Title: Wasserstein Regression and Inference
Description: Implementation of the methodologies described in 1) Alexander Petersen, Xi Liu and Afshin A. Divani (2021) <doi:10.1214/20-aos1971>, including global F tests, partial F tests, intrinsic Wasserstein-infinity bands and Wasserstein density bands, and 2) Chao Zhang, Piotr Kokoszka and Alexander Petersen (2022) <doi:10.1111/jtsa.12590>, including estimation, prediction, and inference of the Wasserstein autoregressive models.
Author: Xi Liu [aut, cre],
Chao Zhang [aut],
Matthew Coleman [aut],
Alexander Petersen [aut]
Maintainer: Xi Liu <xiliu@ucsb.edu>
Diff between WRI versions 0.1.0 dated 2020-11-23 and 0.2.0 dated 2022-07-08
DESCRIPTION | 18 - MD5 | 34 + NAMESPACE | 3 NEWS.md | 5 R/Exp_Map.R |only R/confidenceBands.R | 2 R/partialFtest.R | 5 R/warEst.R |only R/warPred.R |only R/warSim.R |only R/wass_R2.R | 2 build/vignette.rds |binary inst/doc/WRI-vignette.html | 416 ++++++++++++++---------- man/Exp_Map_Barycenter_Method.Rd |only man/Exp_Map_Barycenter_Method_pw.Rd |only man/Sample_ACV.Rd |only man/WARp.Rd |only man/WARp_acvfs.Rd |only man/WARp_forecast_tangent.Rd |only man/getInnovation.Rd |only man/predict.WARp.Rd |only man/strokeCTdensity.Rd | 6 man/warSim.Rd |only src/RcppExports.cpp | 5 tests/testthat/test-Exp_Map_Barycenter_Method.R |only 25 files changed, 306 insertions(+), 190 deletions(-)
Title: Mediation Analysis Confidence Intervals
Description: We provide functions to compute confidence
intervals (CIs) for a well-defined nonlinear function of the model
parameters (e.g., product of k coefficients) in single--level and
multilevel structural equation models.
Author: Davood Tofighi <dtofighi@gmail.com>
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Diff between RMediation versions 1.1.4 dated 2016-03-14 and 1.2.0 dated 2022-07-08
RMediation-1.1.4/RMediation/R/ci.lavaan.R |only RMediation-1.2.0/RMediation/DESCRIPTION | 27 +- RMediation-1.2.0/RMediation/MD5 | 52 ++-- RMediation-1.2.0/RMediation/NAMESPACE | 24 +- RMediation-1.2.0/RMediation/NEWS | 13 - RMediation-1.2.0/RMediation/R/RMediation-package.R |only RMediation-1.2.0/RMediation/R/ci.R | 107 ++++++--- RMediation-1.2.0/RMediation/R/mbco.R |only RMediation-1.2.0/RMediation/R/mbco_asymp.R |only RMediation-1.2.0/RMediation/R/mbco_parametric.R |only RMediation-1.2.0/RMediation/R/mbco_semi.R |only RMediation-1.2.0/RMediation/R/medci.R | 84 +++++++ RMediation-1.2.0/RMediation/R/medciAsymp.R | 10 RMediation-1.2.0/RMediation/R/medciMC.R | 2 RMediation-1.2.0/RMediation/R/medciMeeker.R | 8 RMediation-1.2.0/RMediation/R/memory_exp.R |only RMediation-1.2.0/RMediation/R/pMC.R | 12 - RMediation-1.2.0/RMediation/R/pprodnormal.R | 43 +++ RMediation-1.2.0/RMediation/R/qMC.R | 14 - RMediation-1.2.0/RMediation/R/qprodnormal.R | 49 ++++ RMediation-1.2.0/RMediation/R/qprodnormalMeeker.R | 22 + RMediation-1.2.0/RMediation/README.md |only RMediation-1.2.0/RMediation/build |only RMediation-1.2.0/RMediation/data |only RMediation-1.2.0/RMediation/man/RMediation-package.Rd | 40 ++- RMediation-1.2.0/RMediation/man/ci.Rd | 129 +++++++--- RMediation-1.2.0/RMediation/man/mbco.Rd |only RMediation-1.2.0/RMediation/man/medci.Rd | 214 ++++++++---------- RMediation-1.2.0/RMediation/man/memory_exp.Rd |only RMediation-1.2.0/RMediation/man/pMC.Rd | 9 RMediation-1.2.0/RMediation/man/pprodnormal.Rd | 145 +++++------- RMediation-1.2.0/RMediation/man/qMC.Rd | 9 RMediation-1.2.0/RMediation/man/qprodnormal.Rd | 159 +++++-------- 33 files changed, 715 insertions(+), 457 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.109.2 dated 2022-06-10 and 0.109.6 dated 2022-07-08
DESCRIPTION | 12 MD5 | 20 NEWS.md | 18 R/getscene.R | 12 README.md | 7 build/vignette.rds |binary inst/doc/WebGL.html | 7354 ----------------------------- inst/doc/rgl.html | 175 inst/htmlwidgets/lib/rglClass/mouse.src.js | 39 src/x11gui.cpp | 33 src/x11gui.h | 3 11 files changed, 200 insertions(+), 7473 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.8.3 dated 2022-03-17 and 1.0.9 dated 2022-07-08
ChangeLog | 62 +++++++++++++++++++++++++++ DESCRIPTION | 11 ++-- MD5 | 74 ++++++++++++++++---------------- README.md | 22 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 12 ++++- inst/bib/Rcpp.bib | 33 ++++++++++++++ inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/String.h | 81 ++++++++++++++++++++++++++++++------ inst/include/Rcpp/config.h | 8 +-- inst/include/RcppCommon.h | 1 inst/tinytest/cpp/String.cpp | 29 ++++++++++++ inst/tinytest/test_string.R | 20 ++++++++ man/dependsAttribute.Rd | 7 +-- man/exportAttribute.Rd | 14 +++--- man/interfacesAttribute.Rd | 15 +++--- src/barrier.cpp | 3 - tests/tinytest.R | 2 vignettes/pdf/Rcpp-FAQ.pdf |binary vignettes/pdf/Rcpp-attributes.pdf |binary vignettes/pdf/Rcpp-extending.pdf |binary vignettes/pdf/Rcpp-introduction.pdf |binary vignettes/pdf/Rcpp-jss-2011.pdf |binary vignettes/pdf/Rcpp-libraries.pdf |binary vignettes/pdf/Rcpp-modules.pdf |binary vignettes/pdf/Rcpp-package.pdf |binary vignettes/pdf/Rcpp-quickref.pdf |binary vignettes/pdf/Rcpp-sugar.pdf |binary 38 files changed, 300 insertions(+), 94 deletions(-)
Title: Robust PCA by Projection Pursuit
Description: Provides functions for robust PCA by projection pursuit.
The methods are described in Croux et al. (2006) <doi:10.2139/ssrn.968376>,
Croux et al. (2013) <doi:10.1080/00401706.2012.727746>,
Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>.
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between pcaPP versions 2.0-1 dated 2022-04-26 and 2.0-2 dated 2022-07-08
pcaPP-2.0-1/pcaPP/build |only pcaPP-2.0-2/pcaPP/ChangeLog | 9 +++++++++ pcaPP-2.0-2/pcaPP/DESCRIPTION | 10 ++++++---- pcaPP-2.0-2/pcaPP/MD5 | 8 ++++---- pcaPP-2.0-2/pcaPP/README.md |only pcaPP-2.0-2/pcaPP/man/cor.fk.Rd | 2 +- 6 files changed, 20 insertions(+), 9 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre], Antonio Canale [ctb], Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 1.0.0 dated 2021-11-23 and 1.0.1 dated 2022-07-08
DESCRIPTION | 10 +++--- MD5 | 12 +++---- build/vignette.rds |binary inst/doc/BNPmix.pdf |binary src/DdpFunctions.cpp | 79 +++++++-------------------------------------------- src/RcppExports.cpp | 5 +++ src/cDDP.cpp | 65 ++++++++--------------------------------- 7 files changed, 40 insertions(+), 131 deletions(-)
Title: Port of the S+ "Robust Library"
Description: Methods for robust statistics, a state of the art in the early
2000s, notably for robust regression and robust multivariate analysis.
Author: Jiahui Wang,
Ruben Zamar <ruben@stat.ubc.ca>,
Alfio Marazzi <Alfio.Marazzi@inst.hospvd.ch>,
Victor Yohai <vyohai@dm.uba.ar>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Ricardo Maronna <maron@mate.unlp.edu.ar>,
Eric Zivot <ezivot@u.washington.edu>, [...truncated...]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between robust versions 0.7-0 dated 2022-02-01 and 0.7-1 dated 2022-07-08
robust-0.7-0/robust/README |only robust-0.7-1/robust/DESCRIPTION | 10 ++++++---- robust-0.7-1/robust/MD5 | 12 ++++++------ robust-0.7-1/robust/NEWS.md | 12 ++++++++++-- robust-0.7-1/robust/README.md |only robust-0.7-1/robust/src/compatibility.c | 11 ++++++++++- robust-0.7-1/robust/src/mmprnt.c | 12 ++++++++++++ robust-0.7-1/robust/src/rb.c | 9 +++++++++ 8 files changed, 53 insertions(+), 13 deletions(-)
Title: Educational Assessment Tools for Replication Methods
Description: Replication methods to compute some basic statistic operations (means, standard deviations,
frequency tables, percentiles and generalized linear models) in complex survey designs comprising multiple
imputed variables and/or a clustered sampling structure which both deserve special procedures at least in
estimating standard errors. See the package documentation for a more detailed description along with references.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Benjamin Becker [aut]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatRep versions 0.14.4 dated 2022-06-29 and 0.14.5 dated 2022-07-08
DESCRIPTION | 8 +++---- MD5 | 8 +++---- NEWS.md | 4 +++ R/groupToTotalMeanComparisonLavaan_0.0.3.R | 33 ++++++----------------------- man/eatRep-package.rd | 4 +-- 5 files changed, 21 insertions(+), 36 deletions(-)
Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of stepped wedge cluster randomized trials (SW CRT) based on a repeated cross-sectional sampling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Trials 28:182-191. <doi:10.1016/j.cct.2006.05.007>).
Author: Jim Hughes, Navneet R. Hakhu, Emily Voldal, and Fan Xia
Maintainer: Jim Hughes <jphughes@uw.edu>
Diff between swCRTdesign versions 3.2 dated 2022-05-25 and 3.3 dated 2022-07-08
swCRTdesign-3.2/swCRTdesign/R/swPwr.R |only swCRTdesign-3.3/swCRTdesign/DESCRIPTION | 8 - swCRTdesign-3.3/swCRTdesign/MD5 | 12 - swCRTdesign-3.3/swCRTdesign/R/swGlmPwr.R | 118 ++++++++++++----- swCRTdesign-3.3/swCRTdesign/R/swPwr.r |only swCRTdesign-3.3/swCRTdesign/man/swCRTdesign-package.Rd | 10 + swCRTdesign-3.3/swCRTdesign/man/swGlmPwr.Rd | 17 +- swCRTdesign-3.3/swCRTdesign/man/swPwr.Rd | 15 +- 8 files changed, 122 insertions(+), 58 deletions(-)
Title: Recurrent Event Data Analysis
Description: Contains implementations of recurrent event data analysis routines
including (1) survival and recurrent event data simulation from
stochastic process point of view by the thinning method
proposed by Lewis and Shedler (1979) <doi:10.1002/nav.3800260304>
and the inversion method introduced in Cinlar (1975, ISBN:978-0486497976),
(2) the mean cumulative function (MCF) estimation by the
Nelson-Aalen estimator of the cumulative hazard rate function,
(3) two-sample recurrent event responses comparison with the pseudo-score
tests proposed by Lawless and Nadeau (1995) <doi:10.2307/1269617>,
(4) gamma frailty model with spline rate function following
Fu, et al. (2016) <doi:10.1080/10543406.2014.992524>.
Author: Wenjie Wang [aut, cre] ,
Haoda Fu [aut],
Sy Han Chiou [ctb],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between reda versions 0.5.3 dated 2021-04-02 and 0.5.4 dated 2022-07-08
DESCRIPTION | 13 MD5 | 78 - NAMESPACE | 2 NEWS.md | 12 R/Recur.R | 4 R/Survr.R | 2 R/aic.R | 2 R/baseline.R | 20 R/class.R | 2 R/coef.R | 2 R/data.R | 2 R/mcf-formula.R | 2 R/mcf-generic.R | 2 R/mcf-rateReg.R | 33 R/mcfDiff.R | 2 R/misc.R | 16 R/plot.R | 2 R/rateReg.R | 168 +-- R/reda.R | 2 R/show.R | 2 R/simEvent.R | 53 - R/summary.R | 2 R/zzz.R | 2 README.md | 2 build/vignette.rds |binary inst/CITATION | 4 inst/doc/reda-Recur.html | 1446 ++++++++++++++++++++++++++++- inst/doc/reda-intro.html | 1681 +++++++++++++++++++++++++++++++-- inst/doc/reda-simulate.html | 1690 ++++++++++++++++++++++++++++++++-- inst/include/reda.h | 2 inst/include/reda/Process.h | 4 inst/include/reda/nonparametric_mcf.h | 4 inst/include/reda/utils.h | 4 inst/tinytest/test_rateReg.R | 7 man/rateReg.Rd | 78 - man/simEvent.Rd | 7 src/RcppExports.cpp | 5 src/nonparametric_mcf.cpp | 4 src/relativeRisk.cpp | 2 src/utils.cpp | 2 40 files changed, 4883 insertions(+), 484 deletions(-)
Title: Multiomics Data Integration
Description: Provides functions to do 'O2PLS-DA' analysis for multiple omics data integration.
The algorithm came from "O2-PLS, a two-block (X±Y) latent variable regression (LVR) method with an integral OSC filter"
which published by Johan Trygg and Svante Wold at 2003 <doi:10.1002/cem.775>.
'O2PLS' is a bidirectional multivariate regression method that aims to separate the covariance between
two data sets (it was recently extended to multiple data sets) (Löfstedt and Trygg, 2011 <doi:10.1002/cem.1388>; Löfstedt et al., 2012 <doi:10.1016/j.aca.2013.06.026>)
from the systematic sources of variance being specific for each data set separately.
Author: Kai Guo [aut, cre],
Junguk Hur [aut],
Eva Feldman [aut]
Maintainer: Kai Guo <guokai8@gmail.com>
Diff between o2plsda versions 0.0.15 dated 2022-03-02 and 0.0.16 dated 2022-07-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/o2pls.R | 14 ++++++++++++-- R/o2plscv.R | 5 ++++- build/vignette.rds |binary inst/doc/o2plsda.html | 8 ++++---- man/o2pls.Rd | 2 +- 7 files changed, 31 insertions(+), 18 deletions(-)
Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input
data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] ,
Brent Thorne [ctb] ,
Diego Hernangomez [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between ggspatial versions 1.1.5 dated 2021-01-04 and 1.1.6 dated 2022-07-08
ggspatial-1.1.5/ggspatial/tests/testthat/rosm.cache/osm/13_2635_2917.png |only ggspatial-1.1.5/ggspatial/tests/testthat/rosm.cache/osm/13_2636_2917.png |only ggspatial-1.1.6/ggspatial/DESCRIPTION | 21 ggspatial-1.1.6/ggspatial/MD5 | 176 +++-- ggspatial-1.1.6/ggspatial/NAMESPACE | 8 ggspatial-1.1.6/ggspatial/NEWS.md | 8 ggspatial-1.1.6/ggspatial/R/annotation-map-tile.R | 4 ggspatial-1.1.6/ggspatial/R/annotation-north-arrow.R | 1 ggspatial-1.1.6/ggspatial/R/df-spatial-raster.R | 13 ggspatial-1.1.6/ggspatial/R/df-spatial-stars.R | 41 - ggspatial-1.1.6/ggspatial/R/df-spatial-terra.R |only ggspatial-1.1.6/ggspatial/R/df-spatial.R | 17 ggspatial-1.1.6/ggspatial/R/geom-polypath.R | 4 ggspatial-1.1.6/ggspatial/R/geom-spatial-xline.R | 1 ggspatial-1.1.6/ggspatial/R/layer-spatial-bbox.R | 4 ggspatial-1.1.6/ggspatial/R/layer-spatial-raster.R | 7 ggspatial-1.1.6/ggspatial/R/layer-spatial-stars.R | 339 +++++----- ggspatial-1.1.6/ggspatial/R/layer-spatial-terra.R |only ggspatial-1.1.6/ggspatial/R/layer-spatial.R | 15 ggspatial-1.1.6/ggspatial/R/longlake-data.R | 11 ggspatial-1.1.6/ggspatial/R/utils.R |only ggspatial-1.1.6/ggspatial/inst/longlake/LongLakeMarshWetlands.gpkg |only ggspatial-1.1.6/ggspatial/man/annotation_map_tile.Rd | 4 ggspatial-1.1.6/ggspatial/man/annotation_spatial_hline.Rd | 2 ggspatial-1.1.6/ggspatial/man/df_spatial.Rd | 4 ggspatial-1.1.6/ggspatial/man/figures/README-fig-layer-spatial-sf-1.png |binary ggspatial-1.1.6/ggspatial/man/geom_polypath.Rd | 4 ggspatial-1.1.6/ggspatial/man/geom_spatial_rect.Rd | 4 ggspatial-1.1.6/ggspatial/man/geom_spatial_segment.Rd | 4 ggspatial-1.1.6/ggspatial/man/ggspatial-package.Rd | 4 ggspatial-1.1.6/ggspatial/man/layer_spatial.Raster.Rd | 4 ggspatial-1.1.6/ggspatial/man/layer_spatial.Rd | 15 ggspatial-1.1.6/ggspatial/man/layer_spatial.SpatRaster.Rd |only ggspatial-1.1.6/ggspatial/man/layer_spatial.bbox.Rd | 4 ggspatial-1.1.6/ggspatial/man/layer_spatial.stars.Rd | 22 ggspatial-1.1.6/ggspatial/man/load_longlake_data.Rd | 4 ggspatial-1.1.6/ggspatial/tests/testthat/_snaps |only ggspatial-1.1.6/ggspatial/tests/testthat/rosm.cache/osm/13_1296_2773.png |binary ggspatial-1.1.6/ggspatial/tests/testthat/rosm.cache/osm/13_1296_2774.png |binary ggspatial-1.1.6/ggspatial/tests/testthat/rosm.cache/osm/13_1297_2773.png |binary ggspatial-1.1.6/ggspatial/tests/testthat/rosm.cache/osm/13_1297_2774.png |binary ggspatial-1.1.6/ggspatial/tests/testthat/test-annotation-map-tile.R | 27 ggspatial-1.1.6/ggspatial/tests/testthat/test-annotation-north-arrow.R | 21 ggspatial-1.1.6/ggspatial/tests/testthat/test-annotation-scale.R | 28 ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial-raster.R | 29 ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial-sf.R | 43 - ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial-sp.R | 11 ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial-stars.R | 176 ++++- ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial-terra.R |only ggspatial-1.1.6/ggspatial/tests/testthat/test-df-spatial.R | 11 ggspatial-1.1.6/ggspatial/tests/testthat/test-fixed-aspect.R | 11 ggspatial-1.1.6/ggspatial/tests/testthat/test-geom-polypath.R | 5 ggspatial-1.1.6/ggspatial/tests/testthat/test-geom-spatial-rect.R | 16 ggspatial-1.1.6/ggspatial/tests/testthat/test-geom-spatial-segment.R | 13 ggspatial-1.1.6/ggspatial/tests/testthat/test-geom-spatial-xline.R | 18 ggspatial-1.1.6/ggspatial/tests/testthat/test-geom-spatial.R | 23 ggspatial-1.1.6/ggspatial/tests/testthat/test-layer-spatial-bbox.R | 14 ggspatial-1.1.6/ggspatial/tests/testthat/test-layer-spatial-raster.R | 40 - ggspatial-1.1.6/ggspatial/tests/testthat/test-layer-spatial-stars.R | 308 ++++----- ggspatial-1.1.6/ggspatial/tests/testthat/test-layer-spatial-terra.R |only ggspatial-1.1.6/ggspatial/tests/testthat/test-layer-spatial.R | 11 ggspatial-1.1.6/ggspatial/tests/testthat/test-longlake-data.R | 24 62 files changed, 963 insertions(+), 611 deletions(-)
Title: Dose-Response Data Analysis
Description: Fit logistic functions to observed dose-response continuous
data and evaluate goodness-of-fit measures. See Malyutina A., Tang J.,
and Pessia A. (2021) <doi:10.1101/2021.06.07.447323>.
Author: Alberto Pessia [aut, cre] ,
Alina Malyutina [ctb]
Maintainer: Alberto Pessia <dev@albertopessia.com>
Diff between drda versions 2.0.0 dated 2022-06-17 and 2.0.1 dated 2022-07-08
DESCRIPTION | 6 MD5 | 26 +-- NAMESPACE | 270 ++++++++++++++++++------------------- inst/doc/drda.pdf |binary tests/testthat/test_gompertz.R | 132 +++++++++--------- tests/testthat/test_loggompertz.R | 134 +++++++++--------- tests/testthat/test_logistic2.R | 120 ++++++++-------- tests/testthat/test_logistic4.R | 152 +++++++++----------- tests/testthat/test_logistic5.R | 132 +++++++++--------- tests/testthat/test_logistic6.R | 88 ++++++------ tests/testthat/test_loglogistic2.R | 132 +++++++++--------- tests/testthat/test_loglogistic4.R | 132 +++++++++--------- tests/testthat/test_loglogistic5.R | 122 ++++++++-------- tests/testthat/test_loglogistic6.R | 88 ++++++------ 14 files changed, 757 insertions(+), 777 deletions(-)
Title: Independent Component Analysis
Description: Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between ica versions 1.0-2 dated 2018-05-24 and 1.0-3 dated 2022-07-08
ica-1.0-2/ica/man/ica-package.Rd |only ica-1.0-3/ica/ChangeLog | 17 ++++ ica-1.0-3/ica/DESCRIPTION | 8 - ica-1.0-3/ica/MD5 | 25 +++--- ica-1.0-3/ica/NAMESPACE | 4 ica-1.0-3/ica/R/ica.R |only ica-1.0-3/ica/R/icafast.R | 143 +++++++++++++++++++++-------------- ica-1.0-3/ica/R/icaimax.R | 153 ++++++++++++++++++++++---------------- ica-1.0-3/ica/R/icajade.R | 123 ++++++++++++++++++------------ ica-1.0-3/ica/build/partial.rdb |binary ica-1.0-3/ica/man/ica-internal.Rd | 3 ica-1.0-3/ica/man/ica.Rd |only ica-1.0-3/ica/man/icafast.Rd | 68 +++++++++------- ica-1.0-3/ica/man/icaimax.Rd | 70 +++++++++-------- ica-1.0-3/ica/man/icajade.Rd | 64 ++++++++------- 15 files changed, 402 insertions(+), 276 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Fenny Ong, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 2.2 dated 2022-06-18 and 2.3 dated 2022-07-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++-- R/ICA.BinCont.R | 4 +++- man/ICABinCont.Rd | 3 +-- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling
techniques or better understand data generating processes. The user
specifies a set of relationships between covariates, and generates
data based on these specifications. The final data sets can represent
data from randomized control trials, repeated measure (longitudinal)
designs, and cluster randomized trials. Missingness can be generated
using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] ,
Jacob Wujciak-Jens [aut]
Maintainer: Keith Goldfeld <keith.goldfeld@nyulangone.org>
Diff between simstudy versions 0.4.0 dated 2022-01-20 and 0.5.0 dated 2022-07-08
DESCRIPTION | 13 MD5 | 96 - NAMESPACE | 5 R/add_data.R | 120 + R/asserts.R | 499 +++++--- R/conditions.R | 308 +++- R/define_data.R | 49 R/generate_correlated_data.R | 4 R/generate_data.R | 368 ++++- R/generate_dist.R | 2 R/glue.R | 46 R/group_data.R | 16 R/missing_data.R | 32 R/utility.R | 227 +++ build/vignette.rds |binary inst/doc/clustered.html | 264 +++- inst/doc/correlated.html | 264 ++++ inst/doc/double_dot_extension.html | 277 ++++ inst/doc/longitudinal.html | 239 +++ inst/doc/missing.html | 273 ++++ inst/doc/ordinal.R | 5 inst/doc/ordinal.Rmd | 5 inst/doc/ordinal.html | 365 +++++ inst/doc/simstudy.html | 582 ++++++++- inst/doc/spline.html | 252 +++- inst/doc/survival.R | 327 ++--- inst/doc/survival.Rmd | 418 +++--- inst/doc/survival.html | 2049 +++++++++++++++++++++++++++++++-- inst/doc/treat_and_exposure.html | 347 ++++- man/addCompRisk.Rd |only man/addSynthetic.Rd |only man/defSurv.Rd | 13 man/genFormula.Rd | 8 man/genMarkov.Rd | 7 man/genMiss.Rd | 12 man/genSurv.Rd | 38 man/genSynthetic.Rd |only man/survGetParams.Rd |only man/survParamPlot.Rd |only tests/testthat/test-add_data.R | 120 + tests/testthat/test-asserts.R | 34 tests/testthat/test-conditions.R | 2 tests/testthat/test-define_data.R | 22 tests/testthat/test-generate_data.R | 425 ++++++ tests/testthat/test-generate_dist.R | 2 tests/testthat/test-glue.R | 6 tests/testthat/test-internal_utility.R | 2 tests/testthat/test-missing_data.R | 150 ++ tests/testthat/test-survival.R |only tests/testthat/test-utility.R | 42 vignettes/ordinal.Rmd | 5 vignettes/survival.Rmd | 418 +++--- 52 files changed, 7300 insertions(+), 1458 deletions(-)
Title: Integrative Pathway Enrichment Analysis of Multivariate Omics
Data
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.
Author: Juri Reimand [aut, cre],
Jonathan Barenboim [aut],
Mykhaylo Slobodyanyuk [ctb]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Diff between ActivePathways versions 1.1.0 dated 2022-04-20 and 1.1.1 dated 2022-07-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++-- R/ActivePathways.r | 5 +++++ R/cytoscape.r | 6 ++++++ inst/doc/ActivePathways-vignette.html | 4 ++-- tests/testthat/test_validation.r | 5 +++++ 7 files changed, 33 insertions(+), 13 deletions(-)
More information about ActivePathways at CRAN
Permanent link
Title: Virtual Machines for R
Description: Manage, provision and use Virtual Machines pre-configured for R.
Develop, test and build package in a clean environment.
'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.
Author: Jean-Francois Rey [cre, aut]
Maintainer: Jean-Francois Rey <jf.rey.public@gmail.com>
Diff between vmr versions 0.0.3 dated 2021-03-18 and 0.0.4 dated 2022-07-08
DESCRIPTION | 9 ++--- MD5 | 56 +++++++++++++++++++----------------- R/package.R | 2 - R/vagrant.R | 27 +++++++++-------- R/virtualbox.R | 17 +++++++--- R/vmr-methods.R | 20 ++++++++++++ R/vmr.R | 4 +- README.md | 16 ++++++++-- build/vignette.rds |binary inst/doc/O1-workwithvmr.Rmd | 4 +- inst/doc/O1-workwithvmr.html | 2 + inst/doc/O2-vmrFirstStep.html | 10 +++++- inst/doc/O3-vmrManagevmr.html | 10 +++++- inst/doc/O4-vmrManageBoxes.html | 10 +++++- inst/doc/O5-vmrManageProviders.R | 2 - inst/doc/O5-vmrManageProviders.Rmd | 2 - inst/doc/O5-vmrManageProviders.html | 12 ++++++- inst/doc/O6-vmrDev.html | 10 +++++- inst/doc/O7-vmrcicd.R | 6 +++ inst/doc/O7-vmrcicd.Rmd | 20 ++++++++++-- inst/doc/O7-vmrcicd.html | 29 +++++++++++++++--- inst/doc/O8-vmrResume.html | 10 +++++- inst/doc/vmrPoster.Rnw |only inst/doc/vmrPoster.pdf |only man/vmr-package.Rd | 4 +- man/vmrPackageCheck.Rd | 3 + vignettes/O1-workwithvmr.Rmd | 4 +- vignettes/O5-vmrManageProviders.Rmd | 2 - vignettes/O7-vmrcicd.Rmd | 20 ++++++++++-- vignettes/VMRPosteruseR2022.pdf |only vignettes/vmrPoster.Rnw |only 31 files changed, 230 insertions(+), 81 deletions(-)
Title: A Toolkit for Behavioral Scientists
Description: A collection of functions for analyzing data typically collected
or used by behavioral scientists. Examples of the functions include
a function that compares groups in a factorial experimental design,
a function that conducts (robust) two-way analysis of variance (ANOVA),
and a function that cleans a data set generated by Qualtrics surveys.
Some of the functions will require installing additional package(s).
Such packages and other references are cited within the section
describing the relevant functions. Many functions in this package
rely heavily on these two popular R packages:
Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>.
Wickham et al. (2021) <https://CRAN.R-project.org/package=ggplot2>.
Author: Jin Kim [aut, cre]
Maintainer: Jin Kim <jin.m.kim@yale.edu>
Diff between kim versions 0.5.3 dated 2022-03-18 and 0.5.55 dated 2022-07-08
DESCRIPTION | 8 MD5 | 76 ++++--- NAMESPACE | 7 NEWS.md | 21 + R/akaike_weights.R |only R/check_modes.R |only R/compare_datasets.R | 54 ++--- R/compare_groups.R | 8 R/floodlight_2_by_continuous.R | 226 +++++++++++---------- R/forest_plot.R | 5 R/ggsave_quick.R | 33 ++- R/histogram_w_outlier_bins.R | 45 ++-- R/identical_all.R |only R/install_all_dependencies.R | 4 R/loglinear_analysis.R |only R/mann_whitney.R | 61 ++++- R/modes_of_objects.R |only R/overlapping_interval.R |only R/parallel_analysis.R | 7 R/read_csv.R | 42 +++ R/regex_match.R | 13 - R/repeated_measures_anova.R | 14 + R/scatterplot.R | 4 R/spotlight_2_by_continuous.R | 400 +++++++++++++++++++++++++------------- R/standardized_regression.R |only R/t_test_pairwise.R | 12 - R/und.R | 154 ++++++++++++++ build/partial.rdb |binary inst/CITATION | 4 man/akaike_weights.Rd |only man/check_modes.Rd |only man/compare_groups.Rd | 4 man/floodlight_2_by_continuous.Rd | 8 man/forest_plot.Rd | 3 man/ggsave_quick.Rd | 8 man/identical_all.Rd |only man/loglinear_analysis.Rd |only man/mann_whitney.Rd | 12 + man/modes_of_objects.Rd |only man/overlapping_interval.Rd |only man/read_csv.Rd | 5 man/scatterplot.Rd | 3 man/spotlight_2_by_continuous.Rd | 5 man/standardized_regression.Rd |only man/t_test_pairwise.Rd | 6 man/und.Rd | 5 46 files changed, 894 insertions(+), 363 deletions(-)
Title: Tools for the R Developer
Description: Reporting tools for the R developer to evaluate their packages in terms of complexity, usage, and performance. Developers can generate an HTML report that displays CRAN downloads, number of open GitHub issues and pull requests, package dependencies, and so on, with each component of the report available as independent functions.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between devtoolbox versions 0.1.0 dated 2021-09-07 and 0.2.0 dated 2022-07-08
DESCRIPTION | 11 MD5 | 28 + NEWS.md | 4 R/create_pkg_report.R | 11 R/extract_argument.R | 45 +- R/extract_desc.R | 32 + R/extract_family.R | 38 +- R/extract_title.R | 31 + README.md | 11 inst/rmd_template/package_summary/cran_stats.Rmd |only inst/rmd_template/package_summary/fnc_summary.Rmd |only inst/rmd_template/package_summary/issues.Rmd |only inst/rmd_template/package_summary/main.Rmd | 367 ---------------------- inst/rmd_template/package_summary/pkg_deps.Rmd |only inst/rmd_template/package_summary/pkg_desc.Rmd |only inst/rmd_template/package_summary/pr.Rmd |only man/create_pkg_report.Rd | 13 man/run_rmd.Rd | 4 18 files changed, 166 insertions(+), 429 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.76 dated 2021-10-11 and 0.80 dated 2022-07-08
broman-0.76/broman/NEWS |only broman-0.80/broman/DESCRIPTION | 10 +++++----- broman-0.80/broman/MD5 | 14 +++++++------- broman-0.80/broman/NEWS.md |only broman-0.80/broman/R/jiggle.R | 2 +- broman-0.80/broman/data/numbers-cap.RData |binary broman-0.80/broman/data/numbers.RData |binary broman-0.80/broman/man/jiggle.Rd | 2 +- broman-0.80/broman/src/compare_rows.c | 1 + 9 files changed, 15 insertions(+), 14 deletions(-)
More information about ThresholdROCsurvival at CRAN
Permanent link
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.1-3 dated 2021-10-16 and 1.1-7 dated 2022-07-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/ModisDownload.R | 8 ++++---- R/utils.R | 6 +++--- R/writerts.R | 16 +++++++++------- build/vignette.rds |binary inst/doc/rts.pdf.asis | 2 +- vignettes/rts.pdf.asis | 2 +- 8 files changed, 29 insertions(+), 27 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.8.1 dated 2022-03-13 and 2.9.0 dated 2022-07-08
DESCRIPTION | 10 MD5 | 30 NAMESPACE | 6 R/BAT.R | 3046 +++++++++++++++++++++++++++++----------------------- man/contribution.Rd | 12 man/gamma.Rd |only man/hull.gamma.Rd |only man/hull.sad.Rd |only man/kernel.build.Rd | 8 man/kernel.gamma.Rd |only man/kernel.sad.Rd |only man/mixture.Rd |only man/originality.Rd | 9 man/sad.Rd | 18 man/ses.Rd | 7 man/tree.build.Rd | 44 man/tree.quality.Rd | 16 man/tree.zero.Rd | 4 man/uniqueness.Rd | 5 19 files changed, 1829 insertions(+), 1386 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA) and the World Database on Other Effective Area-Based
Conservation Measures (WDOECM). Data is obtained from Protected Planet
<https://www.protectedplanet.net/en>. To augment data cleaning procedures,
users can install the 'prepr' R package (available at
<https://github.com/dickoa/prepr>).
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 1.3.2 dated 2021-12-05 and 1.3.3 dated 2022-07-08
DESCRIPTION | 13 + MD5 | 40 ++--- NEWS.md | 26 +++ R/internal.R | 25 +++ R/package.R | 2 R/wdpa_fetch.R | 4 R/wdpa_latest_version.R | 2 R/wdpa_url.R | 11 + README.md | 17 +- build/vignette.rds |binary inst/doc/wdpar.Rmd | 6 inst/doc/wdpar.html | 241 ++++++++++++++++++------------------ man/figures/README-readme-map-1.png |binary man/st_repair_geometry.Rd | 6 man/wdpar.Rd | 2 tests/testthat/test_internal.R | 5 tests/testthat/test_wdpa_clean.R | 14 ++ tests/testthat/test_wdpa_dissolve.R | 12 + tests/testthat/test_wdpa_fetch.R | 7 - tests/testthat/test_wdpa_read.R | 4 vignettes/wdpar.Rmd | 6 21 files changed, 266 insertions(+), 177 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2020) <arXiv:2004.02653> and Sigrist (2021) <arXiv:2105.08966> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the included version of Eigen [ctb, cph],
Timot [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 0.7.7 dated 2022-06-10 and 0.7.8 dated 2022-07-08
gpboost-0.7.7/gpboost/tests/testthat/_snaps |only gpboost-0.7.8/gpboost/DESCRIPTION | 8 gpboost-0.7.8/gpboost/MD5 | 52 - gpboost-0.7.8/gpboost/R/GPModel.R | 135 +- gpboost-0.7.8/gpboost/R/gpb.cv.R | 14 gpboost-0.7.8/gpboost/configure.ac | 2 gpboost-0.7.8/gpboost/demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 12 gpboost-0.7.8/gpboost/man/GPModel_shared_params.Rd | 7 gpboost-0.7.8/gpboost/man/fit.GPModel.Rd | 4 gpboost-0.7.8/gpboost/man/fit.Rd | 4 gpboost-0.7.8/gpboost/man/fitGPModel.Rd | 4 gpboost-0.7.8/gpboost/man/gpb.cv.Rd | 3 gpboost-0.7.8/gpboost/man/gpb.grid.search.tune.parameters.Rd | 1 gpboost-0.7.8/gpboost/man/predict.GPModel.Rd | 6 gpboost-0.7.8/gpboost/man/set_prediction_data.GPModel.Rd | 18 gpboost-0.7.8/gpboost/man/set_prediction_data.Rd | 18 gpboost-0.7.8/gpboost/src/c_api.cpp | 86 + gpboost-0.7.8/gpboost/src/gpboost_R.cpp | 62 - gpboost-0.7.8/gpboost/src/gpboost_R.h | 43 gpboost-0.7.8/gpboost/src/include/GPBoost/likelihoods.h | 45 gpboost-0.7.8/gpboost/src/include/GPBoost/re_model.h | 113 +- gpboost-0.7.8/gpboost/src/include/GPBoost/re_model_template.h | 465 +++++++--- gpboost-0.7.8/gpboost/src/include/LightGBM/c_api.h | 41 gpboost-0.7.8/gpboost/src/metric/binary_metric.hpp | 52 - gpboost-0.7.8/gpboost/src/metric/regression_metric.hpp | 52 - gpboost-0.7.8/gpboost/src/re_model.cpp | 284 ++---- gpboost-0.7.8/gpboost/tests/testthat/test_GPModel_gaussian_process.R | 16 gpboost-0.7.8/gpboost/tests/testthat/test_GPModel_grouped_random_effects.R | 8 28 files changed, 994 insertions(+), 561 deletions(-)
Title: Optimizing Consistency and Coverage in Configurational Causal
Modeling
Description: This is an add-on to the 'cna' package <https://CRAN.R-project.org/package=cna> comprising various functions for optimizing consistency and coverage scores of models of configurational comparative methods as Coincidence Analysis (CNA) and Qualitative Comparative Analysis (QCA). The function conCovOpt() calculates con-cov optima, selectMax() selects con-cov maxima among the con-cov optima, DNFbuild() can be used to build models actually reaching those optima, and findOutcomes() identifies those factor values in analyzed data that can be modeled as outcomes. For a theoretical introduction to these functions see Baumgartner and Ambuehl (2021) <doi:10.1177/0049124121995554>.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cnaOpt versions 0.5.1 dated 2022-04-21 and 0.5.2 dated 2022-07-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/conCovOpt.R | 4 ++-- R/conCovOpt_utils.R | 2 +- inst/NEWS | 3 +++ 5 files changed, 14 insertions(+), 11 deletions(-)
Title: A Parallelized General-Purpose Optimization Based on
Marquardt-Levenberg Algorithm
Description: This algorithm provides a numerical solution to the
problem of unconstrained local minimization (or maximization). It is particularly suited for complex problems and more efficient than
the Gauss-Newton-like algorithm when starting from points very
far from the final minimum (or maximum). Each iteration is parallelized and convergence relies on a stringent stopping criterion based on the first and second derivatives. See Philipps et al, 2021 <doi:10.32614/RJ-2021-089>.
Author: Viviane Philipps, Cecile Proust-Lima, Melanie Prague, Boris Hejblum, Daniel Commenges, Amadou Diakite
Maintainer: Viviane Philipps <viviane.philipps@u-bordeaux.fr>
Diff between marqLevAlg versions 2.0.6 dated 2022-03-09 and 2.0.7 dated 2022-07-08
marqLevAlg-2.0.6/marqLevAlg/inst/doc/mla.pdf |only marqLevAlg-2.0.7/marqLevAlg/DESCRIPTION | 10 +- marqLevAlg-2.0.7/marqLevAlg/MD5 | 20 ++--- marqLevAlg-2.0.7/marqLevAlg/R/marqLevAlg.R | 64 +++++++++--------- marqLevAlg-2.0.7/marqLevAlg/R/summary.marqLevAlg.R | 13 ++- marqLevAlg-2.0.7/marqLevAlg/build/partial.rdb |binary marqLevAlg-2.0.7/marqLevAlg/build/vignette.rds |binary marqLevAlg-2.0.7/marqLevAlg/inst/doc/mla.Rmd | 71 +++++++-------------- marqLevAlg-2.0.7/marqLevAlg/inst/doc/mla.html |only marqLevAlg-2.0.7/marqLevAlg/man/marqLevAlg.Rd | 6 + marqLevAlg-2.0.7/marqLevAlg/vignettes/mla.Rmd | 71 +++++++-------------- marqLevAlg-2.0.7/marqLevAlg/vignettes/mla.bib | 28 +------- 12 files changed, 116 insertions(+), 167 deletions(-)
Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with
complex sampling and assessment design (see 'Rutkowski', 2010
<doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the
package, see 'Mirazchiyski', 2021b (<doi:10.3390/psych3020018>).
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.2.0 dated 2022-05-04 and 1.3.0 dated 2022-07-08
DESCRIPTION | 14 MD5 | 40 NAMESPACE | 10 NEWS.md | 108 + R/RALSA.r | 7 R/common.r | 121 + R/lsa.bench.r | 3 R/lsa.bin.log.reg.r | 3 R/lsa.convert.data.r | 74 R/lsa.corr.r | 18 R/lsa.crosstabs.r | 95 + R/lsa.data.diag.r | 2 R/lsa.lin.reg.r | 2 R/lsa.pcts.means.r | 2 R/lsa.prctls.r | 2 R/lsa.recode.vars.r | 2 R/lsa.vars.dict.r | 2 inst/shiny/GUI/server.r | 702 ++++++-- inst/shiny/GUI/ui.r | 3809 ++++++++++++++++++++++++------------------------ man/RALSA.Rd | 2 man/lsa.crosstabs.Rd | 14 21 files changed, 2880 insertions(+), 2152 deletions(-)
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2018) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 3.3.0 dated 2021-12-17 and 3.4.0 dated 2022-07-08
DESCRIPTION | 8 MD5 | 53 NAMESPACE | 3 R/cna.r | 81 + R/condition.r | 2 R/configTable.R | 17 R/ct2df.r | 4 R/full.ct.R | 101 + R/group.by.outcome.r | 16 R/print.condList.R | 39 R/print.condition.R | 4 build/vignette.rds |binary inst/NEWS | 6 inst/doc/cna.R | 6 inst/doc/cna.Rnw | 2863 +++++++++++++++++++++++------------------------- inst/doc/cna.pdf |binary man/cna-internals.Rd | 2 man/cna-package.Rd | 6 man/cna.Rd | 20 man/condList-methods.Rd |only man/condition.Rd | 39 man/full.ct.Rd | 41 man/is.submodel.Rd | 4 man/makeFuzzy.Rd | 112 - man/randomConds.Rd | 382 +++--- man/rreduce.Rd | 2 man/shortcuts.Rd | 106 - vignettes/cna.Rnw | 2863 +++++++++++++++++++++++------------------------- 28 files changed, 3457 insertions(+), 3323 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-07 1.2020.0
2022-04-01 0.3.5
2022-03-16 0.3.4
2021-11-12 0.3.3
2021-09-15 0.3.2
Title: Calculate Federal and State Income Taxes in the United States
Description: Calculates federal and state income taxes in the United States. It acts as a wrapper
to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts
the calculations, while 'usincometaxes' prepares the data for TAXSIM 35, sends the data to
TAXSIM 35's server or communicates with the Web Assembly file, retrieves the data, and places it
into a data frame. All without the user worrying about this process.
Author: Shane Orr [aut, cre, cph],
Thomas Wells [ctb]
Maintainer: Shane Orr <shane.j.orr@gmail.com>
Diff between usincometaxes versions 0.4.0 dated 2022-05-30 and 0.5.0 dated 2022-07-08
DESCRIPTION | 21 +- LICENSE | 4 MD5 | 44 ++-- NEWS.md | 9 R/calculate_taxes.R | 73 +++++-- R/utils_check_data.R | 22 +- R/utils_clean_data.R | 2 R/utils_connect_server.R | 68 ++++++ README.md | 19 - build/vignette.rds |binary inst/doc/interface-options.R |only inst/doc/interface-options.Rmd |only inst/doc/interface-options.html |only inst/doc/send-data-to-taxsim.Rmd | 2 inst/doc/send-data-to-taxsim.html | 226 +++++++++++++++++++++ inst/doc/taxsim-input.html | 350 +++++++++++++++++++++++++++++----- inst/doc/taxsim-output.html | 294 +++++++++++++++++++++++++--- inst/doc/using-usincometaxes.html | 293 ++++++++++++++++++++++++++-- inst/taxsim |only man/calculate_taxes_http.Rd |only man/calculate_taxes_wasm.Rd |only man/check_parameters.Rd | 4 man/taxsim_calculate_taxes.Rd | 16 + tests/testthat/test-calculate_taxes.R | 31 +++ vignettes/interface-options.Rmd |only vignettes/send-data-to-taxsim.Rmd | 2 26 files changed, 1302 insertions(+), 178 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph]
,
Andreas Sand [ant],
Gerth Stoelting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant],
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.2.4 dated 2022-05-02 and 1.2.5 dated 2022-07-08
DESCRIPTION | 10 +- MD5 | 38 ++++----- NEWS.md | 4 R/zzz.R | 10 -- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Quartet-Distance.pdf |binary inst/doc/Using-Quartet.html | 4 src/EdgeParser.cpp | 2 src/QuartetDistanceCalculator.cpp | 130 +++++++++++++++++++++----------- src/TripletDistanceCalculator.cpp | 80 +++++++++++++++---- src/rTripletDist.cpp | 18 ++-- src/unrooted_tree.h | 4 tests/testthat/test-1-tqdist.R | 44 +++++----- tests/testthat/test-PartitionDistance.R | 4 tests/testthat/test-QuartetDistance.R | 13 +-- tests/testthat/test-QuartetStates.R | 6 - tests/testthat/test-ResolvedQuartets.R | 8 - tests/testthat/test-TernaryPoints.R | 29 +++---- tests/testthat/test-VisualizeQuartet.R | 8 - 20 files changed, 253 insertions(+), 159 deletions(-)
Title: Analytic Insurance Rating Techniques
Description: Methods for insurance rating. It helps actuaries to implement GLMs within all relevant steps needed to construct
a risk premium from raw data. It provides a data driven strategy for the construction of insurance tariff classes.
This strategy is based on the work by Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>. It also provides recipes
on how to easily perform one-way, or univariate, analyses on an insurance portfolio. In addition it adds functionality
to include reference categories in the levels of the coefficients in the output of a generalized linear regression analysis.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.6.9 dated 2021-12-11 and 0.7.0 dated 2022-07-08
DESCRIPTION | 8 +-- MD5 | 19 ++++----- NEWS.md | 5 ++ R/model_get_data.R | 72 +++++++++++++---------------------- R/time_reduce.R | 4 - R/utils.R | 5 ++ R/utils_refinement.R | 29 ++++++++------ man/construct_model_points.Rd | 14 +++--- man/figures/bootstraprmse-1.png |binary man/figures/example3c-1.png |binary tests/testthat/test_model_get_data.R |only 11 files changed, 78 insertions(+), 78 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: From Biological Sequences and Simulations to Correlation
Analysis
Description: Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi: 10.1371/journal.pcbi.1006209>. An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) <doi: 10.1038/s41598-020-72766-1>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).
Author: Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [aut,cre]
Maintainer: Marie Chabbert <marie.chabbert@univ-angers.fr>
Diff between Bios2cor versions 2.2 dated 2020-10-02 and 2.2.1 dated 2022-07-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/elsc.Rd | 10 +++++----- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Analysis of Overdispersed Data using S3 Methods
Description: Provides functions to analyse overdispersed
counts or proportions. These functions should be considered as
complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect
models (GLMM). aods3 is an S3 re-implementation of the
deprecated S4 package aod.
Author: Matthieu Lesnoff <matthieu.lesnoff@cirad.fr> and Renaud
Lancelot <renaud.lancelot@cirad.fr>
Maintainer: Renaud Lancelot <renaud.lancelot@cirad.fr>
Diff between aods3 versions 0.4-1.1 dated 2018-08-30 and 0.4-1.2 dated 2022-07-08
DESCRIPTION | 9 +++++---- MD5 | 24 ++++++++++++------------ data/antibio.rda |binary data/cohorts.rda |binary data/dja.rda |binary data/lizards.rda |binary data/mice.rda |binary data/orob1.rda |binary data/orob2.rda |binary data/rabbits.rda |binary data/rats.rda |binary data/salmonella.rda |binary man/salmonella.Rd | 2 +- 13 files changed, 18 insertions(+), 17 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.4 dated 2016-07-16 and 1.0.4.1 dated 2022-07-08
DESCRIPTION |only MD5 |only NAMESPACE |only R |only data |only inst/doc/tutorial.pdf |binary man |only src |only 8 files changed
Title: Tools of Utilization and Cost in Healthcare
Description: R implementation of the software tools developed in the H-CUP
(Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov>
and AHRQ (Agency for Healthcare Research and Quality)
<https://www.ahrq.gov>. It currently contains functions for mapping ICD-9
codes to the AHRQ comorbidity measures and translating ICD-9
(resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General
Equivalence Mappings) from CMS (Centers for Medicare and Medicaid
Services).
Author: Wenjie Wang [aut, cre] ,
Yan Li [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between touch versions 0.1-5 dated 2019-11-17 and 0.1-6 dated 2022-07-08
DESCRIPTION | 24 ++++++++++++------------ MD5 | 36 ++++++++++++++++++------------------ R/RcppExports.R | 17 ----------------- R/cmbd.R | 2 +- R/crosswalk.R | 14 +++++++------- R/data.R | 2 +- R/format.R | 2 +- R/sysdata.rda |binary R/utils.R | 2 +- R/zzz.R | 2 +- README.md | 23 ++++++----------------- data/dxDat.rda |binary inst/CITATION | 4 ++-- inst/ahrq/misc.R | 2 +- man/dxDat.Rd | 4 +++- man/icd_map.Rd | 12 ++++++------ src/RcppExports.cpp | 22 +++++----------------- src/apply_gems.cpp | 2 +- src/initialize_gems.cpp | 2 +- 19 files changed, 67 insertions(+), 105 deletions(-)
Title: Small-Area-Estimation Unit/Area Models and Methods for
Estimation in R
Description: Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645> and Li et al. (2020) <arXiv:2007.05117>.
Author: Zehang R Li [cre, aut],
Bryan D Martin [aut],
Yuan Hsiao [aut],
Jessica Godwin [aut],
John Paige [aut],
Peter Gao [aut],
Jon Wakefield [aut],
Samuel J Clark [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>
Diff between SUMMER versions 1.2.1 dated 2022-02-14 and 1.3.0 dated 2022-07-08
DESCRIPTION | 14 - MD5 | 25 +- NAMESPACE | 5 R/fitINLA2.R | 2 R/fitspace.R | 6 R/mapPlot.R | 3 R/smoothArea.R |only R/smoothUnit.R |only README.md | 31 +-- build/vignette.rds |binary inst/doc/small-area-estimation.html |only inst/doc/small-area-estimation.html.asis |only inst/doc/u5mr-vignette.html | 288 +++++++++++++++--------------- man/smoothArea.Rd |only man/smoothCluster.Rd | 2 man/smoothUnit.Rd |only vignettes/small-area-estimation.html.asis |only 17 files changed, 202 insertions(+), 174 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-29 dated 2022-04-07 and 1.1-30 dated 2022-07-08
DESCRIPTION | 13 ++++++----- MD5 | 46 +++++++++++++++++++++--------------------- R/AllClass.R | 2 - R/allFit.R | 23 +++++++++++++-------- R/bootMer.R | 4 ++- R/checkConv.R | 6 ++++- R/lmer.R | 5 ++++ R/plot.R | 9 ++++---- R/predict.R | 13 +++++++++-- R/utilities.R | 1 inst/NEWS.Rd | 29 +++++++++++++++++++++++++- inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.pdf |binary man/allFit.Rd | 5 +++- man/cake.Rd | 2 - man/mkReTrms.Rd | 2 + tests/nlmer.R | 39 +++++++++++++++++++---------------- tests/nlmer.Rout.save | 45 +++++++++++++++++++++-------------------- tests/testthat/test-allFit.R | 8 +++++++ tests/testthat/test-glmer.R | 12 ++++++++++ tests/testthat/test-glmernb.R | 12 ++++++++++ tests/testthat/test-methods.R | 14 ++++++++++-- tests/testthat/test-utils.R | 14 ++++++++++++ 24 files changed, 213 insertions(+), 91 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-20 1.1.0
2021-09-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-17 1.0.0