Title: Computation and Visualization of Package Download Counts and
Percentiles
Description: Compute and visualize the cross-sectional and longitudinal number
and rank percentile of package downloads from RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.8.0 dated 2023-02-14 and 0.8.1 dated 2023-03-28
DESCRIPTION | 8 +- MD5 | 59 ++++++++------ NAMESPACE | 5 + NEWS.md | 41 ++++++++++ R/archivePackages.R | 2 R/checkPackage.R | 74 ++++++++++-------- R/countryDistribution.R | 9 +- R/countryPackage.R | 9 +- R/cranDownloads.R | 18 ++++ R/cranDownloadsPlotFunctions.R | 8 +- R/cranPackageSize.R | 2 R/filteredDownloads.R | 9 +- R/ipPackage.R | 9 +- R/logInfo.R | 16 ++-- R/packageHistory.R | 105 +++++++++++++++++--------- R/packageLog.R | 11 ++ R/packagesFunctions.R |only R/sizeFilter.R | 139 ++++++++++++++++++++++------------- R/validatePackage.R | 15 ++- README.md | 52 +++++++------ man/countryDistribution.Rd | 5 + man/countryPackage.Rd | 4 - man/extractArchiveDate.Rd |only man/figures/README-sundays-1.png |binary man/figures/README-sundays_mac-1.png |binary man/figures/README-sundays_mac-2.png |only man/figures/README-sundays_src-1.png |binary man/figures/README-sundays_src-2.png |only man/figures/README-sundays_win-1.png |binary man/figures/README-sundays_win-2.png |only man/ipPackage.Rd | 4 - man/packages_in_Archive.Rd |only man/packages_observed_in_logs.Rd |only man/packages_on_CRAN.Rd |only man/packages_partitioned.Rd |only 35 files changed, 399 insertions(+), 205 deletions(-)
Title: Variable Selection under Ranked Sparsity Principles for
Interactions and Polynomials
Description: An implementation of ranked sparsity methods, including
penalized regression methods such as the sparsity-ranked lasso, its
non-convex alternatives, and elastic net, as well as the sparsity-ranked
Bayesian Information Criterion. As described in Peterson and
Cavanaugh (2022) <doi:10.1007/s10182-021-00431-7>, ranked
sparsity is a philosophy with methods primarily useful for
variable selection in the presence of prior informational
asymmetry, which occurs in the context of trying to perform variable
selection in the presence of interactions and/or polynomials. Ultimately,
this package attempts to facilitate dealing with cumbersome interactions
and polynomials while not avoiding them entirely. Typically, models
selected under ranked sparsity principles will also be more transparent,
having fewer falsely selected interactions and polynomials than other
methods.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between sparseR versions 0.2.1 dated 2022-11-10 and 0.2.2 dated 2023-03-28
DESCRIPTION | 10 MD5 | 14 NEWS.md | 4 README.md | 6 inst/CITATION | 2 inst/doc/sparseR.html | 538 ++++++++++++++++++------------------- tests/testthat/Rplots.pdf |binary tests/testthat/test_sparseR_surv.R | 16 - 8 files changed, 301 insertions(+), 289 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb], Shaobo Li [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 3.1.1 dated 2023-03-03 and 3.1.2 dated 2023-03-28
rqPen-3.1.1/rqPen/inst/doc |only rqPen-3.1.2/rqPen/DESCRIPTION | 8 ++-- rqPen-3.1.2/rqPen/MD5 | 36 ++++++++++------------ rqPen-3.1.2/rqPen/NAMESPACE | 1 rqPen-3.1.2/rqPen/NEWS | 5 +++ rqPen-3.1.2/rqPen/R/QICD_functions.R | 3 + rqPen-3.1.2/rqPen/R/mainFunctions.R | 42 +++++++++++++++++++++----- rqPen-3.1.2/rqPen/build/partial.rdb |binary rqPen-3.1.2/rqPen/man/QICD.Rd | 1 rqPen-3.1.2/rqPen/man/coef.cv.rq.group.pen.Rd | 1 rqPen-3.1.2/rqPen/man/coef.cv.rq.pen.Rd | 1 rqPen-3.1.2/rqPen/man/cv_plots.Rd | 1 rqPen-3.1.2/rqPen/man/plot.cv.rq.group.pen.Rd | 1 rqPen-3.1.2/rqPen/man/predict.cv.rq.pen.Rd | 1 rqPen-3.1.2/rqPen/man/predict.rq.pen.Rd | 1 rqPen-3.1.2/rqPen/man/print.cv.rq.pen.Rd | 1 rqPen-3.1.2/rqPen/man/print.rq.pen.Rd | 1 rqPen-3.1.2/rqPen/man/rq.group.fit.Rd | 1 rqPen-3.1.2/rqPen/man/rq.group.pen.Rd | 4 +- 19 files changed, 76 insertions(+), 33 deletions(-)
Title: Predictive Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [ctb, prg],
Andres Navarro [ctb, prg],
Joseline Quiros [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between predictoR versions 3.0.0 dated 2023-02-16 and 3.0.1 dated 2023-03-28
DESCRIPTION | 21 +++++++++++---------- MD5 | 16 ++++++++-------- R/app_ui.R | 2 +- R/mod_acercade.R | 9 ++++----- R/mod_poder_pred_utils.R | 2 +- R/mod_varerr.R | 3 ++- R/predictoR.R | 4 ++-- inst/golem-config.yml | 2 +- man/predictoR.Rd | 2 +- 9 files changed, 31 insertions(+), 30 deletions(-)
Title: Lan-DeMets Method for Group Sequential Boundaries
Description: Computations related to group sequential boundaries.
Includes calculation of bounds using the Lan-DeMets
alpha spending function approach. Based on FORTRAN
program ld98 implemented by Reboussin, et al. (2000) <doi:10.1016/s0197-2456(00)00057-x>.
Author: Charlie Casper, Thomas Cook and Oscar A. Perez. Based on FORTRAN
program ld98.
Maintainer: Charlie Casper <charlie.casper@hsc.utah.edu>
Diff between ldbounds versions 2.0.0 dated 2022-02-24 and 2.0.1 dated 2023-03-28
ldbounds-2.0.0/ldbounds/NEWS |only ldbounds-2.0.1/ldbounds/DESCRIPTION | 8 ++++---- ldbounds-2.0.1/ldbounds/MD5 | 12 ++++++------ ldbounds-2.0.1/ldbounds/NEWS.md |only ldbounds-2.0.1/ldbounds/R/condpower.R | 4 ++-- ldbounds-2.0.1/ldbounds/R/ldBounds.R | 3 +-- ldbounds-2.0.1/ldbounds/inst/doc/ldbounds.pdf |binary ldbounds-2.0.1/ldbounds/man/condpower.Rd | 4 ++-- 8 files changed, 15 insertions(+), 16 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.6.1 dated 2023-01-05 and 3.6.2 dated 2023-03-28
MSEtool-3.6.1/MSEtool/man/MSYCalcs.Rd |only MSEtool-3.6.2/MSEtool/DESCRIPTION | 6 MSEtool-3.6.2/MSEtool/MD5 | 89 ++--- MSEtool-3.6.2/MSEtool/NEWS.md | 25 + MSEtool-3.6.2/MSEtool/R/B_Low_functions.R | 19 - MSEtool-3.6.2/MSEtool/R/Data_fit_index.R | 35 +- MSEtool-3.6.2/MSEtool/R/Data_make_update.R | 90 ++++- MSEtool-3.6.2/MSEtool/R/MMSE_Object.r | 4 MSEtool-3.6.2/MSEtool/R/MOM_object.r | 11 MSEtool-3.6.2/MSEtool/R/MSE_functions.R | 9 MSEtool-3.6.2/MSEtool/R/Misc_Exported.R | 30 + MSEtool-3.6.2/MSEtool/R/Misc_Internal.R | 34 ++ MSEtool-3.6.2/MSEtool/R/OM_Plotting.R | 2 MSEtool-3.6.2/MSEtool/R/RcppExports.R | 32 -- MSEtool-3.6.2/MSEtool/R/SS2OM.R | 4 MSEtool-3.6.2/MSEtool/R/SampleOM.R | 18 - MSEtool-3.6.2/MSEtool/R/multiMSE.R | 415 +++++++++++++++------------ MSEtool-3.6.2/MSEtool/R/multiMSE_internal.R | 10 MSEtool-3.6.2/MSEtool/R/multi_q_estimation.R | 17 - MSEtool-3.6.2/MSEtool/R/popdyn.R | 166 ++++++---- MSEtool-3.6.2/MSEtool/R/popdyn_MICE.R | 70 +++- MSEtool-3.6.2/MSEtool/R/runMSE.R | 345 +++++++++------------- MSEtool-3.6.2/MSEtool/R/sysdata.rda |binary MSEtool-3.6.2/MSEtool/inst/Rmd/Obs/Obs.Rmd | 18 - MSEtool-3.6.2/MSEtool/man/Blow_opt.Rd | 5 MSEtool-3.6.2/MSEtool/man/CheckOM.Rd | 48 +-- MSEtool-3.6.2/MSEtool/man/Lag_Data.Rd | 114 +++---- MSEtool-3.6.2/MSEtool/man/MMSE-class.Rd | 2 MSEtool-3.6.2/MSEtool/man/MOM-class.Rd | 16 - MSEtool-3.6.2/MSEtool/man/MSE-class.Rd | 2 MSEtool-3.6.2/MSEtool/man/SubCpars.Rd | 6 MSEtool-3.6.2/MSEtool/man/getBlow.Rd | 5 MSEtool-3.6.2/MSEtool/man/getnIVs.Rd | 38 +- MSEtool-3.6.2/MSEtool/man/multiMSE.Rd | 10 MSEtool-3.6.2/MSEtool/man/optMSY_eq.Rd | 41 -- MSEtool-3.6.2/MSEtool/man/optQ.Rd | 5 MSEtool-3.6.2/MSEtool/man/optYield.Rd | 5 MSEtool-3.6.2/MSEtool/man/plot.MOM.Rd | 44 +- MSEtool-3.6.2/MSEtool/man/plotRel.Rd | 54 +-- MSEtool-3.6.2/MSEtool/man/popdynCPP.Rd | 5 MSEtool-3.6.2/MSEtool/man/popdynMICE.Rd | 3 MSEtool-3.6.2/MSEtool/man/qestMICE.Rd | 3 MSEtool-3.6.2/MSEtool/man/summary-MMSE.Rd | 40 +- MSEtool-3.6.2/MSEtool/src/MSYcalcs.cpp | 346 +++++++++++----------- MSEtool-3.6.2/MSEtool/src/RcppExports.cpp | 27 - MSEtool-3.6.2/MSEtool/src/popddynCPP.cpp | 142 ++++----- 46 files changed, 1329 insertions(+), 1081 deletions(-)
Title: Exploring and Testing the Toolchain and System Libraries
Description: A collection of helper functions that interface with the appropriate
system utilities to learn about the build environment. Lets you explore 'make'
rules to test the local configuration, or query 'pkg-config' to find compiler
flags and libs needed for building packages with external dependencies. Also
contains tools to analyze which libraries that a installed R package linked to
by inspecting output from 'ldd' in combination with information from your
distribution package manager, e.g. 'rpm' or 'dpkg'. Finally the package provides
Windows-specific utilities to automatically find or install the suitable version
of the 'Rtools' build environment, and diagnose some common problems.
Author: Jeroen Ooms [aut, cre, cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between maketools versions 1.2.2 dated 2022-02-25 and 1.2.4 dated 2023-03-28
DESCRIPTION | 8 - MD5 | 12 +- R/rtools.R | 68 ++++++-------- R/sysdeps.R | 14 ++ build/vignette.rds |binary inst/doc/sysdeps.html | 199 +++++++++++++++++++++++++----------------- tests/testthat/test-sysdeps.R | 1 7 files changed, 176 insertions(+), 126 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
The package does not require any installation of Microsoft products to be able to write Microsoft
files.
Author: David Gohel [aut, cre],
ArData [cph],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Stefan Moog [ctb] ,
Greg Leleu [ctb] ,
Hong [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.6.1 dated 2023-03-08 and 0.6.2 dated 2023-03-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ R/ooxml.R | 2 +- R/ooxml_run_objects.R | 6 +++++- R/rtf.R | 2 +- 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Cytoscape.js Shiny Widget (cyjShiny)
Description: Wraps cytoscape.js as a shiny widget. cytoscape.js <https://js.cytoscape.org/> is a Javascript-based graph theory (network) library for visualization and analysis. This package supports the visualization of networks with custom visual styles and several available layouts. Demo Shiny applications are provided in the package code.
Author: Omar Shah [ctb],
Paul Shannon [aut],
Augustin Luna [aut, cre]
Maintainer: Augustin Luna <augustin_luna@hms.harvard.edu>
Diff between cyjShiny versions 1.0.34 dated 2022-01-20 and 1.0.42 dated 2023-03-28
cyjShiny-1.0.34/cyjShiny/inst/demos/basicDemo/cyjShinyDemo.R |only cyjShiny-1.0.34/cyjShiny/inst/demos/rmarkdownDemo/cyjshiny_rmarkdown.html |only cyjShiny-1.0.34/cyjShiny/inst/demos/tinyApp/foo.png |only cyjShiny-1.0.42/cyjShiny/DESCRIPTION | 15 cyjShiny-1.0.42/cyjShiny/MD5 | 65 - cyjShiny-1.0.42/cyjShiny/R/cyjShiny.R | 8 cyjShiny-1.0.42/cyjShiny/R/graphsToJSON.R | 1 cyjShiny-1.0.42/cyjShiny/README.md | 106 +- cyjShiny-1.0.42/cyjShiny/inst/demos/basicDemo/app.R |only cyjShiny-1.0.42/cyjShiny/inst/demos/basicDemo/basicStyle.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/basicDemo/deploy_shinyappsio.R |only cyjShiny-1.0.42/cyjShiny/inst/demos/basicDemo/rsconnect |only cyjShiny-1.0.42/cyjShiny/inst/demos/basicDemo/yeastGalactoseStyle.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/dataFrameGraphWithAnimation/app.R | 15 cyjShiny-1.0.42/cyjShiny/inst/demos/dataFrameGraphWithPresetNodePositions/app.R | 15 cyjShiny-1.0.42/cyjShiny/inst/demos/fromCytoscapeDesktop/app.R | 12 cyjShiny-1.0.42/cyjShiny/inst/demos/fromCytoscapeDesktop/simple/app.R | 5 cyjShiny-1.0.42/cyjShiny/inst/demos/fromCytoscapeDesktop/small |only cyjShiny-1.0.42/cyjShiny/inst/demos/galFiltered-fromBioconductorGraphNEL/galFiltered.R | 18 cyjShiny-1.0.42/cyjShiny/inst/demos/jsonGraphWithAnimation/app.R | 11 cyjShiny-1.0.42/cyjShiny/inst/demos/loadGraphFromJSONfile/app.R | 11 cyjShiny-1.0.42/cyjShiny/inst/demos/quickStartDemo |only cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/cyjshiny_rmarkdown.Rmd | 21 cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/preset_graph.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/preset_style.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/style.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/yeastGalactose.cyjs |only cyjShiny-1.0.42/cyjShiny/inst/demos/rmarkdownDemo/yeastGalactoseStyle.js |only cyjShiny-1.0.42/cyjShiny/inst/demos/rstudio/dataFrameDemo/demo.R | 4 cyjShiny-1.0.42/cyjShiny/inst/demos/saveAndRestoreLayout/app.R | 14 cyjShiny-1.0.42/cyjShiny/inst/demos/tiny.R |only cyjShiny-1.0.42/cyjShiny/inst/demos/tinyApp/tinyApp.R | 39 cyjShiny-1.0.42/cyjShiny/inst/demos/withDT/app.R | 125 -- cyjShiny-1.0.42/cyjShiny/inst/doc/basicIntro.R | 102 + cyjShiny-1.0.42/cyjShiny/inst/doc/basicIntro.Rmd | 181 ++- cyjShiny-1.0.42/cyjShiny/inst/doc/basicIntro.html | 524 ++++++++-- cyjShiny-1.0.42/cyjShiny/inst/docker/app/app.R | 4 cyjShiny-1.0.42/cyjShiny/inst/docs/ygModelImage.png |binary cyjShiny-1.0.42/cyjShiny/inst/htmlwidgets/cyjShiny.js | 86 - cyjShiny-1.0.42/cyjShiny/man/cyjShiny.Rd | 2 cyjShiny-1.0.42/cyjShiny/vignettes/basicIntro.Rmd | 181 ++- 41 files changed, 1065 insertions(+), 500 deletions(-)
More information about SparseFunClust at CRAN
Permanent link
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.8.2 dated 2023-02-20 and 0.9.1 dated 2023-03-28
DESCRIPTION | 11 ++++++----- MD5 | 19 +++++++++++-------- NAMESPACE | 7 +++++++ NEWS.md | 5 +++++ R/biotech.R |only R/pkgstart.R | 7 ++++++- R/tests.R | 6 +++++- build/vignette.rds |binary inst/doc/wrappedtools.html | 6 +++--- man/plot_LB.Rd |only man/plot_MM.Rd |only tests/testthat/test-glm_CI.R | 2 +- 12 files changed, 44 insertions(+), 19 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.
Author: Sergey Kucheryavskiy [aut, cre]
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.13.1 dated 2022-11-09 and 0.14.0 dated 2023-03-28
mdatools-0.13.1/mdatools/R/pcv.R |only mdatools-0.13.1/mdatools/man/eye.Rd |only mdatools-0.13.1/mdatools/man/getR.Rd |only mdatools-0.13.1/mdatools/man/pcv.Rd |only mdatools-0.13.1/mdatools/man/rotationMatrixToX1.Rd |only mdatools-0.14.0/mdatools/DESCRIPTION | 20 +++++++++++--------- mdatools-0.14.0/mdatools/MD5 | 19 +++++++------------ mdatools-0.14.0/mdatools/NAMESPACE | 2 -- mdatools-0.14.0/mdatools/NEWS.md | 16 ++++++++++++++++ mdatools-0.14.0/mdatools/R/crossval.R | 3 ++- mdatools-0.14.0/mdatools/R/prep.R | 4 +++- mdatools-0.14.0/mdatools/R/simcares.R | 2 +- mdatools-0.14.0/mdatools/man/mdatools.Rd | 1 - 13 files changed, 40 insertions(+), 27 deletions(-)
Title: Estimation of Vaccine Efficacy using Negative Control Outcomes
Description: Methods to reduce confounding bias from unmeasured confounders in observational studies of vaccine efficacy using negative control outcomes.
Author: Lola Etievant [aut],
Mitchell H. Gail [aut],
Joshua N. Sampson [aut],
Bill Wheeler [cre]
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Diff between NegativeControlOutcomeAdjustment versions 0.0.4 dated 2022-02-08 and 0.0.5 dated 2023-03-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/NegativeControlOutcomeAdjustment-package.Rd | 5 +++-- man/negativecontroladjustment.Rd | 6 +++--- 4 files changed, 13 insertions(+), 12 deletions(-)
More information about NegativeControlOutcomeAdjustment at CRAN
Permanent link
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022, <arxiv:1910.09219>).
Multivariate conditional transformation models (Klein et al, 2022, <DOI:10.1111/sjos.12501>)
can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.8-1 dated 2023-03-09 and 0.8-2 dated 2023-03-28
DESCRIPTION | 8 - MD5 | 18 +- NAMESPACE | 1 R/methods.R | 4 build/partial.rdb |binary build/vignette.rds |binary demo/stram.R | 345 ++++++++++++++++++++++++++++++++++------------------- inst/NEWS.Rd | 6 inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary 10 files changed, 247 insertions(+), 135 deletions(-)
Title: The Reinert Method for Textual Data Clustering
Description: An R implementation of the Reinert text clustering method. For more
details about the algorithm see the included vignettes or Reinert (1990)
<doi:10.1177/075910639002600103>.
Author: Julien Barnier [aut, cre],
Florian Prive [ctb]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rainette versions 0.3.1 dated 2023-03-17 and 0.3.1.1 dated 2023-03-28
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/algorithmes.html | 4 ++-- inst/doc/algorithms_en.html | 4 ++-- inst/doc/introduction_en.html | 4 ++-- inst/doc/introduction_usage.html | 4 ++-- 8 files changed, 21 insertions(+), 20 deletions(-)
Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the
L0-Pseudonorm
Description: Optimal Subset Cardinality Regression (OSCAR) models offer
regularized linear regression using the L0-pseudonorm, conventionally
known as the number of non-zero coefficients. The package estimates an
optimal subset of features using the L0-penalization via
cross-validation, bootstrapping and visual diagnostics. Effective
Fortran implementations are offered along the package for finding
optima for the DC-decomposition, which is used for transforming the
discrete L0-regularized optimization problem into a continuous
non-convex optimization task. These optimization modules include DBDC
('Double Bundle method for nonsmooth DC optimization' as described in
Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited
Memory Bundle Method for large-scale nonsmooth optimization' as
in Haarala et al. (2004) <doi:10.1080/10556780410001689225>). The
OSCAR models are comprehensively exemplified in Halkola et al. (2023)
<doi:10.1371/journal.pcbi.1010333>). Multiple regression m [...truncated...]
Author: Teemu Daniel Laajala [aut, cre]
,
Kaisa Joki [aut],
Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between oscar versions 1.1.2-2 dated 2023-03-12 and 1.1.4 dated 2023-03-28
DESCRIPTION | 15 ++++++++------- MD5 | 13 +++++++------ R/fitS4.R | 2 +- R/pckg.R | 2 +- build/partial.rdb |only inst/CITATION | 3 ++- inst/doc/example.html | 6 +++--- man/oscar-package.Rd | 2 +- 8 files changed, 23 insertions(+), 20 deletions(-)
Title: Automated Classification of Mass Spectra
Description: Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values. Three vignettes illustrating how to use the functions of this package from real data sets are also available online to help users: <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Ecrobiav3.html>, <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Klebsiellav3.html> and <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_DAv3.html>.
Author: Alexandre Godmer [aut, cre],
Quentin Giai Gianetto [aut],
Karen Druart [aut]
Maintainer: Alexandre Godmer <alexandre.godmer@aphp.fr>
Diff between MSclassifR versions 0.3.1 dated 2022-09-29 and 0.3.2 dated 2023-03-28
DESCRIPTION | 22 - MD5 | 32 +- NAMESPACE | 10 R/LogReg.R | 42 ++ R/PeakDetection.R | 30 +- R/PredictFastClass.R | 306 ++++++++++----------- R/PredictLogReg.R | 88 +++--- R/SelectionVar.R | 696 +++++++++++++++++++++++++++--------------------- R/SelectionVarStat.R | 61 ++++ build/partial.rdb |binary man/LogReg.Rd | 13 man/PeakDetection.Rd | 25 + man/PlotSpectra.Rd | 2 man/PredictFastClass.Rd | 76 +---- man/PredictLogReg.Rd | 25 - man/SelectionVar.Rd | 143 ++++++--- man/SelectionVarStat.Rd | 82 ++++- 17 files changed, 954 insertions(+), 699 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.2 dated 2023-01-23 and 1.9.3 dated 2023-03-28
DESCRIPTION | 10 +-- MD5 | 42 +++++++------- NAMESPACE | 2 NEWS | 17 +++++ R/TMB.R | 2 R/checker.R | 113 ++++++++++++++++++++++++++++++++++++--- R/validation.R | 71 ++++++++++++------------ inst/include/TMB.hpp | 9 ++- inst/include/distributions_R.hpp | 14 +++- inst/include/tmb_core.hpp | 104 +++++++++++++++++++++++------------ man/MakeADFun.Rd | 33 ++++++++--- man/benchmark.Rd | 3 - man/checkConsistency.Rd | 22 +++++++ man/compile.Rd | 21 +++++-- man/newton.Rd | 26 +++++++- man/oneStepPredict.Rd | 21 +++++-- man/precompile.Rd | 3 - man/runExample.Rd | 12 +++- man/sdreport.Rd | 14 +++- man/summary.sdreport.Rd | 8 ++ man/tmbprofile.Rd | 16 ++++- man/tmbroot.Rd | 13 +++- 22 files changed, 423 insertions(+), 153 deletions(-)
Title: Cast '(R)Markdown' Files to 'XML' and Back Again
Description: Parsing '(R)Markdown' files with numerous regular expressions can
be fraught with peril, but it does not have to be this way. Converting
'(R)Markdown' files to 'XML' using the 'commonmark' package allows
in-memory editing via of 'markdown' elements via 'XPath' through the
extensible 'R6' class called 'yarn'. These modified 'XML' representations
can be written to '(R)Markdown' documents via an 'xslt' stylesheet which
implements an extended version of 'GitHub'-flavoured 'markdown' so that you
can tinker to your hearts content.
Author: Maelle Salmon [aut] ,
Zhian N. Kamvar [aut, cre] ,
Jeroen Ooms [aut],
Nick Wellnhofer [cph] ,
rOpenSci [fnd] ,
Peter Daengeli [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between tinkr versions 0.1.0 dated 2022-08-19 and 0.2.0 dated 2023-03-28
DESCRIPTION | 12 - MD5 | 53 +++--- NAMESPACE | 1 NEWS.md | 27 +++ R/asis-nodes.R | 284 ++++++++++++++++++++++++++++------ R/attr-nodes.R |only R/class-yarn.R | 51 ++++-- R/resolve-links.R | 2 R/to_md.R | 4 R/to_xml.R | 41 ++-- R/utils-string.R |only R/utils.R | 24 +- build/vignette.rds |binary inst/doc/tinkr.html | 15 + inst/extdata/basic-curly.md |only inst/extdata/basic-curly2.Rmd |only inst/extdata/link-test.md | 6 inst/stylesheets/xml2md_gfm.xsl | 41 ++-- man/protect_curly.Rd |only man/protect_unescaped.Rd |only man/to_xml.Rd | 21 ++ man/yarn.Rd | 70 ++++++++ tests/testthat/_snaps/anchor-links.md | 22 +- tests/testthat/_snaps/asis-nodes.md | 2 tests/testthat/_snaps/attr-nodes |only tests/testthat/_snaps/attr-nodes.md |only tests/testthat/_snaps/class-yarn.md | 24 ++ tests/testthat/test-anchor-links.R | 18 ++ tests/testthat/test-asis-nodes.R | 11 + tests/testthat/test-attr-nodes.R |only tests/testthat/test-class-yarn.R | 19 ++ tests/testthat/test-utils-string.R |only 32 files changed, 590 insertions(+), 158 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included (Langsrud, 2020) <doi:10.13140/RG.2.2.27313.61283>. The hierarchy specification functions are useful within statistical disclosure control.
Author: Oyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Bjoern-Helge Mevik [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.4.2 dated 2023-02-16 and 1.4.4 dated 2023-03-28
DESCRIPTION | 8 MD5 | 42 +-- NAMESPACE | 2 R/Div.R | 14 - R/GaussSuppression.R | 454 +++++++++++++++++++++++++++++++++----- R/Hierarchies2ModelMatrix.R | 42 +++ R/HierarchyCompute.R | 33 ++ R/ModelMatrix.R | 88 ++++++- R/NumSingleton.R |only R/aggregate_multiple_fun.R | 91 ++++--- R/dummy_aggregate.R | 32 +- R/model_aggregate.R | 5 R/quantile_weighted.R | 26 ++ man/GaussSuppression.Rd | 39 ++- man/Hierarchies2ModelMatrix.Rd | 26 +- man/ModelMatrix.Rd | 21 + man/NumSingleton.Rd |only man/aggregate_multiple_fun.Rd | 68 +++-- man/dummy_aggregate.Rd | 42 +-- man/fix_vars_amf.Rd | 12 - man/model_aggregate.Rd | 5 man/quantile_weighted.Rd | 5 tests/testthat/test-ModelMatrix.R | 100 ++++++++ 23 files changed, 944 insertions(+), 211 deletions(-)
Title: Parsing and Code Generation Functions for 'rxode2'
Description: Provides the parsing needed for 'rxode2' (Wang, Hallow and
James (2016) <doi:10.1002/psp4.12052>). It also provides the 'stan'
based advan linear compartment model solutions with gradients
(Carpenter et al (2015), <arXiv:1509.07164>) needed in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>).
This split will reduce computational burden of recompiling 'rxode2'.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Richard Upton [ctb],
Gabriel Staples [ctb],
Goro Fuji [ctb],
Morwenn [ctb],
Igor Kushnir [ctb],
Kevin Ushey [ctb],
David Cooley [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2parse versions 2.0.15 dated 2023-03-19 and 2.0.16 dated 2023-03-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/utils.R | 1 + inst/include/rxode2parseVer.h | 2 +- 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Building a Concordance of Terms in a Series of Texts
Description: Compute the frequency distribution of a search term in a series of texts. For example, Arthur Conan Doyle wrote a total of 60 Sherlock Holmes stories, comprised of 54 short stories and 4 longer novels. I wanted to test my own subjective impression that, in many of the stories, Sherlock Holmes' popularity was used as bait to induce the reader to read a story that is essentially not primarily a Sherlock Holmes story. I used the term "Holmes" as a search pattern, since Watson would frequently address him by name, or use his name to describe something that he was doing. My hypothesis is that the frequency distribution of the search pattern "Holmes" is a good proxy for the degree to which a story is or is not truly a Sherlock Holmes story. The results are presented in a manuscript that is available as a vignette and online at <https://barryzee.github.io/Concordance/index.html>.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between SherlockHolmes versions 1.0 dated 2023-03-27 and 1.0.1 dated 2023-03-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/doc/Sherlock.html | 4 ++-- inst/doc/Sherlock2.html | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-)
More information about SherlockHolmes at CRAN
Permanent link
Title: Analyzing Multiple Omics Data with an Offset Approach
Description: Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block. Also offers options to deal with blockwise missingness in multi-omics data.
Author: Simon Klau, Roman Hornung, Alina Bauer, Jonas Hagenberg
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between prioritylasso versions 0.2.5 dated 2020-11-09 and 0.3.0 dated 2023-03-28
DESCRIPTION | 20 MD5 | 68 + NAMESPACE | 11 NEWS |only R/calculate_offsets.R |only R/coef.prioritylasso.R |only R/compare_boolean.R |only R/cvm_prioritylasso.R | 251 +++--- R/data.R | 70 - R/makeCVdivision.R | 9 R/make_imputation_available_cases.R |only R/make_imputation_model.R |only R/missing.control.R |only R/predict.prioritylasso.R | 512 +++++++++++++ R/prioritylasso.R | 1029 +++++++++++++++------------ README.md |only build/vignette.rds |binary inst/doc/explanation_blockwise_missing.R |only inst/doc/explanation_blockwise_missing.Rmd |only inst/doc/explanation_blockwise_missing.html |only inst/doc/prioritylasso_vignette.Rmd | 394 +++++----- inst/doc/prioritylasso_vignette.html | 1041 ++++++++++++++++------------ man/calculate_offsets.Rd |only man/coef.prioritylasso.Rd |only man/compare_boolean.Rd |only man/cvm_prioritylasso.Rd | 14 man/missing.control.Rd |only man/predict.prioritylasso.Rd | 24 man/prioritylasso.Rd | 37 tests |only vignettes/algorithm_1.PNG |only vignettes/algorithm_2.PNG |only vignettes/algorithm_3.PNG |only vignettes/explanation_blockwise_missing.Rmd |only vignettes/prioritylasso_vignette.Rmd | 394 +++++----- vignettes/references.bib |only 36 files changed, 2379 insertions(+), 1495 deletions(-)
Title: Convert Files to Parquet Format
Description: Collection of functions to get files in parquet format.
Parquet is a columnar storage file format <https://parquet.apache.org/>.
The files to convert can be of several formats
("csv", "RData", "rds", "RSQLite",
"json", "ndjson", "SAS", "SPSS"...).
Author: Damien Dotta [aut, cre],
Nicolas Chuche [aut]
Maintainer: Damien Dotta <damien.dotta@live.fr>
Diff between parquetize versions 0.5.4 dated 2023-03-13 and 0.5.5 dated 2023-03-28
parquetize-0.5.4/parquetize/tests/testthat/Data/REG=01 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=02 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=03 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=04 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=06 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=11 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=24 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=27 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=28 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=32 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=44 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=52 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=53 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=75 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=76 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=84 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=93 |only parquetize-0.5.4/parquetize/tests/testthat/Data/REG=94 |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=1 |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=2 |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=3 |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=setosa |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=versic |only parquetize-0.5.4/parquetize/tests/testthat/Data/Species=virgin |only parquetize-0.5.4/parquetize/tests/testthat/Data/census.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/centres-vaccination.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/departement_2022.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/iris.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/iris101-250.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/iris51-100.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/parquetize0.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/parquetize100.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/parquetize50.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/parquetize500000.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/region_2022.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/research-and-development-survey-2021-csv.parquet |only parquetize-0.5.4/parquetize/tests/testthat/Data/species=versicolor |only parquetize-0.5.4/parquetize/tests/testthat/Data/species=virginica |only parquetize-0.5.4/parquetize/tests/testthat/Data_test |only parquetize-0.5.4/parquetize/tests/testthat/output |only parquetize-0.5.4/parquetize/tests/testthat/test-bychunk.R |only parquetize-0.5.5/parquetize/DESCRIPTION | 18 parquetize-0.5.5/parquetize/MD5 | 132 --- parquetize-0.5.5/parquetize/NAMESPACE | 70 - parquetize-0.5.5/parquetize/NEWS.md | 78 + parquetize-0.5.5/parquetize/R/csv_to_parquet.R | 171 +--- parquetize-0.5.5/parquetize/R/download_extract.R |only parquetize-0.5.5/parquetize/R/json_to_parquet.R | 33 parquetize-0.5.5/parquetize/R/rds_to_parquet.R | 24 parquetize-0.5.5/parquetize/R/sqlite_to_parquet.R | 30 parquetize-0.5.5/parquetize/R/table_to_parquet.R | 259 ++---- parquetize-0.5.5/parquetize/R/utilities.R | 151 ++- parquetize-0.5.5/parquetize/inst/doc/aa-conversions.R | 18 parquetize-0.5.5/parquetize/inst/doc/aa-conversions.Rmd | 54 + parquetize-0.5.5/parquetize/inst/doc/aa-conversions.html | 108 +- parquetize-0.5.5/parquetize/man/csv_to_parquet.Rd | 26 parquetize-0.5.5/parquetize/man/download_extract.Rd |only parquetize-0.5.5/parquetize/man/table_to_parquet.Rd | 72 + parquetize-0.5.5/parquetize/tests/testthat/Data/iris101-150.parquet |binary parquetize-0.5.5/parquetize/tests/testthat/_snaps/csv_to_parquet.md | 241 ++--- parquetize-0.5.5/parquetize/tests/testthat/_snaps/download_extract.md |only parquetize-0.5.5/parquetize/tests/testthat/_snaps/json_to_parquet.md | 125 +-- parquetize-0.5.5/parquetize/tests/testthat/_snaps/rds_to_parquet.md | 81 - parquetize-0.5.5/parquetize/tests/testthat/_snaps/sqlite_to_parquet.md | 117 +- parquetize-0.5.5/parquetize/tests/testthat/_snaps/table_to_parquet.md | 413 ++++------ parquetize-0.5.5/parquetize/tests/testthat/_snaps/utilities.md |only parquetize-0.5.5/parquetize/tests/testthat/test-csv_to_parquet.R | 49 - parquetize-0.5.5/parquetize/tests/testthat/test-download_extract.R |only parquetize-0.5.5/parquetize/tests/testthat/test-json_to_parquet.R | 2 parquetize-0.5.5/parquetize/tests/testthat/test-sqlite_to_parquet.R | 11 parquetize-0.5.5/parquetize/tests/testthat/test-table_to_parquet.R | 115 ++ parquetize-0.5.5/parquetize/tests/testthat/test-utilities.R |only parquetize-0.5.5/parquetize/vignettes/aa-conversions.Rmd | 54 + 73 files changed, 1340 insertions(+), 1112 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.2.0 dated 2023-02-22 and 1.2.2 dated 2023-03-28
DESCRIPTION | 8 MD5 | 15 - NAMESPACE | 5 R/functions.R | 614 ++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/corto_vignette.html | 2 man/barplot2.Rd | 4 man/scatter.Rd | 2 man/textrepel.Rd |only 9 files changed, 420 insertions(+), 230 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.1 dated 2022-03-25 and 1.1.3 dated 2023-03-28
DESCRIPTION | 10 +-- MD5 | 47 ++++++++--------- NAMESPACE | 6 ++ NEWS | 12 ++++ R/confrontation.R | 20 ++++--- R/expressionset.R | 1 R/syntax.R | 4 - R/utils.R | 41 +++++++++++++-- R/validate_pkg.R | 12 +--- R/validator.R | 21 ++++--- build/vignette.rds |binary inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.R | 2 inst/doc/cookbook.Rmd | 48 ++++++++--------- inst/doc/cookbook.html | 101 ++++++++++++++++++------------------- inst/tinytest/pocrules/rule_18.txt | 3 - inst/tinytest/test_confrontation.R | 10 +++ inst/tinytest/test_genericrules.R | 12 ++++ inst/tinytest/test_validator.R | 7 ++ inst/tinytest/txttests |only man/syntax.Rd | 4 - man/validate.Rd | 11 +--- man/variables.Rd | 12 ++-- vignettes/cookbook.Rmd | 48 ++++++++--------- vignettes/jss3483.pdf |binary 25 files changed, 255 insertions(+), 177 deletions(-)
Title: Apply Functions to Multiple Multidimensional Arrays or Vectors
Description: The base apply function and its variants, as well as the related
functions in the 'plyr' package, typically apply user-defined functions to a
single argument (or a list of vectorized arguments in the case of mapply). The
'multiApply' package extends this paradigm with its only function, Apply, which
efficiently applies functions taking one or a list of multiple unidimensional
or multidimensional arrays (or combinations thereof) as input. The input
arrays can have different numbers of dimensions as well as different dimension
lengths, and the applied function can return one or a list of unidimensional or
multidimensional arrays as output. This saves development time by preventing the
R user from writing often error-prone and memory-inefficient loops dealing with
multiple complex arrays. Also, a remarkable feature of Apply is the transparent
use of multi-core through its parameter 'ncores'. In contrast to the base apply
function, this package suggests the use of 'target dimensions' as op [...truncated...]
Author: BSC-CNS [aut, cph],
Nicolau Manubens [aut],
Alasdair Hunter [aut],
An-Chi Ho [ctb, cre],
Nuria Perez [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>
Diff between multiApply versions 2.1.3 dated 2021-02-01 and 2.1.4 dated 2023-03-28
multiApply-2.1.3/multiApply/tests |only multiApply-2.1.4/multiApply/DESCRIPTION | 19 ++++++++-------- multiApply-2.1.4/multiApply/MD5 | 14 +++++------- multiApply-2.1.4/multiApply/NAMESPACE | 1 multiApply-2.1.4/multiApply/NEWS.md |only multiApply-2.1.4/multiApply/R/Apply.R | 36 ++++++++++++++++++++++++++++++- multiApply-2.1.4/multiApply/README.md | 12 ++++------ multiApply-2.1.4/multiApply/man/Apply.Rd | 17 +++++++++++--- 8 files changed, 70 insertions(+), 29 deletions(-)
Title: Thermophysical Properties of Water and Steam
Description: Functions for Water and Steam Properties based on the
International Association for the Properties of Water (IAPWS) Formulation
1995 for the Thermodynamic Properties of Ordinary Water Substance for General and
Scientific Use and on the releases for viscosity, conductivity, surface tension and
melting pressure.
Author: Benedito Baptista [aut],
Shawn Way [cre]
Maintainer: Shawn Way <shawnway@yahoo.com>
Diff between IAPWS95 versions 1.2.0 dated 2022-06-24 and 1.2.1 dated 2023-03-28
DESCRIPTION | 8 +-- MD5 | 10 ++-- NEWS.md | 10 +++- build/vignette.rds |binary inst/doc/IAPWS95.html | 124 ++++++++++++++++++++++++++------------------------ src/IAPWS95_init.c | 2 6 files changed, 84 insertions(+), 70 deletions(-)
Title: Handling, Visualisation and Analysis of Epidemiological Contacts
Description: A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Author: Finlay Campbell [aut, cre],
Thibaut Jombart [aut],
Nistara Randhawa [aut],
Bertrand Sudre [aut],
VP Nagraj [aut],
Thomas Crellen [aut],
Zhian N. Kamvar [aut]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between epicontacts versions 1.1.2 dated 2021-10-21 and 1.1.3 dated 2023-03-28
DESCRIPTION | 10 MD5 | 108 NAMESPACE | 56 NEWS.md | 108 R/as.igraph.epicontacts.R | 164 R/colors.R | 272 R/get_clusters.R | 214 R/get_degree.R | 158 R/get_pairwise.R | 196 R/graph3D.R | 370 R/handling.R | 336 R/internals.R | 258 R/make_epicontacts.R | 348 R/plot.R | 168 R/print.epicontacts.R | 60 R/subset.epicontacts.R | 454 R/subset_clusters_by_id.R | 118 R/subset_clusters_by_size.R | 202 R/summary.epicontacts.R | 90 R/thin.R | 110 R/vis_epicontacts.R | 700 - build/vignette.rds |binary inst/CITATION | 31 inst/doc/epicontacts.R | 192 inst/doc/epicontacts.html |12844 ++++++++++++++++++++++++-- inst/doc/epicontacts_class.R | 86 inst/doc/epicontacts_class.html | 949 + man/as.igraph.epicontacts.Rd | 102 man/codeawesome.Rd | 40 man/colors.Rd | 136 man/get_clusters.Rd | 134 man/get_id.Rd | 112 man/graph3D.Rd | 172 man/make_epicontacts.Rd | 188 man/plot.epicontacts.Rd | 140 man/sub-.epicontacts.Rd | 224 man/subset.epicontacts.Rd | 204 man/subset_clusters_by_id.Rd | 82 man/vis_epicontacts.Rd | 272 tests/testthat/helper.R | 20 tests/testthat/test_as.igraph.epicontacts.R | 76 tests/testthat/test_colors.R | 82 tests/testthat/test_get_clusters.R | 384 tests/testthat/test_get_degree.R | 100 tests/testthat/test_get_pairwise.R | 134 tests/testthat/test_graph3D.R | 126 tests/testthat/test_handling.R | 140 tests/testthat/test_make_epicontacts.R | 248 tests/testthat/test_plot.epicontacts.R | 100 tests/testthat/test_print.epicontacts.R | 28 tests/testthat/test_subset_clusters_by_id.R | 34 tests/testthat/test_subset_clusters_by_size.R | 108 tests/testthat/test_summary.epicontacts.R | 48 tests/testthat/test_thin.R | 76 tests/testthat/test_vis_epicontacts.R | 136 55 files changed, 17023 insertions(+), 5225 deletions(-)
Title: Stepwise Selection for Large Data Sets
Description: Selecting linear and generalized linear models for large data sets
using modified stepwise procedure and modern selection criteria (like
modifications of Bayesian Information Criterion). Selection can be
performed on data which exceed RAM capacity.
Author: Piotr Szulc [aut, cre]
Maintainer: Piotr Szulc <piotr.michal.szulc@gmail.com>
Diff between bigstep versions 1.0.3 dated 2019-07-25 and 1.1.0 dated 2023-03-28
DESCRIPTION | 18 - MD5 | 38 +-- NAMESPACE | 2 NEWS.md |only R/bigstep.R | 7 R/fit_model.R | 71 ++--- R/prep_data.R | 14 - README.md | 197 +++++++++++----- build/vignette.rds |binary inst/doc/bigstep.R | 53 +--- inst/doc/bigstep.Rmd | 35 -- inst/doc/bigstep.html | 482 +++++++++++++++++++++++++--------------- man/bigstep.Rd | 7 man/get_model.Rd |only man/prepare_data.Rd | 14 - man/reexports.Rd | 4 man/summary.big.Rd | 4 tests/testthat/test_all.R | 34 -- tests/testthat/test_fit_model.R | 75 ------ tests/testthat/test_prep_data.R | 36 +- vignettes/bigstep.Rmd | 35 -- 21 files changed, 586 insertions(+), 540 deletions(-)
Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.
Author: Ozvan Bocher and Herve Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>
Diff between Ravages versions 1.1.2 dated 2023-02-01 and 1.1.3 dated 2023-03-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/p_valeur_moments_liu.r | 2 +- inst/doc/Ravages_Simulations_vignette.pdf |binary inst/doc/Ravages_vignette.pdf |binary 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Query the Breeding Management System(s)
Description: Linking data management systems to analytics is an important step in breeding
digitization. Breeders can use this R package to Query the Breeding Management
System(s) like 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and
'GIGWA' <https://southgreen.fr/content/gigwa> (using 'BrAPI' <https://brapi.org> calls)
and help them to retrieve phenotypic and genotypic data directly into their analyzing
pipelines.
Author: Khaled Al-Shamaa [aut, cre],
Mariano Omar Crimi [ctb],
Zakaria Kehel [ctb],
Johan Aparicio [ctb],
ICARDA [cph]
Maintainer: Khaled Al-Shamaa <k.el-shamaa@cgiar.org>
Diff between QBMS versions 0.9.0 dated 2023-03-27 and 0.9.1 dated 2023-03-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/qbms.R | 6 +++--- README.md | 6 ++++++ 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <arXiv:2303.10388>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 1.4.8 dated 2023-03-24 and 1.4.9 dated 2023-03-28
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 2 ++ R/pathway_errorbar.R | 10 +++++----- 4 files changed, 16 insertions(+), 14 deletions(-)
Title: Functions to Facilitate the Simulation of Large Scale Assessment
Data
Description: Provides functions to simulate data from large-scale educational
assessments, including background questionnaire data and cognitive item
responses that adhere to a multiple-matrix sampled design. The theoretical
foundation can be found on
Matta, T.H., Rutkowski, L., Rutkowski, D. et al. (2018)
<doi:10.1186/s40536-018-0068-8>.
Author: Tyler Matta [aut],
Leslie Rutkowski [aut],
David Rutkowski [aut],
Yuan-Ling Linda Liaw [aut],
Kondwani Kajera Mughogho [ctb],
Waldir Leoncio [aut, cre],
Sinan Yavuz [ctb],
Paul Bailey [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between lsasim versions 2.1.2 dated 2021-11-09 and 2.1.3 dated 2023-03-28
DESCRIPTION | 9 MD5 | 47 +- R/beta_gen.R | 12 R/calc_var_between.R | 6 R/check_n_N_class.R | 4 R/cluster_gen.R | 4 R/cluster_gen_separate.R | 20 - R/cluster_gen_together.R | 16 R/cluster_message.R | 10 R/convert_vector_to_list.R | 10 R/draw_cluster_structure.R | 4 R/item_gen.R | 104 ++--- R/questionnaire_gen.R | 2 R/replicate_var.R | 12 R/sample_within_range.R | 4 R/summary.R | 4 R/validate.R | 4 build/vignette.rds |binary inst/doc/ex1_BackgroundQuestionnaireGeneration.html | 308 +++++++++++++++-- inst/doc/ex2_UnderstandingElementsOutput.html | 309 +++++++++++++++-- inst/doc/ex3_RetrievingRegressionCoefficients.html | 256 +++++++++++++- inst/doc/ex4_GeneratingClusterSamples.html | 356 +++++++++++++++++--- man/beta_gen.Rd | 10 man/item_gen.Rd | 12 tests/testthat/test.issue48.R |only 25 files changed, 1252 insertions(+), 271 deletions(-)
Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and
tidy reports. This package offers a framework for exploring and
validating data frame like objects using 'dplyr' grammar of data
manipulation.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between ruler versions 0.2.4 dated 2020-11-25 and 0.3.0 dated 2023-03-28
DESCRIPTION | 13 MD5 | 46 +- NEWS.md | 5 R/expose-helpers.R | 2 R/expose.R | 14 R/exposure.R | 4 R/packs.R | 2 R/rules.R | 67 -- R/spread-groups.R | 2 R/utils.R | 8 README.md | 129 ++--- build/vignette.rds |binary inst/doc/design-and-format.html | 506 ++++++++++++++-------- inst/doc/rule-packs.R | 4 inst/doc/rule-packs.Rmd | 8 inst/doc/rule-packs.html | 900 ++++++++++++++++++++++++---------------- inst/doc/validation.html | 894 +++++++++++++++++++++++---------------- man/expose.Rd | 4 man/row-pack.Rd | 2 man/rules.Rd | 58 -- tests/testthat/test-exposure.R | 4 tests/testthat/test-packs.R | 2 tests/testthat/test-rules.R | 38 - vignettes/rule-packs.Rmd | 8 24 files changed, 1558 insertions(+), 1162 deletions(-)
Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group.
This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see <https://qmethod.org/>).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
The package allows to choose either principal components or centroid factor extraction, manual or automatic flagging, a number of mathematical methods for rotation (or none), and a number of correlation coefficients for the initial correlation matrix, among many other options.
Additional functions are available to import and export data (from raw *.CSV, 'HTMLQ' and 'FlashQ' *.CSV, 'PQMethod' *.DAT and 'easy-h [...truncated...]
Author: Aiora Zabala [aut, cre] ,
Maximilian Held [aut] ,
Frans Hermans [aut]
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.8 dated 2021-03-14 and 1.8.4 dated 2023-03-28
DESCRIPTION | 16 +- MD5 | 59 +++++----- NAMESPACE | 5 R/import.easyhtml.R | 6 - R/plot.QmethodRes.R | 12 +- R/q.fnames.R | 2 R/qbstep.R | 4 R/qflag.R | 5 R/qmboots.R | 7 - R/qpcrustes.R | 7 - R/runInterface.R | 3 build/partial.rdb |binary inst/CITATION | 3 inst/shiny-examples/qmethod-gui/rsconnect |only inst/shiny-examples/qmethod-gui/server.R | 177 +++--------------------------- inst/shiny-examples/qmethod-gui/ui.R | 110 +----------------- man/build.q.set.Rd | 3 man/import.q.concourse.Rd | 2 man/import.q.feedback.Rd | 2 man/import.q.sorts.Rd | 3 man/importexample.Rd | 2 man/make.cards.Rd | 3 man/plot.QmethodRes.Rd | 2 man/qbstep.Rd | 4 man/qflag.Rd | 7 + man/qindtest.Rd | 4 man/qmethod-package.Rd | 12 +- man/qmethod.Rd | 6 - man/qpcrustes.Rd | 12 +- man/qzscores.Rd | 2 man/runInterface.Rd | 2 31 files changed, 136 insertions(+), 346 deletions(-)
Title: Estimating the Number of Factors in EFA with Out-of-Sample
Prediction Errors
Description: Estimating the number of factors in Exploratory Factor Analysis (EFA) with out-of-sample prediction errors using a cross-validation scheme. Haslbeck & van Bork (Preprint) <https://psyarxiv.com/qktsd>.
Author: Jonas Haslbeck [aut, cre],
Riet van Bork [ctb]
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between fspe versions 0.1.1 dated 2022-06-15 and 0.1.2 dated 2023-03-28
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 3 ++- NEWS |only R/fspe.R | 13 +++++-------- man/fspe.Rd | 9 ++++++++- 6 files changed, 24 insertions(+), 18 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.12.0 dated 2023-02-09 and 1.13.0 dated 2023-03-28
DESCRIPTION | 8 MD5 | 34 - NEWS.md | 622 +++++++++---------- R/marginal_tidiers.R | 117 +++ R/tidy_add_estimate_to_reference_rows.R | 65 + R/tidy_add_pairwise_contrasts.R | 10 build/vignette.rds |binary data/supported_models.rda |binary inst/doc/tidy.R | 1 inst/doc/tidy.Rmd | 1 inst/doc/tidy.html | 471 +++++++------- man/supported_models.Rd | 2 man/tidy_add_estimate_to_reference_rows.Rd | 6 man/tidy_add_pairwise_contrasts.Rd | 4 tests/testthat/test-add_estimate_to_reference_rows.R | 33 + tests/testthat/test-marginal_tidiers.R | 197 ++++++ tests/testthat/test-tidy_plus_plus.R | 4 vignettes/tidy.Rmd | 1 18 files changed, 984 insertions(+), 592 deletions(-)
Title: Analysis of Massive SNP Arrays
Description: Easy-to-use, efficient, flexible and scalable tools for analyzing
massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.
Author: Florian Prive [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths],
Bjarni Johann Vilhjalmsson [ths]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigsnpr versions 1.11.6 dated 2022-11-07 and 1.12.2 dated 2023-03-28
DESCRIPTION | 20 +++--- MD5 | 97 +++++++++++++++---------------- NAMESPACE | 2 NEWS.md | 38 ++++++++++++ R/LDpred2.R | 86 +++++++++++++++------------ R/RcppExports.R | 36 ++++++----- R/bed-mat-acc.R |only R/external-software.R | 16 +++-- R/get-save-infos.R | 26 ++++---- R/lassosum2.R | 5 + R/ldsc.R | 11 ++- R/man-qq-gc.R | 6 - R/match-alleles.R | 12 ++- R/read-bgen.R | 18 +++-- R/split-LD.R | 11 ++- R/utils-assert.R | 16 ----- R/utils.R | 3 README.md | 8 +- inst/CITATION | 19 +++--- inst/WORDLIST | 1 man/LDpred2.Rd | 17 ++++- man/bigsnpr-package.Rd | 2 man/download_plink.Rd | 6 + man/seq_log.Rd | 6 - man/snp_getSampleInfos.Rd | 22 +++---- man/snp_lassosum2.Rd | 4 + man/snp_ldsc.Rd | 12 +++ man/snp_ldsplit.Rd | 8 ++ man/snp_match.Rd | 12 ++- man/snp_plinkRmSamples.Rd | 8 +- man/snp_prodBGEN.Rd | 5 - man/snp_readBGEN.Rd | 17 +++-- man/sub-bed-ANY-ANY-ANY-method.Rd |only src/Makevars | 2 src/RcppExports.cpp | 97 ++++++++++++++++++------------- src/bed-fun.cpp | 24 ------- src/bed-mat-acc.cpp |only src/clumping-utils.h | 4 - src/lassosum2.cpp | 24 ++++--- src/ld-scores-sfbm.cpp | 36 +++++++---- src/ldpred2-auto.cpp | 55 +++++++++-------- src/ldpred2-sampling.cpp | 22 ++----- src/ldpred2.cpp | 35 +++++------ src/split-LD.cpp | 19 ++++-- tests/testthat/test-1-readBed.R | 25 +++++++ tests/testthat/test-2-bed-clumping-SVD.R | 7 ++ tests/testthat/test-2-ld-scores.R | 13 +--- tests/testthat/test-4-split-LD.R | 40 +++++++++++- tests/testthat/test-7-OpenMP.R | 17 +++-- tests/testthat/test-8-LDpred2.R | 84 ++++++++++++++++++++++++++ tests/testthat/test-9-lassosum2.R | 10 +++ 51 files changed, 685 insertions(+), 379 deletions(-)
Title: Diagnostic Ability Assessment with Right-Censored Data at a
Fixed Time t
Description: We focus on the diagnostic ability assessment of medical tests when the outcome of interest is the status (alive or dead) of the subjects at a certain time-point t. This binary status is determined by right-censored times to event and it is missing for those subjects censored before t. Here we provide three methods (missing exclusion, imputation of censored times and using time-dependent ROC curves) to evaluate the diagnostic ability of binary and continuous tests in this context. Two references for the methods used here are Skaltsa et al. (2010) <doi:10.1002/bimj.200900294> and Heagerty et al. (2000) <doi:10.1111/j.0006-341x.2000.00337.x>.
Author: Sara Perez-Jaume [aut, cre],
Josep L Carrasco [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROCsurvival versions 1.1.0 dated 2023-03-21 and 1.1.1 dated 2023-03-28
DESCRIPTION | 8 MD5 | 4 man/diagnostic_assessment_continuous.Rd | 283 ++++++++++++++++---------------- 3 files changed, 155 insertions(+), 140 deletions(-)
More information about ThresholdROCsurvival at CRAN
Permanent link
Title: Random Number Generation Functions for 'rxode2'
Description: Provides the random number generation (in parallel) needed for
'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>).
This split will reduce computational burden of recompiling 'rxode2'.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [ctb],
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2random versions 2.0.10 dated 2023-03-17 and 2.0.11 dated 2023-03-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/init.c | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of
'amt' includes methods to calculate home ranges, track statistics
(e.g. step lengths, speed, or turning angles), prepare data for
fitting habitat selection analyses, and simulation of space-use from
fitted step-selection functions.
Author: Johannes Signer [aut, cre],
Brian Smith [ctb],
Bjoern Reineking [ctb],
Ulrike Schlaegel [ctb],
John Fieberg [ctb],
Josh O'Brien [ctb],
Bernardo Niebuhr [ctb],
Alec Robitaille [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.2 dated 2023-03-03 and 0.2.1.0 dated 2023-03-28
DESCRIPTION | 6 - MD5 | 24 +++---- NEWS.md | 4 + R/random_steps.R | 18 +++-- R/simulate.R | 4 - build/partial.rdb |binary inst/doc/p1_getting_started.html | 12 +-- inst/doc/p2_hr.html | 12 +-- inst/doc/p3_rsf.html | 34 +++++------ inst/doc/p4_SSF.html | 116 +++++++++++++++++++------------------- inst/doc/p5_other_packages.html | 12 +-- inst/tinytest/test_random_steps.R | 5 + man/random_steps.Rd | 3 13 files changed, 133 insertions(+), 117 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.58 dated 2023-03-07 and 2.0.59 dated 2023-03-28
DESCRIPTION | 8 ++-- MD5 | 18 +++++---- NAMESPACE | 1 NEWS | 7 +++ R/epi.2by2.R | 2 - R/epi.realrisk.r |only inst/doc/epiR_descriptive.html | 41 ++++++++++------------ inst/doc/epiR_measures_of_association.html | 44 +++++++++++------------ inst/doc/epiR_sample_size.html | 4 +- inst/doc/epiR_surveillance.html | 54 ++++++++++++++--------------- man/epi.realrisk.Rd |only 11 files changed, 93 insertions(+), 86 deletions(-)
Title: Empirical Bayes Estimation of Dynamic Bayesian Networks
Description: Infer the adjacency matrix of a
network from time course data using an empirical Bayes
estimation procedure based on Dynamic Bayesian Networks.
Author: Andrea Rau <andrea.rau@inra.fr>
Maintainer: Andrea Rau <andrea.rau@inra.fr>
Diff between ebdbNet versions 1.2.6 dated 2021-10-15 and 1.2.7 dated 2023-03-28
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 3 ++- NEWS | 9 ++++++++- R/ebdbn.R | 16 +--------------- R/plot.ebdbNet.R | 2 +- inst/CITATION | 7 +++---- src/init.c | 18 +++++++++--------- 8 files changed, 36 insertions(+), 43 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.8-4 dated 2023-01-19 and 1.9-2 dated 2023-03-28
DESCRIPTION | 8 MD5 | 18 R/book.menu.r | 4 R/see.tcdf.r | 2 R/selftest.ANOVAreview.R |only R/selftest.regGLM.R |only R/selftest.regapproaches.R | 307 ++++++++++++ R/selftest_reg_char.R | 1066 +++++++++++++++++++++++++++------------------ inst/doc/ranef.cov.pdf |binary inst/doc/simpson.pdf |binary man/selftest.se.tck1.rd | 2 11 files changed, 983 insertions(+), 424 deletions(-)
Title: Flexible and Coherent Test/Estimation Procedure Based on
Restricted Mean Survival Times
Description: Estimates the restricted mean survival time (RMST) with the time window [0, tau], where tau is adaptively selected from the procedure, proposed by Horiguchi et al. (2018) <doi:10.1002/sim.7661>. It also estimates the RMST with the time window [tau1, tau2], where tau1 is adaptively selected from the procedure, proposed by Horiguchi et al. (2023) <doi:10.1002/sim.9662>.
Author: Miki Horiguchi [aut, cre] ,
Lu Tian [aut] ,
Hajime Uno [aut]
Maintainer: Miki Horiguchi <horiguchimiki@gmail.com>
Diff between survRM2adapt versions 1.0-1 dated 2018-05-08 and 1.1.0 dated 2023-03-28
survRM2adapt-1.0-1/survRM2adapt/R/rmst2adapt-ver001.R |only survRM2adapt-1.1.0/survRM2adapt/DESCRIPTION | 29 +++++-- survRM2adapt-1.1.0/survRM2adapt/INDEX |only survRM2adapt-1.1.0/survRM2adapt/MD5 | 38 +++++++--- survRM2adapt-1.1.0/survRM2adapt/NAMESPACE | 3 survRM2adapt-1.1.0/survRM2adapt/NEWS.md | 9 ++ survRM2adapt-1.1.0/survRM2adapt/R/data.R |only survRM2adapt-1.1.0/survRM2adapt/R/ltrmst1.R |only survRM2adapt-1.1.0/survRM2adapt/R/ltrmst2.R |only survRM2adapt-1.1.0/survRM2adapt/R/ltrmst2adapt.R |only survRM2adapt-1.1.0/survRM2adapt/R/print.ltrmst2adapt.R |only survRM2adapt-1.1.0/survRM2adapt/R/print.rmst2adapt.R |only survRM2adapt-1.1.0/survRM2adapt/R/rmst1_edit.R |only survRM2adapt-1.1.0/survRM2adapt/R/rmst2_edit.R |only survRM2adapt-1.1.0/survRM2adapt/R/rmst2adapt.R |only survRM2adapt-1.1.0/survRM2adapt/R/rmst2adapt.sample.data.R |only survRM2adapt-1.1.0/survRM2adapt/R/shuffle.flat.R |only survRM2adapt-1.1.0/survRM2adapt/R/survRM2adapt-package.R |only survRM2adapt-1.1.0/survRM2adapt/README.md |only survRM2adapt-1.1.0/survRM2adapt/build |only survRM2adapt-1.1.0/survRM2adapt/data |only survRM2adapt-1.1.0/survRM2adapt/inst |only survRM2adapt-1.1.0/survRM2adapt/man/cm214_pfs.Rd |only survRM2adapt-1.1.0/survRM2adapt/man/ltrmst2adapt.Rd |only survRM2adapt-1.1.0/survRM2adapt/man/print.ltrmst2adapt.Rd |only survRM2adapt-1.1.0/survRM2adapt/man/print.rmst2adapt.Rd | 5 + survRM2adapt-1.1.0/survRM2adapt/man/rmst2adapt.Rd | 36 ++++----- survRM2adapt-1.1.0/survRM2adapt/man/rmst2adapt.sample.data.Rd | 10 ++ survRM2adapt-1.1.0/survRM2adapt/man/survRM2adapt-package.Rd | 27 ++++--- survRM2adapt-1.1.0/survRM2adapt/vignettes |only 30 files changed, 110 insertions(+), 47 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Cleve Moler [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Gilber [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.0.11 dated 2022-11-01 and 2.0.12 dated 2023-03-28
rxode2-2.0.11/rxode2/R/etTran.R |only rxode2-2.0.11/rxode2/man/dot-getLastIdLvl.Rd |only rxode2-2.0.11/rxode2/man/dot-iniHandleFixOrUnfix.Rd |only rxode2-2.0.11/rxode2/man/forderForceBase.Rd |only rxode2-2.0.11/rxode2/man/rxDerived.Rd |only rxode2-2.0.11/rxode2/man/rxSetIni0.Rd |only rxode2-2.0.11/rxode2/src/rxode2random.c |only rxode2-2.0.11/rxode2/tests/testthat/test-et.R |only rxode2-2.0.12/rxode2/DESCRIPTION | 22 rxode2-2.0.12/rxode2/MD5 | 258 - rxode2-2.0.12/rxode2/NAMESPACE | 55 rxode2-2.0.12/rxode2/NEWS.md | 133 rxode2-2.0.12/rxode2/R/RcppExports.R | 61 rxode2-2.0.12/rxode2/R/asIni.R |only rxode2-2.0.12/rxode2/R/asModel.R |only rxode2-2.0.12/rxode2/R/asRxui.R |only rxode2-2.0.12/rxode2/R/assert.R | 46 rxode2-2.0.12/rxode2/R/err-sim.R | 5 rxode2-2.0.12/rxode2/R/err.R | 3 rxode2-2.0.12/rxode2/R/genShinyApp.template.R | 2 rxode2-2.0.12/rxode2/R/geom-amt.R | 26 rxode2-2.0.12/rxode2/R/getBaseSim.R |only rxode2-2.0.12/rxode2/R/modlib.R | 4 rxode2-2.0.12/rxode2/R/mu.R | 38 rxode2-2.0.12/rxode2/R/nearpd.R |only rxode2-2.0.12/rxode2/R/piping-ini.R | 394 + rxode2-2.0.12/rxode2/R/piping-model.R | 160 rxode2-2.0.12/rxode2/R/piping.R | 145 rxode2-2.0.12/rxode2/R/reexport.R | 20 rxode2-2.0.12/rxode2/R/rxLinCmt.R | 145 rxode2-2.0.12/rxode2/R/rxUiBlessed.R |only rxode2-2.0.12/rxode2/R/rxUiGet.R | 77 rxode2-2.0.12/rxode2/R/rxode-options.R | 20 rxode2-2.0.12/rxode2/R/rxode2.R | 16 rxode2-2.0.12/rxode2/R/rxode2_md5.R | 2 rxode2-2.0.12/rxode2/R/rxrandom.R | 2 rxode2-2.0.12/rxode2/R/rxsolve.R | 151 rxode2-2.0.12/rxode2/R/symengine.R | 6 rxode2-2.0.12/rxode2/R/ui-assign-parts.R |only rxode2-2.0.12/rxode2/R/ui-rename.R | 62 rxode2-2.0.12/rxode2/R/ui.R | 78 rxode2-2.0.12/rxode2/R/utils.R | 49 rxode2-2.0.12/rxode2/README.md | 24 rxode2-2.0.12/rxode2/build/vignette.rds |binary rxode2-2.0.12/rxode2/inst/doc/rxode2-syntax.html | 79 rxode2-2.0.12/rxode2/inst/tools/workaround.R | 2 rxode2-2.0.12/rxode2/man/as.ini.Rd |only rxode2-2.0.12/rxode2/man/as.model.Rd |only rxode2-2.0.12/rxode2/man/as.rxUi.Rd |only rxode2-2.0.12/rxode2/man/assertRxUi.Rd | 34 rxode2-2.0.12/rxode2/man/dot-assertRenameErrorModelLine.Rd |only rxode2-2.0.12/rxode2/man/dot-iniHandleAppend.Rd |only rxode2-2.0.12/rxode2/man/dot-iniHandleLine.Rd |only rxode2-2.0.12/rxode2/man/dot-modelHandleModelLines.Rd | 5 rxode2-2.0.12/rxode2/man/dot-quoteCallInfoLines.Rd | 5 rxode2-2.0.12/rxode2/man/etTrans.Rd | 2 rxode2-2.0.12/rxode2/man/getBaseSimModel.Rd |only rxode2-2.0.12/rxode2/man/ini-set.Rd |only rxode2-2.0.12/rxode2/man/ini.Rd | 86 rxode2-2.0.12/rxode2/man/model-set.Rd |only rxode2-2.0.12/rxode2/man/model.Rd | 5 rxode2-2.0.12/rxode2/man/reexports.Rd | 9 rxode2-2.0.12/rxode2/man/rmdhunks/rxode2-intro-chunk.Rmd | 136 rxode2-2.0.12/rxode2/man/rxModelVars.Rd | 2 rxode2-2.0.12/rxode2/man/rxRename.Rd | 20 rxode2-2.0.12/rxode2/man/rxUiGet.Rd | 24 rxode2-2.0.12/rxode2/man/rxode2-set.Rd |only rxode2-2.0.12/rxode2/man/stat_amt.Rd | 16 rxode2-2.0.12/rxode2/man/stat_cens.Rd | 14 rxode2-2.0.12/rxode2/man/zeroRe.Rd |only rxode2-2.0.12/rxode2/src/Makevars.in | 2 rxode2-2.0.12/rxode2/src/RcppExports.cpp | 33 rxode2-2.0.12/rxode2/src/etTran.cpp | 2063 ---------- rxode2-2.0.12/rxode2/src/expm.cpp | 2 rxode2-2.0.12/rxode2/src/handle_evid.c | 6 rxode2-2.0.12/rxode2/src/init.c | 12 rxode2-2.0.12/rxode2/src/install.libs.R | 9 rxode2-2.0.12/rxode2/src/nearPD.cpp |only rxode2-2.0.12/rxode2/src/nearPD.h |only rxode2-2.0.12/rxode2/src/rxData.cpp | 136 rxode2-2.0.12/rxode2/src/rxData.h | 3 rxode2-2.0.12/rxode2/src/rxode2_df.cpp | 111 rxode2-2.0.12/rxode2/src/rxode2parse.cpp | 90 rxode2-2.0.12/rxode2/src/rxode2random.cpp |only rxode2-2.0.12/rxode2/src/sbuf.c | 23 rxode2-2.0.12/rxode2/tests/testthat/test-100-cmt.R | 6 rxode2-2.0.12/rxode2/tests/testthat/test-alag.R | 1 rxode2-2.0.12/rxode2/tests/testthat/test-as-ini.R |only rxode2-2.0.12/rxode2/tests/testthat/test-as-model.R |only rxode2-2.0.12/rxode2/tests/testthat/test-assert.R |only rxode2-2.0.12/rxode2/tests/testthat/test-bad-dose.R | 4 rxode2-2.0.12/rxode2/tests/testthat/test-basic.R | 12 rxode2-2.0.12/rxode2/tests/testthat/test-cmt-order.R | 17 rxode2-2.0.12/rxode2/tests/testthat/test-cov.R | 127 rxode2-2.0.12/rxode2/tests/testthat/test-data-table.R | 22 rxode2-2.0.12/rxode2/tests/testthat/test-deSolve-events.R | 20 rxode2-2.0.12/rxode2/tests/testthat/test-derived.R | 18 rxode2-2.0.12/rxode2/tests/testthat/test-dfRep.R | 2 rxode2-2.0.12/rxode2/tests/testthat/test-dollar-names.R | 30 rxode2-2.0.12/rxode2/tests/testthat/test-drop.R | 22 rxode2-2.0.12/rxode2/tests/testthat/test-etTrans.R | 816 --- rxode2-2.0.12/rxode2/tests/testthat/test-evid3.R | 12 rxode2-2.0.12/rxode2/tests/testthat/test-example-6.R | 61 rxode2-2.0.12/rxode2/tests/testthat/test-factorial.R | 6 rxode2-2.0.12/rxode2/tests/testthat/test-fixef.R | 11 rxode2-2.0.12/rxode2/tests/testthat/test-focei-variances.R | 735 +-- rxode2-2.0.12/rxode2/tests/testthat/test-geom-amt.R |only rxode2-2.0.12/rxode2/tests/testthat/test-infusion-bolus.R |only rxode2-2.0.12/rxode2/tests/testthat/test-infusion-bolus.qs |only rxode2-2.0.12/rxode2/tests/testthat/test-keep.R | 200 rxode2-2.0.12/rxode2/tests/testthat/test-lincmt-solve.R | 27 rxode2-2.0.12/rxode2/tests/testthat/test-logical.R | 10 rxode2-2.0.12/rxode2/tests/testthat/test-mu.R | 122 rxode2-2.0.12/rxode2/tests/testthat/test-nearpd.R |only rxode2-2.0.12/rxode2/tests/testthat/test-nopred-ui.R | 9 rxode2-2.0.12/rxode2/tests/testthat/test-null-assign.R |only rxode2-2.0.12/rxode2/tests/testthat/test-occ.R | 99 rxode2-2.0.12/rxode2/tests/testthat/test-opt-expr.R | 4 rxode2-2.0.12/rxode2/tests/testthat/test-pheno.R | 4 rxode2-2.0.12/rxode2/tests/testthat/test-pipeline.R | 111 rxode2-2.0.12/rxode2/tests/testthat/test-piping-ini.R |only rxode2-2.0.12/rxode2/tests/testthat/test-plot.R | 11 rxode2-2.0.12/rxode2/tests/testthat/test-print.R | 2 rxode2-2.0.12/rxode2/tests/testthat/test-random.R | 11 rxode2-2.0.12/rxode2/tests/testthat/test-rxStack-factor.R | 16 rxode2-2.0.12/rxode2/tests/testthat/test-rxode-issue-349.R | 28 rxode2-2.0.12/rxode2/tests/testthat/test-rxode-issue-398.R | 10 rxode2-2.0.12/rxode2/tests/testthat/test-sim-zeros.R |only rxode2-2.0.12/rxode2/tests/testthat/test-symmetric.R | 13 rxode2-2.0.12/rxode2/tests/testthat/test-transit.R | 8 rxode2-2.0.12/rxode2/tests/testthat/test-ui-assert.R | 117 rxode2-2.0.12/rxode2/tests/testthat/test-ui-assign-model-parts.R |only rxode2-2.0.12/rxode2/tests/testthat/test-ui-bad.R | 131 rxode2-2.0.12/rxode2/tests/testthat/test-ui-drop-lines.R | 96 rxode2-2.0.12/rxode2/tests/testthat/test-ui-err.R | 162 rxode2-2.0.12/rxode2/tests/testthat/test-ui-fix-unfix.R | 35 rxode2-2.0.12/rxode2/tests/testthat/test-ui-good.R | 77 rxode2-2.0.12/rxode2/tests/testthat/test-ui-ini-lotri.R | 36 rxode2-2.0.12/rxode2/tests/testthat/test-ui-ini-str.R | 17 rxode2-2.0.12/rxode2/tests/testthat/test-ui-lhs.R |only rxode2-2.0.12/rxode2/tests/testthat/test-ui-mod-functions.R | 73 rxode2-2.0.12/rxode2/tests/testthat/test-ui-mv.R | 26 rxode2-2.0.12/rxode2/tests/testthat/test-ui-piping-single-endpoint.R | 18 rxode2-2.0.12/rxode2/tests/testthat/test-ui-piping.R | 806 ++- rxode2-2.0.12/rxode2/tests/testthat/test-ui-pred-err.R | 81 rxode2-2.0.12/rxode2/tests/testthat/test-ui-promote.R | 28 rxode2-2.0.12/rxode2/tests/testthat/test-ui-rename.R | 39 rxode2-2.0.12/rxode2/tests/testthat/test-ui-simulation.R | 138 rxode2-2.0.12/rxode2/tests/testthat/test-ui.R | 102 rxode2-2.0.12/rxode2/tests/testthat/test-unary-noop.R | 23 rxode2-2.0.12/rxode2/tests/testthat/test-utils.R |only 151 files changed, 3938 insertions(+), 5607 deletions(-)
Title: 'Rstudio' Addin for Version Control and Assignment Management
using Git
Description: An 'Rstudio' addin for version control that allows users to clone
repositories, create and delete branches, and sync forks on GitHub, GitLab, etc.
Furthermore, the addin uses the GitLab API to allow instructors to create
forks and merge requests for all students/teams with one click of a button.
Author: Vincent Nijs [aut, cre],
Sanjiv Erat [aut]
Maintainer: Vincent Nijs <vnijs@ucsd.edu>
Diff between gitgadget versions 0.7.5 dated 2022-08-15 and 0.7.6 dated 2023-03-28
gitgadget-0.7.5/gitgadget/R/interactive_testing.R |only gitgadget-0.7.6/gitgadget/DESCRIPTION | 10 - gitgadget-0.7.6/gitgadget/MD5 | 11 - gitgadget-0.7.6/gitgadget/R/git.R | 51 ++++++-- gitgadget-0.7.6/gitgadget/README.md | 2 gitgadget-0.7.6/gitgadget/build/vignette.rds |binary gitgadget-0.7.6/gitgadget/inst/doc/gitgadget.html | 129 +++++++++++----------- 7 files changed, 114 insertions(+), 89 deletions(-)
Title: Create Flashcards of Terms and Definitions
Description: Provides functions for creating flashcard decks of terms and
definitions. This package creates HTML slides using 'revealjs' that can be
viewed in the 'RStudio' viewer or a web browser. Users can create
flashcards from either existing built-in decks or create their own from CSV
files or vectors of function names.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between flashr versions 0.1.0 dated 2022-11-22 and 0.1.1 dated 2023-03-28
DESCRIPTION | 8 ++-- MD5 | 27 +++++++-------- NEWS.md | 7 +++ R/flashcard.R | 5 +- R/list_decks.R | 5 +- README.md | 19 ++++++++-- build/vignette.rds |binary man/choose_deck.Rd | 2 + man/create_deck.Rd | 2 + man/figures/logo.png |only man/flashcard.Rd | 5 ++ man/list_decks.Rd | 2 + tests/testthat/test-flashcard.R | 69 ++++++--------------------------------- tests/testthat/test-list_decks.R | 5 ++ tests/testthat/test-utils.R | 1 15 files changed, 72 insertions(+), 85 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: A 'ggplot2' extension for drawing gene arrow maps.
Author: David Wilkins [aut, cre],
Zachary Kurtz [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.4.1 dated 2020-12-10 and 0.5.0 dated 2023-03-28
DESCRIPTION | 11 MD5 | 116 +-- NAMESPACE | 9 NEWS.md | 21 R/data.R | 28 R/expect_doppelganger.R | 2 R/geom_feature.R |only R/geom_feature_label.R |only R/geom_gene_arrow.R | 84 ++ R/geom_gene_label.R | 47 - R/geom_subgene_arrow.R | 167 ++++ R/geom_subgene_label.R | 46 - R/make_alignment_dummies.R | 9 R/theme_genes.R | 28 README.md | 56 + build/vignette.rds |binary data/example_dummies.rda |only data/example_features.rda |only data/example_genes.rda |binary data/example_subgenes.rda |binary inst/WORDLIST | 14 inst/doc/introduction-to-gggenes.R | 16 inst/doc/introduction-to-gggenes.Rmd | 30 inst/doc/introduction-to-gggenes.html | 385 +++++----- man/example_dummies.Rd |only man/example_features.Rd |only man/figures/README-geom_gene_arrow-1.png |binary man/figures/README-labelled_genes-1.png |binary man/figures/README-make_alignment_dummies-1.png |binary man/figures/README-reversing_direction-1.png |binary man/figures/README-subgenes-1.png |binary man/figures/README-theme_genes-1.png |binary man/figures/README-unnamed-chunk-2-1.png |only man/geom_feature.Rd |only man/geom_feature_label.Rd |only man/geom_gene_label.Rd | 1 man/geom_subgene_arrow.Rd | 5 man/theme_genes.Rd | 6 tests/figs/deps.txt | 4 tests/figs/geom-subgene-arrow |only tests/figs/visual-tests-of-plots/basic-plot-with-features.svg |only tests/figs/visual-tests-of-plots/basic-plot-with-labelled-features.svg |only tests/figs/visual-tests-of-plots/basic-plot.svg | 8 tests/figs/visual-tests-of-plots/plot-in-flipped-coordinates.svg |only tests/figs/visual-tests-of-plots/plot-using-forward-aesthetic.svg | 2 tests/figs/visual-tests-of-plots/plot-with-features-and-non-logical-forward.svg |only tests/figs/visual-tests-of-plots/plot-with-geom-gene-label.svg | 16 tests/figs/visual-tests-of-plots/plot-with-make-alignment-dummies.svg | 8 tests/figs/visual-tests-of-plots/plot-with-subgenes.svg | 8 tests/figs/visual-tests-of-plots/plot-with-theme-genes.svg | 8 tests/figs/visual-tests-of-plots/subgene-plot-in-flipped-coords.svg |only tests/testthat/_snaps |only tests/testthat/test-geom_feature.R |only tests/testthat/test-geom_feature_label.R |only tests/testthat/test-geom_gene_arrow.R | 2 tests/testthat/test-geom_gene_label.R | 2 tests/testthat/test-geom_subgene_arrow.R | 31 tests/testthat/test-geom_subgene_label.R | 2 tests/testthat/test-make_alignment_dummies.R | 2 tests/testthat/test-plots.R | 85 ++ tests/testthat/test-theme_genes.R | 2 vignettes/introduction-to-gggenes.Rmd | 30 62 files changed, 970 insertions(+), 321 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-03 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-07 1.1.1
2019-09-08 1.1.0
2019-06-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-20 1.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-31 0.3.0
2021-02-15 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-02 0.1.2-1
2020-04-05 0.1.2
2020-02-19 0.1.1
2020-01-22 0.1.0