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 - httr2-1.1.1/httr2/R/pooled-request.R |only httr2-1.1.1/httr2/R/req-auth-aws.R | 5 httr2-1.1.1/httr2/R/req-auth-sign.R | 19 httr2-1.1.1/httr2/R/req-auth.R | 4 httr2-1.1.1/httr2/R/req-cache.R | 4 httr2-1.1.1/httr2/R/req-dry-run.R |only httr2-1.1.1/httr2/R/req-error.R | 16 httr2-1.1.1/httr2/R/req-headers.R | 21 - httr2-1.1.1/httr2/R/req-options.R | 110 ----- httr2-1.1.1/httr2/R/req-perform-connection.R | 39 + httr2-1.1.1/httr2/R/req-perform-iterative.R |only httr2-1.1.1/httr2/R/req-perform-parallel.R |only httr2-1.1.1/httr2/R/req-perform-sequential.R |only httr2-1.1.1/httr2/R/req-perform.R | 158 +++---- httr2-1.1.1/httr2/R/req-progress.R |only httr2-1.1.1/httr2/R/req-promise.R | 68 --- httr2-1.1.1/httr2/R/req-throttle.R | 159 +++++-- httr2-1.1.1/httr2/R/req-verbose.R |only httr2-1.1.1/httr2/R/req.R | 3 httr2-1.1.1/httr2/R/resp-headers.R | 5 httr2-1.1.1/httr2/R/resp-status.R | 18 httr2-1.1.1/httr2/R/resp-stream-aws.R | 2 httr2-1.1.1/httr2/R/resp-stream.R | 109 ++++- httr2-1.1.1/httr2/R/resp.R | 13 httr2-1.1.1/httr2/R/test.R | 17 httr2-1.1.1/httr2/R/utils.R | 75 +-- httr2-1.1.1/httr2/R/verbosity.R |only httr2-1.1.1/httr2/README.md | 18 httr2-1.1.1/httr2/build/vignette.rds |binary httr2-1.1.1/httr2/inst/doc/httr2.Rmd | 4 httr2-1.1.1/httr2/inst/doc/httr2.html | 81 ++- httr2-1.1.1/httr2/man/example_url.Rd | 2 httr2-1.1.1/httr2/man/multi_req_perform.Rd | 14 httr2-1.1.1/httr2/man/req_dry_run.Rd | 29 + httr2-1.1.1/httr2/man/req_headers.Rd | 4 httr2-1.1.1/httr2/man/req_perform_connection.Rd | 4 httr2-1.1.1/httr2/man/req_perform_iterative.Rd | 2 httr2-1.1.1/httr2/man/req_perform_parallel.Rd | 52 +- httr2-1.1.1/httr2/man/req_perform_promise.Rd | 5 httr2-1.1.1/httr2/man/req_perform_sequential.Rd | 5 httr2-1.1.1/httr2/man/req_progress.Rd | 2 httr2-1.1.1/httr2/man/req_throttle.Rd | 30 + httr2-1.1.1/httr2/man/req_verbose.Rd | 2 httr2-1.1.1/httr2/man/resp_stream_raw.Rd | 4 httr2-1.1.1/httr2/man/throttle_status.Rd | 8 httr2-1.1.1/httr2/man/with_verbosity.Rd | 27 + httr2-1.1.1/httr2/tests/testthat/_snaps/curl.md | 20 httr2-1.1.1/httr2/tests/testthat/_snaps/headers.md | 20 httr2-1.1.1/httr2/tests/testthat/_snaps/oauth-client.md | 32 + httr2-1.1.1/httr2/tests/testthat/_snaps/oauth-token.md | 18 httr2-1.1.1/httr2/tests/testthat/_snaps/req-auth-aws.md | 18 httr2-1.1.1/httr2/tests/testthat/_snaps/req-dry-run.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-headers.md | 13 httr2-1.1.1/httr2/tests/testthat/_snaps/req-options.md | 11 httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform-connection.md | 10 httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform-iterative-helpers.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform-iterative.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform-parallel.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform-sequential.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-perform.md | 41 - httr2-1.1.1/httr2/tests/testthat/_snaps/req-throttle.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req-verbose.md |only httr2-1.1.1/httr2/tests/testthat/_snaps/req.md | 6 httr2-1.1.1/httr2/tests/testthat/_snaps/resp-stream.md | 51 +- httr2-1.1.1/httr2/tests/testthat/_snaps/utils.md | 2 httr2-1.1.1/httr2/tests/testthat/helper-promise.R | 10 httr2-1.1.1/httr2/tests/testthat/helper-webfakes.R | 10 httr2-1.1.1/httr2/tests/testthat/helper.R | 9 httr2-1.1.1/httr2/tests/testthat/test-content-type.R | 6 httr2-1.1.1/httr2/tests/testthat/test-curl.R | 16 httr2-1.1.1/httr2/tests/testthat/test-headers.R | 16 httr2-1.1.1/httr2/tests/testthat/test-oauth-client.R | 54 -- httr2-1.1.1/httr2/tests/testthat/test-oauth-flow-auth-code.R | 10 httr2-1.1.1/httr2/tests/testthat/test-oauth-flow-refresh.R | 10 httr2-1.1.1/httr2/tests/testthat/test-oauth-token.R | 5 httr2-1.1.1/httr2/tests/testthat/test-req-auth-aws.R | 21 + httr2-1.1.1/httr2/tests/testthat/test-req-auth.R | 6 httr2-1.1.1/httr2/tests/testthat/test-req-cookies.R | 6 httr2-1.1.1/httr2/tests/testthat/test-req-dry-run.R |only httr2-1.1.1/httr2/tests/testthat/test-req-headers.R | 60 ++ httr2-1.1.1/httr2/tests/testthat/test-req-options.R | 44 -- httr2-1.1.1/httr2/tests/testthat/test-req-perform-connection.R | 15 httr2-1.1.1/httr2/tests/testthat/test-req-perform-iterative-helpers.R |only httr2-1.1.1/httr2/tests/testthat/test-req-perform-iterative-responses.R |only httr2-1.1.1/httr2/tests/testthat/test-req-perform-iterative.R |only httr2-1.1.1/httr2/tests/testthat/test-req-perform-parallel.R |only httr2-1.1.1/httr2/tests/testthat/test-req-perform-sequential.R |only httr2-1.1.1/httr2/tests/testthat/test-req-perform-stream.R | 2 httr2-1.1.1/httr2/tests/testthat/test-req-perform.R | 57 -- httr2-1.1.1/httr2/tests/testthat/test-req-promise.R | 2 httr2-1.1.1/httr2/tests/testthat/test-req-throttle.R | 90 ++-- httr2-1.1.1/httr2/tests/testthat/test-req-verbose.R |only httr2-1.1.1/httr2/tests/testthat/test-resp-headers.R | 7 httr2-1.1.1/httr2/tests/testthat/test-resp-stream.R | 62 ++ httr2-1.1.1/httr2/tests/testthat/test-resp-url.R | 2 httr2-1.1.1/httr2/tests/testthat/test-utils.R | 13 httr2-1.1.1/httr2/tests/testthat/test-verbosity.R |only httr2-1.1.1/httr2/vignettes/httr2.Rmd | 4 125 files changed, 1314 insertions(+), 984 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-18 1.6.1
2024-06-13 1.6.0
2024-05-17 1.5.2
2024-04-24 1.5.1
2023-12-11 1.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-05 0.98
2022-01-10 0.92
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-13 0.1.0