Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks
(walk, bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks engine
<https://github.com/conveyal/r5>. The package allows users to generate
detailed routing analysis or calculate travel time and monetary cost matrices
using seamless parallel computing on top of the R5 Java machine. While R5
is developed by Conveyal, the package r5r is independently developed
by a team at the Institute for Applied Economic Research (Ipea) with
contributions from collaborators. Apart from the documentation in this
package, users will find additional information on R5 documentation at
<https://docs.conveyal.com/>. Although we try to keep new releases of
r5r in synchrony with R5, the development of R5 follows Conveyal's
independent update process. Hence, users should confirm the R5 version
implied by the Conveyal user manual (see
<https://docs.conveyal.com/changelog>) correspon [...truncated...]
Author: Marcus Saraiva [aut] ,
Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Carlos Kaue Vieira Braga [aut]
,
Matthew Wigginton Bhagat-Conway [aut]
,
Luyu Liu [ctb] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 2.0 dated 2024-04-11 and 2.1.0 dated 2025-03-08
DESCRIPTION | 16 MD5 | 182 + NAMESPACE | 2 NEWS.md | 8 R/accessibility.R | 567 +++--- R/detailed_itineraries.R | 6 R/download_r5.R | 206 +- R/expanded_travel_time_matrix.R | 6 R/find_snap.R | 120 - R/isochrone.R | 574 +++--- R/onLoad.R | 66 R/pareto_frontier.R | 408 ++-- R/r5r.R | 7 R/r5r_cache.R | 146 - R/r5r_sitrep.R | 140 - R/travel_time_matrix.R | 480 ++--- R/utils.R | 24 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 inst/doc/accessibility.R | 258 +- inst/doc/accessibility.Rmd | 450 ++-- inst/doc/accessibility.html | 75 inst/doc/detailed_itineraries.R | 160 - inst/doc/detailed_itineraries.Rmd | 354 +-- inst/doc/detailed_itineraries.html | 37 inst/doc/faq.Rmd | 208 +- inst/doc/faq.html | 4 inst/doc/fare_structure.R | 406 ++-- inst/doc/fare_structure.html | 192 -- inst/doc/isochrones.R | 228 +- inst/doc/isochrones.Rmd | 412 ++-- inst/doc/isochrones.html | 34 inst/doc/pareto_frontier.R | 208 +- inst/doc/pareto_frontier.Rmd | 488 ++--- inst/doc/pareto_frontier.html | 43 inst/doc/r5r.R | 245 +- inst/doc/r5r.Rmd | 55 inst/doc/r5r.html | 197 -- inst/doc/time_window.R | 174 - inst/doc/time_window.Rmd | 415 ++-- inst/doc/time_window.html | 84 inst/doc/travel_time_matrix.R | 140 - inst/doc/travel_time_matrix.Rmd | 350 +-- inst/doc/travel_time_matrix.html | 90 inst/extdata/poa/network_settings.json | 2 inst/extdata/spo/network_settings.json | 2 inst/jar/r5r.jar |binary man/accessibility.Rd | 6 man/expanded_travel_time_matrix.Rd | 4 man/isochrone.Rd | 549 +++-- man/r5r.Rd | 1 man/r5r_cache.Rd | 74 man/roxygen/templates/common_arguments.R | 136 - man/roxygen/templates/draws_per_minute.R | 12 man/roxygen/templates/lts_section.R | 64 man/roxygen/templates/mcraptor_algorithm_section.R | 44 man/roxygen/templates/raptor_algorithm_section.R | 38 man/roxygen/templates/time_window_related_args.R | 12 man/set_fare_cutoffs.Rd | 84 man/travel_time_matrix.Rd | 4 tests/tests_rafa/isochrone_lines.R |only tests/tests_rafa/line_mid_point.R |only tests/tests_rafa/test_rafa.R | 1928 ++++++++++----------- tests/tests_rafa/v7.0_vs_7.1.R | 162 - tests/testthat.R | 16 tests/testthat/setup.R | 50 tests/testthat/test-accessibility.R | 93 - tests/testthat/test-detailed_itineraries.R | 575 +++--- tests/testthat/test-download_r5.R | 56 tests/testthat/test-expanded_travel_time_matrix.R | 420 ++-- tests/testthat/test-isochrone.R | 228 +- tests/testthat/test-pareto_frontier.R | 11 tests/testthat/test-set_max_lts.R | 208 +- tests/testthat/test-set_max_rides.R | 340 +-- tests/testthat/test-set_monte_carlo_draws.R | 614 +++--- tests/testthat/test-set_percentiles.R | 336 +-- tests/testthat/test-set_progress.R | 130 - tests/testthat/test-set_speed.R | 466 ++--- tests/testthat/test-set_time_window.R | 452 ++-- tests/testthat/test-set_verbose.R | 130 - tests/testthat/test-travel_time_matrix.R | 600 +++--- tests/testthat/test-write_fare_structure.R | 68 tests/testthat/test-z_r5r_cache.R | 112 - vignettes/accessibility.Rmd | 450 ++-- vignettes/detailed_itineraries.Rmd | 354 +-- vignettes/faq.Rmd | 208 +- vignettes/isochrones.Rmd | 412 ++-- vignettes/pareto_frontier.Rmd | 488 ++--- vignettes/r5r.Rmd | 55 vignettes/references.json | 14 vignettes/time_window.Rmd | 415 ++-- vignettes/travel_time_matrix.Rmd | 350 +-- 93 files changed, 9462 insertions(+), 9600 deletions(-)
Title: Multivariate Version of the Diebold-Mariano Test
Description: Allows to perform the multivariate version of the Diebold-Mariano test for equal predictive ability of multiple forecast comparison. Main reference: Mariano, R.S., Preve, D. (2012) <doi:10.1016/j.jeconom.2012.01.014>.
Author: Krzysztof Drachal [aut, cre]
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between multDM versions 1.1.4 dated 2022-06-09 and 1.1.5 dated 2025-03-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/DM.test.R | 2 +- inst/CITATION | 4 ++-- 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Laboratory of Teaching to Statistics and Mathematics
Description: An educational package for teaching statistics and mathematics in both primary and higher education. The objective is to assist in the teaching/learning process, both for student study planning and teacher teaching strategies. The leem package aims to provide, in a simple yet in-depth manner, knowledge of statistics and mathematics to anyone who wants to study these areas of knowledge.
Author: Ben Deivide [aut, cre] ,
Andre Barboza [aut] ,
Alexandre Celestino [ctb] ,
Juliane Nassarala [ctb]
Maintainer: Ben Deivide <ben.deivide@gmail.com>
Diff between leem versions 0.1.0 dated 2022-03-02 and 0.2.0 dated 2025-03-08
leem-0.1.0/leem/inst/etc/iconstatscience.gif |only leem-0.1.0/leem/inst/etc/statscience.gif |only leem-0.2.0/leem/DESCRIPTION | 24 leem-0.2.0/leem/MD5 | 98 + leem-0.2.0/leem/NAMESPACE | 139 ++ leem-0.2.0/leem/NEWS.md |only leem-0.2.0/leem/R/additional_distributions.R |only leem-0.2.0/leem/R/anypfcdfdiscrete.R |only leem-0.2.0/leem/R/aux_probability.R |only leem-0.2.0/leem/R/aux_quantile.R |only leem-0.2.0/leem/R/boxplot.R |only leem-0.2.0/leem/R/confidence_interval.R |only leem-0.2.0/leem/R/error_warning_note.R |only leem-0.2.0/leem/R/globalvariables.R | 33 leem-0.2.0/leem/R/gui.R | 666 ++++++------ leem-0.2.0/leem/R/insert2.R |only leem-0.2.0/leem/R/measures_of_dispersion.R |only leem-0.2.0/leem/R/measures_of_position.R |only leem-0.2.0/leem/R/ogive.R |only leem-0.2.0/leem/R/plot1st2st.R | 1057 +++++++++++--------- leem-0.2.0/leem/R/plots.R |only leem-0.2.0/leem/R/print.R |only leem-0.2.0/leem/R/probability.R |only leem-0.2.0/leem/R/probnormal.R |only leem-0.2.0/leem/R/propofnormal.R |only leem-0.2.0/leem/R/quantile.R |only leem-0.2.0/leem/R/regions_prob.R |only leem-0.2.0/leem/R/showboxplot.R |only leem-0.2.0/leem/R/showcdf.R |only leem-0.2.0/leem/R/showci.R |only leem-0.2.0/leem/R/showkur.R |only leem-0.2.0/leem/R/showpar.R |only leem-0.2.0/leem/R/showskew.R |only leem-0.2.0/leem/R/showtabnormal.R |only leem-0.2.0/leem/R/skewness.R |only leem-0.2.0/leem/R/tabfreq.R |only leem-0.2.0/leem/R/temporario1.R |only leem-0.2.0/leem/R/test_of_hypothesis.R |only leem-0.2.0/leem/R/tkplotleem.R |only leem-0.2.0/leem/R/utils.R |only leem-0.2.0/leem/R/zzz.r | 128 +- leem-0.2.0/leem/inst/po/pt_BR/LC_MESSAGES/R-leem.mo |binary leem-0.2.0/leem/man/Gumbel_distribution.Rd |only leem-0.2.0/leem/man/P.Rd |only leem-0.2.0/leem/man/Q.Rd |only leem-0.2.0/leem/man/Regions_of_probability.Rd |only leem-0.2.0/leem/man/amplitude.Rd |only leem-0.2.0/leem/man/apf.Rd |only leem-0.2.0/leem/man/barplot.leem.Rd |only leem-0.2.0/leem/man/boxplot.leem.Rd |only leem-0.2.0/leem/man/cdfd.Rd |only leem-0.2.0/leem/man/cv.Rd |only leem-0.2.0/leem/man/hist.leem.Rd |only leem-0.2.0/leem/man/insert.Rd |only leem-0.2.0/leem/man/insert.leem.Rd |only leem-0.2.0/leem/man/leem.Rd | 2 leem-0.2.0/leem/man/madev.Rd |only leem-0.2.0/leem/man/mean.leem.Rd |only leem-0.2.0/leem/man/medev.Rd |only leem-0.2.0/leem/man/median.leem.Rd |only leem-0.2.0/leem/man/mfreq.Rd |only leem-0.2.0/leem/man/mpos.Rd |only leem-0.2.0/leem/man/mstde.Rd |only leem-0.2.0/leem/man/new_leem.Rd |only leem-0.2.0/leem/man/ogive.Rd |only leem-0.2.0/leem/man/piechart.Rd |only leem-0.2.0/leem/man/polyfreq.Rd |only leem-0.2.0/leem/man/polyfreq.leem.Rd |only leem-0.2.0/leem/man/probnormal.Rd |only leem-0.2.0/leem/man/propofnormal.Rd |only leem-0.2.0/leem/man/sdev.Rd |only leem-0.2.0/leem/man/showboxplot.Rd |only leem-0.2.0/leem/man/showcdf.Rd |only leem-0.2.0/leem/man/showci.Rd |only leem-0.2.0/leem/man/showkur.Rd |only leem-0.2.0/leem/man/showpar.Rd |only leem-0.2.0/leem/man/showskew.Rd |only leem-0.2.0/leem/man/showtabnormal.Rd |only leem-0.2.0/leem/man/skewness.Rd |only leem-0.2.0/leem/man/stickchart.Rd |only leem-0.2.0/leem/man/tabfreq.Rd |only leem-0.2.0/leem/man/tabfreq.leem.Rd |only leem-0.2.0/leem/man/variance.Rd |only leem-0.2.0/leem/po/R-leem.mo |binary leem-0.2.0/leem/po/R-leem.pot | 901 +++++++++++++---- leem-0.2.0/leem/po/R-pt_BR.po | 352 +++++- leem-0.2.0/leem/po/comando.txt |only leem-0.2.0/leem/po/utils.R |only 88 files changed, 2327 insertions(+), 1073 deletions(-)
Title: Comparison Functions for Clustering and Record Linkage
Description: Implements functions for comparing strings, sequences and
numeric vectors for clustering and record linkage applications.
Supported comparison functions include: generalized edit distances
for comparing sequences/strings, Monge-Elkan similarity for fuzzy
comparison of token sets, and L-p distances for comparing numeric
vectors. Where possible, comparison functions are implemented in
C/C++ to ensure good performance.
Author: Neil Marchant [aut, cre]
Maintainer: Neil Marchant <ngmarchant@gmail.com>
Diff between comparator versions 0.1.3 dated 2025-03-06 and 0.1.4 dated 2025-03-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/CppSeqComparator.R | 7 ++++++- src/IComparator.h | 2 ++ 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Select an Optimal Block-Length to Bootstrap Dependent Data
(Block Bootstrap)
Description: A set of functions to select the optimal block-length for a
dependent bootstrap (block-bootstrap). Includes the Hall, Horowitz, and Jing
(1995) <doi:10.1093/biomet/82.3.561> subsampling-based cross-validation method, the
Politis and White (2004) <doi:10.1081/ETC-120028836> Spectral Density
Plug-in method, including the Patton, Politis, and White (2009)
<doi:10.1080/07474930802459016> correction, and the Lahiri, Furukawa, and Lee
(2007) <doi:10.1016/j.stamet.2006.08.002> nonparametric plug-in method, with
a corresponding set of S3 plot methods.
Author: Alec Stashevsky [aut, cre] ,
Sergio Armella [ctb]
Maintainer: Alec Stashevsky <alec@alecstashevsky.com>
Diff between blocklength versions 0.2.1 dated 2025-03-08 and 0.2.2 dated 2025-03-08
DESCRIPTION | 11 ++-- MD5 | 17 +++--- NEWS.md | 12 ++++ R/nppi.R | 2 R/plot.nppi.R | 68 +++++++++++++++++++++++-- README.md | 111 +++++++++--------------------------------- man/figures/README-nppi-2.svg |only tests/testthat/Rplots.pdf |binary tests/testthat/test-nppi.R | 36 ++++++------- tests/testthat/test-plots.R | 19 ++++++- 10 files changed, 149 insertions(+), 127 deletions(-)
Title: Select an Optimal Block-Length to Bootstrap Dependent Data
(Block Bootstrap)
Description: A set of functions to select the optimal block-length for a
dependent bootstrap (block-bootstrap). Includes the Hall, Horowitz, and Jing
(1995) <doi:10.1093/biomet/82.3.561> subsampling-based cross-validation method, the
Politis and White (2004) <doi:10.1081/ETC-120028836> Spectral Density
Plug-in method, including the Patton, Politis, and White (2009)
<doi:10.1080/07474930802459016> correction, and the Lahiri, Furukawa, and Lee
(2007) <doi:10.1016/j.stamet.2006.08.002> nonparametric plug-in method, with
a corresponding set of S3 plot methods.
Author: Alec Stashevsky [aut, cre] ,
Sergio Armella [ctb]
Maintainer: Alec Stashevsky <alec@alecstashevsky.com>
Diff between blocklength versions 0.2.0 dated 2025-02-17 and 0.2.1 dated 2025-03-08
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 15 +++++++ R/nppi.R | 17 +++++--- README.md | 90 +++++++++++++++++++++++++++++++++++++++++++-- man/nppi.Rd | 35 +++++++++-------- tests/testthat/Rplots.pdf |binary tests/testthat/test-nppi.R | 2 - 8 files changed, 143 insertions(+), 36 deletions(-)
Title: Multidimensional Penalized Splines for (Excess) Hazard Models,
Relative Mortality Ratio Models and Marginal Intensity Models
Description: Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (than [...truncated...]
Author: Mathieu Fauvernier [aut, cre],
Laurent Roche [aut],
Laurent Remontet [aut],
Zoe Uhry [ctb],
Nadine Bossard [ctb],
Elsa Coz [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 2.0.1 dated 2025-01-21 and 2.0.2 dated 2025-03-08
survPen-2.0.1/survPen/R/survPenV2_01.r |only survPen-2.0.2/survPen/DESCRIPTION | 6 survPen-2.0.2/survPen/MD5 | 80 +++++----- survPen-2.0.2/survPen/NEWS | 7 survPen-2.0.2/survPen/R/survPenV2_02.r |only survPen-2.0.2/survPen/inst/doc/survival_analysis_with_survPen.R | 2 survPen-2.0.2/survPen/inst/doc/survival_analysis_with_survPen.Rmd | 6 survPen-2.0.2/survPen/inst/doc/survival_analysis_with_survPen.html | 10 - survPen-2.0.2/survPen/man/HeartFailure.Rd | 2 survPen-2.0.2/survPen/man/NR.beta.Rd | 2 survPen-2.0.2/survPen/man/NR.rho.Rd | 2 survPen-2.0.2/survPen/man/constraint.Rd | 2 survPen-2.0.2/survPen/man/cor.var.Rd | 2 survPen-2.0.2/survPen/man/crs.FP.Rd | 2 survPen-2.0.2/survPen/man/crs.Rd | 2 survPen-2.0.2/survPen/man/datCancer.Rd | 2 survPen-2.0.2/survPen/man/design.matrix.Rd | 2 survPen-2.0.2/survPen/man/expected.table.Rd | 2 survPen-2.0.2/survPen/man/instr.Rd | 2 survPen-2.0.2/survPen/man/inv.repam.Rd | 2 survPen-2.0.2/survPen/man/list.wicss.Rd | 2 survPen-2.0.2/survPen/man/model.cons.Rd | 2 survPen-2.0.2/survPen/man/predSNS.Rd | 2 survPen-2.0.2/survPen/man/predict.survPen.Rd | 2 survPen-2.0.2/survPen/man/print.summary.survPen.Rd | 2 survPen-2.0.2/survPen/man/pwcst.Rd | 2 survPen-2.0.2/survPen/man/rd.Rd | 2 survPen-2.0.2/survPen/man/repam.Rd | 2 survPen-2.0.2/survPen/man/robust.var.Rd | 2 survPen-2.0.2/survPen/man/smf.Rd | 2 survPen-2.0.2/survPen/man/smooth.cons.Rd | 2 survPen-2.0.2/survPen/man/smooth.cons.integral.Rd | 2 survPen-2.0.2/survPen/man/smooth.spec.Rd | 2 survPen-2.0.2/survPen/man/splitmult.Rd | 2 survPen-2.0.2/survPen/man/summary.survPen.Rd | 2 survPen-2.0.2/survPen/man/survPen.Rd | 2 survPen-2.0.2/survPen/man/survPen.fit.Rd | 2 survPen-2.0.2/survPen/man/survPenObject.Rd | 2 survPen-2.0.2/survPen/man/tensor.in.Rd | 2 survPen-2.0.2/survPen/man/tensor.prod.S.Rd | 2 survPen-2.0.2/survPen/man/tensor.prod.X.Rd | 2 survPen-2.0.2/survPen/vignettes/survival_analysis_with_survPen.Rmd | 6 42 files changed, 95 insertions(+), 88 deletions(-)
Title: R Library for 'Harmony'
Description: 'Harmony' is a tool using AI which allows you to compare items from questionnaires and identify similar content. You can try 'Harmony' at <https://harmonydata.ac.uk/app/> and you can read our blog at <https://harmonydata.ac.uk/blog/> or at <https://fastdatascience.com/how-does-harmony-work/>. Documentation at <https://harmonydata.ac.uk/harmony-r-released/>.
Author: Omar Hassoun [aut, cre],
Thomas Wood [ctb],
Alex, Nikic [ctb],
Ulster University [cph]
Maintainer: Omar Hassoun <omtarful@gmail.com>
Diff between harmonydata versions 0.1.1 dated 2023-10-19 and 0.2.1 dated 2025-03-08
DESCRIPTION | 13 + MD5 | 19 +- NAMESPACE | 35 ++-- NEWS.md |only R/create_instrument_from_list.R |only R/generate_crosswalk_table.R |only R/get_example_instruments.R | 129 ++++++++------- R/globals.R | 104 ++++++------ R/load_instruments_for_file.R | 304 +++++++++++++++++-------------------- R/match_instruments.R | 210 ++++++++++++------------- man/create_instrument_from_list.Rd |only man/generate_crosswalk_table.Rd |only man/match_instruments.Rd | 51 ++---- 13 files changed, 430 insertions(+), 435 deletions(-)
Title: 'Rcpp' Bindings to Parser for "Tom's Obvious Markup Language"
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format
(described at <https://toml.io/en/>) suitable for both human editing
as well as the common uses of a machine-readable format. This package
uses 'Rcpp' to connect to the 'toml++' parser written by Mark Gillard
to R.
Author: Dirk Eddelbuettel [aut, cre] ,
Mark Gillard [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.2.2 dated 2023-01-29 and 0.2.3 dated 2025-03-08
ChangeLog | 29 +++++++++++++++++++++++++++++ DESCRIPTION | 19 ++++++++++++------- MD5 | 12 ++++++------ README.md | 2 +- inst/NEWS.Rd | 9 +++++++++ inst/include/toml++/impl/parser.h | 4 ++-- inst/include/toml++/impl/path.h | 2 +- 7 files changed, 60 insertions(+), 17 deletions(-)
Title: A Pipeline to Process Single Cell RNAseq Data
Description: A pipeline that can process single or multiple Single Cell RNAseq
samples primarily specializes in Clustering and Dimensionality Reduction.
Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells,
Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte,
Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling
them by biological names. Once users named each cluster, they can evaluate the
quality of them again and find the de novo marker genes also.
Author: Jianming Zeng [aut],
Yonghe Xia [ctb, cre],
Biotrainee group [cph, fnd]
Maintainer: Yonghe Xia <xiayh17@gmail.com>
Diff between scRNAstat versions 0.1.1 dated 2021-09-22 and 0.1.1.1 dated 2025-03-08
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- data/AJ064_small_last_sce.rda |binary data/AJ064_small_sce.rda |binary 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Tools for Analyzing Finite Mixture Models
Description: Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).
Author: Derek Young [aut, cre] ,
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Kedai Cheng [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young <derek.young@uky.edu>
Diff between mixtools versions 2.0.0 dated 2022-12-05 and 2.0.0.1 dated 2025-03-08
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- build/vignette.rds |binary data/CO2data.RData |binary data/Habituationdata.RData |binary data/NOdata.RData |binary data/RTdata.RData |binary data/RTdata2.RData |binary data/RanEffdata.RData |binary data/RodFramedata.RData |binary data/Waterdata.RData |binary data/WaterdataFull.RData |binary data/tonedata.RData |binary inst/doc/mixtools.Rnw | 2 +- inst/doc/mixtools.pdf |binary man/CO2data.Rd | 2 +- man/NOdata.Rd | 2 +- man/mvnpEM.Rd | 2 +- man/normalmixMMlc.Rd | 2 +- man/summary.mvnpEM.Rd | 2 +- vignettes/mixtools.Rnw | 2 +- 21 files changed, 30 insertions(+), 30 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 1.1.0 dated 2025-02-20 and 1.2.0 dated 2025-03-08
IncidencePrevalence-1.1.0/IncidencePrevalence/inst/doc/a06_benchmark.R |only IncidencePrevalence-1.1.0/IncidencePrevalence/inst/doc/a06_benchmark.Rmd |only IncidencePrevalence-1.1.0/IncidencePrevalence/inst/doc/a06_benchmark.html |only IncidencePrevalence-1.1.0/IncidencePrevalence/vignettes/a06_benchmark.Rmd |only IncidencePrevalence-1.2.0/IncidencePrevalence/DESCRIPTION | 14 IncidencePrevalence-1.2.0/IncidencePrevalence/MD5 | 85 IncidencePrevalence-1.2.0/IncidencePrevalence/NEWS.md | 18 IncidencePrevalence-1.2.0/IncidencePrevalence/R/benchmarkIncidencePrevalence.R | 7 IncidencePrevalence-1.2.0/IncidencePrevalence/R/estimateIncidence.R | 1107 - IncidencePrevalence-1.2.0/IncidencePrevalence/R/estimatePrevalence.R | 2 IncidencePrevalence-1.2.0/IncidencePrevalence/R/generateDenominatorCohortSet.R | 9 IncidencePrevalence-1.2.0/IncidencePrevalence/R/getDenominatorCohorts.R | 910 - IncidencePrevalence-1.2.0/IncidencePrevalence/R/getIncidence.R | 52 IncidencePrevalence-1.2.0/IncidencePrevalence/R/inputValidation.R | 20 IncidencePrevalence-1.2.0/IncidencePrevalence/R/mockIncidencePrevalence.R | 30 IncidencePrevalence-1.2.0/IncidencePrevalence/R/plotting.R | 8 IncidencePrevalence-1.2.0/IncidencePrevalence/R/tables.R | 822 - IncidencePrevalence-1.2.0/IncidencePrevalence/build/vignette.rds |binary IncidencePrevalence-1.2.0/IncidencePrevalence/data/IncidencePrevalenceBenchmarkResults.rda |binary IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.html | 6 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.html | 34 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.html | 26 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.R | 15 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.Rmd | 551 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.html | 149 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.R | 37 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.Rmd | 608 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a05_Calculating_incidence.html | 375 IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a06_Working_with_IncidencePrevalence_Results.R |only IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a06_Working_with_IncidencePrevalence_Results.Rmd |only IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a06_Working_with_IncidencePrevalence_Results.html |only IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a07_benchmark.R |only IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a07_benchmark.Rmd |only IncidencePrevalence-1.2.0/IncidencePrevalence/inst/doc/a07_benchmark.html |only IncidencePrevalence-1.2.0/IncidencePrevalence/man/estimateIncidence.Rd | 12 IncidencePrevalence-1.2.0/IncidencePrevalence/man/mockIncidencePrevalence.Rd | 4 IncidencePrevalence-1.2.0/IncidencePrevalence/tests/manual/test-dbms.R | 8 IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-benchmarkIncidencePrevalence.R | 152 IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-dateUtilities.R | 252 IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-estimateIncidence.R | 7382 +++++----- IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-estimatePrevalence.R | 3096 ++-- IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-generateDenominatorCohortSet.R | 4932 +++--- IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-mockIncidencePrevalence.R | 12 IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-plotting.R | 824 - IncidencePrevalence-1.2.0/IncidencePrevalence/tests/testthat/test-tables.R | 10 IncidencePrevalence-1.2.0/IncidencePrevalence/vignettes/a04_Calculating_prevalence.Rmd | 551 IncidencePrevalence-1.2.0/IncidencePrevalence/vignettes/a05_Calculating_incidence.Rmd | 608 IncidencePrevalence-1.2.0/IncidencePrevalence/vignettes/a06_Working_with_IncidencePrevalence_Results.Rmd |only IncidencePrevalence-1.2.0/IncidencePrevalence/vignettes/a07_benchmark.Rmd |only IncidencePrevalence-1.2.0/IncidencePrevalence/vignettes/inc_rep_some_washout_censor.png |only 50 files changed, 11623 insertions(+), 11105 deletions(-)
More information about IncidencePrevalence at CRAN
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Title: "Mixture and Hidden Markov Models with R" Datasets and Example
Code
Description: Datasets and code examples that accompany our book Visser & Speekenbrink (2021), "Mixture and Hidden Markov Models with R", <https://depmix.github.io/hmmr/>.
Author: Ingmar Visser [aut, cre],
Maarten Speekenbrink [aut]
Maintainer: Ingmar Visser <i.visser@uva.nl>
Diff between hmmr versions 1.0-0 dated 2021-05-27 and 1.0-0.1 dated 2025-03-08
DESCRIPTION | 8 +++--- MD5 | 46 +++++++++++++++++++-------------------- data/IGT.rda |binary data/MAR_simulation_results.rda |binary data/MNAR_simulation_results.rda |binary data/SEsamples.rda |binary data/WPT.rda |binary data/balance8.rda |binary data/balance8pars.rda |binary data/confint.rda |binary data/conservation.rda |binary data/dccs.rda |binary data/dccs_boot_LR.rda |binary data/dccslong.rda |binary data/disc42.rda |binary data/discrimination.rda |binary data/perth.rda |binary data/simplehmm.rda |binary data/speed1.rda |binary data/speed_boot_LR.rda |binary data/speed_boot_LR_extra.rda |binary data/speed_boot_par.rda |binary man/disc42.Rd | 2 - man/discrimination.Rd | 2 - 24 files changed, 29 insertions(+), 29 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get star [...truncated...]
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
Rider Johnson [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 16.3 dated 2024-09-30 and 16.3.1 dated 2025-03-08
DESCRIPTION | 7 ++++--- MD5 | 30 +++++++++++++++--------------- data/CO2.rda |binary data/COmonthlyMet.rda |binary data/NorthAmericanRainfall.rda |binary data/NorthAmericanRainfall2.rda |binary data/PRISMelevation.rda |binary data/RCMexample.rda |binary data/RMelevation.rda |binary data/US.dat.rda |binary data/WorldBankCO2.rda |binary data/glacier.rda |binary data/lennon.rda |binary data/ozone2.rda |binary data/rat.diet.rda |binary data/world.dat.rda |binary 16 files changed, 19 insertions(+), 18 deletions(-)
Title: Dependent Gaussian Processes for Longitudinal Correlated Factors
Description: Functionalities for analyzing high-dimensional and longitudinal biomarker data to facilitate precision medicine, using a joint model of Bayesian sparse factor analysis and dependent Gaussian processes. This paper illustrates the method in detail: J Cai, RJB Goudie, C Starr, BDM Tom (2023) <doi:10.48550/arXiv.2307.02781>.
Author: Jiachen Cai [aut, cre]
Maintainer: Jiachen Cai <jiachen.cai@mrc-bsu.cam.ac.uk>
Diff between DGP4LCF versions 1.0.0 dated 2024-05-28 and 1.0.0.1 dated 2025-03-08
DESCRIPTION | 6 MD5 | 24 +-- build/vignette.rds |binary data/sim_fcs_init.rda |binary data/sim_fcs_results_irregular_6_8.rda |binary data/sim_fcs_results_regular_8.rda |binary data/sim_fcs_truth.rda |binary inst/doc/bsfadgp_irregular_data_example.R | 184 +++++++++++------------ inst/doc/bsfadgp_irregular_data_example.html | 3 inst/doc/bsfadgp_regular_data_example.R | 212 +++++++++++++-------------- inst/doc/bsfadgp_regular_data_example.html | 7 src/Makevars | 2 src/Makevars.win | 2 13 files changed, 221 insertions(+), 219 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.1.0 dated 2025-01-18 and 1.1.1 dated 2025-03-08
httr2-1.1.0/httr2/R/iterate.R |only httr2-1.1.0/httr2/R/multi-req.R |only httr2-1.1.0/httr2/R/progress.R |only httr2-1.1.0/httr2/R/sequential.R |only httr2-1.1.0/httr2/tests/testthat/_snaps/iterate-helpers.md |only httr2-1.1.0/httr2/tests/testthat/_snaps/iterate.md |only httr2-1.1.0/httr2/tests/testthat/_snaps/multi-req.md |only httr2-1.1.0/httr2/tests/testthat/_snaps/sequential.md |only httr2-1.1.0/httr2/tests/testthat/azure-cert.rds |only httr2-1.1.0/httr2/tests/testthat/azure-key.rds |only httr2-1.1.0/httr2/tests/testthat/test-iterate-helpers.R |only httr2-1.1.0/httr2/tests/testthat/test-iterate-responses.R |only httr2-1.1.0/httr2/tests/testthat/test-iterate.R |only httr2-1.1.0/httr2/tests/testthat/test-multi-req.R |only httr2-1.1.0/httr2/tests/testthat/test-sequential.R |only httr2-1.1.1/httr2/DESCRIPTION | 8 httr2-1.1.1/httr2/MD5 | 210 +++++----- httr2-1.1.1/httr2/NAMESPACE | 4 httr2-1.1.1/httr2/NEWS.md | 25 + httr2-1.1.1/httr2/R/content-type.R | 26 + httr2-1.1.1/httr2/R/curl.R | 5 httr2-1.1.1/httr2/R/headers.R | 56 ++ httr2-1.1.1/httr2/R/httr2-package.R | 2 httr2-1.1.1/httr2/R/oauth-client.R | 2 httr2-1.1.1/httr2/R/oauth-flow-auth-code.R | 4 httr2-1.1.1/httr2/R/oauth-token.R | 15 httr2-1.1.1/httr2/R/oauth.R | 24 - 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Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>, the beta method based on signal detection theory by Li and Chen (2024) <DOI:10.1111/bmsp.12371> and Q-matrix validation based on relative fit index by Chen et la. (2013) <DOI:10.1111/j.1745-3984.2012.00185.x>. Different research methods and iterative procedures during Q-matrix validating are avai [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 1.1.1 dated 2025-01-09 and 1.2.0 dated 2025-03-07
Qval-1.1.1/Qval/R/GDI.R |only Qval-1.1.1/Qval/R/Hull.R |only Qval-1.1.1/Qval/R/MLR-B.R |only Qval-1.1.1/Qval/R/P.R |only Qval-1.1.1/Qval/R/PVAF.R |only Qval-1.1.1/Qval/R/Pattern.R |only Qval-1.1.1/Qval/R/R2.R |only Qval-1.1.1/Qval/R/Wald.R |only Qval-1.1.1/Qval/R/beta.R |only Qval-1.1.1/Qval/R/cov.R |only Qval-1.1.1/Qval/R/priority.R |only Qval-1.1.1/Qval/R/validation.R |only Qval-1.1.1/Qval/man/plot.Hull.Rd |only Qval-1.2.0/Qval/DESCRIPTION | 19 +- Qval-1.2.0/Qval/MD5 | 108 +++++++-------- Qval-1.2.0/Qval/NAMESPACE | 11 + Qval-1.2.0/Qval/NEWS.md | 43 +++--- Qval-1.2.0/Qval/R/CDM.R | 157 +++++++++++---------- Qval-1.2.0/Qval/R/IndexBeta.R |only Qval-1.2.0/Qval/R/IndexPVAF.R |only Qval-1.2.0/Qval/R/IndexPriority.R |only Qval-1.2.0/Qval/R/IndexR2.R |only Qval-1.2.0/Qval/R/MLRlasso.R | 3 Qval-1.2.0/Qval/R/Mmatrix.R | 18 +- Qval-1.2.0/Qval/R/QvalBeta.R |only Qval-1.2.0/Qval/R/QvalGDI.R |only Qval-1.2.0/Qval/R/QvalHull.R |only Qval-1.2.0/Qval/R/QvalMLRB.R |only Qval-1.2.0/Qval/R/QvalWald.R |only Qval-1.2.0/Qval/R/Qvalindex.R | 113 ++++++--------- Qval-1.2.0/Qval/R/Qvalvalidation.R |only Qval-1.2.0/Qval/R/Rmatrix.R | 26 +-- Qval-1.2.0/Qval/R/S3.R |only Qval-1.2.0/Qval/R/Wald.test.R | 72 +++++----- Qval-1.2.0/Qval/R/fit.R | 40 ++--- Qval-1.2.0/Qval/R/plot.Hull.R | 74 +++++----- Qval-1.2.0/Qval/R/sim.MQ.R | 8 - Qval-1.2.0/Qval/R/sim.Q.R | 11 - Qval-1.2.0/Qval/R/sim.data.R | 60 ++++++-- Qval-1.2.0/Qval/R/zzz.R | 4 Qval-1.2.0/Qval/man/CDM.Rd | 135 +++++++++--------- Qval-1.2.0/Qval/man/Wald.test.Rd | 29 ++-- Qval-1.2.0/Qval/man/extract.Rd |only Qval-1.2.0/Qval/man/fit.Rd | 37 ++--- Qval-1.2.0/Qval/man/get.Mmatrix.Rd | 11 - Qval-1.2.0/Qval/man/get.PVAF.Rd | 38 ++--- Qval-1.2.0/Qval/man/get.R2.Rd | 48 +++--- Qval-1.2.0/Qval/man/get.Rmatrix.Rd | 12 - Qval-1.2.0/Qval/man/get.beta.Rd |only Qval-1.2.0/Qval/man/get.priority.Rd | 44 ++++-- Qval-1.2.0/Qval/man/parallel_iter.Rd | 63 ++++---- Qval-1.2.0/Qval/man/plot.validation.Rd |only Qval-1.2.0/Qval/man/print.CDM.Rd |only Qval-1.2.0/Qval/man/print.sim.data.Rd |only Qval-1.2.0/Qval/man/print.validation.Rd |only Qval-1.2.0/Qval/man/sim.MQ.Rd | 8 - Qval-1.2.0/Qval/man/sim.Q.Rd | 10 - Qval-1.2.0/Qval/man/sim.data.Rd | 35 ++-- Qval-1.2.0/Qval/man/validation.Rd | 229 ++++++++++++++++++-------------- Qval-1.2.0/Qval/man/zOSR.Rd | 8 - Qval-1.2.0/Qval/man/zQRR.Rd | 6 Qval-1.2.0/Qval/man/zTNR.Rd | 10 - Qval-1.2.0/Qval/man/zTPR.Rd | 10 - Qval-1.2.0/Qval/man/zUSR.Rd | 10 - Qval-1.2.0/Qval/man/zVRR.Rd | 10 - Qval-1.2.0/Qval/src/PGDINA.cpp | 4 Qval-1.2.0/Qval/src/calculatePEst.cpp | 2 Qval-1.2.0/Qval/tests/building.R | 9 - Qval-1.2.0/Qval/tests/demo.R | 58 ++++---- Qval-1.2.0/Qval/tests/repeat.R | 10 - 70 files changed, 863 insertions(+), 740 deletions(-)
Title: Seasonal Mid-Summer Drought Characteristics
Description: Characterization of a mid-summer drought (MSD) with precipitation
based statistics. The MSD is a phenomenon of decreased rainfall during a
typical rainy season. It is a feature of rainfall in much of Central America
and is also found in other locations, typically those with a Mediterranean
climate. Details on the metrics are in Maurer et al. (2022)
<doi:10.5194/hess-26-1425-2022>.
Author: Turner Uyeda [aut],
Ed Maurer [aut, cre, cph],
Iris Stewart-Frey [aut],
Kenneth Joseph [aut],
Alex Avila [aut]
Maintainer: Ed Maurer <emaurer@scu.edu>
Diff between msdrought versions 0.1.0 dated 2024-05-27 and 0.1.1 dated 2025-03-07
msdrought-0.1.0/msdrought/inst/doc/sample-walkthrough.R |only msdrought-0.1.0/msdrought/inst/doc/sample-walkthrough.Rmd |only msdrought-0.1.0/msdrought/inst/doc/sample-walkthrough.html |only msdrought-0.1.0/msdrought/vignettes/sample-walkthrough.Rmd |only msdrought-0.1.1/msdrought/DESCRIPTION | 16 msdrought-0.1.1/msdrought/LICENSE | 4 msdrought-0.1.1/msdrought/MD5 | 74 msdrought-0.1.1/msdrought/NAMESPACE | 14 msdrought-0.1.1/msdrought/NEWS.md | 13 msdrought-0.1.1/msdrought/R/msdDates.R | 8 msdrought-0.1.1/msdrought/R/msdFilter.R | 80 msdrought-0.1.1/msdrought/R/msdGraph.R | 244 +- msdrought-0.1.1/msdrought/R/msdMain.R | 172 - msdrought-0.1.1/msdrought/R/msdStats.R | 29 msdrought-0.1.1/msdrought/R/timeseries.R | 28 msdrought-0.1.1/msdrought/R/which_max.R |only msdrought-0.1.1/msdrought/README.md | 236 +- msdrought-0.1.1/msdrought/build/vignette.rds |binary msdrought-0.1.1/msdrought/inst/doc/Sample-Walkthrough.R |only msdrought-0.1.1/msdrought/inst/doc/Sample-Walkthrough.Rmd |only msdrought-0.1.1/msdrought/inst/doc/Sample-Walkthrough.html |only msdrought-0.1.1/msdrought/inst/doc/average-daily.R | 125 - msdrought-0.1.1/msdrought/inst/doc/average-daily.Rmd | 73 msdrought-0.1.1/msdrought/inst/doc/average-daily.html | 876 ++++------ msdrought-0.1.1/msdrought/inst/doc/raster-sample.R | 76 msdrought-0.1.1/msdrought/inst/doc/raster-sample.Rmd | 46 msdrought-0.1.1/msdrought/inst/doc/raster-sample.html | 812 ++++----- msdrought-0.1.1/msdrought/inst/doc/vector-from-raster.R | 133 - msdrought-0.1.1/msdrought/inst/doc/vector-from-raster.Rmd | 44 msdrought-0.1.1/msdrought/inst/doc/vector-from-raster.html | 739 +++++--- msdrought-0.1.1/msdrought/inst/extdata/prcp_cropped.tif.aux.json | 8 msdrought-0.1.1/msdrought/man/f.which.max.Rd |only msdrought-0.1.1/msdrought/man/figures/README-example-1.png |binary msdrought-0.1.1/msdrought/man/msdDates.Rd | 66 msdrought-0.1.1/msdrought/man/msdFilter.Rd | 66 msdrought-0.1.1/msdrought/man/msdGraph.Rd | 90 - msdrought-0.1.1/msdrought/man/msdMain.Rd | 82 msdrought-0.1.1/msdrought/man/msdStats.Rd | 1 msdrought-0.1.1/msdrought/man/timeseries.Rd | 50 msdrought-0.1.1/msdrought/vignettes/Sample-Walkthrough.Rmd |only msdrought-0.1.1/msdrought/vignettes/average-daily.Rmd | 73 msdrought-0.1.1/msdrought/vignettes/raster-sample.Rmd | 46 msdrought-0.1.1/msdrought/vignettes/vector-from-raster.Rmd | 44 43 files changed, 2218 insertions(+), 2150 deletions(-)
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.8.0 dated 2024-12-04 and 1.9.0 dated 2025-03-07
DESCRIPTION | 6 MD5 | 33 - NAMESPACE | 1 NEWS.md | 13 R/mrbin.R | 1117 +++++++++++++++++++++++++++++++++----------- inst/doc/mrbin.R | 255 +++++----- inst/doc/mrbin.Rnw | 247 ++++++--- inst/doc/mrbin.pdf |binary inst/extdata/data |only inst/extdata/example.csv |only man/annotatemrbin.Rd | 47 + man/editmetabolitesmrbin.Rd | 14 man/mrheatmap.Rd |only man/mrplot.Rd | 23 man/plotMultiNMR.Rd | 6 man/plotNMR.Rd | 6 man/plotPCA.Rd | 3 vignettes/mrbin.Rnw | 247 ++++++--- 18 files changed, 1448 insertions(+), 570 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.8-5 dated 2023-11-28 and 0.8-6 dated 2025-03-07
units-0.8-5/units/man/ud_are_convertible.Rd |only units-0.8-6/units/DESCRIPTION | 10 units-0.8-6/units/MD5 | 74 units-0.8-6/units/NAMESPACE | 3 units-0.8-6/units/NEWS.md | 33 units-0.8-6/units/R/RcppExports.R | 12 units-0.8-6/units/R/arith.R | 27 units-0.8-6/units/R/conversion.R | 14 units-0.8-6/units/R/helpers.R | 34 units-0.8-6/units/R/make_units.R | 4 units-0.8-6/units/R/math.R | 2 units-0.8-6/units/R/misc.R | 93 - units-0.8-6/units/R/mixed.R | 8 units-0.8-6/units/R/plot.R | 1 units-0.8-6/units/R/scale_units.R | 54 units-0.8-6/units/R/summaries.R | 8 units-0.8-6/units/R/symbolic_units.R | 70 units-0.8-6/units/R/tidyverse.R | 1 units-0.8-6/units/R/udunits.R | 73 units-0.8-6/units/build/vignette.rds |binary units-0.8-6/units/configure | 877 +++++---- units-0.8-6/units/configure.ac | 30 units-0.8-6/units/inst/doc/measurement_units_in_R.html | 915 ++++++---- units-0.8-6/units/inst/doc/units.html | 670 +++---- units-0.8-6/units/man/cbind.units.Rd |only units-0.8-6/units/man/deparse_unit.Rd | 2 units-0.8-6/units/man/keep_units.Rd | 20 units-0.8-6/units/man/udunits2.Rd |only units-0.8-6/units/man/units.Rd | 4 units-0.8-6/units/src/RcppExports.cpp | 62 units-0.8-6/units/src/udunits.cpp | 69 units-0.8-6/units/tests/testthat/_snaps/plot/ggplot2-limits-other-units.svg |only units-0.8-6/units/tests/testthat/_snaps/plot/ggplot2-limits-via-scale-with-units.svg |only units-0.8-6/units/tests/testthat/_snaps/plot/ggplot2-limits-via-scale.svg |only units-0.8-6/units/tests/testthat/_snaps/plot/ggplot2-limits-via-xlim.svg |only units-0.8-6/units/tests/testthat/test_arith.R | 15 units-0.8-6/units/tests/testthat/test_conversion.R | 19 units-0.8-6/units/tests/testthat/test_helpers.R | 15 units-0.8-6/units/tests/testthat/test_misc.R | 49 units-0.8-6/units/tests/testthat/test_plot.R | 30 units-0.8-6/units/tests/testthat/test_summaries.R | 2 units-0.8-6/units/tests/testthat/test_udunits.R |only 42 files changed, 1962 insertions(+), 1338 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Groq','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://groq.com>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.3.1 dated 2025-02-24 and 0.3.2 dated 2025-03-07
tidyllm-0.3.1/tidyllm/tests/testthat/groq/api.groq.com/openai/v1/chat/completions-cc1a7b-POST.R |only tidyllm-0.3.2/tidyllm/DESCRIPTION | 19 tidyllm-0.3.2/tidyllm/MD5 | 82 +- tidyllm-0.3.2/tidyllm/NAMESPACE | 6 tidyllm-0.3.2/tidyllm/NEWS.md | 73 ++ tidyllm-0.3.2/tidyllm/R/api_azure_openai.R | 55 + tidyllm-0.3.2/tidyllm/R/api_claude.R | 126 +++ tidyllm-0.3.2/tidyllm/R/api_deepseek.R |only tidyllm-0.3.2/tidyllm/R/api_gemini.R | 171 ++++- tidyllm-0.3.2/tidyllm/R/api_groq.R | 35 - tidyllm-0.3.2/tidyllm/R/api_mistral.R | 37 - tidyllm-0.3.2/tidyllm/R/api_ollama.R | 82 ++ tidyllm-0.3.2/tidyllm/R/api_openai.R | 97 ++- tidyllm-0.3.2/tidyllm/R/api_voyage.R |only tidyllm-0.3.2/tidyllm/R/embedding_helpers.R |only tidyllm-0.3.2/tidyllm/R/llm_verbs.R | 10 tidyllm-0.3.2/tidyllm/R/media.R | 52 + tidyllm-0.3.2/tidyllm/R/perform_api_requests.R | 1 tidyllm-0.3.2/tidyllm/R/tidyllm_schema.R | 5 tidyllm-0.3.2/tidyllm/R/tools.R |only tidyllm-0.3.2/tidyllm/R/utilites.R | 41 - tidyllm-0.3.2/tidyllm/README.md | 4 tidyllm-0.3.2/tidyllm/inst/doc/tidyllm.R | 5 tidyllm-0.3.2/tidyllm/inst/doc/tidyllm.Rmd | 8 tidyllm-0.3.2/tidyllm/inst/doc/tidyllm.html | 322 +++++----- tidyllm-0.3.2/tidyllm/man/azure_openai_chat.Rd | 8 tidyllm-0.3.2/tidyllm/man/chat.Rd | 3 tidyllm-0.3.2/tidyllm/man/deepseek.Rd |only tidyllm-0.3.2/tidyllm/man/deepseek_chat.Rd |only tidyllm-0.3.2/tidyllm/man/embed.Rd | 2 tidyllm-0.3.2/tidyllm/man/gemini_chat.Rd | 5 tidyllm-0.3.2/tidyllm/man/groq_chat.Rd | 8 tidyllm-0.3.2/tidyllm/man/img.Rd |only tidyllm-0.3.2/tidyllm/man/mistral_chat.Rd | 8 tidyllm-0.3.2/tidyllm/man/ollama_chat.Rd | 3 tidyllm-0.3.2/tidyllm/man/openai_chat.Rd | 8 tidyllm-0.3.2/tidyllm/man/tidyllm_tool.Rd |only tidyllm-0.3.2/tidyllm/man/voyage.Rd |only tidyllm-0.3.2/tidyllm/man/voyage_embedding.Rd |only tidyllm-0.3.2/tidyllm/tests/testthat/deepseek |only tidyllm-0.3.2/tidyllm/tests/testthat/groq/api.groq.com/openai/v1/chat/completions-adc488-POST.R |only tidyllm-0.3.2/tidyllm/tests/testthat/perplexity |only tidyllm-0.3.2/tidyllm/tests/testthat/test_api_claude.R | 3 tidyllm-0.3.2/tidyllm/tests/testthat/test_api_deepseek.R |only tidyllm-0.3.2/tidyllm/tests/testthat/test_api_gemini.R | 2 tidyllm-0.3.2/tidyllm/tests/testthat/test_api_groq.R | 10 tidyllm-0.3.2/tidyllm/tests/testthat/test_api_perplexity.R |only tidyllm-0.3.2/tidyllm/tests/testthat/test_api_voyage.R |only tidyllm-0.3.2/tidyllm/tests/testthat/test_tidyllm_schema.R |only tidyllm-0.3.2/tidyllm/tests/testthat/test_tooldef.R |only tidyllm-0.3.2/tidyllm/tests/testthat/voyage_embedding_text |only tidyllm-0.3.2/tidyllm/vignettes/tidyllm.Rmd | 8 52 files changed, 972 insertions(+), 327 deletions(-)
Title: Tool for the U.S. SEC EDGAR Retrieval and Parsing of Corporate
Filings
Description: In the USA, companies file different forms with the U.S.
Securities and Exchange Commission (SEC) through EDGAR (Electronic
Data Gathering, Analysis, and Retrieval system). The EDGAR
database automated system collects all the different necessary
filings and makes it publicly available. This package facilitates
retrieving, storing, searching, and parsing of all the available
filings on the EDGAR server. It downloads filings from SEC
server in bulk with a single query. Additionally, it provides
various useful functions: extracts 8-K triggering events, extract
"Business (Item 1)" and "Management's Discussion and Analysis(Item 7)"
sections of annual statements, searches filings for desired
keywords, provides sentiment measures, parses filing header
information, and provides HTML view of SEC filings.
Author: Gunratan Lonare [aut, cre],
Bharat Patil [aut]
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 2.0.7 dated 2023-10-14 and 2.0.8 dated 2025-03-07
DESCRIPTION | 22 +++-- MD5 | 46 +++++------ R/get8KItems.R | 38 +++++++-- R/getBusinessDescr.R | 47 ++++++++--- R/getDailyMaster.R | 58 +++++++++----- R/getFilingHeader.R | 18 ++-- R/getFilingInfo.R | 20 ++--- R/getFilings.R | 52 ++++++++----- R/getFilingsHTML.R | 18 ++-- R/getMasterIndex.R | 64 ++++++++++------ R/getMgmtDisc.R | 19 ++-- R/getSentiment.R | 16 ++-- R/searchFilings.R | 15 ++- man/get8KItems.Rd | 86 +++++++++++---------- man/getBusinDescr.Rd | 104 +++++++++++++------------- man/getDailyMaster.Rd | 68 ++++++++--------- man/getFilingHeader.Rd | 98 ++++++++++++------------ man/getFilingInfo.Rd | 14 ++- man/getFilings.Rd | 14 ++- man/getFilingsHTML.Rd | 104 +++++++++++++------------- man/getMasterIndex.Rd | 92 ++++++++++++----------- man/getMgmtDisc.Rd | 16 ++-- man/getSentiment.Rd | 196 ++++++++++++++++++++++++------------------------- man/searchFilings.Rd | 106 +++++++++++++------------- 24 files changed, 738 insertions(+), 593 deletions(-)
Title: Spatial Bayesian Methods for Task Functional MRI Studies
Description: Performs a spatial Bayesian general linear model (GLM) for task
functional magnetic resonance imaging (fMRI) data on the cortical surface.
Additional models include group analysis and inference to detect thresholded
areas of activation. Includes direct support for the 'CIFTI' neuroimaging
file format. For more information see A. F. Mejia, Y. R. Yue, D. Bolin, F.
Lindgren, M. A. Lindquist (2020) <doi:10.1080/01621459.2019.1611582> and D.
Spencer, Y. R. Yue, D. Bolin, S. Ryan, A. F. Mejia (2022)
<doi:10.1016/j.neuroimage.2022.118908>.
Author: Amanda Mejia [aut, cre],
Damon Pham [ctb] ,
David Bolin [ctb],
Yu Yue [ctb],
Daniel Spencer [aut] ,
Sarah Ryan [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between BayesfMRI versions 0.3.11 dated 2023-12-18 and 0.10.1 dated 2025-03-07
BayesfMRI-0.10.1/BayesfMRI/DESCRIPTION | 54 BayesfMRI-0.10.1/BayesfMRI/MD5 | 250 + BayesfMRI-0.10.1/BayesfMRI/NAMESPACE | 86 BayesfMRI-0.10.1/BayesfMRI/NEWS.md | 16 BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM.R | 1382 +++++----- BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM2.R | 429 ++- BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM2_Bayes_utils.R |only BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM_check_data_inputs.R |only BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM_format_cifti.R |only BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM_session_names.R |only BayesfMRI-0.10.1/BayesfMRI/R/BayesGLM_utils.R | 412 +- BayesfMRI-0.10.1/BayesfMRI/R/BayesfMRI-package.R | 2 BayesfMRI-0.10.1/BayesfMRI/R/EM_utils.R | 15 BayesfMRI-0.10.1/BayesfMRI/R/GLM_Bayesian_EM.R |only BayesfMRI-0.10.1/BayesfMRI/R/GLM_FIR.R |only BayesfMRI-0.10.1/BayesfMRI/R/GLM_classical.R |only BayesfMRI-0.10.1/BayesfMRI/R/GLM_compare.R |only BayesfMRI-0.10.1/BayesfMRI/R/GLM_est_resid_var_pw.R |only BayesfMRI-0.10.1/BayesfMRI/R/RcppExports.R | 6 BayesfMRI-0.10.1/BayesfMRI/R/SPDE_from_vertex.R |only BayesfMRI-0.10.1/BayesfMRI/R/SPDE_from_voxel.R |only BayesfMRI-0.10.1/BayesfMRI/R/activations.R |only BayesfMRI-0.10.1/BayesfMRI/R/activations.methods.R |only BayesfMRI-0.10.1/BayesfMRI/R/checkX.R |only BayesfMRI-0.10.1/BayesfMRI/R/fit_bayesglm.R |only BayesfMRI-0.10.1/BayesfMRI/R/fit_bayesglm_utils.R |only BayesfMRI-0.10.1/BayesfMRI/R/intersect_mask.R |only BayesfMRI-0.10.1/BayesfMRI/R/make_A_mat.R |only BayesfMRI-0.10.1/BayesfMRI/R/make_mesh.R | 68 BayesfMRI-0.10.1/BayesfMRI/R/make_spde_vol.R |only BayesfMRI-0.10.1/BayesfMRI/R/methods.BayesGLM.R |only BayesfMRI-0.10.1/BayesfMRI/R/methods.BayesGLM2.R |only BayesfMRI-0.10.1/BayesfMRI/R/methods.fit_bglm.R |only BayesfMRI-0.10.1/BayesfMRI/R/nV_definitions.R |only BayesfMRI-0.10.1/BayesfMRI/R/plot.R | 173 - BayesfMRI-0.10.1/BayesfMRI/R/prevalence.R |only BayesfMRI-0.10.1/BayesfMRI/R/prevalence.methods.R |only BayesfMRI-0.10.1/BayesfMRI/R/prevalence_utils.R |only 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Title: Access Data from the Norwegian Parliament API
Description: Functions for retrieving general and specific data from the Norwegian Parliament,
through the Norwegian Parliament API at <https://data.stortinget.no>.
Author: Martin Soeyland [aut, cre]
Maintainer: Martin Soeyland <martin.soyland@stv.uio.no>
Diff between stortingscrape versions 0.3.0 dated 2024-01-18 and 0.4.0 dated 2025-03-07
DESCRIPTION | 17 ++++---- MD5 | 43 +++++++++++---------- NEWS.md | 26 ++++++++++++ R/data.R | 32 +++++++++++++++ R/get_case.R | 8 ++- R/get_meeting_agenda.R | 40 ++++++++++--------- R/get_mp_pic.R | 10 ++-- R/get_proposal_votes.R | 2 R/get_publication.R | 7 ++- R/get_question.R | 87 ++++++++++++++++++++++++------------------- R/get_question_hour.R | 70 ++++++++++++++++++---------------- R/get_session_cases.R | 23 ++++++++++- README.md | 21 ++++++++-- build/vignette.rds |binary data/st_party_colors.rda |only inst/CITATION |only inst/doc/stortingscrape.R | 16 +++---- inst/doc/stortingscrape.Rmd | 2 inst/doc/stortingscrape.html | 14 +++--- man/get_meeting_agenda.Rd | 1 man/get_publication.Rd | 5 +- man/get_question.Rd | 4 + man/st_party_colors.Rd |only vignettes/stortingscrape.Rmd | 2 24 files changed, 279 insertions(+), 151 deletions(-)
More information about stortingscrape at CRAN
Permanent link
Title: Tidy Plots for Scientific Papers
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Diff between tidyplots versions 0.2.1 dated 2025-01-19 and 0.2.2 dated 2025-03-07
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tidyplots-0.2.2/tidyplots/R/helpers.R | 193 +-- tidyplots-0.2.2/tidyplots/R/labels.R | 230 ++-- tidyplots-0.2.2/tidyplots/R/plot.R | 141 +- tidyplots-0.2.2/tidyplots/R/remove.R | 142 +- tidyplots-0.2.2/tidyplots/R/themes.R | 72 - tidyplots-0.2.2/tidyplots/R/tidycolor.R | 6 tidyplots-0.2.2/tidyplots/README.md | 102 + tidyplots-0.2.2/tidyplots/build/vignette.rds |binary tidyplots-0.2.2/tidyplots/inst/doc/tidyplots.R | 196 +-- tidyplots-0.2.2/tidyplots/inst/doc/tidyplots.Rmd | 192 +-- tidyplots-0.2.2/tidyplots/inst/doc/tidyplots.html | 196 +-- tidyplots-0.2.2/tidyplots/man/add.Rd | 4 tidyplots-0.2.2/tidyplots/man/add_annotation_text.Rd | 24 tidyplots-0.2.2/tidyplots/man/add_areastack_absolute.Rd | 24 tidyplots-0.2.2/tidyplots/man/add_barstack_absolute.Rd | 32 tidyplots-0.2.2/tidyplots/man/add_boxplot.Rd | 20 tidyplots-0.2.2/tidyplots/man/add_count_bar.Rd | 84 - tidyplots-0.2.2/tidyplots/man/add_curve_fit.Rd | 16 tidyplots-0.2.2/tidyplots/man/add_data_labels.Rd | 30 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tidyplots-0.2.2/tidyplots/man/reverse_x_axis_labels.Rd | 54 tidyplots-0.2.2/tidyplots/man/save_plot.Rd | 40 tidyplots-0.2.2/tidyplots/man/sort_x_axis_labels.Rd | 54 tidyplots-0.2.2/tidyplots/man/split_plot.Rd | 30 tidyplots-0.2.2/tidyplots/man/theme_tidyplot.Rd | 50 tidyplots-0.2.2/tidyplots/man/tidyplot.Rd | 16 tidyplots-0.2.2/tidyplots/man/view_plot.Rd | 26 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-annotation/add-annotation-text.svg | 8 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-count-x.svg | 2 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-grouped-count-x.svg | 6 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-grouped-mean-xy.svg | 6 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-grouped-median-xy.svg | 6 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-grouped-sum-xy.svg | 6 tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/add-general/add-mean-xy.svg | 2 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tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/helpers/highlight-the-first-3-animals-in-the-dataset.svg |only tidyplots-0.2.2/tidyplots/tests/testthat/_snaps/helpers/highlight-the-last-3-animals-in-the-dataset.svg |only tidyplots-0.2.2/tidyplots/tests/testthat/test-add-annotation.R | 64 - tidyplots-0.2.2/tidyplots/tests/testthat/test-add-general.R | 552 +++++----- tidyplots-0.2.2/tidyplots/tests/testthat/test-add-heatmap.R | 114 +- tidyplots-0.2.2/tidyplots/tests/testthat/test-add-misc.R | 38 tidyplots-0.2.2/tidyplots/tests/testthat/test-add-points.R | 116 +- tidyplots-0.2.2/tidyplots/tests/testthat/test-add-proportional.R | 382 +++--- tidyplots-0.2.2/tidyplots/tests/testthat/test-add-stats.R | 38 tidyplots-0.2.2/tidyplots/tests/testthat/test-adjust.R | 218 ++- tidyplots-0.2.2/tidyplots/tests/testthat/test-helpers.R | 71 - tidyplots-0.2.2/tidyplots/tests/testthat/test-labels.R | 228 ++-- tidyplots-0.2.2/tidyplots/vignettes/tidyplots.Rmd | 192 +-- 131 files changed, 3451 insertions(+), 3341 deletions(-)
Title: Tests of Equal Predictive Accuracy for Panels of Forecasts
Description: Allows to perform the tests of equal predictive accuracy for panels of forecasts. Main references: Qu et al. (2024) <doi:10.1016/j.ijforecast.2023.08.001> and Akgun et al. (2024) <doi:10.1016/j.ijforecast.2023.02.001>.
Author: Krzysztof Drachal [aut, cre]
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between pEPA versions 1.0 dated 2024-07-09 and 1.2 dated 2025-03-07
DESCRIPTION | 12 +++--- MD5 | 15 +++++--- NAMESPACE | 2 + NEWS | 9 ++++ R/RcppExports.R |only R/onUnload.R |only R/tests.R | 105 ++++++++++++++++++++++++++++++-------------------------- inst/include |only src |only 9 files changed, 86 insertions(+), 57 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.0.3 dated 2025-01-13 and 0.0.4 dated 2025-03-07
DESCRIPTION | 11 MD5 | 32 + NAMESPACE | 1 NEWS.md | 9 R/aaa-generics-surface.R | 598 ++++++++++++++++++++++++---------- R/aaa-generics-volume.R | 205 +++++++++++ R/aaa.R | 14 R/as_ieegio_surface.R | 107 +++--- R/math-volume.R | 258 +++++++++----- R/xml.R | 7 build/vignette.rds |binary man/imaging-surface.Rd | 16 man/merge.ieegio_surface.Rd |only man/merge.ieegio_volume.Rd |only tests/testthat.R | 2 tests/testthat/setup.R |only tests/testthat/test-hdf5.R | 2 tests/testthat/test-resample_volume.R |only tests/testthat/test-volume.R | 3 19 files changed, 933 insertions(+), 332 deletions(-)
Title: Calculate Genetic Interactions for Paired CRISPR Targets
Description: Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.
Author: Candace Savonen [aut, cre],
Phoebe Parrish [aut],
Kate Isaac [aut],
Howard Baek [aut],
Daniel Grosso [aut],
Siobhan O'Brien [aut],
Alice Berger [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between gimap versions 1.0.2 dated 2025-02-18 and 1.0.3 dated 2025-03-07
gimap-1.0.2/gimap/man/crtl_genes.Rd |only gimap-1.0.2/gimap/man/gimap_rep_stats.Rd |only gimap-1.0.3/gimap/DESCRIPTION | 6 gimap-1.0.3/gimap/MD5 | 110 ++- gimap-1.0.3/gimap/NAMESPACE | 2 gimap-1.0.3/gimap/NEWS.md | 5 gimap-1.0.3/gimap/R/00-setup_data.R | 16 gimap-1.0.3/gimap/R/01-qc.R | 11 gimap-1.0.3/gimap/R/02-gimap_filter.R | 8 gimap-1.0.3/gimap/R/03-annotate.R | 127 +++- gimap-1.0.3/gimap/R/04-normalize.R | 83 +- gimap-1.0.3/gimap/R/05-calculate_gi.R | 283 +++++++--- gimap-1.0.3/gimap/R/plots-gi.R | 198 ++++-- gimap-1.0.3/gimap/R/plots-norm.R | 4 gimap-1.0.3/gimap/R/plots-qc.R | 7 gimap-1.0.3/gimap/R/utils.R | 69 +- gimap-1.0.3/gimap/README.md | 14 gimap-1.0.3/gimap/inst/doc/quick-start.R | 12 gimap-1.0.3/gimap/inst/doc/quick-start.Rmd | 13 gimap-1.0.3/gimap/inst/doc/quick-start.html | 17 gimap-1.0.3/gimap/inst/doc/timepoint-example.R | 10 gimap-1.0.3/gimap/inst/doc/timepoint-example.Rmd | 10 gimap-1.0.3/gimap/inst/doc/timepoint-example.html | 12 gimap-1.0.3/gimap/inst/doc/treatment_example.R | 6 gimap-1.0.3/gimap/inst/doc/treatment_example.Rmd | 6 gimap-1.0.3/gimap/inst/doc/treatment_example.html | 6 gimap-1.0.3/gimap/inst/extdata/Achilles_common_essentials.csv |only gimap-1.0.3/gimap/man/calc_gi.Rd | 17 gimap-1.0.3/gimap/man/cn_setup.Rd | 8 gimap-1.0.3/gimap/man/ctrl_genes.Rd |only gimap-1.0.3/gimap/man/delete_annotation.Rd |only gimap-1.0.3/gimap/man/delete_example_data.Rd |only gimap-1.0.3/gimap/man/get_example_data.Rd | 13 gimap-1.0.3/gimap/man/get_figshare.Rd | 14 gimap-1.0.3/gimap/man/gimap_annotate.Rd | 42 + gimap-1.0.3/gimap/man/gimap_filter.Rd | 2 gimap-1.0.3/gimap/man/gimap_normalize.Rd | 17 gimap-1.0.3/gimap/man/gimap_stats.Rd |only gimap-1.0.3/gimap/man/plot_crispr.Rd | 2 gimap-1.0.3/gimap/man/plot_exp_v_obs_scatter.Rd | 10 gimap-1.0.3/gimap/man/plot_rank_scatter.Rd | 6 gimap-1.0.3/gimap/man/plot_targets_bar.Rd | 4 gimap-1.0.3/gimap/man/plot_volcano.Rd | 8 gimap-1.0.3/gimap/man/qc_cdf.Rd | 1 gimap-1.0.3/gimap/man/qc_constructs_countzero_bar.Rd | 1 gimap-1.0.3/gimap/man/qc_cor_heatmap.Rd | 1 gimap-1.0.3/gimap/man/qc_filter_plasmid.Rd | 2 gimap-1.0.3/gimap/man/qc_filter_zerocounts.Rd | 2 gimap-1.0.3/gimap/man/qc_sample_hist.Rd | 1 gimap-1.0.3/gimap/man/qc_variance_hist.Rd | 1 gimap-1.0.3/gimap/man/run_qc.Rd | 7 gimap-1.0.3/gimap/man/setup_data.Rd | 14 gimap-1.0.3/gimap/man/tpm_setup.Rd | 8 gimap-1.0.3/gimap/tests/testthat/test-gi-calc.R | 36 + gimap-1.0.3/gimap/tests/testthat/test-normalize.R | 25 gimap-1.0.3/gimap/vignettes/example_qc_report.html |only gimap-1.0.3/gimap/vignettes/images/results_table.png |binary gimap-1.0.3/gimap/vignettes/quick-start.Rmd | 13 gimap-1.0.3/gimap/vignettes/timepoint-example.Rmd | 10 gimap-1.0.3/gimap/vignettes/treatment_example.Rmd | 6 60 files changed, 868 insertions(+), 438 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.4 dated 2024-12-12 and 0.1.5 dated 2025-03-07
ChangeLog | 6 + DESCRIPTION | 8 +- MD5 | 57 ++++++++-------- NAMESPACE | 2 R/RcppExports.R | 66 ++++++++++++++++--- R/qopt.R |only R/qx_functions.R | 151 ++++++++++++++++++++++++-------------------- README.md | 36 ++++++++++ inst/doc/vignette.R | 4 + inst/doc/vignette.html | 25 +++++++ inst/doc/vignette.rmd | 34 +++++++++ inst/include/qs2_external.h | 49 ++++++++++++++ man/blosc_shuffle_raw.Rd | 2 man/qd_deserialize.Rd | 19 +++-- man/qd_read.Rd | 19 +++-- man/qd_save.Rd | 29 ++++---- man/qd_serialize.Rd | 28 ++++---- man/qopt.Rd |only man/qs_deserialize.Rd | 16 ++-- man/qs_read.Rd | 16 ++-- man/qs_save.Rd | 25 ++++--- man/qs_serialize.Rd | 24 ++++-- man/qx_dump.Rd | 6 - man/xxhash_raw.Rd | 6 - man/zstd_compress_bound.Rd | 2 man/zstd_compress_raw.Rd | 2 src/RcppExports.cpp | 136 +++++++++++++++++++++++++++++++++++++-- src/io/io_common.h | 2 src/qoptions.h |only src/qx_functions.cpp | 102 ++++++++++++++++------------- vignettes/vignette.rmd | 34 +++++++++ 31 files changed, 660 insertions(+), 246 deletions(-)
Title: Color Palettes, Colormaps, and Tools to Evaluate Them
Description: A comprehensive collection of color palettes, colormaps, and
tools to evaluate them. See Kovesi (2015) <doi:10.48550/arXiv.1509.03700>.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between pals versions 1.9 dated 2024-07-16 and 1.10 dated 2025-03-07
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NEWS.md | 6 ++- build/vignette.rds |binary inst/doc/bivariate_choropleths.html | 14 +++---- inst/doc/pals_examples.html | 70 ++++++++++++++++++------------------ 6 files changed, 57 insertions(+), 53 deletions(-)
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Description: Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forth [...truncated...]
Author: Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
Kristina Wicke [aut],
John Rhodes [aut, cre]
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Diff between MSCquartets versions 3.0 dated 2024-10-30 and 3.1 dated 2025-03-07
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + R/ToBtoLevel1.R | 14 ++------------ R/evonetMisc.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/NANUQplus.R | 8 ++++---- inst/doc/NANUQplus.Rmd | 2 +- inst/doc/NANUQplus.html | 18 +++++++++--------- inst/doc/TINNIK.html | 10 +++++----- man/suppressNetBinaryNodes.Rd |only vignettes/NANUQplus.Rmd | 2 +- 13 files changed, 38 insertions(+), 45 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [aut] ,
Susanne Dandl [aut],
Keno Mersmann [ctb],
Maximilian Muecke [ctb] ,
Lona Koers [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.7.1 dated 2024-11-14 and 0.7.2 dated 2025-03-07
DESCRIPTION | 35 + MD5 | 368 ++++++++++----------- NAMESPACE | 4 NEWS.md | 20 + R/Graph.R | 56 +-- R/GraphLearner.R | 2 R/LearnerAvg.R | 14 R/PipeOp.R | 144 ++++---- R/PipeOpADAS.R | 4 R/PipeOpBLSmote.R | 4 R/PipeOpBoxCox.R | 4 R/PipeOpBranch.R | 9 R/PipeOpChunk.R | 4 R/PipeOpClassBalancing.R | 5 R/PipeOpClassWeights.R | 5 R/PipeOpClassifAvg.R | 8 R/PipeOpColApply.R | 8 R/PipeOpColRoles.R | 133 +++++-- R/PipeOpCollapseFactors.R | 65 +++ R/PipeOpCopy.R | 19 - R/PipeOpDateFeatures.R | 13 R/PipeOpDecode.R |only R/PipeOpEncode.R | 6 R/PipeOpEncodeImpact.R | 6 R/PipeOpEncodeLmer.R | 11 R/PipeOpEncodePL.R |only R/PipeOpEnsemble.R | 8 R/PipeOpFeatureUnion.R | 8 R/PipeOpFilter.R | 5 R/PipeOpFixFactors.R | 4 R/PipeOpHistBin.R | 3 R/PipeOpICA.R | 3 R/PipeOpImpute.R | 12 R/PipeOpImputeConstant.R | 3 R/PipeOpImputeHist.R | 3 R/PipeOpImputeMean.R | 3 R/PipeOpImputeMedian.R | 3 R/PipeOpImputeMode.R | 5 R/PipeOpImputeOOR.R | 3 R/PipeOpImputeSample.R | 3 R/PipeOpKernelPCA.R | 7 R/PipeOpLearner.R | 7 R/PipeOpLearnerCV.R | 10 R/PipeOpLearnerPICVPlus.R | 18 - R/PipeOpLearnerQuantiles.R | 10 R/PipeOpMissingIndicators.R | 4 R/PipeOpModelMatrix.R | 3 R/PipeOpMutate.R | 4 R/PipeOpNMF.R | 8 R/PipeOpNOP.R | 8 R/PipeOpNearmiss.R | 2 R/PipeOpOVR.R | 1 R/PipeOpPCA.R | 3 R/PipeOpProxy.R | 7 R/PipeOpQuantileBin.R | 7 R/PipeOpRandomProjection.R | 3 R/PipeOpRegrAvg.R | 3 R/PipeOpRemoveConstants.R | 2 R/PipeOpRenameColumns.R | 10 R/PipeOpRowApply.R | 9 R/PipeOpScale.R | 6 R/PipeOpScaleRange.R | 3 R/PipeOpSelect.R | 3 R/PipeOpSmote.R | 2 R/PipeOpSmoteNC.R | 2 R/PipeOpSpatialSign.R | 4 R/PipeOpSubsample.R | 71 +++- R/PipeOpTaskPreproc.R | 83 ++-- R/PipeOpTextVectorizer.R | 100 ++--- R/PipeOpThreshold.R | 1 R/PipeOpTomek.R | 2 R/PipeOpTrafo.R | 75 ++-- R/PipeOpTuneThreshold.R | 3 R/PipeOpUnbranch.R | 7 R/PipeOpVtreat.R | 23 - R/PipeOpYeoJohnson.R | 3 R/bibentries.R | 29 + R/mlr_graphs.R | 1 R/mlr_pipeops.R | 27 + R/po.R | 4 R/ppl.R | 4 R/utils.R | 70 +++ inst/doc/extending.R | 76 ++-- man/Graph.Rd | 56 +-- man/PipeOp.Rd | 148 ++++---- man/PipeOpEncodePL.Rd |only man/PipeOpEnsemble.Rd | 12 man/PipeOpImpute.Rd | 16 man/PipeOpTargetTrafo.Rd | 46 +- man/PipeOpTaskPreproc.Rd | 44 +- man/PipeOpTaskPreprocSimple.Rd | 32 + man/mlr_learners_graph.Rd | 2 man/mlr_pipeops.Rd | 33 + man/mlr_pipeops_adas.Rd | 8 man/mlr_pipeops_blsmote.Rd | 12 man/mlr_pipeops_boxcox.Rd | 9 man/mlr_pipeops_branch.Rd | 12 man/mlr_pipeops_chunk.Rd | 8 man/mlr_pipeops_classbalancing.Rd | 8 man/mlr_pipeops_classifavg.Rd | 10 man/mlr_pipeops_classweights.Rd | 8 man/mlr_pipeops_colapply.Rd | 12 man/mlr_pipeops_collapsefactors.Rd | 48 ++ man/mlr_pipeops_colroles.Rd | 48 ++ man/mlr_pipeops_copy.Rd | 23 - man/mlr_pipeops_datefeatures.Rd | 18 - man/mlr_pipeops_decode.Rd |only man/mlr_pipeops_encode.Rd | 11 man/mlr_pipeops_encodeimpact.Rd | 12 man/mlr_pipeops_encodelmer.Rd | 17 man/mlr_pipeops_encodeplquantiles.Rd |only man/mlr_pipeops_encodepltree.Rd |only man/mlr_pipeops_featureunion.Rd | 12 man/mlr_pipeops_filter.Rd | 6 man/mlr_pipeops_fixfactors.Rd | 9 man/mlr_pipeops_histbin.Rd | 9 man/mlr_pipeops_ica.Rd | 9 man/mlr_pipeops_imputeconstant.Rd | 9 man/mlr_pipeops_imputehist.Rd | 9 man/mlr_pipeops_imputelearner.Rd | 4 man/mlr_pipeops_imputemean.Rd | 9 man/mlr_pipeops_imputemedian.Rd | 9 man/mlr_pipeops_imputemode.Rd | 9 man/mlr_pipeops_imputeoor.Rd | 9 man/mlr_pipeops_imputesample.Rd | 9 man/mlr_pipeops_kernelpca.Rd | 13 man/mlr_pipeops_learner.Rd | 10 man/mlr_pipeops_learner_cv.Rd | 10 man/mlr_pipeops_learner_pi_cvplus.Rd | 22 - man/mlr_pipeops_learner_quantiles.Rd | 14 man/mlr_pipeops_missind.Rd | 8 man/mlr_pipeops_modelmatrix.Rd | 9 man/mlr_pipeops_multiplicityexply.Rd | 4 man/mlr_pipeops_multiplicityimply.Rd | 4 man/mlr_pipeops_mutate.Rd | 6 man/mlr_pipeops_nearmiss.Rd | 6 man/mlr_pipeops_nmf.Rd | 14 man/mlr_pipeops_nop.Rd | 12 man/mlr_pipeops_ovrsplit.Rd | 4 man/mlr_pipeops_ovrunite.Rd | 4 man/mlr_pipeops_pca.Rd | 9 man/mlr_pipeops_proxy.Rd | 8 man/mlr_pipeops_quantilebin.Rd | 11 man/mlr_pipeops_randomprojection.Rd | 9 man/mlr_pipeops_randomresponse.Rd | 4 man/mlr_pipeops_regravg.Rd | 6 man/mlr_pipeops_removeconstants.Rd | 6 man/mlr_pipeops_renamecolumns.Rd | 14 man/mlr_pipeops_replicate.Rd | 4 man/mlr_pipeops_rowapply.Rd | 12 man/mlr_pipeops_scale.Rd | 11 man/mlr_pipeops_scalemaxabs.Rd | 4 man/mlr_pipeops_scalerange.Rd | 9 man/mlr_pipeops_select.Rd | 7 man/mlr_pipeops_smote.Rd | 6 man/mlr_pipeops_smotenc.Rd | 6 man/mlr_pipeops_spatialsign.Rd | 9 man/mlr_pipeops_subsample.Rd | 27 + man/mlr_pipeops_targetinvert.Rd | 12 man/mlr_pipeops_targetmutate.Rd | 6 man/mlr_pipeops_targettrafoscalerange.Rd | 9 man/mlr_pipeops_textvectorizer.Rd | 102 +++-- man/mlr_pipeops_threshold.Rd | 4 man/mlr_pipeops_tomek.Rd | 6 man/mlr_pipeops_tunethreshold.Rd | 4 man/mlr_pipeops_unbranch.Rd | 10 man/mlr_pipeops_updatetarget.Rd | 9 man/mlr_pipeops_vtreat.Rd | 13 man/mlr_pipeops_yeojohnson.Rd | 9 man/mlr_tasks_boston_housing.Rd | 3 tests/testthat/test_GraphLearner.R | 25 - tests/testthat/test_PipeOp.R | 12 tests/testthat/test_dictionary.R | 15 tests/testthat/test_multiplicities.R | 4 tests/testthat/test_parvals.R | 8 tests/testthat/test_pipeop_blsmote.R | 2 tests/testthat/test_pipeop_collapsefactors.R |only tests/testthat/test_pipeop_colroles.R | 97 ++++- tests/testthat/test_pipeop_decode.R |only tests/testthat/test_pipeop_encodepl.R |only tests/testthat/test_pipeop_learner.R | 6 tests/testthat/test_pipeop_learnerpicvplus.R | 1 tests/testthat/test_pipeop_subsample.R | 179 +++++++++- tests/testthat/test_pipeop_targetmutate.R | 70 ++- tests/testthat/test_pipeop_targettrafoscalerange.R | 10 tests/testthat/test_pipeop_task_preproc.R | 27 + tests/testthat/test_po.R | 8 tests/testthat/test_ppl.R | 10 tests/testthat/test_typecheck.R | 2 tests/testthat/test_utils.R |only 190 files changed, 2350 insertions(+), 1118 deletions(-)
Title: Isotopic Tracer Analysis Using MCMC
Description: Implements Bayesian models to analyze data from tracer addition
experiments. The implemented method was originally described in the article
"A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from
Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020)
<doi:10.1086/708546>.
Author: Andres Lopez-Sepulcre [aut] ,
Matthieu Bruneaux [aut, cre]
Maintainer: Matthieu Bruneaux <matthieu.bruneaux@gmail.com>
Diff between isotracer versions 1.1.7 dated 2024-11-04 and 1.1.8 dated 2025-03-07
DESCRIPTION | 6 MD5 | 106 +++++----- NEWS.md | 12 + data/aquarium_run.rda |binary inst/doc/case-study-collins-2016.Rmd | 2 inst/doc/case-study-collins-2016.html | 4 inst/doc/tutorial-010-quick-start.Rmd | 2 inst/doc/tutorial-010-quick-start.html | 4 inst/doc/tutorial-020-replication.Rmd | 2 inst/doc/tutorial-020-replication.html | 4 inst/doc/tutorial-030-steady-state-comps.Rmd | 2 inst/doc/tutorial-030-steady-state-comps.html | 4 inst/doc/tutorial-040-pulse-drip-events.Rmd | 2 inst/doc/tutorial-040-pulse-drip-events.html | 4 inst/doc/tutorial-050-fixed-effects.Rmd | 2 inst/doc/tutorial-050-fixed-effects.html | 4 inst/doc/tutorial-060-units-priors.Rmd | 2 inst/doc/tutorial-060-units-priors.html | 4 inst/doc/tutorial-070-prior-predictive-checks.Rmd | 2 inst/doc/tutorial-070-prior-predictive-checks.html | 4 inst/doc/tutorial-080-mcmc-output-format.Rmd | 2 inst/doc/tutorial-080-mcmc-output-format.html | 4 inst/doc/tutorial-090-post-run-analyses.Rmd | 2 inst/doc/tutorial-090-post-run-analyses.html | 4 inst/doc/tutorial-100-posterior-predictive-checks.Rmd | 2 inst/doc/tutorial-100-posterior-predictive-checks.html | 14 - inst/doc/tutorial-110-derived-parameters.Rmd | 2 inst/doc/tutorial-110-derived-parameters.html | 4 inst/doc/tutorial-120-howto-simulations.Rmd | 2 inst/doc/tutorial-120-howto-simulations.html | 4 inst/doc/tutorial-130-parameter-identifiability.Rmd | 9 inst/doc/tutorial-130-parameter-identifiability.html | 45 ++-- vignettes/case-study-collins-2016.Rmd | 2 vignettes/figures/z-fig-100-unnamed-chunk-12-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-12-2.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-13-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-14-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-2.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-23-1.jpeg |binary vignettes/tutorial-010-quick-start.Rmd | 2 vignettes/tutorial-020-replication.Rmd | 2 vignettes/tutorial-030-steady-state-comps.Rmd | 2 vignettes/tutorial-040-pulse-drip-events.Rmd | 2 vignettes/tutorial-050-fixed-effects.Rmd | 2 vignettes/tutorial-060-units-priors.Rmd | 2 vignettes/tutorial-070-prior-predictive-checks.Rmd | 2 vignettes/tutorial-080-mcmc-output-format.Rmd | 2 vignettes/tutorial-090-post-run-analyses.Rmd | 2 vignettes/tutorial-100-posterior-predictive-checks.Rmd | 2 vignettes/tutorial-110-derived-parameters.Rmd | 2 vignettes/tutorial-120-howto-simulations.Rmd | 2 vignettes/tutorial-130-parameter-identifiability.Rmd | 9 54 files changed, 165 insertions(+), 136 deletions(-)
Title: Simulate, Evaluate, and Analyze Dose Finding Trials with
Bayesian MCPMod
Description: Bayesian MCPMod (Fleischer et al. (2022)
<doi:10.1002/pst.2193>) is an innovative method that improves the
traditional MCPMod by systematically incorporating historical data,
such as previous placebo group data. This R package offers functions
for simulating, analyzing, and evaluating Bayesian MCPMod trials with
normally distributed endpoints. It enables the assessment of trial
designs incorporating historical data across various true
dose-response relationships and sample sizes. Robust mixture prior
distributions, such as those derived with the Meta-Analytic-Predictive
approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be
specified for each dose group. Resulting mixture posterior
distributions are used in the Bayesian Multiple Comparison Procedure
and modeling steps. The modeling step also includes a weighted model
averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>).
Estimated dose-response relationships can be bootstrapped and
visualiz [...truncated...]
Author: Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd],
Stephan Wojciekowski [aut, cre],
Lars Andersen [aut],
Jonas Schick [ctb],
Sebastian Bossert [aut]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>
Diff between BayesianMCPMod versions 1.0.2 dated 2025-02-06 and 1.1.0 dated 2025-03-07
BayesianMCPMod-1.0.2/BayesianMCPMod/R/Quarto |only BayesianMCPMod-1.1.0/BayesianMCPMod/DESCRIPTION | 16 BayesianMCPMod-1.1.0/BayesianMCPMod/MD5 | 86 - BayesianMCPMod-1.1.0/BayesianMCPMod/NAMESPACE | 2 BayesianMCPMod-1.1.0/BayesianMCPMod/NEWS.md | 15 BayesianMCPMod-1.1.0/BayesianMCPMod/R/BMCPMod.R | 566 ++++++---- BayesianMCPMod-1.1.0/BayesianMCPMod/R/bootstrapping.R | 183 ++- BayesianMCPMod-1.1.0/BayesianMCPMod/R/modeling.R | 245 +++- BayesianMCPMod-1.1.0/BayesianMCPMod/R/plot.R | 105 - BayesianMCPMod-1.1.0/BayesianMCPMod/R/posterior.R | 11 BayesianMCPMod-1.1.0/BayesianMCPMod/R/s3methods.R | 405 ++++--- BayesianMCPMod-1.1.0/BayesianMCPMod/inst/PSI_Poster_2024.pdf |only BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Comparison.R | 22 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Comparison.Rmd | 23 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Comparison.html | 20 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Example.R | 15 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Example.Rmd | 45 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/Simulation_Example.html | 243 +++- BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/analysis_normal.R | 49 BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/analysis_normal.Rmd | 107 - BayesianMCPMod-1.1.0/BayesianMCPMod/inst/doc/analysis_normal.html | 114 +- BayesianMCPMod-1.1.0/BayesianMCPMod/man/assessDesign.Rd | 49 BayesianMCPMod-1.1.0/BayesianMCPMod/man/getBootstrapQuantiles.Rd | 25 BayesianMCPMod-1.1.0/BayesianMCPMod/man/getBootstrapSamples.Rd |only BayesianMCPMod-1.1.0/BayesianMCPMod/man/getContr.Rd | 3 BayesianMCPMod-1.1.0/BayesianMCPMod/man/getCritProb.Rd | 1 BayesianMCPMod-1.1.0/BayesianMCPMod/man/getMED.Rd |only BayesianMCPMod-1.1.0/BayesianMCPMod/man/getModelFits.Rd | 13 BayesianMCPMod-1.1.0/BayesianMCPMod/man/getPosterior.Rd | 3 BayesianMCPMod-1.1.0/BayesianMCPMod/man/performBayesianMCP.Rd | 4 BayesianMCPMod-1.1.0/BayesianMCPMod/man/performBayesianMCPMod.Rd | 32 BayesianMCPMod-1.1.0/BayesianMCPMod/man/plot.modelFits.Rd | 35 BayesianMCPMod-1.1.0/BayesianMCPMod/tests/testthat/test-bootstrapping.R | 2 BayesianMCPMod-1.1.0/BayesianMCPMod/tests/testthat/test-s3methods.R | 50 BayesianMCPMod-1.1.0/BayesianMCPMod/vignettes/Simulation_Comparison.Rmd | 23 BayesianMCPMod-1.1.0/BayesianMCPMod/vignettes/Simulation_Example.Rmd | 45 BayesianMCPMod-1.1.0/BayesianMCPMod/vignettes/analysis_normal.Rmd | 107 - 37 files changed, 1769 insertions(+), 895 deletions(-)
More information about BayesianMCPMod at CRAN
Permanent link
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library <https://github.com/libxls/libxls> and '.xlsx' via
the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net/>.
Works on Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Posit, PBC [cph, fnd] ,
Marcin Kalicinski [ctb, cph] ,
Komarov Valery [ctb, cph] ,
Christophe Leitienne [ctb, cph] ,
Bob Colbert [ctb, cph] ,
David Hoerl [ctb, cph] ,
Evan Miller [ctb, cph]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between readxl versions 1.4.4 dated 2025-02-27 and 1.4.5 dated 2025-03-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 21 +++++++++++++-------- src/libxls/xls.c | 15 +++++++++++---- src/libxls/xlsstruct.h | 30 ++++++++++++++++++++++++++++++ 5 files changed, 61 insertions(+), 19 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates to be annotated
to express unspecified date components,
approximate or uncertain date components,
date ranges, and sets of dates.
This is useful for describing and analysing temporal information,
whether historical or recent, where date precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Nathan Werth [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 0.4.1 dated 2024-04-19 and 0.5.2 dated 2025-03-07
messydates-0.4.1/messydates/R/annotate.R |only messydates-0.4.1/messydates/R/battles.R |only messydates-0.4.1/messydates/R/class.R |only messydates-0.4.1/messydates/R/contract.R |only messydates-0.4.1/messydates/R/duration.R |only messydates-0.4.1/messydates/R/expand.R |only messydates-0.4.1/messydates/R/extract.R |only messydates-0.4.1/messydates/R/logical.R |only messydates-0.4.1/messydates/R/operate.R |only messydates-0.4.1/messydates/R/proportional.R |only messydates-0.4.1/messydates/R/report.R |only messydates-0.4.1/messydates/R/resolve.R |only messydates-0.4.1/messydates/R/set.R |only messydates-0.4.1/messydates/build |only messydates-0.4.1/messydates/inst/doc |only messydates-0.4.1/messydates/man/annotate.Rd |only messydates-0.4.1/messydates/man/class.Rd |only messydates-0.4.1/messydates/man/contract.Rd |only messydates-0.4.1/messydates/man/duration_class.Rd |only messydates-0.4.1/messydates/man/expand.Rd |only messydates-0.4.1/messydates/man/extract.Rd |only messydates-0.4.1/messydates/man/from_messydate.Rd |only messydates-0.4.1/messydates/man/logical_tests.Rd |only messydates-0.4.1/messydates/man/messydate.Rd |only messydates-0.4.1/messydates/man/mreport.Rd |only messydates-0.4.1/messydates/man/operate.Rd |only messydates-0.4.1/messydates/man/proportional.Rd |only messydates-0.4.1/messydates/man/resolve.Rd |only messydates-0.4.1/messydates/man/set.Rd |only messydates-0.4.1/messydates/tests/testthat/test-annotate.R |only messydates-0.4.1/messydates/tests/testthat/test-class.R |only messydates-0.4.1/messydates/tests/testthat/test-coerce-from.R |only messydates-0.4.1/messydates/tests/testthat/test-coerce-to.R |only messydates-0.4.1/messydates/tests/testthat/test-contract.R |only messydates-0.4.1/messydates/tests/testthat/test-expand.R |only messydates-0.4.1/messydates/tests/testthat/test-extract.R |only messydates-0.4.1/messydates/tests/testthat/test-logical.R |only messydates-0.4.1/messydates/tests/testthat/test-messydate-make.R |only messydates-0.4.1/messydates/tests/testthat/test-operate.R |only messydates-0.4.1/messydates/tests/testthat/test-proportional.R |only messydates-0.4.1/messydates/tests/testthat/test-report.R |only messydates-0.4.1/messydates/tests/testthat/test-resolve.R |only messydates-0.4.1/messydates/tests/testthat/test-set.R |only messydates-0.4.1/messydates/tests/testthat/test_duration.R |only messydates-0.4.1/messydates/vignettes |only messydates-0.5.2/messydates/DESCRIPTION | 27 messydates-0.5.2/messydates/MD5 | 109 - messydates-0.5.2/messydates/NAMESPACE | 36 messydates-0.5.2/messydates/NEWS.md | 63 + messydates-0.5.2/messydates/R/class_duration.R |only messydates-0.5.2/messydates/R/class_mdate.R |only messydates-0.5.2/messydates/R/class_methods.R |only messydates-0.5.2/messydates/R/coerce_extrema.R |only messydates-0.5.2/messydates/R/coerce_from_messydate.R | 119 +- messydates-0.5.2/messydates/R/coerce_tendency.R |only messydates-0.5.2/messydates/R/coerce_to_messydate.R | 588 ++++------ messydates-0.5.2/messydates/R/component_annotate.R |only messydates-0.5.2/messydates/R/component_extract.R |only messydates-0.5.2/messydates/R/convert_contract.R |only messydates-0.5.2/messydates/R/convert_expand.R |only messydates-0.5.2/messydates/R/convert_sequence.R |only messydates-0.5.2/messydates/R/data_battles.R |only messydates-0.5.2/messydates/R/operate_arithmetic.R |only messydates-0.5.2/messydates/R/operate_inequalities.R |only messydates-0.5.2/messydates/R/operate_proportional.R |only messydates-0.5.2/messydates/R/operate_set.R |only messydates-0.5.2/messydates/R/operate_statements.R |only messydates-0.5.2/messydates/README.md | 88 - messydates-0.5.2/messydates/man/battles.Rd | 14 messydates-0.5.2/messydates/man/class_create.Rd |only messydates-0.5.2/messydates/man/class_duration.Rd |only messydates-0.5.2/messydates/man/class_make.Rd |only messydates-0.5.2/messydates/man/coerce_extrema.Rd |only messydates-0.5.2/messydates/man/coerce_from.Rd |only messydates-0.5.2/messydates/man/coerce_tendency.Rd |only messydates-0.5.2/messydates/man/coerce_to.Rd |only messydates-0.5.2/messydates/man/component_annotate.Rd |only messydates-0.5.2/messydates/man/component_extract.Rd |only messydates-0.5.2/messydates/man/convert_contract.Rd |only messydates-0.5.2/messydates/man/convert_expand.Rd |only messydates-0.5.2/messydates/man/convert_sequence.Rd |only messydates-0.5.2/messydates/man/operate_arithmetic.Rd |only messydates-0.5.2/messydates/man/operate_inequalities.Rd |only messydates-0.5.2/messydates/man/operate_proportional.Rd |only messydates-0.5.2/messydates/man/operate_set.Rd |only messydates-0.5.2/messydates/man/operate_statements.Rd |only messydates-0.5.2/messydates/tests/testthat/test-class_create.R |only messydates-0.5.2/messydates/tests/testthat/test-class_duration.R |only messydates-0.5.2/messydates/tests/testthat/test-class_make.R |only messydates-0.5.2/messydates/tests/testthat/test-coerce_from.R |only messydates-0.5.2/messydates/tests/testthat/test-coerce_resolve.R |only messydates-0.5.2/messydates/tests/testthat/test-coerce_to.R |only messydates-0.5.2/messydates/tests/testthat/test-component_annotate.R |only messydates-0.5.2/messydates/tests/testthat/test-component_extract.R |only messydates-0.5.2/messydates/tests/testthat/test-convert_contract.R |only messydates-0.5.2/messydates/tests/testthat/test-convert_expand.R |only messydates-0.5.2/messydates/tests/testthat/test-operate_arithmetic.R |only messydates-0.5.2/messydates/tests/testthat/test-operate_operators.R |only messydates-0.5.2/messydates/tests/testthat/test-operate_proportional.R |only messydates-0.5.2/messydates/tests/testthat/test-operate_set.R |only messydates-0.5.2/messydates/tests/testthat/test-operate_statements.R |only 101 files changed, 558 insertions(+), 486 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.16.0 dated 2025-01-22 and 0.17.0 dated 2025-03-07
DESCRIPTION | 6 +- MD5 | 24 +++++------ src/c/driver/framework/objects.cc | 1 src/c/driver/postgresql/database.cc | 1 src/c/driver/postgresql/error.cc | 2 src/c/driver/postgresql/result_helper.cc | 2 src/c/driver/postgresql/statement.cc | 1 src/c/driver/sqlite/sqlite.cc | 9 +++- src/c/include/arrow-adbc/adbc.h | 52 +++++++++++++++++++++++++ src/c/validation/adbc_validation_connection.cc | 4 + src/c/validation/adbc_validation_statement.cc | 3 + src/c/validation/adbc_validation_util.cc | 5 ++ src/driver_test.cc | 1 13 files changed, 93 insertions(+), 18 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides a
high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<doi:10.48550/arXiv.1902.08318> paper for more details about 'simdjson'. This
package parses 'JSON' from string, file, or remote URLs under a variety of
settings.
Author: Dirk Eddelbuettel [aut, cre] ,
Brendan Knapp [aut] ,
Daniel Lemire [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.12 dated 2024-07-07 and 0.1.13 dated 2025-03-07
RcppSimdJson-0.1.12/RcppSimdJson/demo |only RcppSimdJson-0.1.13/RcppSimdJson/ChangeLog | 32 RcppSimdJson-0.1.13/RcppSimdJson/DESCRIPTION | 20 RcppSimdJson-0.1.13/RcppSimdJson/MD5 | 21 RcppSimdJson-0.1.13/RcppSimdJson/README.md | 10 RcppSimdJson-0.1.13/RcppSimdJson/build/partial.rdb |binary RcppSimdJson-0.1.13/RcppSimdJson/inst/NEWS.Rd | 14 RcppSimdJson-0.1.13/RcppSimdJson/inst/examples |only RcppSimdJson-0.1.13/RcppSimdJson/inst/include/RcppSimdJson/deserialize/scalar.hpp | 20 RcppSimdJson-0.1.13/RcppSimdJson/inst/include/simdjson.cpp | 394 RcppSimdJson-0.1.13/RcppSimdJson/inst/include/simdjson.h |16307 ++++++---- 11 files changed, 11093 insertions(+), 5725 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.0.0 dated 2025-02-21 and 1.0.1 dated 2025-03-07
DESCRIPTION | 8 MD5 | 410 +++++++++++------------ NEWS.md | 77 ++++ R/RLum-class.R | 11 R/RLum.Analysis-class.R | 42 +- R/Risoe.BINfileData-class.R | 6 R/analyse_Al2O3C_CrossTalk.R | 2 R/analyse_FadingMeasurement.R | 18 - R/analyse_baSAR.R | 4 R/analyse_pIRIRSequence.R | 30 + R/calc_CosmicDoseRate.R | 27 - R/calc_FadingCorr.R | 46 +- R/calc_FastRatio.R | 2 R/calc_MinDose.R | 8 R/extract_IrradiationTimes.R | 2 R/fit_SurfaceExposure.R | 2 R/github.R | 4 R/internals_Thermochronometry.R | 12 R/methods_RLum.R | 86 ++-- R/plot_AbanicoPlot.R | 15 R/plot_DRCSummary.R | 4 R/plot_RLum.Analysis.R | 4 R/plot_RLum.Data.Spectrum.R | 14 R/read_BIN2R.R | 3 R/read_Daybreak2R.R | 3 R/read_HeliosOSL2R.R | 2 R/read_SPE2R.R | 2 R/read_TIFF2R.R | 2 R/read_XSYG2R.R | 4 R/use_DRAC.R | 1 R/write_R2BIN.R | 24 - README.md | 5 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/crosstalk.Rmd | 2 inst/doc/crosstalk.html | 60 +-- man/Analyse_SAR.OSLdata.Rd | 2 man/GitHub-API.Rd | 2 man/RLum-class.Rd | 2 man/RLum.Analysis-class.Rd | 2 man/RLum.Data-class.Rd | 2 man/RLum.Data.Curve-class.Rd | 2 man/RLum.Data.Image-class.Rd | 2 man/RLum.Data.Spectrum-class.Rd | 2 man/RLum.Results-class.Rd | 2 man/Risoe.BINfileData-class.Rd | 2 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 2 man/analyse_Al2O3C_ITC.Rd | 2 man/analyse_Al2O3C_Measurement.Rd | 2 man/analyse_FadingMeasurement.Rd | 8 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 2 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 2 man/analyse_pIRIRSequence.Rd | 6 man/analyse_portableOSL.Rd | 2 man/apply_CosmicRayRemoval.Rd | 2 man/apply_Crosstalk.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CobbleDoseRate.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 4 man/calc_EED_Model.Rd | 2 man/calc_FadingCorr.Rd | 26 - man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_MoransI.Rd | 2 man/calc_OSLLxTxDecomposed.Rd | 2 man/calc_OSLLxTxRatio.Rd | 2 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/calc_gSGC_feldspar.Rd | 2 man/combine_De_Dr.Rd | 2 man/convert_Activity2Concentration.Rd | 2 man/convert_BIN2CSV.Rd | 2 man/convert_CW2pHMi.Rd | 2 man/convert_CW2pLM.Rd | 2 man/convert_CW2pLMi.Rd | 2 man/convert_CW2pPMi.Rd | 2 man/convert_Concentration2DoseRate.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 2 man/convert_PSL2Risoe.BINfileData.Rd | 2 man/convert_RLum2Risoe.BINfileData.Rd | 2 man/convert_SG2MG.Rd | 2 man/convert_Second2Gray.Rd | 2 man/convert_Wavelength2Energy.Rd | 2 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/extract_ROI.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_DoseResponseCurve.Rd | 2 man/fit_EmissionSpectra.Rd | 2 man/fit_LMCurve.Rd | 2 man/fit_OSLLifeTimes.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/fit_ThermalQuenching.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 2 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/import_Data.Rd | 2 man/length_RLum.Rd | 2 man/melt_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Data.Spectrum.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/metadata.Rd | 2 man/names_RLum.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_DRCSummary.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_DoseResponseCurve.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_MoranScatterplot.Rd | 2 man/plot_NRt.Rd | 2 man/plot_OSLAgeSummary.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 14 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_ROI.Rd | 2 man/plot_RadialPlot.Rd | 2 man/plot_Risoe.BINfileData.Rd | 2 man/plot_SingleGrainDisc.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 2 man/read_Daybreak2R.Rd | 2 man/read_HeliosOSL2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_RF2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_TIFF2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/scale_GammaDose.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 2 man/sort_RLum.Rd | 2 man/structure_RLum.Rd | 2 man/subset_SingleGrainData.Rd | 2 man/template_DRAC.Rd | 2 man/trim_RLum.Data.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/view.Rd | 2 man/write_R2BIN.Rd | 2 man/write_R2TIFF.Rd | 2 man/write_RLum2CSV.Rd | 2 tests/testthat/_snaps/calc_CosmicDoseRate.md | 414 +++++++++++++++++++++++- tests/testthat/_snaps/calc_FadingCorr.md | 142 ++++++++ tests/testthat/test_RLum.Analysis-class.R | 14 tests/testthat/test_Risoe.BINfileData-class.R | 6 tests/testthat/test_analyse_FadingMeasurement.R | 12 tests/testthat/test_analyse_baSAR.R | 9 tests/testthat/test_analyse_pIRIRSequence.R | 6 tests/testthat/test_calc_CosmicDoseRate.R | 36 +- tests/testthat/test_calc_FadingCorr.R | 23 + tests/testthat/test_calc_FastRatio.R | 5 tests/testthat/test_calc_MinDose.R | 29 + tests/testthat/test_convert_Daybreak2CSV.R | 3 tests/testthat/test_convert_XSYG2CSV.R | 3 tests/testthat/test_extract_IrradiationTimes.R | 2 tests/testthat/test_github.R | 4 tests/testthat/test_plot_AbanicoPlot.R | 15 tests/testthat/test_plot_DRCSummary.R | 6 tests/testthat/test_plot_DRTResults.R | 5 tests/testthat/test_plot_RLum.Data.Spectrum.R | 10 tests/testthat/test_read_BIN2R.R | 2 tests/testthat/test_read_Daybreak2R.R | 2 tests/testthat/test_read_HeliosOSL2R.R | 2 tests/testthat/test_read_SPE2R.R | 2 tests/testthat/test_read_TIFF2R.R | 2 tests/testthat/test_read_XSYG2R.R | 2 tests/testthat/test_use_DRAC.R | 2 vignettes/crosstalk.Rmd | 2 206 files changed, 1421 insertions(+), 616 deletions(-)
Title: Functions and Datasets for the Data Science Course at IBAW
Description: A collection of useful functions and datasets for the Data Science
Course at IBAW.
Author: Stefan Lanz [aut, cre]
Maintainer: Stefan Lanz <slanz1137@gmail.com>
Diff between ibawds versions 1.0.0 dated 2024-09-30 and 1.1.0 dated 2025-03-07
DESCRIPTION | 19 +++-- MD5 | 44 +++++++++---- NAMESPACE | 7 ++ R/checks.R |only R/cran_packages.R | 8 +- R/data.R | 27 ++++++++ R/install.R | 116 +++++++++++++++++++++++++++++++++++- R/throw_dice.R |only README.md | 15 ++++ build/partial.rdb |binary data/cran_history.rda |binary data/dice_data.rda |only inst/WORDLIST | 5 + inst/extdata/evaluation_wordlist |only inst/extdata/slides_wordlist |only man/check_lecture_packages.Rd |only man/check_links_in_file.Rd |only man/check_links_in_slides.Rd |only man/check_url.Rd |only man/cran_history.Rd | 2 man/dice_data.Rd |only man/ibawds-package.Rd | 1 man/spell_check_evaluation.Rd |only man/throw_dice.Rd |only tests/testthat/data |only tests/testthat/test-checks.R |only tests/testthat/test-cran_packages.R | 25 ++++++- tests/testthat/test-install.R | 60 +++++++++++++++++- tests/testthat/test-throw_dice.R |only 29 files changed, 292 insertions(+), 37 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.4.1 dated 2025-02-05 and 1.4.2 dated 2025-03-07
grates-1.4.1/grates/R/epiweek.R |only grates-1.4.1/grates/R/int_period.R |only grates-1.4.1/grates/R/isoweek.R |only grates-1.4.1/grates/R/month.R |only grates-1.4.1/grates/R/period.R |only grates-1.4.1/grates/R/scale-epiweek.R |only grates-1.4.1/grates/R/scale-int_period.R |only grates-1.4.1/grates/R/scale-isoweek.R |only grates-1.4.1/grates/R/scale-month.R |only grates-1.4.1/grates/R/scale-period.R |only grates-1.4.1/grates/R/scale-year.R |only grates-1.4.1/grates/R/scale-yearmonth.R |only grates-1.4.1/grates/R/scale-yearquarter.R |only grates-1.4.1/grates/R/scale-yearweek.R |only grates-1.4.1/grates/R/utils-general.R |only grates-1.4.1/grates/R/utils-month.R |only grates-1.4.1/grates/R/year.R |only grates-1.4.1/grates/R/yearmonth.R |only grates-1.4.1/grates/R/yearquarter.R |only grates-1.4.1/grates/R/yearweek.R |only grates-1.4.1/grates/man/as_epiweek.Rd |only grates-1.4.1/grates/man/as_int_period.Rd |only grates-1.4.1/grates/man/as_isoweek.Rd |only grates-1.4.1/grates/man/as_month.Rd |only grates-1.4.1/grates/man/as_period.Rd |only grates-1.4.1/grates/man/as_year.Rd |only grates-1.4.1/grates/man/as_yearmonth.Rd |only grates-1.4.1/grates/man/as_yearquarter.Rd |only grates-1.4.1/grates/man/as_yearweek.Rd |only grates-1.4.1/grates/man/epiweek.Rd |only grates-1.4.1/grates/man/isoweek.Rd |only grates-1.4.1/grates/man/new_epiweek.Rd |only grates-1.4.1/grates/man/new_int_period.Rd |only grates-1.4.1/grates/man/new_isoweek.Rd |only grates-1.4.1/grates/man/new_month.Rd |only grates-1.4.1/grates/man/new_period.Rd |only grates-1.4.1/grates/man/new_yearmonth.Rd |only grates-1.4.1/grates/man/new_yearquarter.Rd |only grates-1.4.1/grates/man/new_yearweek.Rd |only grates-1.4.1/grates/man/print.grates_int_period.Rd |only grates-1.4.1/grates/man/print.grates_year.Rd |only grates-1.4.1/grates/man/print.grates_yearquarter.Rd |only grates-1.4.1/grates/man/year.Rd |only grates-1.4.1/grates/man/yearmonth.Rd |only grates-1.4.1/grates/man/yearquarter.Rd |only grates-1.4.1/grates/man/yearweek.Rd |only grates-1.4.2/grates/DESCRIPTION | 13 grates-1.4.2/grates/MD5 | 121 - grates-1.4.2/grates/NEWS.md | 5 grates-1.4.2/grates/R/boundaries.R | 32 grates-1.4.2/grates/R/during.R |only grates-1.4.2/grates/R/epiweek-class.R |only grates-1.4.2/grates/R/epiweek-scale.R |only grates-1.4.2/grates/R/int_period-class.R |only grates-1.4.2/grates/R/int_period-scale.R |only grates-1.4.2/grates/R/isoweek-class.R |only grates-1.4.2/grates/R/isoweek-scale.R |only grates-1.4.2/grates/R/month-class.R |only grates-1.4.2/grates/R/month-scale.R |only grates-1.4.2/grates/R/month-utils.R |only grates-1.4.2/grates/R/period-class.R |only grates-1.4.2/grates/R/period-scale.R |only grates-1.4.2/grates/R/utils.R |only grates-1.4.2/grates/R/year-class.R |only grates-1.4.2/grates/R/year-scale.R |only grates-1.4.2/grates/R/yearmonth-class.R |only grates-1.4.2/grates/R/yearmonth-scale.R |only grates-1.4.2/grates/R/yearquarter-class.R |only grates-1.4.2/grates/R/yearquarter-scale.R |only grates-1.4.2/grates/R/yearweek-class.R |only grates-1.4.2/grates/R/yearweek-scale.R |only grates-1.4.2/grates/README.md | 2 grates-1.4.2/grates/build/vignette.rds |binary grates-1.4.2/grates/inst/doc/grates.R | 150 - grates-1.4.2/grates/inst/doc/grates.Rmd | 398 ++- grates-1.4.2/grates/inst/doc/grates.html | 1828 ++++++++++++++---- grates-1.4.2/grates/man/boundaries.Rd | 21 grates-1.4.2/grates/man/epiweek_class.Rd |only grates-1.4.2/grates/man/grapes-during-grapes.Rd |only grates-1.4.2/grates/man/int_period_class.Rd |only grates-1.4.2/grates/man/isoweek_class.Rd |only grates-1.4.2/grates/man/month_class.Rd |only grates-1.4.2/grates/man/period_class.Rd |only grates-1.4.2/grates/man/print.grates_month.Rd | 11 grates-1.4.2/grates/man/print.grates_period.Rd | 2 grates-1.4.2/grates/man/print.grates_yearmonth.Rd | 15 grates-1.4.2/grates/man/scale_x_grates_epiweek.Rd | 24 grates-1.4.2/grates/man/scale_x_grates_int_period.Rd | 7 grates-1.4.2/grates/man/scale_x_grates_isoweek.Rd | 24 grates-1.4.2/grates/man/scale_x_grates_month.Rd | 32 grates-1.4.2/grates/man/scale_x_grates_period.Rd | 37 grates-1.4.2/grates/man/scale_x_grates_year.Rd | 27 grates-1.4.2/grates/man/scale_x_grates_yearmonth.Rd | 4 grates-1.4.2/grates/man/scale_x_grates_yearquarter.Rd | 32 grates-1.4.2/grates/man/scale_x_grates_yearweek.Rd | 24 grates-1.4.2/grates/man/year_class.Rd |only grates-1.4.2/grates/man/yearmonth_class.Rd |only grates-1.4.2/grates/man/yearquarter_class.Rd |only grates-1.4.2/grates/man/yearweek_class.Rd |only grates-1.4.2/grates/vignettes/grates.Rmd | 398 ++- 100 files changed, 2275 insertions(+), 932 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.2 dated 2024-10-25 and 1.0.3 dated 2025-03-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/findStartData.R | 22 +++++++++++++--------- R/readActiwatchCount.R | 19 +++++++++++++++---- R/readPHBCount.R | 9 ++++++--- man/GGIRread-package.Rd | 4 ++-- tests/testthat/test_readActiwatchCount.R | 5 +++-- 8 files changed, 58 insertions(+), 31 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.1.0 dated 2024-11-09 and 2.2.0 dated 2025-03-07
DESCRIPTION | 22 +- MD5 | 42 ++-- NAMESPACE | 7 NEWS | 13 + R/EBICglasso.qgraph.R | 467 ++++++++++++++++++++++++++++++++++++----------- R/EGAnet.R | 2 R/EGM.R | 130 ++++++++++++- R/S3plots.R | 15 + R/bootEGA.R | 66 ++++-- R/color_palette_EGA.R | 4 R/community.detection.R | 37 +++ R/itemStability.R | 381 ++++++++++++++++++++++++-------------- R/net.loads.R | 37 ++- R/network.nonconvex.R |only R/simEGM.R | 6 R/tefi.compare.R |only data/boot.wmt.RData |binary inst/CITATION | 8 man/EBICglasso.qgraph.Rd | 20 +- man/EGAnet-plot.Rd | 15 + man/EGM.Rd | 4 man/bootEGA.Rd | 2 man/network.nonconvex.Rd |only man/tefi.compare.Rd |only 24 files changed, 954 insertions(+), 324 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/> [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 1.0.0 dated 2024-12-17 and 1.1.0 dated 2025-03-07
archeofrag-1.0.0/archeofrag/data/Tai.RData |only archeofrag-1.0.0/archeofrag/man/Tai.Rd |only archeofrag-1.1.0/archeofrag/DESCRIPTION | 8 archeofrag-1.1.0/archeofrag/MD5 | 67 archeofrag-1.1.0/archeofrag/NAMESPACE | 10 archeofrag-1.1.0/archeofrag/NEWS.md | 17 archeofrag-1.1.0/archeofrag/R/frag.get.parameters.R | 78 archeofrag-1.1.0/archeofrag/R/frag.graph.plot.R | 4 archeofrag-1.1.0/archeofrag/R/frag.graph.reduce.R | 36 archeofrag-1.1.0/archeofrag/R/frag.layers.admixture.R | 15 archeofrag-1.1.0/archeofrag/R/frag.layers.cohesion.R | 16 archeofrag-1.1.0/archeofrag/R/frag.observer.failure.R | 2 archeofrag-1.1.0/archeofrag/R/frag.simul.compare.R | 9 archeofrag-1.1.0/archeofrag/R/frag.simul.process.R | 10 archeofrag-1.1.0/archeofrag/TODO | 19 archeofrag-1.1.0/archeofrag/build/vignette.rds |binary archeofrag-1.1.0/archeofrag/data/CuzoulCave.RData |only archeofrag-1.1.0/archeofrag/data/CuzoulSouth.RData |only archeofrag-1.1.0/archeofrag/data/TaiCave.RData |only archeofrag-1.1.0/archeofrag/data/TaiSouth.RData |only archeofrag-1.1.0/archeofrag/inst/doc/archeofrag-vignette.R | 1 archeofrag-1.1.0/archeofrag/inst/doc/archeofrag-vignette.Rmd | 3 archeofrag-1.1.0/archeofrag/inst/doc/archeofrag-vignette.html | 904 +++------- archeofrag-1.1.0/archeofrag/man/CuzoulCave.Rd |only archeofrag-1.1.0/archeofrag/man/CuzoulSouth.Rd |only archeofrag-1.1.0/archeofrag/man/FontJuvenal.Rd | 10 archeofrag-1.1.0/archeofrag/man/GrandeRivoire.Rd | 6 archeofrag-1.1.0/archeofrag/man/TaiCave.Rd |only archeofrag-1.1.0/archeofrag/man/TaiSouth.Rd |only archeofrag-1.1.0/archeofrag/man/frag.get.parameters.Rd | 26 archeofrag-1.1.0/archeofrag/man/frag.layers.cohesion.Rd | 4 archeofrag-1.1.0/archeofrag/man/frag.observer.failure.Rd | 2 archeofrag-1.1.0/archeofrag/man/frag.simul.compare.Rd | 1 archeofrag-1.1.0/archeofrag/man/frag.simul.process.Rd | 4 archeofrag-1.1.0/archeofrag/tests/testthat/test-frag.edges.weighting.R | 3 archeofrag-1.1.0/archeofrag/tests/testthat/test-frag.graph.reduce.R |only archeofrag-1.1.0/archeofrag/tests/testthat/test-frag.simul.compare.R | 11 archeofrag-1.1.0/archeofrag/tests/testthat/test-frag.simul.summarise.R | 2 archeofrag-1.1.0/archeofrag/tests/testthat/test.frag.get.parameters.R | 25 archeofrag-1.1.0/archeofrag/vignettes/archeofrag-vignette.Rmd | 3 40 files changed, 591 insertions(+), 705 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.16.0 dated 2025-01-22 and 0.17.0 dated 2025-03-07
adbcsqlite-0.16.0/adbcsqlite/src/arrow-adbc |only adbcsqlite-0.16.0/adbcsqlite/src/common |only adbcsqlite-0.17.0/adbcsqlite/DESCRIPTION | 6 - adbcsqlite-0.17.0/adbcsqlite/MD5 | 26 ++--- adbcsqlite-0.17.0/adbcsqlite/src/c/driver/framework/objects.cc | 1 adbcsqlite-0.17.0/adbcsqlite/src/c/driver/postgresql/database.cc | 1 adbcsqlite-0.17.0/adbcsqlite/src/c/driver/postgresql/error.cc | 2 adbcsqlite-0.17.0/adbcsqlite/src/c/driver/postgresql/result_helper.cc | 2 adbcsqlite-0.17.0/adbcsqlite/src/c/driver/postgresql/statement.cc | 1 adbcsqlite-0.17.0/adbcsqlite/src/c/driver/sqlite/sqlite.cc | 9 + adbcsqlite-0.17.0/adbcsqlite/src/c/include/arrow-adbc/adbc.h | 52 ++++++++++ adbcsqlite-0.17.0/adbcsqlite/src/c/validation/adbc_validation_connection.cc | 4 adbcsqlite-0.17.0/adbcsqlite/src/c/validation/adbc_validation_statement.cc | 3 adbcsqlite-0.17.0/adbcsqlite/src/c/validation/adbc_validation_util.cc | 5 14 files changed, 91 insertions(+), 21 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.16.0 dated 2025-01-22 and 0.17.0 dated 2025-03-07
adbcpostgresql-0.16.0/adbcpostgresql/src/arrow-adbc |only adbcpostgresql-0.17.0/adbcpostgresql/DESCRIPTION | 6 - adbcpostgresql-0.17.0/adbcpostgresql/MD5 | 23 ++-- adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/framework/objects.cc | 1 adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/postgresql/database.cc | 1 adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/postgresql/error.cc | 2 adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/postgresql/result_helper.cc | 2 adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/postgresql/statement.cc | 1 adbcpostgresql-0.17.0/adbcpostgresql/src/c/driver/sqlite/sqlite.cc | 9 + adbcpostgresql-0.17.0/adbcpostgresql/src/c/include/arrow-adbc/adbc.h | 52 ++++++++++ adbcpostgresql-0.17.0/adbcpostgresql/src/c/validation/adbc_validation_connection.cc | 4 adbcpostgresql-0.17.0/adbcpostgresql/src/c/validation/adbc_validation_statement.cc | 3 adbcpostgresql-0.17.0/adbcpostgresql/src/c/validation/adbc_validation_util.cc | 5 13 files changed, 91 insertions(+), 18 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Detect Aberrant Behavior in Test Data
Description: Detect several types of aberrant behavior, including answer
copying, answer similarity, nonparametric misfit, parametric misfit,
preknowledge, rapid guessing, and test tampering.
Author: Kylie Gorney [aut, cph, cre] ,
Jiayi Deng [aut, cph]
Maintainer: Kylie Gorney <kgorney@msu.edu>
Diff between aberrance versions 0.2.0 dated 2025-02-07 and 0.2.1 dated 2025-03-07
DESCRIPTION | 11 +- MD5 | 21 +++-- NAMESPACE | 66 ++++++++--------- NEWS.md | 6 + R/RcppExports.R |only R/aberrance-package.R | 58 +++++++-------- R/checks.R | 192 +++++++++++++++++++++++++------------------------- R/compute.R | 45 ----------- R/detect-ac.R | 52 +++++++------ R/detect-as.R | 122 +++++++++++++++++-------------- R/detect-pm.R | 4 - src |only 12 files changed, 278 insertions(+), 299 deletions(-)
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Description: Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and
PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically
access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types.
Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between PubChemR versions 2.1.3 dated 2024-12-16 and 2.1.4 dated 2025-03-07
DESCRIPTION | 7 MD5 | 16 inst/doc/Enhancing_Chemical_Data_Access_with_PubChemR.html | 60 inst/doc/Exploring_Chemical_Data_with_PubChemR.R | 32 inst/doc/Exploring_Chemical_Data_with_PubChemR.html |11167 ++++++------ inst/doc/Working_with_PubChemR_to_Access_Chemical_Data.R | 6 inst/doc/Working_with_PubChemR_to_Access_Chemical_Data.html | 1423 - tests/testthat/test-get_aids.R | 129 tests/testthat/test-get_compounds.R | 202 9 files changed, 7251 insertions(+), 5791 deletions(-)
Title: Model Checking for High-Dimensional GLMs via Random Projections
Description: Provides methods for testing the goodness-of-fit
of generalized linear models (GLMs) using random projections. It is
specifically designed for high-dimensional scenarios where the number
of predictors substantially exceeds the sample size. The statistical
methodologies implemented in this package are detailed in the paper by
Wen Chen and Falong Tan (2024, <doi:10.48550/arXiv.2412.10721>).
Author: Wen Chen [aut, cre],
Jie Liu [aut],
Heng Peng [aut],
FaLong Tan [aut],
Lixing Zhu [aut]
Maintainer: Wen Chen <tlqdcw@gmail.com>
Diff between PLStests versions 0.1.0 dated 2025-01-14 and 0.1.1 dated 2025-03-07
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NAMESPACE | 30 +++++++++++++++--------------- NEWS.md |only R/PLStests.R | 4 ++-- man/PLStests.Rd | 2 +- 6 files changed, 26 insertions(+), 25 deletions(-)
Title: Mixture and Non Mixture Parametric Cure Models to Estimate Cure
Indicators
Description: Fits a variety of cure models using excess hazard modeling methodology such as the mixture model proposed by Phillips et al. (2002) <doi:10.1002/sim.1101> The Weibull distribution is used to represent the survival function of the uncured patients; Fits also non-mixture cure model such as the time-to-null excess hazard model proposed by Boussari et al. (2020) <doi:10.1111/biom.13361>.
Author: Juste Goungounga [aut, cre] ,
Judith Breaud [aut] ,
Olayide Boussari [aut] ,
Laura Botta [ctb] ,
Valerie Jooste [aut]
Maintainer: Juste Goungounga <juste.goungounga@ehesp.fr>
Diff between curesurv versions 0.1.1 dated 2024-09-17 and 0.1.2 dated 2025-03-07
DESCRIPTION | 10 + MD5 | 186 ++++++++++++++++++------------------- NEWS.md | 2 R/TTC_adtneh2.R | 2 R/TTC_ic_adtneh2.R | 2 R/TTC_ic_adtneh2_log.R | 2 R/TTC_ic_multneh.R | 2 R/TTC_ic_multneh_log.R | 2 R/TTC_multneh.R | 2 R/TTC_wei.R | 2 R/cumLexc_alphaweibull.R | 2 R/cumLexc_alphaweibull_topred.R | 2 R/curesurv-package.R | 4 R/curesurv.R | 2 R/dpttcdtheta_adtneh2.R | 2 R/dpttcdtheta_multneh.R | 2 R/dsndtheta_adtneh2.R | 2 R/dsndtheta_multneh.R | 2 R/exhaz_ic_wei.R | 3 R/exhaz_ic_wei_log.R | 4 R/exhaz_ic_wei_loglog.R | 4 R/pi_ic_wei.R | 2 R/plot.predCuresurv.R | 2 R/predcall_tneh.R | 2 R/predcall_wei.R | 2 R/predict.curesurv.R | 2 R/print.curesurv.R | 2 R/pt_cure_ic_adtneh2.R | 2 R/pt_cure_ic_adtneh2_loglog.R | 2 R/pt_cure_ic_multneh.R | 2 R/pt_cure_ic_multneh_loglog.R | 2 R/pt_cure_ic_wei.R | 2 R/sn_ic_adtneh2.R | 2 R/sn_ic_adtneh2_log.R | 2 R/sn_ic_adtneh2_loglog.R | 2 R/sn_ic_multneh.R | 2 R/sn_ic_multneh_log.R | 2 R/sn_ic_multneh_loglog.R | 2 R/summary.curesurv.R | 2 R/var_TTC_multneh.R | 2 R/var_TTC_tneh2.R | 2 R/varexhaz_adtneh2.R | 2 R/z_alpha.R | 2 R/z_riskpop.alpha.R | 2 R/z_tau.R | 2 build/vignette.rds |binary inst/CITATION | 33 +----- inst/doc/Vignette_tneh.html | 72 +++++++------- inst/doc/vignette_mixture.R | 2 inst/doc/vignette_mixture.Rmd | 2 inst/doc/vignette_mixture.html | 65 ++++++------ man/TTC_adtneh2.Rd | 2 man/TTC_ic_adtneh2.Rd | 2 man/TTC_ic_adtneh2_log.Rd | 2 man/TTC_ic_multneh.Rd | 2 man/TTC_ic_multneh_log.Rd | 2 man/TTC_multneh.Rd | 2 man/TTC_wei.Rd | 2 man/cumLexc_alphaweibull.Rd | 2 man/cumLexc_alphaweibull_topred.Rd | 2 man/curesurv-package.Rd | 4 man/curesurv.Rd | 2 man/dpttcdtheta_adtneh2.Rd | 2 man/dpttcdtheta_multneh.Rd | 2 man/dsndtheta_adtneh2.Rd | 2 man/dsndtheta_multneh.Rd | 2 man/exhaz_ic_wei.Rd | 2 man/exhaz_ic_wei_log.Rd | 2 man/exhaz_ic_wei_loglog.Rd | 2 man/pi_ic_wei.Rd | 2 man/plot.predCuresurv.Rd | 2 man/predcall_tneh.Rd | 2 man/predcall_wei.Rd | 2 man/predict.curesurv.Rd | 2 man/print.curesurv.Rd | 2 man/pt_cure_ic_adtneh2.Rd | 2 man/pt_cure_ic_adtneh2_loglog.Rd | 2 man/pt_cure_ic_multneh.Rd | 2 man/pt_cure_ic_multneh_loglog.Rd | 2 man/pt_cure_ic_wei.Rd | 2 man/sn_ic_adtneh2.Rd | 2 man/sn_ic_adtneh2_log.Rd | 2 man/sn_ic_adtneh2_loglog.Rd | 2 man/sn_ic_multneh.Rd | 2 man/sn_ic_multneh_log.Rd | 2 man/sn_ic_multneh_loglog.Rd | 2 man/summary.curesurv.Rd | 2 man/var_TTC_multneh.Rd | 2 man/var_TTC_tneh2.Rd | 2 man/varexhaz_adtneh2.Rd | 2 man/z_alpha.Rd | 2 man/z_riskpop.alpha.Rd | 2 man/z_tau.Rd | 2 vignettes/vignette_mixture.Rmd | 2 94 files changed, 270 insertions(+), 281 deletions(-)
Title: Output Results from 'rms' Models for Medical Journals
Description: This takes the output of models performed using the 'rms' package and
returns a dataframe with the results. This output is in the format required by medical
journals. For example for cox regression models, the hazard ratios, their 95%
confidence intervals, and p values will be provided. There are additional functions for outputs when the model included restricted
cubic spline (RCS) terms. Models using imputed data (eg from aregimpute()) and
fitted used fit.mult.impute() can also be processed. The dataframe which is returned can easily be turned into a publication ready table
with packages 'flextable' and 'officer'.
Author: Samuel Tingle [aut, cre],
Georgios Kourounis [aut]
Maintainer: Samuel Tingle <samjamestingle@gmail.com>
Diff between rmsMD versions 0.1.1 dated 2025-03-03 and 0.1.2 dated 2025-03-07
DESCRIPTION | 7 MD5 | 12 - build/vignette.rds |binary inst/doc/modelsummary_rms-vignette.R | 5 inst/doc/modelsummary_rms-vignette.Rmd | 19 -- inst/doc/modelsummary_rms-vignette.html | 273 +++++++++++++++----------------- vignettes/modelsummary_rms-vignette.Rmd | 19 -- 7 files changed, 152 insertions(+), 183 deletions(-)
Title: Fast Machine Learning Model Training and Evaluation
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing
comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning.
It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.4.0 dated 2025-01-08 and 0.5.0 dated 2025-03-07
DESCRIPTION | 10 MD5 | 61 NAMESPACE | 461 ++--- R/evaluate_models.R | 189 -- R/fastexplain.R | 598 +++---- R/fastexplore.R | 3228 +++++++++++++++++++-------------------- R/fastml.R | 435 ++++- R/helper_functions.R | 1063 ++++++++++++ R/models.R | 898 +++++++--- R/sanitize.R | 138 - R/save_model.R | 48 R/summary.fastml_model.R | 513 +++--- R/train_models.R | 803 ++++----- README.md | 112 - man/availableMethods.Rd |only man/evaluate_models.Rd | 82 man/fastexplore.Rd | 270 +-- man/fastml.Rd | 277 +-- man/flatten_and_rename_models.Rd |only man/get_best_model_idx.Rd |only man/get_best_model_names.Rd |only man/get_best_workflows.Rd |only man/get_default_engine.Rd |only man/get_default_params.Rd |only man/get_default_tune_params.Rd |only man/get_engine_names.Rd |only man/get_model_engine_names.Rd |only man/load_model.Rd | 34 man/plot.fastml_model.Rd | 38 man/predict.fastml_model.Rd | 48 man/process_model.Rd |only man/sanitize.Rd | 56 man/save_model.Rd | 38 man/summary.fastml_model.Rd | 97 - man/train_models.Rd | 137 - tests/testthat.R | 24 tests/testthat/test-fastml.R | 149 - 37 files changed, 5705 insertions(+), 4102 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.6.3 dated 2025-01-14 and 1.7.0 dated 2025-03-07
DESCRIPTION | 8 MD5 | 32 +- NEWS.md | 8 R/plot_confusion_matrix.R | 137 ++++---- R/plotting_utilities.R | 10 README.md | 160 +++++----- build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 4 inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.html | 8 inst/doc/evaluate_by_id.html | 4 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 4 man/figures/README-unnamed-chunk-27-1.png |binary man/figures/README-unnamed-chunk-32-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/plot_confusion_matrix.Rd | 15 man/sum_tile_settings.Rd | 15 17 files changed, 228 insertions(+), 181 deletions(-)
Title: Analysis of Conflicting Claims
Description: The analysis of conflicting claims arises when an amount has
to be divided among a set of agents with claims that exceed what is
available. A rule is a way of selecting a division among the
claimants. This package computes the main rules introduced in the
literature from ancient times to the present. The inventory of rules
covers the proportional and the adjusted proportional rules, the
constrained equal awards and the constrained equal losses rules, the
constrained egalitarian, the Piniles’ and the minimal overlap rules,
the random arrival and the Talmud rules. Besides, the Dominguez and
Thomson and the average-of-awards rules are also included. All of
them can be found in the book by W. Thomson (2019), How to divide when
there isn't enough. From Aristotle, the Talmud, and Maimonides to the
axiomatics of resource allocation', except for the average-of-awards
rule, introduced by Mirás Calvo et al. (2022),
<doi:10.1007/s00355-022-01414-6>. In addition, graphical diagrams
allow t [...truncated...]
Author: Estela Sanchez Rodriguez [cre, aut]
,
Iago Nunez Lugilde [aut] ,
Miguel Angel Miras Calvo [aut]
,
Carmen Quinteiro Sandomingo [aut]
,
MCIN/AEI/10.13039/501100011033 [fnd]
Maintainer: Estela Sanchez Rodriguez <esanchez@uvigo.es>
Diff between ClaimsProblems versions 0.2.1 dated 2023-01-12 and 1.0.0 dated 2025-03-07
ClaimsProblems-0.2.1/ClaimsProblems/build |only ClaimsProblems-1.0.0/ClaimsProblems/DESCRIPTION | 78 ++++-- ClaimsProblems-1.0.0/ClaimsProblems/MD5 | 142 ++++++----- ClaimsProblems-1.0.0/ClaimsProblems/NAMESPACE | 5 ClaimsProblems-1.0.0/ClaimsProblems/NEWS.md |only ClaimsProblems-1.0.0/ClaimsProblems/R/AA.R | 150 +++++------- ClaimsProblems-1.0.0/ClaimsProblems/R/APRO.R | 40 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/AV.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/Bankruptcy.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/CD.R | 21 - ClaimsProblems-1.0.0/ClaimsProblems/R/CE.R | 46 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/CEA.R | 16 - ClaimsProblems-1.0.0/ClaimsProblems/R/CEL.R | 18 - ClaimsProblems-1.0.0/ClaimsProblems/R/CO2emissions.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/DT.R | 30 +- ClaimsProblems-1.0.0/ClaimsProblems/R/MO.R | 52 ++-- ClaimsProblems-1.0.0/ClaimsProblems/R/PIN.R | 23 - ClaimsProblems-1.0.0/ClaimsProblems/R/PRO.R | 12 ClaimsProblems-1.0.0/ClaimsProblems/R/Peso.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/RA.R | 34 +- ClaimsProblems-1.0.0/ClaimsProblems/R/RTalmud.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/Talmud.R | 25 +- ClaimsProblems-1.0.0/ClaimsProblems/R/Universityfunds.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/allrules.R | 39 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/axioms.R |only ClaimsProblems-1.0.0/ClaimsProblems/R/coalitionalgame.R | 57 +--- ClaimsProblems-1.0.0/ClaimsProblems/R/cumawardscurve.R | 38 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/deviationindex.R | 41 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/dynamicplot.R | 35 +- ClaimsProblems-1.0.0/ClaimsProblems/R/giniindex.R | 27 +- ClaimsProblems-1.0.0/ClaimsProblems/R/indexgpath.R | 39 +-- ClaimsProblems-1.0.0/ClaimsProblems/R/indexpath.R | 2 ClaimsProblems-1.0.0/ClaimsProblems/R/lorenzcurve.R | 31 +- ClaimsProblems-1.0.0/ClaimsProblems/R/lorenzdominance.R | 37 +- ClaimsProblems-1.0.0/ClaimsProblems/R/pathawards.R | 14 - ClaimsProblems-1.0.0/ClaimsProblems/R/pathawards3.R | 13 - ClaimsProblems-1.0.0/ClaimsProblems/R/plotrule.R | 20 - ClaimsProblems-1.0.0/ClaimsProblems/R/problemdata.R | 28 +- ClaimsProblems-1.0.0/ClaimsProblems/R/schedrule.R | 17 - ClaimsProblems-1.0.0/ClaimsProblems/R/schedrules.R | 21 - ClaimsProblems-1.0.0/ClaimsProblems/R/setofawards.R | 35 +- ClaimsProblems-1.0.0/ClaimsProblems/R/verticalruleplot.R | 25 -- ClaimsProblems-1.0.0/ClaimsProblems/R/volume.R |only ClaimsProblems-1.0.0/ClaimsProblems/data |only ClaimsProblems-1.0.0/ClaimsProblems/man/AA.Rd | 40 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/APRO.Rd | 42 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/AV.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/Bankruptcy.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/CD.Rd | 21 - ClaimsProblems-1.0.0/ClaimsProblems/man/CE.Rd | 47 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/CEA.Rd | 16 - ClaimsProblems-1.0.0/ClaimsProblems/man/CEL.Rd | 16 - ClaimsProblems-1.0.0/ClaimsProblems/man/CO2emissions.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/DT.Rd | 30 +- ClaimsProblems-1.0.0/ClaimsProblems/man/MO.Rd | 47 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/PIN.Rd | 23 - ClaimsProblems-1.0.0/ClaimsProblems/man/PRO.Rd | 12 ClaimsProblems-1.0.0/ClaimsProblems/man/RA.Rd | 35 +- ClaimsProblems-1.0.0/ClaimsProblems/man/RTalmud.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/Talmud.Rd | 21 - ClaimsProblems-1.0.0/ClaimsProblems/man/Universityfunds.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/allrules.Rd | 28 -- ClaimsProblems-1.0.0/ClaimsProblems/man/axioms.Rd |only ClaimsProblems-1.0.0/ClaimsProblems/man/coalitionalgame.Rd | 57 +--- ClaimsProblems-1.0.0/ClaimsProblems/man/cumawardscurve.Rd | 41 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/deviationindex.Rd | 40 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/dynamicplot.Rd | 33 +- ClaimsProblems-1.0.0/ClaimsProblems/man/giniindex.Rd | 27 +- ClaimsProblems-1.0.0/ClaimsProblems/man/indexgpath.Rd | 39 +-- ClaimsProblems-1.0.0/ClaimsProblems/man/lorenzcurve.Rd | 30 +- ClaimsProblems-1.0.0/ClaimsProblems/man/lorenzdominance.Rd | 37 +- ClaimsProblems-1.0.0/ClaimsProblems/man/pathawards.Rd | 12 ClaimsProblems-1.0.0/ClaimsProblems/man/pathawards3.Rd | 12 ClaimsProblems-1.0.0/ClaimsProblems/man/plotrule.Rd | 18 - ClaimsProblems-1.0.0/ClaimsProblems/man/problemdata.Rd | 28 +- ClaimsProblems-1.0.0/ClaimsProblems/man/schedrule.Rd | 16 - ClaimsProblems-1.0.0/ClaimsProblems/man/schedrules.Rd | 18 - ClaimsProblems-1.0.0/ClaimsProblems/man/setofawards.Rd | 35 +- ClaimsProblems-1.0.0/ClaimsProblems/man/verticalruleplot.Rd | 25 -- ClaimsProblems-1.0.0/ClaimsProblems/man/volume.Rd |only 80 files changed, 1011 insertions(+), 1046 deletions(-)
More information about ClaimsProblems at CRAN
Permanent link
Title: Modular Crop Growth Simulations
Description: A cross-platform representation of models as sets of equations
that facilitates modularity in model building and allows users to harness
modern techniques for numerical integration and data visualization.
Documentation is provided by several vignettes included in this package;
also see Lochocki et al. (2022) <doi:10.1093/insilicoplants/diac003>.
Author: Justin M. McGrath [cre, aut] ,
Edward B. Lochocki [aut] ,
Yufeng He [aut] ,
Scott W. Oswald [aut] ,
Scott Rohde [aut] ,
Deepak Jaiswal [aut] ,
Megan L. Matthews [aut] ,
Fernando E. Miguez [aut] ,
Stephen P. Long [aut] ,
Dan Wang [ctb],
David LeBauer [...truncated...]
Maintainer: Justin M. McGrath <jmcgrath@illinois.edu>
Diff between BioCro versions 3.1.3 dated 2024-04-30 and 3.2.0 dated 2025-03-07
BioCro-3.1.3/BioCro/src/module_library/c3EvapoTrans.cpp |only BioCro-3.1.3/BioCro/src/module_library/leaf_gbw_thornley.h |only BioCro-3.1.3/BioCro/tests/module_test_cases/BioCro_fake_solar.csv |only BioCro-3.1.3/BioCro/tests/module_test_cases/BioCro_leaf_gbw_thornley.csv |only BioCro-3.1.3/BioCro/tests/module_test_cases/BioCro_soil_type_selector.csv |only BioCro-3.1.3/BioCro/tests/testthat/crop_model_testing_helper_functions.R |only BioCro-3.2.0/BioCro/DESCRIPTION | 14 BioCro-3.2.0/BioCro/MD5 | 316 +++--- BioCro-3.2.0/BioCro/NAMESPACE | 5 BioCro-3.2.0/BioCro/NEWS.md | 228 +++- BioCro-3.2.0/BioCro/R/add_time_to_weather_data.R | 5 BioCro-3.2.0/BioCro/R/get_all.R | 4 BioCro-3.2.0/BioCro/R/input_checking_functions.R | 86 + BioCro-3.2.0/BioCro/R/model_testing.R |only BioCro-3.2.0/BioCro/R/module_creators.R | 2 BioCro-3.2.0/BioCro/R/module_paste.R | 2 BioCro-3.2.0/BioCro/R/module_testing.R | 35 BioCro-3.2.0/BioCro/R/module_write.R |only BioCro-3.2.0/BioCro/R/modules.R | 12 BioCro-3.2.0/BioCro/R/run_biocro.R | 75 + BioCro-3.2.0/BioCro/R/system_derivatives.R | 8 BioCro-3.2.0/BioCro/R/validate_dynamical_system_inputs.R | 10 BioCro-3.2.0/BioCro/README.md | 24 BioCro-3.2.0/BioCro/build/partial.rdb |binary BioCro-3.2.0/BioCro/build/vignette.rds |binary BioCro-3.2.0/BioCro/data/cmi_weather_data.rdata |binary BioCro-3.2.0/BioCro/data/default_ode_solvers.rda |binary BioCro-3.2.0/BioCro/data/miscanthus_x_giganteus.rda |binary BioCro-3.2.0/BioCro/data/soil_parameters.rda |binary BioCro-3.2.0/BioCro/data/soybean.rda |binary BioCro-3.2.0/BioCro/data/soybean_clock.rda |binary BioCro-3.2.0/BioCro/data/soybean_weather.rdata |binary BioCro-3.2.0/BioCro/data/willow.rda |binary BioCro-3.2.0/BioCro/inst/doc/BioCro.R | 1 BioCro-3.2.0/BioCro/inst/doc/BioCro.Rmd | 1 BioCro-3.2.0/BioCro/inst/doc/BioCro.html | 7 BioCro-3.2.0/BioCro/inst/extdata/get_soybean_weather_data.R |only BioCro-3.2.0/BioCro/inst/extdata/rounding_weather_values.R | 1 BioCro-3.2.0/BioCro/man/add_time_to_weather_data.Rd | 56 - BioCro-3.2.0/BioCro/man/cmi_soybean_weather_data.Rd | 8 BioCro-3.2.0/BioCro/man/compare_model_output.Rd |only BioCro-3.2.0/BioCro/man/model_test_case.Rd |only BioCro-3.2.0/BioCro/man/model_testing.Rd |only BioCro-3.2.0/BioCro/man/module_case_files.Rd | 5 BioCro-3.2.0/BioCro/man/module_testing.Rd | 3 BioCro-3.2.0/BioCro/man/module_write.Rd |only BioCro-3.2.0/BioCro/man/partial_application.Rd | 2 BioCro-3.2.0/BioCro/man/run_biocro.Rd | 17 BioCro-3.2.0/BioCro/man/run_model_test_cases.Rd |only BioCro-3.2.0/BioCro/man/soybean.Rd | 24 BioCro-3.2.0/BioCro/man/system_derivatives.Rd | 7 BioCro-3.2.0/BioCro/man/test_module.Rd | 7 BioCro-3.2.0/BioCro/man/test_module_library.Rd | 12 BioCro-3.2.0/BioCro/man/time_variable.rd |only BioCro-3.2.0/BioCro/man/update_stored_model_results.Rd |only BioCro-3.2.0/BioCro/src/R_system_derivatives.cpp | 2 BioCro-3.2.0/BioCro/src/inc/boost/concept/detail/general.hpp | 22 BioCro-3.2.0/BioCro/src/inc/boost/concept/usage.hpp | 10 BioCro-3.2.0/BioCro/src/inc/boost/graph/detail/adj_list_edge_iterator.hpp | 30 BioCro-3.2.0/BioCro/src/inc/boost/graph/detail/adjacency_list.hpp | 6 BioCro-3.2.0/BioCro/src/module_library/AuxBioCro.cpp | 355 ------- BioCro-3.2.0/BioCro/src/module_library/AuxBioCro.h | 61 - BioCro-3.2.0/BioCro/src/module_library/BioCro.h | 25 BioCro-3.2.0/BioCro/src/module_library/CanAC.cpp | 155 +-- BioCro-3.2.0/BioCro/src/module_library/CanAC.h | 71 - BioCro-3.2.0/BioCro/src/module_library/ball_berry.h | 2 BioCro-3.2.0/BioCro/src/module_library/ball_berry_gs.cpp | 8 BioCro-3.2.0/BioCro/src/module_library/boundary_layer_conductance.cpp |only BioCro-3.2.0/BioCro/src/module_library/boundary_layer_conductance.h |only BioCro-3.2.0/BioCro/src/module_library/c3CanAC.cpp | 208 ++-- BioCro-3.2.0/BioCro/src/module_library/c3CanAC.h | 82 - BioCro-3.2.0/BioCro/src/module_library/c3_assimilation.h | 179 ++- BioCro-3.2.0/BioCro/src/module_library/c3_canopy.cpp | 192 ++- BioCro-3.2.0/BioCro/src/module_library/c3_canopy.h | 178 ++- BioCro-3.2.0/BioCro/src/module_library/c3_leaf_photosynthesis.cpp | 146 +- BioCro-3.2.0/BioCro/src/module_library/c3_leaf_photosynthesis.h | 132 +- BioCro-3.2.0/BioCro/src/module_library/c3_parameters.h |only BioCro-3.2.0/BioCro/src/module_library/c3_temperature_response.cpp |only BioCro-3.2.0/BioCro/src/module_library/c3_temperature_response.h |only BioCro-3.2.0/BioCro/src/module_library/c3photo.cpp | 74 - BioCro-3.2.0/BioCro/src/module_library/c3photo.h | 5 BioCro-3.2.0/BioCro/src/module_library/c4_assimilation.h | 2 BioCro-3.2.0/BioCro/src/module_library/c4_canopy.h | 317 +++--- BioCro-3.2.0/BioCro/src/module_library/c4_leaf_photosynthesis.cpp | 95 - BioCro-3.2.0/BioCro/src/module_library/c4_leaf_photosynthesis.h | 90 - BioCro-3.2.0/BioCro/src/module_library/c4photo.cpp | 12 BioCro-3.2.0/BioCro/src/module_library/canopy_gbw_thornley.h |only BioCro-3.2.0/BioCro/src/module_library/canopy_photosynthesis_outputs.h | 2 BioCro-3.2.0/BioCro/src/module_library/carbon_assimilation_to_biomass.h |only BioCro-3.2.0/BioCro/src/module_library/development_index_from_thermal_time.h |only BioCro-3.2.0/BioCro/src/module_library/fake_solar.h | 6 BioCro-3.2.0/BioCro/src/module_library/format_time.h |only BioCro-3.2.0/BioCro/src/module_library/grimm_soybean_flowering_calculator.h | 14 BioCro-3.2.0/BioCro/src/module_library/height_from_lai.h |only BioCro-3.2.0/BioCro/src/module_library/leaf_energy_balance.cpp |only BioCro-3.2.0/BioCro/src/module_library/leaf_energy_balance.h |only BioCro-3.2.0/BioCro/src/module_library/leaf_evapotranspiration.h |only BioCro-3.2.0/BioCro/src/module_library/leaf_gbw_nikolov.h | 47 BioCro-3.2.0/BioCro/src/module_library/maintenance_respiration.h |only BioCro-3.2.0/BioCro/src/module_library/module_library.cpp | 274 ++--- BioCro-3.2.0/BioCro/src/module_library/multilayer_canopy_integrator.h | 45 BioCro-3.2.0/BioCro/src/module_library/multilayer_canopy_properties.cpp | 66 - BioCro-3.2.0/BioCro/src/module_library/multilayer_canopy_properties.h | 28 BioCro-3.2.0/BioCro/src/module_library/no_leaf_resp_neg_assim_partitioning_growth_calculator.h | 18 BioCro-3.2.0/BioCro/src/module_library/oscillator_clock_calculator.h | 120 +- BioCro-3.2.0/BioCro/src/module_library/parameter_calculator.h | 78 - BioCro-3.2.0/BioCro/src/module_library/photosynthesis_outputs.h | 2 BioCro-3.2.0/BioCro/src/module_library/rue_leaf_photosynthesis.cpp | 93 - BioCro-3.2.0/BioCro/src/module_library/rue_leaf_photosynthesis.h | 38 BioCro-3.2.0/BioCro/src/module_library/senescence_coefficient_logistic.h | 2 BioCro-3.2.0/BioCro/src/module_library/sla_linear.h |only BioCro-3.2.0/BioCro/src/module_library/sla_logistic.h |only BioCro-3.2.0/BioCro/src/module_library/solar_position_michalsky.h | 16 BioCro-3.2.0/BioCro/src/module_library/soybean_development_rate_calculator.h | 46 BioCro-3.2.0/BioCro/src/module_library/stefan_boltzmann_longwave.h |only BioCro-3.2.0/BioCro/src/module_library/sunML.cpp | 506 +++++++--- BioCro-3.2.0/BioCro/src/module_library/sunML.h | 100 + BioCro-3.2.0/BioCro/src/module_library/temperature_response_functions.h |only BioCro-3.2.0/BioCro/src/module_library/thermal_time_and_frost_senescence.h | 9 BioCro-3.2.0/BioCro/src/module_library/thermal_time_beta.h | 33 BioCro-3.2.0/BioCro/src/module_library/thermal_time_bilinear.h | 31 BioCro-3.2.0/BioCro/src/module_library/thermal_time_development_rate_calculator.h | 38 BioCro-3.2.0/BioCro/src/module_library/thermal_time_linear.h | 23 BioCro-3.2.0/BioCro/src/module_library/thermal_time_linear_extended.h | 29 BioCro-3.2.0/BioCro/src/module_library/thermal_time_trilinear.h | 35 BioCro-3.2.0/BioCro/src/module_library/water_and_air_properties.h | 126 ++ BioCro-3.2.0/BioCro/tests/README.md | 24 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ball_berry.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c3_assimilation.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c3_canopy.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c3_leaf_photosynthesis.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c3_parameters.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c4_assimilation.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c4_canopy.csv | 4 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_c4_leaf_photosynthesis.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_canopy_gbw_thornley.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_carbon_assimilation_to_biomass.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_development_index_from_thermal_time.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_format_time.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_grimm_soybean_flowering_calculator.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_height_from_lai.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_leaf_evapotranspiration.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_leaf_gbw_nikolov.csv | 4 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_maintenance_respiration.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_no_leaf_resp_neg_assim_partitioning_growth_calculator.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_oscillator_clock_calculator.csv | 4 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_parameter_calculator.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_rue_leaf_photosynthesis.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_sla_linear.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_sla_logistic.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_soil_evaporation.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_solar_position_michalsky.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_soybean_development_rate_calculator.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_stefan_boltzmann_longwave.csv |only BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ten_layer_c3_canopy.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ten_layer_c4_canopy.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ten_layer_canopy_integrator.csv | 4 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ten_layer_canopy_properties.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_ten_layer_rue_canopy.csv | 6 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_and_frost_senescence.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_beta.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_bilinear.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_development_rate_calculator.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_linear.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_linear_extended.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_thermal_time_trilinear.csv | 2 BioCro-3.2.0/BioCro/tests/module_test_cases/BioCro_total_biomass.csv | 2 BioCro-3.2.0/BioCro/tests/test_data/miscanthus_x_giganteus_simulation.csv | 360 +++---- BioCro-3.2.0/BioCro/tests/test_data/soybean_simulation.csv | 276 ++--- BioCro-3.2.0/BioCro/tests/test_data/testmod.h |only BioCro-3.2.0/BioCro/tests/test_data/willow_simulation.csv | 360 +++---- BioCro-3.2.0/BioCro/tests/testthat/test.CropModels.R | 95 + BioCro-3.2.0/BioCro/tests/testthat/test.HarmonicOscillationModeling.R | 3 BioCro-3.2.0/BioCro/tests/testthat/test.Modules.R | 6 BioCro-3.2.0/BioCro/tests/testthat/test.PartialApplication.R | 4 BioCro-3.2.0/BioCro/tests/testthat/test.SystemConstruction.R | 22 BioCro-3.2.0/BioCro/tests/testthat/test.c3photo.R | 50 BioCro-3.2.0/BioCro/tests/testthat/test.canopy_modules.R |only BioCro-3.2.0/BioCro/tests/testthat/test.check_is_sequential.R |only BioCro-3.2.0/BioCro/tests/testthat/test.model_testing.R |only BioCro-3.2.0/BioCro/tests/testthat/test.module_write.R |only BioCro-3.2.0/BioCro/tests/testthat/test.time_format.R |only BioCro-3.2.0/BioCro/tests/testthat/test.weather.R |only BioCro-3.2.0/BioCro/vignettes/BioCro.Rmd | 1 BioCro-3.2.0/BioCro/vignettes/building_the_vignettes.md | 89 + 185 files changed, 3796 insertions(+), 2861 deletions(-)
Title: Compare Ordinal Endpoints Using Simulations
Description: Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included 'shiny' application allows users to simulate outcomes given different ordinal data distributions.
Author: Pat Callahan [aut, cre, cph]
Maintainer: Pat Callahan <patricktcallahan18@gmail.com>
Diff between ordinalsimr versions 0.1.3 dated 2025-01-29 and 0.2.0 dated 2025-03-07
DESCRIPTION | 16 +- MD5 | 44 +++-- NAMESPACE | 1 NEWS.md | 11 + R/app_server.R | 34 ++++ R/app_ui.R | 15 - R/mod_kill_simulations.R |only R/mod_plot_distributions.R | 11 + R/mod_progress_modal.R |only R/mod_shinyapps_modal_notice.R |only R/mod_simulation_inputs_page.R | 4 R/mod_start_simulation.R | 2 R/mod_stats_calculations.R | 286 ++++++++++++++++++++++-------------- R/ordinal_tests.R | 4 R/run_simulations.R | 59 ++++++- R/utils.R | 36 +++- README.md | 2 inst/CITATION | 2 inst/doc/coding-simulations.html | 40 ++--- inst/doc/ordinalsimr-options.R | 40 ++--- inst/homepage.Rmd | 2 inst/homepage.html | 42 +++-- inst/scratch/trial_data.R |only man/ordinal_tests.Rd | 2 tests/testthat/test-ordinal_tests.R | 3 25 files changed, 422 insertions(+), 234 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Thomas J. Faulkenberry [rev],
Robert Garrett [rev]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 1.0.0 dated 2025-01-10 and 1.0.1 dated 2025-03-07
DESCRIPTION | 8 MD5 | 18 NEWS.md | 1849 ++++++++++++++++++------------------- R/data_arrange.R | 236 ++-- R/data_modify.R | 812 ++++++++-------- R/select_nse.R | 1258 ++++++++++++------------- README.md | 1247 ++++++++++++------------ inst/WORDLIST | 253 ++--- tests/testthat/helper-state.R | 96 - tests/testthat/test-data_arrange.R | 270 ++--- 10 files changed, 3032 insertions(+), 3015 deletions(-)
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.3.3 dated 2024-11-08 and 2.3.4 dated 2025-03-07
admix-2.3.3/admix/inst/doc/admixture-clustering.R |only admix-2.3.3/admix/inst/doc/test-hypothesis.R |only admix-2.3.4/admix/DESCRIPTION | 6 admix-2.3.4/admix/MD5 | 58 +-- admix-2.3.4/admix/R/IBM_k_samples_test.R | 40 +- admix-2.3.4/admix/R/admix_cluster.R | 24 - admix-2.3.4/admix/R/admix_estim.R | 58 +-- admix-2.3.4/admix/R/admix_test.R | 28 - admix-2.3.4/admix/R/estim_BVdk.R | 141 ++++--- admix-2.3.4/admix/R/estim_IBM.R | 221 +++++++----- admix-2.3.4/admix/R/estim_PS.R | 17 admix-2.3.4/admix/R/gaussianity_test.R | 58 +-- admix-2.3.4/admix/R/orthobasis_test.R | 15 admix-2.3.4/admix/build/partial.rdb |binary admix-2.3.4/admix/build/vignette.rds |binary admix-2.3.4/admix/inst/doc/admixture-clustering.Rmd | 28 - admix-2.3.4/admix/inst/doc/admixture-clustering.html | 107 ++--- admix-2.3.4/admix/inst/doc/admixture-weight-estimation.R | 10 admix-2.3.4/admix/inst/doc/admixture-weight-estimation.Rmd | 10 admix-2.3.4/admix/inst/doc/admixture-weight-estimation.html | 38 +- admix-2.3.4/admix/inst/doc/test-hypothesis.Rmd | 43 +- admix-2.3.4/admix/inst/doc/test-hypothesis.html | 18 admix-2.3.4/admix/man/IBM_k_samples_test.Rd | 8 admix-2.3.4/admix/man/admix_estim.Rd | 2 admix-2.3.4/admix/man/estim_BVdk.Rd | 18 admix-2.3.4/admix/man/estim_IBM.Rd | 8 admix-2.3.4/admix/man/orthobasis_test.Rd | 8 admix-2.3.4/admix/vignettes/admixture-clustering.Rmd | 28 - admix-2.3.4/admix/vignettes/admixture-clustering.Rmd.orig |only admix-2.3.4/admix/vignettes/admixture-weight-estimation.Rmd | 10 admix-2.3.4/admix/vignettes/test-hypothesis.Rmd | 43 +- admix-2.3.4/admix/vignettes/test-hypothesis.Rmd.orig |only 32 files changed, 601 insertions(+), 444 deletions(-)
Title: Create Interface for 'RBMI' and 'tern'
Description: 'RBMI' implements standard and reference based multiple
imputation methods for continuous longitudinal endpoints (Gower-Page
et al. (2022) <doi:10.21105/joss.04251>). This package provides an
interface for 'RBMI' uses the 'tern'
<https://cran.r-project.org/package=tern> framework by Zhu et al.
(2023) and tabulate results easily using 'rtables'
<https://cran.r-project.org/package=rtables> by Becker et al. (2023).
Author: Joe Zhu [aut, cre] ,
Jana Stoilova [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern.rbmi versions 0.1.4 dated 2024-11-26 and 0.1.5 dated 2025-03-06
DESCRIPTION | 33 ++++++++++--------- MD5 | 22 ++++++------- NEWS.md | 4 ++ README.md | 9 ++--- build/vignette.rds |binary data/rbmi_test_data.rda |binary inst/WORDLIST | 11 +++--- inst/doc/tern-rbmi.R | 6 +-- inst/doc/tern-rbmi.Rmd | 4 +- inst/doc/tern-rbmi.html | 79 ++++++++++++++++++++++++----------------------- man/tern.rbmi-package.Rd | 2 - vignettes/tern-rbmi.Rmd | 4 +- 12 files changed, 93 insertions(+), 81 deletions(-)
Title: Comparison Functions for Clustering and Record Linkage
Description: Implements functions for comparing strings, sequences and
numeric vectors for clustering and record linkage applications.
Supported comparison functions include: generalized edit distances
for comparing sequences/strings, Monge-Elkan similarity for fuzzy
comparison of token sets, and L-p distances for comparing numeric
vectors. Where possible, comparison functions are implemented in
C/C++ to ensure good performance.
Author: Neil Marchant [aut, cre]
Maintainer: Neil Marchant <ngmarchant@gmail.com>
Diff between comparator versions 0.1.2 dated 2022-03-16 and 0.1.3 dated 2025-03-06
comparator-0.1.2/comparator/src/Makevars |only comparator-0.1.3/comparator/DESCRIPTION | 8 ++++---- comparator-0.1.3/comparator/MD5 | 7 +++---- comparator-0.1.3/comparator/NEWS.md | 3 +++ comparator-0.1.3/comparator/src/Jaro.h | 2 +- 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 2.1.0 dated 2024-10-14 and 3.0.0 dated 2025-03-06
EMC2-2.1.0/EMC2/R/IS2.R |only EMC2-2.1.0/EMC2/R/variant_lm.R |only EMC2-2.1.0/EMC2/man/mapped_par.Rd |only EMC2-2.1.0/EMC2/man/plot_defective_density.Rd |only EMC2-2.1.0/EMC2/man/plot_fit.Rd |only EMC2-2.1.0/EMC2/man/plot_prior.Rd |only EMC2-2.1.0/EMC2/man/posterior_summary.Rd |only EMC2-2.1.0/EMC2/man/sampled_p_vector.Rd |only EMC2-2.1.0/EMC2/src/log_likelihood_race.cpp |only EMC2-2.1.0/EMC2/tests/testthat/_snaps/plot_defective_density |only EMC2-2.1.0/EMC2/tests/testthat/_snaps/plot_fit/cdfs-plot-fit.svg |only EMC2-2.1.0/EMC2/tests/testthat/test-plot_defective_density.R |only EMC2-3.0.0/EMC2/DESCRIPTION | 10 EMC2-3.0.0/EMC2/MD5 | 273 +- EMC2-3.0.0/EMC2/NAMESPACE | 49 EMC2-3.0.0/EMC2/NEWS.md | 27 EMC2-3.0.0/EMC2/R/EMC2-package.R | 6 EMC2-3.0.0/EMC2/R/MRI.R |only EMC2-3.0.0/EMC2/R/RcppExports.R | 52 EMC2-3.0.0/EMC2/R/SBC.R | 33 EMC2-3.0.0/EMC2/R/bridge_sampling.R | 28 EMC2-3.0.0/EMC2/R/data.R | 13 EMC2-3.0.0/EMC2/R/define_variants.R |only EMC2-3.0.0/EMC2/R/design.R | 860 +++++---- EMC2-3.0.0/EMC2/R/design_plot.R |only EMC2-3.0.0/EMC2/R/factor_analysis.R | 2 EMC2-3.0.0/EMC2/R/fitting.R | 591 +++--- EMC2-3.0.0/EMC2/R/get_type_objects.R | 58 EMC2-3.0.0/EMC2/R/joint.R | 7 EMC2-3.0.0/EMC2/R/likelihood.R | 36 EMC2-3.0.0/EMC2/R/make_data.R | 60 EMC2-3.0.0/EMC2/R/map.R | 438 +++- EMC2-3.0.0/EMC2/R/model_DDM.R | 75 EMC2-3.0.0/EMC2/R/model_LBA.R | 30 EMC2-3.0.0/EMC2/R/model_LNR.R | 18 EMC2-3.0.0/EMC2/R/model_RDM.R | 22 EMC2-3.0.0/EMC2/R/model_SDT.R | 4 EMC2-3.0.0/EMC2/R/objects.R | 91 EMC2-3.0.0/EMC2/R/plot_data.R |only EMC2-3.0.0/EMC2/R/plotting.R | 391 ---- EMC2-3.0.0/EMC2/R/priors.R | 330 +++ EMC2-3.0.0/EMC2/R/s3_funcs.R | 348 ++- EMC2-3.0.0/EMC2/R/sampling.R | 933 ++++------ EMC2-3.0.0/EMC2/R/statistics.R | 105 - 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Title: R Library for Spatial Data Analysis
Description: Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis,
Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code
of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis.
The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
Author: Xun Li [aut, cre],
Luc Anselin [aut]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between rgeoda versions 0.0.11-1 dated 2024-12-19 and 0.1.0 dated 2025-03-06
DESCRIPTION | 8 +-- MD5 | 29 ++++++------ NAMESPACE | 1 R/RcppExports.R | 4 + R/utils.R | 24 ++++++++++ man/eb_rates_standardization.Rd |only src/RcppExports.cpp | 13 +++++ src/libgeoda/clustering/redcap_wrapper.cpp | 17 ++++--- src/libgeoda/clustering/schc_wrapper.cpp | 27 +++++++---- src/libgeoda/gda_clustering.cpp | 22 +++++---- src/libgeoda/gda_clustering.h | 18 +++---- src/libgeoda/gda_data.cpp | 68 +++++++++++++++++++++++++++++ src/libgeoda/gda_data.h | 49 ++++++++++++-------- src/libgeoda/sa/BatchLISA.h | 7 ++ src/libgeoda/sa/LISA.h | 7 ++ src/rcpp_lisa.cpp | 21 ++++++++ 16 files changed, 243 insertions(+), 72 deletions(-)
Title: Create and Query a Local Copy of 'GenBank' in R
Description: Download large sections of
'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local
SQL-based database. A user can then query this database using 'restez'
functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez>
wrappers.
Author: Joel H. Nitta [aut, cre] ,
Dom Bennett [aut]
Maintainer: Joel H. Nitta <joelnitta@gmail.com>
Diff between restez versions 2.1.4 dated 2023-10-25 and 2.1.5 dated 2025-03-06
DESCRIPTION | 8 - MD5 | 158 ++++++++++++++++----------------- NEWS.md | 15 ++- R/entrez-tools.R | 10 +- R/gb-get-tools.R | 5 + R/gb-setup-tools.R | 7 + README.md | 2 man/add_rcrd_log.Rd | 4 man/cat_line.Rd | 4 man/char.Rd | 4 man/check_connection.Rd | 4 man/cleanup.Rd | 4 man/connected.Rd | 4 man/connection_get.Rd | 4 man/db_download_intern.Rd | 4 man/db_sqlngths_get.Rd | 4 man/db_sqlngths_log.Rd | 4 man/dir_size.Rd | 4 man/dwnld_path_get.Rd | 4 man/dwnld_rcrd_log.Rd | 4 man/entrez_fasta_get.Rd | 4 man/entrez_gb_get.Rd | 4 man/extract_accession.Rd | 4 man/extract_by_patterns.Rd | 4 man/extract_clean_sequence.Rd | 4 man/extract_definition.Rd | 4 man/extract_features.Rd | 4 man/extract_inforecpart.Rd | 4 man/extract_keywords.Rd | 4 man/extract_locus.Rd | 4 man/extract_organism.Rd | 4 man/extract_seqrecpart.Rd | 4 man/extract_sequence.Rd | 4 man/extract_version.Rd | 4 man/file_download.Rd | 4 man/filename_log.Rd | 4 man/flatfile_read.Rd | 4 man/gb_build.Rd | 4 man/gb_df_create.Rd | 4 man/gb_df_generate.Rd | 4 man/gb_sql_add.Rd | 4 man/gb_sql_query.Rd | 4 man/gbrelease_check.Rd | 4 man/gbrelease_get.Rd | 4 man/gbrelease_log.Rd | 4 man/has_data.Rd | 4 man/identify_downloadable_files.Rd | 4 man/last_add_get.Rd | 4 man/last_dwnld_get.Rd | 4 man/last_entry_get.Rd | 4 man/latest_genbank_release.Rd | 2 man/latest_genbank_release_notes.Rd | 2 man/message_missing.Rd | 4 man/mock_def.Rd | 4 man/mock_gb_df_generate.Rd | 4 man/mock_org.Rd | 4 man/mock_rec.Rd | 4 man/mock_seq.Rd | 4 man/predict_datasizes.Rd | 4 man/readme_log.Rd | 4 man/restez.Rd | 2 man/restez_connect.Rd | 4 man/restez_disconnect.Rd | 4 man/restez_path_check.Rd | 4 man/restez_rl.Rd | 4 man/search_gz.Rd | 4 man/seshinfo_log.Rd | 4 man/setup.Rd | 4 man/slctn_get.Rd | 4 man/slctn_log.Rd | 4 man/sql_path_get.Rd | 4 man/stat.Rd | 2 man/status_class.Rd | 2 man/testdatadir_get.Rd | 6 - tests/testthat/test-biomartr-tools.R | 19 ++- tests/testthat/test-entrez-tools.R | 22 +--- tests/testthat/test-gb-setup-tools.R | 23 +--- tests/testthat/test-get-tools.R | 6 + tests/testthat/test-log-tools.R | 12 +- tests/testthat/test-rentrez-wrappers.R | 8 - 80 files changed, 290 insertions(+), 265 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.4 dated 2024-01-09 and 0.2.5 dated 2025-03-06
riskmetric-0.2.4/riskmetric/man/figures/hex-riskmetric-aspconfig.png |only riskmetric-0.2.4/riskmetric/tests/testthat/testPackage1 |only riskmetric-0.2.5/riskmetric/DESCRIPTION | 8 riskmetric-0.2.5/riskmetric/MD5 | 34 riskmetric-0.2.5/riskmetric/NEWS.md | 4 riskmetric-0.2.5/riskmetric/R/assess_dependencies.R | 4 riskmetric-0.2.5/riskmetric/R/assess_size_codebase.R | 9 riskmetric-0.2.5/riskmetric/R/pkg_ref_cache_news.R | 4 riskmetric-0.2.5/riskmetric/R/pkg_ref_class.R | 4 riskmetric-0.2.5/riskmetric/README.md | 8 riskmetric-0.2.5/riskmetric/build/vignette.rds |binary riskmetric-0.2.5/riskmetric/inst/doc/extending-riskmetric.R | 6 riskmetric-0.2.5/riskmetric/inst/doc/extending-riskmetric.html | 429 +++----- riskmetric-0.2.5/riskmetric/inst/doc/riskmetric.R | 16 riskmetric-0.2.5/riskmetric/inst/doc/riskmetric.html | 482 +++------- riskmetric-0.2.5/riskmetric/man/determine_pkg_source.Rd | 2 riskmetric-0.2.5/riskmetric/man/figures/logo.png |only riskmetric-0.2.5/riskmetric/man/metric_score.pkg_metric_size_codebase.Rd | 2 riskmetric-0.2.5/riskmetric/man/riskmetric.Rd | 2 19 files changed, 416 insertions(+), 598 deletions(-)
Title: Tools for R Package Developers
Description: R-hub v2 uses GitHub Actions to run 'R CMD check' and
similar package checks. The 'rhub' package helps you set up
R-hub v2 for your R package, and start running checks.
Author: Gabor Csardi [aut, cre],
Maelle Salmon [aut] ,
R Consortium [fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rhub versions 2.0.0 dated 2024-04-11 and 2.0.1 dated 2025-03-06
DESCRIPTION | 8 +++---- MD5 | 36 +++++++++++++++++++------------- NEWS.md | 7 ++++++ R/aaa-async.R | 6 ++--- R/check.R | 2 - R/doctor.R | 2 - R/platforms.R | 13 +++++++---- man/figures/rhub-check-dark.svg |only man/figures/rhub-check.svg |only man/figures/rhub-doctor-dark.svg |only man/figures/rhub-doctor.svg |only man/figures/rhub-platforms-dark.svg |only man/figures/rhub-platforms.svg |only man/figures/rhub-setup-dark.svg |only man/figures/rhub-setup.svg |only man/rhub-package.Rd | 2 - man/rhub_check.Rd | 2 - man/rhubv2.Rd | 8 +++---- tests/testthat/_snaps/doctor.md | 2 - tests/testthat/_snaps/platforms.md | 12 +++++----- tests/testthat/fixtures/pkg/DESCRIPTION | 4 +-- tests/testthat/helpers.R | 3 +- tests/testthat/test-utils.R | 2 - 23 files changed, 64 insertions(+), 45 deletions(-)
Title: Wicked-Fast Streaming 'JSON' ('ndjson') Reader
Description: Streaming 'JSON' ('ndjson') has one 'JSON' record per-line
and many modern 'ndjson' files contain large numbers of records.
These constructs may not be columnar in nature, but it is often
useful to read in these files and "flatten" the structure out to
enable working with the data in an R 'data.frame'-like context.
Functions are provided that make it possible to read in plain
'ndjson' files or compressed ('gz') 'ndjson' files and either
validate the format of the records or create "flat" 'data.table'
structures from them.
Author: Bob Rudis [aut, cre] ,
Niels Lohmann [aut] ,
Deepak Bandyopadhyay [aut] ,
Lutz Kettner [aut] ,
Neal Fultz [ctb] ,
Maarten Demeyer [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between ndjson versions 0.9.0 dated 2022-10-17 and 0.9.1 dated 2025-03-06
DESCRIPTION | 10 MD5 | 18 R/ndjson-package.R | 3 R/ndjson.R | 4 inst/include/json.h |21477 ++++++++++++++++++++++++++++------------------------ man/ndjson.Rd | 9 man/stream_in.Rd | 2 man/validate.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 10 files changed, 11605 insertions(+), 9922 deletions(-)
Title: Scalar-on-Function Regression with Measurement Error Correction
Description: Solve scalar-on-function linear models,
including generalized linear mixed effect model and quantile linear regression model,
and bias correction estimation methods due to measurement error.
Details about the measurement error bias correction methods, see
Luan et al. (2023) <doi:10.48550/arXiv.2305.12624>,
Tekwe et al. (2022) <doi:10.1093/biostatistics/kxac017>,
Zhang et al. (2023) <doi:10.5705/ss.202021.0246>,
Tekwe et al. (2019) <doi:10.1002/sim.8179>.
Author: Heyang Ji [aut, cre, ctb, dtc]
,
Ufuk Beyaztas [aut, ctb, rev] ,
Nicolas Escobar-Velasquez [com]
,
Yuanyuan Luan [aut, ctb],
Xiwei Chen [aut, ctb],
Mengli Zhang [aut, ctb],
Roger Zoh [aut, ths],
Lan Xue [aut, ths],
Carmen Tekwe [aut, ths]
Maintainer: Heyang Ji <jihx1015@outlook.com>
Diff between MECfda versions 0.1.0 dated 2024-10-21 and 0.2.0 dated 2025-03-06
DESCRIPTION | 43 - MD5 | 94 +- NAMESPACE | 17 NEWS.md |only R/FPC_basis_expansion.R |only R/FourierSeries2fun.R | 2 R/ME.fcLR_IV.R | 6 R/ME.fcQR_CLS.R | 8 R/ME.fcQR_IV.SIMEX.R | 27 R/ME.fcRegression_MEM.R | 8 R/MECfda_simDataGen_ME.R |only R/MECfda_simDataGen_fcReg.R |only R/MEM_X_hat.R |only R/basis2fun.R | 14 R/bsplineSeries2fun.R | 4 R/bspline_basis_expansion.R | 4 R/classDefintions.R | 90 ++ R/fcQR.R | 49 + R/fcRegression.R | 60 + R/fourier_basis_expansion.R | 8 R/functional_variable.R | 2 R/initialize.numeric_basis.R |only R/numericBasisSeries2fun.R |only R/numeric_basis_expansion.R |only R/plot.bspline_series.R | 4 R/plot.numeric_series.R |only R/predict.fcQR.R | 11 R/predict.fcRegression.R | 11 build/vignette.rds |binary inst/doc/MECfda.R | 168 ++-- inst/doc/MECfda.Rmd | 892 ++++++++++++------------ inst/doc/MECfda.html | 1188 ++++++++++++++++++++------------- man/FPC_basis_expansion.Rd |only man/FourierSeries2fun.Rd | 2 man/ME.fcLR_IV.Rd | 6 man/ME.fcQR_CLS.Rd | 8 man/ME.fcQR_IV.SIMEX.Rd | 4 man/ME.fcRegression_MEM.Rd | 8 man/MECfda_simDataGen_ME.Rd |only man/MECfda_simDataGen_fcReg.Rd |only man/MEM_X_hat.Rd |only man/basis2fun.Rd | 8 man/bsplineSeries2fun.Rd | 4 man/bspline_basis-class.Rd | 2 man/bspline_basis_expansion.Rd | 2 man/fcQR.Rd | 17 man/fcRegression.Rd | 23 man/fourier_basis_expansion.Rd | 2 man/functional_variable-class.Rd | 2 man/numericBasisSeries2fun.Rd |only man/numericBasis_series-class.Rd |only man/numeric_basis-class.Rd |only man/numeric_basis_expansion.Rd |only man/plot-bspline_series-method.Rd | 4 man/plot-numericBasis_series-method.Rd |only man/predict.fcRegression.Rd | 86 +- vignettes/MECfda.Rmd | 892 ++++++++++++------------ 57 files changed, 2175 insertions(+), 1605 deletions(-)
Title: Bindings to 'OpenCV' Computer Vision Library
Description: Exposes some of the available 'OpenCV' <https://opencv.org/> algorithms,
such as a QR code scanner, and edge, body or face detection. These can either be
applied to analyze static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] ,
Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between opencv versions 0.4.1 dated 2024-10-04 and 0.5.0 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 31 +++++++++++++++++++++++-------- 4 files changed, 32 insertions(+), 14 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Bethany A. Johnson [aut],
Daniel F. Lopez-Lozano [aut],
Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Andrea Paz [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [ [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Diff between wallace versions 2.1.3 dated 2024-07-18 and 2.2.0 dated 2025-03-06
DESCRIPTION | 16 +++-- MD5 | 84 +++++++++++++++--------------- NEWS.md | 6 ++ R/model_bioclim.R | 3 - R/model_maxent.R | 5 + R/part_partitionOccs.R | 18 +++--- R/vis_bioclimPlot.R | 1 R/xfer_area.R | 27 ++++++--- R/xfer_time.R | 20 +++---- R/xfer_userEnvs.R | 24 +++++--- README.md | 4 - inst/module_skeleton/skeleton.R | 2 inst/shiny/Rmd/text_about.Rmd | 2 inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/envs_userEnvs.md | 4 - inst/shiny/modules/model_bioclim.yml | 2 inst/shiny/modules/model_maxent.yml | 2 inst/shiny/modules/part_nonSpat.yml | 2 inst/shiny/modules/part_spat.yml | 2 inst/shiny/modules/vis_bioclimPlot.yml | 2 inst/shiny/modules/vis_mapPreds.R | 12 ++-- inst/shiny/modules/vis_mapPreds.Rmd | 18 +++--- inst/shiny/modules/vis_mapPreds.yml | 2 inst/shiny/modules/vis_maxentEvalPlot.yml | 2 inst/shiny/modules/vis_responsePlot.R | 2 inst/shiny/modules/vis_responsePlot.Rmd | 2 inst/shiny/modules/vis_responsePlot.yml | 2 inst/shiny/modules/xfer_area.R | 2 inst/shiny/modules/xfer_time.md | 2 inst/shiny/server.R | 2 man/model_bioclim.Rd | 2 man/model_maxent.Rd | 2 man/part_partitionOccs.Rd | 6 +- man/vis_bioclimPlot.Rd | 2 man/xfer_area.Rd | 19 +++++- man/xfer_time.Rd | 12 ++-- man/xfer_userEnvs.Rd | 16 ++++- tests/testthat/test_model_bioclim.R | 8 +- tests/testthat/test_model_maxent.R | 4 - tests/testthat/test_xfer_area.R | 17 ++++-- tests/testthat/test_xfer_time.R | 15 +++-- tests/testthat/test_xfer_userEnvs.R | 20 +++++-- 43 files changed, 249 insertions(+), 150 deletions(-)
Title: Mapping Data for 'usmap' Package
Description: Provides a container for data used by the 'usmap' package.
The data used by 'usmap' has been extracted into this package so that the
file size of the 'usmap' package can be reduced greatly. The data in this
package will be updated roughly once per year as new map data files are
provided by the US Census Bureau.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.org>
Diff between usmapdata versions 0.3.0 dated 2024-05-17 and 0.4.0 dated 2025-03-06
usmapdata-0.3.0/usmapdata/inst/extdata/us_counties.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_counties_centroids.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_states.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_states_centroids.gpkg |only usmapdata-0.4.0/usmapdata/DESCRIPTION | 12 usmapdata-0.4.0/usmapdata/MD5 | 54 - usmapdata-0.4.0/usmapdata/NAMESPACE | 13 usmapdata-0.4.0/usmapdata/NEWS.md | 144 +- usmapdata-0.4.0/usmapdata/R/create-us-map.R | 525 +++++----- usmapdata-0.4.0/usmapdata/R/fips-data.R | 51 usmapdata-0.4.0/usmapdata/R/us-map.R | 232 ++-- usmapdata-0.4.0/usmapdata/R/usmapdata-package.R | 2 usmapdata-0.4.0/usmapdata/README.md | 196 +-- usmapdata-0.4.0/usmapdata/inst/WORDLIST | 24 usmapdata-0.4.0/usmapdata/inst/extdata/2021 |only usmapdata-0.4.0/usmapdata/inst/extdata/2022 |only usmapdata-0.4.0/usmapdata/inst/extdata/2023 |only usmapdata-0.4.0/usmapdata/man/available_map_years.Rd |only usmapdata-0.4.0/usmapdata/man/centroid_labels.Rd | 58 - usmapdata-0.4.0/usmapdata/man/create_us_map.Rd | 153 +- usmapdata-0.4.0/usmapdata/man/fips_data.Rd | 70 - usmapdata-0.4.0/usmapdata/man/select_map_year.Rd |only usmapdata-0.4.0/usmapdata/man/us_map.Rd | 109 +- usmapdata-0.4.0/usmapdata/man/usmapdata.Rd | 104 - usmapdata-0.4.0/usmapdata/tests/spelling.R | 2 usmapdata-0.4.0/usmapdata/tests/testthat.R | 24 usmapdata-0.4.0/usmapdata/tests/testthat/test-fips-data.R | 82 - usmapdata-0.4.0/usmapdata/tests/testthat/test-usmap.R | 175 +-- 28 files changed, 1095 insertions(+), 935 deletions(-)
Title: Mathematics PhD Genealogy Data and Plotting
Description: Query, extract, and plot genealogical data from The Mathematics
Genealogy Project <https://mathgenealogy.org/>. Data is gathered from the
'WebSocket' server run by the 'geneagrapher-core' project
<https://github.com/davidalber/geneagrapher-core>.
Author: Louis Aslett [aut, cre]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Diff between maths.genealogy versions 0.1.1 dated 2025-03-03 and 0.1.2 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/get_genealogy.R | 4 ++++ R/plot_gg.R | 4 ++++ R/plot_gg_path.R | 4 ++++ R/plot_grviz.R | 4 ++++ R/search_id.R | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.html | 8 ++++---- man/get_genealogy.Rd | 4 ++++ man/maths.genealogy-package.Rd | 2 +- man/plot_gg.Rd | 4 ++++ man/plot_gg_path.Rd | 4 ++++ man/plot_grviz.Rd | 4 ++++ man/search_id.Rd | 4 ++++ 17 files changed, 71 insertions(+), 26 deletions(-)
More information about maths.genealogy at CRAN
Permanent link
Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between dfr versions 0.1.4 dated 2025-02-06 and 0.1.5 dated 2025-03-06
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------- R/dfr_adap_sgl.R | 31 ++++++++++++++++-- R/dfr_sgl.R | 25 +++++++++++++- R/fitting_code.R | 24 ++------------ R/global_wrapper_code.R | 81 +++++++++++++++++++++++++++++++++++------------- R/run_algorithm.R | 4 +- R/screen.R | 14 ++------ R/utils.R | 66 ++++++++++++++++++++++++++++++++------- build/partial.rdb |binary man/dfr_adap_sgl.Rd | 6 +-- man/dfr_sgl.Rd | 4 +- 12 files changed, 193 insertions(+), 92 deletions(-)
Title: Conditional Binary Quantile Models
Description: Estimates conditional binary quantile models developed by Lu (2020) <doi:10.1017/pan.2019.29>. The estimation procedure is implemented based on Markov chain Monte Carlo methods.
Author: Xiao Lu [aut, cre]
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Diff between cbq versions 0.2.0.3 dated 2023-04-02 and 0.2.0.4 dated 2025-03-06
DESCRIPTION | 14 +++++++++----- MD5 | 14 +++++++------- inst/stan/cbqfixd.stan | 18 +++++++++--------- inst/stan/cbqfixdv.stan | 18 +++++++++--------- inst/stan/cbqpaneld.stan | 18 +++++++++--------- inst/stan/cbqpaneldv.stan | 18 +++++++++--------- inst/stan/cbqrandomd.stan | 18 +++++++++--------- inst/stan/cbqrandomdv.stan | 18 +++++++++--------- 8 files changed, 70 insertions(+), 66 deletions(-)
Title: Interface to the 'Zoltar' Forecast Repository API
Description: 'Zoltar' <https://www.zoltardata.com/> is a website that provides a repository of model forecast results
in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time
series forecasts for prediction challenges of interest to the modeling community. This package provides functions
for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects,
models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.
Author: Matthew Cornell [aut, cre],
Nicholas Reich [aut, cph]
Maintainer: Matthew Cornell <cornell@umass.edu>
Diff between zoltr versions 1.0.1 dated 2024-06-27 and 1.0.2 dated 2025-03-06
DESCRIPTION | 6 MD5 | 32 +-- NAMESPACE | 5 NEWS.md | 6 R/connection.R | 14 - R/model.R | 9 R/project.R | 14 - inst/doc/getting-started.html | 4 inst/doc/project-owners.html | 22 +- tests/testthat/test-cdc.R | 2 tests/testthat/test-connection.R | 134 +++++-------- tests/testthat/test-csv.R | 2 tests/testthat/test-forecast.R | 152 +++++++------- tests/testthat/test-job.R | 75 +++---- tests/testthat/test-model.R | 234 ++++++++++------------- tests/testthat/test-project.R | 396 ++++++++++++++++++--------------------- tests/testthat/test-quantile.R | 2 17 files changed, 523 insertions(+), 586 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>. Functio [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian M Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.9-0 dated 2024-12-20 and 1.9-1 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 9 +++++++++ inst/doc/disclosure.pdf |binary inst/doc/inference.Rnw | 8 +++----- inst/doc/inference.pdf |binary inst/doc/synthpop.pdf |binary inst/doc/utility.pdf |binary man/synthpop-package.Rd | 4 ++-- vignettes/inference.Rnw | 8 +++----- 10 files changed, 30 insertions(+), 25 deletions(-)
Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between rollupTree versions 0.2.0 dated 2025-02-04 and 0.3.0 dated 2025-03-06
DESCRIPTION | 6 +- MD5 | 22 +++++---- NAMESPACE | 1 NEWS.md | 11 ++-- R/rollup.R | 20 +++++++- R/test_dag.R |only README.md | 4 + data/test_dag.rda |only inst/doc/rollupTree.Rmd | 2 inst/doc/rollupTree.html | 6 ++ man/default_validate_dag.Rd |only man/test_dag.Rd |only tests/testthat/test-rollup.R | 103 +++++++++++++++++++++++++++++++++++++++++++ vignettes/rollupTree.Rmd | 2 14 files changed, 159 insertions(+), 18 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a
penalized likelihood estimation on the hazard function but also a
parametric estimation can be fit using this R package: 1) A shared
frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can
be studied. 2) Additive frailty models for proportional hazard models
with two correlated random effects (intercept random effect with
random slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma random
effects. 4) Joint frailty models in the context of the joint
modelling for recurrent events with terminal event for clustered data
or not. A joint frailty model for two semi-competing risks and
clustered data is also proposed. 5) Joint general frailty models in
the context of the joint modelling for recurrent events with terminal
event data with two independent frailty terms. 6) Joint Neste [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.6.5 dated 2024-12-14 and 3.7.0 dated 2025-03-06
DESCRIPTION | 147 ++++++++++++++++++++++++++---------------- MD5 | 26 ++++--- NAMESPACE | 18 +++++ NEWS | 31 +++++--- R/frailtyDesign.R |only R/frailtypack-package.R | 20 ++++- R/print.frailtyDesign.R |only R/summary.frailtyDesign.R |only build/vignette.rds |binary inst/doc/Package_summary.Rmd | 30 ++++---- inst/doc/Package_summary.html | 123 ++++++++++++++++++++--------------- man/frailtyDesign.Rd |only man/frailtypack-package.Rd | 17 ++++ man/print.frailtyDesign.Rd |only man/print.prediction.Rd | 62 ++++++++--------- man/summary.frailtyDesign.Rd |only vignettes/Package_summary.Rmd | 30 ++++---- 17 files changed, 315 insertions(+), 189 deletions(-)
Title: Analyse Open-Ended Survey Responses in Finnish
Description: Annotates Finnish textual survey responses into CoNLL-U format using Finnish treebanks from <https://universaldependencies.org/format.html> using UDPipe as described in Straka and Straková (2017) <doi:10.18653/v1/K17-3009>. Formatted data is then analysed using single or comparison n-gram plots, wordclouds, summary tables and Concept Network plots. The Concept Network plots use the TextRank algorithm as outlined in Mihalcea, Rada & Tarau, Paul (2004) <https://aclanthology.org/W04-3252/>.
Author: Adeline Clarke [cre, aut],
Krista Lagus [aut],
Katja Laine [aut],
Maria Litova [aut],
Matti Nelimarkka [aut],
Joni Oksanen [aut],
Jaakko Peltonen [aut],
Tuukka Oikarinen [aut],
Jani-Matti Tirkkonen [aut],
Ida Toivanen [aut],
Maria Valaste [aut],
Shan [...truncated...]
Maintainer: Adeline Clarke <adelinepclarke@gmail.com>
Diff between finnsurveytext versions 2.1.0 dated 2024-11-08 and 2.1.1 dated 2025-03-06
DESCRIPTION | 6 MD5 | 56 ++++---- NEWS.md | 4 R/01_prepare.R | 30 ++-- R/01b_prepare_svydesign.R | 26 ++- R/02_data_exploration.R | 35 +++-- R/03_concept_network.R | 4 R/04_comparison_functions.R | 4 README.md | 16 +- inst/doc/Overview-PackageTutorial.R | 2 inst/doc/Overview-PackageTutorial.Rmd | 20 ++ inst/doc/Overview-PackageTutorial.html | 112 ++++++++++------ inst/doc/ReadMe.Rmd | 16 +- inst/doc/ReadMe.html | 27 +++ man/fst_find_stopwords.Rd | 2 man/fst_format.Rd | 9 - man/fst_format_svydesign.Rd | 10 - man/fst_freq_table.Rd | 2 man/fst_prepare.Rd | 13 + man/fst_prepare_svydesign.Rd | 16 +- man/fst_rm_stop_punct.Rd | 6 vignettes/Overview-PackageTutorial.Rmd | 20 ++ vignettes/ReadMe.Rmd | 16 +- vignettes/web_only/Extra-AnalysingOtherLanguages.Rmd | 109 +++++++++------ vignettes/web_only/Extra-UseWithSurveyPackage.Rmd | 3 vignettes/web_only/InDetail1-DataPreparation.Rmd | 15 +- vignettes/web_only/InDetail2-DataExploration.Rmd | 2 vignettes/web_only/InDetail3-ConceptNetworkOverview.Rmd | 6 vignettes/web_only/InDetail6-AnalysisExample2.Rmd | 1 29 files changed, 375 insertions(+), 213 deletions(-)
More information about finnsurveytext at CRAN
Permanent link
Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate
spectra for use in teaching or testing. 2. Functions to process files created by
'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson [aut, cre]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.2.7 dated 2017-07-26 and 0.3.1 dated 2025-03-06
SpecHelpers-0.2.7/SpecHelpers/inst |only SpecHelpers-0.3.1/SpecHelpers/DESCRIPTION | 20 ++++--- SpecHelpers-0.3.1/SpecHelpers/MD5 | 42 +++++++-------- SpecHelpers-0.3.1/SpecHelpers/NAMESPACE | 1 SpecHelpers-0.3.1/SpecHelpers/NEWS | 5 + SpecHelpers-0.3.1/SpecHelpers/R/CIExyz.R | 5 + SpecHelpers-0.3.1/SpecHelpers/R/SpecHelpers-package.R | 3 - SpecHelpers-0.3.1/SpecHelpers/R/emSpectrum.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/getGamutValues.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/multiplet.R |only SpecHelpers-0.3.1/SpecHelpers/R/plotCIEchrom.R | 4 - SpecHelpers-0.3.1/SpecHelpers/R/prepCIEgradient.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/sysdata.rda |binary SpecHelpers-0.3.1/SpecHelpers/build |only SpecHelpers-0.3.1/SpecHelpers/data/CIExyz.RData |binary SpecHelpers-0.3.1/SpecHelpers/man/CIExyz.Rd | 17 +++--- SpecHelpers-0.3.1/SpecHelpers/man/SpecHelpers-package.Rd | 8 ++ SpecHelpers-0.3.1/SpecHelpers/man/getGamutValues.Rd | 1 SpecHelpers-0.3.1/SpecHelpers/man/makeSpec.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/multiplet.Rd |only SpecHelpers-0.3.1/SpecHelpers/man/plot2DNMRspec.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/plotCIEchrom.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/plotNMRspec.Rd | 13 +++- SpecHelpers-0.3.1/SpecHelpers/man/qMS.Rd | 3 - 24 files changed, 109 insertions(+), 55 deletions(-)
Title: TK Rplot
Description: Simple mechanism for placing R graphics in a Tk widget.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between tkrplot versions 0.0-27 dated 2022-10-18 and 0.0-29 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/TkRplot.Rd | 7 +++++++ src/tcltkimg.c | 10 ++++++---- 4 files changed, 19 insertions(+), 10 deletions(-)
Title: Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Description: Implementation of methods for estimation of quantitative maps
from Multi-Parameter Mapping (MPM) acquisitions (Weiskopf et al. (2013)
<doi:10.3389/fnins.2013.00095>) and analysis of Inversion Recovery MRI data.
Usage of the package is described in
Polzehl and Tabelow (2023),
"Magnetic Resonance Brain Imaging", 2nd Edition, Chapter 6 and 7, Springer, Use R! Series.
<doi:10.1007/978-3-031-38949-8>.
J. Polzehl and K. Tabelow (2023), "Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data."
<doi:10.20347/WIAS.DATA.6> provides extensive example code and data.
Author: Joerg Polzehl [aut],
Karsten Tabelow [aut, cre],
WIAS Berlin [cph, fnd]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between qMRI versions 1.2.7.8 dated 2024-12-09 and 1.2.7.9 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- build/partial.rdb |binary inst/doc/IRMRI-Example.R | 2 +- inst/doc/IRMRI-Example.Rnw | 2 +- inst/doc/IRMRI-Example.pdf |binary inst/doc/qMRI-Example.pdf |binary man/estimateIR.Rd | 2 +- man/estimateIRfluid.Rd | 2 +- man/estimateIRsolid.Rd | 2 +- man/estimateIRsolidfixed.Rd | 2 +- man/readIRData.Rd | 2 +- man/smoothIRSolid.Rd | 2 +- vignettes/IRMRI-Example-2.pdf |binary vignettes/IRMRI-Example-9.pdf |binary vignettes/IRMRI-Example.Rnw | 2 +- vignettes/qMRI-Example-11.pdf |binary vignettes/qMRI-Example-8.pdf |binary 18 files changed, 30 insertions(+), 30 deletions(-)
Title: Simulation of Matrix Population Models with Defined Life History
Characteristics
Description: Allows users to simulate matrix population models with
particular characteristics based on aspects of life history such as
mortality trajectories and fertility trajectories. Also allows the
exploration of sampling error due to small sample size.
Author: Owen Jones [aut, cre]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between mpmsim versions 3.1.0 dated 2024-10-12 and 3.2.0 dated 2025-03-06
mpmsim-3.1.0/mpmsim/R/generate_mpm_set.R |only mpmsim-3.1.0/mpmsim/R/random_mpm.R |only mpmsim-3.1.0/mpmsim/man/generate_mpm_set.Rd |only mpmsim-3.1.0/mpmsim/man/random_mpm.Rd |only mpmsim-3.1.0/mpmsim/tests/testthat/test-generate_mpm_set.R |only mpmsim-3.1.0/mpmsim/tests/testthat/test-random_mpm.R |only mpmsim-3.2.0/mpmsim/DESCRIPTION | 10 - mpmsim-3.2.0/mpmsim/MD5 | 65 +++--- mpmsim-3.2.0/mpmsim/NAMESPACE | 2 mpmsim-3.2.0/mpmsim/NEWS.md | 5 mpmsim-3.2.0/mpmsim/R/make_leslie_mpm.R | 11 + mpmsim-3.2.0/mpmsim/R/plot_matrix.R | 6 mpmsim-3.2.0/mpmsim/R/rand_lefko_mpm.R | 13 + mpmsim-3.2.0/mpmsim/R/rand_lefko_set.R | 48 ++++- mpmsim-3.2.0/mpmsim/R/rand_leslie_set.R | 60 +++--- mpmsim-3.2.0/mpmsim/README.md | 55 +++-- mpmsim-3.2.0/mpmsim/build/partial.rdb |binary mpmsim-3.2.0/mpmsim/build/vignette.rds |binary mpmsim-3.2.0/mpmsim/inst/WORDLIST | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_lefkovitch_models.Rmd | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_lefkovitch_models.html | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.R | 9 mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.Rmd | 20 +- mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.html | 23 +- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.R | 30 +-- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.Rmd | 44 ++-- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.html | 94 +++++----- mpmsim-3.2.0/mpmsim/man/figures/logo_mpmsim.png |only mpmsim-3.2.0/mpmsim/man/make_leslie_mpm.Rd | 12 + mpmsim-3.2.0/mpmsim/man/model_fecundity.Rd | 8 mpmsim-3.2.0/mpmsim/man/rand_lefko_mpm.Rd | 15 + mpmsim-3.2.0/mpmsim/man/rand_lefko_set.Rd | 36 ++- mpmsim-3.2.0/mpmsim/man/rand_leslie_set.Rd | 21 +- mpmsim-3.2.0/mpmsim/tests/testthat/test-rand_lefko_set.R | 10 - mpmsim-3.2.0/mpmsim/vignettes/generating_lefkovitch_models.Rmd | 4 mpmsim-3.2.0/mpmsim/vignettes/generating_leslie_models.Rmd | 20 +- mpmsim-3.2.0/mpmsim/vignettes/sampling_error_propagation.Rmd | 44 ++-- 37 files changed, 389 insertions(+), 288 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre],
Simon Urbanek [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.10.7 dated 2025-01-08 and 0.10.8 dated 2025-03-06
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS.md | 1 man/ModeC.Rd | 2 - src/fastmatch_fastmatch.c | 59 ++++++++++++++++++++++++---------------------- 5 files changed, 41 insertions(+), 37 deletions(-)
Title: Download Colombian Demographic, Climate and Geospatial Data
Description: Downloads wrangled Colombian socioeconomic, geospatial,population
and climate data from DANE <https://www.dane.gov.co/> (National
Administrative Department of Statistics) and IDEAM (Institute of Hydrology,
Meteorology and Environmental Studies). It solves the problem of Colombian
data being issued in different web pages and sources by using functions that
allow the user to select the desired database and download it without having
to do the exhausting acquisition process.
Author: Maria Camila Tavera-Cifuentes [aut, cre, cph]
,
Julian Otero [aut, cph] ,
Natalia Nino-Machado [ctb] ,
Catalina Gonzalez-Uribe [ctb] ,
Juan Manuel Cordovez [ctb] ,
Hugo Gruson [rev] ,
Chris Hartgerink [rev] ,
Karim Mane [rev] ,
Joshua W. Lambert [rev [...truncated...]
Maintainer: Maria Camila Tavera-Cifuentes <mc.tavera@uniandes.edu.co>
Diff between ColOpenData versions 0.3.1 dated 2024-10-30 and 1.0.0 dated 2025-03-06
DESCRIPTION | 16 MD5 | 56 NEWS.md | 34 R/download_climate.R | 640 +- R/download_demographic.R | 14 R/download_geospatial.R | 255 R/download_population_projections.R | 222 README.md | 56 build/vignette.rds |binary inst/WORDLIST | 247 inst/doc/climate_data.Rmd | 2 inst/doc/climate_data.html | 4 inst/doc/demographic_data.Rmd | 2 inst/doc/demographic_data.html | 4 inst/doc/design_principles.R |only inst/doc/design_principles.Rmd |only inst/doc/design_principles.html |only inst/doc/documentation_and_dictionaries.Rmd | 6 inst/doc/documentation_and_dictionaries.html | 21 inst/doc/geospatial_data.Rmd | 2 inst/doc/geospatial_data.html | 4 tests/testthat/_snaps/download_climate.md | 452 - tests/testthat/_snaps/download_demographic.md | 2484 ++++---- tests/testthat/_snaps/download_geospatial.md | 30 tests/testthat/_snaps/download_population_projections.md | 4400 +++++++-------- tests/testthat/_snaps/merge_geo_demographic.md | 108 vignettes/climate_data.Rmd | 2 vignettes/demographic_data.Rmd | 2 vignettes/design_principles.Rmd |only vignettes/documentation_and_dictionaries.Rmd | 6 vignettes/geospatial_data.Rmd | 2 31 files changed, 4598 insertions(+), 4473 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle [aut, cre]
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.3-3 dated 2023-11-16 and 2.3-4 dated 2025-03-06
DESCRIPTION | 15 MD5 | 70 +-- NAMESPACE | 36 + R/aictab.R | 132 ++++++ R/anovaOD.R | 237 +++++++++++ R/bictab.R | 102 ++++ R/detHist.R | 390 +++++++++++++++++-- R/extractCN.R | 3 R/extractX.R | 282 +++++++++++++ R/importance.R | 181 ++++++++ R/mb.gof.test.R | 4 R/modavg.R | 612 +++++++++++++++++++++++++++++ R/modavgEffect.R | 528 +++++++++++++++++++++++++ R/modavgPred.R | 780 ++++++++++++++++++++++++++++++++++++++ R/modavgShrink.R | 359 +++++++++++++++++ R/summaryOD.R | 121 +++++ build/vignette.rds |binary inst/NEWS | 8 inst/NEWS.Rd | 21 - inst/doc/AICcmodavg-unmarked.R | 16 inst/doc/AICcmodavg-unmarked.Rnw | 11 inst/doc/AICcmodavg-unmarked.pdf |binary inst/doc/AICcmodavg.pdf |binary man/AICcmodavg-package.Rd | 20 man/aictab.Rd | 8 man/anovaOD.Rd | 8 man/bictab.Rd | 10 man/detHist.Rd | 33 + man/extractX.Rd | 69 +-- man/importance.Rd | 22 - man/modavg.Rd | 42 +- man/modavgEffect.Rd | 134 +++++- man/modavgPred.Rd | 123 +++++ man/modavgShrink.Rd | 49 +- man/summaryOD.Rd | 14 vignettes/AICcmodavg-unmarked.Rnw | 11 36 files changed, 4221 insertions(+), 230 deletions(-)
Title: 'date' C++ Header Library for Date and Time Functionality
Description: A header-only C++ library is provided with support
for dates, time zones, ISO weeks, Julian dates, and Islamic dates.
'date' offers extensive date and time functionality for the C++11,
C++14 and C++17 standards and was written by Howard Hinnant and released
under the MIT license. A slightly modified version has been accepted
(along with 'tz.h') as part of C++20. This package regroups all
header files from the upstream repository by Howard Hinnant so that
other R packages can use them in their C++ code. At present, few of
the types have explicit 'Rcpp' wrappers though these may be added as
needed.
Author: Dirk Eddelbuettel [aut, cre] ,
Howard Hinnant [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDate versions 0.0.4 dated 2024-10-14 and 0.0.5 dated 2025-03-06
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ inst/include/date.h | 8 ++++---- inst/include/islamic.h | 8 ++++---- inst/include/iso_week.h | 4 ++-- inst/include/julian.h | 8 ++++---- inst/include/solar_hijri.h | 8 ++++---- inst/include/tz.h | 12 ++++++------ 11 files changed, 67 insertions(+), 38 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/cctest.R | 2 +- man/cctest.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre]
,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.0.1 dated 2025-02-27 and 1.0.2 dated 2025-03-06
DESCRIPTION | 32 - MD5 | 37 - R/datatableInternal.R | 140 ++-- R/formatEstimateValue.R | 2 R/mockResults.R | 5 R/plot.R | 4 R/plottingThemes.R | 2 R/utilities.R | 550 +++++++++-------- R/visOmopTable.R | 536 ++++++++--------- R/visTable.R | 389 ++++++------ inst/doc/a01_tables.html | 925 +++++++++++++++--------------- inst/doc/a02_plots.R | 6 man/visOmopResults-package.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-datatableInternal.R |only tests/testthat/test-formatEstimateName.R | 4 tests/testthat/test-formatEstimateValue.R | 4 tests/testthat/test-formatTable.R | 181 ++--- tests/testthat/test-visOmopTable.R | 732 ++++++++++++----------- tests/testthat/test-visTable.R | 297 ++++----- 20 files changed, 1974 insertions(+), 1874 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph]
,
Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Diff between snvecR versions 3.10.0 dated 2025-03-01 and 3.10.1 dated 2025-03-06
snvecR-3.10.0/snvecR/man/PT-ZB18a.Rd |only snvecR-3.10.0/snvecR/man/ZB23.Rxx.Rd |only snvecR-3.10.1/snvecR/DESCRIPTION | 6 snvecR-3.10.1/snvecR/MD5 | 33 ++- snvecR-3.10.1/snvecR/NEWS.md | 38 +++- snvecR-3.10.1/snvecR/R/data.R | 7 snvecR-3.10.1/snvecR/R/get_solution.R | 34 ++- snvecR-3.10.1/snvecR/README.md | 102 ++++++++++- snvecR-3.10.1/snvecR/build/vignette.rds |binary snvecR-3.10.1/snvecR/inst/doc/analyze_grid_td-ed.html | 112 ++++++------- snvecR-3.10.1/snvecR/inst/doc/compare_with_c.R |only snvecR-3.10.1/snvecR/inst/doc/compare_with_c.Rmd |only snvecR-3.10.1/snvecR/inst/doc/compare_with_c.html |only snvecR-3.10.1/snvecR/man/PT_ZB18a.Rd |only snvecR-3.10.1/snvecR/man/ZB23.Rd |only snvecR-3.10.1/snvecR/man/get_solution.Rd | 8 snvecR-3.10.1/snvecR/tests/testthat/_snaps/get_solution.md | 73 ++++++++ snvecR-3.10.1/snvecR/tests/testthat/_snaps/snvec.md | 64 +++++++ snvecR-3.10.1/snvecR/tests/testthat/test-get_solution.R | 14 + snvecR-3.10.1/snvecR/tests/testthat/test-globals.R |only snvecR-3.10.1/snvecR/tests/testthat/test-snvec.R | 25 ++ snvecR-3.10.1/snvecR/vignettes/compare_with_c.Rmd |only 22 files changed, 387 insertions(+), 129 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Andrea Gilardi [ctb] ,
Shane Saunders [cph] ,
Stanislaw Adaszewski [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.4.1 dated 2024-07-07 and 0.4.2 dated 2025-03-06
DESCRIPTION | 12 +- MD5 | 118 ++++++++++---------- NEWS.md | 18 ++- R/centrality.R | 2 R/dists-nearest.R | 14 -- R/dists.R | 108 +++++++++++------- R/flows.R | 50 ++++++-- R/fund-cycles.R | 1 R/graph-contraction.R | 74 +++++++----- R/graph-conversion.R | 7 + R/graph-functions-misc.R | 35 ++++++ R/graph-functions.R | 11 + R/match-points.R | 7 - R/times.R | 10 - R/weight-streetnet.R | 186 +++++++++++++++++++++++--------- README.md | 47 +++++++- build/vignette.rds |binary inst/doc/dists-categorical.R | 2 inst/doc/dists-categorical.html | 18 +-- inst/doc/dodgr.R | 86 +++++++------- inst/doc/dodgr.html | 89 ++++++--------- inst/doc/flows.R | 72 ++++++------ inst/doc/flows.html | 8 - inst/doc/parallel.R | 2 inst/doc/parallel.html | 4 inst/doc/times.R | 28 ++-- inst/doc/times.html | 8 - man/dodgr.Rd | 1 man/dodgr_centrality.Rd | 2 man/dodgr_distances.Rd | 100 ++++++++++------- man/dodgr_dists.Rd | 100 ++++++++++------- man/dodgr_dists_categorical.Rd | 17 ++ man/dodgr_dists_nearest.Rd | 45 ++++++- man/dodgr_flows_aggregate.Rd | 34 ++++- man/dodgr_flows_disperse.Rd | 10 + man/dodgr_flows_si.Rd | 33 ++++- man/dodgr_times.Rd | 95 +++++++++------- man/dodgr_uncontract_graph.Rd | 13 ++ man/weight_streetnet.Rd | 140 ++++++++++++++++-------- src/deduplicate.cpp | 5 src/heaps/bheap.cpp | 1 src/heaps/fheap.cpp | 1 src/heaps/heap23.cpp | 1 src/heaps/triheap.cpp | 1 src/heaps/triheap_ext.cpp | 1 tests/testthat/test-cache.R | 45 ++++--- tests/testthat/test-centrality.R | 6 - tests/testthat/test-cycles.R | 2 tests/testthat/test-deduplicate.R | 4 tests/testthat/test-dists-categorical.R | 14 +- tests/testthat/test-dists-nearest.R | 6 - tests/testthat/test-dists.R | 82 +++++++++----- tests/testthat/test-flows.R | 6 - tests/testthat/test-graph-conversion.R | 6 - tests/testthat/test-graph-fns.R | 27 +++- tests/testthat/test-iso.R | 10 - tests/testthat/test-match-pts-fns.R | 7 - tests/testthat/test-save-load.R | 6 - tests/testthat/test-sc.R | 8 - tests/testthat/test-streetnet.R | 27 +++- 60 files changed, 1191 insertions(+), 682 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 0.0.7 dated 2025-03-01 and 0.0.8 dated 2025-03-06
DESCRIPTION | 6 +- MD5 | 36 ++++++++--------- NEWS.md | 7 +-- R/gradient.R | 15 +++---- R/helpers.R | 3 - R/zzz.R | 10 +++- build/partial.rdb |binary inst/CITATION | 16 +++---- inst/doc/compatibility-with-numDeriv.R | 13 +++--- inst/doc/compatibility-with-numDeriv.Rmd | 23 +++++++--- inst/doc/compatibility-with-numDeriv.html | 63 ++++++++++++++++++++---------- inst/doc/fast-and-accurate.html | 2 inst/doc/step-size-selection.html | 2 man/GenD.Rd | 2 man/Grad.Rd | 2 man/Jacobian.Rd | 2 man/checkDimensions.Rd | 2 tests/testthat/Rplots.pdf |binary vignettes/compatibility-with-numDeriv.Rmd | 23 +++++++--- 19 files changed, 136 insertions(+), 91 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.3 dated 2024-08-28 and 1.3.4 dated 2025-03-06
lsirm12pl-1.3.3/lsirm12pl/data/BFPT.csv |only lsirm12pl-1.3.3/lsirm12pl/data/TDRI.csv |only lsirm12pl-1.3.4/lsirm12pl/DESCRIPTION | 18 lsirm12pl-1.3.4/lsirm12pl/MD5 | 10 lsirm12pl-1.3.4/lsirm12pl/R/lsirm.R | 561 +++++++++++++---- lsirm12pl-1.3.4/lsirm12pl/R/lsirm1pl_fixed_gamma_mar.R | 300 ++++----- lsirm12pl-1.3.4/lsirm12pl/data/BFPT.csv.gz |only lsirm12pl-1.3.4/lsirm12pl/data/TDRI.csv.gz |only 8 files changed, 613 insertions(+), 276 deletions(-)
Title: Data Visualisation on 'Lifemap' Tree
Description: Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Author: Cassandra Bompard [aut],
Damien M. de Vienne [aut] ,
Julien Barnier [aut] ,
Aurelie Siberchicot [ctb, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between LifemapR versions 1.1.4 dated 2024-07-31 and 1.1.5 dated 2025-03-06
DESCRIPTION | 21 - MD5 | 38 +- R/build_Lifemap.R | 178 ++++----- R/create_matrix.R | 19 - R/data.R | 246 ++++++------- R/display_map.R | 50 +- R/draw_Lifemap.R | 850 +++++++++++++++++++++++----------------------- R/lifemap_obj.R | 16 R/lm_branches.R | 6 R/lm_piecharts.R | 1 R/make_newick.R | 6 README.md | 55 +- build/vignette.rds |binary inst/doc/runLifemapR.R | 116 +++--- inst/doc/runLifemapR.Rmd | 15 inst/doc/runLifemapR.html | 29 - man/build_Lifemap.Rd | 6 man/display_map.Rd | 10 man/draw_Lifemap.Rd | 4 vignettes/runLifemapR.Rmd | 15 20 files changed, 835 insertions(+), 846 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.19.0 dated 2025-01-29 and 1.20.0 dated 2025-03-06
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Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Michael Chirico [aut, cre],
Jens Oehlschlaegel [aut],
Brian Ripley [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between bit versions 4.5.0.1 dated 2024-12-03 and 4.6.0 dated 2025-03-06
bit-4.5.0.1/bit/NEWS |only bit-4.5.0.1/bit/inst/doc/bit-demo.pdf |only bit-4.5.0.1/bit/inst/doc/bit-performance.pdf |only bit-4.5.0.1/bit/inst/doc/bit-usage.pdf |only bit-4.6.0/bit/DESCRIPTION | 32 bit-4.6.0/bit/MD5 | 201 - bit-4.6.0/bit/NEWS.md |only bit-4.6.0/bit/R/attrutil.R | 106 bit-4.6.0/bit/R/bit-package.R | 13 bit-4.6.0/bit/R/bit.R | 3100 +++++++++++------------- bit-4.6.0/bit/R/bitsort.R | 755 ++--- bit-4.6.0/bit/R/chunkutil.R | 519 +--- bit-4.6.0/bit/R/clone.R | 43 bit-4.6.0/bit/R/generics.R | 410 +-- bit-4.6.0/bit/R/integerutil.R | 116 bit-4.6.0/bit/R/merge.R | 300 +- bit-4.6.0/bit/R/rle.R | 196 - bit-4.6.0/bit/R/timeutil.R | 72 bit-4.6.0/bit/R/zzz.R | 41 bit-4.6.0/bit/build/vignette.rds |binary bit-4.6.0/bit/inst/doc/bit-demo.R | 28 bit-4.6.0/bit/inst/doc/bit-demo.Rmd | 39 bit-4.6.0/bit/inst/doc/bit-demo.html |only bit-4.6.0/bit/inst/doc/bit-performance.R | 543 ++-- bit-4.6.0/bit/inst/doc/bit-performance.Rmd | 556 ++-- bit-4.6.0/bit/inst/doc/bit-performance.html |only bit-4.6.0/bit/inst/doc/bit-usage.R | 276 +- bit-4.6.0/bit/inst/doc/bit-usage.Rmd | 335 +- bit-4.6.0/bit/inst/doc/bit-usage.html |only bit-4.6.0/bit/man/CoercionToStandard.Rd | 16 bit-4.6.0/bit/man/Extract.Rd | 28 bit-4.6.0/bit/man/Metadata.Rd | 13 bit-4.6.0/bit/man/PhysVirt.Rd | 11 bit-4.6.0/bit/man/Sorting.Rd | 68 bit-4.6.0/bit/man/Summaries.Rd | 43 bit-4.6.0/bit/man/as.bit.Rd | 36 bit-4.6.0/bit/man/as.bitwhich.Rd | 37 bit-4.6.0/bit/man/as.booltype.Rd | 5 bit-4.6.0/bit/man/as.character.bit.Rd | 2 bit-4.6.0/bit/man/as.character.bitwhich.Rd | 2 bit-4.6.0/bit/man/as.ri.Rd | 10 bit-4.6.0/bit/man/as.which.Rd | 32 bit-4.6.0/bit/man/bbatch.Rd | 14 bit-4.6.0/bit/man/bit-package.Rd | 9 bit-4.6.0/bit/man/bit.Rd | 8 bit-4.6.0/bit/man/bit_in.Rd | 10 bit-4.6.0/bit/man/bit_init.Rd | 6 bit-4.6.0/bit/man/bit_rangediff.Rd | 18 bit-4.6.0/bit/man/bit_setops.Rd | 14 bit-4.6.0/bit/man/bit_sort.Rd | 14 bit-4.6.0/bit/man/bit_sort_unique.Rd | 34 bit-4.6.0/bit/man/bit_unidup.Rd | 62 bit-4.6.0/bit/man/bitsort.Rd | 11 bit-4.6.0/bit/man/bitwhich.Rd | 36 bit-4.6.0/bit/man/bitwhich_representation.Rd | 6 bit-4.6.0/bit/man/booltype.Rd | 33 bit-4.6.0/bit/man/booltypes.Rd | 27 bit-4.6.0/bit/man/c.booltype.Rd | 8 bit-4.6.0/bit/man/chunk.Rd | 30 bit-4.6.0/bit/man/chunks.Rd | 28 bit-4.6.0/bit/man/clone.Rd | 20 bit-4.6.0/bit/man/copy_vector.Rd | 9 bit-4.6.0/bit/man/countsort.Rd | 8 bit-4.6.0/bit/man/firstNA.Rd | 4 bit-4.6.0/bit/man/get_length.Rd | 3 bit-4.6.0/bit/man/getsetattr.Rd | 28 bit-4.6.0/bit/man/in.bitwhich.Rd | 11 bit-4.6.0/bit/man/intrle.Rd | 40 bit-4.6.0/bit/man/is.booltype.Rd | 20 bit-4.6.0/bit/man/is.na.bit.Rd | 6 bit-4.6.0/bit/man/length.bit.Rd | 127 bit-4.6.0/bit/man/maxindex.Rd | 36 bit-4.6.0/bit/man/merge_rev.Rd | 168 - bit-4.6.0/bit/man/print.bitwhich.Rd | 2 bit-4.6.0/bit/man/quicksort2.Rd | 8 bit-4.6.0/bit/man/quicksort3.Rd | 8 bit-4.6.0/bit/man/range_na.Rd | 15 bit-4.6.0/bit/man/range_nanozero.Rd | 16 bit-4.6.0/bit/man/range_sortna.Rd | 30 bit-4.6.0/bit/man/rep.booltype.Rd | 12 bit-4.6.0/bit/man/repeat.time.Rd | 10 bit-4.6.0/bit/man/repfromto.Rd | 8 bit-4.6.0/bit/man/rev.booltype.Rd | 6 bit-4.6.0/bit/man/reverse_vector.Rd | 4 bit-4.6.0/bit/man/ri.Rd | 6 bit-4.6.0/bit/man/rlepack.Rd | 25 bit-4.6.0/bit/man/still.identical.Rd | 4 bit-4.6.0/bit/man/str.bit.Rd | 2 bit-4.6.0/bit/man/str.bitwhich.Rd | 2 bit-4.6.0/bit/man/symdiff.Rd | 12 bit-4.6.0/bit/man/unattr.Rd | 4 bit-4.6.0/bit/man/vecseq.Rd | 32 bit-4.6.0/bit/man/xor.Rd | 84 bit-4.6.0/bit/src/attrutil.c | 4 bit-4.6.0/bit/src/integerutil.c | 4 bit-4.6.0/bit/src/merge.h | 8 bit-4.6.0/bit/tests/ff_tests.R |only bit-4.6.0/bit/tests/testthat.R | 4 bit-4.6.0/bit/tests/testthat/test-bit.R | 611 ++-- bit-4.6.0/bit/tests/testthat/test-bitsort.R | 394 +-- bit-4.6.0/bit/tests/testthat/test-merge.R | 276 +- bit-4.6.0/bit/tests/testthat/test-old-regtest.R | 369 +- bit-4.6.0/bit/tests/testthat/test-rle.R | 98 bit-4.6.0/bit/vignettes/bit-demo.Rmd | 39 bit-4.6.0/bit/vignettes/bit-performance.Rmd | 556 ++-- bit-4.6.0/bit/vignettes/bit-usage.Rmd | 335 +- 106 files changed, 6141 insertions(+), 5679 deletions(-)
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.1.0 dated 2025-01-07 and 1.1.1 dated 2025-03-06
DESCRIPTION | 6 - MD5 | 18 ++-- NEWS.md | 11 ++- R/extract_opportunities.R | 8 ++ R/run_law.R | 9 ++ R/run_law_model.R | 9 ++ R/run_model.R | 9 ++ README.md | 18 ++-- build/vignette.rds |binary inst/doc/TDLM.html | 168 +++++++++++++++++++++++----------------------- 10 files changed, 149 insertions(+), 107 deletions(-)
Title: CORe Multiple Sclerosis Outcomes Toolkit
Description: Enable operationalized evaluation of disease outcomes in
multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded
clinical data structured in long format. The package is based on the
research developed at Clinical Outcomes Research unit (CORe),
University of Melbourne and Neuroimmunology Centre, Royal Melbourne
Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>.
Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al.
(2022) <doi:10.1111/ene.15406>. Dzau et al. (2023)
<doi:10.1136/jnnp-2023-331748>.
Author: Sifat Sharmin [aut],
Johannes Lorscheider [aut],
Nathaniel Lizak [aut],
Sam Harding-Forrester [aut],
Winston Dzau [aut],
Jannis Mueller [aut],
Izanne Roos [aut],
Tomas Kalincik [aut, cre, cph]
Maintainer: Tomas Kalincik <tomas.kalincik@unimelb.edu.au>
Diff between MSoutcomes versions 0.2.0 dated 2024-02-29 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 +++++++++----- LICENSE | 2 +- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/CDEseq.R | 59 ++++++++++++++++++++++++++++++++++++----------------------- R/CDI.R | 34 +++++++++++++++++++++------------- R/CDW.R | 34 +++++++++++++++++++++------------- R/PIRA.R | 34 +++++++++++++++++++++------------- 9 files changed, 130 insertions(+), 76 deletions(-)
Title: PD-Clustering and Related Methods
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Author: Cristina Tortora [aut, cre, cph],
Noe Vidales [aut],
Francesco Palumbo [aut],
Tina Kalra [aut],
Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 2.3.4 dated 2025-02-13 and 2.3.5 dated 2025-03-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PDQ.R | 5 ++--- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Free Knot-Bayesian Model Averaging
Description: Analysis of Bayesian adaptive enrichment clinical trial using Free-Knot Bayesian Model Averaging (FK-BMA) method of Maleyeff et al. (2024) for Gaussian data. Maleyeff, L., Golchi, S., Moodie, E. E. M., & Hudson, M. (2024) "An adaptive enrichment design using Bayesian model averaging for selection and threshold-identification of predictive variables" <doi:10.1093/biomtc/ujae141>.
Author: Lara Maleyeff [aut, cre],
Shirin Golchi [aut],
Erica E. M. Moodie [aut]
Maintainer: Lara Maleyeff <lara.maleyeff@mcgill.ca>
Diff between fkbma versions 0.1.0 dated 2025-01-31 and 0.2.0 dated 2025-03-05
fkbma-0.1.0/fkbma/man/fittedTrtEff.Rd |only fkbma-0.1.0/fkbma/man/predictTrtEff.Rd |only fkbma-0.2.0/fkbma/DESCRIPTION | 6 fkbma-0.2.0/fkbma/MD5 | 44 +- fkbma-0.2.0/fkbma/NAMESPACE | 5 fkbma-0.2.0/fkbma/R/data_generate.R | 4 fkbma-0.2.0/fkbma/R/rjMCMC.R | 81 ++-- fkbma-0.2.0/fkbma/R/s3-methods.R | 495 +++++++++++++------------ fkbma-0.2.0/fkbma/data/simulated_data.rda |binary fkbma-0.2.0/fkbma/man/coef.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/credint.Rd | 7 fkbma-0.2.0/fkbma/man/fitted.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/fittedExposureEff.Rd |only fkbma-0.2.0/fkbma/man/getEffectiveSubspace.Rd | 20 - fkbma-0.2.0/fkbma/man/pip.Rd | 25 - fkbma-0.2.0/fkbma/man/plot.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/plotHistTrace.Rd | 8 fkbma-0.2.0/fkbma/man/predict.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/predictExposureEff.Rd |only fkbma-0.2.0/fkbma/man/print.rjMCMC.Rd | 16 fkbma-0.2.0/fkbma/man/rhats.Rd | 33 - fkbma-0.2.0/fkbma/man/rjMCMC.Rd | 27 - fkbma-0.2.0/fkbma/man/simulated_data.Rd | 2 fkbma-0.2.0/fkbma/man/summary.rjMCMC.Rd | 26 - fkbma-0.2.0/fkbma/tests/testthat/test-rjMCMC.R | 18 25 files changed, 491 insertions(+), 422 deletions(-)
Title: An Extension of the Gap Statistic for Ordinal/Categorical Data
Description: The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.
Author: Jeffrey Miecznikowski [aut],
Eduardo Cortes [aut, cre]
Maintainer: Eduardo Cortes <ecortesg@buffalo.edu>
Diff between DiscreteGapStatistic versions 1.0.0 dated 2024-12-09 and 1.1.2 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 66 +++++------ R/AuxFuns.R | 11 + R/DiscreteClusGapFuns.R | 10 + R/DistanceFuns.R | 76 ++++++++---- R/SimDataFun.R | 3 R/VisualFuns.R | 35 ++++- R/data.R | 13 +- README.md | 185 +++++++++++++++++++------------ man/BhattacharyyaDist.Rd | 2 man/ChisqDist.Rd | 2 man/CramerV.Rd | 2 man/HellingerDist.Rd | 2 man/ResHeatmap.Rd | 21 ++- man/SimData.Rd | 3 man/clusGapDiscr.Rd | 4 man/clusGapDiscr0.Rd | 4 man/clusterFunSel.Rd | 5 man/concussion.Rd | 6 - man/cramersVmod.Rd | 8 - man/dissbhattacharyya.Rd | 8 - man/disschisquare.Rd | 8 - man/disscramerv.Rd | 8 - man/disshamming.Rd | 8 - man/disshellinger.Rd | 8 - man/distanceHeat.Rd | 15 +- man/distancematrix.Rd | 9 - man/figures/README-clusGapDiscrFit-1.png |binary man/figures/README-clusGapDiscrFit-2.png |binary man/figures/README-clusGapDiscrFit-3.png |binary man/findK.Rd | 2 man/kmodesD.Rd | 5 man/likert.heat.plot2.Rd | 8 - man/mass.Rd | 11 - 34 files changed, 320 insertions(+), 234 deletions(-)
More information about DiscreteGapStatistic at CRAN
Permanent link
Title: Tools and Metrics for 3D Surfaces and Objects
Description: A collection of functions for sampling and simulating 3D surfaces and objects
and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity,
second moments of area and volume, and more.
Author: Joshua Madin [aut] ,
Nina Schiettekatte [aut, cre]
Maintainer: Nina Schiettekatte <nina.schiettekatte@gmail.com>
Diff between habtools versions 1.0.7 dated 2024-11-15 and 1.1.1 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 6 +++ R/entropy.R |only R/fd_boxes.R | 6 +-- R/fd_cubes.R | 13 ++++--- R/fd_diagnose.R | 36 +++++++++++--------- R/planar.R | 7 ---- R/rg.R | 2 - R/smv.R | 4 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DEM_intro.html | 6 +-- inst/doc/fractal_intro.html | 76 ++++++++++++++++++++++---------------------- inst/doc/mesh_intro.html | 38 +++++++++++----------- man/entropy.Rd |only man/entropy_1d.Rd |only man/entropy_2d.Rd |only man/entropy_3d.Rd |only man/fd_cubes.Rd | 2 - man/fd_diagnose.Rd | 6 ++- man/smv.Rd | 4 +- 23 files changed, 138 insertions(+), 119 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut] ,
Leonardo Ramirez-Lopez [aut, cre]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.7 dated 2024-02-16 and 0.2.8 dated 2025-03-05
prospectr-0.2.7/prospectr/build/prospectr.pdf |only prospectr-0.2.8/prospectr/DESCRIPTION | 29 +++++++---- prospectr-0.2.8/prospectr/LICENSE | 2 prospectr-0.2.8/prospectr/MD5 | 30 +++++------ prospectr-0.2.8/prospectr/NEWS.md | 15 +++++ prospectr-0.2.8/prospectr/R/gapDer.R | 10 +-- prospectr-0.2.8/prospectr/R/kenstone.R | 5 + prospectr-0.2.8/prospectr/README.md | 14 ++--- prospectr-0.2.8/prospectr/build/stage23.rdb |only prospectr-0.2.8/prospectr/build/vignette.rds |binary prospectr-0.2.8/prospectr/inst/doc/prospectr.R | 46 ++++++++--------- prospectr-0.2.8/prospectr/inst/doc/prospectr.html | 54 ++++++++++----------- prospectr-0.2.8/prospectr/man/gapDer.Rd | 6 +- prospectr-0.2.8/prospectr/man/kenStone.Rd | 5 + prospectr-0.2.8/prospectr/man/prospectr-package.Rd | 2 prospectr-0.2.8/prospectr/src/Makevars | 1 prospectr-0.2.8/prospectr/src/Makevars.win | 1 17 files changed, 122 insertions(+), 98 deletions(-)
Title: Power Analysis for PLS Classification
Description: It estimates power and sample size for Partial Least Squares-based methods described in Andreella, et al., (2024), <doi:10.48550/arXiv.2403.10289>.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unitn.it>
Diff between powerPLS versions 0.2.0 dated 2024-09-30 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 ++-- MD5 | 62 +++++++++++++-------- NAMESPACE | 10 +++ NEWS.md | 4 + R/AUCTest.R |only R/F1Test.R |only R/FMTest.R |only R/IDA.R | 25 ++++---- R/PLSc.R | 91 ++++++++++++++----------------- R/R2Test.R | 75 ++++++++++++++----------- R/computePower.R | 136 ++++++++++++++++++++++------------------------- R/computeSampleSize.R | 35 +++++------- R/computeWT.R | 55 ++++++++----------- R/dQ2Test.R |only R/global.R | 2 R/mccTest.R | 113 +++++++++++++++++++++------------------ R/ptPLSc.R | 64 +++++++++++----------- R/repeatedCV_test.R |only R/scoreTest.R | 109 ++++++++++++++++++++----------------- R/sensitivityTest.R |only R/sim_Tscore.R | 25 ++++---- R/sim_XY.R | 99 ++++++++++++++++------------------ R/simulatePilotData.R | 34 ++++++----- R/specificityTest.R |only R/utils.R | 128 ++++++++++++++++++++++++++++++++------------ README.md | 2 man/AUCTest.Rd |only man/F1Test.Rd |only man/FMTest.Rd |only man/PLSc.Rd | 8 +- man/R2Test.Rd | 16 ++++- man/computePower.Rd | 14 ++-- man/computeSampleSize.Rd | 8 +- man/dQ2Test.Rd |only man/mccTest.Rd | 18 ++++-- man/repeatedCV_test.Rd |only man/scoreTest.Rd | 16 ++++- man/sensitivityTest.Rd |only man/specificityTest.Rd |only 39 files changed, 645 insertions(+), 518 deletions(-)
Title: Download Official Data on Brazil's Federal Budget
Description: Allows users to download and analyze official data on Brazil's federal budget through the 'SPARQL' endpoint
provided by the Integrated Budget and Planning System ('SIOP'). This package enables access to detailed information on budget
allocations and expenditures of the federal government, making it easier to analyze and visualize these data. Technical
information on the Brazilian federal budget is available (Portuguese only) at <https://www1.siop.planejamento.gov.br/mto/>.
The 'SIOP' endpoint is available at <https://www1.siop.planejamento.gov.br/sparql/>.
Author: Daniel Gersten Reiss [aut, cre]
,
Bernardo Borba de Andrade [ctb]
,
Gustavo Jose de Guimaraes e Souza [ctb]
,
Ministerio do Planejamento e Orcamento [cph, fnd]
Maintainer: Daniel Gersten Reiss <daniel.reiss@planejamento.gov.br>
Diff between orcamentoBR versions 1.0.2 dated 2025-02-20 and 1.0.3 dated 2025-03-05
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ R/orcamentoBR.R | 8 +++++--- R/quaisDimensoes.R | 4 ++-- man/despesaDetalhada.Rd | 2 ++ man/quaisMembros.Rd | 2 +- man/whichMembers.Rd | 2 +- 7 files changed, 24 insertions(+), 19 deletions(-)
Title: Diagnostic Tools for a Multivariate Negative Binomial Regression
Model
Description: Diagnostic tools as residual analysis, global,
local and total-local influence for the multivariate model
from the random intercept Poisson generalized log gamma model
are available in this package. Including also, the estimation
process by maximum likelihood method, for details see
Fabio, L. C; Villegas, C. L.; Carrasco, J.M.F and de Castro, M. (2023)
<doi:10.1080/03610926.2021.1939380> and Fábio, L. C.; Villegas, C.;
Mamun, A. S. M. A. and Carrasco, J. M. F. (2025) <doi:10.28951/bjb.v43i1.728>.
Author: Jalmar Carrasco [aut, cre],
Cristian Lobos [aut],
Lizandra Fabio [aut]
Maintainer: Jalmar Carrasco <carrascojalmar@gmail.com>
Diff between MNB versions 1.1.0 dated 2022-04-22 and 1.2.0 dated 2025-03-05
DESCRIPTION | 18 - MD5 | 38 +-- R/Local.R | 650 ++++++++++++++++++++++++++-------------------------- R/MNB.R | 217 ++++++++--------- R/enveSim.R | 277 +++++++++++----------- R/estimate.R | 219 ++++++++--------- R/global.R | 180 +++++++------- R/qMNB.R | 215 ++++++++--------- R/rMNB.R | 96 +++---- R/residual.R | 393 +++++++++++++++---------------- man/MNB.Rd | 11 man/alzheimer.Rd | 7 man/envelope.MNB.Rd | 11 man/fit.MNB.Rd | 11 man/global.MNB.Rd | 8 man/local.MNB.Rd | 8 man/qMNB.Rd | 11 man/rMNB.Rd | 4 man/re.MNB.Rd | 11 man/seizures.Rd | 11 20 files changed, 1216 insertions(+), 1180 deletions(-)
Title: Assessing Complex Heterogeneity in Surrogacy
Description: Provides functions to assess and test for complex heterogeneity in the utility of a surrogate marker with respect to multiple baseline covariates, using both a parametric model and a semiparametric two-step model. More details are available in: Knowlton, R., Tian, L., & Parast, L. (2025). "A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker," Statistics in Medicine, 44(5), e70001 <doi:10.1002/sim.70001>. A tutorial for this package can be found at <https://laylaparast.com/home/cohetsurr.html>.
Author: Rebecca Knowlton [aut],
Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between cohetsurr versions 1.0 dated 2024-11-21 and 1.1 dated 2025-03-05
DESCRIPTION | 17 ++-- MD5 | 4 - man/complex.heterogeneity.Rd | 158 +++++++++++++++++++++---------------------- 3 files changed, 90 insertions(+), 89 deletions(-)
Title: Calculate Mass Properties and Uncertainties of Tree Structures
Description: Recursively calculates mass properties (mass, center of mass, moments and products of inertia, and optionally, their uncertainties) for arbitrary decomposition trees. R. L. Zimmerman, J. H. Nakai. (2005) <https://www.sawe.org/product/paper-3360/>).
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between massProps versions 0.2.0 dated 2025-01-30 and 0.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 57 + NAMESPACE | 6 NEWS.md | 17 R/massprops.R | 42 - R/mp_table_small.R |only R/mp_tree_small.R |only R/radii.R |only R/test_unc_table.R |only README.md | 114 +++ data/mp_table_small.rda |only data/mp_tree.rda |binary data/mp_tree_small.rda |only data/test_tree.rda |binary data/test_unc_table.rda |only inst/doc/massProps.R | 142 +++- inst/doc/massProps.Rmd | 692 +++++++++++++++-------- inst/doc/massProps.html | 719 +++++++++++++++--------- man/add_radii_of_gyration.Rd |only man/get_mass_props_and_unc_and_radii.Rd |only man/get_mass_props_and_unc_and_radii_and_unc.Rd |only man/mp_table_small.Rd |only man/mp_tree_small.Rd |only man/rollup_mass_props.Rd | 2 man/rollup_mass_props_and_unc.Rd | 2 man/rollup_mass_props_and_unc_fast.Rd | 2 man/rollup_mass_props_unc.Rd | 4 man/rollup_radii_of_gyration_unc.Rd |only man/set_mass_props_unc.Rd | 2 man/set_radii_of_gyration.Rd |only man/set_radii_of_gyration_unc.Rd |only man/test_unc_table.Rd |only man/validate_mass_props_and_unc_table.Rd | 2 man/validate_mass_props_table.Rd | 2 tests/testthat/test-massProps.R | 1 tests/testthat/test-radii.R |only vignettes/massProps.Rmd | 692 +++++++++++++++-------- vignettes/references.bib | 8 38 files changed, 1709 insertions(+), 803 deletions(-)
Title: Retrieve Data from the Census APIs
Description: A wrapper for the U.S. Census Bureau APIs that returns data frames of
Census data and metadata. Available datasets include the
Decennial Census, American Community Survey, Small Area Health Insurance Estimates,
Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
Author: Hannah Recht [aut, cre]
Maintainer: Hannah Recht <censusapi.rstats@gmail.com>
Diff between censusapi versions 0.8.0 dated 2022-08-09 and 0.9.0 dated 2025-03-05
DESCRIPTION | 13 - MD5 | 36 ++-- NAMESPACE | 3 NEWS.md | 34 +++- R/api-key.R |only R/datasets.R | 2 R/getcensus_functions.R | 371 +++++++++++++++++++++++++++++++--------------- R/makevar_functions.R | 32 ++- R/metadata_functions.R | 250 ++++++++++++++++++++++-------- README.md | 146 +++++++++++++++++- build |only inst |only man/fips.Rd | 2 man/getCensus.Rd | 104 ++++++------ man/getFunction.Rd | 7 man/get_api_key.Rd |only man/has_api_key.Rd |only man/listCensusApis.Rd | 58 ++++++- man/listCensusMetadata.Rd | 128 +++++++++------ man/makeVarlist.Rd | 33 ++-- vignettes |only 21 files changed, 868 insertions(+), 351 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 3.1.0 dated 2025-02-25 and 3.1.1 dated 2025-03-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/Makevars.in | 2 +- src/osx/Makevars | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by
the National 'Phenology' Network (<https://usanpn.org/>), which
includes data on various life history events that occur at specific
times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
Eric R Scott [aut] ,
David LeBauer [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.9.0 dated 2024-08-19 and 1.3.0 dated 2025-03-05
rnpn-1.2.9.0/rnpn/man/check_geo_service.Rd |only rnpn-1.2.9.0/rnpn/man/check_service.Rd |only rnpn-1.2.9.0/rnpn/tests/test-all.R |only rnpn-1.3.0/rnpn/DESCRIPTION | 47 rnpn-1.3.0/rnpn/LICENSE | 4 rnpn-1.3.0/rnpn/MD5 | 194 - rnpn-1.3.0/rnpn/NAMESPACE | 8 rnpn-1.3.0/rnpn/NEWS.md | 78 rnpn-1.3.0/rnpn/R/base-reqs.R |only rnpn-1.3.0/rnpn/R/defunct.R | 12 rnpn-1.3.0/rnpn/R/lookup_names.R | 24 rnpn-1.3.0/rnpn/R/npn_data_download.R | 1460 ++++++------ rnpn-1.3.0/rnpn/R/npn_dataset.R | 21 rnpn-1.3.0/rnpn/R/npn_geoserver.R | 897 +++---- rnpn-1.3.0/rnpn/R/npn_get_species.R | 180 - rnpn-1.3.0/rnpn/R/npn_partner_groups.R | 47 rnpn-1.3.0/rnpn/R/npn_phenophases.R | 269 +- rnpn-1.3.0/rnpn/R/npn_stations.R | 121 rnpn-1.3.0/rnpn/R/release-reminders.R |only rnpn-1.3.0/rnpn/R/rnpn-package.R | 17 rnpn-1.3.0/rnpn/R/test-helpers.R |only rnpn-1.3.0/rnpn/R/utils.R |only rnpn-1.3.0/rnpn/R/zzz.R | 180 - rnpn-1.3.0/rnpn/README.md | 20 rnpn-1.3.0/rnpn/inst/CITATION |only rnpn-1.3.0/rnpn/inst/doc/III_individual_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/II_status_intensity.html | 2 rnpn-1.3.0/rnpn/inst/doc/IV_site_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/I_introduction.html | 2 rnpn-1.3.0/rnpn/inst/doc/VIII_data_cleaning.html | 2 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.R | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.html | 47 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.html | 40 rnpn-1.3.0/rnpn/inst/doc/V_magnitude_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/release-tasks.R |only rnpn-1.3.0/rnpn/man/get_additional_rasters.Rd | 13 rnpn-1.3.0/rnpn/man/npn_abundance_categories.Rd | 11 rnpn-1.3.0/rnpn/man/npn_check_point_cached.Rd | 8 rnpn-1.3.0/rnpn/man/npn_datasets.Rd | 9 rnpn-1.3.0/rnpn/man/npn_download_geospatial.Rd | 35 rnpn-1.3.0/rnpn/man/npn_download_individual_phenometrics.Rd | 183 - rnpn-1.3.0/rnpn/man/npn_download_magnitude_phenometrics.Rd | 155 - rnpn-1.3.0/rnpn/man/npn_download_site_phenometrics.Rd | 207 + rnpn-1.3.0/rnpn/man/npn_download_status_data.Rd | 169 - rnpn-1.3.0/rnpn/man/npn_get_agdd_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_get_common_query_vars.Rd | 5 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_raster.Rd | 42 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_time_series.Rd | 55 rnpn-1.3.0/rnpn/man/npn_get_data.Rd | 28 rnpn-1.3.0/rnpn/man/npn_get_data_by_year.Rd | 63 rnpn-1.3.0/rnpn/man/npn_get_download_url.Rd | 10 rnpn-1.3.0/rnpn/man/npn_get_layer_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_get_phenophases_for_taxon.Rd | 57 rnpn-1.3.0/rnpn/man/npn_get_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_groups.Rd | 20 rnpn-1.3.0/rnpn/man/npn_lookup_names.Rd | 17 rnpn-1.3.0/rnpn/man/npn_merge_geo_data.Rd | 8 rnpn-1.3.0/rnpn/man/npn_pheno_classes.Rd | 12 rnpn-1.3.0/rnpn/man/npn_phenophase_definitions.Rd | 10 rnpn-1.3.0/rnpn/man/npn_phenophase_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_phenophases.Rd | 9 rnpn-1.3.0/rnpn/man/npn_phenophases_by_species.Rd | 21 rnpn-1.3.0/rnpn/man/npn_species.Rd | 57 rnpn-1.3.0/rnpn/man/npn_species_types.Rd | 14 rnpn-1.3.0/rnpn/man/npn_stations.Rd | 6 rnpn-1.3.0/rnpn/man/npn_stations_by_location.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_by_state.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_with_spp.Rd | 8 rnpn-1.3.0/rnpn/man/resolve_six_raster.Rd | 31 rnpn-1.3.0/rnpn/man/rnpn-defunct.Rd | 12 rnpn-1.3.0/rnpn/man/rnpn-package.Rd | 29 rnpn-1.3.0/rnpn/tests/fixtures |only rnpn-1.3.0/rnpn/tests/testthat.R |only rnpn-1.3.0/rnpn/tests/testthat/test-npn-datasets.R | 13 rnpn-1.3.0/rnpn/tests/testthat/test-npn-defunct.R | 15 rnpn-1.3.0/rnpn/tests/testthat/test-npn-geoserver.R | 181 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-get-species.R | 96 rnpn-1.3.0/rnpn/tests/testthat/test-npn-observations.R | 506 +--- rnpn-1.3.0/rnpn/tests/testthat/test-npn-partners.R | 20 rnpn-1.3.0/rnpn/tests/testthat/test-npn-phenophases.R | 154 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-stations.R | 68 rnpn-1.3.0/rnpn/vignettes/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd.orig | 44 86 files changed, 3478 insertions(+), 3020 deletions(-)
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] ,
Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MoEClust versions 1.5.2 dated 2023-12-11 and 1.6.0 dated 2025-03-05
MoEClust-1.5.2/MoEClust/R/MoEClust.R |only MoEClust-1.6.0/MoEClust/DESCRIPTION | 14 MoEClust-1.6.0/MoEClust/MD5 | 66 +- MoEClust-1.6.0/MoEClust/NAMESPACE | 7 MoEClust-1.6.0/MoEClust/R/Functions.R | 452 +++++++++++-------- MoEClust-1.6.0/MoEClust/R/MoEClust-package.R |only MoEClust-1.6.0/MoEClust/R/Plotting_Functions.R | 553 ++++++++++++++---------- MoEClust-1.6.0/MoEClust/R/data.R | 4 MoEClust-1.6.0/MoEClust/README.md | 2 MoEClust-1.6.0/MoEClust/build/partial.rdb |binary MoEClust-1.6.0/MoEClust/build/vignette.rds |binary MoEClust-1.6.0/MoEClust/inst/NEWS.md | 81 +++ MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.R | 87 +-- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.Rmd | 61 +- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.html | 75 +-- MoEClust-1.6.0/MoEClust/man/CO2data.Rd | 2 MoEClust-1.6.0/MoEClust/man/FARI.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoEClust-package.Rd | 210 ++++----- MoEClust-1.6.0/MoEClust/man/MoE_Uncertainty.Rd | 130 +++-- MoEClust-1.6.0/MoEClust/man/MoE_clust.Rd | 26 - MoEClust-1.6.0/MoEClust/man/MoE_compare.Rd | 16 MoEClust-1.6.0/MoEClust/man/MoE_control.Rd | 396 ++++++++--------- MoEClust-1.6.0/MoEClust/man/MoE_crit.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_cstep.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_estep.Rd | 6 MoEClust-1.6.0/MoEClust/man/MoE_gpairs.Rd | 107 ++-- MoEClust-1.6.0/MoEClust/man/MoE_news.Rd | 4 MoEClust-1.6.0/MoEClust/man/MoE_plotCrit.Rd | 11 MoEClust-1.6.0/MoEClust/man/MoE_stepwise.Rd | 4 MoEClust-1.6.0/MoEClust/man/ais.Rd | 84 +-- MoEClust-1.6.0/MoEClust/man/as.Mclust.Rd | 51 +- MoEClust-1.6.0/MoEClust/man/expert_covar.Rd | 4 MoEClust-1.6.0/MoEClust/man/noise_vol.Rd | 2 MoEClust-1.6.0/MoEClust/man/plot.MoEClust.Rd | 8 MoEClust-1.6.0/MoEClust/vignettes/MoEClust.Rmd | 61 +- 35 files changed, 1423 insertions(+), 1107 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and
convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] ,
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 1.1.1 dated 2024-10-20 and 1.2.0 dated 2025-03-05
divest-1.1.1/divest/R/attribs.R |only divest-1.1.1/divest/build |only divest-1.1.1/divest/inst/tinytest/attributes.json |only divest-1.1.1/divest/man/bidsJson.Rd |only divest-1.1.1/divest/man/imageAttributes.Rd |only divest-1.2.0/divest/DESCRIPTION | 10 +++--- divest-1.2.0/divest/MD5 | 28 ++++++++----------- divest-1.2.0/divest/NAMESPACE | 4 ++ divest-1.2.0/divest/NEWS | 16 ++++++++++ divest-1.2.0/divest/R/read.R | 21 ++++++++------ divest-1.2.0/divest/R/zzz.R | 9 ++++++ divest-1.2.0/divest/configure | 20 ++++++------- divest-1.2.0/divest/configure.ac | 4 +- divest-1.2.0/divest/inst/tinytest/test-05-read.R | 7 ---- divest-1.2.0/divest/man/readDicom.Rd | 5 ++- divest-1.2.0/divest/man/reexports.Rd |only divest-1.2.0/divest/src/dcm2niix/nii_dicom_batch.cpp | 2 - divest-1.2.0/divest/src/main.cpp | 2 - 18 files changed, 76 insertions(+), 52 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.5.0 dated 2025-02-20 and 2.5.1 dated 2025-03-05
DESCRIPTION | 18 MD5 | 280 +-- NEWS.md | 25 R/000_options.R | 24 R/acc_loess.R | 34 R/acc_margins.R | 8 R/acc_varcomp.R | 26 R/dq_report_by.R | 31 R/prep_check_for_dataquieR_updates.R | 1 R/summary.dataquieR_resultset2.R | 149 + R/util_acc_loess_bin.R | 64 R/util_acc_loess_continuous.R | 44 R/util_acc_varcomp.R | 16 R/util_compress_ggplots_in_res.R | 2 R/util_condition_constructor_factory.R | 9 R/util_eval_to_dataquieR_result.R | 3 R/util_evaluate_calls.R | 4 R/util_generate_pages_from_report.R | 2 R/util_generate_table_indicators_descriptors.R | 26 R/util_get_rule_sets.R | 13 R/util_interpret_limits.R | 2 R/util_margins_bin.R | 83 - R/util_margins_lm.R | 42 R/util_margins_nom.R | 19 R/util_margins_ord.R | 6 R/util_margins_poi.R | 39 R/util_view_file.R | 20 R/zzz_globs.R | 2 build/vignette.rds |binary inst/grading_rulesets.xlsx |binary inst/hovertext.rds |binary inst/menu/script.js | 3 inst/templates/default/grading_ruleset_text.html | 4 inst/templates/default/ruleset_formats_text.html | 4 man/acc_loess.Rd | 14 man/acc_varcomp.Rd | 3 man/dataquieR.CONDITIONS_LEVEL_TRHESHOLD.Rd | 2 man/dataquieR.CONDITIONS_WITH_STACKTRACE.Rd | 2 man/dataquieR.ELEMENT_MISSMATCH_CHECKTYPE.Rd | 2 man/dataquieR.ERRORS_WITH_CALLER.Rd | 2 man/dataquieR.GAM_for_LOESS.Rd | 2 man/dataquieR.MAX_LABEL_LEN.Rd | 2 man/dataquieR.MAX_VALUE_LABEL_LEN.Rd | 2 man/dataquieR.MESSAGES_WITH_CALLER.Rd | 2 man/dataquieR.MULTIVARIATE_OUTLIER_CHECK.Rd | 2 man/dataquieR.Rd | 6 man/dataquieR.VALUE_LABELS_htmlescaped.Rd | 2 man/dataquieR.WARNINGS_WITH_CALLER.Rd | 2 man/dataquieR.acc_loess.exclude_constant_subgroups.Rd | 2 man/dataquieR.acc_loess.mark_time_points.Rd | 2 man/dataquieR.acc_loess.min_bw.Rd |only man/dataquieR.acc_loess.min_proportion.Rd |only man/dataquieR.acc_loess.plot_format.Rd | 2 man/dataquieR.acc_loess.plot_observations.Rd | 2 man/dataquieR.acc_margins_num.Rd | 2 man/dataquieR.acc_margins_sort.Rd | 2 man/dataquieR.acc_multivariate_outlier.scale.Rd | 2 man/dataquieR.col_con_con_empirical.Rd | 2 man/dataquieR.col_con_con_logical.Rd | 2 man/dataquieR.debug.Rd | 2 man/dataquieR.des_summary_hard_lim_remove.Rd | 2 man/dataquieR.dontwrapresults.Rd | 2 man/dataquieR.fix_column_type_on_read.Rd | 2 man/dataquieR.flip_mode.Rd | 2 man/dataquieR.force_item_specific_missing_codes.Rd | 2 man/dataquieR.force_label_col.Rd | 2 man/dataquieR.grading_formats.Rd | 2 man/dataquieR.grading_rulesets.Rd | 2 man/dataquieR.guess_missing_codes.Rd | 2 man/dataquieR.lang.Rd | 2 man/dataquieR.max_group_var_levels_in_plot.Rd | 2 man/dataquieR.max_group_var_levels_with_violins.Rd | 2 man/dataquieR.min_obs_per_group_var_in_plot.Rd | 2 man/dataquieR.non_disclosure.Rd | 2 man/dataquieR.progress_fkt.Rd | 2 man/dataquieR.progress_msg_fkt.Rd | 2 man/dataquieR.scale_level_heuristics_control_binaryrecodelimit.Rd | 2 man/dataquieR.scale_level_heuristics_control_metriclevels.Rd | 2 man/dataquieR.testdebug.Rd | 2 man/util_acc_loess_bin.Rd | 14 man/util_acc_loess_continuous.Rd | 8 man/util_acc_varcomp.Rd | 4 man/util_generate_table_indicators_descriptors.Rd | 4 man/util_margins_bin.Rd | 8 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-both-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg | 39 tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-both-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-facets-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-with-covars-ok.svg | 139 - 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tests/testthat/_snaps/R4.5/acc_loess/loess-plot-for-crp-0-auto1-ok.svg | 47 tests/testthat/_snaps/R4.5/acc_loess/loess-plot-for-crp-0-auto2-ok.svg | 71 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-all-quest-dt.svg | 4 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-low-quest-dt.svg | 6 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-upp-quest-dt.svg | 6 tests/testthat/_snaps/R4.5/plots/loess-def-dbp0.svg | 52 tests/testthat/_snaps/R4.5/plots/loess-def-edu0.svg | 90 - tests/testthat/_snaps/R4.5/plots/loess-fac-dbp0.svg | 322 ++-- tests/testthat/_snaps/R4.5/plots/loess-fac-edu0.svg | 761 +++++----- tests/testthat/_snaps/R4.5/plots/margins-dbp0.svg | 293 +-- tests/testthat/_snaps/R4.5/plots/margins-edu0.svg | 14 tests/testthat/test-acc_loess.R | 6 tests/testthat/test-acc_margins.R | 350 ++++ tests/testthat/test-acc_varcomp.R | 4 tests/testthat/test-dataquieR_resultset2.R | 2 tests/testthat/test-dq_report_by_m.R | 19 tests/testthat/test-prep_add_missing_codes.R | 1 tests/testthat/test-statichtmlWidget.R | 2 142 files changed, 4881 insertions(+), 4145 deletions(-)
Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for large data sets that
cannot be loaded into memory. Designed to be more memory- and
computation-efficient than existing lasso-fitting packages like 'glmnet' and
'ncvreg', thus allowing the user to analyze big data with limited RAM
<doi:10.32614/RJ-2021-001>.
Author: Yaohui Zeng [aut],
Chuyi Wang [aut],
Tabitha Peter [aut],
Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between biglasso versions 1.6.0 dated 2024-04-21 and 1.6.1 dated 2025-03-05
DESCRIPTION | 37 +++++++++--------- MD5 | 39 +++++++++++-------- NAMESPACE | 3 - NEWS.md | 9 ++++ R/biglasso-package.R | 34 ++++++++++++----- R/biglasso.R | 18 ++++++--- R/cv-biglasso.R | 7 --- R/predict.R | 7 ++- R/setupX.R | 2 - README.md |only build/partial.rdb |only build/vignette.rds |binary inst/doc/biglasso.html | 24 ++++++------ inst/tinytest |only man/biglasso-package.Rd | 32 +++++++++++----- man/biglasso.Rd | 6 +++ man/setupX.Rd | 2 - src/binomial.cpp | 9 ---- src/init.c | 6 ++- src/utilities.cpp | 95 +++++++++++++----------------------------------- tests |only 21 files changed, 168 insertions(+), 162 deletions(-)
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 0.9.5 dated 2024-06-23 and 1.0.0 dated 2025-03-05
tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_future_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_present_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_sf.RDS |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_land_mask.nc |only tidysdm-0.9.5/tidysdm/inst/notes |only tidysdm-1.0.0/tidysdm/DESCRIPTION | 34 tidysdm-1.0.0/tidysdm/MD5 | 349 - tidysdm-1.0.0/tidysdm/NAMESPACE | 6 tidysdm-1.0.0/tidysdm/NEWS.md | 20 tidysdm-1.0.0/tidysdm/R/add_member.R | 37 tidysdm-1.0.0/tidysdm/R/add_repeat.R | 18 tidysdm-1.0.0/tidysdm/R/autoplot_simple_ensemble.R | 11 tidysdm-1.0.0/tidysdm/R/autoplot_spatial_initial_split.R | 5 tidysdm-1.0.0/tidysdm/R/blockcv2rsample.R | 42 tidysdm-1.0.0/tidysdm/R/boyce_cont.R | 103 tidysdm-1.0.0/tidysdm/R/calib_class_thresh.R | 63 tidysdm-1.0.0/tidysdm/R/check_coords_names.R | 5 tidysdm-1.0.0/tidysdm/R/check_sdm_presence.R | 15 tidysdm-1.0.0/tidysdm/R/check_split_balance.R | 77 tidysdm-1.0.0/tidysdm/R/clamp_predictors.R | 88 tidysdm-1.0.0/tidysdm/R/collect_metrics.R | 10 tidysdm-1.0.0/tidysdm/R/confusion_matrix_df.R | 3 tidysdm-1.0.0/tidysdm/R/datasets_docs.R | 5 tidysdm-1.0.0/tidysdm/R/dist_pres_vs_bg.R | 20 tidysdm-1.0.0/tidysdm/R/explain_tidysdm.R | 74 tidysdm-1.0.0/tidysdm/R/extrapol_mess.R | 301 - tidysdm-1.0.0/tidysdm/R/filter_caret.R | 83 tidysdm-1.0.0/tidysdm/R/filter_collinear.R | 273 - tidysdm-1.0.0/tidysdm/R/filter_high_cor.R | 61 tidysdm-1.0.0/tidysdm/R/filter_vif.R | 82 tidysdm-1.0.0/tidysdm/R/gam_formula.R | 10 tidysdm-1.0.0/tidysdm/R/geom_split_violin.R | 46 tidysdm-1.0.0/tidysdm/R/grid_cellsize.R | 22 tidysdm-1.0.0/tidysdm/R/grid_offset.R | 15 tidysdm-1.0.0/tidysdm/R/kap_max.R | 86 tidysdm-1.0.0/tidysdm/R/make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/R/make_maxent.R | 17 tidysdm-1.0.0/tidysdm/R/maxent.R | 28 tidysdm-1.0.0/tidysdm/R/maxent_params.R | 15 tidysdm-1.0.0/tidysdm/R/maxnet_fit.R | 28 tidysdm-1.0.0/tidysdm/R/niche_overlap.R | 60 tidysdm-1.0.0/tidysdm/R/optim_thresh.R | 54 tidysdm-1.0.0/tidysdm/R/out_of_range_warning.R | 50 tidysdm-1.0.0/tidysdm/R/pairs.R |only tidysdm-1.0.0/tidysdm/R/plot_pres_vs_bg.R | 18 tidysdm-1.0.0/tidysdm/R/predict_raster.R | 42 tidysdm-1.0.0/tidysdm/R/predict_repeat_ensemble.R | 37 tidysdm-1.0.0/tidysdm/R/predict_simple_ensemble.R | 151 tidysdm-1.0.0/tidysdm/R/prob_metrics.R | 24 tidysdm-1.0.0/tidysdm/R/recipe_sf.R | 46 tidysdm-1.0.0/tidysdm/R/recipes_sf_methods.R | 54 tidysdm-1.0.0/tidysdm/R/repeat_ensemble.R | 8 tidysdm-1.0.0/tidysdm/R/sample_background.R | 92 tidysdm-1.0.0/tidysdm/R/sample_background_time.R | 180 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs.R | 107 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs_time.R | 147 tidysdm-1.0.0/tidysdm/R/sdm_spec_boost_tree.R | 52 tidysdm-1.0.0/tidysdm/R/sdm_spec_gam.R | 26 tidysdm-1.0.0/tidysdm/R/sdm_spec_glm.R | 15 tidysdm-1.0.0/tidysdm/R/sdm_spec_maxent.R | 24 tidysdm-1.0.0/tidysdm/R/sdm_spec_rand_forest.R | 13 tidysdm-1.0.0/tidysdm/R/simple_ensemble.R | 16 tidysdm-1.0.0/tidysdm/R/spatial_initial_split.R | 29 tidysdm-1.0.0/tidysdm/R/thin_by_cell.R | 68 tidysdm-1.0.0/tidysdm/R/thin_by_cell_time.R | 75 tidysdm-1.0.0/tidysdm/R/thin_by_dist.R | 51 tidysdm-1.0.0/tidysdm/R/thin_by_dist_time.R | 68 tidysdm-1.0.0/tidysdm/R/tidysdm-package.R | 3 tidysdm-1.0.0/tidysdm/R/tss.R | 50 tidysdm-1.0.0/tidysdm/R/tss_max.R | 63 tidysdm-1.0.0/tidysdm/R/zzz.R | 10 tidysdm-1.0.0/tidysdm/README.md | 62 tidysdm-1.0.0/tidysdm/build/partial.rdb |binary tidysdm-1.0.0/tidysdm/build/vignette.rds |binary tidysdm-1.0.0/tidysdm/data/horses.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_ensemble.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_rep_ens.rda |binary tidysdm-1.0.0/tidysdm/data/lacertidae_background.rda |binary tidysdm-1.0.0/tidysdm/inst/WORDLIST | 10 tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.R | 402 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.html | 2337 ++-------- tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.R | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.html | 26 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.R | 136 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.html | 649 +- tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.R | 19 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.Rmd | 15 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.html | 149 tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_future_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_present_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_land_mask.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin_all_vars.rds |only tidysdm-1.0.0/tidysdm/man/autoplot.simple_ensemble.Rd | 2 tidysdm-1.0.0/tidysdm/man/blockcv2rsample.Rd | 8 tidysdm-1.0.0/tidysdm/man/boyce_cont.Rd | 67 tidysdm-1.0.0/tidysdm/man/calib_class_thresh.Rd | 19 tidysdm-1.0.0/tidysdm/man/check_sdm_presence.Rd | 7 tidysdm-1.0.0/tidysdm/man/check_splits_balance.Rd | 12 tidysdm-1.0.0/tidysdm/man/clamp_predictors.Rd | 25 tidysdm-1.0.0/tidysdm/man/collect_metrics.simple_ensemble.Rd | 9 tidysdm-1.0.0/tidysdm/man/conf_matrix_df.Rd | 3 tidysdm-1.0.0/tidysdm/man/dist_pres_vs_bg.Rd | 13 tidysdm-1.0.0/tidysdm/man/explain_tidysdm.Rd | 16 tidysdm-1.0.0/tidysdm/man/extrapol_mess.Rd | 30 tidysdm-1.0.0/tidysdm/man/filter_collinear.Rd | 87 tidysdm-1.0.0/tidysdm/man/filter_high_cor.Rd | 44 tidysdm-1.0.0/tidysdm/man/form_resp.Rd | 3 tidysdm-1.0.0/tidysdm/man/geom_split_violin.Rd | 31 tidysdm-1.0.0/tidysdm/man/grid_cellsize.Rd | 15 tidysdm-1.0.0/tidysdm/man/grid_offset.Rd | 15 tidysdm-1.0.0/tidysdm/man/kap_max.Rd | 73 tidysdm-1.0.0/tidysdm/man/lacertidae_background.Rd | 5 tidysdm-1.0.0/tidysdm/man/make_mask_from_presence.Rd |only tidysdm-1.0.0/tidysdm/man/maxent.Rd | 24 tidysdm-1.0.0/tidysdm/man/maxent_params.Rd | 11 tidysdm-1.0.0/tidysdm/man/maxnet_fit.Rd | 20 tidysdm-1.0.0/tidysdm/man/niche_overlap.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh_kap_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_sens.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_tss_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/pairs-stars.Rd |only tidysdm-1.0.0/tidysdm/man/plot_pres_vs_bg.Rd | 7 tidysdm-1.0.0/tidysdm/man/predict.repeat_ensemble.Rd | 37 tidysdm-1.0.0/tidysdm/man/predict.simple_ensemble.Rd | 41 tidysdm-1.0.0/tidysdm/man/predict_raster.Rd | 14 tidysdm-1.0.0/tidysdm/man/prob_metrics_sf.Rd | 22 tidysdm-1.0.0/tidysdm/man/recipe.sf.Rd | 34 tidysdm-1.0.0/tidysdm/man/repeat_ensemble.Rd | 4 tidysdm-1.0.0/tidysdm/man/sample_background.Rd | 43 tidysdm-1.0.0/tidysdm/man/sample_background_time.Rd | 86 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs.Rd | 47 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs_time.Rd | 79 tidysdm-1.0.0/tidysdm/man/sdm_spec_boost_tree.Rd | 18 tidysdm-1.0.0/tidysdm/man/sdm_spec_gam.Rd | 27 tidysdm-1.0.0/tidysdm/man/sdm_spec_glm.Rd | 13 tidysdm-1.0.0/tidysdm/man/sdm_spec_maxent.Rd | 14 tidysdm-1.0.0/tidysdm/man/simple_ensemble.Rd | 10 tidysdm-1.0.0/tidysdm/man/spatial_initial_split.Rd | 15 tidysdm-1.0.0/tidysdm/man/thin_by_cell.Rd | 38 tidysdm-1.0.0/tidysdm/man/thin_by_cell_time.Rd | 61 tidysdm-1.0.0/tidysdm/man/thin_by_dist.Rd | 35 tidysdm-1.0.0/tidysdm/man/thin_by_dist_time.Rd | 47 tidysdm-1.0.0/tidysdm/man/tidysdm-package.Rd | 8 tidysdm-1.0.0/tidysdm/man/tss.Rd | 58 tidysdm-1.0.0/tidysdm/man/tss_max.Rd | 63 tidysdm-1.0.0/tidysdm/tests/spelling.R | 9 tidysdm-1.0.0/tidysdm/tests/testthat/Rplots.pdf |only tidysdm-1.0.0/tidysdm/tests/testthat/test_blockcv2rsample.R | 104 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_sdm_presence.R | 6 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_split_balance.R | 39 tidysdm-1.0.0/tidysdm/tests/testthat/test_clamp_predictors.R | 181 tidysdm-1.0.0/tidysdm/tests/testthat/test_dist_pres_vs_bg.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_explain_tidysdm.R | 105 tidysdm-1.0.0/tidysdm/tests/testthat/test_extrapol_mess.R | 117 tidysdm-1.0.0/tidysdm/tests/testthat/test_filter_collinear.R | 109 tidysdm-1.0.0/tidysdm/tests/testthat/test_initial_spatial_split.R | 56 tidysdm-1.0.0/tidysdm/tests/testthat/test_make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_maxnet_fit.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_out_of_range_warning.R | 26 tidysdm-1.0.0/tidysdm/tests/testthat/test_overlap_niche.R | 33 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_repeat_ensemble.R | 49 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_simple_ensemble.R | 83 tidysdm-1.0.0/tidysdm/tests/testthat/test_prob_metrics_sf.R | 28 tidysdm-1.0.0/tidysdm/tests/testthat/test_recipe_sf.R | 48 tidysdm-1.0.0/tidysdm/tests/testthat/test_repeat_ensemble.R | 16 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background.R | 82 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background_time.R | 239 - tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs.R | 85 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs_time.R | 245 - tidysdm-1.0.0/tidysdm/tests/testthat/test_simple_ensemble.R | 37 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell_time.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist.R | 35 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist_time.R | 48 tidysdm-1.0.0/tidysdm/vignettes/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/vignettes/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/vignettes/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/vignettes/a3_troubleshooting.Rmd | 15 184 files changed, 6935 insertions(+), 5019 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.8 dated 2024-09-06 and 0.0.9 dated 2025-03-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 7 +++++++ NEWS.md | 7 +++++-- R/gloss_example.R | 44 ++++++++++++++++++++++++++++++++++++++++++-- data/glosses_df.RData |binary man/gloss_example.Rd | 1 + 7 files changed, 66 insertions(+), 15 deletions(-)
Title: Multivariate Markov Chains
Description: Provides routines to estimate the Mixture Transition Distribution Model based on Raftery (1985) <http://www.jstor.org/stable/2345788> and Nicolau (2014) <doi:10.1111/sjos.12087> specifications, for multivariate data. Additionally, provides a function for the estimation of a new model for multivariate non-homogeneous Markov chains. This new specification, Generalized Multivariate Markov Chains (GMMC) was proposed by Carolina Vasconcelos and Bruno Damasio and considers (continuous or discrete) covariates exogenous to the Markov chain.
Author: Carolina Vasconcelos [aut, cre],
Bruno Damasio [aut]
Maintainer: Carolina Vasconcelos <cvasconcelos@novaims.unl.pt>
Diff between GenMarkov versions 0.2.0 dated 2023-12-19 and 0.2.1 dated 2025-03-05
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- R/CalculateInitialValues.R | 12 ++++++++- R/ProbValuesXDependent.R | 55 ++++++++++++++++++++++++++++++++++++++------- R/multi.mtd.R | 7 ++++- build/partial.rdb |binary 6 files changed, 71 insertions(+), 19 deletions(-)
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.1.1 dated 2025-02-06 and 1.1.2 dated 2025-03-05
Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.Rd |only Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.list.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.list.Rd |only Coxmos-1.1.2/Coxmos/DESCRIPTION | 15 Coxmos-1.1.2/Coxmos/MD5 | 144 Coxmos-1.1.2/Coxmos/NAMESPACE | 233 Coxmos-1.1.2/Coxmos/R/Coxmos_common_functions.R | 249 Coxmos-1.1.2/Coxmos/R/Coxmos_coxEN.R | 44 Coxmos-1.1.2/Coxmos/R/Coxmos_evaluation_functions.R | 28 Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdacox_dynamic.R | 1206 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox.R | 1218 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox_dynamic.R | 1284 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsicox.R | 1220 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_multiblock_functions.R | 1878 +++--- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions.R | 1276 +++- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions_others.R | 16 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox.R | 1620 ++--- Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsicox.R | 50 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdacox_dynamic.R | 52 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_dynamic.R | 2127 +++---- Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_median.R | 2777 +++++----- Coxmos-1.1.2/Coxmos/R/Coxmos_splsicox.R | 64 Coxmos-1.1.2/Coxmos/README.md | 6 Coxmos-1.1.2/Coxmos/build/partial.rdb |binary Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.R | 72 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.html | 427 - Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.R | 20 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.Rmd | 30 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.html | 253 Coxmos-1.1.2/Coxmos/man/cv.coxEN.Rd | 18 Coxmos-1.1.2/Coxmos/man/cv.isb.splsdacox.Rd | 356 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox_penalty.Rd | 390 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsicox.Rd | 12 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdacox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdrcox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.sb.splsdacox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox_penalty.Rd | 454 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsicox.Rd | 16 Coxmos-1.1.2/Coxmos/man/cv.splsdacox.Rd | 448 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox.Rd | 466 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox_penalty.Rd | 636 +- Coxmos-1.1.2/Coxmos/man/cv.splsicox.Rd | 30 Coxmos-1.1.2/Coxmos/man/getAutoKM.Rd | 3 Coxmos-1.1.2/Coxmos/man/getAutoKM.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/getTestKM.Rd | 5 Coxmos-1.1.2/Coxmos/man/getTestKM.list.Rd | 3 Coxmos-1.1.2/Coxmos/man/loadingplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/man/loadingplot.fromVector.Coxmos.Rd | 5 Coxmos-1.1.2/Coxmos/man/mb.splsdacox.Rd | 4 Coxmos-1.1.2/Coxmos/man/mb.splsdrcox.Rd | 4 Coxmos-1.1.2/Coxmos/man/plot_evaluation.Rd | 19 Coxmos-1.1.2/Coxmos/man/plot_evaluation.list.Rd | 18 Coxmos-1.1.2/Coxmos/man/plot_events.Rd | 25 Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.Rd |only Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.Rd | 31 Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.list.Rd | 36 Coxmos-1.1.2/Coxmos/man/plot_time.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/sb.splsdacox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/sb.splsdrcox.Rd | 420 - Coxmos-1.1.2/Coxmos/man/splsdacox.Rd | 406 - Coxmos-1.1.2/Coxmos/man/splsdrcox.Rd | 428 - Coxmos-1.1.2/Coxmos/man/splsdrcox_penalty.Rd | 4 Coxmos-1.1.2/Coxmos/man/w.starplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-pipeline.Rmd | 30 77 files changed, 11996 insertions(+), 10898 deletions(-)
Title: Local Regression, Likelihood and Density Estimation
Description: Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Author: Catherine Loader [aut],
Jiayang Sun [ctb],
Lucent Technologies [cph],
Andy Liaw [cre]
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between locfit versions 1.5-9.11 dated 2025-02-03 and 1.5-9.12 dated 2025-03-05
DESCRIPTION | 8 - MD5 | 54 ++++---- src/S_enter.c | 14 ++ src/band.c | 10 - src/cversion.h | 30 ++++ src/dbinom.c | 15 ++ src/dens_int.c | 1 src/density.c | 5 src/design.h | 2 src/ev_kdtre.c | 1 src/ev_trian.c | 14 ++ src/frend.c | 4 src/lf_nbhd.c | 1 src/lffuns.h | 346 +++++++++++++++++++++++++++++++++++++++++++++----------- src/m_eigen.c | 2 src/m_icirc.c | 4 src/m_imont.c | 2 src/m_isimp.c | 7 + src/m_isphr.c | 8 + src/m_jacob.c | 2 src/math.c | 2 src/mutil.h | 22 ++- src/prob.c | 5 src/scb.c | 1 src/scb_iface.c | 2 src/smisc.c | 4 src/tube.h | 33 ++++- src/weight.c | 1 28 files changed, 465 insertions(+), 135 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 25.1.1 dated 2025-01-29 and 25.3.1 dated 2025-03-05
DESCRIPTION | 17 +- MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 10 + R/REDCap_split.r | 5 R/as_factor.R | 21 ++ R/as_logical.R |only R/ds2dd_detailed.R | 49 +++-- R/easy_redcap.R | 39 ++++ R/read_redcap_tables.R | 69 ++++---- README.md | 3 inst/WORDLIST | 2 inst/doc/Database-creation.html | 5 inst/doc/REDCapCAST.html | 335 ++++++++++++++++++++-------------------- inst/doc/Shiny-app.html | 5 man/as_factor.Rd | 11 + man/as_logical.Rd |only man/ds2dd.Rd | 2 man/ds2dd_detailed.Rd | 7 man/easy_redcap.Rd | 16 + man/format_redcap_factor.Rd | 2 man/read_redcap_tables.Rd | 4 22 files changed, 376 insertions(+), 269 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-05
DESCRIPTION | 10 MD5 | 118 +++++----- NAMESPACE | 18 - R/learner_glmnet.R | 24 +- R/learner_xgboost.R | 14 - R/zzz.R | 58 ++--- build/vignette.rds |binary inst/doc/mllrnrs_glmnet_binary.html | 5 inst/doc/mllrnrs_glmnet_binary.qmd | 1 inst/doc/mllrnrs_glmnet_multiclass.R | 29 +- inst/doc/mllrnrs_glmnet_multiclass.html | 68 ++--- inst/doc/mllrnrs_glmnet_multiclass.qmd | 30 +- inst/doc/mllrnrs_glmnet_regression.html | 5 inst/doc/mllrnrs_glmnet_regression.qmd | 1 inst/doc/mllrnrs_lightgbm_binary.html | 5 inst/doc/mllrnrs_lightgbm_binary.qmd | 1 inst/doc/mllrnrs_lightgbm_multiclass.R | 39 +-- inst/doc/mllrnrs_lightgbm_multiclass.html | 78 +++--- inst/doc/mllrnrs_lightgbm_multiclass.qmd | 40 +-- inst/doc/mllrnrs_lightgbm_regression.html | 5 inst/doc/mllrnrs_lightgbm_regression.qmd | 1 inst/doc/mllrnrs_ranger_binary.html | 5 inst/doc/mllrnrs_ranger_binary.qmd | 1 inst/doc/mllrnrs_ranger_multiclass.R | 25 +- inst/doc/mllrnrs_ranger_multiclass.html | 68 ++--- inst/doc/mllrnrs_ranger_multiclass.qmd | 26 +- inst/doc/mllrnrs_ranger_regression.html | 5 inst/doc/mllrnrs_ranger_regression.qmd | 1 inst/doc/mllrnrs_xgboost_binary.html | 5 inst/doc/mllrnrs_xgboost_binary.qmd | 1 inst/doc/mllrnrs_xgboost_multiclass.R | 34 +- inst/doc/mllrnrs_xgboost_multiclass.html | 73 ++---- inst/doc/mllrnrs_xgboost_multiclass.qmd | 35 +-- inst/doc/mllrnrs_xgboost_regression.html | 5 inst/doc/mllrnrs_xgboost_regression.qmd | 1 man/LearnerGlmnet.Rd | 296 ++++++++++++------------- man/LearnerLightgbm.Rd | 342 +++++++++++++++--------------- man/LearnerRanger.Rd | 298 +++++++++++++------------- man/LearnerXgboost.Rd | 342 +++++++++++++++--------------- tests/testthat.R | 27 +- tests/testthat/test-glmnet_binary.R | 288 ++++++++++++------------- tests/testthat/test-glmnet_regression.R | 300 +++++++++++++------------- tests/testthat/test-lightgbm_regression.R | 314 +++++++++++++-------------- tests/testthat/test-lints.R | 26 +- tests/testthat/test-ranger_regression.R | 284 ++++++++++++------------ tests/testthat/test-xgboost_binary.R | 211 ++++++++---------- tests/testthat/test-xgboost_multiclass.R | 15 - tests/testthat/test-xgboost_regression.R | 295 ++++++++++++------------- vignettes/mllrnrs_glmnet_binary.qmd | 1 vignettes/mllrnrs_glmnet_multiclass.qmd | 30 +- vignettes/mllrnrs_glmnet_regression.qmd | 1 vignettes/mllrnrs_lightgbm_binary.qmd | 1 vignettes/mllrnrs_lightgbm_multiclass.qmd | 40 +-- vignettes/mllrnrs_lightgbm_regression.qmd | 1 vignettes/mllrnrs_ranger_binary.qmd | 1 vignettes/mllrnrs_ranger_multiclass.qmd | 26 +- vignettes/mllrnrs_ranger_regression.qmd | 1 vignettes/mllrnrs_xgboost_binary.qmd | 1 vignettes/mllrnrs_xgboost_multiclass.qmd | 35 +-- vignettes/mllrnrs_xgboost_regression.qmd | 1 60 files changed, 1955 insertions(+), 2057 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.3.1 dated 2024-12-07 and 0.4.2 dated 2025-03-05
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More information about tutorial.helpers at CRAN
Permanent link
Title: Expression Data Analysis and Visualization
Description: The Gene Expression Omnibus (<https://www.ncbi.nlm.nih.gov/geo/>) and The Cancer Genome Atlas (<https://portal.gdc.cancer.gov/>) are widely used medical public databases. Our platform integrates routine analysis and visualization tools for expression data to provide concise and intuitive data analysis and presentation.
Author: Xiaojie Sun [aut, cre]
Maintainer: Xiaojie Sun <18763899370@163.com>
Diff between tinyarray versions 2.4.2 dated 2024-06-13 and 2.4.3 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 17 +++++---- NAMESPACE | 2 + NEWS.md | 6 +++ R/2_geo_id.R | 83 +++++++++++++++++++++++++++++++++++++++++++--- R/7_quick_double_enrich.R | 7 ++- R/get_anno.R |only R/start_massage.R | 2 - R/tmp.R |only man/double_enrich.Rd | 4 +- man/geo_parser.Rd |only 11 files changed, 109 insertions(+), 20 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 1.4.0 dated 2025-02-03 and 1.4.3 dated 2025-03-05
DESCRIPTION | 6 LICENSE | 4 MD5 | 102 - NAMESPACE | 44 NEWS.md | 8 R/adhoc-core.R | 405 +++---- R/adhoc-utils.R | 154 +- R/build-core.R | 414 +++---- R/build-quick.R | 454 ++++---- R/log-core.R | 172 +-- R/main-core.R | 104 - R/main-utils.R | 502 ++++---- R/strata-package.R | 18 R/survey-core.R | 372 +++--- R/survey-utils.R | 236 ++-- R/toml-core.R | 272 ++-- R/toml-io.R | 274 ++-- R/toml-utils.R | 300 ++--- README.md | 1852 ++++++++++++++++----------------- man/adhoc.Rd | 86 - man/adhoc_lamina.Rd | 72 - man/adhoc_stratum.Rd | 72 - man/build_lamina.Rd | 60 - man/build_outlined_strata_project.Rd | 116 +- man/build_quick_strata_project.Rd | 66 - man/build_stratum.Rd | 54 man/edit_toml.Rd | 146 +- man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/log_error.Rd | 58 - man/log_message.Rd | 74 - man/log_total_time.Rd | 64 - man/main.Rd | 114 +- man/strata-package.Rd | 48 man/survey_log.Rd | 82 - man/survey_strata.Rd | 82 - man/survey_tomls.Rd | 58 - man/view_toml.Rd | 48 tests/testthat.R | 24 tests/testthat/test-adhoc-core.R | 440 +++---- tests/testthat/test-adhoc-utils.R | 154 +- tests/testthat/test-build-core.R | 250 ++-- tests/testthat/test-build-quick.R | 718 ++++++------ tests/testthat/test-log-core.R | 72 - tests/testthat/test-main-core.R | 148 +- tests/testthat/test-main-utils.R | 107 + tests/testthat/test-survey-core.R | 264 ++-- tests/testthat/test-survey-utils.R | 104 - tests/testthat/test-toml-core.R | 368 +++--- tests/testthat/test-toml-utils.R | 200 +-- 52 files changed, 5022 insertions(+), 5004 deletions(-)
Title: A Package for Analyzing Skew Factor Models
Description: Generates Skew Factor Models data and applies Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Projected Principal Component (PPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods to estimate model parameters. It includes capabilities for calculating mean squared error, relative error, and sparsity of the loading matrix.The philosophy of the package is described in Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Yu Jin [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between SFM versions 0.1.0 dated 2024-11-12 and 0.2.0 dated 2025-03-05
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Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.3.0 dated 2025-02-26 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/addCategories.R | 305 +++++++++++++++++++----------------- R/checks.R | 62 ------- R/filterCohortId.R | 1 R/summariseResult.R | 4 inst/doc/cohort-intersect.html | 64 +++---- inst/doc/concept-intersect.html | 94 +++++------ inst/doc/demographics.html | 220 ++++++++++++------------- inst/doc/summarise.html | 196 +++++++++++------------ inst/doc/table-intersect.html | 86 +++++----- man/addCategories.Rd | 6 tests/testthat/test-addCategories.R | 6 14 files changed, 529 insertions(+), 553 deletions(-)
More information about PatientProfiles at CRAN
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Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.0 dated 2025-01-12 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 115 ++++++++++++++++++------------------ R/clusterCharts.R | 3 inst/examples/sidebar_app.R | 10 ++- tests/testthat/test-clustercharts.R | 2 6 files changed, 78 insertions(+), 68 deletions(-)
More information about leaflet.extras2 at CRAN
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Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.5.7 dated 2024-10-01 and 5.6.0 dated 2025-03-05
huxtable-5.5.7/huxtable/tests/testthat/404.html |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.aux |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.log |only huxtable-5.6.0/huxtable/DESCRIPTION | 6 huxtable-5.6.0/huxtable/MD5 | 54 huxtable-5.6.0/huxtable/NEWS.md | 15 huxtable-5.6.0/huxtable/R/Workbook.R | 5 huxtable-5.6.0/huxtable/R/dplyr.R | 60 - huxtable-5.6.0/huxtable/R/latex-dependencies.R | 11 huxtable-5.6.0/huxtable/R/zzz.R | 10 huxtable-5.6.0/huxtable/README.md | 68 - huxtable-5.6.0/huxtable/build/vignette.rds |binary huxtable-5.6.0/huxtable/inst/doc/design-principles-html.html | 10 huxtable-5.6.0/huxtable/inst/doc/design-principles-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxreg-html.html | 19 huxtable-5.6.0/huxtable/inst/doc/huxreg-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxtable-html.html | 46 huxtable-5.6.0/huxtable/inst/doc/huxtable-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/themes-html.html | 6 huxtable-5.6.0/huxtable/man/as_Workbook.Rd | 3 huxtable-5.6.0/huxtable/man/huxtable-news.Rd | 21 huxtable-5.6.0/huxtable/tests/testthat/filecec5332acc3.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec53854bfe2.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec567db13c6.log |only huxtable-5.6.0/huxtable/tests/testthat/multirow.rds |binary huxtable-5.6.0/huxtable/tests/testthat/quarto-test-tex-labels-out.pdf |binary huxtable-5.6.0/huxtable/tests/testthat/table-tester-2.log | 550 +++++----- huxtable-5.6.0/huxtable/tests/testthat/test-dplyr.R | 11 huxtable-5.6.0/huxtable/tests/testthat/test-latex-dependencies.R | 42 huxtable-5.6.0/huxtable/tests/testthat/test-openxlsx.R | 8 huxtable-5.6.0/huxtable/tests/testthat/test-print.R | 11 31 files changed, 488 insertions(+), 468 deletions(-)
Title: Bootstrap p-Values
Description: Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models and tests of location.
Author: Mans Thulin [aut, cre]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between boot.pval versions 0.6 dated 2025-01-14 and 0.7.0 dated 2025-03-05
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Title: Create Tests According to QTI 2.1 Standard
Description: Create tests and tasks compliant with the Question & Test Interoperability (QTI) information model version 2.1. Input sources are Rmd/md description files or S4-class objects. Output formats include standalone zip or xml files. Supports the generation of basic task types (single and multiple choice, order, pair association, matching tables, filling gaps and essay) and provides a comprehensive set of attributes for customizing tests.
Author: Andrey Shevandrin [aut, cre, cph]
,
Petr Bondarenko [ctb] ,
Ivonne Ojeda [ctb],
Johannes Titz [aut, cph] ,
Brian Mottershead [cph] ,
Stiftung fuer Innovation in der Hochschullehre [fnd]
Maintainer: Andrey Shevandrin <shevandrin@gmail.com>
Diff between rqti versions 0.3.0 dated 2024-07-19 and 1.0.0 dated 2025-03-05
rqti-0.3.0/rqti/R/api_opal.R |only rqti-0.3.0/rqti/man/auth_opal.Rd |only rqti-0.3.0/rqti/man/get_course_elements.Rd |only rqti-0.3.0/rqti/man/get_course_results.Rd |only rqti-0.3.0/rqti/man/get_resource_url.Rd |only rqti-0.3.0/rqti/man/get_resources.Rd |only rqti-0.3.0/rqti/man/publish_course.Rd |only rqti-0.3.0/rqti/man/update_course_test.Rd |only rqti-0.3.0/rqti/tests/testthat/test-api_opal.R |only rqti-1.0.0/rqti/DESCRIPTION | 24 rqti-1.0.0/rqti/MD5 | 259 rqti-1.0.0/rqti/NAMESPACE | 253 rqti-1.0.0/rqti/NEWS.md | 86 rqti-1.0.0/rqti/R/AssessmentItem.R | 21 rqti-1.0.0/rqti/R/AssessmentSection.R | 49 rqti-1.0.0/rqti/R/AssessmentTest.R | 87 rqti-1.0.0/rqti/R/AssessmentTestOpal.R | 93 rqti-1.0.0/rqti/R/CorrectFeedback.R | 7 rqti-1.0.0/rqti/R/DirectedPair.R | 274 rqti-1.0.0/rqti/R/Entry.R | 7 rqti-1.0.0/rqti/R/Essay.R | 327 rqti-1.0.0/rqti/R/LMS.R |only rqti-1.0.0/rqti/R/ModalFeedback.R | 7 rqti-1.0.0/rqti/R/MultipleChoice.R | 7 rqti-1.0.0/rqti/R/MultipleChoiceTable.R | 345 rqti-1.0.0/rqti/R/OneInColTable.R | 247 rqti-1.0.0/rqti/R/OneInRowTable.R | 247 rqti-1.0.0/rqti/R/Opal.R |only rqti-1.0.0/rqti/R/Ordering.R | 345 rqti-1.0.0/rqti/R/QtiMetadata.R | 70 rqti-1.0.0/rqti/R/SingleChoice.R | 291 rqti-1.0.0/rqti/R/WrongFeedback.R | 7 rqti-1.0.0/rqti/R/character.R | 39 rqti-1.0.0/rqti/R/extract_results.R | 31 rqti-1.0.0/rqti/R/knit_functions.R | 8 rqti-1.0.0/rqti/R/object_builder.R | 25 rqti-1.0.0/rqti/R/qti_task.R | 44 rqti-1.0.0/rqti/R/qti_test.R | 479 rqti-1.0.0/rqti/R/response_processing.R | 20 rqti-1.0.0/rqti/R/rqti_project.R | 3 rqti-1.0.0/rqti/R/section_builder.R | 741 rqti-1.0.0/rqti/inst/QTIJS/index.xml | 315 rqti-1.0.0/rqti/inst/QTIJS/qti.js | 32 rqti-1.0.0/rqti/inst/QTIJS/rqti.js | 2 rqti-1.0.0/rqti/inst/QTIJS/themecc/style.css | 12 rqti-1.0.0/rqti/inst/exercises/metadata_template.Rmd | 38 rqti-1.0.0/rqti/inst/imsqti_v2p1p2.xsd |20968 +++++----- rqti-1.0.0/rqti/inst/qti_v2p1p2_extension.xsd |only 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rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/skeleton/skeleton.Rmd | 26 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/skeleton/skeleton.Rmd | 3 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/skeleton/skeleton.Rmd | 9 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/skeleton/skeleton.Rmd | 6 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/skeleton/skeleton.Rmd | 61 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/skeleton/skeleton.Rmd | 15 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/test_results.zip |binary rqti-1.0.0/rqti/man/AssessmentItem-class.Rd | 2 rqti-1.0.0/rqti/man/AssessmentTest-class.Rd | 8 rqti-1.0.0/rqti/man/AssessmentTestOpal-class.Rd | 8 rqti-1.0.0/rqti/man/DirectedPair-class.Rd | 2 rqti-1.0.0/rqti/man/Entry-class.Rd | 2 rqti-1.0.0/rqti/man/Essay-class.Rd | 2 rqti-1.0.0/rqti/man/LMS-class.Rd |only rqti-1.0.0/rqti/man/MatchTable-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoiceTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInColTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInRowTable-class.Rd | 2 rqti-1.0.0/rqti/man/Opal-class.Rd |only rqti-1.0.0/rqti/man/Ordering-class.Rd | 2 rqti-1.0.0/rqti/man/QtiContributor-class.Rd | 2 rqti-1.0.0/rqti/man/SingleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/assessmentSection.Rd |only rqti-1.0.0/rqti/man/assessmentTest.Rd |only rqti-1.0.0/rqti/man/assessmentTestOpal.Rd |only rqti-1.0.0/rqti/man/authLMS-methods.Rd |only rqti-1.0.0/rqti/man/correctFeedback.Rd | 6 rqti-1.0.0/rqti/man/createQtiTask-methods.Rd | 6 rqti-1.0.0/rqti/man/create_qti_task.Rd | 5 rqti-1.0.0/rqti/man/create_question_object.Rd |only rqti-1.0.0/rqti/man/directedPair.Rd | 11 rqti-1.0.0/rqti/man/essay.Rd | 29 rqti-1.0.0/rqti/man/extract_results.Rd | 11 rqti-1.0.0/rqti/man/getCourseElements-methods.Rd |only rqti-1.0.0/rqti/man/getCourseResult-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourceURL-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResources-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourcesByName-methods.Rd |only rqti-1.0.0/rqti/man/isUserLoggedIn-methods.Rd |only rqti-1.0.0/rqti/man/modalFeedback.Rd | 6 rqti-1.0.0/rqti/man/multipleChoice.Rd | 6 rqti-1.0.0/rqti/man/multipleChoiceTable.Rd | 8 rqti-1.0.0/rqti/man/oneInColTable.Rd | 8 rqti-1.0.0/rqti/man/oneInRowTable.Rd | 8 rqti-1.0.0/rqti/man/opal.Rd |only rqti-1.0.0/rqti/man/ordering.Rd | 6 rqti-1.0.0/rqti/man/publishCourse-Opal-method.Rd |only rqti-1.0.0/rqti/man/publishCourse-missing-method.Rd |only rqti-1.0.0/rqti/man/publishCourse.Rd |only rqti-1.0.0/rqti/man/qtiContributor.Rd |only rqti-1.0.0/rqti/man/qtiMetadata.Rd |only rqti-1.0.0/rqti/man/qti_contributor.Rd | 6 rqti-1.0.0/rqti/man/qti_metadata.Rd | 2 rqti-1.0.0/rqti/man/singleChoice.Rd | 6 rqti-1.0.0/rqti/man/test.Rd | 12 rqti-1.0.0/rqti/man/test4opal.Rd | 12 rqti-1.0.0/rqti/man/updateCourseElementResource-Opal-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource-missing-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource.Rd |only rqti-1.0.0/rqti/man/upload2LMS-methods.Rd |only rqti-1.0.0/rqti/man/upload2opal.Rd | 18 rqti-1.0.0/rqti/man/verify_qti.Rd |only rqti-1.0.0/rqti/man/wrongFeedback.Rd | 6 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice_sign_more_less.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/NumericGap.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/TextGapOpal.xml | 8 rqti-1.0.0/rqti/tests/testthat/test-api_lms.R |only rqti-1.0.0/rqti/tests/testthat/test-assessment_test.R | 98 rqti-1.0.0/rqti/tests/testthat/test-extract_results.R | 18 rqti-1.0.0/rqti/tests/testthat/test-qti_metadata.R | 8 rqti-1.0.0/rqti/tests/testthat/test-qti_task.R | 2 rqti-1.0.0/rqti/tests/testthat/test-text_gap.R | 835 rqti-1.0.0/rqti/tests/testthat/test-text_inline_choice.R | 524 149 files changed, 14224 insertions(+), 13549 deletions(-)
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph]
,
Tilman M. Davies [aut, ctb, cph]
,
Martin L. Hazelton [aut, ctb, cph]
,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.1-1 dated 2024-11-04 and 3.1-2 dated 2025-03-05
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS | 8 + R/adaptive.R | 6 + inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/densityBC.Rd | 181 +++++++++++++++++++++++++++++++++++++-------- man/macros/newdefns.Rd | 4 8 files changed, 179 insertions(+), 46 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.4.1 dated 2025-02-13 and 2.4.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 10 R/hbam.R | 8 R/inits.R | 2 R/prep_data.R | 6 inst/doc/hbamr.R | 3 inst/doc/hbamr.Rmd | 12 inst/doc/hbamr.html | 91 ++--- inst/stan/omni.stan | 27 - man/hbam.Rd | 5 src/stanExports_omni.h | 835 ++++++++++++++++++++++++------------------------- vignettes/hbamr.Rmd | 12 13 files changed, 521 insertions(+), 520 deletions(-)
Title: Two Highly Customizable 'rmarkdown' Themes for Scientific
Reports
Description: Offers 'markdown' output formats designed with various styles, allowing users to generate HTML reports tailored for scientific or machine learning showcase. The output has a contemporary appearance with vibrant visuals, providing numerous styles for effective highlighting. Created using the 'tufte' <https://rstudio.github.io/tufte/> package code as a starting point.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between scientific versions 2025.0 dated 2025-02-02 and 2025.1 dated 2025-03-05
DESCRIPTION | 6 +-- MD5 | 20 ++++++----- NEWS.md | 13 +++++-- R/base_func.R | 4 -- R/markdown.R | 11 +++++- README.md | 2 + inst/doc/Introduction.html | 6 +-- inst/rmarkdown/templates/html/layout/template1.tpl2 |only inst/rmarkdown/templates/html/layout/template2.tpl | 36 +------------------- inst/rmarkdown/templates/html/layout/template2.tpl2 |only inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/html/template.yaml | 2 - 12 files changed, 43 insertions(+), 59 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.2.1 dated 2025-01-24 and 0.2.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/dijkstras-path.R | 1 src/vcglib/vcg/complex/algorithms/parametrization/voronoi_atlas.h | 6 src/vcglib/vcg/complex/algorithms/voronoi_processing.h | 20 +- src/vcglib/vcg/complex/allocate.h | 72 +++++----- src/vcglib/wrap/callback.h | 37 ++--- 8 files changed, 83 insertions(+), 77 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]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.8 dated 2024-12-11 and 1.3.9 dated 2025-03-05
DESCRIPTION | 8 +- MD5 | 21 ++++-- NEWS.md | 3 R/cox2.R | 8 +- build/vignette.rds |binary inst/doc/jstable.html | 88 +++++++++++++------------- inst/doc/jstable_competing_risk_analysis.R |only inst/doc/jstable_competing_risk_analysis.Rmd |only inst/doc/jstable_competing_risk_analysis.html |only inst/doc/jstable_options.R |only inst/doc/jstable_options.Rmd |only inst/doc/jstable_options.html |only tests/testthat/test-forestcox.R | 1 vignettes/jstable_competing_risk_analysis.Rmd |only vignettes/jstable_options.Rmd |only vignettes/vignette-styles.css |only 16 files changed, 73 insertions(+), 56 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are also implemented, provided there is no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.6.7 dated 2025-01-07 and 0.7.0 dated 2025-03-05
DESCRIPTION | 6 MD5 | 76 ++++---- NAMESPACE | 2 NEWS.md | 11 + R/IWP.R |only R/as_hce.data.frame.R | 13 - R/as_hce.default.R |only R/calcWINS_data_frame.R | 121 ++++++++---- R/calcWINS_formula.R | 24 +- R/calcWINS_hce.R | 22 +- R/data.R | 2 R/plot_hce.R | 37 +++ R/simHCE.R | 126 +++++++++---- README.md | 2 inst/doc/Introduction.R | 6 inst/doc/Introduction.Rmd | 18 + inst/doc/Introduction.html | 106 +++++++++-- inst/doc/Wins.R | 2 inst/doc/Wins.Rmd | 2 inst/doc/Wins.html | 6 inst/doc/hce.R | 24 +- inst/doc/hce.Rmd | 117 ++++++++++-- inst/doc/hce.html | 391 +++++++++++++++++++----------------------- inst/doc/maraca.R | 2 inst/doc/maraca.Rmd | 2 inst/doc/maraca.html | 6 man/ADLB.Rd | 2 man/IWP.Rd |only man/as_hce.data.frame.Rd | 3 man/as_hce.default.Rd |only man/calcWINS.data.frame.Rd | 57 +++++- man/calcWINS.formula.Rd | 20 +- man/calcWINS.hce.Rd | 20 +- man/plot.hce.Rd | 16 + man/simHCE.Rd | 8 tests/testthat/test-test-WO.R | 51 +++++ vignettes/Introduction.Rmd | 18 + vignettes/REFERENCES.bib | 93 +++++++++ vignettes/Wins.Rmd | 2 vignettes/hce.Rmd | 117 ++++++++++-- vignettes/maraca.Rmd | 2 41 files changed, 1045 insertions(+), 488 deletions(-)
Title: Permutation Test for Weighted Quantile Sum Regression
Description: Implements a permutation test method for the weighted quantile sum (WQS) regression, building off the 'gWQS' package (Renzetti et al. <https://CRAN.R-project.org/package=gWQS>). Weighted quantile sum regression is a statistical technique to evaluate the effect of complex exposure mixtures on an outcome (Carrico et al. 2015 <doi:10.1007/s13253-014-0180-3>). The model features a statistical power and Type I error (i.e., false positive) rate trade-off, as there is a machine learning step to determine the weights that optimize the linear model fit. This package provides an alternative method based on a permutation test that should reliably allow for both high power and low false positive rate when utilizing WQS regression (Day et al. 2022 <doi:10.1289/EHP10570>).
Author: Drew Day [aut, cre],
James Peng [aut],
Adam Szpiro [aut]
Maintainer: Drew Day <dday612@gmail.com>
Diff between wqspt versions 1.0.1 dated 2023-03-06 and 1.0.2 dated 2025-03-05
DESCRIPTION | 17 - MD5 | 36 ++- NAMESPACE | 43 ++-- NEWS.md |only R/utils.R |only R/wqs_full_perm.R | 123 ++++++++----- R/wqs_pt.R | 182 +++++++++++-------- R/wqs_sim.R | 29 +-- R/wqspt_plot.R | 90 ++++++--- README.md | 109 +++++------ build/vignette.rds |binary inst/WORDLIST | 14 - inst/doc/introduction.R | 215 +++++++++++----------- inst/doc/introduction.Rmd | 201 ++++++++++++++------- inst/doc/introduction.html | 425 +++++++++++++++++++++++++-------------------- man/wqs_full_perm.Rd | 271 ++++++++++++++++------------ man/wqs_pt.Rd | 287 ++++++++++++++++-------------- man/wqs_sim.Rd | 275 ++++++++++++++--------------- man/wqspt_plot.Rd | 185 ++++++++++++------- vignettes/introduction.Rmd | 201 ++++++++++++++------- 20 files changed, 1571 insertions(+), 1132 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths]
,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.4 dated 2022-05-18 and 2.1.5 dated 2025-03-05
DESCRIPTION | 14 MD5 | 36 NEWS.md | 11 R/utils.R | 7 build/vignette.rds |binary inst/CITATION | 39 inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 10 inst/GerminaQuant/ui.R | 49 inst/doc/GerminaQuant.R | 2 inst/doc/GerminaQuant.Rmd | 2 inst/doc/GerminaQuant.html | 75 - inst/doc/GerminaR.R | 14 inst/doc/GerminaR.html | 611 +++++----- inst/doc/introduction.html | 63 - inst/rstudio/addins.dcf | 4 man/figures/logo.png |binary man/gquant_analysis.Rd | 122 - vignettes/GerminaQuant.Rmd | 2 vignettes/files/pkgs.bib | 332 ----- 19 files changed, 598 insertions(+), 795 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.1 dated 2025-02-08 and 0.8.2 dated 2025-03-04
DESCRIPTION | 6 MD5 | 155 +- NAMESPACE | 3 NEWS.md | 7 R/RcppExports.R | 12 R/cache.R | 6 R/client.R | 168 +- R/config.R | 64 - R/convert.R | 6 R/credential_providers.R | 213 +-- R/credential_sso.R | 36 R/credential_sts.R | 72 - R/custom_rds.R | 18 R/custom_s3.R | 162 -- R/dateutil.R | 5 R/error.R | 4 R/handlers.R | 10 R/handlers_ec2query.R | 9 R/handlers_jsonrpc.R | 8 R/handlers_query.R | 14 R/handlers_rest.R | 36 R/handlers_restxml.R | 3 R/handlers_stream.R | 30 R/head_bucket.R | 61 R/iniutil.R | 10 R/jsonutil.R | 12 R/logging.R | 28 R/mock_bindings.R | 4 R/net.R | 30 R/onLoad.R | 2 R/paginate.R | 83 - R/populate.R | 11 R/queryutil.R | 3 R/request.R | 22 R/retry.R | 5 R/service.R | 41 R/signer_v1.R | 40 R/signer_v4.R | 75 - R/tags.R | 7 R/url.R | 9 R/util.R | 18 R/xmlutil.R | 97 + src/RcppExports.cpp | 19 src/ini_utils.cpp | 18 src/resolve_endpoint.cpp | 30 src/set_partition_name.cpp |only tests/testthat/helper.R | 5 tests/testthat/test_aws_error.R | 10 tests/testthat/test_cache.R | 6 tests/testthat/test_client.R | 106 + tests/testthat/test_config.R | 328 ++--- tests/testthat/test_convert.R | 13 tests/testthat/test_credential_providers.R | 37 tests/testthat/test_credentials.R | 69 - tests/testthat/test_custom_s3.R | 138 +- tests/testthat/test_dateutil.R | 20 tests/testthat/test_endpoint_vendor.R | 72 - tests/testthat/test_escape.R | 24 tests/testthat/test_handlers_core.R | 5 tests/testthat/test_handlers_ec2query.R | 196 +-- tests/testthat/test_handlers_jsonrpc.R | 285 +--- tests/testthat/test_handlers_query.R | 388 +++--- tests/testthat/test_handlers_rest.R | 41 tests/testthat/test_handlers_restjson.R | 401 +++--- tests/testthat/test_handlers_restxml.R | 414 +++--- tests/testthat/test_handlers_sse.R | 45 tests/testthat/test_handlers_stream.R | 1776 ++++++++++++++++++++++++++--- tests/testthat/test_iniutil.R | 13 tests/testthat/test_logging.R | 44 tests/testthat/test_net.R | 36 tests/testthat/test_paginate.R | 279 ++-- tests/testthat/test_populateutil.R | 6 tests/testthat/test_request.R | 5 tests/testthat/test_retry.R | 51 tests/testthat/test_service.R | 41 tests/testthat/test_signer_query.R | 521 ++++---- tests/testthat/test_signer_v4.R | 92 - tests/testthat/test_util.R | 5 tests/testthat/test_xmlutil.R | 42 79 files changed, 4197 insertions(+), 2989 deletions(-)
Title: Statistical Functions for the Design of Studies with Composite
Endpoints
Description: It has been designed to calculate the required sample size in randomized clinical trials with composite endpoints. It also calculates the expected effect and the probability of observing the composite endpoint, among others. The methodology can be found in Bofill & Gómez (2019) <doi:10.1002/sim.8092> and Gómez & Lagakos (2013) <doi:10.1002/sim.5547>.
Author: Marta Bofill Roig [aut, cre],
Jordi Cortes Martinez [aut],
Guadalupe Gomez Melis [ctb]
Maintainer: Marta Bofill Roig <marta.bofill.roig@upc.edu>
Diff between CompAREdesign versions 2.3.1 dated 2024-02-15 and 2.4.0 dated 2025-03-04
DESCRIPTION | 27 +++++-- MD5 | 54 +++++++++------ R/ARE_tte.R | 57 ++++++---------- R/MarginalsSelection.R | 47 +++++++------ R/effectsize_tte.R | 111 ++++++++++++++++--------------- R/get_prob1.R | 6 - R/plot_tte.R | 126 +++++++++++++++++++++++------------ R/sample_size_tte.R | 64 +++++++++--------- R/simula_cbe.R | 24 +++--- R/simula_tte.R | 17 +++- R/surv_tte.R | 152 ++++++++++++++++++++++--------------------- build |only inst |only man/ARE_tte.Rd | 16 ++-- man/CompAREdesign-package.Rd | 25 ++++++- man/MarginalsSelection.Rd | 5 + man/effectsize_tte.Rd | 20 +++-- man/figures |only man/get_prob1.Rd | 12 +++ man/plot_tte.Rd | 26 +++++-- man/samplesize_tte.Rd | 26 +++++-- man/simula_tte.Rd | 11 ++- man/surv_tte.Rd | 27 +++++-- vignettes |only 24 files changed, 520 insertions(+), 333 deletions(-)
Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones.
Includes a function for every PX keyword, making metadata manipulation
simple and human-readable.
Author: Johan Ejstrud [cre, aut],
Lars Pedersen [aut],
Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Diff between pxmake versions 0.15.1 dated 2025-02-17 and 0.16.0 dated 2025-03-04
DESCRIPTION | 12 +++--- MD5 | 26 ++++++------- NEWS.md | 15 +++++++ R/data_df.R | 28 ++++++++------ R/px.R | 21 +++++++--- R/px_file.R | 3 - README.md | 19 ++------- inst/doc/first-px-file.html | 42 ++++++++++----------- inst/doc/micro-files.html | 26 ++++++------- man/px.Rd | 21 +++++++--- tests/testthat/test-50-px.R | 2 + tests/testthat/test-52-px-ordering.R | 64 ++++++++++++++++++++++++++++++--- tests/testthat/test-55-modify-cells1.R | 2 - tests/testthat/test-91-micromake.R | 3 - 14 files changed, 180 insertions(+), 104 deletions(-)
Title: Extended Legends and Axes for 'ggplot2'
Description: A 'ggplot2' extension that focusses on expanding the
plotter's arsenal of guides. Guides in 'ggplot2' include axes and
legends. 'legendry' offers new axes and annotation options, as well as
new legends and colour displays.
Author: Teun van den Brand [aut, cre, cph]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between legendry versions 0.2.0 dated 2024-12-14 and 0.2.1 dated 2025-03-04
DESCRIPTION | 6 MD5 | 100 - NEWS.md | 19 R/aaa.R | 2 R/compose-.R | 2 R/compose-crux.R | 486 +++--- R/compose-sandwich.R | 228 +- R/compose-stack.R | 15 R/gizmo-density.R | 6 R/gizmo-histogram.R | 45 R/guide-circles.R | 790 +++++----- R/guide-colring.R | 5 R/guide-legend-base.R | 4 R/guide-legend-cross.R | 4 R/guide-legend-group.R | 4 R/key-.R | 744 ++++----- R/key-group.R | 4 R/key-range.R | 6 R/key-segment.R | 44 R/primitive-bracket.R | 614 +++---- R/primitive-labels.R | 5 R/primitive-line.R | 389 ++-- R/primitive-segments.R | 28 R/themes.R | 3 R/utils-checks.R | 33 R/utils-ggplot2.R | 531 +++--- R/utils.R | 10 man/figures/README-composition-1.svg | 1 man/figures/README-full_guides-1.svg | 1 man/gizmo_density.Rd | 5 man/gizmo_histogram.Rd | 15 man/key_group.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/compose-sandwich/horizontal-sandwich-flipped.svg | 1 tests/testthat/_snaps/compose-sandwich/horizontal-sandwich.svg | 1 tests/testthat/_snaps/compose-sandwich/vertical-sandwich-flipped.svg | 1 tests/testthat/_snaps/compose-sandwich/vertical-sandwich.svg | 1 tests/testthat/_snaps/compose-stack/compose-stack-cartesian.svg | 16 tests/testthat/_snaps/guide-circles.md |only tests/testthat/_snaps/guide-colbar/bottom-position.svg | 4 tests/testthat/_snaps/guide-colbar/left-position.svg | 4 tests/testthat/_snaps/guide-colbar/right-position.svg | 4 tests/testthat/_snaps/guide-colbar/top-position.svg | 4 tests/testthat/_snaps/guide-colsteps/bottom-position.svg | 4 tests/testthat/_snaps/guide-colsteps/left-position.svg | 4 tests/testthat/_snaps/guide-colsteps/right-position.svg | 4 tests/testthat/_snaps/guide-colsteps/top-position.svg | 4 tests/testthat/test-aaa.R | 3 tests/testthat/test-guide-circles.R | 142 - tests/testthat/test-key-range.R | 14 tests/testthat/test-key-segment.R | 14 tests/testthat/test-themes.R |only 52 files changed, 2293 insertions(+), 2085 deletions(-)
Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials.
Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the
probability that a jury will find a defendant guilty given jurors' preferences for a guilty
verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical
trial conditions to conduct harmful error analysis. The relationship between individual jurors'
verdict preferences and the probability that a jury returns a guilty verdict has been studied
by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>,
and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>
Diff between sate versions 2.3.0 dated 2025-02-06 and 2.4.0 dated 2025-03-04
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NEWS.md | 14 ++++++++++++-- R/data.R | 26 ++++++++++++++++++++++++++ data/observed.deliberations.rda |only man/observed.deliberations.Rd |only 6 files changed, 46 insertions(+), 8 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.4 dated 2025-02-06 and 0.3.5 dated 2025-03-04
DESCRIPTION | 8 ++-- MD5 | 28 +++++++------- R/fit_goscar.R | 26 +++++++++++-- R/fit_gslope.R | 24 +++++++++++- R/fit_sgo.R | 24 +++++++++++- R/fit_sgs.R | 23 +++++++++++- R/fitting_code.R | 22 +---------- R/global_wrapper_code.R | 41 ++++++++++++++------- R/screen.R | 2 - R/utils.R | 70 +++++++++++++++++++++++++++++-------- inst/doc/reproducible_example.html | 12 +++--- man/fit_goscar.Rd | 2 - man/fit_gslope.Rd | 2 - man/fit_sgo.Rd | 2 - man/fit_sgs.Rd | 2 - 15 files changed, 201 insertions(+), 87 deletions(-)
Title: A Spotlight 'React' Widget for 'shiny' Apps
Description: Creates a contextual menu that can be triggered with keyboard shortcuts or programmatically.
This can replace traditional sidebars or navigation bars, thereby enhancing the
user experience with lighter user interfaces.
Author: David Granjon [aut, cre],
Adenekan Wonderful [cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between scoutbaR versions 0.0.1 dated 2024-11-21 and 0.1.0 dated 2025-03-04
scoutbaR-0.0.1/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002_.new.png |only scoutbaR-0.1.0/scoutbaR/DESCRIPTION | 6 scoutbaR-0.1.0/scoutbaR/MD5 | 22 scoutbaR-0.1.0/scoutbaR/NEWS.md | 7 scoutbaR-0.1.0/scoutbaR/R/scoutbar.R | 2 scoutbaR-0.1.0/scoutbaR/inst/examples/simple/app.R | 2 scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js | 2659 ---------- scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js.LICENSE.txt |only scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js.map | 2 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-001.json | 3 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002.json | 1 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002_.png |binary scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-003.json | 1 13 files changed, 30 insertions(+), 2675 deletions(-)
Title: Ternary Plots
Description: Ternary plots made simple. This package allows to create
ternary plots using 'graphics'. It provides functions to display the
data in the ternary space, to add or tune graphical elements and to
display statistical summaries. It also includes common ternary
diagrams which are useful for the archaeologist (e.g. soil texture
charts, ceramic phase diagram).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between isopleuros versions 1.3.0 dated 2024-11-22 and 1.4.0 dated 2025-03-04
DESCRIPTION | 30 ++- MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 7 R/AllGenerics.R | 49 +++++- R/coordinates.R | 2 R/isopleuros-internal.R | 38 ++++ R/isopleuros-package.R | 2 R/ternary_contour.R | 5 R/ternary_image.R | 245 ++++++++++++++++++++---------- R/ternary_window.R | 2 README.md | 38 +++- build/partial.rdb |binary inst/CITATION | 2 inst/examples/ex-tile.R |only inst/po |only inst/tinytest/_tinysnapshot/image_bin.svg |only inst/tinytest/test_tiles.R | 13 + man/isopleuros-package.Rd | 6 man/ternary_contour.Rd | 2 man/ternary_image.Rd | 3 man/ternary_tile.Rd |only po |only 23 files changed, 354 insertions(+), 133 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 1.0.4 dated 2025-01-16 and 1.0.5 dated 2025-03-04
DESCRIPTION | 8 +++---- LICENSE |only MD5 | 25 +++++++++++----------- NEWS.md | 4 +++ R/base.R | 16 -------------- R/secret.R | 16 -------------- README.md | 28 ++++++++---------------- build/partial.rdb |binary src/base.c | 35 +++++++++--------------------- src/init.c | 16 -------------- src/secret.c | 16 -------------- src/secret.h | 18 --------------- src/secret2.c | 16 -------------- src/secret3.c | 61 ++++++++++++++++++++++-------------------------------- 14 files changed, 67 insertions(+), 192 deletions(-)
Title: Search and Retrieve Spatial Data from 'GUGiK'
Description: Automatic open data acquisition from resources of Polish Head Office
of Geodesy and Cartography ('Główny Urząd Geodezji i Kartografii')
(<https://www.gov.pl/web/gugik>).
Available datasets include various types of numeric, raster and vector data,
such as orthophotomaps, digital elevation models (digital terrain models,
digital surface model, point clouds), state register of borders, spatial
databases, geometries of cadastral parcels, 3D models of buildings, and more.
It is also possible to geocode addresses or objects using the geocodePL_get()
function.
Author: Krzysztof Dyba [aut, cre] ,
Jakub Nowosad [aut] ,
Maciej Beresewicz [ctb] ,
Grzegorz Sapijaszko [ctb],
GUGiK [ctb]
Maintainer: Krzysztof Dyba <adres7@gmail.com>
Diff between rgugik versions 0.4.1 dated 2024-05-11 and 0.4.2 dated 2025-03-04
DESCRIPTION | 15 ++++++--- MD5 | 57 ++++++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 13 ++++++++ R/DEM_request.R | 10 ++++-- R/borders_download.R | 6 +-- R/commune_names.R | 2 - R/egib_download.R |only R/egib_layers.R |only R/geodb_download.R | 2 - R/geonames_download.R | 2 - R/minmaxDTM_get.R | 3 + R/topodb_download.R | 2 - README.md | 33 +++++++++++--------- build/vignette.rds |binary data/commune_names.rda |binary data/egib_layers.rda |only inst/doc/DEM.html | 4 +- inst/doc/orthophotomap.html | 2 - inst/doc/topodb.html | 2 - man/borders_download.Rd | 2 - man/commune_names.Rd | 4 +- man/egib_download.Rd |only man/egib_layers.Rd |only man/figures/README-f1-1.png |binary man/figures/README-f2-1.png |binary man/geonames_download.Rd | 2 - man/rgugik-package.Rd | 1 tests/test-tile_download.R |only tests/testthat/test-DEM_request.R | 2 - tests/testthat/test-egib_download.R |only tests/testthat/test-geocodePL_get.R | 6 +-- tests/testthat/test-tile_download.R | 8 +---- 33 files changed, 106 insertions(+), 73 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.24.1 dated 2025-01-14 and 0.24.2 dated 2025-03-04
DESCRIPTION | 30 +++--- MD5 | 116 +++++++++++++-------------- NAMESPACE | 2 NEWS.md | 15 +++ R/1_model_parameters.R | 15 --- R/dof_kenward.R | 8 - R/extract_random_variances.R | 2 R/format.R | 5 + R/group_level_total.R |only R/methods_aod.R | 7 - R/methods_aov.R | 12 ++ R/methods_averaging.R | 7 - R/methods_betareg.R | 7 - R/methods_bfsl.R | 7 - R/methods_brglm2.R | 14 --- R/methods_brms.R | 20 ++-- R/methods_cplm.R | 7 - R/methods_fixest.R | 14 --- R/methods_glmmTMB.R | 24 +++-- R/methods_hglm.R | 7 - R/methods_lme4.R | 20 ++-- R/methods_marginaleffects.R | 37 +++++++- R/methods_mclogit.R | 7 - R/methods_mmrm.R | 7 - R/methods_mvord.R | 7 - R/methods_nestedLogit.R | 7 - R/methods_ordinal.R | 7 - R/methods_panelr.R | 1 R/methods_rstanarm.R | 8 + R/methods_selection.R | 7 - R/methods_survey.R | 7 - R/methods_svy2lme.R | 4 R/methods_systemfit.R | 7 - R/print.parameters_model.R | 7 + R/print_html.R | 1 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 man/compare_parameters.Rd | 12 +- man/display.parameters_model.Rd | 5 - man/equivalence_test.lm.Rd | 7 - man/model_parameters.BFBayesFactor.Rd | 10 +- man/model_parameters.befa.Rd | 10 +- man/model_parameters.brmsfit.Rd | 24 ++--- man/model_parameters.default.Rd | 3 man/model_parameters.glimML.Rd | 3 man/model_parameters.glmmTMB.Rd | 10 -- man/model_parameters.zcpglm.Rd | 3 man/p_function.Rd | 7 - man/pool_parameters.Rd | 7 - man/print.compare_parameters.Rd | 5 - man/print.parameters_model.Rd | 5 - man/simulate_parameters.Rd | 10 +- tests/testthat/_snaps/marginaleffects.md | 2 tests/testthat/_snaps/weightit.md | 2 tests/testthat/test-group_level_total.R |only tests/testthat/test-marginaleffects.R | 19 ++++ tests/testthat/test-model_parameters.aov.R | 48 +++++++++++ tests/testthat/test-model_parameters.mixed.R | 8 + 60 files changed, 324 insertions(+), 332 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] ,
Eva Cantagallo [aut],
William Anderson [aut],
Julien Peron [ctb],
Johan Verbeeck [ctb]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 3.0.5 dated 2024-10-13 and 3.1.0 dated 2025-03-04
BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getCount.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getIid.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getPairScore.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getPseudovalue.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getSurvival.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-sensitivity.Rd |only BuyseTest-3.1.0/BuyseTest/DESCRIPTION | 16 BuyseTest-3.1.0/BuyseTest/MD5 | 304 - BuyseTest-3.1.0/BuyseTest/NAMESPACE | 193 BuyseTest-3.1.0/BuyseTest/NEWS | 540 +- BuyseTest-3.1.0/BuyseTest/R/0-onLoad.R | 22 BuyseTest-3.1.0/BuyseTest/R/1-setGeneric.R | 118 BuyseTest-3.1.0/BuyseTest/R/BuyseMultComp.R | 996 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTTEM.R | 1403 +++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-Peron.R | 714 +- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-check.R | 1139 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-inference.R | 1028 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-initialization.R | 1738 +++---- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-package.R | 142 BuyseTest-3.1.0/BuyseTest/R/BuyseTest-print.R | 357 - BuyseTest-3.1.0/BuyseTest/R/BuyseTest.R | 1557 +++--- BuyseTest-3.1.0/BuyseTest/R/BuyseTest.options.R | 222 BuyseTest-3.1.0/BuyseTest/R/CasinoTest.R | 666 +- BuyseTest-3.1.0/BuyseTest/R/PairScore.R | 108 BuyseTest-3.1.0/BuyseTest/R/RcppExports.R | 462 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-model.tables.R | 338 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-nobs.R | 96 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-print.R | 66 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-show.R | 64 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-summary.R | 350 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower.R | 166 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-coef.R | 678 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-confint.R | 2166 ++++---- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-get.R | 1706 +++---- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-model.tables.R | 564 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-nobs.R | 204 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-plot.R | 178 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-print.R | 70 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-sensitivity.R | 730 +-- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-show.R | 98 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-summary.R | 947 +-- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest.R | 612 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest.options.R | 464 - BuyseTest-3.1.0/BuyseTest/R/as.data.table.performance.R | 282 - BuyseTest-3.1.0/BuyseTest/R/auc.R | 792 +-- BuyseTest-3.1.0/BuyseTest/R/autoplot.S4BuyseTest.R | 342 - BuyseTest-3.1.0/BuyseTest/R/brier.R | 604 +- BuyseTest-3.1.0/BuyseTest/R/constStrata.R | 178 BuyseTest-3.1.0/BuyseTest/R/discreteRoot.R | 580 +- BuyseTest-3.1.0/BuyseTest/R/doc-data.R |only BuyseTest-3.1.0/BuyseTest/R/efronlim.R |only BuyseTest-3.1.0/BuyseTest/R/iid.S3sensitivity.R | 50 BuyseTest-3.1.0/BuyseTest/R/iid.prodlim.R | 404 - BuyseTest-3.1.0/BuyseTest/R/normexp.R | 424 - BuyseTest-3.1.0/BuyseTest/R/performance.R | 2424 +++++----- BuyseTest-3.1.0/BuyseTest/R/performanceResample.R | 572 +- BuyseTest-3.1.0/BuyseTest/R/plot.S3sensitivity.R | 358 - BuyseTest-3.1.0/BuyseTest/R/powerBuyseTest.R | 1621 +++--- BuyseTest-3.1.0/BuyseTest/R/predict.logit.R | 564 +- BuyseTest-3.1.0/BuyseTest/R/rbind.performanceResample.R | 226 BuyseTest-3.1.0/BuyseTest/R/sim.simBuyseTest.R | 66 BuyseTest-3.1.0/BuyseTest/R/simBuyseTest.R | 1470 +++--- BuyseTest-3.1.0/BuyseTest/R/simCompetingRisks.R | 284 - BuyseTest-3.1.0/BuyseTest/R/summary.performance.R | 228 BuyseTest-3.1.0/BuyseTest/R/valid.R | 960 +-- BuyseTest-3.1.0/BuyseTest/build/vignette.rds |binary BuyseTest-3.1.0/BuyseTest/data |only BuyseTest-3.1.0/BuyseTest/inst/CITATION | 116 BuyseTest-3.1.0/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-3.1.0/BuyseTest/inst/doc/overview.pdf.asis | 1118 ++-- BuyseTest-3.1.0/BuyseTest/inst/doc/wilcoxonTest.pdf.asis | 210 BuyseTest-3.1.0/BuyseTest/inst/source |only BuyseTest-3.1.0/BuyseTest/man/BuyseMultComp.Rd | 230 BuyseTest-3.1.0/BuyseTest/man/BuyseTTEM.Rd | 157 BuyseTest-3.1.0/BuyseTest/man/BuyseTest-package.Rd | 166 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.Rd | 635 +- BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options-class.Rd | 32 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options-methods.Rd | 44 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options.Rd | 66 BuyseTest-3.1.0/BuyseTest/man/CasinoTest.Rd | 224 BuyseTest-3.1.0/BuyseTest/man/GPC_cpp.Rd | 380 - BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-class.Rd | 34 BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-nobs.Rd | 50 BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-summary.Rd | 118 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-class.Rd | 34 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-coef.Rd | 132 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-confint.Rd | 254 - BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-nobs.Rd | 62 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-plot.Rd | 136 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-print.Rd | 52 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-show.Rd | 72 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-summary.Rd | 284 - BuyseTest-3.1.0/BuyseTest/man/as.data.table.performance.Rd | 66 BuyseTest-3.1.0/BuyseTest/man/auc.Rd | 166 BuyseTest-3.1.0/BuyseTest/man/autoplot-S4BuyseTest.Rd | 82 BuyseTest-3.1.0/BuyseTest/man/calcIntegralSurv2_cpp.Rd | 94 BuyseTest-3.1.0/BuyseTest/man/coef.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/coef.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/confint.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/confint.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/constStrata.Rd | 122 BuyseTest-3.1.0/BuyseTest/man/data-CHARM.Rd |only BuyseTest-3.1.0/BuyseTest/man/data-EB.Rd |only BuyseTest-3.1.0/BuyseTest/man/data-prodige.Rd |only BuyseTest-3.1.0/BuyseTest/man/dot-calcIntegralCif_cpp.Rd | 98 BuyseTest-3.1.0/BuyseTest/man/dot-calcIntegralSurv_cpp.Rd | 84 BuyseTest-3.1.0/BuyseTest/man/dot-colCenter_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-colCumSum_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-colMultiply_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-colScale_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowCenter_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowCumProd_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-rowCumSum_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-rowMultiply_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowScale_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/efronlim.Rd |only BuyseTest-3.1.0/BuyseTest/man/getCount.Rd |only BuyseTest-3.1.0/BuyseTest/man/getIid.Rd |only BuyseTest-3.1.0/BuyseTest/man/getPairScore.Rd |only BuyseTest-3.1.0/BuyseTest/man/getPseudovalue.Rd |only BuyseTest-3.1.0/BuyseTest/man/getSurvival.Rd |only BuyseTest-3.1.0/BuyseTest/man/iid.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/iid.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/iid.prodlim.Rd | 110 BuyseTest-3.1.0/BuyseTest/man/performance.Rd | 212 BuyseTest-3.1.0/BuyseTest/man/performanceResample.Rd | 114 BuyseTest-3.1.0/BuyseTest/man/powerBuyseTest.Rd | 314 - BuyseTest-3.1.0/BuyseTest/man/predict.BuyseTTEM.Rd | 62 BuyseTest-3.1.0/BuyseTest/man/rbind.performance.Rd | 122 BuyseTest-3.1.0/BuyseTest/man/sensitivity.Rd |only BuyseTest-3.1.0/BuyseTest/man/simBuyseTest.Rd | 422 - BuyseTest-3.1.0/BuyseTest/man/simCompetingRisks.Rd | 212 BuyseTest-3.1.0/BuyseTest/man/summary.performance.Rd | 46 BuyseTest-3.1.0/BuyseTest/man/validFCTs.Rd | 312 - BuyseTest-3.1.0/BuyseTest/tests/testthat.R | 84 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuysePower.R | 400 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTTEM.R | 568 +- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 468 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R | 240 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 1204 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 1148 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 450 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-engine.R | 214 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-iid.R | 1601 +++--- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-multcomp.R | 178 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 206 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 202 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 1556 +++--- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 1198 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-restricted.R | 188 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-strata.R | 864 +-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-weightObs.R | 130 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-auc.R | 268 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-initSurvival.R | 438 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-initThreshold.R | 168 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-otherPackages.R | 394 - BuyseTest-3.1.0/BuyseTest/tests/testthat/testthat-problems.rds |only BuyseTest-3.1.0/BuyseTest/vignettes/overview.pdf.asis | 1118 ++-- BuyseTest-3.1.0/BuyseTest/vignettes/vignette_CR.Rmd | 146 BuyseTest-3.1.0/BuyseTest/vignettes/wilcoxonTest.pdf.asis | 210 160 files changed, 27637 insertions(+), 27481 deletions(-)
Title: Maximum Likelihood Estimation for Univariate Densities
Description: User-friendly maximum likelihood estimation (Fisher (1921)
<doi:10.1098/rsta.1922.0009>) of univariate densities.
Author: Jonas Moss [aut, cre] ,
Thomas Nagler [ctb],
Chitu Okoli [ctb]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between univariateML versions 1.1.1 dated 2022-01-25 and 1.5.0 dated 2025-03-04
univariateML-1.1.1/univariateML/R/imports.R |only univariateML-1.1.1/univariateML/man/ml_input_checker.Rd |only univariateML-1.5.0/univariateML/DESCRIPTION | 16 univariateML-1.5.0/univariateML/LICENSE | 4 univariateML-1.5.0/univariateML/MD5 | 339 ++- univariateML-1.5.0/univariateML/NAMESPACE | 118 - univariateML-1.5.0/univariateML/R/aaa.R |only univariateML-1.5.0/univariateML/R/bootstrap.R | 189 +- univariateML-1.5.0/univariateML/R/data-abalone.R | 62 univariateML-1.5.0/univariateML/R/data-corbet.R |only univariateML-1.5.0/univariateML/R/data-egypt.R | 58 univariateML-1.5.0/univariateML/R/densities.R | 4 univariateML-1.5.0/univariateML/R/functions.R | 168 - univariateML-1.5.0/univariateML/R/generics.R | 372 ++-- univariateML-1.5.0/univariateML/R/helpers.R | 291 +-- univariateML-1.5.0/univariateML/R/mlbeta.R | 177 -- univariateML-1.5.0/univariateML/R/mlbetapr.R | 101 - univariateML-1.5.0/univariateML/R/mlbinom.R |only univariateML-1.5.0/univariateML/R/mlburr.R |only univariateML-1.5.0/univariateML/R/mlcauchy.R | 111 - univariateML-1.5.0/univariateML/R/mldunif.R |only univariateML-1.5.0/univariateML/R/mlexp.R | 84 univariateML-1.5.0/univariateML/R/mlfatigue.R |only univariateML-1.5.0/univariateML/R/mlgamma.R | 151 - univariateML-1.5.0/univariateML/R/mlged.R | 86 - univariateML-1.5.0/univariateML/R/mlgeom.R |only univariateML-1.5.0/univariateML/R/mlgompertz.R |only univariateML-1.5.0/univariateML/R/mlgumbel.R | 163 - univariateML-1.5.0/univariateML/R/mlinvburr.R |only univariateML-1.5.0/univariateML/R/mlinvgamma.R | 99 - univariateML-1.5.0/univariateML/R/mlinvgauss.R | 101 - univariateML-1.5.0/univariateML/R/mlinvweibull.R | 117 - univariateML-1.5.0/univariateML/R/mlkumar.R | 178 -- univariateML-1.5.0/univariateML/R/mllaplace.R | 91 - univariateML-1.5.0/univariateML/R/mllgamma.R | 105 - univariateML-1.5.0/univariateML/R/mllgser.R |only univariateML-1.5.0/univariateML/R/mlllogis.R | 109 - univariateML-1.5.0/univariateML/R/mllnorm.R | 96 - univariateML-1.5.0/univariateML/R/mllogis.R | 104 - univariateML-1.5.0/univariateML/R/mllogitnorm.R | 106 - univariateML-1.5.0/univariateML/R/mllomax.R | 196 -- univariateML-1.5.0/univariateML/R/mlnaka.R | 121 - univariateML-1.5.0/univariateML/R/mlnbinom.R |only univariateML-1.5.0/univariateML/R/mlnorm.R | 93 - univariateML-1.5.0/univariateML/R/mlparalogis.R |only univariateML-1.5.0/univariateML/R/mlpareto.R | 94 - univariateML-1.5.0/univariateML/R/mlpois.R |only univariateML-1.5.0/univariateML/R/mlpower.R | 131 - univariateML-1.5.0/univariateML/R/mlrayleigh.R | 85 univariateML-1.5.0/univariateML/R/mlsged.R | 86 - univariateML-1.5.0/univariateML/R/mlsnorm.R | 80 univariateML-1.5.0/univariateML/R/mlsstd.R | 81 univariateML-1.5.0/univariateML/R/mlstd.R | 80 univariateML-1.5.0/univariateML/R/mlunif.R | 84 univariateML-1.5.0/univariateML/R/mlweibull.R | 140 - univariateML-1.5.0/univariateML/R/mlzip.R |only univariateML-1.5.0/univariateML/R/mlzipf.R |only univariateML-1.5.0/univariateML/R/model_select.R | 205 +- univariateML-1.5.0/univariateML/R/probability_plots.R | 308 ++- univariateML-1.5.0/univariateML/R/univariateML-package.R | 44 univariateML-1.5.0/univariateML/R/utility.R | 173 +- univariateML-1.5.0/univariateML/R/zzz.R |only univariateML-1.5.0/univariateML/README.md | 290 +-- univariateML-1.5.0/univariateML/build/vignette.rds |binary univariateML-1.5.0/univariateML/data/corbet.rda |only univariateML-1.5.0/univariateML/inst/CITATION | 33 univariateML-1.5.0/univariateML/inst/doc/copula.R | 86 - univariateML-1.5.0/univariateML/inst/doc/copula.Rmd | 218 +- univariateML-1.5.0/univariateML/inst/doc/copula.html | 770 +++++--- univariateML-1.5.0/univariateML/inst/doc/distributions.R | 25 univariateML-1.5.0/univariateML/inst/doc/distributions.Rmd | 124 - univariateML-1.5.0/univariateML/inst/doc/distributions.html | 659 ++----- univariateML-1.5.0/univariateML/inst/doc/overview.R | 185 +- univariateML-1.5.0/univariateML/inst/doc/overview.Rmd | 411 ++-- univariateML-1.5.0/univariateML/inst/doc/overview.html | 859 ++++------ univariateML-1.5.0/univariateML/man/MaximumLikelihoodDistribution.Rd | 138 - univariateML-1.5.0/univariateML/man/ProbabilityPlots.Rd | 189 +- univariateML-1.5.0/univariateML/man/abalone.Rd | 88 - univariateML-1.5.0/univariateML/man/bootstrapml.Rd | 184 +- univariateML-1.5.0/univariateML/man/confint.univariateML.Rd | 98 - univariateML-1.5.0/univariateML/man/corbet.Rd |only univariateML-1.5.0/univariateML/man/decorator.Rd |only univariateML-1.5.0/univariateML/man/egypt.Rd | 84 univariateML-1.5.0/univariateML/man/figures/README-weibull_plot-1.png |binary univariateML-1.5.0/univariateML/man/get_start.Rd |only univariateML-1.5.0/univariateML/man/inverse_digamma.Rd |only univariateML-1.5.0/univariateML/man/listmerge.Rd | 50 univariateML-1.5.0/univariateML/man/mlbeta.Rd | 95 - univariateML-1.5.0/univariateML/man/mlbetapr.Rd | 98 - univariateML-1.5.0/univariateML/man/mlbinom.Rd |only univariateML-1.5.0/univariateML/man/mlburr.Rd |only univariateML-1.5.0/univariateML/man/mlcauchy.Rd | 94 - univariateML-1.5.0/univariateML/man/mldunif.Rd |only univariateML-1.5.0/univariateML/man/mlexp.Rd | 89 - univariateML-1.5.0/univariateML/man/mlfatigue.Rd |only univariateML-1.5.0/univariateML/man/mlgamma.Rd | 100 - univariateML-1.5.0/univariateML/man/mlged.Rd | 92 - univariateML-1.5.0/univariateML/man/mlgeom.Rd |only univariateML-1.5.0/univariateML/man/mlgompertz.Rd |only univariateML-1.5.0/univariateML/man/mlgumbel.Rd | 93 - univariateML-1.5.0/univariateML/man/mlinvburr.Rd |only univariateML-1.5.0/univariateML/man/mlinvgamma.Rd | 88 - univariateML-1.5.0/univariateML/man/mlinvgauss.Rd | 92 - univariateML-1.5.0/univariateML/man/mlinvweibull.Rd | 102 - univariateML-1.5.0/univariateML/man/mlkumar.Rd | 106 - univariateML-1.5.0/univariateML/man/mllaplace.Rd | 90 - univariateML-1.5.0/univariateML/man/mllgamma.Rd | 92 - univariateML-1.5.0/univariateML/man/mllgser.Rd |only univariateML-1.5.0/univariateML/man/mlllogis.Rd | 102 - univariateML-1.5.0/univariateML/man/mllnorm.Rd | 92 - univariateML-1.5.0/univariateML/man/mllogis.Rd | 90 - univariateML-1.5.0/univariateML/man/mllogitnorm.Rd | 92 - univariateML-1.5.0/univariateML/man/mllomax.Rd | 113 - univariateML-1.5.0/univariateML/man/mlnaka.Rd | 103 - univariateML-1.5.0/univariateML/man/mlnbinom.Rd |only univariateML-1.5.0/univariateML/man/mlnorm.Rd | 90 - univariateML-1.5.0/univariateML/man/mlparalogis.Rd |only univariateML-1.5.0/univariateML/man/mlpareto.Rd | 90 - univariateML-1.5.0/univariateML/man/mlpois.Rd |only univariateML-1.5.0/univariateML/man/mlpower.Rd | 106 - univariateML-1.5.0/univariateML/man/mlrayleigh.Rd | 88 - univariateML-1.5.0/univariateML/man/mlsged.Rd | 92 - univariateML-1.5.0/univariateML/man/mlsnorm.Rd | 86 - univariateML-1.5.0/univariateML/man/mlsstd.Rd | 86 - univariateML-1.5.0/univariateML/man/mlstd.Rd | 86 - univariateML-1.5.0/univariateML/man/mlunif.Rd | 86 - univariateML-1.5.0/univariateML/man/mlweibull.Rd | 94 - univariateML-1.5.0/univariateML/man/mlzip.Rd |only univariateML-1.5.0/univariateML/man/mlzipf.Rd |only univariateML-1.5.0/univariateML/man/model_select.Rd | 126 - univariateML-1.5.0/univariateML/man/newton_raphson_1d.Rd |only univariateML-1.5.0/univariateML/man/plot.univariateML.Rd | 68 univariateML-1.5.0/univariateML/man/plot_wrangler.Rd | 38 univariateML-1.5.0/univariateML/man/ppqq_wrangler.Rd | 42 univariateML-1.5.0/univariateML/man/simulate_default.Rd |only univariateML-1.5.0/univariateML/man/to_univariateML.Rd | 34 univariateML-1.5.0/univariateML/man/univariateML-package.Rd | 93 - univariateML-1.5.0/univariateML/man/univariateML_construct.Rd |only univariateML-1.5.0/univariateML/man/univariateML_metadata.Rd |only univariateML-1.5.0/univariateML/man/univariateML_models.Rd | 38 univariateML-1.5.0/univariateML/man/univariateML_to_function.Rd | 44 univariateML-1.5.0/univariateML/man/univariateML_to_string.Rd | 44 univariateML-1.5.0/univariateML/tests/testthat.R | 8 univariateML-1.5.0/univariateML/tests/testthat/Rplots.pdf |binary univariateML-1.5.0/univariateML/tests/testthat/test_bootstrap.R | 99 - univariateML-1.5.0/univariateML/tests/testthat/test_confint.R | 28 univariateML-1.5.0/univariateML/tests/testthat/test_functions.R | 95 - univariateML-1.5.0/univariateML/tests/testthat/test_generics.R | 80 univariateML-1.5.0/univariateML/tests/testthat/test_helpers.R | 77 univariateML-1.5.0/univariateML/tests/testthat/test_input_checks.R | 33 univariateML-1.5.0/univariateML/tests/testthat/test_mlbeta.R | 83 univariateML-1.5.0/univariateML/tests/testthat/test_mlbetapr.R | 135 - univariateML-1.5.0/univariateML/tests/testthat/test_mlbinom.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlcauchy.R | 146 - univariateML-1.5.0/univariateML/tests/testthat/test_mlexp.R | 58 univariateML-1.5.0/univariateML/tests/testthat/test_mlgamma.R | 90 - univariateML-1.5.0/univariateML/tests/testthat/test_mlged.R | 103 - univariateML-1.5.0/univariateML/tests/testthat/test_mlgumbel.R | 118 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvgamma.R | 86 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvgauss.R | 138 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvweibull.R | 72 univariateML-1.5.0/univariateML/tests/testthat/test_mlkumar.R | 122 - univariateML-1.5.0/univariateML/tests/testthat/test_mllaplace.R | 56 univariateML-1.5.0/univariateML/tests/testthat/test_mllgamma.R | 82 univariateML-1.5.0/univariateML/tests/testthat/test_mllgser.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlllogis.R | 89 - univariateML-1.5.0/univariateML/tests/testthat/test_mllnorm.R | 60 univariateML-1.5.0/univariateML/tests/testthat/test_mllogis.R | 184 +- univariateML-1.5.0/univariateML/tests/testthat/test_mllogitnorm.R | 64 univariateML-1.5.0/univariateML/tests/testthat/test_mllomax.R | 112 - univariateML-1.5.0/univariateML/tests/testthat/test_mlnaka.R | 90 - univariateML-1.5.0/univariateML/tests/testthat/test_mlnbinom.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlnorm.R | 56 univariateML-1.5.0/univariateML/tests/testthat/test_mlpareto.R | 122 - univariateML-1.5.0/univariateML/tests/testthat/test_mlpower.R | 128 - univariateML-1.5.0/univariateML/tests/testthat/test_mlrayleigh.R | 58 univariateML-1.5.0/univariateML/tests/testthat/test_mlsged.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlsnorm.R | 103 - univariateML-1.5.0/univariateML/tests/testthat/test_mlsstd.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlstd.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlunif.R | 111 - univariateML-1.5.0/univariateML/tests/testthat/test_mlweibull.R | 92 - univariateML-1.5.0/univariateML/tests/testthat/test_mlzip.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlzipf.R |only univariateML-1.5.0/univariateML/tests/testthat/test_model_select.R | 97 - univariateML-1.5.0/univariateML/tests/testthat/test_probability_plots.R | 172 +- univariateML-1.5.0/univariateML/tests/testthat/test_utility.R | 45 univariateML-1.5.0/univariateML/vignettes/copula.Rmd | 218 +- univariateML-1.5.0/univariateML/vignettes/copula.bib | 12 univariateML-1.5.0/univariateML/vignettes/copula.md | 234 +- univariateML-1.5.0/univariateML/vignettes/copula_files/figure-html/make_data-1.png |binary univariateML-1.5.0/univariateML/vignettes/distributions.Rmd | 124 - univariateML-1.5.0/univariateML/vignettes/overview.Rmd | 411 ++-- 193 files changed, 9068 insertions(+), 8875 deletions(-)
Title: Routines for Common fMRI Processing Tasks
Description: Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Mark Fiecas [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRItools versions 0.4.7 dated 2024-05-30 and 0.5.3 dated 2025-03-04
fMRItools-0.4.7/fMRItools/man/detrend.Rd |only fMRItools-0.4.7/fMRItools/man/image.scale.Rd |only fMRItools-0.5.3/fMRItools/DESCRIPTION | 8 fMRItools-0.5.3/fMRItools/MD5 | 34 ++- fMRItools-0.5.3/fMRItools/NAMESPACE | 3 fMRItools-0.5.3/fMRItools/R/DCT_FFT_detrending.R | 199 +++++++++++++++++------ fMRItools-0.5.3/fMRItools/R/UT.R | 20 +- fMRItools-0.5.3/fMRItools/R/carpetplot.R | 1 fMRItools-0.5.3/fMRItools/R/dual_reg.R | 36 ++-- fMRItools-0.5.3/fMRItools/R/expand_RPs.R |only fMRItools-0.5.3/fMRItools/R/fsl_bptf.R | 131 ++++++++++----- fMRItools-0.5.3/fMRItools/R/norm_BOLD.R | 85 ++++++--- fMRItools-0.5.3/fMRItools/R/plot_FC.R | 15 + fMRItools-0.5.3/fMRItools/man/UT2mat.Rd | 13 - fMRItools-0.5.3/fMRItools/man/dct_bases.Rd | 2 fMRItools-0.5.3/fMRItools/man/dual_reg.Rd | 15 + fMRItools-0.5.3/fMRItools/man/expand_RPs.Rd |only fMRItools-0.5.3/fMRItools/man/fsl_bptf.Rd | 13 + fMRItools-0.5.3/fMRItools/man/image_scale.Rd |only fMRItools-0.5.3/fMRItools/man/norm_BOLD.Rd | 24 +- fMRItools-0.5.3/fMRItools/man/temporal_filter.Rd |only 21 files changed, 411 insertions(+), 188 deletions(-)
Title: Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Description: Handles univariate non-parametric density estimation with
parametric starts and asymmetric kernels in a simple and flexible way.
Kernel density estimation with parametric starts involves fitting a
parametric density to the data before making a correction with kernel
density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
Asymmetric kernels make kernel density estimation more efficient on bounded
intervals such as (0, 1) and the positive half-line. Supported asymmetric
kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
User-supplied kernels, parametric starts, and bandwidths are supported.
Author: Jonas Moss [aut, cre] ,
Martin Tveten [ctb]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between kdensity versions 1.1.0 dated 2020-09-30 and 1.1.1 dated 2025-03-04
DESCRIPTION | 19 LICENSE | 2 MD5 | 103 +-- NAMESPACE | 30 NEWS.md | 28 R/builtin_bandwidths.R | 396 ++++++------ R/builtin_bandwidths_get_bw.R | 136 ++-- R/builtin_bandwidths_ucv_helpers.R | 47 - R/builtin_kernels.R | 427 ++++++------- R/builtin_kernels_get_kernel.R | 85 +- R/builtin_starts_get_start.R | 89 +- R/builtin_starts_list.R | 229 +++---- R/cran.r |only R/generics.R | 532 ++++++++-------- R/kdensity.R | 611 +++++++++--------- R/kdensity_helpers.R | 241 +++---- R/utility_functions.R | 239 +++---- README.md | 403 ++++++------ build/vignette.rds |binary inst/doc/tutorial.R | 171 ++--- inst/doc/tutorial.Rmd | 317 ++++----- inst/doc/tutorial.html | 1000 ++++++++++++++++--------------- man/add_bw.Rd | 40 - man/add_kernel.Rd | 40 - man/add_start.Rd | 40 - man/bandwidths.Rd | 138 ++-- man/get_bw.Rd | 36 - man/get_kernel.Rd | 38 - man/get_kernel_start_support.Rd | 60 - man/get_range.Rd | 36 - man/get_standard_bw.Rd | 44 - man/get_start.Rd | 36 - man/kdensity.Rd | 274 ++++---- man/kernels.Rd | 174 ++--- man/listmerge.Rd | 50 - man/parametric_starts.Rd | 106 +-- man/plot.kdensity.Rd | 90 +- man/plot_helper.Rd | 72 +- man/recycle.Rd | 46 - man/support_compatible.Rd | 38 - tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/test_assignments.R | 32 tests/testthat/test_bandwidth.r | 48 - tests/testthat/test_generics.r | 23 tests/testthat/test_generics_invisible.R | 16 tests/testthat/test_kdensity.R | 108 +-- tests/testthat/test_kdensity_helpers.R | 16 tests/testthat/test_kernels.r | 42 - tests/testthat/test_starts.r | 60 - tests/testthat/test_univariateML.R | 83 +- tests/testthat/test_utility_functions.R | 60 - vignettes/tutorial.Rmd | 317 ++++----- 53 files changed, 3727 insertions(+), 3549 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Includes functionality to estimate latent class analyses.
Author: Caspar J. van Lissa [aut, cre]
,
Mauricio Garnier-Villarreal [ctb]
,
Frank C Gootjes [ctb]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between tidySEM versions 0.2.7 dated 2024-06-04 and 0.2.8 dated 2025-03-04
DESCRIPTION | 16 MD5 | 157 +- NAMESPACE | 19 R/blrt.R | 15 R/dagitty.R | 100 + R/lr_vml.R | 16 R/mixture-3step.R | 24 R/mixture-pseudo_class.R | 976 ++++++++-------- R/mixture_gradient.R | 10 R/mixture_predict.R | 2 R/mx_dummies.R | 6 R/mx_mixture.R | 117 + R/mx_simple_thresholds.R | 230 +-- R/mx_switch_labels.R | 2 R/mx_temp_start.R | 30 R/openmx_functions.R | 28 R/plot-bivariate.R | 21 R/plot-plot_sem.R | 29 R/results-table_fit.R | 2 R/results-table_results_mx_model.R | 21 R/syntax-add_paths.R | 26 R/syntax-run.R | 27 R/syntax_data_dictionary.R | 4 R/syntax_factor.R | 1 R/utilities.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Generating_syntax.R | 72 - inst/doc/Generating_syntax.Rmd | 2 inst/doc/Generating_syntax.html | 10 inst/doc/Plotting_graphs.R | 218 +-- inst/doc/Plotting_graphs.html | 34 inst/doc/SMART_LCA_checklist.Rmd | 256 ++-- inst/doc/SMART_LCA_checklist.html | 4 inst/doc/Tabulating_results.R | 70 - inst/doc/Tabulating_results.Rmd | 2 inst/doc/Tabulating_results.html | 2 inst/doc/lca_confirmatory.R | 252 ++-- inst/doc/lca_confirmatory.html | 2 inst/doc/lca_exploratory.R | 230 +-- inst/doc/lca_exploratory.html | 2 inst/doc/lca_lcga.R | 412 +++--- inst/doc/lca_lcga.html | 2 inst/doc/lca_ordinal.R | 156 +- inst/doc/lca_ordinal.html | 2 inst/doc/sem_graph.R | 58 inst/doc/sem_graph.html | 20 man/BCH.Rd | 2 man/add_paths.Rd | 16 man/append_class_draws.Rd | 2 man/lr_lmr.Rd | 2 man/lr_test.Rd | 2 man/mixture_starts.Rd | 12 man/mx_dummies.Rd | 2 man/mx_growth_mixture.Rd | 4 man/mx_lca.Rd | 4 man/mx_mixture.Rd | 2 man/mx_profiles.Rd | 2 man/plot_bivariate.Rd | 2 man/pseudo_class.Rd | 2 man/tidy_sem.Rd | 4 tests/testthat.R | 2 tests/testthat/test-BLRT_lr_lmr.R | 35 tests/testthat/test-dagitty_nodes_edges.R |only tests/testthat/test-lr_test_negative_df.R | 28 tests/testthat/test-lrt_bch.R | 69 - tests/testthat/test-lrt_multigroup.R | 21 tests/testthat/test-multigroup_mx.R | 89 - tests/testthat/test-namespace_checks_dominique.R | 34 tests/testthat/test-openmx_binary.R | 243 ++- tests/testthat/test-openmx_ordinal.R | 133 +- tests/testthat/test-openmx_ordinal_and_cont.R | 134 +- tests/testthat/test-openmx_ordinal_methods.R | 346 ++--- tests/testthat/test-openmx_ordinal_thresh_constraints.R | 101 - tests/testthat/test-plot_plot_prob.R | 1 tests/testthat/test-plot_profiles_varyingcov.R | 1 tests/testthat/test-pseudo_class_technique.R | 2 vignettes/Generating_syntax.Rmd | 2 vignettes/SMART_LCA_checklist.Rmd | 256 ++-- vignettes/Tabulating_results.Rmd | 2 80 files changed, 2681 insertions(+), 2565 deletions(-)
Title: Estimating (Time-Dependent) Drift Diffusion Models
Description: Fit and explore Drift Diffusion Models (DDMs),
a common tool in psychology for describing decision processes in simple
tasks. It can handle both time-independent and time-dependent DDMs. You
either choose prebuilt models or create your own, and the package takes
care of model predictions and parameter estimation. Model predictions
are derived via the numerical solutions provided by Richter, Ulrich, and
Janczyk (2023, <doi:10.1016/j.jmp.2023.102756>).
Author: Valentin Koob [cre, aut, cph],
Thomas Richter [aut, cph],
Markus Janczyk [aut]
Maintainer: Valentin Koob <v.koob@web.de>
Diff between dRiftDM versions 0.2.1 dated 2025-01-08 and 0.2.2 dated 2025-03-04
dRiftDM-0.2.1/dRiftDM/R/formatting_dm_fits_ids.R |only dRiftDM-0.2.1/dRiftDM/R/formatting_rest.R |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.R |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.Rmd |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.html |only dRiftDM-0.2.1/dRiftDM/man/plot.list_stats_dm.Rd |only dRiftDM-0.2.1/dRiftDM/tests/testthat/_snaps/formatting_rest.md |only dRiftDM-0.2.1/dRiftDM/tests/testthat/fixtures/dm_fits_ids |only dRiftDM-0.2.1/dRiftDM/tests/testthat/fixtures/dm_fits_ids.R |only dRiftDM-0.2.1/dRiftDM/tests/testthat/test-formatting_rest.R |only dRiftDM-0.2.1/dRiftDM/vignettes/use_ddm_models.Rmd |only dRiftDM-0.2.2/dRiftDM/DESCRIPTION | 14 dRiftDM-0.2.2/dRiftDM/MD5 | 168 +-- dRiftDM-0.2.2/dRiftDM/NAMESPACE | 45 dRiftDM-0.2.2/dRiftDM/NEWS.md | 29 dRiftDM-0.2.2/dRiftDM/R/core_dm.R | 552 ++++++++-- dRiftDM-0.2.2/dRiftDM/R/core_estimate.R | 2 dRiftDM-0.2.2/dRiftDM/R/core_estimate_wrapper.R | 14 dRiftDM-0.2.2/dRiftDM/R/core_flex_prms.R | 23 dRiftDM-0.2.2/dRiftDM/R/core_stats.R | 91 + dRiftDM-0.2.2/dRiftDM/R/dRiftDM-package.R | 19 dRiftDM-0.2.2/dRiftDM/R/extended_s3_methods.R | 51 dRiftDM-0.2.2/dRiftDM/R/formatting_coefs_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_drift_dm.R | 39 dRiftDM-0.2.2/dRiftDM/R/formatting_fits_ids_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_flex_prms.R | 6 dRiftDM-0.2.2/dRiftDM/R/formatting_stats_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_traces_dm.R |only dRiftDM-0.2.2/dRiftDM/R/models.R | 16 dRiftDM-0.2.2/dRiftDM/R/plotting.R | 46 dRiftDM-0.2.2/dRiftDM/R/utils.R | 4 dRiftDM-0.2.2/dRiftDM/README.md | 75 - 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Title: Clean and Standardize Epidemiological Data
Description: Cleaning and standardizing tabular data package, tailored
specifically for curating epidemiological data. It streamlines various
data cleaning tasks that are typically expected when working with
datasets in epidemiology. It returns the processed data in the same
format, and generates a comprehensive report detailing the outcomes of
each cleaning task.
Author: Karim Mane [aut, cre] ,
Thibaut Jombart [ctb] .),
Abdoelnaser Degoot [aut] ,
Bankole Ahadzie [aut],
Nuredin Mohammed [aut],
Bubacarr Bah [aut] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [rev] ,
James M. Azam [rev] ,
Joshua W. Lambert [rev] ,
Chris Ha [...truncated...]
Maintainer: Karim Mane <karim.mane@lshtm.ac.uk>
Diff between cleanepi versions 1.0.2 dated 2024-06-17 and 1.1.0 dated 2025-03-04
cleanepi-1.0.2/cleanepi/man/date_check_column_existence.Rd |only cleanepi-1.0.2/cleanepi/man/date_convert_and_update.Rd |only cleanepi-1.0.2/cleanepi/man/date_i_extract_string.Rd |only cleanepi-1.0.2/cleanepi/man/date_i_find_format.Rd |only cleanepi-1.0.2/cleanepi/man/default_cleanepi_settings.Rd |only cleanepi-1.0.2/cleanepi/man/get_sum.Rd |only cleanepi-1.0.2/cleanepi/man/make_readcap_dictionary.Rd |only cleanepi-1.0.2/cleanepi/man/scan_columns.Rd |only cleanepi-1.1.0/cleanepi/DESCRIPTION | 62 cleanepi-1.1.0/cleanepi/LICENSE | 2 cleanepi-1.1.0/cleanepi/MD5 | 224 cleanepi-1.1.0/cleanepi/NAMESPACE | 2 cleanepi-1.1.0/cleanepi/NEWS.md |only cleanepi-1.1.0/cleanepi/R/check_date_sequence.R | 105 cleanepi-1.1.0/cleanepi/R/clean_data.R | 241 - cleanepi-1.1.0/cleanepi/R/clean_data_helpers.R | 246 - cleanepi-1.1.0/cleanepi/R/cleanepi-package.R | 1 cleanepi-1.1.0/cleanepi/R/column_name_standardization.R | 213 cleanepi-1.1.0/cleanepi/R/convert_numeric_to_date.R | 29 cleanepi-1.1.0/cleanepi/R/convert_to_numeric.R | 121 cleanepi-1.1.0/cleanepi/R/date_standardization_helpers.R | 525 +- cleanepi-1.1.0/cleanepi/R/default_cleanepi_settings.R | 56 cleanepi-1.1.0/cleanepi/R/dictionary_based_cleaning.R | 271 - cleanepi-1.1.0/cleanepi/R/find_and_remove_duplicates.R | 116 cleanepi-1.1.0/cleanepi/R/guess_dates.R | 391 - cleanepi-1.1.0/cleanepi/R/print_report.R | 172 cleanepi-1.1.0/cleanepi/R/remove_constants.R | 195 cleanepi-1.1.0/cleanepi/R/replace_missing_values.R | 78 cleanepi-1.1.0/cleanepi/R/span.R | 107 cleanepi-1.1.0/cleanepi/R/standardize_date.R | 160 cleanepi-1.1.0/cleanepi/R/standardize_subject_ids.R | 197 cleanepi-1.1.0/cleanepi/R/utils-pipe.R |only cleanepi-1.1.0/cleanepi/R/utils-potools.R |only cleanepi-1.1.0/cleanepi/R/utils.R | 201 cleanepi-1.1.0/cleanepi/README.md | 494 +- cleanepi-1.1.0/cleanepi/build/vignette.rds |binary cleanepi-1.1.0/cleanepi/inst/WORDLIST | 17 cleanepi-1.1.0/cleanepi/inst/doc/cleanepi.R | 518 +- 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cleanepi-1.1.0/cleanepi/tests/testthat/test-clean_data.R | 156 cleanepi-1.1.0/cleanepi/tests/testthat/test-clean_data_helpers.R | 64 cleanepi-1.1.0/cleanepi/tests/testthat/test-column_name_standardization.R | 50 cleanepi-1.1.0/cleanepi/tests/testthat/test-convert_numeric_to_date.R | 44 cleanepi-1.1.0/cleanepi/tests/testthat/test-convert_to_numeric.R | 37 cleanepi-1.1.0/cleanepi/tests/testthat/test-dictionary_based_cleaning.R | 91 cleanepi-1.1.0/cleanepi/tests/testthat/test-find_and_remove_duplicates.R | 23 cleanepi-1.1.0/cleanepi/tests/testthat/test-print_report.R | 90 cleanepi-1.1.0/cleanepi/tests/testthat/test-remove_constants.R | 126 cleanepi-1.1.0/cleanepi/tests/testthat/test-replace_missing_values.R | 25 cleanepi-1.1.0/cleanepi/tests/testthat/test-span.R | 151 cleanepi-1.1.0/cleanepi/tests/testthat/test-standardize_date.R | 232 cleanepi-1.1.0/cleanepi/tests/testthat/test-standardize_subject_ids.R | 215 cleanepi-1.1.0/cleanepi/tests/testthat/test-utils.R | 84 cleanepi-1.1.0/cleanepi/vignettes/cleanepi.Rmd | 617 +- cleanepi-1.1.0/cleanepi/vignettes/design_principle.Rmd | 403 - 124 files changed, 6750 insertions(+), 5895 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.8 dated 2024-11-21 and 0.2.9 dated 2025-03-04
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++------------ NEWS.md | 24 +++++++++------ R/AcqFunction.R | 12 +++---- R/AcqOptimizer.R | 4 +- R/ResultAssignerSurrogate.R | 10 +++--- man/AcqFunction.Rd | 12 +++---- man/AcqOptimizer.Rd | 4 +- tests/testthat.R | 1 tests/testthat/helper.R | 16 ++++++++-- tests/testthat/setup.R | 19 ++++++++++-- tests/testthat/teardown.R | 5 +-- tests/testthat/test_AcqFunctionMulti.R | 2 - tests/testthat/test_ResultAssignerArchive.R | 16 +++++----- tests/testthat/test_ResultAssignerSurrogate.R | 16 +++++----- tests/testthat/test_SurrogateLearnerCollection.R | 8 ++--- tests/testthat/test_TunerADBO.R | 2 - tests/testthat/test_TunerAsyncMbo.R | 2 - tests/testthat/test_TunerMbo.R | 2 - 19 files changed, 117 insertions(+), 82 deletions(-)
Title: Generalized Linear Mixed Models using Adaptive Gaussian
Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under
maximum likelihood approximating the integrals over the random effects with an
adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995)
<doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between GLMMadaptive versions 0.9-1 dated 2023-10-17 and 0.9-7 dated 2025-03-04
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 2 +- R/Functions.R | 12 +++++++----- R/methods.R | 18 ++++++++++-------- R/mixed_fit.R | 2 +- R/mixed_model.R | 4 ++-- build/vignette.rds |binary inst/doc/GLMMadaptive.R | 6 +++--- inst/doc/GLMMadaptive.html | 10 +++++----- man/GLMMadaptive.Rd | 4 ++-- 11 files changed, 45 insertions(+), 41 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 0.2.2 dated 2025-01-28 and 0.3.0 dated 2025-03-04
OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.html |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.html |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.html |only OmopSketch-0.2.2/OmopSketch/vignettes/A-summarise_clinical_tables_records.Rmd |only OmopSketch-0.2.2/OmopSketch/vignettes/B-summarise_concept_set_counts.Rmd |only OmopSketch-0.2.2/OmopSketch/vignettes/C-summarise_observation_period.Rmd |only OmopSketch-0.3.0/OmopSketch/DESCRIPTION | 14 OmopSketch-0.3.0/OmopSketch/MD5 | 74 ++-- OmopSketch-0.3.0/OmopSketch/NEWS.md |only OmopSketch-0.3.0/OmopSketch/R/documentationHelper.R | 9 OmopSketch-0.3.0/OmopSketch/R/summariseClinicalRecords.R | 3 OmopSketch-0.3.0/OmopSketch/R/summariseConceptCounts.R | 2 OmopSketch-0.3.0/OmopSketch/R/summariseConceptIdCounts.R | 57 ++- OmopSketch-0.3.0/OmopSketch/R/summariseConceptSetCounts.R | 15 OmopSketch-0.3.0/OmopSketch/R/summariseInObservation.R | 14 OmopSketch-0.3.0/OmopSketch/R/summariseMissingData.R | 167 ++++++---- OmopSketch-0.3.0/OmopSketch/R/summariseRecordCount.R | 4 OmopSketch-0.3.0/OmopSketch/R/tableClinicalRecords.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableConceptIdCounts.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableMissingData.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableObservationPeriod.R | 9 OmopSketch-0.3.0/OmopSketch/R/tableOmopSnapshot.R | 14 OmopSketch-0.3.0/OmopSketch/build/vignette.rds |binary OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.html |only OmopSketch-0.3.0/OmopSketch/man/interval.Rd |only OmopSketch-0.3.0/OmopSketch/man/summariseConceptIdCounts.Rd | 11 OmopSketch-0.3.0/OmopSketch/man/summariseMissingData.Rd | 7 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseClinicalRecords.R | 2 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseConceptIdCounts.R | 120 ++++++- OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseInObservation.R | 1 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseMissingData.R | 108 ++++++ OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseObservationPeriod.R | 3 OmopSketch-0.3.0/OmopSketch/vignettes/characterisation.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_clinical_tables_records.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_concept_set_counts.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_observation_period.Rmd |only 53 files changed, 506 insertions(+), 158 deletions(-)
Title: Format BibTeX Entries and Files
Description: Format BibTeX entries and files in an opinionated way.
Author: Wenjie Wang [aut, cre]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between formatBibtex versions 0.1.0 dated 2023-02-03 and 0.1.1 dated 2025-03-03
formatBibtex-0.1.0/formatBibtex/R/zzz.R |only formatBibtex-0.1.1/formatBibtex/DESCRIPTION | 11 +- formatBibtex-0.1.1/formatBibtex/MD5 | 26 +++--- formatBibtex-0.1.1/formatBibtex/NAMESPACE | 2 formatBibtex-0.1.1/formatBibtex/NEWS.md |only formatBibtex-0.1.1/formatBibtex/R/bibtex.R | 12 +-- formatBibtex-0.1.1/formatBibtex/R/default_options.R |only formatBibtex-0.1.1/formatBibtex/R/format_string.R | 39 +++++++--- formatBibtex-0.1.1/formatBibtex/R/misc.R | 5 + formatBibtex-0.1.1/formatBibtex/README.md | 6 - formatBibtex-0.1.1/formatBibtex/inst/CITATION | 4 - formatBibtex-0.1.1/formatBibtex/inst/examples/ex-bibtex.R | 24 ++---- formatBibtex-0.1.1/formatBibtex/inst/examples/ex-format_string.R | 12 +-- formatBibtex-0.1.1/formatBibtex/man/format_bibtex_entry.Rd | 28 +++---- formatBibtex-0.1.1/formatBibtex/man/format_options.Rd |only formatBibtex-0.1.1/formatBibtex/man/format_string.Rd | 27 +++--- 16 files changed, 108 insertions(+), 88 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [ctb],
Ching Ching Lau [ [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 0.98 dated 2024-09-19 and 1.0.5 dated 2025-03-03
dartR.base-0.98/dartR.base/R/gl.prop.shared.r |only dartR.base-0.98/dartR.base/R/gl2svdquartets.r |only dartR.base-0.98/dartR.base/man/gl2svdquartets.Rd |only dartR.base-1.0.5/dartR.base/DESCRIPTION | 16 dartR.base-1.0.5/dartR.base/MD5 | 230 +-- dartR.base-1.0.5/dartR.base/NAMESPACE | 18 dartR.base-1.0.5/dartR.base/R/gl.compliance.check.r | 12 dartR.base-1.0.5/dartR.base/R/gl.diagnostics.hwe.r | 10 dartR.base-1.0.5/dartR.base/R/gl.dist.phylo.r | 20 dartR.base-1.0.5/dartR.base/R/gl.dist.pop.r | 71 - dartR.base-1.0.5/dartR.base/R/gl.drop.ind.r | 24 dartR.base-1.0.5/dartR.base/R/gl.drop.pop.r | 61 dartR.base-1.0.5/dartR.base/R/gl.filter.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.filter.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.filter.monomorphs.r | 3 dartR.base-1.0.5/dartR.base/R/gl.filter.rdepth.r | 20 dartR.base-1.0.5/dartR.base/R/gl.filter.reproducibility.r | 28 dartR.base-1.0.5/dartR.base/R/gl.filter.secondaries.r | 21 dartR.base-1.0.5/dartR.base/R/gl.join.r | 346 +++-- dartR.base-1.0.5/dartR.base/R/gl.keep.ind.r | 32 dartR.base-1.0.5/dartR.base/R/gl.keep.pop.r | 51 dartR.base-1.0.5/dartR.base/R/gl.load.r | 26 dartR.base-1.0.5/dartR.base/R/gl.map.interactive.r | 75 - dartR.base-1.0.5/dartR.base/R/gl.pcoa.r | 186 ++ dartR.base-1.0.5/dartR.base/R/gl.propShared.r |only dartR.base-1.0.5/dartR.base/R/gl.read.PLINK.r | 1 dartR.base-1.0.5/dartR.base/R/gl.read.csv.r | 17 dartR.base-1.0.5/dartR.base/R/gl.read.dart.r | 3 dartR.base-1.0.5/dartR.base/R/gl.read.vcf.r | 15 dartR.base-1.0.5/dartR.base/R/gl.report.allelerich.r |only dartR.base-1.0.5/dartR.base/R/gl.report.allna.r | 8 dartR.base-1.0.5/dartR.base/R/gl.report.bases.r | 2 dartR.base-1.0.5/dartR.base/R/gl.report.callrate.r | 50 dartR.base-1.0.5/dartR.base/R/gl.report.diversity.r | 98 - dartR.base-1.0.5/dartR.base/R/gl.report.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.report.heterozygosity.r | 18 dartR.base-1.0.5/dartR.base/R/gl.report.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.report.ld.map.r | 11 dartR.base-1.0.5/dartR.base/R/gl.report.maf.r | 6 dartR.base-1.0.5/dartR.base/R/gl.report.pa.r | 135 + dartR.base-1.0.5/dartR.base/R/gl.report.polyploid_heterozygosity.r | 24 dartR.base-1.0.5/dartR.base/R/gl.report.reproducibility.r | 31 dartR.base-1.0.5/dartR.base/R/gl.report.shannon.r |only dartR.base-1.0.5/dartR.base/R/gl.save.r | 5 dartR.base-1.0.5/dartR.base/R/gl.sort.r | 78 - dartR.base-1.0.5/dartR.base/R/gl.subsample.ind.r | 145 +- dartR.base-1.0.5/dartR.base/R/gl.subsample.loc.r | 84 - dartR.base-1.0.5/dartR.base/R/gl.tree.fitch.r | 7 dartR.base-1.0.5/dartR.base/R/gl.tree.nj.r | 37 dartR.base-1.0.5/dartR.base/R/gl2bpp.r | 101 + dartR.base-1.0.5/dartR.base/R/gl2fasta.r | 21 dartR.base-1.0.5/dartR.base/R/gl2genepop.r | 4 dartR.base-1.0.5/dartR.base/R/gl2paup.parsimony.r |only dartR.base-1.0.5/dartR.base/R/gl2paup.svdquartets.r |only dartR.base-1.0.5/dartR.base/R/utils.check.datatype.R | 4 dartR.base-1.0.5/dartR.base/R/utils.collapse.matrix.r |only dartR.base-1.0.5/dartR.base/R/utils.dart2genlight.r | 56 dartR.base-1.0.5/dartR.base/R/utils.het.report.r | 16 dartR.base-1.0.5/dartR.base/R/utils.read.dart.r | 14 dartR.base-1.0.5/dartR.base/R/utils.read.ped.r | 15 dartR.base-1.0.5/dartR.base/man/gl.alf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.allele.freq.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.dist.phylo.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.dist.pop.Rd | 10 dartR.base-1.0.5/dartR.base/man/gl.filter.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.filter.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.join.Rd | 21 dartR.base-1.0.5/dartR.base/man/gl.load.Rd | 13 dartR.base-1.0.5/dartR.base/man/gl.map.interactive.Rd | 31 dartR.base-1.0.5/dartR.base/man/gl.prop.shared.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.read.csv.Rd | 6 dartR.base-1.0.5/dartR.base/man/gl.read.vcf.Rd | 14 dartR.base-1.0.5/dartR.base/man/gl.report.allelerich.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.allna.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.bases.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.report.basics.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.callrate.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.diversity.Rd | 26 dartR.base-1.0.5/dartR.base/man/gl.report.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.heterozygosity.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.report.ld.map.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl.report.locmetric.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.overshoot.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.pa.Rd | 39 dartR.base-1.0.5/dartR.base/man/gl.report.polyploid_heterozygosity.Rd | 684 ++++------ dartR.base-1.0.5/dartR.base/man/gl.report.rdepth.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.reproducibility.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.secondaries.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.shannon.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.taglength.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.sort.Rd | 42 dartR.base-1.0.5/dartR.base/man/gl.subsample.ind.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.subsample.loc.Rd | 8 dartR.base-1.0.5/dartR.base/man/gl.tree.fitch.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.tree.nj.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl2bpp.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2genepop.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2paup.parsimony.Rd |only dartR.base-1.0.5/dartR.base/man/gl2paup.svdquartets.Rd |only dartR.base-1.0.5/dartR.base/man/utils.check.datatype.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.collapse.matrix.Rd |only dartR.base-1.0.5/dartR.base/man/utils.dart2genlight.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.dist.binary.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.flag.start.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.het.pop.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.impute.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.is.fixed.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.jackknife.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.n.var.invariant.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.plot.save.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.fasta.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.ped.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.avgpic.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.callrate.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhets.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomref.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomsnp.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.reset.flags.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.transpose.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.vcfr2genlight.polyploid.Rd | 1 125 files changed, 2112 insertions(+), 1143 deletions(-)
Title: Load and Process Passive Acoustic Data
Description: Tools for loading and processing passive acoustic data. Read in data
that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
processing functions, and export data for reports or external modeling tools. Parameter
calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
<doi:10.1121/1.3479549>.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Emily Griffiths [ctb],
Michael Oswald [ctb],
Simone Baumann-Pickering [ctb],
Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMpal versions 1.2.1 dated 2024-07-11 and 1.4.4 dated 2025-03-03
DESCRIPTION | 8 - MD5 | 58 ++++----- NAMESPACE | 10 + NEWS.md | 41 ++++++ R/PAMpalSettings.R | 7 - R/addFunction.R | 16 ++ R/addRecordings.R | 41 ++++-- R/calculateAverageSpectra.R | 5 R/calculateEchoDepth.R | 242 ++++++++++++++++++++++++++++++++------- R/calculateICI.R | 38 +++--- R/calculateModuleData.R | 51 -------- R/getClipData.R | 2 R/getDetectorData.R | 4 R/plotGram.R | 15 +- R/processPgDetections.R | 170 +++++++++++++++++++-------- R/runDepthReview.R | 124 +++++++++++++++---- R/runIciReview.R |only R/setSpecies.R | 7 - R/standardClickCalcs.R | 6 R/updateFiles.R | 22 +++ R/utils.R | 4 R/wavUtils.R | 2 man/PAMpalSettings.Rd | 3 man/addFunction.Rd | 4 man/addRecordings.Rd | 7 + man/calculateEchoDepth.Rd | 10 + man/calculateICI.Rd | 6 man/getDetectorData.Rd | 4 man/processPgDetections.Rd | 14 +- man/runIciReview.Rd |only tests/testthat/test-processPps.R | 28 +++- 31 files changed, 681 insertions(+), 268 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.1.8 dated 2024-04-08 and 0.1.9 dated 2025-03-03
DESCRIPTION | 11 - MD5 | 63 +++++---- NEWS.md | 50 +++++++ R/approx_check.R | 11 - R/est_change_plot.R | 4 R/est_change_raw_user.R | 46 +++++-- R/generic_index_plot.R | 6 R/influence_plot.R | 4 R/lavaan_rerun.R | 60 +++++++-- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.html | 14 +- inst/doc/selecting_cases.html | 8 - inst/doc/semfindr.R | 40 +++--- inst/doc/semfindr.Rmd | 2 inst/doc/semfindr.html | 38 ++--- inst/doc/user_id.R | 2 inst/doc/user_id.html | 8 - man/approx_check.Rd | 8 - man/est_change_plot.Rd | 4 man/index_plot.Rd | 2 man/influence_plot.Rd | 4 man/lavaan_rerun.Rd | 17 ++ man/pars_id_to_lorg.Rd | 6 man/semfindr-package.Rd | 2 man/user_change_raw.Rd | 22 ++- tests/testthat/test-approx_check.R | 2 tests/testthat/test-est_change_raw_loo_single_user_function.R | 64 ++++++++++ tests/testthat/test-lavaan_rerun_parallel.R |only vignettes/articles/user_fun-1.png |only vignettes/articles/user_fun2-1.png |only vignettes/articles/user_function.Rmd |only vignettes/articles/user_function.Rmd.original |only vignettes/semfindr.Rmd | 2 35 files changed, 354 insertions(+), 148 deletions(-)
Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX',
'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and
'Citation File Format'. A low level 'R6' class is provided, as well
as stand-alone functions for each citation format for both read
and write.
Author: Scott Chamberlain [aut] ,
Brenton M. Wiernik [aut, cre] ,
Thierry Onkelinx [ctb]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between handlr versions 0.3.0 dated 2020-10-15 and 0.3.1 dated 2025-03-03
DESCRIPTION | 27 ++++--- MD5 | 66 ++++++++--------- NEWS.md | 9 ++ R/a_types.R | 2 R/cff_reader.R | 76 +++++++++++++------- R/cff_writer.R | 64 +++++++++++----- R/codemeta_reader.R | 12 +-- R/codemeta_writer.R | 16 ++-- R/doi_utils.R | 17 ++-- R/handlr-package.r | 20 ++--- R/schema_org_writer.R | 34 ++++---- R/translations.R | 12 +-- README.md | 75 ++++++++----------- inst/extdata/bib-many.bib | 4 - inst/extdata/citation_1.2.0.cff |only inst/extdata/citation_1.2.0_project.cff |only inst/extdata/citeproc-many.json | 2 inst/extdata/citeproc2.json | 2 inst/extdata/codemeta-many.json | 36 ++++----- inst/extdata/codemeta.json | 18 ++-- inst/extdata/crosscite.json | 4 - inst/extdata/crossref.bib | 4 - inst/extdata/crossref.ris | 2 inst/extdata/elsevier.ris | 2 man/HandlrClient.Rd | 36 ++++----- man/cff_reader.Rd | 14 ++- man/cff_reference_types.Rd | 2 man/cff_writer.Rd | 20 ++++- man/codemeta_writer.Rd | 2 man/handl.Rd | 6 + man/handlr-package.Rd | 12 ++- man/schema_org_writer.Rd | 2 tests/testthat/test-cff_reader.R | 121 +++++++++++++++++++++++++++++--- tests/testthat/test-cff_writer.R | 70 +++++++++++++++++- tests/testthat/test-client.R | 3 35 files changed, 528 insertions(+), 264 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Davis Vaughan [aut, cre] ,
Jim Hester [aut] ,
Romain Francois [aut] ,
Benjamin Kietzman [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between cpp11 versions 0.5.1 dated 2024-12-04 and 0.5.2 dated 2025-03-03
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 4 + inst/doc/FAQ.R | 6 + inst/doc/FAQ.html | 6 - inst/doc/cpp11.Rmd | 2 inst/doc/cpp11.html | 25 +++--- inst/doc/motivations.R | 148 +++++++++++++++++++-------------------- inst/doc/motivations.html | 99 ++++++++++++++++---------- inst/include/cpp11/R.hpp | 2 inst/include/cpp11/named_arg.hpp | 2 inst/include/fmt/format.h | 4 - vignettes/cpp11.Rmd | 2 13 files changed, 180 insertions(+), 150 deletions(-)
Title: Output Space-Filling Design
Description: Methods to generate a design in the input space that sequentially fills the output space of a black-box function. The output space-filling designs are helpful in inverse design or feature-based modeling problems.
See Wang, Shangkun, Adam P. Generale, Surya R. Kalidindi, and V. Roshan Joseph. (2024), Sequential designs for filling output spaces, Technometrics, 66, 65–76. for details. This work is supported by U.S. National Foundation grant CMMI-1921646.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <sk_wang@gatech.edu>
Diff between OSFD versions 3.0 dated 2025-01-15 and 3.1 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/OSFD.cpp | 11 ++++++++--- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Machine Learning Experiments
Description: Provides 'R6' objects to perform parallelized hyperparameter
optimization and cross-validation. Hyperparameter optimization can be
performed with Bayesian optimization (via 'ParBayesianOptimization'
<https://cran.r-project.org/package=ParBayesianOptimization>) and grid
search. The optimized hyperparameters can be validated using k-fold
cross-validation. Alternatively, hyperparameter optimization and
validation can be performed with nested cross-validation. While
'mlexperiments' focuses on core wrappers for machine learning
experiments, additional learner algorithms can be supplemented by
inheriting from the provided learner base class.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlexperiments versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 108 +-- NAMESPACE | 38 - R/MLTuneParameters.R | 410 ++++++------ R/cv_helper_base.R | 14 R/cv_performance.R | 390 ++++++------ R/cv_predictions.R | 282 ++++---- R/learner_lm.R | 4 R/optimizer_class_base.R | 84 +- R/optimizer_class_bayesian.R | 70 +- R/optimizer_helper_base.R | 102 +-- R/utils_handle_cat_vars.R | 66 +- R/utils_method_params_refactor.R | 22 R/utils_metrics.R | 472 +++++++------- R/utils_validate_fold_equality.R | 260 ++++---- R/zzz.R | 40 - build/vignette.rds |binary inst/doc/mlexperiments_knn_binary.html | 5 inst/doc/mlexperiments_knn_multiclass.html | 5 inst/doc/mlexperiments_knn_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_binary.html | 7 inst/doc/mlexperiments_rpart_multiclass.html | 5 inst/doc/mlexperiments_rpart_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_regression.R | 6 inst/doc/mlexperiments_rpart_regression.html | 23 inst/doc/mlexperiments_rpart_regression.qmd | 6 inst/doc/mlexperiments_starter.R | 262 ++++---- inst/doc/mlexperiments_starter.html | 7 inst/doc/mlexperiments_starter.qmd | 1 man/LearnerGlm.Rd | 210 +++--- man/LearnerKnn.Rd | 242 +++---- man/LearnerLm.Rd | 210 +++--- man/LearnerRpart.Rd | 272 ++++---- man/MLBase.Rd | 132 ++-- man/MLCrossValidation.Rd | 716 +++++++++++----------- man/MLExperimentsBase.Rd | 208 +++--- man/MLLearnerBase.Rd | 792 ++++++++++++------------- man/MLNestedCV.Rd | 852 +++++++++++++-------------- man/MLTuneParameters.Rd | 584 +++++++++--------- man/handle_cat_vars.Rd | 66 +- man/metric_types_helper.Rd | 94 +- man/performance.Rd | 216 +++--- man/predictions.Rd | 168 ++--- man/validate_fold_equality.Rd | 186 ++--- tests/testthat.R | 3 tests/testthat/test-fold_equality.R | 194 +++--- tests/testthat/test-glm_predictions.R | 438 ++++++------- tests/testthat/test-knn.R | 602 +++++++++---------- tests/testthat/test-lints.R | 26 tests/testthat/test-lm.R | 73 ++ tests/testthat/test-rpart_regression.R | 502 +++++++-------- vignettes/mlexperiments_knn_multiclass.qmd | 1 vignettes/mlexperiments_rpart_multiclass.qmd | 1 vignettes/mlexperiments_rpart_regression.qmd | 6 vignettes/mlexperiments_starter.qmd | 1 55 files changed, 4787 insertions(+), 4709 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.9.0 dated 2025-02-19 and 1.9.1 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ build/vignette.rds |binary inst/doc/json-aaquickstart.html | 2 +- inst/doc/json-mapping.pdf |binary tests/testthat/test-fromJSON-datasets.R | 6 +++--- 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.3.0 dated 2024-11-14 and 1.4.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 115 ++++---- NAMESPACE | 3 NEWS.md | 19 + R/AlleleTrim.R | 16 - R/BDtoPyPop.R | 4 R/GIANT.R | 29 +- R/GLStoUNI.R | 4 R/GLupdater.R | 590 ++++++++++++++++++++---------------------- R/SearchandBuildAlignments.R | 26 + R/ThirdPartyFunctions.R | 3 R/VersionValidation.R | 8 R/accessoryFunctions.R | 51 ++- R/atlasMaker.R | 2 R/buildGazeteer.R | 2 R/compareSequences.R | 2 R/data.R | 4 R/locusValidator.R | 2 R/relRisk.R | 2 README.md | 40 +- build/vignette.rds |binary data/HLAatlas.rda |binary data/HLAgazeteer.rda |binary data/alleleListHistory.rda |binary data/fragmentFeatureNames.rda |binary inst/doc/HLAtools.Rmd | 22 + inst/doc/HLAtools.html | 43 ++- man/GIANT.Rd | 4 man/GLSC.ex.Rd | 2 man/GLV.Rd | 4 man/GLV2.Rd | 4 man/GLVhelper.Rd | 4 man/GLupdate.Rd | 34 -- man/GLvalidate.Rd | 6 man/HLAatlas.Rd | 2 man/alignmentSearch.Rd | 12 man/atlasMaker.Rd | 2 man/compareSequences.Rd | 2 man/convertAny.Rd | 6 man/countSpaces.Rd | 3 man/customAlign.Rd | 10 man/formatHead.Rd | 6 man/getAlignmentNames.Rd | 2 man/getField.Rd | 2 man/multiAlign.Rd | 2 man/multiTranslateGLstring.Rd |only man/multiUpdateGL.Rd | 23 - man/parseAlignmentHead.Rd | 2 man/redec.Rd | 2 man/relRisk.Rd | 2 man/repoVersion.Rd | 4 man/squashVersion.Rd | 4 man/translateAllele.Rd |only man/translateGLstring.Rd |only man/uniAlign.Rd | 2 man/updateGL.Rd | 29 -- man/validateAllele.Rd | 4 man/validateLocus.Rd | 2 man/verifyAllele.Rd | 16 - vignettes/HLAtools.Rmd | 22 + 60 files changed, 660 insertions(+), 554 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.6 dated 2025-02-10 and 3.6.7 dated 2025-03-03
DESCRIPTION | 8 MD5 | 93 - NEWS.md | 11 inst/doc/ConditionalErrorSpending.R | 4 inst/doc/ConditionalErrorSpending.Rmd | 4 inst/doc/ConditionalErrorSpending.html | 1367 +++++++++++++++-- inst/doc/ConditionalPowerPlot.R | 4 inst/doc/ConditionalPowerPlot.Rmd | 4 inst/doc/ConditionalPowerPlot.html | 607 +++++++ inst/doc/GentleIntroductionToGSD.R | 4 inst/doc/GentleIntroductionToGSD.Rmd | 4 inst/doc/GentleIntroductionToGSD.html | 2 inst/doc/PoissonMixtureModel.R | 4 inst/doc/PoissonMixtureModel.Rmd | 4 inst/doc/PoissonMixtureModel.html | 1818 ++++++++++++++++++++++- inst/doc/SpendingFunctionOverview.R | 4 inst/doc/SpendingFunctionOverview.Rmd | 4 inst/doc/SurvivalOverview.R | 4 inst/doc/SurvivalOverview.Rmd | 4 inst/doc/SurvivalOverview.html | 651 ++++++++ inst/doc/VaccineEfficacy.R | 4 inst/doc/VaccineEfficacy.Rmd | 4 inst/doc/VaccineEfficacy.html | 442 ++--- inst/doc/binomialSPRTExample.R | 4 inst/doc/binomialSPRTExample.Rmd | 4 inst/doc/binomialSPRTExample.html | 1763 ++++++++++++++++++++-- inst/doc/gsDesignPackageOverview.R | 4 inst/doc/gsDesignPackageOverview.Rmd | 4 inst/doc/gsDesignPackageOverview.html | 512 ++++++ inst/doc/gsSurvBasicExamples.R | 4 inst/doc/gsSurvBasicExamples.Rmd | 4 inst/doc/gsSurvBasicExamples.html | 1224 +++++++++++++-- inst/doc/nNormal.R | 4 inst/doc/nNormal.Rmd | 4 inst/doc/nNormal.html | 328 ++++ inst/doc/toInteger.html | 2 tests/testthat/test-independent-test-toInteger.R |only vignettes/ConditionalErrorSpending.Rmd | 4 vignettes/ConditionalPowerPlot.Rmd | 4 vignettes/GentleIntroductionToGSD.Rmd | 4 vignettes/PoissonMixtureModel.Rmd | 4 vignettes/SpendingFunctionOverview.Rmd | 4 vignettes/SurvivalOverview.Rmd | 4 vignettes/VaccineEfficacy.Rmd | 4 vignettes/binomialSPRTExample.Rmd | 4 vignettes/gsDesignPackageOverview.Rmd | 4 vignettes/gsSurvBasicExamples.Rmd | 4 vignettes/nNormal.Rmd | 4 48 files changed, 8066 insertions(+), 894 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.2.0 dated 2023-12-06 and 0.3.0 dated 2025-03-03
fwb-0.2.0/fwb/build/fwb.pdf |only fwb-0.3.0/fwb/DESCRIPTION | 16 fwb-0.3.0/fwb/MD5 | 53 +- fwb-0.3.0/fwb/NAMESPACE | 1 fwb-0.3.0/fwb/NEWS.md | 26 + fwb-0.3.0/fwb/R/fwb.R | 323 ++++++++++++---- fwb-0.3.0/fwb/R/fwb.ci.R | 130 ++++-- fwb-0.3.0/fwb/R/plot.fwb.R | 12 fwb-0.3.0/fwb/R/set_fwb_wtype.R | 8 fwb-0.3.0/fwb/R/summary.fwb.R | 83 ++-- fwb-0.3.0/fwb/R/utils.R | 287 ++++++++------ fwb-0.3.0/fwb/R/vcovFWB.R | 145 +++++-- fwb-0.3.0/fwb/README.md | 61 +-- fwb-0.3.0/fwb/build/stage23.rdb |binary fwb-0.3.0/fwb/build/vignette.rds |only fwb-0.3.0/fwb/inst |only fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-10-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-5-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-9-1.png |binary fwb-0.3.0/fwb/man/fwb-package.Rd | 1 fwb-0.3.0/fwb/man/fwb.Rd | 36 + fwb-0.3.0/fwb/man/fwb.ci.Rd | 5 fwb-0.3.0/fwb/man/get_ci.Rd | 2 fwb-0.3.0/fwb/man/set_fwb_wtype.Rd | 8 fwb-0.3.0/fwb/man/summary.fwb.Rd | 17 fwb-0.3.0/fwb/man/vcovFWB.Rd | 40 + fwb-0.3.0/fwb/tests |only fwb-0.3.0/fwb/vignettes |only 28 files changed, 871 insertions(+), 383 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.5.0 dated 2025-01-15 and 1.5.1 dated 2025-03-03
DESCRIPTION | 9 MD5 | 50 ++-- NEWS.md | 7 R/CFCalendar.R | 9 R/CFCalendarProleptic.R | 2 R/CFCalendarStandard.R | 4 R/CFCalendarUTC.R | 22 +- R/CFtime.R | 113 +++++----- R/api.R | 16 - R/deprecated.R | 4 README.md | 133 +++++------- TODO | 5 inst/doc/CFtime.R | 63 +++--- inst/doc/CFtime.Rmd | 79 +++---- inst/doc/CFtime.html | 263 ++++++++++++++++++------- inst/doc/Processing.R | 74 +++---- inst/doc/Processing.Rmd | 116 +++++------ inst/doc/Processing.html | 376 +++++++++++++++++++++++------------- man/CFCalendar.Rd | 2 man/CFTime.Rd | 30 +- tests/testthat/test-CFformat.R | 17 + tests/testthat/test-CFtime.R | 31 +- tests/testthat/test-functions.R | 16 + tests/testthat/test-parse_deparse.R | 44 ++++ vignettes/CFtime.Rmd | 79 +++---- vignettes/Processing.Rmd | 116 +++++------ 26 files changed, 1005 insertions(+), 675 deletions(-)
Title: R6-Based ML Survival Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners for survival analysis. The package
provides R6-based survival learners for the following algorithms:
'glmnet' <https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'rpart'
<https://CRAN.R-project.org/package=rpart>. These can be used directly
with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlsurvlrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 52 +-- NAMESPACE | 24 - R/learner_surv_coxph_cox.R | 316 +++++++++++----------- R/surv_c_index.R | 54 +-- R/zzz.R | 50 +-- build/vignette.rds |binary inst/doc/mlsurvlrnrs_glmnet_survival.html | 5 inst/doc/mlsurvlrnrs_ranger_survival.html | 5 inst/doc/mlsurvlrnrs_rpart_survival.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_aft.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_cox.html | 5 man/LearnerSurvCoxPHCox.Rd | 284 +++++++++---------- man/LearnerSurvGlmnetCox.Rd | 308 ++++++++++----------- man/LearnerSurvRangerCox.Rd | 314 +++++++++++----------- man/LearnerSurvRpartCox.Rd | 342 ++++++++++++------------ man/LearnerSurvXgboostAft.Rd | 356 ++++++++++++------------- man/LearnerSurvXgboostCox.Rd | 348 ++++++++++++------------ man/c_index.Rd | 66 ++-- tests/testthat.R | 27 + tests/testthat/test-lints.R | 26 - tests/testthat/test-surv_coxph_cox.R | 128 ++++---- tests/testthat/test-surv_glmnet_cox.R | 214 +++++++-------- tests/testthat/test-surv_ranger_cox.R | 236 ++++++++-------- tests/testthat/test-surv_rpart_cox.R | 230 ++++++++-------- tests/testthat/test-surv_xgboost_aft.R | 248 ++++++++--------- tests/testthat/test-surv_xgboost_cox.R | 246 ++++++++--------- 27 files changed, 1951 insertions(+), 1953 deletions(-)
Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but
instead of geospatial coordinates, we use isotopic coordinates. The estimation
methods include: 1) 2-dimensional bivariate normal kernel utilization density
estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon
estimator, all applied to stable isotope data. Additionally, functions to
determine niche area, polygon overlap between groups and levels (confidence
contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>
Diff between rKIN versions 1.0.3 dated 2025-02-14 and 1.0.4 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/getColors.R | 17 ++++++----------- 3 files changed, 12 insertions(+), 17 deletions(-)
Title: Color-Based Image Segmentation
Description: Automatic, semi-automatic, and manual functions for
generating color maps from images. The idea is to simplify
the colors of an image according to a metric that is useful for
the user, using deterministic methods whenever possible.
Many images will be clustered well using the out-of-the-box
functions, but the package also includes a toolbox of functions
for making manual adjustments (layer merging/isolation, blurring,
fitting to provided color clusters or those from another image, etc).
Also includes export methods for other color/pattern analysis packages
(pavo, patternize, colordistance).
Author: Hannah Weller [aut, cre]
Maintainer: Hannah Weller <hannahiweller@gmail.com>
Diff between recolorize versions 0.1.0 dated 2021-12-07 and 0.2.0 dated 2025-03-03
DESCRIPTION | 15 MD5 | 200 ++--- NAMESPACE | 3 NEWS.md | 9 R/absorbLayer.R | 60 + R/apply_imager_operation.R | 10 R/assignPixels.R | 4 R/backgroundCondition.R | 2 R/backgroundIndex.R | 14 R/blurImage.R | 16 R/brick_to_array.R | 11 R/cimgConversions.R | 2 R/colorClusters.R | 70 + R/colorResiduals.R | 6 R/editLayers.R | 28 R/imDist.R | 20 R/imposeColors.R | 5 R/medianColors.R |only R/mergeLayers.R | 31 R/pixelAssignMatrix.R | 4 R/plotColorPalette.R | 4 R/plotImageArray.R | 4 R/plot_recolorize.R | 6 R/raster_array_conversions.R | 4 R/readImage.R | 17 R/recluster.R | 22 R/recolorImage.R | 4 R/recolorize-package.R |only R/recolorize.R | 27 R/recolorize2.R | 8 R/recolorizeVector.R | 19 R/recolorize_adjacency.R | 1 R/reorder_colors.R |only R/rerun_recolorize.R | 2 R/splitByColor.R | 19 R/thresholdRecolor.R | 6 R/wernerColor.R | 16 README.md | 113 ++ build/vignette.rds |binary inst/doc/Introduction.R | 223 ++--- inst/doc/Introduction.Rmd | 11 inst/doc/Introduction.html | 1166 ++++++++++++++++-------------- inst/doc/step00_prep.R | 79 +- inst/doc/step00_prep.Rmd | 1 inst/doc/step00_prep.html | 715 ++++++++++-------- inst/doc/step01_loading.R | 83 +- inst/doc/step01_loading.Rmd | 1 inst/doc/step01_loading.html | 835 +++++++++++---------- inst/doc/step02_initial_cluster.R | 253 +++--- inst/doc/step02_initial_cluster.Rmd | 1 inst/doc/step02_initial_cluster.html | 1095 ++++++++++++++++------------ inst/doc/step03_refinement.R | 79 +- inst/doc/step03_refinement.Rmd | 1 inst/doc/step03_refinement.html | 848 +++++++++++---------- inst/doc/step04_manual_tweak.R | 82 +- inst/doc/step04_manual_tweak.Rmd | 6 inst/doc/step04_manual_tweak.html | 858 +++++++++++----------- inst/doc/step05_visualization_export.R | 139 +-- inst/doc/step05_visualization_export.Rmd | 1 inst/doc/step05_visualization_export.html | 965 +++++++++++++----------- inst/extdata/msc/corbetti_vector.rds |binary man/absorbLayer.Rd | 9 man/apply_imager_operation.Rd | 10 man/array_to_RasterStack.Rd | 2 man/array_to_cimg.Rd | 2 man/assignPixels.Rd | 4 man/backgroundCondition.Rd | 2 man/backgroundIndex.Rd | 6 man/blurImage.Rd | 14 man/col2col.Rd | 7 man/colorClusters.Rd | 14 man/colorClustersHist.Rd | 12 man/colorClustersKMeans.Rd | 6 man/colorResiduals.Rd | 6 man/editLayer.Rd | 12 man/editLayers.Rd | 12 man/figures |only man/imDist.Rd | 10 man/imHeatmap.Rd | 6 man/imposeColors.Rd | 5 man/match_colors.Rd |only man/medianColors.Rd |only man/mergeLayers.Rd | 12 man/pixelAssignMatrix.Rd | 4 man/plot.recolorize.Rd | 6 man/plotColorPalette.Rd | 4 man/plotImageArray.Rd | 4 man/readImage.Rd | 2 man/recluster.Rd | 20 man/recoloredImage.Rd | 2 man/recolorize-package.Rd |only man/recolorize.Rd | 14 man/recolorize2.Rd | 8 man/reorder_colors.Rd |only man/splitByColor.Rd | 14 man/thresholdRecolor.Rd | 2 man/wernerColor.Rd | 10 vignettes/Introduction.Rmd | 11 vignettes/step00_prep.Rmd | 1 vignettes/step01_loading.Rmd | 1 vignettes/step02_initial_cluster.Rmd | 1 vignettes/step03_refinement.Rmd | 1 vignettes/step04_manual_tweak.Rmd | 6 vignettes/step05_visualization_export.Rmd | 1 104 files changed, 4692 insertions(+), 3795 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Isaac Gravestock [aut, cre],
Craig Gower-Page [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between rbmi versions 1.4.0 dated 2025-02-07 and 1.4.1 dated 2025-03-03
DESCRIPTION | 16 +++++----- MD5 | 24 ++++++++-------- NEWS.md | 5 +++ R/utilities.R | 26 ++++++++++------- build/vignette.rds |binary inst/doc/advanced.html | 2 - inst/doc/quickstart.html | 50 +++++++++++++++++----------------- inst/stan/MMRM.stan | 2 - man/rbmi-package.Rd | 4 +- man/rbmi-settings.Rd | 10 ++++++ tests/testthat.R | 5 +++ tests/testthat/test-reproducibility.R | 5 +++ tests/testthat/test-utilities.R | 10 +++--- 13 files changed, 95 insertions(+), 64 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.3.7 dated 2024-10-03 and 2.0.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 81 +++--- NAMESPACE | 6 NEWS.md | 12 R/class_plot.R | 407 +++++++++++++++++++++++++++++-- R/class_print.R | 20 + R/class_summary.R | 11 R/data_countryside.R |only R/obs_shape.R | 9 R/sar_countryside.R |only R/sar_habitat.R | 67 ++--- README.md | 102 +++---- build/vignette.rds |binary data/countryside.rda |only inst/doc/sars-r-package.Rmd | 23 + inst/doc/sars-r-package.html | 155 ++--------- man/coleman.Rd | 108 ++++---- man/countryside.Rd |only man/countryside_extrap.Rd |only man/display_sars_models.Rd | 56 ++-- man/figures/README-unnamed-chunk-5-1.png |binary man/gdm.Rd | 356 +++++++++++++-------------- man/lin_pow.Rd | 144 +++++----- man/plot.habitat.Rd | 213 ++++++++++++++-- man/sar_countryside.Rd |only man/sar_habitat.Rd | 335 ++++++++++++------------- man/sar_linear.Rd | 148 +++++------ man/sar_logistic.Rd | 194 +++++++------- man/sar_multi.Rd | 142 +++++----- tests/testthat.R | 10 tests/testthat/Rplots.pdf |only tests/testthat/test_coleman.R | 2 tests/testthat/test_countryside.R |only tests/testthat/test_fit_collection.R | 6 tests/testthat/test_gdm.R | 12 tests/testthat/test_habitat.R |only tests/testthat/test_lin_pow.R | 14 - tests/testthat/test_loga.R | 4 tests/testthat/test_monod.R | 1 tests/testthat/test_multi.R | 52 +++ tests/testthat/test_power.R | 13 tests/testthat/test_pred.R | 2 tests/testthat/test_sar_linear.R | 6 tests/testthat/test_thresholds.R | 32 ++ tests/testthat/test_weibull3.R | 22 + vignettes/sars-r-package.Rmd | 23 + 46 files changed, 1734 insertions(+), 1062 deletions(-)
Title: Rating and Evaluating Texts Using Large Language Models
Description: Generates ratings and psycholinguistic metrics for textual stimuli using large language models.
It enables users to evaluate idioms and other language materials by combining context, prompts, and stimulus inputs.
It supports multiple LLM APIs (such as 'OpenAI', 'DeepSeek', 'Anthropic', 'Cohere', 'Google PaLM', and 'Ollama')
by allowing users to switch models with a single parameter. In addition to generating numeric ratings,
'chatRater' provides functions for obtaining detailed psycholinguistic metrics including word frequency (with optional corpus input),
lexical coverage (with customizable vocabulary size and test basis), Zipf metric, Levenshtein distance, and semantic transparency.
Author: Shiyang Zheng [aut, cre]
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Diff between chatRater versions 1.0.0 dated 2025-02-17 and 1.1.0 dated 2025-03-03
DESCRIPTION | 20 - MD5 | 19 NAMESPACE | 9 R/chatRater.R | 762 +++++++++++++++++++++++++++++++-------- README.md | 70 +++ man/chatRater-package.Rd |only man/generate_ratings.Rd | 51 +- man/generate_ratings_for_all.Rd | 47 +- man/get_levenshtein_d.Rd |only man/get_lexical_coverage.Rd |only man/get_semantic_transparency.Rd |only man/get_word_frequency.Rd |only man/get_zipf_metric.Rd |only man/llm_api_call.Rd |only 14 files changed, 763 insertions(+), 215 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson [aut, cre]
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 3.1.1 dated 2022-11-05 and 3.1.2 dated 2025-03-03
DESCRIPTION | 17 - MD5 | 42 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BHSBVAR.Rnw | 1 inst/doc/BHSBVAR.pdf |binary man/BHSBVAR-package.Rd | 50 ++--- man/BH_SBVAR.Rd | 372 ++++++++++++++++++++--------------------- man/Dist_Plots.Rd | 268 ++++++++++++++--------------- man/FEVD_Plots.Rd | 292 ++++++++++++++++---------------- man/HD_Plots.Rd | 308 ++++++++++++++++----------------- man/IRF_Plots.Rd | 274 +++++++++++++++--------------- man/USLMData.Rd | 54 ++--- src/BHSBVAR.cpp | 2 src/Makevars | 12 - src/Makevars.win | 12 - vignettes/BHSBVAR.Rnw | 1 vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/FEVD_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 22 files changed, 842 insertions(+), 863 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Facilitate the evaluation of forecasts in a convenient
framework based on data.table. It allows user to to check their forecasts
and diagnose issues, to visualise forecasts and missing data, to transform
data before scoring, to handle missing forecasts, to aggregate scores, and
to visualise the results of the evaluation. The package mostly focuses on
the evaluation of probabilistic forecasts and allows evaluating several
different forecast types and input formats. Find more information about the
package in the Vignettes as well as in the accompanying paper,
<doi:10.48550/arXiv.2205.07090>.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Toshiaki Asakura [ctb] ,
James Mba Azam [ctb] ,
Sebastian Funk [aut],
Michael Chirico [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 2.0.0 dated 2024-10-31 and 2.1.0 dated 2025-03-03
scoringutils-2.0.0/scoringutils/R/z-packageStartupMessage.R |only scoringutils-2.1.0/scoringutils/DESCRIPTION | 34 scoringutils-2.1.0/scoringutils/MD5 | 148 +-- scoringutils-2.1.0/scoringutils/NAMESPACE | 13 scoringutils-2.1.0/scoringutils/NEWS.md | 78 - scoringutils-2.1.0/scoringutils/R/class-forecast-binary.R | 29 scoringutils-2.1.0/scoringutils/R/class-forecast-nominal.R | 50 - scoringutils-2.1.0/scoringutils/R/class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/R/class-forecast-point.R | 11 scoringutils-2.1.0/scoringutils/R/class-forecast-quantile.R | 18 scoringutils-2.1.0/scoringutils/R/class-forecast-sample.R | 42 scoringutils-2.1.0/scoringutils/R/class-forecast.R | 30 scoringutils-2.1.0/scoringutils/R/documentation-templates.R | 15 scoringutils-2.1.0/scoringutils/R/get-forecast-type.R | 9 scoringutils-2.1.0/scoringutils/R/get-pit-histogram.R | 6 scoringutils-2.1.0/scoringutils/R/helper-quantile-interval-range.R | 3 scoringutils-2.1.0/scoringutils/R/metrics-nominal.R | 76 + scoringutils-2.1.0/scoringutils/R/metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/R/metrics-quantile.R | 11 scoringutils-2.1.0/scoringutils/R/metrics-sample.R | 24 scoringutils-2.1.0/scoringutils/R/score.R | 2 scoringutils-2.1.0/scoringutils/README.md | 7 scoringutils-2.1.0/scoringutils/build/partial.rdb |binary scoringutils-2.1.0/scoringutils/build/vignette.rds |binary scoringutils-2.1.0/scoringutils/data/example_ordinal.rda |only scoringutils-2.1.0/scoringutils/inst/create-example-data.R | 14 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-functions.html | 5 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.R | 478 +++++----- scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.html | 9 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.Rmd | 6 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.html | 15 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.Rmd | 23 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.aux | 70 - scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.log | 228 ++-- scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.tex | 85 + scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/calibration-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/correlation-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/coverage-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pairwise-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pit-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/plot-forecast-counts-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/score-heatmap-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/wis-components-1.pdf |binary scoringutils-2.1.0/scoringutils/man/as_forecast_binary.Rd | 12 scoringutils-2.1.0/scoringutils/man/as_forecast_generic.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_nominal.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/as_forecast_point.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_quantile.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_sample.Rd | 15 scoringutils-2.1.0/scoringutils/man/assert_input_categorical.Rd |only scoringutils-2.1.0/scoringutils/man/assert_input_nominal.Rd | 26 scoringutils-2.1.0/scoringutils/man/assert_input_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/example_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/figures/metrics-ordinal.png |only scoringutils-2.1.0/scoringutils/man/figures/workflow.png |binary scoringutils-2.1.0/scoringutils/man/get_metrics.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_binary.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_nominal.Rd | 3 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_point.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_quantile.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_sample.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.scores.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_pit_histogram.Rd | 6 scoringutils-2.1.0/scoringutils/man/illustration-input-metric-ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/is_forecast.Rd | 8 scoringutils-2.1.0/scoringutils/man/logs_sample.Rd | 2 scoringutils-2.1.0/scoringutils/man/rps_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/score.Rd | 8 scoringutils-2.1.0/scoringutils/man/scoring-functions-binary.Rd | 2 scoringutils-2.1.0/scoringutils/man/scoring-functions-nominal.Rd | 31 scoringutils-2.1.0/scoringutils/tests/testthat/setup.R | 2 scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-quantile.R | 19 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-nominal.R | 14 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-sample.R | 10 scoringutils-2.1.0/scoringutils/vignettes/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/vignettes/scoring-rules.Rmd | 6 82 files changed, 1004 insertions(+), 763 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.2.0 dated 2025-02-18 and 4.2.1 dated 2025-03-03
plmmr-4.2.0/plmmr/tests/tinytest.R |only plmmr-4.2.1/plmmr/DESCRIPTION | 8 ++++---- plmmr-4.2.1/plmmr/MD5 | 14 +++++++------- plmmr-4.2.1/plmmr/NEWS.md | 4 ++++ plmmr-4.2.1/plmmr/build/partial.rdb |binary plmmr-4.2.1/plmmr/build/vignette.rds |binary plmmr-4.2.1/plmmr/inst/doc/getting-started.html | 10 +++++----- plmmr-4.2.1/plmmr/src/plmm_init.c | 9 ++++++--- plmmr-4.2.1/plmmr/tests/test.R |only 9 files changed, 26 insertions(+), 19 deletions(-)
Title: Generates Expectations for 'testthat' Unit Testing
Description: Helps systematize and ease the process of
building unit tests with the 'testthat' package by providing
tools for generating expectations.
Author: Ludvig Renbo Olsen [aut, cre] ,
R. Mark Sharp [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between xpectr versions 0.4.3 dated 2022-11-18 and 0.4.4 dated 2025-03-03
xpectr-0.4.3/xpectr/build/xpectr.pdf |only xpectr-0.4.3/xpectr/man/xpectr.Rd |only xpectr-0.4.4/xpectr/DESCRIPTION | 13 xpectr-0.4.4/xpectr/MD5 | 38 xpectr-0.4.4/xpectr/NEWS.md | 8 xpectr-0.4.4/xpectr/R/create_expectations.R | 2 xpectr-0.4.4/xpectr/R/do_if.R | 9 xpectr-0.4.4/xpectr/R/element_descriptors.R | 20 xpectr-0.4.4/xpectr/R/package_info.R | 4 xpectr-0.4.4/xpectr/R/strip.R | 1 xpectr-0.4.4/xpectr/R/strip_side_effect_messages.R | 10 xpectr-0.4.4/xpectr/README.md | 135 - xpectr-0.4.4/xpectr/build/stage23.rdb |only xpectr-0.4.4/xpectr/build/vignette.rds |binary xpectr-0.4.4/xpectr/inst/doc/readme.R | 986 ++++---- xpectr-0.4.4/xpectr/inst/doc/readme.Rmd | 2 xpectr-0.4.4/xpectr/inst/doc/readme.html | 1204 +++++----- xpectr-0.4.4/xpectr/man/stop_if.Rd | 9 xpectr-0.4.4/xpectr/man/strip_msg.Rd | 10 xpectr-0.4.4/xpectr/man/xpectr-package.Rd |only xpectr-0.4.4/xpectr/tests/testthat/test_capture_side_effects.R | 3 xpectr-0.4.4/xpectr/vignettes/readme.Rmd | 2 22 files changed, 1247 insertions(+), 1209 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics.
These can be used to run survival models under a frequentist (based on maximum likelihood)
or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian
Monte Carlo). To run the Bayesian models, the user needs to install additional modules
(packages), i.e. 'survHEinla' and 'survHEhmc'. These can be installed using
'remotes::install_github' from their GitHub repositories:
(<https://github.com/giabaio/survHEhmc> and <https://github.com/giabaio/survHEinla/>
respectively). 'survHEinla' is based on the package INLA, which is available for download at
<https://inla.r-inla-download.org/R/stable/>. The user can specify a set of parametric models
using a common notation and select the preferred mode of inference. The results can also be
post-processed to produce probabilistic sensitivity analysis and can be used to export the
output to an Excel file (e.g. for a Markov model, [...truncated...]
Author: Gianluca Baio [aut, cre],
Andrea Berardi [ctb],
Philip Cooney [ctb],
Andrew Jones [ctb],
Nathan Green [ctb]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between survHE versions 2.0.2 dated 2024-10-04 and 2.0.3 dated 2025-03-03
survHE-2.0.2/survHE/inst |only survHE-2.0.3/survHE/DESCRIPTION | 12 ++-- survHE-2.0.3/survHE/MD5 | 17 +++--- survHE-2.0.3/survHE/NEWS.md | 64 ++++++++++++++++++++++++-- survHE-2.0.3/survHE/R/make.transition.probs.R | 2 survHE-2.0.3/survHE/R/psa.plot.R | 6 +- survHE-2.0.3/survHE/R/utils_plot_survHE.R | 6 +- survHE-2.0.3/survHE/R/write.surv.R | 2 survHE-2.0.3/survHE/README.md | 4 + survHE-2.0.3/survHE/build/partial.rdb |binary 10 files changed, 86 insertions(+), 27 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.7.1). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.7.1.1.1 dated 2025-02-10 and 0.7.1.1.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/include/vinecopulib/misc/nlohmann_json.hpp | 4 ++-- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.3.0 dated 2024-11-21 and 1.4.0 dated 2025-03-03
rTwig-1.3.0/rTwig/R/import_qsm.R |only rTwig-1.3.0/rTwig/R/qsm_summary.R |only rTwig-1.3.0/rTwig/R/standardize_qsm.R |only rTwig-1.3.0/rTwig/man/standardize_qsm.Rd |only rTwig-1.4.0/rTwig/DESCRIPTION | 6 rTwig-1.4.0/rTwig/MD5 | 115 +-- rTwig-1.4.0/rTwig/NAMESPACE | 5 rTwig-1.4.0/rTwig/NEWS.md | 424 ++++++------ rTwig-1.4.0/rTwig/R/RcppExports.R | 73 ++ rTwig-1.4.0/rTwig/R/box_dimension.R | 12 rTwig-1.4.0/rTwig/R/cluster_cloud.R | 18 rTwig-1.4.0/rTwig/R/correct_radii.R | 5 rTwig-1.4.0/rTwig/R/export_mat.R | 4 rTwig-1.4.0/rTwig/R/export_mesh.R | 353 +++++++--- rTwig-1.4.0/rTwig/R/import_leaves.R |only rTwig-1.4.0/rTwig/R/import_treeqsm.R |only rTwig-1.4.0/rTwig/R/plot_qsm.R | 466 ++++++++++--- rTwig-1.4.0/rTwig/R/prune_qsm.R | 37 - rTwig-1.4.0/rTwig/R/run_rtwig.R | 73 +- rTwig-1.4.0/rTwig/R/smooth_qsm.R | 5 rTwig-1.4.0/rTwig/R/standardise_qsm.R |only rTwig-1.4.0/rTwig/R/summarise_qsm.R |only rTwig-1.4.0/rTwig/R/tools.R | 13 rTwig-1.4.0/rTwig/R/tree_metrics.R | 298 ++++++-- rTwig-1.4.0/rTwig/R/twigs.R | 21 rTwig-1.4.0/rTwig/R/update_cylinders.R | 7 rTwig-1.4.0/rTwig/README.md | 15 rTwig-1.4.0/rTwig/build/partial.rdb |binary rTwig-1.4.0/rTwig/data/twigs_index.rda |only rTwig-1.4.0/rTwig/inst/REFERENCES.bib | 50 + rTwig-1.4.0/rTwig/inst/doc/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/inst/doc/Dictionary.html | 328 +++++++++ rTwig-1.4.0/rTwig/inst/doc/Metrics.html | 6 rTwig-1.4.0/rTwig/inst/doc/Overview.R | 10 rTwig-1.4.0/rTwig/inst/doc/Overview.Rmd | 16 rTwig-1.4.0/rTwig/inst/doc/Overview.html | 39 - rTwig-1.4.0/rTwig/inst/doc/Twigs.R | 49 + rTwig-1.4.0/rTwig/inst/doc/Twigs.Rmd | 73 ++ rTwig-1.4.0/rTwig/inst/doc/Twigs.html | 97 ++ rTwig-1.4.0/rTwig/inst/doc/Validation.html | 770 +++++++++++----------- rTwig-1.4.0/rTwig/inst/include/helper_functions.h | 1 rTwig-1.4.0/rTwig/man/box_dimension.Rd | 9 rTwig-1.4.0/rTwig/man/cluster_cloud.Rd | 6 rTwig-1.4.0/rTwig/man/correct_radii.Rd | 5 rTwig-1.4.0/rTwig/man/export_mat.Rd | 4 rTwig-1.4.0/rTwig/man/export_mesh.Rd | 93 ++ rTwig-1.4.0/rTwig/man/import_leaves.Rd |only rTwig-1.4.0/rTwig/man/import_qsm.Rd | 26 rTwig-1.4.0/rTwig/man/import_treeqsm.Rd |only rTwig-1.4.0/rTwig/man/plot_qsm.Rd | 113 ++- rTwig-1.4.0/rTwig/man/prune_qsm.Rd | 24 rTwig-1.4.0/rTwig/man/qsm_summary.Rd | 28 rTwig-1.4.0/rTwig/man/run_rtwig.Rd | 24 rTwig-1.4.0/rTwig/man/smooth_qsm.Rd | 5 rTwig-1.4.0/rTwig/man/standardise_qsm.Rd |only rTwig-1.4.0/rTwig/man/summarise_qsm.Rd |only rTwig-1.4.0/rTwig/man/tree_metrics.Rd | 15 rTwig-1.4.0/rTwig/man/twigs.Rd | 4 rTwig-1.4.0/rTwig/man/twigs_index.Rd |only rTwig-1.4.0/rTwig/man/update_cylinders.Rd | 7 rTwig-1.4.0/rTwig/src/RcppExports.cpp | 65 + rTwig-1.4.0/rTwig/src/helper_functions.cpp | 67 + rTwig-1.4.0/rTwig/src/io.cpp |only rTwig-1.4.0/rTwig/vignettes/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/vignettes/Overview.Rmd | 16 rTwig-1.4.0/rTwig/vignettes/Twigs.Rmd | 73 ++ 66 files changed, 3363 insertions(+), 1154 deletions(-)
Title: Rearranging Data
Description: Arrange data by a set of methods. Use rearrangers to reorder
data points and mutators to change their values. From basic utilities,
to centering the greatest value, to swirling in 3-dimensional space,
'rearrr' enables creativity when plotting and experimenting with data.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between rearrr versions 0.3.4 dated 2024-02-07 and 0.3.5 dated 2025-03-03
rearrr-0.3.4/rearrr/build/rearrr.pdf |only rearrr-0.3.5/rearrr/DESCRIPTION | 13 - rearrr-0.3.5/rearrr/MD5 | 37 +-- rearrr-0.3.5/rearrr/NEWS.md | 6 rearrr-0.3.5/rearrr/R/transfer_centroids.R | 2 rearrr-0.3.5/rearrr/README.md | 111 +++++----- rearrr-0.3.5/rearrr/build/stage23.rdb |only rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-11-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-14-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-16-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-19-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-21-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-27-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-29-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-31-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-33-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-35-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-6-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-9-1.png |binary rearrr-0.3.5/rearrr/man/figures/rearrr_square_logo_242x225_259dpi.png |only rearrr-0.3.5/rearrr/tests/testthat/test_n_fn.R | 24 -- 21 files changed, 92 insertions(+), 101 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.5.0 dated 2024-12-19 and 1.5.1-1 dated 2025-03-03
DESCRIPTION | 11 MD5 | 72 +++-- NEWS.md | 43 +++ R/GMAT.R | 2 R/GMAT2test.R | 2 R/GMATtest.R | 4 R/NLR.R | 612 +++++++++++++++++++------------------------------- R/ORD.R | 2 R/difNLR-package.R | 31 +- R/difNLR.R | 77 +++--- R/difORD.R | 5 R/estimNLR.R | 4 R/formulaNLR.R | 10 R/genNLR.R | 2 R/private.R | 2 README.md | 48 ++- build/partial.rdb |binary man/GMAT.Rd | 2 man/GMAT2test.Rd | 2 man/GMATtest.Rd | 4 man/NLR.Rd | 6 man/ORD.Rd | 2 man/coef.difNLR.Rd | 5 man/difNLR-package.Rd | 31 +- man/difNLR.Rd | 2 man/difORD.Rd | 5 man/estimNLR.Rd | 2 man/genNLR.Rd | 2 tests |only 29 files changed, 478 insertions(+), 512 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem. References: Makowski et al. (2020) <doi:10.21105/joss.02306>.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Remi Theriault [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.6 dated 2024-10-26 and 0.8.7 dated 2025-03-03
correlation-0.8.6/correlation/tests/testthat/_snaps/as.list.md |only correlation-0.8.6/correlation/tests/testthat/test-as.list.R |only correlation-0.8.7/correlation/DESCRIPTION | 12 correlation-0.8.7/correlation/MD5 | 56 +-- correlation-0.8.7/correlation/NEWS.md | 10 correlation-0.8.7/correlation/R/cor_sort.R | 90 ++++- correlation-0.8.7/correlation/R/cormatrix_to_excel.R | 22 - correlation-0.8.7/correlation/R/correlation.R | 82 ++-- correlation-0.8.7/correlation/R/display.R | 3 correlation-0.8.7/correlation/R/methods_format.R | 25 + correlation-0.8.7/correlation/R/methods_print.R | 10 correlation-0.8.7/correlation/README.md | 49 +- correlation-0.8.7/correlation/inst/doc/multilevel.R | 42 +- correlation-0.8.7/correlation/inst/doc/multilevel.html | 64 ++- correlation-0.8.7/correlation/inst/doc/types.R | 154 ++++---- correlation-0.8.7/correlation/inst/doc/types.html | 175 +++++----- correlation-0.8.7/correlation/man/correlation-package.Rd | 12 correlation-0.8.7/correlation/man/correlation.Rd | 21 - correlation-0.8.7/correlation/man/display.easycormatrix.Rd | 3 correlation-0.8.7/correlation/man/figures/README-12-1.png |binary correlation-0.8.7/correlation/man/figures/README-7-1.png |binary correlation-0.8.7/correlation/man/figures/README-corr-1.png |binary correlation-0.8.7/correlation/tests/testthat/_snaps/as_list.md |only correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_dataframe.md | 54 --- correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_matrix.md | 27 - correlation-0.8.7/correlation/tests/testthat/_snaps/methods.md | 14 correlation-0.8.7/correlation/tests/testthat/_snaps/windows |only correlation-0.8.7/correlation/tests/testthat/test-as_list.R |only correlation-0.8.7/correlation/tests/testthat/test-cor_sort.R |only correlation-0.8.7/correlation/tests/testthat/test-correlation.R | 13 correlation-0.8.7/correlation/tests/testthat/test-display_print_dataframe.R | 12 correlation-0.8.7/correlation/tests/testthat/test-display_print_matrix.R | 21 - 32 files changed, 543 insertions(+), 428 deletions(-)
Title: Topic Inference to Identify Tissue Architecture in Multiplexed
Images
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see <https://xiyupeng.github.io/SpaTopic/>.
Author: Xiyu Peng [aut, cre]
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Diff between SpaTopic versions 1.1.0 dated 2024-04-22 and 1.2.0 dated 2025-03-03
SpaTopic-1.1.0/SpaTopic/man/gibbs.res-class.Rd |only SpaTopic-1.2.0/SpaTopic/DESCRIPTION | 10 SpaTopic-1.2.0/SpaTopic/MD5 | 38 SpaTopic-1.2.0/SpaTopic/NAMESPACE | 3 SpaTopic-1.2.0/SpaTopic/NEWS.md | 5 SpaTopic-1.2.0/SpaTopic/R/Gibbs_sampler.R | 981 ++++++++++--------- SpaTopic-1.2.0/SpaTopic/R/RcppExports.R | 46 SpaTopic-1.2.0/SpaTopic/R/SpaTopic-package.R | 27 SpaTopic-1.2.0/SpaTopic/R/class.R | 10 SpaTopic-1.2.0/SpaTopic/R/prepare_SpaTopic_input.R | 28 SpaTopic-1.2.0/SpaTopic/README.md | 209 +--- SpaTopic-1.2.0/SpaTopic/build/vignette.rds |binary SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.R | 41 SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.Rmd | 145 +- SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.html | 672 ++++++++----- SpaTopic-1.2.0/SpaTopic/man/SpaTopic-Package.Rd | 34 SpaTopic-1.2.0/SpaTopic/man/SpaTopic-class.Rd |only SpaTopic-1.2.0/SpaTopic/man/SpaTopic_inference.Rd | 4 SpaTopic-1.2.0/SpaTopic/man/print.SpaTopic.Rd |only SpaTopic-1.2.0/SpaTopic/man/spatopic_message.Rd |only SpaTopic-1.2.0/SpaTopic/src/Makevars | 4 SpaTopic-1.2.0/SpaTopic/vignettes/Intro_SpaTopic.Rmd | 145 +- 22 files changed, 1388 insertions(+), 1014 deletions(-)
Title: A Collection of Loss Functions for Assessing Point Forecasts
Description: Implements multiple consistent scoring functions
(Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>) for assessing point
forecasts and point predictions. Detailed documentation of scoring
functions' properties is included for facilitating interpretation of
results.
Author: Hristos Tyralis [aut, cre] ,
Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>
Diff between scoringfunctions versions 1.0 dated 2024-12-01 and 1.1 dated 2025-03-03
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++++++----- NAMESPACE | 5 +++++ R/meanlog_if.R |only R/serrexp_sf.R |only R/serrlog_sf.R |only R/serrpower_sf.R |only R/serrsq_sf.R |only build/partial.rdb |binary man/mean_if.Rd | 4 ++-- man/meanlog_if.Rd |only man/scoringfunctions-package.Rd | 14 ++++++++++++-- man/serrexp_sf.Rd |only man/serrlog_sf.Rd |only man/serrpower_sf.Rd |only man/serrsq_sf.Rd |only 16 files changed, 39 insertions(+), 14 deletions(-)
More information about scoringfunctions at CRAN
Permanent link
Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or
point-related data. There are multiple models implemented for two bark
beetle species. The models can be customized and their submodels (onset of
infestation, beetle development, diapause initiation, mortality) can be
combined. The following models are available in the package:
PHENIPS-Clim (first-time release in this package),
PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>,
RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>,
CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>,
BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>,
Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>,
Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>.
The package may be expanded by models for other bark beetle species in the
future.
Author: Jakob Jentschke [aut, cre],
FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>
Diff between barrks versions 1.0.1 dated 2024-11-04 and 1.1.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 68 ++--- NEWS.md | 32 ++ R/model-joensson.R | 10 R/model-lange.R | 6 R/model-phenips-clim.R | 73 ++++- R/model-phenips.R | 21 + R/phenology-results.R | 12 R/phenology.R | 5 R/plot-development-diagram.R | 69 ++++- R/utils-log.R | 86 +++--- R/utils-model-functions.R | 272 ++++++++++++---------- build/partial.rdb |binary inst/doc/bso.html | 10 inst/doc/model-comparison.html | 33 +- inst/doc/model-customization.html | 12 inst/doc/stations.html | 4 inst/doc/storage.html | 4 inst/tinytest/data/test-data-phenips-clim.rda |binary inst/tinytest/data/test-data-spring-mortality.rda |binary inst/tinytest/storage-test.R | 72 ++--- inst/tinytest/test-model-phenips-clim.R | 25 +- inst/tinytest/test-models-min.R | 46 +-- inst/tinytest/test-spring-mortality.R | 5 inst/tinytest/test-storage-chapy.R | 36 +- inst/tinytest/test-storage-combine.R | 48 +-- inst/tinytest/test-storage-joensson.R | 36 +- inst/tinytest/test-storage-lange.R | 36 +- inst/tinytest/test-storage-phenips-clim.R | 36 +- inst/tinytest/test-storage-phenips.R | 36 +- inst/tinytest/test-storage-rity.R | 36 +- man/get_generations.Rd | 10 man/model.joensson.customize.Rd | 4 man/model.phenips_clim.customize.Rd | 12 tests/tinytest.R | 12 35 files changed, 671 insertions(+), 502 deletions(-)
Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.6.1 dated 2025-02-16 and 0.6.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/multi-scale-assessment.R | 6 +++++- inst/doc/multi-scale-assessment.Rmd | 6 +++++- inst/doc/multi-scale-assessment.html | 8 ++++++-- vignettes/multi-scale-assessment.Rmd | 6 +++++- 7 files changed, 34 insertions(+), 14 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.1.0 dated 2025-02-10 and 0.3.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 R/globals.R | 2 R/readARS.R | 49 - README.md | 36 inst/extdata/ADAE.csv | 2384 +++++++++++++++++++++++++------------------------- man/ARS_example.Rd | 44 man/readARS.Rd | 3 9 files changed, 1275 insertions(+), 1269 deletions(-)
Title: A Mini-Dictionary for 'R', 'shiny' and 'rmarkdown' Documents
Description: Despite the predominant use of R for data manipulation and various robust statistical calculations, in recent years, more people from various disciplines are beginning to use R for other purposes. In doing this seemlessly, further tools are needed users to easily and freely write in R for all kinds of purposes. The r2dictionary introduces a means for users to directly search for definitions of terms within the R environment.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2dictionary versions 0.2 dated 2023-07-16 and 0.3 dated 2025-03-03
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/complete.dic |binary inst/doc/simple_samples.html | 4 ++-- man/defineSelected.Rd | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting
text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering
of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further
processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.4.1 dated 2024-09-20 and 3.5.0 dated 2025-03-03
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 42 ++++++++++++++++++++++++------------------ 4 files changed, 39 insertions(+), 30 deletions(-)
Title: Exact Matching and Matching-Adjusted Indirect Comparison (MAIC)
Description: The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2025)). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2021) <doi:10.1002/pst.2210>.)
Author: Lillian Yau [aut, cre],
Ekkehard Glimm [aut],
Xinlei Deng [aut]
Maintainer: Lillian Yau <maicChecks@gmail.com>
Diff between maicChecks versions 0.1.2 dated 2022-01-04 and 0.2.0 dated 2025-03-03
DESCRIPTION | 28 ++++-- MD5 | 51 +++++++----- NAMESPACE | 19 ++-- R/eAD.R | 40 +++++---- R/eIPD.R | 40 +++++---- R/exmLP.2ipd.R |only R/exmWt.2ipd.R |only R/maicChecks-package.R |only R/maicLP.R | 73 ++++++++++++------ R/maicMD.R | 184 +++++++++++++++++++++++++-------------------- R/maicPCA.R | 186 ++++++++++++++++++++++++++-------------------- R/maicT2Test.R | 82 +++++++++++--------- R/maicWt.R | 102 +++++++++++++++---------- R/maxessWt.R | 92 +++++++++++++--------- R/sim110.R |only README.md |only build |only data/eAD.txt | 8 - data/eIPD.txt | 86 ++++++++++----------- data/sim110.rda |only man/eAD.Rd | 47 ++++++----- man/eIPD.Rd | 45 ++++++----- man/exmLP.2ipd.Rd |only man/exmWt.2ipd.Rd |only man/maicChecks-package.Rd |only man/maicLP.Rd | 60 +++++++------- man/maicMD.Rd | 66 +++++++++------- man/maicPCA.Rd | 78 +++++++++---------- man/maicT2Test.Rd | 66 ++++++++-------- man/maicWt.Rd | 67 ++++++++-------- man/maxessWt.Rd | 57 +++++++------- man/sim110.Rd |only 32 files changed, 832 insertions(+), 645 deletions(-)
Title: Generate Simulated Sawn Timber Strength Grading Data
Description: Tools for generating simulated sawn timber
strength grading data with a main focus on statistical simulation based on
covariance matrices. Simulation data
for Norway spruce sawn timber from Austria and reference values of means and
standard deviations of grade determining properties from literature
for a number of European countries are provided, as well.
Author: Andreas Weidenhiller [cre, aut]
,
Anton Wegscheider [aut]
Maintainer: Andreas Weidenhiller <a.weidenhiller@holzforschung.at>
Diff between WoodSimulatR versions 0.6.1 dated 2023-12-04 and 0.6.2 dated 2025-03-03
DESCRIPTION | 10 MD5 | 42 NEWS.md | 113 +- R/data.r | 4 R/stat_sim_dataset.r | 945 ++++++++++----------- R/statistical_simulation.r | 1296 ++++++++++++++--------------- R/subsample_data.r | 436 ++++----- README.md | 7 build/vignette.rds |binary inst/doc/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ inst/doc/woodsimulatr_basics.html | 11 man/gdp_data.Rd | 2 man/get_subsample_definitions.Rd | 6 man/get_transform_names.Rd | 6 man/simbase.Rd | 2 man/simbase_covar.Rd | 12 man/simbase_labeler.Rd | 2 man/simbase_list.Rd | 12 man/simulate_conditionally.Rd | 2 man/simulate_conditionally.simbase_list.Rd | 6 man/simulate_dataset.Rd | 28 vignettes/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ 22 files changed, 2546 insertions(+), 2540 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.7 dated 2025-02-10 and 0.3.8 dated 2025-03-03
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 4 + R/gg_scatter.R | 2 R/locus.R | 7 ++ inst/doc/locuszoomr.R | 104 ++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.html | 53 +++++++--------------- man/locus.Rd | 5 +- vignettes/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- 10 files changed, 311 insertions(+), 114 deletions(-)
Title: 'ade4' Tcl/Tk Graphical User Interface
Description: A Tcl/Tk GUI for some basic functions in the 'ade4' package.
Author: Jean Thioulouse [aut] ,
Stephane Dray [aut] ,
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4TkGUI versions 0.3-1 dated 2020-12-03 and 0.3.3 dated 2025-03-03
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 10 +++++----- NAMESPACE | 30 +++++++++++++++++++++++++++++- R/choose.R | 10 +++++----- R/ordiClust.R | 14 +++++++------- inst/CITATION | 41 +++++++++++++++++------------------------ 6 files changed, 82 insertions(+), 50 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.1.1 dated 2024-09-08 and 2.2.0 dated 2025-03-03
DESCRIPTION | 14 +++--- MD5 | 27 ++++++------ NEWS.md | 15 ++++++ R/launchApp.R | 2 R/realisedCoeffs.R | 49 ++++++++++++---------- README.md | 17 +++---- build/partial.rdb |binary inst/shiny/R/plot-functions.R | 2 inst/shiny/R/saveData.R | 8 +-- inst/shiny/app.R | 28 +++++++----- inst/shiny/www/custom.css | 2 inst/shiny/www/scripts.js |only man/figures/README-ibdsim2-example-distplot-1.png |binary man/ibdsim2-package.Rd | 2 man/realised.Rd | 11 +++- 15 files changed, 103 insertions(+), 74 deletions(-)