Title: Kernel Approaches for Nonlinear Genetic Association Regression
Description: Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel).
Author: Juliane Manitz [aut, cre],
Benjamin Hofner [aut],
Stefanie Friedrichs [aut],
Patricia Burger [aut],
Ngoc Thuy Ha [aut],
Saskia Freytag [ctb],
Heike Bickeboeller [ctb]
Maintainer: Juliane Manitz <r@manitz.org>
Diff between kangar00 versions 1.4.1 dated 2022-12-06 and 1.4.2 dated 2024-05-08
DESCRIPTION | 40 + MD5 | 12 NAMESPACE | 5 R/GWASdata.r | 1184 ++++++++++++++++++++++++------------------------- R/get_network_matrix.r | 406 ++++++++-------- R/pathway.r | 1088 ++++++++++++++++++++++----------------------- inst/CITATION | 186 +++---- 7 files changed, 1465 insertions(+), 1456 deletions(-)
Title: Wrapper for SQL Server bcp Utility
Description: Provides functions to utilize a command line utility that does bulk inserts and exports from SQL Server databases.
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas@roh.engineering>
Diff between bcputility versions 0.4.0 dated 2023-01-16 and 0.4.3 dated 2024-05-08
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ NEWS.md | 9 +++++ R/bcp.R | 80 ++++++++++++++++++++++++++++++------------------- R/sysdata.rda |binary README.md | 2 - man/makeConnectArgs.Rd | 6 +++ tests/a-init-db.R | 2 - tests/b-import-db.R | 1 tests/c-export-db.R | 1 tests/d-types.R | 1 11 files changed, 83 insertions(+), 49 deletions(-)
Title: Temporal Tensor Decomposition, a Dimensionality Reduction Tool
for Longitudinal Multivariate Data
Description: TEMPoral TEnsor Decomposition (TEMPTED), is a dimension reduction method for multivariate longitudinal data with varying temporal sampling. It formats the data into a temporal tensor and decomposes it into a summation of low-dimensional components, each consisting of a subject loading vector, a feature loading vector, and a continuous temporal loading function. These loadings provide a low-dimensional representation of subjects or samples and can be used to identify features associated with clusters of subjects or samples. TEMPTED provides the flexibility of allowing subjects to have different temporal sampling, so time points do not need to be binned, and missing time points do not need to be imputed.
Author: Pixu Shi
Maintainer: Pixu Shi <pixu.shi@duke.edu>
Diff between tempted versions 0.1.0 dated 2024-01-11 and 0.1.1 dated 2024-05-08
DESCRIPTION | 10 ++--- MD5 | 7 ++-- NAMESPACE | 1 R/TEMPTED.R | 91 +++++++++++++++++++++++++++++++++++++++++++++++++++++ man/reconstruct.Rd |only 5 files changed, 101 insertions(+), 8 deletions(-)
Title: Goodness-of-Fit Functions for Comparison of Simulated and
Observed Hydrological Time Series
Description: S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph]
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
Diff between hydroGOF versions 0.5-4 dated 2024-01-21 and 0.6-0 dated 2024-05-08
DESCRIPTION | 6 - MD5 | 100 +++++++++++---------- NAMESPACE | 18 +++ NEWS.md | 24 +++++ R/APFB.R |only R/HFB.R |only R/KGE.R | 24 +++-- R/KGEkm.R |only R/KGElf.R | 14 +-- R/ggof.R | 52 ++++++++--- R/gof.R | 185 ++++++++++++++++++++++++---------------- R/pbiasfdc.R | 13 +- R/plot2.R | 49 +++++++--- R/sKGE.R | 72 +++++++++++---- R/wsNSE.R |only build/vignette.rds |binary inst/CITATION | 7 - inst/doc/hydroGOF_Vignette.Rmd | 2 inst/doc/hydroGOF_Vignette.pdf |binary man/APFB.Rd |only man/HFB.Rd |only man/KGE.Rd | 73 +++++++++------ man/KGEkm.Rd |only man/KGElf.Rd | 26 +++-- man/KGEnp.Rd | 13 +- man/NSE.Rd | 16 ++- man/R2.Rd | 6 - man/VE.Rd | 3 man/br2.Rd | 4 man/cp.Rd | 4 man/d.Rd | 8 - man/dr.Rd | 11 +- man/ggof.Rd | 145 +++++++++++++++++++++++++------ man/gof.Rd | 162 +++++++++++++++++++++++++++-------- man/hydroGOF-package.Rd | 112 ++++++++++++++++-------- man/mNSE.rd | 4 man/mae.Rd | 6 + man/md.Rd | 15 +-- man/me.Rd | 2 man/mse.Rd | 6 + man/pbias.Rd | 2 man/pbiasfdc.Rd | 12 +- man/pfactor.Rd | 8 - man/rNSE.rd | 4 man/rPearson.Rd | 4 man/rd.Rd | 10 +- man/rfactor.Rd | 8 - man/rmse.Rd | 6 + man/rsr.Rd | 2 man/sKGE.Rd | 41 ++++++-- man/ssq.Rd | 11 +- man/ubRMSE.Rd | 4 man/wNSE.Rd | 8 - man/wsNSE.Rd |only vignettes/hydroGOF_Vignette.Rmd | 2 55 files changed, 886 insertions(+), 418 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 1.0.0.1 dated 2023-12-04 and 1.1.0.0 dated 2024-05-08
DESCRIPTION | 6 MD5 | 14 +- src/RlibMVL.c | 264 ++++++++++++++++++++++++++++++++---------- src/libMVL.c | 166 ++++++++++++++++++++------ src/libMVL.h | 68 ++++++++-- src/libMVL_sort.cc | 54 -------- tests/test_bracket2.R | 22 +-- tests/test_bracket2.Rout.save | 24 +-- 8 files changed, 423 insertions(+), 195 deletions(-)
Title: Lyrics and Song Data for Taylor Swift's Discography
Description: A comprehensive resource for data on Taylor Swift songs. Data
is included for all officially released studio albums, extended plays
(EPs), and individual singles are included. Data comes from 'Genius'
(lyrics) and 'Spotify' (song characteristics). Additional functions
are included for easily creating data visualizations with color
palettes inspired by Taylor Swift's album covers.
Author: W. Jake Thompson [aut, cre, cph]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between taylor versions 3.0.0 dated 2023-11-06 and 3.1.0 dated 2024-05-08
taylor-3.0.0/taylor/inst/album-covers |only taylor-3.1.0/taylor/DESCRIPTION | 31 taylor-3.1.0/taylor/LICENSE | 4 taylor-3.1.0/taylor/MD5 | 204 taylor-3.1.0/taylor/NEWS.md | 88 taylor-3.1.0/taylor/R/data.R | 19 taylor-3.1.0/taylor/R/ggplot2-color-scales.R | 30 taylor-3.1.0/taylor/R/taylor-album-palettes.R | 103 taylor-3.1.0/taylor/R/taylor-package.R | 3 taylor-3.1.0/taylor/README.md | 32 taylor-3.1.0/taylor/build |only taylor-3.1.0/taylor/data/eras_tour_surprise.rda |binary taylor-3.1.0/taylor/data/taylor_album_songs.rda |binary taylor-3.1.0/taylor/data/taylor_albums.rda |binary taylor-3.1.0/taylor/data/taylor_all_songs.rda |binary taylor-3.1.0/taylor/inst/WORDLIST | 7 taylor-3.1.0/taylor/inst/doc |only taylor-3.1.0/taylor/man/album_levels.Rd | 2 taylor-3.1.0/taylor/man/album_palettes.Rd | 4 taylor-3.1.0/taylor/man/eras_tour_surprise.Rd | 7 taylor-3.1.0/taylor/man/figures/logo.png |binary taylor-3.1.0/taylor/man/taylor_albums.Rd | 2 taylor-3.1.0/taylor/man/taylor_songs.Rd | 20 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Title: Regression Model Diagnostics for Survey Data
Description: Diagnostics for fixed effects linear regression models fitted with survey data. Extensions of standard diagnostics to complex survey data are included: standardized residuals, leverages, Cook's D, dfbetas, dffits, condition indexes, and variance inflation factors as found in Li and Valliant (Surv. Meth., 2009, 35(1), pp. 15-24; Jnl. of Off. Stat., 2011, 27(1), pp. 99-119; Jnl. of Off. Stat., 2015, 31(1), pp. 61-75); Liao and Valliant (Surv. Meth., 2012, 38(1), pp. 53-62; Surv. Meth., 2012, 38(2), pp. 189-202). Variance inflation factors are also computed for some general linear models (binomial, gaussian, poisson, quasibinomial, and quasipoisson) as described in Liao (U. Maryland thesis, 2010).
Author: Richard Valliant [aut, cre]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between svydiags versions 0.5 dated 2024-03-12 and 0.6 dated 2024-05-08
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/svyvif.R | 52 ++++++++++++++++++++++++++++++++++++++-------------- man/svyvif.Rd | 38 ++++++++++++++++++++++++++++---------- 5 files changed, 82 insertions(+), 34 deletions(-)
Title: Highly Customizable 'rmarkdown' Theme for Scientific Reporting
Description: Offers 'markdown' output formats designed with various scientific styles, allowing users to generate PDF and HTML outputs. The output has a contemporary appearance with vibrant visuals, providing numerous styles for effective highlighting. The package also includes additional features specifically tailored for front-page slides, enhancing the overall presentation and customization options. The package was created using the 'tufte' <https://rstudio.github.io/tufte/> package code as a starting point.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between scientific versions 2024.1 dated 2024-02-22 and 2024.2 dated 2024-05-08
DESCRIPTION | 8 MD5 | 18 README.md | 4 build/vignette.rds |binary inst/doc/Introduction.Rmd | 4 inst/doc/Introduction.html | 12 inst/rmarkdown/templates/html/layout/index.ohtml | 76 inst/rmarkdown/templates/html/layout/scientific1.css |81316 +++++++++---------- inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 5 vignettes/Introduction.Rmd | 4 10 files changed, 40743 insertions(+), 40704 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the 'ped
suite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.9.3 dated 2024-04-02 and 0.9.4 dated 2024-05-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/peel.R | 31 +++++++++++-------------------- build/partial.rdb |binary tests/testthat/test-likelihood.R | 13 ++++++++++--- 6 files changed, 36 insertions(+), 32 deletions(-)
Title: Sample Size and Power Calculation for Common Non-Parametric
Tests in Survival Analysis
Description: A number of statistical tests have been proposed to compare two
survival curves, including the difference in (or ratio of) t-year
survival, difference in (or ratio of) p-th percentile survival, difference in
(or ratio of) restricted mean survival time, and the weighted log-rank test.
Despite the multitude of options, the convention in survival studies is to assume
proportional hazards and to use the unweighted log-rank test for design and
analysis. This package provides sample size and power
calculation for all of the above statistical tests with allowance for
flexible accrual, censoring, and survival (eg. Weibull, piecewise-exponential,
mixture cure). It is the companion R package to the paper by Yung and Liu (2020)
<doi:10.1111/biom.13196>. Specific to the weighted log-rank test, users may
specify which approximations they wish to use to estimate the large-sample mean
and variance. The default option has been shown to provide substantial
improvement over the conventional sample [...truncated...]
Author: Godwin Yung [aut, cre],
Yi Liu [aut]
Maintainer: Godwin Yung <godwin.y.yung@gmail.com>
Diff between npsurvSS versions 1.0.1 dated 2019-12-18 and 1.1.0 dated 2024-05-08
DESCRIPTION | 17 MD5 | 80 +- NAMESPACE | 68 +- R/calc_central_moments.R | 464 +++++++------- R/calc_counting_processes.R | 226 +++---- R/calc_events_and_duration.R | 224 +++---- R/calc_interval.R | 40 - R/calc_maxU_and_minimaxU.R | 216 +++--- R/calc_power_and_sample_size.R | 606 +++++++++---------- R/class_arm.R | 649 ++++++++++---------- R/dist_accr.R | 162 ++--- R/dist_loss.R | 88 +- R/dist_surv.R | 242 +++---- R/simulation.R | 240 +++---- build/vignette.rds |binary inst/doc/basic_functionalities.R | 270 ++++---- inst/doc/basic_functionalities.Rmd | 374 +++++------ inst/doc/basic_functionalities.html | 1147 +++++++++++++++++++----------------- inst/doc/example1.R | 362 +++++------ inst/doc/example1.Rmd | 420 ++++++------- inst/doc/example1.html | 1080 +++++++++++++++++---------------- inst/doc/example2.R | 254 ++++--- inst/doc/example2.Rmd | 304 ++++----- inst/doc/example2.html | 988 ++++++++++++++++--------------- man/create_arm.Rd | 233 +++---- man/create_arm_lachin.Rd | 190 +++-- man/daccr.Rd | 84 +- man/dloss.Rd | 90 +- man/dmaxU.Rd | 84 +- man/dminimaxU.Rd | 106 +-- man/dsurv.Rd | 98 +-- man/exp_duration.Rd | 92 +- man/exp_events.Rd | 70 +- man/per2haz.Rd | 56 - man/power_two_arm.Rd | 130 ++-- man/simulate_arm.Rd | 72 +- man/simulate_trial.Rd | 94 +- man/size_two_arm.Rd | 149 ++-- vignettes/basic_functionalities.Rmd | 374 +++++------ vignettes/example1.Rmd | 420 ++++++------- vignettes/example2.Rmd | 304 ++++----- 41 files changed, 5731 insertions(+), 5436 deletions(-)
Title: Next Generation Clustered Heat Maps
Description: Next-Generation Clustered Heat Maps (NG-CHMs) allow for
dynamic exploration of heat map data in a web browser. 'NGCHM' allows
users to create both stand-alone HTML files containing a
Next-Generation Clustered Heat Map, and .ngchm files to view in the
NG-CHM viewer. See Ryan MC, Stucky M, et al (2020)
<doi:10.12688/f1000research.20590.2> for more details.
Author: Bradley M Broom [aut] ,
Mary A Rohrdanz [ctb, cre],
Chris Wakefield [ctb],
James Melott [ctb],
MD Anderson Cancer Center [cph]
Maintainer: Mary A Rohrdanz <marohrdanz@mdanderson.org>
Diff between NGCHM versions 1.0.2 dated 2024-03-28 and 1.0.3 dated 2024-05-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/functions.R | 9 +++------ 3 files changed, 8 insertions(+), 11 deletions(-)
Title: Process Analysis for Exponential Random Graph Models
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM).
Includes functions to conduct mediation and moderation analyses and to diagnose
multicollinearity.
URL: <https://github.com/sduxbury/ergMargins>.
BugReports: <https://github.com/sduxbury/ergMargins/issues>.
Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>.
Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>.
Mize, Trenton D. (2019) <doi:10.15195/v6.a4>.
Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>.
Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
Duxbury, Scott W, Jenna Wertsching (2023) <doi:10.1016/j.socnet.2023.02.003>.
Huang, Peng, Carter Butts (2023) <doi:10.1016/j.socnet.2023.07.001>.
Author: Scott Duxbury [aut, cre, cph]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Diff between ergMargins versions 1.2 dated 2024-02-23 and 1.3 dated 2024-05-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ergmAME.R | 38 +++++++++++++++++++++++++------------- R/ergmMEM.R | 49 +++++++++++++++++++++++++++++++------------------ R/vif.ergm.R | 13 +++++++------ 5 files changed, 70 insertions(+), 44 deletions(-)
Title: Flexible Time-to-Event Figures
Description: Ease the creation of time-to-event (i.e. survival) endpoint
figures. The modular functions create figures ready for publication.
Each of the functions that add to or modify the figure are written as
proper 'ggplot2' geoms or stat methods, allowing the functions from
this package to be combined with any function or customization from
'ggplot2' and other 'ggplot2' extension packages.
Author: Daniel D. Sjoberg [aut, cre, cph]
,
Mark Baillie [aut],
Charlotta Fruechtenicht [aut] ,
Steven Haesendonckx [aut] ,
Tim Treis [aut]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between ggsurvfit versions 1.0.0 dated 2023-10-30 and 1.1.0 dated 2024-05-08
DESCRIPTION | 12 MD5 | 262 +- NEWS.md | 14 R/add_censor_mark.R | 6 R/add_confidence_interval.R | 2 R/add_legend_title.R | 2 R/add_pvalue.R | 2 R/add_quantile.R | 2 R/add_risktable.R | 2 R/ggcuminc.R | 3 R/ggsurvfit.R | 2 R/ggsurvfit_align_plots.R | 10 R/tidy_survfit.R | 44 R/utils-add_risktable.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/themes.html | 12 man/figures/README-gt-related-pkgs.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/ggcuminc.Rd | 2 man/ggsurvfit-package.Rd | 1 man/ggsurvfit.Rd | 3 man/survfit2.Rd | 13 man/tidy_survfit.Rd | 9 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_censor_mark/cuminc1-censor-mark-all-outcomes.svg | 14 tests/testthat/_snaps/add_censor_mark/cuminc2-censor-mark-all-outcomes.svg | 24 tests/testthat/_snaps/add_censor_mark/cuminc2-censor-mark.svg | 22 tests/testthat/_snaps/add_censor_mark/cuminc3-censor-mark-all-outcomes.svg | 896 +++++----- tests/testthat/_snaps/add_censor_mark/cuminc3-censor-mark.svg | 518 ++--- tests/testthat/_snaps/add_censor_mark/sf2-censor-mark.svg | 22 tests/testthat/_snaps/add_censor_mark/sf3-censor-mark.svg | 420 ++-- tests/testthat/_snaps/add_confidence_interval/cuminc1-confidence-interval-all-outcomes.svg | 18 tests/testthat/_snaps/add_confidence_interval/cuminc2-confidence-interval-all-outcomes.svg | 20 tests/testthat/_snaps/add_confidence_interval/cuminc2-confidence-interval.svg | 18 tests/testthat/_snaps/add_confidence_interval/cuminc3-confidence-interval-all-outcomes.svg | 248 +- tests/testthat/_snaps/add_confidence_interval/cuminc3-confidence-interval.svg | 182 +- tests/testthat/_snaps/add_confidence_interval/sf2-confidence-interval.svg | 18 tests/testthat/_snaps/add_confidence_interval/sf3-confidence-interval.svg | 194 +- tests/testthat/_snaps/add_pvalue/cuminc2-pvalue.svg | 72 tests/testthat/_snaps/add_pvalue/sf2-pvalue-annotation-risk.svg | 14 tests/testthat/_snaps/add_pvalue/sf2-pvalue-annotation.svg | 14 tests/testthat/_snaps/add_pvalue/sf2-pvalue-caption.svg | 14 tests/testthat/_snaps/add_pvalue/sf2-pvalue-with-survfit.svg | 14 tests/testthat/_snaps/add_quantile/cuminc1-quantile-all-outcomes.svg | 14 tests/testthat/_snaps/add_quantile/cuminc2-quantile-all-outcomes.svg | 16 tests/testthat/_snaps/add_quantile/cuminc2-quantile.svg | 14 tests/testthat/_snaps/add_quantile/cuminc3-quantile-all-outcomes.svg | 192 +- tests/testthat/_snaps/add_quantile/cuminc3-quantile.svg | 154 - 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Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.8.2 dated 2024-04-16 and 0.8.3 dated 2024-05-08
DESCRIPTION | 6 - MD5 | 45 ++++---- NEWS.md | 9 + R/boot_log_TOST.R | 5 R/boot_t_TOST.R | 5 R/brunner_munzel.R | 14 ++ R/cohend_calcs.R | 45 +++++++- R/methods.TOSTt.R | 12 ++ R/plot_smd.R | 19 +++ R/simple_htest.R | 13 ++ inst/doc/IntroTOSTt.html | 17 +-- inst/doc/IntroductionToTOSTER.html | 8 - inst/doc/SMD_calcs.R | 5 inst/doc/SMD_calcs.Rmd | 58 +++++------ inst/doc/SMD_calcs.html | 186 ++++++++++++++++++++++++------------- inst/doc/correlations.html | 9 - inst/doc/robustTOST.Rmd | 6 - inst/doc/robustTOST.html | 37 +++---- inst/doc/the_ftestTOSTER.html | 9 - man/simple_htest.Rd | 4 tests/testthat/test-smd-se.R |only vignettes/SMD_calcs.Rmd | 58 +++++------ vignettes/references.bib | 48 ++++++++- vignettes/robustTOST.Rmd | 6 - 24 files changed, 404 insertions(+), 220 deletions(-)
Title: Query 'Snowflake' Databases with 'SQL'
Description: A wrapper allowing 'SQL' queries to be run on a 'Snowflake' instance directly from an 'R' script, by using the 'snowflake-connector-python' package in the background.
Author: Dani Mermelstein [aut, cre, cph]
Maintainer: Dani Mermelstein <dmermelstein@hey.com>
Diff between snowquery versions 1.0.0 dated 2023-07-20 and 1.2.0 dated 2024-05-08
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 1 NEWS.md | 8 +++++ R/queryDB.R | 73 ++++++++++++++++++++++++++++++++++++-------------- R/snowquery-package.R | 10 +++--- README.md | 67 ++++++++++++++++++++++++++++++++------------- man/queryDB.Rd | 9 ++++-- 8 files changed, 132 insertions(+), 58 deletions(-)
Title: Particle Tracking and Demography
Description: Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in evolutionary and ecological studies.
Author: Marjolein Bruijning, Marco D. Visser, Caspar A. Hallmann, Eelke Jongejans
Maintainer: Marjolein Bruijning <m.bruijning@uva.nl>
Diff between trackdem versions 0.6 dated 2021-09-24 and 0.7.2 dated 2024-05-08
DESCRIPTION | 12 MD5 | 16 R/resultsFunctions.R | 2 build/vignette.rds |binary inst/doc/tutorial.R | 1 inst/doc/tutorial.pdf |binary inst/python/createImageSeq.py | 818 +++++++++++++++++++++--------------------- man/trackdem.Rd | 9 src/RcppExports.cpp | 5 9 files changed, 438 insertions(+), 425 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>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.
Author: Paul Hoffman [aut] ,
Rahul Satija [aut, cre] ,
David Collins [aut] ,
Yuhan Hao [aut] ,
Austin Hartman [aut] ,
Gesmira Molla [aut] ,
Andrew Butler [aut] ,
Tim Stuart [aut] ,
Madeline Kowalski [ctb] ,
Saket Choudhary [ctb] ,
Skylar Li [ctb],
Longda Jia [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between SeuratObject versions 5.0.1 dated 2023-11-17 and 5.0.2 dated 2024-05-08
DESCRIPTION | 30 LICENSE | 4 MD5 | 553 NAMESPACE | 1287 - NEWS.md | 232 R/RcppExports.R | 22 R/assay.R | 3913 ++-- R/assay5.R | 6610 +++---- R/centroids.R | 964 - R/command.R | 654 R/compliance.R | 126 R/data.R | 50 R/default.R | 612 R/dimreduc.R | 2328 +- R/fov.R | 2173 +- R/generics.R | 3311 +-- R/graph.R | 446 R/jackstraw.R | 348 R/keymixin.R | 626 R/layers.R | 754 R/logmap.R | 1406 - R/molecules.R | 870 R/neighbor.R | 386 R/segmentation.R | 724 R/seurat.R |11841 ++++++------- R/sparse.R | 344 R/spatial.R | 786 R/utils.R | 5591 +++--- R/zzz.R | 1103 - build/SeuratObject.pdf |binary build/partial.rdb |binary man/AddMetaData-StdAssay.Rd | 54 man/AddMetaData.Rd | 94 man/Assay-class.Rd | 104 man/Assay-validity.Rd | 138 man/Assay5-class.Rd | 122 man/Assay5-validity.Rd | 86 man/Assay5T-class.Rd | 114 man/AssayData-StdAssay.Rd | 96 man/AssayData.Rd | 208 man/AttachDeps.Rd | 78 man/Boundaries.Rd | 106 man/CastAssay-StdAssay.Rd | 56 man/CastAssay.Rd | 60 man/Cells-StdAssay.Rd | 64 man/Cells.Rd | 116 man/CellsByIdentities.Rd | 62 man/CellsByImage.Rd | 58 man/Centroids-class.Rd | 76 man/Centroids-methods.Rd | 260 man/CheckDots.Rd | 100 man/CheckFeaturesNames.Rd | 36 man/CheckGC.Rd | 36 man/CheckLayersName.Rd | 34 man/CheckMatrix.Rd | 80 man/ClassKey.Rd | 64 man/Command.Rd | 56 man/CreateAssay5Object.Rd | 84 man/CreateAssayObject.Rd | 142 man/CreateCentroids.Rd | 50 man/CreateDimReducObject.Rd | 140 man/CreateFOV.Rd | 166 man/CreateMolecules.Rd | 74 man/CreateSegmentation.Rd | 48 man/CreateSeuratObject.Rd | 220 man/Crop.Rd | 68 man/DefaultAssay-StdAssay.Rd | 56 man/DefaultAssay.Rd | 148 man/DefaultDimReduc.Rd | 56 man/DefaultFOV.Rd | 74 man/DefaultLayer-StdAssay.Rd | 56 man/DefaultLayer.Rd | 72 man/DimReduc-class.Rd | 102 man/DimReduc-validity.Rd | 108 man/Distances.Rd | 46 man/Embeddings.Rd | 72 man/EmptyDF.Rd | 50 man/EmptyMatrix.Rd |only man/ExtractField.Rd | 60 man/FOV-class.Rd | 76 man/FOV-methods.Rd | 364 man/FOV-validity.Rd | 46 man/FetchData.Rd | 124 man/FilterObjects.Rd | 68 man/GetImage.Rd | 98 man/GetTissueCoordinates.Rd | 52 man/Graph-class.Rd | 48 man/Idents.Rd | 292 man/Images.Rd | 56 man/Indices.Rd | 46 man/IsGlobal.Rd | 68 man/IsMatrixEmpty.Rd | 57 man/IsNamedList.Rd | 72 man/IsSparse.Rd | 58 man/JS.Rd | 86 man/JackStrawData-class.Rd | 44 man/JackStrawData-methods.Rd | 114 man/Key-validity.Rd | 62 man/Key.Rd | 154 man/KeyMixin-class.Rd | 124 man/Layers-StdAssay.Rd | 130 man/Layers.Rd | 200 man/Loadings.Rd | 106 man/LogMap-class.Rd | 214 man/LogMap-validity.Rd | 88 man/LogSeuratCommand.Rd | 64 man/MatchCells.Rd | 66 man/Misc-StdAssay.Rd | 60 man/Misc.Rd | 124 man/Molecules-class.Rd | 56 man/Molecules-methods.Rd | 132 man/NNIndex.Rd | 66 man/Neighbor-class.Rd | 58 man/Neighbor-methods.Rd | 66 man/ObjectAccess.Rd | 88 man/Overlay.Rd | 104 man/PackageCheck.Rd | 66 man/PolyVtx.Rd | 93 man/Project.Rd | 66 man/Radius.Rd | 38 man/RandomName.Rd | 62 man/RegisterSparseMatrix.Rd | 54 man/RenameAssays.Rd | 72 man/RenameCells-StdAssay.Rd | 56 man/RenameCells.Rd | 156 man/RowMergeSparseMatrices.Rd | 50 man/SaveSeuratRds.Rd | 250 man/Segmentation-class.Rd | 40 man/Segmentation-methods.Rd | 270 man/Seurat-class.Rd | 134 man/Seurat-validity.Rd | 50 man/SeuratCommand-class.Rd | 70 man/SeuratObject-options.Rd | 100 man/SeuratObject-package.Rd | 91 man/Simplify.Rd | 58 man/SparseEmptyMatrix.Rd | 34 man/SpatialImage-class.Rd | 58 man/SpatialImage-methods.Rd | 438 man/SplitLayers.Rd | 64 man/StdAssay-class.Rd | 136 man/StdAssay-validity.Rd | 90 man/Stdev.Rd | 72 man/StitchMatrix.Rd | 56 man/Theta.Rd | 30 man/Tool.Rd | 130 man/UpdateSeuratObject.Rd | 52 man/UpdateSlots.Rd | 36 man/VariableFeatures-StdAssay.Rd | 152 man/VariableFeatures.Rd | 350 man/Version.Rd | 48 man/WhichCells.Rd | 142 man/aggregate.Rd | 122 man/angles.Rd | 76 man/as.Centroids.Rd | 80 man/as.Graph.Rd | 102 man/as.Neighbor.Rd | 46 man/as.Seurat.Rd | 40 man/as.list.SeuratCommand.Rd | 76 man/as.matrix.LogMap.Rd | 76 man/as.sparse.Rd | 70 man/cash-.Assay.Rd | 102 man/cash-.Assay5.Rd | 78 man/cash-.Seurat.Rd | 148 man/cash-.SeuratCommand.Rd | 66 man/cash-.StdAssay.Rd | 82 man/colMeans-Assay-method.Rd | 120 man/colMeans-Seurat-method.Rd | 120 man/dim.Assay.Rd | 74 man/dim.Assay5.Rd | 62 man/dim.DimReduc.Rd | 142 man/dim.Seurat.Rd | 80 man/dim.StdAssay.Rd | 66 man/dimnames.Assay.Rd | 126 man/dimnames.Assay5.Rd | 96 man/dimnames.Seurat.Rd | 122 man/dimnames.StdAssay.Rd | 92 man/dot-AssayClass.Rd | 48 man/dot-BPMatrixMode.Rd | 56 man/dot-CalcN.Rd | 50 man/dot-CheckFmargin.Rd | 56 man/dot-ClassPkg.Rd | 68 man/dot-Collections.Rd | 68 man/dot-Contains.Rd | 46 man/dot-CreateStdAssay.Rd | 218 man/dot-DefaultFOV.Rd | 40 man/dot-Deprecate.Rd | 152 man/dot-DiskLoad.Rd | 98 man/dot-DollarNames.Assay.Rd | 54 man/dot-DollarNames.Assay5.Rd | 52 man/dot-DollarNames.Seurat.Rd | 52 man/dot-DollarNames.SeuratCommand.Rd | 62 man/dot-DollarNames.StdAssay.Rd | 72 man/dot-FileMove.Rd | 72 man/dot-FilePath.Rd | 56 man/dot-FilterObjects.Rd | 66 man/dot-FindObject.Rd | 70 man/dot-GetMethod.Rd | 54 man/dot-IsFutureSeurat.Rd | 62 man/dot-KeyPattern.Rd | 46 man/dot-MARGIN.Rd | 36 man/dot-PropagateList.Rd | 70 man/dot-RandomKey.Rd | 64 man/dot-SelectFeatures.Rd | 46 man/dot-SparseSlots.Rd | 70 man/dot-Subobjects.Rd | 76 man/droplevels.LogMap.Rd | 80 man/intersect.LogMap.Rd | 80 man/labels.LogMap.Rd | 120 man/merge.Assay.Rd | 104 man/merge.Assay5.Rd | 94 man/merge.DimReduc.Rd | 74 man/merge.Seurat.Rd | 186 man/merge.StdAssay.Rd | 78 man/names.Seurat.Rd | 82 man/old-assign.Rd | 58 man/oldseurat-class.Rd | 150 man/pbmc_small.Rd | 72 man/print.DimReduc.Rd | 94 man/reexports.Rd | 46 man/roxygen/meta.R | 38 man/roxygen/templates/desc-validity.R | 4 man/roxygen/templates/lifecycle-deprecated.R | 10 man/roxygen/templates/lifecycle-experimental.R | 12 man/roxygen/templates/lifecycle-superseded.R | 6 man/roxygen/templates/method-cells.R | 6 man/roxygen/templates/method-features.R | 8 man/roxygen/templates/method-lengths.R | 10 man/roxygen/templates/method-show.R | 6 man/roxygen/templates/method-stdassay.R | 16 man/roxygen/templates/name-oldv.R | 16 man/roxygen/templates/note-reqdpkg.R | 6 man/roxygen/templates/param-dots-ignored.R | 2 man/roxygen/templates/param-dots-method.R | 2 man/roxygen/templates/param-verbose.R | 2 man/roxygen/templates/return-null.R | 2 man/roxygen/templates/return-show.R | 4 man/roxygen/templates/section-future.R | 26 man/roxygen/templates/section-progressr.R | 16 man/roxygen/templates/seealso-methods.R | 2 man/roxygen/templates/slot-key.R | 8 man/roxygen/templates/slot-misc.R | 2 man/roxygen/templates/slot-stdassay.R | 40 man/s4list.Rd | 154 man/set-if-na.Rd | 90 man/set-if-null.Rd | 88 man/show-Assay-method.Rd | 50 man/show-DimReduc-method.Rd | 54 man/show-Graph-method.Rd | 42 man/show-LogMap-method.Rd | 38 man/show-Seurat-method.Rd | 42 man/show-SeuratCommand-method.Rd | 44 man/show-StdAssay-method.Rd | 66 man/show-oldseurat-method.Rd | 40 man/split.Assay.Rd | 98 man/split.Assay5.Rd | 166 man/split.Seurat.Rd | 116 man/split.StdAssay.Rd | 190 man/sub-.Assay.Rd | 120 man/sub-.Assay5.Rd | 90 man/sub-.DimReduc.Rd | 100 man/sub-.SeuratCommand.Rd | 70 man/sub-.StdAssay.Rd | 90 man/sub-LogMap-method.Rd | 132 man/sub-sub-.Assay.Rd | 156 man/sub-sub-.Assay5.Rd | 116 man/sub-sub-.DimReduc.Rd | 90 man/sub-sub-.Seurat.Rd | 174 man/sub-sub-.StdAssay.Rd | 156 man/sub-sub-LogMap-internal-method.Rd | 54 man/sub-subset-Seurat-NULL.Rd | 94 man/sub-subset-Seurat-character-missing-StdAssay-method.Rd | 96 man/sub-subset-Seurat.Rd | 138 man/subset.Assay.Rd | 88 man/subset.Assay5.Rd | 78 man/subset.DimReduc.Rd | 66 man/subset.Seurat.Rd | 146 man/subset.StdAssay.Rd | 82 man/v5-assay-summaries.Rd | 86 278 files changed, 34592 insertions(+), 34453 deletions(-)
Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation
and initialization of the following models
(1)- hidden hybrid Markov/semi-Markov model,
introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>,
(2)- nonparametric mixture of B-splines emissions (Langrock et al., 2015
<doi:10.1111/biom.12282>),
(3)- regime switching regression model
(Kim et al., 2008 <doi:10.1016/j.jeconom.2007.10.002>) and auto-regressive
hidden hybrid Markov/semi-Markov model,
(4)- spline-based nonparametric
estimation of additive state-switching models
(Langrock et al., 2018 <doi:10.1111/stan.12133>)
(5)- robust emission model proposed by
Qin et al, 2024 <doi:10.1007/s10479-024-05989-4>
(6)- several emission distributions, including mixture of multivariate normal
(which can also handle missing data using EM algorithm) and multi-nomial emission
(for modeling polymer or DNA sequences)
(7)- tools for prediction of future state sequence, computing the score of a new sequence,
spli [...truncated...]
Author: Morteza Amini [aut, cre, cph],
Afarin Bayat [aut],
Reza Salehian [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>
Diff between hhsmm versions 0.3.7 dated 2024-05-01 and 0.4.0 dated 2024-05-08
DESCRIPTION | 29 +++++++++++++++++++---------- MD5 | 8 ++++++-- NAMESPACE | 3 +++ R/drobust.R |only R/robust-mstep.R |only man/drobust.Rd |only man/robust_mstep.Rd |only 7 files changed, 28 insertions(+), 12 deletions(-)
Title: Evidential Regression
Description: An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.1109/TFUZZ.2023.3268200>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).
Author: Thierry Denoeux [aut, cre]
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evreg versions 1.0.4 dated 2024-04-22 and 1.1.0 dated 2024-05-08
evreg-1.0.4/evreg/R/evreg.R |only evreg-1.0.4/evreg/man/evreg.Rd |only evreg-1.1.0/evreg/DESCRIPTION | 10 - evreg-1.1.0/evreg/MD5 | 25 ++-- evreg-1.1.0/evreg/NEWS | 10 + evreg-1.1.0/evreg/R/Bel.R | 10 + evreg-1.1.0/evreg/R/evreg-package.R |only evreg-1.1.0/evreg/R/foncgrad_musigh.R | 32 ++++-- evreg-1.1.0/evreg/R/intervals.R | 12 +- evreg-1.1.0/evreg/build/partial.rdb |only evreg-1.1.0/evreg/inst/doc/Introduction.R | 34 +++--- evreg-1.1.0/evreg/inst/doc/Introduction.Rmd | 36 +++--- evreg-1.1.0/evreg/inst/doc/Introduction.html | 139 +++++++++++++-------------- evreg-1.1.0/evreg/man/evreg-package.Rd |only evreg-1.1.0/evreg/man/intervals.Rd | 1 evreg-1.1.0/evreg/vignettes/Introduction.Rmd | 36 +++--- 16 files changed, 195 insertions(+), 150 deletions(-)
Title: Univariate GARCH Models
Description: Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsgarch versions 1.0.0 dated 2024-04-24 and 1.0.2 dated 2024-05-08
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 12 ++++++++++++ build/partial.rdb |binary inst/doc/benchmark.html | 14 +++++++------- inst/doc/demonstration.html | 36 ++++++++++++++++++------------------ inst/doc/garch_models.pdf |binary src/TMB/tsgarch_TMBExports.cpp | 2 +- tests/testthat/test-simulation.R | 23 +++++++++++------------ 9 files changed, 60 insertions(+), 49 deletions(-)
Title: 'Rcpp' Integration for the 'Blaze' High-Performance 'C++' Math
Library
Description: Blaze is an open-source, high-performance 'C++' math library for dense and sparse arithmetic.
With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and
ease of use of a domain-specific language with HPC-grade performance, making it one of the most
intuitive and fastest 'C++' math libraries available. The 'RcppBlaze' package includes the header files
from the 'Blaze' library with disabling some functionalities related to link to the thread and system
libraries which make 'RcppBlaze' be a header-only library. Therefore, users do not need to install
'Blaze'.
Author: Ching-Chuan Chen [aut, cre, ctr]
,
Klaus Iglberger [aut] ,
Georg Georg [aut] ,
Tobias Scharpff [aut]
Maintainer: Ching-Chuan Chen <zw12356@gmail.com>
Diff between RcppBlaze versions 1.0.0 dated 2024-05-02 and 1.0.1 dated 2024-05-08
DESCRIPTION | 8 - MD5 | 44 +++++---- NAMESPACE | 6 + NEWS.md | 6 + R/RcppExports.R | 35 +++++++ R/flags.R | 9 +- README.md | 61 ++++++------- build/partial.rdb |binary inst/examples/lmBenchmark.R | 1 inst/include/RcppBlazeAs.h | 4 inst/include/RcppBlazeWrap.h | 6 - inst/tinytest/cpp/test-matrices.cpp | 10 -- inst/tinytest/cpp/test-vectors.cpp | 11 -- inst/tinytest/test_expr.R | 13 ++ inst/tinytest/test_matrix.R | 25 ++--- inst/tinytest/test_vector.R | 16 ++- inst/tinytest/test_views.R | 13 ++ man/blaze_seed.Rd |only man/blaze_threads.Rd |only man/fastLmPure.Rd | 2 src/RcppBlaze.cpp | 45 ++++++++++ src/RcppExports.cpp | 46 +++++++++- src/fastLm.cpp | 160 ++++++++++++++++++++---------------- src/registerDynamicSymbols.c | 8 + 24 files changed, 348 insertions(+), 181 deletions(-)
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Noah Greifer [ctb] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.20.0 dated 2024-05-06 and 0.20.1 dated 2024-05-08
DESCRIPTION | 56 +++++++++++++++++++++++------------------------ MD5 | 23 ++++++++++--------- NAMESPACE | 2 + NEWS.md | 6 +++++ R/bootstrap_simulation.R | 9 +++++-- R/get_contrasts.R | 5 ++++ R/inferences.R | 26 +++++++++++---------- R/methods_AER.R |only R/methods_survival.R | 20 ++++++++++++++++ R/predictions.R | 27 +++++++++------------- R/sanitize_type.R | 5 ++-- R/sanitize_variables.R | 2 - man/set_coef.Rd | 10 ++++++-- 13 files changed, 117 insertions(+), 74 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Create Tests According to QTI 2.1 Standard
Description: Create tests and tasks compliant with the Question & Test Interoperability (QTI) information model version 2.1. Input sources are Rmd/md description files or S4-class objects. Output formats include standalone zip or xml files. Supports the generation of basic task types (single and multiple choice, order, pair association, matching tables, filling gaps and essay) and provides a comprehensive set of attributes for customizing tests.
Author: Andrey Shevandrin [aut, cre, cph]
,
Petr Bondarenko [ctb] ,
Ivonne Ojeda [ctb],
Johannes Titz [aut, cph] ,
Brian Mottershead [cph] ,
Stiftung fuer Innovation in der Hochschullehre [fnd]
Maintainer: Andrey Shevandrin <shevandrin@gmail.com>
Diff between rqti versions 0.1.1 dated 2024-03-21 and 0.2.0 dated 2024-05-08
rqti-0.1.1/rqti/R/Order.R |only rqti-0.1.1/rqti/inst/imsqti_v2p1.xsd |only rqti-0.1.1/rqti/man/Order-class.Rd |only rqti-0.2.0/rqti/DESCRIPTION | 14 rqti-0.2.0/rqti/MD5 | 267 rqti-0.2.0/rqti/NAMESPACE | 194 rqti-0.2.0/rqti/NEWS.md | 27 rqti-0.2.0/rqti/R/AssessmentItem.R | 56 rqti-0.2.0/rqti/R/AssessmentSection.R | 9 rqti-0.2.0/rqti/R/AssessmentTest.R | 14 rqti-0.2.0/rqti/R/AssessmentTestOpal.R | 10 rqti-0.2.0/rqti/R/CorrectFeedback.R | 79 rqti-0.2.0/rqti/R/DirectedPair.R | 96 rqti-0.2.0/rqti/R/Entry.R | 57 rqti-0.2.0/rqti/R/Essay.R | 89 rqti-0.2.0/rqti/R/Gap.R | 4 rqti-0.2.0/rqti/R/InlineChoice.R | 53 rqti-0.2.0/rqti/R/MatchTable.R | 16 rqti-0.2.0/rqti/R/ModalFeedback.R | 21 rqti-0.2.0/rqti/R/MultipleChoice.R | 81 rqti-0.2.0/rqti/R/MultipleChoiceTable.R | 91 rqti-0.2.0/rqti/R/NumericGap.R | 221 rqti-0.2.0/rqti/R/OneInColTable.R | 91 rqti-0.2.0/rqti/R/OneInRowTable.R | 91 rqti-0.2.0/rqti/R/Ordering.R |only rqti-0.2.0/rqti/R/QtiMetadata.R |only rqti-0.2.0/rqti/R/SingleChoice.R | 83 rqti-0.2.0/rqti/R/TextGap.R | 163 rqti-0.2.0/rqti/R/TextGapOpal.R | 115 rqti-0.2.0/rqti/R/WrongFeedback.R | 81 rqti-0.2.0/rqti/R/api_opal.R | 65 rqti-0.2.0/rqti/R/character.R | 9 rqti-0.2.0/rqti/R/extract_results.R | 2 rqti-0.2.0/rqti/R/helpers.R | 6 rqti-0.2.0/rqti/R/knit_functions.R | 10 rqti-0.2.0/rqti/R/object_builder.R | 25 rqti-0.2.0/rqti/R/qti_task.R | 621 rqti-0.2.0/rqti/R/qti_test.R | 478 rqti-0.2.0/rqti/R/rqti.R | 6 rqti-0.2.0/rqti/R/rqti_project.R | 6 rqti-0.2.0/rqti/R/section_builder.R | 71 rqti-0.2.0/rqti/README.md | 8 rqti-0.2.0/rqti/inst/QTIJS/id_task_2599.xml |only rqti-0.2.0/rqti/inst/QTIJS/id_task_5293.xml |only rqti-0.2.0/rqti/inst/QTIJS/imsmanifest.xml |only rqti-0.2.0/rqti/inst/QTIJS/index.xml | 186 rqti-0.2.0/rqti/inst/QTIJS/qti.js |11476 +++++----- rqti-0.2.0/rqti/inst/QTIJS/rqti.js |only rqti-0.2.0/rqti/inst/QTIJS/test_identifier.xml |only rqti-0.2.0/rqti/inst/QTIJS/themecc/style.css | 601 rqti-0.2.0/rqti/inst/imsqti_v2p1p2.xsd |only rqti-0.2.0/rqti/inst/xsd |only rqti-0.2.0/rqti/man/AssessmentItem-class.Rd | 10 rqti-0.2.0/rqti/man/AssessmentSection-class.Rd | 2 rqti-0.2.0/rqti/man/AssessmentTest-class.Rd | 6 rqti-0.2.0/rqti/man/AssessmentTestOpal-class.Rd | 10 rqti-0.2.0/rqti/man/DirectedPair-class.Rd | 10 rqti-0.2.0/rqti/man/Entry-class.Rd | 12 rqti-0.2.0/rqti/man/Essay-class.Rd | 10 rqti-0.2.0/rqti/man/InlineChoice-class.Rd | 3 rqti-0.2.0/rqti/man/MatchTable-class.Rd | 10 rqti-0.2.0/rqti/man/MultipleChoice-class.Rd | 14 rqti-0.2.0/rqti/man/MultipleChoiceTable-class.Rd | 10 rqti-0.2.0/rqti/man/OneInColTable-class.Rd | 10 rqti-0.2.0/rqti/man/OneInRowTable-class.Rd | 10 rqti-0.2.0/rqti/man/Ordering-class.Rd |only rqti-0.2.0/rqti/man/QtiContributor-class.Rd |only rqti-0.2.0/rqti/man/QtiMetadata-class.Rd |only rqti-0.2.0/rqti/man/SingleChoice-class.Rd | 14 rqti-0.2.0/rqti/man/auth_opal.Rd | 4 rqti-0.2.0/rqti/man/correctFeedback.Rd |only rqti-0.2.0/rqti/man/createItemBody-methods.Rd | 10 rqti-0.2.0/rqti/man/createMetadata-methods.Rd |only rqti-0.2.0/rqti/man/createOutcomeDeclaration-methods.Rd | 2 rqti-0.2.0/rqti/man/createQtiTask-methods.Rd | 2 rqti-0.2.0/rqti/man/createResponseDeclaration-methods.Rd | 10 rqti-0.2.0/rqti/man/createResponseProcessing-methods.Rd | 10 rqti-0.2.0/rqti/man/create_qti_task.Rd | 2 rqti-0.2.0/rqti/man/directedPair.Rd |only rqti-0.2.0/rqti/man/entry.Rd |only rqti-0.2.0/rqti/man/essay.Rd |only rqti-0.2.0/rqti/man/extract_results.Rd | 2 rqti-0.2.0/rqti/man/gap_text.Rd | 102 rqti-0.2.0/rqti/man/getCalculator-methods.Rd | 2 rqti-0.2.0/rqti/man/getContributors-methods.Rd |only rqti-0.2.0/rqti/man/getFiles-methods.Rd | 2 rqti-0.2.0/rqti/man/getIdentifier-methods.Rd | 2 rqti-0.2.0/rqti/man/getObject-methods.Rd | 2 rqti-0.2.0/rqti/man/getPoints-methods.Rd | 2 rqti-0.2.0/rqti/man/get_resource_url.Rd | 4 rqti-0.2.0/rqti/man/get_resources.Rd | 4 rqti-0.2.0/rqti/man/inlineChoice.Rd |only rqti-0.2.0/rqti/man/modalFeedback.Rd |only rqti-0.2.0/rqti/man/multipleChoice.Rd |only rqti-0.2.0/rqti/man/multipleChoiceTable.Rd |only rqti-0.2.0/rqti/man/numericGap_doc.Rd |only rqti-0.2.0/rqti/man/oneInColTable.Rd |only rqti-0.2.0/rqti/man/oneInRowTable.Rd |only rqti-0.2.0/rqti/man/ordering.Rd |only rqti-0.2.0/rqti/man/qti_contributor.Rd |only rqti-0.2.0/rqti/man/qti_metadata.Rd |only rqti-0.2.0/rqti/man/singleChoice.Rd |only rqti-0.2.0/rqti/man/test.Rd | 19 rqti-0.2.0/rqti/man/test4opal.Rd | 25 rqti-0.2.0/rqti/man/textGapOpal_doc.Rd |only rqti-0.2.0/rqti/man/textGap_doc.Rd |only rqti-0.2.0/rqti/man/upload2opal.Rd | 11 rqti-0.2.0/rqti/man/wrongFeedback.Rd |only rqti-0.2.0/rqti/tests/testthat/file/csv/test_result_items_all_type_q.csv | 302 rqti-0.2.0/rqti/tests/testthat/file/rmd/DirectedPair_SimpleCalc.Rmd | 36 rqti-0.2.0/rqti/tests/testthat/file/rmd/DirectedPair_SimpleCalc_pdf.Rmd | 42 rqti-0.2.0/rqti/tests/testthat/file/xml/DirectedPair.xml | 170 rqti-0.2.0/rqti/tests/testthat/file/xml/DirectedPair_abbr.xml | 178 rqti-0.2.0/rqti/tests/testthat/file/xml/DirectedPair_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/Essay.xml | 50 rqti-0.2.0/rqti/tests/testthat/file/xml/Essay_without_Maxscore_Minscore.xml | 50 rqti-0.2.0/rqti/tests/testthat/file/xml/InlineChoice.xml | 132 rqti-0.2.0/rqti/tests/testthat/file/xml/InlineChoice_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/MultipleChoice.xml | 158 rqti-0.2.0/rqti/tests/testthat/file/xml/MultipleChoiceTable.xml | 230 rqti-0.2.0/rqti/tests/testthat/file/xml/MultipleChoiceTable_abbr.xml | 244 rqti-0.2.0/rqti/tests/testthat/file/xml/MultipleChoiceTable_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/MultipleChoice_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/NumericGap.xml | 124 rqti-0.2.0/rqti/tests/testthat/file/xml/OneInColTable.xml | 190 rqti-0.2.0/rqti/tests/testthat/file/xml/OneInColTable_abbr.xml | 192 rqti-0.2.0/rqti/tests/testthat/file/xml/OneInColTable_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/OneInRowTable.xml | 188 rqti-0.2.0/rqti/tests/testthat/file/xml/OneInRowTable_abbr.xml | 174 rqti-0.2.0/rqti/tests/testthat/file/xml/OneInRowTable_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/Order.xml | 264 rqti-0.2.0/rqti/tests/testthat/file/xml/Order_output_createQtiTask.xml | 152 rqti-0.2.0/rqti/tests/testthat/file/xml/Order_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/SingleChoice.xml | 144 rqti-0.2.0/rqti/tests/testthat/file/xml/SingleChoice_sign_more_less.xml |only rqti-0.2.0/rqti/tests/testthat/file/xml/TextGapOpal.xml | 136 rqti-0.2.0/rqti/tests/testthat/test-One_in_col_table.R | 14 rqti-0.2.0/rqti/tests/testthat/test-One_in_row_table.R | 14 rqti-0.2.0/rqti/tests/testthat/test-assessment_section.R | 602 rqti-0.2.0/rqti/tests/testthat/test-assessment_test.R | 1350 - rqti-0.2.0/rqti/tests/testthat/test-character.R | 54 rqti-0.2.0/rqti/tests/testthat/test-correct_feedback.R | 18 rqti-0.2.0/rqti/tests/testthat/test-directed_pair.R | 12 rqti-0.2.0/rqti/tests/testthat/test-essay.R | 147 rqti-0.2.0/rqti/tests/testthat/test-multiple_choice.R | 8 rqti-0.2.0/rqti/tests/testthat/test-multiple_choice_table.R | 21 rqti-0.2.0/rqti/tests/testthat/test-object_builder.R | 11 rqti-0.2.0/rqti/tests/testthat/test-qti_exam.R | 258 rqti-0.2.0/rqti/tests/testthat/test-qti_task.R | 692 rqti-0.2.0/rqti/tests/testthat/test-section_builder.R | 362 rqti-0.2.0/rqti/tests/testthat/test-single_choice.R | 378 rqti-0.2.0/rqti/tests/testthat/test-text_gap.R | 63 rqti-0.2.0/rqti/tests/testthat/test-text_order.R | 18 rqti-0.2.0/rqti/tests/testthat/test-wrong_feedback.R | 25 rqti-0.2.0/rqti/tests/testthat/test-xml_verification.R | 416 155 files changed, 12598 insertions(+), 10962 deletions(-)
Title: Logging for 'dplyr' and 'tidyr' Functions
Description: Provides feedback about 'dplyr' and 'tidyr' operations.
Author: Benjamin Elbers [aut, cre] ,
Damiano Oldoni [ctb]
Maintainer: Benjamin Elbers <elbersb@gmail.com>
Diff between tidylog versions 1.0.2 dated 2020-07-03 and 1.1.0 dated 2024-05-08
DESCRIPTION | 14 - MD5 | 57 ++-- NAMESPACE | 4 NEWS.md | 14 + R/filter.R | 11 R/group_by.R | 2 R/join.R | 62 +++- R/longer_wider.R | 16 + R/mutate.R | 12 R/tidylog.R | 15 + README.md | 92 ++++--- build/vignette.rds |binary inst/doc/benchmarks.R | 2 inst/doc/benchmarks.html | 459 +++++++++++++++++++++++-------------- man/count.Rd | 6 man/drop_na.Rd | 6 man/fill.Rd | 6 man/gather.Rd | 6 man/pivot_longer.Rd | 6 man/pivot_wider.Rd | 6 man/replace_na.Rd | 6 man/separate_wider_delim.Rd |only man/separate_wider_position.Rd |only man/separate_wider_regex.Rd |only man/spread.Rd | 6 man/transmute.Rd | 6 man/uncount.Rd | 6 tests/testthat/test_filter.R | 10 tests/testthat/test_join.R | 86 +++++- tests/testthat/test_longer_wider.R | 189 ++++++--------- tests/testthat/test_mutate.R | 30 ++ 31 files changed, 712 insertions(+), 423 deletions(-)
Title: Extract and Analyze Rivers from Elevation Data
Description: Seamless extraction of river networks from digital
elevation models data. The package allows analysis of digital
elevation models that can be either externally provided or
downloaded from open source repositories (thus interfacing
with the 'elevatr' package). Extraction is performed via the
'D8' flow direction algorithm of TauDEM (Terrain Analysis Using
Digital Elevation Models), thus interfacing with the 'traudem'
package. Resulting river networks are compatible with functions
from the 'OCNet' package. See Carraro (2023)
<doi:10.5194/hess-27-3733-2023> for a presentation of the package.
Author: Luca Carraro [cre, aut],
University of Zurich [cph, fnd]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between rivnet versions 0.4.1 dated 2024-04-16 and 0.4.2 dated 2024-05-08
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/doc/rivnet.html | 41 ++++++++++++++++++++--------------------- 4 files changed, 34 insertions(+), 29 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 1.3.0 dated 2024-05-03 and 1.3.1 dated 2024-05-08
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/oa2df.R | 24 ++++++++++++++---------- README.md | 29 +++++++++++++++++++---------- inst |only tests/testthat/test-oa_fetch.R | 6 ++++-- 7 files changed, 50 insertions(+), 30 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for rich multivariate data.
Credits to Mu Sigma for their continuous support throughout the development of the package.
Author: Zubin Dowlaty [aut],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between HVT versions 23.11.1 dated 2023-11-19 and 24.5.1 dated 2024-05-08
HVT-23.11.1/HVT/R/HVT.R |only HVT-23.11.1/HVT/R/exploded_hmap.R |only HVT-23.11.1/HVT/R/get_cell_id.R |only HVT-23.11.1/HVT/R/hvtHmap.R |only HVT-23.11.1/HVT/R/mlayerHVT.R |only HVT-23.11.1/HVT/R/multiNormalDist.R |only HVT-23.11.1/HVT/R/plotCells.R |only HVT-23.11.1/HVT/R/plotDiag.R |only HVT-23.11.1/HVT/R/predictHVT.R |only HVT-23.11.1/HVT/R/predictLayerHVT.R |only HVT-23.11.1/HVT/R/qeHistPlot.R |only HVT-23.11.1/HVT/R/removeOutliers.R |only HVT-23.11.1/HVT/R/sammonsProjection.R |only HVT-23.11.1/HVT/man/HVT.Rd |only HVT-23.11.1/HVT/man/diagPlot.Rd |only HVT-23.11.1/HVT/man/exploded_hmap.Rd |only HVT-23.11.1/HVT/man/get_cell_id.Rd |only HVT-23.11.1/HVT/man/hvtHmap.Rd |only HVT-23.11.1/HVT/man/mlayerHVT.Rd |only HVT-23.11.1/HVT/man/multiNormalDist.Rd |only HVT-23.11.1/HVT/man/plotCells.Rd |only HVT-23.11.1/HVT/man/plotDiag.Rd |only HVT-23.11.1/HVT/man/predictHVT.Rd |only HVT-23.11.1/HVT/man/predictLayerHVT.Rd |only HVT-23.11.1/HVT/man/qeHistPlot.Rd |only HVT-23.11.1/HVT/man/removeOutliers.Rd |only HVT-23.11.1/HVT/man/sammonsProjection.Rd |only HVT-23.11.1/HVT/vignettes/heatmaps |only HVT-23.11.1/HVT/vignettes/interactive.png |only HVT-23.11.1/HVT/vignettes/mlayer1.png |only HVT-23.11.1/HVT/vignettes/predictLayerHVT_function.png |only HVT-23.11.1/HVT/vignettes/predictLayerHVT_function_mapA.png |only HVT-23.11.1/HVT/vignettes/predictLayerHVT_function_mapB.png |only HVT-23.11.1/HVT/vignettes/predictLayerHVT_function_mapC.png |only HVT-23.11.1/HVT/vignettes/sample_dataset |only HVT-23.11.1/HVT/vignettes/torus.png |only HVT-23.11.1/HVT/vignettes/torus1.png |only HVT-23.11.1/HVT/vignettes/torus_donut.png |only HVT-24.5.1/HVT/DESCRIPTION | 28 HVT-24.5.1/HVT/MD5 | 139 - HVT-24.5.1/HVT/NAMESPACE | 41 HVT-24.5.1/HVT/R/Add_boundary_points.R | 55 HVT-24.5.1/HVT/R/Corrected_Tessellations.R | 66 HVT-24.5.1/HVT/R/DelaunayInfo.R | 114 - HVT-24.5.1/HVT/R/Delete_Outpoints.R | 4 HVT-24.5.1/HVT/R/Transform_Coordinates.R | 28 HVT-24.5.1/HVT/R/VQ_codebookSplit.R | 5 HVT-24.5.1/HVT/R/diagPlot.R | 42 HVT-24.5.1/HVT/R/displayTable.R |only HVT-24.5.1/HVT/R/edaPlots.R |only HVT-24.5.1/HVT/R/getCellId.R |only HVT-24.5.1/HVT/R/getCentroids.R | 3 HVT-24.5.1/HVT/R/getOptimalCentroids.R | 1 HVT-24.5.1/HVT/R/getTransitionProbability.R |only HVT-24.5.1/HVT/R/global.R | 11 HVT-24.5.1/HVT/R/hvq.R | 103 - HVT-24.5.1/HVT/R/madPlot.R | 43 HVT-24.5.1/HVT/R/plotAnimatedFlowmap.R |only HVT-24.5.1/HVT/R/plotHVT.R | 867 +++++++++++- HVT-24.5.1/HVT/R/plotModelDiagnostics.R |only HVT-24.5.1/HVT/R/plotNovelCells.R |only HVT-24.5.1/HVT/R/plotQuantErrorHistogram.R |only HVT-24.5.1/HVT/R/plotStateTransition.R |only HVT-24.5.1/HVT/R/reconcileTransitionProbability.R |only HVT-24.5.1/HVT/R/removeNovelty.R | 121 - HVT-24.5.1/HVT/R/scoreHVT.R |only HVT-24.5.1/HVT/R/scoreLayeredHVT.R |only HVT-24.5.1/HVT/R/trainHVT.R |only HVT-24.5.1/HVT/README.md | 163 +- HVT-24.5.1/HVT/build/vignette.rds |binary HVT-24.5.1/HVT/inst/doc/HVT.R | 9 HVT-24.5.1/HVT/inst/doc/HVT.Rmd | 124 + HVT-24.5.1/HVT/inst/doc/HVT.html | 367 ++--- HVT-24.5.1/HVT/man/VQ_codebookSplit.Rd | 2 HVT-24.5.1/HVT/man/displayTable.Rd |only HVT-24.5.1/HVT/man/edaPlots.Rd |only HVT-24.5.1/HVT/man/getCellId.Rd |only HVT-24.5.1/HVT/man/getTransitionProbability.Rd |only HVT-24.5.1/HVT/man/hvq.Rd | 16 HVT-24.5.1/HVT/man/madPlot.Rd | 38 HVT-24.5.1/HVT/man/plotAnimatedFlowmap.Rd |only HVT-24.5.1/HVT/man/plotHVT.Rd | 107 + HVT-24.5.1/HVT/man/plotModelDiagnostics.Rd |only HVT-24.5.1/HVT/man/plotNovelCells.Rd |only HVT-24.5.1/HVT/man/plotQuantErrorHistogram.Rd |only HVT-24.5.1/HVT/man/plotStateTransition.Rd |only HVT-24.5.1/HVT/man/reconcileTransitionProbability.Rd |only HVT-24.5.1/HVT/man/removeNovelty.Rd | 45 HVT-24.5.1/HVT/man/scoreHVT.Rd |only HVT-24.5.1/HVT/man/scoreLayeredHVT.Rd |only HVT-24.5.1/HVT/man/trainHVT.Rd |only HVT-24.5.1/HVT/tests/testthat/testhvt.R | 16 HVT-24.5.1/HVT/vignettes/HVT.Rmd | 124 + HVT-24.5.1/HVT/vignettes/hvt_result_diag.png |only HVT-24.5.1/HVT/vignettes/hvt_results_list.png |only HVT-24.5.1/HVT/vignettes/hvt_results_list_score.png |only HVT-24.5.1/HVT/vignettes/reference.png |binary HVT-24.5.1/HVT/vignettes/scoreLayeredHVT_function.png |only HVT-24.5.1/HVT/vignettes/scoreLayeredHVT_function_mapA.png |only HVT-24.5.1/HVT/vignettes/scoreLayeredHVT_function_mapB.png |only HVT-24.5.1/HVT/vignettes/scoreLayeredHVT_function_mapC.png |only 101 files changed, 1764 insertions(+), 918 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.8.2.1 dated 2024-04-15 and 0.12.8.3.0 dated 2024-05-08
ChangeLog | 16 +++++++++++ DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++----------- R/inline.R | 13 ++------- build/partial.rdb |binary build/vignette.rds |binary configure | 18 ++++++------ configure.ac | 2 - inst/NEWS.Rd | 12 ++++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/arma_version.hpp | 2 - inst/include/armadillo_bits/compiler_setup.hpp | 3 -- inst/include/armadillo_bits/config.hpp | 5 +++ inst/include/armadillo_bits/debug.hpp | 8 ++--- inst/include/armadillo_bits/fft_engine_fftw3.hpp | 32 ++++++++++++++++++++++- 16 files changed, 102 insertions(+), 47 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <ByrneL54@tcd.ie>
Diff between DImodelsMulti versions 1.1.0 dated 2024-04-15 and 1.1.1 dated 2024-05-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/DImulti_fit.R | 18 +++++++++++++++--- inst/doc/DImulti_onTheta.R | 10 ++++++++++ inst/doc/DImulti_onTheta.Rmd | 17 ++++++++++++++++- inst/doc/DImulti_onTheta.html | 14 +++++++++++++- vignettes/DImulti_onTheta.Rmd | 17 ++++++++++++++++- 7 files changed, 79 insertions(+), 15 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detail data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored an shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.0.7 dated 2023-02-16 and 1.1.7 dated 2024-05-08
TKCat-1.0.7/TKCat/inst/doc/TKCat-User-guide.R |only TKCat-1.0.7/TKCat/inst/doc/TKCat-User-guide.Rmd |only TKCat-1.0.7/TKCat/inst/doc/TKCat-User-guide.html |only TKCat-1.0.7/TKCat/inst/www/cerulean.css |only TKCat-1.0.7/TKCat/vignettes/TKCat-User-guide.Rmd |only TKCat-1.1.7/TKCat/DESCRIPTION | 15 TKCat-1.1.7/TKCat/MD5 | 101 ++++-- TKCat-1.1.7/TKCat/NAMESPACE | 44 ++ TKCat-1.1.7/TKCat/R/ClickHouse.R | 53 +-- TKCat-1.1.7/TKCat/R/KM-specifications.R |only TKCat-1.1.7/TKCat/R/KMR.R |only TKCat-1.1.7/TKCat/R/MDB.R | 29 + TKCat-1.1.7/TKCat/R/POK.R |only TKCat-1.1.7/TKCat/R/TKCat.R | 6 TKCat-1.1.7/TKCat/R/chMDB.R | 371 +++++++++++------------ TKCat-1.1.7/TKCat/R/chTKCat.R | 265 +++++++++++++--- TKCat-1.1.7/TKCat/R/file-management.R |only TKCat-1.1.7/TKCat/R/fileMDB.R | 22 - TKCat-1.1.7/TKCat/R/generics.R | 58 +++ TKCat-1.1.7/TKCat/R/km-data-model.R |only TKCat-1.1.7/TKCat/R/memoMDB.R | 1 TKCat-1.1.7/TKCat/R/metaMDB.R | 1 TKCat-1.1.7/TKCat/R/namespace.R | 4 TKCat-1.1.7/TKCat/R/other-helpers.R |only TKCat-1.1.7/TKCat/R/shiny-helpers.R | 274 ++++++++++++++-- TKCat-1.1.7/TKCat/build/vignette.rds |binary TKCat-1.1.7/TKCat/inst/ClickHouse/users.xml | 3 TKCat-1.1.7/TKCat/inst/KM-Data-Model |only TKCat-1.1.7/TKCat/inst/doc/TKCat-KMR-POK.R |only TKCat-1.1.7/TKCat/inst/doc/TKCat-KMR-POK.Rmd |only TKCat-1.1.7/TKCat/inst/doc/TKCat-KMR-POK.html |only TKCat-1.1.7/TKCat/inst/doc/TKCat.R |only TKCat-1.1.7/TKCat/inst/doc/TKCat.Rmd |only TKCat-1.1.7/TKCat/inst/doc/TKCat.html |only TKCat-1.1.7/TKCat/inst/pkgdown.yml | 9 TKCat-1.1.7/TKCat/inst/www/format_bytes.js |only TKCat-1.1.7/TKCat/man/add_feature_def.Rd |only TKCat-1.1.7/TKCat/man/add_helpers.Rd |only TKCat-1.1.7/TKCat/man/add_km_feature.Rd |only TKCat-1.1.7/TKCat/man/add_km_spec.Rd |only TKCat-1.1.7/TKCat/man/add_km_table.Rd |only TKCat-1.1.7/TKCat/man/add_property_values.Rd |only TKCat-1.1.7/TKCat/man/add_table_def.Rd |only TKCat-1.1.7/TKCat/man/add_table_features.Rd |only TKCat-1.1.7/TKCat/man/add_unit_def.Rd |only TKCat-1.1.7/TKCat/man/as_KMR.Rd |only TKCat-1.1.7/TKCat/man/create_KMR.Rd |only TKCat-1.1.7/TKCat/man/create_POK.Rd |only TKCat-1.1.7/TKCat/man/create_chTKCat_user.Rd | 2 TKCat-1.1.7/TKCat/man/db_reconnect.Rd | 8 TKCat-1.1.7/TKCat/man/decode_bin.Rd |only TKCat-1.1.7/TKCat/man/dims.Rd | 3 TKCat-1.1.7/TKCat/man/dot-format_bytes.Rd |only TKCat-1.1.7/TKCat/man/encode_bin.Rd |only TKCat-1.1.7/TKCat/man/get_KMR.Rd |only TKCat-1.1.7/TKCat/man/get_POK.Rd |only TKCat-1.1.7/TKCat/man/get_R_helpers.Rd |only TKCat-1.1.7/TKCat/man/get_chMDB_metadata.Rd |only TKCat-1.1.7/TKCat/man/get_km_spec.Rd |only TKCat-1.1.7/TKCat/man/has_km_spec.Rd |only TKCat-1.1.7/TKCat/man/is.KMR.Rd |only TKCat-1.1.7/TKCat/man/is.POK.Rd |only TKCat-1.1.7/TKCat/man/list_POKs.Rd |only TKCat-1.1.7/TKCat/man/list_feature_properties.Rd |only TKCat-1.1.7/TKCat/man/list_measurement_units.Rd |only TKCat-1.1.7/TKCat/man/list_measurements.Rd |only TKCat-1.1.7/TKCat/man/list_property_values.Rd |only TKCat-1.1.7/TKCat/man/list_table_features.Rd |only TKCat-1.1.7/TKCat/man/list_table_types.Rd |only TKCat-1.1.7/TKCat/man/list_tables.Rd | 19 - TKCat-1.1.7/TKCat/man/parse_R_helpers.Rd |only TKCat-1.1.7/TKCat/man/read_KMR.Rd |only TKCat-1.1.7/TKCat/man/rm_km_feature.Rd |only TKCat-1.1.7/TKCat/man/rm_km_table.Rd |only TKCat-1.1.7/TKCat/vignettes/EBKM-helpers.R |only TKCat-1.1.7/TKCat/vignettes/KMR-data-model.png |only TKCat-1.1.7/TKCat/vignettes/MDB-helpers.R |only TKCat-1.1.7/TKCat/vignettes/TKCat-KMR-POK.Rmd |only TKCat-1.1.7/TKCat/vignettes/TKCat.Rmd |only TKCat-1.1.7/TKCat/vignettes/TKCat.png |binary 80 files changed, 918 insertions(+), 370 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-24 0.3.17