Title: Regression Models with Break-Points / Change-Points (with
Possibly Random Effects) Estimation
Description: Given a regression model, segmented `updates' it by adding one or more segmented
(i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in
in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 1.6-2 dated 2022-12-09 and 1.6-3 dated 2023-03-26
DESCRIPTION | 8 MD5 | 22 - NEWS | 794 +++++++++++++++++++++++------------------------ R/seg.num.fit.boot.r | 4 R/segmented.lme.r | 2 R/segmented.numeric.R | 29 + R/selgmented.r | 466 +++++++++++++-------------- R/slope.R | 2 inst/CITATION | 146 ++++---- man/segmented-package.Rd | 162 ++++----- man/segmented.Rd | 12 man/selgmented.Rd | 244 +++++++------- 12 files changed, 954 insertions(+), 937 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 1.0.1 dated 2023-01-18 and 1.1.3 dated 2023-03-26
rgl-1.0.1/rgl/demo/abundance.r |only rgl-1.0.1/rgl/demo/bivar.r |only rgl-1.0.1/rgl/demo/envmap.r |only rgl-1.0.1/rgl/demo/hist3d.r |only rgl-1.0.1/rgl/demo/lollipop3d.R |only rgl-1.0.1/rgl/demo/lsystem.r |only rgl-1.0.1/rgl/demo/shapes3d.R |only rgl-1.0.1/rgl/demo/subdivision.r |only rgl-1.0.1/rgl/src/Makevars.win |only rgl-1.0.1/rgl/src/ext/GLsdk |only rgl-1.1.3/rgl/DESCRIPTION | 6 rgl-1.1.3/rgl/MD5 | 197 rgl-1.1.3/rgl/NAMESPACE | 3 rgl-1.1.3/rgl/NEWS.md | 58 rgl-1.1.3/rgl/R/as.mesh3d.default.R | 34 rgl-1.1.3/rgl/R/as.triangles3d.R | 4 rgl-1.1.3/rgl/R/convertScene.R | 8 rgl-1.1.3/rgl/R/enum.R | 4 rgl-1.1.3/rgl/R/getscene.R | 4 rgl-1.1.3/rgl/R/hover3d.R |only rgl-1.1.3/rgl/R/indices.R |only rgl-1.1.3/rgl/R/material.R | 16 rgl-1.1.3/rgl/R/mesh3d.R | 13 rgl-1.1.3/rgl/R/obj.R | 35 rgl-1.1.3/rgl/R/par3d.R | 2 rgl-1.1.3/rgl/R/ply.R | 53 rgl-1.1.3/rgl/R/r3d.rgl.R | 30 rgl-1.1.3/rgl/R/rglwidget.R | 21 rgl-1.1.3/rgl/R/selectpoints3d.R | 9 rgl-1.1.3/rgl/R/setUserShaders.R | 16 rgl-1.1.3/rgl/R/stl.R | 16 rgl-1.1.3/rgl/README.md | 39 rgl-1.1.3/rgl/build/vignette.rds |binary rgl-1.1.3/rgl/configure | 3325 +++++----- rgl-1.1.3/rgl/configure.ac | 6 rgl-1.1.3/rgl/configure.win | 3 rgl-1.1.3/rgl/demo/00Index | 10 rgl-1.1.3/rgl/demo/rgl.r | 10 rgl-1.1.3/rgl/inst/doc/WebGL.html | 377 - rgl-1.1.3/rgl/inst/doc/demos.R |only rgl-1.1.3/rgl/inst/doc/demos.Rmd |only rgl-1.1.3/rgl/inst/doc/demos.html |only rgl-1.1.3/rgl/inst/doc/deprecation.html | 4 rgl-1.1.3/rgl/inst/doc/pkgdown.html | 2 rgl-1.1.3/rgl/inst/doc/rgl.R | 3 rgl-1.1.3/rgl/inst/doc/rgl.Rmd | 60 rgl-1.1.3/rgl/inst/doc/rgl.html | 361 - rgl-1.1.3/rgl/inst/doc/transparency.html | 8 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/draw.src.js | 2 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/init.src.js | 2 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/rglClass.min.js | 6 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/shaders.src.js | 18 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/shaders/rgl_fragment.glsl | 119 rgl-1.1.3/rgl/inst/htmlwidgets/lib/rglClass/shaders/rgl_vertex.glsl | 12 rgl-1.1.3/rgl/man/figures/READMEpolyhedra-1-rgl.png |binary rgl-1.1.3/rgl/man/hover3d.Rd |only rgl-1.1.3/rgl/man/material.Rd | 40 rgl-1.1.3/rgl/man/scene.Rd | 2 rgl-1.1.3/rgl/man/select3d.Rd | 2 rgl-1.1.3/rgl/man/selectpoints3d.Rd | 2 rgl-1.1.3/rgl/src/ABCLineSet.cpp | 6 rgl-1.1.3/rgl/src/Background.cpp | 2 rgl-1.1.3/rgl/src/ClipPlane.cpp | 2 rgl-1.1.3/rgl/src/Color.cpp | 1 rgl-1.1.3/rgl/src/Makevars.in | 5 rgl-1.1.3/rgl/src/Makevars.ucrt | 3 rgl-1.1.3/rgl/src/Makevars.win.in |only rgl-1.1.3/rgl/src/Material.cpp | 5 rgl-1.1.3/rgl/src/Material.h | 3 rgl-1.1.3/rgl/src/PlaneSet.cpp | 14 rgl-1.1.3/rgl/src/SphereMesh.cpp | 1 rgl-1.1.3/rgl/src/String.cpp | 2 rgl-1.1.3/rgl/src/Texture.cpp | 80 rgl-1.1.3/rgl/src/Texture.h | 10 rgl-1.1.3/rgl/src/api.cpp | 17 rgl-1.1.3/rgl/src/device.cpp | 2 rgl-1.1.3/rgl/src/ext/glad |only rgl-1.1.3/rgl/src/gl.c |only rgl-1.1.3/rgl/src/opengl.h | 24 rgl-1.1.3/rgl/src/par3d.cpp | 11 rgl-1.1.3/rgl/src/pixmap.cpp | 1 rgl-1.1.3/rgl/src/platform.h | 4 rgl-1.1.3/rgl/src/rglmath.h | 2 rgl-1.1.3/rgl/src/scene.cpp | 4 rgl-1.1.3/rgl/src/subscene.cpp | 11 rgl-1.1.3/rgl/src/useNULL/Makevars | 2 rgl-1.1.3/rgl/src/useNULL/Makevars.in | 2 rgl-1.1.3/rgl/src/win32gui.cpp | 18 rgl-1.1.3/rgl/src/x11gui.cpp | 41 rgl-1.1.3/rgl/tests/indices.R | 21 rgl-1.1.3/rgl/tests/testthat/testdata/mergeVertices.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/obj.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/qmesh3d.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/r3d.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/shade3detc.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/subscenes.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/tmesh3d.rds |binary rgl-1.1.3/rgl/tests/testthat/testdata/transformations.rds |binary rgl-1.1.3/rgl/tools/configure.R |only rgl-1.1.3/rgl/vignettes/demos.Rmd |only rgl-1.1.3/rgl/vignettes/rgl.Rmd | 60 101 files changed, 2891 insertions(+), 2405 deletions(-)
Title: Haplotype Trend Regression with eXtra Flexibility (HTRX)
Description: Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) <doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Attfield K E, et al (2022) <doi:10.1101/2022.09.23.509097>.
Author: Yaoling Yang [aut, cre] ,
Daniel Lawson [aut]
Maintainer: Yaoling Yang <yaoling.yang@bristol.ac.uk>
Diff between HTRX versions 1.2.1 dated 2023-02-14 and 1.2.2 dated 2023-03-26
DESCRIPTION | 8 +++---- MD5 | 22 +++++++++---------- R/do_cumulative_htrx.R | 26 +++++++++++----------- R/do_cv.R | 19 +++++++++------- R/pkgname.R | 2 - inst/doc/HTRX_vignette.R | 40 +++++++++++++++++------------------ inst/doc/HTRX_vignette.Rmd | 50 ++++++++++++++++++++++---------------------- inst/doc/HTRX_vignette.pdf |binary man/HTRX-package.Rd | 2 - man/do_cumulative_htrx.Rd | 18 +++++++-------- man/do_cv.Rd | 17 +++++++++----- vignettes/HTRX_vignette.Rmd | 50 ++++++++++++++++++++++---------------------- 12 files changed, 131 insertions(+), 123 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],
Karoline Sachse [aut],
Benjamin Becker [aut]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatRep versions 0.14.6 dated 2022-11-18 and 0.14.7 dated 2023-03-26
eatRep-0.14.6/eatRep/data/datalist |only eatRep-0.14.7/eatRep/DESCRIPTION | 9 - eatRep-0.14.7/eatRep/MD5 | 29 +++--- eatRep-0.14.7/eatRep/NEWS.md | 9 + eatRep-0.14.7/eatRep/R/2_doTrends.r | 102 +++++++++++----------- eatRep-0.14.7/eatRep/R/bifie.r | 18 +++ eatRep-0.14.7/eatRep/R/jk2.R | 132 ++++++++++++++++------------- eatRep-0.14.7/eatRep/R/report.r | 104 ++++++++++------------ eatRep-0.14.7/eatRep/data/lsa.rda |binary eatRep-0.14.7/eatRep/man/eatRep-package.rd | 4 eatRep-0.14.7/eatRep/man/repGlm.Rd | 10 +- eatRep-0.14.7/eatRep/man/repLmer.Rd | 21 +++- eatRep-0.14.7/eatRep/man/repMean.Rd | 70 ++++++--------- eatRep-0.14.7/eatRep/man/repQuantile.Rd | 25 ++--- eatRep-0.14.7/eatRep/man/repTable.Rd | 78 +++++++---------- eatRep-0.14.7/eatRep/man/report.Rd | 13 -- 16 files changed, 317 insertions(+), 307 deletions(-)
Title: Automatically Retrieve Multidimensional Distributed Data Sets
Description: Tool to automatically fetch, transform and arrange subsets of
multi- dimensional data sets (collections of files) stored in local and/or
remote file systems or servers, using multicore capabilities where possible.
The tool provides an interface to perceive a collection of data sets as a single
large multidimensional data array, and enables the user to request for automatic
retrieval, processing and arrangement of subsets of the large array. Wrapper
functions to add support for custom file formats can be plugged in/out, making
the tool suitable for any research field where large multidimensional data sets
are involved.
Author: Nicolau Manubens [aut],
An-Chi Ho [aut, cre],
Nuria Perez-Zanon [aut] ,
Javier Vegas [ctb],
Pierre-Antoine Bretonniere [ctb],
Roberto Serrano [ctb],
Eva Rifa [ctb],
BSC-CNS [aut, cph]
Maintainer: An-Chi Ho <an.ho@bsc.es>
Diff between startR versions 2.2.1 dated 2022-11-18 and 2.2.2 dated 2023-03-26
DESCRIPTION | 8 +- MD5 | 12 +-- NEWS.md | 4 + R/CDORemapper.R | 2 R/NcDataReader.R | 160 +++++++++++++++++++++++++++++++++++++---------------- R/Start.R | 13 ++-- man/CDORemapper.Rd | 2 7 files changed, 138 insertions(+), 63 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.20 dated 2023-01-19 and 2.21 dated 2023-03-26
rmarkdown-2.20/rmarkdown/R/rmarkdown.R |only rmarkdown-2.20/rmarkdown/inst/rmd/h/fontawesome |only rmarkdown-2.21/rmarkdown/DESCRIPTION | 42 +-- rmarkdown-2.21/rmarkdown/MD5 | 41 +-- rmarkdown-2.21/rmarkdown/NEWS.md | 8 rmarkdown-2.21/rmarkdown/R/html_dependencies.R | 10 rmarkdown-2.21/rmarkdown/R/render.R | 8 rmarkdown-2.21/rmarkdown/R/rmarkdown-package.R |only rmarkdown-2.21/rmarkdown/R/shiny_prerendered.R | 2 rmarkdown-2.21/rmarkdown/README.md | 8 rmarkdown-2.21/rmarkdown/build/vignette.rds |binary rmarkdown-2.21/rmarkdown/inst/CITATION | 32 -- rmarkdown-2.21/rmarkdown/inst/doc/lua-filters.html | 226 ++++++++++----------- rmarkdown-2.21/rmarkdown/man/figures/logo.png |binary rmarkdown-2.21/rmarkdown/man/rmarkdown-package.Rd | 2 15 files changed, 174 insertions(+), 205 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 0.7.0 dated 2021-10-11 and 0.8.0 dated 2023-03-26
DESCRIPTION | 10 - MD5 | 22 +- NEWS.md | 9 + R/ApiData.R | 61 ++++-- R/fromJSONstatExtra.R | 63 ++++++- build/vignette.rds |binary inst/doc/Introduction.R | 62 +++++-- inst/doc/Introduction.Rmd | 144 ++++++++++------ inst/doc/Introduction.html | 371 +++++++++++++++++++++++++----------------- man/ApiData.Rd | 23 +- tests/testthat/test-ApiData.R | 150 +++++++++------- vignettes/Introduction.Rmd | 144 ++++++++++------ 12 files changed, 687 insertions(+), 372 deletions(-)
Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then
applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU.
The relevant papers are
a) Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>.
b) Tsagris M. (2022). The FEDHC Bayesian Network Learning Algorithm. Mathematics 2022, 10(15): 2604. <doi:10.3390/math10152604>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 0.9 dated 2023-03-22 and 1.0 dated 2023-03-26
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- man/big_cor.Rd | 8 +++----- man/big_read.Rd | 5 +++-- man/dcor.fedhc.skel.Rd | 4 ++-- man/fedhc.Rd | 2 +- man/fedhc.boot.Rd | 2 +- man/fedhc.skel.Rd | 2 +- man/pchc-package.Rd | 6 +++--- 10 files changed, 29 insertions(+), 30 deletions(-)
Title: Hydrological Codes
Description: Pfafstetter Hydrological Codes
as cited in Verdin and Verdin (1999) <doi: 10.1016/S0022-1694(99)00011-6>
are decoded for upstream or downstream queries.
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between HydroCode versions 1.0.2 dated 2020-08-31 and 1.0.3 dated 2023-03-26
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/rhineCCM2.R | 2 +- R/rhineHYBASlev08.R | 2 +- build/partial.rdb |binary data/rhineCCM2.rda |binary data/rhineHYBASlev08.rda |binary inst/NEWS.Rd | 5 +++++ man/rhineCCM2.Rd | 2 +- man/rhineHYBASlev08.Rd | 2 +- 10 files changed, 23 insertions(+), 18 deletions(-)
Title: Authentication in Shiny with Auth0
Description: Uses Auth0 API (see <https://auth0.com> for more
information) to use a simple authentication system. It provides
tools to log in and out a shiny application using social networks or a list
of e-mails.
Author: Julio Trecenti [cre],
Daniel Falbel [aut],
Jose Jesus [ctb],
Dean Attali [ctb],
C Lente [ctb]
Maintainer: Julio Trecenti <julio.trecenti@gmail.com>
Diff between auth0 versions 0.2.1 dated 2019-09-26 and 0.2.3 dated 2023-03-26
DESCRIPTION | 16 LICENSE | 4 MD5 | 98 +-- NAMESPACE | 28 NEWS.md |only R/auth0.R | 313 +++++----- R/logout.R | 167 ++--- R/shiny.R | 396 +++++++------ R/utils.R | 110 +-- build/vignette.rds |binary inst/bookmark/_auth0.yml | 14 inst/bookmark/app.R | 44 - inst/doc/tutorial.R | 12 inst/doc/tutorial.Rmd | 214 +++---- inst/doc/tutorial.html | 865 ++++++++++++++++-------------- inst/logout/_auth0.yml | 14 inst/logout/app.R | 16 inst/simple/_auth0.yml | 14 inst/simple/app.R | 28 inst/ui-server-bookmark/_auth0.yml | 14 inst/ui-server-bookmark/server.R | 34 - inst/ui-server-bookmark/ui.R | 38 - inst/ui-server-userinfo/_auth0.yml | 14 inst/ui-server-userinfo/global.R | 2 inst/ui-server-userinfo/server.R | 10 inst/ui-server-userinfo/ui.R | 8 inst/ui-server/_auth0.yml | 14 inst/ui-server/server.R | 18 inst/ui-server/ui.R | 8 inst/userinfo/_auth0.yml | 16 inst/userinfo/app.R | 38 - man/auth0_config.Rd | 38 - man/auth0_find_config_file.Rd | 42 - man/auth0_info.Rd | 50 - man/auth0_logout_url.Rd | 111 +-- man/figures/logo.png |only man/logout.Rd | 40 - man/logoutButton.Rd | 86 +- man/logout_url.Rd | 46 - man/shinyAppAuth0.Rd | 70 +- man/shinyAuth0App.Rd | 38 - man/ui-server.Rd | 95 +-- man/use_auth0.Rd | 91 +-- vignettes/examples/bookmark.Rmd | 66 +- vignettes/examples/logout.Rmd | 66 +- vignettes/examples/simple.Rmd | 66 +- vignettes/examples/ui-server-bookmark.Rmd | 84 +- vignettes/examples/ui-server-userinfo.Rmd | 92 +-- vignettes/examples/ui-server.Rmd | 78 +- vignettes/examples/userinfo.Rmd | 66 +- vignettes/tutorial.Rmd | 214 +++---- 51 files changed, 2052 insertions(+), 1954 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10. [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 5.8 dated 2023-02-07 and 5.9 dated 2023-03-26
DESCRIPTION | 15 ++++++++------- MD5 | 40 ++++++++++++++++++++-------------------- R/esag.reg.R | 5 +---- R/iag.reg.R | 2 +- R/makefolds.R | 8 +++++--- R/spher.esag.contour.R | 2 +- R/spher.kent.contour.R | 2 +- R/spher.mixvmf.contour.R | 2 +- R/spher.purka.contour.R | 2 +- R/spher.sespc.contour.R | 2 +- R/spher.spcauchy.contour.R | 2 +- R/spher.vmf.contour.R | 2 +- man/Directional-package.Rd | 4 ++-- man/dsespc.Rd | 2 +- man/dvm.Rd | 2 +- man/pc.test.Rd | 2 +- man/read.fbm.Rd | 7 ++++--- man/sespc.mle.Rd | 5 +++-- man/spher.sespc.contour.Rd | 2 +- man/vmf.contour.Rd | 6 +++--- man/vmf.mle.Rd | 2 +- 21 files changed, 59 insertions(+), 57 deletions(-)
Title: Inhomogeneous K- And Pair Correlation Functions Using Global
Estimators
Description: Second-order summary statistics K- and pair-correlation functions describe
interactions in point pattern data. This package provides computations to estimate those
statistics on inhomogeneous point processes, using the methods of
in T Shaw, J Møller, R Waagepetersen, 2020 <arXiv:2004.00527>.
Author: Thomas Shaw [aut, cre],
Ege Rubak [ctb],
Adrian Baddeley [ctb],
Rolf Turner [ctb]
Maintainer: Thomas Shaw <shawtr@umich.edu>
Diff between globalKinhom versions 0.1.5 dated 2022-11-18 and 0.1.6 dated 2023-03-26
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 +- R/rho_rho.R | 2 +- build/partial.rdb |binary 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.5.0 dated 2022-08-16 and 0.6.0 dated 2023-03-26
crosstable-0.5.0/crosstable/man/body_add_crosstable_list.Rd |only crosstable-0.6.0/crosstable/DESCRIPTION | 14 crosstable-0.6.0/crosstable/MD5 | 139 crosstable-0.6.0/crosstable/NAMESPACE | 579 +- crosstable-0.6.0/crosstable/NEWS.md | 61 crosstable-0.6.0/crosstable/R/burgled.R | 2 crosstable-0.6.0/crosstable/R/compact.R | 58 crosstable-0.6.0/crosstable/R/cross_by.R | 25 crosstable-0.6.0/crosstable/R/cross_categorical.R | 241 crosstable-0.6.0/crosstable/R/cross_numeric.R | 44 crosstable-0.6.0/crosstable/R/cross_survival.R | 41 crosstable-0.6.0/crosstable/R/crosstable-package.R | 12 crosstable-0.6.0/crosstable/R/crosstable.R | 58 crosstable-0.6.0/crosstable/R/dataset.R | 153 crosstable-0.6.0/crosstable/R/effect.R | 37 crosstable-0.6.0/crosstable/R/flextable.R | 106 crosstable-0.6.0/crosstable/R/funs.R | 5 crosstable-0.6.0/crosstable/R/gt.R | 23 crosstable-0.6.0/crosstable/R/labels.R | 66 crosstable-0.6.0/crosstable/R/methods.R |only crosstable-0.6.0/crosstable/R/officer.R | 180 crosstable-0.6.0/crosstable/R/openxlsx.R | 13 crosstable-0.6.0/crosstable/R/options.R | 16 crosstable-0.6.0/crosstable/R/pivot.R |only crosstable-0.6.0/crosstable/R/reexport.R | 64 crosstable-0.6.0/crosstable/R/test.R | 34 crosstable-0.6.0/crosstable/R/utils.R | 146 crosstable-0.6.0/crosstable/README.md | 366 - crosstable-0.6.0/crosstable/build/vignette.rds |binary crosstable-0.6.0/crosstable/inst/IMPORTLIST |only crosstable-0.6.0/crosstable/inst/WORDLIST | 8 crosstable-0.6.0/crosstable/inst/doc/crosstable-install.html | 128 crosstable-0.6.0/crosstable/inst/doc/crosstable-report.html | 128 crosstable-0.6.0/crosstable/inst/doc/crosstable-selection.html | 898 --- crosstable-0.6.0/crosstable/inst/doc/crosstable.Rmd | 502 - crosstable-0.6.0/crosstable/inst/doc/crosstable.html | 756 -- crosstable-0.6.0/crosstable/inst/doc/percent_pattern.R |only crosstable-0.6.0/crosstable/inst/doc/percent_pattern.Rmd |only crosstable-0.6.0/crosstable/inst/doc/percent_pattern.html |only crosstable-0.6.0/crosstable/man/as_flextable.Rd | 11 crosstable-0.6.0/crosstable/man/as_gt.Rd | 6 crosstable-0.6.0/crosstable/man/body_add_legend.Rd | 4 crosstable-0.6.0/crosstable/man/body_add_table_list.Rd |only crosstable-0.6.0/crosstable/man/clean_names_with_labels.Rd | 8 crosstable-0.6.0/crosstable/man/crosstable-package.Rd | 1 crosstable-0.6.0/crosstable/man/crosstable.Rd | 3 crosstable-0.6.0/crosstable/man/crosstable_options.Rd | 9 crosstable-0.6.0/crosstable/man/ct_compact.Rd | 2 crosstable-0.6.0/crosstable/man/effect_summary.Rd | 10 crosstable-0.6.0/crosstable/man/effect_tabular.Rd | 8 crosstable-0.6.0/crosstable/man/get_percent_pattern.Rd |only crosstable-0.6.0/crosstable/man/iris2.Rd | 5 crosstable-0.6.0/crosstable/man/is.crosstable.Rd | 13 crosstable-0.6.0/crosstable/man/mtcars2.Rd | 8 crosstable-0.6.0/crosstable/man/pivot_crosstable.Rd |only crosstable-0.6.0/crosstable/man/reexports.Rd | 4 crosstable-0.6.0/crosstable/man/set_label.Rd | 4 crosstable-0.6.0/crosstable/man/summaryFunctions.Rd | 12 crosstable-0.6.0/crosstable/man/transpose_crosstable.Rd |only crosstable-0.6.0/crosstable/tests/testthat/_snaps/by_factor.md | 2843 ++-------- crosstable-0.6.0/crosstable/tests/testthat/_snaps/by_numeric.md | 20 crosstable-0.6.0/crosstable/tests/testthat/_snaps/compact.md |only crosstable-0.6.0/crosstable/tests/testthat/_snaps/flextable.md | 84 crosstable-0.6.0/crosstable/tests/testthat/_snaps/methods.md |only crosstable-0.6.0/crosstable/tests/testthat/_snaps/options.md | 18 crosstable-0.6.0/crosstable/tests/testthat/_snaps/pivot.md |only crosstable-0.6.0/crosstable/tests/testthat/_snaps/selection.md | 18 crosstable-0.6.0/crosstable/tests/testthat/helper-init_dataset.R | 51 crosstable-0.6.0/crosstable/tests/testthat/test-by_factor.R | 189 crosstable-0.6.0/crosstable/tests/testthat/test-compact.R | 52 crosstable-0.6.0/crosstable/tests/testthat/test-flextable.R | 45 crosstable-0.6.0/crosstable/tests/testthat/test-labels.R | 28 crosstable-0.6.0/crosstable/tests/testthat/test-methods.R |only crosstable-0.6.0/crosstable/tests/testthat/test-officer.R | 78 crosstable-0.6.0/crosstable/tests/testthat/test-options.R | 6 crosstable-0.6.0/crosstable/tests/testthat/test-pivot.R |only crosstable-0.6.0/crosstable/tests/testthat/test-selection.R | 15 crosstable-0.6.0/crosstable/vignettes/crosstable.Rmd | 502 - crosstable-0.6.0/crosstable/vignettes/percent_pattern.Rmd |only 79 files changed, 3278 insertions(+), 5682 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.4 dated 2020-09-17 and 1.1.5 dated 2023-03-26
DESCRIPTION | 12 ++++++------ MD5 | 35 ++++++++++++++++++----------------- R/csmk.test.R | 9 --------- R/hcb.R | 3 +-- R/mk.test.R | 2 +- R/mult.mk.test.R | 2 +- R/partial.mk.test.R | 2 +- R/smk.test.R | 2 +- build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 11 +++++++++++ inst/doc/trend.pdf |binary man/csmk.test.Rd | 2 +- man/hcb.Rd | 3 +-- man/mk.test.Rd | 2 +- man/mult.mk.test.Rd | 2 +- man/partial.mk.test.Rd | 2 +- man/smk.test.Rd | 2 +- src/init.c | 1 - 19 files changed, 46 insertions(+), 46 deletions(-)
Title: Data Frames with Persistent Columns and Attributes
Description: Provides data frames that hold certain columns and attributes
persistently for data processing in 'dplyr'.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between stickyr versions 0.1.1 dated 2023-01-13 and 0.1.2 dated 2023-03-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/dplyr.R | 15 ++++++--------- 4 files changed, 17 insertions(+), 16 deletions(-)
Title: Regression Spline Functions and Classes
Description: Constructs basis matrix of B-splines, M-splines,
I-splines, convex splines (C-splines), periodic M-splines,
natural cubic splines, generalized Bernstein polynomials,
and their integrals (except C-splines) and derivatives
of given order by close-form recursive formulas.
It also contains a C++ head-only library integrated with Rcpp.
See Wang and Yan (2021) <doi:10.6339/21-JDS1020> for details.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between splines2 versions 0.4.7 dated 2023-01-14 and 0.4.8 dated 2023-03-26
DESCRIPTION | 10 MD5 | 49 ++- NEWS.md | 11 README.md | 66 ++--- build/vignette.rds |binary inst/CITATION | 4 inst/bib/splines2.bib | 12 inst/doc/splines2-intro.html | 285 +++++++++++------------ inst/doc/splines2-wi-rcpp.Rmd | 29 +- inst/doc/splines2-wi-rcpp.html | 185 +++++++------- inst/include/splines2Armadillo.h | 4 inst/include/splines2Armadillo/PeriodicMSpline.h | 38 ++- inst/include/splines2Armadillo/SplineBase.h | 14 - inst/rcpp-tests/test-BSpline.cpp | 6 inst/rcpp-tests/test-BernsteinPoly.cpp | 6 inst/rcpp-tests/test-CSpline.cpp | 6 inst/rcpp-tests/test-ISpline.cpp | 6 inst/rcpp-tests/test-MSpline.cpp | 6 inst/rcpp-tests/test-NaturalSpline.cpp | 6 inst/rcpp-tests/test-PeriodicMSpline.R | 16 + inst/rcpp-tests/test-PeriodicMSpline.cpp | 56 +++- inst/run_rcpp_test.R |only src/Makevars | 1 src/Makevars.win | 1 tests/tinytest.R | 13 - vignettes/splines2-wi-rcpp.Rmd | 29 +- 26 files changed, 466 insertions(+), 393 deletions(-)
Title: Drag-and-Drop in 'shiny' Apps with 'SortableJS'
Description: Enables drag-and-drop behaviour in Shiny apps, by exposing the
functionality of the 'SortableJS' <https://sortablejs.github.io/Sortable/>
JavaScript library as an 'htmlwidget'.
You can use this in Shiny apps and widgets, 'learnr' tutorials as well as
R Markdown. In addition, provides a custom 'learnr' question type -
'question_rank()' - that allows ranking questions with drag-and-drop.
Author: Andrie de Vries [cre, aut],
Barret Schloerke [aut],
Kenton Russell [aut, ccp] ,
RStudio [cph, fnd],
Lebedev Konstantin [cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between sortable versions 0.4.6 dated 2022-08-14 and 0.5.0 dated 2023-03-26
sortable-0.4.6/sortable/inst/shiny-examples/update_rank_list |only sortable-0.5.0/sortable/DESCRIPTION | 10 sortable-0.5.0/sortable/MD5 | 72 +- sortable-0.5.0/sortable/NAMESPACE | 1 sortable-0.5.0/sortable/NEWS.md | 12 sortable-0.5.0/sortable/R/bucket_list.R | 29 sortable-0.5.0/sortable/R/dependencies.R | 11 sortable-0.5.0/sortable/R/question_rank.R | 10 sortable-0.5.0/sortable/R/rank_list.R | 84 ++ sortable-0.5.0/sortable/build/vignette.rds |binary sortable-0.5.0/sortable/inst/doc/built_in.R | 6 sortable-0.5.0/sortable/inst/doc/built_in.html | 275 +++---- sortable-0.5.0/sortable/inst/doc/cloning.R | 2 sortable-0.5.0/sortable/inst/doc/cloning.Rmd | 2 sortable-0.5.0/sortable/inst/doc/cloning.html | 126 +-- sortable-0.5.0/sortable/inst/doc/novel_solutions.html | 126 +-- sortable-0.5.0/sortable/inst/doc/understanding_sortable_js.R | 11 sortable-0.5.0/sortable/inst/doc/understanding_sortable_js.Rmd | 17 sortable-0.5.0/sortable/inst/doc/understanding_sortable_js.html | 253 +++---- sortable-0.5.0/sortable/inst/doc/updating_rank_list.R | 47 - sortable-0.5.0/sortable/inst/doc/updating_rank_list.html | 162 ---- sortable-0.5.0/sortable/inst/doc/using_custom_css.html | 126 +-- sortable-0.5.0/sortable/inst/htmlwidgets/plugins/sortable-rstudio/bucket_list.css | 1 sortable-0.5.0/sortable/inst/htmlwidgets/plugins/sortable-rstudio/rank_list.css | 9 sortable-0.5.0/sortable/inst/htmlwidgets/plugins/sortable-rstudio/rank_list_binding.js |only sortable-0.5.0/sortable/inst/htmlwidgets/sortable.js | 15 sortable-0.5.0/sortable/inst/shiny-examples/bucket_list/app.R | 4 sortable-0.5.0/sortable/inst/shiny-examples/horizontal |only sortable-0.5.0/sortable/inst/shiny-examples/rank_list/app.R | 2 sortable-0.5.0/sortable/inst/shiny-examples/update |only sortable-0.5.0/sortable/man/add_rank_list.Rd | 64 + sortable-0.5.0/sortable/man/bucket_list.Rd | 13 sortable-0.5.0/sortable/man/figures/logo.svg | 129 +-- sortable-0.5.0/sortable/man/question_rank.Rd | 8 sortable-0.5.0/sortable/man/rank_list.Rd | 13 sortable-0.5.0/sortable/man/update_bucket_list.Rd |only sortable-0.5.0/sortable/man/update_rank_list.Rd |only sortable-0.5.0/sortable/vignettes/cloning.Rmd | 2 sortable-0.5.0/sortable/vignettes/grouped_lists.html | 355 ++++++++-- sortable-0.5.0/sortable/vignettes/understanding_sortable_js.Rmd | 17 40 files changed, 1092 insertions(+), 922 deletions(-)
Title: Select Intervals Suited for Functional Regression
Description: Interval fusion and selection procedures for regression with
functional inputs. Methods include a semiparametric approach based
on Sliced Inverse Regression (SIR), as described in
<doi:10.1007/s11222-018-9806-6> (standard ridge and sparse SIR are
also included in the package) and a random forest based approach.
Author: Victor Picheny [aut],
Remi Servien [aut],
Nathalie Vialaneix [aut, cre]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SISIR versions 0.2.1 dated 2023-03-12 and 0.2.2 dated 2023-03-26
SISIR-0.2.1/SISIR/tests/test_ridge.R |only SISIR-0.2.2/SISIR/DESCRIPTION | 9 +++--- SISIR-0.2.2/SISIR/MD5 | 19 ++++++++----- SISIR-0.2.2/SISIR/NEWS.md | 16 +++++++++++ SISIR-0.2.2/SISIR/R/helpers_sfcb.R | 1 SISIR-0.2.2/SISIR/R/plot_functions.R | 48 +++++++++++++++++++++++++++++------ SISIR-0.2.2/SISIR/R/sfcb_methods.R | 6 ++-- SISIR-0.2.2/SISIR/man/SFCB-class.Rd | 4 ++ SISIR-0.2.2/SISIR/tests/testthat |only SISIR-0.2.2/SISIR/tests/testthat.R |only 10 files changed, 81 insertions(+), 22 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. [...truncated...]
Maintainer: Julia Wrobel <julia.wrobel@cuanschutz.edu>
Diff between refund versions 0.1-29 dated 2023-01-17 and 0.1-30 dated 2023-03-26
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 3 +-- R/pffr-methods.R | 1 - man/qq.pffr.Rd | 2 +- 5 files changed, 11 insertions(+), 13 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.9.1 dated 2022-11-20 and 0.9.2 dated 2023-03-26
DESCRIPTION | 8 ++-- MD5 | 30 +++++++-------- NAMESPACE | 2 + NEWS.md | 11 +++++ R/create.R | 16 ++++---- R/exists.R | 9 +--- R/nodbi-package.R | 2 + R/query.R | 87 +++++++++++++++++++++++++++++--------------- R/src.R | 2 - R/src_duckdb.R | 26 ++++++++++++- man/docdb_create.Rd | 16 ++++---- man/docdb_exists.Rd | 2 - man/docdb_query.Rd | 25 +++++++----- man/src.Rd | 2 - tests/testthat/core-nodbi.R | 12 ++++-- tests/testthat/helper.R | 8 +++- 16 files changed, 169 insertions(+), 89 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.0.15 dated 2022-11-30 and 0.0.16 dated 2023-03-26
DESCRIPTION | 12 - MD5 | 43 +++--- NEWS.md | 25 +++ R/NMcheckData.R | 64 ++++++--- R/NMextractText.R | 12 + R/NMreadSection.R | 1 R/NMscanInput.R | 8 - R/NMscanMultiple.R | 2 R/NMwriteSection.R | 68 ++++++++-- R/compareCols.R | 12 + R/fnAppend.R | 10 - man/NMextractText.Rd | 6 man/NMscanMultiple.Rd | 2 man/NMwriteSection.Rd | 5 man/compareCols.Rd | 13 + tests/testthat/testData/data/pred_data1.csv |only tests/testthat/testData/data/pred_data1.rds |only tests/testthat/testData/data/pred_data1_meta.txt |only tests/testthat/testData/nonmem/pred030.mod |only tests/testthat/testData/simulations/NMsimData_xgxr014_testsim1.rds |binary tests/testthat/testOutput/xgxr011_update3.mod |only tests/testthat/testOutput/xgxr011_update5.mod |only tests/testthat/testOutput/xgxr011_update6.mod |only tests/testthat/testReference/NMscanInput_10.rds |only tests/testthat/testReference/NMwriteSection_6.rds |only tests/testthat/test_NMscanInput.R | 12 + tests/testthat/test_NMwriteSection.R | 23 ++- 27 files changed, 245 insertions(+), 73 deletions(-)
Title: Navigation Menu for Pipe-Friendly Data Processing
Description: Provides a navigation menu to enable pipe-friendly data processing for hierarchical data structures.
By activating the menu items, you can perform operations on each item while maintaining the overall structure in attributes.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between navigatr versions 0.2.0 dated 2022-11-19 and 0.2.1 dated 2023-03-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/nav_input.R | 2 +- R/nav_menu.R | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Mod [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver@ife.uzh.ch>
Diff between ctsem versions 3.7.2 dated 2022-11-06 and 3.7.6 dated 2023-03-26
ctsem-3.7.2/ctsem/R/zzz.R |only ctsem-3.7.2/ctsem/man/w32chk.Rd |only ctsem-3.7.2/ctsem/src/Makevars |only ctsem-3.7.2/ctsem/src/Makevars.win |only ctsem-3.7.2/ctsem/src/init.cpp |only ctsem-3.7.2/ctsem/src/stan_files |only ctsem-3.7.2/ctsem/tools |only ctsem-3.7.6/ctsem/DESCRIPTION | 25 ctsem-3.7.6/ctsem/MD5 | 221 +- ctsem-3.7.6/ctsem/NAMESPACE | 1 ctsem-3.7.6/ctsem/NEWS | 7 ctsem-3.7.6/ctsem/R/JKalman.R |only ctsem-3.7.6/ctsem/R/ctCheckFit.R | 2 ctsem-3.7.6/ctsem/R/ctChisqTest.R | 2 ctsem-3.7.6/ctsem/R/ctDiscretePars.R | 23 ctsem-3.7.6/ctsem/R/ctFitMultiModel.R | 2 ctsem-3.7.6/ctsem/R/ctGuessPriors.R |only ctsem-3.7.6/ctsem/R/ctJacobian.R | 31 ctsem-3.7.6/ctsem/R/ctKalman.R | 93 - ctsem-3.7.6/ctsem/R/ctPlotArray.R | 212 +- ctsem-3.7.6/ctsem/R/ctStanContinuousPars.R | 2 ctsem-3.7.6/ctsem/R/ctStanFit.R | 767 ++++------ ctsem-3.7.6/ctsem/R/ctStanGenerateFromFit.R | 9 ctsem-3.7.6/ctsem/R/ctStanKalman.R | 7 ctsem-3.7.6/ctsem/R/ctStanModelWriter.R | 236 --- ctsem-3.7.6/ctsem/R/ctStanTIpredeffects.R | 3 ctsem-3.7.6/ctsem/R/ctsemUtils.R | 14 ctsem-3.7.6/ctsem/R/ctsmupdate.R | 105 - ctsem-3.7.6/ctsem/R/extract.ctStanFit.R | 4 ctsem-3.7.6/ctsem/R/isdiag.R | 2 ctsem-3.7.6/ctsem/R/llsurface.R |only ctsem-3.7.6/ctsem/R/stanWplot.R | 2 ctsem-3.7.6/ctsem/R/stanmodels.R | 64 ctsem-3.7.6/ctsem/R/stanoptimis.R | 15 ctsem-3.7.6/ctsem/R/summary.ctStanFit.R | 3 ctsem-3.7.6/ctsem/configure |only ctsem-3.7.6/ctsem/configure.win |only ctsem-3.7.6/ctsem/data/ctstantestfit.rda |binary ctsem-3.7.6/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.7.6/ctsem/inst/doc/hierarchicalmanual.rnw | 56 ctsem-3.7.6/ctsem/inst/include |only ctsem-3.7.6/ctsem/inst/stan |only ctsem-3.7.6/ctsem/man/AnomAuth.Rd | 30 ctsem-3.7.6/ctsem/man/Oscillating.Rd | 30 ctsem-3.7.6/ctsem/man/ctAddSamples.Rd | 52 ctsem-3.7.6/ctsem/man/ctCheckFit.Rd | 212 +- ctsem-3.7.6/ctsem/man/ctChisqTest.Rd | 66 ctsem-3.7.6/ctsem/man/ctCollapse.Rd | 56 ctsem-3.7.6/ctsem/man/ctDeintervalise.Rd | 40 ctsem-3.7.6/ctsem/man/ctDensity.Rd | 64 ctsem-3.7.6/ctsem/man/ctDiscretiseData.Rd | 82 - ctsem-3.7.6/ctsem/man/ctDocs.Rd | 34 ctsem-3.7.6/ctsem/man/ctExample1.Rd | 24 ctsem-3.7.6/ctsem/man/ctExample1TIpred.Rd | 26 ctsem-3.7.6/ctsem/man/ctExample2.Rd | 28 ctsem-3.7.6/ctsem/man/ctExample2level.Rd | 28 ctsem-3.7.6/ctsem/man/ctExample3.Rd | 24 ctsem-3.7.6/ctsem/man/ctExample4.Rd | 24 ctsem-3.7.6/ctsem/man/ctExtract.Rd | 66 ctsem-3.7.6/ctsem/man/ctFit.Rd | 50 ctsem-3.7.6/ctsem/man/ctFitMultiModel.Rd | 134 - ctsem-3.7.6/ctsem/man/ctGenerate.Rd | 116 - ctsem-3.7.6/ctsem/man/ctIndplot.Rd | 144 - ctsem-3.7.6/ctsem/man/ctIntervalise.Rd | 170 +- ctsem-3.7.6/ctsem/man/ctKalman.Rd | 170 +- ctsem-3.7.6/ctsem/man/ctLOO.Rd | 82 - ctsem-3.7.6/ctsem/man/ctLongToWide.Rd | 108 - ctsem-3.7.6/ctsem/man/ctModel.Rd | 444 ++--- ctsem-3.7.6/ctsem/man/ctModelHigherOrder.Rd | 88 - ctsem-3.7.6/ctsem/man/ctModelLatex.Rd | 152 - ctsem-3.7.6/ctsem/man/ctPlotArray.Rd | 130 - ctsem-3.7.6/ctsem/man/ctPoly.Rd | 70 ctsem-3.7.6/ctsem/man/ctStanContinuousPars.Rd | 70 ctsem-3.7.6/ctsem/man/ctStanDiscretePars.Rd | 132 - ctsem-3.7.6/ctsem/man/ctStanDiscreteParsPlot.Rd | 151 - ctsem-3.7.6/ctsem/man/ctStanFit.Rd | 744 ++++----- ctsem-3.7.6/ctsem/man/ctStanFitUpdate.Rd | 61 ctsem-3.7.6/ctsem/man/ctStanGenerate.Rd | 90 - ctsem-3.7.6/ctsem/man/ctStanGenerateFromFit.Rd | 73 ctsem-3.7.6/ctsem/man/ctStanKalman.Rd | 104 - ctsem-3.7.6/ctsem/man/ctStanModel.Rd | 84 - ctsem-3.7.6/ctsem/man/ctStanParnames.Rd | 98 - ctsem-3.7.6/ctsem/man/ctStanPlotPost.Rd | 102 - ctsem-3.7.6/ctsem/man/ctStanPostPredict.Rd | 112 - ctsem-3.7.6/ctsem/man/ctStanSubjectPars.Rd | 66 ctsem-3.7.6/ctsem/man/ctStanTIpredeffects.Rd | 167 +- ctsem-3.7.6/ctsem/man/ctStanUpdModel.Rd | 40 ctsem-3.7.6/ctsem/man/ctWideNames.Rd | 74 ctsem-3.7.6/ctsem/man/ctWideToLong.Rd | 130 - ctsem-3.7.6/ctsem/man/ctsem.Rd | 56 ctsem-3.7.6/ctsem/man/ctstantestdat.Rd | 22 ctsem-3.7.6/ctsem/man/ctstantestfit.Rd | 22 ctsem-3.7.6/ctsem/man/datastructure.Rd | 30 ctsem-3.7.6/ctsem/man/inv_logit.Rd | 34 ctsem-3.7.6/ctsem/man/isdiag.Rd | 88 - ctsem-3.7.6/ctsem/man/log1p_exp.Rd | 34 ctsem-3.7.6/ctsem/man/longexample.Rd | 28 ctsem-3.7.6/ctsem/man/plot.ctKalmanDF.Rd | 150 - ctsem-3.7.6/ctsem/man/plot.ctStanFit.Rd | 90 - ctsem-3.7.6/ctsem/man/plot.ctStanModel.Rd | 132 - ctsem-3.7.6/ctsem/man/sdpcor2cov.Rd | 52 ctsem-3.7.6/ctsem/man/stanWplot.Rd | 80 - ctsem-3.7.6/ctsem/man/stan_checkdivergences.Rd | 96 - ctsem-3.7.6/ctsem/man/stan_postcalc.Rd | 68 ctsem-3.7.6/ctsem/man/stan_reinitsf.Rd | 51 ctsem-3.7.6/ctsem/man/stan_unconstrainsamples.Rd | 92 - ctsem-3.7.6/ctsem/man/standatact_specificsubjects.Rd | 51 ctsem-3.7.6/ctsem/man/stanoptimis.Rd | 226 +- ctsem-3.7.6/ctsem/man/summary.ctStanFit.Rd | 87 - ctsem-3.7.6/ctsem/src/RcppExports.cpp |only ctsem-3.7.6/ctsem/tests/testthat/test-bivariatetrait_hmc.R |only ctsem-3.7.6/ctsem/tests/testthat/test-bootHessian.R |only ctsem-3.7.6/ctsem/tests/testthat/test-runExamples.R | 5 ctsem-3.7.6/ctsem/tests/testthat/test-sunspots.R | 5 ctsem-3.7.6/ctsem/tests/testthat/test-tdeffectvariation_covtest.R |only ctsem-3.7.6/ctsem/tests/testthat/test-timevarying.R | 44 ctsem-3.7.6/ctsem/tests/testthat/test_behavGenNLcor.R |only ctsem-3.7.6/ctsem/vignettes/hierarchicalmanual.rnw | 56 118 files changed, 4132 insertions(+), 4417 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut, cre],
Martijn Schuemie [aut],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Adam Black <black@ohdsi.org>
Diff between Andromeda versions 0.6.1 dated 2022-05-24 and 0.6.3 dated 2023-03-26
DESCRIPTION | 13 +++++++------ MD5 | 15 ++++++++------- NAMESPACE | 1 + R/Object.R | 22 ++++++++++++++++++++++ README.md | 2 +- build/vignette.rds |binary inst/doc/UsingAndromeda.pdf |binary man/isAndromedaTable.Rd |only tests/testthat/test-object.R | 21 +++++++++++++++++++++ 9 files changed, 60 insertions(+), 14 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.2.6 dated 2023-03-10 and 0.2.7 dated 2023-03-26
stdmod-0.2.6/stdmod/inst/doc/cond_effect.R |only stdmod-0.2.6/stdmod/vignettes/stdmod_lm_std2_boot.rds |only stdmod-0.2.7/stdmod/DESCRIPTION | 6 stdmod-0.2.7/stdmod/MD5 | 109 +- stdmod-0.2.7/stdmod/NEWS.md | 19 stdmod-0.2.7/stdmod/R/coef_condeff.R | 2 stdmod-0.2.7/stdmod/R/condeff.R | 2 stdmod-0.2.7/stdmod/R/condeff_boot.R | 3 stdmod-0.2.7/stdmod/R/confint_condeff.R | 4 stdmod-0.2.7/stdmod/R/confint_stdmod.R | 24 stdmod-0.2.7/stdmod/R/plotmod.R | 3 stdmod-0.2.7/stdmod/R/print_summary_stdmod.R | 2 stdmod-0.2.7/stdmod/R/std_selected.R | 32 stdmod-0.2.7/stdmod/R/std_selected_boot.R | 26 stdmod-0.2.7/stdmod/README.md | 4 stdmod-0.2.7/stdmod/build/partial.rdb |binary stdmod-0.2.7/stdmod/build/vignette.rds |binary stdmod-0.2.7/stdmod/inst/doc/cond_effect.Rmd | 144 ++- stdmod-0.2.7/stdmod/inst/doc/cond_effect.html | 39 stdmod-0.2.7/stdmod/inst/doc/moderation.R | 21 stdmod-0.2.7/stdmod/inst/doc/moderation.Rmd | 55 - stdmod-0.2.7/stdmod/inst/doc/moderation.html | 318 +++--- stdmod-0.2.7/stdmod/inst/doc/plotmod.R | 37 stdmod-0.2.7/stdmod/inst/doc/plotmod.Rmd | 50 - stdmod-0.2.7/stdmod/inst/doc/plotmod.html | 48 - stdmod-0.2.7/stdmod/inst/doc/std_selected.R | 47 - stdmod-0.2.7/stdmod/inst/doc/std_selected.Rmd | 78 + stdmod-0.2.7/stdmod/inst/doc/std_selected.html | 277 +++--- stdmod-0.2.7/stdmod/inst/doc/stdmod.R | 14 stdmod-0.2.7/stdmod/inst/doc/stdmod.Rmd | 72 + stdmod-0.2.7/stdmod/inst/doc/stdmod.html | 458 +++++----- stdmod-0.2.7/stdmod/inst/doc/stdmod_lavaan.R | 2 stdmod-0.2.7/stdmod/inst/doc/stdmod_lavaan.Rmd | 12 stdmod-0.2.7/stdmod/inst/doc/stdmod_lavaan.html | 19 stdmod-0.2.7/stdmod/man/coef.cond_effect.Rd | 2 stdmod-0.2.7/stdmod/man/cond_effect.Rd | 5 stdmod-0.2.7/stdmod/man/confint.cond_effect.Rd | 4 stdmod-0.2.7/stdmod/man/confint.std_selected.Rd | 23 stdmod-0.2.7/stdmod/man/figures |only stdmod-0.2.7/stdmod/man/plotmod.Rd | 3 stdmod-0.2.7/stdmod/man/std_selected.Rd | 36 stdmod-0.2.7/stdmod/tests/testthat/test_condeff.R | 16 stdmod-0.2.7/stdmod/tests/testthat/test_condeff_boot.R | 8 stdmod-0.2.7/stdmod/tests/testthat/test_stdmod_selected_boot.R | 38 stdmod-0.2.7/stdmod/tests/testthat/test_stdmod_selected_boot_fac.R | 11 stdmod-0.2.7/stdmod/tests/testthat/test_stdmod_selected_confint.R | 5 stdmod-0.2.7/stdmod/tests/testthat/test_stdmod_selectedj_to_std.R |only stdmod-0.2.7/stdmod/vignettes/cond_effect.Rmd | 144 ++- stdmod-0.2.7/stdmod/vignettes/cond_effect.Rmd.original |only stdmod-0.2.7/stdmod/vignettes/eg2_lm_xwy_std_ci.rds |binary stdmod-0.2.7/stdmod/vignettes/eg_lm_xwy_std_ci.rds |binary stdmod-0.2.7/stdmod/vignettes/moderation.Rmd | 55 - stdmod-0.2.7/stdmod/vignettes/plotmod.Rmd | 50 - stdmod-0.2.7/stdmod/vignettes/std_selected.Rmd | 78 + stdmod-0.2.7/stdmod/vignettes/stdmod.Rmd | 72 + stdmod-0.2.7/stdmod/vignettes/stdmod_lavaan.Rmd | 12 stdmod-0.2.7/stdmod/vignettes/stdmod_lm_std1_boot.rds |binary stdmod-0.2.7/stdmod/vignettes/stdmod_lm_stdall_boot.rds |binary 58 files changed, 1583 insertions(+), 906 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>.
The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.2.0 dated 2022-08-06 and 1.3.1 dated 2023-03-26
FastJM-1.2.0/FastJM/R/plot.survfitjmcs.R |only FastJM-1.2.0/FastJM/man/plot.survfitjmcs.Rd |only FastJM-1.2.0/FastJM/src/GetBreslowInit.cpp |only FastJM-1.2.0/FastJM/src/getEWsik.cpp |only FastJM-1.2.0/FastJM/src/updateH0.cpp |only FastJM-1.3.1/FastJM/DESCRIPTION | 23 FastJM-1.3.1/FastJM/MD5 | 52 +- FastJM-1.3.1/FastJM/NAMESPACE | 11 FastJM-1.3.1/FastJM/NEWS.md | 6 FastJM-1.3.1/FastJM/R/FastJM.R | 5 FastJM-1.3.1/FastJM/R/GetEmpiricalCIF.R |only FastJM-1.3.1/FastJM/R/MAEQjmcs.R |only FastJM-1.3.1/FastJM/R/PEjmcs.R |only FastJM-1.3.1/FastJM/R/RcppExports.R | 24 FastJM-1.3.1/FastJM/R/jmcs.R | 27 - FastJM-1.3.1/FastJM/R/print.survfitjmcs.R | 67 +- FastJM-1.3.1/FastJM/R/summary.MAEQjmcs.R |only FastJM-1.3.1/FastJM/R/summary.PEjmcs.R |only FastJM-1.3.1/FastJM/R/summary.jmcs.R | 32 - FastJM-1.3.1/FastJM/R/survfitjmcs.R | 673 +++++++--------------------- FastJM-1.3.1/FastJM/README.md | 119 ++-- FastJM-1.3.1/FastJM/inst/WORDLIST | 4 FastJM-1.3.1/FastJM/man/MAEQjmcs.Rd |only FastJM-1.3.1/FastJM/man/PEjmcs.Rd |only FastJM-1.3.1/FastJM/man/jmcs.Rd | 29 - FastJM-1.3.1/FastJM/man/summary.MAEQjmcs.Rd |only FastJM-1.3.1/FastJM/man/summary.PEjmcs.Rd |only FastJM-1.3.1/FastJM/man/summary.Rd | 2 FastJM-1.3.1/FastJM/man/survfitjmcs.Rd | 27 - FastJM-1.3.1/FastJM/src/Makevars | 2 FastJM-1.3.1/FastJM/src/RcppExports.cpp | 137 +++-- FastJM-1.3.1/FastJM/src/basics.cpp | 110 ++++ FastJM-1.3.1/FastJM/src/basics.h | 16 FastJM-1.3.1/FastJM/src/getECIF.cpp |only FastJM-1.3.1/FastJM/src/getES.cpp |only 35 files changed, 637 insertions(+), 729 deletions(-)
Title: Calculate Phenotype Risk Scores
Description: Use phenotype risk scores based on linked clinical and genetic data
to study Mendelian disease and rare genetic variants. See Bastarache et al.
2018 <doi:10.1126/science.aal4043>.
Author: Jake Hughey [aut, cre],
Layla Aref [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between phers versions 1.0.0 dated 2022-12-14 and 1.0.2 dated 2023-03-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 3 +-- NEWS.md | 6 ++++++ R/utils.R | 3 +-- R/weights.R | 2 +- data/demoSample.rda |binary data/icdSample.rda |binary 8 files changed, 20 insertions(+), 16 deletions(-)
Title: Functions for the Grid Square Codes in Japan
Description: Provides functions for grid square codes in Japan
(<https://www.stat.go.jp/english/data/mesh/index.html>).
Generates the grid square codes from longitude/latitude, geometries, and
the grid square codes of different scales, and vice versa.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between jpgrid versions 0.3.0 dated 2023-02-11 and 0.3.1 dated 2023-03-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/grid.R | 14 +++++++------- R/sf.R | 31 +++++++++++++------------------ 5 files changed, 32 insertions(+), 32 deletions(-)
Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions.
Provides access to 'RStudio' public repositories at
<https://packagemanager.rstudio.com>, and transparent management of
system requirements without administrative privileges. Currently supported
distributions are 'CentOS' / 'RHEL' 7-9, and several 'RHEL' derivatives
('Rocky Linux', 'AlmaLinux', 'Oracle Linux', and 'Amazon Linux' 2),
'openSUSE' / 'SLES' 15.3-4, and 'Ubuntu' 18.04, 20.04 and 22.04.
Author: Inaki Ucar [aut, cph, cre] ,
R Core Team [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between rspm versions 0.3.0 dated 2022-12-22 and 0.3.1 dated 2023-03-26
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 5 +++++ R/integration.R | 2 +- R/utils.R | 1 + R/zzz_centos_base.R | 3 ++- inst/tinytest/test_integration.R | 5 ++++- inst/tinytest/test_integration_ci.R |only inst/tinytest/test_manager_ci.R | 1 - 9 files changed, 24 insertions(+), 14 deletions(-)
Title: Utilities for using the 'COM(P)ADRE' Matrix Model Database
Description: Utility functions for interacting with the 'COMPADRE' and
'COMADRE' databases of matrix population models. Described in Jones et
al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] ,
Danny Buss [aut],
Roberto Salguero-Gomez [aut] ,
Iain Stott [aut] ,
William K. Petry [aut] ,
Tamora James [aut] ,
Owen Jones [aut, cre] ,
Julia Jones [aut] ,
Gesa Roemer [aut] ,
Sam Levin [aut]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rcompadre versions 1.2.0 dated 2023-01-18 and 1.2.1 dated 2023-03-26
DESCRIPTION | 8 +- MD5 | 32 ++++----- NEWS.md | 6 + R/CompadreDB-Methods.R | 17 ++++- R/cdb_build_cdb.R | 14 ++-- README.md | 7 -- build/vignette.rds |binary inst/CITATION | 29 +++++--- inst/doc/a01_GettingStarted.R | 4 - inst/doc/a01_GettingStarted.Rmd | 4 - inst/doc/a01_GettingStarted.html | 111 +++++++++++++++++---------------- inst/doc/a02_RcompadreTidy.html | 19 +++-- inst/doc/a03_VectorisingRcompadre.html | 17 +++-- inst/doc/a04_ObtainingReferences.html | 51 +++++---------- inst/doc/a05_UsingYourOwnData.html | 25 ++++--- man/CompadreDB-Methods.Rd | 14 +++- vignettes/a01_GettingStarted.Rmd | 4 - 17 files changed, 209 insertions(+), 153 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.17 dated 2022-10-29 and 0.3.18 dated 2023-03-26
ChangeLog | 54 ++++++++++++++ DESCRIPTION | 8 +- MD5 | 34 ++++---- build/vignette.rds |binary configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 22 +++++ inst/doc/littler-examples.html | 144 +++++++++++++++++++++++++++----------- inst/doc/littler-faq.html | 65 +++++++++++++---- inst/examples/getRStudioDesktop.r | 26 ------ inst/examples/getRStudioServer.r | 25 ------ inst/examples/install2.r | 26 ++++-- inst/examples/installGithub.r | 7 + inst/examples/installRub.r |only inst/examples/r2u.r | 43 +++++++++-- inst/examples/rcc.r | 4 - inst/examples/roxy.r | 3 inst/examples/tt.r | 6 - inst/examples/tttl.r |only 19 files changed, 333 insertions(+), 154 deletions(-)
Title: Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary
Tables
Description: Quickly and easily perform exploratory data analysis by uploading your
data as a 'csv' file. Start generating insights using 'ggplot2' plots and
'table1' tables with descriptive stats, all using an easy-to-use point and click
'Shiny' interface.
Author: Samer Mouksassi [aut, cre] ,
Dean Attali [aut],
Benjamin Rich [aut] ,
Michael Sachs [aut] ,
James Craig [aut]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between ggquickeda versions 0.2.2 dated 2022-05-16 and 0.3.0 dated 2023-03-26
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Title: Multivariate Conditional Volatility Modelling and Forecasting
Description: Methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndt–Hall–Hall–Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>.
Author: Markus J. Fuelle [aut, cre],
Alexander Lange [aut],
Christian M. Hafner [aut],
Helmut Herwartz [aut]
Maintainer: Markus J. Fuelle <fuelle@uni-goettingen.de>
Diff between BEKKs versions 1.4.2 dated 2023-03-20 and 1.4.3 dated 2023-03-26
DESCRIPTION | 6 +- MD5 | 8 +-- R/bekk_fit_methods.R | 102 ++++++++++++++++++++++++------------------------ build/BEKKs.pdf |binary man/bekk_fit_methods.Rd | 23 +++------- 5 files changed, 67 insertions(+), 72 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
See Nunes and Prangle (2015) <doi:10.32614/RJ-2015-030> and Rodrigues, Prangle and Sisson (2018) <doi:10.1016/j.csda.2018.04.004>.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut],
Guilherme Rodrigues [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between abctools versions 1.1.4 dated 2022-11-02 and 1.1.6 dated 2023-03-26
DESCRIPTION | 21 ++++++++++----------- MD5 | 8 ++++---- R/mincrit.R | 2 +- R/nn.ent.R | 4 ++-- inst/CITATION | 23 +++++++++-------------- 5 files changed, 26 insertions(+), 32 deletions(-)
Title: Combine and Export Data Frames
Description: Functions to combine data.frames in ways that require additional effort in
base R, and to add metadata (id, title, ...) that can be used for printing and
xlsx export. The 'Tatoo_report' class is provided as a
convenient helper to write several such tables to a workbook, one table per
worksheet. Tatoo is built on top of 'openxlsx', but intimate knowledge of
that package is not required to use tatoo.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between tatoo versions 1.1.1 dated 2019-03-29 and 1.1.2 dated 2023-03-26
tatoo-1.1.1/tatoo/vignettes/Thumbs.db |only tatoo-1.1.1/tatoo/vignettes/report_example.xlsx |only tatoo-1.1.2/tatoo/DESCRIPTION | 9 tatoo-1.1.2/tatoo/LICENSE | 4 tatoo-1.1.2/tatoo/MD5 | 139 tatoo-1.1.2/tatoo/NAMESPACE | 200 - tatoo-1.1.2/tatoo/NEWS.md | 137 tatoo-1.1.2/tatoo/R/Composite_table.R | 1263 ++++---- tatoo-1.1.2/tatoo/R/Mashed_table.R | 1528 +++++----- tatoo-1.1.2/tatoo/R/Stacked_table.R | 394 +- tatoo-1.1.2/tatoo/R/Tagged_table.R | 896 ++--- tatoo-1.1.2/tatoo/R/Tatoo_report.R | 192 - tatoo-1.1.2/tatoo/R/Tatoo_table.R | 94 tatoo-1.1.2/tatoo/R/as_latex.R | 802 ++--- tatoo-1.1.2/tatoo/R/as_lines.R | 790 ++--- tatoo-1.1.2/tatoo/R/as_workbook.R | 1312 ++++---- tatoo-1.1.2/tatoo/R/regions.R | 138 tatoo-1.1.2/tatoo/R/styles.R | 12 tatoo-1.1.2/tatoo/R/tatoo-package.R | 76 tatoo-1.1.2/tatoo/R/utils-hammr.R | 806 ++--- tatoo-1.1.2/tatoo/R/utils-sfmisc.R | 1151 +++---- tatoo-1.1.2/tatoo/R/utils.R | 277 - tatoo-1.1.2/tatoo/R/walk_regions.R | 202 - tatoo-1.1.2/tatoo/README.md | 99 tatoo-1.1.2/tatoo/build/vignette.rds |binary tatoo-1.1.2/tatoo/inst/WORDLIST |only tatoo-1.1.2/tatoo/inst/doc/named_regions.R | 122 tatoo-1.1.2/tatoo/inst/doc/named_regions.Rmd | 302 - tatoo-1.1.2/tatoo/inst/doc/named_regions.html | 723 +++- tatoo-1.1.2/tatoo/inst/doc/tatoo.R | 308 +- tatoo-1.1.2/tatoo/inst/doc/tatoo.Rmd | 608 +-- tatoo-1.1.2/tatoo/inst/doc/tatoo.html | 1303 +++++--- tatoo-1.1.2/tatoo/inst/templates/save_tex.Rmd | 26 tatoo-1.1.2/tatoo/man/Composite_table.Rd | 8 tatoo-1.1.2/tatoo/man/Mashed_table.Rd | 34 tatoo-1.1.2/tatoo/man/Stacked_table.Rd | 8 tatoo-1.1.2/tatoo/man/Tagged_table.Rd | 8 tatoo-1.1.2/tatoo/man/Tatoo_report.Rd | 2 tatoo-1.1.2/tatoo/man/as.data.table.Composite_table.Rd | 23 tatoo-1.1.2/tatoo/man/as.data.table.Mashed_table.Rd | 41 tatoo-1.1.2/tatoo/man/as_Composite_table.Rd | 11 tatoo-1.1.2/tatoo/man/as_latex.Composite_table.Rd | 17 tatoo-1.1.2/tatoo/man/as_latex.Mashed_table.Rd | 27 tatoo-1.1.2/tatoo/man/as_latex.Rd | 40 tatoo-1.1.2/tatoo/man/as_latex.Tagged_table.Rd | 13 tatoo-1.1.2/tatoo/man/as_latex.Tatoo_report.Rd | 13 tatoo-1.1.2/tatoo/man/as_latex.data.frame.Rd | 14 tatoo-1.1.2/tatoo/man/as_lines.Rd | 11 tatoo-1.1.2/tatoo/man/as_workbook.Rd | 5 tatoo-1.1.2/tatoo/man/cmash.Rd | 9 tatoo-1.1.2/tatoo/man/multinames.Rd | 2 tatoo-1.1.2/tatoo/man/print.Mashed_table.Rd | 10 tatoo-1.1.2/tatoo/man/sanitize_excel_sheet_names.Rd | 4 tatoo-1.1.2/tatoo/man/tatoo.Rd | 7 tatoo-1.1.2/tatoo/man/tatoo_table.Rd | 10 tatoo-1.1.2/tatoo/man/tt_meta.Rd | 10 tatoo-1.1.2/tatoo/man/write_worksheet.Rd | 83 tatoo-1.1.2/tatoo/tests/testthat.R | 8 tatoo-1.1.2/tatoo/tests/testthat/manual_tests/test_named_region_names.R | 32 tatoo-1.1.2/tatoo/tests/testthat/manual_tests/test_output_formats.R | 260 - tatoo-1.1.2/tatoo/tests/testthat/manual_tests/test_print_methods.R | 64 tatoo-1.1.2/tatoo/tests/testthat/test_Composite_table.R | 380 +- tatoo-1.1.2/tatoo/tests/testthat/test_Mashed_table.R | 572 +-- tatoo-1.1.2/tatoo/tests/testthat/test_Stacked_table.R | 46 tatoo-1.1.2/tatoo/tests/testthat/test_Tagged_table.R | 304 - tatoo-1.1.2/tatoo/tests/testthat/test_as_workbook.R | 218 - tatoo-1.1.2/tatoo/tests/testthat/test_save_xlsx.R | 64 tatoo-1.1.2/tatoo/tests/testthat/test_utils-regions.R | 36 tatoo-1.1.2/tatoo/tests/testthat/test_utils.R | 74 tatoo-1.1.2/tatoo/tests/testthat/testdata/testdata.R | 318 +- tatoo-1.1.2/tatoo/vignettes/named_regions.Rmd | 302 - tatoo-1.1.2/tatoo/vignettes/tatoo.Rmd | 608 +-- 72 files changed, 9160 insertions(+), 8449 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.7.1 dated 2022-11-29 and 0.7.2 dated 2023-03-26
wnl-0.7.1/wnl/inst/doc/NCA.pdf |only wnl-0.7.2/wnl/DESCRIPTION | 8 - wnl-0.7.2/wnl/MD5 | 25 ++-- wnl-0.7.2/wnl/NAMESPACE | 2 wnl-0.7.2/wnl/R/BasicUtil.R | 112 ++++++---------------- wnl-0.7.2/wnl/R/EnvObj.R |only wnl-0.7.2/wnl/R/nlr.R | 172 ++++++++++++++++++---------------- wnl-0.7.2/wnl/R/pProf.R |only wnl-0.7.2/wnl/R/sysdata.rda |binary wnl-0.7.2/wnl/R/wnl5.R | 2 wnl-0.7.2/wnl/inst/NEWS.Rd | 10 + wnl-0.7.2/wnl/inst/doc/wnl-manual.pdf |binary wnl-0.7.2/wnl/man/BasicUtil.Rd | 3 wnl-0.7.2/wnl/man/EnvObj.Rd |only wnl-0.7.2/wnl/man/nlr.Rd | 7 - wnl-0.7.2/wnl/man/pProf.Rd |only 16 files changed, 160 insertions(+), 181 deletions(-)
Title: An Interface to the 'DescribeDisplay' 'GGobi' Plugin
Description: Produce publication quality graphics from output of 'GGobi'
describe display plugin.
Author: Di Cook [aut, cre],
Hadley Wickham [aut],
Andreas Buja [aut],
Barret Schloerke [aut]
Maintainer: Di Cook <dicook@monash.edu>
Diff between DescribeDisplay versions 0.2.7 dated 2018-09-23 and 0.2.9 dated 2023-03-26
DescribeDisplay-0.2.7/DescribeDisplay/README.md |only DescribeDisplay-0.2.9/DescribeDisplay/DESCRIPTION | 16 +-- DescribeDisplay-0.2.9/DescribeDisplay/MD5 | 41 ++++------ DescribeDisplay-0.2.9/DescribeDisplay/NEWS | 5 + DescribeDisplay-0.2.9/DescribeDisplay/R/DescribeDisplay-package.R | 6 - DescribeDisplay-0.2.9/DescribeDisplay/R/axis-geom.R | 2 DescribeDisplay-0.2.9/DescribeDisplay/R/ggplot-barchart.R | 8 - DescribeDisplay-0.2.9/DescribeDisplay/R/ggplot-parcoords.R | 6 - DescribeDisplay-0.2.9/DescribeDisplay/R/ggplot-timeseries.R | 4 DescribeDisplay-0.2.9/DescribeDisplay/R/ggplot.R | 4 DescribeDisplay-0.2.9/DescribeDisplay/R/plots.R | 6 - DescribeDisplay-0.2.9/DescribeDisplay/man/addbrush.Rd | 12 ++ DescribeDisplay-0.2.9/DescribeDisplay/man/ddpanelGrob.Rd | 8 + DescribeDisplay-0.2.9/DescribeDisplay/man/describedisplayreshape.Rd | 6 - DescribeDisplay-0.2.9/DescribeDisplay/man/geom_axis.Rd | 2 DescribeDisplay-0.2.9/DescribeDisplay/man/ggplot.barplot.Rd | 6 - DescribeDisplay-0.2.9/DescribeDisplay/man/ggplot.ddplot.Rd | 8 - DescribeDisplay-0.2.9/DescribeDisplay/man/ggplot.histogram.Rd | 6 - DescribeDisplay-0.2.9/DescribeDisplay/man/ggplot.parcoords.Rd | 7 - DescribeDisplay-0.2.9/DescribeDisplay/man/ggplot.timeseries.Rd | 6 - DescribeDisplay-0.2.9/DescribeDisplay/man/plot.dd.Rd | 14 ++- DescribeDisplay-0.2.9/DescribeDisplay/man/plot.ddplot.Rd | 12 ++ 22 files changed, 109 insertions(+), 76 deletions(-)
More information about DescribeDisplay at CRAN
Permanent link
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
three public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>) and
the 'ISRCTN' (<http://www.isrctn.com/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Functions are included to identify deduplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries.
The package can be used for meta-analysis and trend-analysis of
the design and conduct as well as for results of clinical trials.
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.11.1 dated 2022-11-20 and 1.12.0 dated 2023-03-26
DESCRIPTION | 12 MD5 | 33 - NAMESPACE | 5 NEWS.md | 6 R/ctrdata-registers.R | 26 R/main.R | 466 ++++++++++------- R/utils.R | 46 + README.md | 149 +++-- build/vignette.rds |binary exec/euctr2ndjson_results.php | 2 inst/tinytest/ctrdata_ctgov.R | 49 + inst/tinytest/ctrdata_ctis.R |only inst/tinytest/ctrdata_isrctn.R | 5 inst/tinytest/more_test_ctrdata_duckdb_ctis.R |only inst/tinytest/more_test_ctrdata_mongo_remote_rw_ctis.R |only inst/tinytest/more_test_ctrdata_postgres_ctis.R |only inst/tinytest/test_ctrdata_mongo_local_ctis.R |only man/ctrGetQueryUrl.Rd | 4 man/ctrLoadQueryIntoDb.Rd | 29 - man/ctrdata-registers.Rd | 26 20 files changed, 530 insertions(+), 328 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for: 1. single response multiple regression, see Papageorgiou, G. (2018) <doi: 10.32614/RJ-2018-069>, 2. multivariate response multiple regression, with nonparametric models for the means, the variances and the correlation matrix, with variable selection, see Papageorgiou, G. and Marshall, B. C. (2020) <doi: 10.1080/10618600.2020.1739534>, 3. joint mean-covariance models for multivariate responses, see Papageorgiou, G. (2022) <doi: 10.1002/sim.9376>, and 4.Dirichlet process mixtures, see Papageorgiou, G. (2019) <doi: 10.1111/anzs.12273>.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.2.1 dated 2023-02-28 and 2.2.2 dated 2023-03-26
DESCRIPTION | 8 +++---- MD5 | 8 +++---- R/bnpMulti.R | 13 ++++++------ man/BNSP-package.Rd | 4 +-- src/Univariate.c | 53 +++++++++++++++++++++++++++------------------------- 5 files changed, 45 insertions(+), 41 deletions(-)
Title: Effect Estimates from All Models
Description: Estimates and plots effect estimates from models with all possible
combinations of a list of variables. It can be used for assessing treatment
effects in clinical trials or risk factors in bio-medical and epidemiological
research. Like Stata command 'confall' (Wang Z (2007) <doi:10.1177/1536867X0700700203> ),
'allestimates' calculates and stores all effect estimates, and plots them against p values or
Akaike information criterion (AIC) values. It currently has functions for linear
regression: all_lm(), logistic and Poisson regression: all_glm(),
and Cox proportional hazards regression: all_cox().
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <menzies.uq@gmail.com>
Diff between allestimates versions 0.2.2 dated 2022-03-04 and 0.2.3 dated 2023-03-26
allestimates-0.2.2/allestimates/R/all_speedglm.R |only allestimates-0.2.2/allestimates/man/all_speedglm.Rd |only allestimates-0.2.3/allestimates/DESCRIPTION | 15 allestimates-0.2.3/allestimates/MD5 | 46 - allestimates-0.2.3/allestimates/NAMESPACE | 2 allestimates-0.2.3/allestimates/NEWS.md | 4 allestimates-0.2.3/allestimates/R/all_cox.R | 140 +-- allestimates-0.2.3/allestimates/R/all_glm.R | 2 allestimates-0.2.3/allestimates/R/all_lm.R | 170 ++-- allestimates-0.2.3/allestimates/R/all_plot.R | 132 +-- allestimates-0.2.3/allestimates/R/all_plot2.R | 4 allestimates-0.2.3/allestimates/R/all_plot_aic.R | 86 +- allestimates-0.2.3/allestimates/R/all_plot_aic2.R | 126 +-- allestimates-0.2.3/allestimates/build/vignette.rds |binary allestimates-0.2.3/allestimates/inst/doc/allestimates-vignette.R | 10 allestimates-0.2.3/allestimates/inst/doc/allestimates-vignette.Rmd | 199 ++-- allestimates-0.2.3/allestimates/inst/doc/allestimates-vignette.html | 402 +++++++--- allestimates-0.2.3/allestimates/man/all_cox.Rd | 4 allestimates-0.2.3/allestimates/man/all_glm.Rd | 2 allestimates-0.2.3/allestimates/man/all_lm.Rd | 2 allestimates-0.2.3/allestimates/man/all_plot.Rd | 2 allestimates-0.2.3/allestimates/man/all_plot2.Rd | 4 allestimates-0.2.3/allestimates/man/all_plot_aic.Rd | 2 allestimates-0.2.3/allestimates/man/all_plot_aic2.Rd | 4 allestimates-0.2.3/allestimates/vignettes/allestimates-vignette.Rmd | 199 ++-- 25 files changed, 884 insertions(+), 673 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-22 1.0.1
Title: Longitudinal Drift-Diffusion Mixed Models (LDDMM)
Description: Implementation of the drift-diffusion mixed model for category learning as described in Paulon et al. (2021) <doi:10.1080/01621459.2020.1801448>.
Author: Giorgio Paulon [aut, cre],
Abhra Sarkar [aut, ctb]
Maintainer: Giorgio Paulon <giorgio.paulon@utexas.edu>
Diff between lddmm versions 0.2.1 dated 2023-01-31 and 0.3.0 dated 2023-03-26
DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 6 - R/RcppExports.R | 19 +++ R/fcts.R | 236 +++++++++++++++++++++++++++------------------- README.md | 14 +- man/compute_WAIC.Rd |only man/log_likelihood_ind.Rd |only src/RcppExports.cpp | 17 +++ src/drift_diff_fcts.cpp | 110 +++++++++++++++++++++ 10 files changed, 307 insertions(+), 119 deletions(-)