Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-18 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-03 0.1.0
2023-07-13 0.0.2
Title: Easy, Fast, and Pretty Specification Curve Analysis
Description: Making specification curve analysis easy, fast, and pretty. It
improves upon existing offerings with additional features and 'tidyverse'
integration. Users can easily visualize and evaluate how their models behave
under different specifications with a high degree of customization. For a
description and applications of specification curve analysis see Simonsohn,
Simmons, and Nelson (2020) <doi:10.1038/s41562-020-0912-z>.
Author: Zayne Sember [aut, cre, cph]
Maintainer: Zayne Sember <zsember@ucsd.edu>
Diff between speccurvieR versions 0.3.0 dated 2024-01-24 and 0.4.0 dated 2024-09-18
DESCRIPTION | 10 - MD5 | 25 ++- NAMESPACE | 7 NEWS.md | 8 R/functions.R | 386 ++++++++++++++++++++++++++++++++++++++++++++++++ R/helpers.R | 144 ++++++++++++++++- R/speccurvieR-package.R | 5 man/figures |only man/se_boot.Rd |only man/se_compare.Rd |only 10 files changed, 565 insertions(+), 20 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In the process, causal effects, adjacency matrices, and other essential parameters of the complex biological networks, [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.2 dated 2024-03-02 and 0.0.3 dated 2024-09-18
DESCRIPTION | 8 MD5 | 29 R/NetworkMotif.R | 72 +- R/RGM.R | 520 ++++++++------- R/RcppExports.R | 182 ++--- README.md | 989 +++++++++++++++++------------- build/partial.rdb |binary man/NetworkMotif.Rd | 52 - man/RGM.Rd | 299 ++++----- man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-11-2.png |binary man/figures/README-unnamed-chunk-11-3.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |only man/figures/README-unnamed-chunk-8-1.png |binary src/Generate.cpp | 4 16 files changed, 1192 insertions(+), 963 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut] ,
Christian Kleiber [aut] ,
Achim Zeileis [aut, cre] ,
Nikolas Kuschnig [ctb] ,
R Core Team [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ivreg versions 0.6-3 dated 2024-04-20 and 0.6-4 dated 2024-09-18
DESCRIPTION | 10 MD5 | 22 +- NEWS.md | 6 R/ivregDiagnostics.R | 2 R/ivregMethods.R | 10 build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.html | 32 +-- inst/doc/ivreg.html | 277 ++++++++------------------ man/figures/README-2sls.svg | 269 +++++++++++++------------ man/figures/README-effects-1.png |binary man/figures/README-influenceplot-1.png |binary man/figures/README-qqplot-1.png |binary 12 files changed, 275 insertions(+), 353 deletions(-)
Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
Mark Clements [aut],
R Core Team [ctb]
Maintainer: Devin Incerti <devin.incerti@gmail.com>
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hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-21_7acb799340fc4819aa1be6bfa3c49f7f.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-21_7acb799340fc4819aa1be6bfa3c49f7f.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-21_7acb799340fc4819aa1be6bfa3c49f7f.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-22_15bfd3329de6a7234843bd4829e9d5aa.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-22_15bfd3329de6a7234843bd4829e9d5aa.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-22_15bfd3329de6a7234843bd4829e9d5aa.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-2_21e3ed77d8c10fbf474233dd92bd6514.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-2_21e3ed77d8c10fbf474233dd92bd6514.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-2_21e3ed77d8c10fbf474233dd92bd6514.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-3_d8c315d20ace9e6dfe0e84f24bd56312.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-3_d8c315d20ace9e6dfe0e84f24bd56312.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-3_d8c315d20ace9e6dfe0e84f24bd56312.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-4_81769f87d7d47fc1fafdcdac45e5ba48.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-4_81769f87d7d47fc1fafdcdac45e5ba48.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-4_81769f87d7d47fc1fafdcdac45e5ba48.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-5_54ef0287be3e20de5138a54e85ae434d.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-5_54ef0287be3e20de5138a54e85ae434d.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-5_54ef0287be3e20de5138a54e85ae434d.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-6_bee98aff225bf6c6b929a72c9a39bc7b.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-6_bee98aff225bf6c6b929a72c9a39bc7b.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-6_bee98aff225bf6c6b929a72c9a39bc7b.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-7_76e39a13e78a5fc2311c4adb030cdf3f.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-7_76e39a13e78a5fc2311c4adb030cdf3f.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-7_76e39a13e78a5fc2311c4adb030cdf3f.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-8_e41084ae0a945e7bce88c067e244697d.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-8_e41084ae0a945e7bce88c067e244697d.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-8_e41084ae0a945e7bce88c067e244697d.rdx |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-9_479b182feead027ca1fcaa5ebdc057af.RData |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-9_479b182feead027ca1fcaa5ebdc057af.rdb |only hesim-0.5.5/hesim/vignettes/intro_cache/html/unnamed-chunk-9_479b182feead027ca1fcaa5ebdc057af.rdx |only 171 files changed, 516 insertions(+), 405 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general adaptive three operator splitting (ATOS) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.2.0 dated 2024-07-13 and 0.3.0 dated 2024-09-18
DESCRIPTION | 16 - MD5 | 64 ++-- NAMESPACE | 4 R/atos.R | 8 R/coef.R | 3 R/fit_goscar.R |only R/fit_goscar_cv.R |only R/fit_gslope.R | 60 ++-- R/fit_gslope_cv.R | 8 R/fit_sgo.R |only R/fit_sgo_cv.R |only R/fit_sgs.R | 30 +- R/fit_sgs_cv.R | 8 R/gen_toy_data.R | 10 R/global_wrapper_code.R | 10 R/plot.R | 4 R/predict.R | 4 R/print.R | 16 - R/run_algorithm.R | 8 inst/doc/reproducible_example.html | 474 +++---------------------------------- man/as_sgs.Rd | 4 man/atos.Rd | 8 man/coef.sgs.Rd | 7 man/fit_goscar.Rd |only man/fit_goscar_cv.Rd |only man/fit_gslope.Rd | 30 +- man/fit_gslope_cv.Rd | 12 man/fit_sgo.Rd |only man/fit_sgo_cv.Rd |only man/fit_sgs.Rd | 31 +- man/fit_sgs_cv.Rd | 10 man/gen_toy_data.Rd | 10 man/plot.sgs.Rd | 8 man/predict.sgs.Rd | 8 man/print.sgs.Rd | 12 man/scaled_sgs.Rd | 4 man/sgs-package.Rd | 7 37 files changed, 296 insertions(+), 582 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
Huijuan Xu [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Teun Post [ctb],
Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 2.1.2 dated 2024-05-29 and 3.0.0 dated 2024-09-18
DESCRIPTION | 8 ++++---- MD5 | 25 ++++++++++++++----------- NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/hardReexports.R | 26 ++++++++++++++++++++++++-- R/nlmixr2CheckInstall.R | 2 +- R/utils.R | 3 +++ README.md | 21 +++++++++------------ man/foceiControl.Rd | 23 ++++++++++++++++++++++- man/nlsControl.Rd | 2 +- man/profileFixed.Rd |only man/profileFixedSingle.Rd |only man/profileLlp.Rd |only man/reexports.Rd | 2 +- man/vpcSim.Rd | 2 +- 15 files changed, 87 insertions(+), 34 deletions(-)
Title: Information Analysis for Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.3.3 dated 2024-03-20 and 3.3.5 dated 2024-09-18
DESCRIPTION | 8 - MD5 | 31 ++-- NAMESPACE | 2 R/Analyze.R | 40 +++-- R/Sbinsmth.R | 104 +++++++------ R/Sbinsmth.init.R |only R/TG_analysis.R | 13 + R/index_search.R | 7 R/make_dataList.R | 4 R/nominal_surpmat.R |only R/smooth.surp.R | 379 ++++++++++++++++++--------------------------------- R/surp.fit.R |only README.md | 11 + man/Analyze.Rd | 134 ++++++++++-------- man/Sbinsmth.Rd | 2 man/Sbinsmth.init.Rd |only man/TG_density.fd.Rd | 3 man/smooth.surp.Rd | 71 ++++----- man/surp.fit.Rd |only 19 files changed, 374 insertions(+), 435 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 2.0.9 dated 2024-05-29 and 3.0.0 dated 2024-09-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ tests/testthat/test-plots-cens.R | 2 +- tests/testthat/test-plots.R | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to
integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between toastui versions 0.3.3 dated 2024-03-28 and 0.3.4 dated 2024-09-18
DESCRIPTION | 8 MD5 | 42 - NEWS.md | 134 ++--- R/chart.R | 176 +++---- R/data.R | 8 R/datagrid.R | 6 R/grid-editor.R | 422 ++++++++--------- R/onLoad.R | 122 ++-- R/shiny.R | 254 +++++----- README.md | 156 +++--- build/vignette.rds |binary inst/doc/toastui.R | 29 - inst/doc/toastui.Rmd | 6 inst/doc/toastui.html | 790 ++++++++++++++++---------------- inst/examples/calendar-edit-schedules.R | 284 +++++------ inst/examples/calendar-popup-shiny.R | 36 - man/cal_props.Rd | 20 man/countries.Rd | 2 man/ps3_games.Rd | 2 man/rolling_stones_50.Rd | 2 man/rolling_stones_500.Rd | 2 vignettes/toastui.Rmd | 6 22 files changed, 1254 insertions(+), 1253 deletions(-)
Title: Simulate Data from R or 'JAGS' Code
Description: Generates data from R or 'JAGS' code for use in simulation
studies. The data are returned as an 'nlist::nlists' object and/or
saved to file as individual '.rds' files. Parallelization is
implemented using the 'future' package. Progress is reported using
the 'progressr' package.
Author: Audrey Beliveau [aut, cre],
Joe Thorley [aut]
Maintainer: Audrey Beliveau <audrey.beliveau@uwaterloo.ca>
Diff between sims versions 0.0.3 dated 2021-09-20 and 0.0.4 dated 2024-09-18
sims-0.0.3/sims/tests/testthat/data0000001.rds |only sims-0.0.4/sims/DESCRIPTION | 41 +- sims-0.0.4/sims/MD5 | 15 sims-0.0.4/sims/NEWS.md | 6 sims-0.0.4/sims/README.md | 5 sims-0.0.4/sims/build/vignette.rds |binary sims-0.0.4/sims/inst/doc/sims.R | 6 sims-0.0.4/sims/inst/doc/sims.html | 479 ++++++++++++++++++------- sims-0.0.4/sims/tests/testthat/test-add.R | 2 9 files changed, 386 insertions(+), 168 deletions(-)
Title: 'nonmem2rx' Converts 'NONMEM' Models to 'rxode2'
Description: 'NONMEM' has been a tool for running nonlinear mixed
effects models since the 80s and is still used today (Bauer 2019
<doi:10.1002/psp4.12404>). This tool allows you to convert
'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016)
<doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax
(Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2'
syntax requires the residual specification to be included and it
is not always translated. If available, the 'rxode2' model will
read in the 'NONMEM' data and compare the simulation for the
population model ('PRED') individual model ('IPRED') and residual
model ('IWRES') to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rx [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Philip Delff [ctb],
Gabriel Staples [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nonmem2rx versions 0.1.4 dated 2024-05-29 and 0.1.5 dated 2024-09-18
nonmem2rx-0.1.4/nonmem2rx/src/dparser3.h |only nonmem2rx-0.1.5/nonmem2rx/DESCRIPTION | 10 nonmem2rx-0.1.5/nonmem2rx/MD5 | 49 nonmem2rx-0.1.5/nonmem2rx/NEWS.md | 8 nonmem2rx-0.1.5/nonmem2rx/R/buildParser.R | 10 nonmem2rx-0.1.5/nonmem2rx/R/rxSolve.R | 87 nonmem2rx-0.1.5/nonmem2rx/R/validate.R | 39 nonmem2rx-0.1.5/nonmem2rx/R/zzz.R | 9 nonmem2rx-0.1.5/nonmem2rx/build/vignette.rds |binary nonmem2rx-0.1.5/nonmem2rx/inst/doc/import-nonmem.html | 905 +++++----- nonmem2rx-0.1.5/nonmem2rx/src/abbrec.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/abbrev.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/data.c | 4 nonmem2rx-0.1.5/nonmem2rx/src/init.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/input.c | 6 nonmem2rx-0.1.5/nonmem2rx/src/lst.c | 4 nonmem2rx-0.1.5/nonmem2rx/src/mem.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/model.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/omega.c | 10 nonmem2rx-0.1.5/nonmem2rx/src/records.c | 6 nonmem2rx-0.1.5/nonmem2rx/src/sub.c | 4 nonmem2rx-0.1.5/nonmem2rx/src/tab.c | 2 nonmem2rx-0.1.5/nonmem2rx/src/theta.c | 2 nonmem2rx-0.1.5/nonmem2rx/tests/testthat/test-external-models.R | 27 nonmem2rx-0.1.5/nonmem2rx/tests/testthat/test-omega.R | 24 nonmem2rx-0.1.5/nonmem2rx/tests/testthat/test-rxsolve.R | 6 26 files changed, 646 insertions(+), 576 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 2.0.10 dated 2024-05-29 and 3.0.0 dated 2024-09-18
DESCRIPTION | 13 ++++++------- MD5 | 25 +++++++++++++++++-------- NAMESPACE | 19 +++++++++++++++++++ NEWS.md | 4 ++++ R/computingutil.R | 6 +----- R/knit_printEquation.R | 10 ++++++++++ R/profile.R |only R/reexport.R | 4 ++++ R/utils.R |only man/fixedControl.Rd |only man/llpControl.Rd |only man/profile.nlmixr2FitCore.Rd |only man/profileFixed.Rd |only man/profileLlp.Rd |only man/profileNlmixr2FitCoreRet.Rd |only man/reexports.Rd | 3 ++- tests/testthat/test-bootstrap.R | 8 ++++---- tests/testthat/test-profile.R |only 18 files changed, 67 insertions(+), 25 deletions(-)
Title: Generalized Entropy Calibration
Description: Generalized Entropy Calibration produces calibration weights
using generalized entropy as the objective function for optimization.
This approach, as implemented in the 'GECal' package, is based on
Kwon, Kim, and Qiu (2024) <doi:10.48550/arXiv.2404.01076>. Unlike
traditional methods, 'GECal' incorporates design weights into the
constraints to maintain design consistency, rather than including
them in the objective function itself.
Author: Yonghyun Kwon [aut, cre] ,
Jae Kwang Kim [aut] ,
Yumou Qiu [aut]
Maintainer: Yonghyun Kwon <yhkwon@kma.ac.kr>
Diff between GECal versions 0.1.3 dated 2024-09-18 and 0.1.4 dated 2024-09-18
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ R/G.R | 2 +- R/GEcalib.R | 16 ++++++++-------- R/estimate.R | 2 -- man/GEcalib.Rd | 11 +++++------ man/estimate.Rd | 2 -- 7 files changed, 26 insertions(+), 30 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder [aut, cre],
Steve Horvath [aut],
Chaochao Cai [aut],
Jun Dong [aut],
Jeremy Miller [aut],
Lin Song [aut],
Andy Yip [aut],
Bin Zhang [aut]
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.72-5 dated 2023-12-07 and 1.73 dated 2024-09-18
Changelog | 14 +++++++ DESCRIPTION | 44 ++++++++++++++++++++--- MD5 | 22 ++++++----- R/empiricalBayesLM.R | 74 ++++++++++++++++++++++++++++++++++++++++ build |only man/bicor.Rd | 3 - man/chooseOneHubInEachModule.Rd | 5 +- man/chooseTopHubInEachModule.Rd | 2 - man/consensusCalculation.Rd | 2 - man/empiricalBayesLM.Rd | 2 - man/modifiedBisquareWeights.Rd |only src/parallelQuantile.cc | 2 - src/pivot.c | 4 +- 13 files changed, 146 insertions(+), 28 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.0-5 dated 2024-08-17 and 1.0-6 dated 2024-09-18
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 26 +-- R/Compris.R | 16 +- R/internal.R | 2 R/mmlt.R | 365 +++++++++++++++++++++++------------------------- demo/hcc.R | 4 demo/npn.R | 14 + demo/undernutrition.R | 4 inst/NEWS.Rd | 10 + inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary man/Compris.Rd | 8 - man/mmlt.Rd | 40 ++--- tests/bugfixes.R | 10 - tests/mmlt-Ex.R | 68 ++++---- tests/mmlt-Ex.Rout.save | 86 +++++------ tests/mmlt_ll_sc.R | 6 18 files changed, 362 insertions(+), 341 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 2.2.2 dated 2024-05-28 and 3.0.0 dated 2024-09-18
nlmixr2est-2.2.2/nlmixr2est/R/onLoad.R |only nlmixr2est-2.2.2/nlmixr2est/R/poped.R |only nlmixr2est-2.2.2/nlmixr2est/man/dot-popedFree.Rd |only nlmixr2est-2.2.2/nlmixr2est/man/dot-popedSetup.Rd |only nlmixr2est-2.2.2/nlmixr2est/man/dot-popedSolveIdME.Rd |only nlmixr2est-2.2.2/nlmixr2est/man/dot-popedSolveIdN.Rd |only nlmixr2est-2.2.2/nlmixr2est/src/poped.cpp |only nlmixr2est-2.2.2/nlmixr2est/tests/testthat/test-saem-regressor.R |only nlmixr2est-3.0.0/nlmixr2est/DESCRIPTION | 20 nlmixr2est-3.0.0/nlmixr2est/MD5 | 179 +-- nlmixr2est-3.0.0/nlmixr2est/NAMESPACE | 27 nlmixr2est-3.0.0/nlmixr2est/NEWS.md | 27 nlmixr2est-3.0.0/nlmixr2est/R/RcppExports.R | 24 nlmixr2est-3.0.0/nlmixr2est/R/addCwres.R | 14 nlmixr2est-3.0.0/nlmixr2est/R/augPred.R | 31 nlmixr2est-3.0.0/nlmixr2est/R/bobyqa.R | 7 nlmixr2est-3.0.0/nlmixr2est/R/deparse.R |only nlmixr2est-3.0.0/nlmixr2est/R/focei.R | 30 nlmixr2est-3.0.0/nlmixr2est/R/foceiControl.R | 86 + nlmixr2est-3.0.0/nlmixr2est/R/lbfgsb3c.R | 7 nlmixr2est-3.0.0/nlmixr2est/R/mu2.R | 54 - nlmixr2est-3.0.0/nlmixr2est/R/n1qn1.R | 18 nlmixr2est-3.0.0/nlmixr2est/R/newuoa.R | 7 nlmixr2est-3.0.0/nlmixr2est/R/nlm.R | 36 nlmixr2est-3.0.0/nlmixr2est/R/nlme.R | 8 nlmixr2est-3.0.0/nlmixr2est/R/nlmeRxUiGet.R | 11 nlmixr2est-3.0.0/nlmixr2est/R/nlminb.R | 7 nlmixr2est-3.0.0/nlmixr2est/R/nlmixr2.R | 2 nlmixr2est-3.0.0/nlmixr2est/R/nlmixr2Est.R | 21 nlmixr2est-3.0.0/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-3.0.0/nlmixr2est/R/nlmixr2output.R | 11 nlmixr2est-3.0.0/nlmixr2est/R/nls.R | 34 nlmixr2est-3.0.0/nlmixr2est/R/optim.R | 17 nlmixr2est-3.0.0/nlmixr2est/R/reexports.R | 4 nlmixr2est-3.0.0/nlmixr2est/R/resid.R | 93 + nlmixr2est-3.0.0/nlmixr2est/R/rxsolve.R | 67 + nlmixr2est-3.0.0/nlmixr2est/R/saem.R | 11 nlmixr2est-3.0.0/nlmixr2est/R/saemControl.R | 29 nlmixr2est-3.0.0/nlmixr2est/R/saemRxUiGet.R | 2 nlmixr2est-3.0.0/nlmixr2est/R/saemRxUiGetModel.R | 54 - nlmixr2est-3.0.0/nlmixr2est/R/sessioninfo.R |only nlmixr2est-3.0.0/nlmixr2est/R/uobyqa.R | 20 nlmixr2est-3.0.0/nlmixr2est/R/utils.R | 5 nlmixr2est-3.0.0/nlmixr2est/R/vpc.R | 15 nlmixr2est-3.0.0/nlmixr2est/R/zzz.R |only nlmixr2est-3.0.0/nlmixr2est/configure | 3 nlmixr2est-3.0.0/nlmixr2est/inst/include/nlmixr2est_RcppExports.h | 1 nlmixr2est-3.0.0/nlmixr2est/inst/tools/workaround.R | 2 nlmixr2est-3.0.0/nlmixr2est/man/dot-addPkgNlmixr2.Rd |only nlmixr2est-3.0.0/nlmixr2est/man/dot-augPredIpredModel.Rd |only nlmixr2est-3.0.0/nlmixr2est/man/dot-deparseDifferent.Rd |only nlmixr2est-3.0.0/nlmixr2est/man/dot-deparseFinal.Rd |only nlmixr2est-3.0.0/nlmixr2est/man/foceiControl.Rd | 23 nlmixr2est-3.0.0/nlmixr2est/man/nlmixr2AugPredSolve.Rd | 13 nlmixr2est-3.0.0/nlmixr2est/man/nlsControl.Rd | 2 nlmixr2est-3.0.0/nlmixr2est/man/nmNearPD.Rd | 14 nlmixr2est-3.0.0/nlmixr2est/man/reexports.Rd | 3 nlmixr2est-3.0.0/nlmixr2est/man/vpcSim.Rd | 2 nlmixr2est-3.0.0/nlmixr2est/src/Makevars.in | 2 nlmixr2est-3.0.0/nlmixr2est/src/RcppExports.cpp | 85 - nlmixr2est-3.0.0/nlmixr2est/src/armahead.h | 2 nlmixr2est-3.0.0/nlmixr2est/src/censResid.h | 29 nlmixr2est-3.0.0/nlmixr2est/src/init.c | 28 nlmixr2est-3.0.0/nlmixr2est/src/inner.cpp | 529 +++++----- nlmixr2est-3.0.0/nlmixr2est/src/inner.h | 20 nlmixr2est-3.0.0/nlmixr2est/src/nearPD.cpp | 160 --- nlmixr2est-3.0.0/nlmixr2est/src/nearPD.h | 1 nlmixr2est-3.0.0/nlmixr2est/src/nlm.cpp | 141 +- nlmixr2est-3.0.0/nlmixr2est/src/npde.cpp | 27 nlmixr2est-3.0.0/nlmixr2est/src/npde.h | 3 nlmixr2est-3.0.0/nlmixr2est/src/saem.cpp | 160 +-- nlmixr2est-3.0.0/nlmixr2est/src/scale.h | 5 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-augpred.R | 19 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-cwres.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-focei-llik.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-issue-281.R | 77 + nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-manual-back-transform.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-nlm.R | 73 + nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-nlme.R | 59 + nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-nls.R | 47 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-nmobj.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-nonmu.R | 4 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-np.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-npde.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-optim.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-resume-bobyqa.R |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-resume-bobyqa.qs |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-rx-model-props.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-rxsolve.R | 46 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-rxuideparse.R |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-aic.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-funny-mu.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-mu.R |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-no-pop.R |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-theo_sd.R | 393 +++---- nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-theo_sd.qs |binary nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-saem-translate.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-split.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-str-est.R |only nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-ui-est-change.R | 2 nlmixr2est-3.0.0/nlmixr2est/tests/testthat/test-vpcSim.R | 2 101 files changed, 1775 insertions(+), 1206 deletions(-)
Title: Scoring Rules for Parametric and Simulated Distribution
Forecasts
Description: Dictionary-like reference for computing scoring rules in a wide
range of situations. Covers both parametric forecast distributions (such as
mixtures of Gaussians) and distributions generated via simulation. Further
details can be found in the package vignettes <doi:10.18637/jss.v090.i12>,
<doi:10.18637/jss.v110.i08>.
Author: Alexander I. Jordan [aut] ,
Fabian Krueger [aut, cre] ,
Sebastian Lerch [aut] ,
Sam Allen [aut] ,
Maximiliane Graeter [ctb]
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>
Diff between scoringRules versions 1.1.2 dated 2024-09-05 and 1.1.3 dated 2024-09-18
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/scores_norm.R | 28 ++++++++++++++++++++++++++++ R/scores_sample_multiv_weighted.R | 6 ++---- R/scores_sample_univ_weighted.R | 5 ++--- R/scores_t.R | 6 +++--- inst/doc/article.pdf |binary inst/doc/article_weighted_scores.pdf |binary inst/doc/gettingstarted.pdf |binary man/scores_norm.Rd | 29 +++++++++++++++++++++++++++++ man/scores_sample_multiv_weighted.Rd | 6 ++---- man/scores_sample_univ_weighted.Rd | 5 ++--- man/scores_t.Rd | 2 +- tests/testthat/test-rps.R | 20 +++++++++++--------- tests/testthat/test-scores_quantiles.R | 2 +- 15 files changed, 99 insertions(+), 46 deletions(-)
Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics.
You can quickly visualize your data accordingly to their type, export in various formats,
and retrieve the code to reproduce the plot.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Ian Carroll [ctb] ,
Xiangnan Dang [ctb] ,
Nicolas Bevacqua [cph] ,
Daybrush [cph] ,
Zeno Rocha [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between esquisse versions 2.0.0 dated 2024-05-25 and 2.0.1 dated 2024-09-18
DESCRIPTION | 8 - MD5 | 50 ++++---- NEWS.md | 8 + R/esquisse-server.R | 2 R/esquisse-ui.R | 28 ++-- R/input-colors.R | 66 ++++++----- R/module-controls-axes.R | 13 +- R/module-controls-geoms.R | 13 +- R/module-controls-options.R | 2 R/module-controls-theme.R | 26 ++-- R/module-controls.R | 19 ++- R/module-utils.R | 2 README.md | 4 build/vignette.rds |binary inst/i18n/al.csv | 204 +++++++++++++++++++---------------- inst/i18n/cn.csv | 205 +++++++++++++++++++---------------- inst/i18n/de.csv | 204 +++++++++++++++++++---------------- inst/i18n/es.csv | 256 +++++++++++++++++++------------------------- inst/i18n/extract_labels.R |only inst/i18n/fr.csv | 208 +++++++++++++++++++---------------- inst/i18n/kr.csv | 204 +++++++++++++++++++---------------- inst/i18n/maj_csv.R |only inst/i18n/mk.csv | 204 +++++++++++++++++++---------------- inst/i18n/pl.csv | 205 +++++++++++++++++++---------------- inst/i18n/pt.csv | 203 +++++++++++++++++++--------------- inst/i18n/tr.csv | 204 +++++++++++++++++++---------------- man/esquisse-module.Rd | 2 27 files changed, 1281 insertions(+), 1059 deletions(-)
Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>)
by geography, state, measure, and release year. This package also contains a
function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>
Diff between CDCPLACES versions 1.1.7 dated 2024-08-26 and 1.1.8 dated 2024-09-18
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- NEWS.md | 9 +++++-- R/get_places.R | 65 ++++++++++++++++++++++++++++++++++++------------------ R/sysdata.rda |binary man/get_places.Rd | 12 +++++++-- 6 files changed, 68 insertions(+), 34 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.1.3 dated 2024-05-28 and 3.0.0 dated 2024-09-18
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rxode2-3.0.0/rxode2/R/modelExtract.R | 39 rxode2-3.0.0/rxode2/R/modlib.R | 2 rxode2-3.0.0/rxode2/R/parseFuns.R |only rxode2-3.0.0/rxode2/R/piping-ini.R | 161 rxode2-3.0.0/rxode2/R/piping-model.R | 5 rxode2-3.0.0/rxode2/R/piping.R | 122 rxode2-3.0.0/rxode2/R/print.R | 133 rxode2-3.0.0/rxode2/R/reexport.R | 174 rxode2-3.0.0/rxode2/R/register-s3.R |only rxode2-3.0.0/rxode2/R/rudf.R |only rxode2-3.0.0/rxode2/R/rxCbindStudyIndividual.R |only rxode2-3.0.0/rxode2/R/rxParams.R | 44 rxode2-3.0.0/rxode2/R/rxParseSuppressMsg.R |only rxode2-3.0.0/rxode2/R/rxPrune.R | 111 rxode2-3.0.0/rxode2/R/rxReq.R |only rxode2-3.0.0/rxode2/R/rxStack.R |only rxode2-3.0.0/rxode2/R/rxSymInv.R | 1 rxode2-3.0.0/rxode2/R/rxSyntaxFunctions.R | 2 rxode2-3.0.0/rxode2/R/rxUiGet.R | 119 rxode2-3.0.0/rxode2/R/rxValidate.R | 5 rxode2-3.0.0/rxode2/R/rxode-options.R | 77 rxode2-3.0.0/rxode2/R/rxode2.R | 24 rxode2-3.0.0/rxode2/R/rxode2_md5.R | 2 rxode2-3.0.0/rxode2/R/rxrandom.R | 543 + rxode2-3.0.0/rxode2/R/rxsolve.R | 322 rxode2-3.0.0/rxode2/R/symengine.R | 198 rxode2-3.0.0/rxode2/R/tran.R |only rxode2-3.0.0/rxode2/R/ui-assign-parts.R | 1 rxode2-3.0.0/rxode2/R/ui.R | 33 rxode2-3.0.0/rxode2/R/utils.R | 421 + rxode2-3.0.0/rxode2/README.md | 19 rxode2-3.0.0/rxode2/build/partial.rdb |only rxode2-3.0.0/rxode2/build/vignette.rds |binary rxode2-3.0.0/rxode2/data/rxReservedKeywords.rda |binary rxode2-3.0.0/rxode2/data/rxResidualError.rda |binary rxode2-3.0.0/rxode2/data/rxSyntaxFunctions.rda |binary rxode2-3.0.0/rxode2/inst/CITATION | 5 rxode2-3.0.0/rxode2/inst/doc/rxode2-syntax.html | 324 rxode2-3.0.0/rxode2/inst/include/rxode2.h | 41 rxode2-3.0.0/rxode2/inst/include/rxode2_RcppExports.h | 22 rxode2-3.0.0/rxode2/inst/include/rxode2_control.h | 8 rxode2-3.0.0/rxode2/inst/include/rxode2_model_shared.c |only rxode2-3.0.0/rxode2/inst/include/rxode2_model_shared.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parse.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parseGetTime.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parseHandleEvid.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parseSbuf.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parseStruct.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parseVer.h |only rxode2-3.0.0/rxode2/inst/include/rxode2parse_control.h |only rxode2-3.0.0/rxode2/inst/include/rxode2ptr.h |only rxode2-3.0.0/rxode2/inst/include/rxode2random_fillVec.h |only rxode2-3.0.0/rxode2/inst/include/sbuf.c |only rxode2-3.0.0/rxode2/inst/po/en@quot/LC_MESSAGES/R-rxode2.mo |binary rxode2-3.0.0/rxode2/inst/tools/workaround.R | 144 rxode2-3.0.0/rxode2/inst/tran.g | 39 rxode2-3.0.0/rxode2/man/add.dosing.Rd |only rxode2-3.0.0/rxode2/man/add.sampling.Rd |only rxode2-3.0.0/rxode2/man/as.et.Rd |only rxode2-3.0.0/rxode2/man/assertCompartmentExists.Rd |only rxode2-3.0.0/rxode2/man/assertCompartmentName.Rd |only rxode2-3.0.0/rxode2/man/assertCompartmentNew.Rd |only rxode2-3.0.0/rxode2/man/assertRxUi.Rd | 32 rxode2-3.0.0/rxode2/man/assertVariableExists.Rd |only rxode2-3.0.0/rxode2/man/assertVariableNew.Rd |only rxode2-3.0.0/rxode2/man/boxCox.Rd |only rxode2-3.0.0/rxode2/man/cvPost.Rd |only rxode2-3.0.0/rxode2/man/dfWishart.Rd |only rxode2-3.0.0/rxode2/man/dot-cbindOme.Rd |only rxode2-3.0.0/rxode2/man/dot-clearPipe.Rd |only rxode2-3.0.0/rxode2/man/dot-collectWarnings.Rd |only rxode2-3.0.0/rxode2/man/dot-convertId.Rd |only rxode2-3.0.0/rxode2/man/dot-expandPars.Rd |only rxode2-3.0.0/rxode2/man/dot-extraC.Rd |only rxode2-3.0.0/rxode2/man/dot-extraCnow.Rd |only rxode2-3.0.0/rxode2/man/dot-getLastIdLvl.Rd |only rxode2-3.0.0/rxode2/man/dot-getWh.Rd |only rxode2-3.0.0/rxode2/man/dot-linCmtSensB.Rd |only rxode2-3.0.0/rxode2/man/dot-pipeRx.Rd |only rxode2-3.0.0/rxode2/man/dot-rxC.Rd |only rxode2-3.0.0/rxode2/man/dot-rxPrune.Rd | 4 rxode2-3.0.0/rxode2/man/dot-rxSEeqUsr.Rd |only rxode2-3.0.0/rxode2/man/dot-rxTransInfo.Rd |only rxode2-3.0.0/rxode2/man/dot-rxTransform.Rd |only rxode2-3.0.0/rxode2/man/dot-rxode2ptrs.Rd |only rxode2-3.0.0/rxode2/man/dot-s3register.Rd |only rxode2-3.0.0/rxode2/man/dot-symengineFs.Rd |only rxode2-3.0.0/rxode2/man/dot-toClassicEvid.Rd |only rxode2-3.0.0/rxode2/man/dot-udfCallFunArg.Rd |only rxode2-3.0.0/rxode2/man/dot-udfEnvReset.Rd |only rxode2-3.0.0/rxode2/man/dot-udfEnvSet.Rd |only rxode2-3.0.0/rxode2/man/dot-udfEnvSetUdf.Rd |only rxode2-3.0.0/rxode2/man/dot-udfExists.Rd |only rxode2-3.0.0/rxode2/man/dot-udfMd5Info.Rd |only rxode2-3.0.0/rxode2/man/dot-vecDf.Rd |only rxode2-3.0.0/rxode2/man/et.Rd |only rxode2-3.0.0/rxode2/man/etExpand.Rd |only rxode2-3.0.0/rxode2/man/etRbind.Rd |only rxode2-3.0.0/rxode2/man/etRep.Rd |only rxode2-3.0.0/rxode2/man/etSeq.Rd |only rxode2-3.0.0/rxode2/man/etTrans.Rd | 9 rxode2-3.0.0/rxode2/man/eventTable.Rd |only rxode2-3.0.0/rxode2/man/forderForceBase.Rd |only rxode2-3.0.0/rxode2/man/ini.Rd | 26 rxode2-3.0.0/rxode2/man/invWR1d.Rd |only rxode2-3.0.0/rxode2/man/is.rxEt.Rd |only rxode2-3.0.0/rxode2/man/is.rxStackData.Rd |only rxode2-3.0.0/rxode2/man/logit.Rd | 1 rxode2-3.0.0/rxode2/man/phi.Rd |only rxode2-3.0.0/rxode2/man/print.rxModelVars.Rd |only rxode2-3.0.0/rxode2/man/rLKJ1.Rd |only rxode2-3.0.0/rxode2/man/reexports.Rd | 45 rxode2-3.0.0/rxode2/man/rinvchisq.Rd |only rxode2-3.0.0/rxode2/man/rmdhunks/rxode2-syntax-hunk.Rmd | 90 rxode2-3.0.0/rxode2/man/rxCbindStudyIndividual.Rd |only rxode2-3.0.0/rxode2/man/rxCombineErrorLines.Rd | 9 rxode2-3.0.0/rxode2/man/rxDerived.Rd |only rxode2-3.0.0/rxode2/man/rxEtDispatchSolve.Rd |only rxode2-3.0.0/rxode2/man/rxEvid.Rd |only rxode2-3.0.0/rxode2/man/rxFun.Rd | 19 rxode2-3.0.0/rxode2/man/rxFunParse.Rd |only rxode2-3.0.0/rxode2/man/rxGetSeed.Rd |only rxode2-3.0.0/rxode2/man/rxIs.Rd | 12 rxode2-3.0.0/rxode2/man/rxParams.Rd | 3 rxode2-3.0.0/rxode2/man/rxParseSetSilentErr.Rd |only rxode2-3.0.0/rxode2/man/rxParseSuppressMsg.Rd |only rxode2-3.0.0/rxode2/man/rxRateDur.Rd |only rxode2-3.0.0/rxode2/man/rxReq.Rd |only rxode2-3.0.0/rxode2/man/rxRmvn.Rd |only rxode2-3.0.0/rxode2/man/rxSeedEng.Rd |only rxode2-3.0.0/rxode2/man/rxSetIni0.Rd |only rxode2-3.0.0/rxode2/man/rxSetSeed.Rd |only rxode2-3.0.0/rxode2/man/rxSolve.Rd | 53 rxode2-3.0.0/rxode2/man/rxStack.Rd |only rxode2-3.0.0/rxode2/man/rxSyntaxFunctions.Rd | 2 rxode2-3.0.0/rxode2/man/rxUiDeparse.Rd |only rxode2-3.0.0/rxode2/man/rxUiGet.Rd | 19 rxode2-3.0.0/rxode2/man/rxWithSeed.Rd |only rxode2-3.0.0/rxode2/man/rxode2.Rd | 123 rxode2-3.0.0/rxode2/man/rxode2parse.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseAssignPackagesToLoad.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseAssignPointerTranslation.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseAssignTranslation.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseD.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseGetPointerAssignment.Rd |only rxode2-3.0.0/rxode2/man/rxode2parseGetTranslation.Rd |only rxode2-3.0.0/rxode2/man/stat_amt.Rd | 47 rxode2-3.0.0/rxode2/man/stat_cens.Rd | 47 rxode2-3.0.0/rxode2/man/swapMatListWithCube.Rd |only rxode2-3.0.0/rxode2/man/testRxLinCmt.Rd |only rxode2-3.0.0/rxode2/man/testRxUnbounded.Rd |only rxode2-3.0.0/rxode2/man/toTrialDuration.Rd |only rxode2-3.0.0/rxode2/po/R-rxode2.pot | 272 rxode2-3.0.0/rxode2/po/rxode2.pot | 1156 ++- rxode2-3.0.0/rxode2/po/zh_CN.po | 1794 ++-- rxode2-3.0.0/rxode2/src/Makevars.in | 8 rxode2-3.0.0/rxode2/src/RcppExports.cpp | 781 +- rxode2-3.0.0/rxode2/src/approx.c | 145 rxode2-3.0.0/rxode2/src/call_dvode.c | 13 rxode2-3.0.0/rxode2/src/cbindThetaOmega.cpp |only rxode2-3.0.0/rxode2/src/checkmate.cpp |only rxode2-3.0.0/rxode2/src/checkmate.h | 20 rxode2-3.0.0/rxode2/src/checkmate_stub.c |only rxode2-3.0.0/rxode2/src/codegen.c |only rxode2-3.0.0/rxode2/src/codegen.h |only rxode2-3.0.0/rxode2/src/codegen2.h |only rxode2-3.0.0/rxode2/src/cvPost.cpp |only rxode2-3.0.0/rxode2/src/et.cpp |only rxode2-3.0.0/rxode2/src/etTran.cpp | 2746 +++++++ rxode2-3.0.0/rxode2/src/expm.cpp | 1 rxode2-3.0.0/rxode2/src/fast_factor.cpp |only rxode2-3.0.0/rxode2/src/genModelVars.c |only rxode2-3.0.0/rxode2/src/genModelVars.h |only rxode2-3.0.0/rxode2/src/getOption.c |only rxode2-3.0.0/rxode2/src/getOption.h |only rxode2-3.0.0/rxode2/src/handle_evid.c | 2 rxode2-3.0.0/rxode2/src/init.c | 446 - rxode2-3.0.0/rxode2/src/isEt.c |only rxode2-3.0.0/rxode2/src/lincmt.c |only rxode2-3.0.0/rxode2/src/lincmtB.cpp |only rxode2-3.0.0/rxode2/src/lincmtB1.h |only rxode2-3.0.0/rxode2/src/nearPD.cpp | 17 rxode2-3.0.0/rxode2/src/needSortDefines.h | 4 rxode2-3.0.0/rxode2/src/par_solve.cpp | 99 rxode2-3.0.0/rxode2/src/par_solve.h | 10 rxode2-3.0.0/rxode2/src/parseAllowAssign.h |only rxode2-3.0.0/rxode2/src/parseAssignStr.h |only rxode2-3.0.0/rxode2/src/parseCmtProperties.h |only rxode2-3.0.0/rxode2/src/parseDdt.h |only rxode2-3.0.0/rxode2/src/parseDfdy.h |only rxode2-3.0.0/rxode2/src/parseFuns.h |only rxode2-3.0.0/rxode2/src/parseFunsDiff.h |only rxode2-3.0.0/rxode2/src/parseFunsDosing.h |only rxode2-3.0.0/rxode2/src/parseFunsLinCmt.h |only rxode2-3.0.0/rxode2/src/parseFunsNa.h |only rxode2-3.0.0/rxode2/src/parseFunsRandom.h |only rxode2-3.0.0/rxode2/src/parseIdentifier.h |only rxode2-3.0.0/rxode2/src/parseIndLin.h |only rxode2-3.0.0/rxode2/src/parseLevels.h |only rxode2-3.0.0/rxode2/src/parseLinCmt.c |only rxode2-3.0.0/rxode2/src/parseLinCmt.h |only rxode2-3.0.0/rxode2/src/parseLinCmtAB.h |only rxode2-3.0.0/rxode2/src/parseLinCmtAdjustPars.h |only rxode2-3.0.0/rxode2/src/parseLinCmtCl.h |only rxode2-3.0.0/rxode2/src/parseLinCmtTransAlpha.h |only rxode2-3.0.0/rxode2/src/parseLinCmtTransCl.h |only rxode2-3.0.0/rxode2/src/parseLinCmtTransK.h |only rxode2-3.0.0/rxode2/src/parseLinCmtV.h |only rxode2-3.0.0/rxode2/src/parseLogical.h |only rxode2-3.0.0/rxode2/src/parseStatements.h |only rxode2-3.0.0/rxode2/src/parseSyntaxErrors.h |only rxode2-3.0.0/rxode2/src/parseVars.h |only rxode2-3.0.0/rxode2/src/print_node.c |only rxode2-3.0.0/rxode2/src/print_node.h |only rxode2-3.0.0/rxode2/src/qs.cpp |only rxode2-3.0.0/rxode2/src/rx2api.c |only rxode2-3.0.0/rxode2/src/rx2api.h |only rxode2-3.0.0/rxode2/src/rxData.cpp | 613 + rxode2-3.0.0/rxode2/src/rxData.h | 2 rxode2-3.0.0/rxode2/src/rxInv.cpp | 10 rxode2-3.0.0/rxode2/src/rxStack.cpp |only rxode2-3.0.0/rxode2/src/rxode2_df.cpp | 72 rxode2-3.0.0/rxode2/src/rxthreefry.cpp |only rxode2-3.0.0/rxode2/src/rxthreefry.h |only rxode2-3.0.0/rxode2/src/sbuf.c | 36 rxode2-3.0.0/rxode2/src/seed.cpp |only rxode2-3.0.0/rxode2/src/seed.h | 14 rxode2-3.0.0/rxode2/src/strncmpi.c |only rxode2-3.0.0/rxode2/src/strncmpi.h |only rxode2-3.0.0/rxode2/src/timsort.h |only rxode2-3.0.0/rxode2/src/tran.c |only rxode2-3.0.0/rxode2/src/tran.g.d_parser.h |only rxode2-3.0.0/rxode2/src/tran.h |only rxode2-3.0.0/rxode2/src/udf.cpp |only rxode2-3.0.0/rxode2/src/utilc.c | 341 rxode2-3.0.0/rxode2/src/utilcpp.cpp | 66 rxode2-3.0.0/rxode2/tests/testthat/etTrans-drop.qs |only rxode2-3.0.0/rxode2/tests/testthat/keep-756.qs |only rxode2-3.0.0/rxode2/tests/testthat/test-000-modelVars.R | 6 rxode2-3.0.0/rxode2/tests/testthat/test-as-ini.R | 140 rxode2-3.0.0/rxode2/tests/testthat/test-as-model.R | 112 rxode2-3.0.0/rxode2/tests/testthat/test-assert.R | 193 rxode2-3.0.0/rxode2/tests/testthat/test-assignReserved.R |only rxode2-3.0.0/rxode2/tests/testthat/test-backward.R | 8 rxode2-3.0.0/rxode2/tests/testthat/test-binomProb.R | 314 rxode2-3.0.0/rxode2/tests/testthat/test-cholperm.R |only rxode2-3.0.0/rxode2/tests/testthat/test-cmt-order.R | 129 rxode2-3.0.0/rxode2/tests/testthat/test-convertId.R | 1 rxode2-3.0.0/rxode2/tests/testthat/test-cov.R | 254 rxode2-3.0.0/rxode2/tests/testthat/test-derived.R | 5 rxode2-3.0.0/rxode2/tests/testthat/test-dfRep.R | 108 rxode2-3.0.0/rxode2/tests/testthat/test-dollar-names.R | 17 rxode2-3.0.0/rxode2/tests/testthat/test-dsl.R | 29 rxode2-3.0.0/rxode2/tests/testthat/test-et.R |only rxode2-3.0.0/rxode2/tests/testthat/test-etTrans-1.qs |only rxode2-3.0.0/rxode2/tests/testthat/test-etTrans-780.qs |only rxode2-3.0.0/rxode2/tests/testthat/test-etTrans.R | 1383 +++ rxode2-3.0.0/rxode2/tests/testthat/test-example-3-1.R | 78 rxode2-3.0.0/rxode2/tests/testthat/test-example-3-3.R | 34 rxode2-3.0.0/rxode2/tests/testthat/test-factorial.R | 36 rxode2-3.0.0/rxode2/tests/testthat/test-geom-amt.R | 54 rxode2-3.0.0/rxode2/tests/testthat/test-getindex.R | 30 rxode2-3.0.0/rxode2/tests/testthat/test-iCov.R | 92 rxode2-3.0.0/rxode2/tests/testthat/test-ignore-state.R | 349 rxode2-3.0.0/rxode2/tests/testthat/test-infusion-bolus.R | 100 rxode2-3.0.0/rxode2/tests/testthat/test-interp.R |only rxode2-3.0.0/rxode2/tests/testthat/test-keep.R | 367 rxode2-3.0.0/rxode2/tests/testthat/test-lag.R | 203 rxode2-3.0.0/rxode2/tests/testthat/test-lhs-str.R |only rxode2-3.0.0/rxode2/tests/testthat/test-lincmt-solve.R | 2 rxode2-3.0.0/rxode2/tests/testthat/test-lock.R | 78 rxode2-3.0.0/rxode2/tests/testthat/test-logical.R | 38 rxode2-3.0.0/rxode2/tests/testthat/test-logit.R | 15 rxode2-3.0.0/rxode2/tests/testthat/test-mdv.R | 54 rxode2-3.0.0/rxode2/tests/testthat/test-meanProb.R | 172 rxode2-3.0.0/rxode2/tests/testthat/test-mtime.R | 68 rxode2-3.0.0/rxode2/tests/testthat/test-mu2.R | 112 rxode2-3.0.0/rxode2/tests/testthat/test-nearpd.R | 5 rxode2-3.0.0/rxode2/tests/testthat/test-newind.R | 80 rxode2-3.0.0/rxode2/tests/testthat/test-nmtest.R | 298 rxode2-3.0.0/rxode2/tests/testthat/test-npde-mac.R | 2 rxode2-3.0.0/rxode2/tests/testthat/test-occ.R | 75 rxode2-3.0.0/rxode2/tests/testthat/test-omegaCubeConvert.R |only rxode2-3.0.0/rxode2/tests/testthat/test-omegaRse.R |only rxode2-3.0.0/rxode2/tests/testthat/test-par-solve.R | 21 rxode2-3.0.0/rxode2/tests/testthat/test-parsing.R | 735 + rxode2-3.0.0/rxode2/tests/testthat/test-pheno.R | 18 rxode2-3.0.0/rxode2/tests/testthat/test-piping-ini.R | 1613 ++-- rxode2-3.0.0/rxode2/tests/testthat/test-random.R | 104 rxode2-3.0.0/rxode2/tests/testthat/test-resample.R | 33 rxode2-3.0.0/rxode2/tests/testthat/test-rhs.R | 94 rxode2-3.0.0/rxode2/tests/testthat/test-rlkj.R | 652 - rxode2-3.0.0/rxode2/tests/testthat/test-rxFix.R | 260 rxode2-3.0.0/rxode2/tests/testthat/test-rxUiDeparse.R |only rxode2-3.0.0/rxode2/tests/testthat/test-rxode-issue-349.R | 9 rxode2-3.0.0/rxode2/tests/testthat/test-rxode-issue-375.R | 56 rxode2-3.0.0/rxode2/tests/testthat/test-safeZero.R |only rxode2-3.0.0/rxode2/tests/testthat/test-statePropDf.R |only rxode2-3.0.0/rxode2/tests/testthat/test-strncmpi.R |only rxode2-3.0.0/rxode2/tests/testthat/test-symmetric.R | 2 rxode2-3.0.0/rxode2/tests/testthat/test-tad.R | 286 rxode2-3.0.0/rxode2/tests/testthat/test-udf.R | 31 rxode2-3.0.0/rxode2/tests/testthat/test-ui-modelExtract.R | 52 rxode2-3.0.0/rxode2/tests/testthat/test-ui-piping.R | 3774 +++++----- rxode2-3.0.0/rxode2/tests/testthat/test-ui-props.R |only 330 files changed, 19884 insertions(+), 7558 deletions(-)
Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics.
Groups individual data, merges registry data and population data, calculates age-specific rate, age-standardized rate, cumulative risk, estimated annual percentage rate with standards error. Creates graphics across variable and
time, such as age-specific trends, bar chart and period-cohort trends.
Author: Mathieu Laversanne [aut, cre],
Jerome Vignat [aut],
Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.who.int>
Diff between Rcan versions 1.3.82 dated 2020-05-19 and 1.3.90 dated 2024-09-18
Rcan-1.3.82/Rcan/data/csu_CI5XI_data.rda |only Rcan-1.3.82/Rcan/man/csu_CI5XI_data.Rd |only Rcan-1.3.90/Rcan/DESCRIPTION | 14 +-- Rcan-1.3.90/Rcan/MD5 | 46 ++++++------ Rcan-1.3.90/Rcan/NAMESPACE | 2 Rcan-1.3.90/Rcan/R/csu_ageSpecific.r | 2 Rcan-1.3.90/Rcan/R/csu_cumrisk.R | 78 ++++++++++---------- Rcan-1.3.90/Rcan/R/helper.r | 82 +++++++++++++++------- Rcan-1.3.90/Rcan/R/zzz.R | 4 - Rcan-1.3.90/Rcan/build/partial.rdb |binary Rcan-1.3.90/Rcan/data/csu_CI5XII_data.rda |only Rcan-1.3.90/Rcan/data/csu_ci5_mean.rda |binary Rcan-1.3.90/Rcan/data/datalist | 2 Rcan-1.3.90/Rcan/inst/testdata/csu_eapc_test1.rds |binary Rcan-1.3.90/Rcan/man/ICD_group_CI5.Rd | 2 Rcan-1.3.90/Rcan/man/Rcan-package.Rd | 4 - Rcan-1.3.90/Rcan/man/csu_CI5XII_data.Rd |only Rcan-1.3.90/Rcan/man/csu_ageSpecific.Rd | 10 +- Rcan-1.3.90/Rcan/man/csu_ageSpecific_top.Rd | 14 +-- Rcan-1.3.90/Rcan/man/csu_ci5_mean.Rd | 6 - Rcan-1.3.90/Rcan/man/csu_eapc.Rd | 2 Rcan-1.3.90/Rcan/man/csu_registry_data_1.Rd | 2 Rcan-1.3.90/Rcan/man/csu_registry_data_2.Rd | 2 Rcan-1.3.90/Rcan/man/csu_time_trend.Rd | 2 Rcan-1.3.90/Rcan/man/csu_trendCohortPeriod.Rd | 2 Rcan-1.3.90/Rcan/tests/testthat/test-Rcan.R | 2 26 files changed, 156 insertions(+), 122 deletions(-)
Title: Download Flight and Airport Data from Brazil
Description: Download flight and airport data from Brazil’s Civil Aviation Agency
(ANAC) <https://www.gov.br/anac/pt-br>. The data includes detailed
information on all aircrafts, aerodromes, airports, and airport
movements registered in ANAC, on airfares and on every international
flight to and from Brazil, as well as domestic flights within the country.
Author: Rafael H. M. Pereira [aut, cre]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between flightsbr versions 0.4.1 dated 2024-04-23 and 0.5.0 dated 2024-09-18
DESCRIPTION | 14 MD5 | 88 - NEWS.md | 18 R/flightsbr.R | 2 R/read_aircrafts.R | 91 - R/read_airport_movements.R | 84 - R/read_airports.R | 126 +- R/read_flights.R | 99 - R/utils.R | 691 ------------- R/utils_aircrafts.R |only R/utils_airfares.R |only R/utils_airport_movement.R |only R/utils_flightst.R |only build/vignette.rds |binary inst/doc/airports.html | 2 inst/doc/flights.R | 48 inst/doc/flights.Rmd | 48 inst/doc/flights.html | 74 - inst/doc/intro_flightsbr.html | 2 inst/img/vig_output_flights.png |binary man/download_aircrafts_data.Rd | 7 man/download_airfares_data.Rd | 2 man/download_airport_movement_data.Rd | 8 man/download_flights_data.Rd | 2 man/download_flightsbr_file.Rd | 7 man/flightsbr.Rd | 2 man/generate_all_months.Rd | 9 man/get_aircrafts_dates_available.Rd | 2 man/get_aircrafts_url.Rd | 10 man/get_airfares_dates_available.Rd | 2 man/get_airfares_url.Rd | 2 man/get_airport_movement_dates_available.Rd | 9 man/get_airport_movements_url.Rd | 11 man/get_flight_dates_available.Rd | 2 man/get_flights_url.Rd | 13 man/read_aircrafts.Rd | 13 man/read_airfares.Rd | 3 man/read_airport_movements.Rd | 3 man/read_airports.Rd | 6 man/read_flights.Rd | 2 man/roxygen/templates/date.R | 3 tests/testthat/test_get_airport_movement_dates_available.R | 4 tests/testthat/test_read_aircrafts.R | 10 tests/testthat/test_read_airport_movements.R | 18 tests/testthat/test_read_airports.R | 1 tests/testthat/test_read_flights.R | 1 vignettes/flights.Rmd | 48 47 files changed, 465 insertions(+), 1122 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong [aut],
Dirk Eddelbuettel [aut, cre] ,
John Laing [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.14 dated 2022-10-06 and 0.3.15 dated 2024-09-18
ChangeLog | 76 DESCRIPTION | 28 MD5 | 126 - R/bsrch.R | 2 R/lookup.R | 1 README.md | 41 build/vignette.rds |binary configure | 23 inst/NEWS.Rd | 25 inst/doc/rblpapi-intro.html | 275 +- inst/doc/rblpapi-intro.md | 10 inst/include/blpapi_abstractsession.h | 987 ++++++---- inst/include/blpapi_authoptions.h |only inst/include/blpapi_call.h | 434 ++-- inst/include/blpapi_constant.h | 673 +++--- inst/include/blpapi_correlationid.h | 658 +++--- inst/include/blpapi_datetime.h | 2780 ++++++++++++++-------------- inst/include/blpapi_defs.h | 188 + inst/include/blpapi_diagnosticsutil.h | 93 inst/include/blpapi_dispatchtbl.h | 758 ++++++- inst/include/blpapi_element.h | 2940 ++++++++++++++++-------------- inst/include/blpapi_error.h | 106 - inst/include/blpapi_event.h | 840 +++++--- inst/include/blpapi_eventdispatcher.h | 170 + inst/include/blpapi_eventformatter.h | 1951 +++++++++++++------ inst/include/blpapi_exception.h | 539 +++-- inst/include/blpapi_highresolutionclock.h | 94 inst/include/blpapi_identity.h | 396 ++-- inst/include/blpapi_logging.h | 220 +- inst/include/blpapi_message.h | 819 +++++--- inst/include/blpapi_messageformatter.h |only inst/include/blpapi_name.h | 507 ++--- inst/include/blpapi_names.h |only inst/include/blpapi_providersession.h | 1749 ++++++++++------- inst/include/blpapi_request.h | 789 ++++---- inst/include/blpapi_requesttemplate.h |only inst/include/blpapi_resolutionlist.h | 627 +++--- inst/include/blpapi_schema.h | 868 ++++---- inst/include/blpapi_service.h | 934 +++++---- inst/include/blpapi_session.h | 1795 +++++++++++------- inst/include/blpapi_sessionoptions.h | 1395 +++++++++----- inst/include/blpapi_socks5config.h |only inst/include/blpapi_streamproxy.h | 91 inst/include/blpapi_subscriptionlist.h | 762 ++++--- inst/include/blpapi_testutil.h |only inst/include/blpapi_timepoint.h | 156 + inst/include/blpapi_tlsoptions.h |only inst/include/blpapi_topic.h | 219 +- inst/include/blpapi_topiclist.h | 453 ++-- inst/include/blpapi_types.h | 528 ++++- inst/include/blpapi_versioninfo.h | 397 ++-- inst/include/blpapi_versionmacros.h | 57 inst/include/blpapi_zfputil.h |only man/bsrch.Rd | 2 src/Makevars.in | 8 src/Makevars.win | 9 src/authenticate.cpp | 20 src/bdh.cpp | 20 src/bdp.cpp | 12 src/bds.cpp | 24 src/beqs.cpp | 38 src/blpapi_utils.cpp | 53 src/bsrch.cpp | 18 src/fieldsearch.cpp | 9 src/getBars.cpp | 16 src/getTicks.cpp | 28 src/lookup.cpp | 15 vignettes/rblpapi-intro.md | 10 68 files changed, 16080 insertions(+), 10782 deletions(-)
Title: Query the Breeding Management System(s)
Description: This R package assists breeders in linking data systems with their analytic pipelines,
a crucial step in digitizing breeding processes. It supports querying and retrieving
phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>,
'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and
'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls).
Extra helper functions support environmental data sources, including
'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO'
'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Author: Khaled Al-Shamaa [aut, cre],
Mariano Omar Crimi [ctb],
Zakaria Kehel [ctb],
Johan Aparicio [ctb],
ICARDA [cph]
Maintainer: Khaled Al-Shamaa <k.el-shamaa@cgiar.org>
Diff between QBMS versions 1.0.0 dated 2024-03-07 and 1.5.0 dated 2024-09-18
DESCRIPTION | 14 MD5 | 170 + NAMESPACE | 3 NEWS.md | 38 R/auth.R |only R/brapi.R |only R/gigwa.R |only R/http.R |only R/hwsd.R |only R/pedigree.R |only R/qbms.R | 2998 ++-------------------------------- R/terraclimate.R |only README.md | 56 build/partial.rdb |binary build/vignette.rds |binary inst/doc/bms_example.Rmd | 8 inst/doc/bms_example.html | 146 - inst/doc/breedbase_example.Rmd | 6 inst/doc/breedbase_example.html | 125 - inst/doc/ebs_example.Rmd | 6 inst/doc/ebs_example.html | 105 - inst/doc/gigwa_example.Rmd | 54 inst/doc/gigwa_example.html | 195 +- inst/doc/hwsd2_example.Rmd | 6 inst/doc/hwsd2_example.html | 89 - inst/doc/terraclimate_example.Rmd | 17 inst/doc/terraclimate_example.html | 102 - man/brapi_get_call.Rd | 24 man/brapi_headers.Rd | 28 man/brapi_map.Rd |only man/brapi_post_search_allelematrix.Rd |only man/brapi_post_search_call.Rd |only man/build_pedigree_table.Rd | 18 man/calc_biovars.Rd | 89 - man/debug_qbms.Rd | 16 man/get_async_page.Rd | 19 man/get_async_pages.Rd | 20 man/get_brapi_url.Rd |only man/get_germplasm_attributes.Rd | 16 man/get_germplasm_data.Rd | 19 man/get_germplasm_id.Rd | 6 man/get_germplasm_list.Rd | 26 man/get_hwsd2.Rd | 48 man/get_login_details.Rd | 7 man/get_parents.Rd | 11 man/get_pedigree_table.Rd | 40 man/get_program_studies.Rd | 24 man/get_program_trials.Rd | 11 man/get_qbms_connection.Rd | 32 man/get_study_data.Rd | 27 man/get_study_info.Rd | 27 man/get_terraclimate.Rd | 73 man/get_trial_data.Rd | 24 man/get_trial_obs_ontology.Rd | 24 man/gigwa_get_allelematrix.Rd |only man/gigwa_get_markers.Rd |only man/gigwa_get_metadata.Rd | 17 man/gigwa_get_samples.Rd | 22 man/gigwa_get_sequences.Rd |only man/gigwa_get_variants.Rd | 35 man/gigwa_list_dbs.Rd | 10 man/gigwa_list_projects.Rd | 13 man/gigwa_list_runs.Rd | 15 man/gigwa_set_db.Rd | 13 man/gigwa_set_project.Rd | 16 man/gigwa_set_run.Rd | 17 man/ini_hwsd2.Rd | 21 man/ini_terraclimate.Rd | 51 man/list_crops.Rd | 22 man/list_locations.Rd | 8 man/list_programs.Rd | 26 man/list_studies.Rd | 35 man/list_trials.Rd | 41 man/login_bms.Rd | 29 man/login_breedbase.Rd | 8 man/login_gigwa.Rd | 18 man/login_oauth2.Rd | 28 man/rbindlistx.Rd | 2 man/rbindx.Rd | 2 man/scan_brapi_endpoints.Rd | 13 man/set_crop.Rd | 22 man/set_program.Rd | 27 man/set_qbms_config.Rd | 26 man/set_qbms_connection.Rd | 31 man/set_study.Rd | 37 man/set_token.Rd | 17 man/set_trial.Rd | 30 vignettes/bms_example.Rmd | 8 vignettes/breedbase_example.Rmd | 6 vignettes/ebs_example.Rmd | 6 vignettes/gigwa_example.Rmd | 54 vignettes/hwsd2_example.Rmd | 6 vignettes/terraclimate_example.Rmd | 17 93 files changed, 1450 insertions(+), 4066 deletions(-)
Title: Bayesian Spatial Analysis
Description: For spatial data analysis; provides exploratory spatial analysis tools, spatial regression models, disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health surveillance data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
Author: Connor Donegan [aut, cre] ,
Mitzi Morris [ctb],
Amy Tims [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between geostan versions 0.6.2 dated 2024-06-04 and 0.7.0 dated 2024-09-18
geostan-0.6.2/geostan/inst/stan/parts/gen_quants_declaration.stan |only geostan-0.6.2/geostan/inst/stan/parts/gen_quants_expression.stan |only geostan-0.6.2/geostan/vignettes/autonormal.stan |only geostan-0.6.2/geostan/vignettes/car_poisson.stan |only geostan-0.6.2/geostan/vignettes/sar-lpdf.stan |only geostan-0.6.2/geostan/vignettes/sar_model.stan |only geostan-0.7.0/geostan/DESCRIPTION | 8 geostan-0.7.0/geostan/MD5 | 139 geostan-0.7.0/geostan/NAMESPACE | 7 geostan-0.7.0/geostan/NEWS.md | 18 geostan-0.7.0/geostan/R/check-data.R | 4 geostan-0.7.0/geostan/R/convenience-functions.R | 89 geostan-0.7.0/geostan/R/geary.R | 19 geostan-0.7.0/geostan/R/geostan_fit-methods.R | 169 geostan-0.7.0/geostan/R/information-criteria.R |only geostan-0.7.0/geostan/R/internal-functions.R | 89 geostan-0.7.0/geostan/R/make-me-data.R | 3 geostan-0.7.0/geostan/R/moran.R | 4 geostan-0.7.0/geostan/R/priors.R | 11 geostan-0.7.0/geostan/R/raster-analysis.R | 54 geostan-0.7.0/geostan/R/stan_car.R | 37 geostan-0.7.0/geostan/R/stan_esf.R | 47 geostan-0.7.0/geostan/R/stan_glm.R | 33 geostan-0.7.0/geostan/R/stan_icar.R | 31 geostan-0.7.0/geostan/R/stan_sar.R | 50 geostan-0.7.0/geostan/README.md | 96 geostan-0.7.0/geostan/build/partial.rdb |binary geostan-0.7.0/geostan/build/vignette.rds |binary geostan-0.7.0/geostan/inst/doc/custom-spatial-models.R | 37 geostan-0.7.0/geostan/inst/doc/custom-spatial-models.Rmd | 144 geostan-0.7.0/geostan/inst/doc/custom-spatial-models.html | 180 geostan-0.7.0/geostan/inst/doc/measuring-sa.Rmd | 4 geostan-0.7.0/geostan/inst/doc/measuring-sa.html | 16 geostan-0.7.0/geostan/inst/doc/raster-regression.html | 51 geostan-0.7.0/geostan/inst/doc/spatial-me-models.R | 22 geostan-0.7.0/geostan/inst/doc/spatial-me-models.Rmd | 69 geostan-0.7.0/geostan/inst/doc/spatial-me-models.html | 343 geostan-0.7.0/geostan/inst/stan/foundation.stan | 42 geostan-0.7.0/geostan/inst/stan/parts/data.stan | 52 geostan-0.7.0/geostan/inst/stan/parts/gen_quants.stan |only geostan-0.7.0/geostan/inst/stan/parts/model.stan | 60 geostan-0.7.0/geostan/inst/stan/parts/params.stan | 18 geostan-0.7.0/geostan/inst/stan/parts/priors.stan | 115 geostan-0.7.0/geostan/inst/stan/parts/trans_data.stan | 28 geostan-0.7.0/geostan/inst/stan/parts/trans_params_declaration.stan | 19 geostan-0.7.0/geostan/inst/stan/parts/trans_params_expression_auto-model.stan | 30 geostan-0.7.0/geostan/man/aple.Rd | 4 geostan-0.7.0/geostan/man/expected_mc.Rd | 2 geostan-0.7.0/geostan/man/figures/README-unnamed-chunk-5-1.png |binary geostan-0.7.0/geostan/man/gr.Rd | 10 geostan-0.7.0/geostan/man/lg.Rd | 8 geostan-0.7.0/geostan/man/log_lik.Rd |only geostan-0.7.0/geostan/man/mc.Rd | 2 geostan-0.7.0/geostan/man/me_diag.Rd | 2 geostan-0.7.0/geostan/man/prep_car_data.Rd | 5 geostan-0.7.0/geostan/man/priors.Rd | 11 geostan-0.7.0/geostan/man/resid_geostan_fit.Rd | 15 geostan-0.7.0/geostan/man/shape2mat.Rd | 2 geostan-0.7.0/geostan/man/sim_sar.Rd | 2 geostan-0.7.0/geostan/man/sp_diag.Rd | 9 geostan-0.7.0/geostan/man/stan_car.Rd | 3 geostan-0.7.0/geostan/man/stan_esf.Rd | 18 geostan-0.7.0/geostan/man/stan_glm.Rd | 3 geostan-0.7.0/geostan/man/stan_icar.Rd | 5 geostan-0.7.0/geostan/man/stan_sar.Rd | 3 geostan-0.7.0/geostan/man/waic.Rd | 36 geostan-0.7.0/geostan/src/stanExports_foundation.h | 3814 +++++----- geostan-0.7.0/geostan/tests/testthat/test-information-criteria.R |only geostan-0.7.0/geostan/tests/testthat/test-stan-car.R | 3 geostan-0.7.0/geostan/vignettes/custom-spatial-models-files |only geostan-0.7.0/geostan/vignettes/custom-spatial-models.Rmd | 144 geostan-0.7.0/geostan/vignettes/measuring-sa.Rmd | 4 geostan-0.7.0/geostan/vignettes/spatial-me-models.Rmd | 69 geostan-0.7.0/geostan/vignettes/wcar-lpdf.stan | 36 74 files changed, 3374 insertions(+), 2974 deletions(-)
Title: Self-Organizing Map
Description: Self-Organizing Map (with application in gene clustering).
Author: Jun Yan [aut, cre]
Maintainer: Jun Yan <jyan@stat.uconn.edu>
Diff between som versions 0.3-5.1 dated 2016-07-06 and 0.3-5.2 dated 2024-09-18
som-0.3-5.1/som/INDEX |only som-0.3-5.2/som/DESCRIPTION | 14 +++++++++----- som-0.3-5.2/som/MD5 | 11 +++++------ som-0.3-5.2/som/R/som.R | 2 +- som-0.3-5.2/som/man/plot.som.Rd | 2 +- som-0.3-5.2/som/man/som.Rd | 2 +- som-0.3-5.2/som/src/som.cc | 18 +++++++++--------- 7 files changed, 26 insertions(+), 23 deletions(-)
Title: Linear Time Series Analysis
Description: Methods of developing linear time series modelling.
Methods are given for loglikelihood computation, forecasting
and simulation.
Author: A.I. McLeod [aut, cre],
Hao Yu [aut],
Zinovi Krougly [aut]
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between ltsa versions 1.4.6 dated 2015-12-21 and 1.4.6.1 dated 2024-09-18
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 14 +++++++------- inst/CITATION | 18 ++++-------------- inst/doc/index.html | 2 +- inst/doc/v23i05.pdf |binary man/DLSimulate.Rd | 2 +- man/exactLoglikelihood.Rd | 1 - src/nrutil.c | 12 ++++++------ 8 files changed, 36 insertions(+), 35 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>
Diff between cotram versions 0.5-1 dated 2024-07-19 and 0.5-2 dated 2024-09-18
cotram-0.5-1/cotram/R/mcotram.R |only cotram-0.5-1/cotram/demo |only cotram-0.5-1/cotram/man/mcotram.Rd |only cotram-0.5-1/cotram/tests/Examples |only cotram-0.5-2/cotram/DESCRIPTION | 8 ++++---- cotram-0.5-2/cotram/MD5 | 13 ++++--------- cotram-0.5-2/cotram/NAMESPACE | 4 ++-- cotram-0.5-2/cotram/inst/NEWS.Rd | 7 +++++++ cotram-0.5-2/cotram/inst/doc/cotram.pdf |binary 9 files changed, 17 insertions(+), 15 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (100+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained
RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecolog [...truncated...]
Author: Thomas Yee [aut, cre] ,
Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-11 dated 2024-05-15 and 1.1-12 dated 2024-09-18
VGAM-1.1-11/VGAM/man/alaplace3.Rd |only VGAM-1.1-11/VGAM/man/alaplaceUC.Rd |only VGAM-1.1-11/VGAM/man/loglapUC.Rd |only VGAM-1.1-11/VGAM/man/loglaplace.Rd |only VGAM-1.1-11/VGAM/man/triangle.Rd |only VGAM-1.1-12/VGAM/DESCRIPTION | 10 VGAM-1.1-12/VGAM/MD5 | 201 - VGAM-1.1-12/VGAM/NAMESPACE | 27 VGAM-1.1-12/VGAM/NEWS | 25 VGAM-1.1-12/VGAM/R/family.gaitd.R | 36 VGAM-1.1-12/VGAM/R/family.qreg.R | 3801 ++++-------------------------- VGAM-1.1-12/VGAM/R/hdeff.R | 154 - VGAM-1.1-12/VGAM/R/links.q | 33 VGAM-1.1-12/VGAM/R/rootogramsubset.R | 10 VGAM-1.1-12/VGAM/R/summary.vglm.q | 2 VGAM-1.1-12/VGAM/build/partial.rdb |binary VGAM-1.1-12/VGAM/data/Huggins89.t1.rda |binary VGAM-1.1-12/VGAM/data/Huggins89table1.rda |binary VGAM-1.1-12/VGAM/data/alclevels.rda |binary VGAM-1.1-12/VGAM/data/alcoff.rda |binary VGAM-1.1-12/VGAM/data/auuc.rda |binary VGAM-1.1-12/VGAM/data/backPain.rda |binary VGAM-1.1-12/VGAM/data/backPain2.rda |binary VGAM-1.1-12/VGAM/data/beggs.rda |binary VGAM-1.1-12/VGAM/data/budworm.rda |binary VGAM-1.1-12/VGAM/data/car.all.rda |binary VGAM-1.1-12/VGAM/data/cfibrosis.rda |binary VGAM-1.1-12/VGAM/data/corbet.rda |binary VGAM-1.1-12/VGAM/data/crashbc.rda |binary VGAM-1.1-12/VGAM/data/crashf.rda |binary VGAM-1.1-12/VGAM/data/crashi.rda |binary VGAM-1.1-12/VGAM/data/crashmc.rda |binary VGAM-1.1-12/VGAM/data/crashp.rda |binary VGAM-1.1-12/VGAM/data/crashtr.rda |binary VGAM-1.1-12/VGAM/data/deermice.rda |binary VGAM-1.1-12/VGAM/data/ducklings.rda |binary VGAM-1.1-12/VGAM/data/finney44.rda |binary VGAM-1.1-12/VGAM/data/flourbeetle.rda |binary VGAM-1.1-12/VGAM/data/hspider.rda |binary VGAM-1.1-12/VGAM/data/lakeO.rda |binary VGAM-1.1-12/VGAM/data/leukemia.rda |binary VGAM-1.1-12/VGAM/data/lpossums.rda |binary VGAM-1.1-12/VGAM/data/marital.nz.rda |binary VGAM-1.1-12/VGAM/data/melbmaxtemp.rda |binary VGAM-1.1-12/VGAM/data/pneumo.rda |binary VGAM-1.1-12/VGAM/data/prinia.rda |binary VGAM-1.1-12/VGAM/data/ruge.rda |binary VGAM-1.1-12/VGAM/data/toxop.rda |binary VGAM-1.1-12/VGAM/data/venice.rda |binary VGAM-1.1-12/VGAM/data/venice90.rda |binary VGAM-1.1-12/VGAM/data/wine.rda |binary VGAM-1.1-12/VGAM/man/AR1.Rd | 2 VGAM-1.1-12/VGAM/man/AR1UC.Rd | 2 VGAM-1.1-12/VGAM/man/Links.Rd | 15 VGAM-1.1-12/VGAM/man/Opt.Rd | 2 VGAM-1.1-12/VGAM/man/alteredvglm.Rd | 3 VGAM-1.1-12/VGAM/man/amlbinomial.Rd | 2 VGAM-1.1-12/VGAM/man/amlexponential.Rd | 2 VGAM-1.1-12/VGAM/man/amlnormal.Rd | 2 VGAM-1.1-12/VGAM/man/amlpoisson.Rd | 2 VGAM-1.1-12/VGAM/man/betageometric.Rd | 2 VGAM-1.1-12/VGAM/man/cens.poisson.Rd | 13 VGAM-1.1-12/VGAM/man/expexpff.Rd | 2 VGAM-1.1-12/VGAM/man/exponential.Rd | 2 VGAM-1.1-12/VGAM/man/extlogF.UC.Rd | 2 VGAM-1.1-12/VGAM/man/extlogF1.Rd | 13 VGAM-1.1-12/VGAM/man/fill1.Rd | 8 VGAM-1.1-12/VGAM/man/gaitdlog.Rd | 6 VGAM-1.1-12/VGAM/man/gaitdpoisson.Rd | 6 VGAM-1.1-12/VGAM/man/gengamma.Rd | 2 VGAM-1.1-12/VGAM/man/genrayleigh.Rd | 4 VGAM-1.1-12/VGAM/man/grc.Rd | 2 VGAM-1.1-12/VGAM/man/hdeff.Rd | 8 VGAM-1.1-12/VGAM/man/hdeffsev.Rd | 91 VGAM-1.1-12/VGAM/man/huber.Rd | 2 VGAM-1.1-12/VGAM/man/inv.paralogistic.Rd | 3 VGAM-1.1-12/VGAM/man/laplace.Rd | 14 VGAM-1.1-12/VGAM/man/laplaceUC.Rd | 4 VGAM-1.1-12/VGAM/man/lindley.Rd | 2 VGAM-1.1-12/VGAM/man/lms.bcn.Rd | 2 VGAM-1.1-12/VGAM/man/logitlink.Rd | 2 VGAM-1.1-12/VGAM/man/negbinomial.Rd | 9 VGAM-1.1-12/VGAM/man/notdocumentedyet.Rd | 2 VGAM-1.1-12/VGAM/man/paralogistic.Rd | 3 VGAM-1.1-12/VGAM/man/posbernoulli.b.Rd | 2 VGAM-1.1-12/VGAM/man/rootogram4vglm.Rd | 4 VGAM-1.1-12/VGAM/man/simplex.Rd | 7 VGAM-1.1-12/VGAM/man/simulate.vlm.Rd | 6 VGAM-1.1-12/VGAM/man/sinmad.Rd | 3 VGAM-1.1-12/VGAM/man/summarydrrvglm.Rd | 4 VGAM-1.1-12/VGAM/man/summarypvgam.Rd | 2 VGAM-1.1-12/VGAM/man/topple.Rd | 2 VGAM-1.1-12/VGAM/man/toppleUC.Rd | 2 VGAM-1.1-12/VGAM/man/triangleUC.Rd | 11 VGAM-1.1-12/VGAM/man/truncweibull.Rd | 2 VGAM-1.1-12/VGAM/man/vgam.Rd | 6 VGAM-1.1-12/VGAM/man/wald.stat.Rd | 2 VGAM-1.1-12/VGAM/man/weibull.mean.Rd | 3 VGAM-1.1-12/VGAM/man/zipebcom.Rd | 6 VGAM-1.1-12/VGAM/src/caqo3.c | 85 VGAM-1.1-12/VGAM/src/rgam.f | 11 VGAM-1.1-12/VGAM/src/rgam3.c | 22 VGAM-1.1-12/VGAM/src/vgam3.c | 184 - VGAM-1.1-12/VGAM/src/vmux3.c | 46 104 files changed, 1255 insertions(+), 3690 deletions(-)
Title: Genotype by Environment (GxE) Analysis
Description: Analysis of multi environment data of plant breeding experiments
following the analyses described in Malosetti, Ribaut,
and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>.
One of a series of statistical genetic packages for streamlining the analysis of
typical plant breeding experiments developed by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb],
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGxE versions 1.0.8 dated 2024-05-06 and 1.0.9 dated 2024-09-18
DESCRIPTION | 12 +-- MD5 | 42 ++++++------ NEWS.md | 5 + R/createFW.R | 4 - R/createStability.R | 4 - R/gxeAmmi.R | 2 R/gxeFw.R | 150 +++++++++++++++++++++----------------------- README.md | 22 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenGxE.html | 111 ++++++++++++++++---------------- man/FW.Rd | 4 - man/gxeAmmi.Rd | 2 man/gxeFw.Rd | 2 man/gxeGGE.Rd | 2 man/gxeMegaEnv.Rd | 2 man/gxeStability.Rd | 2 man/gxeVarComp.Rd | 2 man/gxeVarCov.Rd | 2 man/statgenGxE-package.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-gxeFW.R | 30 ++++---- 22 files changed, 202 insertions(+), 200 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.4.1 dated 2024-01-10 and 3.4.2 dated 2024-09-18
DESCRIPTION | 12 MD5 | 276 ++++++++++----------- R/opal.R | 18 + build/partial.rdb |only build/vignette.rds |binary inst/doc/datashield-admin.html | 331 +++++++++++++------------ inst/doc/opal-files.html | 194 +++++++-------- inst/doc/opal-projects.html | 374 +++++++++++++++-------------- inst/doc/opal-rsession.html | 213 ++++++++-------- man/dsadmin.get_method.Rd | 6 man/dsadmin.get_methods.Rd | 6 man/dsadmin.get_options.Rd | 8 man/dsadmin.install_github_package.Rd | 8 man/dsadmin.install_local_package.Rd | 8 man/dsadmin.install_package.Rd | 8 man/dsadmin.installed_package.Rd | 8 man/dsadmin.package_description.Rd | 6 man/dsadmin.package_descriptions.Rd | 6 man/dsadmin.profile.Rd | 2 man/dsadmin.profile_access.Rd | 6 man/dsadmin.profile_create.Rd | 6 man/dsadmin.profile_delete.Rd | 6 man/dsadmin.profile_enable.Rd | 6 man/dsadmin.profile_exists.Rd | 6 man/dsadmin.profile_init.Rd | 6 man/dsadmin.profile_perm.Rd | 4 man/dsadmin.profile_perm_add.Rd | 6 man/dsadmin.profile_perm_delete.Rd | 6 man/dsadmin.profile_rparser.Rd | 6 man/dsadmin.profiles.Rd | 6 man/dsadmin.publish_package.Rd | 8 man/dsadmin.remove_package.Rd | 8 man/dsadmin.rm_method.Rd | 6 man/dsadmin.rm_methods.Rd | 6 man/dsadmin.rm_option.Rd | 6 man/dsadmin.rm_options.Rd | 6 man/dsadmin.rm_package_methods.Rd | 8 man/dsadmin.set_method.Rd | 8 man/dsadmin.set_option.Rd | 8 man/dsadmin.set_package_methods.Rd | 8 man/dsadmin.unpublish_package.Rd | 8 man/oadmin.install_bioconductor_package.Rd | 2 man/oadmin.install_cran_package.Rd | 2 man/oadmin.install_devtools.Rd | 2 man/oadmin.install_github_package.Rd | 2 man/oadmin.install_local_package.Rd | 2 man/oadmin.install_package.Rd | 2 man/oadmin.installed_devtools.Rd | 2 man/oadmin.package_description.Rd | 2 man/oadmin.remove_package.Rd | 2 man/opal.annotate.Rd | 8 man/opal.annotations.Rd | 8 man/opal.assign.Rd | 4 man/opal.assign.data.Rd | 4 man/opal.assign.resource.Rd | 4 man/opal.assign.script.Rd | 4 man/opal.assign.table.Rd | 4 man/opal.assign.table.tibble.Rd | 4 man/opal.attribute_values.Rd | 8 man/opal.command.Rd | 4 man/opal.command_result.Rd | 4 man/opal.command_rm.Rd | 4 man/opal.commands.Rd | 4 man/opal.commands_rm.Rd | 4 man/opal.datasource.Rd | 6 man/opal.datasources.Rd | 6 man/opal.file.Rd | 2 man/opal.file_cp.Rd | 6 man/opal.file_download.Rd | 6 man/opal.file_ls.Rd | 6 man/opal.file_mkdir.Rd | 4 man/opal.file_mkdir_tmp.Rd | 4 man/opal.file_mv.Rd | 6 man/opal.file_read.Rd | 6 man/opal.file_rm.Rd | 6 man/opal.file_unzip.Rd | 6 man/opal.file_upload.Rd | 6 man/opal.file_write.Rd | 6 man/opal.load_package.Rd | 2 man/opal.perms.Rd | 2 man/opal.project.Rd | 4 man/opal.project_create.Rd | 4 man/opal.project_delete.Rd | 4 man/opal.project_exists.Rd | 4 man/opal.projects.Rd | 4 man/opal.projects_databases.Rd | 4 man/opal.resource.Rd | 8 man/opal.resource_create.Rd | 10 man/opal.resource_delete.Rd | 10 man/opal.resource_exists.Rd | 10 man/opal.resource_extension_create.Rd | 10 man/opal.resource_get.Rd | 10 man/opal.resource_perm.Rd | 8 man/opal.resource_perm_add.Rd | 10 man/opal.resource_perm_delete.Rd | 10 man/opal.resource_view_create.Rd | 2 man/opal.resource_view_reconnect.Rd | 2 man/opal.resources.Rd | 8 man/opal.resources_perm.Rd | 8 man/opal.resources_perm_add.Rd | 8 man/opal.resources_perm_delete.Rd | 8 man/opal.table.Rd | 6 man/opal.table_create.Rd | 2 man/opal.table_delete.Rd | 2 man/opal.table_dictionary_get.Rd | 2 man/opal.table_dictionary_update.Rd | 2 man/opal.table_exists.Rd | 2 man/opal.table_export.Rd | 2 man/opal.table_get.Rd | 2 man/opal.table_import.Rd | 2 man/opal.table_perm_add.Rd | 2 man/opal.table_perm_delete.Rd | 2 man/opal.table_save.Rd | 2 man/opal.table_truncate.Rd | 2 man/opal.table_view_create.Rd | 2 man/opal.table_view_update.Rd | 2 man/opal.tables.Rd | 6 man/opal.task_cancel.Rd | 4 man/opal.task_wait.Rd | 4 man/opal.tasks.Rd | 4 man/opal.taxonomies.Rd | 2 man/opal.taxonomy_delete.Rd | 2 man/opal.taxonomy_download.Rd | 2 man/opal.taxonomy_upload.Rd | 2 man/opal.terms.Rd | 2 man/opal.token_datashield_create.Rd | 4 man/opal.token_delete.Rd | 4 man/opal.token_r_create.Rd | 4 man/opal.token_renew.Rd | 4 man/opal.token_sql_create.Rd | 4 man/opal.tokens.Rd | 4 man/opal.unload_package.Rd | 2 man/opal.valueset.Rd | 8 man/opal.variable.Rd | 4 man/opal.variable_summary.Rd | 8 man/opal.variables.Rd | 8 man/opal.vocabularies.Rd | 2 man/opal.vocabulary.Rd | 2 man/opalr-package.Rd | 4 tests/testthat/test-url.R |only 140 files changed, 1055 insertions(+), 1009 deletions(-)
Title: Chacko Test for Order-Restriction with Permutation
Description: Implements an extension of the Chacko chi-square test for
ordered vectors (Chacko, 1966, <https://www.jstor.org/stable/25051572>).
Our extension brings the Chacko test to the computer age by implementing
a permutation test to offer a numeric estimate of the p-value, which is
particularly useful when the analytic solution is not available.
Author: Waldir Leoncio [aut, cre] ,
Graeme Ruxton [aut],
Morten Wang Fagerland [aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between permChacko versions 1.0.0 dated 2024-04-17 and 1.0.1 dated 2024-09-18
DESCRIPTION | 11 +- MD5 | 22 ++--- NAMESPACE | 1 NEWS.md | 6 + R/chackoStatistic.R | 16 +-- R/permChacko-package.R | 5 - R/permChacko.R | 2 R/reduceVector.R | 2 build/vignette.rds |binary inst/doc/improving_chacko.html | 135 +++++++++++++++----------------- tests/testthat/test-customExamples.R | 9 ++ tests/testthat/test-print-and-summary.R | 12 +- 12 files changed, 118 insertions(+), 103 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.3-1 dated 2024-07-15 and 3.3-2 dated 2024-09-18
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS | 15 +++++++++++++++ R/random.R | 9 ++++++--- inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/rSSI.Rd | 6 +++++- man/reach.Rd | 2 +- man/spatstat.random-package.Rd | 2 ++ 9 files changed, 44 insertions(+), 18 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.3-2 dated 2024-07-15 and 3.3-3 dated 2024-09-18
DESCRIPTION | 10 ++++----- MD5 | 24 ++++++++++++---------- NAMESPACE | 2 + NEWS | 29 +++++++++++++++++++++++++++ R/persp.ppp.R |only R/randombasic.R | 46 +++++++++++++++++++++++++++++-------------- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/as.tess.Rd | 6 +++-- man/markstat.Rd | 8 +++---- man/persp.ppp.Rd |only man/rjitter.Rd | 28 ++++++++++++++++++++++---- man/spatstat.geom-package.Rd | 4 +++ man/unitname.Rd | 10 ++++----- 14 files changed, 124 insertions(+), 45 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-02 1.0.0
Title: Provides Some Useful Functions for Making Statistical Tables
Description: You can use the functions provided by the package to make various statistical tables,
such as baseline data tables. Creates 'Table 1', i.e., a description of the baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences.
This method was described by Mary L McHugh (2013) <doi:10.11613/bm.2013.018>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between scitb versions 0.1.8 dated 2024-06-02 and 0.2.0 dated 2024-09-18
DESCRIPTION | 6 +++--- MD5 | 4 +++- R/Maddala.Cox.Snell.R |only R/modeldata.R |only 4 files changed, 6 insertions(+), 4 deletions(-)
Title: R Interface to MPI for HPC Clusters (Programming with Big Data
Project)
Description: A simplified, efficient, interface to MPI for HPC clusters. It is
a derivation and rethinking of the Rmpi package. pbdMPI embraces the
prevalent parallel programming style on HPC clusters. Beyond the
interface, a collection of functions for global work with
distributed data and resource-independent RNG reproducibility is
included. It is based on S4 classes and methods.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] ,
Brian Ripley [ctb] ,
R Core team [ctb] ,
Sebastien Lamy de la Chapelle [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.5-1 dated 2023-12-10 and 0.5-2 dated 2024-09-18
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 2 +- src/comm_errors.c | 27 +++++++++++++++++++-------- src/spmd.c | 24 ++++++++++++------------ src/spmd_communicator_spawn.c | 4 ++-- 7 files changed, 48 insertions(+), 33 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., confidence intervals, collinearity and residual diag [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.6.6 dated 2024-08-25 and 0.6.7 dated 2024-09-18
DESCRIPTION | 8 +-- MD5 | 58 +++++++++++------------ NEWS.md | 55 ++++++++++++++++----- R/blimp.R | 65 +++++++++++++++---------- R/blimp.bayes.R | 14 +++-- R/blimp.plot.R | 123 +++++++++++++++++++++++++++++++++++++++---------- R/blimp.print.R | 23 +++++---- R/blimp.run.R | 6 +- R/center.R | 4 - R/item.invar.R | 7 ++ R/mplus.R | 116 ++++++++++++++++++++++++++++++---------------- R/mplus.bayes.R | 16 +++--- R/mplus.lca.R | 2 R/mplus.print.R | 9 +-- R/na.auxiliary.R | 11 ++-- R/na.indicator.R | 110 ++++++++++++++++++++++++++++++++++++------- R/na.test.R | 6 +- R/print.misty.object.R | 80 +++++++------------------------ R/rec.R | 2 R/utils.R | 9 +-- man/blimp.Rd | 20 +++---- man/blimp.bayes.Rd | 6 +- man/blimp.plot.Rd | 18 ++++--- man/blimp.run.Rd | 4 - man/center.Rd | 10 +-- man/mplus.Rd | 30 +++++------ man/mplus.bayes.Rd | 4 + man/mplus.print.Rd | 7 +- man/na.indicator.Rd | 23 +++++++-- man/na.test.Rd | 7 +- 30 files changed, 537 insertions(+), 316 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block
diagonal matrices (often used for covariance matrices). This is based
on the domain specific language implemented in 'nlmixr2' but expanded
to create matrices in R generally instead of specifying parts of
matrices to estimate. It has expanded to include some matrix manipulation
functions that are generally useful for 'rxode2' and 'nlmixr2'.
Author: Matthew L. Fidler [aut, cre] ,
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 0.4.3 dated 2023-03-20 and 1.0.0 dated 2024-09-18
DESCRIPTION | 24 MD5 | 50 + NAMESPACE | 5 NEWS.md | 93 +++ R/as.expression.R | 163 ++++++ R/err.R | 4 R/lotri.R | 655 ++++++++++++++++++++++---- R/lotriMatInv.R | 51 ++ R/lotriNearPD.R |only R/lotriPtrs.R |only R/rcm.R |only README.md | 512 ++++++++++---------- build/vignette.rds |binary inst/doc/lotri-motivation.html | 16 inst/include |only man/dot-lotriPointers.Rd |only man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/lotri.Rd | 29 + man/lotriAsExpression.Rd |only man/lotriIsBlockMat.Rd |only man/lotriNearPD.Rd |only man/rcm.Rd |only src/Makevars |only src/Makevars.win |only src/matlist.c | 103 +++- src/nearPD.cpp |only src/nearPD.h |only src/rcm.cpp |only src/rcm.h |only tests/testthat/test-line-form.R |only tests/testthat/test-lotriCov.R |only tests/testthat/test-nearPD.R |only tests/testthat/test-omega-nse.R |only tests/testthat/test-rcm.R |only tests/testthat/test-theta-lhs-as.expression.R | 123 ++-- 36 files changed, 1374 insertions(+), 454 deletions(-)