Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Wesley Gardiner [ctb] (Unit tests),
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <jdahlke@humrro.org>
Diff between psychmeta versions 2.5.0 dated 2021-05-02 and 2.5.1 dated 2021-05-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 21 +++++++++++++-------- R/ma_d_bb.R | 8 ++++---- R/ma_generic.R | 8 ++++---- R/ma_r.R | 8 ++++---- R/ma_r_bb.R | 8 ++++---- R/ma_r_ic.R | 20 ++++++++++---------- R/remove_dependency.R | 9 +++++---- R/wrangle_data.R | 4 ++-- build/partial.rdb |binary inst/doc/ma_r.html | 4 ++-- tests/testthat/test-ma_r.R | 32 ++++++++++++++++++++++++++++++-- 13 files changed, 94 insertions(+), 60 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.16.0 dated 2021-04-27 and 1.17.0 dated 2021-05-08
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Shadow-Test Approach to Computerized Adaptive Testing
Description: As an advanced approach to computerized adaptive testing (CAT),
shadow testing (van der Linden(2005) <doi:10.1007/0-387-29054-0>) dynamically
assembles entire shadow tests as a part of
selecting items throughout the testing process.
Selecting items from shadow tests guarantees the compliance of all content
constraints defined by the blueprint. 'RSCAT' is an R package for the
shadow-test approach to CAT. The objective of
'RSCAT' is twofold: 1) Enhancing the effectiveness of shadow-test CAT simulation;
2) Contributing to the academic and scientific community for CAT research.
Author: Bingnan Jiang [aut, cre],
ACT, Inc. [cph]
Maintainer: Bingnan Jiang <bnjiangece@gmail.com>
Diff between RSCAT versions 1.1.0 dated 2020-01-17 and 1.1.1 dated 2021-05-08
RSCAT-1.1.0/RSCAT/inst/java/RSCAT-1.1.0.jar |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/cat |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/mip |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/sim |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/sol |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/testdef |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/util |only RSCAT-1.1.0/RSCAT/java/src/test/java/org/act/sim |only RSCAT-1.1.1/RSCAT/DESCRIPTION | 8 RSCAT-1.1.1/RSCAT/MD5 | 171 +++++++++---------- RSCAT-1.1.1/RSCAT/R/runSim.R | 4 RSCAT-1.1.1/RSCAT/R/scoreMethodConfig.R | 10 - RSCAT-1.1.1/RSCAT/README.md | 16 - RSCAT-1.1.1/RSCAT/inst/java/RSCAT-1.1.1.jar |only RSCAT-1.1.1/RSCAT/java/pom.xml | 16 - RSCAT-1.1.1/RSCAT/java/src/main/java/org/act/rscat |only RSCAT-1.1.1/RSCAT/java/src/test/java/org/act/rscat |only RSCAT-1.1.1/RSCAT/man/launchApp.Rd | 30 +-- RSCAT-1.1.1/RSCAT/man/result2CSV.Rd | 32 +-- RSCAT-1.1.1/RSCAT/man/runSim.Rd | 2 RSCAT-1.1.1/RSCAT/man/scoreMethodConfig.Rd | 4 RSCAT-1.1.1/RSCAT/man/shinyAppUI.Rd | 28 +-- RSCAT-1.1.1/RSCAT/man/summary-SimResult-method.Rd | 28 +-- 23 files changed, 176 insertions(+), 173 deletions(-)
Title: Czech Interest Rates
Description: Interface to interest and foreign exchange rates published by the Czech National Bank.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between czechrates versions 0.1.10 dated 2020-08-26 and 0.2.0 dated 2021-05-08
DESCRIPTION | 13 - MD5 | 35 +-- NAMESPACE | 1 NEWS.md | 6 R/cnbfxrate.R |only R/czechrates.R | 7 R/ok_to_proceed.R |only R/pribor.R | 26 +- R/repo2w.R | 14 - README.md | 92 ++++++-- build/vignette.rds |binary inst/doc/vignette.R | 32 ++ inst/doc/vignette.Rmd | 60 ++++- inst/doc/vignette.html | 460 ++++++++++++++-------------------------- man/cnbfxrate.Rd |only man/czechrates-package.Rd | 2 man/ok_to_proceed.Rd |only tests/testthat/test-cnbfxrate.R |only tests/testthat/test-pribor.R | 5 tests/testthat/test-repo2w.R | 4 vignettes/vignette.Rmd | 60 ++++- 21 files changed, 435 insertions(+), 382 deletions(-)
Title: Analysis of Tidal Datasets
Description: Contains functions for analysis and summary of tidal datasets. Also provides access to tidal data collected by the National Oceanic and Atmospheric Administration's Center for Operational Oceanographic Products and Services and the Permanent Service for Mean Sea Level. For detailed description and application examples, see Hill, T.D. and S.C. Anisfeld (2021) <doi:10.6084/m9.figshare.14161202.v1> and Hill, T.D. and S.C. Anisfeld (2015) <doi:10.1016/j.ecss.2015.06.004>.
Author: Troy Hill [aut, cre] (<https://orcid.org/0000-0003-2980-4099>),
Shimon Anisfeld [ctb]
Maintainer: Troy Hill <Hill.Troy@gmail.com>
Diff between VulnToolkit versions 1.1.2 dated 2021-04-16 and 1.1.3 dated 2021-05-08
VulnToolkit-1.1.2/VulnToolkit/R/noaa_stations.R |only VulnToolkit-1.1.2/VulnToolkit/man/noaa.stations.Rd |only VulnToolkit-1.1.3/VulnToolkit/DESCRIPTION | 8 - VulnToolkit-1.1.3/VulnToolkit/MD5 | 70 +++++++----- VulnToolkit-1.1.3/VulnToolkit/NAMESPACE | 13 ++ VulnToolkit-1.1.3/VulnToolkit/NEWS | 9 + VulnToolkit-1.1.3/VulnToolkit/R/HL.r | 93 ++++++++++++++--- VulnToolkit-1.1.3/VulnToolkit/R/HL_plot.R | 38 +++++- VulnToolkit-1.1.3/VulnToolkit/R/dur_bias.R |only VulnToolkit-1.1.3/VulnToolkit/R/fldDurEvents.R | 3 VulnToolkit-1.1.3/VulnToolkit/R/fld_frq.R | 3 VulnToolkit-1.1.3/VulnToolkit/R/floodDepth.R | 2 VulnToolkit-1.1.3/VulnToolkit/R/form_no.R | 6 - VulnToolkit-1.1.3/VulnToolkit/R/harcon.R | 4 VulnToolkit-1.1.3/VulnToolkit/R/noaa.r | 5 VulnToolkit-1.1.3/VulnToolkit/R/noaaParameters.R | 2 VulnToolkit-1.1.3/VulnToolkit/R/noaa_datums.R | 6 - VulnToolkit-1.1.3/VulnToolkit/R/number_tides.R | 1 VulnToolkit-1.1.3/VulnToolkit/R/psmsl.R |only VulnToolkit-1.1.3/VulnToolkit/R/psmsl_stations.R |only VulnToolkit-1.1.3/VulnToolkit/build/vignette.rds |binary VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.R |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.Rmd |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.html |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/Tidal_data.Rmd | 2 VulnToolkit-1.1.3/VulnToolkit/inst/doc/Tidal_data.html | 6 - VulnToolkit-1.1.3/VulnToolkit/man/HL.Rd | 49 +++++++- VulnToolkit-1.1.3/VulnToolkit/man/HL.plot.Rd | 39 ++++++- VulnToolkit-1.1.3/VulnToolkit/man/dur.bias.Rd |only VulnToolkit-1.1.3/VulnToolkit/man/dur.events.Rd | 3 VulnToolkit-1.1.3/VulnToolkit/man/fld.depth.Rd | 2 VulnToolkit-1.1.3/VulnToolkit/man/fld.frq.Rd | 3 VulnToolkit-1.1.3/VulnToolkit/man/form.no.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/harcon.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/noaa.Rd | 5 VulnToolkit-1.1.3/VulnToolkit/man/noaa.datums.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/noaa.parameters.Rd | 2 VulnToolkit-1.1.3/VulnToolkit/man/number.tides.Rd | 1 VulnToolkit-1.1.3/VulnToolkit/man/psmsl.Rd |only VulnToolkit-1.1.3/VulnToolkit/man/psmsl.stations.Rd |only VulnToolkit-1.1.3/VulnToolkit/vignettes/NOAA_PSMSL.Rmd |only VulnToolkit-1.1.3/VulnToolkit/vignettes/Tidal_data.Rmd | 2 42 files changed, 275 insertions(+), 120 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Krzysiek G [ctb] (https://github.com/storaged),
Manuela Hummel [ctb] (https://github.com/hummelma),
Chase Clark [ctb] (https://github.com/chasemc),
Lucas Graybuck [ctb] (https://github.com/hypercompetent),
jdetribol [ctb] (https://github.com/jdetribol),
Ben Ho [ctb] (https://github.com/SplitInf),
Samuel Perreault [ctb] (https://github.com/samperochkin),
Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/),
David Bradley [ctb] (https://github.com/DBradley27),
Houyun Huang [ctb] (https://github.com/houyunhuang)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.14.0 dated 2020-08-26 and 1.15.1 dated 2021-05-08
ChangeLog | 1545 +++++++++++++++++++------------ DESCRIPTION | 8 MD5 | 35 NEWS | 15 NEWS.md | 10 R/colored_dots.R | 6 R/data.R | 6 R/get_subdendrograms.R | 44 README.md | 16 inst/doc/Cluster_Analysis.html | 663 ++++++------- inst/doc/FAQ.html | 593 ++++++----- inst/doc/Quick_Introduction.html | 123 +- inst/doc/dendextend.Rmd | 2 inst/doc/dendextend.html | 1335 +++++++++++++------------- man/colored_dots.Rd | 3 man/get_subdendrograms.Rd | 39 man/khan.Rd | 4 tests/testthat/test-get_subdendrograms.R |only vignettes/dendextend.Rmd | 2 19 files changed, 2550 insertions(+), 1899 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.3.5 dated 2020-03-13 and 0.3.6 dated 2021-05-08
DESCRIPTION | 19 - LICENSE | 2 MD5 | 63 ++- NAMESPACE | 7 NEWS.md | 71 +--- R/cansim.R | 405 ++++++++++++++++++++--- R/cansim_helpers.R | 51 ++ R/cansim_sql.R |only R/cansim_tables_list.R | 98 +++-- R/cansim_vectors.R | 171 ++++++---- R/sysdata.rda |binary README.md | 21 - build/vignette.rds |binary inst/doc/cansim.R | 9 inst/doc/cansim.Rmd | 30 - inst/doc/cansim.html | 426 +++++++------------------ inst/doc/working_with_large_tables.R |only inst/doc/working_with_large_tables.Rmd |only inst/doc/working_with_large_tables.html |only man/collect_and_normalize.Rd |only man/create_index.Rd |only man/csv2sqlite.Rd |only man/disconnect_cansim_sqlite.Rd |only man/fold_in_metadata_for_columns.Rd |only man/get_cansim.Rd | 25 - man/get_cansim_changed_tables.Rd | 5 man/get_cansim_data_for_table_coord_periods.Rd | 17 man/get_cansim_ndm.Rd | 14 man/get_cansim_sqlite.Rd |only man/get_cansim_vector.Rd | 19 - man/get_cansim_vector_for_latest_periods.Rd | 20 + man/list_cansim_sqlite_cached_tables.Rd |only man/normalize_cansim_values.Rd | 5 man/parse_and_fold_in_metadata.Rd | 4 man/parse_metadata.Rd |only man/remove_cansim_sqlite_cached_table.Rd |only man/view_cansim_webpage.Rd | 5 vignettes/cansim.Rmd | 30 - vignettes/precompile.R |only vignettes/working_with_large_tables.Rmd |only 40 files changed, 919 insertions(+), 598 deletions(-)
Title: Using R to Install Stuff on Windows OS (Such As: R, 'Rtools',
'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool),
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Tom Allard [ctb],
ChingChuan Chen [ctb],
Jonathan Hill [ctb],
Chan-Yub Park [ctb] (https://github.com/mrchypark),
Gerhard Nachtmann [ctb],
Russ Hyde [ctb],
Lyndon D'Arcy [ctb] (https://github.com/logworthy),
Gerhard Burger [ctb] (https://github.com/burgerga),
Adrian Hordyk [ctb] (https://github.com/AdrianHordyk)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.22.0 dated 2019-08-02 and 0.23.2 dated 2021-05-08
ChangeLog | 305 ++ DESCRIPTION | 36 MD5 | 239 +- NAMESPACE | 215 - NEWS | 1739 +++++++------- NEWS.md | 1727 +++++++------- R/RStudio_CRAN_data.R | 1052 ++++---- R/create.global.library.R | 1109 ++++----- R/geo_functions.R | 474 +-- R/install.R | 3223 +++++++++++++-------------- R/install.inno.R | 110 R/installNodejs.R | 120 - R/installOpenJdk.R | 204 - R/installPython.R | 132 - R/installRtools.R |only R/installr-package.R | 71 R/is.x.R | 319 +- R/kill_pid.R | 566 ++-- R/os.manage.R | 526 ++-- R/rename_r_to_R.R | 222 - R/startup.R | 624 ++--- R/updateR.R | 1864 +++++++-------- R/xlsx2csv.R | 216 - R/zzz.R | 444 +-- README.md | 220 - TODO | 24 man/R_version_in_a_folder.Rd | 56 man/add.installr.GUI.Rd | 58 man/add_load_installr_on_startup_menu.Rd | 28 man/add_remove_installr_from_startup_menu.Rd | 28 man/add_to_.First_in_Rprofile.site.Rd | 74 man/ask.user.for.a.row.Rd | 84 man/ask.user.yn.question.Rd | 90 man/barplot_package_users_per_day.Rd | 98 man/browse.latest.R.NEWS.Rd | 49 man/check.for.updates.R.Rd | 73 man/check.integer.Rd | 76 man/checkMD5sums2.Rd | 72 man/copy.packages.between.libraries.Rd | 101 man/cranometer.Rd | 174 - man/create.global.library.Rd | 44 man/download_RStudio_CRAN_data.Rd | 119 man/fetch_tag_from_Rd.Rd | 102 man/file.name.from.url.Rd | 65 man/format_RStudio_CRAN_data.Rd | 102 man/freegeoip.Rd | 105 man/get.installed.R.folders.Rd | 77 man/get_Rscript_PID.Rd | 76 man/get_latest_r_version.Rd |only man/get_pid.Rd | 78 man/get_tasklist.Rd | 76 man/install.7zip.Rd | 97 man/install.CMake.Rd | 84 man/install.Cygwin.Rd | 66 man/install.FFmpeg.Rd | 71 man/install.GitHub.Rd | 73 man/install.GraphicsMagick.Rd | 74 man/install.ImageMagick.Rd | 73 man/install.LaTeX2RTF.Rd | 71 man/install.LyX.Rd | 83 man/install.MikTeX.Rd | 69 man/install.R.Rd | 106 man/install.RStudio.Rd | 68 man/install.Rdevel.Rd | 77 man/install.Rtools.Rd | 98 man/install.SWFTools.Rd | 75 man/install.Texmaker.Rd | 75 man/install.URL.Rd | 105 man/install.conda.Rd | 68 man/install.git.Rd | 66 man/install.inno.Rd | 74 man/install.java.Rd | 134 - man/install.nodejs.Rd | 76 man/install.notepadpp.Rd | 69 man/install.npptor.Rd | 70 man/install.packages.zip.Rd | 64 man/install.pandoc.Rd | 90 man/install.python.Rd | 81 man/installr-package.Rd | 27 man/installr.Rd | 62 man/is.RStudio.Rd | 50 man/is.Rgui.Rd | 56 man/is.empty.Rd | 106 man/is.exe.installed.Rd | 46 man/is.windows.Rd | 52 man/is.x64.Rd | 50 man/is_in_.First_in_Rprofile.site.Rd | 76 man/kill_all_Rscript_s.Rd | 90 man/kill_pid.Rd | 94 man/kill_process.Rd | 102 man/lineplot_package_downloads.Rd | 116 man/load_installr_on_startup.Rd | 56 man/most_downloaded_packages.Rd | 94 man/myip.Rd | 60 man/os.hibernate.Rd | 82 man/os.lock.Rd | 78 man/os.manage.Rd | 82 man/os.restart.Rd | 72 man/os.shutdown.Rd | 92 man/os.sleep.Rd | 82 man/package_authors.Rd | 145 - man/pkgDNLs_worldmapcolor.Rd | 100 man/read_RStudio_CRAN_data.Rd | 116 man/remove.installr.GUI.Rd | 46 man/remove_from_.First_in_Rprofile.site.Rd | 76 man/rename_r_to_R.Rd | 132 - man/require2.Rd | 66 man/restart_RGui.Rd | 48 man/rm_installr_from_startup.Rd | 58 man/source.https.Rd | 82 man/system.PATH.Rd | 44 man/turn.number.version.Rd | 46 man/turn.version.to.number.Rd | 44 man/turn.version.to.number1.Rd | 52 man/uninstall.R.Rd | 70 man/uninstall.packages.Rd | 74 man/up_folder.Rd | 50 man/updateR.Rd | 192 - man/xlsx2csv.Rd | 64 tests |only 120 files changed, 11727 insertions(+), 11246 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar
constructs are implemented. Block-diagonal matrices can be extracted or removed
using two small functions implemented here. In addition, non-square matrices
are supported. Block diagonal matrices occur when two dimensions of a data set
are combined along one edge of a matrix. For example, trade-flow data in the
'decompr' and 'gvc' packages have each country-industry combination occur along
both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 5.2.0 dated 2020-04-28 and 6.0.0 dated 2021-05-08
DESCRIPTION | 11 +- MD5 | 12 +- NEWS.md | 6 + README.md | 3 build/vignette.rds |binary inst/CITATION | 2 inst/doc/fatdiag.html | 236 ++++++-------------------------------------------- 7 files changed, 50 insertions(+), 220 deletions(-)
Title: Markov Chain-Based Cost-Optimal Control Charts
Description: Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.
Author: Balazs Dobi & Andras Zempleni
Maintainer: Balazs Dobi <dobibalazs@inf.elte.hu>
Diff between Markovchart versions 2.0.0 dated 2021-04-23 and 2.0.1 dated 2021-05-08
Markovchart-2.0.0/Markovchart/R/Markovchart_functions_20210310.r |only Markovchart-2.0.1/Markovchart/DESCRIPTION | 6 +++--- Markovchart-2.0.1/Markovchart/MD5 | 8 ++++---- Markovchart-2.0.1/Markovchart/R/Markovchart_functions_20210502.r |only Markovchart-2.0.1/Markovchart/man/Markovstat.Rd | 2 +- Markovchart-2.0.1/Markovchart/man/plot.Markov_grid.Rd | 7 +++++-- 6 files changed, 13 insertions(+), 10 deletions(-)
Title: Desirable Dietary Pattern
Description: The desirable Dietary Pattern (DDP)/ PPH score
measures the variety of food consumption. The (weighted) score is calculated
based on the type of food. This package is intended to calculate
the DDP/ PPH score that is faster than traditional method via
a manual calculation by BKP (2017) <http://bkp.pertanian.go.id/storage/app/uploads/public/5bf/ca9/06b/5bfca906bc654274163456.pdf> and is simpler than the nutrition survey
<http://www.nutrisurvey.de>. The database to create weights and baseline values
is the Indonesia national survey in 2017.
Author: Weksi Budiaji [aut, cre]
Maintainer: Weksi Budiaji <budiaji@untirta.ac.id>
Diff between ddp versions 0.0.2 dated 2020-08-03 and 0.0.3 dated 2021-05-08
DESCRIPTION | 9 - MD5 | 17 +-- NAMESPACE | 3 NEWS.md |only R/valid.R |only build/vignette.rds |binary inst/doc/ddp.R | 5 inst/doc/ddp.Rmd | 12 ++ inst/doc/ddp.html | 278 +++++++++++++---------------------------------------- man/valid.Rd |only vignettes/ddp.Rmd | 12 ++ 11 files changed, 120 insertions(+), 216 deletions(-)
Title: Composite Grid Gaussian Processes
Description: Run computer experiments using the adaptive composite grid
algorithm with a Gaussian process model.
The algorithm works best when running an experiment that can evaluate thousands
of points from a deterministic computer simulation.
This package is an implementation of a forthcoming paper by Plumlee,
Erickson, Ankenman, et al. For a preprint of the paper,
contact the maintainer of this package.
Author: Collin Erickson [aut, cre],
Matthew Plumlee [aut]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between CGGP versions 1.0.2 dated 2020-03-29 and 1.0.3 dated 2021-05-08
DESCRIPTION | 11 - MD5 | 16 - NEWS.md | 8 R/CGGP_calc_lS_cholS_valo_etc.R | 6 R/CGGP_corr_fs.R | 72 ++++--- R/CGGP_fastcalcassist_fs.R | 12 + build/vignette.rds |binary inst/doc/CGGP.html | 387 +++++++++++----------------------------- tests/testthat/testcorr.R | 139 ++++++++------ 9 files changed, 274 insertions(+), 377 deletions(-)
Title: Variable-Lag Time Series Causality Inference Framework
Description: A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2021) <doi:10.1145/3441452> when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between VLTimeCausality versions 0.1.2 dated 2021-03-29 and 0.1.3 dated 2021-05-08
VLTimeCausality-0.1.2/VLTimeCausality/vignettes/VLTimeCausality_demo.nb.html |only VLTimeCausality-0.1.3/VLTimeCausality/DESCRIPTION | 8 VLTimeCausality-0.1.3/VLTimeCausality/MD5 | 39 +-- VLTimeCausality-0.1.3/VLTimeCausality/NEWS.md | 3 VLTimeCausality-0.1.3/VLTimeCausality/R/MultipleTSsimulation.R | 16 - VLTimeCausality-0.1.3/VLTimeCausality/R/multipleVLGranger.R | 8 VLTimeCausality-0.1.3/VLTimeCausality/R/multipleVLTransferEntropy.R | 10 VLTimeCausality-0.1.3/VLTimeCausality/README.md | 29 ++ VLTimeCausality-0.1.3/VLTimeCausality/build/vignette.rds |binary VLTimeCausality-0.1.3/VLTimeCausality/inst/CITATION | 17 - VLTimeCausality-0.1.3/VLTimeCausality/inst/doc/VLTimeCausality_demo.html | 6 VLTimeCausality-0.1.3/VLTimeCausality/man/GrangerFunc.Rd | 118 ++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/MultipleSimulationVLtimeseries.Rd | 96 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/SimpleSimulationVLtimeseries.Rd | 102 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/VLGrangerFunc.Rd | 120 +++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/VLTransferEntropy.Rd | 118 ++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/checkMultipleSimulationVLtimeseries.Rd | 62 ++--- VLTimeCausality-0.1.3/VLTimeCausality/man/followingRelation.Rd | 84 +++---- VLTimeCausality-0.1.3/VLTimeCausality/man/multipleVLGrangerFunc.Rd | 102 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/multipleVLTransferEntropy.Rd | 98 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/plotTimeSeries.Rd | 60 ++--- 21 files changed, 562 insertions(+), 534 deletions(-)
More information about VLTimeCausality at CRAN
Permanent link
Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>); and genetic simulations.
Author: Ozvan Bocher and Hervé Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>
Diff between Ravages versions 0.1.3 dated 2021-04-08 and 0.1.4 dated 2021-05-08
DESCRIPTION | 8 ++--- MD5 | 40 ++++++++++++++--------------- NEWS | 3 ++ R/zzz.r | 4 +- inst/doc/Ravages_Simulations_vignette.html | 2 - inst/doc/Ravages_vignette.html | 10 +++---- man/SKAT.Rd | 4 +- man/burden.mlogit.Rd | 4 +- src/allelecounter.cpp | 1 src/allelecounter.h | 1 src/allelecounter2.cpp | 1 src/allelecounter2.h | 1 src/alleles_by_group.cpp | 1 src/count_alternative_alleles.cpp | 1 src/jaccard.cpp | 1 src/skat.cpp | 1 src/skatBootstrap.cpp | 1 src/sum_fst.cpp | 1 src/sum_fst1.cpp | 1 src/weighted_left_product.cpp | 1 src/weighted_left_product.h | 1 21 files changed, 39 insertions(+), 49 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statics and p-values; creating specialized plots for correlation
or regression trees. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] (<https://orcid.org/0000-0001-9650-6919>)
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.7.6 dated 2021-05-05 and 0.7.8 dated 2021-05-08
DESCRIPTION | 15 +++----- MD5 | 20 +++++----- NEWS.md | 8 ++++ R/pkgstart.R | 82 +++++++++++++++++++++++---------------------- R/tests.R | 4 +- README.md | 60 ++++++++++++++++++++++++++++---- inst/doc/wrappedtools.R | 11 ++++++ inst/doc/wrappedtools.Rmd | 23 ++++++++++++ inst/doc/wrappedtools.html | 45 ++++++++++++++++++++---- man/cortestR.Rd | 2 - vignettes/wrappedtools.Rmd | 23 ++++++++++++ 11 files changed, 217 insertions(+), 76 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering the GCV procedure), functions to compute
the multivariate skewness, kurtosis, Mahalanobis distance (checking the positive
defineteness) and the Wilson-Hilferty transformation of chi squared variables. Furthermore,
the package provides interfaces to C code callable by another C code from other R packages.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.3-81 dated 2021-02-05 and 0.3-819 dated 2021-05-08
fastmatrix-0.3-81/fastmatrix/R/cholesky.R |only fastmatrix-0.3-81/fastmatrix/R/geomean.R |only fastmatrix-0.3-81/fastmatrix/src/hadamard.f |only fastmatrix-0.3-819/fastmatrix/ChangeLog | 10 fastmatrix-0.3-819/fastmatrix/DESCRIPTION | 21 - fastmatrix-0.3-819/fastmatrix/MD5 | 65 ++- fastmatrix-0.3-819/fastmatrix/NAMESPACE | 14 fastmatrix-0.3-819/fastmatrix/R/asSymmetric.R |only fastmatrix-0.3-819/fastmatrix/R/cg.R |only fastmatrix-0.3-819/fastmatrix/R/hadamard.R | 16 fastmatrix-0.3-819/fastmatrix/R/jacobi.R |only fastmatrix-0.3-819/fastmatrix/R/ldl.R |only fastmatrix-0.3-819/fastmatrix/R/moments.R |only fastmatrix-0.3-819/fastmatrix/R/seidel.R |only fastmatrix-0.3-819/fastmatrix/R/whitening.R |only fastmatrix-0.3-819/fastmatrix/inst/CITATION | 4 fastmatrix-0.3-819/fastmatrix/inst/include/fastmatrix.h | 11 fastmatrix-0.3-819/fastmatrix/inst/include/fastmatrix_API.h | 134 ++++-- fastmatrix-0.3-819/fastmatrix/man/asSymmetric.Rd |only fastmatrix-0.3-819/fastmatrix/man/cg.Rd |only fastmatrix-0.3-819/fastmatrix/man/jacobi.Rd |only fastmatrix-0.3-819/fastmatrix/man/kurtosis.Rd | 10 fastmatrix-0.3-819/fastmatrix/man/ldl.Rd |only fastmatrix-0.3-819/fastmatrix/man/minkowski.Rd | 14 fastmatrix-0.3-819/fastmatrix/man/moments.Rd |only fastmatrix-0.3-819/fastmatrix/man/ols.Rd | 4 fastmatrix-0.3-819/fastmatrix/man/ols.fit-methods.Rd | 2 fastmatrix-0.3-819/fastmatrix/man/seidel.Rd |only fastmatrix-0.3-819/fastmatrix/man/whitening.Rd |only fastmatrix-0.3-819/fastmatrix/src/R_init_fastmatrix.c | 14 fastmatrix-0.3-819/fastmatrix/src/blas_1.c | 237 +++++++++++- fastmatrix-0.3-819/fastmatrix/src/brent.c | 4 fastmatrix-0.3-819/fastmatrix/src/cholesky.c | 2 fastmatrix-0.3-819/fastmatrix/src/cov.c | 10 fastmatrix-0.3-819/fastmatrix/src/fastmatrix.h | 37 + fastmatrix-0.3-819/fastmatrix/src/hadamard.c |only fastmatrix-0.3-819/fastmatrix/src/ldl_decomp.f |only fastmatrix-0.3-819/fastmatrix/src/linear_iterative.c |only fastmatrix-0.3-819/fastmatrix/src/norms.c | 2 fastmatrix-0.3-819/fastmatrix/src/ols.c | 71 ++- fastmatrix-0.3-819/fastmatrix/src/products.c | 6 fastmatrix-0.3-819/fastmatrix/src/ridge.c | 2 fastmatrix-0.3-819/fastmatrix/src/stats_API.c | 69 ++- fastmatrix-0.3-819/fastmatrix/src/whitening.c |only 44 files changed, 585 insertions(+), 174 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.1.2 dated 2021-01-06 and 1.1.3 dated 2021-05-08
dexter-1.1.2/dexter/tests/testthat/test_interaction.R |only dexter-1.1.2/dexter/tests/testthat/test_oplike.r |only dexter-1.1.3/dexter/DESCRIPTION | 26 + dexter-1.1.3/dexter/MD5 | 75 ++--- dexter-1.1.3/dexter/NAMESPACE | 5 dexter-1.1.3/dexter/NEWS | 18 - dexter-1.1.3/dexter/R/RcppExports.R | 8 dexter-1.1.3/dexter/R/anon_plausible_values.R | 33 ++ dexter-1.1.3/dexter/R/data_selection.R | 3 dexter-1.1.3/dexter/R/database.R | 2 dexter-1.1.3/dexter/R/dexter.R | 6 dexter-1.1.3/dexter/R/enorm.R | 149 +++++++++- dexter-1.1.3/dexter/R/equating.R | 61 ++-- dexter-1.1.3/dexter/R/interaction_model.R | 36 +- dexter-1.1.3/dexter/R/misc.R | 85 +++++ dexter-1.1.3/dexter/R/plausible_values.R | 38 +- dexter-1.1.3/dexter/R/plots.R | 4 dexter-1.1.3/dexter/R/reparam.R | 10 dexter-1.1.3/dexter/R/resp_data.R | 4 dexter-1.1.3/dexter/R/suf_stats.R | 43 +- dexter-1.1.3/dexter/R/tia.R | 17 - dexter-1.1.3/dexter/README.md | 77 +++-- dexter-1.1.3/dexter/build/vignette.rds |binary dexter-1.1.3/dexter/inst/doc/DIF_vignette.html | 53 --- dexter-1.1.3/dexter/inst/doc/Equating.html | 57 --- dexter-1.1.3/dexter/inst/doc/Plausible_Values.html | 63 +--- dexter-1.1.3/dexter/inst/doc/Test_Individual_differences.html | 61 +--- dexter-1.1.3/dexter/inst/doc/dexter.R | 8 dexter-1.1.3/dexter/inst/doc/dexter.Rmd | 10 dexter-1.1.3/dexter/inst/doc/dexter.html | 145 ++++----- dexter-1.1.3/dexter/inst/doc/profile-plots.html | 44 -- dexter-1.1.3/dexter/man/dexter-package.Rd | 15 - dexter-1.1.3/dexter/man/fit_enorm.Rd | 5 dexter-1.1.3/dexter/man/latent_cor.Rd |only dexter-1.1.3/dexter/man/tia_tables.Rd | 4 dexter-1.1.3/dexter/src/RcppExports.cpp | 43 ++ dexter-1.1.3/dexter/src/roger.cpp | 107 ++++++- dexter-1.1.3/dexter/tests/testthat.R | 4 dexter-1.1.3/dexter/tests/testthat/test_ability.R | 40 -- dexter-1.1.3/dexter/vignettes/dexter.Rmd | 10 40 files changed, 838 insertions(+), 531 deletions(-)
Title: Analysis of Single-Cell Viral Growth Curves
Description: Aims to quantify time intensity data by using sigmoidal and
double sigmoidal curves. It fits straight lines, sigmoidal,
and double sigmoidal curves on to time vs intensity data.
Then all the fits are used to make decision on which model
best describes the data. This method was first developed
in the context of single-cell viral growth analysis (for
details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>),
and the package name stands for "SIngle CEll Growth Analysis in R".
Author: M. Umut Caglar [aut],
Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between sicegar versions 0.2.3 dated 2019-08-23 and 0.2.4 dated 2021-05-08
DESCRIPTION | 22 ++- MD5 | 47 ++++---- R/sicegar.R | 1 README.md | 6 - build/vignette.rds |binary inst/CITATION |only inst/doc/additional_parameters.R | 12 +- inst/doc/additional_parameters.html | 96 +++++++++++------ inst/doc/categorizing_fits.R | 14 +- inst/doc/categorizing_fits.html | 164 +++++++++++++++++------------ inst/doc/fitting_individual_models.R | 16 +- inst/doc/fitting_individual_models.html | 152 ++++++++++++++++----------- inst/doc/introduction.R | 14 +- inst/doc/introduction.html | 148 ++++++++++++++++---------- inst/doc/plotting_fitted_models.R | 6 - inst/doc/plotting_fitted_models.html | 180 ++++++++++++++++++-------------- man/categorize.Rd | 11 + man/doublesigmoidalFitFormula.Rd | 11 + man/doublesigmoidalFitFunction.Rd | 23 ++-- man/figureModelCurves.Rd | 14 +- man/fitAndCategorize.Rd | 46 ++++---- man/multipleFitFunction.Rd | 11 + man/preCategorize.Rd | 7 - man/sameSourceDataCheck.Rd | 3 man/sigmoidalFitFunction.Rd | 14 +- 25 files changed, 615 insertions(+), 403 deletions(-)
Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rwhois versions 1.0.4 dated 2020-04-16 and 1.0.5 dated 2021-05-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/functions.R | 5 +++-- README.md | 2 +- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.84 dated 2017-10-16 and 0.87 dated 2021-05-08
DESCRIPTION | 24 LICENSE |only MD5 | 71 - NAMESPACE | 24 R/colorlegend.R | 210 +-- R/cor-mtest.R | 90 - R/corrMatOrder.R | 158 +- R/corrRect.R | 52 R/corrRect.hclust.R | 90 - R/corrplot-package.R | 86 - R/corrplot.R | 2015 ++++++++++++++++++------------------ R/corrplot.mixed.R | 161 +- build/vignette.rds |binary inst/CITATION | 48 inst/NEWS | 178 +-- inst/doc/corrplot-intro.R | 408 +++---- inst/doc/corrplot-intro.Rmd | 698 ++++++------ inst/doc/corrplot-intro.html | 1114 +++++++++---------- man/colorlegend.Rd | 152 +- man/cor.mtest.Rd | 68 - man/corrMatOrder.Rd | 157 +- man/corrRect.Rd | 120 +- man/corrRect.hclust.Rd | 141 +- man/corrplot-package.Rd | 80 - man/corrplot.Rd | 950 ++++++++-------- man/corrplot.mixed.Rd | 140 +- tests/testthat.R | 8 tests/testthat/test-colorlegend.R | 112 +- tests/testthat/test-cor-mtest.R | 50 tests/testthat/test-corrplot.R | 470 ++++---- vignettes/corrplot-intro.Rmd | 698 ++++++------ vignettes/example-colorlegend.R | 48 vignettes/example-corrMatOrder.R | 56 - vignettes/example-corrRect.R | 62 - vignettes/example-corrRect.hclust.R | 62 - vignettes/example-corrplot.R | 372 +++--- vignettes/example-corrplot.mixed.R | 26 37 files changed, 4662 insertions(+), 4537 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for
more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between SeuratObject versions 4.0.0 dated 2021-01-15 and 4.0.1 dated 2021-05-08
SeuratObject-4.0.0/SeuratObject/README.md |only SeuratObject-4.0.1/SeuratObject/DESCRIPTION | 28 SeuratObject-4.0.1/SeuratObject/MD5 | 35 - SeuratObject-4.0.1/SeuratObject/NAMESPACE | 9 SeuratObject-4.0.1/SeuratObject/NEWS.md |only SeuratObject-4.0.1/SeuratObject/R/assay.R | 131 ---- SeuratObject-4.0.1/SeuratObject/R/generics.R | 17 SeuratObject-4.0.1/SeuratObject/R/seurat.R | 386 ++---------- SeuratObject-4.0.1/SeuratObject/R/utils.R | 90 +- SeuratObject-4.0.1/SeuratObject/R/zzz.R | 24 SeuratObject-4.0.1/SeuratObject/man/Assay-methods.Rd | 24 SeuratObject-4.0.1/SeuratObject/man/AttachDeps.Rd |only SeuratObject-4.0.1/SeuratObject/man/CellsByIdentities.Rd | 5 SeuratObject-4.0.1/SeuratObject/man/CreateAssayObject.Rd | 4 SeuratObject-4.0.1/SeuratObject/man/CreateSeuratObject.Rd | 5 SeuratObject-4.0.1/SeuratObject/man/IsMatrixEmpty.Rd |only SeuratObject-4.0.1/SeuratObject/man/Seurat-methods.Rd | 35 + SeuratObject-4.0.1/SeuratObject/man/SeuratObject-package.Rd | 8 SeuratObject-4.0.1/SeuratObject/man/Version.Rd |only SeuratObject-4.0.1/SeuratObject/man/WhichCells.Rd | 13 SeuratObject-4.0.1/SeuratObject/man/as.sparse.Rd | 5 21 files changed, 350 insertions(+), 469 deletions(-)
Title: Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Diff between Rsurrogate versions 2.0 dated 2016-10-20 and 3.0 dated 2021-05-08
DESCRIPTION | 11 MD5 | 38 +- NAMESPACE | 5 R/Functions_Rsurrogate.R | 787 ++++++++++++++++++++++++++++++++++++++---- data/d_example_me.RData |only data/d_example_multiple.RData |only man/Aug.R.s.surv.estimate.Rd | 11 man/R.multiple.surv.Rd |only man/R.s.estimate.Rd | 12 man/R.s.estimate.me.Rd |only man/R.s.surv.estimate.Rd | 12 man/R.t.surv.estimate.Rd | 9 man/calculate.var.np.Rd |only man/censor.weight.Rd | 7 man/d_example_me.Rd |only man/d_example_multiple.Rd |only man/delta.multiple.surv.Rd |only man/delta.s.estimate.Rd | 2 man/delta.s.surv.estimate.Rd | 19 - man/delta.surv.estimate.Rd | 5 man/delta.t.surv.estimate.Rd | 9 man/fieller.calculate.me.Rd |only man/me.variance.estimate.Rd |only man/pred.smooth.Rd | 4 man/pred.smooth.surv.Rd | 16 25 files changed, 837 insertions(+), 110 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>),
Fanny Chow [aut],
Max Kuhn [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between rsample versions 0.0.9 dated 2021-02-17 and 0.1.0 dated 2021-05-08
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Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph], Jean-Sebastien Roy [cph], Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.3.0 dated 2021-04-06 and 0.3.0-1 dated 2021-05-08
poismf-0.3.0-1/poismf/DESCRIPTION | 10 poismf-0.3.0-1/poismf/MD5 | 17 - poismf-0.3.0-1/poismf/NAMESPACE | 6 poismf-0.3.0-1/poismf/R/poismf.R | 395 +++++++------------------ poismf-0.3.0-1/poismf/configure | 18 - poismf-0.3.0-1/poismf/man/poismf.Rd | 25 - poismf-0.3.0-1/poismf/man/poismf_unsafe.Rd | 7 poismf-0.3.0-1/poismf/man/poisson.llk.Rd | 4 poismf-0.3.0-1/poismf/man/predict.poismf.Rd | 2 poismf-0.3.0/poismf/man/get.all.predictions.Rd |only 10 files changed, 164 insertions(+), 320 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future and includes facilities
for local prototyping and testing. Web applications are provided (via 'shiny') for
the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 1.1 dated 2019-09-23 and 1.3-1 dated 2021-05-08
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