Title: Analysing Equity Portfolios
Description: Classes for analysing and implementing equity portfolios,
including routines for generating tradelists and calculating
exposures to user-specified risk factors.
Author: Jeff Enos [aut],
David Kane [aut],
Daniel Gerlanc [aut, cre],
Kyle Campbell [ctb]
Maintainer: Daniel Gerlanc <dan@gerlanc.com>
Diff between portfolio versions 0.5-2 dated 2021-07-10 and 0.5-3 dated 2024-08-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/trellis.multiplot.R | 2 +- build/vignette.rds |binary inst/doc/matching_portfolio.pdf |binary inst/doc/portfolio.pdf |binary inst/doc/tradelist.pdf |binary man/tradelist-class.Rd | 2 +- tests/tradelist.calcSwaps.test.R | 37 ++++++++++++++++++++----------------- 9 files changed, 34 insertions(+), 31 deletions(-)
Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference,
including distance correlation, one-sample, two-sample, and multi-sample tests for
comparing multivariate distributions, are implemented. Measuring and testing
multivariate independence based on distance correlation, partial distance correlation,
multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy
distance, testing for multivariate normality, distance components (disco) for non-parametric
analysis of structured data, and other energy statistics/methods are implemented.
Author: Maria Rizzo [aut, cre],
Gabor Szekely [aut]
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>
Diff between energy versions 1.7-11 dated 2022-12-22 and 1.7-12 dated 2024-08-23
energy-1.7-11/energy/R/Eindep.R |only energy-1.7-11/energy/man/indep.test.Rd |only energy-1.7-11/energy/src/Eindep.c |only energy-1.7-12/energy/DESCRIPTION | 11 energy-1.7-12/energy/MD5 | 45 +-- energy-1.7-12/energy/NAMESPACE | 2 energy-1.7-12/energy/NEWS.md | 14 energy-1.7-12/energy/R/RcppExports.R | 102 +++---- energy-1.7-12/energy/R/disco.R | 366 +++++++++++++------------- energy-1.7-12/energy/R/energy-defunct.R | 30 -- energy-1.7-12/energy/R/energy-deprecated.R | 124 +++----- energy-1.7-12/energy/R/indep-deprecated.R |only energy-1.7-12/energy/R/mvI.R |only energy-1.7-12/energy/build/partial.rdb |binary energy-1.7-12/energy/man/U_product.Rd | 4 energy-1.7-12/energy/man/centering.Rd | 1 energy-1.7-12/energy/man/energy-defunct.Rd | 72 +---- energy-1.7-12/energy/man/energy-deprecated.Rd | 54 +-- energy-1.7-12/energy/man/energy-package.Rd | 5 energy-1.7-12/energy/man/indep-deprecated.Rd |only energy-1.7-12/energy/man/mvI.test.Rd | 170 +++++++----- energy-1.7-12/energy/src/RcppExports.cpp | 25 + energy-1.7-12/energy/src/dcov.c | 9 energy-1.7-12/energy/src/energy.c | 124 ++++---- energy-1.7-12/energy/src/energy_init.c | 10 energy-1.7-12/energy/src/mvI.cpp |only energy-1.7-12/energy/src/utilities.c | 22 - 27 files changed, 598 insertions(+), 592 deletions(-)
Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions for probability
distributions in R.
Primary focus is on (central and non-central) beta, gamma and related
distributions such as the chi-squared, F, and t.
--
For several distribution functions, provide functions implementing formulas from
Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207> and
Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous
distributions respectively.
This is for the use of researchers in these numerical approximation
implementations, notably for my own use in order to improve standard
R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] ,
Morten Welinder [ctb] ),
Wolfgang Viechtbauer [ctb] , 2002),
Ross Ihaka [ctb] ,
Marius Hofert [ctb] , lssum),
R-core [ctb] ,
R Foundation [cph]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQ versions 0.5-8 dated 2023-12-01 and 0.5-9 dated 2024-08-23
DESCRIPTION | 14 MD5 | 120 +-- NAMESPACE | 28 R/beta-fns.R | 338 +++++---- R/dbinom-nbinom.R | 79 +- R/dgamma.R | 288 ++++++-- R/expm1x.R |only R/qchisqAppr.R | 9 R/qgamma-fn.R | 9 R/t-nonc-fn.R | 737 ++++++++++++++++++++- R/utils.R | 11 TODO | 34 build/partial.rdb |binary build/vignette.rds |binary data |only inst/NEWS.Rd | 84 ++ inst/doc/Noncentral-Chisq.pdf |binary inst/doc/comp-beta.pdf |binary inst/doc/log1pmx-etc.Rnw | 29 inst/doc/log1pmx-etc.pdf |binary inst/doc/qnorm-asymp.pdf |binary inst/extraR/relErr-plots.R |only inst/test-tools.R | 16 man/Ixpq.Rd |only man/algdiv.Rd | 3 man/bpser.Rd | 4 man/chebyshevPoly.Rd | 4 man/dbinom_raw.Rd | 16 man/dchisqApprox.Rd | 2 man/dgamma-utils.Rd | 86 -- man/dgamma.R.Rd | 11 man/dnt.Rd | 36 - man/dtWV.Rd | 6 man/expm1x.Rd |only man/gam1d.Rd |only man/gamln1.Rd |only man/gammaVer.Rd | 22 man/lbeta.Rd | 91 ++ man/lgamma1p.Rd | 95 ++ man/lgammaAsymp.Rd | 27 man/log1pmx.Rd | 7 man/pbetaRv1.Rd | 2 man/pnbeta.Rd | 6 man/pnt.Rd | 178 ++++- man/pow.Rd |only man/pow1p.Rd |only man/pt_Witkovsky_Tab1.Rd |only man/stirlerr.Rd |only src/DPQ-misc.c | 82 +- src/DPQpkg.h | 42 - src/bd0.c | 8 src/bpser.c | 87 +- src/chebyshev.c | 4 src/dpsifn.c | 2 src/gamma-variants.c | 25 src/init.c | 11 src/stirlerr.c | 127 +++ tests/bd0-tst.R |only tests/chisq-nonc-ex.R | 1 tests/dgamma-tst.R |only tests/dt-ex.R |only tests/expm1x-tst.R |only tests/pow-tst.R |only tests/pqnorm_extreme.R | 2 tests/qbeta-dist.R | 4 tests/qgamma-ex.R | 3 tests/stirlerr-tst.R | 1473 +++++++++++++++++++++++++++++------------- tests/t-nonc-tst.R | 18 vignettes/log1pmx-etc.Rnw | 29 69 files changed, 3291 insertions(+), 1019 deletions(-)
Title: Find Differences Between R Objects
Description: Compare complex R objects and reveal the key differences.
Designed particularly for use in testing packages where being able to
quickly isolate key differences makes understanding test failures much
easier.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between waldo versions 0.5.2 dated 2023-11-02 and 0.5.3 dated 2024-08-23
DESCRIPTION | 12 ++++----- MD5 | 16 ++++++------ NAMESPACE | 1 NEWS.md | 72 ++++++++++++++++++++++++++++-------------------------- R/compare-class.R | 2 - R/compare.R | 22 ++++++++-------- R/diff.R | 8 +++--- R/utils.R | 4 +-- R/waldo-package.R | 1 9 files changed, 70 insertions(+), 68 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.3.0 dated 2024-05-17 and 0.4.0 dated 2024-08-23
tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/escape-html.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/group_rows.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-html_tutorial_01.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue165_html_centering_style.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-alignment.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-bootstrap_css.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-borders.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-built_in_plots.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-caption.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-conditional_styling.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-font_size.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-footnote.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-formatting.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-heatmap.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-images.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-individual_cells.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-issue58.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-issue88.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-issue92.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-line_break.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-merge_cells.txt |only tinytable-0.3.0/tinytable/inst/tinytest/_tinysnapshot/html-missing_value.txt |only 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tinytable-0.4.0/tinytable/R/format_numeric.R |only tinytable-0.4.0/tinytable/R/format_tt.R | 302 ++++------ tinytable-0.4.0/tinytable/R/group_bootstrap.R | 36 - tinytable-0.4.0/tinytable/R/group_grid.R | 27 tinytable-0.4.0/tinytable/R/group_tabularray.R | 28 tinytable-0.4.0/tinytable/R/group_tt.R | 32 - tinytable-0.4.0/tinytable/R/group_typst.R | 40 - tinytable-0.4.0/tinytable/R/package.R |only tinytable-0.4.0/tinytable/R/plot_tt.R | 40 - tinytable-0.4.0/tinytable/R/print.R | 36 - tinytable-0.4.0/tinytable/R/sanity.R | 251 +++++--- tinytable-0.4.0/tinytable/R/save_tt.R | 71 +- tinytable-0.4.0/tinytable/R/style_bootstrap.R | 292 ++++----- tinytable-0.4.0/tinytable/R/style_grid.R | 5 tinytable-0.4.0/tinytable/R/style_tabularray.R | 20 tinytable-0.4.0/tinytable/R/style_tt.R | 28 tinytable-0.4.0/tinytable/R/style_typst.R | 285 +++++---- tinytable-0.4.0/tinytable/R/theme_tt.R | 157 ++++- tinytable-0.4.0/tinytable/R/tt.R | 29 tinytable-0.4.0/tinytable/R/tt_bootstrap.R | 21 tinytable-0.4.0/tinytable/R/tt_grid.R | 7 tinytable-0.4.0/tinytable/R/tt_tabularray.R | 6 tinytable-0.4.0/tinytable/R/tt_typst.R | 14 tinytable-0.4.0/tinytable/R/utils.R | 23 tinytable-0.4.0/tinytable/README.md | 71 +- tinytable-0.4.0/tinytable/build/partial.rdb |binary tinytable-0.4.0/tinytable/inst/templates/bootstrap.html | 45 - tinytable-0.4.0/tinytable/inst/templates/typst.typ | 32 - tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/colrowspan-markdown_multiple.txt | 2 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/docx-issue98_01.txt | 2 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/docx-issue98_02.txt | 2 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/docx-issue98_03.txt | 2 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/docx-issue98_04.txt | 2 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption_escape_03.txt | 1 tinytable-0.4.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-fn.txt | 2 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8 tinytable-0.4.0/tinytable/inst/tinytest/test-latex.R | 17 tinytable-0.4.0/tinytable/inst/tinytest/test-markdown.R | 15 tinytable-0.4.0/tinytable/inst/tinytest/test-misc.R | 10 tinytable-0.4.0/tinytable/inst/tinytest/test-pdf.R |only tinytable-0.4.0/tinytable/inst/tinytest/test-print.R | 1 tinytable-0.4.0/tinytable/inst/tinytest/test-tibble.R | 2 tinytable-0.4.0/tinytable/inst/tinytest/test-typst.R | 6 tinytable-0.4.0/tinytable/man/format_tt.Rd | 54 + tinytable-0.4.0/tinytable/man/group_eval-tinytable_typst-method.Rd | 2 tinytable-0.4.0/tinytable/man/group_tt.Rd | 18 tinytable-0.4.0/tinytable/man/initialize-tinytable-method.Rd | 2 tinytable-0.4.0/tinytable/man/knit_print.tinytable.Rd | 2 tinytable-0.4.0/tinytable/man/print.tinytable.Rd | 2 tinytable-0.4.0/tinytable/man/save_tt.Rd | 2 tinytable-0.4.0/tinytable/man/style_tt.Rd | 6 tinytable-0.4.0/tinytable/man/theme_tt.Rd | 62 +- tinytable-0.4.0/tinytable/man/tt.Rd | 40 + tinytable-0.4.0/tinytable/tests/tinytest.R | 2 186 files changed, 2305 insertions(+), 1369 deletions(-)
Title: Sparse Family and Selection Index
Description: Here we provide tools for the estimation of coefficients in penalized regressions when the (co)variance matrix of predictors and the covariance vector between predictors and response, are provided. These methods are extended to the context of a Selection Index (commonly used for breeding value prediction). The approaches offer opportunities such as the integration of high-throughput traits in genetic evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2> and solutions for training set optimization in Genomic Prediction ('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.
Author: Marco Lopez-Cruz [aut, cre],
Gustavo de los Campos [aut],
Paulino Perez-Rodriguez [ctb]
Maintainer: Marco Lopez-Cruz <maraloc@gmail.com>
Diff between SFSI versions 1.4 dated 2024-06-25 and 1.4.1 dated 2024-08-23
DESCRIPTION | 8 +- MD5 | 59 ++++++++-------- NEWS.md | 7 + R/LARS.R | 18 ++-- R/SGP.CV.R | 1 R/SGP.R | 3 R/fitBLUP.R | 5 - R/getGenCov.R | 1 R/methods.R | 16 +++- R/multitrait.plot.R | 17 ++-- R/nsup.plot.R | 3 R/path.plot.R | 30 ++++---- R/plot.net.R | 34 ++++----- R/rrr_functions.R | 2 R/solveEN.R | 26 ++++--- build/vignette.rds |binary inst/doc/SGP-documentation.Rmd |only inst/doc/SSI-documentation.R | 26 +++---- inst/doc/SSI-documentation.Rmd |only man/LARS.Rd | 13 ++- man/SGP.Rd | 2 man/getGenCov.Rd | 2 man/path.plot.Rd | 2 man/plot.net.Rd | 4 - man/solveEN.Rd | 15 ++-- src/Makevars | 1 src/SFSI.h | 41 +++++------ src/c_lars.c | 150 ++++++++++++++++++++++------------------- src/c_solveEN.c | 134 ++++++++++++++++++------------------ src/c_solveEN_sparse.c |only src/init.c | 6 + src/utils.c | 41 +++++++++++ 32 files changed, 383 insertions(+), 284 deletions(-)
Title: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over
Time
Description: Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.
Author: Matheus Lima Araujo [aut, cre, cph]
,
Luiz Gabriel Souza e Souza Ferreira [aut]
,
Gabriel Nakamura [aut] ,
Marco Tulio Pacheco Coelho [aut]
,
Thiago Fernando Rangel [aut]
Maintainer: Matheus Lima Araujo <matheusaraujolima@live.com>
Diff between treesliceR versions 1.0.1 dated 2024-02-08 and 1.0.2 dated 2024-08-23
DESCRIPTION | 8 MD5 | 32 - NEWS.md | 3 R/CpD.R | 4 R/CpE.R | 4 build/vignette.rds |binary inst/doc/Intro-treesliceR.Rmd | 8 inst/doc/Intro-treesliceR.html | 138 +++---- inst/doc/Passeriformes-distribution.R | 2 inst/doc/Passeriformes-distribution.Rmd | 2 inst/doc/Passeriformes-distribution.html | 160 ++++---- inst/doc/Passeriformes-diversification.R | 313 ++++++++++------ inst/doc/Passeriformes-diversification.Rmd | 338 ++++++++++------- inst/doc/Passeriformes-diversification.html | 546 ++++++++++++++++------------ vignettes/Intro-treesliceR.Rmd | 8 vignettes/Passeriformes-distribution.Rmd | 2 vignettes/Passeriformes-diversification.Rmd | 338 ++++++++++------- 17 files changed, 1126 insertions(+), 780 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas [aut, cre] ,
Immanuel Scholz [aut],
Rainer Boehme [ctb],
Sylvain Jasson [ctb],
Martin Maechler [ctb]
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.7-4 dated 2024-01-15 and 0.7-5 dated 2024-08-23
ChangeLog | 10 + DESCRIPTION | 22 ++- MD5 | 38 +++--- R/Stirling-n-etc.R | 2 R/biginteger.R | 25 +++- R/matrixq.R | 4 R/matrixz.R | 21 ++- man/extract.Rd | 35 ++---- man/matrix.Rd | 15 ++ src/apply.cc | 168 +++++++++++++++-------------- src/bigintegerR.cc | 267 +++++++++++++++++++++++++++-------------------- src/bigmod.cc | 16 +- src/bigrationalR.cc | 100 ++++++++++------- src/extract_matrix.cc | 18 +-- src/factor.cc | 3 src/matrix.cc | 30 +++-- src/matrixq.cc | 36 +++--- src/solve.cc | 14 +- tests/basic-ex.R | 37 ++++-- tests/gmp-test.Rout.save | 12 +- 20 files changed, 513 insertions(+), 360 deletions(-)
Title: Parse 'YMD' Format Number or String to Date
Description: Convert 'YMD' format number or string to Date efficiently, using Rust's
standard library. It also provides helper functions to handle Date, e.g., quick
finding the beginning or end of the given period, adding months to Date, etc.
Author: Xianying Tan [aut, cre] ,
Hiroaki Yutani [ctb] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Xianying Tan <shrektan@126.com>
Diff between ymd versions 0.1.1 dated 2024-08-17 and 0.1.2 dated 2024-08-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ configure | 12 ++++++++++-- configure.win | 12 ++++++++++-- 5 files changed, 31 insertions(+), 11 deletions(-)
Title: Tables and Graphs for Generalized Estimating Equations (GEE)
Model Fits
Description: Generalized estimating equations (GEE) are a popular choice
for analyzing longitudinal binary outcomes. This package provides an
interface for fitting GEE, currently for logistic regression, within
the 'tern' <https://cran.r-project.org/package=tern> framework (Zhu,
Sabanés Bové et al., 2023) and tabulate results easily using 'rtables'
<https://cran.r-project.org/package=rtables> (Becker, Waddell et al.,
2023). It builds on 'geepack' <doi:10.18637/jss.v015.i02> (Højsgaard,
Halekoh and Yan, 2006) for the actual GEE model fitting.
Author: Daniel Sabanes Bove [aut],
Joe Zhu [aut, cre],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern.gee versions 0.1.4 dated 2024-06-12 and 0.1.5 dated 2024-08-23
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/lsmeans.R | 8 +++++--- inst/doc/tern-gee.html | 14 +++++++++----- man/lsmeans.Rd | 18 ++++++++++++++++-- 6 files changed, 55 insertions(+), 26 deletions(-)
Title: A Financial Calculator
Description: A financial calculator that provides very fast implementations
of common financial indicators using 'Rust' code. It includes functions for
bond-related indicators, such as yield to maturity ('YTM'), modified duration,
and Macaulay duration, as well as functions for calculating time-weighted
and money-weighted rates of return (using 'Modified Dietz' method) for multiple portfolios,
given their market values and profit and loss ('PnL') data. 'fcl' is designed
to be efficient and accurate for financial analysis and computation. The methods
used in this package are based on the following references:
<https://en.wikipedia.org/wiki/Modified_Dietz_method>,
<https://en.wikipedia.org/wiki/Time-weighted_return>.
Author: Xianying Tan [aut, cre] ,
Raymon Mina [ctb] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Xianying Tan <shrektan@126.com>
Diff between fcl versions 0.1.1 dated 2024-08-23 and 0.1.2 dated 2024-08-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ configure | 10 ++++++++++ configure.win | 10 ++++++++++ 5 files changed, 31 insertions(+), 7 deletions(-)
Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology (Pinheiro et al. (2014)
<doi:10.1002/sim.6052>).
Author: Bjoern Bornkamp [aut] ,
Jose Pinheiro [aut],
Frank Bretz [aut],
Ludger Sandig [aut],
Marius Thomas [aut, cre],
Novartis Pharma AG [cph, fnd]
Maintainer: Marius Thomas <marius.thomas@novartis.com>
Diff between DoseFinding versions 1.1-1 dated 2023-11-02 and 1.2-1 dated 2024-08-23
DoseFinding-1.1-1/DoseFinding/ChangeLog |only DoseFinding-1.2-1/DoseFinding/DESCRIPTION | 28 DoseFinding-1.2-1/DoseFinding/MD5 | 199 DoseFinding-1.2-1/DoseFinding/NAMESPACE | 122 DoseFinding-1.2-1/DoseFinding/NEWS.md |only DoseFinding-1.2-1/DoseFinding/R/DesignMCPModApp.R | 18 DoseFinding-1.2-1/DoseFinding/R/DoseFinding-package.R |only DoseFinding-1.2-1/DoseFinding/R/MCPMod.R | 649 +-- DoseFinding-1.2-1/DoseFinding/R/MCTtest.R | 588 +- DoseFinding-1.2-1/DoseFinding/R/MCTtest_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/Mods.R | 1568 ++----- DoseFinding-1.2-1/DoseFinding/R/Mods_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/bFitMod.R | 898 +--- DoseFinding-1.2-1/DoseFinding/R/bFitMod_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/bMCTtest.R | 562 +- DoseFinding-1.2-1/DoseFinding/R/bMCTtest_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/drmodels.R | 296 - DoseFinding-1.2-1/DoseFinding/R/fitMod.R | 2035 ++++------ DoseFinding-1.2-1/DoseFinding/R/fitMod_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/guesst.R | 314 + DoseFinding-1.2-1/DoseFinding/R/optContr.R | 483 +- DoseFinding-1.2-1/DoseFinding/R/optContr_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/optDesign.R | 1103 ++--- DoseFinding-1.2-1/DoseFinding/R/optDesign_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/planMod.R | 996 ++-- DoseFinding-1.2-1/DoseFinding/R/planMod_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/powMCT.R | 458 -- DoseFinding-1.2-1/DoseFinding/R/powMCT_helpers.R |only DoseFinding-1.2-1/DoseFinding/R/sampSize.R | 712 ++- DoseFinding-1.2-1/DoseFinding/README.md |only DoseFinding-1.2-1/DoseFinding/build/vignette.rds |binary DoseFinding-1.2-1/DoseFinding/inst/doc/analysis_normal.R | 208 - DoseFinding-1.2-1/DoseFinding/inst/doc/analysis_normal.Rmd | 634 +-- DoseFinding-1.2-1/DoseFinding/inst/doc/analysis_normal.html | 1338 +++--- DoseFinding-1.2-1/DoseFinding/inst/doc/binary_data.R | 320 - DoseFinding-1.2-1/DoseFinding/inst/doc/binary_data.Rmd | 662 +-- DoseFinding-1.2-1/DoseFinding/inst/doc/binary_data.html | 1437 +++---- DoseFinding-1.2-1/DoseFinding/inst/doc/faq.R | 14 DoseFinding-1.2-1/DoseFinding/inst/doc/faq.Rmd | 792 +-- DoseFinding-1.2-1/DoseFinding/inst/doc/faq.html | 1152 +++-- DoseFinding-1.2-1/DoseFinding/inst/doc/mult_regimen.R | 396 - DoseFinding-1.2-1/DoseFinding/inst/doc/mult_regimen.Rmd | 610 +- DoseFinding-1.2-1/DoseFinding/inst/doc/mult_regimen.html | 1318 +++--- DoseFinding-1.2-1/DoseFinding/inst/doc/overview.R | 92 DoseFinding-1.2-1/DoseFinding/inst/doc/overview.Rmd | 162 DoseFinding-1.2-1/DoseFinding/inst/doc/overview.html | 958 ++-- DoseFinding-1.2-1/DoseFinding/inst/doc/sample_size.R | 204 - DoseFinding-1.2-1/DoseFinding/inst/doc/sample_size.Rmd | 452 +- DoseFinding-1.2-1/DoseFinding/inst/doc/sample_size.html | 1111 ++--- DoseFinding-1.2-1/DoseFinding/man/DesignMCPModApp.Rd | 36 DoseFinding-1.2-1/DoseFinding/man/DoseFinding-package.Rd | 201 DoseFinding-1.2-1/DoseFinding/man/IBScovars.Rd | 37 DoseFinding-1.2-1/DoseFinding/man/MCPMod.Rd | 532 +- DoseFinding-1.2-1/DoseFinding/man/MCTpval.Rd | 133 DoseFinding-1.2-1/DoseFinding/man/MCTtest.Rd | 358 - DoseFinding-1.2-1/DoseFinding/man/Mods.Rd | 458 +- DoseFinding-1.2-1/DoseFinding/man/bFitMod.Rd | 468 +- DoseFinding-1.2-1/DoseFinding/man/bMCTtest.Rd | 424 -- DoseFinding-1.2-1/DoseFinding/man/biom.Rd | 31 DoseFinding-1.2-1/DoseFinding/man/critVal.Rd | 93 DoseFinding-1.2-1/DoseFinding/man/defBnds.Rd | 96 DoseFinding-1.2-1/DoseFinding/man/drmodels.Rd | 500 +- DoseFinding-1.2-1/DoseFinding/man/figures |only DoseFinding-1.2-1/DoseFinding/man/fitMod.Rd | 356 - DoseFinding-1.2-1/DoseFinding/man/glycobrom.Rd | 53 DoseFinding-1.2-1/DoseFinding/man/guesst.Rd | 129 DoseFinding-1.2-1/DoseFinding/man/migraine.Rd | 38 DoseFinding-1.2-1/DoseFinding/man/mvpostmix.Rd | 64 DoseFinding-1.2-1/DoseFinding/man/mvtnorm-control.Rd | 50 DoseFinding-1.2-1/DoseFinding/man/neurodeg.Rd | 77 DoseFinding-1.2-1/DoseFinding/man/optContr.Rd | 290 - DoseFinding-1.2-1/DoseFinding/man/optDesign.Rd | 591 +- DoseFinding-1.2-1/DoseFinding/man/planMod.Rd | 380 - DoseFinding-1.2-1/DoseFinding/man/powMCT.Rd | 258 - DoseFinding-1.2-1/DoseFinding/man/sampSize.Rd | 385 - DoseFinding-1.2-1/DoseFinding/man/targdose.Rd | 181 DoseFinding-1.2-1/DoseFinding/tests/testgFit.R | 198 DoseFinding-1.2-1/DoseFinding/tests/testplanMod.R | 322 - DoseFinding-1.2-1/DoseFinding/tests/testsFitting.R | 940 ++-- DoseFinding-1.2-1/DoseFinding/tests/testsMCPMod.R | 360 - DoseFinding-1.2-1/DoseFinding/tests/testsMCT.R | 552 +- DoseFinding-1.2-1/DoseFinding/tests/testsoptContr.R | 254 - DoseFinding-1.2-1/DoseFinding/tests/testsplotDRMod.R | 176 DoseFinding-1.2-1/DoseFinding/tests/testssampSize.R | 220 - DoseFinding-1.2-1/DoseFinding/tests/testssamplMod.R | 244 - DoseFinding-1.2-1/DoseFinding/tests/testthat.R | 24 DoseFinding-1.2-1/DoseFinding/tests/testthat/generate_test_datasets.R | 206 - DoseFinding-1.2-1/DoseFinding/tests/testthat/test-MCTtest.R | 490 +- DoseFinding-1.2-1/DoseFinding/tests/testthat/test-bMCTtest.R | 550 +- DoseFinding-1.2-1/DoseFinding/tests/testthat/test-drmodels.R | 68 DoseFinding-1.2-1/DoseFinding/tests/testthat/test-fitMod.R | 580 +- DoseFinding-1.2-1/DoseFinding/tests/testthat/test-guesst.R | 144 DoseFinding-1.2-1/DoseFinding/tests/testthat/test-optContr.R | 274 - DoseFinding-1.2-1/DoseFinding/tests/testthat/test-optDesign.R | 370 - DoseFinding-1.2-1/DoseFinding/tests/testthat/test-planMod.R | 156 DoseFinding-1.2-1/DoseFinding/tests/testthat/test-powMCTBinCount.R | 232 - DoseFinding-1.2-1/DoseFinding/vignettes/american-statistical-association.csl | 378 - DoseFinding-1.2-1/DoseFinding/vignettes/analysis_normal.Rmd | 634 +-- DoseFinding-1.2-1/DoseFinding/vignettes/binary_data.Rmd | 662 +-- DoseFinding-1.2-1/DoseFinding/vignettes/children/settings.txt | 16 DoseFinding-1.2-1/DoseFinding/vignettes/faq.Rmd | 792 +-- DoseFinding-1.2-1/DoseFinding/vignettes/mult_regimen.Rmd | 610 +- DoseFinding-1.2-1/DoseFinding/vignettes/overview.Rmd | 162 DoseFinding-1.2-1/DoseFinding/vignettes/refs.bib | 252 - DoseFinding-1.2-1/DoseFinding/vignettes/sample_size.Rmd | 452 +- 105 files changed, 19820 insertions(+), 19606 deletions(-)
Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models.
References.
Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>.
Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>.
Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>.
Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>.
Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>.
Santolino, M. (2023) <doi:10.3390/risks11100170>.
Author: David Atance [aut, cre] ,
Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>
Diff between CvmortalityMult versions 1.0.5 dated 2024-08-23 and 1.0.6 dated 2024-08-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/fitLCmulti.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
More information about CvmortalityMult at CRAN
Permanent link
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.8-0.1 dated 2023-11-28 and 0.9-0 dated 2024-08-23
rlibkriging-0.8-0.1/rlibkriging/src/libK/bindings/R/bench_perf-full.Rmd |only rlibkriging-0.8-0.1/rlibkriging/src/libK/bindings/R/bench_perf-full.sh |only rlibkriging-0.8-0.1/rlibkriging/src/libK/src/lib/include/libKriging/utils/hdf5utils.hpp |only rlibkriging-0.8-0.1/rlibkriging/src/libK/src/lib/utils/hdf5utils.cpp |only rlibkriging-0.8-0.1/rlibkriging/tools/HDF5_LICENSE |only rlibkriging-0.9-0/rlibkriging/DESCRIPTION | 16 rlibkriging-0.9-0/rlibkriging/MD5 | 461 +- rlibkriging-0.9-0/rlibkriging/NAMESPACE | 8 rlibkriging-0.9-0/rlibkriging/R/KMClass.R | 10 rlibkriging-0.9-0/rlibkriging/R/KrigingClass.R | 322 + rlibkriging-0.9-0/rlibkriging/R/NoiseKMClass.R | 10 rlibkriging-0.9-0/rlibkriging/R/NoiseKrigingClass.R | 305 + rlibkriging-0.9-0/rlibkriging/R/NuggetKMClass.R | 8 rlibkriging-0.9-0/rlibkriging/R/NuggetKrigingClass.R | 298 + rlibkriging-0.9-0/rlibkriging/R/RcppExports.R | 112 rlibkriging-0.9-0/rlibkriging/R/allGenerics.R | 74 rlibkriging-0.9-0/rlibkriging/R/miscUtils.R | 8 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Title: Companion Package to Probability and Statistics for Economics
and Business
Description: Utilities for multiple hypothesis testing, companion datasets from "Probability and Statistics for Economics and Business: An Introduction Using R" by Jason Abrevaya (MIT Press, under contract).
Author: Jason Abrevaya [aut, cph],
Nathan Gardner Hattersley [aut, cre]
Maintainer: Nathan Gardner Hattersley <nhattersley@utexas.edu>
Diff between probstats4econ versions 0.2.0 dated 2024-05-23 and 0.3.1 dated 2024-08-23
probstats4econ-0.2.0/probstats4econ/data/names2022.RData |only probstats4econ-0.2.0/probstats4econ/data/premier2020.RData |only probstats4econ-0.2.0/probstats4econ/man/names2022.Rd |only probstats4econ-0.2.0/probstats4econ/man/premier2020.Rd |only probstats4econ-0.3.1/probstats4econ/DESCRIPTION | 10 - probstats4econ-0.3.1/probstats4econ/MD5 | 93 +++++----- probstats4econ-0.3.1/probstats4econ/NAMESPACE | 3 probstats4econ-0.3.1/probstats4econ/NEWS.md | 10 + probstats4econ-0.3.1/probstats4econ/R/build/build_r_files.R | 27 ++ probstats4econ-0.3.1/probstats4econ/R/build/knitr_parsing.R | 19 +- probstats4econ-0.3.1/probstats4econ/R/build/package_cran_version.R |only probstats4econ-0.3.1/probstats4econ/R/build/rmd_r_code_template.R | 22 +- probstats4econ-0.3.1/probstats4econ/R/data.R | 23 +- probstats4econ-0.3.1/probstats4econ/R/se_meanx.R |only probstats4econ-0.3.1/probstats4econ/R/se_rxy.R |only probstats4econ-0.3.1/probstats4econ/R/se_sx.R |only probstats4econ-0.3.1/probstats4econ/R/test_linear_restrictions.R | 10 - probstats4econ-0.3.1/probstats4econ/R/utils.R | 8 probstats4econ-0.3.1/probstats4econ/R/wald_test.R | 12 - probstats4econ-0.3.1/probstats4econ/build/partial.rdb |binary probstats4econ-0.3.1/probstats4econ/data/auctions.RData |binary probstats4econ-0.3.1/probstats4econ/data/babynames.RData |only probstats4econ-0.3.1/probstats4econ/data/baseball.RData |binary probstats4econ-0.3.1/probstats4econ/data/births.RData |binary probstats4econ-0.3.1/probstats4econ/data/bitcoin.RData |binary probstats4econ-0.3.1/probstats4econ/data/brands.RData |binary probstats4econ-0.3.1/probstats4econ/data/cigdata.RData |binary probstats4econ-0.3.1/probstats4econ/data/congress.RData |binary probstats4econ-0.3.1/probstats4econ/data/cps.RData |binary probstats4econ-0.3.1/probstats4econ/data/dictator.RData |binary probstats4econ-0.3.1/probstats4econ/data/exams.RData |binary probstats4econ-0.3.1/probstats4econ/data/houseprices.RData |binary probstats4econ-0.3.1/probstats4econ/data/hrs.RData |binary probstats4econ-0.3.1/probstats4econ/data/inflation.RData |binary probstats4econ-0.3.1/probstats4econ/data/inflation_expectations.RData |binary probstats4econ-0.3.1/probstats4econ/data/married.RData |binary probstats4econ-0.3.1/probstats4econ/data/metricsgrades.RData |binary probstats4econ-0.3.1/probstats4econ/data/mutualfunds.RData |binary probstats4econ-0.3.1/probstats4econ/data/premier.RData |only probstats4econ-0.3.1/probstats4econ/data/resume.RData |binary probstats4econ-0.3.1/probstats4econ/data/sp500.RData |binary probstats4econ-0.3.1/probstats4econ/data/strikes.RData |binary probstats4econ-0.3.1/probstats4econ/data/website.RData |binary probstats4econ-0.3.1/probstats4econ/data/widgets.RData |binary probstats4econ-0.3.1/probstats4econ/man/babynames.Rd |only probstats4econ-0.3.1/probstats4econ/man/cigdata.Rd | 9 probstats4econ-0.3.1/probstats4econ/man/premier.Rd |only probstats4econ-0.3.1/probstats4econ/man/se_meanx.Rd |only probstats4econ-0.3.1/probstats4econ/man/test_linear_restrictions.Rd | 4 probstats4econ-0.3.1/probstats4econ/man/wald_test.Rd | 6 probstats4econ-0.3.1/probstats4econ/tests/testthat/_snaps/se_functions.md |only probstats4econ-0.3.1/probstats4econ/tests/testthat/setup.R | 2 probstats4econ-0.3.1/probstats4econ/tests/testthat/test-se_functions.R |only probstats4econ-0.3.1/probstats4econ/tests/testthat/test-utils.R | 14 - probstats4econ-0.3.1/probstats4econ/tests/testthat/test-wald_test.R | 4 55 files changed, 169 insertions(+), 107 deletions(-)
More information about probstats4econ at CRAN
Permanent link
Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution as described in Hong (2013) <doi: 10.1016/j.csda.2012.10.006>. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution. The C code for fast Fourier transformation (FFT) is written by R Core Team (2019)<https://www.R-project.org/>, which implements the FFT algorithm in Singleton (1969) <doi: 10.1109/TAU.1969.1162042>.
Author: Yili Hong [aut, cre],
R Core Team [aut, cph]
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between poibin versions 1.5 dated 2020-01-08 and 1.6 dated 2024-08-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/dftcf.c | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9 dated 2024-08-19 and 10.9.1 dated 2024-08-23
DESCRIPTION | 8 MD5 | 184 +++++++++---------- R/ANOVA.R | 6 R/ARMA.R | 6 R/ARMA_optim.R | 4 R/Boost.R | 3 R/Causation.R | 3 R/Copula.R | 2 R/Dependence.R | 3 R/FSD.R | 4 R/LPM_UPM_VaR.R | 5 R/NNS_MC.R | 3 R/NNS_VAR.R | 18 - R/NNS_meboot.R | 6 R/NNS_term_matrix.R | 3 R/Normalization.R | 3 R/Nowcast.R | 9 R/Numerical_Differentiation.R | 3 R/Partial_Moments.R | 11 - R/Partition_Map.R | 3 R/RcppExports.R | 33 +-- R/Regression.R | 19 + R/SD_Efficient_Set.R | 5 R/SSD.R | 2 R/Seasonality_Test.R | 3 R/Stack.R | 3 R/TSD.R | 2 R/Uni_SD_Routines.R | 8 R/dy_d_wrt.R | 6 R/dy_dx.R | 6 README.md | 10 - inst/doc/NNSvignette_Classification.Rmd | 10 - inst/doc/NNSvignette_Classification.html | 12 - inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 10 - inst/doc/NNSvignette_Clustering_and_Regression.html | 12 - inst/doc/NNSvignette_Comparing_Distributions.Rmd | 6 inst/doc/NNSvignette_Comparing_Distributions.html | 9 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 8 inst/doc/NNSvignette_Correlation_and_Dependence.html | 10 - inst/doc/NNSvignette_Forecasting.Rmd | 6 inst/doc/NNSvignette_Forecasting.html | 6 inst/doc/NNSvignette_Partial_Moments.Rmd | 10 - inst/doc/NNSvignette_Partial_Moments.html | 10 - inst/doc/NNSvignette_Sampling.Rmd | 6 inst/doc/NNSvignette_Sampling.html | 6 man/Co.LPM.Rd | 3 man/Co.UPM.Rd | 3 man/D.LPM.Rd | 3 man/D.UPM.Rd | 3 man/LPM.Rd | 3 man/LPM.VaR.Rd | 3 man/LPM.ratio.Rd | 6 man/NNS.ANOVA.Rd | 6 man/NNS.ARMA.Rd | 6 man/NNS.ARMA.optim.Rd | 3 man/NNS.CDF.Rd | 6 man/NNS.FSD.Rd | 4 man/NNS.FSD.uni.Rd | 4 man/NNS.MC.Rd | 3 man/NNS.SD.efficient.set.Rd | 4 man/NNS.SSD.Rd | 2 man/NNS.SSD.uni.Rd | 2 man/NNS.TSD.Rd | 2 man/NNS.TSD.uni.Rd | 2 man/NNS.VAR.Rd | 18 - man/NNS.boost.Rd | 3 man/NNS.caus.Rd | 3 man/NNS.copula.Rd | 2 man/NNS.dep.Rd | 3 man/NNS.diff.Rd | 3 man/NNS.meboot.Rd | 6 man/NNS.moments.Rd | 3 man/NNS.norm.Rd | 3 man/NNS.nowcast.Rd | 9 man/NNS.part.Rd | 3 man/NNS.reg.Rd | 9 man/NNS.seas.Rd | 3 man/NNS.stack.Rd | 3 man/NNS.term.matrix.Rd | 3 man/PM.matrix.Rd | 6 man/UPM.Rd | 3 man/UPM.VaR.Rd | 6 man/UPM.ratio.Rd | 3 man/dy.d_.Rd | 6 man/dy.dx.Rd | 6 src/partial_moments_rcpp.cpp | 33 +-- vignettes/NNSvignette_Classification.Rmd | 10 - vignettes/NNSvignette_Clustering_and_Regression.Rmd | 10 - vignettes/NNSvignette_Comparing_Distributions.Rmd | 6 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 8 vignettes/NNSvignette_Forecasting.Rmd | 6 vignettes/NNSvignette_Partial_Moments.Rmd | 10 - vignettes/NNSvignette_Sampling.Rmd | 6 93 files changed, 337 insertions(+), 429 deletions(-)
Title: Explanation Groves
Description: Compute surrogate explanation groves for predictive machine learning models and analyze complexity vs. explanatory power of an explanation according to Szepannek, G. and von Holt, B. (2023) <doi:10.1007/s41237-023-00205-2>.
Author: Gero Szepannek [aut, cre]
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between xgrove versions 0.1-7 dated 2023-09-13 and 0.1-11 dated 2024-08-23
xgrove-0.1-11/xgrove/DESCRIPTION | 19 +++- xgrove-0.1-11/xgrove/MD5 | 15 +-- xgrove-0.1-11/xgrove/NAMESPACE | 1 xgrove-0.1-11/xgrove/NEWS | 17 +++- xgrove-0.1-11/xgrove/R/xgrove.R | 53 +++++++++++-- xgrove-0.1-11/xgrove/man/plot.sgtree.Rd | 78 +++++++++---------- xgrove-0.1-11/xgrove/man/sgtree.Rd | 128 ++++++++++++++++---------------- xgrove-0.1-11/xgrove/man/xgrove.Rd | 29 ++++++- xgrove-0.1-7/xgrove/inst |only 9 files changed, 209 insertions(+), 131 deletions(-)
Title: Prediction Model Validation and Updating
Description: Evaluate the predictive performance of an existing (i.e. previously
developed) prediction/ prognostic model given relevant information about the
existing prediction model (e.g. coefficients) and a new dataset. Provides a
range of model updating methods that help tailor the existing model to the
new dataset; see Su et al. (2018) <doi:10.1177/0962280215626466>. Techniques
to aggregate multiple existing prediction models on the new data are also
provided; see Debray et al. (2014) <doi:10.1002/sim.6080> and Martin et al.
(2018) <doi:10.1002/sim.7586>).
Author: Glen P. Martin [aut, cre, cph]
,
David Jenkins [aut, cph],
Matthew Sperrin [aut, cph]
Maintainer: Glen P. Martin <glen.martin31@gmail.com>
Diff between predRupdate versions 0.1.1 dated 2023-12-12 and 0.2.0 dated 2024-08-23
DESCRIPTION | 8 MD5 | 62 +- NAMESPACE | 1 NEWS.md | 11 R/clean_variable_names.R |only R/flex_calplot.R | 53 + R/map_newdata.R | 552 ++++++++++---------- R/pred_input_info.R | 481 +++++++++-------- R/pred_input_info_input_checks.R | 192 +++---- R/pred_val_probs.R |only R/pred_validate.R | 214 +++++-- R/validate_logistic.R | 42 + R/validate_survival.R | 39 + inst/doc/predRupdate.R | 63 ++ inst/doc/predRupdate.Rmd | 575 +++++++++++---------- inst/doc/predRupdate.html | 655 +++++++++++++----------- inst/doc/predRupdate_splineIllustration.html | 36 - man/map_newdata.Rd | 166 +++--- man/pred_val_probs.Rd |only man/pred_validate.Rd | 35 + tests/testthat/_snaps/pred_validate_logistic.md | 66 +- tests/testthat/_snaps/pred_validate_survival.md | 48 - tests/testthat/test-clean_variable_names.R |only tests/testthat/test-flex_calplot.R |only tests/testthat/test-map_newdata.R | 392 ++++++++------ tests/testthat/test-pred_input_info.R | 122 ++-- tests/testthat/test-pred_input_info_checks.R | 200 +++---- tests/testthat/test-pred_predict.R | 288 +++++----- tests/testthat/test-pred_stacked_regression.R | 140 +++-- tests/testthat/test-pred_update.R | 176 +++--- tests/testthat/test-pred_val_probs.R |only tests/testthat/test-pred_validate_logistic.R | 136 ++-- tests/testthat/test-pred_validate_survival.R | 108 ++- tests/testthat/test-validate_survival.R | 115 ++-- vignettes/predRupdate.Rmd | 575 +++++++++++---------- 35 files changed, 3116 insertions(+), 2435 deletions(-)
Title: Visualize and Parse the Output of 'BeXY'
Description: Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.
Author: Madleina Caduff [aut, cre],
Raphael Eckel [ctb],
Christoph Leuenberger [ctb],
Daniel Wegmann [aut]
Maintainer: Madleina Caduff <madleina.caduff@unifr.ch>
Diff between bexy versions 0.1.2 dated 2023-11-29 and 0.1.3 dated 2024-08-23
bexy-0.1.2/bexy/man/plotXY.Rd |only bexy-0.1.3/bexy/DESCRIPTION | 8 bexy-0.1.3/bexy/MD5 | 38 - bexy-0.1.3/bexy/NAMESPACE | 2 bexy-0.1.3/bexy/NEWS.md | 9 bexy-0.1.3/bexy/R/bexy.R | 232 +++++++--- bexy-0.1.3/bexy/man/dot-getIndexScaffold.bexy.Rd |only bexy-0.1.3/bexy/man/dot-getIndexScaffoldAutosomalTrisomy.bexy.Rd | 6 bexy-0.1.3/bexy/man/dot-getSamplesToHighlight.bexy.Rd | 2 bexy-0.1.3/bexy/man/dot-getSamplesToHighlightAutosomalTrisomy.bexy.Rd | 2 bexy-0.1.3/bexy/man/dot-openFile.bexy.Rd | 4 bexy-0.1.3/bexy/man/dot-plotAutosomalTrisomy.bexy.Rd | 2 bexy-0.1.3/bexy/man/dot-plotTernary.bexy.Rd | 2 bexy-0.1.3/bexy/man/dot-plotTernaryAndTicTacToe.bexy.Rd | 2 bexy-0.1.3/bexy/man/dot-plotXVsY.bexy.Rd | 8 bexy-0.1.3/bexy/man/plot.bexy.Rd | 21 bexy-0.1.3/bexy/man/plotAutosomalTrisomy.Rd | 2 bexy-0.1.3/bexy/man/plotAutosomalTrisomyCounts.Rd | 2 bexy-0.1.3/bexy/man/plotAutosomalTrisomyPosteriorProbabilities.Rd | 2 bexy-0.1.3/bexy/man/plotBars.Rd |only bexy-0.1.3/bexy/man/plotCounts.Rd |only bexy-0.1.3/bexy/man/plotTernary.Rd | 2 22 files changed, 240 insertions(+), 106 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Advanced statistical tools for Bayesian structure learning in undirected graphical models, accommodating continuous, ordinal, discrete, count, and mixed data. It integrates recent advancements in Bayesian graphical models as presented in the literature, including the works of Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2021) <doi:10.1080/01621459.2021.1996377>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, and Mohammadi et al. (2023) <doi:10.48550/arXiv.2307.00127>.
Author: Reza Mohammadi [aut, cre] ,
Ernst Wit [aut] ,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.72 dated 2022-12-25 and 2.73 dated 2024-08-23
DESCRIPTION | 8 MD5 | 134 ++--- NAMESPACE | 1 NEWS.md | 4 R/bdgraph.R | 4 R/bdgraph.dw.R | 39 + R/bdgraph.mpl.R | 5 R/bdgraph.sim.R | 58 +- R/bdw.reg.R | 2 R/compare.R | 2 R/mse.R |only R/select.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 - inst/doc/BDgraph-Examples.Rmd | 2 inst/doc/BDgraph-Examples.html | 476 ++++++++++++++----- inst/doc/Introduction-BDgraph.Rmd | 26 - inst/doc/Introduction-BDgraph.html | 882 +++++++++++++++++++++++++++---------- man/BDgraph-package.Rd | 10 man/adj2link.Rd | 20 man/auc.Rd | 10 man/bdgraph.Rd | 10 man/bdgraph.dw.Rd | 14 man/bdgraph.mpl.Rd | 8 man/bdgraph.npn.Rd | 2 man/bdgraph.sim.Rd | 2 man/bdw.reg.Rd | 20 man/bf.Rd | 8 man/compare.Rd | 8 man/conf.mat.Rd | 8 man/conf.mat.plot.Rd | 8 man/covariance.Rd | 6 man/ddweibull.Rd | 2 man/gnorm.Rd | 4 man/graph.sim.Rd | 2 man/link2adj.Rd | 6 man/mse.Rd |only man/pgraph.Rd | 8 man/plinks.Rd | 6 man/plot.bdgraph.Rd | 4 man/plot.graph.Rd | 4 man/plot.sim.Rd | 6 man/plotcoda.Rd | 4 man/plotroc.Rd | 12 man/posterior.predict.Rd | 10 man/precision.Rd | 4 man/predict.bdgraph.Rd | 12 man/print.bdgraph.Rd | 4 man/print.sim.Rd | 4 man/rgwish.Rd | 8 man/rmvnorm.Rd | 2 man/roc.Rd | 24 - man/rwish.Rd | 2 man/select.Rd | 6 man/sparsity.Rd | 8 man/summary.bdgraph.Rd | 6 man/traceplot.Rd | 6 man/trensfer.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/copula.cpp | 672 ++++++++++++++-------------- src/ggm_mpl_bd.cpp | 405 ++++++++++++++-- src/matrix.cpp | 2 src/matrix.h | 22 src/rgwish.cpp | 4 vignettes/BDgraph-Examples.Rmd | 2 vignettes/Introduction-BDgraph.Rmd | 26 - 69 files changed, 2051 insertions(+), 1061 deletions(-)
Title: Translate Text
Description: Provide easy methods to translate pieces of text.
Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between polyglotr versions 1.5.1 dated 2024-07-27 and 1.5.2 dated 2024-08-23
polyglotr-1.5.1/polyglotr/tests/testthat/test-google_translate.R |only polyglotr-1.5.1/polyglotr/tests/testthat/test-language_detect.R |only polyglotr-1.5.2/polyglotr/DESCRIPTION | 12 polyglotr-1.5.2/polyglotr/LICENSE | 4 polyglotr-1.5.2/polyglotr/MD5 | 156 - polyglotr-1.5.2/polyglotr/NAMESPACE | 58 polyglotr-1.5.2/polyglotr/NEWS.md | 81 polyglotr-1.5.2/polyglotr/R/batch_translate.R | 52 polyglotr-1.5.2/polyglotr/R/create_translation_table.R | 64 polyglotr-1.5.2/polyglotr/R/create_transliteration_table.R | 64 polyglotr-1.5.2/polyglotr/R/google_get_supported_languages.R | 58 polyglotr-1.5.2/polyglotr/R/google_is_valid_language_code.R | 48 polyglotr-1.5.2/polyglotr/R/google_supported_languages.R | 16 polyglotr-1.5.2/polyglotr/R/google_translate.R | 130 - polyglotr-1.5.2/polyglotr/R/google_translate_file.R | 86 - polyglotr-1.5.2/polyglotr/R/google_translate_long_text.R | 126 - polyglotr-1.5.2/polyglotr/R/google_transliterate.R | 132 - polyglotr-1.5.2/polyglotr/R/language_detect.R | 54 polyglotr-1.5.2/polyglotr/R/linguee_external_sources.R | 84 polyglotr-1.5.2/polyglotr/R/linguee_translation_examples.R | 102 - polyglotr-1.5.2/polyglotr/R/linguee_word_translation.R | 92 - polyglotr-1.5.2/polyglotr/R/microsoft_supported_languages.R | 62 polyglotr-1.5.2/polyglotr/R/mymemory_translate.R | 64 polyglotr-1.5.2/polyglotr/R/pons_dictionaries.R | 66 polyglotr-1.5.2/polyglotr/R/pons_translate.R | 138 - polyglotr-1.5.2/polyglotr/R/qcri_api_key.R | 20 polyglotr-1.5.2/polyglotr/R/qcri_get_domains.R | 88 - polyglotr-1.5.2/polyglotr/R/qcri_get_language_pairs.R | 72 polyglotr-1.5.2/polyglotr/R/qcri_translate_text.R | 98 - polyglotr-1.5.2/polyglotr/R/translate_to_morse.R | 86 - polyglotr-1.5.2/polyglotr/R/translate_to_morse_audio.R | 92 - polyglotr-1.5.2/polyglotr/R/utils-pipe.R | 28 polyglotr-1.5.2/polyglotr/R/wikimedia_detect_language.R | 90 - polyglotr-1.5.2/polyglotr/R/wikipedia_get_language_names.R | 84 polyglotr-1.5.2/polyglotr/R/wmcloud_translate.R | 188 +- polyglotr-1.5.2/polyglotr/README.md | 132 - polyglotr-1.5.2/polyglotr/build/vignette.rds |binary polyglotr-1.5.2/polyglotr/inst/doc/Linguee.R | 49 polyglotr-1.5.2/polyglotr/inst/doc/Linguee.Rmd | 125 - polyglotr-1.5.2/polyglotr/inst/doc/Linguee.html | 814 ++++----- polyglotr-1.5.2/polyglotr/inst/doc/Movie_Reviews.R | 59 polyglotr-1.5.2/polyglotr/inst/doc/Movie_Reviews.Rmd | 137 - polyglotr-1.5.2/polyglotr/inst/doc/Movie_Reviews.html | 857 ++++------ polyglotr-1.5.2/polyglotr/inst/doc/polyglotr.R | 51 polyglotr-1.5.2/polyglotr/inst/doc/polyglotr.Rmd | 115 - polyglotr-1.5.2/polyglotr/inst/doc/polyglotr.html | 814 ++++----- polyglotr-1.5.2/polyglotr/man/batch_translate.Rd | 52 polyglotr-1.5.2/polyglotr/man/create_translation_table.Rd | 52 polyglotr-1.5.2/polyglotr/man/create_transliteration_table.Rd | 52 polyglotr-1.5.2/polyglotr/man/google_get_supported_languages.Rd | 28 polyglotr-1.5.2/polyglotr/man/google_is_valid_language_code.Rd | 46 polyglotr-1.5.2/polyglotr/man/google_supported_languages.Rd | 38 polyglotr-1.5.2/polyglotr/man/google_translate.Rd | 62 polyglotr-1.5.2/polyglotr/man/google_translate_long_text.Rd | 76 polyglotr-1.5.2/polyglotr/man/google_transliterate.Rd | 54 polyglotr-1.5.2/polyglotr/man/language_detect.Rd | 34 polyglotr-1.5.2/polyglotr/man/linguee_external_sources.Rd | 64 polyglotr-1.5.2/polyglotr/man/linguee_translation_examples.Rd | 86 - polyglotr-1.5.2/polyglotr/man/linguee_word_translation.Rd | 76 polyglotr-1.5.2/polyglotr/man/microsoft_supported_languages.Rd | 44 polyglotr-1.5.2/polyglotr/man/mymemory_translate.Rd | 52 polyglotr-1.5.2/polyglotr/man/pipe.Rd | 40 polyglotr-1.5.2/polyglotr/man/pons_dictionaries.Rd | 44 polyglotr-1.5.2/polyglotr/man/pons_translate.Rd | 60 polyglotr-1.5.2/polyglotr/man/qcri_api_key.Rd | 28 polyglotr-1.5.2/polyglotr/man/qcri_get_domains.Rd | 56 polyglotr-1.5.2/polyglotr/man/qcri_get_language_pairs.Rd | 46 polyglotr-1.5.2/polyglotr/man/qcri_translate_text.Rd | 68 polyglotr-1.5.2/polyglotr/man/translate_file.Rd | 60 polyglotr-1.5.2/polyglotr/man/translate_to_morse.Rd | 38 polyglotr-1.5.2/polyglotr/man/translate_to_morse_audio.Rd | 38 polyglotr-1.5.2/polyglotr/man/wikimedia_detect_language.Rd | 46 polyglotr-1.5.2/polyglotr/man/wikipedia_get_language_names.Rd | 38 polyglotr-1.5.2/polyglotr/man/wmcloud_translate.Rd | 120 - polyglotr-1.5.2/polyglotr/tests/testthat.R | 20 polyglotr-1.5.2/polyglotr/tests/testthat/helpers.R | 30 polyglotr-1.5.2/polyglotr/tests/testthat/test-mymemory_translate.R | 20 polyglotr-1.5.2/polyglotr/vignettes/Linguee.Rmd | 125 - polyglotr-1.5.2/polyglotr/vignettes/Movie_Reviews.Rmd | 137 - polyglotr-1.5.2/polyglotr/vignettes/polyglotr.Rmd | 115 - 80 files changed, 3824 insertions(+), 3869 deletions(-)
Title: Tools for Working with Points and Intervals
Description: Tools for working with and comparing sets of points and intervals.
Author: Richard Bourgon [aut],
Edzer Pebesma [cre]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between intervals versions 0.15.4 dated 2023-06-29 and 0.15.5 dated 2024-08-23
DESCRIPTION | 19 ++++++++++++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/intervals_overview.pdf |binary src/Endpoint.h | 3 +++ src/plot_overlap.cpp | 4 ++-- src/reduce.cpp | 16 ++++++++-------- src/which_nearest.cpp | 18 +++++++++--------- 8 files changed, 43 insertions(+), 31 deletions(-)
Title: Spatially Smoothed MRCD Estimator
Description: Estimation of the Spatially Smoothed Minimum Regularized Determinant (ssMRCD) estimator and its usage in an ssMRCD-based outlier detection method as described in Puchhammer and Filzmoser (2023) <doi:10.1080/10618600.2023.2277875> and for sparse robust PCA for multi-source data described in Puchhammer, Wilms and Filzmoser (2024) <doi:10.48550/arXiv.2407.16299>. Included are also complementary visualization and parameter tuning tools.
Author: Patricia Puchhammer [aut, cre, cph],
Peter Filzmoser [aut]
Maintainer: Patricia Puchhammer <patricia.puchhammer@tuwien.ac.at>
Diff between ssMRCD versions 0.1.0 dated 2023-05-15 and 1.1.0 dated 2024-08-23
ssMRCD-0.1.0/ssMRCD/R/helper_functions_application.R |only ssMRCD-0.1.0/ssMRCD/R/helper_functions_ssMRCD.R |only ssMRCD-0.1.0/ssMRCD/R/local_outliers_ssMRCD.R |only ssMRCD-0.1.0/ssMRCD/R/parameter_tuning.R |only ssMRCD-0.1.0/ssMRCD/man/N_structure_gridbased.Rd |only ssMRCD-1.1.0/ssMRCD/DESCRIPTION | 11 ssMRCD-1.1.0/ssMRCD/MD5 | 89 +++++-- ssMRCD-1.1.0/ssMRCD/NAMESPACE | 46 +++- ssMRCD-1.1.0/ssMRCD/R/check_input.R | 54 ---- ssMRCD-1.1.0/ssMRCD/R/data.R | 48 +++- ssMRCD-1.1.0/ssMRCD/R/general_helpers.R |only ssMRCD-1.1.0/ssMRCD/R/locOuts.R |only ssMRCD-1.1.0/ssMRCD/R/locOuts_methods.R | 10 ssMRCD-1.1.0/ssMRCD/R/select_parameters.R |only ssMRCD-1.1.0/ssMRCD/R/sparsePCA_ADMM.R |only ssMRCD-1.1.0/ssMRCD/R/sparsePCA_helpers.R |only ssMRCD-1.1.0/ssMRCD/R/sparsePCAloc.R |only ssMRCD-1.1.0/ssMRCD/R/sparsePCAloc_methods.R |only ssMRCD-1.1.0/ssMRCD/R/ssMRCD.R | 35 ++- ssMRCD-1.1.0/ssMRCD/R/ssMRCD_helpers.R |only ssMRCD-1.1.0/ssMRCD/R/ssMRCD_methods.R | 217 +++++++++++++++++-- ssMRCD-1.1.0/ssMRCD/build/partial.rdb |binary ssMRCD-1.1.0/ssMRCD/build/vignette.rds |binary ssMRCD-1.1.0/ssMRCD/data/weatherHoheWarte.rda |only ssMRCD-1.1.0/ssMRCD/inst/doc/ssMRCD.R | 8 ssMRCD-1.1.0/ssMRCD/inst/doc/ssMRCD.Rmd | 12 - ssMRCD-1.1.0/ssMRCD/inst/doc/ssMRCD.html | 35 +-- ssMRCD-1.1.0/ssMRCD/man/align_PC.Rd |only ssMRCD-1.1.0/ssMRCD/man/biplot.PCAloc.Rd |only ssMRCD-1.1.0/ssMRCD/man/contamination_random.Rd | 5 ssMRCD-1.1.0/ssMRCD/man/eval_objective.Rd |only ssMRCD-1.1.0/ssMRCD/man/explained_var.Rd |only ssMRCD-1.1.0/ssMRCD/man/geo_weights.Rd | 10 ssMRCD-1.1.0/ssMRCD/man/groups_gridbased.Rd |only ssMRCD-1.1.0/ssMRCD/man/local_outliers_ssMRCD.Rd | 12 - ssMRCD-1.1.0/ssMRCD/man/objective_matrix.Rd | 2 ssMRCD-1.1.0/ssMRCD/man/parameter_tuning.Rd | 12 - ssMRCD-1.1.0/ssMRCD/man/plot.PCAloc.Rd |only ssMRCD-1.1.0/ssMRCD/man/plot.locOuts.Rd | 6 ssMRCD-1.1.0/ssMRCD/man/plot.ssMRCD.Rd | 4 ssMRCD-1.1.0/ssMRCD/man/plot_loadings.Rd |only ssMRCD-1.1.0/ssMRCD/man/plot_score_distances.Rd |only ssMRCD-1.1.0/ssMRCD/man/plot_scores.Rd |only ssMRCD-1.1.0/ssMRCD/man/rescale_weights.Rd | 2 ssMRCD-1.1.0/ssMRCD/man/residuals.ssMRCD.Rd |only ssMRCD-1.1.0/ssMRCD/man/restructure_as_list.Rd | 8 ssMRCD-1.1.0/ssMRCD/man/scale_ssMRCD.Rd |only ssMRCD-1.1.0/ssMRCD/man/scores.OD.Rd |only ssMRCD-1.1.0/ssMRCD/man/scores.Rd |only ssMRCD-1.1.0/ssMRCD/man/scores.SD.Rd |only ssMRCD-1.1.0/ssMRCD/man/screeplot.PCAloc.Rd |only ssMRCD-1.1.0/ssMRCD/man/select_smoothing.Rd |only ssMRCD-1.1.0/ssMRCD/man/select_sparsity.Rd |only ssMRCD-1.1.0/ssMRCD/man/sparsePCAloc.Rd |only ssMRCD-1.1.0/ssMRCD/man/sparsity_entries.Rd |only ssMRCD-1.1.0/ssMRCD/man/sparsity_group.Rd |only ssMRCD-1.1.0/ssMRCD/man/sparsity_mixed.Rd |only ssMRCD-1.1.0/ssMRCD/man/sparsity_summary.Rd |only ssMRCD-1.1.0/ssMRCD/man/ssMRCD.Rd | 6 ssMRCD-1.1.0/ssMRCD/man/summary.PCAloc.Rd |only ssMRCD-1.1.0/ssMRCD/man/summary.locOuts.Rd | 4 ssMRCD-1.1.0/ssMRCD/man/time_weights.Rd |only ssMRCD-1.1.0/ssMRCD/man/weatherAUT2021.Rd | 4 ssMRCD-1.1.0/ssMRCD/man/weatherHoheWarte.Rd |only ssMRCD-1.1.0/ssMRCD/vignettes/ssMRCD.Rmd | 12 - 65 files changed, 465 insertions(+), 187 deletions(-)
Title: Intuitive Construction of Joint Priors for Variance Parameters
Description: Tool for easy prior construction and visualization. It helps to formulates joint prior distributions for variance parameters in latent Gaussian models. The resulting prior is robust and can be created in an intuitive way. A graphical user interface (GUI) can be used to choose the joint prior, where the user can click through the model and select priors. An extensive guide is available in the GUI. The package allows for direct inference with the specified model and prior. Using a hierarchical variance decomposition, we formulate a joint variance prior that takes the whole model structure into account. In this way, existing knowledge can intuitively be incorporated at the level it applies to. Alternatively, one can use independent variance priors for each model components in the latent Gaussian model. Details can be found in the accompanying scientific paper: Hem, Fuglstad, Riebler (2024, Journal of Statistical Software, <doi:10.18637/jss.v110.i03>).
Author: Ingeborg Hem [cre, aut] ,
Geir-Arne Fuglstad [aut] ,
Andrea Riebler [aut]
Maintainer: Ingeborg Hem <ingeborg.hem@ntnu.no>
Diff between makemyprior versions 1.2.1 dated 2024-04-09 and 1.2.2 dated 2024-08-23
DESCRIPTION | 23 ++++++++++++----------- MD5 | 13 +++++++------ NEWS.md | 5 +++++ inst/CITATION |only inst/doc/latin_square.html | 14 +++++++------- inst/doc/make_prior.html | 18 +++++++++--------- inst/doc/neonatal_mortality.html | 2 +- inst/doc/wheat_breeding.html | 10 +++++----- 8 files changed, 46 insertions(+), 39 deletions(-)
Title: Conditional Distance Correlation Based Feature Screening and
Conditional Independence Inference
Description: Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <https://www3.stat.sinica.edu.tw/statistica/J28N1/J28N114/J28N114.html>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.
Author: Wenhao Hu [aut],
Mian Huang [aut],
Wenliang Pan [aut],
Xueqin Wang [aut] ,
Canhong Wen [aut, cre],
Yuan Tian [aut],
Heping Zhang [aut] ,
Jin Zhu [aut]
Maintainer: Canhong Wen <wench@ustc.edu.cn>
Diff between cdcsis versions 2.0.4 dated 2024-07-07 and 2.0.5 dated 2024-08-23
DESCRIPTION | 31 ++++++++++++++++++++++++------- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/cdcsis-package.R | 2 +- R/utility.R | 2 +- man/cdcsis-package.Rd | 2 +- src/RcppExports.cpp | 5 +++++ 7 files changed, 41 insertions(+), 16 deletions(-)
Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting. The package is described in
Vollering et al. (2019; <doi:10.1002/ece3.5654>).
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph],
Michael Bedward [ctb]
Maintainer: Julien Vollering <julienvollering@gmail.com>
Diff between MIAmaxent versions 1.3.0 dated 2024-07-29 and 1.3.1 dated 2024-08-23
DESCRIPTION | 6 MD5 | 12 NEWS.md | 150 +-- R/projectModel.R | 3 README.md | 6 inst/doc/a-modeling-example.html | 1788 +++++++++++++++++++++++---------------- vignettes/a-modeling-example.Rmd | 9 7 files changed, 1191 insertions(+), 783 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.0 dated 2024-03-18 and 1.0.1 dated 2024-08-23
DESCRIPTION | 10 ++-- MD5 | 29 ++++++----- NEWS.md | 10 ++++ R/dot_plot.R | 4 + R/relative_risk.R | 12 +++- README.md | 11 ++++ build/vignette.rds |binary inst/doc/eudract.Rmd | 4 - inst/doc/eudract.html | 21 ++++---- inst/doc/standard_reporting.html | 56 +++++++++++------------ man/relative_risk.Rd | 9 ++- tests/testthat/Rplots.pdf |only tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg |only tests/testthat/_snaps/dotplot/dotplot-ref.svg |only tests/testthat/test_dotplot.R | 17 ++++++ tests/testthat/test_relative_risk.R | 3 - vignettes/eudract.Rmd | 4 - 17 files changed, 123 insertions(+), 67 deletions(-)
Title: Easy Dockerfile Creation from R
Description: Build a Dockerfile straight from your R session.
'dockerfiler' allows you to create step by step a Dockerfile, and
provide convenient tools to wrap R code inside this Dockerfile.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Josiah Parry [aut] ,
Sebastien Rochette [aut]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between dockerfiler versions 0.2.3 dated 2024-07-09 and 0.2.4 dated 2024-08-23
dockerfiler-0.2.3/dockerfiler/inst/renv_Dockefile |only dockerfiler-0.2.4/dockerfiler/DESCRIPTION | 8 - dockerfiler-0.2.4/dockerfiler/MD5 | 28 ++-- dockerfiler-0.2.4/dockerfiler/NEWS.md | 5 dockerfiler-0.2.4/dockerfiler/R/add.R | 2 dockerfiler-0.2.4/dockerfiler/R/dock_from_desc.R | 2 dockerfiler-0.2.4/dockerfiler/R/dock_from_renv.R | 31 ++-- dockerfiler-0.2.4/dockerfiler/R/parse-dockerfile.R | 2 dockerfiler-0.2.4/dockerfiler/R/utils.R | 3 dockerfiler-0.2.4/dockerfiler/build/vignette.rds |binary dockerfiler-0.2.4/dockerfiler/inst/doc/dockerfile-from-renv-lock.html | 2 dockerfiler-0.2.4/dockerfiler/inst/doc/dockerfiler.html | 6 dockerfiler-0.2.4/dockerfiler/man/dockerfiles.Rd | 3 dockerfiler-0.2.4/dockerfiler/tests/testthat/renv_Dockerfile |only dockerfiler-0.2.4/dockerfiler/tests/testthat/test-dock_from_desc.R | 4 dockerfiler-0.2.4/dockerfiler/tests/testthat/test-dock_from_renv.R | 63 ++-------- 16 files changed, 76 insertions(+), 83 deletions(-)
Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models.
References.
Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>.
Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>.
Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>.
Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>.
Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>.
Santolino, M. (2023) <doi:10.3390/risks11100170>.
Author: David Atance [aut, cre] ,
Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>
Diff between CvmortalityMult versions 1.0.3 dated 2024-07-16 and 1.0.5 dated 2024-08-23
CvmortalityMult-1.0.3/CvmortalityMult/data/SpainNat.RData |only CvmortalityMult-1.0.3/CvmortalityMult/data/SpainRegions.RData |only CvmortalityMult-1.0.3/CvmortalityMult/data/regions.RData |only CvmortalityMult-1.0.5/CvmortalityMult/DESCRIPTION | 10 - CvmortalityMult-1.0.5/CvmortalityMult/MD5 | 23 +-- CvmortalityMult-1.0.5/CvmortalityMult/NAMESPACE | 2 CvmortalityMult-1.0.5/CvmortalityMult/R/SpainNat.R | 7 CvmortalityMult-1.0.5/CvmortalityMult/R/SpainRegions.R | 5 CvmortalityMult-1.0.5/CvmortalityMult/R/fitLCmulti.R | 21 +- CvmortalityMult-1.0.5/CvmortalityMult/R/residSVD2.R |only CvmortalityMult-1.0.5/CvmortalityMult/data/SpainNat.rda |binary CvmortalityMult-1.0.5/CvmortalityMult/data/SpainRegions.rda |binary CvmortalityMult-1.0.5/CvmortalityMult/man/SpainMap.Rd | 76 +++++----- CvmortalityMult-1.0.5/CvmortalityMult/man/fitLCmulti.Rd | 1 CvmortalityMult-1.0.5/CvmortalityMult/man/residSVD2.Rd |only 15 files changed, 80 insertions(+), 65 deletions(-)
More information about CvmortalityMult at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-18 2.5.1
2013-08-08 1.13-8-8
2011-12-07 1.11-12-7
2011-11-28 1.11-11-27
2011-11-20 1.11-11-19
2011-11-18 1.11-11-17
2011-11-05 1.1-1
2011-11-02 1.1
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.151 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 6.9 dated 2024-07-08 and 7.0 dated 2024-08-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/diri.reg.R | 21 +++++++++++++-------- R/kl.compreg.R | 25 ++++++++++++++++++++++--- man/Compositional-package.Rd | 7 +++++-- man/zad.est.Rd | 4 ++-- 6 files changed, 51 insertions(+), 24 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
and More
Description: Functions used to fit and test the phenology of species based on counts. Based on Girondot, M. (2010) <doi:10.3354/esr00292> for the phenology function, Girondot, M. (2017) <doi:10.1016/j.ecolind.2017.05.063> for the convolution of negative binomial, Girondot, M. and Rizzo, A. (2015) <doi:10.2993/etbi-35-02-337-353.1> for Bayesian estimate, Pfaller JB, ..., Girondot M (2019) <doi:10.1007/s00227-019-3545-x> for tag-loss estimate, Hancock J, ..., Girondot M (2019) <doi:10.1016/j.ecolmodel.2019.04.013> for nesting history, Laloe J-O, ..., Girondot M, Hays GC (2020) <doi:10.1007/s00227-020-03686-x> for aggregating several seasons.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between phenology versions 9.1 dated 2023-10-16 and 10.1 dated 2024-08-23
DESCRIPTION | 19 - MD5 | 186 ++++++------ NEWS | 12 R/Likelihood_phenology.R | 5 R/Lnegbin.R | 79 +++-- R/Tagloss_fit.R | 2 R/Tagloss_simulate.R | 2 R/add_phenology.R | 617 +++++++++++++++++++++++-------------------- R/fit_phenology.R | 6 R/format_par.R | 9 R/map_phenology.R | 2 R/onAttach.R | 30 +- R/phenology-package.R | 5 R/plot.fitRMU.R | 2 R/plot.phenology.R | 4 R/summary.phenology.R | 62 ++-- man/AutoFitPhenology.Rd | 14 man/BE_to_LBLE.Rd | 18 - man/CI.RMU.Rd | 32 +- man/ECFOCF_f.Rd | 4 man/ECFOCF_full.Rd | 4 man/ExponentialRegression.Rd | 8 man/Gratiot.Rd | 28 - man/IPFit.Rd | 10 man/IPModel.Rd | 24 - man/IPPredict.Rd | 2 man/LBLE_to_BE.Rd | 18 - man/LBLE_to_L.Rd | 16 - man/L_to_LBLE.Rd | 16 - man/MarineTurtles_2002.Rd | 18 - man/MinBMinE_to_Min.Rd | 18 - man/Parameter_Global_Year.Rd | 6 man/RI.Rd | 6 man/TableECFOCF.Rd | 12 man/Tagloss_L.Rd | 10 man/Tagloss_LengthObs.Rd | 6 man/Tagloss_cumul.Rd | 12 man/Tagloss_daymax.Rd | 8 man/Tagloss_fit.Rd | 24 - man/Tagloss_format.Rd | 8 man/Tagloss_mcmc.Rd | 20 - man/Tagloss_mcmc_p.Rd | 6 man/Tagloss_model.Rd | 10 man/Tagloss_simulate.Rd | 14 man/adapt_parameters.Rd | 14 man/add_SE.Rd | 14 man/add_phenology.Rd | 104 +++++-- man/extract_result.Rd | 14 man/fitCF.Rd | 100 +++--- man/fitCF_MHmcmc.Rd | 4 man/fitCF_MHmcmc_p.Rd | 4 man/fitRMU.Rd | 32 +- man/fitRMU_MHmcmc.Rd | 2 man/fitRMU_MHmcmc_p.Rd | 6 man/fit_phenology.Rd | 18 - man/generateCF.Rd | 68 ++-- man/likelihood_phenology.Rd | 17 - man/lnLCF.Rd | 6 man/logLik.ECFOCF.Rd | 6 man/logLik.Tagloss.Rd | 8 man/logLik.fitRMU.Rd | 4 man/logLik.phenology.Rd | 14 man/map_Gratiot.Rd | 22 - man/map_phenology.Rd | 28 - man/o_4p_p1p2.Rd | 8 man/outLR.Rd | 4 man/par_init.Rd | 40 +- man/phenology-package.Rd | 85 ++--- man/phenology.Rd | 12 man/phenology2fitRMU.Rd | 22 - man/phenology_MHmcmc.Rd | 12 man/phenology_MHmcmc_p.Rd | 12 man/plot.ECFOCF.Rd | 10 man/plot.TableECFOCF.Rd | 6 man/plot.Tagloss.Rd | 4 man/plot.TaglossData.Rd | 4 man/plot.fitRMU.Rd | 4 man/plot.phenology.Rd | 17 - man/plot.phenologymap.Rd | 12 man/plot_delta.Rd | 14 man/plot_phi.Rd | 14 man/print.phenology.Rd | 12 man/print.phenologymap.Rd | 14 man/print.phenologyout.Rd | 14 man/remove_site.Rd | 14 man/result_Gratiot.Rd | 20 - man/result_Gratiot1.Rd | 24 - man/result_Gratiot2.Rd | 24 - man/result_Gratiot_Flat.Rd | 22 - man/result_Gratiot_mcmc.Rd | 22 - man/summary.phenology.Rd | 17 - man/summary.phenologymap.Rd | 14 man/summary.phenologyout.Rd | 14 man/toggle_Min_PMin.Rd | 4 94 files changed, 1293 insertions(+), 1101 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.3.0 dated 2023-08-22 and 3.3.1 dated 2024-08-23
DESCRIPTION | 10 MD5 | 144 ++--- NAMESPACE | 102 +-- NEWS.md | 338 ++++++------ R/Appenders.R | 452 ++++++++-------- R/Args.R | 835 +++++++++++++++---------------- R/Cluster.R | 534 +++++++++---------- R/Layouts.R | 460 ++++++++--------- R/Loggers.R | 362 ++++++------- R/Logging.R | 636 +++++++++++------------ R/ParallelLogger.R | 54 +- R/ShinyApps.R | 146 ++--- README.md | 196 +++---- build/vignette.rds |binary inst/doc/Logging.R | 458 ++++++++--------- inst/doc/Logging.Rmd | 742 +++++++++++++-------------- inst/doc/Logging.pdf |binary inst/doc/Parallel.R | 78 +- inst/doc/Parallel.Rmd | 232 ++++---- inst/doc/Parallel.pdf |binary inst/shinyApps/LogViewer/global.R | 22 inst/shinyApps/LogViewer/server.R | 446 ++++++++-------- inst/shinyApps/LogViewer/ui.R | 46 - man/ParallelLogger-package.Rd | 68 +- man/addDefaultConsoleLogger.Rd | 48 - man/addDefaultEmailLogger.Rd | 130 ++-- man/addDefaultErrorReportLogger.Rd | 48 - man/addDefaultFileLogger.Rd | 42 - man/clearLoggers.Rd | 22 man/clusterApply.Rd | 96 +-- man/clusterRequire.Rd | 32 - man/convertJsonToSettings.Rd | 42 - man/convertSettingsToJson.Rd | 42 - man/createArgFunction.Rd | 88 +-- man/createConsoleAppender.Rd | 56 +- man/createEmailAppender.Rd | 144 ++--- man/createFileAppender.Rd | 56 +- man/createLogger.Rd | 86 +-- man/excludeFromList.Rd | 32 - man/getLoggers.Rd | 28 - man/launchLogViewer.Rd | 64 +- man/layoutEmail.Rd | 34 - man/layoutErrorReport.Rd | 36 - man/layoutParallel.Rd | 34 - man/layoutSimple.Rd | 32 - man/layoutStackTrace.Rd | 32 - man/layoutTimestamp.Rd | 54 +- man/loadSettingsFromJson.Rd | 40 - man/logDebug.Rd | 36 - man/logError.Rd | 36 - man/logFatal.Rd | 40 - man/logInfo.Rd | 60 +- man/logTrace.Rd | 58 +- man/logWarn.Rd | 40 - man/makeCluster.Rd | 72 +- man/matchInList.Rd | 92 +-- man/registerLogger.Rd | 58 +- man/saveSettingsToJson.Rd | 40 - man/selectFromList.Rd | 78 +- man/stopCluster.Rd | 46 - man/unregisterLogger.Rd | 68 +- tests/testthat.R | 6 tests/testthat/test-Appenders.R | 30 - tests/testthat/test-ShinyApps.R | 30 - tests/testthat/test-args.R | 14 tests/testthat/test-cluster.R | 178 +++--- tests/testthat/test-layouts.R | 130 ++-- tests/testthat/test-loggers.R | 172 +++--- tests/testthat/test-logging.R | 270 +++++----- tests/testthat/test-parallelProcessing.R | 28 - tests/testthat/test-saveAndLoadJson.R | 291 +++++----- vignettes/Logging.Rmd | 742 +++++++++++++-------------- vignettes/Parallel.Rmd | 232 ++++---- 73 files changed, 5277 insertions(+), 5249 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Statistical Methods for Auditing
Description: Provides statistical methods for auditing as implemented in JASP
for Audit (Derks et al., 2021 <doi:10.21105/joss.02733>). First, the package
makes it easy for an auditor to plan a statistical sample, select the sample
from the population, and evaluate the misstatement in the sample compliant
with international auditing standards. Second, the package provides
statistical methods for auditing data, including tests of digit
distributions and repeated values. Finally, the package includes methods for
auditing algorithms on the aspect of fairness and bias. Next to classical
statistical methodology, the package implements Bayesian equivalents of
these methods whose statistical underpinnings are described in Derks et al.
(2021) <doi:10.1111/ijau.12240>, Derks et al. (2024)
<doi:10.2308/AJPT-2021-086>, and Derks et al. (2022)
<doi:10.31234/osf.io/8nf3e>.
Author: Koen Derks [aut, cre]
Maintainer: Koen Derks <k.derks@nyenrode.nl>
Diff between jfa versions 0.7.1 dated 2024-03-07 and 0.7.2 dated 2024-08-23
DESCRIPTION | 14 ++++---- MD5 | 50 +++++++++++++++---------------- NEWS.md | 7 ++++ R/auditPrior.R | 44 +++++++++++++-------------- R/evaluation.R | 6 +-- R/jfa-internal.R | 2 - R/jfa-methods.R | 26 ++++++++-------- R/methods.R | 4 +- R/selection.R | 16 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 7 ++-- inst/stan/beta_zero_one.stan | 4 +- inst/stan/pp_error.stan | 4 +- inst/stan/pp_taint.stan | 4 +- man/auditPrior.Rd | 22 ++++++------- man/evaluation.Rd | 6 +-- man/selection.Rd | 2 - src/stanExports_beta_zero_one.h | 10 +++--- src/stanExports_pp_error.h | 14 ++++---- src/stanExports_pp_taint.h | 14 ++++---- tests/testthat/test-auditPrior.R | 8 ++-- tests/testthat/test-evaluation.R | 2 - tests/testthat/test-planning.R | 4 +- tests/testthat/test-selection.R | 38 ++++++++++++++++++++++- tests/testthat/test-statistical-tables.R | 6 +-- 26 files changed, 175 insertions(+), 139 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.1 dated 2024-01-30 and 6.2 dated 2024-08-23
DESCRIPTION | 19 ++++++++++++------- MD5 | 26 +++++++++++++------------- NEWS | 11 +++++++++-- R/HelpersMG-package.R | 5 ++--- R/IC_threshold_matrix.R | 11 +++++++---- R/RM_get.R | 16 ++++++++++++++-- R/onAttach.R | 30 +++++++++++++++--------------- R/read_folder.R | 2 ++ R/sysdata.rda |binary inst/shiny/cutter/ui.R | 2 +- man/HelpersMG-package.Rd | 6 ++---- man/IC_threshold_matrix.Rd | 4 ++-- man/RM_get.Rd | 2 +- man/read_folder.Rd | 2 ++ 14 files changed, 82 insertions(+), 54 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between embryogrowth versions 9.1 dated 2023-10-24 and 9.5 dated 2024-08-23
DESCRIPTION | 28 +- MD5 | 159 +++++++------- NAMESPACE | 3 NEWS | 24 ++ R/DatabaseNestingArea.R | 14 - R/DatabaseTSD.R | 13 - R/DatabaseTSD.version.R | 2 R/P_TRT.R | 447 +++++++++++++++++++++++++-------------- R/ROSIE.R |only R/ROSIE.version.R |only R/STRN_fit.R | 9 R/TSP.list.R | 7 R/calibrate.datalogger.R | 2 R/embryogrowth-package.R | 52 +--- R/hist.Nests.R | 1 R/info.nests.R | 33 ++ R/modelTSD.R | 35 +++ R/movement.R | 8 R/onAttach.R | 30 +- R/plot.HatchingSuccess.R | 11 R/plot.NestsResult.R | 4 R/plot.tsd.R | 448 +++++++++++++++++++++++++++++----------- R/resultNest_3p_Weibull.R | 4 R/searchR.R | 13 - R/tempConst.R | 2 R/tsd.R | 270 +++++++++++++++--------- R/tsd_MHmcmc_p.R | 154 +++++++++---- R/tsd_fit.R | 26 +- R/uncertainty.datalogger.R | 2 build |only data/DatabaseNestingArea.rda |binary data/DatabaseTSD.rda |binary data/ROSIE.rda |only data/TSP.list.rda |binary data/stages.rda |binary inst/REFERENCES.bib |only inst/shiny/server.R | 48 ++-- inst/shiny/ui.R | 19 + man/DatabaseNestingArea.Rd | 13 - man/DatabaseTSD.Rd | 71 +++--- man/DatabaseTSD.version.Rd | 8 man/GenerateAnchor.Rd | 2 man/HatchingSuccess.MHmcmc.Rd | 1 man/HatchingSuccess.MHmcmc_p.Rd | 1 man/HatchingSuccess.fit.Rd | 13 - man/HatchingSuccess.lnL.Rd | 3 man/HatchingSuccess.model.Rd | 3 man/P_TRT.Rd | 16 - man/ROSIE.Rd |only man/ROSIE.version.Rd |only man/STRN.Rd | 48 ++-- man/TSP.list.Rd | 20 - man/calibrate.datalogger.Rd | 3 man/embryogrowth-package.Rd | 68 +----- man/hist.Nests.Rd | 2 man/hist.NestsResult.Rd | 2 man/info.nests.Rd | 138 ++++++------ man/logLik.HatchingSuccess.Rd | 3 man/movement.Rd | 3 man/nest.Rd | 6 man/nobs.HatchingSuccess.Rd | 3 man/plot.HatchingSuccess.Rd | 16 - man/plot.NestsResult.Rd | 18 - man/plot.tsd.Rd | 53 ++-- man/predict.HatchingSuccess.Rd | 5 man/predict.tsd.Rd | 14 - man/resultNest_3p_Weibull.Rd | 12 - man/resultNest_4p_SSM.Rd | 6 man/resultNest_4p_normal.Rd | 8 man/resultNest_4p_transition.Rd | 8 man/resultNest_4p_trigo.Rd | 8 man/resultNest_4p_weight.Rd | 8 man/resultNest_mcmc_4p_SSM.Rd | 8 man/resultNest_mcmc_6p_SSM.Rd | 8 man/resultNest_mcmc_newp.Rd | 8 man/resultNest_newp.Rd | 8 man/searchR.Rd | 46 +--- man/stages.Rd | 28 +- man/summary.Nests.Rd | 4 man/tempConst.Rd | 4 man/tsd.Rd | 123 ++++++---- man/tsd_MHmcmc.Rd | 8 man/tsd_MHmcmc_p.Rd | 14 - man/uncertainty.datalogger.Rd | 9 84 files changed, 1669 insertions(+), 1050 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.9.0 dated 2024-08-17 and 1.9.1 dated 2024-08-23
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/help.R | 4 +--- R/trans_diff.R | 2 +- R/trans_env.R | 2 +- R/trans_func.R | 1 - R/trans_venn.R | 2 +- man/microeco.Rd | 4 +--- man/trans_diff.Rd | 4 ++-- man/trans_func.Rd | 2 -- man/trans_venn.Rd | 4 ++-- 11 files changed, 22 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-22 0.3
Title: Draw Variable-Width Lines
Description: Provides R functions to draw lines and curves with the width
of the curve allowed to vary along the length of the curve.
Author: Paul Murrell [aut, cre]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between vwline versions 0.2-2 dated 2019-07-25 and 0.2-4 dated 2024-08-23
DESCRIPTION | 12 - MD5 | 10 R/endsjoins.R | 322 ++++++++++++++++--------------- R/vwline.R | 150 ++++++++++---- inst/NEWS.rd | 10 inst/regression-tests/bug-joins.R |only inst/regression-tests/bug-joins.save.pdf |only 7 files changed, 303 insertions(+), 201 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.8-1 dated 2024-05-27 and 6.8-2 dated 2024-08-23
DESCRIPTION | 18 +++++++++++------- MD5 | 27 ++++++++++++++------------- NEWS | 4 ++++ R/impactPO.r | 4 ++-- R/validate.cph.s | 4 ++-- inst/tests/survest2.r |only man/Gls.Rd | 4 ++-- man/bj.Rd | 4 ++-- man/cph.Rd | 2 +- man/impactPO.Rd | 4 ++-- man/npsurv.Rd | 4 ++-- man/plot.Predict.Rd | 2 +- man/psm.Rd | 8 ++++---- man/residuals.cph.Rd | 4 ++-- man/survplot.Rd | 2 +- 15 files changed, 50 insertions(+), 41 deletions(-)
Title: Location Scale Standardized Distributions
Description: Location-Scale based distributions parameterized in terms of mean, standard deviation, skew and shape parameters and estimation using automatic differentiation. Distributions include the Normal, Student and GED as well as their skewed variants ('Fernandez and Steel'), the 'Johnson SU', and the Generalized Hyperbolic. Also included is the semi-parametric piece wise distribution ('spd') with Pareto tails and kernel interior.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsdistributions versions 1.0.1 dated 2024-05-13 and 1.0.2 dated 2024-08-23
tsdistributions-1.0.1/tsdistributions/src/distributions.c |only tsdistributions-1.0.1/tsdistributions/src/tsdistributions_init.c |only tsdistributions-1.0.2/tsdistributions/DESCRIPTION | 19 tsdistributions-1.0.2/tsdistributions/MD5 | 40 - tsdistributions-1.0.2/tsdistributions/NAMESPACE | 8 tsdistributions-1.0.2/tsdistributions/NEWS.md | 7 tsdistributions-1.0.2/tsdistributions/R/RcppExports.R |only tsdistributions-1.0.2/tsdistributions/R/pdqr.R | 317 ++++------ tsdistributions-1.0.2/tsdistributions/R/spd.R | 2 tsdistributions-1.0.2/tsdistributions/R/tsdistributions-package.R | 4 tsdistributions-1.0.2/tsdistributions/build/partial.rdb |binary tsdistributions-1.0.2/tsdistributions/build/vignette.rds |binary tsdistributions-1.0.2/tsdistributions/inst/doc/estimation_demo.html | 8 tsdistributions-1.0.2/tsdistributions/inst/doc/location_scale_distributions.pdf |binary tsdistributions-1.0.2/tsdistributions/inst/doc/profile_demo.html | 8 tsdistributions-1.0.2/tsdistributions/inst/doc/spd_demo.html | 24 tsdistributions-1.0.2/tsdistributions/man/gh.Rd | 2 tsdistributions-1.0.2/tsdistributions/man/ghyp.Rd |only tsdistributions-1.0.2/tsdistributions/man/spd_modelspec.Rd | 2 tsdistributions-1.0.2/tsdistributions/man/tsdistributions-package.Rd | 2 tsdistributions-1.0.2/tsdistributions/src/RcppExports.cpp |only tsdistributions-1.0.2/tsdistributions/src/TMB/tsdistributions_TMBExports.cpp | 2 tsdistributions-1.0.2/tsdistributions/src/distributions.cpp |only tsdistributions-1.0.2/tsdistributions/src/distributions.h | 207 ++---- 24 files changed, 297 insertions(+), 355 deletions(-)
More information about tsdistributions at CRAN
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Title: Open Trade Statistics API Wrapper and Utility Program
Description: Access 'Open Trade Statistics' API from R to download
international trade data.
Author: Mauricio Vargas [aut, cre, cph]
,
Joshua Kunst [ctb] ,
Alexey Kravchenko [ctb] ,
Emma Mendelsohn [ctb] ,
Daniela de los Santos [ctb] ,
Emily Riederer [rev] ,
Mark Padgham [rev] ,
Amanda Dobbyn [rev] ,
Jorge Cimentada [rev] ,
UN Comtrade [dtc],
The Wo [...truncated...]
Maintainer: Mauricio Vargas <mavargas11@uc.cl>
Diff between tradestatistics versions 4.5.0 dated 2023-06-29 and 5.0.0 dated 2024-08-23
tradestatistics-4.5.0/tradestatistics/data/ots_distances.rda |only tradestatistics-4.5.0/tradestatistics/man/ots_distances.Rd |only tradestatistics-5.0.0/tradestatistics/DESCRIPTION | 8 tradestatistics-5.0.0/tradestatistics/MD5 | 90 - tradestatistics-5.0.0/tradestatistics/NEWS.md | 9 tradestatistics-5.0.0/tradestatistics/R/ots_create_tidy_data.R | 8 tradestatistics-5.0.0/tradestatistics/R/ots_gdp_deflator_adjustment.R | 11 tradestatistics-5.0.0/tradestatistics/R/ots_read_from_api.R | 4 tradestatistics-5.0.0/tradestatistics/R/ots_strings_processing.R | 20 tradestatistics-5.0.0/tradestatistics/R/tradestatistics-package.R | 91 - tradestatistics-5.0.0/tradestatistics/build/vignette.rds |binary tradestatistics-5.0.0/tradestatistics/data/ots_commodities.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_commodities_short.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_countries.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_countries_colors.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_gdp_deflator.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_sections.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_sections_colors.rda |binary tradestatistics-5.0.0/tradestatistics/data/ots_tables.rda |binary tradestatistics-5.0.0/tradestatistics/inst/doc/basic-usage.R | 2 tradestatistics-5.0.0/tradestatistics/inst/doc/basic-usage.Rmd | 2 tradestatistics-5.0.0/tradestatistics/inst/doc/basic-usage.html | 523 ++++------ tradestatistics-5.0.0/tradestatistics/inst/references.bib | 74 - tradestatistics-5.0.0/tradestatistics/man/ots_commodities.Rd | 12 tradestatistics-5.0.0/tradestatistics/man/ots_commodities_short.Rd | 8 tradestatistics-5.0.0/tradestatistics/man/ots_countries.Rd | 12 tradestatistics-5.0.0/tradestatistics/man/ots_countries_colors.Rd | 8 tradestatistics-5.0.0/tradestatistics/man/ots_create_tidy_data.Rd | 2 tradestatistics-5.0.0/tradestatistics/man/ots_gdp_deflator.Rd | 8 tradestatistics-5.0.0/tradestatistics/man/ots_sections.Rd | 6 tradestatistics-5.0.0/tradestatistics/man/ots_sections_colors.Rd | 6 tradestatistics-5.0.0/tradestatistics/man/ots_tables.Rd | 4 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_all_2002_yrp.yml | 20 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yr.yml | 40 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yr_apple.yml | 10 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrp.yml | 10 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc.yml | 50 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_cache.yml | 20 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_fish.yml | 10 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_wheat.yml | 8 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2004_yr.yml | 10 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2004_yrpc.yml | 10 tradestatistics-5.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_myt_2002_yrp.yml | 8 tradestatistics-5.0.0/tradestatistics/tests/testthat/test-ots_create_tidy_data.R | 12 tradestatistics-5.0.0/tradestatistics/tests/testthat/test-ots_inflation_adjustment.R | 6 tradestatistics-5.0.0/tradestatistics/tests/testthat/test-ots_strings_processing.R | 4 tradestatistics-5.0.0/tradestatistics/vignettes/basic-usage.Rmd | 2 47 files changed, 543 insertions(+), 585 deletions(-)
More information about tradestatistics at CRAN
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Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.5 dated 2024-05-01 and 0.0.6 dated 2024-08-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/expect_snapshot_print.R | 5 ++++- R/utils.R | 12 +++--------- build/partial.rdb |binary 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching.
The contents include themes for plots, functions for simulating
quantities of interest from regression models, functions for simulating various
forms of fake data for instructional/research purposes, and many more. All told, the functions
provided here are broadly useful for data organization, data presentation, data recoding,
and data simulation.
Author: Steve Miller [aut, cre],
Ben Bolker [ctb],
Dave Armstrong [ctb],
John Fox [ctb],
Winston Chang [ctb],
Brian Ripley [ctb],
Bill Venables [ctb],
Pascal van Kooten [ctb],
Gerko Vink [ctb],
Paul Williamson [ctb],
Andreas Beger [ctb] ,
Vincent Arel-Bundoc [...truncated...]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevemisc versions 1.7.0 dated 2023-11-06 and 1.8.0 dated 2024-08-23
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 6 R/linloess_plot.R | 99 ++++-- R/p_z.R | 2 R/rd_plot.R | 2 README.md | 733 --------------------------------------------------- man/linloess_plot.Rd | 59 +++- man/p_z.Rd | 2 9 files changed, 136 insertions(+), 789 deletions(-)
Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation,
model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs,
correlation between graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Grover E. Castro Guzman [aut],
Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 1.0.3 dated 2024-07-26 and 1.0.4 dated 2024-08-23
statGraph-1.0.3/statGraph/R/plot.statGraph.R |only statGraph-1.0.4/statGraph/DESCRIPTION | 8 +++--- statGraph-1.0.4/statGraph/MD5 | 19 ++++++-------- statGraph-1.0.4/statGraph/NAMESPACE | 1 statGraph-1.0.4/statGraph/R/graph.cem.R | 4 +-- statGraph-1.0.4/statGraph/R/graph.hclust.R | 26 +++++++++++++------- statGraph-1.0.4/statGraph/R/graph.kmeans.R | 10 ++++--- statGraph-1.0.4/statGraph/R/graph.model.selection.R | 2 - statGraph-1.0.4/statGraph/man/graph.cem.Rd | 2 - statGraph-1.0.4/statGraph/man/graph.hclust.Rd | 11 +++++--- statGraph-1.0.4/statGraph/man/graph.kmeans.Rd | 5 ++- 11 files changed, 50 insertions(+), 38 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.7.4 dated 2024-07-08 and 0.7.5 dated 2024-08-23
DESCRIPTION | 6 - MD5 | 57 ++++++------- NAMESPACE | 1 NEWS.md | 39 +++++++++ R/RcppExports.R | 6 + R/client.R | 18 +++- R/custom_s3.R | 58 +++++++++++++ R/error.R | 2 R/handlers_rest.R | 2 R/idempotency.R | 19 ---- R/net.R | 23 ++++- R/queryutil.R | 3 R/request.R | 4 R/service.R | 9 +- R/service_parameter_helper.R | 62 ++++++-------- R/signer_v4.R | 15 --- R/time.R | 4 man/new_operation.Rd | 3 man/new_service.Rd | 6 + man/set_service_parameter.Rd | 12 +- src/RcppExports.cpp | 12 ++ src/utils.cpp | 20 ++++ src/uuid.h |only tests/testthat/test_custom_s3.R | 135 ++++++++++++++++++++++++++++++++ tests/testthat/test_dateutil.R | 36 ++++++++ tests/testthat/test_handlers_ec2query.R | 6 - tests/testthat/test_handlers_jsonrpc.R | 6 - tests/testthat/test_handlers_query.R | 3 tests/testthat/test_handlers_restjson.R | 6 - tests/testthat/test_signer_v4.R | 2 30 files changed, 443 insertions(+), 132 deletions(-)
Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between mMARCH.AC versions 2.9.2.0 dated 2023-08-16 and 2.9.4.0 dated 2024-08-23
DESCRIPTION | 12 ++--- MD5 | 26 +++++------ R/RA2.R | 2 R/module0_maincall.R | 21 +++++++-- R/module1_csv_data_transform.R | 4 - R/module2_summary.pipeline.R | 39 +++++++++-------- R/r.jive.predict.edit.R | 3 - build/vignette.rds |binary inst/doc/features.dictionary.xlsx |binary inst/doc/mMARCH.AC.html | 44 +++++++++---------- inst/template/features.dictionary.xlsx |binary inst/template/module7a_calculate_newfeatures.Rmd | 2 inst/template/module7c_runJIVE.Rmd | 52 +++++++++++++++-------- man/get_mean_sd_hour.Rd | 2 14 files changed, 121 insertions(+), 86 deletions(-)
Title: Fitting and Forecasting Gegenbauer ARMA Time Series Models
Description: Methods for estimating univariate long memory-seasonal/cyclical
Gegenbauer time series processes. See for example (2022) <doi:10.1007/s00362-022-01290-3>.
Refer to the vignette for details of fitting these processes.
Author: Richard Hunt [aut, cre]
Maintainer: Richard Hunt <maint@huntemail.id.au>
Diff between garma versions 0.9.13 dated 2023-08-19 and 0.9.20 dated 2024-08-23
garma-0.9.13/garma/R/garma_css.R |only garma-0.9.13/garma/R/garma_qml.R |only garma-0.9.13/garma/R/garma_whittle.R |only garma-0.9.13/garma/R/garma_wll.R |only garma-0.9.13/garma/R/generic_optim.R |only garma-0.9.13/garma/R/semipara.R |only garma-0.9.13/garma/man/predict2.Rd |only garma-0.9.13/garma/man/print.garma_semipara.Rd |only garma-0.9.13/garma/man/version.Rd |only garma-0.9.20/garma/DESCRIPTION | 17 garma-0.9.20/garma/MD5 | 106 + garma-0.9.20/garma/NAMESPACE | 18 garma-0.9.20/garma/NEWS.md | 10 garma-0.9.20/garma/R/AIC.R |only garma-0.9.20/garma/R/coef.R |only garma-0.9.20/garma/R/extract_arma.R |only garma-0.9.20/garma/R/fitted.R |only garma-0.9.20/garma/R/forecast.R |only garma-0.9.20/garma/R/garma-package.R | 13 garma-0.9.20/garma/R/garma_ggtsdisplay.R | 10 garma-0.9.20/garma/R/garma_main.R | 1238 ++++++++--------------- garma-0.9.20/garma/R/gg_raw_pgram.R | 28 garma-0.9.20/garma/R/ggbr_semipara.R |only garma-0.9.20/garma/R/gof.R | 22 garma-0.9.20/garma/R/internal_css_ggbr_obj.R |only garma-0.9.20/garma/R/internal_fitted_values.R |only garma-0.9.20/garma/R/internal_functions.R | 207 +++ garma-0.9.20/garma/R/internal_generic_optim.R |only garma-0.9.20/garma/R/internal_whittle_obj.R |only garma-0.9.20/garma/R/internal_wll_ggbr_obj.R |only garma-0.9.20/garma/R/logLik.R |only garma-0.9.20/garma/R/plot.R | 129 +- garma-0.9.20/garma/R/predict.R |only garma-0.9.20/garma/R/print.R | 100 - garma-0.9.20/garma/R/residuals.R |only garma-0.9.20/garma/R/tsdiag.R | 41 garma-0.9.20/garma/R/vcov.R |only garma-0.9.20/garma/build/vignette.rds |binary garma-0.9.20/garma/inst/doc/introduction.Rmd | 4 garma-0.9.20/garma/inst/doc/introduction.html | 11 garma-0.9.20/garma/inst/garma.pdf |binary garma-0.9.20/garma/man/AIC.garma_model.Rd | 4 garma-0.9.20/garma/man/autoplot.garma_model.Rd | 4 garma-0.9.20/garma/man/coef.garma_model.Rd | 2 garma-0.9.20/garma/man/extract_arma.Rd | 10 garma-0.9.20/garma/man/fitted.garma_model.Rd | 4 garma-0.9.20/garma/man/forecast.garma_model.Rd | 15 garma-0.9.20/garma/man/garma.Rd | 133 +- garma-0.9.20/garma/man/garma_ggtsdisplay.Rd | 2 garma-0.9.20/garma/man/gg_raw_pgram.Rd | 6 garma-0.9.20/garma/man/ggbr_semipara.Rd | 39 garma-0.9.20/garma/man/gof.Rd | 4 garma-0.9.20/garma/man/logLik.garma_model.Rd | 4 garma-0.9.20/garma/man/plot.garma_model.Rd | 4 garma-0.9.20/garma/man/predict.garma_model.Rd | 35 garma-0.9.20/garma/man/print.garma_model.Rd | 4 garma-0.9.20/garma/man/print.ggbr_factors.Rd | 2 garma-0.9.20/garma/man/residuals.garma_model.Rd | 2 garma-0.9.20/garma/man/summary.garma_model.Rd | 4 garma-0.9.20/garma/man/tsdiag.garma_model.Rd | 4 garma-0.9.20/garma/man/vcov.garma_model.Rd | 2 garma-0.9.20/garma/tests/testthat.R | 8 garma-0.9.20/garma/tests/testthat/_snaps |only garma-0.9.20/garma/tests/testthat/test-predict.R |only garma-0.9.20/garma/tests/testthat/test_garma.R | 260 +++- garma-0.9.20/garma/tests/testthat/test_garma2.R |only garma-0.9.20/garma/vignettes/introduction.Rmd | 4 67 files changed, 1266 insertions(+), 1244 deletions(-)
Title: Mixed Effects Cox Models
Description: Fit Cox proportional hazards models containing both
fixed and random effects. The random effects can have a general form, of which
familial interactions (a "kinship" matrix) is a particular special case.
Note that the simplest case of a mixed effects Cox model, i.e. a single random
per-group intercept, is also called a "frailty" model. The approach is based
on Ripatti and Palmgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau.terry@mayo.edu>
Diff between coxme versions 2.2-20 dated 2024-03-05 and 2.2-22 dated 2024-08-23
coxme-2.2-20/coxme/inst/NEWS.Rd.orig |only coxme-2.2-20/coxme/man/summary.coxme.Rd |only coxme-2.2-20/coxme/noweb/all.nw |only coxme-2.2-20/coxme/noweb/all.pdf |only coxme-2.2-20/coxme/noweb/all.tex |only coxme-2.2-20/coxme/noweb/code.nw |only coxme-2.2-20/coxme/noweb/test2.r |only coxme-2.2-20/coxme/src/bdsmatrix.h |only coxme-2.2-22/coxme/DESCRIPTION | 6 ++-- coxme-2.2-22/coxme/MD5 | 26 +++++++-------------- coxme-2.2-22/coxme/build/vignette.rds |binary coxme-2.2-22/coxme/inst/NEWS.Rd | 4 +++ coxme-2.2-22/coxme/inst/doc/coxme.pdf |binary coxme-2.2-22/coxme/inst/doc/laplace.pdf |binary coxme-2.2-22/coxme/inst/doc/lmekin.pdf |binary coxme-2.2-22/coxme/inst/doc/variance.pdf |binary coxme-2.2-22/coxme/src/coxfit6a.c | 32 +++++++++++++------------- coxme-2.2-22/coxme/src/coxfit6c.c | 38 +++++++++++++++---------------- 18 files changed, 51 insertions(+), 55 deletions(-)