Title: Fit Text Inside a Box in 'ggplot2'
Description: A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Author: David Wilkins [aut, cre],
Brady Johnston [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.10.1 dated 2023-09-05 and 0.10.2 dated 2024-01-31
DESCRIPTION | 10 - MD5 | 28 ++--- NAMESPACE | 16 +++ NEWS.md | 8 + R/geom_bar_text.R | 4 R/geom_fit_text.R | 33 ++---- R/polar.R | 10 - R/utilities.R | 51 +++++++++- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/introduction-to-ggfittext.R | 22 ++-- inst/doc/introduction-to-ggfittext.html | 4 tests/testthat/_snaps/richtext/complex-rich-text-with-grow-and-reflow.svg | 4 tests/testthat/_snaps/richtext/complex-rich-text-with-reflow-only.svg | 4 tests/testthat/test-richtext.R | 4 15 files changed, 131 insertions(+), 69 deletions(-)
Title: Point Process Models with LASSO-Type Penalties
Description: Toolkit for fitting point process models with sequences of LASSO penalties ("regularisation paths"), as described in Renner, I.W. and Warton, D.I. (2013) <doi:10.1111/j.1541-0420.2012.01824.x>. Regularisation paths of Poisson point process models or area-interaction models can be fitted with LASSO, adaptive LASSO or elastic net penalties. A number of criteria are available to judge the bias-variance tradeoff.
Author: Ian Renner
Maintainer: Ian Renner <Ian.Renner@newcastle.edu.au>
Diff between ppmlasso versions 1.3 dated 2022-12-01 and 1.4 dated 2024-01-31
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++++++++++++++++++++++++----- R/ppmlasso |only data/BlueMountains.RData |binary inst/CITATION | 34 +++++++++++++---------------- inst/NEWS | 5 +--- man/ppmlasso-internal.Rd | 1 7 files changed, 71 insertions(+), 31 deletions(-)
Title: Probabilistic Sampling Design and Strategies
Description: It allows the user to determine sample sizes, select probabilistic samples,
make estimates of different parameters for the total finite population and in studio domains,
using the main design drawings.
Author: Jorge Baron [aut, cre, cph],
Guillermo Martinez [aut]
Maintainer: Jorge Baron <jorgeabaron@correo.unicordoba.edu.co>
Diff between ProbSamplingI versions 0.1.0 dated 2021-03-09 and 2.0 dated 2024-01-31
DESCRIPTION | 16 +++--- MD5 | 16 +++--- R/ESTRAT.r | 15 ++--- R/M.MET.r | 8 +-- R/PiPT.r | 143 ++++++++++++++++++++++++++---------------------------- R/R.SIS.r | 2 R/n.MAS.r | 18 +++--- build/partial.rdb |binary man/ESTRAT.rd | 16 +++--- 9 files changed, 116 insertions(+), 118 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-49 dated 2022-08-09 and 3.1-51 dated 2024-01-31
HH-3.1-49/HH/R/likertWeighted47.R |only HH-3.1-49/HH/R/mmc.explain.R |only HH-3.1-49/HH/man/HH-defunct.Rd |only HH-3.1-49/HH/man/likertWeighted47.Rd |only HH-3.1-49/HH/man/seqplot.forecast.Rd |only HH-3.1-51/HH/DESCRIPTION | 8 - HH-3.1-51/HH/MD5 | 49 ++++---- HH-3.1-51/HH/NAMESPACE | 6 - HH-3.1-51/HH/NEWS | 66 +++++++++++ HH-3.1-51/HH/R/AAAAAAA.if.R.R | 4 HH-3.1-51/HH/R/ARIMA-trellis.R | 4 HH-3.1-51/HH/R/ToBW.likert.R | 2 HH-3.1-51/HH/R/as.likert.R | 14 +- HH-3.1-51/HH/R/interaction2wt.R | 33 ++++- HH-3.1-51/HH/R/intxplot.R | 58 ++++++---- HH-3.1-51/HH/R/likert.formula.DataFrame.r | 118 -------------------- HH-3.1-51/HH/R/likert.formula.R | 3 HH-3.1-51/HH/R/mmc_explain.R |only HH-3.1-51/HH/R/panel.interaction2wt.R | 165 +++++++++++++---------------- HH-3.1-51/HH/build/partial.rdb |binary HH-3.1-51/HH/inst/CITATION | 10 - HH-3.1-51/HH/man/ToBW.likert.Rd | 2 HH-3.1-51/HH/man/if.R.Rd | 18 ++- HH-3.1-51/HH/man/interaction2wt.Rd | 36 +++++- HH-3.1-51/HH/man/intxplot.Rd | 43 ++++--- HH-3.1-51/HH/man/panel.interaction2wt.Rd | 21 +-- HH-3.1-51/HH/man/residual.plots.lattice.Rd | 3 HH-3.1-51/HH/man/seqplotForecast.Rd |only HH-3.1-51/HH/man/sufficient.Rd | 2 29 files changed, 345 insertions(+), 320 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.3.1 dated 2023-11-02 and 1.3.2 dated 2024-01-31
greeks-1.3.1/greeks/tests/testthat/test-.R |only greeks-1.3.2/greeks/DESCRIPTION | 6 greeks-1.3.2/greeks/MD5 | 36 +- greeks-1.3.2/greeks/R/BS_European_Greeks.R | 28 - greeks-1.3.2/greeks/R/BS_Malliavin_Asian_Greeks.R | 23 - greeks-1.3.2/greeks/R/Greeks.R | 8 greeks-1.3.2/greeks/R/Malliavin_European_Greeks.R | 158 +++++----- greeks-1.3.2/greeks/R/Malliavin_Geometric_Asian_Greeks.R | 67 ---- greeks-1.3.2/greeks/README.md |only greeks-1.3.2/greeks/build/vignette.rds |binary greeks-1.3.2/greeks/inst/doc/using_greeks.R | 2 greeks-1.3.2/greeks/man/BS_Malliavin_Asian_Greeks.Rd | 4 greeks-1.3.2/greeks/man/Greeks.Rd | 6 greeks-1.3.2/greeks/man/Malliavin_European_Greeks.Rd | 3 greeks-1.3.2/greeks/man/Malliavin_Geometric_Asian_Greeks.Rd | 2 greeks-1.3.2/greeks/src/Binomial_American_Greeks.cpp | 7 greeks-1.3.2/greeks/tests/testthat/test-BS_Malliavin_Asian_Greeks.R |only greeks-1.3.2/greeks/tests/testthat/test-Greeks.R |only greeks-1.3.2/greeks/tests/testthat/test-Implied_Volatility.R | 3 greeks-1.3.2/greeks/tests/testthat/test-Malliavin_Asian_Greeks.R |only greeks-1.3.2/greeks/tests/testthat/test-Malliavin_European_Greeks.R | 21 - greeks-1.3.2/greeks/tests/testthat/test-Malliavin_Geometric_Asian_Greeks.R |only 22 files changed, 171 insertions(+), 203 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.2.0 dated 2023-12-14 and 1.2.1 dated 2024-01-31
DESCRIPTION | 11 +- MD5 | 22 ++--- NEWS.md | 9 ++ R/appMetadata-quarto.R | 40 ++++++--- R/bundlePackageRenv.R | 8 - R/http.R | 5 - README.md | 2 inst/doc/custom-http.html | 2 man/rsconnect-package.Rd | 1 tests/testthat/_snaps/appMetadata-quarto.md | 18 ++++ tests/testthat/test-appMetadata-quarto.R | 114 ++++++++++++++++++++-------- tests/testthat/test-http.R | 9 ++ 12 files changed, 173 insertions(+), 68 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph] ,
Matthew Collins [aut] ,
Scott Chamberlain [ctb],
Kevin Love [ctb],
Hem Nalini Morzaria-Luna [ctb],
Michelle L. Gaynor [ctb],
Jesse Bennett [cre]
Maintainer: Jesse Bennett <j3553@ufl.edu>
Diff between ridigbio versions 0.3.7 dated 2023-10-06 and 0.3.8 dated 2024-01-31
DESCRIPTION | 11 +++++++---- MD5 | 14 +++++++------- R/idig_search_records.R | 23 +++++++++++++++++++++-- R/ridigbio.R | 2 +- README.md | 15 +++++++++++++++ man/idig_search_records.Rd | 17 ++++++++++++++++- man/ridigbio-package.Rd | 1 + man/ridigbio.Rd | 2 +- 8 files changed, 69 insertions(+), 16 deletions(-)
Title: Helper Functions for Org Files
Description: Helper functions for Org files (<https://orgmode.org/>):
a generic function 'toOrg' for transforming R objects into Org
markup (most useful for data frames; there are also methods for
Dates/POSIXt) and a function to read Org tables into data frames.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between orgutils versions 0.4-1 dated 2017-03-21 and 0.5-0 dated 2024-01-31
DESCRIPTION | 17 ++- MD5 | 30 +++--- NEWS | 15 +++ R/toOrg.R | 173 ++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/orgutils_examples.R | 2 inst/doc/orgutils_examples.Rnw | 20 ++-- inst/doc/orgutils_examples.pdf |binary inst/unitTests/orgtable10.org |only inst/unitTests/runTests.R | 4 inst/unitTests/test_results.txt | 8 - inst/unitTests/ut_orgutils.R | 57 +++++++------ man/orgutils-package.Rd | 22 ++--- man/readOrg.Rd | 40 +++++++-- man/toOrg.Rd | 9 +- vignettes/auto |only vignettes/orgutils_examples.Rnw | 20 ++-- 17 files changed, 307 insertions(+), 110 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Data
Description: Datasets for 'nlmixr2' and 'rxode2'. 'nlmixr2' is used for fitting and comparing
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] ,
Rik Schoemaker [ctb] ,
Kyle Baron [ctb],
Thierry Wendling [ctb],
Ted Grasella [ctb],
C Weil [ctb],
Yaning Wang [ctb],
R O'Reilly [ctb],
David D'Argenio [ctb],
Rodriguez-Vera [ctb],
D Gaver [ctb],
Yuan Xiong [ctb],
Wenping [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2data versions 2.0.8 dated 2023-08-30 and 2.0.9 dated 2024-01-31
DESCRIPTION | 16 +++++++++------- MD5 | 3 ++- NEWS.md |only 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Edgar Merkle [ctb],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Ad [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-15 dated 2023-08-29 and 0.7-16 dated 2024-01-31
gimme-0.7-15/gimme/R/setupFinalDataChecks.R |only gimme-0.7-15/gimme/inst/doc/hrfgimme-vignette.R |only gimme-0.7-15/gimme/inst/doc/hrfgimme-vignette.Rmd |only gimme-0.7-15/gimme/inst/doc/hrfgimme-vignette.html |only gimme-0.7-15/gimme/man/setupFinalDataChecks.Rd |only gimme-0.7-15/gimme/vignettes/hrfgimme-vignette.Rmd |only gimme-0.7-15/gimme/vignettes/hrfgimme_vignette.R |only gimme-0.7-16/gimme/DESCRIPTION | 12 - gimme-0.7-16/gimme/MD5 | 60 +++--- gimme-0.7-16/gimme/R/aggSEM.R | 19 -- gimme-0.7-16/gimme/R/determine.subgroups.R | 23 +- gimme-0.7-16/gimme/R/final.org.R | 9 - gimme-0.7-16/gimme/R/get.params.R | 25 ++ gimme-0.7-16/gimme/R/gimme.R | 58 ------ gimme-0.7-16/gimme/R/indSEM.R | 32 --- gimme-0.7-16/gimme/R/indiv.search.R | 2 gimme-0.7-16/gimme/R/sFIR.R | 17 + gimme-0.7-16/gimme/R/search.paths.ms.R | 3 gimme-0.7-16/gimme/R/setup.R | 6 gimme-0.7-16/gimme/R/setupBaseSyntax.R | 2 gimme-0.7-16/gimme/R/setupConvolve.R | 7 gimme-0.7-16/gimme/R/setupPrepPaths.R | 116 ++++--------- gimme-0.7-16/gimme/R/setupTransformData.R | 28 ++- gimme-0.7-16/gimme/R/simulateVAR.R | 8 gimme-0.7-16/gimme/build/vignette.rds |binary gimme-0.7-16/gimme/inst/doc/gimme_vignette.html | 4 gimme-0.7-16/gimme/man/aggSEM.Rd | 16 - gimme-0.7-16/gimme/man/gimmeSEM.Rd | 50 ----- gimme-0.7-16/gimme/man/indSEM.Rd | 29 --- gimme-0.7-16/gimme/tests/testthat.R |only gimme-0.7-16/gimme/tests/testthat/Rplots.pdf |only gimme-0.7-16/gimme/tests/testthat/rds/run1_path_counts.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run1_path_matrix.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run2_path_counts.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run2_path_matrix.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run3_path_counts.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run3_path_matrix.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run4_path_counts.rds |only gimme-0.7-16/gimme/tests/testthat/rds/run4_path_matrix.rds |only gimme-0.7-16/gimme/tests/testthat/test-gimme.R |only 40 files changed, 179 insertions(+), 347 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: JJ Allaire [aut, cph],
Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
Dirk Eddelbuettel [ctb, cph],
Yuan Tang [aut, cph] ,
Nick Golding [ctb, cph],
Google Inc. [ctb, cph] ,
Posit, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@posit.co>
Diff between tensorflow versions 2.14.0 dated 2023-09-28 and 2.15.0 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 12 ++++++++++++ NEWS.md | 5 +++++ R/generics.R | 14 ++++++++++++++ R/install.R | 11 +++++++++-- R/seed.R | 6 ++++-- man/install_tensorflow.Rd | 2 +- man/tensorflow.Rd | 1 - 9 files changed, 57 insertions(+), 18 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace
Approximation, Monte Carlo Expectation Maximization, and some other tools.
The nimbleFunction system makes it easy to do things like implement new MCMC
samplers from R, customize the assignment of samplers to different parts of
a model from R, and compile the new samplers automatically via C++ alongside
the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language
by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think
of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models,
one can use 'NIMBLE' for writing arbitrary other kinds of model-generic
algorithms as well. A full User Manual [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodriguez [aut] ,
Duncan Temple Lang [aut] ,
Wei Zhang [aut] ,
[...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 1.0.1 dated 2023-06-15 and 1.1.0 dated 2024-01-31
nimble-1.0.1/nimble/inst/include/Eigen/CMakeLists.txt |only nimble-1.0.1/nimble/inst/include/Eigen/src/Core/arch/CUDA/Half.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/Core/arch/CUDA/MathFunctions.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/Core/arch/CUDA/PacketMath.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/Core/arch/CUDA/TypeCasting.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h |only nimble-1.0.1/nimble/inst/include/Eigen/src/LU/arch/Inverse_SSE.h |only nimble-1.0.1/nimble/man/nimble.Rd |only nimble-1.1.0/nimble/DESCRIPTION | 34 nimble-1.1.0/nimble/INSTALL | 6 nimble-1.1.0/nimble/LICENSE | 4 nimble-1.1.0/nimble/MD5 | 754 - nimble-1.1.0/nimble/NAMESPACE | 6 nimble-1.1.0/nimble/R/BNP_distributions.R | 6 nimble-1.1.0/nimble/R/BNP_samplers.R | 2 nimble-1.1.0/nimble/R/BUGS_BUGSdecl.R | 17 nimble-1.1.0/nimble/R/BUGS_contexts.R | 2 nimble-1.1.0/nimble/R/BUGS_macros.R | 555 + nimble-1.1.0/nimble/R/BUGS_model.R | 31 nimble-1.1.0/nimble/R/BUGS_modelDef.R | 259 nimble-1.1.0/nimble/R/BUGS_readBUGS.R | 21 nimble-1.1.0/nimble/R/CAR.R | 124 nimble-1.1.0/nimble/R/Laplace.R | 55 nimble-1.1.0/nimble/R/MCEM_build.R | 18 nimble-1.1.0/nimble/R/MCMC_build.R | 44 nimble-1.1.0/nimble/R/MCMC_configuration.R | 182 nimble-1.1.0/nimble/R/MCMC_conjugacy.R | 47 nimble-1.1.0/nimble/R/MCMC_samplers.R | 438 nimble-1.1.0/nimble/R/MCMC_utils.R | 6 nimble-1.1.0/nimble/R/NF_utils.R | 10 nimble-1.1.0/nimble/R/RCfunction_compile.R | 14 nimble-1.1.0/nimble/R/RCfunction_core.R | 11 nimble-1.1.0/nimble/R/all_utils.R | 5 nimble-1.1.0/nimble/R/cppDefs_RCfunction.R | 1 nimble-1.1.0/nimble/R/cppDefs_core.R | 26 nimble-1.1.0/nimble/R/cppDefs_cppProject.R | 26 nimble-1.1.0/nimble/R/cppDefs_nimbleFunction.R | 283 nimble-1.1.0/nimble/R/cppInterfaces_otherTypes.R | 8 nimble-1.1.0/nimble/R/crossValidation.R | 16 nimble-1.1.0/nimble/R/distributions_implementations.R | 2 nimble-1.1.0/nimble/R/distributions_processInputList.R | 61 nimble-1.1.0/nimble/R/genCpp_eigenization.R | 20 nimble-1.1.0/nimble/R/genCpp_generateCpp.R | 9 nimble-1.1.0/nimble/R/genCpp_operatorLists.R | 9 nimble-1.1.0/nimble/R/genCpp_processSpecificCalls.R | 11 nimble-1.1.0/nimble/R/genCpp_sizeProcessing.R | 407 nimble-1.1.0/nimble/R/genCpp_toEigenize.R | 11 nimble-1.1.0/nimble/R/nimble-package.r | 24 nimble-1.1.0/nimble/R/nimbleFunction_Rderivs.R | 2 nimble-1.1.0/nimble/R/nimbleFunction_Rexecution.R | 107 nimble-1.1.0/nimble/R/nimbleFunction_compile.R | 18 nimble-1.1.0/nimble/R/nimbleFunction_core.R | 14 nimble-1.1.0/nimble/R/nimbleFunction_keywordProcessing.R | 36 nimble-1.1.0/nimble/R/nimbleFunction_nodeFunctionNew.R | 30 nimble-1.1.0/nimble/R/nimbleList_core.R | 61 nimble-1.1.0/nimble/R/nimbleProject.R | 22 nimble-1.1.0/nimble/R/options.R | 18 nimble-1.1.0/nimble/R/parameterTransform.R | 10 nimble-1.1.0/nimble/inst/COPYRIGHTS | 147 nimble-1.1.0/nimble/inst/CppCode/GNUmakefile | 2 nimble-1.1.0/nimble/inst/CppCode/RcppUtils.cpp | 4 nimble-1.1.0/nimble/inst/CppCode/Utils.cpp | 56 nimble-1.1.0/nimble/inst/CppCode/dists.cpp | 155 nimble-1.1.0/nimble/inst/CppCode/eigenUsingClasses.cpp | 8 nimble-1.1.0/nimble/inst/CppCode/nimDerivs_atomic_classes.cpp | 30 nimble-1.1.0/nimble/inst/CppCode/nimDerivs_atomic_dyn_ind.cpp |only nimble-1.1.0/nimble/inst/CppCode/nimDists.cpp | 28 nimble-1.1.0/nimble/inst/CppCode/nimIntegrate.cpp |only nimble-1.1.0/nimble/inst/CppCode/nimbleCppAD.cpp | 2 nimble-1.1.0/nimble/inst/NEWS.md | 142 nimble-1.1.0/nimble/inst/include/Eigen/Cholesky | 1 nimble-1.1.0/nimble/inst/include/Eigen/Core | 382 nimble-1.1.0/nimble/inst/include/Eigen/Eigenvalues | 5 nimble-1.1.0/nimble/inst/include/Eigen/Geometry | 12 nimble-1.1.0/nimble/inst/include/Eigen/Householder | 1 nimble-1.1.0/nimble/inst/include/Eigen/Jacobi | 1 nimble-1.1.0/nimble/inst/include/Eigen/LU | 7 nimble-1.1.0/nimble/inst/include/Eigen/OrderingMethods | 3 nimble-1.1.0/nimble/inst/include/Eigen/QR | 5 nimble-1.1.0/nimble/inst/include/Eigen/QtAlignedMalloc | 1 nimble-1.1.0/nimble/inst/include/Eigen/SVD | 1 nimble-1.1.0/nimble/inst/include/Eigen/Sparse | 2 nimble-1.1.0/nimble/inst/include/Eigen/SparseCholesky | 8 nimble-1.1.0/nimble/inst/include/Eigen/SparseLU | 4 nimble-1.1.0/nimble/inst/include/Eigen/SparseQR | 1 nimble-1.1.0/nimble/inst/include/Eigen/src/Cholesky/LDLT.h | 78 nimble-1.1.0/nimble/inst/include/Eigen/src/Cholesky/LLT.h | 61 nimble-1.1.0/nimble/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 76 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ArithmeticSequence.h | 143 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Array.h | 112 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ArrayBase.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ArrayWrapper.h | 42 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/AssignEvaluator.h | 175 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Assign_MKL.h | 26 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/BandMatrix.h | 32 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Block.h | 116 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/BooleanRedux.h | 16 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CommaInitializer.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ConditionEstimator.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CoreEvaluators.h | 449 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CwiseBinaryOp.h | 38 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CwiseNullaryOp.h | 133 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CwiseUnaryOp.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/CwiseUnaryView.h | 24 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/DenseBase.h | 170 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/DenseCoeffsBase.h | 46 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/DenseStorage.h | 224 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Diagonal.h | 39 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/DiagonalMatrix.h | 48 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Dot.h | 21 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/EigenBase.h | 19 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ForceAlignedAccess.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/GeneralProduct.h | 23 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/GenericPacketMath.h | 746 + nimble-1.1.0/nimble/inst/include/Eigen/src/Core/GlobalFunctions.h | 23 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/IO.h | 47 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/IndexedView.h | 40 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Inverse.h | 19 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Map.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/MapBase.h | 19 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/MathFunctions.h | 1016 +- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/MathFunctionsImpl.h | 145 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Matrix.h | 158 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/MatrixBase.h | 42 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/NestByValue.h | 73 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/NoAlias.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/NumTraits.h | 93 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/PartialReduxEvaluator.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/PermutationMatrix.h | 34 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/PlainObjectBase.h | 211 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Product.h | 61 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ProductEvaluators.h | 334 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Random.h | 36 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Redux.h | 338 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Ref.h | 140 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Replicate.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Reshaped.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/ReturnByValue.h | 10 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Reverse.h | 24 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Select.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/SelfAdjointView.h | 55 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Solve.h | 28 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/SolveTriangular.h | 33 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/SolverBase.h | 44 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/StableNorm.h | 170 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/StlIterators.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Stride.h | 13 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Swap.h | 9 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Transpose.h | 109 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Transpositions.h | 75 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/TriangularMatrix.h | 153 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/VectorBlock.h | 10 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/VectorwiseOp.h | 225 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/Visitor.h | 166 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX/Complex.h | 179 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX/MathFunctions.h | 467 - nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX/PacketMath.h | 1255 ++ nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX/TypeCasting.h | 66 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX512/Complex.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 446 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 1811 +++ nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AVX512/TypeCasting.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/Complex.h | 317 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/MathFunctions.h | 270 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProduct.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 2390 ++++- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/CUDA/Complex.h | 315 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/BFloat16.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/ConjHelper.h | 116 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/Half.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/Settings.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/Default/TypeCasting.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/GPU |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/HIP |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/MSA |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 536 - nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/NEON/MathFunctions.h | 212 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 4626 +++++++++- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/NEON/TypeCasting.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SSE/Complex.h | 243 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 495 - nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SSE/PacketMath.h | 1160 +- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h | 93 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SVE |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/SYCL |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/ZVector/Complex.h | 187 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/ZVector/MathFunctions.h | 17 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/arch/ZVector/PacketMath.h | 239 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/functors/AssignmentFunctors.h | 13 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/functors/BinaryFunctors.h | 183 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/functors/NullaryFunctors.h | 61 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/functors/StlFunctors.h | 36 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/functors/UnaryFunctors.h | 335 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 1664 ++- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 63 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 70 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h | 187 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/Parallelizer.h | 27 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h | 83 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h | 24 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/SelfadjointProduct.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/SelfadjointRank2Update.h | 7 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 84 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h | 26 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularMatrixVector.h | 22 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 70 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/products/TriangularSolverVector.h | 23 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/BlasUtil.h | 422 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/ConfigureVectorization.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/Constants.h | 30 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 57 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 37 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/IndexedViewHelper.h | 65 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/IntegralConstant.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/Macros.h | 943 +- nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/Memory.h | 236 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/Meta.h | 386 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/ReshapedHelper.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/StaticAssert.h | 17 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/SymbolicIndex.h | 25 nimble-1.1.0/nimble/inst/include/Eigen/src/Core/util/XprHelper.h | 87 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h | 11 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/EigenSolver.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h | 5 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 15 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/RealSchur.h | 34 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 120 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h | 25 nimble-1.1.0/nimble/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h | 35 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/AlignedBox.h | 102 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/AngleAxis.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/EulerAngles.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Homogeneous.h | 26 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Hyperplane.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/OrthoMethods.h | 5 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/ParametrizedLine.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Quaternion.h | 84 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Rotation2D.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Scaling.h | 28 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Transform.h | 141 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Translation.h | 18 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/Umeyama.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/Geometry/arch/Geometry_SIMD.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/Householder/BlockHouseholder.h | 11 nimble-1.1.0/nimble/inst/include/Eigen/src/Householder/Householder.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/Householder/HouseholderSequence.h | 173 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 30 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 30 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 30 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h | 88 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 111 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h | 90 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h | 22 nimble-1.1.0/nimble/inst/include/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h | 20 nimble-1.1.0/nimble/inst/include/Eigen/src/Jacobi/Jacobi.h | 35 nimble-1.1.0/nimble/inst/include/Eigen/src/KLUSupport/KLUSupport.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/LU/Determinant.h | 54 nimble-1.1.0/nimble/inst/include/Eigen/src/LU/FullPivLU.h | 70 nimble-1.1.0/nimble/inst/include/Eigen/src/LU/InverseImpl.h | 35 nimble-1.1.0/nimble/inst/include/Eigen/src/LU/PartialPivLU.h | 129 nimble-1.1.0/nimble/inst/include/Eigen/src/LU/arch/InverseSize4.h |only nimble-1.1.0/nimble/inst/include/Eigen/src/OrderingMethods/Amd.h | 24 nimble-1.1.0/nimble/inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h | 582 - nimble-1.1.0/nimble/inst/include/Eigen/src/OrderingMethods/Ordering.h | 16 nimble-1.1.0/nimble/inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/PardisoSupport/PardisoSupport.h | 16 nimble-1.1.0/nimble/inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 60 nimble-1.1.0/nimble/inst/include/Eigen/src/QR/CompleteOrthogonalDecomposition.h | 125 nimble-1.1.0/nimble/inst/include/Eigen/src/QR/FullPivHouseholderQR.h | 72 nimble-1.1.0/nimble/inst/include/Eigen/src/QR/HouseholderQR.h | 62 nimble-1.1.0/nimble/inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 28 nimble-1.1.0/nimble/inst/include/Eigen/src/SVD/BDCSVD.h | 139 nimble-1.1.0/nimble/inst/include/Eigen/src/SVD/JacobiSVD.h | 36 nimble-1.1.0/nimble/inst/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h | 5 nimble-1.1.0/nimble/inst/include/Eigen/src/SVD/SVDBase.h | 106 nimble-1.1.0/nimble/inst/include/Eigen/src/SVD/UpperBidiagonalization.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 26 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h | 49 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/AmbiVector.h | 5 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/CompressedStorage.h | 16 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h | 12 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseAssign.h | 104 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseBlock.h | 82 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseCompressedBase.h | 35 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 6 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h | 38 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseMatrix.h | 143 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 17 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseProduct.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseRef.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 15 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseUtil.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseVector.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseCore/SparseView.h | 1 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU.h | 176 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU_Memory.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 78 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU_column_dfs.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 2 nimble-1.1.0/nimble/inst/include/Eigen/src/SparseQR/SparseQR.h | 53 nimble-1.1.0/nimble/inst/include/Eigen/src/StlSupport/StdDeque.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/StlSupport/StdList.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/StlSupport/StdVector.h | 4 nimble-1.1.0/nimble/inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h | 18 nimble-1.1.0/nimble/inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h | 208 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 30 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 149 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/BlockMethods.h | 404 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/CommonCwiseUnaryOps.h | 14 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/IndexedViewMethods.h | 17 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 8 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 10 nimble-1.1.0/nimble/inst/include/Eigen/src/plugins/ReshapedMethods.h |only nimble-1.1.0/nimble/inst/include/nimble/RcppNimbleUtils.h | 14 nimble-1.1.0/nimble/inst/include/nimble/Utils.h | 41 nimble-1.1.0/nimble/inst/include/nimble/dists.h | 7 nimble-1.1.0/nimble/inst/include/nimble/nimDerivs_atomic_classes.h | 1 nimble-1.1.0/nimble/inst/include/nimble/nimDerivs_atomic_dyn_ind.h |only nimble-1.1.0/nimble/inst/include/nimble/nimDerivs_dists.h | 193 nimble-1.1.0/nimble/inst/include/nimble/nimDists.h | 7 nimble-1.1.0/nimble/inst/include/nimble/nimIntegrate.h |only nimble-1.1.0/nimble/inst/include/nimble/nimbleCppAD.h | 16 nimble-1.1.0/nimble/inst/include/nimble/nimbleCppADbaseClass.cpp | 11 nimble-1.1.0/nimble/inst/include/nimble/nimbleEigen.h | 90 nimble-1.1.0/nimble/inst/include/nimble/nimbleEigenNimArr.h | 2 nimble-1.1.0/nimble/man/ChineseRestaurantProcess.Rd | 6 nimble-1.1.0/nimble/man/MCMCconf-class.Rd | 81 nimble-1.1.0/nimble/man/as.carAdjacency.Rd | 2 nimble-1.1.0/nimble/man/buildMCEM.Rd | 18 nimble-1.1.0/nimble/man/buildMCMC.Rd | 4 nimble-1.1.0/nimble/man/compileNimble.Rd | 2 nimble-1.1.0/nimble/man/deregisterDistributions.Rd | 6 nimble-1.1.0/nimble/man/getMacroParameters.Rd |only nimble-1.1.0/nimble/man/laplace.Rd | 55 nimble-1.1.0/nimble/man/modelBaseClass-class.Rd | 14 nimble-1.1.0/nimble/man/model_macro_builder.Rd | 14 nimble-1.1.0/nimble/man/nimDerivs.Rd | 2 nimble-1.1.0/nimble/man/nimIntegrate.Rd |only nimble-1.1.0/nimble/man/nimNumeric.Rd | 2 nimble-1.1.0/nimble/man/nimOptim.Rd | 4 nimble-1.1.0/nimble/man/nimOptimDefaultControl.Rd | 4 nimble-1.1.0/nimble/man/nimble-package.Rd |only nimble-1.1.0/nimble/man/nimbleList.Rd | 2 nimble-1.1.0/nimble/man/readBUGSmodel.Rd | 5 nimble-1.1.0/nimble/man/registerDistributions.Rd | 28 nimble-1.1.0/nimble/man/runCrossValidate.Rd | 16 nimble-1.1.0/nimble/man/samplers.Rd | 64 nimble-1.1.0/nimble/man/simNodesMV.Rd | 10 nimble-1.1.0/nimble/tests/testthat/AD_math_test_lists.R | 1 nimble-1.1.0/nimble/tests/testthat/AD_test_utils.R | 16 nimble-1.1.0/nimble/tests/testthat/mathTestLists.R | 18 nimble-1.1.0/nimble/tests/testthat/mcmcTestLog_Correct.Rout | 11 nimble-1.1.0/nimble/tests/testthat/test-ADbasics.R | 153 nimble-1.1.0/nimble/tests/testthat/test-ADdists.R | 2 nimble-1.1.0/nimble/tests/testthat/test-ADerrorTrapping.R | 52 nimble-1.1.0/nimble/tests/testthat/test-ADfunctions.R | 439 nimble-1.1.0/nimble/tests/testthat/test-ADlaplace.R | 46 nimble-1.1.0/nimble/tests/testthat/test-ADmodels-bigmv.R | 13 nimble-1.1.0/nimble/tests/testthat/test-ADmodels.R | 86 nimble-1.1.0/nimble/tests/testthat/test-bnp.R | 34 nimble-1.1.0/nimble/tests/testthat/test-car.R | 41 nimble-1.1.0/nimble/tests/testthat/test-checkDSL.R | 21 nimble-1.1.0/nimble/tests/testthat/test-coreR.R | 27 nimble-1.1.0/nimble/tests/testthat/test-distributions.R | 4 nimble-1.1.0/nimble/tests/testthat/test-errors.R | 58 nimble-1.1.0/nimble/tests/testthat/test-getParam.R | 46 nimble-1.1.0/nimble/tests/testthat/test-integrate.R |only nimble-1.1.0/nimble/tests/testthat/test-macros.R | 688 + nimble-1.1.0/nimble/tests/testthat/test-math.R | 1 nimble-1.1.0/nimble/tests/testthat/test-mcmc.R | 348 nimble-1.1.0/nimble/tests/testthat/test-misc.R | 6 nimble-1.1.0/nimble/tests/testthat/test-models.R | 27 nimble-1.1.0/nimble/tests/testthat/test-nimbleList.R | 9 nimble-1.1.0/nimble/tests/testthat/test-optim.R | 41 nimble-1.1.0/nimble/tests/testthat/test-user.R | 64 nimble-1.1.0/nimble/tests/testthat/test_utils.R | 50 394 files changed, 28444 insertions(+), 11869 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.19.7 dated 2023-11-26 and 0.19.8 dated 2024-01-31
DESCRIPTION | 22 +-- MD5 | 91 +++++++------ NAMESPACE | 9 + NEWS.md | 25 +++ R/all_equal_models.R | 8 - R/apply_table_theme.R |only R/check_if_installed.R | 4 R/clean_names.R | 2 R/clean_parameters.R | 76 +++++------ R/compute_variances.R | 2 R/export_table.R | 59 ++++---- R/find_algorithm.R | 12 - R/find_formula.R | 113 ++++++++-------- R/find_variables.R | 2 R/get_auxiliary.R | 13 + R/get_data.R | 149 ++++++++++------------ R/helper_functions.R | 24 ++- R/is_multivariate.R | 10 + R/link_function.R | 18 ++ R/link_inverse.R | 22 ++- R/model_info.R | 32 ++-- R/n_obs.R | 49 +------ R/null_model.R | 14 -- R/utils_model_info.R | 42 +----- inst/WORDLIST | 2 inst/doc/display.html | 216 +++++++++++++++----------------- inst/doc/export.html | 2 inst/doc/insight.html | 2 man/export_table.Rd | 25 ++- man/find_formula.Rd | 2 man/insight-package.Rd | 1 man/model_info.Rd | 2 tests/testthat/_snaps/format_table.md | 32 ++-- tests/testthat/_snaps/mipo.md | 52 +++---- tests/testthat/test-afex_aov.R | 6 tests/testthat/test-averaging.R |only tests/testthat/test-betareg.R | 79 ++++++----- tests/testthat/test-factor_to_numeric.R |only tests/testthat/test-find_formula.R |only tests/testthat/test-find_variables.R |only tests/testthat/test-gam.R | 144 ++++++++++----------- tests/testthat/test-get_loglikelihood.R | 77 ++++++++--- tests/testthat/test-glmmPQL.R |only tests/testthat/test-glmmTMB.R | 26 +++ tests/testthat/test-marginaleffects.R | 2 tests/testthat/test-rms.R | 36 +++-- tests/testthat/test-rq.R | 25 +-- tests/testthat/test-rqs.R |only tests/testthat/test-vgam.R | 9 - tests/testthat/test-zeroinfl.R | 34 ++--- 50 files changed, 836 insertions(+), 736 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.34.0 dated 2023-10-12 and 1.35.0 dated 2024-01-31
DESCRIPTION | 8 MD5 | 53 ++--- NEWS.md | 40 ++++ R/RcppExports.R | 4 R/conversion.R | 1 R/knitr-engine.R | 110 +++++++---- R/miniconda.R | 4 R/package.R | 3 R/pyenv.R | 2 R/python.R | 16 + R/seed.R | 4 R/utils.R | 42 ++++ R/virtualenv.R | 28 ++ build/vignette.rds |binary inst/doc/python_primer.html | 46 ++-- man/py_set_seed.Rd | 2 man/reticulate.Rd | 30 +++ man/with.python.builtin.object.Rd | 2 src/RcppExports.cpp | 9 src/python.cpp | 195 ++++++++++++-------- tests/testthat/resources/altair-example.Rmd | 49 ++++- tests/testthat/resources/eng-reticulate-example.Rmd | 30 ++- tests/testthat/resources/figure |only tests/testthat/resources/test-custom-root-dir.Rmd |only tests/testthat/resources/test-custom-root-dir.md |only tests/testthat/test-python-knitr-engine.R | 22 ++ tests/testthat/test-python-objects.R | 23 +- tests/testthat/test-python-scipy-sparse-matrix.R | 105 ++++++++++ tests/testthat/test-r-extptr-capsule.R |only 29 files changed, 627 insertions(+), 201 deletions(-)
Title: Integration of Geography, Environment, and Remote Sensing
Description: Handling and manipulation polygons, coordinates, and other geographical objects. The tools include: polygon areas, barycentric and trilinear coordinates (Hormann and Floater, 2006, <doi:10.1145/1183287.1183295>), convex hull for polygons (Graham and Yao, 1983, <doi:10.1016/0196-6774(83)90013-5>), polygon triangulation (Toussaint, 1991, <doi:10.1007/BF01905693>), great circle and geodesic distances, Hausdorff distance, and reduced major axis.
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between tigers versions 0.1-2 dated 2024-01-26 and 0.1-3 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 10 ++++++++++ R/FUNs.R | 5 ++++- 4 files changed, 21 insertions(+), 8 deletions(-)
Title: Download Datasets from the Swiss National Science Foundation
(SNF, FNS, SNSF)
Description: Download and read datasets from the Swiss National
Science Foundation (SNF, FNS, SNSF; <https://snf.ch>). The
package is lightweight and without dependencies. Downloaded
data can optionally be cached, to avoid repeated downloads of
the same files. There are also utilities for comparing
different versions of datasets, i.e. to report added, removed
and changed entries.
Author: Silvia Martens [ctb] ,
Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between SNSFdatasets versions 0.1.0 dated 2023-09-23 and 0.1.1 dated 2024-01-31
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 5 +++++ R/functions.R | 2 +- man/SNSFdatasets.Rd | 28 +++++++++++++++------------- 5 files changed, 30 insertions(+), 23 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.8.0 dated 2023-09-12 and 2.8.4 dated 2024-01-31
redcapAPI-2.8.0/redcapAPI/R/cleanseMetaData.R |only redcapAPI-2.8.0/redcapAPI/man/cleanseMetaData.Rd |only redcapAPI-2.8.4/redcapAPI/DESCRIPTION | 40 - redcapAPI-2.8.4/redcapAPI/MD5 | 393 +++++----- redcapAPI-2.8.4/redcapAPI/NAMESPACE | 20 redcapAPI-2.8.4/redcapAPI/NEWS | 39 redcapAPI-2.8.4/redcapAPI/R/assembleCodebook.R |only redcapAPI-2.8.4/redcapAPI/R/changedRecords.R |only redcapAPI-2.8.4/redcapAPI/R/constructLinkToRedcapForm.R |only redcapAPI-2.8.4/redcapAPI/R/createFileRepositoryFolder.R | 5 redcapAPI-2.8.4/redcapAPI/R/createRedcapProject.R |only redcapAPI-2.8.4/redcapAPI/R/deleteArms.R | 10 redcapAPI-2.8.4/redcapAPI/R/deleteDags.R | 3 redcapAPI-2.8.4/redcapAPI/R/deleteEvents.R | 8 redcapAPI-2.8.4/redcapAPI/R/deleteFiles.R | 2 redcapAPI-2.8.4/redcapAPI/R/deleteFromFileRepository.R | 2 redcapAPI-2.8.4/redcapAPI/R/deleteRecords.R | 4 redcapAPI-2.8.4/redcapAPI/R/deleteUserRoles.R | 2 redcapAPI-2.8.4/redcapAPI/R/deleteUsers.R | 2 redcapAPI-2.8.4/redcapAPI/R/docsArmsMethods.R | 6 redcapAPI-2.8.4/redcapAPI/R/docsDagAssignmentMethods.R | 3 redcapAPI-2.8.4/redcapAPI/R/docsDagMethods.R | 6 redcapAPI-2.8.4/redcapAPI/R/docsEventMethods.R | 6 redcapAPI-2.8.4/redcapAPI/R/docsFileMethods.R | 17 redcapAPI-2.8.4/redcapAPI/R/docsFileRepositoryMethods.R | 18 redcapAPI-2.8.4/redcapAPI/R/docsFromFileRepository.R | 9 redcapAPI-2.8.4/redcapAPI/R/docsMappingMethods.R | 1 redcapAPI-2.8.4/redcapAPI/R/docsMetaDataMethods.R | 8 redcapAPI-2.8.4/redcapAPI/R/docsProjectInformationMethods.R | 3 redcapAPI-2.8.4/redcapAPI/R/docsRecordsManagementMethods.R | 4 redcapAPI-2.8.4/redcapAPI/R/docsRecordsMethods.R | 5 redcapAPI-2.8.4/redcapAPI/R/docsRecordsTypedMethods.R | 36 redcapAPI-2.8.4/redcapAPI/R/docsRepeatingInstrumentEventMethods.R | 3 redcapAPI-2.8.4/redcapAPI/R/docsUserMethods.R | 6 redcapAPI-2.8.4/redcapAPI/R/docsUserRoleAssignmentMethods.R | 3 redcapAPI-2.8.4/redcapAPI/R/docsUserRoleMethods.R | 7 redcapAPI-2.8.4/redcapAPI/R/documentation-common-args.R | 14 redcapAPI-2.8.4/redcapAPI/R/exportArms.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportDags.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportEvents.R | 9 redcapAPI-2.8.4/redcapAPI/R/exportExternalCoding.R |only redcapAPI-2.8.4/redcapAPI/R/exportFieldNames.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportFileRepository.R | 3 redcapAPI-2.8.4/redcapAPI/R/exportFileRepositoryListing.R | 8 redcapAPI-2.8.4/redcapAPI/R/exportFiles.R | 8 redcapAPI-2.8.4/redcapAPI/R/exportFilesMultiple.R |only redcapAPI-2.8.4/redcapAPI/R/exportFromFileRepository.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportInstruments.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportLogging.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportMappings.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportMetaData.R | 18 redcapAPI-2.8.4/redcapAPI/R/exportPDF.R | 7 redcapAPI-2.8.4/redcapAPI/R/exportProjectInformation.R | 4 redcapAPI-2.8.4/redcapAPI/R/exportProjectXml.R |only redcapAPI-2.8.4/redcapAPI/R/exportRecords.R | 27 redcapAPI-2.8.4/redcapAPI/R/exportRecordsTyped.R | 206 +++-- 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redcapAPI-2.8.4/redcapAPI/R/importRecords.R | 16 redcapAPI-2.8.4/redcapAPI/R/importRepeatingInstrumentsEvents.R | 5 redcapAPI-2.8.4/redcapAPI/R/importToFileRepository.R | 1 redcapAPI-2.8.4/redcapAPI/R/importUserDagAssignments.R | 3 redcapAPI-2.8.4/redcapAPI/R/importUserRoleAssignments.R | 3 redcapAPI-2.8.4/redcapAPI/R/importUserRoles.R | 13 redcapAPI-2.8.4/redcapAPI/R/importUsers.R | 4 redcapAPI-2.8.4/redcapAPI/R/invalid.R | 9 redcapAPI-2.8.4/redcapAPI/R/isZeroCodedCheckField.R | 17 redcapAPI-2.8.4/redcapAPI/R/makeApiCall.R | 68 + redcapAPI-2.8.4/redcapAPI/R/missingSummary.R | 3 redcapAPI-2.8.4/redcapAPI/R/prepUserImportData.R | 2 redcapAPI-2.8.4/redcapAPI/R/preserveProject.R |only redcapAPI-2.8.4/redcapAPI/R/purgeRestoreProject.R | 82 -- redcapAPI-2.8.4/redcapAPI/R/redcapConnection.R | 189 ++++ redcapAPI-2.8.4/redcapAPI/R/redcapDataStructure.R | 17 redcapAPI-2.8.4/redcapAPI/R/renameRecord.R | 2 redcapAPI-2.8.4/redcapAPI/R/switchDag.R | 5 redcapAPI-2.8.4/redcapAPI/R/unlockREDCap.R | 7 redcapAPI-2.8.4/redcapAPI/README.md | 120 ++- redcapAPI-2.8.4/redcapAPI/build/vignette.rds |binary redcapAPI-2.8.4/redcapAPI/inst/CITATION | 27 redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-best-practices.pdf |binary redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-casting-data.Rnw |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-casting-data.pdf |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-data-validation.Rnw |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-data-validation.pdf |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-faq.Rnw |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-faq.pdf |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-getting-started-connecting.Rnw |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-getting-started-connecting.pdf |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-missing-data-detection.Rnw |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-missing-data-detection.pdf |only redcapAPI-2.8.4/redcapAPI/inst/doc/redcapAPI-offline-connection.Rnw 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redcapAPI-2.8.4/redcapAPI/tests/testthat/test-059-isZeroCodedCheckField.R | 43 - redcapAPI-2.8.4/redcapAPI/tests/testthat/test-100-projectInfo-functionality.R | 16 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-101-userMethods-Functionality.R | 36 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-102-userRoleMethods-Functionality.R | 17 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-103-userRoleAssignmentMethods-Functionality.R | 20 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-104-dagMethods-Functionality.R | 20 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-105-dagAssignment-Functionality.R | 12 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-106-armsMethods-Functionality.R | 124 +-- redcapAPI-2.8.4/redcapAPI/tests/testthat/test-107-eventsMethods-Functionality.R | 116 +- redcapAPI-2.8.4/redcapAPI/tests/testthat/test-108-metadataMethods-Functionality.R | 15 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-109-instrumentMethods-Functionality.R | 80 +- redcapAPI-2.8.4/redcapAPI/tests/testthat/test-110-repeatingInstruments-Functionality.R | 12 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-200-exportTypedRecords-Functionality.R | 66 + redcapAPI-2.8.4/redcapAPI/tests/testthat/test-201-exportTypedRecords-withDAGs.R | 15 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-204-exportTypedRecords-withRepeatingInstruments.R | 5 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-205-exportTypedRecords-offline-Functionality.R | 138 +++ redcapAPI-2.8.4/redcapAPI/tests/testthat/test-206-exportBulkRecords.R | 6 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-254-mChoiceCast.R | 12 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-257-exportExternalCoding.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-258-assembleCodebook.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-301-fileMethods-Functionality.R | 127 ++- redcapAPI-2.8.4/redcapAPI/tests/testthat/test-304-fileRepository-BulkFileMethods-Functionality.R | 9 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-307-exportFilesMultiple.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-352-savePurgeRestoreProject-ArgumentValidation.R | 29 redcapAPI-2.8.4/redcapAPI/tests/testthat/test-352-savePurgeRestoreProject-Functionality.R | 118 ++- redcapAPI-2.8.4/redcapAPI/tests/testthat/test-359-exportProjectXml-ArgumentValidation.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-359-exportProjectXml-Functionality.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-360-createRedcapProject-ArgumentValidation.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-361-userStructureVersion.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/test-801-changedRecords.R |only redcapAPI-2.8.4/redcapAPI/tests/testthat/testdata/offlineConnectionFiles/TestRedcapAPI_Arms.csv | 2 redcapAPI-2.8.4/redcapAPI/tests/testthat/testdata/offlineConnectionFiles/TestRedcapAPI_DAGs.csv | 4 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redcapAPI-2.8.4/redcapAPI/vignettes/redcapAPI-offline-connection.Rnw |only 211 files changed, 2657 insertions(+), 1225 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 2.0.7 dated 2022-10-19 and 2.0.8 dated 2024-01-31
nlmixr2plot-2.0.7/nlmixr2plot/R/zzz.R |only nlmixr2plot-2.0.8/nlmixr2plot/DESCRIPTION | 16 nlmixr2plot-2.0.8/nlmixr2plot/MD5 | 83 +-- nlmixr2plot-2.0.8/nlmixr2plot/NAMESPACE | 16 nlmixr2plot-2.0.8/nlmixr2plot/NEWS.md | 13 nlmixr2plot-2.0.8/nlmixr2plot/R/nlmixr2plot.R | 1 nlmixr2plot-2.0.8/nlmixr2plot/R/plot.nlmixr2.R | 274 ++++------ nlmixr2plot-2.0.8/nlmixr2plot/R/plot.nlmixr2AugPred.R | 4 nlmixr2plot-2.0.8/nlmixr2plot/R/vpcPlot.R | 39 - nlmixr2plot-2.0.8/nlmixr2plot/README.md | 143 ++--- nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-1.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-10.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-11.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-12.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-13.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-14.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-15.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-16.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-17.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-18.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-19.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-2.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-20.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-21.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-22.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-23.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-24.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-25.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-26.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-27.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-28.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-3.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-4.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-5.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-6.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-7.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-8.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/figures/README-example-9.png |binary nlmixr2plot-2.0.8/nlmixr2plot/man/plot.nlmixr2FitData.Rd | 17 nlmixr2plot-2.0.8/nlmixr2plot/man/vpcPlot.Rd | 24 nlmixr2plot-2.0.8/nlmixr2plot/tests/testthat/test-plots-cens.R | 79 ++ nlmixr2plot-2.0.8/nlmixr2plot/tests/testthat/test-plots-multiple-endpoints.R | 42 - nlmixr2plot-2.0.8/nlmixr2plot/tests/testthat/test-plots.R | 72 +- 43 files changed, 423 insertions(+), 400 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.1 dated 2023-11-20 and 0.15.2 dated 2024-01-31
eq5d-0.15.1/eq5d/man/getDimensionsFromHealthStates.Rd |only eq5d-0.15.1/eq5d/man/getHealthStates.Rd |only eq5d-0.15.1/eq5d/man/getHealthStatesFromDimensions.Rd |only eq5d-0.15.2/eq5d/DESCRIPTION | 10 - eq5d-0.15.2/eq5d/MD5 | 100 +++++++------- eq5d-0.15.2/eq5d/NAMESPACE | 3 eq5d-0.15.2/eq5d/NEWS.md | 12 + eq5d-0.15.2/eq5d/R/data.R | 10 - eq5d-0.15.2/eq5d/R/eq5d.R | 14 - eq5d-0.15.2/eq5d/R/eq5d3l.R | 2 eq5d-0.15.2/eq5d/R/eq5d5l.R | 2 eq5d-0.15.2/eq5d/R/eq5dcf.R | 6 eq5d-0.15.2/eq5d/R/eq5dcw.R | 2 eq5d-0.15.2/eq5d/R/eq5dds.R | 18 +- eq5d-0.15.2/eq5d/R/eq5dlfs.R | 18 +- eq5d-0.15.2/eq5d/R/eq5dlss.R | 12 - eq5d-0.15.2/eq5d/R/eq5dmap.R | 8 - eq5d-0.15.2/eq5d/R/eq5drcw.R | 2 eq5d-0.15.2/eq5d/R/eq5dy.R | 2 eq5d-0.15.2/eq5d/R/eqhpg.R | 12 - eq5d-0.15.2/eq5d/R/eqpchc.R | 18 +- eq5d-0.15.2/eq5d/R/eqps.R | 2 eq5d-0.15.2/eq5d/R/eqshannon.R | 18 +- eq5d-0.15.2/eq5d/R/helpers.R | 43 +++--- eq5d-0.15.2/eq5d/R/sysdata.rda |binary eq5d-0.15.2/eq5d/README.md | 36 ++--- eq5d-0.15.2/eq5d/inst/doc/eq5d.R | 4 eq5d-0.15.2/eq5d/inst/doc/eq5d.Rmd | 12 - eq5d-0.15.2/eq5d/inst/doc/eq5d.html | 34 ++-- eq5d-0.15.2/eq5d/inst/doc/eq5d_nice_dsu.R | 2 eq5d-0.15.2/eq5d/inst/doc/eq5d_nice_dsu.Rmd | 2 eq5d-0.15.2/eq5d/inst/doc/eq5d_nice_dsu.html | 2 eq5d-0.15.2/eq5d/inst/shiny/server.R | 50 +++---- eq5d-0.15.2/eq5d/man/CW.Rd | 2 eq5d-0.15.2/eq5d/man/DSU3L.Rd | 2 eq5d-0.15.2/eq5d/man/DSU5L.Rd | 2 eq5d-0.15.2/eq5d/man/RCW.Rd | 2 eq5d-0.15.2/eq5d/man/TTO.Rd | 2 eq5d-0.15.2/eq5d/man/VT.Rd | 2 eq5d-0.15.2/eq5d/man/eq5d-package.Rd | 2 eq5d-0.15.2/eq5d/man/get_all_health_states.Rd |only eq5d-0.15.2/eq5d/man/get_dimensions_from_health_states.Rd |only eq5d-0.15.2/eq5d/man/get_health_states_from_dimensions.Rd |only eq5d-0.15.2/eq5d/man/hpg.Rd | 2 eq5d-0.15.2/eq5d/man/pchc.Rd | 2 eq5d-0.15.2/eq5d/man/ps.Rd | 2 eq5d-0.15.2/eq5d/man/shannon.Rd | 2 eq5d-0.15.2/eq5d/tests/testthat/test-eq5d5l.R | 22 ++- eq5d-0.15.2/eq5d/tests/testthat/test-eq5dcf.R | 4 eq5d-0.15.2/eq5d/tests/testthat/test-eq5dds.R | 4 eq5d-0.15.2/eq5d/tests/testthat/test-eqshannon.R | 2 eq5d-0.15.2/eq5d/tests/testthat/test-helpers.R | 32 ++-- eq5d-0.15.2/eq5d/vignettes/eq5d.Rmd | 12 - eq5d-0.15.2/eq5d/vignettes/eq5d_nice_dsu.Rmd | 2 54 files changed, 289 insertions(+), 267 deletions(-)
Title: Visualisation, Exploration, and Web Communication of
Archaeological Spatial Data
Description: An R 'Shiny' application for the visualisation, interactive exploration, and web communication of archaeological spatial data. It includes interactive 3D and 2D visualisations, generation of cross sections and maps of the remains, and display an interactive timeline of the work made in a site. Simple spatial statistics can be performed (convex hull, regression surfaces, 2D kernel density estimation), as well as exporting data to other online applications for more complex methods. 'archeoViz' can be used locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
Author: Sebastien Plutniak [aut, cre] ,
Renata Araujo [ctb] ,
Laura Coltofean [ctb] ,
Nicolas Delsol [ctb] ,
Sara Giardino [ctb] ,
Julian Laabs [ctb]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeoViz versions 1.3.2 dated 2023-09-18 and 1.3.4 dated 2024-01-31
archeoViz-1.3.2/archeoViz/TODO |only archeoViz-1.3.4/archeoViz/DESCRIPTION | 13 archeoViz-1.3.4/archeoViz/MD5 | 60 archeoViz-1.3.4/archeoViz/NAMESPACE | 4 archeoViz-1.3.4/archeoViz/NEWS.md | 19 archeoViz-1.3.4/archeoViz/R/app_server.R | 352 ++ archeoViz-1.3.4/archeoViz/R/app_ui.R | 7 archeoViz-1.3.4/archeoViz/R/archeoViz.R | 16 archeoViz-1.3.4/archeoViz/R/do_map_plot.R | 58 archeoViz-1.3.4/archeoViz/R/do_objects_dataset.R | 8 archeoViz-1.3.4/archeoViz/R/do_r_command.R | 2 archeoViz-1.3.4/archeoViz/R/do_section_plot.R | 19 archeoViz-1.3.4/archeoViz/R/do_square_list.R | 7 archeoViz-1.3.4/archeoViz/R/load_interface_terms.R | 1325 +++++----- archeoViz-1.3.4/archeoViz/R/rotate.R |only archeoViz-1.3.4/archeoViz/inst/CITATION | 18 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-es.R | 23 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-es.Rmd | 64 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-es.html | 65 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-fr.R | 23 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-fr.Rmd | 67 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz-fr.html | 64 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz.R | 21 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz.Rmd | 70 archeoViz-1.3.4/archeoViz/inst/doc/archeoViz.html | 74 archeoViz-1.3.4/archeoViz/man/archeoViz.Rd | 8 archeoViz-1.3.4/archeoViz/tests/testthat/test.do_objects_dataset.R | 4 archeoViz-1.3.4/archeoViz/tests/testthat/test.do_r_command.R |only archeoViz-1.3.4/archeoViz/tests/testthat/test.do_section_plot.R | 80 archeoViz-1.3.4/archeoViz/tests/testthat/test.do_square_list.R |only archeoViz-1.3.4/archeoViz/vignettes/archeoViz-es.Rmd | 64 archeoViz-1.3.4/archeoViz/vignettes/archeoViz-fr.Rmd | 67 archeoViz-1.3.4/archeoViz/vignettes/archeoViz.Rmd | 70 33 files changed, 1628 insertions(+), 1044 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa [aut, cre],
Hans Van de Velde [aut]
Maintainer: Wilbert Heeringa <wheeringa@fryske-akademy.nl>
Diff between visvow versions 1.3.10 dated 2023-10-16 and 1.3.11 dated 2024-01-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/visvow.R | 36 +++++++++++++++++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary 5 files changed, 38 insertions(+), 12 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.7-65 dated 2023-12-15 and 1.7-71 dated 2024-01-31
DESCRIPTION | 12 +-- MD5 | 152 +++++++++++++++++++------------------- NAMESPACE | 4 - NEWS.md | 33 ++++++++ R/Agenerics.R | 5 + R/click.R | 54 ++++++------- R/extract.R | 4 - R/focal.R | 8 +- R/hist.R | 2 R/k_means.R | 4 - R/layerCor.R | 1 R/levels.R | 10 +- R/lines.R | 2 R/options.R | 6 - R/plot_legend.R | 71 ++++++++++++++++- R/plot_let.R | 9 +- R/plot_raster.R | 24 ++++-- R/princomp.R | 9 ++ R/rast.R | 14 ++- R/rasterize.R | 1 R/sample.R | 19 +++- R/tiles.R | 35 +++++++- R/values.R | 26 +++++- R/vect.R | 14 +-- R/xapp.R |only inst/tinytest/test_multivariate.R |only man/SpatExtent-class.Rd | 2 man/add.Rd | 4 - man/all.equal.Rd | 6 - man/arith-generic.Rd | 2 man/box.Rd |only man/collapse.Rd | 2 man/compare-generics.Rd | 2 man/contour.Rd | 4 - man/expanse.Rd | 2 man/extend.Rd | 6 + man/identical.Rd |only man/init.Rd | 2 man/layerCor.Rd | 9 ++ man/makeTiles.Rd | 25 ++++-- man/math-generics.Rd | 2 man/merge.Rd | 2 man/plet.Rd | 2 man/plot.Rd | 26 +++++- man/plotRGB.Rd | 2 man/prcomp.Rd |only man/predict.Rd | 2 man/princomp.Rd | 10 +- man/project.Rd | 2 man/rast.Rd | 2 man/sds.Rd | 2 man/setValues.Rd | 2 man/sprc.Rd | 6 - man/summarize-generics.Rd | 2 man/terra-package.Rd | 10 +- man/tmpFile.Rd | 2 man/union.Rd | 2 man/vect.Rd | 3 man/vrt.Rd | 2 man/writeRaster.Rd | 4 - man/xapp.Rd |only man/xyCellFrom.Rd | 4 - src/RcppModule.cpp | 4 - src/arith.cpp | 1 src/file_utils.cpp | 14 ++- src/file_utils.h | 2 src/focal.cpp | 20 ++++- src/gdal_algs.cpp | 26 +----- src/gdalio.cpp | 10 +- src/raster_methods.cpp | 118 ++++++++++++++++++++++++++++- src/rasterize.cpp | 2 src/read_gdal.cpp | 2 src/read_ogr.cpp | 14 ++- src/spatBase.cpp | 2 src/spatBase.h | 2 src/spatRaster.cpp | 2 src/spatRaster.h | 8 +- src/spatVector.h | 3 src/write.cpp | 2 src/write_ogr.cpp | 2 80 files changed, 634 insertions(+), 274 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the
'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged; it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.6.1 dated 2023-10-30 and 2.0.0 dated 2024-01-31
DESCRIPTION | 12 +- MD5 | 100 ++++++++++---------- NEWS.md | 6 + R/alphord.R | 56 +++++++---- R/arg-match.R | 75 ++++++++++----- R/c-wrappers.R | 13 +- R/currency.R | 2 R/extract-non-nums.R | 53 ++++++---- R/extract-nums.R | 141 +++++++++++++++++------------ R/num-after.R | 91 +++++++++++------- R/num-before.R | 96 ++++++++++++------- R/split-by-nums.R | 17 ++- R/trim.R | 26 ++--- R/utils.R | 24 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alphordering-numbers.R | 4 inst/doc/alphordering-numbers.Rmd | 4 inst/doc/alphordering-numbers.html | 4 inst/doc/argument-matching.html | 4 inst/doc/before-and-after.R | 4 inst/doc/before-and-after.Rmd | 4 inst/doc/before-and-after.html | 8 - inst/doc/detection.R | 2 inst/doc/detection.html | 9 - inst/doc/important-miscellany.R | 16 +-- inst/doc/important-miscellany.Rmd | 14 +- inst/doc/important-miscellany.html | 18 +-- inst/doc/numbers-in-strings.R | 11 +- inst/doc/numbers-in-strings.Rmd | 14 ++ inst/doc/numbers-in-strings.html | 73 ++++++++------- man/str_extract_non_numerics.Rd | 20 ++-- man/str_extract_numbers.Rd | 31 +++--- man/str_nth_non_numeric.Rd | 23 +++- man/str_nth_number.Rd | 36 ++++--- man/str_nth_number_after_mth.Rd | 57 +++++++---- man/str_nth_number_before_mth.Rd | 57 +++++++---- man/str_split_by_numbers.Rd | 13 ++ src/list-utils.c | 32 +++--- src/stringi-imports.h | 2 tests/testthat/test-c-wrappers.R | 4 tests/testthat/test-camel-case.R | 11 +- tests/testthat/test-currency.R | 17 +-- tests/testthat/test-detect.R | 42 +++++--- tests/testthat/test-elem.R | 30 +++--- tests/testthat/test-extract-non-numerics.R | 8 - tests/testthat/test-extract-nums.R | 15 +-- vignettes/alphordering-numbers.Rmd | 4 vignettes/before-and-after.Rmd | 4 vignettes/important-miscellany.Rmd | 14 +- vignettes/numbers-in-strings.Rmd | 14 ++ 51 files changed, 797 insertions(+), 538 deletions(-)
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.6.0 dated 2022-08-31 and 1.7.0 dated 2024-01-31
PhylogeneticEM-1.6.0/PhylogeneticEM/man/extract.variance_covariance.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/prod.index.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/qr.solve_exact.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/sum.partitions.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/sum.partitions.cardFixed.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/sum.prod.comb.Rd |only PhylogeneticEM-1.6.0/PhylogeneticEM/man/sum.simplex.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/DESCRIPTION | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/MD5 | 143 - PhylogeneticEM-1.7.0/PhylogeneticEM/NAMESPACE | 1 PhylogeneticEM-1.7.0/PhylogeneticEM/NEWS.md | 7 PhylogeneticEM-1.7.0/PhylogeneticEM/R/E_step.R | 62 PhylogeneticEM-1.7.0/PhylogeneticEM/R/M_step.R | 14 PhylogeneticEM-1.7.0/PhylogeneticEM/R/estimateEM.R | 42 PhylogeneticEM-1.7.0/PhylogeneticEM/R/generic_functions.R | 5 PhylogeneticEM-1.7.0/PhylogeneticEM/R/init_EM.R | 16 PhylogeneticEM-1.7.0/PhylogeneticEM/R/model_selection.R | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/R/parsimonyNumber.R | 16 PhylogeneticEM-1.7.0/PhylogeneticEM/R/partitionsNumber.R | 46 PhylogeneticEM-1.7.0/PhylogeneticEM/R/plot_functions.R | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/R/shifts_manipulations.R | 66 PhylogeneticEM-1.7.0/PhylogeneticEM/R/shutoff.R | 82 - PhylogeneticEM-1.7.0/PhylogeneticEM/R/simulate.R | 20 PhylogeneticEM-1.7.0/PhylogeneticEM/build/vignette.rds |binary PhylogeneticEM-1.7.0/PhylogeneticEM/inst/CITATION | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/monkeys.R | 118 - PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/monkeys.Rmd | 119 - PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/monkeys.html | 730 +++++++--- PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/tutorial.R | 31 PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/tutorial.Rmd | 32 PhylogeneticEM-1.7.0/PhylogeneticEM/inst/doc/tutorial.html | 338 ++-- PhylogeneticEM-1.7.0/PhylogeneticEM/man/allocate_subset_node.simulate.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/check_data.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_E.simple.Rd | 10 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_actualization_matrix_ultrametric.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_betas_from_shifts.Rd | 5 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_expectations.BM.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_expectations.scOU.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_gauss_lasso.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_log_likelihood.simple.Rd | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_mahalanobis_distance.simple.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_residuals.simple.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/compute_sum_var_diff.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/enlight.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/equivalent_shifts_values.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/estimateEM.Rd | 14 PhylogeneticEM-1.7.0/PhylogeneticEM/man/extract_variance_covariance.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/find_grid_alpha.Rd | 3 PhylogeneticEM-1.7.0/PhylogeneticEM/man/find_shift_values.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/go_back_to_original_process.Rd | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/man/imputed_traits.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/incidence_matrix_actualization_factors.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/init.compute_betas_from_shifts.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/init.parsimonyCost.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/init.parsimonyNumber.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/init.simulate.OU.Rd | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/man/init.simulate.StateAndExp.Rd | 8 PhylogeneticEM-1.7.0/PhylogeneticEM/man/is.in.ranges.Rd | 67 PhylogeneticEM-1.7.0/PhylogeneticEM/man/log_likelihood.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/merge_params_independent.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/man/model_selection.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/node_optimal_values.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/params_BM.Rd | 3 PhylogeneticEM-1.7.0/PhylogeneticEM/man/params_OU.Rd | 3 PhylogeneticEM-1.7.0/PhylogeneticEM/man/penalty_pBIC.Rd | 3 PhylogeneticEM-1.7.0/PhylogeneticEM/man/prod_index.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/qr_solve_exact.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/segmentation.OU.specialCase.lasso.Rd | 5 PhylogeneticEM-1.7.0/PhylogeneticEM/man/segmentation.OU.specialCase.same_shifts.Rd | 5 PhylogeneticEM-1.7.0/PhylogeneticEM/man/simul_process.Rd | 6 PhylogeneticEM-1.7.0/PhylogeneticEM/man/simulate_internal.Rd | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/man/sum_partitions.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/sum_partitions.cardFixed.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/sum_prod.comb.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/sum_simplex.Rd |only PhylogeneticEM-1.7.0/PhylogeneticEM/man/update.partitionsNumber.gen.Rd | 2 PhylogeneticEM-1.7.0/PhylogeneticEM/tests/testthat/test-core-log_likelihood.R | 4 PhylogeneticEM-1.7.0/PhylogeneticEM/tests/testthat/test-utilities-rotations.R | 5 PhylogeneticEM-1.7.0/PhylogeneticEM/vignettes/monkeys.Rmd | 119 - PhylogeneticEM-1.7.0/PhylogeneticEM/vignettes/tutorial.Rmd | 32 80 files changed, 1248 insertions(+), 1060 deletions(-)
More information about PhylogeneticEM at CRAN
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Title: Basic Functions to Investigate Metabolomics Data Matrices
Description: A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between MetabolomicsBasics versions 1.4.3 dated 2023-10-27 and 1.4.5 dated 2024-01-31
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++++----- NAMESPACE | 2 +- R/PolarPlot.R |only R/unique_subformula_masses.R | 16 +++++++++++----- README.md | 29 +++++++++++++++++++++++------ man/PolarCoordHeterPlot.Rd |only man/figures/README-example1-1.png |only man/figures/README-example2-1.png |only man/unique_subformula_masses.Rd | 10 ++++++++-- 10 files changed, 57 insertions(+), 24 deletions(-)
More information about MetabolomicsBasics at CRAN
Permanent link
Title: Geographically-Weighted Models
Description: Techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. 'GWmodel' includes functions to calibrate: GW summary statistics (Brunsdon et al., 2002)<doi: 10.1016/s0198-9715(01)00009-6>, GW principal components analysis (Harris et al., 2011)<doi: 10.1080/13658816.2011.554838>, GW discriminant analysis (Brunsdon et al., 2007)<doi: 10.1111/j.1538-4632.2007.00709.x> and various forms of GW regression (Brunsdon et al., 1996)<doi: 10.1111/j.1538-4632.1996.tb00936.x>; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Daisuke Murakami[aut],Isabella Gollini[ctb], Yigong Hu[ctb], Fiona H Evans[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 2.3-1 dated 2023-07-05 and 2.3-2 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/gtwr.R | 2 +- R/gwr.mixed.r | 5 ++++- R/zzz.r | 2 +- build/partial.rdb |binary man/GWmodel-package.Rd | 4 ++-- man/USelect.rd | 3 +-- 8 files changed, 20 insertions(+), 18 deletions(-)
Title: 'data.table' Time-Series
Description: High-frequency time-series support via 'nanotime' and 'data.table'.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dtts versions 0.1.1 dated 2023-08-08 and 0.1.2 dated 2024-01-31
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/NEWS.Rd | 8 ++++++++ src/align.cpp | 4 ++-- 5 files changed, 34 insertions(+), 12 deletions(-)
Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] ,
Tejasvi Gupta [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpecUtils versions 1.0.3 dated 2023-05-30 and 1.0.4 dated 2024-01-31
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/ChemoSpecUtils-package.R | 3 +-- R/check4Gaps.R | 2 +- R/chkArgs.R | 2 +- build/partial.rdb |binary data/Col12.RData |binary data/Col7.RData |binary data/Col8.RData |binary data/Sym12.RData |binary data/Sym8.RData |binary man/ChemoSpecUtils-package.Rd | 8 ++++++++ man/check4Gaps.Rd | 2 +- man/dot-chkArgs.Rd | 2 +- 15 files changed, 37 insertions(+), 26 deletions(-)
More information about ChemoSpecUtils at CRAN
Permanent link
Title: Interactive Assessments of Models
Description: Launch a 'shiny' application for 'tidymodels' results. For
classification or regression models, the app can be used to determine
if there is lack of fit or poorly predicted points.
Author: Max Kuhn [aut] ,
Shisham Adhikari [aut],
Julia Silge [aut] ,
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between shinymodels versions 0.1.0 dated 2021-11-17 and 0.1.1 dated 2024-01-31
DESCRIPTION | 31 LICENSE | 4 MD5 | 100 NEWS.md | 4 R/explore.R | 2 R/multi_class_diag_plots.R | 6 R/regression_diag_plots.R | 8 R/shiny_models.R | 1 R/two_class_diag_plots.R | 6 README.md | 41 inst/welcome/welcome_tab.Rmd | 10 man/ames_mlp_itr.Rd | 6 man/cars_bag_vfld.Rd | 6 man/cell_race.Rd | 6 man/explore.Rd | 4 man/plot_multiclass_obs_pred.Rd | 2 man/plot_multiclass_pred_factorcol.Rd | 2 man/plot_multiclass_pred_numcol.Rd | 2 man/plot_numeric_obs_pred.Rd | 2 man/plot_numeric_res_factorcol.Rd | 2 man/plot_numeric_res_numcol.Rd | 2 man/plot_numeric_res_pred.Rd | 2 man/plot_twoclass_obs_pred.Rd | 2 man/plot_twoclass_pred_factorcol.Rd | 2 man/plot_twoclass_pred_numcol.Rd | 2 man/scat_fda_bt.Rd | 6 man/shiny_models.Rd | 2 man/shinymodels-package.Rd | 9 man/two_class_final.Rd | 6 tests/testthat/_snaps/display_selected.md |only tests/testthat/_snaps/first_level.md |only tests/testthat/_snaps/first_level_prob_name.md |only tests/testthat/_snaps/multiclass_plots |only tests/testthat/_snaps/multiclass_plots.md | 3738 ------------------------- tests/testthat/_snaps/organize_data.md |only tests/testthat/_snaps/reg_plots |only tests/testthat/_snaps/reg_plots.md | 843 ----- tests/testthat/_snaps/twoclass_plots |only tests/testthat/_snaps/twoclass_plots.md | 1691 ----------- tests/testthat/helper.R | 12 tests/testthat/misc.R | 6 tests/testthat/test-display_selected.R | 18 tests/testthat/test-first_level.R | 53 tests/testthat/test-first_level_prob_name.R | 23 tests/testthat/test-multiclass_plots.R | 105 tests/testthat/test-organize_data.R | 21 tests/testthat/test-reg_plots.R | 70 tests/testthat/test-twoclass_plots.R | 117 48 files changed, 513 insertions(+), 6462 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 2.3.1.1 dated 2023-07-18 and 2.4.0 dated 2024-01-31
DESCRIPTION | 10 - MD5 | 39 +++--- NAMESPACE | 1 NEWS.md | 7 + R/rstan_config.R | 2 R/rstan_create_package.R | 2 R/rstan_package_utils.R | 21 +++ R/use_rstan.R | 15 ++ build/vignette.rds |binary inst/doc/developer-guidelines.html | 2 inst/doc/minimal-rstan-package.R | 39 ++---- inst/doc/minimal-rstan-package.Rmd | 7 - inst/doc/minimal-rstan-package.html | 179 ++++++++++++++--------------- inst/include/sys/rstanpkg-package.R | 2 man/rstan_create_package.Rd | 2 man/rstantools-package.Rd | 27 ++++ man/rstantools_load_code.Rd |only man/use_rstan.Rd | 1 tests/testthat/RStanTest/NAMESPACE | 2 tests/testthat/test-rstan_create_package.R | 3 vignettes/minimal-rstan-package.Rmd | 7 - 21 files changed, 219 insertions(+), 149 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of implementation can
be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.1-2 dated 2023-11-22 and 3.0.1-3 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 26 +++++++++++++++++--------- R/pRecipe.R | 6 ++---- R/trend.R | 14 ++++++++------ inst/doc/introduction.html | 4 ++-- man/pRecipe-package.Rd | 10 ++++++++++ 7 files changed, 49 insertions(+), 31 deletions(-)
Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using
an expressive statistical grammar that coheres with the tidy design
framework.
Author: Andrew Bray [aut],
Chester Ismay [aut] ,
Evgeni Chasnovski [aut] ,
Simon Couch [aut, cre] ,
Ben Baumer [aut] ,
Mine Cetinkaya-Rundel [aut] ,
Ted Laderas [ctb] ,
Nick Solomon [ctb],
Johanna Hardin [ctb],
Albert Y. Kim [ctb] ,
Neal Fultz [ctb],
Doug Fr [...truncated...]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between infer versions 1.0.5 dated 2023-09-05 and 1.0.6 dated 2024-01-31
DESCRIPTION | 14 - MD5 | 114 +++++++------- NAMESPACE | 8 - NEWS.md | 12 + R/assume.R | 67 ++++---- R/calculate.R | 64 ++++---- R/deprecated.R | 2 R/fit.R | 11 - R/generate.R | 88 +++++------ R/get_confidence_interval.R | 92 +++++++---- R/get_p_value.R | 32 ++-- R/hypothesize.R | 88 ++++++----- R/infer.R | 2 R/rep_sample_n.R | 10 - R/set_params.R | 8 - R/shade_confidence_interval.R | 4 R/shade_p_value.R | 22 +- R/specify.R | 92 ++++++----- R/utils.R | 165 +++++++++++---------- R/visualize.R | 126 ++++++++-------- R/wrappers.R | 128 +++++----------- README.md | 34 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/anova.html | 8 - inst/doc/chi_squared.html | 6 inst/doc/infer.R | 8 - inst/doc/observed_stat_examples.R | 16 -- inst/doc/observed_stat_examples.Rmd | 25 --- inst/doc/observed_stat_examples.html | 39 +--- inst/doc/t_test.R | 4 inst/doc/t_test.Rmd | 4 inst/doc/t_test.html | 10 - man/chisq_stat.Rd | 7 man/chisq_test.Rd | 7 man/deprecated.Rd | 2 man/infer.Rd | 2 man/prop_test.Rd | 21 -- man/shade_confidence_interval.Rd | 4 man/shade_p_value.Rd | 4 man/t_stat.Rd | 9 - man/t_test.Rd | 7 man/visualize.Rd | 4 tests/testthat/_snaps/assume.md | 8 - tests/testthat/_snaps/calculate.md | 22 +- tests/testthat/_snaps/fit.md | 3 tests/testthat/_snaps/generate.md | 12 - tests/testthat/_snaps/get_confidence_interval.md | 18 +- tests/testthat/_snaps/get_p_value.md | 24 ++- tests/testthat/_snaps/rep_sample_n.md | 2 tests/testthat/_snaps/shade_confidence_interval.md | 12 + tests/testthat/_snaps/shade_p_value.md | 18 +- tests/testthat/_snaps/specify.md | 16 +- tests/testthat/_snaps/visualize.md | 37 ++-- tests/testthat/_snaps/wrappers.md | 6 tests/testthat/test-get_confidence_interval.R | 19 ++ vignettes/observed_stat_examples.Rmd | 25 --- vignettes/t_test.Rmd | 4 58 files changed, 845 insertions(+), 751 deletions(-)
Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional
data (e.g. portions of substances) and positive numbers (e.g. concentrations)
in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart <boogaart@hzdr.de>,
Raimon Tolosana-Delgado, Matevz Bren
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between compositions versions 2.0-7 dated 2024-01-09 and 2.0-8 dated 2024-01-31
compositions-2.0-7/compositions/tests/RobustTest.Rout.save |only compositions-2.0-7/compositions/tests/missings.R |only compositions-2.0-7/compositions/tests/missings.Rout.save |only compositions-2.0-8/compositions/ChangeLog | 7 compositions-2.0-8/compositions/DESCRIPTION | 8 compositions-2.0-8/compositions/MD5 | 33 compositions-2.0-8/compositions/R/compositions.R | 5 compositions-2.0-8/compositions/build/partial.rdb |binary compositions-2.0-8/compositions/inst/doc/UsingCompositions.pdf |binary compositions-2.0-8/compositions/tests/AitchisonTest.R | 2 compositions-2.0-8/compositions/tests/CheckGeometry.R | 6 compositions-2.0-8/compositions/tests/CheckGeometry.Rout.save | 21 compositions-2.0-8/compositions/tests/RobustTest.R | 1 compositions-2.0-8/compositions/tests/Rplots.pdf |binary compositions-2.0-8/compositions/tests/TestMissing.R | 88 compositions-2.0-8/compositions/tests/TestMissing.Rout.save | 395 compositions-2.0-8/compositions/tests/TestSimp.R | 189 compositions-2.0-8/compositions/tests/TestSimp.Rout.save | 7898 +--------- compositions-2.0-8/compositions/tests/geostat.R | 72 19 files changed, 1503 insertions(+), 7222 deletions(-)
Title: ROBustness in Network
Description: Assesses the robustness of the community structure of a network found by one or more community detection algorithm to give indications about their reliability. It detects if the community structure found by a set of algorithms is statistically significant and compares the different selected detection algorithms on the same network. robin helps to choose among different community detection algorithms the one that better fits the network of interest. Reference in Policastro V., Righelli D., Carissimo A., Cutillo L., De Feis I. (2021) <https://journal.r-project.org/archive/2021/RJ-2021-040/index.html>.
Author: Valeria Policastro [aut, cre],
Dario Righelli [aut],
Luisa Cutillo [aut],
Italia De Feis [aut],
Annamaria Carissimo [aut]
Maintainer: Valeria Policastro <valeria.policastro@gmail.com>
Diff between robin versions 1.1.1 dated 2022-05-16 and 1.1.2 dated 2024-01-31
DESCRIPTION | 8 MD5 | 33 R/ROBIN.R | 150 ++- R/ROBINFast.R | 2 README.md | 23 build/vignette.rds |binary inst/NEWS | 2 inst/doc/robin.R | 2 inst/doc/robin.Rmd | 5 inst/doc/robin.html | 1875 ++++++++++++++++++++++++++++++++++++++----- man/createITPSplineResult.Rd | 3 man/img |only man/membershipCommunities.Rd | 10 man/methodCommunity.Rd | 8 man/rewireCompl.Rd | 6 man/robinCompareFast.Rd | 164 +-- man/robinRobust.Rd | 8 vignettes/robin.Rmd | 5 18 files changed, 1932 insertions(+), 372 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 2.0.8 dated 2022-10-22 and 2.0.9 dated 2024-01-31
nlmixr2extra-2.0.8/nlmixr2extra/R/bootstrap.R |only nlmixr2extra-2.0.9/nlmixr2extra/DESCRIPTION | 20 nlmixr2extra-2.0.9/nlmixr2extra/MD5 | 54 nlmixr2extra-2.0.9/nlmixr2extra/NAMESPACE | 4 nlmixr2extra-2.0.9/nlmixr2extra/NEWS.md | 21 nlmixr2extra-2.0.9/nlmixr2extra/R/SCM.R | 213 nlmixr2extra-2.0.9/nlmixr2extra/R/bayesiancovsel.R | 169 nlmixr2extra-2.0.9/nlmixr2extra/R/computingutil.R | 874 nlmixr2extra-2.0.9/nlmixr2extra/R/knit_printEquation.R |only nlmixr2extra-2.0.9/nlmixr2extra/R/lassocov.R | 513 nlmixr2extra-2.0.9/nlmixr2extra/README.md |100210 ---------- nlmixr2extra-2.0.9/nlmixr2extra/man/adaptivelassoCoefficients.Rd | 17 nlmixr2extra-2.0.9/nlmixr2extra/man/adjustedlassoCoefficients.Rd | 16 nlmixr2extra-2.0.9/nlmixr2extra/man/bootplot.Rd | 15 nlmixr2extra-2.0.9/nlmixr2extra/man/bootstrapFit.Rd | 103 nlmixr2extra-2.0.9/nlmixr2extra/man/covarSearchAuto.Rd | 20 nlmixr2extra-2.0.9/nlmixr2extra/man/foldgen.Rd | 17 nlmixr2extra-2.0.9/nlmixr2extra/man/horseshoeSummardf.Rd | 17 nlmixr2extra-2.0.9/nlmixr2extra/man/knit_print.nlmixr2FitCore.Rd |only nlmixr2extra-2.0.9/nlmixr2extra/man/lassoCoefficients.Rd | 20 nlmixr2extra-2.0.9/nlmixr2extra/man/lassoSummardf.Rd | 16 nlmixr2extra-2.0.9/nlmixr2extra/man/normalizedData.Rd | 3 nlmixr2extra-2.0.9/nlmixr2extra/man/optimUnisampling.Rd | 6 nlmixr2extra-2.0.9/nlmixr2extra/man/reexports.Rd | 5 nlmixr2extra-2.0.9/nlmixr2extra/man/regularmodel.Rd | 17 nlmixr2extra-2.0.9/nlmixr2extra/src/Makevars.in | 3 nlmixr2extra-2.0.9/nlmixr2extra/tests/testthat/test-bootstrap.R | 108 nlmixr2extra-2.0.9/nlmixr2extra/tests/testthat/test-computing.R | 21 nlmixr2extra-2.0.9/nlmixr2extra/tests/testthat/test-knit_printEquation.R |only nlmixr2extra-2.0.9/nlmixr2extra/tests/testthat/test-lasso.R | 29 30 files changed, 1124 insertions(+), 101387 deletions(-)
Title: Bayesian Causal Mediation Analysis using 'Stan'
Description: Performs parametric mediation analysis using the Bayesian g-formula approach for binary and continuous outcomes. The methodology is based on Comment (2018) <doi:10.5281/zenodo.1285275> and a demonstration of its application can be found at Yimer et al. (2022) <doi:10.48550/arXiv.2210.08499>.
Author: Belay Birlie Yimer [aut, cre] ,
Mark Lunt [aut],
Marcus Beasley [aut],
Gary J Macfarlane [aut],
John McBeth [aut]
Maintainer: Belay Birlie Yimer <belaybirlie.yimer@manchester.ac.uk>
Diff between BayesGmed versions 0.0.2 dated 2023-11-10 and 0.0.3 dated 2024-01-31
DESCRIPTION | 6 - MD5 | 30 ++--- NEWS.md | 4 inst/doc/Intro_to_BayesGmed.html | 50 ++++----- inst/stan/BY_BM_single.stan | 182 ++++++++++++++++----------------- inst/stan/BY_BM_single_sens.stan | 6 - inst/stan/BY_NM_single.stan | 194 ++++++++++++++++++------------------ inst/stan/BY_NM_single_sens.stan | 4 inst/stan/NY_BM_single.stan | 194 ++++++++++++++++++------------------ inst/stan/NY_BM_single_sens.stan | 4 src/stanExports_BY_BM_single.h | 8 - src/stanExports_BY_BM_single_sens.h | 8 - src/stanExports_BY_NM_single.h | 4 src/stanExports_BY_NM_single_sens.h | 4 src/stanExports_NY_BM_single.h | 4 src/stanExports_NY_BM_single_sens.h | 4 16 files changed, 355 insertions(+), 351 deletions(-)
Title: Alternating Optimization
Description: Alternating optimization of (high-dimensional) functions is an
iterative procedure for optimizing jointly over all parameters by
alternately optimizing parameter subsets.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 0.3.0 dated 2023-11-08 and 0.3.1 dated 2024-01-31
DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 1 NEWS.md | 206 ++++++++++--------- R/ao-package.R | 29 +- R/ao.R | 500 ++++++++++++++++++++++++----------------------- README.md | 98 ++++++--- build/vignette.rds |binary inst/doc/ao.R | 4 inst/doc/ao.Rmd | 138 ++++++------ inst/doc/ao.html | 62 +++-- man/ao-package.Rd | 52 ++-- man/ao.Rd | 4 tests/testthat/test-ao.R | 314 ++++++++++++++--------------- vignettes/ao.Rmd | 138 ++++++------ 15 files changed, 832 insertions(+), 752 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-20 0.2.1
Title: Construct Parsers for Structured Text Files
Description: Construct parser combinator functions, higher order functions that
parse input. Construction of such parsers is transparent and easy. Their main
application is the parsing of structured text files like those generated by
laboratory instruments. Based on a paper by Hutton (1992)
<doi:10.1017/S0956796800000411>.
Author: Douwe Molenaar [aut, cre, cph]
Maintainer: Douwe Molenaar <d.molenaar@vu.nl>
Diff between parcr versions 0.5.0 dated 2024-01-16 and 0.5.1 dated 2024-01-31
DESCRIPTION | 10 ++++----- MD5 | 20 +++++++++--------- NEWS.md | 8 +++++++ README.md | 11 ++++++++-- inst/doc/Creating_parser_combinators.R | 8 +++---- inst/doc/Creating_parser_combinators.Rmd | 27 ++++++++++++++----------- inst/doc/Creating_parser_combinators.html | 32 +++++++++++++++--------------- inst/doc/Design_details.Rmd | 5 +++- inst/doc/Design_details.html | 17 ++++++++++++++- vignettes/Creating_parser_combinators.Rmd | 27 ++++++++++++++----------- vignettes/Design_details.Rmd | 5 +++- 11 files changed, 105 insertions(+), 65 deletions(-)
Title: Interpreting High Resolution Mass Spectra
Description: High resolution mass spectrometry yields often large data sets of
spectra from compounds which are not present in available libraries. These
spectra need to be annotated and interpreted.
'InterpretMSSpectrum' provides a set of functions to perform such tasks for
Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived
data in positive and negative ionization mode.
Author: Jan Lisec [aut, cre] ,
Jaeger Carsten [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between InterpretMSSpectrum versions 1.3.8 dated 2023-07-07 and 1.4.5 dated 2024-01-31
InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/ExtractChemicalElements.R |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/plot.findMAIN.R |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/print.findMAIN.R |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/PlausibleFormula.Rd |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/DESCRIPTION | 27 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/MD5 | 62 - InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/NAMESPACE | 3 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/CountChemicalElements.R | 1 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/DetermineIsomainPeaks.R | 15 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/GenerateMetaboliteSQLiteDB.R | 4 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/InterpretMSSpectrum.R | 545 +++------- InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/InterpretTP.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/PlausibleFormula.R | 131 +- InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/PlotSpec.R | 46 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/ReadSpecClipboard.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/ScoreFormulaCombination.R | 1 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/check_param.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/findMAIN.r | 149 ++ InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/getNeutralMass.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/get_exactmass.R | 2 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/is.subformula.R | 4 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/R/summary.findMAIN.R | 1 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/README.md |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/inst/CITATION |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/InterpretMSSpectrum.Rd | 65 - InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/InterpretTP.Rd |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/PlotSpec.Rd | 29 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/ReadSpecClipboard.Rd |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/figures |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/findMAIN.Rd | 33 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/man/get_exactmass.Rd | 2 InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/_snaps |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-CountChemicalElements.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-DetermineIsomainPeaks.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-GetIsotopeDistribution.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-InterpretMSSpectrum.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-InterpretTP.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-PlotSpec.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-ReadSpecClipboard.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-check_param.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-findMAIN.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-get_exactmass.R |only InterpretMSSpectrum-1.4.5/InterpretMSSpectrum/tests/testthat/test-is.subformula.R |only 43 files changed, 586 insertions(+), 534 deletions(-)
More information about InterpretMSSpectrum at CRAN
Permanent link
Title: Penalized Composite Link Model for Efficient Estimation of
Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data)
assuming that counts are Poisson distributed and that the underlying sequence
on a fine grid to be estimated is smooth. The method is based on the composite
link model and estimation is achieved by maximizing a penalized likelihood.
Smooth detailed sequences of counts and rates are so estimated from the binned
counts. Ungrouping binned data can be desirable for many reasons: Bins can be
too coarse to allow for accurate analysis; comparisons can be hindered when
different grouping approaches are used in different histograms; and the last
interval is often wide and open-ended and, thus, covers a lot of information
in the tail area. Age-at-death distributions grouped in age classes and
abridged life tables are examples of binned data. Because of modest assumptions,
the approach is suitable for many demographic and epidemiological applications.
For a detailed description of the method and applications see
Rizzi et al. (2015) &l [...truncated...]
Author: Marius D. Pascariu [aut, cre] ,
Silvia Rizzi [aut],
Jonas Schoeley [aut] ,
Maciej J. Danko [aut]
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between ungroup versions 1.4.2 dated 2021-06-28 and 1.4.4 dated 2024-01-31
DESCRIPTION | 9 LICENSE | 4 MD5 | 142 +++++----- NAMESPACE | 114 ++++---- NEWS | 42 +-- R/MortalitySmooth_fun.R | 166 +++++------ R/RcppExports.R | 22 - R/pclm_1D.R | 572 ++++++++++++++++++++--------------------- R/pclm_2D.R | 434 +++++++++++++++---------------- R/pclm_CI.R | 298 ++++++++++----------- R/pclm_control.R | 172 ++++++------ R/pclm_fit.R | 452 ++++++++++++++++---------------- R/pclm_graphics.R | 418 ++++++++++++++--------------- R/pclm_optim.R | 194 ++++++------- R/ungroup-data.R | 82 ++--- R/ungroup-package.r | 45 +-- R/utils.R | 316 +++++++++++----------- README.md | 116 ++++---- THANKS | 38 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 68 ++-- inst/REFERENCES.bib | 194 ++++++------- inst/doc/Intro.R | 118 ++++---- inst/doc/Intro.Rmd | 292 ++++++++++---------- inst/doc/Intro.pdf |binary man/AIC.pclm.Rd | 160 +++++------ man/AIC.pclm2D.Rd | 160 +++++------ man/BIC.pclm.Rd | 154 +++++------ man/BIC.pclm2D.Rd | 160 +++++------ man/MortSmooth_tpower.Rd | 4 man/build_B_spline_basis.Rd | 72 ++--- man/build_C_matrix.Rd | 66 ++-- man/build_P_matrix.Rd | 46 +-- man/compute_standard_errors.Rd | 38 +- man/control.pclm.Rd | 102 +++---- man/control.pclm2D.Rd | 102 +++---- man/create.artificial.bin.Rd | 44 +-- man/delete.artificial.bin.Rd | 30 +- man/frac.Rd | 30 +- man/map.bins.Rd | 46 +-- man/ofun.Rd | 40 +- man/optimize_par.Rd | 52 +-- man/pclm.Rd | 290 ++++++++++---------- man/pclm.confidence.Rd | 66 ++-- man/pclm.confidence.dx.Rd | 30 +- man/pclm.confidence.mx.Rd | 30 +- man/pclm.fit.Rd | 138 ++++----- man/pclm.input.check.Rd | 30 +- man/pclm2D.Rd | 264 +++++++++--------- man/plot.pclm.Rd | 94 +++--- man/plot.pclm2D.Rd | 136 ++++----- man/print.pclm.Rd | 34 +- man/print.pclm2D.Rd | 34 +- man/print.summary.pclm.Rd | 34 +- man/print.summary.pclm2D.Rd | 34 +- man/print.ungroup.data.Rd | 34 +- man/residuals.pclm.Rd | 56 ++-- man/residuals.pclm2D.Rd | 74 ++--- man/seqlast.Rd | 42 +-- man/suggest.valid.out.step.Rd | 38 +- man/summary.pclm.Rd | 34 +- man/summary.pclm2D.Rd | 42 +-- man/ungroup.Rd | 86 ++---- man/ungroup.data.Rd | 66 ++-- man/validate.nlast.Rd | 50 +-- src/RcppExports.cpp | 5 tests/testthat.R | 8 tests/testthat/test_pclm.R | 198 +++++++------- tests/testthat/test_pclm2D.R | 134 ++++----- vignettes/Intro.Rmd | 292 ++++++++++---------- vignettes/REFERENCES.bib | 192 ++++++------- 72 files changed, 4076 insertions(+), 4103 deletions(-)
Title: Interface for the 'QuickJS' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript' engine.
The engine is bundled entirely within the package, requiring no external system
dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
Fabrice Bellard [ctb, cph] ,
Charlie Gordon [ctb, cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.1.0 dated 2024-01-21 and 1.1.3 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/Makevars | 25 ++++++++++++++++++++++++- src/quickjs/quickjs-libc.c | 2 +- src/quickjs/quickjs.c | 8 +++++++- 6 files changed, 45 insertions(+), 12 deletions(-)
Title: Markov Models for Health Economic Evaluations
Description: An implementation of the modelling and reporting features described
in reference textbook and guidelines (Briggs, Andrew, et al. Decision
Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011;
Siebert, U. et al. State-Transition Modeling. Medical Decision Making
32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis,
heterogeneity analysis, time dependency on state-time and model-time
(semi-Markov and non-homogeneous Markov models), etc.
Author: Kevin Zarca [aut, cre],
Antoine Filipovic-Pierucci [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb],
Jordan Amdahl [ctb],
Yonatan Carranza Alarcon [ctb],
Vince Daniels [ctb]
Maintainer: Kevin Zarca <kevin.zarca@gmail.com>
Diff between heemod versions 0.16.0 dated 2023-07-18 and 1.0.1 dated 2024-01-31
heemod-0.16.0/heemod/inst/tabular/thr/output |only heemod-0.16.0/heemod/man/define_spline_survival.Rd |only heemod-0.16.0/heemod/man/define_survival.Rd |only heemod-0.16.0/heemod/man/heemod.Rd |only heemod-0.16.0/heemod/man/plot.surv_obj.Rd |only heemod-1.0.1/heemod/DESCRIPTION | 14 heemod-1.0.1/heemod/MD5 | 257 +- heemod-1.0.1/heemod/NAMESPACE | 95 heemod-1.0.1/heemod/NEWS.md | 34 heemod-1.0.1/heemod/R/cluster.R | 4 heemod-1.0.1/heemod/R/combine.R | 19 heemod-1.0.1/heemod/R/density.R | 125 + heemod-1.0.1/heemod/R/dispatch_strategy.R | 3 heemod-1.0.1/heemod/R/efficiency_frontier.R | 1 heemod-1.0.1/heemod/R/evpi.R | 2 heemod-1.0.1/heemod/R/expand.R | 47 heemod-1.0.1/heemod/R/heemod.R | 27 heemod-1.0.1/heemod/R/look_up.R | 4 heemod-1.0.1/heemod/R/matrix_define.R | 4 heemod-1.0.1/heemod/R/matrix_eval.R | 8 heemod-1.0.1/heemod/R/newdata.R | 27 heemod-1.0.1/heemod/R/param_define.R | 23 heemod-1.0.1/heemod/R/param_eval.R | 14 heemod-1.0.1/heemod/R/part_surv.R | 13 heemod-1.0.1/heemod/R/resamp_define.R | 29 heemod-1.0.1/heemod/R/resamp_eval.R | 191 + heemod-1.0.1/heemod/R/resamp_print.R | 3 heemod-1.0.1/heemod/R/run_model_define.R | 20 heemod-1.0.1/heemod/R/states_define.R | 3 heemod-1.0.1/heemod/R/states_eval.R | 1 heemod-1.0.1/heemod/R/strategy_define.R | 6 heemod-1.0.1/heemod/R/strategy_eval.R | 8 heemod-1.0.1/heemod/R/survival_define.R | 75 heemod-1.0.1/heemod/R/survival_eval.R | 179 + heemod-1.0.1/heemod/R/survival_operations.R | 256 +- heemod-1.0.1/heemod/R/tabular_input.R | 2 heemod-1.0.1/heemod/R/transform.R | 7 heemod-1.0.1/heemod/R/update.R | 6 heemod-1.0.1/heemod/R/utils.R | 115 + heemod-1.0.1/heemod/R/zzz.R | 7 heemod-1.0.1/heemod/build/vignette.rds |binary heemod-1.0.1/heemod/inst/doc/a_introduction.Rmd | 8 heemod-1.0.1/heemod/inst/doc/a_introduction.html | 16 heemod-1.0.1/heemod/inst/doc/b_time_dependency.Rmd | 2 heemod-1.0.1/heemod/inst/doc/b_time_dependency.html | 10 heemod-1.0.1/heemod/inst/doc/c_homogeneous.Rmd | 2 heemod-1.0.1/heemod/inst/doc/c_homogeneous.html | 6 heemod-1.0.1/heemod/inst/doc/d_non_homogeneous.Rmd | 4 heemod-1.0.1/heemod/inst/doc/d_non_homogeneous.html | 8 heemod-1.0.1/heemod/inst/doc/e_probabilistic.html | 4 heemod-1.0.1/heemod/inst/doc/f_sensitivity.Rmd | 4 heemod-1.0.1/heemod/inst/doc/f_sensitivity.html | 8 heemod-1.0.1/heemod/inst/doc/g_heterogeneity.Rmd | 2 heemod-1.0.1/heemod/inst/doc/g_heterogeneity.html | 160 - heemod-1.0.1/heemod/inst/doc/h_tabular.R | 20 heemod-1.0.1/heemod/inst/doc/h_tabular.Rmd | 22 heemod-1.0.1/heemod/inst/doc/h_tabular.html | 18 heemod-1.0.1/heemod/inst/doc/i_reproduction.html | 4 heemod-1.0.1/heemod/inst/doc/j_survival.R | 39 heemod-1.0.1/heemod/inst/doc/j_survival.Rmd | 59 heemod-1.0.1/heemod/inst/doc/j_survival.html | 273 +- heemod-1.0.1/heemod/inst/doc/j_survival_2_psa.R |only heemod-1.0.1/heemod/inst/doc/j_survival_2_psa.Rmd |only heemod-1.0.1/heemod/inst/doc/j_survival_2_psa.html |only heemod-1.0.1/heemod/inst/doc/k_calibration.R | 2 heemod-1.0.1/heemod/inst/doc/k_calibration.Rmd | 2 heemod-1.0.1/heemod/inst/doc/k_calibration.html | 6 heemod-1.0.1/heemod/inst/examples/example_plot.surv_object.R |only heemod-1.0.1/heemod/inst/tabular/surv/example_use_fits_explicit_dists.csv | 8 heemod-1.0.1/heemod/inst/tabular/surv/use_fits_mixed.csv | 2 heemod-1.0.1/heemod/man/add_hazards.Rd | 4 heemod-1.0.1/heemod/man/apply_af.Rd | 4 heemod-1.0.1/heemod/man/apply_hr.Rd | 2 heemod-1.0.1/heemod/man/apply_or.Rd | 2 heemod-1.0.1/heemod/man/apply_shift.Rd | 2 heemod-1.0.1/heemod/man/check_matrix.Rd | 2 heemod-1.0.1/heemod/man/cluster.Rd | 4 heemod-1.0.1/heemod/man/combine_models.Rd | 2 heemod-1.0.1/heemod/man/compute_counts.Rd | 10 heemod-1.0.1/heemod/man/compute_surv.Rd | 4 heemod-1.0.1/heemod/man/compute_values.Rd | 4 heemod-1.0.1/heemod/man/create_demographic_table.Rd | 2 heemod-1.0.1/heemod/man/define_correlation.Rd | 2 heemod-1.0.1/heemod/man/define_part_surv.Rd | 6 heemod-1.0.1/heemod/man/define_psa.Rd | 2 heemod-1.0.1/heemod/man/define_surv_dist.Rd |only heemod-1.0.1/heemod/man/define_surv_fit.Rd |only heemod-1.0.1/heemod/man/define_surv_spline.Rd |only heemod-1.0.1/heemod/man/define_transition.Rd | 2 heemod-1.0.1/heemod/man/distributions.Rd | 2 heemod-1.0.1/heemod/man/eval_strategy_newdata.Rd | 6 heemod-1.0.1/heemod/man/eval_surv.Rd | 10 heemod-1.0.1/heemod/man/expand_state.Rd | 6 heemod-1.0.1/heemod/man/extract_strata.Rd | 2 heemod-1.0.1/heemod/man/extract_stratum.Rd | 5 heemod-1.0.1/heemod/man/get_state_value_names.Rd | 2 heemod-1.0.1/heemod/man/heemod-package.Rd |only heemod-1.0.1/heemod/man/is.wholenumber.Rd | 4 heemod-1.0.1/heemod/man/join.Rd | 10 heemod-1.0.1/heemod/man/look_up.Rd | 4 heemod-1.0.1/heemod/man/mix.Rd | 10 heemod-1.0.1/heemod/man/plot.psa.Rd | 2 heemod-1.0.1/heemod/man/plot.surv_object.Rd |only heemod-1.0.1/heemod/man/probability.Rd | 4 heemod-1.0.1/heemod/man/resample_surv.Rd |only heemod-1.0.1/heemod/man/run_bcea.Rd | 2 heemod-1.0.1/heemod/man/run_psa.Rd | 15 heemod-1.0.1/heemod/man/set_covariates.Rd | 2 heemod-1.0.1/heemod/man/update_model.Rd | 4 heemod-1.0.1/heemod/man/wtd_summary.Rd | 2 heemod-1.0.1/heemod/tests/testthat/Rplots.pdf |binary heemod-1.0.1/heemod/tests/testthat/test_dmhee.R | 4 heemod-1.0.1/heemod/tests/testthat/test_model.R | 24 heemod-1.0.1/heemod/tests/testthat/test_part_surv.R | 30 heemod-1.0.1/heemod/tests/testthat/test_run_model.R | 14 heemod-1.0.1/heemod/tests/testthat/test_starting_values.R | 54 heemod-1.0.1/heemod/tests/testthat/test_states.R | 6 heemod-1.0.1/heemod/tests/testthat/test_surv_eval.R | 1068 +++------- heemod-1.0.1/heemod/tests/testthat/test_surv_psa.R |only heemod-1.0.1/heemod/tests/testthat/test_tabular_input.R | 4 heemod-1.0.1/heemod/tests/testthat/test_transform.R | 2 heemod-1.0.1/heemod/vignettes/a_introduction.Rmd | 8 heemod-1.0.1/heemod/vignettes/b_time_dependency.Rmd | 2 heemod-1.0.1/heemod/vignettes/c_homogeneous.Rmd | 2 heemod-1.0.1/heemod/vignettes/d_non_homogeneous.Rmd | 4 heemod-1.0.1/heemod/vignettes/f_sensitivity.Rmd | 4 heemod-1.0.1/heemod/vignettes/g_heterogeneity.Rmd | 2 heemod-1.0.1/heemod/vignettes/h_tabular.Rmd | 22 heemod-1.0.1/heemod/vignettes/j_survival.Rmd | 59 heemod-1.0.1/heemod/vignettes/j_survival_2_psa.Rmd |only heemod-1.0.1/heemod/vignettes/k_calibration.Rmd | 2 131 files changed, 2093 insertions(+), 1682 deletions(-)
Title: Processing Force-Plate Data
Description: Process raw force-plate data (txt-files) by segmenting them into trials and, if needed, calculating (user-defined) descriptive
statistics of variables for user-defined time bins (relative to trigger onsets) for each trial. When segmenting the data a baseline
correction, a filter, and a data imputation can be applied if needed. Experimental data can also be processed and combined with the
segmented force-plate data. This procedure is suggested by Johannsen et al. (2023) <doi:10.6084/m9.figshare.22190155> and some of the
options (e.g., choice of low-pass filter) are also suggested by Winter (2009) <doi:10.1002/9780470549148>.
Author: Raphae Hartmann [aut, cre] ,
Anton Koger [aut, ctb] ,
Leif Johannsen [ctb]
Maintainer: Raphae Hartmann <raphael.hartmann@protonmail.com>
Diff between forceplate versions 1.0-0 dated 2023-12-19 and 1.1-0 dated 2024-01-31
forceplate-1.0-0/forceplate/man/time_lock_fp_data.Rd |only forceplate-1.1-0/forceplate/DESCRIPTION | 8 ++++---- forceplate-1.1-0/forceplate/MD5 | 12 ++++++++---- forceplate-1.1-0/forceplate/NAMESPACE | 2 +- forceplate-1.1-0/forceplate/R/time_lock_bioware.R | 8 ++++---- forceplate-1.1-0/forceplate/README.md |only forceplate-1.1-0/forceplate/man/figures |only forceplate-1.1-0/forceplate/man/time_lock_stats.Rd |only 8 files changed, 17 insertions(+), 13 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Theresa Burkard [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.0.2 dated 2024-01-14 and 1.0.3 dated 2024-01-31
DrugExposureDiagnostics-1.0.2/DrugExposureDiagnostics/R/getIngredientsOverview.R |only DrugExposureDiagnostics-1.0.2/DrugExposureDiagnostics/man/getIngredientOverview.Rd |only DrugExposureDiagnostics-1.0.2/DrugExposureDiagnostics/man/getIngredientPresence.Rd |only DrugExposureDiagnostics-1.0.2/DrugExposureDiagnostics/tests/testthat/test-IngredientOverview.R |only DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/DESCRIPTION | 12 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/MD5 | 50 +-- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/NEWS.md | 6 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/R/executeChecks.R | 26 - DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/R/mockDrugExposure.R | 94 +++--- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/R/obscureCounts.R | 4 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/R/utils.R | 11 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/README.md | 79 +++-- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.R | 2 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 2 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 6 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/SummaryOfChecks.R | 10 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/SummaryOfChecks.Rmd | 42 -- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/inst/doc/SummaryOfChecks.html | 155 ---------- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/man/DrugExposureDiagnostics-package.Rd | 9 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/man/figures/DrugExposureDiagnostics.png |binary DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-Eunomia.R | 6 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-GetDrugRecords.R | 5 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-MockDrugExposure.R | 3 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-ObscureCounts.R | 32 -- DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 2 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/tests/testthat/test-getHistogram.R | 1 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 2 DrugExposureDiagnostics-1.0.3/DrugExposureDiagnostics/vignettes/SummaryOfChecks.Rmd | 42 -- 28 files changed, 190 insertions(+), 411 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.0.2 dated 2024-01-14 and 1.0.3 dated 2024-01-31
DESCRIPTION | 6 MD5 | 28 +- NEWS.md | 12 + R/backward_compatibility.R | 21 + R/objective.R | 28 +- R/optimizer.R | 49 ++-- README.md | 7 man/Objective.Rd | 12 - man/apply_optimizer.Rd | 88 +++---- man/define_optimizer.Rd | 308 +++++++++++++-------------- man/new_optimizer.Rd | 190 ++++++++-------- man/validate_optimizer.Rd | 92 ++++---- tests/testthat/test-backward_compatibility.R | 25 +- tests/testthat/test-objective.R | 4 tests/testthat/test-optimizer.R | 32 ++ 15 files changed, 503 insertions(+), 399 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM).
Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli,
Poisson or Gaussian emission laws on the edges, and possibly covariate for Simple and Bipartite SBM).
See Léger (2016) <arxiv:1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and
'Bar-Hen et al.' (2020) <arxiv:1807.10138>.
Author: Julien Chiquet [aut, cre] ,
Sophie Donnet [aut] ,
grossBM team [ctb],
Pierre Barbillon [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.4.5 dated 2023-01-09 and 0.4.6 dated 2024-01-31
DESCRIPTION | 6 MD5 | 90 ++-- NEWS.md | 5 R/R6Class-BipartiteSBM_fit.R | 11 R/R6Class-MultipartiteSBM_fit.R | 10 R/R6Class-MultiplexSBM_fit.R | 14 R/R6Class-SBM.R | 4 R/R6Class-SimpleSBM_fit.R | 12 R/estimate.R | 75 +--- R/fungusTreeNetwork.R | 13 R/multipartiteEcologicalNetwork.R | 14 R/plotAlluvial.R | 12 R/plotMyMatrix.R | 19 - R/plotMyMultipartiteMatrix.R | 21 - R/plotMyMultiplexMatrix.R | 21 - R/utils_plot.R | 11 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 10 inst/doc/Multipartite_EcologicalNetwork.R | 2 inst/doc/Multipartite_EcologicalNetwork.html | 283 +++++++-------- inst/doc/MultiplexNetwork_principle.R | 22 - inst/doc/MultiplexNetwork_principle.html | 305 ++++++++-------- inst/doc/Multiplex_allianceNwar_case_study.R | 6 inst/doc/Multiplex_allianceNwar_case_study.html | 448 ++++++++++++------------ inst/doc/SBM_fungus_tree_network.R | 2 inst/doc/SBM_fungus_tree_network.html | 390 ++++++++++---------- man/BipartiteSBM_fit.Rd | 11 man/MultipartiteSBM_fit.Rd | 10 man/MultiplexSBM_fit.Rd | 12 man/SimpleSBM_fit.Rd | 11 man/estimateBipartiteSBM.Rd | 15 man/estimateMultipartiteSBM.Rd | 12 man/estimateMultiplexSBM.Rd | 24 - man/estimateSimpleSBM.Rd | 16 man/fungusTreeNetwork.Rd | 12 man/multipartiteEcologicalNetwork.Rd | 13 man/plot.SBM.Rd | 4 man/plotAlluvial.Rd | 10 man/plotMyMatrix.Rd | 16 man/plotMyMultipartiteMatrix.Rd | 18 man/plotMyMultiplexMatrix.Rd | 18 src/Makevars | 1 src/Makevars.win | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-MultipartiteSBM.R | 5 46 files changed, 970 insertions(+), 1045 deletions(-)
Title: Market Matching and Causal Impact Inference
Description: For a given test market find the best control markets using time series matching and analyze the impact of an intervention. The intervention could be a marketing event or some other local business tactic that is being tested. The workflow implemented in the Market Matching package utilizes dynamic time warping (the 'dtw' package) to do the matching and the 'CausalImpact' package to analyze the causal impact. In fact, this package can be considered a "workflow wrapper" for those two packages. In addition, if you don't have a chosen set of test markets to match, the Market Matching package can provide suggested test/control market pairs and pseudo prospective power analysis (measuring causal impact at fake interventions).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between MarketMatching versions 1.2.0 dated 2021-01-08 and 1.2.1 dated 2024-01-31
DESCRIPTION | 13 MD5 | 20 NAMESPACE | 3 R/MarketMatching.R | 3 R/functions.R | 54 + README.md | 4 build/vignette.rds |binary inst/doc/MarketMatching-Vignette.html | 1012 ++++++++++++++++++++++------------ man/MarketMatching.Rd | 3 man/inference.Rd | 2 man/test_fake_lift.Rd | 2 11 files changed, 741 insertions(+), 375 deletions(-)
More information about MarketMatching at CRAN
Permanent link
Title: Dose Response for Omics
Description: Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, [...truncated...]
Author: Marie-Laure Delignette-Muller [aut]
,
Elise Billoir [aut] ,
Floriane Larras [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between DRomics versions 2.5-0 dated 2023-01-24 and 2.5-2 dated 2024-01-31
DRomics-2.5-0/DRomics/inst/NEWS |only DRomics-2.5-2/DRomics/DESCRIPTION | 15 DRomics-2.5-2/DRomics/MD5 | 139 DRomics-2.5-2/DRomics/NAMESPACE | 2 DRomics-2.5-2/DRomics/NEWS.md | 25 DRomics-2.5-2/DRomics/R/PCAdataplot.R | 4 DRomics-2.5-2/DRomics/R/RNAseqdata.R | 16 DRomics-2.5-2/DRomics/R/bmdboot.R | 204 DRomics-2.5-2/DRomics/R/bmdcalc.R | 49 DRomics-2.5-2/DRomics/R/bmdfilter.R |only DRomics-2.5-2/DRomics/R/bmdplot.R | 76 DRomics-2.5-2/DRomics/R/bmdplotwithgradient.R | 49 DRomics-2.5-2/DRomics/R/continuousanchoringdata.R | 8 DRomics-2.5-2/DRomics/R/curvesplot.R | 89 DRomics-2.5-2/DRomics/R/drcfit.R | 2086 ++++----- DRomics-2.5-2/DRomics/R/ecdfplotwithCI.R | 14 DRomics-2.5-2/DRomics/R/ecdfquantileplot.R | 12 DRomics-2.5-2/DRomics/R/itemselect.R | 26 DRomics-2.5-2/DRomics/R/metabolomicdata.R | 14 DRomics-2.5-2/DRomics/R/microarraydata.R | 18 DRomics-2.5-2/DRomics/R/onAttach.R |only DRomics-2.5-2/DRomics/R/selectgroups.R | 4 DRomics-2.5-2/DRomics/R/sensitivityplot.R | 80 DRomics-2.5-2/DRomics/R/targetplot.R | 4 DRomics-2.5-2/DRomics/R/trendplot.R | 38 DRomics-2.5-2/DRomics/R/util-basicandfitfunc.R | 73 DRomics-2.5-2/DRomics/R/util-plotfunc.R | 25 DRomics-2.5-2/DRomics/build/partial.rdb |binary DRomics-2.5-2/DRomics/build/vignette.rds |binary DRomics-2.5-2/DRomics/inst/CITATION | 39 DRomics-2.5-2/DRomics/inst/DRomics-shiny/global.R | 1 DRomics-2.5-2/DRomics/inst/DRomics-shiny/install.R | 9 DRomics-2.5-2/DRomics/inst/DRomics-shiny/rinstall.txt | 1 DRomics-2.5-2/DRomics/inst/DRomics-shiny/server.R | 169 DRomics-2.5-2/DRomics/inst/DRomics-shiny/ui.R | 136 DRomics-2.5-2/DRomics/inst/DRomics-shiny/www/informations_datafile_input.txt | 18 DRomics-2.5-2/DRomics/inst/DRomics-shiny/www/informations_z_x.txt | 12 DRomics-2.5-2/DRomics/inst/DRomicsInterpreter-shiny/global.R | 3 DRomics-2.5-2/DRomics/inst/DRomicsInterpreter-shiny/install.R | 1 DRomics-2.5-2/DRomics/inst/DRomicsInterpreter-shiny/rinstall.txt | 1 DRomics-2.5-2/DRomics/inst/DRomicsInterpreter-shiny/server.R | 1627 +++---- DRomics-2.5-2/DRomics/inst/DRomicsInterpreter-shiny/ui.R | 703 +-- DRomics-2.5-2/DRomics/inst/WORDLIST |only DRomics-2.5-2/DRomics/inst/doc/DRomics_vignette.R | 145 DRomics-2.5-2/DRomics/inst/doc/DRomics_vignette.Rmd | 290 + DRomics-2.5-2/DRomics/inst/doc/DRomics_vignette.html | 2112 +++++++--- DRomics-2.5-2/DRomics/man/RNAseqdata.Rd | 3 DRomics-2.5-2/DRomics/man/Zhou.Rd | 2 DRomics-2.5-2/DRomics/man/bmdboot.Rd | 13 DRomics-2.5-2/DRomics/man/bmdcalc.Rd | 18 DRomics-2.5-2/DRomics/man/bmdfilter.Rd |only DRomics-2.5-2/DRomics/man/bmdplot.Rd | 56 DRomics-2.5-2/DRomics/man/bmdplotwithgradient.Rd | 39 DRomics-2.5-2/DRomics/man/continuousanchoringdata.Rd | 3 DRomics-2.5-2/DRomics/man/curvesplot.Rd | 116 DRomics-2.5-2/DRomics/man/drcfit.Rd | 17 DRomics-2.5-2/DRomics/man/metabolomicdata.Rd | 3 DRomics-2.5-2/DRomics/man/microarraydata.Rd | 3 DRomics-2.5-2/DRomics/man/selectgroups.Rd | 4 DRomics-2.5-2/DRomics/man/sensitivityplot.Rd | 29 DRomics-2.5-2/DRomics/man/targetplot.Rd | 9 DRomics-2.5-2/DRomics/tests/examplewithRNAseq.R | 8 DRomics-2.5-2/DRomics/tests/examplewithanchoringdata.R | 2 DRomics-2.5-2/DRomics/tests/examplewithmicroarray.R | 6 DRomics-2.5-2/DRomics/tests/testAIC.R | 2 DRomics-2.5-2/DRomics/tests/test_selectgroups.R | 6 DRomics-2.5-2/DRomics/tests/testbmdcalc.R | 19 DRomics-2.5-2/DRomics/tests/testplotfit.R | 13 DRomics-2.5-2/DRomics/tests/testscaling.R | 2 DRomics-2.5-2/DRomics/tests/testthat/test_bmdcalc.R | 11 DRomics-2.5-2/DRomics/tests/testthat/test_drcfit.R | 38 DRomics-2.5-2/DRomics/tests/testthat/test_itemselect.R | 2 DRomics-2.5-2/DRomics/vignettes/DRomics_vignette.Rmd | 290 + 73 files changed, 5223 insertions(+), 3828 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between coda versions 0.19-4 dated 2020-09-30 and 0.19-4.1 dated 2024-01-31
DESCRIPTION | 6 +- MD5 | 8 +- R/gelman.R | 46 ++++++++-------- R/output.R | 166 ++++++++++++++++++++++++++++++------------------------------ R/util.R | 112 ++++++++++++++++++++-------------------- 5 files changed, 171 insertions(+), 167 deletions(-)
Title: Create Interactive Web Maps Using 'The National Map' Services
Description: Creates interactive web maps using the 'JavaScript' 'Leaflet'
library with base layers of 'The National Map' ('TNM'). 'TNM' services
provide access to base geospatial information that describes the landscape
of the United States and its territories. This package is dependent on, and
intended to be used with, the 'leaflet' package.
Author: Jason C. Fisher [aut, cre] ,
Stefano Cudini [ctb, cph] ,
John Firebaugh [ctb, cph]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between webmap versions 1.0.3 dated 2023-09-01 and 1.0.7 dated 2024-01-31
webmap-1.0.3/webmap/build |only webmap-1.0.3/webmap/inst/doc |only webmap-1.0.3/webmap/inst/extdata |only webmap-1.0.3/webmap/vignettes |only webmap-1.0.7/webmap/DESCRIPTION | 16 ++--- webmap-1.0.7/webmap/MD5 | 31 ++++------ webmap-1.0.7/webmap/NEWS.md | 21 +++++++ webmap-1.0.7/webmap/R/add_cluster_button.R | 8 +- webmap-1.0.7/webmap/R/add_legend.R | 16 ++--- webmap-1.0.7/webmap/R/add_search_button.R | 8 +- webmap-1.0.7/webmap/R/make_map.R | 63 ++++++++++----------- webmap-1.0.7/webmap/R/us_cities.R |only webmap-1.0.7/webmap/README.md | 76 +++++++++++++------------- webmap-1.0.7/webmap/data |only webmap-1.0.7/webmap/man/add_cluster_button.Rd | 8 +- webmap-1.0.7/webmap/man/add_legend.Rd | 16 ++--- webmap-1.0.7/webmap/man/add_search_button.Rd | 8 +- webmap-1.0.7/webmap/man/make_map.Rd | 30 +++++----- webmap-1.0.7/webmap/man/us_cities.Rd |only 19 files changed, 154 insertions(+), 147 deletions(-)
Title: Multivariate Statistical Methods
Description: Algorithms to build set partitions and commutator matrices and their use in the
construction of multivariate d-Hermite polynomials; estimation and derivation of theoretical vector moments and vector
cumulants of multivariate distributions; conversion formulae for multivariate moments and cumulants. Applications to
estimation and derivation of multivariate measures of skewness and kurtosis; estimation and derivation of asymptotic
covariances for d-variate Hermite polynomials, multivariate moments and cumulants and measures of skewness and kurtosis.
The formulae implemented are discussed in Terdik (2021, ISBN:9783030813925), "Multivariate Statistical Methods".
Author: Gyorgy Terdik [aut],
Emanuele Taufer [aut, cre]
Maintainer: Emanuele Taufer <emanuele.taufer@unitn.it>
Diff between MultiStatM versions 1.2.0 dated 2023-06-12 and 1.2.1 dated 2024-01-31
MultiStatM-1.2.0/MultiStatM/inst/doc/Introduction.R |only MultiStatM-1.2.0/MultiStatM/inst/doc/Introduction.Rmd |only MultiStatM-1.2.0/MultiStatM/inst/doc/Introduction.html |only MultiStatM-1.2.0/MultiStatM/vignettes/Introduction.Rmd |only MultiStatM-1.2.1/MultiStatM/DESCRIPTION | 8 ++++---- MultiStatM-1.2.1/MultiStatM/MD5 | 16 ++++++++-------- MultiStatM-1.2.1/MultiStatM/NEWS.md | 5 +++++ MultiStatM-1.2.1/MultiStatM/R/Commutators.R | 6 ++++-- MultiStatM-1.2.1/MultiStatM/build/vignette.rds |binary MultiStatM-1.2.1/MultiStatM/inst/doc/Overview.R |only MultiStatM-1.2.1/MultiStatM/inst/doc/Overview.Rmd |only MultiStatM-1.2.1/MultiStatM/inst/doc/Overview.html |only MultiStatM-1.2.1/MultiStatM/vignettes/Overview.Rmd |only 13 files changed, 21 insertions(+), 14 deletions(-)
Title: Generate Feasible Samples of a Knapsack Problem
Description: The sampl.mcmc function creates samples of the feasible region of a knapsack problem with both equalities and inequalities constraints.
Author: Chin Soon Lim [aut]
Maintainer: Chin Soon Lim <chinsoon12@hotmail.com>
Diff between KnapsackSampling versions 0.1.0 dated 2016-10-16 and 0.1.1 dated 2024-01-31
KnapsackSampling-0.1.0/KnapsackSampling/man/grapes-sub-sub-grapes.Rd |only KnapsackSampling-0.1.0/KnapsackSampling/man/unlist.constr.Rd |only KnapsackSampling-0.1.1/KnapsackSampling/DESCRIPTION | 14 +-- KnapsackSampling-0.1.1/KnapsackSampling/MD5 | 12 +- KnapsackSampling-0.1.1/KnapsackSampling/R/knapsackSampling.R | 42 ++++------ KnapsackSampling-0.1.1/KnapsackSampling/man/flip01.Rd | 1 KnapsackSampling-0.1.1/KnapsackSampling/man/initState.Rd | 1 KnapsackSampling-0.1.1/KnapsackSampling/man/sampl.mcmc.Rd | 5 - 8 files changed, 34 insertions(+), 41 deletions(-)
More information about KnapsackSampling at CRAN
Permanent link
Title: Generalized Berk-Jones Test for Set-Based Inference in Genetic
Association Studies
Description: Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic
association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ),
Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence
Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented
in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests.
The GBJ has been shown to outperform other tests in genetic association studies when signals
are correlated and moderately sparse. Please see the vignette for a quickstart guide or Sun and Lin
(2017) <arXiv:1710.02469> for more details.
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between GBJ versions 0.5.3 dated 2020-01-13 and 0.5.4 dated 2024-01-31
GBJ-0.5.3/GBJ/src/Makevars |only GBJ-0.5.3/GBJ/src/Makevars.win |only GBJ-0.5.4/GBJ/DESCRIPTION | 16 GBJ-0.5.4/GBJ/MD5 | 32 - GBJ-0.5.4/GBJ/NAMESPACE | 1 GBJ-0.5.4/GBJ/R/calc_score_stats.R | 5 GBJ-0.5.4/GBJ/R/data.R | 4 GBJ-0.5.4/GBJ/R/score_stats_only.R | 4 GBJ-0.5.4/GBJ/build/vignette.rds |binary GBJ-0.5.4/GBJ/inst/doc/GBJ_tutorial.Rmd | 2 GBJ-0.5.4/GBJ/inst/doc/GBJ_tutorial.html | 528 +++++++++++++++++----- GBJ-0.5.4/GBJ/man/FGFR2.Rd | 6 GBJ-0.5.4/GBJ/man/calc_score_stats.Rd | 1 GBJ-0.5.4/GBJ/man/gbr_pcs.Rd | 4 GBJ-0.5.4/GBJ/src/RcppExports.cpp | 5 GBJ-0.5.4/GBJ/tests/testthat/test_omnibus.R | 8 GBJ-0.5.4/GBJ/tests/testthat/test_variance_calc.R | 2 GBJ-0.5.4/GBJ/vignettes/GBJ_tutorial.Rmd | 2 18 files changed, 473 insertions(+), 147 deletions(-)
Title: Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones
Maintainer: E. Jones <edmundjones79@gmail.com>
Diff between cchs versions 0.4.3 dated 2024-01-29 and 0.4.4 dated 2024-01-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/cchs.Rd | 5 ++++- man/cchsData.Rd | 8 +++++--- 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Political Science Computational Laboratory
Description: Bayesian analysis of item-response theory (IRT) models,
roll call analysis; computing highest density regions;
maximum likelihood estimation of zero-inflated and hurdle models for count data;
goodness-of-fit measures for GLMs;
data sets used in writing and teaching; seats-votes curves.
Author: Simon Jackman [aut, cre] ,
Alex Tahk [ctb] ,
Achim Zeileis [ctb] ,
Christina Maimone [ctb] ,
James Fearon [ctb],
Zoe Meers [ctb]
Maintainer: Simon Jackman <simon.jackman@sydney.edu.au>
Diff between pscl versions 1.5.5.1 dated 2023-05-10 and 1.5.9 dated 2024-01-31
pscl-1.5.5.1/pscl/NEWS |only pscl-1.5.9/pscl/DESCRIPTION | 43 pscl-1.5.9/pscl/MD5 | 71 - pscl-1.5.9/pscl/R/dropUnanimous.r | 28 pscl-1.5.9/pscl/R/hurdle.R | 4 pscl-1.5.9/pscl/R/ideal.r | 58 - pscl-1.5.9/pscl/R/plot.ideal.r | 2 pscl-1.5.9/pscl/R/postProcess.r | 8 pscl-1.5.9/pscl/R/predprob.R | 2 pscl-1.5.9/pscl/R/rollcall.r | 2 pscl-1.5.9/pscl/R/summary.ideal.r | 9 pscl-1.5.9/pscl/R/zeroinfl.R | 1444 +++++++++++++-------------- pscl-1.5.9/pscl/R/zzz.R | 8 pscl-1.5.9/pscl/README.md |only pscl-1.5.9/pscl/build/partial.rdb |only pscl-1.5.9/pscl/build/vignette.rds |binary pscl-1.5.9/pscl/inst/CITATION | 35 pscl-1.5.9/pscl/inst/NEWS_old |only pscl-1.5.9/pscl/inst/News.md |only pscl-1.5.9/pscl/inst/doc/countreg.pdf |binary pscl-1.5.9/pscl/man/AustralianElections.Rd | 2 pscl-1.5.9/pscl/man/ca2006.Rd | 2 pscl-1.5.9/pscl/man/hurdle.Rd | 2 pscl-1.5.9/pscl/man/iraqVote.Rd | 2 pscl-1.5.9/pscl/man/nj07.Rd | 2 pscl-1.5.9/pscl/man/pR2.Rd | 2 pscl-1.5.9/pscl/man/partycodes.Rd | 4 pscl-1.5.9/pscl/man/predict.hurdle.Rd | 2 pscl-1.5.9/pscl/man/presidentialElections.Rd | 8 pscl-1.5.9/pscl/man/readKH.Rd | 6 pscl-1.5.9/pscl/man/sc9497.Rd | 4 pscl-1.5.9/pscl/man/state.info.Rd | 2 pscl-1.5.9/pscl/man/unionDensity.Rd | 2 pscl-1.5.9/pscl/man/vote92.Rd | 2 pscl-1.5.9/pscl/man/zeroinfl.Rd | 4 pscl-1.5.9/pscl/src/IDEAL.c | 8 pscl-1.5.9/pscl/src/crossprod.c | 2 pscl-1.5.9/pscl/src/util.c | 3 pscl-1.5.9/pscl/src/util.h | 2 39 files changed, 902 insertions(+), 873 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-27 0.1.2
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 2.2.0 dated 2023-12-12 and 2.2.1 dated 2024-01-31
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++++-------------- NEWS.md | 10 ++++ R/focei.R | 1 R/nlmixr2.R | 2 R/nls.R | 3 + R/onLoad.R | 4 - R/vpc.R | 5 ++ man/nlmixr2.Rd | 2 man/nlsControl.Rd | 3 + man/vpcSim.Rd | 5 ++ tests/testthat/test-augpred.R | 13 ++++-- tests/testthat/test-cwres.R | 2 tests/testthat/test-focei-llik.R | 22 +++++----- tests/testthat/test-manual-back-transform.R | 2 tests/testthat/test-nlm.R | 2 tests/testthat/test-nlme.R | 2 tests/testthat/test-nls.R | 1 tests/testthat/test-nmobj.R | 1 tests/testthat/test-nonmu.R | 4 + tests/testthat/test-np.R | 2 tests/testthat/test-npde.R | 2 tests/testthat/test-optim.R | 2 tests/testthat/test-rx-model-props.R | 3 + tests/testthat/test-rxsolve.R | 3 + tests/testthat/test-saem-aic.R | 3 + tests/testthat/test-saem-funny-mu.R | 3 + tests/testthat/test-saem-translate.R | 2 tests/testthat/test-split.R | 9 ++-- tests/testthat/test-ui-est-change.R | 4 + tests/testthat/test-vpcSim.R | 2 31 files changed, 132 insertions(+), 55 deletions(-)
Title: Handy File and String Manipulation
Description: This started out as a package for file and string
manipulation. Since then, the 'fs' and 'strex' packages emerged,
offering functionality previously given by this package (but it's done
better in these new ones). Those packages have hence almost pushed
'filesstrings' into extinction. However, it still has a small number
of unique, handy file manipulation functions which can be seen in the
vignette. One example is a function to remove spaces from all file
names in a directory.
Author: Rory Nolan [aut, cre, cph] ,
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 3.2.4 dated 2023-01-25 and 3.3.0 dated 2024-01-31
filesstrings-3.2.4/filesstrings/man/give_ext.Rd |only filesstrings-3.2.4/filesstrings/man/nice_nums.Rd |only filesstrings-3.2.4/filesstrings/man/remove_quoted.Rd |only filesstrings-3.2.4/filesstrings/man/singleize.Rd |only filesstrings-3.2.4/filesstrings/man/trim_anything.Rd |only filesstrings-3.3.0/filesstrings/DESCRIPTION | 6 filesstrings-3.3.0/filesstrings/MD5 | 96 ++-- filesstrings-3.3.0/filesstrings/NEWS.md | 6 filesstrings-3.3.0/filesstrings/R/arg-match.R | 8 filesstrings-3.3.0/filesstrings/R/can-be-num.R | 8 filesstrings-3.3.0/filesstrings/R/str-after.R | 28 - filesstrings-3.3.0/filesstrings/R/str-before.R | 41 + filesstrings-3.3.0/filesstrings/R/str-currency.R | 33 + filesstrings-3.3.0/filesstrings/R/str-elem.R | 24 - filesstrings-3.3.0/filesstrings/R/str-extract-non-nums.R | 20 filesstrings-3.3.0/filesstrings/R/str-extract-nums.R | 21 filesstrings-3.3.0/filesstrings/R/str-give-ext.R | 12 filesstrings-3.3.0/filesstrings/R/str-locate.R | 24 - filesstrings-3.3.0/filesstrings/R/str-nice-nums.R | 18 filesstrings-3.3.0/filesstrings/R/str-num-after.R | 72 ++- filesstrings-3.3.0/filesstrings/R/str-num-before.R | 72 ++- filesstrings-3.3.0/filesstrings/R/str-remove.R | 12 filesstrings-3.3.0/filesstrings/R/str-singleize.R | 12 filesstrings-3.3.0/filesstrings/R/str-split-by-nums.R | 8 filesstrings-3.3.0/filesstrings/R/str-to-vec.R | 8 filesstrings-3.3.0/filesstrings/R/str-trim.R | 14 filesstrings-3.3.0/filesstrings/README.md | 3 filesstrings-3.3.0/filesstrings/build/partial.rdb |binary filesstrings-3.3.0/filesstrings/build/vignette.rds |binary filesstrings-3.3.0/filesstrings/inst/CITATION | 15 filesstrings-3.3.0/filesstrings/inst/doc/files.R | 2 filesstrings-3.3.0/filesstrings/inst/doc/files.html | 30 - filesstrings-3.3.0/filesstrings/man/before_last_dot.Rd | 8 filesstrings-3.3.0/filesstrings/man/can_be_numeric.Rd | 8 filesstrings-3.3.0/filesstrings/man/currency.Rd | 23 filesstrings-3.3.0/filesstrings/man/extract_non_numerics.Rd | 105 ---- filesstrings-3.3.0/filesstrings/man/extract_numbers.Rd | 114 ---- filesstrings-3.3.0/filesstrings/man/locate_braces.Rd | 8 filesstrings-3.3.0/filesstrings/man/match_arg.Rd | 31 - filesstrings-3.3.0/filesstrings/man/nth_number_after_mth.Rd | 264 +---------- filesstrings-3.3.0/filesstrings/man/nth_number_before_mth.Rd | 264 +---------- filesstrings-3.3.0/filesstrings/man/str_after_nth.Rd | 29 - filesstrings-3.3.0/filesstrings/man/str_before_nth.Rd | 29 - filesstrings-3.3.0/filesstrings/man/str_elem.Rd | 11 filesstrings-3.3.0/filesstrings/man/str_elems.Rd | 14 filesstrings-3.3.0/filesstrings/man/str_give_ext.Rd |only filesstrings-3.3.0/filesstrings/man/str_locate_nth.Rd | 29 - filesstrings-3.3.0/filesstrings/man/str_nice_nums.Rd |only filesstrings-3.3.0/filesstrings/man/str_paste_elems.Rd | 13 filesstrings-3.3.0/filesstrings/man/str_remove_quoted.Rd |only filesstrings-3.3.0/filesstrings/man/str_singleize.Rd |only filesstrings-3.3.0/filesstrings/man/str_split_by_nums.Rd | 56 -- filesstrings-3.3.0/filesstrings/man/str_to_vec.Rd | 8 filesstrings-3.3.0/filesstrings/man/str_trim_anything.Rd |only 54 files changed, 528 insertions(+), 1079 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-16 1.0
2021-12-08 0.9
2021-12-03 0.8
2021-12-02 0.7