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 1.0 dated 2023-06-19 and 2.0 dated 2025-01-14
DESCRIPTION | 14 - MD5 | 22 - NAMESPACE | 20 - R/OSFD.R | 576 ++++++++++++++++++++++++++++---------------- R/RcppExports.R | 8 man/IOSFD.Rd |only man/OSFD-package.Rd | 38 +- man/OSFD.Rd | 18 - man/ball_unif.Rd | 14 - man/mMdist.Rd | 10 man/space_filling_points.Rd |only src/OSFD.cpp | 249 +++++++++++-------- src/RcppExports.cpp | 28 +- 13 files changed, 628 insertions(+), 369 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho [aut, cre]
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.9-7 dated 2024-01-19 and 1.11 dated 2025-01-14
DESCRIPTION | 14 ++-- MD5 | 151 +++++++++++++++++++++++------------------------ R/anm.ExpDesign.r | 24 ++++--- R/anm.LV.r | 5 - R/anm.ci.r | 36 ++++++----- R/anm.coin.r | 23 +++---- R/anm.cont.pdf.r | 36 +++++------ R/anm.die.r | 11 ++- R/anm.loglik.r | 72 +++++++++++----------- R/anm.ls.r | 41 ++++++------ R/anm.ls.reg.r | 48 +++++++------- R/anm.mc.bvn.r | 23 +++---- R/anm.popgrowth.r | 6 + R/anm.samp.design.R | 9 +- R/anm.transM.r | 3 R/dec2bin.R |only R/loglik.exp.plot.r | 89 ++++++++++++++------------- R/loglik.norm.plot.r | 130 ++++++++++++++++++++-------------------- R/plotAncova.r | 5 - R/see.Fcdf.r | 46 +++++++------- R/see.HW.r | 18 +++-- R/see.M.r | 21 +++--- R/see.accPrec.tck.r | 43 ++++++------- R/see.adddel.r | 21 +++--- R/see.ancova.tck.r | 82 ++++++++++++------------- R/see.anova.tck.r | 118 ++++++++++++++++++------------------ R/see.betacdf.r | 65 ++++++++++---------- R/see.bincdf.r | 85 +++++++++++++------------- R/see.chicdf.r | 43 +++++++------ R/see.cor.range.tck.r | 12 ++- R/see.expcdf.r | 57 +++++++++-------- R/see.exppower.r | 24 ++++--- R/see.gamcdf.r | 77 ++++++++++++----------- R/see.geocdf.r | 59 +++++++++--------- R/see.hypercdf.r | 71 +++++++++++----------- R/see.lnormcdf.r | 71 +++++++++++----------- R/see.logiscdf.r | 63 +++++++++---------- R/see.mixedII.r | 28 ++++---- R/see.mnom.tck.r | 26 ++++---- R/see.nbincdf.r | 65 ++++++++++---------- R/see.nlm.r | 59 +++++++++--------- R/see.normcdf.r | 84 +++++++++++++------------- R/see.poiscdf.r | 62 +++++++++---------- R/see.power.r | 83 +++++++++++++------------ R/see.rEffect.tck.r | 16 ++-- R/see.regression.tck.r | 55 ++++++++--------- R/see.roc.tck.r | 89 +++++++++++++-------------- R/see.smooth.tck.r | 65 ++++++++++---------- R/see.tcdf.r | 74 +++++++++++------------ R/see.ttest.tck.r | 98 +++++++++++++++--------------- R/see.unifcdf.r | 65 ++++++++++---------- R/see.weibcdf.r | 67 ++++++++++---------- R/see_discunifcdf.R | 81 +++++++++++++------------ R/selftest.pdfs.r | 111 ++++++++++++++++++++++++++-------- R/selftest.regGLM.R | 2 R/selftest.stats.tck.R | 8 +- build/vignette.rds |binary inst/doc/ranefCov.pdf |binary inst/doc/simpson.pdf |binary inst/doc/typeISS_key.pdf |binary man/anm.LV.rd | 24 +++---- man/anm.ci.rd | 14 ++-- man/anm.coin.Rd | 2 man/anm.cont.pdf.rd | 6 - man/anm.geo.growth.rd | 8 +- man/anm.loglik.rd | 56 ++++++++--------- man/anm.samp.design.Rd | 2 man/bin2dec.rd | 20 +++++- man/bvn.plot.rd | 11 +-- man/plot.pairw.rd | 30 ++++----- man/plotAncova.rd | 6 + man/pseudo.v.Rd | 8 +- man/qq.Plot.Rd | 30 ++++----- man/r.pb.rd | 8 +- man/see.power.rd | 4 - man/see.typeI_II.rd | 4 - man/world.emissions.Rd | 8 +- 77 files changed, 1628 insertions(+), 1453 deletions(-)
Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to
develop continuous-time agent based models. Its high performance
allows it to simulate millions of agents efficiently. Agents are
defined by their states (arbitrary R lists). The events are handled in
chronological order. This avoids the multi-event interaction problem
in a time step of discrete-time simulations, and gives precise
outcomes. The states are modified by provided or user-defined events.
The framework provides a flexible and customizable implementation of
state transitions (either spontaneous or caused by agent
interactions), making the framework suitable to apply to epidemiology
and ecology, e.g., to model life history stages, competition and
cooperation, and disease and information spread. The agent
interactions are flexible and extensible. The framework provides
random mixing and network interactions, and supports multi-level
mixing patterns. It can be easily extended to other interactions such
as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>
Diff between ABM versions 0.4.1 dated 2024-03-14 and 0.4.2 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 19 +++++++++++++++++++ inst/include/XP.h | 2 +- src/Agent.cpp | 4 ++-- src/Event.cpp | 4 ++-- src/RNG.cpp | 1 + src/Simulation.cpp | 8 ++++---- src/Transition.cpp | 15 +++++++++------ 9 files changed, 50 insertions(+), 27 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve Saeboe¸ [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.4.1 dated 2025-01-08 and 1.4.2 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ R/lm.R | 49 +++++-------------------------------------------- 4 files changed, 19 insertions(+), 51 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Elizabeth Chun [aut],
Steve Broll [aut],
David Buchanan [aut],
John Muschelli [aut] ,
Nathaniel Fernandes [aut] ,
Jung Hoon Seo [ctb],
Johnathan Shih [ctb],
Jacek Urbanek [ctb],
John Schwenck [ctb],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Pa [...truncated...]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between iglu versions 4.2.0 dated 2024-10-15 and 4.2.2 dated 2025-01-14
DESCRIPTION | 6 MD5 | 28 - NEWS.md | 3 R/active_percent.R | 14 R/mage.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/AGP_and_Episodes.html | 2 inst/doc/MAGE.html | 46 - inst/doc/iglu.R | 8 inst/doc/iglu.html | 262 +++++----- inst/shiny_iglu/rsconnect/shinyapps.io/irinagain/shiny_iglu.dcf | 2 man/active_percent.Rd | 4 man/mage.Rd | 1 vignettes/iglu_files/figure-html/unnamed-chunk-27-1.png |binary 15 files changed, 197 insertions(+), 186 deletions(-)
Title: Characterizing Observed and Expected Representation
Description: A system for analyzing descriptive representation, especially for comparing the composition of a political body to the population it represents. Users can compute the expected degree of representation for a body under a random sampling model, the expected degree of representation variability, as well as representation scores from observed political bodies. The package is based on Gerring, Jerzak, and Oncel (2024) <doi:10.1017/S0003055423000680>.
Author: Connor Jerzak [aut, cre] ,
John Gerring [aut] ,
Erzen Oncel [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between DescriptiveRepresentationCalculator versions 1.0.0 dated 2023-10-23 and 1.1.0 dated 2025-01-14
DESCRIPTION | 15 ++++++++------- MD5 | 22 ++++++++++++++-------- R/ExpectedRep.R | 19 ++++++++++++++----- R/ObservedRep.R | 25 ++++++++++++++++--------- R/VarRep.R | 20 +++++++++++++++----- build/partial.rdb |binary build/vignette.rds |only inst |only man/ExpectedRepresentation.Rd | 14 ++++++++++---- man/ObservedRepresentation.Rd | 10 ++++++++-- man/SDRepresentation.Rd | 14 ++++++++++---- vignettes |only 12 files changed, 95 insertions(+), 44 deletions(-)
More information about DescriptiveRepresentationCalculator at CRAN
Permanent link
Title: Analytical Methods for Stream DAGs
Description: Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.
Author: Ken Aho [aut, cre],
Arya Legg [dtc, ctb],
Rob Ramos [dtc],
Maggi Kraft [dtc],
Charles T. Bond [dtc],
Rebecca L. Hale [dtc]
Maintainer: Ken Aho <ahoken@isu.edu>
Diff between streamDAG versions 1.5 dated 2023-10-06 and 1.5-9 dated 2025-01-14
DESCRIPTION | 10 ++-- MD5 | 96 ++++++++++++++++++++++------------------- NAMESPACE | 4 + R/STIC.RFimpute.R |only R/arc_pa_from_nodes.R | 4 - R/delete_nodes_pa.R | 9 +++ R/get.AIMS.data.R |only R/intact_to_sink.R | 35 +++++++++----- R/size_intact_to_arc.R |only R/streamDAGs.R | 28 ++++++++--- R/vector_segments.R |only build/vignette.rds |binary data/AIMS.node.coords.rda |binary data/dc_arc_pres_abs.rda |binary data/dc_lengths.rda |binary data/dc_node_pres_abs.rda |binary data/gj_coords16.rda |binary data/gj_lengths.rda |binary data/gj_lengths_piezo_full.rda |only data/gj_node_pres_abs.rda |binary data/gj_node_pres_abs16.rda |binary data/jd_lengths.rda |binary data/jd_lengths_2023.rda |only data/jd_lengths_full.rda |binary data/jd_node_pres_abs.rda |binary data/kon_coords.rda |binary data/kon_lengths.rda |binary data/mur_arc_pres_abs.rda |binary data/mur_coords.rda |binary data/mur_lengths.rda |binary data/mur_node_pres_abs.rda |binary data/mur_seasons_arc_pa.rda |binary inst/CITATION | 5 -- inst/doc/streamDAG.R | 9 ++- inst/doc/streamDAG.Rmd | 16 +++--- inst/doc/streamDAG.html | 65 ++++++++++++++------------- man/AIMS.node.coords.Rd | 1 man/STIC.RFimpute.Rd |only man/dc_lengths.Rd | 2 man/dc_node_pres_abs.Rd | 13 ++++- man/delete.nodes.pa.Rd | 6 +- man/get.AIMS.data.rd |only man/gj_lengths.Rd | 7 +- man/gj_node_pres_abs.Rd | 15 ++++-- man/intact_to_sink.Rd | 14 +++-- man/isle.Rd | 2 man/jd_lengths.Rd | 5 +- man/jd_node_pres_abs.Rd | 21 ++++++++ man/path.lengths.sink.Rd | 2 man/size.intact.to.arc.Rd |only man/spatial.plot.Rd | 9 ++- man/streamDAGs.Rd | 96 ++++++++++++++++++++++++++++++++--------- man/vector_segments.Rd |only vignettes/streamDAG.Rmd | 16 +++--- 54 files changed, 318 insertions(+), 172 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>. d) Tsagris M., Papadakis M., Alenazi A. and Alzeley O. (2024). Computationally Efficient Outlier Detection for High-Dimensional Data Using the [...truncated...]
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [ctb],
Stefanos Fafalios [aut],
Matteo Fasiolo [ctb],
Morgan Jacob [ctb],
Giorgos Borboudakis [ctb],
John Burkardt [ctb],
Changliang Zou [ctb],
Kleanthi Lakiotaki [ctb],
Chris [...truncated...]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.3 dated 2024-12-31 and 2.1.4 dated 2025-01-14
Rfast-2.1.3/Rfast/man/dcor.Rd |only Rfast-2.1.3/Rfast/man/spml.regs.Rd |only Rfast-2.1.4/Rfast/DESCRIPTION | 8 - Rfast-2.1.4/Rfast/MD5 | 97 ++++++++--------- Rfast-2.1.4/Rfast/NAMESPACE | 2 Rfast-2.1.4/Rfast/NEWS.md | 20 +++ Rfast-2.1.4/Rfast/R/auc.R | 2 Rfast-2.1.4/Rfast/R/distance_cov_cor.R | 30 ++++- Rfast-2.1.4/Rfast/R/hd.eigen.R | 29 ++--- Rfast-2.1.4/Rfast/R/system_and_package.R | 78 +++++++++----- Rfast-2.1.4/Rfast/build/partial.rdb |binary Rfast-2.1.4/Rfast/inst/include/Rfast/FactorVector.hpp | 10 + Rfast-2.1.4/Rfast/inst/include/Rfast/helpers.hpp | 74 +++++++++++-- Rfast-2.1.4/Rfast/inst/include/Rfast/templates.h | 8 + Rfast-2.1.4/Rfast/man/Lgamma.Rd | 2 Rfast-2.1.4/Rfast/man/acg.mle.Rd | 15 +- Rfast-2.1.4/Rfast/man/beta.mle.Rd | 10 - Rfast-2.1.4/Rfast/man/circlin.cor.Rd | 10 - Rfast-2.1.4/Rfast/man/colvarcomps.mom.Rd | 2 Rfast-2.1.4/Rfast/man/colwatsons.Rd | 4 Rfast-2.1.4/Rfast/man/dcor.ttest.Rd | 4 Rfast-2.1.4/Rfast/man/dcov.Rd | 34 ++++-- Rfast-2.1.4/Rfast/man/dmvnorm.Rd | 4 Rfast-2.1.4/Rfast/man/edist.Rd | 2 Rfast-2.1.4/Rfast/man/fish.kent.Rd | 4 Rfast-2.1.4/Rfast/man/hd.eigen.Rd | 10 - Rfast-2.1.4/Rfast/man/kuiper.Rd | 10 - Rfast-2.1.4/Rfast/man/mahala.Rd | 2 Rfast-2.1.4/Rfast/man/mat.mult.Rd | 2 Rfast-2.1.4/Rfast/man/mediandir.Rd | 4 Rfast-2.1.4/Rfast/man/mvkurtosis.Rd | 2 Rfast-2.1.4/Rfast/man/mvt.mle.Rd | 6 - Rfast-2.1.4/Rfast/man/ompr.Rd | 4 Rfast-2.1.4/Rfast/man/pc.skel.Rd | 2 Rfast-2.1.4/Rfast/man/pdcor.Rd |only Rfast-2.1.4/Rfast/man/permcor.Rd | 3 Rfast-2.1.4/Rfast/man/racg.Rd | 6 - Rfast-2.1.4/Rfast/man/rmdp.Rd | 2 Rfast-2.1.4/Rfast/man/rvmf.Rd | 5 Rfast-2.1.4/Rfast/man/rvonmises.Rd | 4 Rfast-2.1.4/Rfast/man/score.glms.Rd | 14 +- Rfast-2.1.4/Rfast/man/spml.reg.Rd | 31 ++++- Rfast-2.1.4/Rfast/src/col_row_utilities.cpp | 98 ++++++++++++------ Rfast-2.1.4/Rfast/src/dista.cpp | 76 ++++++++++--- Rfast-2.1.4/Rfast/src/dists.cpp | 61 +++++++---- Rfast-2.1.4/Rfast/src/energy.cpp | 4 Rfast-2.1.4/Rfast/src/gaussian_nb.cpp | 4 Rfast-2.1.4/Rfast/src/maha.cpp | 17 +-- Rfast-2.1.4/Rfast/src/maha_ex.cpp | 51 ++++----- Rfast-2.1.4/Rfast/src/rmdp.cpp | 9 + Rfast-2.1.4/Rfast/src/rvmf.cpp | 11 +- 51 files changed, 565 insertions(+), 322 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al.(2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
log-normal log-normal mixture. Multiple distributions can be averaged
using Akaike Information Criteria. Confidence intervals on hazard
concentrations and proportions are produced by bootstrapping.
Author: Joe Thorley [aut, cre] ,
Rebecca Fisher [aut],
David Fox [aut],
Carl Schwarz [aut],
Angeline Tillmanns [ctb],
Seb Dalgarno [ctb] ,
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb],
Ali Azizishi [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 2.1.0 dated 2024-10-21 and 2.2.0 dated 2025-01-14
ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.R |only ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.html |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.R |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.html |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.R |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.html |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.R |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.html |only ssdtools-2.1.0/ssdtools/inst/doc/small-sample-bias.pdf |only ssdtools-2.1.0/ssdtools/inst/doc/small-sample-bias.pdf.asis |only ssdtools-2.1.0/ssdtools/src/gompertz.cpp |only ssdtools-2.1.0/ssdtools/src/gumbel.cpp |only ssdtools-2.1.0/ssdtools/vignettes/additional-technical-details.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/customising-plots.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/distributions.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/images |only ssdtools-2.1.0/ssdtools/vignettes/model-averaging.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/small-sample-bias.pdf.asis |only ssdtools-2.2.0/ssdtools/DESCRIPTION | 34 - ssdtools-2.2.0/ssdtools/MD5 | 225 ++++------ ssdtools-2.2.0/ssdtools/NAMESPACE | 2 ssdtools-2.2.0/ssdtools/NEWS.md | 25 - ssdtools-2.2.0/ssdtools/R/RcppExports.R | 8 ssdtools-2.2.0/ssdtools/R/censor.R | 14 ssdtools-2.2.0/ssdtools/R/censored.R | 2 ssdtools-2.2.0/ssdtools/R/d.R | 30 - ssdtools-2.2.0/ssdtools/R/devtools-helpers.R | 2 ssdtools-2.2.0/ssdtools/R/dists.R | 15 ssdtools-2.2.0/ssdtools/R/ggplot.R | 35 - ssdtools-2.2.0/ssdtools/R/gof.R | 2 ssdtools-2.2.0/ssdtools/R/gompertz.R | 22 ssdtools-2.2.0/ssdtools/R/hc-burrlioz.R | 18 ssdtools-2.2.0/ssdtools/R/lgumbel.R | 17 ssdtools-2.2.0/ssdtools/R/params.R | 16 ssdtools-2.2.0/ssdtools/R/plot-cf.R | 13 ssdtools-2.2.0/ssdtools/R/plot.R | 2 ssdtools-2.2.0/ssdtools/R/scales.R | 28 + ssdtools-2.2.0/ssdtools/R/ssd-plot.R | 98 +++- ssdtools-2.2.0/ssdtools/R/utils.R | 3 ssdtools-2.2.0/ssdtools/R/wqg.R | 43 - ssdtools-2.2.0/ssdtools/README.md | 74 +-- ssdtools-2.2.0/ssdtools/build/vignette.rds |binary ssdtools-2.2.0/ssdtools/data/boron_pred.rda |binary ssdtools-2.2.0/ssdtools/data/dist_data.rda |binary ssdtools-2.2.0/ssdtools/inst/WORDLIST | 13 ssdtools-2.2.0/ssdtools/inst/doc/faqs.R |only ssdtools-2.2.0/ssdtools/inst/doc/faqs.Rmd |only ssdtools-2.2.0/ssdtools/inst/doc/faqs.html |only ssdtools-2.2.0/ssdtools/inst/doc/ssdtools.R | 8 ssdtools-2.2.0/ssdtools/inst/doc/ssdtools.html | 15 ssdtools-2.2.0/ssdtools/man/comma_signif.Rd | 5 ssdtools-2.2.0/ssdtools/man/dist_data.Rd | 3 ssdtools-2.2.0/ssdtools/man/figures/README-unnamed-chunk-4-1.png |binary ssdtools-2.2.0/ssdtools/man/figures/README-unnamed-chunk-8-1.png |binary ssdtools-2.2.0/ssdtools/man/geom_hcintersect.Rd | 2 ssdtools-2.2.0/ssdtools/man/geom_ssd.Rd | 8 ssdtools-2.2.0/ssdtools/man/params.Rd | 23 - ssdtools-2.2.0/ssdtools/man/pgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/plgumbel.Rd | 3 ssdtools-2.2.0/ssdtools/man/predict.fitburrlioz.Rd | 2 ssdtools-2.2.0/ssdtools/man/predict.fitdists.Rd | 2 ssdtools-2.2.0/ssdtools/man/qgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/qlgumbel.Rd | 3 ssdtools-2.2.0/ssdtools/man/rgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/rlgumbel.Rd | 7 ssdtools-2.2.0/ssdtools/man/scale_colour_ssd.Rd | 10 ssdtools-2.2.0/ssdtools/man/ssd_censor_data.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists_all.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists_shiny.Rd |only ssdtools-2.2.0/ssdtools/man/ssd_gof.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_hc.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_hc_burrlioz.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_label_comma_hc.Rd |only ssdtools-2.2.0/ssdtools/man/ssd_plot.Rd | 25 - ssdtools-2.2.0/ssdtools/man/ssd_plot_cf.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_plot_data.Rd | 4 ssdtools-2.2.0/ssdtools/man/ssd_wqg_bc.Rd | 18 ssdtools-2.2.0/ssdtools/man/ssd_wqg_burrlioz.Rd | 17 ssdtools-2.2.0/ssdtools/man/ssdtools-package.Rd | 5 ssdtools-2.2.0/ssdtools/man/stat_ssd.Rd | 6 ssdtools-2.2.0/ssdtools/src/RcppExports.cpp | 26 - 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Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
,
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.7.0 dated 2023-11-14 and 0.8.0 dated 2025-01-14
DESCRIPTION | 8 +-- MD5 | 37 ++++++++-------- NAMESPACE | 1 NEWS.md | 5 ++ R/auk-country.R | 2 R/auk-filter.R | 1 R/auk-version.R | 6 +- R/process_barcharts.R |only build/vignette.rds |binary data/ebird_taxonomy.rda |binary inst/doc/auk.R | 88 +++++++++++++++++++-------------------- inst/doc/auk.html | 16 +++---- inst/doc/development.R | 52 +++++++++++------------ inst/doc/development.html | 4 - inst/extdata/barchart-sample.txt |only man/auk_country.Rd | 2 man/auk_ebd_version.Rd | 3 - man/auk_version.Rd | 3 - man/ebird_species.Rd | 3 - man/get_ebird_taxonomy.Rd | 3 - man/process_barcharts.Rd |only 21 files changed, 124 insertions(+), 110 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of
'Protocol Buffers' library is required; currently version 3.3.0 from 2017
is the stated minimum.
Author: Romain Francois [aut] ,
Dirk Eddelbuettel [aut, cre] ,
Murray Stokely [aut] ,
Jeroen Ooms [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.22 dated 2024-01-21 and 0.4.23 dated 2025-01-14
ChangeLog | 77 +++ DESCRIPTION | 23 MD5 | 62 +- R/00classes.R | 4 R/extensions.R | 10 R/field_count.R | 2 R/wrapper_ServiceDescriptor.R | 4 README.md | 2 build/vignette.rds |binary configure | 851 +++++++++++++++++++----------------- configure.ac | 10 inst/NEWS.Rd | 25 - inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/tinytest/test_addressbook.R | 4 src/DescriptorPoolLookup.cpp | 6 src/DescriptorPoolLookup.h | 8 src/RWarningErrorCollector.cpp | 16 src/RWarningErrorCollector.h | 6 src/init.c | 8 src/mutators.cpp | 22 src/rprotobuf.cpp | 6 src/rprotobuf.h | 3 src/wrapper_Descriptor.cpp | 14 src/wrapper_EnumDescriptor.cpp | 6 src/wrapper_EnumValueDescriptor.cpp | 2 src/wrapper_FieldDescriptor.cpp | 2 src/wrapper_FileDescriptor.cpp | 18 src/wrapper_Message.cpp | 8 src/wrapper_MethodDescriptor.cpp | 2 src/wrapper_ServiceDescriptor.cpp | 6 32 files changed, 706 insertions(+), 501 deletions(-)
Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.
Author: Matthias Kohl [cre, cph, aut],
Peter Ruckdeschel [aut, cph],
Mykhailo Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
R Core Team [ctb, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobAStBase versions 1.2.6 dated 2024-09-02 and 1.2.7 dated 2025-01-14
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- inst/CITATION | 3 ++- inst/NEWS | 10 ++++++++++ man/0RobAStBase-package.Rd | 8 ++++---- 5 files changed, 29 insertions(+), 18 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.0.9 dated 2025-01-07 and 2.1.0 dated 2025-01-14
DESCRIPTION | 14 - MD5 | 36 +-- R/GeoCompositeLik2.R | 16 - R/GeoCorrFct.r | 18 - R/GeoCorrFct_Cop.R | 30 +- R/GeoCovmatrix.r | 104 +++++--- R/GeoKrig.r | 65 +++-- R/GeoLik.r | 304 ++----------------------- R/GeoSim.r | 4 R/GeoSimapprox.r | 2 R/GeoVariogram.r | 96 +++++--- R/TB.R | 40 ++- R/Utility.r | 104 ++++---- src/CompositeLikelihood2_ani.c | 78 +++--- src/CompositeLikelihoodCond2_ani.c | 70 ++--- src/CorrelationFunction.c | 9 src/Distributions.c | 13 - src/GeoModels_init.c | 444 +++++++++++++++++++------------------ src/Utility.c | 26 -- 19 files changed, 653 insertions(+), 820 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.3.0 dated 2024-12-12 and 0.4.0 dated 2025-01-14
DESCRIPTION | 6 MD5 | 29 - NEWS.md | 19 + R/padronizar_enderecos.R | 15 R/padronizar_numeros.R | 68 +++- README.md | 2 inst/doc/enderecobr.R | 37 ++ inst/doc/enderecobr.Rmd | 80 ++++ inst/doc/enderecobr.html | 430 +++++++++++++++----------- man/padronizar_enderecos.Rd | 6 man/padronizar_numeros.Rd | 6 tests/testthat/_snaps/padronizar_enderecos.md | 12 tests/testthat/_snaps/padronizar_numeros.md |only tests/testthat/test-padronizar_enderecos.R | 41 ++ tests/testthat/test-padronizar_numeros.R | 90 +++++ vignettes/enderecobr.Rmd | 80 ++++ 16 files changed, 689 insertions(+), 232 deletions(-)
Title: At-Risk
Description: The at-Risk (aR) approach is based on a two-step parametric estimation procedure that allows to forecast the full conditional distribution of an economic variable at a given horizon, as a function of a set of factors. These density forecasts are then be used to produce coherent forecasts for any downside risk measure, e.g., value-at-risk, expected shortfall, downside entropy. Initially introduced by Adrian et al. (2019) <doi:10.1257/aer.20161923> to reveal the vulnerability of economic growth to financial conditions, the aR approach is currently extensively used by international financial institutions to provide Value-at-Risk (VaR) type forecasts for GDP growth (Growth-at-Risk) or inflation (Inflation-at-Risk). This package provides methods for estimating these models. Datasets for the US and the Eurozone are available to allow testing of the Adrian et al. (2019) model. This package constitutes a useful toolbox (data and functions) for private practitioners, scholars as well as p [...truncated...]
Author: Quentin Lajaunie [aut, cre],
Guillaume Flament [aut, ctb],
Christophe Hurlin [aut],
Souzan Kazemi [rev]
Maintainer: Quentin Lajaunie <quentin_lajaunie@hotmail.fr>
Diff between atRisk versions 0.1.0 dated 2023-08-08 and 0.2.0 dated 2025-01-14
atRisk-0.1.0/atRisk/R/f_param_histo.R |only atRisk-0.1.0/atRisk/data/data_param_histo.rda |only atRisk-0.1.0/atRisk/man/data_param_histo.Rd |only atRisk-0.1.0/atRisk/man/f_param_histo.Rd |only atRisk-0.2.0/atRisk/DESCRIPTION | 9 atRisk-0.2.0/atRisk/MD5 | 46 +- atRisk-0.2.0/atRisk/NAMESPACE | 6 atRisk-0.2.0/atRisk/R/f_ES.R | 82 ++--- atRisk-0.2.0/atRisk/R/f_VaR.R | 92 +++-- atRisk-0.2.0/atRisk/R/f_compile_quantile.R | 179 +++++------ atRisk-0.2.0/atRisk/R/f_distrib.R | 291 ++++++++++-------- atRisk-0.2.0/atRisk/R/f_histo_RM.R | 52 +-- atRisk-0.2.0/atRisk/R/f_nadaraya_watson_quantile.R |only atRisk-0.2.0/atRisk/R/f_plot_distrib_2D.R | 73 ++-- atRisk-0.2.0/atRisk/R/f_plot_distrib_3D.R | 75 ++-- atRisk-0.2.0/atRisk/data/data_US.rda |binary atRisk-0.2.0/atRisk/data/data_param_histo_US.rda |only atRisk-0.2.0/atRisk/man/data_US.Rd | 8 atRisk-0.2.0/atRisk/man/data_euro.Rd | 2 atRisk-0.2.0/atRisk/man/data_param_histo_US.Rd |only atRisk-0.2.0/atRisk/man/f_ES.Rd | 6 atRisk-0.2.0/atRisk/man/f_VaR.Rd | 2 atRisk-0.2.0/atRisk/man/f_compile_quantile.Rd | 13 atRisk-0.2.0/atRisk/man/f_distrib.Rd | 28 - atRisk-0.2.0/atRisk/man/f_histo_RM.Rd | 29 - atRisk-0.2.0/atRisk/man/f_nadaraya_watson_quantile.Rd |only atRisk-0.2.0/atRisk/man/f_plot_distrib_2D.Rd | 29 + atRisk-0.2.0/atRisk/man/f_plot_distrib_3D.Rd | 28 - 28 files changed, 579 insertions(+), 471 deletions(-)
Title: FDR Power
Description: Computing Average and TPX Power under various BHFDR type sequential
procedures. All of these procedures involve control of some summary of the
distribution of the FDP, e.g. the proportion of discoveries which are false
in a given experiment. The most widely known of these, the BH-FDR procedure,
controls the FDR which is the mean of the FDP. A lesser known procedure, due
to Lehmann and Romano, controls the FDX, or probability that the FDP exceeds
a user provided threshold. This is less conservative than FWE control
procedures but much more conservative than the BH-FDR proceudre. This
package and the references supporting it introduce a new procedure for
controlling the FDX which we call the BH-FDX procedure. This procedure
iteratively identifies, given alpha and lower threshold delta, an alpha*
less than alpha at which BH-FDR guarantees FDX control. This uses
asymptotic approximation and is only slightly more conservative than the
BH-FDR procedure. Likewise, we can think of the power i [...truncated...]
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between pwrFDR versions 3.2.2 dated 2024-12-18 and 3.2.4 dated 2025-01-14
DESCRIPTION | 6 MD5 | 14 - R/pwrFDR.R | 354 ++++++++++++++++++++------------- inst/doc/pwrFDR-vignette.R | 171 +++++++++++++--- inst/doc/pwrFDR-vignette.Rnw | 438 +++++++++++++++++++++++++++++------------- inst/doc/pwrFDR-vignette.pdf |binary man/Ch01-pwrFDR.Rd | 2 vignettes/pwrFDR-vignette.Rnw | 438 +++++++++++++++++++++++++++++------------- 8 files changed, 988 insertions(+), 435 deletions(-)
Title: Curved Text in 'ggplot2'
Description: A 'ggplot2' extension that allows text to follow curved paths.
Curved text makes it easier to directly label paths or neatly annotate in
polar co-ordinates.
Author: Allan Cameron [aut, cre],
Teun van den Brand [aut]
Maintainer: Allan Cameron <Allan.Cameron@nhs.scot>
Diff between geomtextpath versions 0.1.4 dated 2024-06-13 and 0.1.5 dated 2025-01-14
DESCRIPTION | 8 +- MD5 | 58 ++++++++++---------- NEWS.md | 97 +++++++++++++++++++---------------- R/geom_labelpath.R | 2 R/geom_textabline.R | 1 R/geom_textpath.R | 2 R/geom_textsf.R | 37 +++++++++---- R/grob_labelpath.R | 9 ++- R/grob_textpath.R | 11 +++ R/path_handling.R | 25 ++++++++- R/sf_helpers.R | 41 +++++++++----- R/text_helpers.R | 17 +++++- R/text_placement.R | 4 - README.md | 3 - build/vignette.rds |binary inst/doc/aesthetics.R | 2 inst/doc/aesthetics.Rmd | 2 inst/doc/aesthetics.html | 46 ++++++++-------- inst/doc/curved_polar.R | 2 inst/doc/curved_polar.Rmd | 2 inst/doc/curved_polar.html | 20 +++---- inst/doc/geomtextpath.R | 2 inst/doc/geomtextpath.Rmd | 2 inst/doc/geomtextpath.html | 14 ++--- man/figures/README-geom_textsf-1.png |binary man/geom_textsf.Rd | 45 ++++++++-------- tests/testthat/Rplots.pdf |binary vignettes/aesthetics.Rmd | 2 vignettes/curved_polar.Rmd | 2 vignettes/geomtextpath.Rmd | 2 30 files changed, 273 insertions(+), 185 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.17 dated 2024-02-20 and 0.2.18 dated 2025-01-14
DESCRIPTION | 8 MD5 | 64 ++-- NAMESPACE | 6 NEWS.md | 10 R/JAGS-diagnostics.R | 24 + R/JAGS-fit.R | 457 ++++++++++++++++++++++++++--- R/JAGS-formula.R | 55 +-- R/JAGS-marglik.R | 136 ++++---- R/interpret.R | 52 +++ R/marginal-distributions.R | 634 +++++++++++++++++++++++++++++++++++++++-- R/model-averaging-plots.R | 57 +++ R/model-averaging.R | 484 ++++++++++++++++++++++++++++++- R/priors-plot.R | 50 ++- R/priors-print.R | 46 ++ R/priors-tools.R | 88 +++++ R/priors.R | 334 +++++++++++++++++---- R/summary-tables.R | 623 ++++++++++++++++++++++++++++------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/ComparisonR.html | 21 - inst/doc/SpikeAndSlab.html | 30 - man/BayesTools.Rd | 1 man/BayesTools_model_tables.Rd | 9 man/JAGS_check_convergence.Rd | 9 man/as_marginal_inference.Rd |only man/as_mixed_posteriors.Rd |only man/interpret.Rd | 3 man/is.prior.Rd | 3 man/marginal_inference.Rd | 5 man/marginal_posterior.Rd | 2 man/mix_posteriors.Rd | 2 man/prior_mixture.Rd |only man/prior_weightfunction.Rd | 8 man/update.BayesTools_table.Rd |only man/weightfunctions_mapping.Rd | 4 35 files changed, 2708 insertions(+), 517 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 0.24.0 dated 2024-11-27 and 0.24.1 dated 2025-01-14
DESCRIPTION | 30 +- MD5 | 221 +++++++-------- NAMESPACE | 1 NEWS.md | 22 + R/1_model_parameters.R | 198 ++++++------- R/4_standard_error.R | 6 R/5_simulate_model.R | 5 R/bootstrap_model.R | 4 R/ci_kenward.R | 1 R/ci_profile_boot.R | 3 R/cluster_analysis.R | 3 R/cluster_discrimination.R | 1 R/cluster_meta.R | 4 R/convert_efa_to_cfa.R | 5 R/display.R | 14 R/dof_kenward.R | 2 R/dof_ml1.R | 8 R/dominance_analysis.R | 76 ++--- R/equivalence_test.R | 18 - R/extract_parameters.R | 14 R/extract_parameters_anova.R | 4 R/extract_random_parameters.R | 1 R/extract_random_variances.R | 13 R/factor_analysis.R | 16 - R/format.R | 14 R/format_p_adjust.R | 5 R/format_parameters.R | 3 R/methods_BayesFM.R | 49 +-- R/methods_BayesFactor.R | 2 R/methods_aov.R | 7 R/methods_base.R | 4 R/methods_brglm2.R | 4 R/methods_cplm.R | 4 R/methods_emmeans.R | 2 R/methods_fixest.R | 57 +-- R/methods_gam.R | 2 R/methods_glmmTMB.R | 6 R/methods_glmx.R | 1 R/methods_hclust.R | 1 R/methods_htest.R | 26 - R/methods_kmeans.R | 8 R/methods_lavaan.R | 9 R/methods_lm.R | 2 R/methods_lme4.R | 1 R/methods_lqmm.R | 2 R/methods_lrm.R | 4 R/methods_mass.R | 3 R/methods_metaplus.R | 9 R/methods_mfx.R | 4 R/methods_mhurdle.R | 1 R/methods_mice.R | 11 R/methods_mmrm.R | 53 +-- R/methods_model_fit.R | 4 R/methods_nlme.R | 2 R/methods_ordinal.R | 5 R/methods_other.R | 2 R/methods_panelr.R | 5 R/methods_plm.R | 2 R/methods_posterior.R | 3 R/methods_pscl.R | 5 R/methods_quantreg.R | 7 R/methods_survey.R | 6 R/methods_survival.R | 58 +++ R/methods_varest.R | 5 R/methods_vgam.R | 5 R/n_clusters.R | 6 R/n_clusters_easystats.R | 13 R/n_factors.R | 4 R/p_function.R | 44 +- R/p_significance.R | 1 R/p_value_kenward.R | 4 R/parameters_type.R | 6 R/pool_parameters.R | 3 R/principal_components.R | 6 R/print.parameters_model.R | 11 R/print_html.R | 1 R/print_md.R | 14 R/random_parameters.R | 2 R/reduce_parameters.R | 18 - R/reshape_loadings.R | 4 R/select_parameters.R | 1 R/standardize_info.R | 12 R/standardize_parameters.R | 5 R/utils.R | 2 R/utils_cleaners.R | 2 R/utils_format.R | 14 R/utils_model_parameters.R | 9 R/utils_pca_efa.R | 31 -- man/p_function.Rd | 41 +- tests/testthat/_snaps/brms.md | 8 tests/testthat/_snaps/model_parameters.fixest.md | 25 + tests/testthat/_snaps/model_parameters_ordinal.md | 28 - tests/testthat/_snaps/printing-stan.md | 74 ++++- tests/testthat/_snaps/printing.md | 21 + tests/testthat/_snaps/windows/model_parameters.logitr.md |only tests/testthat/test-GLMMadaptive.R | 1 tests/testthat/test-dominance_analysis.R | 1 tests/testthat/test-geeglm.R | 15 - tests/testthat/test-glmer.R | 1 tests/testthat/test-glmmTMB.R | 2 tests/testthat/test-model_parameters.anova.R | 1 tests/testthat/test-model_parameters.fixest.R | 14 tests/testthat/test-model_parameters.logitr.R |only tests/testthat/test-model_parameters_df.R | 1 tests/testthat/test-p_value.R | 1 tests/testthat/test-polr.R |only tests/testthat/test-pool_parameters.R | 4 tests/testthat/test-printing-stan.R | 13 tests/testthat/test-printing.R | 10 tests/testthat/test-quantreg.R | 1 tests/testthat/test-random_effects_ci.R | 10 tests/testthat/test-robust.R | 6 tests/testthat/test-standardize_parameters.R | 3 113 files changed, 662 insertions(+), 905 deletions(-)
Title: Easily Install and Load the 'mlr3' Package Family
Description: The 'mlr3' package family is a set of packages for
machine-learning purposes built in a modular fashion. This wrapper
package is aimed to simplify the installation and loading of the core
'mlr3' packages. Get more information about the 'mlr3' project at
<https://mlr3book.mlr-org.com/>.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3verse versions 0.3.0 dated 2024-06-30 and 0.3.1 dated 2025-01-14
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/mlr3verse_info.R | 24 ++++++++++++++++-------- R/zzz.R | 19 +------------------ README.md | 28 ++++++++++++++++++++++------ man/mlr3verse-package.Rd | 26 -------------------------- man/mlr3verse_info.Rd | 3 ++- 9 files changed, 70 insertions(+), 77 deletions(-)
Title: Control of the Median of the FDP
Description: Methods for controlling the median of the false discovery proportion (mFDP).
Depending on the method, simultaneous or non-simultaneous inference is provided.
The methods take a vector of p-values or test statistics as input.
Author: Jesse Hemerik [aut, cre]
Maintainer: Jesse Hemerik <hemerik@ese.eur.nl>
Diff between mFDP versions 0.1.0 dated 2022-08-22 and 0.2.0 dated 2025-01-14
DESCRIPTION | 21 ++++++++++----------- MD5 | 6 +++++- R/mFDP.direc.R |only R/mFDP.equiv.R |only man/mFDP.direc.Rd |only man/mFDP.equiv.Rd |only 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations. Important applications are the use of splines to model spatial or temporal
trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.8 dated 2024-08-26 and 1.0.9 dated 2025-01-14
DESCRIPTION | 13 MD5 | 111 ++- NAMESPACE | 1 NEWS.md | 11 R/DifferentiationCholesky.R | 2 R/LMMsolve-class.R | 150 ++-- R/LMMsolve.R | 506 +++------------- R/RcppExports.R | 2 R/chkInputLMMsolve.R |only R/chkResponse.R |only R/chkSplinesFormula.R |only R/constructFixed.R |only R/constructGinv.R |only R/constructRandom.R |only R/diagnosticsMME.R |only R/displayMME.R |only R/fitLMM.R |only R/getWeights.R |only R/multinomial.R |only R/obtainSmoothTrend.R | 6 R/predictFunctions.R | 21 R/spl1D.R | 2 R/splinesFunctions.R | 4 R/utils.R | 67 +- README.md | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Solving_Linear_Mixed_Models.R | 156 ++++- inst/doc/Solving_Linear_Mixed_Models.Rmd | 260 ++++++-- inst/doc/Solving_Linear_Mixed_Models.html | 929 +++++++++++++++++------------- inst/tinytest/GLMMFull |binary inst/tinytest/LMMsolve0 |binary inst/tinytest/LMMsolve1 |binary inst/tinytest/LMMsolve2 |binary inst/tinytest/LMMsolve3 |binary inst/tinytest/LMMsolve4 |binary inst/tinytest/LMMsolve5 |binary inst/tinytest/binomial1 |only inst/tinytest/binomial2 |only inst/tinytest/binomial3 |only inst/tinytest/cfFull |binary inst/tinytest/effDims |binary inst/tinytest/gam1DFull |binary inst/tinytest/modCoefs |binary inst/tinytest/modCoefsSe |binary inst/tinytest/modFit |binary inst/tinytest/modResid |binary inst/tinytest/multinomial1 |only inst/tinytest/smooth3D1 |binary inst/tinytest/smooth3D2 |binary inst/tinytest/spl1DFull |binary inst/tinytest/spl2DFull |binary inst/tinytest/spl3DFull |binary inst/tinytest/test_binomial.R |only inst/tinytest/test_multinomial.R |only inst/tinytest/test_offset.R |only man/LMMsolve.Rd | 14 man/LMMsolveObject.Rd | 1 man/constructRinv.Rd | 24 man/diagnosticsMME.Rd | 2 man/displayMME.Rd | 2 man/multinomial.Rd |only man/predict.LMMsolve.Rd | 20 src/ADcholesky.cpp | 2 vignettes/Solving_Linear_Mixed_Models.Rmd | 260 ++++++-- vignettes/bibliography.bib | 17 66 files changed, 1515 insertions(+), 1083 deletions(-)
Title: Methods for Closed Testing with Simes Inequality, in Particular
Hommel's Method
Description: Provides methods for closed testing using Simes local tests. In particular, calculates adjusted p-values for Hommel's multiple testing method, and provides lower confidence bounds for true discovery proportions. A robust but more conservative variant of the closed testing procedure that does not require the assumption of Simes inequality is also implemented. The methods have been described in detail in Goeman et al (Biometrika 106, 841-856, 2019).
Author: Jelle Goeman [aut, cre],
Rosa Meijer [aut],
Thijmen Krebs [aut]
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between hommel versions 1.6 dated 2021-12-17 and 1.8 dated 2025-01-14
ChangeLog | 9 +++ DESCRIPTION | 24 ++++++-- MD5 | 22 +++---- R/concentration-function.R | 8 ++ R/discoveries-function.R | 4 - man/concentration-function.Rd | 7 +- man/fdp-function.Rd | 118 +++++++++++++++++++++--------------------- man/hommel-class.Rd | 4 - man/hommel-function.Rd | 2 man/hommel-package.Rd | 60 +++++++++++---------- man/localtest-function.Rd | 2 src/hommel.cpp | 5 + 12 files changed, 148 insertions(+), 117 deletions(-)
Title: Build a Package from Rmarkdown Files
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut] ,
Vincent Guyader [aut, cre] ,
Yohann Mansiaux [aut],
ThinkR [cph]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between fusen versions 0.6.0 dated 2024-05-14 and 0.7.0 dated 2025-01-14
DESCRIPTION | 32 MD5 | 167 +- NAMESPACE | 5 NEWS.md | 147 +- R/add_flat_template.R | 112 + R/build_fusen_chunks.R | 32 R/create_fusen_rsproject.R | 31 R/deprecate_flat_file.R | 18 R/fill_description.R | 10 R/get_all_created_funs.R | 5 R/get_package_structure.R | 36 R/globals.R | 5 R/inflate-utils.R | 116 + R/inflate.R | 124 + R/inflate_all.R | 44 R/inflate_all_utils.R | 2 R/init_share_on_github.R | 5 R/load_flat_functions.R | 3 R/pre_inflate_all_diagnosis_eval.R | 10 R/register_config_file.R | 113 + R/rename_flat_file.R | 27 R/sepuku.R |only R/sepuku_utils.R |only README.md | 197 +- build/vignette.rds |binary inst/doc/How-to-use-fusen.html | 308 ++-- inst/doc/Maintain-packages-with-fusen.html | 353 +++-- inst/doc/deal-with-a-fusen-flat-file.R | 8 inst/doc/deal-with-a-fusen-flat-file.Rmd | 10 inst/doc/deal-with-a-fusen-flat-file.html | 226 +-- inst/doc/draw-a-tree-of-your-package-files-and-functions.R | 6 inst/doc/draw-a-tree-of-your-package-files-and-functions.Rmd | 6 inst/doc/draw-a-tree-of-your-package-files-and-functions.html | 354 ++--- inst/doc/inflate-all-your-flat-files.R | 6 inst/doc/inflate-all-your-flat-files.Rmd | 10 inst/doc/inflate-all-your-flat-files.html | 313 ++-- inst/doc/register-files-in-config.R | 12 inst/doc/register-files-in-config.Rmd | 12 inst/doc/register-files-in-config.html | 459 +++--- inst/doc/share-on-a-github-website.html | 231 +-- inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.R |only inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.Rmd |only inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.html |only inst/doc/tips-and-tricks.Rmd | 8 inst/doc/tips-and-tricks.html | 659 +++++----- inst/flat-template-additional.Rmd | 4 inst/flat-template-full.Rmd | 18 inst/flat-template-minimal_package.Rmd | 4 inst/flat-template-teaching.Rmd | 7 inst/rmarkdown/templates/additional/skeleton/skeleton.Rmd | 4 inst/the-dev-history.Rmd | 8 man/check_not_registered_files.Rd | 6 man/deprecate_flat_file.Rd | 4 man/fill_description.Rd | 7 man/fusen-package.Rd | 8 man/get_package_structure.Rd | 6 man/inflate.Rd | 10 man/inflate_all.Rd | 11 man/register_all_to_config.Rd | 6 man/rename_flat_file.Rd | 4 man/sepuku.Rd |only man/sepuku_utils.Rd |only tests/testthat/config_fusen_register.yaml | 78 - tests/testthat/test-add_flat_template.R | 126 + tests/testthat/test-build_fusen_chunks.R | 66 - tests/testthat/test-deprecate_flat_file.R | 18 tests/testthat/test-fill_description.R | 36 tests/testthat/test-get_all_created_funs.R | 2 tests/testthat/test-get_package_structure.R | 8 tests/testthat/test-inflate-part1.R | 176 +- tests/testthat/test-inflate-part2.R | 220 ++- tests/testthat/test-inflate-part3.R |only tests/testthat/test-inflate_all.R | 257 +++ tests/testthat/test-inflate_all_utils.R | 77 - tests/testthat/test-inflate_qmd.R | 6 tests/testthat/test-inflate_utils.R | 43 tests/testthat/test-init_share_on_github.R | 2 tests/testthat/test-pre_inflate_all_diagnosis_eval.R | 11 tests/testthat/test-register_config_file.R | 287 ++-- tests/testthat/test-rename_flat_file.R | 23 tests/testthat/test-sepuku.R |only tests/testthat/test-sepuku_utils.R |only tests/testthat/test-skeleton.R | 3 tests/testthat/test-user-story.R | 12 vignettes/deal-with-a-fusen-flat-file.Rmd | 10 vignettes/draw-a-tree-of-your-package-files-and-functions.Rmd | 6 vignettes/inflate-all-your-flat-files.Rmd | 10 vignettes/register-files-in-config.Rmd | 12 vignettes/switch-from-a-package-developed-with-fusen-to-a-classical-package.Rmd |only vignettes/tips-and-tricks.Rmd | 8 90 files changed, 3512 insertions(+), 2314 deletions(-)
Title: Joint Clustering and Alignment of Functional Data
Description: Implementations of the k-means, hierarchical agglomerative and
DBSCAN clustering methods for functional data which allows for jointly
aligning and clustering curves. It supports functional data defined on
one-dimensional domains but possibly evaluating in multivariate codomains.
It supports functional data defined in arrays but also via the 'fd' and
'funData' classes for functional data defined in the 'fda' and 'funData'
packages respectively. It currently supports shift, dilation and affine
warping functions for functional data defined on the real line and uses the
SRVF framework to handle boundary-preserving warping for functional data
defined on a specific interval. Main reference for the k-means algorithm:
Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment
for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for
the SRVF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013)
"Generative models for functional data using phase and [...truncated...]
Author: Aymeric Stamm [aut, cre] ,
Laura Sangalli [ctb],
Piercesare Secchi [ctb],
Simone Vantini [ctb],
Valeria Vitelli [ctb],
Alessandro Zito [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between fdacluster versions 0.4.0 dated 2025-01-12 and 0.4.1 dated 2025-01-14
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++--------------- NEWS.md | 7 +++++++ R/compare-caps.R | 4 ++-- R/fdadbscan.R | 2 +- R/fdadist.R | 6 +++--- R/fdahclust.R | 2 +- R/fdakmeans.R | 34 +++++++++++++++++----------------- R/utils.R | 11 ++++++----- man/compare_caps.Rd | 8 ++++---- man/fdacluster-package.Rd | 2 +- man/fdadbscan.Rd | 20 ++++++++++---------- man/fdadist.Rd | 6 +++--- man/fdahclust.Rd | 20 ++++++++++---------- man/fdakmeans.Rd | 20 ++++++++++---------- src/kumaraswamyWarpingClass.cpp |only src/kumaraswamyWarpingClass.h |only tests/testthat/test-fdakmeans.R | 2 +- 18 files changed, 98 insertions(+), 88 deletions(-)
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.20 dated 2024-01-13 and 1.0.21 dated 2025-01-14
pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/baseline/pubmed24n1219.xml.gz |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/baseline/pubmed24n1219.xml.gz.md5 |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/pubmed24n1219.rds |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/pubmed24n1220.rds |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed24n1220.xml.gz |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed24n1220.xml.gz.md5 |only pmparser-1.0.21/pmparser/DESCRIPTION | 8 pmparser-1.0.21/pmparser/MD5 | 38 pmparser-1.0.21/pmparser/NEWS.md | 3 pmparser-1.0.21/pmparser/build/vignette.rds |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/get_parsing_tables_no_suffix.rds |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/get_parsing_tables_with_suffix.rds |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz.md5 |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_postdown.csv | 8 pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_predown_all.csv | 2536 +++++----- pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_predown_baseline.csv | 2493 +++++---- pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/open_citation_collection.zip |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pmdb_sample_create.db |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pmdb_sample_update.db |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pubmed25n1274.rds |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pubmed25n1275.rds |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz.md5 |only 26 files changed, 2583 insertions(+), 2503 deletions(-)
Title: Co-Data Learning for Bayesian Additive Regression Trees
Description: Estimate prior variable weights for Bayesian Additive Regression
Trees (BART). These weights correspond to the probabilities of the variables
being selected in the splitting rules of the sum-of-trees.
Weights are estimated using empirical Bayes and external information on
the explanatory variables (co-data).
BART models are fitted using the 'dbarts' 'R' package.
See Goedhart and others (2023) <doi:10.48550/arXiv.2311.09997> for details.
Author: Jeroen M. Goedhart [aut, cre, cph]
,
Thomas Klausch [aut],
Mark A. van de Wiel [aut],
Vincent Dorie [ctb] ,
Hanarth Fonds [fnd]
Maintainer: Jeroen M. Goedhart <jeroengoed@gmail.com>
Diff between EBcoBART versions 1.1.0 dated 2024-09-26 and 1.1.1 dated 2025-01-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/EBcoBART_Functions.R | 30 +++++++++++++++--------------- R/data.R | 6 +++--- man/Bloodplatelet.Rd | 2 +- man/Dat_EBcoBART.Rd | 20 ++++++++++---------- man/EBcoBART.Rd | 4 ++-- man/Lymphoma.Rd | 4 ++-- 9 files changed, 49 insertions(+), 44 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.1.2 dated 2024-11-12 and 2.2.0 dated 2025-01-14
GitStats-2.1.2/GitStats/inst/roche_get_commits_workflow.R |only GitStats-2.1.2/GitStats/inst/roche_get_files_workflow.R |only GitStats-2.1.2/GitStats/inst/roche_get_release_logs_workflow.R |only GitStats-2.1.2/GitStats/man/get_files_content.Rd |only GitStats-2.1.2/GitStats/man/get_files_structure.Rd |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_commits-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_commits-GitStats.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_content-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_content-GitLab.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitLab.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitStats.md |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitStats.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitStats.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitStats.R |only GitStats-2.2.0/GitStats/DESCRIPTION | 6 GitStats-2.2.0/GitStats/MD5 | 194 - 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Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.9.6 dated 2024-10-23 and 2.9.7 dated 2025-01-14
DESCRIPTION | 10 +-- MD5 | 12 +-- inst/CITATION | 4 - inst/NEWS | 11 +++ inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 8 +- tests/Examples/distrMod-Ex.Rout.save | 116 ++++++++++++----------------------- 7 files changed, 68 insertions(+), 93 deletions(-)
Title: Bootstrap p-Values
Description: Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models.
Author: Mans Thulin [aut, cre]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between boot.pval versions 0.5 dated 2023-09-28 and 0.6 dated 2025-01-14
DESCRIPTION | 12 ++++++++---- MD5 | 32 +++++++++++++++++++------------- NEWS.md | 3 +++ R/boot.pval.R | 6 +++--- R/boot_summary.R | 22 +++++++++++++--------- R/censboot_summary.R | 7 ++++--- R/summary_to_gt.R | 4 ---- README.md | 29 ++++++++++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |only inst/REFERENCES.bib | 8 ++++---- inst/doc |only man/boot.pval.Rd | 4 ++-- man/boot_summary.Rd | 6 +++--- man/censboot_summary.Rd | 2 +- man/figures |only man/summary_to_gt.Rd | 9 +-------- vignettes |only 18 files changed, 87 insertions(+), 57 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural point estimators, which are neural networks that map data to a point summary of the posterior distribution. These estimators are likelihood-free and amortised, in the sense that, after an initial setup cost, inference from observed data can be made in a fraction of the time required by conventional approaches; see Sainsbury-Dale, Zammit-Mangion, and Huser (2024) <doi:10.1080/00031305.2023.2249522> for further details and an accessible introduction. The package also enables the construction of neural networks that approximate the likelihood-to-evidence ratio in an amortised manner, allowing one to perform inference based on the likelihood function or the entire posterior distribution; see Zammit-Mangion, Sainsbury-Dale, and Huser (2024, Sec. 5.2) <doi:10.48550/arXiv.2404.12484>, and the references therein. The package accommodates any model for which [...truncated...]
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.1.2 dated 2024-12-19 and 0.1.3 dated 2025-01-14
DESCRIPTION | 8 MD5 | 18 NAMESPACE | 2 R/core.R | 10 R/missingdata.R | 203 +++++++++++ README.md | 76 ++-- inst/doc/NeuralEstimators.html | 698 ++++++++++++++++++++++++++------------ man/spatialgraph.Rd |only man/spatialgraphlist.Rd |only tests/testthat/test-core.R | 1 tests/testthat/test-missingdata.R | 62 +++ 11 files changed, 802 insertions(+), 276 deletions(-)
More information about NeuralEstimators at CRAN
Permanent link
Title: Documentation for 'distr' Family of R Packages
Description: Provides documentation in form of a common vignette to packages 'distr',
'distrEx', 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrDoc versions 2.8.4 dated 2024-10-24 and 2.8.5 dated 2025-01-14
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- inst/CITATION | 8 ++++---- inst/NEWS | 10 ++++++++++ inst/doc/distr.pdf |binary man/0distrDoc-package.Rd | 8 ++++---- 6 files changed, 32 insertions(+), 22 deletions(-)
Title: Sourcing Archaeological Materials by Chemical Composition
Description: Exploration and analysis of compositional data in the
framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package
provides tools for chemical fingerprinting and source tracking of
ancient materials.
Author: Nicolas Frerebeau [aut, cre] ,
Anne Philippe [aut] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between nexus versions 0.3.0 dated 2024-09-03 and 0.4.0 dated 2025-01-14
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Title: Utility-Based Optimal Phase II/III Drug Development Planning
Description: Plan optimal sample size allocation and go/no-go decision rules
for phase II/III drug development programs with time-to-event, binary or
normally distributed endpoints when assuming fixed treatment effects or a
prior distribution for the treatment effect, using methods from Kirchner et al.
(2016) <doi:10.1002/sim.6624> and Preussler (2020). Optimal is in the sense of
maximal expected utility, where the utility is a function taking into account
the expected cost and benefit of the program. It is possible to extend to more
complex settings with bias correction (Preussler S et al. (2020)
<doi:10.1186/s12874-020-01093-w>), multiple phase III trials (Preussler et
al. (2019) <doi:10.1002/bimj.201700241>), multi-arm trials (Preussler et al.
(2019) <doi:10.1080/19466315.2019.1702092>), and multiple endpoints
(Kieser et al. (2018) <doi:10.1002/pst.1861>).
Author: Stella Erdmann [aut],
Johannes Cepicka [aut],
Marietta Kirchner [aut],
Meinhard Kieser [aut],
Lukas D. Sauer [aut, cre]
Maintainer: Lukas D. Sauer <sauer@imbi.uni-heidelberg.de>
Diff between drugdevelopR versions 1.0.1 dated 2024-01-10 and 1.0.2 dated 2025-01-14
DESCRIPTION | 8 MD5 | 191 +++---- NAMESPACE | 288 +++++----- NEWS.md | 14 R/drugdevelopR-package.R |only R/optimal_bias.R | 44 - R/optimal_bias_binary.R | 539 ++++++++++++++------ R/optimal_bias_generic.R | 50 - R/optimal_bias_normal.R | 43 - R/optimal_binary.R | 12 R/optimal_generic.R | 46 - R/optimal_multiarm.R | 17 R/optimal_multiarm_binary.R | 17 R/optimal_multiarm_generic.R | 40 - R/optimal_multiarm_normal.R | 21 R/optimal_multiple_normal.R | 17 R/optimal_multiple_tte.R | 15 R/optimal_multitrial.R | 586 ++++++++++++++++------ R/optimal_multitrial_binary.R | 37 + R/optimal_multitrial_normal.R | 31 + R/optimal_normal.R | 14 R/optimal_return_doc.R | 6 R/optimal_tte.R | 14 R/print.drugdevelopResult.R | 547 ++++++++++---------- README.md | 262 ++++----- build/partial.rdb |only build/vignette.rds |binary inst/doc/Bias_adjustment.R | 28 - inst/doc/Bias_adjustment.Rmd | 248 ++++----- inst/doc/Bias_adjustment.html | 6 inst/doc/Binary_outcomes.R | 26 inst/doc/Binary_outcomes.html | 4 inst/doc/Fixed_and_prior_distributions.R | 24 inst/doc/Fixed_and_prior_distributions.html | 4 inst/doc/Interpreting_Output.R | 24 inst/doc/Interpreting_Output.html | 4 inst/doc/Introduction-to-drugdevelopR.R | 24 inst/doc/Introduction-to-drugdevelopR.Rmd | 238 ++++---- inst/doc/Introduction-to-drugdevelopR.html | 4 inst/doc/More_Parameters.R | 140 ++--- inst/doc/More_Parameters.html | 14 inst/doc/Multiarm_Trials.R | 16 inst/doc/Multiarm_Trials.html | 2 inst/doc/Multiple_Endpoints.R | 52 - inst/doc/Multiple_Endpoints.html | 8 inst/doc/Multitrial.R | 22 inst/doc/Multitrial.html | 8 inst/doc/Package_validation.R | 4 inst/doc/Package_validation.Rmd | 98 +-- inst/doc/Package_validation.html | 6 inst/doc/Time-to-event_outcomes.R | 26 inst/doc/Time-to-event_outcomes.html | 4 man/drugdevelopR-package.Rd |only man/drugdevelopResult.Rd | 38 - man/get_sample_multiple_normal.Rd | 52 - man/get_sample_multiple_tte.Rd | 52 - man/optimal_bias.Rd | 6 man/optimal_bias_binary.Rd | 4 man/optimal_bias_normal.Rd | 4 man/optimal_binary.Rd | 6 man/optimal_generic.Rd | 70 +- man/optimal_multiarm.Rd | 4 man/optimal_multiarm_binary.Rd | 4 man/optimal_multiarm_normal.Rd | 4 man/optimal_multiple_generic.Rd | 56 +- man/optimal_multiple_normal.Rd | 4 man/optimal_multiple_tte.Rd | 4 man/optimal_multitrial.Rd | 6 man/optimal_multitrial_binary.Rd | 4 man/optimal_multitrial_generic.Rd | 54 +- man/optimal_multitrial_normal.Rd | 4 man/optimal_normal.Rd | 5 man/optimal_return_doc.Rd | 46 - man/optimal_tte.Rd | 6 man/print.drugdevelopResult.Rd | 88 +-- man/print_drugdevelopResult_helper.Rd | 40 - tests/testthat/test-function_bias_binary.R | 272 +++++----- tests/testthat/test-function_bias_normal.R | 304 +++++------ tests/testthat/test-functions_bias.R | 134 ++--- tests/testthat/test-functions_binary.R | 82 +-- tests/testthat/test-functions_multiple_normal.R | 72 +- tests/testthat/test-functions_multiple_tte.R | 134 ++--- tests/testthat/test-functions_multitrial.R | 412 +++++++-------- tests/testthat/test-functions_multitrial_binary.R | 356 ++++++------- tests/testthat/test-functions_multitrial_normal.R | 350 ++++++------- tests/testthat/test-optimal_bias.R | 168 +++--- tests/testthat/test-optimal_bias_binary.R | 92 +-- tests/testthat/test-optimal_bias_normal.R | 92 +-- tests/testthat/test-optimal_multiarm.R | 26 tests/testthat/test-optimal_multiarm_binary.R | 24 tests/testthat/test-optimal_multiarm_normal.R | 26 tests/testthat/test-optimal_multitrial_binary.R | 2 tests/testthat/test-optimal_multitrial_normal.R | 26 tests/testthat/test-optimal_return_doc.R | 46 - tests/testthat/test-print.drugdevelopResult.R | 2 vignettes/Bias_adjustment.Rmd | 248 ++++----- vignettes/Introduction-to-drugdevelopR.Rmd | 238 ++++---- vignettes/Package_validation.Rmd | 98 +-- 98 files changed, 4140 insertions(+), 3518 deletions(-)
Title: The Analysis of Dark Adaptation Data
Description: The recovery of visual sensitivity in a dark environment is known
as dark adaptation. In a clinical or research setting the recovery is typically
measured after a dazzling flash of light and can be described by the Mahroo,
Lamb and Pugh (MLP) model of dark adaptation. The functions in this package take
dark adaptation data and use nonlinear regression to find the parameters of the
model that 'best' describe the data. They do this by firstly, generating rapid
initial objective estimates of data adaptation parameters, then a multi-start
algorithm is used to reduce the possibility of a local minimum. There is also a
bootstrap method to calculate parameter confidence intervals. The functions rely
upon a 'dark' list or object. This object is created as the first step in the
workflow and parts of the object are updated as it is processed.
Author: Jeremiah MF Kelly [aut, cre, cph]
Maintainer: Jeremiah MF Kelly <emkayoh@mac.com>
Diff between Dark versions 0.9.8 dated 2016-06-02 and 0.9.9 dated 2025-01-14
DESCRIPTION | 24 + MD5 | 53 ++-- NEWS.md |only R/BestFit.R | 4 R/Declutter.R | 2 README.md | 14 - build/vignette.rds |binary inst/WORDLIST |only inst/doc/Workflow.R | 22 - inst/doc/Workflow.html | 548 +++++++++++++++++++++++++++++++++----------- inst/doc/parameter_exp.R | 6 inst/doc/parameter_exp.html | 310 ++++++++++++++++++++++-- man/AICc.Rd | 10 man/BestFit.Rd | 9 man/BootDark.Rd | 11 man/Dark-package.Rd | 6 man/Declutter.Rd | 9 man/GetData.Rd | 7 man/H.Rd | 15 - man/ModelSelect.Rd | 8 man/MultiStart.Rd | 6 man/P3.Rd | 9 man/P5c.Rd | 9 man/P6c.Rd | 9 man/P7c.Rd | 9 man/Start.Rd | 6 man/TestData.Rd | 6 man/dark.Rd | 4 tests/spelling.R |only 29 files changed, 838 insertions(+), 278 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.6 dated 2024-02-16 and 2.4.7 dated 2025-01-14
DESCRIPTION | 17 MD5 | 150 ++-- NAMESPACE | 318 ++++----- NEWS.md | 20 R/CEriskav.R | 47 - R/CEriskav_plot_graph.R | 4 R/bcea.R | 69 - R/ceac_plot_graph.R | 8 R/ceaf.plot.R | 10 R/ceef_plot_graph.R | 5 R/ceplane.plot.R | 56 - R/ceplane_base_params.R | 2 R/ceplane_base_params_xxx.R | 8 R/ceplane_geom_params.R | 4 R/ceplane_ggplot_params.R | 19 R/ceplane_plot_graph.R | 12 R/compute_eib_cri.R | 4 R/contour_graph.R | 2 R/diag.evppi.R | 1 R/eib.plot.R | 27 R/eib_params_ggplot.R | 8 R/eib_plot_graph.R | 9 R/evi.plot.R | 5 R/evi.plot.mixedAn.R | 2 R/evi_plot_graph.R | 16 R/evppi.R | 46 - R/evppi.default.R | 6 R/evppi_plot_ggplot.R | 3 R/helper_ggplot_params.R | 17 R/ib.plot.R | 2 R/info_rank_graph.R | 17 R/inforank_params.R | 8 R/make_legend_ggplot.R | 29 R/mce.plot.R | 34 R/misc_helpers.R | 7 R/plot.bcea.R | 19 R/plot.evppi.R | 5 R/prep_ceplane_params.R | 34 R/prep_contour_params.R | 10 R/prep_eib_params.R | 8 R/prepare_ceac_params.R | 3 R/select_plot_type.R | 5 R/themes_ggplot.R | 2 README.md | 6 build/partial.rdb |binary inst/doc/CEriskav.R | 6 inst/doc/CEriskav.html | 60 - inst/doc/Set_bcea_parameters.R | 14 inst/doc/bcea.html | 18 inst/doc/ceac.R | 10 inst/doc/ceac.Rmd | 17 inst/doc/ceac.html | 170 ++-- inst/doc/ceef.R | 16 inst/doc/ceef.html | 88 +- inst/doc/ceplane.R | 67 + inst/doc/ceplane.Rmd | 155 ++++ inst/doc/ceplane.html | 149 +++- inst/doc/contour.html | 62 - inst/doc/eib.html | 44 - inst/doc/paired_vs_multiple_comps.html | 8 man/BCEA-package.Rd | 1 man/CEriskav_assign.Rd | 45 - man/bcea.Rd | 70 -- man/ceplane.plot.Rd | 51 - man/ceplane_ggplot_params.Rd | 4 man/ceplane_plot_graph.Rd | 2 man/eib.plot.Rd | 2 man/evppi.Rd | 49 - man/get_fitted_.Rd | 30 man/is.rel.Rd |only man/plot.bcea.Rd | 11 man/plot.evppi.Rd | 4 man/prep_ceplane_params.Rd | 4 man/prep_contour_params.Rd |only tests/testthat/test-evppi.R | 1150 ++++++++++++++++----------------- vignettes/ceac.Rmd | 17 vignettes/ceplane.Rmd | 155 ++++ 77 files changed, 2088 insertions(+), 1475 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.2 dated 2024-08-17 and 2.2.3 dated 2025-01-14
DESCRIPTION | 6 +- MD5 | 52 +++++++++---------- NEWS.md | 5 + R/tidy_mcmc.R | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/BayesMallows.html | 36 ++++++------- inst/doc/SMC-Mallows.html | 38 ++++++------- inst/doc/parallel_chains.html | 22 ++++---- inst/examples/compute_mallows_sequentially_example.R | 2 inst/examples/estimate_partition_function_example.R | 2 inst/examples/sample_prior_example.R | 2 man/compute_mallows_sequentially.Rd | 2 man/estimate_partition_function.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/sample_prior.Rd | 2 tests/testthat.R | 6 ++ tests/testthat/test-acceptance_ratio.R | 1 tests/testthat/test-assign_cluster.R | 25 +++++++++ tests/testthat/test-compute_mallows.R | 1 tests/testthat/test-estimate_partition_function.R | 1 tests/testthat/test-plot_top_k.R | 1 tests/testthat/test-setup_rank_data.R | 1 tests/testthat/test-smc_pairwise.R | 1 tests/testthat/test-smc_update_correctness.R | 1 27 files changed, 134 insertions(+), 79 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.3.0 dated 2024-10-14 and 1.4.0 dated 2025-01-14
praatpicture-1.3.0/praatpicture/LICENSE |only praatpicture-1.4.0/praatpicture/DESCRIPTION | 8 praatpicture-1.4.0/praatpicture/MD5 | 44 praatpicture-1.4.0/praatpicture/NEWS.md | 230 - praatpicture-1.4.0/praatpicture/R/emupicture.R | 193 - praatpicture-1.4.0/praatpicture/R/formantplot.R | 371 +- praatpicture-1.4.0/praatpicture/R/intensityplot.R | 196 - praatpicture-1.4.0/praatpicture/R/pitchplot.R | 310 + praatpicture-1.4.0/praatpicture/R/praatanimation.R | 559 +-- praatpicture-1.4.0/praatpicture/R/praatpicture.R | 1611 +++++----- praatpicture-1.4.0/praatpicture/R/specplot.R | 890 +++-- praatpicture-1.4.0/praatpicture/R/tgplot.R | 220 - praatpicture-1.4.0/praatpicture/R/waveplot.R | 254 - praatpicture-1.4.0/praatpicture/inst/CITATION | 18 praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/rsconnect |only praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/server.R | 1413 ++++---- praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/ui.R | 700 ++-- praatpicture-1.4.0/praatpicture/man/formantplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/intensityplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/pitchplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/praatpicture.Rd | 66 praatpicture-1.4.0/praatpicture/man/specplot.Rd | 39 praatpicture-1.4.0/praatpicture/man/tgplot.Rd | 9 praatpicture-1.4.0/praatpicture/man/waveplot.Rd | 11 24 files changed, 3987 insertions(+), 3185 deletions(-)
Title: Secure in-Browser and Database Storage for 'shiny' Inputs,
Outputs, Views and User Likes
Description: Store persistent and synchronized data from 'shiny' inputs within the browser. Refresh 'shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'shiny' input or output values. Store app visitor views, likes and followers.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between shinyStorePlus versions 1.3 dated 2024-12-06 and 1.4 dated 2025-01-14
DESCRIPTION | 6 +- MD5 | 38 ++++++++-------- NAMESPACE | 2 NEWS.md | 6 -- R/includes.R | 4 - R/persistentObserveEvent.R |only R/setup.R | 2 build/vignette.rds |binary inst/doc/introduction_to_shinystoreplus.html | 4 - inst/doc/shinystoreplus_v08.html | 4 - inst/doc/shinystoreplus_v12.html | 4 - inst/doc/store_shiny_visitor_views_likes_followers.Rmd | 4 - inst/doc/store_shiny_visitor_views_likes_followers.html | 10 ++-- inst/doc/using_shinystoreplus.html | 4 - inst/example/shinyObserveOnce |only inst/scripts/misc.js |only inst/scripts/rpkg.js | 9 +++ inst/scripts/shinystoreplus.js | 15 +++++- man/initStore.Rd | 6 +- man/observeonce.Rd |only man/setupStorage.Rd | 2 vignettes/store_shiny_visitor_views_likes_followers.Rmd | 4 - 22 files changed, 74 insertions(+), 50 deletions(-)
More information about shinyStorePlus at CRAN
Permanent link
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Integrated Surface Database
(ISD, see
<https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.8 dated 2023-06-05 and 0.9.9 dated 2025-01-14
worldmet-0.9.8/worldmet/build |only worldmet-0.9.8/worldmet/inst |only worldmet-0.9.8/worldmet/man/figures/README-map.png |only worldmet-0.9.8/worldmet/man/figures/README-windRose-1.png |only worldmet-0.9.8/worldmet/vignettes |only worldmet-0.9.9/worldmet/DESCRIPTION | 46 ++-- worldmet-0.9.9/worldmet/LICENSE |only worldmet-0.9.9/worldmet/MD5 | 31 +- worldmet-0.9.9/worldmet/NEWS.md |only worldmet-0.9.9/worldmet/R/getMeta.R | 14 - worldmet-0.9.9/worldmet/R/metNOAA.R | 19 + worldmet-0.9.9/worldmet/R/weatherCodes.R | 12 - worldmet-0.9.9/worldmet/R/worldmet-package.R | 6 worldmet-0.9.9/worldmet/README.md | 157 +++++--------- worldmet-0.9.9/worldmet/data/weatherCodes.rda |binary worldmet-0.9.9/worldmet/man/figures/feature-banner.png |only worldmet-0.9.9/worldmet/man/figures/logo.png |only worldmet-0.9.9/worldmet/man/importNOAA.Rd | 9 worldmet-0.9.9/worldmet/man/weatherCodes.Rd | 15 + worldmet-0.9.9/worldmet/man/worldmet-package.Rd | 12 - 20 files changed, 153 insertions(+), 168 deletions(-)
Title: Spatial Empirical Dynamic Modeling
Description: Integrates empirical dynamic modeling (EDM) with geospatial cross-sectional data to analyze causality via geographical convergent cross mapping (GCCM) described in Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.1 dated 2024-12-19 and 1.2 dated 2025-01-14
DESCRIPTION | 10 - MD5 | 53 +++---- NAMESPACE | 6 NEWS.md | 12 + R/RcppExports.R | 8 - R/ccm_formatoutput.R |only R/gccm.R | 126 ++++++++--------- R/globals.R | 2 R/spEDM-package.R | 8 - R/variable_check.R |only R/xmapdf.R |only R/zzz.R | 2 inst/doc/GCCM.Rmd | 299 +++++++++------------------------------- inst/doc/GCCM.html | 325 +++++++++++--------------------------------- man/figures/gccm/fig1-1.png |binary man/figures/gccm/fig2-1.png |binary man/figures/gccm/fig3-1.png |binary man/gccm.Rd | 47 +++++- src/CppGridUtils.cpp | 1 src/CppGridUtils.h | 2 src/GCCM4Grid.cpp | 45 +++--- src/GCCM4Grid.h | 16 +- src/GCCM4Lattice.cpp | 44 +++-- src/GCCM4Lattice.h | 15 +- src/GridExp.cpp | 10 + src/LatticeExp.cpp | 17 +- src/RcppExports.cpp | 22 +- vignettes/GCCM.Rmd | 299 +++++++++------------------------------- vignettes/GCCM.Rmd.orig | 87 ++--------- 29 files changed, 512 insertions(+), 944 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 1.6.2 dated 2024-07-31 and 1.6.3 dated 2025-01-14
DESCRIPTION | 22 - MD5 | 48 ++-- NEWS.md | 4 R/get_nested_model_coefficients.R | 12 - build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 26 +- inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.R | 24 +- inst/doc/cross_validating_custom_functions.html | 12 - inst/doc/evaluate_by_id.html | 8 inst/doc/picking_the_number_of_folds_for_cross-validation.R | 48 ++-- inst/doc/picking_the_number_of_folds_for_cross-validation.html | 14 - tests/testthat/test_validate_fn.R | 119 +++++----- vignettes/man/figures/vignette_conf_mat-unnamed-chunk-12-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-13-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-14-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-15-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-2.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-17-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-18-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-5-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-6-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-9-1.png |binary vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |binary 25 files changed, 184 insertions(+), 157 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-03 0.7.2
2024-03-23 0.7.1
2024-02-26 0.7.0
2023-11-20 0.6.5
2023-05-20 0.6.4
2023-03-15 0.6.3
2023-02-19 0.6.2
2023-01-21 0.6.1
2022-11-25 0.6.0
2022-10-31 0.5.1
Title: Hardware-Accelerated Rerandomization for Improved Balance
Description: Provides hardware-accelerated tools for performing rerandomization
and randomization testing in experimental research. Using a 'JAX' backend, the
package enables exact rerandomization inference even for large experiments
with hundreds of billions of possible randomizations. Key functionalities
include generating pools of acceptable rerandomizations based on covariate
balance, conducting exact randomization tests, and performing pre-analysis
evaluations to determine optimal rerandomization acceptance thresholds. The
package supports various hardware acceleration frameworks including 'CPU',
'CUDA', and 'METAL', making it versatile across accelerated computing environments. This
allows researchers to efficiently implement stringent rerandomization designs and
conduct valid inference even with large sample sizes. The package is partly based on Jerzak and Goldstein (2023) <doi:10.48550/arXiv.2310.00861>.
Author: Fucheng Warren Zhu [aut] ,
Aniket Sachin Kamat [aut] ,
Connor Jerzak [aut, cre] ,
Rebecca Goldstein [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between fastrerandomize versions 0.1 dated 2025-01-13 and 0.2 dated 2025-01-14
DESCRIPTION | 6 MD5 | 24 +-- R/FRR_BuildBackend.R | 6 R/FRR_GenerateRandomizations.R | 16 -- R/FRR_GenerateRandomizations_Exact.R | 32 +++- R/FRR_GenerateRandomizations_MonteCarlo.R | 41 +++-- R/FRR_InitializeJAX.R | 64 +++++--- R/FRR_RandomizationTest.R | 15 + inst/doc/MainVignette.html | 236 ++++++++++++++++++++++++------ man/generate_randomizations.Rd | 11 - man/generate_randomizations_exact.Rd | 5 man/generate_randomizations_mc.Rd | 4 man/randomization_test.Rd | 3 13 files changed, 327 insertions(+), 136 deletions(-)
More information about fastrerandomize at CRAN
Permanent link
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut] ,
Nikita G. Platonov [cre]
Maintainer: Nikita G. Platonov <platonov@sev-in.ru>
Diff between ursa versions 3.11.1 dated 2024-09-26 and 3.11.2 dated 2025-01-14
DESCRIPTION | 6 +-- MD5 | 86 +++++++++++++++++++++++++------------------------- NEWS.md | 6 ++- R/allocate.R | 7 ++-- R/classCRS.R | 13 +++++-- R/classGrid.R | 18 ++++++++-- R/classRaster_close.R | 8 ++++ R/classStack.R | 22 ++++++++++-- R/colorize.R | 40 ++++++++++++++++++----- R/compose_panel.R | 2 - R/conn.open_envi.R | 12 ++++++ R/conn.write_gdal.R | 4 +- R/cubehelix.R | 23 +++++++++---- R/glance.R | 2 - R/identify.R | 13 +++++++ R/legend_mtext.R | 13 ++++--- R/package_vapour.R | 4 +- R/panel_annotation.R | 8 ++-- R/panel_coastline.R | 4 +- R/panel_graticule.R | 2 - R/panel_new.R | 3 + R/panel_raster.R | 13 ++++--- R/session.R | 33 ++++++++++++------- R/spatial_engine.R | 11 ++++++ R/trackline.R | 37 ++++++++++++++++++--- R/ursa_info.R | 4 +- R/whiteboxing.R | 2 - R/xxx.browse.R | 5 ++ R/xxx.gdalwarp.R | 4 +- R/xxx.geomap.R | 9 ++++- R/xxx.ncdf.R | 11 ++++-- R/xxx.panel_WMS.R | 25 +++++++++++++- R/xxx.panel_cluster.R | 4 +- R/xxx.panel_legend.R | 4 ++ R/xxx.polarmap.R | 30 +++++++++-------- R/xxx.spatialize.R | 72 +++++++++++++++++++++++++++++------------ R/yyy.cache.R | 13 +++++-- R/yyy.plot.R | 41 ++++++++++++++++++++--- R/yyy.project.R | 1 R/yyy.tile.R | 10 ++++- R/yyy.util.R | 5 ++ man/allocate.Rd | 7 ++-- man/colorize.Rd | 8 ++-- src/ursa.c | 37 +++++++++++++++++++-- 44 files changed, 495 insertions(+), 187 deletions(-)
Title: Implementation of Random Variables
Description: Implements random variables by means of S4 classes and methods.
Author: Matthias Kohl [cre, cph, aut] ,
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RandVar versions 1.2.4 dated 2024-09-02 and 1.2.5 dated 2025-01-14
DESCRIPTION | 27 ++--- MD5 | 14 +- build/vignette.rds |binary inst/CITATION | 5 inst/NEWS | 16 +++ inst/doc/RandVar.pdf |binary man/0RandVar-package.Rd | 92 ++++++++--------- tests/tests.Rout.save | 255 ++++++++++++++++++++++-------------------------- 8 files changed, 203 insertions(+), 206 deletions(-)
Title: Quantitative Text Kit
Description: Support package for the textbook "An Introduction to
Quantitative Text Analysis for Linguists: Reproducible Research Using
R" (Francom, 2024) <doi:10.4324/9781003393764>. Includes functions to
acquire, clean, and analyze text data as well as functions to document
and share the results of text analysis. The package is designed to be
used in conjunction with the book, but can also be used as a standalone
package for text analysis.
Author: Jerid Francom [aut, cre, cph]
Maintainer: Jerid Francom <francojc@wfu.edu>
Diff between qtkit versions 1.1.0 dated 2024-12-07 and 1.1.1 dated 2025-01-14
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 17 ++++- R/calc_assoc_metrics.R | 102 ++++++++++++++++--------------- R/calc_type_metrics.R | 72 ++++++++------------- R/create_data_dictionary.R | 65 ++++++++++++------- man/calculate_bigram_probabilities.Rd | 7 +- man/calculate_metrics.Rd | 13 ++- man/validate_inputs_cam.Rd | 6 - tests/testthat/test-calc_assoc_metrics.R | 4 - 10 files changed, 168 insertions(+), 142 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Nathan Pollesch [ctb] ,
Miyuki Breen [ctb] ,
Shannon Bell [ctb] ,
Xia [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.4.0 dated 2024-09-05 and 2.5.0 dated 2025-01-14
httk-2.4.0/httk/R/onAtttach.R |only httk-2.5.0/httk/DESCRIPTION | 18 httk-2.5.0/httk/MD5 | 175 ++-- httk-2.5.0/httk/NAMESPACE | 5 httk-2.5.0/httk/NEWS.md | 52 + httk-2.5.0/httk/R/armitage.R | 6 httk-2.5.0/httk/R/calc_analytic_css_1comp.R | 23 httk-2.5.0/httk/R/calc_analytic_css_3comp2.R |only httk-2.5.0/httk/R/calc_analytic_css_sumclearances.R |only httk-2.5.0/httk/R/calc_css.R | 215 +++--- httk-2.5.0/httk/R/calc_elimination_rate.R | 89 -- httk-2.5.0/httk/R/calc_half_life.R | 46 + httk-2.5.0/httk/R/calc_hep_bioavailability.R | 2 httk-2.5.0/httk/R/calc_kair.R | 114 ++- httk-2.5.0/httk/R/calc_oral_bioavailability.R | 2 httk-2.5.0/httk/R/calc_total_clearance.R | 89 +- httk-2.5.0/httk/R/calc_volume_of_distribution.R | 15 httk-2.5.0/httk/R/check_model.R | 21 httk-2.5.0/httk/R/create_mc_samples.R | 7 httk-2.5.0/httk/R/data.R | 67 + httk-2.5.0/httk/R/get_cheminfo.R | 12 httk-2.5.0/httk/R/get_weight_class.R | 6 httk-2.5.0/httk/R/modelinfo_1comp.R | 3 httk-2.5.0/httk/R/modelinfo_3comp2.R |only httk-2.5.0/httk/R/modelinfo_gas_pbtk.R | 1 httk-2.5.0/httk/R/modelinfo_sumclearances.R |only httk-2.5.0/httk/R/onAttach.R |only httk-2.5.0/httk/R/parameterize_1comp.R | 34 httk-2.5.0/httk/R/parameterize_3comp.R | 8 httk-2.5.0/httk/R/parameterize_3comp2.R |only httk-2.5.0/httk/R/parameterize_gas_pbtk.R | 15 httk-2.5.0/httk/R/parameterize_pbtk.R | 14 httk-2.5.0/httk/R/parameterize_schmitt.R | 14 httk-2.5.0/httk/R/parameterize_steadystate.R | 5 httk-2.5.0/httk/R/parameterize_sumclearances.R |only httk-2.5.0/httk/R/predict_partitioning_schmitt.R | 6 httk-2.5.0/httk/R/propagate_invitrouv_1comp.R | 43 - httk-2.5.0/httk/R/scale_dosing.R | 2 httk-2.5.0/httk/R/solve_3comp2.R |only httk-2.5.0/httk/R/solve_gas_pbtk.R | 4 httk-2.5.0/httk/R/solve_model.R | 42 - httk-2.5.0/httk/R/sysdata.rda |binary httk-2.5.0/httk/README.md | 8 httk-2.5.0/httk/build/partial.rdb |binary httk-2.5.0/httk/inst/doc/V1_IntroToHTTK.html | 22 httk-2.5.0/httk/inst/doc/Va_Pearce2017.html | 97 +- httk-2.5.0/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.5.0/httk/inst/doc/Ve_Wambaugh2018.html | 4 httk-2.5.0/httk/inst/doc/Vg_Wambaugh2019.html | 4 httk-2.5.0/httk/inst/doc/Vi_Kapraun2022.html | 4 httk-2.5.0/httk/man/armitage_eval.Rd | 2 httk-2.5.0/httk/man/calc_analytic_css_3comp2.Rd |only httk-2.5.0/httk/man/calc_analytic_css_sumclearances.Rd |only httk-2.5.0/httk/man/calc_css.Rd | 66 + httk-2.5.0/httk/man/calc_elimination_rate.Rd | 12 httk-2.5.0/httk/man/calc_half_life.Rd | 9 httk-2.5.0/httk/man/calc_hep_bioavailability.Rd | 1 httk-2.5.0/httk/man/calc_kair.Rd | 14 httk-2.5.0/httk/man/calc_total_clearance.Rd | 16 httk-2.5.0/httk/man/calc_vdist.Rd | 14 httk-2.5.0/httk/man/check_model.Rd | 5 httk-2.5.0/httk/man/get_cheminfo.Rd | 10 httk-2.5.0/httk/man/get_weight_class.Rd | 6 httk-2.5.0/httk/man/httk-package.Rd | 1 httk-2.5.0/httk/man/parameterize_1comp.Rd | 9 httk-2.5.0/httk/man/parameterize_3comp.Rd | 5 httk-2.5.0/httk/man/parameterize_3comp2.Rd |only httk-2.5.0/httk/man/parameterize_gas_pbtk.Rd | 4 httk-2.5.0/httk/man/parameterize_pbtk.Rd | 10 httk-2.5.0/httk/man/parameterize_schmitt.Rd | 24 httk-2.5.0/httk/man/parameterize_sumclearances.Rd |only httk-2.5.0/httk/man/physiology.data.Rd | 33 httk-2.5.0/httk/man/predict_partitioning_schmitt.Rd | 23 httk-2.5.0/httk/man/solve_3comp2.Rd |only httk-2.5.0/httk/man/solve_gas_pbtk.Rd | 4 httk-2.5.0/httk/man/solve_model.Rd | 8 httk-2.5.0/httk/man/tissue.data.Rd | 31 httk-2.5.0/httk/man/wfl.Rd | 4 httk-2.5.0/httk/src/init.c | 35 httk-2.5.0/httk/src/model3comp2.c |only httk-2.5.0/httk/src/model_gas_pbtk.c | 2 httk-2.5.0/httk/src/modelpbtk.c | 2 httk-2.5.0/httk/tests/1comp_test.Rout.save | 296 ++++---- httk-2.5.0/httk/tests/3comp_test.Rout.save | 606 ++++++++--------- httk-2.5.0/httk/tests/caco2_test.Rout.save | 24 httk-2.5.0/httk/tests/cheminfo_test.Rout.save | 8 httk-2.5.0/httk/tests/fetal_pbtk_testing.Rout.save | 270 +++---- httk-2.5.0/httk/tests/montecarlo_tests.R | 2 httk-2.5.0/httk/tests/montecarlo_tests.Rout.save | 22 httk-2.5.0/httk/tests/other_tests.Rout.save | 392 +++++----- httk-2.5.0/httk/tests/pbtk_test.Rout.save | 36 - httk-2.5.0/httk/tests/solve_gas_test.R | 16 httk-2.5.0/httk/tests/solve_gas_test.Rout.save | 114 +-- httk-2.5.0/httk/tests/testthat |only httk-2.5.0/httk/tests/testthat.R |only httk-2.5.0/httk/tests/unit_test.R | 4 httk-2.5.0/httk/tests/unit_test.Rout.save | 41 - 97 files changed, 1986 insertions(+), 1493 deletions(-)
Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using
ExifTool <https://exiftool.org/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP
and ID3, Lyrics3, as well as the maker notes of many digital cameras by
Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson,
Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo,
Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between exiftoolr versions 0.2.6 dated 2024-07-19 and 0.2.7 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 12 ++++++++++++ R/install.R | 3 ++- R/utils.R | 12 ++++++++---- 5 files changed, 30 insertions(+), 13 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.3 dated 2024-12-01 and 1.0.4 dated 2025-01-14
quickcode-1.0.3/quickcode/man/clean.Rd |only quickcode-1.0.4/quickcode/DESCRIPTION | 6 - quickcode-1.0.4/quickcode/MD5 | 24 ++-- quickcode-1.0.4/quickcode/NAMESPACE | 2 quickcode-1.0.4/quickcode/NEWS.md | 4 quickcode-1.0.4/quickcode/R/clean.R | 24 +++- quickcode-1.0.4/quickcode/R/func_chain.R | 60 ++++++++++ quickcode-1.0.4/quickcode/R/track.R | 1 quickcode-1.0.4/quickcode/inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++----- quickcode-1.0.4/quickcode/inst/doc/nullish_coalescing_operator_r.html | 4 quickcode-1.0.4/quickcode/inst/doc/quickcode_r_introduction.html | 4 quickcode-1.0.4/quickcode/inst/doc/track_function_usage_r.html | 4 quickcode-1.0.4/quickcode/man/clearenvironment.Rd |only quickcode-1.0.4/quickcode/man/lastwd.Rd |only quickcode-1.0.4/quickcode/man/simplechaining2.Rd |only 15 files changed, 138 insertions(+), 49 deletions(-)