra-1.8-42/terra/man/map_extent.Rd | 66 terra-1.8-42/terra/man/mappal.Rd | 150 terra-1.8-42/terra/man/mask.Rd | 144 terra-1.8-42/terra/man/match.Rd | 98 terra-1.8-42/terra/man/math-generics.Rd | 206 - terra-1.8-42/terra/man/mem.Rd | 78 terra-1.8-42/terra/man/merge.Rd | 174 terra-1.8-42/terra/man/mergeTime.Rd | 98 terra-1.8-42/terra/man/meta.Rd | 58 terra-1.8-42/terra/man/metags.Rd | 136 terra-1.8-42/terra/man/minmax.Rd | 88 terra-1.8-42/terra/man/modal.Rd | 74 terra-1.8-42/terra/man/mosaic.Rd | 132 terra-1.8-42/terra/man/na.omit.Rd | 84 terra-1.8-42/terra/man/names.Rd | 148 terra-1.8-42/terra/man/nearby.Rd | 92 terra-1.8-42/terra/man/normalize.longitude.Rd | 68 terra-1.8-42/terra/man/north.Rd | 134 terra-1.8-42/terra/man/nseg.Rd | 66 terra-1.8-42/terra/man/origin.Rd | 78 terra-1.8-42/terra/man/pairs.Rd | 94 terra-1.8-42/terra/man/panel.Rd | 104 terra-1.8-42/terra/man/patches.Rd | 156 terra-1.8-42/terra/man/perim.Rd | 74 terra-1.8-42/terra/man/persp.Rd | 74 terra-1.8-42/terra/man/pitfinder.Rd | 162 terra-1.8-42/terra/man/plet.Rd | 256 - terra-1.8-42/terra/man/plot.Rd | 427 +- terra-1.8-42/terra/man/plotRGB.Rd | 118 terra-1.8-42/terra/man/plot_extent.Rd | 74 terra-1.8-42/terra/man/plot_graticule.Rd | 120 terra-1.8-42/terra/man/prcomp.Rd | 98 terra-1.8-42/terra/man/predict.Rd | 310 - terra-1.8-42/terra/man/princomp.Rd | 116 terra-1.8-42/terra/man/project.Rd | 248 - terra-1.8-42/terra/man/quantile.Rd | 114 terra-1.8-42/terra/man/query.Rd | 121 terra-1.8-42/terra/man/rangeFill.Rd | 96 terra-1.8-42/terra/man/rapp.Rd | 128 terra-1.8-42/terra/man/rast.Rd | 279 - terra-1.8-42/terra/man/rasterize.Rd | 175 - terra-1.8-42/terra/man/rasterizeGeom.Rd | 116 terra-1.8-42/terra/man/rasterizeWin.Rd | 144 terra-1.8-42/terra/man/rcl.Rd | 108 terra-1.8-42/terra/man/readwrite.Rd | 174 terra-1.8-42/terra/man/rectify.Rd | 74 terra-1.8-42/terra/man/regress.Rd | 88 terra-1.8-42/terra/man/rep.Rd | 78 terra-1.8-42/terra/man/replace_dollar.Rd | 98 terra-1.8-42/terra/man/replace_layers.Rd | 110 terra-1.8-42/terra/man/replace_values.Rd | 122 terra-1.8-42/terra/man/resample.Rd | 152 terra-1.8-42/terra/man/rescale.Rd | 88 terra-1.8-42/terra/man/roll.Rd | 124 terra-1.8-42/terra/man/rotate.Rd | 128 terra-1.8-42/terra/man/rowSums.Rd | 100 terra-1.8-42/terra/man/same.crs.Rd | 66 terra-1.8-42/terra/man/sample.Rd | 4 terra-1.8-42/terra/man/sapp.Rd | 104 terra-1.8-42/terra/man/sbar.Rd | 122 terra-1.8-42/terra/man/scale.Rd | 86 terra-1.8-42/terra/man/scale_linear.Rd | 78 terra-1.8-42/terra/man/scatter.Rd | 90 terra-1.8-42/terra/man/scoff.Rd | 104 terra-1.8-42/terra/man/sds.Rd | 145 terra-1.8-42/terra/man/segregate.Rd | 84 terra-1.8-42/terra/man/select.Rd | 138 terra-1.8-42/terra/man/selectRange.Rd | 102 terra-1.8-42/terra/man/serialize.Rd | 146 terra-1.8-42/terra/man/setValues.Rd | 144 terra-1.8-42/terra/man/shade.Rd | 118 terra-1.8-42/terra/man/sharedPaths.Rd | 106 terra-1.8-42/terra/man/shift.Rd | 94 terra-1.8-42/terra/man/simplify.Rd | 98 terra-1.8-42/terra/man/sort.Rd | 106 terra-1.8-42/terra/man/spin.Rd | 86 terra-1.8-42/terra/man/split.Rd | 111 terra-1.8-42/terra/man/sprc.Rd | 127 terra-1.8-42/terra/man/stretch.Rd | 106 terra-1.8-42/terra/man/subset.Rd | 152 terra-1.8-42/terra/man/subset_dollar.Rd | 130 terra-1.8-42/terra/man/subset_double.Rd | 160 terra-1.8-42/terra/man/subset_single.Rd | 228 - terra-1.8-42/terra/man/subst.Rd | 102 terra-1.8-42/terra/man/summarize-generics.Rd | 338 - terra-1.8-42/terra/man/summary.Rd | 96 terra-1.8-42/terra/man/surfArea.Rd | 82 terra-1.8-42/terra/man/svc.Rd | 137 terra-1.8-42/terra/man/symdif.Rd | 84 terra-1.8-42/terra/man/tapp.Rd | 120 terra-1.8-42/terra/man/terra-package.Rd | 1363 +++---- terra-1.8-42/terra/man/terrain.Rd | 166 terra-1.8-42/terra/man/text.Rd | 106 terra-1.8-42/terra/man/time.Rd | 156 terra-1.8-42/terra/man/tmpFile.Rd | 76 terra-1.8-42/terra/man/topology.Rd | 146 terra-1.8-42/terra/man/transpose.Rd | 94 terra-1.8-42/terra/man/trim.Rd | 78 terra-1.8-42/terra/man/unique.Rd | 124 terra-1.8-42/terra/man/units.Rd | 102 terra-1.8-42/terra/man/update.Rd | 78 terra-1.8-42/terra/man/values.Rd | 150 terra-1.8-42/terra/man/varnames.Rd | 142 terra-1.8-42/terra/man/vect.Rd | 5 terra-1.8-42/terra/man/vector_layers.Rd | 50 terra-1.8-42/terra/man/viewshed.Rd | 84 terra-1.8-42/terra/man/voronoi.Rd | 104 terra-1.8-42/terra/man/vrt.Rd | 128 terra-1.8-42/terra/man/vrt_tiles.Rd | 60 terra-1.8-42/terra/man/watershed.Rd | 82 terra-1.8-42/terra/man/weighted.mean.Rd | 120 terra-1.8-42/terra/man/where.Rd | 86 terra-1.8-42/terra/man/which.Rd | 72 terra-1.8-42/terra/man/width.Rd | 109 terra-1.8-42/terra/man/window.Rd | 126 terra-1.8-42/terra/man/wrap.Rd | 120 terra-1.8-42/terra/man/wrapCache.Rd | 92 terra-1.8-42/terra/man/writeCDF.Rd | 179 - terra-1.8-42/terra/man/writeRaster.Rd | 198 - terra-1.8-42/terra/man/writeVector.Rd | 96 terra-1.8-42/terra/man/xapp.Rd | 92 terra-1.8-42/terra/man/xmin.Rd | 198 - terra-1.8-42/terra/man/xyCellFrom.Rd | 266 - terra-1.8-42/terra/man/zonal.Rd | 218 - terra-1.8-42/terra/man/zoom.Rd | 80 terra-1.8-42/terra/src/Makevars.ucrt | 6 terra-1.8-42/terra/src/RcppExports.cpp | 11 terra-1.8-42/terra/src/RcppFunctions.cpp | 26 terra-1.8-42/terra/src/RcppModule.cpp | 35 terra-1.8-42/terra/src/arith.cpp | 85 terra-1.8-42/terra/src/crs.cpp | 2 terra-1.8-42/terra/src/distRaster.cpp | 59 terra-1.8-42/terra/src/distValueRaster.cpp | 6 terra-1.8-42/terra/src/distVector.cpp | 299 + terra-1.8-42/terra/src/distance.cpp | 2 terra-1.8-42/terra/src/extract.cpp | 66 terra-1.8-42/terra/src/focal.cpp | 2 terra-1.8-42/terra/src/gdal_algs.cpp | 50 terra-1.8-42/terra/src/gdalio.cpp | 4 terra-1.8-42/terra/src/geodesic.c | 66 terra-1.8-42/terra/src/geos_methods.cpp | 67 terra-1.8-42/terra/src/geos_spat.h | 20 terra-1.8-42/terra/src/math_utils.h | 34 terra-1.8-42/terra/src/memory.cpp | 3 terra-1.8-42/terra/src/raster_methods.cpp | 22 terra-1.8-42/terra/src/raster_stats.cpp | 63 terra-1.8-42/terra/src/rasterize.cpp | 4 terra-1.8-42/terra/src/read.cpp | 4 terra-1.8-42/terra/src/read_gdal.cpp | 142 terra-1.8-42/terra/src/read_ogr.cpp | 30 terra-1.8-42/terra/src/recycle.h | 8 terra-1.8-42/terra/src/sample.cpp | 278 + terra-1.8-42/terra/src/spatBase.cpp | 2 terra-1.8-42/terra/src/spatBase.h | 3 terra-1.8-42/terra/src/spatDataframe.cpp | 114 terra-1.8-42/terra/src/spatDataframe.h | 50 terra-1.8-42/terra/src/spatFactor.cpp | 14 terra-1.8-42/terra/src/spatFactor.h | 18 terra-1.8-42/terra/src/spatRaster.cpp | 106 terra-1.8-42/terra/src/spatRaster.h | 49 terra-1.8-42/terra/src/spatRasterMultiple.cpp | 124 terra-1.8-42/terra/src/spatRasterMultiple.h | 49 terra-1.8-42/terra/src/spatSources.cpp | 49 terra-1.8-42/terra/src/spatTime.cpp | 9 terra-1.8-42/terra/src/spatVector.cpp | 102 terra-1.8-42/terra/src/spatVector.h | 68 terra-1.8-42/terra/src/table_utils.cpp |only terra-1.8-42/terra/src/table_utils.h |only terra-1.8-42/terra/src/vecmath.h | 10 terra-1.8-42/terra/src/vector_methods.cpp | 4 terra-1.8-42/terra/src/write.cpp | 18 terra-1.8-42/terra/src/write_gdal.cpp | 78 terra-1.8-42/terra/tests/tinytest.R | 8 451 files changed, 44361 insertions(+), 42999 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.3-2 dated 2025-02-17 and 1.3-3 dated 2025-04-02
DESCRIPTION | 8 +- MD5 | 75 ++++++++++----------- NEWS.md | 6 + README.md | 42 ++++++++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/consistency.Rmd | 46 +++++++------ inst/doc/consistency.html | 76 +++++++++++---------- inst/doc/gd.Rmd | 18 ----- inst/doc/gd.html | 142 +++++++++++++++++------------------------ inst/doc/idsa.Rmd | 22 ------ inst/doc/idsa.html | 78 ++++++++-------------- inst/doc/opgd.Rmd | 4 - inst/doc/opgd.html | 28 +++----- inst/doc/rgdrid.Rmd | 2 inst/doc/rgdrid.html | 6 - inst/doc/sesu.Rmd | 20 ----- inst/doc/sesu.html | 48 ++++--------- inst/doc/shegd.Rmd | 12 --- inst/doc/shegd.html | 38 +++------- inst/doc/spade.Rmd | 20 ----- inst/doc/spade.html | 76 ++++++++------------- vignettes/consistency.Rmd | 46 +++++++------ vignettes/consistency.Rmd.orig | 21 +++--- vignettes/gd.Rmd | 18 ----- vignettes/gd.Rmd.orig | 1 vignettes/idsa.Rmd | 22 ------ vignettes/idsa.Rmd.orig | 1 vignettes/opgd.Rmd | 4 - vignettes/opgd.Rmd.orig | 1 vignettes/precompile.R | 2 vignettes/rgdrid.Rmd | 2 vignettes/rgdrid.Rmd.orig | 1 vignettes/sesu.Rmd | 20 ----- vignettes/sesu.Rmd.orig | 7 +- vignettes/shegd.Rmd | 12 --- vignettes/shegd.Rmd.orig | 1 vignettes/spade.Rmd | 20 ----- vignettes/spade.Rmd.orig | 1 39 files changed, 372 insertions(+), 575 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.6 dated 2025-02-28 and 5.1 dated 2025-04-02
ChangeLog | 4 DESCRIPTION | 8 MD5 | 16 - R/ETSvalidate.R | 30 + R/TETSvalidate.R | 30 + src/ETSmodel.h | 149 --------- src/TETSmodel.h | 873 ++++++++++++++++++++++++++++++++++++++++++++++--------- src/optim.h | 3 src/stats.h | 6 9 files changed, 812 insertions(+), 307 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak and area under the curve are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.1 dated 2024-08-28 and 1.0.2 dated 2025-04-02
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NEWS.md |only build/vignette.rds |binary inst/CITATION |only 5 files changed, 7 insertions(+), 5 deletions(-)
Title: Semi-Automatic Grading of R and Rmd Scripts
Description: A customisable set of tools for assessing and grading
R or R-markdown scripts from students. It allows for checking correctness
of code output, runtime statistics and static code analysis. The latter
feature is made possible by representing R expressions using a tree
structure.
Author: Vik Gopal [aut, cre],
Samuel Seah [aut],
Viknesh Jeya Kumar [aut],
Gabriel Ang [aut],
Ruofan Liu [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between autoharp versions 0.0.10 dated 2021-11-12 and 0.0.12 dated 2025-04-02
autoharp-0.0.10/autoharp/R/examplify_to_r.R |only autoharp-0.0.10/autoharp/R/lum_local_match.R |only autoharp-0.0.10/autoharp/man/examplify_to_r.Rd |only autoharp-0.0.10/autoharp/man/lum_local_match.Rd |only autoharp-0.0.12/autoharp/DESCRIPTION | 26 ++++++------ autoharp-0.0.12/autoharp/MD5 | 40 +++++++++---------- autoharp-0.0.12/autoharp/NAMESPACE | 4 - autoharp-0.0.12/autoharp/NEWS | 9 ++++ autoharp-0.0.12/autoharp/R/autoharp.R | 3 - autoharp-0.0.12/autoharp/R/extracton_section_text.R |only autoharp-0.0.12/autoharp/R/forestharp.R | 10 ++-- autoharp-0.0.12/autoharp/R/join_treeharp.R | 5 +- autoharp-0.0.12/autoharp/R/populate_soln_env.R | 37 +---------------- autoharp-0.0.12/autoharp/R/tree_routines.R | 19 +++++---- autoharp-0.0.12/autoharp/man/TreeHarp-class.Rd | 12 ++--- autoharp-0.0.12/autoharp/man/autoharp.Rd | 25 +++++++++++ autoharp-0.0.12/autoharp/man/extract_section_text.Rd |only autoharp-0.0.12/autoharp/man/forestharp-helpers.Rd | 30 +++++++------- autoharp-0.0.12/autoharp/man/get_adj_list.Rd | 4 - autoharp-0.0.12/autoharp/man/get_child_ids.Rd | 6 +- autoharp-0.0.12/autoharp/man/get_node_types.Rd | 4 - autoharp-0.0.12/autoharp/man/get_parent_id.Rd | 6 +- autoharp-0.0.12/autoharp/man/populate_soln_env.Rd | 10 +--- autoharp-0.0.12/autoharp/man/rmd_to_forestharp.Rd | 2 24 files changed, 128 insertions(+), 124 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Rodrigo Basa [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.10.1 dated 2024-09-20 and 1.11.0 dated 2025-04-02
DESCRIPTION | 17 + MD5 | 29 ++- NAMESPACE | 3 NEWS.md | 14 + R/destructure.R |only R/node.R | 12 - R/tools.R | 175 +++++++++++++++++++- inst/WORDLIST | 6 inst/templates/app_structure/app/static/favicon.ico |binary man/auto_test_r.Rd |only man/devmode.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/format_r.Rd | 4 man/grapes-set-grapes.Rd |only man/test_r.Rd | 5 tests/testthat/test-destructure.R |only tests/testthat/test-tools.R | 6 20 files changed, 237 insertions(+), 34 deletions(-)
Title: The Double-Gap Life Expectancy Forecasting Model
Description: Life expectancy is highly correlated over time among countries and
between males and females. These associations can be used to improve forecasts.
Here we have implemented a method for forecasting female life expectancy based on
analysis of the gap between female life expectancy in a country compared with
the record level of female life expectancy in the world. Second, to forecast
male life expectancy, the gap between male life expectancy and female life
expectancy in a country is analysed. We named this method the Double-Gap model.
For a detailed description of the method see Pascariu et al. (2018).
<doi:10.1016/j.insmatheco.2017.09.011>.
Author: Marius D. Pascariu [aut, cre]
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between MortalityGaps versions 1.0.0 dated 2018-07-20 and 1.0.7 dated 2025-04-02
MortalityGaps-1.0.0/MortalityGaps/R/Utils.R |only MortalityGaps-1.0.0/MortalityGaps/R/data_and_imports.R |only MortalityGaps-1.0.0/MortalityGaps/man/onAttach.Rd |only MortalityGaps-1.0.7/MortalityGaps/DESCRIPTION | 28 MortalityGaps-1.0.7/MortalityGaps/MD5 | 75 MortalityGaps-1.0.7/MortalityGaps/NAMESPACE | 70 MortalityGaps-1.0.7/MortalityGaps/NEWS | 7 MortalityGaps-1.0.7/MortalityGaps/R/DGM_fit.R | 779 +++++----- MortalityGaps-1.0.7/MortalityGaps/R/DGM_predict.R | 310 +-- MortalityGaps-1.0.7/MortalityGaps/R/Graphics.R | 184 +- MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-data.R |only MortalityGaps-1.0.7/MortalityGaps/R/MortalityGaps-package.R |only MortalityGaps-1.0.7/MortalityGaps/README.md | 115 - MortalityGaps-1.0.7/MortalityGaps/THANKS | 24 MortalityGaps-1.0.7/MortalityGaps/build/partial.rdb |only MortalityGaps-1.0.7/MortalityGaps/build/vignette.rds |binary MortalityGaps-1.0.7/MortalityGaps/inst/REFERENCES.bib |only MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.R | 56 MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.Rmd | 208 +- MortalityGaps-1.0.7/MortalityGaps/inst/doc/Manual.pdf |binary MortalityGaps-1.0.7/MortalityGaps/inst/figures |only MortalityGaps-1.0.7/MortalityGaps/man/DoubleGap.Rd | 283 +-- MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.Rd |only MortalityGaps-1.0.7/MortalityGaps/man/MortalityGaps.data.Rd | 64 MortalityGaps-1.0.7/MortalityGaps/man/bp_gap.model.Rd | 56 MortalityGaps-1.0.7/MortalityGaps/man/compute_CI.Rd | 58 MortalityGaps-1.0.7/MortalityGaps/man/find_fitted_values.Rd | 38 MortalityGaps-1.0.7/MortalityGaps/man/find_observed_values.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_record_ex.Rd | 30 MortalityGaps-1.0.7/MortalityGaps/man/find_tau.Rd | 46 MortalityGaps-1.0.7/MortalityGaps/man/plot.predict.DoubleGap.Rd | 79 - MortalityGaps-1.0.7/MortalityGaps/man/predict.DoubleGap.Rd | 72 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/prepare_data_for_prediction.Rd | 42 MortalityGaps-1.0.7/MortalityGaps/man/print.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.MortalityGaps.data.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.predict.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/print.summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/man/sex_gap.model.Rd | 52 MortalityGaps-1.0.7/MortalityGaps/man/summary.DoubleGap.Rd | 34 MortalityGaps-1.0.7/MortalityGaps/tests/testthat.R | 8 MortalityGaps-1.0.7/MortalityGaps/tests/testthat/testDGM.R | 208 +- MortalityGaps-1.0.7/MortalityGaps/vignettes/Manual.Rmd | 208 +- 43 files changed, 1690 insertions(+), 1644 deletions(-)
Title: Testing for Spatial Independence of Cross-Sectional Qualitative
Data
Description: Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
Author: Fernando Lopez [aut, cre] ,
Roman Minguez [aut] ,
Antonio Paez [aut] ,
Manuel Ruiz [aut]
Maintainer: Fernando Lopez <fernando.lopez@upct.es>
Diff between spqdep versions 0.1.3.5 dated 2025-01-08 and 0.1.3.6 dated 2025-04-02
DESCRIPTION | 13 +- MD5 | 28 +++--- NAMESPACE | 2 R/m.surround.R | 3 R/methods_qmap.R | 5 - R/plot.sprunstest.R | 69 ++++++++------ R/summary.spjctest.R | 20 ++-- R/summary.spqtest.R | 14 +-- R/utils-pipe.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 7 - inst/doc/user-guide.Rmd | 11 +- inst/doc/user-guide.html | 217 +++++++++++++++++++++++------------------------ man/pipe.Rd |only vignettes/user-guide.Rmd | 11 +- 16 files changed, 204 insertions(+), 196 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard '%dopar%' loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.8.6.1 dated 2025-01-13 and 1.8.6.2 dated 2025-04-02
doRNG-1.8.6.1/doRNG/build |only doRNG-1.8.6.1/doRNG/inst/doc |only doRNG-1.8.6.1/doRNG/vignettes |only doRNG-1.8.6.2/doRNG/DESCRIPTION | 9 ++++----- doRNG-1.8.6.2/doRNG/MD5 | 11 +++-------- doRNG-1.8.6.2/doRNG/man/doRNG-package.Rd | 2 +- doRNG-1.8.6.2/doRNG/man/grapes-dorng-grapes.Rd | 8 +++++--- 7 files changed, 13 insertions(+), 17 deletions(-)
Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API
<https://dev.elsevier.com/sc_apis.html> to download
information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between rscopus versions 0.6.6 dated 2019-09-17 and 0.8.1 dated 2025-04-02
rscopus-0.6.6/rscopus/R/read_cto.R |only rscopus-0.8.1/rscopus/DESCRIPTION | 15 rscopus-0.8.1/rscopus/MD5 | 106 +- rscopus-0.8.1/rscopus/NAMESPACE | 5 rscopus-0.8.1/rscopus/NEWS.md | 8 rscopus-0.8.1/rscopus/R/author_df.R | 12 rscopus-0.8.1/rscopus/R/author_retrieval.R | 8 rscopus-0.8.1/rscopus/R/author_search.R | 8 rscopus-0.8.1/rscopus/R/bibtex_core_data.R | 118 +- rscopus-0.8.1/rscopus/R/citation_retrieval.R | 48 rscopus-0.8.1/rscopus/R/elsevier_authenticate.R | 23 rscopus-0.8.1/rscopus/R/generic_elsevier_search.R | 6 rscopus-0.8.1/rscopus/R/get_affiliation_info.R | 4 rscopus-0.8.1/rscopus/R/get_all_coauthors.R |only rscopus-0.8.1/rscopus/R/get_author_info.R | 8 rscopus-0.8.1/rscopus/R/get_next.R | 2 rscopus-0.8.1/rscopus/R/object_retrieval.R | 11 rscopus-0.8.1/rscopus/R/read_cto.r |only rscopus-0.8.1/rscopus/R/scopus_search.R | 39 rscopus-0.8.1/rscopus/R/utils-pipe.R |only rscopus-0.8.1/rscopus/build/vignette.rds |binary rscopus-0.8.1/rscopus/inst/doc/api_key.R | 40 rscopus-0.8.1/rscopus/inst/doc/api_key.Rmd | 36 rscopus-0.8.1/rscopus/inst/doc/api_key.html | 285 +++-- rscopus-0.8.1/rscopus/inst/doc/multi_author.R | 32 rscopus-0.8.1/rscopus/inst/doc/multi_author.Rmd | 13 rscopus-0.8.1/rscopus/inst/doc/multi_author.html | 824 ++++++++-------- rscopus-0.8.1/rscopus/man/abstract_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/affil_df.Rd | 22 rscopus-0.8.1/rscopus/man/affil_search.Rd | 9 rscopus-0.8.1/rscopus/man/affiliation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/article_retrieval.Rd | 10 rscopus-0.8.1/rscopus/man/author_df.Rd | 51 rscopus-0.8.1/rscopus/man/author_retrieval.Rd | 42 rscopus-0.8.1/rscopus/man/author_search.Rd | 27 rscopus-0.8.1/rscopus/man/author_search_by_affil.Rd | 2 rscopus-0.8.1/rscopus/man/bibtex_core_data.Rd | 2 rscopus-0.8.1/rscopus/man/citation_retrieval.Rd | 27 rscopus-0.8.1/rscopus/man/complete_multi_author_info.Rd | 3 rscopus-0.8.1/rscopus/man/elsevier_authenticate.Rd | 22 rscopus-0.8.1/rscopus/man/embase_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/entitlement_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/generic_elsevier_api.Rd | 32 rscopus-0.8.1/rscopus/man/get_affiliation_info.Rd | 13 rscopus-0.8.1/rscopus/man/get_all_coauthors.Rd |only rscopus-0.8.1/rscopus/man/get_complete_author_info.Rd | 26 rscopus-0.8.1/rscopus/man/get_links.Rd | 5 rscopus-0.8.1/rscopus/man/object_retrieval.Rd | 30 rscopus-0.8.1/rscopus/man/pipe.Rd |only rscopus-0.8.1/rscopus/man/process_affiliation_name.Rd | 8 rscopus-0.8.1/rscopus/man/process_author_name.Rd | 16 rscopus-0.8.1/rscopus/man/read_cto.Rd | 2 rscopus-0.8.1/rscopus/man/recommendation_retrieval.Rd | 8 rscopus-0.8.1/rscopus/man/scopus_search.Rd | 47 rscopus-0.8.1/rscopus/tests/testthat/test_author_df.R | 11 rscopus-0.8.1/rscopus/vignettes/api_key.Rmd | 36 rscopus-0.8.1/rscopus/vignettes/multi_author.Rmd | 13 57 files changed, 1285 insertions(+), 862 deletions(-)
Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with
absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre],
Brian Koch [ctb]
Maintainer: Bob Harlow <rharlow86@gmail.com>
Diff between quadprogXT versions 0.0.5 dated 2020-01-15 and 0.0.6 dated 2025-04-02
DESCRIPTION | 18 +++++---- MD5 | 10 ++--- R/convertToCompactQP.R | 68 +++++++++++++++++++++------------- inst/tinytest/test-convertToCompact.R | 17 ++++++-- man/convertToCompact.Rd | 9 ++-- man/solveQPXT.Rd | 23 +++++++++-- 6 files changed, 93 insertions(+), 52 deletions(-)
Title: Person Fit
Description: Several person-fit statistics
(PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>)
are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro [aut, cre]
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>
Diff between PerFit versions 1.4.6 dated 2021-10-15 and 1.4.7 dated 2025-04-02
DESCRIPTION | 17 +-- MD5 | 12 +- R/PerFitPFS.R | 180 ++++++++++++++++----------------- R/SanityChecks.R | 272 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/PerFit-package.Rd | 1 man/lz.Rd | 2 7 files changed, 244 insertions(+), 240 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.8 dated 2024-11-21 and 1.3.9 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 12 ++--- R/addBagPlot.R | 8 +-- R/plotPCAw.R | 25 +++++++---- build/vignette.rds |binary inst/doc/wrGraphVignette1.html | 93 ++++++++++++++++++----------------------- man/addBagPlot.Rd | 2 7 files changed, 73 insertions(+), 73 deletions(-)
Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the
Computational Toxicology and Exposure ('CTX') APIs
<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>.
'ctxR' was developed to streamline the process of accessing the information
available through the 'CTX' APIs without requiring prior knowledge of how to
use APIs. Most data is also available on the CompTox Chemical Dashboard
('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the
EPA Computational Toxicology and Exposure Online Resources
<https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] ,
Caroline Ring [aut] ,
Madison Feshuk [ctb] ,
Carter Thunes [ctb],
Jason Brown [cre]
Maintainer: Jason Brown <brown.jason@epa.gov>
Diff between ctxR versions 1.1.0 dated 2025-01-08 and 1.1.1 dated 2025-04-01
DESCRIPTION | 16 MD5 | 172 NEWS.md | 6 build/vignette.rds |binary inst/doc/Bioactivity.html | 2 inst/doc/Chemical.html | 2 inst/doc/Exposure.html | 2 inst/doc/Hazard.html | 2 inst/doc/Introduction.html | 2 tests/testthat/bioactivity/bioactivity/data/search/by-aeid/1.json | 6 tests/testthat/chemical-batch/chemical/detail/search/by-dtxcid/DTXCID30182-9e51f1.json | 78 tests/testthat/chemical-batch/chemical/detail/search/by-dtxsid-9e51f1-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/fate/search/by-dtxsid-cd40e5-POST.json | 862 tests/testthat/chemical-batch/chemical/fate/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/file/mol/search/by-dtxcid/DTXCID30182.txt | 94 tests/testthat/chemical-batch/chemical/file/mol/search/by-dtxsid/DTXSID7020182.txt | 94 tests/testthat/chemical-batch/chemical/ghslink/to-dtxsid-cd40e5-POST.json | 14 tests/testthat/chemical-batch/chemical/list/chemicals/search/contain/Biosolids2021/Bis.json | 126 tests/testthat/chemical-batch/chemical/list/chemicals/search/equal/Biosolids2021/Bis.json | 6 tests/testthat/chemical-batch/chemical/list/chemicals/search/start-with/Biosolids2021/Bis.json | 60 tests/testthat/chemical-batch/chemical/list/search/by-dtxsid/DTXSID7020182.json | 3700 +- tests/testthat/chemical-batch/chemical/list/search/by-name/BIOSOLIDS2021.json | 24 tests/testthat/chemical-batch/chemical/list/search/by-type/federal.json | 3964 +- tests/testthat/chemical-batch/chemical/msready/search/by-dtxcid/DTXCID30182.json | 52 tests/testthat/chemical-batch/chemical/msready/search/by-formula/8x.json | 6 tests/testthat/chemical-batch/chemical/msready/search/by-formula/CH4.json | 406 tests/testthat/chemical-batch/chemical/msready/search/by-mass-8e72d4-POST.json | 16 tests/testthat/chemical-batch/chemical/msready/search/by-mass/1/1.json | 6 tests/testthat/chemical-batch/chemical/msready/search/by-mass/16.0313/16.0314.json | 406 tests/testthat/chemical-batch/chemical/msready/search/by-mass/16.0314/16.0314.json | 6 tests/testthat/chemical-batch/chemical/property/search/by-dtxsid-cd40e5-POST.json | 1036 tests/testthat/chemical-batch/chemical/property/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical-batch/chemical/search/equal-a5c27e-POST.json | 34 tests/testthat/chemical-batch/chemical/search/equal-b2fb80-POST.json | 42 tests/testthat/chemical-batch/chemical/synonym/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/chemical/chemical/file/mol/search/by-dtxcid/DTXCID30182.txt | 94 tests/testthat/chemical/chemical/file/mol/search/by-dtxsid/DTXSID7020182.txt | 94 tests/testthat/chemical/chemical/ghslink/to-dtxsid/DTXSID7020182.json | 10 tests/testthat/chemical/chemical/list/chemicals/search/equal/Biosolids2021/Bisphenol%20A.json | 6 tests/testthat/chemical/chemical/list/chemicals/search/equal/Biosolids2021/zy.json | 6 tests/testthat/chemical/chemical/list/chemicals/search/start-with/CCL4/Bi.json | 22 tests/testthat/chemical/chemical/list/chemicals/search/start-with/CCL4/zy.json | 6 tests/testthat/chemical/chemical/list/search/by-name/Biosolids2021.json | 24 tests/testthat/chemical/chemical/msready/search/by-dtxcid/DTXCID30182.json | 52 tests/testthat/chemical/chemical/msready/search/by-formula/8x.json | 6 tests/testthat/chemical/chemical/msready/search/by-formula/CH4.json | 406 tests/testthat/chemical/chemical/msready/search/by-mass/1/4.json | 6 tests/testthat/chemical/chemical/msready/search/by-mass/16.0313/16.0314.json | 406 tests/testthat/chemical/chemical/msready/search/by-mass/16.0314/16.0314.json | 6 tests/testthat/chemical/chemical/property/search/by-dtxsid/DTXSID.json | 6 tests/testthat/chemical/chemical/property/search/by-dtxsid/DTXSID7020182-f7c7b7.json | 772 tests/testthat/exposure-batch/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 tests/testthat/exposure-batch/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 tests/testthat/exposure-batch/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 tests/testthat/exposure-batch/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- tests/testthat/exposure/exposure/fun-use/category.json | 1284 tests/testthat/exposure/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 tests/testthat/exposure/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 tests/testthat/exposure/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 tests/testthat/exposure/exposure/list-presence/tags.json | 1876 - tests/testthat/exposure/exposure/product-data/puc.json | 7028 +-- tests/testthat/exposure/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- tests/testthat/hazard-batch/hazard/cancer-summary/search/by-dtxsid-cd40e5-POST.json | 6 tests/testthat/hazard-batch/hazard/cancer-summary/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/eco/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/genetox/details/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/genetox/summary/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/human/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/search/by-dtxsid-ddb193-POST.json | 6 tests/testthat/hazard-batch/hazard/skin-eye/search/by-dtxsid-ddb193-POST.json | 6 vignettes/4/0/bioactivity/assay/search/by-aeid/700.json | 156 vignettes/4/0/bioactivity/assay/search/by-aeid/891.json | 162 vignettes/4/0/bioactivity/data/search/by-aeid/704.json |18414 +++++----- vignettes/4/0/bioactivity/data/search/by-dtxsid/DTXSID30944145.json | 2128 - vignettes/4/0/bioactivity/data/search/by-m4id/739695.json | 430 vignettes/4/0/bioactivity/data/search/by-spid/TP0000904H05.json | 3430 - vignettes/4/0/bioactivity/data/summary/search/by-aeid/700.json | 14 vignettes/4/0/bioactivity/data/summary/search/by-aeid/759.json | 14 vignettes/4/0/bioactivity/data/summary/search/by-aeid/891.json | 14 vignettes/5/0/exposure/fun-use/category.json | 1284 vignettes/5/0/exposure/fun-use/probability/search/by-dtxsid/DTXSID0020232.json | 36 vignettes/5/0/exposure/fun-use/probability/search/by-dtxsid/DTXSID7020182.json | 100 vignettes/5/0/exposure/fun-use/search/by-dtxsid/DTXSID7020182.json | 724 vignettes/5/0/exposure/list-presence/search/by-dtxsid/DTXSID7020182.json | 1278 vignettes/5/0/exposure/list-presence/tags.json | 1876 - vignettes/5/0/exposure/product-data/puc.json | 7028 +-- vignettes/5/0/exposure/product-data/search/by-dtxsid/DTXSID7020182.json |12394 +++--- 87 files changed, 50952 insertions(+), 50946 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.13.0 dated 2024-11-18 and 1.13.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 32 - R/getUPS1acc.R | 4 R/readAlphaPeptFile.R | 9 R/readMaxQuantFile.R | 2 R/readProteomeDiscovererFile.R | 48 + R/readProteomeDiscovererPeptides.R | 7 build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 22 inst/doc/wrProteoVignette1.Rmd | 6 inst/doc/wrProteoVignette1.html | 245 +++----- inst/doc/wrProteoVignetteUPS1.R | 32 - inst/doc/wrProteoVignetteUPS1.Rmd | 2 inst/doc/wrProteoVignetteUPS1.html | 1130 ++++++++++++++++++------------------- man/getUPS1acc.Rd | 4 vignettes/wrProteoVignette1.Rmd | 6 vignettes/wrProteoVignetteUPS1.Rmd | 2 17 files changed, 767 insertions(+), 790 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.2 dated 2025-03-17 and 4.0.0 dated 2025-04-01
DESCRIPTION | 6 ++-- MD5 | 13 +++++----- NEWS | 3 ++ src/Makevars.in | 2 - src/Makevars.win | 56 ++++++++++++++++++++++++++++---------------- src/mongoc/mongoc-openssl.c | 2 - src/osx/Makevars | 2 - tools |only 8 files changed, 52 insertions(+), 32 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.5.2 dated 2025-03-14 and 0.5.3 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 15 ++--- NEWS.md | 6 ++ R/MaestroPipeline.R | 8 ++ inst/doc/maestro-1-quick-start.html | 20 ++----- inst/doc/maestro-4-advanced-scheduling.html | 12 ++-- inst/doc/maestro-5-directed-acyclic-graphs.html | 22 ++++---- inst/doc/maestro-6-logging.html | 66 ++++++++++++------------ vignettes/maestro-8-tag-reference.html |only 9 files changed, 80 insertions(+), 75 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.5.1 dated 2025-02-28 and 1.6.0 dated 2025-04-01
DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 2 NEWS.md | 6 + R/process.r | 201 +++++++++++++++++++++++------------------- R/utils.r | 2 R/validate.r | 7 + build/vignette.rds |binary tests/testthat/test-process.r | 60 ++++++++++-- 9 files changed, 187 insertions(+), 115 deletions(-)
Title: Interface to 'Glassdoor' API
Description: Interacts with the 'Glassdoor' API
<https://www.glassdoor.com/developer/index.htm>. Allows the user to
search job statistics, employer statistics, and job progression,
where 'Glassdoor' provides a breakdown of other jobs a person did
after their current one.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between glassdoor versions 0.8.1 dated 2018-11-21 and 0.9.0 dated 2025-04-01
glassdoor-0.8.1/glassdoor/R/glassdoor_job_prog.R |only glassdoor-0.8.1/glassdoor/man/gd_job_prog.Rd |only glassdoor-0.9.0/glassdoor/DESCRIPTION | 11 glassdoor-0.9.0/glassdoor/MD5 | 34 - glassdoor-0.9.0/glassdoor/NAMESPACE | 1 glassdoor-0.9.0/glassdoor/NEWS.md | 5 glassdoor-0.9.0/glassdoor/R/gdoor.R | 2 glassdoor-0.9.0/glassdoor/R/results.R | 2 glassdoor-0.9.0/glassdoor/README.md | 24 - glassdoor-0.9.0/glassdoor/build/vignette.rds |binary glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.R | 22 glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.Rmd | 20 glassdoor-0.9.0/glassdoor/inst/doc/running-glassdoor.html | 322 +++++++------- glassdoor-0.9.0/glassdoor/man/gd_api.Rd | 18 glassdoor-0.9.0/glassdoor/man/gd_company.Rd | 26 - glassdoor-0.9.0/glassdoor/man/gd_job_stats.Rd | 26 - glassdoor-0.9.0/glassdoor/man/gd_review.Rd | 3 glassdoor-0.9.0/glassdoor/man/results.Rd | 2 glassdoor-0.9.0/glassdoor/vignettes/running-glassdoor.Rmd | 20 19 files changed, 284 insertions(+), 254 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.4.0 dated 2025-02-28 and 0.4.1 dated 2025-04-01
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/tm_a_pca.R | 6 ++++-- R/tm_a_regression.R | 7 +++---- R/tm_g_association.R | 7 +++---- R/tm_g_bivariate.R | 7 +++---- R/tm_g_distribution.R | 7 +++---- R/tm_g_response.R | 7 +++---- R/tm_g_scatterplot.R | 6 ++++-- R/tm_t_crosstable.R | 6 ++++-- build/vignette.rds |binary 12 files changed, 47 insertions(+), 41 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Cole C. Monnahan [ctb, cph] ,
Mollie Brooks [ct [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.6.0 dated 2024-05-29 and 0.7.0 dated 2025-04-01
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Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how
many times a video has been liked, search for videos with particular
content, and much more. You can also scrape captions from a few
videos. To learn more about the YouTube API, see
<https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb],
John Muschelli [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.9.9 dated 2020-06-11 and 1.0.1 dated 2025-04-01
tuber-0.9.9/tuber/tests/testthat/test-pkg-style.R |only tuber-0.9.9/tuber/tests/testthat/token_file.rds |only tuber-0.9.9/tuber/vignettes/tuber-ex.md |only tuber-1.0.1/tuber/DESCRIPTION | 38 tuber-1.0.1/tuber/LICENSE | 2 tuber-1.0.1/tuber/MD5 | 217 + tuber-1.0.1/tuber/NAMESPACE | 148 - tuber-1.0.1/tuber/NEWS.md | 243 +- tuber-1.0.1/tuber/R/add_video_to_playlist.R |only tuber-1.0.1/tuber/R/change_playlist_title.R |only tuber-1.0.1/tuber/R/create_playlist.R |only tuber-1.0.1/tuber/R/delete_captions.R | 58 tuber-1.0.1/tuber/R/delete_channel_sections.R | 60 tuber-1.0.1/tuber/R/delete_comments.R | 58 tuber-1.0.1/tuber/R/delete_playlist_items.R | 58 tuber-1.0.1/tuber/R/delete_playlists.R | 58 tuber-1.0.1/tuber/R/delete_videos.R | 57 tuber-1.0.1/tuber/R/get_all_channel_video_stats.R | 143 - tuber-1.0.1/tuber/R/get_all_comments.R | 183 - tuber-1.0.1/tuber/R/get_captions.R | 84 tuber-1.0.1/tuber/R/get_channel_stats.R | 163 - tuber-1.0.1/tuber/R/get_comment_threads.R | 234 +- tuber-1.0.1/tuber/R/get_comments.R | 180 - tuber-1.0.1/tuber/R/get_playlist_item_ids.R |only tuber-1.0.1/tuber/R/get_playlist_item_videoids.R |only tuber-1.0.1/tuber/R/get_playlist_items.R | 186 - tuber-1.0.1/tuber/R/get_playlists.R | 151 - tuber-1.0.1/tuber/R/get_related_videos.R | 137 - tuber-1.0.1/tuber/R/get_stats.R | 77 tuber-1.0.1/tuber/R/get_subscriptions.R | 120 - tuber-1.0.1/tuber/R/get_video_details.R | 176 + tuber-1.0.1/tuber/R/list_abuse_report_reasons.R | 115 - tuber-1.0.1/tuber/R/list_caption_tracks.R | 107 tuber-1.0.1/tuber/R/list_captions.R | 82 tuber-1.0.1/tuber/R/list_channel_activities.R | 201 - tuber-1.0.1/tuber/R/list_channel_resources.R | 155 - tuber-1.0.1/tuber/R/list_channel_sections.R | 85 tuber-1.0.1/tuber/R/list_channel_videos.R | 88 tuber-1.0.1/tuber/R/list_guidecats.R | 135 - tuber-1.0.1/tuber/R/list_langs.R | 78 tuber-1.0.1/tuber/R/list_my_videos.R | 34 tuber-1.0.1/tuber/R/list_regions.R | 81 tuber-1.0.1/tuber/R/list_videocats.R | 132 - tuber-1.0.1/tuber/R/list_videos.R | 94 tuber-1.0.1/tuber/R/read_sbv.R | 78 tuber-1.0.1/tuber/R/tuber.R | 399 ++- tuber-1.0.1/tuber/R/update_video_metadata.R |only tuber-1.0.1/tuber/R/upload_caption.R | 170 - tuber-1.0.1/tuber/R/upload_video.R | 257 +- tuber-1.0.1/tuber/R/utils-pipe.R |only tuber-1.0.1/tuber/R/yt_oauth.R | 152 - tuber-1.0.1/tuber/R/yt_search.R | 457 ++-- tuber-1.0.1/tuber/R/yt_topic_search.R | 78 tuber-1.0.1/tuber/R/zzz.R |only tuber-1.0.1/tuber/README.md | 169 - tuber-1.0.1/tuber/build/vignette.rds |binary tuber-1.0.1/tuber/inst/CITATION | 31 tuber-1.0.1/tuber/inst/doc/tuber-ex.R | 139 - tuber-1.0.1/tuber/inst/doc/tuber-ex.Rmd | 523 ++-- tuber-1.0.1/tuber/inst/doc/tuber-ex.html | 1087 +++++----- tuber-1.0.1/tuber/man/add_video_to_playlist.Rd |only tuber-1.0.1/tuber/man/change_playlist_title.Rd |only tuber-1.0.1/tuber/man/create_playlist.Rd |only tuber-1.0.1/tuber/man/delete_captions.Rd | 54 tuber-1.0.1/tuber/man/delete_channel_sections.Rd | 56 tuber-1.0.1/tuber/man/delete_comments.Rd | 54 tuber-1.0.1/tuber/man/delete_playlist_items.Rd | 54 tuber-1.0.1/tuber/man/delete_playlists.Rd | 54 tuber-1.0.1/tuber/man/delete_videos.Rd | 54 tuber-1.0.1/tuber/man/get_all_channel_video_stats.Rd | 74 tuber-1.0.1/tuber/man/get_all_comments.Rd | 68 tuber-1.0.1/tuber/man/get_captions.Rd | 76 tuber-1.0.1/tuber/man/get_channel_stats.Rd | 79 tuber-1.0.1/tuber/man/get_comment_threads.Rd | 137 - 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tuber-1.0.1/tuber/man/upload_video.Rd | 120 - tuber-1.0.1/tuber/man/yt_key.Rd |only tuber-1.0.1/tuber/man/yt_oauth.Rd | 104 tuber-1.0.1/tuber/man/yt_search.Rd | 264 +- tuber-1.0.1/tuber/man/yt_token.Rd | 40 tuber-1.0.1/tuber/man/yt_topic_search.Rd | 58 tuber-1.0.1/tuber/tests/testthat.R | 8 tuber-1.0.1/tuber/tests/testthat/test-captions.R | 26 tuber-1.0.1/tuber/tests/testthat/test-get-details.R | 39 tuber-1.0.1/tuber/tests/testthat/test-get-related-videos.R | 24 tuber-1.0.1/tuber/tests/testthat/test-list-channel-activities.R | 26 tuber-1.0.1/tuber/tests/testthat/test-list-channel-sections.R | 52 tuber-1.0.1/tuber/vignettes/tuber-ex.Rmd | 523 ++-- 120 files changed, 6399 insertions(+), 5600 deletions(-)
Title: Grammar of Graphics for Linear Model Diagnostic Plots
Description: Allows for easy creation of diagnostic plots for a variety of model objects using the Grammar of Graphics.
Provides functionality for both individual diagnostic plots and an array of four standard diagnostic plots.
Author: Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between gglm versions 1.0.3 dated 2024-01-16 and 1.0.4 dated 2025-04-01
DESCRIPTION | 14 ++++++++------ MD5 | 2 +- 2 files changed, 9 insertions(+), 7 deletions(-)
Title: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Description: Articles in the 'R Journal' were first authored in 'LaTeX', which performs
admirably for 'PDF' files but is less than ideal for modern online interfaces.
The 'texor' package does all the transitional chores and conversions necessary
to move to the online versions.
Author: Abhishek Ulayil [aut, cre, cph]
,
Heather Turner [ctb] ,
Christophe Dervieux [ctb] ,
Mitchell O'Hara-Wild [ctb] ,
Dianne Cook [ctb] ,
Yinxiang Huang [ctb]
Maintainer: Abhishek Ulayil <perricoq@outlook.com>
Diff between texor versions 1.5.3 dated 2024-12-13 and 1.5.6 dated 2025-04-01
DESCRIPTION | 6 ++--- LICENSE | 2 - MD5 | 26 +++++++++++----------- NEWS.md | 9 +++++++ R/article-tools.R | 2 + R/automation-tools.R | 10 +++++--- R/table-tools.R | 33 +++++++++++++++++++++++++++- build/vignette.rds |binary inst/bookdown_ref.lua | 28 +++++++++++++++++++----- inst/doc/environment-handling.html | 18 +++++++-------- inst/fig_code_chunk.lua | 39 +++++++++++++++++++++++++++++++-- inst/table_caption.lua | 43 ++++++++++++++++++++++++++++++++----- inst/table_code_chunk.lua | 8 ++++-- man/latex_to_web.Rd | 8 +++--- 14 files changed, 182 insertions(+), 50 deletions(-)
Title: XML Generation from Tables
Description: Converting structured data from tables into XML format using
predefined templates ensures consistency and flexibility, making it
ideal for data exchange, reporting, and automated workflows.
Author: Jose Samos [aut, cre] ,
Universidad de Granada [cph]
Maintainer: Jose Samos <jsamos@ugr.es>
Diff between tab2xml versions 1.0.0 dated 2025-02-21 and 1.1.0 dated 2025-04-01
DESCRIPTION | 6 - LICENSE | 4 MD5 | 37 ++++--- NAMESPACE | 7 - NEWS.md | 14 +- R/check.R |only R/keys.R |only R/new.R | 87 +++++++++++------ R/sheet2xml.R | 10 +- R/utils.R | 39 ++++++++ README.md | 208 +++++++++++++++++++++++------------------- inst/doc/tab2xml.R | 10 +- inst/doc/tab2xml.Rmd | 36 ++++++- inst/doc/tab2xml.html | 213 +++++++++++++++++++++++++------------------- man/check_tab.Rd |only man/is_cell_empty.Rd |only man/remove_empty_nodes.Rd |only man/sheet2xml.Rd | 78 ++++++++-------- man/validate_fk.Rd |only man/validate_pk.Rd |only tests/testthat/test-check.R |only tests/testthat/test-keys.R |only tests/testthat/test-utils.R | 45 +++++++++ vignettes/tab2xml.Rmd | 36 ++++++- 24 files changed, 542 insertions(+), 288 deletions(-)
Title: Create Custom 'Rstudio' Keyboard Shortcuts
Description: Create custom keyboard shortcuts to examine code selected in the 'Rstudio' editor.
F3 can for example yield 'str(selection)' and F7 open the source
code of CRAN and base package functions on 'github'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rskey versions 0.4.4 dated 2020-06-05 and 0.4.19 dated 2025-04-01
DESCRIPTION | 12 +- MD5 | 28 +++--- NAMESPACE | 7 + R/addins.R | 32 ++++++- R/href.R |only R/selectobject.R | 2 R/setKeyboardBindings.R | 184 +++++++++++++++++++++------------------------ R/umlaut2ascii.R |only README.md | 15 ++- inst/keyboardRlabels.ods |binary inst/rstudio/addins.dcf | 26 ++++++ man/addins.Rd | 14 +++ man/bdoc.Rd | 40 ++++----- man/href.Rd |only man/selectobject.Rd | 2 man/setKeyboardBindings.Rd | 12 ++ man/umlaut2ascii.Rd |only 17 files changed, 226 insertions(+), 148 deletions(-)
Title: Human 'Connectome' Project Interface
Description: Downloads and reads data from Human 'Connectome' Project
<https://db.humanconnectome.org> using Amazon Web Services ('AWS')
'S3' buckets.
Author: John Muschelli [aut, cre],
Adi Gherman [ctb]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurohcp versions 0.9.0 dated 2020-10-14 and 0.11.0 dated 2025-04-01
DESCRIPTION | 12 MD5 | 32 NEWS.md | 9 R/bucketlist.R | 14 R/download_hcp_file.R | 13 R/get_hcp_file.R | 4 R/hcp_list_files.R | 87 - R/make_aws_call.R | 8 R/parse_list_files.R | 11 README.md | 4102 +++++++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/hcp.R | 32 inst/doc/hcp.html | 303 +-- man/bucketlist.Rd | 2 man/get_hcp_file.Rd | 4 man/hcp_list_files.Rd | 28 man/make_aws_call.Rd | 8 17 files changed, 4441 insertions(+), 228 deletions(-)
Title: Simultaneous Truth and Performance Level Estimation
Description: An implementation of Simultaneous Truth and
Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This
method is used when there are multiple raters for an object, typically an
image, and this method fuses these ratings into one rating. It uses an
expectation-maximization method to estimate this rating and the individual
specificity/sensitivity for each rater.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between stapler versions 0.7.1 dated 2020-01-09 and 0.8.0 dated 2025-04-01
DESCRIPTION | 9 - MD5 | 30 ++-- NEWS.md | 8 + R/staple.R | 59 ++++++++ R/staple_binimg.R | 9 + R/staple_binmat.R | 3 R/staple_multi_mat.R | 55 +++++++- README.md | 11 - build/vignette.rds |binary inst/doc/staple_example.R | 8 - inst/doc/staple_example.html | 260 ++++++++++++++++++++++----------------- man/staple.Rd | 59 ++++++++ man/staple_bin_img.Rd | 8 + man/staple_multi_mat.Rd | 6 tests/testthat/test-binmat-bad.R | 6 tests/testthat/test-binmat.R | 4 16 files changed, 383 insertions(+), 152 deletions(-)
Title: Multi-Model Inference
Description: Tools for model selection and model averaging with support for a
wide range of statistical models. Automated model selection through
subsets of the maximum model, with optional constraints for model
inclusion. Averaging of model parameters and predictions based on
model weights derived from information criteria (AICc and alike)
or custom model weighting schemes.
Author: Kamil Barton [aut, cre]
Maintainer: Kamil Barton <kamil.barton@go2.pl>
Diff between MuMIn versions 1.48.4 dated 2024-06-22 and 1.48.11 dated 2025-04-01
DESCRIPTION | 18 ++--- MD5 | 130 +++++++++++++++++++++------------------- NAMESPACE | 15 +++- NEWS | 39 ++++++++++-- R/class-fitdistr.R |only R/class-glmmTMB.R | 3 R/class-unmarkedFit.R | 53 +++++++--------- R/coefTable.R | 2 R/dredge.R | 41 ++++++------ R/frmsplit.R |only R/getAllTerms.R | 4 - R/getspecs.R |only R/methods-averaging.R | 2 R/model.names.R | 2 R/model.sel.R | 15 ++-- R/model.selection.R | 7 -- R/modelspecs.R |only R/modify.model.selection.R | 3 R/pdredge.R | 2 R/plot.model.selection.R | 19 ----- R/predict.R | 2 R/r.squaredLR.R | 39 ++++++++---- R/rbind.model.selection.R | 8 ++ R/substitution.R | 9 +- R/umf_specs.R | 34 +++++----- R/unfckme.R | 28 +++++--- R/utils-misc.R | 89 ++++++++++++++++++++------- R/utils-models.R | 4 - data/Beetle.rda |binary data/Cement.rda |binary data/GPA.rda |binary demo/pdredge.pcount.R | 5 - man/AICc.Rd | 18 ++--- man/BGweights.Rd | 20 +++--- man/ICs.Rd | 21 +++--- man/MuMIn-package.Rd | 30 ++++----- man/QAIC.Rd | 12 +-- man/QIC.Rd | 25 ++++--- man/Weights.Rd | 56 +++++++++++------ man/arm.glm.Rd | 26 ++++---- man/bootWeights.Rd | 10 +-- man/coefplot.Rd | 8 +- man/cos2weights.Rd | 6 - man/dredge.Rd | 134 +++++++++++++++++++++--------------------- man/exprApply.Rd | 10 +-- man/get.models.Rd | 12 +-- man/jackknifeWeights.Rd | 16 ++--- man/macros/macros.Rd | 24 ++++++- man/manip-formula.Rd | 6 - man/merge.model.selection.Rd | 6 - man/model-utils.Rd | 20 ++++-- man/model.avg.Rd | 28 ++++---- man/model.sel.Rd | 16 ++--- man/model.selection.object.Rd | 12 ++- man/nested.Rd | 6 - man/par.avg.Rd | 2 man/pdredge.Rd | 4 - man/plot.model.selection.Rd | 28 ++++---- man/predict.averaging.Rd | 12 +-- man/r.squaredGLMM.Rd | 25 ++++--- man/r.squaredLR.Rd | 4 - man/stackingWeights.Rd | 6 - man/std.coef.Rd | 6 - man/stdize.Rd | 16 ++--- man/subset.model.selection.Rd | 6 - man/sumofweights.Rd | 4 - man/supported-classes.Rd | 28 +++++--- man/updateable.Rd | 76 ++++++++++++++--------- 68 files changed, 732 insertions(+), 580 deletions(-)
Title: Survival Trees to Fit Left-Truncated and Right-Censored and
Interval-Censored Survival Data
Description: Recursive partition algorithms designed for fitting survival trees with left-truncated and right-censored (LTRC) data, as well as interval-censored data.
The LTRC trees can also be used to fit survival trees with time-varying covariates.
Author: Wei Fu [aut],
Jeffrey Simonoff [aut],
Wenbo Jing [aut, cre]
Maintainer: Wenbo Jing <wj2093@stern.nyu.edu>
Diff between LTRCtrees versions 1.1.1 dated 2021-01-13 and 1.1.2 dated 2025-04-01
DESCRIPTION | 33 - MD5 | 12 R/LTRCART.R | 436 +++++++-------- build/vignette.rds |binary inst/doc/LTRCtrees.R | 278 ++++----- inst/doc/LTRCtrees.html | 1350 ++++++++++++++++++++++++++---------------------- man/LTRCART.Rd | 258 ++++----- 7 files changed, 1255 insertions(+), 1112 deletions(-)
Title: 'Leanpub' API Interface
Description: Provides access to the 'Leanpub' API
<https://leanpub.com/help/api> for gathering information about
publications and submissions to the 'Leanpub' platform.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between leanpubr versions 0.3.1 dated 2018-08-16 and 0.4.0 dated 2025-04-01
DESCRIPTION | 18 +- MD5 | 55 +++--- NAMESPACE | 4 NEWS.md | 8 R/aaa_utils.R | 16 + R/lp_book.R | 2 R/lp_coupons.R | 2 R/lp_download.R | 6 R/lp_get_wrapper.R | 35 ++-- R/lp_job_status.R | 2 R/lp_preview.R | 4 R/lp_publish.R | 5 R/lp_quiz_responses.R |only R/lp_sales.R | 49 +++++ README.md |only build/vignette.rds |binary inst/doc/getting_data_leanpub.R | 7 inst/doc/getting_data_leanpub.Rmd | 6 inst/doc/getting_data_leanpub.html | 312 +++++++++++++++++++------------------ man/lp_book_info.Rd | 7 man/lp_coupons.Rd | 4 man/lp_download.Rd | 16 + man/lp_get_wrapper.Rd | 26 ++- man/lp_job_status.Rd | 7 man/lp_links.Rd | 2 man/lp_preview.Rd | 6 man/lp_publish.Rd | 4 man/lp_quiz_responses.Rd |only man/lp_sales.Rd | 32 +++ vignettes/getting_data_leanpub.Rmd | 6 30 files changed, 387 insertions(+), 254 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.1.9 dated 2024-11-08 and 0.2.0 dated 2025-04-01
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 4 R/load.R | 15 - build/vignette.rds |binary inst/doc/performance.R | 428 +++++++++++++++++++-------------------- inst/doc/performance.Rmd | 6 inst/doc/performance.html | 22 +- man/filearray.Rd | 6 tests/testthat/test-method_add.R | 8 tests/testthat/test-method_sub.R | 8 vignettes/performance.Rmd | 6 12 files changed, 276 insertions(+), 255 deletions(-)
Title: Forward Selection using Concordance/C-Index
Description: Performs forward model selection, using the C-index/concordance
in survival analysis models.
Author: John Muschelli [aut, cre] ,
Andrew Leroux [aut]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between cforward versions 0.1.0 dated 2021-03-29 and 0.2.0 dated 2025-04-01
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/cforward.R | 16 ++++++++-------- README.md | 2 ++ man/cforward.Rd | 8 ++++---- man/estimate_concordance.Rd | 8 ++++---- man/figures/README-pressure-1.png |binary 8 files changed, 33 insertions(+), 27 deletions(-)
Title: A Toolbox for Writing Pretty Papers and Reports
Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based
reports and to prettify the output of various estimated models.
Author: Benjamin Hofner [aut, cre] ,
Romain Francois [ctb],
Kurt Hornik [ctb],
Martin Maechler [ctb],
David Dahl [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between papeR versions 1.0-5 dated 2021-03-22 and 1.0-6 dated 2025-04-01
ChangeLog | 32 +++ DESCRIPTION | 22 +- MD5 | 34 +-- NAMESPACE | 2 R/helpers.R | 4 R/summarize.R | 38 +-- README.md | 1 build/vignette.rds |binary inst/CITATION | 6 inst/NEWS.Rd | 19 + inst/doc/papeR_introduction.R | 14 - inst/doc/papeR_introduction.html | 403 ++++++++++++++++++++++++--------------- inst/doc/papeR_with_latex.pdf |binary man/Anova.lme.Rd | 4 man/confint.Rd | 4 man/labels.data.frame.Rd | 4 man/papeR-package.Rd | 4 man/prettify.Rd | 12 - 18 files changed, 387 insertions(+), 216 deletions(-)
Title: Example T1 Structural Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Structural T1 magnetic resonance imaging ('MRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.t1 versions 1.7.0 dated 2018-08-13 and 1.8.0 dated 2025-04-01
DESCRIPTION | 21 +++++++++++++-------- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/delete_t1_data.R | 2 +- R/download_t1_data.R | 15 ++++++++++++--- R/get_t1_filenames.R | 9 ++++++++- README.md | 8 +++++--- man/delete_t1_data.Rd | 2 +- man/download_t1_data.Rd | 5 ++++- man/get_t1_filenames.Rd | 5 ++++- 11 files changed, 63 insertions(+), 29 deletions(-)
Title: Example Functional Imaging Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Functional magnetic resonance imaging ('fMRI')
data from the 'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.fmri versions 1.7.0 dated 2018-08-13 and 1.8.0 dated 2025-04-01
DESCRIPTION | 19 ++++++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/delete_fmri_data.R | 2 +- R/download_fmri_data.R | 2 +- R/get_fmri_filenames.R | 2 +- README.md | 7 ++++--- man/delete_fmri_data.Rd | 2 +- man/download_fmri_data.Rd | 2 +- man/get_fmri_filenames.Rd | 2 +- 10 files changed, 35 insertions(+), 25 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.11.2 dated 2024-12-12 and 1.0.0 dated 2025-04-01
glmmrBase-0.11.2/glmmrBase/src/heckman.cpp |only glmmrBase-1.0.0/glmmrBase/DESCRIPTION | 8 glmmrBase-1.0.0/glmmrBase/MD5 | 45 +- glmmrBase-1.0.0/glmmrBase/R/R6Model.R | 42 + glmmrBase-1.0.0/glmmrBase/R/RcppExports.R | 44 +- glmmrBase-1.0.0/glmmrBase/R/extrafunctions.R | 8 glmmrBase-1.0.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.0.0/glmmrBase/inst/cmdstan/mcml.stan | 12 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/covariance.hpp | 36 + glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/general.h | 6 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/hsgpcovariance.hpp | 9 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/linearpredictor.hpp | 3 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/maths.h | 36 - glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/matrixfield.h | 4 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 59 +- glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modelmcmc.hpp | 35 - glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 219 ++++++---- glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/nngpcovariance.hpp | 17 glmmrBase-1.0.0/glmmrBase/inst/include/glmmr/optim/lbfgs/Param.h | 12 glmmrBase-1.0.0/glmmrBase/inst/stan/mcml.stan | 12 glmmrBase-1.0.0/glmmrBase/man/Model.Rd | 2 glmmrBase-1.0.0/glmmrBase/src/RcppExports.cpp | 12 glmmrBase-1.0.0/glmmrBase/src/model_module.cpp | 164 +++---- glmmrBase-1.0.0/glmmrBase/src/stanExports_mcml.h | 12 24 files changed, 487 insertions(+), 310 deletions(-)
Title: Google Citation Parser
Description: Scrapes Google Citation pages and creates data frames of
citations over time.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between gcite versions 0.10.1 dated 2019-03-06 and 0.11.0 dated 2025-04-01
DESCRIPTION | 11 ++----- MD5 | 64 ++++++++++++++++++++++---------------------- NEWS.md | 5 +++ R/author_cloud.R | 2 - R/gcite.R | 2 - R/gcite_author_info.R | 8 ++--- R/gcite_citation_index.R | 2 - R/gcite_citation_page.R | 22 ++++++++++----- R/gcite_cite_over_time.R | 2 - R/gcite_graph.R | 5 ++- R/gcite_main_graph.R | 2 - R/gcite_paper_df.R | 2 - R/gcite_papers.R | 2 - R/gcite_user_info.R | 2 - R/gcite_username.R | 21 ++++++++------ R/gcite_wordcloud_spec.R | 4 +- R/set_cookies_txt.R | 4 +- README.md | 11 ++----- man/author_cloud.Rd | 25 ++++++++++++----- man/gcite.Rd | 16 ++++++++--- man/gcite_author_info.Rd | 22 ++++++++++----- man/gcite_citation_index.Rd | 2 - man/gcite_citation_page.Rd | 19 ++++--------- man/gcite_cite_over_time.Rd | 2 - man/gcite_graph.Rd | 2 - man/gcite_main_graph.Rd | 2 - man/gcite_paper_df.Rd | 5 +-- man/gcite_papers.Rd | 2 - man/gcite_user_info.Rd | 14 +++++++-- man/gcite_username.Rd | 5 +-- man/gcite_wordcloud.Rd | 8 ++++- man/gcite_wordcloud_spec.Rd | 17 ++++++++--- man/set_cookies_txt.Rd | 4 +- 33 files changed, 184 insertions(+), 132 deletions(-)
Title: Display Differences Between Two Files using Codediff Library
Description: An R interface to the 'codediff' JavaScript library (a copy of which is included in the package,
see <https://github.com/danvk/codediff.js> for information).
Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between diffr versions 0.1 dated 2017-02-27 and 0.3.0 dated 2025-04-01
DESCRIPTION | 9 ++++----- MD5 | 12 +++++++----- NEWS.md |only R/diffr.R | 4 ++-- inst/htmlwidgets/lib/codediff/codediff.css | 2 +- man/diffr.Rd | 21 +++++++++++++++------ man/diffrOutput.Rd | 4 ++-- man/img |only 8 files changed, 31 insertions(+), 21 deletions(-)
Title: Helper Functions to 'misc3d' and 'rgl' Packages for Brain
Imaging
Description: This includes functions for creating 3D and 4D images using
'WebGL', 'rgl', and 'JavaScript' commands.
This package relies on the X toolkit ('XTK',
<https://github.com/xtk/X#readme>).
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between brainR versions 1.6.0 dated 2019-12-05 and 1.7.0 dated 2025-04-01
DESCRIPTION | 10 ++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/brainR-package.R | 5 ++--- R/makeScene.R | 4 ++-- R/scene4d.R | 1 + R/write4D.R | 16 ++++++++-------- R/write4D.file.R | 6 +++--- R/writeTrianglesSTL.R | 2 +- README.md | 15 +++++++-------- man/brainR-package.Rd | 2 +- man/makeScene.Rd | 4 ++-- man/write4D.Rd | 6 +++--- man/write4D.file.Rd | 4 ++-- man/writeTrianglesSTL.Rd | 2 +- 15 files changed, 55 insertions(+), 54 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.15.2 dated 2024-08-20 and 1.15.3.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 41 +++-- NAMESPACE | 2 R/checkFilePath.R | 296 +++++++++++++++++++++--------------------- R/matchMatrixLinesToRef.R | 22 +-- R/moderTest2grp.R | 14 - R/nonAmbiguousNum.R | 20 +- R/normalizeThis.R | 33 ++-- R/summarizeCols.R | 1 R/top3mean.R |only R/trimRedundText.R | 1 R/trimmedMean.R | 3 build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 28 +-- inst/doc/wrMiscVignette1.html | 73 ++++------ man/checkFilePath.Rd | 14 - man/dot-doubleExt.Rd |only man/dot-normalize.Rd | 4 man/moderTest2grp.Rd | 14 - man/nonAmbiguousNum.Rd | 14 + man/normalizeThis.Rd | 13 - man/top3mean.Rd |only man/trimmedMean.Rd | 1 23 files changed, 316 insertions(+), 284 deletions(-)
Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modelling mutations in
pedigrees with marker data, as used e.g. in likelihood computations
with microsatellite data. Implemented models include equal,
proportional and stepwise models, as well as random models for
experimental work, and custom models allowing the user to apply any
valid mutation matrix. Allele lumping is done following the
lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
Author: Magnus Dehli Vigeland [aut, cre]
,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedmut versions 0.7.1 dated 2023-11-04 and 0.8.0 dated 2025-04-01
DESCRIPTION | 8 MD5 | 38 +- NAMESPACE | 2 NEWS.md | 29 + R/adjustRate.R |only R/makeReversible.R |only R/mutRate.R | 24 - R/mutationMatrix.R | 561 ++++++++++++++++++++++++----------- R/mutationModel.R | 14 R/stepwiseReversible.R | 26 + R/utils.R | 31 - README.md | 69 ++-- man/adjustRate.Rd |only man/makeReversible.Rd |only man/mutRate.Rd | 12 man/mutationMatrix.Rd | 60 ++- man/mutationModel.Rd | 4 man/pedmut-package.Rd | 54 +-- man/stepwiseReversible.Rd | 7 tests/testthat/test-mutationMatrix.R | 30 + tests/testthat/test-mutationModel.R | 6 tests/testthat/test-properties.R | 11 22 files changed, 641 insertions(+), 345 deletions(-)
Title: Data Integration with Two-Way Orthogonal Partial Least Squares
Description: Performs the O2PLS data integration method for two datasets, yielding joint and data-specific parts for each dataset.
The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data.
It provides a rigorous and a faster alternative cross-validation method to select the number of components,
as well as functions to report proportions of explained variation and to construct plots of the results.
See the software article by el Bouhaddani et al (2018) <doi:10.1186/s12859-018-2371-3>,
and Trygg and Wold (2003) <doi:10.1002/cem.775>.
It also performs Sparse Group (Penalized) O2PLS, see Gu et al (2020) <doi:10.1186/s12859-021-03958-3> and cross-validation for the degree of sparsity.
Author: Said el Bouhaddani [aut, cre],
Zander Gu [aut],
Jeanine Houwing-Duistermaat [aut],
Geurt Jongbloed [aut],
Szymon Kielbasa [aut],
Hae-Won Uh [aut]
Maintainer: Said el Bouhaddani <s.elbouhaddani@umcutrecht.nl>
Diff between OmicsPLS versions 2.0.2 dated 2021-05-19 and 2.1.0 dated 2025-04-01
OmicsPLS-2.0.2/OmicsPLS/man/OmicsPLS.Rd |only OmicsPLS-2.1.0/OmicsPLS/DESCRIPTION | 40 + OmicsPLS-2.1.0/OmicsPLS/MD5 | 42 - OmicsPLS-2.1.0/OmicsPLS/NAMESPACE | 2 OmicsPLS-2.1.0/OmicsPLS/R/Crossval_OmicsPLS.R | 25 OmicsPLS-2.1.0/OmicsPLS/R/OmicsPLS.R | 75 +- OmicsPLS-2.1.0/OmicsPLS/R/OmicsPLS_o2m.R | 32 - OmicsPLS-2.1.0/OmicsPLS/build/partial.rdb |binary OmicsPLS-2.1.0/OmicsPLS/build/vignette.rds |binary OmicsPLS-2.1.0/OmicsPLS/inst/CITATION | 26 OmicsPLS-2.1.0/OmicsPLS/inst/doc/OmicsPLS_vignette.html | 489 ++++++++++++---- OmicsPLS-2.1.0/OmicsPLS/man/OmicsPLS-package.Rd |only OmicsPLS-2.1.0/OmicsPLS/man/adjR2.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/crossval_o2m.Rd | 11 OmicsPLS-2.1.0/OmicsPLS/man/crossval_o2m_adjR2.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/impute_matrix.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/loadings.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/loocv.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/loocv_combi.Rd | 5 OmicsPLS-2.1.0/OmicsPLS/man/plot.o2m.Rd | 4 OmicsPLS-2.1.0/OmicsPLS/man/scores.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/man/summary.o2m.Rd | 2 OmicsPLS-2.1.0/OmicsPLS/tests/testthat/Rplots.pdf |binary 23 files changed, 538 insertions(+), 233 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.4 dated 2025-02-27 and 1.1.5 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 114 ++++++++++++++++++++--------------------- NEWS.md | 7 ++ R/LSest.R | 22 +++---- R/STVARconstruction.R | 2 R/data.R | 2 R/geneticAlgorithm.R | 14 ++--- R/loglikelihood.R | 12 ++-- R/miscellaneous.R | 6 +- R/parameterReforms.R | 6 +- R/pickParams.R | 18 +++--- inst/doc/sstvars-vignette.Rnw | 114 ++++++++++++++++++++--------------------- inst/doc/sstvars-vignette.pdf |binary man/GAfit.Rd | 16 ++--- man/STVAR.Rd | 14 ++--- man/alt_stvar.Rd | 2 man/change_parametrization.Rd | 10 +-- man/change_regime.Rd | 14 ++--- man/check_constraints.Rd | 2 man/check_params.Rd | 12 ++-- man/estim_LS.Rd | 6 +- man/estim_NLS.Rd | 6 +- man/filter_estimates.Rd | 2 man/fitSSTVAR.Rd | 2 man/fitSTVAR.Rd | 4 - man/fitbsSSTVAR.Rd | 14 ++--- man/get_boldA_eigens_par.Rd | 12 ++-- man/get_omega_eigens_par.Rd | 12 ++-- man/get_regime_autocovs.Rd | 10 +-- man/get_regime_means.Rd | 12 ++-- man/get_residuals.Rd | 12 ++-- man/in_paramspace.Rd | 10 +-- man/iterate_more.Rd | 2 man/loglikelihood.Rd | 12 ++-- man/pick_Am.Rd | 8 +- man/pick_Ami.Rd | 8 +- man/pick_Omegas.Rd | 8 +- man/pick_W.Rd | 10 +-- man/pick_allA.Rd | 8 +- man/pick_distpars.Rd | 8 +- man/pick_lambdas.Rd | 10 +-- man/pick_phi0.Rd | 12 ++-- man/pick_regime.Rd | 14 ++--- man/pick_weightpars.Rd | 8 +- man/random_ind.Rd | 4 - man/reform_constrained_pars.Rd | 10 +-- man/regime_distance.Rd | 6 +- man/reorder_B_columns.Rd | 2 man/smart_ind.Rd | 14 ++--- man/sort_impactmats.Rd | 10 +-- man/sort_regimes.Rd | 10 +-- man/stab_conds_satisfied.Rd | 8 +- man/standard_errors.Rd | 12 ++-- man/swap_B_signs.Rd | 2 man/swap_parametrization.Rd | 2 man/usacpu.Rd | 2 vignettes/refs.bib | 10 +++ vignettes/sstvars-vignette.Rnw | 114 ++++++++++++++++++++--------------------- 58 files changed, 415 insertions(+), 394 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client written in 'C++' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between RMySQL versions 0.11.0 dated 2025-02-08 and 0.11.1 dated 2025-04-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.in | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Implicit Association Test Scores Using Robust Statistics
Description: Compute several variations of the Implicit Association Test (IAT) scores, including the D scores (Greenwald, Nosek, Banaji, 2003, <doi:10.1037/0022-3514.85.2.197>) and the new scores that were developed using robust statistics (Richetin, Costantini, Perugini, and Schonbrodt, 2015, <doi:10.1371/journal.pone.0129601>).
Author: Giulio Costantini [aut, cre]
Maintainer: Giulio Costantini <costantinigiulio@gmail.com>
Diff between IATscores versions 0.2.7 dated 2020-05-09 and 0.2.8 dated 2025-04-01
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS.md | 5 +++-- inst/CITATION | 35 ++++++++++++----------------------- man/Tgraph.Rd | 5 ++++- 5 files changed, 29 insertions(+), 35 deletions(-)
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <rpackages@fredriksavje.com>
Diff between distances versions 0.1.11 dated 2024-07-31 and 0.1.12 dated 2025-04-01
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ NEWS.md | 5 +++ R/distances-package.R | 5 +-- man/distances-package.Rd | 13 ++++++++ src/Makevars | 2 - src/libann/Makefile | 2 - src/libann/include/ANN/ANNperf.h | 2 - src/libann/src/ANN.cpp | 6 +-- src/libann/src/kd_dump.cpp | 2 - src/libann/src/perf.cpp | 61 +++++++++++++++++++-------------------- 11 files changed, 73 insertions(+), 55 deletions(-)
Title: Spanish version of orloca package. Modelos de localizacion en
investigacion operativa
Description: Help and demo in Spanish of the orloca package. Ayuda y demo en espanol del paquete orloca. Objetos y metodos para manejar y resolver el problema de localizacion de suma minima, tambien conocido como problema de Fermat-Weber. El problema de localizacion de suma minima busca un punto tal que la suma ponderada de las distancias a los puntos de demanda se minimice. Vease "The Fermat-Weber location problem revisited" por Brimberg, Mathematical Programming, 1, pag. 71-76, 1995. <DOI: 10.1007/BF01592245>.
Se usan algoritmos generales de optimizacion global para resolver el problema, junto con el metodo especifico Weiszfeld, vease "Sur le point pour lequel la Somme des distance de n points donnes est minimum", por Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pag. 355-386, 1937 o "On the point for which the sum of the distances to n given points is minimum", por E. Weiszfeld y F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z& [...truncated...]
Author: Manuel Munoz-Marquez [aut, cre]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between orloca.es versions 4.9 dated 2020-03-06 and 5.5 dated 2025-04-01
DESCRIPTION | 28 ++++++++++++------------ MD5 | 51 ++++++++++++++++++++++---------------------- NAMESPACE | 2 + build |only man/andalucia.Rd | 2 - man/as-methods.Rd | 6 ----- man/as.data.frame.loca.p.Rd | 11 ++++----- man/as.loca.p.Rd | 2 - man/as.loca.p.data.frame.Rd | 2 - man/as.loca.p.matrix.Rd | 2 - man/as.matrix.loca.p.Rd | 2 - man/contour.loca.p.Rd | 2 - man/distsum.Rd | 2 - man/distsumgra.Rd | 2 - man/distsuml2.Rd | 2 - man/distsuml2min.Rd | 2 - man/distsumlp.Rd | 2 - man/distsumlpmin.Rd | 2 - man/distsummin.Rd | 2 - man/loca.p.Rd | 4 +-- man/orloca.es-package.Rd | 14 ++++++++---- man/persp.loca.p.Rd | 2 - man/plot.Rd | 4 +-- man/rloca.p.Rd | 2 - man/zsum.Rd | 2 - man/zsumgra.Rd | 2 - man/zsummin.Rd | 2 - 27 files changed, 80 insertions(+), 76 deletions(-)
Title: Optimising Random Forest Stability by Determining the Optimal
Number of Trees
Description: Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.
Author: Thomas Martin Lange [cre, aut]
,
Felix Heinrich [ctb]
Maintainer: Thomas Martin Lange <thomas.lange@uni-goettingen.de>
Diff between optRF versions 1.1.0 dated 2025-02-03 and 1.2.0 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 56 +++++++++++--------- NAMESPACE | 1 NEWS.md | 14 +++++ R/measure_stability.R |only R/opt_importance.R | 37 ++++++++----- R/opt_prediction.R | 42 +++++++++------ R/plot_stability.R | 10 +-- R/utils.R | 31 ++++++++--- README.md | 4 - build/vignette.rds |binary inst/CITATION | 9 +-- inst/doc/optRF.R | 17 ++++++ inst/doc/optRF.Rmd | 31 +++++++++++ inst/doc/optRF.html | 31 +++++++++++ inst/doc/opt_importance.R | 19 ++++++ inst/doc/opt_importance.Rmd | 36 +++++++++++- inst/doc/opt_importance.html | 40 +++++++++++++- inst/doc/opt_prediction.R | 17 ++++++ inst/doc/opt_prediction.Rmd | 32 ++++++++++- inst/doc/opt_prediction.html | 37 ++++++++++++- man/figures |only man/measure_stability.Rd |only man/opt_importance.Rd | 12 ++-- man/opt_prediction.Rd | 12 ++-- man/plot_stability.Rd | 8 +- vignettes/optRF.Rmd | 31 +++++++++++ vignettes/optRF_vignette_stabilityData.Rda |only vignettes/opt_importance.Rmd | 36 +++++++++++- vignettes/opt_importance_vignette_stabilityData.Rda |only vignettes/opt_prediction.Rmd | 32 ++++++++++- vignettes/opt_prediction_vignette_stabilityData.Rda |only 32 files changed, 495 insertions(+), 106 deletions(-)
Title: Compound Annual Growth Rate
Description: A time series usually does not have a uniform growth rate. Compound Annual Growth Rate measures the average annual growth over a given period. More details can be found in Bardhan et al. (2022) <DOI:10.18805/ag.D-5418>.
Author: Debopam Rakshit [aut, cre],
Dwaipayan Bardhan [aut]
Maintainer: Debopam Rakshit <rakshitdebopam@yahoo.com>
Diff between CAGR versions 1.1.0 dated 2024-03-02 and 1.1.1 dated 2025-04-01
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 ++ R/CAGR.R | 51 ++++++++++++++++++++++++++++++++++++++++----------- man/CAGR.Rd | 6 +++--- man/LLTM.Rd |only man/data.first.Rd | 4 ++-- man/data.last.Rd | 4 ++-- man/n.years.Rd | 4 ++-- 9 files changed, 64 insertions(+), 31 deletions(-)
Title: In-Code Documentation for 'GAMS'
Description: A collection of tools which extract a model documentation from 'GAMS' code and comments.
In order to use the package you need to install 'pandoc' and 'pandoc-citeproc'
first (<https://pandoc.org/>).
Author: Jan Philipp Dietrich [aut, cre],
Kristine Karstens [aut],
David Klein [aut],
Lavinia Baumstark [aut],
Falk Benke [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between goxygen versions 1.0.3 dated 2020-08-16 and 1.4.5 dated 2025-04-01
goxygen-1.0.3/goxygen/inst/templates/ming.css |only goxygen-1.0.3/goxygen/inst/templates/template.latex |only goxygen-1.0.3/goxygen/tests/testthat/test-travisCI.R |only goxygen-1.4.5/goxygen/DESCRIPTION | 22 goxygen-1.4.5/goxygen/MD5 | 72 +- goxygen-1.4.5/goxygen/NAMESPACE | 1 goxygen-1.4.5/goxygen/R/appendExtraPageBlocks.R |only goxygen-1.4.5/goxygen/R/buildHTML.R | 169 ++--- goxygen-1.4.5/goxygen/R/buildTEX.R | 23 goxygen-1.4.5/goxygen/R/chooseTemplate.R |only goxygen-1.4.5/goxygen/R/createListModularCode.R | 301 +++++---- goxygen-1.4.5/goxygen/R/createListSimpleCode.R | 46 - goxygen-1.4.5/goxygen/R/createModulePage.R | 95 +- goxygen-1.4.5/goxygen/R/extractDocumentation.R | 165 ++-- goxygen-1.4.5/goxygen/R/flattenPageBlockList.R |only goxygen-1.4.5/goxygen/R/goxygen.R | 140 ++-- goxygen-1.4.5/goxygen/R/helper_functions.R | 108 +-- goxygen-1.4.5/goxygen/R/mergeDocumentation.R | 10 goxygen-1.4.5/goxygen/R/oldBuildHTML.R | 2 goxygen-1.4.5/goxygen/README.md | 19 goxygen-1.4.5/goxygen/build/vignette.rds |binary goxygen-1.4.5/goxygen/inst/doc/goxygen.R | 4 goxygen-1.4.5/goxygen/inst/doc/goxygen.Rmd | 26 goxygen-1.4.5/goxygen/inst/doc/goxygen.html | 332 +++++++--- goxygen-1.4.5/goxygen/inst/templates/classic.latex |only goxygen-1.4.5/goxygen/inst/templates/ming |only goxygen-1.4.5/goxygen/inst/templates/ming.html5 | 10 goxygen-1.4.5/goxygen/man/appendExtraPageBlocks.Rd |only goxygen-1.4.5/goxygen/man/buildHTML.Rd | 13 goxygen-1.4.5/goxygen/man/buildTEX.Rd | 12 goxygen-1.4.5/goxygen/man/chooseTemplate.Rd |only goxygen-1.4.5/goxygen/man/createListModularCode.Rd | 10 goxygen-1.4.5/goxygen/man/createListSimpleCode.Rd | 2 goxygen-1.4.5/goxygen/man/createModulePage.Rd | 2 goxygen-1.4.5/goxygen/man/dot-section.Rd |only goxygen-1.4.5/goxygen/man/extractDocumentation.Rd | 14 goxygen-1.4.5/goxygen/man/flattenPageBlockList.Rd |only goxygen-1.4.5/goxygen/man/goxygen.Rd | 43 - goxygen-1.4.5/goxygen/tests/testthat/test-appendExtraPageBlocks.R |only goxygen-1.4.5/goxygen/tests/testthat/test-flattenPageBlockList.R |only goxygen-1.4.5/goxygen/tests/testthat/test-goxygen.R | 75 +- goxygen-1.4.5/goxygen/vignettes/goxygen.Rmd | 26 42 files changed, 1060 insertions(+), 682 deletions(-)
Title: Generalized Order-Restricted Information Criterion
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
Author: Daniel Gerhard [aut, cre],
Rebecca M. Kuiper [aut]
Maintainer: Daniel Gerhard <00gerhard@gmail.com>
Diff between goric versions 1.1-2 dated 2021-04-19 and 1.1-3 dated 2025-04-01
DESCRIPTION | 8 - MD5 | 18 +-- build/vignette.rds |binary inst/doc/goric.R | 4 inst/doc/goric.Rmd | 4 inst/doc/goric.html | 285 +++++++++++++++++++++++++++++----------------------- man/orgls.Rd | 6 - man/orglsSet.Rd | 4 man/orlm.Rd | 2 vignettes/goric.Rmd | 4 10 files changed, 187 insertions(+), 148 deletions(-)
Title: Simple Animated Plots for R
Description: Simple animated versions of basic R plots, using the 'animation'
package. Includes animated versions of plot, barplot, persp, contour,
filled.contour, hist, curve, points, lines, text, symbols, segments, and
arrows.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between anim.plots versions 0.2.2 dated 2021-04-30 and 0.2.3 dated 2025-04-01
DESCRIPTION | 15 + MD5 | 18 +- NEWS.md | 8 - R/anim.plots.R | 3 R/postprocessing.R | 4 build/vignette.rds |binary inst/doc/anim.plots-stub.R | 8 - inst/doc/anim.plots-stub.html | 331 ++++++++++++++++++++++++++++++++---------- man/anim.plots-package.Rd | 13 + man/anim.save.Rd | 4 10 files changed, 307 insertions(+), 97 deletions(-)
Title: Strategy Estimation
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Author: Fabian Dvorak [aut, cre]
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Diff between stratEst versions 1.1.6 dated 2022-11-29 and 1.1.7 dated 2025-04-01
DESCRIPTION | 19 ++++++++++++------- MD5 | 36 ++++++++++++++++++------------------ R/is_stratEst_check.R | 2 +- R/is_stratEst_data.R | 2 +- R/is_stratEst_model.R | 2 +- R/is_stratEst_strategy.R | 2 +- R/summary_stratEst_data.R | 2 +- R/summary_stratEst_model.R | 2 +- README.md | 5 +++++ configure | 4 ++-- configure.ac | 6 +++--- inst/WORDLIST | 34 +++++++++++++++++++--------------- man/is.stratEst.check.Rd | 2 +- man/is.stratEst.data.Rd | 2 +- man/is.stratEst.model.Rd | 2 +- man/is.stratEst.strategy.Rd | 2 +- man/summary.stratEst.data.Rd | 2 +- man/summary.stratEst.model.Rd | 2 +- src/Makevars.win | 2 +- 19 files changed, 72 insertions(+), 58 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.9.0 dated 2025-01-20 and 0.8.10 dated 2025-04-01
DESCRIPTION | 12 +++--- MD5 | 17 +++++--- NAMESPACE | 2 - R/datasets.R | 27 ++++++++++++++ R/direct_export.R | 6 +-- R/sopls.R | 87 ++++++++++++++++++++++++++++++++++++---------- R/sopls_crossvalidation.R | 4 +- data/mobile.rda |only man/figures/mobile.png |only man/mobile.Rd |only man/reexports.Rd | 3 - 11 files changed, 118 insertions(+), 40 deletions(-)
Title: Analyze Two Choice Reaction Time Data with the D*M Method
Description: A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
Author: Don van den Bergh [aut, cre] ,
Stijn Verdonck [aut] ,
Francis Tuerlinckx [aut]
Maintainer: Don van den Bergh <donvdbergh@hotmail.com>
Diff between DstarM versions 0.4.0 dated 2020-08-28 and 0.5.0 dated 2025-04-01
DstarM-0.4.0/DstarM/R/DstarMmethodsDeprecated.R |only DstarM-0.5.0/DstarM/DESCRIPTION | 22 ++++++++++++++++------ DstarM-0.5.0/DstarM/MD5 | 21 ++++++++++----------- DstarM-0.5.0/DstarM/NAMESPACE | 1 + DstarM-0.5.0/DstarM/NEWS.md | 6 ++++++ DstarM-0.5.0/DstarM/R/Densities.R | 9 +++++---- DstarM-0.5.0/DstarM/R/estDstarM.R | 6 +++--- DstarM-0.5.0/DstarM/R/estND.R | 4 ++-- DstarM-0.5.0/DstarM/man/Voss.density.Rd | 8 ++++---- DstarM-0.5.0/DstarM/man/estDstarM.Rd | 6 +++--- DstarM-0.5.0/DstarM/man/estND.Rd | 4 ++-- DstarM-0.5.0/DstarM/src/RcppExports.cpp | 5 +++++ 12 files changed, 57 insertions(+), 35 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
Diff between CAESAR.Suite versions 0.2.1 dated 2025-03-25 and 0.2.2 dated 2025-04-01
DESCRIPTION | 6 +- MD5 | 8 +-- inst/doc/STMOB.html | 10 ++-- inst/doc/XeniumBC.html | 106 ++++++++++++++++++++++++------------------------- src/imfactor.cpp | 2 5 files changed, 67 insertions(+), 65 deletions(-)
Title: Interact with Peak Flow Data in the United Kingdom
Description: Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/data/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Author: Ilaria Prosdocimi [aut, cre] ,
Luke Shaw [aut]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between winfapReader versions 0.1-5.1 dated 2024-06-19 and 0.1-6 dated 2025-04-01
DESCRIPTION | 10 - MD5 | 28 ++-- NAMESPACE | 1 NEWS.md | 4 R/dateManupulations.R | 312 ++++++++++++++++++++++----------------------- R/get_winfapapi.R | 2 R/readerFuncs.R | 9 - build/vignette.rds |binary inst/doc/winfapReader.R | 98 +++++++------- inst/doc/winfapReader.Rmd | 10 - inst/doc/winfapReader.html | 129 +++++++++++------- man/get_pot.Rd | 2 man/read_cd3.Rd | 2 tests/testthat/testthat.R | 4 vignettes/winfapReader.Rmd | 10 - 15 files changed, 337 insertions(+), 284 deletions(-)
Title: Utilities for Handling Strings and Text
Description: Utilities for handling character vectors
that store human-readable text (either plain or with
markup, such as HTML or LaTeX). The package provides,
in particular, functions that help with the
preparation of plain-text reports, e.g. for expanding
and aligning strings that form the lines of such
reports. The package also provides generic functions for
transforming R objects to HTML and to plain text.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between textutils versions 0.4-1 dated 2024-04-01 and 0.4-2 dated 2025-04-01
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++-------- NAMESPACE | 1 NEWS | 18 ++++++++++- R/functions.R | 69 +++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/btable.pdf |binary inst/tinytest/test_HTMLrm.R | 10 +++--- inst/tinytest/test_insert.R | 5 ++- inst/tinytest/test_toHTML.R | 47 +++++++++++++++++++++++++++++ man/HTMLdecode.Rd | 9 +++-- man/insert.Rd | 4 +- man/toHTML.Rd | 18 +++++++---- 14 files changed, 174 insertions(+), 43 deletions(-)
Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame
Object
Description: An S3 class 'groupedHyperframe' that inherits from
hyper data frame. Batch processes on point-pattern hyper
column. Aggregation of function-value-table hyper
column(s) and numeric hyper column(s) over a nested
grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.1.0 dated 2025-03-25 and 0.2.1 dated 2025-04-01
groupedHyperframe-0.1.0/groupedHyperframe/R/fv_S3.R |only groupedHyperframe-0.1.0/groupedHyperframe/R/key1nonfinite.fv.R |only groupedHyperframe-0.1.0/groupedHyperframe/R/nncross_.R |only groupedHyperframe-0.1.0/groupedHyperframe/man/fvlist.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/groupedHyperframe.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/is.finite.fv.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/key1nonfinite-set.Rd |only groupedHyperframe-0.1.0/groupedHyperframe/man/op_fv.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/DESCRIPTION | 12 groupedHyperframe-0.2.1/groupedHyperframe/MD5 | 81 groupedHyperframe-0.2.1/groupedHyperframe/NAMESPACE | 18 groupedHyperframe-0.2.1/groupedHyperframe/R/0PACKAGE.R | 8 groupedHyperframe-0.2.1/groupedHyperframe/R/aggregate_fv.R | 52 groupedHyperframe-0.2.1/groupedHyperframe/R/aggregate_num.R | 100 - groupedHyperframe-0.2.1/groupedHyperframe/R/as.groupedHyperframe.R | 66 groupedHyperframe-0.2.1/groupedHyperframe/R/data_doc.R | 13 groupedHyperframe-0.2.1/groupedHyperframe/R/fvlist.R | 135 - groupedHyperframe-0.2.1/groupedHyperframe/R/groupedHyperframe.R | 48 groupedHyperframe-0.2.1/groupedHyperframe/R/grouped_ppp.R | 60 groupedHyperframe-0.2.1/groupedHyperframe/R/key1.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/mc_identical_by.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/nncross.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/op_hyperframe.R | 30 groupedHyperframe-0.2.1/groupedHyperframe/R/op_ppp.R | 22 groupedHyperframe-0.2.1/groupedHyperframe/R/op_ppplist.R | 26 groupedHyperframe-0.2.1/groupedHyperframe/R/pmean.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/slice.R |only groupedHyperframe-0.2.1/groupedHyperframe/R/user_hyperframe.R | 25 groupedHyperframe-0.2.1/groupedHyperframe/data/Ki67.rda |binary groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.R | 114 - groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.Rmd | 232 +- groupedHyperframe-0.2.1/groupedHyperframe/inst/doc/intro.html | 968 ++++++---- groupedHyperframe-0.2.1/groupedHyperframe/man/Ki67.Rd | 15 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_by_.Rd | 12 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_fv.Rd | 17 groupedHyperframe-0.2.1/groupedHyperframe/man/aggregate_num.Rd | 7 groupedHyperframe-0.2.1/groupedHyperframe/man/as.groupedHyperframe.Rd | 26 groupedHyperframe-0.2.1/groupedHyperframe/man/check_fvlist.Rd | 8 groupedHyperframe-0.2.1/groupedHyperframe/man/dot-nncross.Rd | 3 groupedHyperframe-0.2.1/groupedHyperframe/man/dot-slice.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/groupedHyperframe-package.Rd | 8 groupedHyperframe-0.2.1/groupedHyperframe/man/grouped_ppp.Rd | 13 groupedHyperframe-0.2.1/groupedHyperframe/man/key1.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/mc_identical_by.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/op_hyperframe.Rd | 23 groupedHyperframe-0.2.1/groupedHyperframe/man/op_ppp.Rd | 4 groupedHyperframe-0.2.1/groupedHyperframe/man/op_ppplist.Rd | 11 groupedHyperframe-0.2.1/groupedHyperframe/man/pmean.Rd |only groupedHyperframe-0.2.1/groupedHyperframe/man/user_hyperframe.Rd | 7 groupedHyperframe-0.2.1/groupedHyperframe/vignettes/intro.Rmd | 232 +- 50 files changed, 1263 insertions(+), 1133 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).
Author: Jenni Niku [aut, cre],
Wesley Brooks [aut],
Riki Herliansyah [aut],
Francis K.C. Hui [aut],
Pekka Korhonen [aut],
Sara Taskinen [aut],
Bert van der Veen [aut],
David I. Warton [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 2.0 dated 2024-11-26 and 2.0.1 dated 2025-04-01
gllvm-2.0.1/gllvm/DESCRIPTION | 10 gllvm-2.0.1/gllvm/MD5 | 98 +-- gllvm-2.0.1/gllvm/NAMESPACE | 9 gllvm-2.0.1/gllvm/NEWS.md | 29 + gllvm-2.0.1/gllvm/R/TMBtrait.R | 159 +++--- gllvm-2.0.1/gllvm/R/VP.gllvm.R | 94 ++- gllvm-2.0.1/gllvm/R/coefplot.gllvm.R | 2 gllvm-2.0.1/gllvm/R/getEnvironCov.gllvm.R | 129 ++-- gllvm-2.0.1/gllvm/R/gllvm.R | 87 +-- gllvm-2.0.1/gllvm/R/gllvm.TMB.R | 138 +++-- gllvm-2.0.1/gllvm/R/gllvm.auxiliary.R | 178 ++++-- gllvm-2.0.1/gllvm/R/gllvm.iter.R | 9 gllvm-2.0.1/gllvm/R/gllvm.makeform.R | 2 gllvm-2.0.1/gllvm/R/goodnessOfFit.gllvm.R |only gllvm-2.0.1/gllvm/R/logLik.gllvm.R | 7 gllvm-2.0.1/gllvm/R/phyloplot.gllvm.R | 8 gllvm-2.0.1/gllvm/R/plotVP.gllvm.R | 40 - gllvm-2.0.1/gllvm/R/predict.gllvm.R | 2 gllvm-2.0.1/gllvm/R/randomCoefplot.R | 16 gllvm-2.0.1/gllvm/R/residuals.gllvm.R | 117 ++-- gllvm-2.0.1/gllvm/R/se.gllvm.R | 71 +- gllvm-2.0.1/gllvm/R/summary.gllvm.R | 29 + gllvm-2.0.1/gllvm/README.md | 12 gllvm-2.0.1/gllvm/inst/doc/vignette1.Rmd | 6 gllvm-2.0.1/gllvm/inst/doc/vignette1.html | 53 +- gllvm-2.0.1/gllvm/inst/doc/vignette2.R | 3 gllvm-2.0.1/gllvm/inst/doc/vignette2.html | 15 gllvm-2.0.1/gllvm/inst/doc/vignette2.rmd | 5 gllvm-2.0.1/gllvm/inst/doc/vignette3.html | 606 +++++++++++------------ gllvm-2.0.1/gllvm/inst/doc/vignette4.html | 146 ++--- gllvm-2.0.1/gllvm/inst/doc/vignette5.html | 4 gllvm-2.0.1/gllvm/inst/doc/vignette6.Rmd | 27 - gllvm-2.0.1/gllvm/inst/doc/vignette6.html | 39 - gllvm-2.0.1/gllvm/inst/doc/vignette8.html | 218 ++++---- gllvm-2.0.1/gllvm/inst/doc/vignette9.Rmd | 12 gllvm-2.0.1/gllvm/inst/doc/vignette9.html | 12 gllvm-2.0.1/gllvm/man/AICc.Rd | 48 - gllvm-2.0.1/gllvm/man/VP.gllvm.Rd |only gllvm-2.0.1/gllvm/man/coefplot.gllvm.Rd | 2 gllvm-2.0.1/gllvm/man/getEnvironCov.gllvm.Rd | 6 gllvm-2.0.1/gllvm/man/gllvm.Rd | 20 gllvm-2.0.1/gllvm/man/goodnessOfFit.Rd |only gllvm-2.0.1/gllvm/man/phyloplot.gllvm.Rd | 3 gllvm-2.0.1/gllvm/src/gllvm.cpp | 210 ++++++- gllvm-2.0.1/gllvm/tests/testthat/test-fitgllvm.R | 14 gllvm-2.0.1/gllvm/vignettes/fit_4th.Rdata |only gllvm-2.0.1/gllvm/vignettes/rcoefs-1.png |binary gllvm-2.0.1/gllvm/vignettes/vignette1.Rmd | 6 gllvm-2.0.1/gllvm/vignettes/vignette2.rmd | 5 gllvm-2.0.1/gllvm/vignettes/vignette6.Rmd | 27 - gllvm-2.0.1/gllvm/vignettes/vignette9.Rmd | 12 gllvm-2.0/gllvm/man/varPartitioning.gllvm.Rd |only gllvm-2.0/gllvm/vignettes/fit_4th.RData |only 53 files changed, 1609 insertions(+), 1136 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] ,
Unicode, Inc. [dtc, cph]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.6-4 dated 2024-04-01 and 0.6-5 dated 2025-04-01
DESCRIPTION | 10 +++++----- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + NEWS | 8 ++++++++ R/data.R | 34 +++++++++++++++++++++++++++++++++- README.md | 20 +++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/tznames.RData |binary inst/doc/datetimeutils_examples.pdf |binary man/Easter.Rd |only man/date1904.Rd | 3 +-- man/rfc822t.Rd | 2 +- man/tznames.Rd | 2 +- 14 files changed, 72 insertions(+), 33 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), geeglm() (from package 'geepack'), ivreg() (from package 'AER'), ivreg() (from package 'ivreg' when
estimated by ordinary least squares), [...truncated...]
Author: James E. Pustejovsky [aut, cre]
,
Samuel Pekofsky [ctb],
Jingru Zhang [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.11 dated 2024-06-20 and 0.6.0 dated 2025-04-01
DESCRIPTION | 21 + MD5 | 51 ++- NEWS.md | 8 R/Wald_test.R | 138 +++++++++- R/coef_test.R | 96 +++++-- R/conf_int.R | 34 ++ R/geeglm.R | 3 R/rma-mv.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Wald-tests-in-clubSandwich.html | 167 ++++++------- inst/doc/meta-analysis-with-CRVE.html | 53 ++-- inst/doc/panel-data-CRVE.Rmd | 10 inst/doc/panel-data-CRVE.html | 95 ++++--- man/Wald_test.Rd | 53 +++- man/coef_test.Rd | 30 +- man/conf_int.Rd | 2 man/linear_contrast.Rd | 13 - tests/testthat/test_Wald.R | 126 +++++++++ tests/testthat/test_Wald_multiple_comparisons.R |only tests/testthat/test_coef.R | 69 +++++ tests/testthat/test_geeglm.R | 92 ++++++- tests/testthat/test_gls.R | 8 tests/testthat/test_impute_covariance_matrix.R | 6 tests/testthat/test_linear_contrast_multiple_comparisons.R |only tests/testthat/test_lm_robust.R |only tests/testthat/test_rma-mv.R | 62 ++-- vignettes/panel-data-CRVE.Rmd | 10 28 files changed, 841 insertions(+), 310 deletions(-)
Title: Small Area Estimation for Key Health and Demographic Indicators
from Household Surveys
Description: Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R 'shiny' application that helps public health analysts, policymakers, and researchers generate subnational estimates and prevalence maps for 150+ binary indicators from Demographic and Health Surveys (DHS). Basing its core SAE analysis workflow on the 'surveyPrev' package, the app ensures methodological rigor through guided model selection, automated fitting, and interactive visualization. For more details, visit <https://sae4health.stat.uw.edu/>.
Author: Yunhan Wu [cre, aut],
Qianyu Dong [aut],
Zehang R Li [aut],
Jon Wakefield [aut]
Maintainer: Yunhan Wu <wu-thomas@outlook.com>
Diff between sae4health versions 1.2.0 dated 2025-03-28 and 1.2.1 dated 2025-04-01
DESCRIPTION | 6 MD5 | 22 R/app_ui.R | 382 +++--- R/fct_analysis_helpers.R | 13 R/fct_helpers.R | 637 +++++----- R/fct_results_visual_helpers.R | 6 R/mod_country_specify.R | 2360 +++++++++++++++++++------------------- R/mod_landing_page.R | 760 ++++++------ R/mod_model_selection.R | 214 ++- R/prepare_preload_dat.R | 8 README.md | 11 tests/testthat/test-app-loading.R | 102 - 12 files changed, 2319 insertions(+), 2202 deletions(-)
Title: Machine Learning for Merging Satellite and Ground Precipitation
Data
Description: A machine learning algorithm that merges satellite and ground precipitation data using Random Forest for spatial prediction, residual modeling for bias correction, and quantile mapping for adjustment, ensuring accurate estimates across temporal scales and regions.
Author: Jonnathan Augusto Landi Bermeo [aut, cre, cph]
,
Alex Aviles [aut] ,
Dario Zhina [aut] ,
Marco Mogro [aut] ,
Anthony Guaman [aut]
Maintainer: Jonnathan Augusto Landi Bermeo <jonnathan.landi@outlook.com>
Diff between RFplus versions 1.4-0 dated 2025-03-10 and 1.5-4 dated 2025-03-31
DESCRIPTION | 8 - MD5 | 38 +++--- NEWS.md | 32 ++++- R/RFplus.R | 164 ++++++++++++++++------------ build/vignette.rds |binary data/BD_Insitu.RData |binary data/Cords_Insitu.RData |binary inst/NEWS | 13 ++ inst/doc/RFplus.Rmd | 224 +++++++++++++++++++------------------- inst/doc/RFplus.html | 91 +++++++-------- inst/extdata/BD_Insitu.csv | 242 +++++++++++++++++++++--------------------- inst/extdata/CHIRPS.nc |binary inst/extdata/Cords_Insitu.csv | 24 +--- inst/extdata/DEM.nc |binary inst/extdata/MSWEP.nc |binary man/BD_Insitu.Rd | 2 man/Cords_Insitu.Rd | 8 + man/RFplus.Rd | 24 +++- tests/testthat/test-RFplus.R | 2 vignettes/RFplus.Rmd | 224 +++++++++++++++++++------------------- 20 files changed, 581 insertions(+), 515 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to
impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable
selection and statistical inference. In this package, we have implemented robust
Bayesian variable selection with spike-and-slab priors under high-dimensional
linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models including robust Bayesian
group LASSO are also included. The Markov Chain Monte Carlo (MCMC) algorithms
of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.1.1 dated 2025-02-23 and 1.1.2 dated 2025-03-31
DESCRIPTION | 15 - MD5 | 73 +++---- NAMESPACE | 24 +- NEWS.md | 88 ++++---- R/NonRobust.R | 150 +++++++------- R/NonRobust_vc.R | 150 +++++++------- R/Robust_vc.R | 164 ++++++++-------- R/coverage.R | 75 +++---- R/coverage_lin.R | 22 +- R/coverage_vc.R | 88 ++++---- R/data.R | 104 +++++----- R/estimation.R | 81 ++++---- R/estimation_lin.R | 24 +- R/estimation_vc.R | 126 ++++++------ R/nonrobust_g.R |only R/nonrobust_lin.R | 75 +++---- R/pqrBayes-package.R | 120 +++++------ R/pqrBayes.R | 54 +++-- R/pqrBayes_g.R |only R/pqrBayes_lin.R | 38 +-- R/pqrBayes_vc.R | 38 +-- R/predict.pqrBayes.R | 99 +++++---- R/predict_lin.R | 114 +++++------ R/predict_vc.R | 148 +++++++------- R/print.pqrBayes.R | 106 +++++----- R/robust_g.R |only R/robust_lin.R | 84 ++++---- R/select.pqrBayes.R | 151 +++++++------- R/select_lin.R | 78 +++---- R/select_vc.R | 88 ++++---- README.md | 455 +++++++++++++++++++++++++-------------------- data/data.rda |binary man/coverage.Rd | 8 man/data.Rd | 18 + man/estimation.pqrBayes.Rd | 6 man/pqrBayes-package.Rd | 10 man/pqrBayes.Rd | 46 +++- man/predict_pqrBayes.Rd | 10 man/select.pqrBayes.Rd | 8 39 files changed, 1548 insertions(+), 1390 deletions(-)
Title: Tools for Analyzing Time Series Data of Just Finance and
Econometrics
Description: Offers procedures to support financial-economic time series modelling and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between JFE versions 2.5.8 dated 2025-01-24 and 2.5.9 dated 2025-03-31
JFE-2.5.8/JFE/man/getBIS.Rd |only JFE-2.5.9/JFE/DESCRIPTION | 8 ++-- JFE-2.5.9/JFE/MD5 | 8 ++-- JFE-2.5.9/JFE/R/dataDownload.R | 81 ++++++++++++++++++++++++++++------------- JFE-2.5.9/JFE/man/getEER.Rd |only JFE-2.5.9/JFE/man/getFed.Rd | 20 +++------- 6 files changed, 70 insertions(+), 47 deletions(-)
Title: Analyze Results Generated by the 'SqueezeMeta' Pipeline
Description: 'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
Author: Fernando Puente-Sanchez [aut, cre],
Natalia Garcia-Garcia [aut]
Maintainer: Fernando Puente-Sanchez <fernando.puente.sanchez@slu.se>
Diff between SQMtools versions 1.6.3 dated 2023-09-18 and 1.7.0 dated 2025-03-31
DESCRIPTION | 10 - MD5 | 90 ++++++---- NAMESPACE | 15 + R/CheckMProkaryote.R |only R/USiCGs.R | 4 R/aggregate_methods.R | 3 R/bin_methods.R |only R/combineSQM.R | 224 +++++++++++++-------------- R/combineSQMlite.R | 4 R/copy_number.R |only R/exportKrona.R | 6 R/exportPathway.R | 48 +++-- R/exportSeqs.R |only R/exportTable.R | 11 - R/extra_methods.R | 57 +++--- R/figures.R | 30 ++- R/genericTable.R | 9 - R/loadSQM.R | 194 +++++++++++++---------- R/loadSQMlite.R | 2 R/seqvec2fasta.R | 6 R/subset_methods.R | 340 ++++++++++++++++++++++++++++------------- R/summary_bunch.R |only R/summary_lite.R | 2 data/CheckMProkaryote.RData |only data/Hadza.RData |binary data/MGKOs.RData |binary data/MGOGs.RData |binary data/RecA.RData |binary data/USiCGs.RData |binary man/CheckMProkaryote.Rd |only man/USiCGs.Rd | 4 man/combineSQM.Rd | 19 +- man/create_bin.Rd |only man/exportBins.Rd |only man/exportContigs.Rd |only man/exportKrona.Rd | 4 man/exportORFs.Rd |only man/exportPathway.Rd | 19 +- man/exportTable.Rd | 11 - man/find_redundant_contigs.Rd |only man/loadSQM.Rd | 20 +- man/loadSQMlite.Rd | 2 man/plotBins.Rd | 4 man/plotFunctions.Rd | 7 man/plotTaxonomy.Rd | 2 man/remove_contigs_from_bin.Rd |only man/seqvec2fasta.Rd | 7 man/subsetBins.Rd | 5 man/subsetContigs.Rd | 8 man/subsetFun.Rd | 14 + man/subsetORFs.Rd | 10 - man/subsetTax.Rd | 14 + man/summary.SQMbunch.Rd |only 53 files changed, 729 insertions(+), 476 deletions(-)
Title: Kidney-Related Functions for Clinical and Epidemiological
Research
Description: Contains kidney care oriented functions.
Current version contains functions for calculation of:
- Estimated glomerular filtration rate by CKD-EPI (2021 and 2009), MDRD, CKiD, FAS, EKFC, etc.
- Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors.
- Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, <https://Scientific-Tools.Org>. <doi:10.32614/CRAN.package.kidney.epi>.
Author: Boris Bikbov [aut, cre]
Maintainer: Boris Bikbov <boris.bikbov@scientific-tools.org>
Diff between kidney.epi versions 1.2.0 dated 2020-03-04 and 1.3.0 dated 2025-03-31
kidney.epi-1.2.0/kidney.epi/R/egfr.R |only kidney.epi-1.2.0/kidney.epi/data/ktx.RData |only kidney.epi-1.2.0/kidney.epi/man/egfr.ckdepi.Rd |only kidney.epi-1.2.0/kidney.epi/man/kidney.epi.Rd |only kidney.epi-1.2.0/kidney.epi/man/ktx.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_obligatory_params.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_param_arguments.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_param_number.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_params_numeric.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_plausibility.age.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.check_plausibility.creatinine.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.count_greater_threshhold.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.count_lowerequal_threshhold.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.is.param_possible.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.is_numeric.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.output_message.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.singular_or_plural.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.strict_to_numeric_threshhold_greater.Rd |only kidney.epi-1.2.0/kidney.epi/man/service.strict_to_numeric_threshhold_lower.Rd |only kidney.epi-1.3.0/kidney.epi/DESCRIPTION | 26 kidney.epi-1.3.0/kidney.epi/MD5 | 107 +- kidney.epi-1.3.0/kidney.epi/NAMESPACE | 34 kidney.epi-1.3.0/kidney.epi/NEWS | 17 kidney.epi-1.3.0/kidney.epi/R/ckd_classify.R |only kidney.epi-1.3.0/kidney.epi/R/data.R | 31 kidney.epi-1.3.0/kidney.epi/R/egfr_ckdepi2009.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ckdepi2021.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ckid.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_ekfc.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_fas.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_mdrd.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_other_adults.R |only kidney.epi-1.3.0/kidney.epi/R/egfr_other_children.R |only kidney.epi-1.3.0/kidney.epi/R/kidney.epi.R | 19 kidney.epi-1.3.0/kidney.epi/R/ktx.kdpi.optn.R | 142 +-- kidney.epi-1.3.0/kidney.epi/R/matrix.R |only kidney.epi-1.3.0/kidney.epi/R/service.check_plausibility.R | 153 ++- kidney.epi-1.3.0/kidney.epi/R/service.general.R | 195 ++-- kidney.epi-1.3.0/kidney.epi/R/sysdata.rda |binary kidney.epi-1.3.0/kidney.epi/README.md | 55 - kidney.epi-1.3.0/kidney.epi/build/vignette.rds |binary kidney.epi-1.3.0/kidney.epi/data/ckd.data.rda |only kidney.epi-1.3.0/kidney.epi/data/ktx.data.rda |only kidney.epi-1.3.0/kidney.epi/inst/CITATION | 20 kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.R | 60 + kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.Rmd | 121 ++ kidney.epi-1.3.0/kidney.epi/inst/doc/gfr.html | 450 +++++++--- kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.R | 31 kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.Rmd | 53 - kidney.epi-1.3.0/kidney.epi/inst/doc/ktx.html | 399 +++++--- kidney.epi-1.3.0/kidney.epi/inst/doc/services.Rmd |only kidney.epi-1.3.0/kidney.epi/inst/doc/services.html |only kidney.epi-1.3.0/kidney.epi/inst/figures |only kidney.epi-1.3.0/kidney.epi/man/ckd.data.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.2009.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.2021.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckdepi.cr_cys.2021.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckid_u25.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ckid_u25.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ekfc.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.ekfc.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cr_cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.fas.cys.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.lm.cr.Rd |only kidney.epi-1.3.0/kidney.epi/man/egfr.mdrd4.Rd | 37 kidney.epi-1.3.0/kidney.epi/man/egfr.schwartz.Rd | 37 kidney.epi-1.3.0/kidney.epi/man/figures |only kidney.epi-1.3.0/kidney.epi/man/ktx.data.Rd |only kidney.epi-1.3.0/kidney.epi/man/ktx.kdpi.optn.Rd | 43 kidney.epi-1.3.0/kidney.epi/man/matrix.cross_table.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.get_named_matrix_value.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.read_excel_to_named_matrix.Rd |only kidney.epi-1.3.0/kidney.epi/man/matrix.save_named_matrix_to_excel.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.albuminuria_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.gfr_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.kdigo_risk_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/nephro.proteinuria_category.Rd |only kidney.epi-1.3.0/kidney.epi/man/service.convert_creatinine.Rd | 20 kidney.epi-1.3.0/kidney.epi/man/service.convert_cystatin.Rd |only kidney.epi-1.3.0/kidney.epi/vignettes/gfr.Rmd | 121 ++ kidney.epi-1.3.0/kidney.epi/vignettes/ktx.Rmd | 53 - kidney.epi-1.3.0/kidney.epi/vignettes/services.Rmd |only 84 files changed, 1472 insertions(+), 752 deletions(-)
Title: Companion Tools for Open-Source Tools for Training Resources
(OTTR)
Description: Tools for converting Open-Source Tools for Training Resources
(OTTR) courses into Leanpub or Coursera courses. 'ottrpal' is for use
with the OTTR Template repository to create courses.
Author: Candace Savonen [aut, cre] ,
Carrie Wright [ctb],
Howard Baek [ctb],
Kate Isaac [ctb]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between ottrpal versions 1.2.1 dated 2024-01-09 and 2.0.0 dated 2025-03-31
ottrpal-1.2.1/ottrpal/R/aaa_utils.R |only ottrpal-1.2.1/ottrpal/R/bookdown_to_leanpub.R |only ottrpal-1.2.1/ottrpal/R/coursera.R |only ottrpal-1.2.1/ottrpal/R/data.R |only ottrpal-1.2.1/ottrpal/R/example_data.R |only ottrpal-1.2.1/ottrpal/R/footnotes.R |only ottrpal-1.2.1/ottrpal/R/gs_png.R |only ottrpal-1.2.1/ottrpal/R/leanpub_checks.R |only ottrpal-1.2.1/ottrpal/R/quiz.R |only ottrpal-1.2.1/ottrpal/R/remove_yaml.R |only ottrpal-1.2.1/ottrpal/R/replace_html.R |only ottrpal-1.2.1/ottrpal/R/set_knitr_image_path.R |only ottrpal-1.2.1/ottrpal/R/set_up.R |only ottrpal-1.2.1/ottrpal/R/simple_references.R |only ottrpal-1.2.1/ottrpal/R/utils-pipe.R |only ottrpal-1.2.1/ottrpal/R/zzz.R |only ottrpal-1.2.1/ottrpal/inst/extdata/01-intro.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/02-example-chapter.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/Book.txt |only ottrpal-1.2.1/ottrpal/inst/extdata/_bookdown.yml |only ottrpal-1.2.1/ottrpal/inst/extdata/index.Rmd |only ottrpal-1.2.1/ottrpal/inst/extdata/references.bib |only ottrpal-1.2.1/ottrpal/inst/extdata/resources/chapt_screen_images |only ottrpal-1.2.1/ottrpal/inst/extdata/resources/chapter_urls.tsv |only ottrpal-1.2.1/ottrpal/inst/extdata/tmp |only ottrpal-1.2.1/ottrpal/inst/extdata/toc_close.css |only ottrpal-1.2.1/ottrpal/man/bookdown_destination.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_file.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_path.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_rmd_files.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_book_txt.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_embed_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/bookdown_to_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/convert_utube_link.Rd |only ottrpal-1.2.1/ottrpal/man/example_repo_cleanup.Rd |only ottrpal-1.2.1/ottrpal/man/example_repo_setup.Rd |only ottrpal-1.2.1/ottrpal/man/figures |only ottrpal-1.2.1/ottrpal/man/footnotes.Rd |only ottrpal-1.2.1/ottrpal/man/get_bookdown_spec.Rd |only ottrpal-1.2.1/ottrpal/man/leanpub_check.Rd |only ottrpal-1.2.1/ottrpal/man/remove_yaml_header.Rd |only ottrpal-1.2.1/ottrpal/man/replace_html.Rd |only ottrpal-1.2.1/ottrpal/man/set_up_leanpub.Rd |only ottrpal-1.2.1/ottrpal/man/simple_references.Rd |only ottrpal-1.2.1/ottrpal/vignettes/manuscript |only ottrpal-2.0.0/ottrpal/DESCRIPTION | 27 ottrpal-2.0.0/ottrpal/MD5 | 191 +++--- ottrpal-2.0.0/ottrpal/NAMESPACE | 66 +- ottrpal-2.0.0/ottrpal/NEWS.md | 9 ottrpal-2.0.0/ottrpal/R/auth.R | 286 +++++++--- ottrpal-2.0.0/ottrpal/R/book_txt.R |only ottrpal-2.0.0/ottrpal/R/borrow_chapter.R |only ottrpal-2.0.0/ottrpal/R/get_data.R |only ottrpal-2.0.0/ottrpal/R/github_handling.R |only ottrpal-2.0.0/ottrpal/R/google_slides.R |only ottrpal-2.0.0/ottrpal/R/leanpub.R |only ottrpal-2.0.0/ottrpal/R/notes_to_fig_alt.R | 33 - ottrpal-2.0.0/ottrpal/R/ottrfy.R |only ottrpal-2.0.0/ottrpal/R/quiz_formatting.R |only ottrpal-2.0.0/ottrpal/R/render_without_toc.R |only ottrpal-2.0.0/ottrpal/R/spell_check.R |only ottrpal-2.0.0/ottrpal/R/token_handlers.R |only ottrpal-2.0.0/ottrpal/R/url_check.R |only ottrpal-2.0.0/ottrpal/R/utils.R |only ottrpal-2.0.0/ottrpal/README.md | 88 --- ottrpal-2.0.0/ottrpal/build/vignette.rds |binary ottrpal-2.0.0/ottrpal/inst/doc/getting-started.html | 22 ottrpal-2.0.0/ottrpal/inst/extdata/_child_doc.Rmd |only ottrpal-2.0.0/ottrpal/inst/extdata/dictionary.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/exclude_files.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/ignore-urls.txt |only ottrpal-2.0.0/ottrpal/inst/extdata/parent_doc.Rmd |only ottrpal-2.0.0/ottrpal/inst/extdata/parent_doc.html |only ottrpal-2.0.0/ottrpal/inst/extdata/resources/other_chapters |only ottrpal-2.0.0/ottrpal/man/app_set_up.Rd |only ottrpal-2.0.0/ottrpal/man/auth_from_secret.Rd | 39 + ottrpal-2.0.0/ottrpal/man/authorize.Rd | 22 ottrpal-2.0.0/ottrpal/man/bad_quiz_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/borrow_chapter.Rd |only ottrpal-2.0.0/ottrpal/man/cache_secrets_folder.Rd |only ottrpal-2.0.0/ottrpal/man/check_all_questions.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_git_repo.Rd |only ottrpal-2.0.0/ottrpal/man/check_question.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz_attributes.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quiz_dir.Rd |only ottrpal-2.0.0/ottrpal/man/check_quiz_question_attributes.Rd | 2 ottrpal-2.0.0/ottrpal/man/check_quizzes.Rd | 5 ottrpal-2.0.0/ottrpal/man/check_spelling.Rd |only ottrpal-2.0.0/ottrpal/man/check_urls.Rd |only ottrpal-2.0.0/ottrpal/man/clean_up.Rd |only ottrpal-2.0.0/ottrpal/man/convert_coursera_quizzes.Rd | 2 ottrpal-2.0.0/ottrpal/man/convert_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/course_path.Rd |only ottrpal-2.0.0/ottrpal/man/course_to_book_txt.Rd |only ottrpal-2.0.0/ottrpal/man/coursera.Rd | 10 ottrpal-2.0.0/ottrpal/man/delete_creds.Rd |only ottrpal-2.0.0/ottrpal/man/encrypt_creds_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/encrypt_creds_user_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/extract_meta.Rd | 2 ottrpal-2.0.0/ottrpal/man/find_issue.Rd |only ottrpal-2.0.0/ottrpal/man/get_chapters.Rd | 12 ottrpal-2.0.0/ottrpal/man/get_github.Rd |only ottrpal-2.0.0/ottrpal/man/get_object_id_notes.Rd | 2 ottrpal-2.0.0/ottrpal/man/get_pages_url.Rd |only ottrpal-2.0.0/ottrpal/man/get_repo_info.Rd |only ottrpal-2.0.0/ottrpal/man/get_slide_id.Rd | 2 ottrpal-2.0.0/ottrpal/man/get_urls.Rd |only ottrpal-2.0.0/ottrpal/man/good_quiz_path.Rd | 9 ottrpal-2.0.0/ottrpal/man/gs_helpers.Rd | 2 ottrpal-2.0.0/ottrpal/man/gs_png_url.Rd | 2 ottrpal-2.0.0/ottrpal/man/key_encrypt_creds_path.Rd | 2 ottrpal-2.0.0/ottrpal/man/make_embed_markdown.Rd | 25 ottrpal-2.0.0/ottrpal/man/make_screenshots.Rd |only ottrpal-2.0.0/ottrpal/man/ottr_check.Rd |only ottrpal-2.0.0/ottrpal/man/ottrfy.Rd |only ottrpal-2.0.0/ottrpal/man/parse_q_tag.Rd | 2 ottrpal-2.0.0/ottrpal/man/parse_quiz.Rd | 2 ottrpal-2.0.0/ottrpal/man/parse_quiz_df.Rd | 2 ottrpal-2.0.0/ottrpal/man/pipe.Rd | 8 ottrpal-2.0.0/ottrpal/man/qrmd_files.Rd |only ottrpal-2.0.0/ottrpal/man/set_knitr_image_path.Rd | 13 ottrpal-2.0.0/ottrpal/man/setup_ottr_template.Rd |only ottrpal-2.0.0/ottrpal/man/supported_endpoints.Rd |only ottrpal-2.0.0/ottrpal/man/test_url.Rd |only ottrpal-2.0.0/ottrpal/man/website_to_embed_leanpub.Rd |only ottrpal-2.0.0/ottrpal/tests |only 127 files changed, 511 insertions(+), 392 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management, ...).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package is described in 'Pérez-Zanón et al. (2023)
<doi:10.1016/j.cliser.2023.100393>' and it was developed in the context of
'H2020 MED-GOLD' (776467) and 'S2S4E' (776787) projects. See 'Lledó et al. (2019)
<doi:10.1016/j.renene.2019.04.13 [...truncated...]
Author: Theertha Kariyathan [cre],
Victoria Agudetse [ctb],
Eva Rifa [ctb],
Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
BSC-CNS [cph]
Maintainer: Theertha Kariyathan <theertha.kariyathan@bsc.es>
Diff between CSIndicators versions 1.1.1 dated 2024-01-24 and 1.1.2 dated 2025-03-31
DESCRIPTION | 14 +++++++----- MD5 | 38 +++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 19 +++++++++++++++++ R/AccumulationExceedingThreshold.R | 10 +++++---- R/MergeRefToExp.R | 9 +++++--- R/PeriodAccumulation.R | 15 ++++++++----- R/PeriodMax.R | 14 +++++++----- R/PeriodMean.R | 9 +++++--- R/PeriodMin.R | 11 ++++++---- R/PeriodPET.R | 8 +++++-- R/PeriodStandardization.R | 27 +++++++++++++++--------- R/PeriodVariance.R | 8 ++++--- R/SelectPeriodOnData.R | 2 - R/SelectPeriodOnDates.R | 2 - R/TotalSpellTimeExceedingThreshold.R | 10 +++++---- R/TotalTimeExceedingThreshold.R | 10 +++++---- build/partial.rdb |binary inst/CITATION | 2 - man/CST_PeriodStandardization.Rd | 8 +++---- 20 files changed, 136 insertions(+), 81 deletions(-)
Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40
different coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
,
CJ Yetman [ctb] ,
Nils Enevoldsen [ctb] ,
Etienne Bacher [ctb] ,
Samuel Meichtry [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.6.0 dated 2024-03-22 and 1.6.1 dated 2025-03-31
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/codelist.R | 4 ++-- R/countrycode.R | 8 +++++++- data/codelist.rda |binary data/codelist_panel.rda |binary man/codelist.Rd | 4 ++-- 8 files changed, 27 insertions(+), 16 deletions(-)
Title: Chromatographic File Converter
Description: Reads chromatograms from binary formats into R objects. Currently supports
conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions',
'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats.
In addition to its internal parsers, chromConverter contains bindings to parsers in
external libraries, such as 'Aston' <https://github.com/bovee/aston>,
'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>,
and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
Author: Ethan Bass [aut, cre] ,
James Dillon [ctb, cph] ,
Evan Shi [ctb, cph]
Maintainer: Ethan Bass <ethanbass@gmail.com>
Diff between chromConverter versions 0.2.1 dated 2022-07-11 and 0.7.5 dated 2025-03-31
chromConverter-0.2.1/chromConverter/R/parsers.R |only chromConverter-0.2.1/chromConverter/man/attach_metadata.Rd |only chromConverter-0.2.1/chromConverter/man/configure_aston.Rd |only chromConverter-0.2.1/chromConverter/tests/testthat/testdata/DAD1.CSV |only chromConverter-0.7.5/chromConverter/DESCRIPTION | 58 chromConverter-0.7.5/chromConverter/MD5 | 115 - chromConverter-0.7.5/chromConverter/NAMESPACE | 42 chromConverter-0.7.5/chromConverter/NEWS.md | 262 +++ chromConverter-0.7.5/chromConverter/R/attach_metadata.R | 855 ++++++++-- chromConverter-0.7.5/chromConverter/R/call_aston.R |only chromConverter-0.7.5/chromConverter/R/call_entab.R |only chromConverter-0.7.5/chromConverter/R/call_openchrom.R | 283 ++- chromConverter-0.7.5/chromConverter/R/call_rainbow.R |only chromConverter-0.7.5/chromConverter/R/olefile_utilities.R |only chromConverter-0.7.5/chromConverter/R/read_agilent_d.R |only chromConverter-0.7.5/chromConverter/R/read_asm.R |only chromConverter-0.7.5/chromConverter/R/read_cdf.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_ch.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_csv.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_ms.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_report.R |only chromConverter-0.7.5/chromConverter/R/read_chemstation_uv.R |only chromConverter-0.7.5/chromConverter/R/read_chromeleon.R |only chromConverter-0.7.5/chromConverter/R/read_chroms.R | 474 ++++- chromConverter-0.7.5/chromConverter/R/read_mdf.R |only chromConverter-0.7.5/chromConverter/R/read_mzml.R |only chromConverter-0.7.5/chromConverter/R/read_peaklist.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_ascii.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_gcd.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_lcd.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_peaktable.R |only chromConverter-0.7.5/chromConverter/R/read_shimadzu_qgd.R |only chromConverter-0.7.5/chromConverter/R/read_thermoraw.R | 163 - chromConverter-0.7.5/chromConverter/R/read_varian_peaklist.R |only chromConverter-0.7.5/chromConverter/R/read_varian_sms.R |only chromConverter-0.7.5/chromConverter/R/read_waters_arw.R |only chromConverter-0.7.5/chromConverter/R/read_waters_raw.R |only chromConverter-0.7.5/chromConverter/R/reshape_chroms.R |only chromConverter-0.7.5/chromConverter/R/utils.R | 422 ++++ chromConverter-0.7.5/chromConverter/R/write_andi_ms.R |only chromConverter-0.7.5/chromConverter/R/write_chroms.R |only chromConverter-0.7.5/chromConverter/R/write_mzml.R |only chromConverter-0.7.5/chromConverter/R/zzz.R | 17 chromConverter-0.7.5/chromConverter/README.md | 147 + chromConverter-0.7.5/chromConverter/build/partial.rdb |binary chromConverter-0.7.5/chromConverter/inst/CITATION | 19 chromConverter-0.7.5/chromConverter/inst/shell/path_to_openchrom_commandline.txt | 2 chromConverter-0.7.5/chromConverter/man/call_entab.Rd | 36 chromConverter-0.7.5/chromConverter/man/call_openchrom.Rd | 85 chromConverter-0.7.5/chromConverter/man/call_rainbow.Rd |only chromConverter-0.7.5/chromConverter/man/configure_openchrom.Rd |only chromConverter-0.7.5/chromConverter/man/configure_python_environment.Rd |only chromConverter-0.7.5/chromConverter/man/extract_metadata.Rd |only chromConverter-0.7.5/chromConverter/man/read_agilent_d.Rd |only chromConverter-0.7.5/chromConverter/man/read_agilent_dx.Rd |only chromConverter-0.7.5/chromConverter/man/read_asm.Rd |only chromConverter-0.7.5/chromConverter/man/read_cdf.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_ch.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_csv.Rd | 34 chromConverter-0.7.5/chromConverter/man/read_chemstation_ms.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_reports.Rd |only chromConverter-0.7.5/chromConverter/man/read_chemstation_uv.Rd |only chromConverter-0.7.5/chromConverter/man/read_chromeleon.Rd | 31 chromConverter-0.7.5/chromConverter/man/read_chroms.Rd | 128 + chromConverter-0.7.5/chromConverter/man/read_mdf.Rd |only chromConverter-0.7.5/chromConverter/man/read_mzml.Rd | 42 chromConverter-0.7.5/chromConverter/man/read_peaklist.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu.Rd | 74 chromConverter-0.7.5/chromConverter/man/read_shimadzu_gcd.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu_lcd.Rd |only chromConverter-0.7.5/chromConverter/man/read_shimadzu_qgd.Rd |only chromConverter-0.7.5/chromConverter/man/read_sz_lcd_2d.Rd |only chromConverter-0.7.5/chromConverter/man/read_sz_lcd_3d.Rd |only chromConverter-0.7.5/chromConverter/man/read_thermoraw.Rd | 39 chromConverter-0.7.5/chromConverter/man/read_varian_peaklist.Rd |only chromConverter-0.7.5/chromConverter/man/read_varian_sms.Rd |only chromConverter-0.7.5/chromConverter/man/read_waters_arw.Rd | 31 chromConverter-0.7.5/chromConverter/man/read_waters_raw.Rd |only chromConverter-0.7.5/chromConverter/man/sp_converter.Rd | 35 chromConverter-0.7.5/chromConverter/man/uv_converter.Rd | 34 chromConverter-0.7.5/chromConverter/man/write_andi_chrom.Rd |only chromConverter-0.7.5/chromConverter/man/write_chroms.Rd |only chromConverter-0.7.5/chromConverter/man/write_mzml.Rd |only chromConverter-0.7.5/chromConverter/tests/testthat/helpers.R | 32 chromConverter-0.7.5/chromConverter/tests/testthat/test-extra.R |only chromConverter-0.7.5/chromConverter/tests/testthat/test-read_chroms.R | 334 +++ chromConverter-0.7.5/chromConverter/tests/testthat/test_utils.R |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/RUTIN2.D |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/chemstation_130.ch |only chromConverter-0.7.5/chromConverter/tests/testthat/testdata/dad1.csv |only 90 files changed, 3065 insertions(+), 729 deletions(-)
More information about chromConverter at CRAN
Permanent link
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael Nussbaumer [ctb] ,
Jurriaan [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.8.1 dated 2024-07-30 and 0.9.0 dated 2025-03-31
DESCRIPTION | 8 MD5 | 84 ++- NAMESPACE | 6 NEWS.md | 40 + R/apply_mistnet.R | 10 R/as.vp.R |only R/as.vpts.R | 63 ++ R/calculate_param.R | 26 - R/calculate_vp.R | 18 R/clean_mixture.R |only R/filter_precip.R |only R/filter_vpts.R | 5 R/integrate_to_ppi.R | 19 R/map.R | 93 ++-- R/nexrad_odim.R | 2 R/nyquist_velocity.R | 1 R/plot.vpi.R | 10 R/read_vpfiles.R | 5 R/regularize_vpts.R | 17 R/utils.R | 17 README.md | 19 build/partial.rdb |binary build/vignette.rds |binary data/example_vp.rda |binary inst/doc/bioRad.html | 21 inst/doc/rad_aero_22.R | 782 +++++++++++++++++----------------- inst/doc/rad_aero_22.Rmd | 2 inst/doc/rad_aero_22.html | 445 +++++++++---------- inst/doc/range_correction.html | 124 ++--- man/apply_mistnet.Rd | 10 man/as.vp.Rd |only man/calculate_param.Rd | 23 - man/calculate_vp.Rd | 2 man/clean_mixture.Rd |only man/filter_precip.Rd |only man/filter_vpts.Rd | 8 man/map.Rd | 5 man/nexrad_to_odim.Rd | 2 man/nyquist_velocity.Rd | 1 man/regularize_vpts.Rd | 17 tests/testthat/test-as.vp.R |only tests/testthat/test-as.vpts.R | 33 + tests/testthat/test-calculate_param.R | 12 tests/testthat/test-clean_mixture.R |only tests/testthat/test-list_vpts_aloft.R | 6 tests/testthat/test-read_vpts.R | 1 vignettes/rad_aero_22.Rmd | 2 47 files changed, 1074 insertions(+), 865 deletions(-)
Title: 'SAS' Interface
Description: Provides a 'SAS' interface, through
'SASPy'(<https://sassoftware.github.io/saspy/>) and
'reticulate'(<https://rstudio.github.io/reticulate/>). This package
helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS'
servers, retrieve execution results and log, and exchange datasets
between 'SAS' and 'R'. It also helps you to install 'SASPy' and
create a configuration file for the connection. Please review the
'SASPy' license file as instructed so that you comply with its
separate and independent license.
Author: Liming Li [aut, cre],
Daniel Sabanes Bove [aut],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd],
AstraZeneca plc [cph, fnd]
Maintainer: Liming Li <liming.li1@astrazeneca.com>
Diff between sasr versions 0.1.4 dated 2025-02-26 and 0.1.5 dated 2025-03-31
DESCRIPTION | 18 ++++++++++-------- MD5 | 8 ++++---- NEWS.md | 4 ++++ man/sasr-package.Rd | 3 ++- tests/testthat/test-rmarkdown.R | 1 + 5 files changed, 21 insertions(+), 13 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of
'Protocol Buffers' library is required; currently version 3.3.0 from 2017
is the stated minimum.
Author: Romain Francois [aut] ,
Dirk Eddelbuettel [aut, cre] ,
Murray Stokely [aut] ,
Jeroen Ooms [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.23 dated 2025-01-14 and 0.4.24 dated 2025-03-31
ChangeLog | 19 +++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/00classes.R | 2 +- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS.Rd | 12 ++++++++++-- inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary src/init.c | 2 ++ src/mutators.cpp | 3 +-- src/rprotobuf.cpp | 4 ++-- src/rprotobuf.h | 28 ++++++++++++---------------- 15 files changed, 75 insertions(+), 51 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong [aut],
Dirk Eddelbuettel [aut, cre] ,
John Laing [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.15 dated 2024-09-18 and 0.3.16 dated 2025-03-31
ChangeLog | 109 +++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 13 +++-- MD5 | 60 +++++++++++++------------- R/RcppExports.R | 13 ++++- R/blpConnect.R | 7 ++- R/init.R | 45 ++++++++++---------- build/vignette.rds |binary configure | 47 +++++++++++---------- inst/NEWS.Rd | 12 +++++ man/blpAuthenticate.Rd | 12 +---- man/blpConnect.Rd | 6 ++ man/getTicks.Rd | 2 man/haveBlp.Rd |only src/Makevars.in | 15 ++++-- src/Makevars.no_blp |only src/Makevars.win | 5 -- src/RcppExports.cpp | 24 ++++++++-- src/authenticate.cpp | 21 ++++++--- src/bdh.cpp | 24 +++++++--- src/bdp.cpp | 41 +++++++++++++----- src/bds.cpp | 31 +++++++++---- src/beqs.cpp | 37 ++++++++-------- src/blpConnect.cpp | 21 +++++++-- src/blpVersion.cpp | 30 ++++++++++++- src/blpapi_utils.cpp | 50 ++++++++++++---------- src/bsrch.cpp | 29 ++++++------- src/fieldsearch.cpp | 14 ++++-- src/getBars.cpp | 13 ++++- src/getFieldInfo.cpp | 44 ++++++++++--------- src/getTicks.cpp | 17 ++++--- src/lookup.cpp | 18 ++++---- src/subscribe.cpp | 22 +++++---- 32 files changed, 531 insertions(+), 251 deletions(-)
Title: Decision Trees with Structural Equation Models Fit in 'Mplus'
Description: Uses recursive partitioning to create homogeneous subgroups based on structural equation models
fit in 'Mplus', a stand-alone program developed by Muthen and Muthen.
Author: Sarfaraz Serang [aut, cre],
Ross Jacobucci [aut],
Kevin J. Grimm [ctb],
Gabriela Stegmann [ctb],
Andreas M. Brandmaier [ctb]
Maintainer: Sarfaraz Serang <sserang@mailbox.sc.edu>
Diff between MplusTrees versions 0.2.2 dated 2022-10-11 and 0.2.3 dated 2025-03-31
DESCRIPTION | 35 ++++++++++++++++++++++++++--------- MD5 | 2 +- 2 files changed, 27 insertions(+), 10 deletions(-)
Title: Sparsed Sliced Inverse Regression via Lasso
Description: Estimate the sufficient dimension reduction space using sparsed sliced inverse regression via Lasso (Lasso-SIR) introduced in Lin, Zhao, and Liu (2019) <doi:10.1080/01621459.2018.1520115>. The Lasso-SIR is consistent and achieve the optimal convergence rate under certain sparsity conditions for the multiple index models.
Author: Zhigen Zhao [aut, cre],
Qian Lin [aut],
Jun Liu [aut]
Maintainer: Zhigen Zhao <zhigen.zhao@gmail.com>
Diff between LassoSIR versions 0.1.1 dated 2017-12-06 and 1.0 dated 2025-03-31
DESCRIPTION | 24 ++++++++++--- MD5 | 12 ++++-- R/LassoSIR.R | 81 +++++++++++++++++++++++++++-------------------- R/predict_Lasso_SIR.R |only build/partial.rdb |binary man/LassoSIR-package.Rd | 14 ++++---- man/LassoSIR.Rd | 40 ++++++++++++----------- man/predict_Lasso_SIR.Rd |only 8 files changed, 101 insertions(+), 70 deletions(-)
Title: Model-Based Clustering for Functional Data with Covariates
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <doi:10.48550/arXiv.1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Author: Natalya Pya [aut, cre],
Per Arnqvist [aut],
Sara Sjoestedt de Luna [aut]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between fdaMocca versions 0.1-1 dated 2022-07-21 and 0.1-2 dated 2025-03-31
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 2 +- 2 files changed, 15 insertions(+), 11 deletions(-)
Title: Fast and Scalable Single Cell Differential Expression Analysis
using Mixed-Effects Models
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm
for analysis of single-cell differential expression. The algorithm uses
summary-level statistics and requires less computer memory to fit the LMM.
Author: Changjiang Xu [aut, cre],
Gary Bader [aut]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Diff between FLASHMM versions 1.1.0 dated 2025-03-11 and 1.2.0 dated 2025-03-31
DESCRIPTION | 9 MD5 | 22 NEWS.md | 6 R/lmm.R | 64 +- R/lmmfit.R | 17 README.md | 39 - inst/doc/FLASHMM-vignette.R | 223 +++----- inst/doc/FLASHMM-vignette.Rmd | 355 +++++-------- inst/doc/FLASHMM-vignette.html | 1114 +++++++++++++++++++++-------------------- man/lmm.Rd | 6 man/lmmfit.Rd | 4 vignettes/FLASHMM-vignette.Rmd | 355 +++++-------- 12 files changed, 1091 insertions(+), 1123 deletions(-)
Title: Bayesian Modeling of Spatio-Temporal Data with R
Description: Fits, validates and compares a number of Bayesian models for
spatial and space time point referenced and areal unit data. Model fitting
is done using several packages: 'rstan', 'INLA', 'spBayes', 'spTimer',
'spTDyn', 'CARBayes' and 'CARBayesST'. Model comparison is performed using
the DIC and WAIC, and K-fold cross-validation where the user is free
to select their own subset of data rows for validation. Sahu (2022)
<doi:10.1201/9780429318443> describes the methods in detail.
Author: Sujit K. Sahu [aut, cre] ,
Duncan P. Lee [aut],
K. Shuvo Bakar [aut]
Maintainer: Sujit K. Sahu <S.K.Sahu@soton.ac.uk>
Diff between bmstdr versions 0.7.9 dated 2023-12-18 and 0.8.2 dated 2025-03-31
DESCRIPTION | 8 MD5 | 37 NAMESPACE | 1 R/Bspatial.R | 2 R/Bsptime.R | 8 R/methods.R | 25 build/partial.rdb |binary build/vignette.rds |binary inst/doc/vigverysmall.R | 308 ++--- inst/doc/vigverysmall.html | 1354 ++++++++++++++++++------- inst/stan/gp_marginal.stan | 16 inst/stan/ind_gpp_marginal.stan | 26 inst/stan/normal.stan | 2 man/Bspatial.Rd | 2 man/Bsptime.Rd | 8 man/resid.bmstdr.Rd |only src/stanExports_gp_marginal.h | 1426 ++++++++++++-------------- src/stanExports_ind_gpp_marginal.h | 1958 +++++++++++++++++-------------------- src/stanExports_normal.h | 639 +++++------- src/stanExports_spatial_model.h | 1082 +++++++++----------- 20 files changed, 3606 insertions(+), 3296 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre]
,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.7 dated 2024-07-27 and 1.2.8 dated 2025-03-31
DESCRIPTION | 10 - MD5 | 18 +- R/wiki_utils.R | 74 ++++----- inst/doc/wiki_utils.R | 18 +- inst/doc/wiki_utils.Rmd | 2 inst/doc/wiki_utils.html | 375 ++++------------------------------------------- man/v_AutoSuggest.Rd | 2 man/v_GetRecord.Rd | 2 man/v_Search.Rd | 2 vignettes/wiki_utils.Rmd | 2 10 files changed, 96 insertions(+), 409 deletions(-)
Title: Data Collection from the Central Bank of Brazil
Description: Provides tools to facilitate the access and processing of data
from the Central Bank of Brazil API. The package allows users
to retrieve economic and financial data, transforming them into usable
tabular formats for further analysis. The data is obtained from the
Central Bank of Brazil API: <https://api.bcb.gov.br/dados/serie/bcdata.sgs.{series_code}/dados?formato=json&dataInicial={start_date}&dataFinal={end_date}>.
Author: Paulo Icaro [aut],
Lissandro Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Sousa <lisandrosousa54@gmail.com>
Diff between BacenAPI versions 0.1.1 dated 2025-03-17 and 0.2.0 dated 2025-03-31
DESCRIPTION | 7 ++++--- MD5 | 9 +++++++-- NAMESPACE | 2 ++ R/bacen_search.R |only R/dataset.R |only data |only man/bacen_search.Rd |only man/dataset.Rd |only 8 files changed, 13 insertions(+), 5 deletions(-)
Title: Fast and Vectorized Base 64 Engine
Description: Provides a fast, lightweight, and vectorized base 64 engine
to encode and decode character and raw vectors as well as files stored
on disk. Common base 64 alphabets are supported out of the box
including the standard, URL-safe, bcrypt, crypt, 'BinHex', and
IMAP-modified UTF-7 alphabets. Custom engines can be created to
support unique base 64 encoding and decoding needs.
Author: Josiah Parry [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between b64 versions 0.1.3 dated 2024-09-26 and 0.1.4 dated 2025-03-31
b64-0.1.3/b64/src/Makevars |only b64-0.1.3/b64/src/Makevars.win |only b64-0.1.4/b64/DESCRIPTION | 13 +++++---- b64-0.1.4/b64/MD5 | 29 ++++++++++---------- b64-0.1.4/b64/NEWS.md | 3 +- b64-0.1.4/b64/R/extendr-wrappers.R | 1 b64-0.1.4/b64/README.md | 42 ++++++++++++++---------------- b64-0.1.4/b64/configure | 2 - b64-0.1.4/b64/configure.win | 2 - b64-0.1.4/b64/man/b64-package.Rd | 12 +++++++- b64-0.1.4/b64/src/Makevars.in |only b64-0.1.4/b64/src/Makevars.win.in |only b64-0.1.4/b64/src/rust/Cargo.lock | 34 ++++++++++++++---------- b64-0.1.4/b64/src/rust/Cargo.toml | 5 ++- b64-0.1.4/b64/src/rust/vendor-config.toml | 4 ++ b64-0.1.4/b64/src/rust/vendor.tar.xz |binary b64-0.1.4/b64/tools/config.R |only b64-0.1.4/b64/tools/msrv.R | 4 +- 18 files changed, 86 insertions(+), 65 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Several approaches are described in the review Dray et al (2012)
<doi:10.1890/11-1183.1>.
Author: Stephane Dray [aut] ,
David Bauman [ctb],
Guillaume Blanchet [ctb],
Daniel Borcard [ctb],
Sylvie Clappe [ctb],
Guillaume Guenard [ctb] ,
Thibaut Jombart [ctb],
Guillaume Larocque [ctb],
Pierre Legendre [ctb] ,
Naima Madi [ctb],
Helene H Wagner [ctb], [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adespatial versions 0.3-26 dated 2025-03-21 and 0.3-27 dated 2025-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/tutorial.html | 4 ++-- src/constr.hclust.c | 1 + src/constr.hclust.h | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Compare Human Performance to Sampling Algorithms
Description: Understand human performance from the perspective of sampling, both looking at how people generate samples and how people use the samples they have generated. A longer overview and other resources can be found at <https://sampling.warwick.ac.uk>.
Author: Lucas Castillo [aut, cre, cph]
,
Yun-Xiao Li [aut, cph] ,
Adam N Sanborn [aut, cph] ,
European Research Council [fnd]
Maintainer: Lucas Castillo <lucas.castillo-marti@warwick.ac.uk>
Diff between samplr versions 1.0.1 dated 2024-08-19 and 1.1.0 dated 2025-03-31
DESCRIPTION | 10 ++-- MD5 | 52 ++++++++++++------------ NEWS.md | 11 +++++ R/ABSClass.R | 6 +- R/Z_identities.R | 62 ++++++++++++++++++++++++----- R/calc_functions.R | 26 +++++++++--- build/partial.rdb |binary inst/REFERENCES.bib | 20 ++++++++- inst/doc/abs-simulations.Rmd | 2 inst/doc/abs-simulations.html | 66 +++++++++++++++++++++++-------- inst/doc/custom-density-functions.html | 20 ++++----- inst/doc/how-to-sample.html | 6 +- inst/doc/multivariate-mixtures.html | 10 ++-- inst/doc/supported-distributions.html | 6 +- inst/doc/time-comparisons.html | 26 ++++++------ man/Bayesian_Sampler.Rd | 22 +++++++++- man/Mean_Variance.Rd | 6 ++ man/Z_identities.Rd | 3 + man/Zhu23ABS.Rd | 5 +- man/calc_PSD.Rd | 8 +++ man/calc_all.Rd | 11 ++++- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/samplr-package.Rd | 2 tests/testthat/test-Z_identities.R | 58 ++++++++++++++++++++++++++- tests/testthat/test-calc_functions.R | 16 +++++-- vignettes/abs-simulations.Rmd | 2 27 files changed, 340 insertions(+), 116 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.1.0 dated 2025-02-05 and 1.2.0 dated 2025-03-31
PlotFTIR-1.1.0/PlotFTIR/vignettes/peak_fitting.Rbak |only PlotFTIR-1.2.0/PlotFTIR/DESCRIPTION | 8 PlotFTIR-1.2.0/PlotFTIR/MD5 | 41 PlotFTIR-1.2.0/PlotFTIR/NAMESPACE | 1 PlotFTIR-1.2.0/PlotFTIR/NEWS.md | 5 PlotFTIR-1.2.0/PlotFTIR/R/io.R | 376 ++- PlotFTIR-1.2.0/PlotFTIR/R/manipulations.R | 304 +- PlotFTIR-1.2.0/PlotFTIR/R/maths.R | 440 ++- PlotFTIR-1.2.0/PlotFTIR/R/plot_ftir.R | 117 PlotFTIR-1.2.0/PlotFTIR/R/utils.R | 104 PlotFTIR-1.2.0/PlotFTIR/R/zzz.R | 5 PlotFTIR-1.2.0/PlotFTIR/README.md | 26 PlotFTIR-1.2.0/PlotFTIR/build/vignette.rds |binary PlotFTIR-1.2.0/PlotFTIR/inst/doc/plotting_ftir_spectra.html | 5 PlotFTIR-1.2.0/PlotFTIR/man/check_ftir_data.Rd | 32 PlotFTIR-1.2.0/PlotFTIR/man/intensity_type.Rd | 3 PlotFTIR-1.2.0/PlotFTIR/tests/testthat.R | 24 PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-io.R | 449 +++ PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-manipulations.R | 206 + PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-maths.R | 1441 +++++++++--- PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-plot_ftir.R | 54 PlotFTIR-1.2.0/PlotFTIR/tests/testthat/test-utils.R | 14 22 files changed, 2907 insertions(+), 748 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced “picture”), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 1.0 dated 2024-12-02 and 1.0.1 dated 2025-03-31
DESCRIPTION | 8 MD5 | 10 NEWS.md | 4 inst/doc/Examples.html | 43 inst/doc/userman.html | 109 +- src/pikchr.c | 2320 ++++++++++++++++++++++++++----------------------- 6 files changed, 1345 insertions(+), 1149 deletions(-)
Title: Geocoding Made Easy
Description: An intuitive interface for getting data from geocoding services.
Author: Jesse Cambon [aut, cre] ,
Diego Hernangomez [aut] ,
Christopher Belanger [aut] ,
Daniel Possenriede [aut] ,
Otto Hansen [ctb]
Maintainer: Jesse Cambon <jesse.cambon@gmail.com>
Diff between tidygeocoder versions 1.0.5 dated 2021-11-02 and 1.0.6 dated 2025-03-31
tidygeocoder-1.0.5/tidygeocoder/R/geo_methods.R |only tidygeocoder-1.0.5/tidygeocoder/man/geo_census.Rd |only tidygeocoder-1.0.6/tidygeocoder/DESCRIPTION | 26 tidygeocoder-1.0.6/tidygeocoder/MD5 | 99 tidygeocoder-1.0.6/tidygeocoder/NAMESPACE | 13 tidygeocoder-1.0.6/tidygeocoder/NEWS.md | 25 tidygeocoder-1.0.6/tidygeocoder/R/api_url.R | 92 tidygeocoder-1.0.6/tidygeocoder/R/batch_geocoding.R | 962 ++++---- tidygeocoder-1.0.6/tidygeocoder/R/data.R | 63 tidygeocoder-1.0.6/tidygeocoder/R/documentation.R | 187 - tidygeocoder-1.0.6/tidygeocoder/R/geo.R | 802 +++--- tidygeocoder-1.0.6/tidygeocoder/R/geocode.R | 222 + tidygeocoder-1.0.6/tidygeocoder/R/geocode_combine.R | 521 ++-- tidygeocoder-1.0.6/tidygeocoder/R/global_variables.R | 31 tidygeocoder-1.0.6/tidygeocoder/R/input_handling.R | 96 tidygeocoder-1.0.6/tidygeocoder/R/query_factory.R | 232 +- tidygeocoder-1.0.6/tidygeocoder/R/results_processing.R | 342 +- tidygeocoder-1.0.6/tidygeocoder/R/reverse_batch_geocoding.R | 736 +++--- tidygeocoder-1.0.6/tidygeocoder/R/reverse_geo.R | 611 ++--- tidygeocoder-1.0.6/tidygeocoder/R/reverse_geocode.R | 161 - tidygeocoder-1.0.6/tidygeocoder/R/tidygeocoder.R | 2 tidygeocoder-1.0.6/tidygeocoder/R/utils.R | 346 +-- tidygeocoder-1.0.6/tidygeocoder/R/zzz.R | 4 tidygeocoder-1.0.6/tidygeocoder/README.md | 107 tidygeocoder-1.0.6/tidygeocoder/build/vignette.rds |binary tidygeocoder-1.0.6/tidygeocoder/data/api_info_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/api_key_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/api_parameter_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/batch_limit_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/data/min_time_reference.rda |binary tidygeocoder-1.0.6/tidygeocoder/inst/CITATION | 33 tidygeocoder-1.0.6/tidygeocoder/inst/WORDLIST |only tidygeocoder-1.0.6/tidygeocoder/inst/doc/tidygeocoder.Rmd | 278 +- tidygeocoder-1.0.6/tidygeocoder/inst/doc/tidygeocoder.html | 1149 ++++++---- tidygeocoder-1.0.6/tidygeocoder/man/api_parameter_reference.Rd | 10 tidygeocoder-1.0.6/tidygeocoder/man/figures/README-usamap-1.png |binary tidygeocoder-1.0.6/tidygeocoder/man/geo.Rd | 128 - tidygeocoder-1.0.6/tidygeocoder/man/geo_combine.Rd | 47 tidygeocoder-1.0.6/tidygeocoder/man/geocode.Rd | 53 tidygeocoder-1.0.6/tidygeocoder/man/geocode_combine.Rd | 76 tidygeocoder-1.0.6/tidygeocoder/man/get_api_query.Rd | 12 tidygeocoder-1.0.6/tidygeocoder/man/louisville.Rd | 3 tidygeocoder-1.0.6/tidygeocoder/man/min_time_reference.Rd | 10 tidygeocoder-1.0.6/tidygeocoder/man/query_api.Rd | 30 tidygeocoder-1.0.6/tidygeocoder/man/reverse_geo.Rd | 90 tidygeocoder-1.0.6/tidygeocoder/man/reverse_geocode.Rd | 36 tidygeocoder-1.0.6/tidygeocoder/man/tidygeocoder-package.Rd | 5 tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-geocode-combine.R | 106 tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-geocode.R | 243 +- tidygeocoder-1.0.6/tidygeocoder/tests/testthat/test-utils.R | 131 - tidygeocoder-1.0.6/tidygeocoder/vignettes/tidygeocoder.Rmd | 278 +- tidygeocoder-1.0.6/tidygeocoder/vignettes/tidygeocoder.Rmd.orig | 4 52 files changed, 4516 insertions(+), 3886 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.10 dated 2024-11-15 and 1.0.11 dated 2025-03-31
DESCRIPTION | 8 ++-- MD5 | 42 ++++++++++----------- NEWS.md | 7 +++ R/EMMA.R | 2 - R/GWASHelp.R | 14 ++++--- R/RcppExports.R | 2 - R/codeMarkers.R | 7 ++- R/createGData.R | 6 +-- R/createGWAS.R | 6 +-- R/fastGLS.R | 94 ++++++++++++++++++++++++------------------------- R/kinship.R | 2 - R/manhattanPlot.R | 2 - R/qtlPlot.R | 2 - R/readPlink.R | 2 - R/runSingleTraitGwas.R | 2 - build/partial.rdb |binary build/vignette.rds |binary configure | 4 +- configure.ac | 4 +- inst/doc/GWAS.html | 38 +++++++++---------- src/utils.cpp | 2 - tests/tinytest.R | 10 ++--- 22 files changed, 133 insertions(+), 123 deletions(-)