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 1.1.0 dated 2024-05-15 and 1.2.0 dated 2025-01-16
DESCRIPTION | 14 ++- MD5 | 71 +++++++++++-------- NAMESPACE | 10 ++ NEWS.md | 39 +++++++--- R/cpp11.R | 16 ++++ R/font_outline.R |only R/match_fonts.R | 71 ++++++++++++------- R/register_font.R | 146 +++++++++++++++++++++++++++++------------ R/web_fonts.R |only R/zzz.R | 3 build/vignette.rds |binary inst/doc/c_interface.html | 2 inst/include/systemfonts-ft.h | 6 + inst/include/systemfonts.h | 20 +++-- man/add_fonts.Rd |only man/as_font_weight.Rd | 4 - man/glyph_outline.Rd |only man/glyph_raster.Rd |only man/glyph_raster_grob.Rd |only man/match_fonts.Rd | 18 +++++ man/register_font.Rd | 24 +++++- man/register_variant.Rd | 23 +++++- man/require_font.Rd |only man/search_web_fonts.Rd |only man/web-fonts.Rd |only src/FontDescriptor.h | 81 ++++++++++++++++++++-- src/Makevars.in | 6 - src/Makevars.win | 34 +++++---- src/caches.cpp | 10 ++ src/caches.h | 2 src/cpp11.cpp | 33 +++++++++ src/font_local.cpp |only src/font_local.h |only src/font_matching.cpp | 70 ++++++++++--------- src/font_outlines.cpp |only src/font_outlines.h |only src/ft_cache.cpp | 88 ++++++++++++------------ src/ft_cache.h | 48 +++++++------ src/mac/FontManagerMac.mm | 9 ++ src/unix/FontManagerLinux.cpp | 15 ++++ src/utils.h | 10 -- src/win/FontManagerWindows.cpp | 130 ++++++++++++++++-------------------- tools/winlibs.R | 2 43 files changed, 667 insertions(+), 338 deletions(-)
Title: Wrangle and Analyze Growth Curve Data
Description: Easy wrangling and model-free analysis of
microbial growth curve data, as commonly output by plate readers.
Tools for reshaping common plate reader outputs into 'tidy' formats and
merging them with design information, making data easy to work with using
'gcplyr' and other packages. Also streamlines common growth curve
processing steps, like smoothing and calculating derivatives, and
facilitates model-free characterization and analysis of growth data.
See methods at <https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Diff between gcplyr versions 1.10.0 dated 2024-07-09 and 1.11.0 dated 2025-01-16
DESCRIPTION | 14 +- MD5 | 78 ++++++++-------- NEWS.md | 6 + R/example_functions.R | 74 ++++++++++++--- R/functions.R | 63 ++++++++++--- README.md | 2 build/vignette.rds |binary inst/doc/gc01_gcplyr.R | 3 inst/doc/gc01_gcplyr.Rmd | 3 inst/doc/gc01_gcplyr.pdf |binary inst/doc/gc02_import_reshape.pdf |binary inst/doc/gc03_incorporate_designs.pdf |binary inst/doc/gc04_preprocess_plot.R | 30 +++++- inst/doc/gc04_preprocess_plot.Rmd | 47 +++++++++ inst/doc/gc04_preprocess_plot.pdf |binary inst/doc/gc05_process.Rmd | 2 inst/doc/gc05_process.pdf |binary inst/doc/gc06_analyze.R | 5 - inst/doc/gc06_analyze.Rmd | 7 - inst/doc/gc06_analyze.pdf |binary inst/doc/gc07_noise.pdf |binary inst/doc/gc08_conclusion.pdf |binary inst/doc/gc09_multiple_plates.pdf |binary inst/doc/gc10_using_make_design.pdf |binary man/lag_time.Rd | 29 ++++- tests/testthat/test_analysisfunctions.R | 74 ++++++++++++--- vignettes/gc01_gcplyr.Rmd | 3 vignettes/gc01_gcplyr.html | 81 ++++++++-------- vignettes/gc02_import_reshape.html | 18 +-- vignettes/gc03_incorporate_designs.html | 4 vignettes/gc04_preprocess_plot.Rmd | 47 +++++++++ vignettes/gc04_preprocess_plot.html | 113 +++++++++++++++++------ vignettes/gc05_process.Rmd | 2 vignettes/gc05_process.html | 21 ++-- vignettes/gc06_analyze.Rmd | 7 - vignettes/gc06_analyze.html | 123 +++++++++++++------------ vignettes/gc07_noise.html | 155 +++++++++++++++++--------------- vignettes/gc08_conclusion.html | 29 ++--- vignettes/gc09_multiple_plates.html | 40 ++++---- vignettes/gc10_using_make_design.html | 4 40 files changed, 721 insertions(+), 363 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.2.0 dated 2025-01-08 and 0.2.1 dated 2025-01-16
DESCRIPTION | 6 MD5 | 64 ++++---- R/mockOmopSketch.R | 6 R/summariseClinicalRecords.R | 5 R/summariseConceptIdCounts.R | 2 R/summariseConceptSetCounts.R | 4 R/summariseInObservation.R | 4 R/summariseInternal.R | 14 - R/summariseOmopSnapshot.R | 2 R/summariseRecordCount.R | 4 R/tableObservationPeriod.R | 4 README.md | 5 build/vignette.rds |binary inst/doc/A-summarise_clinical_tables_records.html | 176 +++++++++++----------- inst/doc/B-summarise_concept_set_counts.R | 2 inst/doc/B-summarise_concept_set_counts.Rmd | 2 inst/doc/B-summarise_concept_set_counts.html | 16 +- inst/doc/C-summarise_observation_period.R |only inst/doc/C-summarise_observation_period.Rmd |only inst/doc/C-summarise_observation_period.html |only man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/mockOmopSketch.Rd | 2 man/summariseClinicalRecords.Rd | 4 man/summariseConceptSetCounts.Rd | 4 tests/testthat/setup.R | 2 tests/testthat/test-summariseClinicalRecords.R | 17 -- tests/testthat/test-summariseConceptIdCounts.R | 6 tests/testthat/test-summariseConceptSetCounts.R | 15 - tests/testthat/test-summariseRecordCount.R | 6 vignettes/B-summarise_concept_set_counts.Rmd | 2 vignettes/C-summarise_observation_period.Rmd |only 35 files changed, 174 insertions(+), 200 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Designed for simplicity, a 'mirai' evaluates an R expression
asynchronously in a parallel process, locally or distributed over the
network, with the result automatically available upon completion. Modern
networking and concurrency built on 'nanonext' and 'NNG' (Nanomsg Next Gen)
ensure reliable and efficient scheduling, over fast inter-process
communications or TCP/IP secured by TLS. Advantages include being inherently
queued thus handling many more tasks than available processes, no storage on
the file system, support for otherwise non-exportable reference objects, an
event-driven promises implementation, and built-in asynchronous parallel
map.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Hibiki AI Limited [cph],
Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 2.0.0 dated 2025-01-08 and 2.0.1 dated 2025-01-16
DESCRIPTION | 6 - MD5 | 54 ++++++++--------- NAMESPACE | 2 NEWS.md | 13 ++++ R/daemon.R | 51 +++++++++++----- R/dispatcher.R | 60 +++++++++---------- R/launchers.R | 4 - R/map.R | 139 +++++++++++++++++++++++++++------------------- R/mirai.R | 60 ++++++++++++------- R/next.R | 28 +++++++++ inst/doc/mirai.Rmd | 142 +++++++++++++++++++++++++---------------------- inst/doc/mirai.html | 139 ++++++++++++++++++++++++---------------------- inst/doc/shiny.Rmd | 115 ++++++++++++++++++++++++++++++-------- inst/doc/shiny.html | 108 ++++++++++++++++++++++++++++------- man/call_mirai.Rd | 7 +- man/collect_mirai.Rd | 17 +++-- man/daemon.Rd | 12 ++- man/dot-flat.Rd | 15 +--- man/everywhere.Rd | 4 - man/is_mirai_error.Rd | 5 - man/mirai.Rd | 19 +++--- man/mirai_map.Rd | 66 +++++++++++---------- man/nextstream.Rd | 13 ++++ tests/tests.R | 38 ++++++++---- vignettes/mirai.Rmd | 142 +++++++++++++++++++++++++---------------------- vignettes/mirai.Rmd.orig | 33 ++++++---- vignettes/shiny.Rmd | 115 ++++++++++++++++++++++++++++++-------- vignettes/shiny.Rmd.orig | 114 ++++++++++++++++++++++++++++++------- 28 files changed, 982 insertions(+), 539 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.3.2 dated 2024-05-01 and 1.4.0 dated 2025-01-16
DESCRIPTION | 12 MD5 | 46 +- NAMESPACE | 7 NEWS.md | 13 R/nls.R | 217 ++++++++-- R/nls_large.R | 20 R/nls_methods.R | 257 ++++++++---- R/nls_rho.R |only configure | 22 - configure.ac | 2 inst/unit_tests/unit_tests_gslnls.R | 362 +++++++++++------ man/cooks.distance.gsl_nls.Rd |only man/gsl_nls.Rd | 61 ++ man/gsl_nls_control.Rd | 13 man/gsl_nls_large.Rd | 9 man/gsl_nls_loss.Rd |only man/summary.gsl_nls.Rd | 2 src/fdf.c |only src/fdfvv.c |only src/fdjac.c |only src/gsl_nls.h | 255 +++++++++--- src/init.c | 4 src/nls.c | 733 ++++++++++++------------------------ src/nls_fit.c |only src/nls_irls.c |only src/nls_large.c | 127 ------ src/nls_mstart.c |only src/nls_utils.c |only src/trust.c | 333 ++++++++++++---- 29 files changed, 1441 insertions(+), 1054 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut, cre] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: Andrew Pulsipher <pulsipher.a@gmail.com>
Diff between epiworldR versions 0.3-2 dated 2024-10-08 and 0.6.0.0 dated 2025-01-16
epiworldR-0.3-2/epiworldR/man/global-actions.Rd |only epiworldR-0.6.0.0/epiworldR/DESCRIPTION | 15 epiworldR-0.6.0.0/epiworldR/MD5 | 138 ++-- epiworldR-0.6.0.0/epiworldR/NAMESPACE | 40 + epiworldR-0.6.0.0/epiworldR/NEWS.md | 24 epiworldR-0.6.0.0/epiworldR/R/LFMCMC.R |only epiworldR-0.6.0.0/epiworldR/R/cpp11.R | 140 ++++ epiworldR-0.6.0.0/epiworldR/R/global-actions.R | 52 + epiworldR-0.6.0.0/epiworldR/R/model-methods.R | 49 + epiworldR-0.6.0.0/epiworldR/R/plot_epi.R | 3 epiworldR-0.6.0.0/epiworldR/README.md | 57 - epiworldR-0.6.0.0/epiworldR/build/vignette.rds |binary epiworldR-0.6.0.0/epiworldR/inst/CITATION | 3 epiworldR-0.6.0.0/epiworldR/inst/doc/getting-started.html | 87 +- epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.R |only epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.Rmd |only epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.html |only epiworldR-0.6.0.0/epiworldR/inst/doc/mixing.html | 14 epiworldR-0.6.0.0/epiworldR/inst/doc/run-multiple.html | 22 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/agent-meat-virus-sampling.hpp | 6 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/database-bones.hpp | 21 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/database-meat.hpp | 18 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/epiworld.hpp | 6 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/distributions.hpp |only epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-bones.hpp | 187 +++--- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp | 90 +- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-meat.hpp | 306 +++++----- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/misc.hpp | 2 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/model-bones.hpp | 20 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/model-meat.hpp | 68 -- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/seirconnected.hpp | 67 ++ epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/sirconnected.hpp | 58 + epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/surveillance.hpp | 2 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/progress.hpp | 12 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/random_graph.hpp | 13 epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-lfmcmc.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-multiple.R | 2 epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-seir.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sir.R | 93 +-- epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sirconn.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sird.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sis.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-tool.R |only epiworldR-0.6.0.0/epiworldR/man/LFMCMC.Rd |only epiworldR-0.6.0.0/epiworldR/man/ModelDiffNet.Rd | 4 epiworldR-0.6.0.0/epiworldR/man/ModelSEIR.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRCONN.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRD.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRDCONN.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSIR.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSIRCONN.Rd | 2 epiworldR-0.6.0.0/epiworldR/man/ModelSIRD.Rd | 14 epiworldR-0.6.0.0/epiworldR/man/ModelSIRDCONN.Rd | 2 epiworldR-0.6.0.0/epiworldR/man/ModelSIRLogit.Rd | 16 epiworldR-0.6.0.0/epiworldR/man/ModelSIS.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSISD.Rd | 16 epiworldR-0.6.0.0/epiworldR/man/ModelSURV.Rd | 6 epiworldR-0.6.0.0/epiworldR/man/agents.Rd | 36 - epiworldR-0.6.0.0/epiworldR/man/agents_smallworld.Rd | 22 epiworldR-0.6.0.0/epiworldR/man/entities.Rd | 14 epiworldR-0.6.0.0/epiworldR/man/epiworld-data.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/epiworld-methods.Rd | 141 ++-- epiworldR-0.6.0.0/epiworldR/man/epiworldR-package.Rd | 3 epiworldR-0.6.0.0/epiworldR/man/figures/README-logit-model-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-multiple-example-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-sir-figures-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-sir-figures-2.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-transmission-net-1.png |binary epiworldR-0.6.0.0/epiworldR/man/global-events.Rd |only epiworldR-0.6.0.0/epiworldR/man/run_multiple.Rd | 4 epiworldR-0.6.0.0/epiworldR/man/tool.Rd | 25 epiworldR-0.6.0.0/epiworldR/man/virus.Rd | 19 epiworldR-0.6.0.0/epiworldR/src/Makevars.in | 2 epiworldR-0.6.0.0/epiworldR/src/Makevars.win | 2 epiworldR-0.6.0.0/epiworldR/src/cpp11.cpp | 280 +++++++++ epiworldR-0.6.0.0/epiworldR/src/lfmcmc.cpp |only epiworldR-0.6.0.0/epiworldR/src/model.cpp | 17 epiworldR-0.6.0.0/epiworldR/vignettes/likelihood-free-mcmc.Rmd |only 78 files changed, 1566 insertions(+), 738 deletions(-)
Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for
R expressions.
Author: Jim Hester [aut],
Davis Vaughan [aut, cre],
Drew Schmidt [ctb] ,
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between bench versions 1.1.3 dated 2023-05-04 and 1.1.4 dated 2025-01-16
DESCRIPTION | 22 ++- LICENSE | 2 MD5 | 55 ++++----- NAMESPACE | 1 NEWS.md | 16 ++ R/autoplot.R | 73 ++++++------ R/bench-package.R | 1 R/bench_time.R | 8 + R/bytes.R | 84 +++++++++++--- R/expression.R | 11 + R/import-standalone-s3-register.R | 54 +++++---- R/load.R | 1 R/mark.R | 135 ++++++++++++++++------- R/press.R | 59 +++++----- R/time.R | 81 +++++++++----- R/utils.R | 31 +++-- R/workout.R | 6 - README.md | 24 ++-- man/autoplot.bench_mark.Rd | 2 man/press.Rd | 10 + tests/testthat/test-autoplot.R |only tests/testthat/test-bench_process_memory.R | 8 - tests/testthat/test-bench_time.R | 4 tests/testthat/test-bytes.R | 5 tests/testthat/test-expression.R | 5 tests/testthat/test-mark.R | 167 ++++++++++++++++++++--------- tests/testthat/test-press.R | 36 +++--- tests/testthat/test-time.R | 5 tests/testthat/test-workout.R | 5 29 files changed, 596 insertions(+), 315 deletions(-)
Title: Create Interactive Web Maps Using 'The National Map' Services
Description: Creates interactive web maps using the 'JavaScript' 'Leaflet'
library with base layers of 'The National Map' ('TNM'). 'TNM' services
provide access to base geospatial information that describes the landscape
of the United States and its territories. This package is dependent on, and
intended to be used with, the 'leaflet' package.
Author: Jason C. Fisher [aut, cre] ,
Stefano Cudini [ctb, cph] ,
John Firebaugh [ctb, cph]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between webmap versions 1.1.0 dated 2024-03-25 and 1.1.1 dated 2025-01-16
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 4 R/add_home_button.R | 7 - R/add_legend.R | 4 R/make_map.R | 2 README.md | 58 +++++----- data/us_cities.rda |binary inst/htmlwidgets/plugins/leaflet-search/leaflet-search.min.css | 2 man/add_cluster_button.Rd | 2 man/add_fullscreen_button.Rd | 2 man/add_home_button.Rd | 7 - man/add_legend.Rd | 6 - man/add_search_button.Rd | 2 man/make_map.Rd | 2 15 files changed, 71 insertions(+), 63 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.5 dated 2024-11-20 and 0.15.6 dated 2025-01-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/data.R | 1 + R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/eq5d.html | 12 ++++++------ man/VT.Rd | 3 ++- man/eq5d-package.Rd | 2 +- tests/testthat/test-eq5d5l.R | 9 +++++++++ 11 files changed, 37 insertions(+), 22 deletions(-)
Title: Accessing and Analyzing Large-Scale Environmental Data
Description: Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.
Author: Mitchell Manware [aut, ctb] ,
Insang Song [aut, ctb] ,
Eva Marques [aut, ctb] ,
Mariana Alifa Kassien [aut, ctb]
,
Elizabeth Scholl [ctb] ,
Kyle Messier [aut, cre] ,
Spatiotemporal Exposures and Toxicology Group [cph]
Maintainer: Kyle Messier <kyle.messier@nih.gov>
Diff between amadeus versions 1.2.2 dated 2025-01-08 and 1.2.3 dated 2025-01-16
DESCRIPTION | 9 - MD5 | 26 ++--- NAMESPACE | 2 R/calculate_covariates.R | 173 ++++++++++++++++++++---------------- R/download_auxiliary.R | 15 --- build/partial.rdb |binary inst/doc/gridmet_workflow.html | 4 inst/doc/narr_workflow.html | 4 inst/doc/terraclimate_workflow.html | 4 man/calculate_nlcd.Rd | 4 man/calculate_terraclimate.Rd | 3 man/calculate_tri.Rd | 6 - man/download_hash.Rd | 7 - man/sum_edc.Rd | 4 14 files changed, 135 insertions(+), 126 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-8 dated 2024-12-02 and 1.3-9 dated 2025-01-16
DESCRIPTION | 11 MD5 | 73 +++--- NEWS.md | 11 R/components.R | 4 R/diffnb.R | 40 ++- R/listw2sn.R | 4 R/nb2listw.R | 2 R/nb2mat.R | 6 R/nblag.R | 4 R/nboperations.R | 44 +-- inst/doc/CO69.R | 4 inst/doc/CO69.Rmd | 4 inst/doc/CO69.html | 8 inst/doc/nb_sf.html | 28 +- inst/doc/sids.html | 4 inst/doc/subgraphs.Rmd | 2 inst/doc/subgraphs.html | 8 inst/tinytest/test_nb_setops.R |only man/diffnb.Rd | 17 + man/localC.Rd | 467 ++++++++++++++++++++++++++++++++++++++++- man/nboperations.Rd | 10 src/card.c | 6 src/dfs_ncomp.c | 12 - src/dnn.c | 12 - src/gabriel.c | 2 src/gearyw.c | 2 src/gsymtest.c | 2 src/jc.c | 2 src/knn.c | 2 src/lagw.c | 6 src/nbdists.c | 8 src/perm_no_replace.c | 4 src/polypoly.c | 111 --------- src/relative.c | 2 src/spdep.h | 9 src/symtest.c | 2 vignettes/CO69.Rmd | 4 vignettes/subgraphs.Rmd | 2 38 files changed, 667 insertions(+), 272 deletions(-)
Title: Radiation and Photovoltaic Systems
Description: Provides tools for calculating solar geometry, solar radiation on horizontal and inclined planes, and simulating the performance of various photovoltaic (PV) systems. Supports daily and intradaily irradiation data, enabling detailed analysis of grid-connected and water-pumping PV systems, including shading effects and solar angle calculations.
Author: Oscar Perpinan-Lamigueiro [aut]
,
Francisco Delgado-Lopez [aut, cre]
Maintainer: Francisco Delgado-Lopez <f.delgadol@alumnos.upm.es>
Diff between solaR2 versions 0.10 dated 2024-09-16 and 0.11 dated 2025-01-16
DESCRIPTION | 15 ++++--- MD5 | 82 +++++++++++++++++++++--------------------- NAMESPACE | 7 +++ R/calcG0.R | 11 ++++- R/fSolD.R | 2 - README.md | 42 +++++++++++++++++++++ man/HQCurve.Rd | 4 +- man/Meteo2Meteo.Rd | 19 +++++---- man/NmgSFB.Rd | 3 + man/as.data.tableD-methods.Rd | 3 + man/as.data.tableI-methods.Rd | 3 + man/as.data.tableM-methods.Rd | 9 +++- man/as.data.tableY-methods.Rd | 5 ++ man/calcG0.Rd | 7 ++- man/calcGef.Rd | 3 + man/calcSol.Rd | 15 ++++--- man/compare-methods.Rd | 13 ++++-- man/compareLosses-methods.Rd | 11 +++-- man/corrFdKt.Rd | 29 ++++++++------ man/fBTd.Rd | 3 + man/fBTi.Rd | 3 + man/fCompD.Rd | 25 +++++++----- man/fCompI.Rd | 2 + man/fProd.Rd | 11 +++-- man/fPump.Rd | 14 +++++-- man/fSolD.Rd | 16 ++++---- man/fSolI.Rd | 18 +++++---- man/fSombra.Rd | 5 ++ man/local2UTC.Rd | 3 + man/mergesolaR-methods.Rd | 11 +++-- man/optimShd.Rd | 34 +++++++++-------- man/prodGCPV.Rd | 4 +- man/readBD.Rd | 3 + man/readG0dm.Rd | 7 ++- man/readSIAR.Rd | 6 ++- man/sample2Diff.Rd | 3 + man/solar2-package.Rd | 1 man/solarAngles.Rd | 2 + man/window-methods.Rd | 7 ++- man/writeSolar.Rd | 2 + tests/testthat.R | 2 + tests/testthat/test-calcG0.R | 2 - 42 files changed, 307 insertions(+), 160 deletions(-)
Title: Create Custom Research Compendiums
Description: Provides functions to create and manage research compendiums for data analysis. Research compendiums are a standard and intuitive folder structure for organizing the digital materials of a research project, which can significantly improve reproducibility. The package offers several compendium structure options that fit different research project as well as the ability of duplicating the folder structure of existing projects or implementing custom structures. It also simplifies the use of version control.
Author: Marcelo Araya-Salas [aut, cre]
,
Andrea Yure Arriaga Madrigal [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between sketchy versions 1.0.4 dated 2024-09-02 and 1.0.5 dated 2025-01-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/add_to_gitignore.R | 5 ++++- R/sysdata.rda |binary data/compendiums.rda |binary 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding / decoding. Hashes strings and raw vectors directly. Stream hashes
files which can be larger than memory, as well as in-memory objects through
R's serialization mechanism. Implementations include the SHA-256, SHA-3 and
'Keccak' cryptographic hash functions, SHAKE256 extendable-output function
(XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.3 dated 2024-10-02 and 1.0.4 dated 2025-01-16
DESCRIPTION | 8 +- MD5 | 42 +++++------ NEWS.md | 4 + R/base.R | 56 +++++++------- R/secret.R | 173 ++++++++++++++++++++++------------------------ README.md | 22 ++--- build/partial.rdb |binary inst/CITATION | 2 man/base64dec.Rd | 23 ++---- man/base64enc.Rd | 21 ++--- man/keccak.Rd | 53 +++++++------- man/secretbase-package.Rd | 12 +-- man/sha256.Rd | 56 +++++++------- man/sha3.Rd | 48 ++++++------ man/shake256.Rd | 47 ++++++------ man/siphash13.Rd | 68 +++++++++--------- src/base.c | 21 +---- src/secret.c | 24 ++---- src/secret.h | 23 +----- src/secret2.c | 15 ++- src/secret3.c | 15 ++- tests/tests.R | 6 - 22 files changed, 359 insertions(+), 380 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.5 dated 2024-11-04 and 2.8.7 dated 2025-01-16
DESCRIPTION | 6 MD5 | 106 +- NAMESPACE | 1 NEWS.md | 31 R/AAAA.R | 30 R/createSSURGO.R | 354 ++++++--- R/createStaticNASIS.R | 93 +- R/fetchNASIS.R | 4 R/fetchNASISLabData.R | 2 R/fetchNASIS_components.R | 6 R/fetchNASIS_pedons.R | 19 R/fetchSOLUS.R | 9 R/fetchSoilGrids.R | 2 R/fetchVegdata.R | 100 +- R/getHzErrorsNASIS.R | 12 R/get_NASIS_table_name_by_purpose.R | 60 - R/get_colors_from_NASIS_db.R | 20 R/get_component_data_from_NASIS_db.R | 6 R/get_ecosite_history_from_NASIS_db.R | 4 R/get_hz_data_from_NASIS_db.R | 20 R/get_hz_data_from_pedon_db.R | 4 R/get_lablayer_data_from_NASIS_db.R | 7 R/get_labpedon_data_from_NASIS_db.R | 4 R/get_site_data_from_NASIS_db.R | 141 ++- R/get_text_notes_from_NASIS_db.R | 8 R/get_veg_data_from_NASIS_db.R | 6 R/get_vegplot_data_from_NASIS_db.R | 206 +++-- R/soilDB-package.R | 4 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/gopheridge.rda |binary data/loafercreek.rda |binary data/mineralKing.rda |binary inst/CITATION | 6 inst/doc/fetchNASIS.R | 2 inst/doc/fetchNASIS.Rmd | 2 inst/doc/fetchNASIS.html | 28 inst/doc/wcs-ssurgo.R | 54 - inst/doc/wcs-ssurgo.html | 1270 +++++++++++++++++----------------- man/createSSURGO.Rd | 52 + man/downloadSSURGO.Rd | 58 + man/fetchNASIS.Rd | 4 man/fetchSOLUS.Rd | 7 man/fetchVegdata.Rd | 25 man/getHzErrorsNASIS.Rd | 2 man/get_colors_from_NASIS_db.Rd | 11 man/get_site_data_from_NASIS_db.Rd | 26 man/loafercreek.Rd | 4 tests/testthat.R | 10 tests/testthat/test-fetchLDM.R | 54 - tests/testthat/test-fetchNASIS.R | 3 tests/testthat/test-soilDBdata.R | 60 + vignettes/fetchNASIS.Rmd | 2 54 files changed, 1709 insertions(+), 1238 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph] [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.8.0 dated 2024-08-26 and 0.8.0.1 dated 2025-01-16
DESCRIPTION | 10 ++-- MD5 | 40 ++++++++--------- NEWS.md | 4 + R/push-packages.R | 49 +++++++++++++++++++++ R/repo.R | 2 man/chunks/install.Rmd | 18 ++++--- man/install.Rd | 4 + man/repo_add.Rd | 2 src/library/curl/configure | 3 - src/library/lpSolve/DESCRIPTION | 15 +++--- src/library/lpSolve/src/commonlib.c | 6 -- src/library/lpSolve/src/lp_lib.c | 2 src/library/lpSolve/src/lp_utils.c | 1 src/library/lpSolve/src/lusol.c | 2 src/library/lpSolve/src/myblas.c | 68 +++--------------------------- src/library/pkgsearch/DESCRIPTION | 9 +-- src/library/pkgsearch/NEWS.md | 5 ++ src/library/pkgsearch/R/advanced_search.R | 6 -- src/library/pkgsearch/R/api.R | 32 ++++++-------- src/library/pkgsearch/R/http.R | 26 ++++++++++- src/library/pkgsearch/R/utils.R | 18 ++++--- 21 files changed, 178 insertions(+), 144 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Trevor L. Davis [aut, cre] ,
Mike FC [aut] ,
ggplot2 authors [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 1.2.2 dated 2024-06-03 and 1.3.1 dated 2025-01-16
DESCRIPTION | 12 ++-- LICENSE | 2 MD5 | 43 ++++++++-------- NAMESPACE | 2 NEWS.md | 8 ++- R/alphaMaskGrob.R | 2 R/grid-pattern.R | 9 ++- R/pattern-pattern-aRtsy.R |only R/utils-ggplot2.R | 12 ++++ R/utils-params.R | 1 README.md | 100 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/developing-patterns.R | 10 +-- inst/doc/developing-patterns.Rmd | 6 +- inst/doc/developing-patterns.html | 8 +-- inst/doc/tiling.R | 38 +++++++------- inst/doc/tiling.Rmd | 38 +++++++------- inst/doc/tiling.html | 38 +++++++------- man/alphaMaskGrob.Rd | 2 man/grid.pattern.Rd | 6 +- man/grid.pattern_aRtsy.Rd |only tests/testthat/test_aRtsy.R |only vignettes/developing-patterns.Rmd | 6 +- vignettes/tiling.Rmd | 38 +++++++------- 24 files changed, 206 insertions(+), 175 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.6-30 dated 2024-10-02 and 3.6-31 dated 2025-01-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS | 3 +++ build/partial.rdb |binary 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates
compilers needed to build R packages on various platforms and ensures
the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgbuild versions 1.4.5 dated 2024-10-28 and 1.4.6 dated 2025-01-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/compile-dll.R | 4 +++- man/compile_dll.Rd | 4 +++- tests/testthat/test-withr.R | 6 ++++++ 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Effective Reproduction Number Estimation
Description: Estimate the effective reproduction number from wastewater
and clinical data sources.
Author: David Champredon [aut, cre] ,
Warsame Yusuf [aut] ,
Irena Papst [aut]
Maintainer: David Champredon <david.champredon@canada.ca>
Diff between ern versions 2.0.0 dated 2024-04-22 and 2.1.2 dated 2025-01-16
ern-2.0.0/ern/R/format_ww.smooth.R |only ern-2.0.0/ern/README.md |only ern-2.0.0/ern/man/summarise_by_date_ens.Rd |only ern-2.1.2/ern/DESCRIPTION | 6 ern-2.1.2/ern/MD5 | 26 +- ern-2.1.2/ern/R/estimate_R_cl_rep.R | 21 -- ern-2.1.2/ern/R/estimate_R_cl_single.R | 151 +++++++-------- ern-2.1.2/ern/R/estimate_R_ww.R | 28 +- ern-2.1.2/ern/R/get_use_dates.R | 21 -- ern-2.1.2/ern/R/globals.R | 1 ern-2.1.2/ern/R/incidence_to_R.R | 68 ++++-- ern-2.1.2/ern/R/summary_postsamples.R |only ern-2.1.2/ern/inst/doc/est-rt.html | 16 - ern-2.1.2/ern/man/sample_post_ee.Rd |only ern-2.1.2/ern/man/summary_postsamples.Rd |only ern-2.1.2/ern/tests/testthat/test-estimate_R_cl_single.R | 25 -- ern-2.1.2/ern/tests/testthat/test-get_use_dates.R | 3 17 files changed, 179 insertions(+), 187 deletions(-)
Title: Tests for Segregation Distortion in Polyploids
Description: Provides a suite of tests for
segregation distortion in F1 polyploid populations (for
now, just tetraploids). This is under different assumptions of
meiosis. Details of these methods are described in
Gerard et al. (2025) <doi:10.1007/s00122-025-04816-z>.
This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The
opinions, findings, and conclusions or recommendations expressed
are those of the author and do not necessarily reflect the views
of the National Science Foundation.
Author: David Gerard [aut, cre] ,
Mira Thakkar [aut],
NSF DBI 2132247 [fnd]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between segtest versions 1.0.1 dated 2024-10-21 and 1.0.2 dated 2025-01-16
DESCRIPTION | 8 - MD5 | 53 ++++---- NAMESPACE | 74 +++++------ R/lrt_gl.R | 200 +++++++++++++++---------------- R/overall.R | 262 ++++++++++++++++++++-------------------- R/segtest-package.R | 18 +- README.md | 18 ++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/intro.Rmd | 6 inst/doc/intro.html | 11 - man/gcount_to_gvec.Rd | 58 ++++----- man/gvec_to_gcount.Rd | 64 ++++----- man/is_valid_2.Rd | 66 +++++----- man/iter.array.Rd | 76 +++++------ man/lrt_men_gl4.Rd | 188 ++++++++++++++--------------- man/multi_lrt.Rd | 270 +++++++++++++++++++++--------------------- man/multidog_to_g.Rd | 140 ++++++++++----------- man/nextElem.arrayiter.Rd | 68 +++++----- man/otest_g.Rd | 186 ++++++++++++++-------------- man/po_gl.Rd | 100 +++++++-------- man/segtest-package.Rd | 2 man/simgl.Rd | 74 +++++------ man/ufit.Rd | 80 ++++++------ tests/testthat/test-corner.R | 66 +++++----- tests/testthat/test-overall.R | 14 +- vignettes/intro.Rmd | 6 28 files changed, 1060 insertions(+), 1048 deletions(-)
Title: Computation and Decomposition of the Mutual Information Index
Description: The Mutual Information Index (M) introduced to social science literature by
Theil and Finizza (1971) <doi:10.1080/0022250X.1971.9989795> is a multigroup
segregation measure that is highly decomposable and that according to Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008> and Mora and Ruiz-Castillo
(2011) <doi:10.1111/j.1467-9531.2011.01237.x> satisfies the Strong Unit
Decomposability and Strong Group Decomposability properties. This package allows
computing and decomposing the total index value into its "between" and
"within" terms. These last terms can also be decomposed into their
contributions, either by group or unit characteristics. The factors that produce
each "within" term can also be displayed at the user's request. The results can
be computed considering a variable or sets of variables that define separate
clusters.
Author: Cristian Angulo-Gonzalez [aut, cre],
Rafael Fuentealba-Chaura [aut],
Ricardo Mora [aut],
Julio Rojas-Mora [aut],
FONDECYT/ANID Project 11170583 [fnd],
MCIN/AEI/10.13039/501100011033 [fnd],
UCT VIP Project FEQUIP2019-INRN-03 [fnd]
Maintainer: Cristian Angulo-Gonzalez <cristian_world@hotmail.cl>
Diff between mutualinf versions 1.2.2 dated 2024-02-02 and 2.0.1 dated 2025-01-16
mutualinf-1.2.2/mutualinf/R/mutual_inv.R |only mutualinf-2.0.1/mutualinf/DESCRIPTION | 25 - mutualinf-2.0.1/mutualinf/MD5 | 48 ++ mutualinf-2.0.1/mutualinf/NAMESPACE | 3 mutualinf-2.0.1/mutualinf/R/M.R | 72 ++-- mutualinf-2.0.1/mutualinf/R/M_within.R | 356 +++++++++++++++++++-- mutualinf-2.0.1/mutualinf/R/M_within_inv.R |only mutualinf-2.0.1/mutualinf/R/RcppExports.R |only mutualinf-2.0.1/mutualinf/R/get_contribution.R | 37 +- mutualinf-2.0.1/mutualinf/R/mutual.R | 5 mutualinf-2.0.1/mutualinf/R/prepare_data.R | 3 mutualinf-2.0.1/mutualinf/README.md | 27 + mutualinf-2.0.1/mutualinf/build/partial.rdb |binary mutualinf-2.0.1/mutualinf/man/mutual.Rd | 3 mutualinf-2.0.1/mutualinf/man/mutualinf-package.Rd | 1 mutualinf-2.0.1/mutualinf/man/prepare_data.Rd | 2 mutualinf-2.0.1/mutualinf/src |only 17 files changed, 478 insertions(+), 104 deletions(-)
Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre],
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
F. [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.1.0 dated 2024-08-21 and 0.2.0 dated 2025-01-16
admiralpeds-0.1.0/admiralpeds/data/dm_peds.rda |only admiralpeds-0.1.0/admiralpeds/data/vs_peds.rda |only admiralpeds-0.1.0/admiralpeds/man/dm_peds.Rd |only admiralpeds-0.1.0/admiralpeds/man/vs_peds.Rd |only admiralpeds-0.2.0/admiralpeds/DESCRIPTION | 8 - admiralpeds-0.2.0/admiralpeds/MD5 | 42 +++---- admiralpeds-0.2.0/admiralpeds/NEWS.md | 14 ++ admiralpeds-0.2.0/admiralpeds/R/data.R | 14 -- admiralpeds-0.2.0/admiralpeds/R/derive_params_growth_age.R | 5 admiralpeds-0.2.0/admiralpeds/R/derive_params_growth_height.R | 7 - admiralpeds-0.2.0/admiralpeds/README.md | 14 ++ admiralpeds-0.2.0/admiralpeds/inst/WORDLIST | 1 admiralpeds-0.2.0/admiralpeds/inst/doc/admiralpeds.R | 8 - admiralpeds-0.2.0/admiralpeds/inst/doc/admiralpeds.Rmd | 4 admiralpeds-0.2.0/admiralpeds/inst/doc/admiralpeds.html | 4 admiralpeds-0.2.0/admiralpeds/inst/doc/advs.R | 60 +++++----- admiralpeds-0.2.0/admiralpeds/inst/doc/advs.Rmd | 16 +- admiralpeds-0.2.0/admiralpeds/inst/doc/advs.html | 21 +-- admiralpeds-0.2.0/admiralpeds/inst/templates/ad_advs.R | 47 ++++--- admiralpeds-0.2.0/admiralpeds/man/adsl_peds.Rd | 5 admiralpeds-0.2.0/admiralpeds/man/derive_params_growth_age.Rd | 5 admiralpeds-0.2.0/admiralpeds/man/derive_params_growth_height.Rd | 7 - admiralpeds-0.2.0/admiralpeds/vignettes/admiralpeds.Rmd | 4 admiralpeds-0.2.0/admiralpeds/vignettes/advs.Rmd | 16 +- 24 files changed, 161 insertions(+), 141 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features
plots for mlr3 objects such as tasks, learners, predictions, benchmark
results, tuning instances and filters via the 'autoplot()' generic of
'ggplot2'. The package draws plots with the 'viridis' color palette
and applies the minimal theme. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3viz versions 0.10.0 dated 2024-11-07 and 0.10.1 dated 2025-01-16
DESCRIPTION | 15 ++- MD5 | 59 +++++++-------- NEWS.md | 7 + R/BenchmarkResult.R | 46 ++++++++++- R/EnsembleFSResult.R | 16 +++- R/Filter.R | 2 R/LearnerClassif.R | 2 R/LearnerClassifCVGlmnet.R | 2 R/LearnerClassifGlmnet.R | 1 R/LearnerClassifRpart.R | 1 R/LearnerClustHierarchical.R | 2 R/LearnerRegr.R | 2 R/LearnerRegrCVGlmnet.R | 1 R/LearnerRegrRpart.R | 1 R/LearnerSurvCoxPH.R | 5 - R/OptimInstanceBatchSingleCrit.R | 2 R/PredictionClassif.R | 2 R/PredictionClust.R | 2 R/PredictionRegr.R | 2 R/ResampleResult.R | 9 +- R/TaskClassif.R | 2 R/TaskClust.R | 2 R/TaskRegr.R | 2 build/partial.rdb |binary man/autoplot.BenchmarkResult.Rd | 4 - man/autoplot.EnsembleFSResult.Rd | 9 ++ man/autoplot.LearnerSurvCoxPH.Rd | 4 - man/autoplot.ResampleResult.Rd | 5 - tests/testthat/_snaps/BenchmarkResult/bmr-holdout-ci.svg |only tests/testthat/test_BenchmarkResult.R | 15 +++ tests/testthat/test_EnsembleFSResult.R | 13 ++- 31 files changed, 168 insertions(+), 67 deletions(-)
Title: Recursive Two-Stage Models to Address Endogeneity
Description: Various recursive two-stage models to address the endogeneity issue of treatment variables in observational study or mediators in experiments. The details of the models are discussed in Peng (2023) <doi:10.1287/isre.2022.1113>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between endogeneity versions 2.1.3 dated 2023-08-21 and 2.1.4 dated 2025-01-16
DESCRIPTION | 16 ++++++++++------ MD5 | 30 +++++++++++++++--------------- R/probit_linear.R | 5 +++-- build/vignette.rds |binary inst/doc/vignette.html | 28 ++++++++++++++-------------- man/bilinear.Rd | 6 +++--- man/biprobit.Rd | 4 ++-- man/biprobit_latent.Rd | 6 +++--- man/biprobit_partial.Rd | 6 +++--- man/linear_probit.Rd | 6 +++--- man/pln_linear.Rd | 6 +++--- man/pln_probit.Rd | 6 +++--- man/probit_linear.Rd | 2 +- man/probit_linearRE.Rd | 6 +++--- man/probit_linear_latent.Rd | 6 +++--- man/probit_linear_partial.Rd | 6 +++--- 16 files changed, 72 insertions(+), 67 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi'
(<https://www.jamovi.org>) aims to make statistical analyses easy and
intuitive. 'jamovi' produces syntax that can directly be used in R (in
connection with the R-package 'jmv'). Having import / export routines for
the data files 'jamovi' produces ('.omv') permits an easy transfer of
data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.4.8 dated 2024-11-09 and 0.4.9 dated 2025-01-16
DESCRIPTION | 6 - MD5 | 26 +++---- NEWS.md | 10 +++ R/arrange_cols_omv.R | 35 ++++++---- R/describe_omv.R | 64 ++++++++++--------- R/distances_omv.R | 48 +++++++++----- R/globals.R | 7 +- R/read_omv.R | 120 +++++++++++++++++++++--------------- R/write_omv.R | 58 +++++++++++------ README.md | 4 - build/vignette.rds |binary inst/CITATION | 4 - inst/doc/jmvReadWrite.html | 8 +- tests/testthat/test-distances_omv.R | 13 ++- 14 files changed, 244 insertions(+), 159 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Michael Chirico [aut, cre],
Jens Oehlschlaegel [aut],
Leonardo Silvestri [ctb],
Ofek Shilon [ctb]
Maintainer: Michael Chirico <michaelchirico4@gmail.com>
Diff between bit64 versions 4.5.2 dated 2024-09-22 and 4.6.0-1 dated 2025-01-16
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Title: UNHCR 'ggplot2' Theme and Colour Palettes
Description: A 'ggplot2' theme and color palettes following
the United Nations High Commissioner for Refugees (UNHCR) Data Visualization Guidelines recommendations.
Author: Cedric Vidonne [aut, cre],
Ahmadou Dicko [aut],
UNHCR [cph]
Maintainer: Cedric Vidonne <cedric@vidonne.me>
Diff between unhcrthemes versions 0.6.2 dated 2023-11-27 and 0.6.3 dated 2025-01-16
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Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 0.2.2 dated 2023-05-04 and 1.0.1 dated 2025-01-16
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|only shapr-1.0.1/shapr/tests/testthat/test-iterative-output.R |only shapr-1.0.1/shapr/tests/testthat/test-iterative-setup.R |only shapr-1.0.1/shapr/tests/testthat/test-plot.R | 335 + shapr-1.0.1/shapr/tests/testthat/test-regression-output.R |only shapr-1.0.1/shapr/tests/testthat/test-regression-setup.R |only shapr-1.0.1/shapr/tests/testthat/test-regular-output.R |only shapr-1.0.1/shapr/tests/testthat/test-regular-setup.R |only shapr-1.0.1/shapr/vignettes/asymmetric_causal.Rmd |only shapr-1.0.1/shapr/vignettes/figure_asymmetric_causal |only shapr-1.0.1/shapr/vignettes/figure_general_usage |only shapr-1.0.1/shapr/vignettes/figure_regression |only shapr-1.0.1/shapr/vignettes/figure_vaeac |only shapr-1.0.1/shapr/vignettes/general_usage.Rmd |only shapr-1.0.1/shapr/vignettes/regression.Rmd |only shapr-1.0.1/shapr/vignettes/vaeac.Rmd |only 293 files changed, 5121 insertions(+), 1782 deletions(-)
Title: Clustering of Sites with Species Data
Description: Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Author: Sebastian Schmidtlein [aut, cre]
,
Jason Collison [aut],
Robin Pfannendoerfer [aut],
Lubomir Tichy [ctb]
Maintainer: Sebastian Schmidtlein <schmidtlein@kit.edu>
Diff between isopam versions 3.1 dated 2025-01-08 and 3.2 dated 2025-01-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/clusters.Rd | 12 +----------- 3 files changed, 6 insertions(+), 16 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.8.1 dated 2024-12-19 and 0.8.2 dated 2025-01-16
DESCRIPTION | 6 MD5 | 10 NEWS.md | 5 R/cohortUtilities.R | 3 inst/doc/create_cohorts.html | 38 inst/doc/drug_utilisation.html | 2374 ++++++++++++++++++++--------------------- 6 files changed, 1221 insertions(+), 1215 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Age-Specific Bayesian Survival Trajectory Analysis from
Incomplete Census or Capture-Recapture/Recovery Data
Description: Estimates survival and mortality with covariates from census or capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots, as described in Colchero, Jones, and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and Colchero et al. (2021) <doi:10.1038/s41467-021-23894-3>.
Author: Fernando Colchero [aut, cre],
Owen Jones [ctb]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Diff between BaSTA versions 2.0.0 dated 2024-07-08 and 2.0.1 dated 2025-01-16
DESCRIPTION | 8 MD5 | 26 +- NAMESPACE | 6 R/basta.R | 543 ++++++++++++++++++++++++++++++++++++---------- data/bastaCMRdat.RData |binary data/bastaCMRout.RData |binary data/bastaCensDat.RData |binary data/bastaCensOut.RData |binary man/BaSTA-package.Rd | 4 man/basta.Rd | 13 - man/bastaCMRout.Rd | 4 man/bastaCensOut.Rd | 4 man/multibasta.Rd |only man/summary.basta.Rd | 28 +- man/summary.multibasta.Rd |only 15 files changed, 476 insertions(+), 160 deletions(-)
Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized
large-N trials with the 'tricot' approach <https://climmob.net/>.
Developed by van Etten et al. (2019) <doi:10.1017/S0014479716000739>, it turns the
research paradigm on its head; instead of a few researchers designing complicated
trials to compare several technologies in search of the best solutions for the
target environment, it enables many participants to carry out reasonably simple
experiments that taken together can offer even more information. 'ClimMobTools'
enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between ClimMobTools versions 1.2 dated 2024-01-25 and 1.4 dated 2025-01-16
DESCRIPTION | 12 - LICENSE | 4 MD5 | 54 +++---- NEWS.md | 7 R/AAA-getDataCM.R | 71 ++++----- R/ClimMobTools.R | 2 R/as.data.frame-climmob_list.R | 302 ++++++++++++++++++++--------------------- R/getProjectProgress.R | 90 +++++------- R/getProjectsCM.R | 76 ++++------ R/getTraitList.R | 39 ++--- R/internal_functions.R | 142 +++++++++---------- R/print.R | 68 ++++----- R/rankTricot.R | 5 R/rmGeoIdentity.R | 96 ++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 14 - inst/doc/Overview.R | 37 ----- inst/doc/Overview.Rmd | 58 +------ inst/doc/Overview.html | 185 ++++++++----------------- man/ClimMobTools.Rd | 4 man/getDataCM.Rd | 36 +--- man/getProjectProgress.Rd | 20 -- man/getProjectsCM.Rd | 13 - man/getTraitList.Rd | 7 man/rankTricot.Rd | 4 man/rmGeoIdentity.Rd | 8 - vignettes/Overview.Rmd | 58 +------ 28 files changed, 600 insertions(+), 812 deletions(-)
Title: A Fast 'WHATWG' Compliant URL Parser
Description: A wrapper for 'ada-url', a 'WHATWG' compliant and fast URL parser written in modern 'C++'. Also contains auxiliary functions such as a public suffix extractor.
Author: David Schoch [aut, cre] ,
Chung-hong Chan [aut] ,
Yagiz Nizipli [ctb, cph] ,
Daniel Lemire [ctb, cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between adaR versions 0.3.3 dated 2024-07-12 and 0.3.4 dated 2025-01-16
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 4 README.md | 54 +-- build/vignette.rds |binary inst/doc/adaR.html | 747 +++++++++++++++++++++++++--------------------------- src/RcppExports.cpp | 2 src/ada/ada.cpp | 41 +- src/ada/ada.h | 64 +++- src/adaR.cpp | 21 + 10 files changed, 502 insertions(+), 455 deletions(-)
More information about NPBBBDAefficiency at CRAN
Permanent link
Title: ADaM in R Asset Library - Ophthalmology
Description: Aids the programming of Clinical Data Standards Interchange
Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM)
datasets in R. ADaM datasets are a mandatory part of any New Drug or
Biologics License Application submitted to the United States Food and
Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Edoardo Mancini [aut, cre] ,
Ritika Aggarwal [aut],
Jane Gao [aut],
William Holmes [aut],
Josie Jackson [aut],
Sonali Jain [aut],
Yuki Matsunaga [aut],
Gordon Miller [aut],
Rachel Linacre [aut],
Lucy Palmen [aut],
Nandini R Thampi [aut],
Aldrich Salv [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiralophtha versions 1.1.0 dated 2024-06-19 and 1.2.0 dated 2025-01-16
DESCRIPTION | 35 +- MD5 | 44 +- NAMESPACE | 2 NEWS.md | 25 + R/admiralophtha-package.R | 1 R/derive_var_afeye.R | 26 - R/derive_var_bcvacritxfl.R | 14 R/derive_var_studyeye.R | 2 README.md | 21 - build/vignette.rds |binary inst/WORDLIST | 121 +------ inst/doc/adbcva.R | 164 +++------ inst/doc/adbcva.Rmd | 209 +++++------- inst/doc/adbcva.html | 563 +++++++++++++++------------------ inst/doc/adoe.html | 100 ++--- inst/doc/advfq.html | 242 +++++++------- inst/templates/ad_adbcva.R | 153 ++++---- man/admiralophtha-package.Rd | 3 man/derive_var_afeye.Rd | 17 man/derive_var_bcvacritxfl.Rd | 4 man/derive_var_bcvacritxfl_util.Rd | 5 tests/testthat/test-derive_var_afeye.R | 43 -- vignettes/adbcva.Rmd | 209 +++++------- 23 files changed, 877 insertions(+), 1126 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.3.2 dated 2025-01-13 and 3.3.3 dated 2025-01-16
DESCRIPTION | 8 MD5 | 20 - R/generic.predict.rfsrc.R | 5 R/partial.rfsrc.R | 2 R/rfsrc.R | 4 configure | 551 +++++++++++++++++++++------------------------- configure.ac | 2 data/follic.rda |binary data/peakVO2.rda |binary inst/NEWS | 4 src/randomForestSRC.c | 24 +- 11 files changed, 294 insertions(+), 326 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Feature Selection for 'mlr3'
Description: Feature selection package of the 'mlr3' ecosystem. It selects
the optimal feature set for any 'mlr3' learner. The package works with
several optimization algorithms e.g. Random Search, Recursive Feature
Elimination, and Genetic Search. Moreover, it can automatically
optimize learners and estimate the performance of optimized feature
sets with nested resampling.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 1.2.1 dated 2024-11-07 and 1.3.0 dated 2025-01-16
DESCRIPTION | 14 - MD5 | 37 +- NAMESPACE | 3 NEWS.md | 7 R/ArchiveBatchFSelect.R | 5 R/EnsembleFSResult.R | 331 +++++++++++++++++++----- R/FSelectInstanceBatchSingleCrit.R | 1 R/bibentries.R | 41 ++ R/embedded_ensemble_fselect.R |only R/ensemble_fselect.R | 113 ++++---- R/zzz.R | 2 README.md | 3 build/partial.rdb |binary man/FSelectInstanceBatchSingleCrit.Rd | 1 man/embedded_ensemble_fselect.Rd |only man/ensemble_fs_result.Rd | 174 +++++++++++- man/ensemble_fselect.Rd | 39 +- man/fselect.Rd | 1 man/fsi.Rd | 1 tests/testthat/test_embedded_ensemble_fselect.R |only tests/testthat/test_ensemble_fselect.R | 306 ++++++++++++++++------ 21 files changed, 816 insertions(+), 263 deletions(-)
Title: Dose-Response Data Analysis
Description: Fit logistic functions to observed dose-response continuous
data and evaluate goodness-of-fit measures. See Malyutina A., Tang J.,
and Pessia A. (2023) <doi:10.18637/jss.v106.i04>.
Author: Alberto Pessia [aut, cre] ,
Alina Malyutina [ctb]
Maintainer: Alberto Pessia <dev@albertopessia.com>
Diff between drda versions 2.0.4 dated 2024-08-21 and 2.0.5 dated 2025-01-16
DESCRIPTION | 6 - MD5 | 16 +- NAMESPACE | 2 R/S3.R | 2 R/plot.R | 301 +++++++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary data/voropm2.rda |binary inst/doc/drda.pdf |binary man/plot.drda.Rd | 17 +- 9 files changed, 239 insertions(+), 105 deletions(-)
Title: R Client for 'Customer Journey Analytics' ('CJA') API
Description: Connect and pull data from the 'CJA' API, which powers 'CJA Workspace' <https://github.com/AdobeDocs/cja-apis>.
The package was developed with the analyst in mind and will
continue to be developed with the guiding principles of iterative,
repeatable, timely analysis. New features are actively being
developed and we value your feedback and contribution to the process.
Author: Ben Woodard [aut, cre],
Charles Gallagher [ctb],
Braxton Butcher [ctb]
Maintainer: Ben Woodard <benrwoodard@gmail.com>
Diff between cjar versions 0.1.2 dated 2022-04-18 and 0.2.0 dated 2025-01-16
cjar-0.1.2/cjar/R/annotation_build.R |only cjar-0.1.2/cjar/R/cja_get_annotations.R |only cjar-0.1.2/cjar/man/annotation_build.Rd |only cjar-0.1.2/cjar/man/cja_get_annotations.Rd |only cjar-0.2.0/cjar/DESCRIPTION | 33 +--- cjar-0.2.0/cjar/MD5 | 40 ++-- cjar-0.2.0/cjar/NAMESPACE | 4 cjar-0.2.0/cjar/NEWS.md | 7 cjar-0.2.0/cjar/R/auth.R | 233 ++++++++++++++++++++++++----- cjar-0.2.0/cjar/R/cja_freeform_table.R | 6 cjar-0.2.0/cjar/R/cja_get_dataviews.R | 2 cjar-0.2.0/cjar/R/cja_get_dimensions.R | 2 cjar-0.2.0/cjar/R/cja_get_metrics.R | 2 cjar-0.2.0/cjar/R/cjar-package.R | 2 cjar-0.2.0/cjar/R/filter_sequence.R | 7 cjar-0.2.0/cjar/R/filter_verbs.R | 2 cjar-0.2.0/cjar/README.md | 85 +++++----- cjar-0.2.0/cjar/man/cja_auth.Rd | 22 +- cjar-0.2.0/cjar/man/cja_auth_with.Rd | 4 cjar-0.2.0/cjar/man/cja_freeform_table.Rd | 6 cjar-0.2.0/cjar/man/cjar-package.Rd | 6 cjar-0.2.0/cjar/man/filter_seq.Rd | 6 cjar-0.2.0/cjar/man/filter_verbs.Rd | 2 23 files changed, 321 insertions(+), 150 deletions(-)
Title: Bitmap Tools
Description: Provides functions for creating, modifying, and displaying bitmaps including printing them in the terminal. There is a special emphasis on monochrome bitmap fonts and their glyphs as well as colored pixel art/sprites. Provides native read/write support for the 'hex' and 'yaff' bitmap font formats and if 'monobit' <https://github.com/robhagemans/monobit> is installed can also read/write several additional bitmap font formats.
Author: Trevor L. Davis [aut, cre] ,
Frederic Cambus [tyg] ,
Markus Kuhn [tyg] ,
josehzz [art]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between bittermelon versions 2.0.2 dated 2024-06-25 and 2.1.1 dated 2025-01-16
DESCRIPTION | 10 LICENSE | 4 MD5 | 61 ++--- NAMESPACE | 9 NEWS.md | 61 +++-- R/as.data.frame.bm_matrix.R |only R/as.matrix.bm_matrix.R | 6 R/as_bm_bitmap.R | 15 + R/as_bm_pixmap.R | 15 + R/bm_distort.R | 2 R/bm_pixel_picker.R |only R/bm_print.R | 5 R/monobit.R | 6 R/print.bm_bitmap.R | 14 + R/utils-color.R | 29 +- README.md | 15 - build/vignette.rds |binary inst/doc/bittermelon.R | 18 - inst/doc/bittermelon.Rmd | 9 inst/doc/bittermelon.html | 202 +++++++---------- man/as.data.frame.bm_matrix.Rd |only man/as_bm_bitmap.Rd | 3 man/as_bm_pixmap.Rd | 3 man/bm_pixel_picker.Rd |only man/bm_print.Rd | 3 man/col2int.Rd | 3 man/monobit.Rd | 2 tests/testthat/_snaps/plot/as-data-frame-bm-bitmap.svg |only tests/testthat/_snaps/plot/as-data-frame-bm-pixmap.svg |only tests/testthat/_snaps/plot/bm-pixel-picker-plot.svg |only tests/testthat/test-monobit.R | 2 tests/testthat/test-plot.R | 30 ++ tests/testthat/test-print.bm_bitmap.R | 2 tests/testthat/txt/plus_space_rl.txt | 2 vignettes/bittermelon.Rmd | 9 35 files changed, 322 insertions(+), 218 deletions(-)
Title: Building Predictive Models with Stacking
Description: Building predictive models with stacking which is a type of ensemble learning. Learners can be specified from those implemented in 'caret'. For more information of the package, see Nukui and Onogi (2023) <doi:10.1101/2023.06.06.543970>.
Author: Taichi Nukui [aut, cph],
Tomohiro Ishibashi [aut, cph],
Akio Onogi [aut, cre, cph]
Maintainer: Akio Onogi <onogiakio@gmail.com>
Diff between stacking versions 0.1.3 dated 2024-09-11 and 0.2.1 dated 2025-01-16
DESCRIPTION | 11 +- MD5 | 18 ++-- R/stacking_predict.R | 166 +++++++++++++++++++++++++++------------ R/stacking_train.R | 6 - R/train_basemodel.R | 202 +++++++++++++++++++++++++++++++++--------------- R/train_metamodel.R | 173 +++++++++++++++++++++++++++++++++-------- man/stacking_predict.Rd | 47 +++++++++-- man/stacking_train.Rd | 69 +++++++++++++--- man/train_basemodel.Rd | 70 +++++++++++++--- man/train_metamodel.Rd | 67 +++++++++++++-- 10 files changed, 622 insertions(+), 207 deletions(-)
Title: Estimate Incidence and Prevalence using the OMOP Common Data
Model
Description: Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
Author: Edward Burn [aut, cre] ,
Berta Raventos [aut] ,
Marti Catala [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Ger Inberg [ctb] ,
Kim Lopez [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between IncidencePrevalence versions 0.9.0 dated 2024-11-27 and 1.0.0 dated 2025-01-16
IncidencePrevalence-0.9.0/IncidencePrevalence/R/obscureCounts.R |only IncidencePrevalence-0.9.0/IncidencePrevalence/inst/doc/a06_Plotting_options.R |only IncidencePrevalence-0.9.0/IncidencePrevalence/inst/doc/a06_Plotting_options.Rmd |only IncidencePrevalence-0.9.0/IncidencePrevalence/inst/doc/a06_Plotting_options.html |only IncidencePrevalence-0.9.0/IncidencePrevalence/man/optionsPlot.Rd |only IncidencePrevalence-0.9.0/IncidencePrevalence/tests/testthat/test-obscureCounts.R |only IncidencePrevalence-0.9.0/IncidencePrevalence/vignettes/a06_Plotting_options.Rmd |only IncidencePrevalence-1.0.0/IncidencePrevalence/DESCRIPTION | 22 IncidencePrevalence-1.0.0/IncidencePrevalence/MD5 | 145 IncidencePrevalence-1.0.0/IncidencePrevalence/NAMESPACE | 8 IncidencePrevalence-1.0.0/IncidencePrevalence/NEWS.md |only IncidencePrevalence-1.0.0/IncidencePrevalence/R/benchmarkIncidencePrevalence.R | 104 IncidencePrevalence-1.0.0/IncidencePrevalence/R/data.R |only IncidencePrevalence-1.0.0/IncidencePrevalence/R/dateUtilities.R | 181 IncidencePrevalence-1.0.0/IncidencePrevalence/R/estimateIncidence.R | 157 IncidencePrevalence-1.0.0/IncidencePrevalence/R/estimatePrevalence.R | 101 IncidencePrevalence-1.0.0/IncidencePrevalence/R/generateDenominatorCohortSet.R | 465 IncidencePrevalence-1.0.0/IncidencePrevalence/R/getDenominatorCohorts.R | 893 - IncidencePrevalence-1.0.0/IncidencePrevalence/R/getIncidence.R | 810 - IncidencePrevalence-1.0.0/IncidencePrevalence/R/getPrevalence.R | 294 IncidencePrevalence-1.0.0/IncidencePrevalence/R/getStudyDays.R | 95 IncidencePrevalence-1.0.0/IncidencePrevalence/R/inputValidation.R | 376 IncidencePrevalence-1.0.0/IncidencePrevalence/R/mockIncidencePrevalence.R | 184 IncidencePrevalence-1.0.0/IncidencePrevalence/R/plotting.R | 836 - IncidencePrevalence-1.0.0/IncidencePrevalence/R/recordAttrition.R | 16 IncidencePrevalence-1.0.0/IncidencePrevalence/R/reexport-omopgenerics.R | 2 IncidencePrevalence-1.0.0/IncidencePrevalence/R/tables.R | 835 - IncidencePrevalence-1.0.0/IncidencePrevalence/R/tidyResults.R |only IncidencePrevalence-1.0.0/IncidencePrevalence/README.md | 42 IncidencePrevalence-1.0.0/IncidencePrevalence/build/vignette.rds |binary IncidencePrevalence-1.0.0/IncidencePrevalence/data |only IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.R | 11 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.Rmd | 9 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.html | 18 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.R | 71 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.Rmd | 71 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.html | 215 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.R | 45 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.Rmd | 45 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.html | 83 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.R | 74 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.Rmd | 83 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.html | 725 - IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.R | 65 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.Rmd | 71 IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.html | 697 - IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a06_benchmark.R |only IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a06_benchmark.Rmd |only IncidencePrevalence-1.0.0/IncidencePrevalence/inst/doc/a06_benchmark.html |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/IncidencePrevalenceBenchmarkResults.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/asIncidenceResult.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/asPrevalenceResult.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/availableIncidenceGrouping.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/availablePrevalenceGrouping.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/figures/README-unnamed-chunk-11-1.png |binary IncidencePrevalence-1.0.0/IncidencePrevalence/man/figures/README-unnamed-chunk-12-1.png |binary IncidencePrevalence-1.0.0/IncidencePrevalence/man/figures/README-unnamed-chunk-13-1.png |binary IncidencePrevalence-1.0.0/IncidencePrevalence/man/mockIncidencePrevalence.Rd | 22 IncidencePrevalence-1.0.0/IncidencePrevalence/man/optionsTableIncidence.Rd | 2 IncidencePrevalence-1.0.0/IncidencePrevalence/man/optionsTablePrevalence.Rd | 2 IncidencePrevalence-1.0.0/IncidencePrevalence/man/plotIncidence.Rd | 28 IncidencePrevalence-1.0.0/IncidencePrevalence/man/plotIncidencePopulation.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/plotPrevalence.Rd | 28 IncidencePrevalence-1.0.0/IncidencePrevalence/man/plotPrevalencePopulation.Rd |only IncidencePrevalence-1.0.0/IncidencePrevalence/man/tableIncidence.Rd | 13 IncidencePrevalence-1.0.0/IncidencePrevalence/man/tableIncidenceAttrition.Rd | 26 IncidencePrevalence-1.0.0/IncidencePrevalence/man/tablePrevalence.Rd | 13 IncidencePrevalence-1.0.0/IncidencePrevalence/man/tablePrevalenceAttrition.Rd | 27 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/manual/test-dbms.R | 311 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/manual/test-eunomia.R | 27 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-benchmarkIncidencePrevalence.R | 29 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-dateUtilities.R | 120 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-estimateIncidence.R | 6886 +++++----- IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-estimatePrevalence.R | 2896 ++-- IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-generateDenominatorCohortSet.R | 4099 +++-- IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-mockIncidencePrevalence.R | 54 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-plotting.R | 666 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-tables.R | 106 IncidencePrevalence-1.0.0/IncidencePrevalence/tests/testthat/test-tidyResults.R |only IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence.Rmd | 9 IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a02_Creating_denominator_populations.Rmd | 71 IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations.Rmd | 45 IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a04_Calculating_prevalence.Rmd | 83 IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a05_Calculating_incidence.Rmd | 71 IncidencePrevalence-1.0.0/IncidencePrevalence/vignettes/a06_benchmark.Rmd |only 85 files changed, 12215 insertions(+), 11268 deletions(-)
More information about IncidencePrevalence at CRAN
Permanent link
Title: Selecting General Circulation Models for Species Distribution
Modeling
Description: Methods to help selecting General Circulation Models (GCMs)
in the context of projecting models to future scenarios. It is provided
clusterization algorithms, distance and correlation metrics, as well as
a tailor-made algorithm to detect the optimum subset of GCMs that recreate
the environment of all GCMs as proposed in Esser et al. (2025) <doi:10.1111/gcb.70008>.
Author: Dayani Bailly [aut] ,
Reginaldo Re [aut] ,
Marcos R. Lima [aut] ,
Luiz Esser [aut, cre, cph]
Maintainer: Luiz Esser <luizesser@gmail.com>
Diff between chooseGCM versions 1.0.1 dated 2024-11-21 and 1.0.2 dated 2025-01-16
chooseGCM-1.0.1/chooseGCM/inst/doc/Resolution.R |only chooseGCM-1.0.1/chooseGCM/inst/doc/Resolution.Rmd |only chooseGCM-1.0.1/chooseGCM/inst/doc/Resolution.html |only chooseGCM-1.0.1/chooseGCM/vignettes/Resolution.Rmd |only chooseGCM-1.0.2/chooseGCM/DESCRIPTION | 16 ++--- chooseGCM-1.0.2/chooseGCM/MD5 | 18 ++--- chooseGCM-1.0.2/chooseGCM/R/WorldClim_data.R | 64 ++++++++++----------- chooseGCM-1.0.2/chooseGCM/README.md | 11 +-- chooseGCM-1.0.2/chooseGCM/build/vignette.rds |binary chooseGCM-1.0.2/chooseGCM/inst/doc/README.R |only chooseGCM-1.0.2/chooseGCM/inst/doc/README.Rmd |only chooseGCM-1.0.2/chooseGCM/inst/doc/README.html |only chooseGCM-1.0.2/chooseGCM/man/worldclim_data.Rd | 61 ++++++++++---------- chooseGCM-1.0.2/chooseGCM/vignettes/README.Rmd |only 14 files changed, 87 insertions(+), 83 deletions(-)
Title: Blocked Weighted Bootstrap
Description: The blocked weighted bootstrap (BBW) is an estimation technique
for use with data from two-stage cluster sampled surveys in which either
prior weighting (e.g. population-proportional sampling or PPS as used in
Standardized Monitoring and Assessment of Relief and Transitions or SMART
surveys) or posterior weighting (e.g. as used in rapid assessment method or
RAM and simple spatial sampling method or S3M surveys) is implemented. See
Cameron et al (2008) <doi:10.1162/rest.90.3.414> for application of
bootstrap to cluster samples. See Aaron et al (2016)
<doi:10.1371/journal.pone.0163176> and Aaron et al (2016)
<doi:10.1371/journal.pone.0162462> for application of the blocked weighted
bootstrap to estimate indicators from two-stage cluster sampled surveys.
Author: Mark Myatt [aut, cph],
Ernest Guevarra [aut, cre, cph]
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between bbw versions 0.2.0 dated 2022-05-29 and 0.3.0 dated 2025-01-16
DESCRIPTION | 25 ++-- MD5 | 96 ++++++++++++------ NAMESPACE | 28 +++++ NEWS.md | 30 ++++- R/bbw.R | 99 +++++++++---------- R/bootBW.r | 106 +++++++++++--------- R/bootClassic.R | 25 +++- R/bootProbit.R | 31 +++--- R/boot_bw.R |only R/boot_bw_estimate.R |only R/data.R | 59 +++++++---- R/post_strat_estimation.R |only R/recode.R | 18 ++- R/utils.R |only README.md | 142 +++++++++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/indicatorsCH1.rda |binary data/indicatorsCH2.rda |binary data/indicatorsHH.rda |binary data/somalia_population.rda |only inst/CITATION |only inst/WORDLIST | 32 +++--- inst/doc/bbw-estimation.Rmd |only inst/doc/bbw-estimation.html |only inst/doc/bbw-parallel.Rmd |only inst/doc/bbw-parallel.html |only inst/doc/bbw.R | 3 inst/doc/bbw.Rmd | 51 +++++----- inst/doc/bbw.html | 122 ++++++++++-------------- man/bbw.Rd | 85 +++++++--------- man/bootBW.Rd | 53 ++++------ man/bootClassic.Rd | 8 + man/bootPROBIT.Rd | 8 + man/boot_bw.Rd |only man/boot_bw_estimate.Rd |only man/boot_percentile.Rd |only man/calc_total_ci.Rd |only man/calc_total_estimate.Rd |only man/calc_total_sd.Rd |only man/check_data.Rd |only man/check_est_df.Rd |only man/check_params.Rd |only man/check_pop_df.Rd |only man/estimate_total.Rd |only man/estimate_total_.Rd |only man/get_strata.Rd |only man/indicatorsCH1.Rd | 4 man/indicatorsCH2.Rd | 4 man/indicatorsHH.Rd | 4 man/recode.Rd | 8 - man/somalia_population.Rd |only man/tidy_boot.Rd |only tests/testthat/test-boot_bw.R |only tests/testthat/test-boot_bw_estimate.R |only tests/testthat/test-post_strat_estimation.R |only tests/testthat/test_bbw.R | 15 ++ tests/testthat/test_bootClassic.R | 24 +++- tests/testthat/test_bootProbit.R | 13 +- tests/testthat/test_recode.R | 16 ++- vignettes/bbw-estimation.Rmd |only vignettes/bbw-estimation.Rmd.orig |only vignettes/bbw-parallel.Rmd |only vignettes/bbw-parallel.Rmd.orig |only vignettes/bbw.Rmd | 51 +++++----- 65 files changed, 694 insertions(+), 466 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-17 0.8.2
2024-06-05 0.8.1
2024-05-22 0.8.0
2023-12-12 0.5.0
2023-11-24 0.4.1
2023-11-19 0.4.0
2023-11-13 0.3.0
2023-10-31 0.2.1
Title: R Client for 'Adobe Analytics' API 2.0
Description: Connect to the 'Adobe Analytics' API v2.0 <https://github.com/AdobeDocs/analytics-2.0-apis>
which powers 'Analysis Workspace'. The package was developed
with the analyst in mind, and it will continue to be
developed with the guiding principles of iterative,
repeatable, timely analysis.
Author: Ben Woodard [aut, cre],
Tim Wilson [aut, ctb],
Charles Gallagher [ctb],
Mark Edmondson [ctb]
Maintainer: Ben Woodard <benrwoodard@gmail.com>
Diff between adobeanalyticsr versions 0.4.0 dated 2023-11-09 and 0.5.0 dated 2025-01-16
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Title: Parametric and Non-Parametric Demographic Functions and
Applications
Description: Calculate parametric mortality and Fertility models, following packages 'BaSTA' in Colchero, Jones and Rebke (2012) <doi:10.1111/j.2041-210X.2012.00186.x> and 'BaFTA' <https://github.com/fercol/BaFTA>, summary statistics (e.g. ageing rates, life expectancy, lifespan equality, etc.), life table and product limit estimators from census data.
Author: Fernando Colchero [aut, cre]
Maintainer: Fernando Colchero <fernando_colchero@eva.mpg.de>
Diff between paramDemo versions 1.0.1 dated 2024-07-09 and 1.0.2 dated 2025-01-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/paramDemo.R | 20 +++++++++++++++++--- man/paramDemo-package.Rd | 4 ++-- 4 files changed, 26 insertions(+), 12 deletions(-)
Title: Chemical Metrics for Microbial Communities
Description: Combines taxonomic classifications of high-throughput 16S rRNA
gene sequences with reference proteomes of archaeal and bacterial taxa to
generate amino acid compositions of community reference proteomes. Calculates
chemical metrics including carbon oxidation state ('Zc'), stoichiometric
oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C
ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'),
protein length, and average molecular weight of amino acid residues. Uses
precomputed reference proteomes for archaea and bacteria derived from the
Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived
from the NCBI Reference Sequence ('RefSeq') database and manual mapping from
the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and
Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic
classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class'
objects from the Bioconductor pa [...truncated...]
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between chem16S versions 1.1.0 dated 2024-07-01 and 1.2.0 dated 2025-01-16
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