Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph],
Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>
Diff between r2redux versions 1.0.16 dated 2023-09-19 and 1.0.17 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/r2_diff2.r | 7 +++++++ R/r_diff.r | 10 +++++++++- man/r2_diff.Rd | 7 +++++++ man/r_diff.Rd | 7 +++++++ 6 files changed, 38 insertions(+), 9 deletions(-)
Title: Dynamic Models for Survival Data
Description: Time-varying coefficient models for interval censored and
right censored survival data including
1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data studied by
Sinha et al. (1999) <doi:10.1111/j.0006-341X.1999.00585.x> and
Wang et al. (2013) <doi:10.1007/s10985-013-9246-8>,
2) Spline based time-varying coefficient Cox model for right censored data
proposed by Perperoglou et al. (2006) <doi:10.1016/j.cmpb.2005.11.006>, and
3) Transformation model with time-varying coefficients for right censored data
using estimating equations proposed by
Peng and Huang (2007) <doi:10.1093/biomet/asm058>.
Author: Wenjie Wang [aut, cre] ,
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between dynsurv versions 0.4-5 dated 2023-08-19 and 0.4-6 dated 2023-11-28
ChangeLog | 7 +++++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/CITATION | 2 +- src/GibbsSampler.h | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: R Interface to Google RE2 (C++) Regular Expression Library
Description: Pattern matching, extraction, replacement and other string
processing operations using Google's RE2 <https://github.com/google/re2>
regular-expression engine. Consistent interface (similar to 'stringr').
RE2 uses finite-automata based techniques, and offers a
fast and safe alternative to backtracking regular-expression engines
like those used in 'stringr', 'stringi' and other PCRE implementations.
Author: Girish Palya [aut, cre],
RE2 developers [ctb] ,
Google Inc. [ctb, cph]
Maintainer: Girish Palya <girishji@gmail.com>
Diff between re2 versions 0.1.2 dated 2022-03-29 and 0.1.3 dated 2023-11-28
re2-0.1.2/re2/src/re2google/benchlog.macbook-air |only re2-0.1.2/re2/src/re2google/benchlog/benchlog.c2 |only re2-0.1.2/re2/src/re2google/benchlog/benchlog.mini |only re2-0.1.2/re2/src/re2google/benchlog/benchlog.r70 |only re2-0.1.2/re2/src/re2google/benchlog/benchlog.wreck |only re2-0.1.2/re2/src/re2google/re2/dfa-e8910e85.o.tmp |only re2-0.1.3/re2/DESCRIPTION | 10 re2-0.1.3/re2/MD5 | 28 re2-0.1.3/re2/build/vignette.rds |binary re2-0.1.3/re2/inst/doc/re2_intro.R | 2 re2-0.1.3/re2/inst/doc/re2_intro.html | 571 ++++++++++++++------ re2-0.1.3/re2/inst/doc/re2_syntax.R | 2 re2-0.1.3/re2/inst/doc/re2_syntax.html | 402 +++++++++++--- re2-0.1.3/re2/man/re2_syntax.Rd | 2 re2-0.1.3/re2/src/Makevars | 2 re2-0.1.3/re2/src/Makevars.win | 2 re2-0.1.3/re2/src/re2google/util/logging.h | 2 re2-0.1.3/re2/tools/RE2Syntax.md | 2 18 files changed, 766 insertions(+), 259 deletions(-)
Title: Local Time Space Kriging
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively. The method is documented in Kumar et al (2013) <https://www.nature.com/articles/jes201352)>.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang <dliang@umces.edu>
Diff between ltsk versions 1.1.0 dated 2023-09-02 and 1.1.1 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/cmp_kriging.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.2.1 dated 2023-07-05 and 1.2.8 dated 2023-11-28
DESCRIPTION | 6 - MD5 | 39 +++++------ NAMESPACE | 5 - NEWS.md | 18 +++++ R/bgplot3d.R | 17 ++++ R/plotmath3d.R | 4 - R/r3d.rgl.R | 4 - R/rglwidget.R | 8 +- R/triangulate.R | 1 R/zzz.R | 16 ++-- inst/doc/WebGL.html | 106 ++++++++---------------------- inst/doc/demos.html | 18 ++--- inst/doc/deprecation.html | 4 - inst/doc/rgl.R | 4 - inst/doc/rgl.Rmd | 2 inst/doc/rgl.html | 12 +-- inst/htmlwidgets/lib/rglClass/init.src.js | 8 +- man/rgl.fns.Rd | 3 man/safe.dev.off.Rd |only src/x11gui.cpp | 2 vignettes/rgl.Rmd | 2 21 files changed, 137 insertions(+), 142 deletions(-)
Title: Compact Standard for Australian Phone Numbers
Description: Phone numbers are often represented as strings because there
is no obvious and suitable native representation for them. This leads
to high memory use and a lack of standard representation. The package
provides integer representation of Australian phone numbers with optional
raw vector calling code. The package name is an extension of 'au' and 'ph'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between dauphin versions 0.3.0 dated 2021-09-06 and 0.3.1 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only man/dauphin-package.Rd | 6 +----- src/CMobileCleaning.c | 8 ++++---- 5 files changed, 13 insertions(+), 16 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) <DOI:10.1186/s12859-017-1863-x> and the package vignette.
Author: Youyi Fong [cre],
Qianqian Chen [aut],
Shuangcheng Hua [aut],
Hyunju Son [aut],
Adam Elder [aut],
Tao Yang [aut],
Zonglin He [aut],
Simone Giannerini [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2023.1-30 dated 2023-01-31 and 2023.11-28 dated 2023-11-28
ChangeLog | 3 ++ DESCRIPTION | 10 ++++----- MD5 | 24 +++++++++++------------ R/chngptm.R | 10 ++++++--- inst/doc/chngpt-vignette.pdf |binary man/chngpt.test.Rd | 14 ++++++------- man/convert.coef.Rd | 24 +++++++++++------------ man/double.hinge.Rd | 44 +++++++++++++++++++++---------------------- man/hinge.test.Rd | 10 ++++----- man/performance.unit.test.Rd | 12 +++++------ man/sim.chngpt.Rd | 28 +++++++++++++-------------- man/sim.hinge.Rd | 20 +++++++++---------- src/error.h | 2 - 13 files changed, 104 insertions(+), 97 deletions(-)
Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform prior [...truncated...]
Author: Merlise Clyde [aut, cre, cph] ,
Michael Littman [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb],
Betsy Bersson [ctb],
Don van de Bergh [ctb],
Quanli Wang [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 1.6.4 dated 2022-11-02 and 1.6.6 dated 2023-11-28
BAS-1.6.4/BAS/R/gordy.R |only BAS-1.6.6/BAS/DESCRIPTION | 22 BAS-1.6.6/BAS/MD5 | 113 +- BAS-1.6.6/BAS/NEWS.md | 35 BAS-1.6.6/BAS/R/EB_global.R | 2 BAS-1.6.6/BAS/R/bas_glm.R | 93 +- BAS-1.6.6/BAS/R/bas_lm.R | 32 BAS-1.6.6/BAS/R/beta_priors.R | 2 BAS-1.6.6/BAS/R/coefficients.R | 26 BAS-1.6.6/BAS/R/cv_summary.R | 1 BAS-1.6.6/BAS/R/glm_fit.R | 22 BAS-1.6.6/BAS/R/hypergeometric2F1.R | 2 BAS-1.6.6/BAS/R/image.R | 4 BAS-1.6.6/BAS/R/plot.R | 2 BAS-1.6.6/BAS/R/plot_coef.R | 4 BAS-1.6.6/BAS/R/predict.R | 2 BAS-1.6.6/BAS/R/update.R | 4 BAS-1.6.6/BAS/README.md | 15 BAS-1.6.6/BAS/build/partial.rdb |binary BAS-1.6.6/BAS/build/vignette.rds |binary BAS-1.6.6/BAS/inst/CITATION | 4 BAS-1.6.6/BAS/inst/doc/BAS-vignette.R | 15 BAS-1.6.6/BAS/inst/doc/BAS-vignette.Rmd | 11 BAS-1.6.6/BAS/inst/doc/BAS-vignette.html | 559 ++++++------- BAS-1.6.6/BAS/man/bas.glm.Rd | 23 BAS-1.6.6/BAS/man/bas.lm.Rd | 9 BAS-1.6.6/BAS/man/bayesglm.fit.Rd | 2 BAS-1.6.6/BAS/man/intrinsic.Rd | 2 BAS-1.6.6/BAS/man/update.Rd | 4 BAS-1.6.6/BAS/src/E_ZS.c | 8 BAS-1.6.6/BAS/src/Makevars | 1 BAS-1.6.6/BAS/src/ZS_approx_full_np.c | 14 BAS-1.6.6/BAS/src/ZS_approx_null_np.c | 33 BAS-1.6.6/BAS/src/bas.h | 26 BAS-1.6.6/BAS/src/bayesglm.c | 21 BAS-1.6.6/BAS/src/betapriorfamily.c | 7 BAS-1.6.6/BAS/src/cch.c | 21 BAS-1.6.6/BAS/src/family.c | 86 +- BAS-1.6.6/BAS/src/glm_fit.c | 21 BAS-1.6.6/BAS/src/glm_lpy.c | 9 BAS-1.6.6/BAS/src/init.c | 4 BAS-1.6.6/BAS/src/lm_deterministic.c | 8 BAS-1.6.6/BAS/src/lm_mcmc.c | 259 ------ BAS-1.6.6/BAS/src/lm_mcmcbas.c | 745 +++++++----------- BAS-1.6.6/BAS/src/lm_sampleworep.c | 176 ---- BAS-1.6.6/BAS/src/mtherr.c | 5 BAS-1.6.6/BAS/src/tree_structures.c | 452 ++++++++++ BAS-1.6.6/BAS/tests/testthat/Rplots.pdf |binary BAS-1.6.6/BAS/tests/testthat/test-bas-glm.R | 85 ++ BAS-1.6.6/BAS/tests/testthat/test-bas-lm.R | 213 +++++ BAS-1.6.6/BAS/tests/testthat/test-coefficients.R | 54 + BAS-1.6.6/BAS/tests/testthat/test-glm-fit.R |only BAS-1.6.6/BAS/tests/testthat/test-image.R | 4 BAS-1.6.6/BAS/tests/testthat/test-outliers.R | 1 BAS-1.6.6/BAS/tests/testthat/test-plot.R | 10 BAS-1.6.6/BAS/tests/testthat/test-predict.R | 20 BAS-1.6.6/BAS/tests/testthat/test-special-functions.R | 11 BAS-1.6.6/BAS/tests/testthat/test-update.R |only BAS-1.6.6/BAS/vignettes/BAS-vignette.Rmd | 11 59 files changed, 1902 insertions(+), 1413 deletions(-)
Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder
reliability coefficient alpha and bootstrapped uncertainty estimates
(Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb]
Maintainer: Alexander Staudt <staudtlex@live.de>
Diff between icr versions 0.6.3 dated 2023-04-23 and 0.6.4 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/krippalpha.R | 31 ++++++++++++++++++++++--------- man/krippalpha.Rd | 2 +- 4 files changed, 30 insertions(+), 17 deletions(-)
Title: Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Description: Simplifies custom 'CSS' styling of both 'shiny' and
'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as
well as their various 'Bootswatch' themes. An interactive widget is
also provided for previewing themes in real time.
Author: Carson Sievert [aut, cre] ,
Joe Cheng [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd],
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Javi Aguilar [ctb, cph] ,
Thomas Park [ctb, cph] ,
PayPal [ctb, cph]
Maintainer: Carson Sievert <carson@posit.co>
Diff between bslib versions 0.6.0 dated 2023-11-21 and 0.6.1 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 ++++++++ R/sysdata.rda |binary inst/builtin/bs5/shiny/_rules.scss | 8 ++++++-- inst/components/dist/components.js | 2 +- inst/components/dist/components.min.js | 2 +- inst/components/dist/web-components.js | 2 +- inst/components/dist/web-components.min.js | 2 +- inst/css-precompiled/5/bootstrap.min.css | 2 +- inst/themer-demo/app.R | 2 +- 11 files changed, 33 insertions(+), 21 deletions(-)
Title: Information Analysis for Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.2.7 dated 2023-11-24 and 3.3.0 dated 2023-11-28
DESCRIPTION | 8 +-- MD5 | 10 ++-- R/ICC_plot.R | 9 +-- R/Sbinsmth.R | 2 R/TG_analysis.R | 15 +++--- R/make_dataList.R | 128 +++++++++++++++++++++++++++++++++++++----------------- 6 files changed, 113 insertions(+), 59 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.32 dated 2023-04-21 and 0.34 dated 2023-11-28
qtl2-0.32/qtl2/R/read_csv.R |only qtl2-0.32/qtl2/R/read_csv_numer.R |only qtl2-0.32/qtl2/man/read_csv.Rd |only qtl2-0.32/qtl2/man/read_csv_numer.Rd |only qtl2-0.34/qtl2/DESCRIPTION | 8 - qtl2-0.34/qtl2/MD5 | 85 +++++++++--------- qtl2-0.34/qtl2/NAMESPACE | 5 - qtl2-0.34/qtl2/NEWS.md | 27 +++++ qtl2-0.34/qtl2/R/RcppExports.R | 4 qtl2-0.34/qtl2/R/calc_geno_freq.R | 2 qtl2-0.34/qtl2/R/calc_het.R | 13 ++ qtl2-0.34/qtl2/R/calc_kinship.R | 7 - qtl2-0.34/qtl2/R/calc_raw_summaries.R | 4 qtl2-0.34/qtl2/R/drop_markers.R | 2 qtl2-0.34/qtl2/R/est_herit.R | 4 qtl2-0.34/qtl2/R/find_dup_markers.R |only qtl2-0.34/qtl2/R/fread_csv.R |only qtl2-0.34/qtl2/R/fread_csv_numer.R |only qtl2-0.34/qtl2/R/read_cross2.R | 32 +++--- qtl2-0.34/qtl2/R/read_pheno.R | 8 - qtl2-0.34/qtl2/R/reduce_markers.R | 2 qtl2-0.34/qtl2/R/scan1.R | 4 qtl2-0.34/qtl2/R/scan1blup.R | 2 qtl2-0.34/qtl2/README.md | 1 qtl2-0.34/qtl2/build/partial.rdb |binary qtl2-0.34/qtl2/data/CCaltcolors.RData |binary qtl2-0.34/qtl2/data/CCcolors.RData |binary qtl2-0.34/qtl2/data/CCorigcolors.RData |binary qtl2-0.34/qtl2/man/calc_geno_freq.Rd | 3 qtl2-0.34/qtl2/man/calc_het.Rd | 10 ++ qtl2-0.34/qtl2/man/calc_kinship.Rd | 7 - qtl2-0.34/qtl2/man/calc_raw_geno_freq.Rd | 2 qtl2-0.34/qtl2/man/calc_raw_het.Rd | 2 qtl2-0.34/qtl2/man/drop_markers.Rd | 2 qtl2-0.34/qtl2/man/est_herit.Rd | 4 qtl2-0.34/qtl2/man/find_dup_markers.Rd |only qtl2-0.34/qtl2/man/fread_csv.Rd |only qtl2-0.34/qtl2/man/fread_csv_numer.Rd |only qtl2-0.34/qtl2/man/reduce_markers.Rd | 3 qtl2-0.34/qtl2/man/scan1.Rd | 4 qtl2-0.34/qtl2/man/scan1blup.Rd | 2 qtl2-0.34/qtl2/src/RcppExports.cpp | 15 +++ qtl2-0.34/qtl2/src/chisq_colpairs.cpp | 2 qtl2-0.34/qtl2/src/cross_risib8.cpp | 2 qtl2-0.34/qtl2/src/find_dup_markers.cpp |only qtl2-0.34/qtl2/src/find_dup_markers.h |only qtl2-0.34/qtl2/src/r_message.cpp | 2 qtl2-0.34/qtl2/tests/testthat/test-chisq_colpairs.R | 6 + qtl2-0.34/qtl2/tests/testthat/test-find_dup_markers.R |only qtl2-0.34/qtl2/tests/testthat/test-read_issues.R | 12 +- 50 files changed, 195 insertions(+), 93 deletions(-)
Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.
Author: Eugenio Lopez-Cortegano [aut, cre]
Maintainer: Eugenio Lopez-Cortegano <elcortegano@gmail.com>
Diff between purgeR versions 1.8 dated 2023-08-16 and 1.8.2 dated 2023-11-28
DESCRIPTION | 8 ++-- MD5 | 29 ++++++++-------- NEWS.md | 9 +++++ R/purgeR.R | 74 +++++++++++++++++++++--------------------- inst/CITATION | 2 - inst/doc/ip.R | 2 - inst/doc/ip.Rmd | 8 ++-- inst/doc/ip.html | 10 ++--- inst/doc/purgeR-tutorial.R | 2 - inst/doc/purgeR-tutorial.Rmd | 6 +-- inst/doc/purgeR-tutorial.html | 8 ++-- inst/shiny |only man/purgeR.Rd | 70 +++++++++++++++++++++------------------ src/error.h | 3 - vignettes/ip.Rmd | 8 ++-- vignettes/purgeR-tutorial.Rmd | 6 +-- 16 files changed, 130 insertions(+), 115 deletions(-)
Title: Cleans and Normalizes FLUOstar DBF and DAT Files
Description: Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Author: Tingwei Adeck [aut, cre],
normfluodbf authors [cph]
Maintainer: Tingwei Adeck <awesome.tingwei@outlook.com>
Diff between normfluodbf versions 1.5.1 dated 2023-11-20 and 1.5.2 dated 2023-11-28
DESCRIPTION | 6 MD5 | 110 +- NAMESPACE | 13 NEWS.md | 4 R/actual_cols_used.R |only R/check_dirs.R |only R/clean_odddat_optimus.R | 7 R/dat_col_names_horizontal.R | 24 R/dat_col_names_optimus.R | 36 R/dat_col_names_prime.R | 27 R/dat_col_names_rigid.R | 19 R/data.R | 160 ++-- R/ggplot_tnp.R | 11 R/normfluodat.R | 1111 ++++++++++++++++++++---------- R/normfluodatfull.R |only R/normfluodatlite.R |only R/normfluordat.R | 151 +++- R/ntdbf_subordinates.R | 386 +++++----- R/resample_dat.R | 8 R/resample_dat_alt.R | 5 R/resample_dat_scale.R | 113 ++- R/resample_dat_scale_alt.R | 124 ++- R/resample_dat_scale_alt_bf.R |only R/resample_dat_scale_optimus.R | 201 ++++- R/time_attribute.R |only README.md | 74 + build/vignette.rds |binary data/dat_4.rda |only data/dat_5.rda |only data/dat_6.rda |only data/dat_7.rda |only inst/doc/normfluodbf.Rmd | 12 inst/doc/normfluodbf.html | 17 inst/doc/test_file.R |only inst/doc/test_file.Rmd |only inst/doc/test_file.html |only inst/extdata/dat_4.dat |only inst/extdata/dat_5.dat |only inst/extdata/dat_6.dat |only inst/extdata/dat_7.dat |only man/actual_cols_used.Rd |only man/check_dat.Rd |only man/check_dbf.Rd |only man/dat_1.Rd | 2 man/dat_2.Rd | 2 man/dat_3.Rd | 2 man/dat_4.Rd |only man/dat_5.Rd |only man/dat_6.Rd |only man/dat_7.Rd |only man/dat_col_names_horizontal.Rd | 6 man/dat_col_names_optimus.Rd | 5 man/dat_col_names_prime.Rd | 8 man/dat_col_names_rigid.Rd | 5 man/ggplot_tnp.Rd | 10 man/norm_applier.Rd |only man/normfluodat.Rd | 18 man/normfluodatfull.Rd |only man/normfluodatlite.Rd |only man/normfluordat.Rd | 116 +-- man/resample_dat.Rd | 6 man/resample_dat_alt.Rd | 5 man/resample_dat_scale.Rd | 2 man/resample_dat_scale_alt.Rd | 4 man/resample_dat_scale_alt_bf_na.Rd |only man/resample_dat_scale_alt_bfv.Rd |only man/resample_dat_scale_alt_na.Rd |only man/resample_dat_scale_naretainer.Rd |only man/resample_dat_scale_optimus_backend.Rd |only man/resample_dat_scale_optimus_na.Rd |only man/time_attribute.Rd |only vignettes/img/qc_fun.jpg |only vignettes/normfluodbf.Rmd | 12 vignettes/test_file.Rmd |only 74 files changed, 1949 insertions(+), 873 deletions(-)
Title: A Seamless Integration of 'EViews' and R
Description: It allows running 'EViews' (<https://eviews.com>) program from R, R Markdown and Quarto documents. 'EViews' (Econometric Views) is a statistical software for Econometric analysis. This package integrates 'EViews' and R and also serves as an 'EViews' Knit-Engine for 'knitr' package. Write all your 'EViews' commands in R, R Markdown or Quarto documents. For details, please consult our peer-review article Mati S., Civcir I. and Abba S.I (2023) <doi:10.32614/RJ-2023-045>.
Author: Sagiru Mati [aut, cre]
Maintainer: Sagiru Mati <sagirumati@gmail.com>
Diff between EviewsR versions 0.1.5 dated 2022-08-23 and 0.1.6 dated 2023-11-28
DESCRIPTION | 14 MD5 | 82 ++-- NEWS.md | 16 R/eng_eviews.R | 42 +- R/eviews_graph.R | 7 R/import_graph.R | 4 R/utils.R | 39 + README.md | 95 +++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 30 + inst/doc/EviewsR.Rmd | 115 +++-- inst/doc/EviewsR.html | 163 ++++---- inst/examples/EVIEWS_IMPORT.wf1 |only inst/examples/EVIEWS_IMPORT1.wf1 |only inst/examples/EVIEWS_WFCREATE.wf1 |only inst/examples/EVIEWS_WFCREATE1.wf1 |only inst/examples/EXEC_COMMANDS.wf1 |only inst/examples/EXPORT_DATAFRAME.wf1 |only inst/examples/EviewsR.pdf |only inst/examples/EviewsR_workfile.wf1 |only inst/examples/eviews_import.csv |only inst/examples/pagesave.csv |only inst/examples/wfsave.csv |only inst/figures/eviewsgraph-eviewsrpage-x.pdf |only inst/figures/eviewsgraph-eviewsrpage-x.png |binary inst/figures/eviewsgraph-eviewsrpage-y.pdf |only inst/figures/eviewsgraph-eviewsrpage-y.png |binary inst/figures/eviewsgraph1-eviewsgraph1-xy.pdf |only inst/figures/eviewsgraph1-eviewsgraph1-xy.png |binary inst/figures/eviewsgraph2-eviewsrpage-xy.pdf |only inst/figures/eviewsgraph2-eviewsrpage-xy.png |binary inst/figures/eviewsreviewsrpage-xx.pdf |only inst/figures/eviewsreviewsrpage-xx.png |binary inst/figures/eviewsreviewsrpage-yy.pdf |only inst/figures/eviewsreviewsrpage-yy.png |binary inst/figures/fig-importgraph-eviewsrpage-xx.pdf |only inst/figures/fig-importgraph-eviewsrpage-xx.png |binary inst/figures/fig-importgraph-eviewsrpage-yy.pdf |only inst/figures/fig-importgraph-eviewsrpage-yy.png |binary inst/figures/fig-importgraph1-eviewspage-x_graph.pdf |only inst/figures/fig-importgraph1-eviewspage-x_graph.png |binary inst/figures/fig-importgraph1-eviewspage1-x_graph.pdf |only inst/figures/fig-importgraph1-eviewspage1-x_graph.png |binary inst/figures/fig-importworkfile-eviewsrpage-xx.pdf |only inst/figures/fig-importworkfile-eviewsrpage-xx.png |binary inst/figures/fig-importworkfile-eviewsrpage-yy.pdf |only inst/figures/fig-importworkfile-eviewsrpage-yy.png |binary inst/figures/fig-rwalk-1.pdf |only inst/figures/fig-rwalk-2.pdf |only inst/figures/fig-rwalk-2.png |binary man/EviewsR-package.Rd | 90 ++-- man/import_kable.Rd | 366 +++++++++--------- vignettes/EviewsR.Rmd | 115 +++-- vignettes/EviewsR_workfile.wf1 |binary 55 files changed, 724 insertions(+), 454 deletions(-)
Title: Create, and Refine Data Nuggets
Description: Creating, and refining data nuggets.
Data nuggets reduce a large dataset into a small collection of nuggets of
data, each containing a center (location), weight (importance), and scale
(variability) parameter. Data nugget centers are created by choosing
observations in the dataset which are as equally spaced apart as possible.
Data nugget weights are created by counting the number observations
closest to a given data nugget’s center. We then say the data nugget
'contains' these observations and the data nugget center is recalculated
as the mean of these observations. Data nugget scales are created by
calculating the trace of the covariance matrix of the observations
contained within a data nugget divided by the dimension of the dataset.
Data nuggets are refined by 'splitting' data nuggets which have scales or
shapes (defined as the ratio of the two largest eigenvalues of the
covariance matrix of the observations contained within the data nugget)
Reference paper: [1] Cherasia, K. E., Ca [...truncated...]
Author: Yajie Duan [cre, ctb],
Traymon Beavers [aut],
Javier Cabrera [aut],
Ge Cheng [aut],
Kunting Qi [aut],
Mariusz Lubomirski [aut]
Maintainer: Yajie Duan <yajieritaduan@gmail.com>
Diff between datanugget versions 1.2.2 dated 2023-10-26 and 1.2.4 dated 2023-11-28
DESCRIPTION | 8 +- MD5 | 4 - R/createDNcenters.R | 149 +++++++++++++++++++++++++++++++++++++++++++--------- 3 files changed, 130 insertions(+), 31 deletions(-)
Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>
Diff between distances versions 0.1.9 dated 2023-01-27 and 0.1.10 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/error.c | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Disk-Based Constrained Change-Point Detection
Description: Disk-based implementation of
Functional Pruning Optimal Partitioning with up-down constraints
<doi:10.18637/jss.v101.i10> for single-sample peak calling
(independently for each sample and genomic problem),
can handle huge data sets (10^7 or more).
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegDisk versions 2023.9.4 dated 2023-09-06 and 2023.11.27 dated 2023-11-28
DESCRIPTION | 6 MD5 | 103 +-- NAMESPACE | 40 - NEWS | 124 ++- R/PeakSegFPOP_df.R | 268 ++++---- R/PeakSegFPOP_dir.R | 564 +++++++++--------- R/PeakSegFPOP_file.R | 250 ++++---- R/PeakSegFPOP_vec.R | 156 ++--- R/col.name.list.R | 88 +- R/fread.R | 242 +++---- R/sequentialSearch_dir.R | 306 ++++----- R/writeBedGraph.R | 118 +-- build/vignette.rds |binary inst/CITATION | 46 - inst/doc/Examples.R | 266 ++++---- inst/doc/Examples.Rnw | 808 +++++++++++++------------- inst/doc/Examples.pdf |binary inst/doc/Spatial_correlation.R | 370 +++++------ inst/doc/Spatial_correlation.Rmd | 514 ++++++++-------- inst/doc/Spatial_correlation.html | 870 ++++++++++++++-------------- inst/doc/Worst_case.R | 152 ++-- inst/doc/Worst_case.Rmd | 200 +++--- inst/doc/Worst_case.html | 552 ++++++++--------- man/ChIPreads.Rd | 72 +- man/Mono27ac.Rd | 78 +- man/PeakSegFPOP_df.Rd | 198 +++--- man/PeakSegFPOP_dir.Rd | 298 ++++----- man/PeakSegFPOP_file.Rd | 150 ++-- man/PeakSegFPOP_vec.Rd | 140 ++-- man/coef.PeakSegFPOP_df.Rd | 42 - man/coef.PeakSegFPOP_dir.Rd | 38 - man/col.name.list.Rd | 88 +- man/fread.first.Rd | 104 +-- man/fread.last.Rd | 104 +-- man/plot.PeakSegFPOP_df.Rd | 38 - man/plot.PeakSegFPOP_dir.Rd | 38 - man/sequentialSearch_dir.Rd | 160 ++--- man/summary.PeakSegFPOP_dir.Rd | 38 - man/wc2int.Rd | 34 - man/writeBedGraph.Rd | 88 +- src/funPieceListLog.cpp | 2 tests/testthat.R | 10 tests/testthat/test-CRAN-PeakSegFPOP_dir.R | 368 +++++------ tests/testthat/test-CRAN-PeakSegFPOP_file.R | 138 ++-- tests/testthat/test-CRAN-PeakSegFPOP_vec.R | 32 - tests/testthat/test-CRAN-bad-paths.R | 36 - tests/testthat/test-CRAN-cpp-errors.R | 406 ++++++------- tests/testthat/test-CRAN-sequentialSearch.R | 52 - tests/testthat/test-CRAN-wc2int.R | 70 +- vignettes/Examples.Rnw | 808 +++++++++++++------------- vignettes/Spatial_correlation.Rmd | 514 ++++++++-------- vignettes/Worst_case.Rmd | 200 +++--- vignettes/seconds.csv |only 53 files changed, 5196 insertions(+), 5191 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written t [...truncated...]
Author: Lucas A. Nell [cph, aut, cre]
Maintainer: Lucas A. Nell <lucnell@gmail.com>
Diff between jackalope versions 1.1.4 dated 2023-10-15 and 1.1.5 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/read_write.R | 18 ++++++++++++++++-- inst/doc/jackalope-intro.html | 2 +- src/io_vcf.cpp | 13 ------------- src/ref_classes.h | 8 +++++--- src/util.cpp | 5 +++-- tests/testthat/test-variants_coal.R | 12 ++++++++++++ tests/testthat/test-vcf_IO.R | 2 ++ 9 files changed, 50 insertions(+), 32 deletions(-)
Title: Access and Analyze Data from 'DeFiLlama'
Description: Provides an interface to access and analyze data from
'DeFiLlama'<https://defillama.com>. This package simplifies the
process of fetching and manipulating 'DeFiLlama' data for further
analysis and visualization.
Author: Alexey Ivanov [aut, cre, cph]
Maintainer: Alexey Ivanov <twor.2r@gmail.com>
Diff between rllama versions 0.2.0 dated 2023-11-17 and 0.4.3 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++++++------- NEWS.md | 22 +++++++++++++++++++++- R/get_defillama_chain_hist_tvl.R |only R/get_defillama_chain_tvl.R | 23 ++++++++++++++++------- R/get_defillama_protocol_hist_tvl.R |only R/get_defillama_protocol_tvl.R | 16 ++++++++++++---- R/get_defillama_stablecoin_data.R |only R/get_defillama_stablecoin_hist_data.R |only README.md | 26 +++++++++++++++----------- man/get_defillama_chain_hist_tvl.Rd |only man/get_defillama_chain_tvl.Rd | 4 ++-- man/get_defillama_protocol_hist_tvl.Rd |only man/get_defillama_protocol_tvl.Rd | 10 +++++++--- man/get_defillama_stablecoin_data.Rd |only man/get_defillama_stablecoin_hist_data.Rd |only 16 files changed, 91 insertions(+), 38 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 fil [...truncated...]
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.21 dated 2023-01-06 and 1.22 dated 2023-11-28
ChangeLog | 2 + DESCRIPTION | 8 +++---- MD5 | 14 ++++++------- R/ncdf4.R | 10 +++++++-- R/ncdf4_priv.R | 2 + R/ncdf4_priv_var.R | 4 +++ man/ancvar_put.Rd | 12 ++++++++++- src/ncdf.c | 55 +++++++++++++++++++++++++++-------------------------- 8 files changed, 67 insertions(+), 40 deletions(-)
Title: Plots of the Empirical Attainment Function
Description: Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Marco Chiarandini [aut],
Carlos Fonseca [aut],
Luis Paquete [aut],
Thomas Stuetzle [aut],
Mickael Binois [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between eaf versions 2.4.1 dated 2023-03-14 and 2.5 dated 2023-11-28
eaf-2.4.1/eaf/src/mo-tools/hv_contrib.h |only eaf-2.4.1/eaf/tests/eafplot.Rout.saved |only eaf-2.4.1/eaf/tests/lin-sph.R |only eaf-2.4.1/eaf/tests/lin.S-sph.S-diff.txt.xz |only eaf-2.4.1/eaf/tests/lin.S.txt |only eaf-2.4.1/eaf/tests/ran.100pts.3d.10 |only eaf-2.4.1/eaf/tests/ran.100pts.3d.10.R |only eaf-2.4.1/eaf/tests/sph.S.txt |only eaf-2.5/eaf/DESCRIPTION | 12 + eaf-2.5/eaf/MD5 | 117 +++++++++-------- eaf-2.5/eaf/NEWS.md | 32 ++-- eaf-2.5/eaf/R/eaf.R | 54 ++++---- eaf-2.5/eaf/R/eafplot.R | 138 ++++++++++----------- eaf-2.5/eaf/R/igd.R | 18 +- eaf-2.5/eaf/R/interactive.R | 2 eaf-2.5/eaf/R/nondominated.R | 2 eaf-2.5/eaf/R/normalise.R | 14 +- eaf-2.5/eaf/R/read_datasets.R | 2 eaf-2.5/eaf/R/vorob.R | 30 ++-- eaf-2.5/eaf/R/whv.R | 5 eaf-2.5/eaf/README.md | 49 +++++-- eaf-2.5/eaf/build/partial.rdb |binary eaf-2.5/eaf/cleanup | 2 eaf-2.5/eaf/inst/REFERENCES.bib | 2 eaf-2.5/eaf/inst/WORDLIST |only eaf-2.5/eaf/man/attsurf2df.Rd | 2 eaf-2.5/eaf/man/choose_eafdiffplot.Rd | 2 eaf-2.5/eaf/man/eafdiffplot.Rd | 2 eaf-2.5/eaf/man/eafplot.Rd | 18 +- eaf-2.5/eaf/man/eafs.Rd | 2 eaf-2.5/eaf/man/igd.Rd | 18 +- eaf-2.5/eaf/man/normalise.Rd | 8 - eaf-2.5/eaf/man/pdf_crop.Rd | 6 eaf-2.5/eaf/man/whv_hype.Rd | 5 eaf-2.5/eaf/man/write_datasets.Rd | 2 eaf-2.5/eaf/src/Reaf.c | 2 eaf-2.5/eaf/src/eaf/eaf.h | 8 - eaf-2.5/eaf/src/eaf/eaf3d.c | 115 +++++++++-------- eaf-2.5/eaf/src/eaf/gcc.mk | 2 eaf-2.5/eaf/src/eaf/svn_version | 2 eaf-2.5/eaf/src/mo-tools/gcc.mk | 2 eaf-2.5/eaf/src/mo-tools/svn_version | 2 eaf-2.5/eaf/src/mo-tools/whv.c | 2 eaf-2.5/eaf/tests/eafplot.R | 24 --- eaf-2.5/eaf/tests/spelling.R |only eaf-2.5/eaf/tests/testthat/_snaps |only eaf-2.5/eaf/tests/testthat/helper-common.R | 30 ++++ eaf-2.5/eaf/tests/testthat/lin.S-sph.S-diff.txt.xz |only eaf-2.5/eaf/tests/testthat/lin.S.txt |only eaf-2.5/eaf/tests/testthat/sph.S.txt |only eaf-2.5/eaf/tests/testthat/test-eaf.R | 26 +++ eaf-2.5/eaf/tests/testthat/test-eafdiffplot.R | 1 eaf-2.5/eaf/tests/testthat/test-eafplot-list.R | 42 ++++-- eaf-2.5/eaf/tests/testthat/test-eafplot.R | 74 +++++++---- eaf-2.5/eaf/tests/testthat/test-hv.R | 2 eaf-2.5/eaf/tests/testthat/test-normalise.R | 3 eaf-2.5/eaf/tests/testthat/test-pareto-rank.R | 1 eaf-2.5/eaf/tests/testthat/test-vorob.R | 3 eaf-2.5/eaf/tests/testthat/test-whv.R | 1 eaf-2.5/eaf/tests/testthat/test-whv_hype.R | 1 eaf-2.5/eaf/tests/testthat/test-write_datasets.R | 1 eaf-2.5/eaf/tools/winlibs.R | 4 62 files changed, 496 insertions(+), 396 deletions(-)
Title: Fitting a Bayesian Sparse Latent Factor Model in Gene Expression
Analysis
Description: Set of tools to find coherent patterns in gene expression (microarray) data using a Bayesian Sparse Latent Factor Model (SLFM) <DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put to build a fast and memory efficient package, which makes this proposal an interesting and computationally convenient alternative to study patterns of gene expressions exhibited in matrices. The package contains the implementation of two versions of the model based on different mixture priors for the loadings: one relies on a degenerate component at zero and the other uses a small variance normal distribution for the spike part of the mixture.
Author: Vinicius Mayrink [aut, cre],
Joao Duarte [aut]
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Diff between slfm versions 1.0.1 dated 2020-03-15 and 1.0.2 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 1 + NEWS | 6 ++++++ R/slfm.r | 8 +++++++- R/slfm_package.r | 1 + man/print.slfm.Rd |only man/slfm_package.Rd | 1 + 8 files changed, 27 insertions(+), 11 deletions(-)
Title: Low-Level Browser Automation Interface
Description: An implementation of 'W3C WebDriver 2.0'
(<https://w3c.github.io/webdriver/>), allowing interaction
with a 'Selenium Server' (<https://www.selenium.dev/documentation/grid/>)
instance from 'R'. Allows a web browser to be automated from 'R'.
Author: Ashby Thorpe [aut, cre, cph]
Maintainer: Ashby Thorpe <ashbythorpe@gmail.com>
Diff between selenium versions 0.1.2 dated 2023-10-28 and 0.1.3 dated 2023-11-28
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 20 ++ R/commands.R | 50 ++--- R/element.R | 165 +++++++++++++---- R/server.R | 70 ++++++- R/session.R | 362 +++++++++++++++++++++++++++++---------- R/status.R | 19 +- README.md | 8 man/SeleniumSession.Rd | 354 +++++++++++++++++++++++++++++++++----- man/ShadowRoot.Rd | 12 + man/WebElement.Rd | 152 ++++++++++++++-- man/selenium_server.Rd | 9 man/selenium_server_available.Rd | 22 +- 14 files changed, 1019 insertions(+), 258 deletions(-)
Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization,
Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a (potentially very sparse
or having many missing values) matrix 'X' as the product of two low-dimensional matrices,
optionally aided with secondary information matrices about rows and/or columns of 'X',
which are also factorized using the same latent components.
The intended usage is for recommender systems, dimensionality reduction, and missing value imputation.
Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce
different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky,
(2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model,
(Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>),
or the enhanced model with 'implicit features' (Rendle, Zhang,
Koren, (2019) <arXiv:1905.01395>), with [...truncated...]
Author: David Cortes [aut, cre, cph],
Jorge Nocedal [cph] ,
Naoaki Okazaki [cph] ,
David Blackman [cph] ,
Sebastiano Vigna [cph] ,
NumPy Developers [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between cmfrec versions 3.5.1-1 dated 2023-04-11 and 3.5.1-2 dated 2023-11-28
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++++--------- R/cmfrec.R |only R/fit.R | 46 +++++++------------------------------------- build/vignette.rds |binary man/cmfrec.Rd |only man/fit.Rd | 55 ++++++++++++++--------------------------------------- src/cmfrec.h | 14 +++++-------- src/collective.c | 29 +++++++++------------------ src/common.c | 37 +++++++++++++++++------------------ src/helpers.c | 35 +++++++++++++-------------------- src/offsets.c | 20 ++++++------------- 12 files changed, 92 insertions(+), 170 deletions(-)
Title: Design Shaded Contour Lines (or Tanaka) Maps
Description: The Tanaka method enhances the representation of topography on
a map using shaded contour lines. In this simplified implementation of
the method, north-west white contours represent illuminated topography
and south-east black contours represent shaded topography. See Tanaka
(1950) <doi:10.2307/211219>.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between tanaka versions 0.3.0 dated 2022-07-04 and 0.4.0 dated 2023-11-28
tanaka-0.3.0/tanaka/R/legend.R |only tanaka-0.4.0/tanaka/DESCRIPTION | 10 +++++----- tanaka-0.4.0/tanaka/MD5 | 15 +++++++-------- tanaka-0.4.0/tanaka/NAMESPACE | 7 +------ tanaka-0.4.0/tanaka/NEWS.md | 6 ++++++ tanaka-0.4.0/tanaka/R/tanaka.R | 24 ++++++++++++++---------- tanaka-0.4.0/tanaka/README.md | 4 ++-- tanaka-0.4.0/tanaka/inst/tinytest/test_tanaka.R | 23 ----------------------- tanaka-0.4.0/tanaka/man/tanaka.Rd | 10 ++++++---- 9 files changed, 41 insertions(+), 58 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.0.0 dated 2023-08-22 and 3.0.1 dated 2023-11-28
DESCRIPTION | 16 +- MD5 | 94 ++++++++-------- NEWS.md | 4 R/AllGenerics.R | 3 R/plot_diceleraas.R | 2 R/plot_ford.R | 19 +-- R/plot_matrix.R | 32 +++-- R/tabula-internal.R | 88 -------------- R/tabula-package.R | 2 README.md | 17 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/bibliography.html | 4 inst/doc/diversity.html | 8 - inst/tinytest/_tinysnapshot/plot_bertin_count.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_bertin_noflip.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_bertin_prop1.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_bertin_prop2.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_bertin_threshold.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_ford_count.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_ford_weights.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_matrigraph.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_matrigraph_reverse.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_mtx_count.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_mtx_incid.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_mtx_occ.svg | 20 +-- inst/tinytest/_tinysnapshot/plot_mtx_prop1.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_mtx_prop2.svg | 74 ++++-------- inst/tinytest/_tinysnapshot/plot_mtx_sim.svg | 36 +++--- inst/tinytest/_tinysnapshot/plot_seriograph.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_spot_occ.svg | 20 +-- inst/tinytest/_tinysnapshot/plot_spot_plain.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_spot_prop1.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_spot_prop2.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_spot_ring.svg | 28 ++-- inst/tinytest/_tinysnapshot/plot_spot_sim_plain.svg | 36 +++--- inst/tinytest/_tinysnapshot/plot_spot_sim_ring.svg | 36 +++--- man/figures/README-ford-1.png |binary man/figures/README-occurrence-1.png |binary man/matrigraph.Rd | 3 man/plot_bertin.Rd | 3 man/plot_ford.Rd | 3 man/plot_heatmap.Rd | 3 man/plot_matrix.Rd | 3 man/plot_spot.Rd | 3 man/seriograph.Rd | 3 man/tabula-package.Rd | 2 48 files changed, 518 insertions(+), 724 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-25 dated 2023-11-03 and 5.2.1-26 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/RcppExports.R | 2 +- man/rmumps-package.Rd | 2 +- src/RcppExports.cpp | 14 +++++++------- src/lib/scotch_6.0.9/src/libscotch/common_file.c | 2 +- 7 files changed, 26 insertions(+), 20 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides
a high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<arXiv:1902.08318> paper for more details about 'simdjson'. This package
parses 'JSON' from string, file, or remote URLs under a variety of settings.
Author: Dirk Eddelbuettel, Brendan Knapp, Daniel Lemire
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.10 dated 2023-05-14 and 0.1.11 dated 2023-11-28
ChangeLog | 10 +++++++++- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RcppExports.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 12 +++++++++--- src/RcppExports.cpp | 7 ++++--- 7 files changed, 33 insertions(+), 18 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface from within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating time spent and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Matthew Fidler [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.0.5 dated 2023-11-11 and 0.0.6 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 13 +++++++++++++ R/NMexecDirectory.R | 4 +++- R/NMsim.R | 23 +++++++++++++++-------- R/NMsim_known.R | 10 +++++----- R/addEVID2.R | 4 ++-- R/genPhiFile.R | 10 ++++++++-- man/NMsim.Rd | 8 +++++++- 9 files changed, 64 insertions(+), 30 deletions(-)
Title: MAle Lineage ANalysis
Description: MAle Lineage ANalysis by simulating
genealogies backwards and imposing short tandem repeats (STR) mutations forwards.
Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses.
Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.
Refer to papers mentioned in citation("malan") (DOI's:
<doi:10.1371/journal.pgen.1007028>,
<doi:10.21105/joss.00684> and
<doi:10.1016/j.fsigen.2018.10.004>).
Author: Mikkel Meyer Andersen [aut, cre]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between malan versions 1.0.2 dated 2020-06-25 and 1.0.3 dated 2023-11-28
DESCRIPTION | 11 MD5 | 60 - NAMESPACE | 5 NEWS | 42 R/RcppExports.R | 90 + R/data.R | 4 R/igraph.R | 9 R/malan.R | 2 README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/case-study-partial.html | 476 ++++---- inst/doc/introduction.html | 594 +++++----- man/infer_generation.Rd |only man/load_haplotypes.Rd |only man/malan-package.Rd | 2 man/meiotic_dist_threshold.Rd |only man/meiotic_radius.Rd |only man/mixture_info_by_individuals_2pers.Rd | 9 man/pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists.Rd | 6 man/set_generation.Rd |only man/ystr_kits.Rd | 2 man/ystr_markers.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 87 + src/api_load_data.cpp | 97 + src/api_utility_haplotypes.cpp | 91 + src/api_utility_mixtures.cpp | 33 src/api_utility_mixtures_analyse.cpp | 5 src/class_Individual.cpp | 179 ++- src/class_Individual.h | 9 tests/testthat/test-family.R | 3 tests/testthat/test-loadpop.R | 197 +++ 34 files changed, 1451 insertions(+), 568 deletions(-)
Title: R Interface to 'lp_solve' Version 5.5.2.0
Description: The lpSolveAPI package provides an R interface to 'lp_solve',
a Mixed Integer Linear Programming (MILP) solver with support for pure
linear, (mixed) integer/binary, semi-continuous and special ordered sets
(SOS) models.
Author: lp_solve <https://lpsolve.sourceforge.net/> [aut],
Kjell Konis [aut],
Florian Schwendinger [aut, cre],
Kurt Hornik [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between lpSolveAPI versions 5.5.2.0-17.10 dated 2023-09-03 and 5.5.2.0-17.11 dated 2023-11-28
ChangeLog | 8 +++++--- DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/RlpSolve.c | 4 ++-- 4 files changed, 13 insertions(+), 11 deletions(-)
Title: Read Data from 'LimeSurvey'
Description: Read data from 'LimeSurvey'
(<https://www.limesurvey.org/>)
in a comfortable way.
Heavily inspired by 'limer'
(<https://github.com/cloudyr/limer/>),
which lacked a few comfort features for me.
Author: Maximilian Hagspiel [aut, cre, cph]
Maintainer: Maximilian Hagspiel <maxhag@mailbox.org>
Diff between ipanema versions 0.2.1 dated 2023-11-18 and 0.3.1 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++++---- NAMESPACE | 3 +++ R/get_sql_varname.R |only R/get_survey_data.R | 6 ++++++ R/get_survey_id.R |only man/get_sql_varname.Rd |only man/get_survey_data.Rd | 6 ++++++ man/get_survey_id.Rd |only 9 files changed, 26 insertions(+), 7 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <Sylvain.Jasson@inrae.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.7-2 dated 2023-07-01 and 0.7-3 dated 2023-11-28
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- man/Stirling.Rd | 2 - src/apply.cc | 4 +- src/bigintegerR.cc | 94 +++++++++++++++++++++++++------------------------- src/bigrationalR.cc | 60 +++++++++++++++---------------- src/extract_matrix.cc | 8 ++-- src/factor.cc | 2 - src/matrix.cc | 12 +++--- src/matrixq.cc | 12 +++--- src/solve.cc | 8 ++-- 11 files changed, 115 insertions(+), 115 deletions(-)
Title: Generalized Linear Models with Clustering
Description: Binomial and Poisson regression for clustered data, fixed
and random effects with bootstrapping.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb],
Henrik Holmberg [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between glmmML versions 1.1.5 dated 2023-09-06 and 1.1.6 dated 2023-11-28
ChangeLog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/glmmML.pdf |binary src/glmmml.c | 16 ++++++++-------- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: Event History Analysis
Description: Parametric proportional hazards fitting with left truncation and
right censoring for common families of distributions, piecewise constant
hazards, and discrete models. Parametric accelerated failure time models
for left truncated and right censored data. Proportional hazards
models for tabular and register data. Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Broström (2022) <doi:10.1201/9780429503764>.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between eha versions 2.11.1 dated 2023-09-30 and 2.11.2 dated 2023-11-28
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/aftreg.R | 4 ++-- inst/doc/eha.html | 4 ++-- inst/doc/gompertz.html | 4 ++-- inst/doc/parametric.html | 4 ++-- inst/doc/parametric1.pdf |binary inst/doc/tpchreg.html | 4 ++-- man/aftreg.Rd | 4 ++-- man/swedeaths.Rd | 2 +- man/swepop.Rd | 2 +- src/coxfun.c | 4 ++-- 13 files changed, 36 insertions(+), 32 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based
spatial clustering of applications with noise) and HDBSCAN (hierarchical
DBSCAN), the ordering algorithm OPTICS (ordering points to identify the
clustering structure), shared nearest neighbor clustering, and the outlier
detection algorithms LOF (local outlier factor) and GLOSH (global-local
outlier score from hierarchies). The implementations use the kd-tree data
structure (from library ANN) for faster k-nearest neighbor search. An R
interface to fast kNN and fixed-radius NN search is also provided.
Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-11 dated 2022-10-27 and 1.1-12 dated 2023-11-28
DESCRIPTION | 11 -- MD5 | 42 ++++---- NEWS.md | 7 + R/pointdensity.R | 3 README.md | 246 +++++++++++++++++++++++++++++++++++++------------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 3 inst/doc/dbscan.Rnw | 5 inst/doc/dbscan.pdf |binary inst/doc/hdbscan.html | 15 -- src/ANN.cpp | 20 +-- src/Makevars | 2 src/R_buildHDBSCAN.cpp | 11 +- src/R_cleanup.cpp | 5 src/R_comps.cpp | 11 +- src/R_dendrogram.cpp | 67 +++++++------ src/R_mrd.cpp | 9 + src/R_optics.cpp | 2 src/R_prims_mst.cpp | 9 + src/utilities.h | 19 ++- vignettes/dbscan.Rnw | 5 22 files changed, 337 insertions(+), 155 deletions(-)
More information about BiostatsUHNplus at CRAN
Permanent link
Title: Tau-Leaping Stochastic Simulation
Description: Implements adaptive tau leaping to approximate the
trajectory of a continuous-time stochastic process as
described by Cao et al. (2007) The Journal of Chemical Physics
<doi:10.1063/1.2745299> (aka. the Gillespie stochastic
simulation algorithm). This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip
Johnson and NIH R01-AI049334 to Rustom Antia.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between adaptivetau versions 2.2-3 dated 2019-03-19 and 2.3 dated 2023-11-28
DESCRIPTION | 8 +-- MD5 | 16 +++--- NEWS | 7 +++ R/ssa.adaptivetau.R | 8 +-- build/vignette.rds |binary inst/doc/adaptivetau.pdf |binary man/ssa.adaptivetau.Rd | 13 +++++ man/ssa.exact.Rd | 14 +++++- src/adaptivetau.cpp | 109 +++++++++++++++++++++++++++++++++++++++++------ 9 files changed, 144 insertions(+), 31 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.8-4 dated 2023-09-13 and 0.8-5 dated 2023-11-28
DESCRIPTION | 6 +- MD5 | 14 ++--- NEWS.md | 4 + build/vignette.rds |binary configure | 26 ++++----- inst/doc/measurement_units_in_R.R | 10 +-- inst/doc/units.html | 102 ++++++++++++++++++-------------------- src/udunits.cpp | 2 8 files changed, 83 insertions(+), 81 deletions(-)
Title: Simple Utilities for Tab-Separated-Value (TSV) Files
Description: Utilities for rapidly loading specified rows and/or columns of data from large tab-separated value (tsv) files (large: e.g. 1 GB file of 10000 x 10000 matrix). 'tsvio' is an R wrapper to 'C' code that creates an index file for the rows of the tsv file, and uses that index file to collect rows and/or columns from the tsv file without reading the whole file into memory.
Author: Bradley M Broom [aut] ,
Mary A Rohrdanz [ctb, cre],
Chris Wakefield [ctb],
James Melott [ctb],
Paul Hsieh [ctb],
MD Anderson Cancer Center [cph]
Maintainer: Mary A Rohrdanz <marohrdanz@mdanderson.org>
Diff between tsvio versions 1.0.4 dated 2023-10-04 and 1.0.6 dated 2023-11-28
tsvio-1.0.4/tsvio/README.md |only tsvio-1.0.6/tsvio/DESCRIPTION | 6 tsvio-1.0.6/tsvio/MD5 | 11 tsvio-1.0.6/tsvio/build/vignette.rds |binary tsvio-1.0.6/tsvio/inst/doc/tsvio.R | 8 tsvio-1.0.6/tsvio/inst/doc/tsvio.html | 421 +++++++++++++++++++++++++++------- tsvio-1.0.6/tsvio/src/tsvlib.c | 20 - 7 files changed, 361 insertions(+), 105 deletions(-)
Title: Bayesian Treed Gaussian Process Models
Description: Bayesian nonstationary, semiparametric nonlinear regression
and design by treed Gaussian processes (GPs) with jumps to the limiting
linear model (LLM). Special cases also implemented include Bayesian
linear models, CART, treed linear models, stationary separable and
isotropic GPs, and GP single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided, including ALM,
ALC, and expected improvement. The latter supports derivative-free
optimization of noisy black-box functions. For details and tutorials,
see Gramacy (2007) <doi:10.18637/jss.v019.i09> and Gramacy & Taddy (2010)
<doi:10.18637/jss.v033.i06>.
Author: Robert B. Gramacy <rbg@vt.edu> and Matt A. Taddy
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between tgp versions 2.4-21 dated 2023-01-06 and 2.4-22 dated 2023-11-28
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/exp2d.rda |binary inst/CITATION | 12 +++++------- inst/doc/tgp.pdf |binary inst/doc/tgp2.pdf |binary src/Makevars | 2 +- src/temper.cc | 2 +- 11 files changed, 28 insertions(+), 23 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.8 dated 2023-05-30 and 0.16.0 dated 2023-11-28
stringfish-0.15.8/stringfish/tests/tests.r |only stringfish-0.16.0/stringfish/ChangeLog | 3 stringfish-0.16.0/stringfish/DESCRIPTION | 10 - stringfish-0.16.0/stringfish/MD5 | 18 - stringfish-0.16.0/stringfish/build/vignette.rds |binary stringfish-0.16.0/stringfish/inst/doc/vignette.html | 13 + stringfish-0.16.0/stringfish/inst/include/sf_internal.h | 10 - stringfish-0.16.0/stringfish/src/PCRE2/pcre2_is_bundled.c | 2 stringfish-0.16.0/stringfish/src/sf_altrep.h | 132 +++++++++++--- stringfish-0.16.0/stringfish/src/sf_functions.cpp | 3 stringfish-0.16.0/stringfish/tests/tests.R |only 11 files changed, 138 insertions(+), 53 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.16.0 dated 2023-10-23 and 2.17.0 dated 2023-11-28
DESCRIPTION | 8 MD5 | 46 +++-- NAMESPACE | 10 + NEWS.md | 5 R/mol_parameters.R | 54 +++++- R/mrs_data_proc.R | 23 ++ R/mrs_read_pfile.R | 2 R/mrs_read_twix.R | 3 R/pulse_sequences.R | 163 ++++++++++++++++++ R/pulse_shapes.R | 21 ++ R/qm_simulation.R | 154 ++++++++++++++--- R/rats.R | 2 R/svs_batch_fit.R | 269 +++++++++++++++++++++++++++++- inst/doc/abfit-baseline-opts.html | 12 - inst/doc/spant-intro.html | 114 ++++++------ inst/doc/spant-metabolite-simulation.html | 22 +- inst/doc/spant-preprocessing.html | 4 man/get_1h_brain_basis_names.Rd |only man/get_1h_braino_basis_names.Rd |only man/get_1h_spectre_basis_names.Rd |only man/get_spin_num.Rd |only man/read_pulse_ascii.Rd |only man/seq_press_2d_shaped.Rd |only man/sim_basis.Rd | 4 man/spin_sys.Rd | 6 man/sub_median_dyns.Rd |only man/svs_1h_brain_analysis_dev.Rd |only man/te.Rd |only man/write_pulse_ascii.Rd |only 29 files changed, 784 insertions(+), 138 deletions(-)
Title: Standard Methods for Use in Public Health Scotland
Description: A collection of methods for commonly undertaken analytical
tasks, primarily developed for Public Health Scotland (PHS) analysts,
but the package is also generally useful to others working in the
healthcare space, particularly since it has functions for working with
Community Health Index (CHI) numbers. The package can help to make
data manipulation and analysis more efficient and reproducible.
Author: Public Health Scotland [cph],
David Caldwell [aut],
Lucinda Lawrie [rev],
Jack Hannah [aut],
Tina Fu [aut, cre],
Ciara Gribben [aut],
Chris Deans [aut],
Jaime Villacampa [aut],
Graeme Gowans [aut],
Alice Byers [ctb],
Alan Yeung [ctb],
James McMahon [ [...truncated...]
Maintainer: Tina Fu <Yuyan.Fu2@phs.scot>
Diff between phsmethods versions 1.0.0 dated 2023-11-03 and 1.0.1 dated 2023-11-28
DESCRIPTION | 10 ++- MD5 | 16 +++-- NEWS.md | 7 ++ R/extract_fin_year.R | 38 ++++-------- build |only inst/doc |only man/extract_fin_year.Rd | 4 - tests/testthat/_snaps/extract_fin_year.md |only tests/testthat/test-extract_fin_year.R | 90 ++++++++++++++++++++++++++++++ vignettes |only 10 files changed, 130 insertions(+), 35 deletions(-)
Title: Line Maps
Description: Create maps made of lines. The package contains one function:
linemap(). linemap() displays a map made of lines using a
raster or gridded data.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between linemap versions 0.2.0 dated 2021-01-19 and 0.3.0 dated 2023-11-28
linemap-0.2.0/linemap/R/getgrid.R |only linemap-0.2.0/linemap/R/package.R |only linemap-0.2.0/linemap/data |only linemap-0.2.0/linemap/inst/gpkg |only linemap-0.2.0/linemap/man/getgrid.Rd |only linemap-0.2.0/linemap/man/linemap-package.Rd |only linemap-0.2.0/linemap/man/popOcc.Rd |only linemap-0.3.0/linemap/DESCRIPTION | 18 -- linemap-0.3.0/linemap/MD5 | 24 +- linemap-0.3.0/linemap/NAMESPACE | 2 linemap-0.3.0/linemap/NEWS.md | 8 linemap-0.3.0/linemap/R/linemap.R | 178 +++++++++++++++------ linemap-0.3.0/linemap/README.md | 110 +++--------- linemap-0.3.0/linemap/inst/tif |only linemap-0.3.0/linemap/inst/tinytest/test_linemap.R | 28 +-- linemap-0.3.0/linemap/man/figures |only linemap-0.3.0/linemap/man/linemap.Rd | 34 ---- 17 files changed, 206 insertions(+), 196 deletions(-)
Title: Limited Memory BFGS Minimizer with Bounds on Parameters with
optim() 'C' Interface
Description: Interfacing to Nocedal et al. L-BFGS-B.3.0
(See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>)
limited memory BFGS minimizer with bounds on parameters.
This is a fork of 'lbfgsb3'.
This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same
function types and optimization as the optim() function (see writing 'R' extensions
and source for details). This package also adds more stopping criteria as well
as allowing the adjustment of more tolerances.
Author: Matthew L Fidler [aut, cre],
John C Nash [aut],
Ciyou Zhu [aut],
Richard Byrd [aut],
Jorge Nocedal [aut],
Jose Luis Morales [aut]
Maintainer: Matthew L Fidler <matthew.fidler@gmail.com>
Diff between lbfgsb3c versions 2020-3.2 dated 2020-03-03 and 2020-3.3 dated 2023-11-28
lbfgsb3c-2020-3.2/lbfgsb3c/NEWS |only lbfgsb3c-2020-3.2/lbfgsb3c/inst/doc/lbfgsb3c.pdf |only lbfgsb3c-2020-3.3/lbfgsb3c/DESCRIPTION | 30 +++-- lbfgsb3c-2020-3.3/lbfgsb3c/LICENSE.note | 2 lbfgsb3c-2020-3.3/lbfgsb3c/MD5 | 36 +++---- lbfgsb3c-2020-3.3/lbfgsb3c/NEWS.md |only lbfgsb3c-2020-3.3/lbfgsb3c/R/lbfgsb3.R | 77 +++++++-------- lbfgsb3c-2020-3.3/lbfgsb3c/README.md | 8 + lbfgsb3c-2020-3.3/lbfgsb3c/build/vignette.rds |binary lbfgsb3c-2020-3.3/lbfgsb3c/inst/doc/lbfgsb3c.R | 4 lbfgsb3c-2020-3.3/lbfgsb3c/inst/doc/lbfgsb3c.Rmd | 47 ++++----- lbfgsb3c-2020-3.3/lbfgsb3c/inst/doc/lbfgsb3c.html |only lbfgsb3c-2020-3.3/lbfgsb3c/src/RcppExports.cpp | 5 lbfgsb3c-2020-3.3/lbfgsb3c/src/lbfgsb.f | 2 lbfgsb3c-2020-3.3/lbfgsb3c/src/lbfgsb3x.cpp | 18 +-- lbfgsb3c-2020-3.3/lbfgsb3c/tests/testthat.R | 8 + lbfgsb3c-2020-3.3/lbfgsb3c/tests/testthat/test-bounds.R | 1 lbfgsb3c-2020-3.3/lbfgsb3c/tests/testthat/test-cyq.R | 2 lbfgsb3c-2020-3.3/lbfgsb3c/tests/testthat/test-genrose.R | 77 ++++++++------- lbfgsb3c-2020-3.3/lbfgsb3c/vignettes/lbfgsb3c.Rmd | 47 ++++----- lbfgsb3c-2020-3.3/lbfgsb3c/vignettes/lbfgsb3c.bib | 55 +++++----- 21 files changed, 224 insertions(+), 195 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current
literature on landscape metrics. This package supports 'terra' SpatRaster objects
as input arguments. It further provides utility functions to visualize patches,
select metrics and building blocks to develop new metrics.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Jakub Nowosad [aut] ,
Sebastian Hanss [aut] ,
Laura J. Graham [ctb] ,
Jeffrey Hollister [ctb] ,
Kimberly A. With [ctb] ,
Florian Prive [ctb] function),
Project Nayuki [ctb] ,
Matt Strima [...truncated...]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between landscapemetrics versions 2.0.0 dated 2023-10-03 and 2.1.0 dated 2023-11-28
DESCRIPTION | 6 MD5 | 380 ++++++++++++++--------------- NAMESPACE | 7 NEWS.md | 31 ++ R/calculate_lsm.R | 25 + R/construct_buffer.R | 8 R/data.R | 1 R/data_info.R | 2 R/get_boundaries.R | 2 R/get_centroids.R | 16 - R/get_circumscribingcircle.R | 10 R/get_nearestneighbour.R | 12 R/get_patches.R | 2 R/get_unique_values.R | 2 R/landscape_as_list.R | 1 R/landscapemetrics-package.R | 2 R/lsm_c_ai.R | 21 - R/lsm_c_area_cv.R | 17 - R/lsm_c_area_mn.R | 17 - R/lsm_c_area_sd.R | 17 - R/lsm_c_ca.R | 17 - R/lsm_c_cai_cv.R | 18 - R/lsm_c_cai_mn.R | 18 - R/lsm_c_cai_sd.R | 18 - R/lsm_c_circle_cv.R | 20 - R/lsm_c_circle_mn.R | 20 - R/lsm_c_circle_sd.R | 21 - R/lsm_c_clumpy.R | 14 - R/lsm_c_cohesion.R | 34 +- R/lsm_c_contig_cv.R | 20 - R/lsm_c_contig_mn.R | 20 - R/lsm_c_contig_sd.R | 20 - R/lsm_c_core_cv.R | 21 - R/lsm_c_core_mn.R | 21 - R/lsm_c_core_sd.R | 21 - R/lsm_c_cpland.R | 30 +- R/lsm_c_dcad.R | 21 - R/lsm_c_dcore_cv.R | 22 - R/lsm_c_dcore_mn.R | 22 - R/lsm_c_dcore_sd.R | 22 - R/lsm_c_division.R | 21 - R/lsm_c_ed.R | 28 +- R/lsm_c_enn_cv.R | 21 - R/lsm_c_enn_mn.R | 21 - R/lsm_c_enn_sd.R | 21 - R/lsm_c_frac_cv.R | 21 - R/lsm_c_frac_mn.R | 21 - R/lsm_c_frac_sd.R | 21 - R/lsm_c_gyrate_cv.R | 22 - R/lsm_c_gyrate_mn.R | 22 - R/lsm_c_gyrate_sd.R | 22 - R/lsm_c_iji.R | 33 +- R/lsm_c_lpi.R | 19 - R/lsm_c_lsi.R | 31 -- R/lsm_c_mesh.R | 19 - R/lsm_c_ndca.R | 20 - R/lsm_c_nlsi.R | 37 +- R/lsm_c_np.R | 30 +- R/lsm_c_pafrac.R | 35 +- R/lsm_c_para_cv.R | 19 - R/lsm_c_para_mn.R | 19 - R/lsm_c_para_sd.R | 21 - R/lsm_c_pd.R | 29 +- R/lsm_c_pladj.R | 17 - R/lsm_c_pland.R | 28 +- R/lsm_c_shape_cv.R | 19 - R/lsm_c_shape_mn.R | 19 - R/lsm_c_shape_sd.R | 19 - R/lsm_c_split.R | 21 - R/lsm_c_tca.R | 22 - R/lsm_c_te.R | 41 +-- R/lsm_l_ai.R | 40 +-- R/lsm_l_area_cv.R | 19 - R/lsm_l_area_mn.R | 21 - R/lsm_l_area_sd.R | 19 - R/lsm_l_cai_cv.R | 19 - R/lsm_l_cai_mn.R | 22 - R/lsm_l_cai_sd.R | 20 - R/lsm_l_circle_cv.R | 19 - R/lsm_l_circle_mn.R | 19 - R/lsm_l_circle_sd.R | 19 - R/lsm_l_cohesion.R | 31 +- R/lsm_l_condent.R | 34 +- R/lsm_l_contag.R | 33 +- R/lsm_l_contig_cv.R | 19 - R/lsm_l_contig_mn.R | 19 - R/lsm_l_contig_sd.R | 19 - R/lsm_l_core_cv.R | 19 - R/lsm_l_core_mn.R | 19 - R/lsm_l_core_sd.R | 19 - R/lsm_l_dcad.R | 23 - R/lsm_l_dcore_cv.R | 20 - R/lsm_l_dcore_mn.R | 20 - R/lsm_l_dcore_sd.R | 20 - R/lsm_l_division.R | 19 - R/lsm_l_ed.R | 30 +- R/lsm_l_enn_cv.R | 19 - R/lsm_l_enn_mn.R | 19 - R/lsm_l_enn_sd.R | 19 - R/lsm_l_ent.R | 27 +- R/lsm_l_frac_cv.R | 19 - R/lsm_l_frac_mn.R | 19 - R/lsm_l_frac_sd.R | 19 - R/lsm_l_gyrate_cv.R | 20 - R/lsm_l_gyrate_mn.R | 20 - R/lsm_l_gyrate_sd.R | 20 - R/lsm_l_iji.R | 27 +- R/lsm_l_joinent.R | 26 - R/lsm_l_lpi.R | 19 - R/lsm_l_lsi.R | 30 +- R/lsm_l_mesh.R | 19 - R/lsm_l_msidi.R | 27 +- R/lsm_l_msiei.R | 26 + R/lsm_l_mutinf.R | 33 +- R/lsm_l_ndca.R | 20 - R/lsm_l_np.R | 19 - R/lsm_l_pafrac.R | 38 +- R/lsm_l_para_cv.R | 19 - R/lsm_l_para_mn.R | 19 - R/lsm_l_para_sd.R | 19 - R/lsm_l_pd.R | 29 +- R/lsm_l_pladj.R | 17 - R/lsm_l_pr.R | 23 + R/lsm_l_prd.R | 21 - R/lsm_l_relmutinf.R | 33 +- R/lsm_l_rpr.R | 18 - R/lsm_l_shape_cv.R | 19 - R/lsm_l_shape_mn.R | 19 - R/lsm_l_shape_sd.R | 19 - R/lsm_l_shdi.R | 19 - R/lsm_l_shei.R | 19 - R/lsm_l_sidi.R | 19 - R/lsm_l_siei.R | 21 - R/lsm_l_split.R | 19 - R/lsm_l_ta.R | 19 - R/lsm_l_tca.R | 19 - R/lsm_l_te.R | 34 +- R/lsm_p_area.R | 44 +-- R/lsm_p_cai.R | 31 +- R/lsm_p_circle.R | 39 +- R/lsm_p_contig.R | 35 +- R/lsm_p_core.R | 46 +-- R/lsm_p_enn.R | 63 +--- R/lsm_p_frac.R | 28 +- R/lsm_p_gyrate.R | 54 ++-- R/lsm_p_ncore.R | 55 ++-- R/lsm_p_para.R | 29 +- R/lsm_p_perim.R | 101 +------ R/lsm_p_shape.R | 35 +- R/matrix_to_raster.R | 2 R/prepare_extras.R |only R/proj_info.R | 6 R/raster_to_points.R | 5 R/sample_lsm.R | 5 R/show_cores.R | 2 R/show_correlation.R | 2 R/show_lsm.R | 1 R/show_patches.R | 19 - R/spatialize_lsm.R | 3 R/sysdata.rda |binary R/window_lsm.R | 103 +++---- inst/doc/get_started.html | 359 +++++++++++++-------------- man/construct_buffer.Rd | 8 man/figures/README-unnamed-chunk-2-1.png |binary man/get_area_patches.Rd |only man/get_boundaries.Rd | 2 man/get_class_patches.Rd |only man/get_complexity.Rd |only man/get_enn_patch.Rd |only man/get_patches.Rd | 2 man/get_perimeter_patch.Rd |only man/get_points.Rd |only man/lsm_l_ai.Rd | 5 man/prepare_extras.Rd |only man/show_correlation.Rd | 2 man/spatialize_lsm.Rd | 3 man/window_lsm.Rd | 2 src/RcppExports.cpp | 40 +-- src/rcpp_create_neighborhood.cpp | 6 src/rcpp_create_neighborhood.h | 2 src/rcpp_get_boundaries.cpp | 2 src/rcpp_get_boundaries.h | 2 src/rcpp_get_circle.cpp | 2 src/rcpp_get_circle.h | 2 src/rcpp_get_composition_vector.cpp | 2 src/rcpp_get_coocurrence_matrix.cpp | 2 src/rcpp_get_coocurrence_matrix.h | 2 src/rcpp_get_coocurrence_matrix_diag.cpp | 2 src/rcpp_get_coocurrence_matrix_diag.h | 2 src/rcpp_get_coocurrence_matrix_single.cpp | 2 src/rcpp_get_coocurrence_matrix_single.h | 2 src/rcpp_get_coocurrence_vector.cpp | 2 src/rcpp_get_coocurrence_vector.h | 2 src/rcpp_get_entropy.cpp | 2 src/rcpp_get_nearest_neighbor.cpp | 4 195 files changed, 2250 insertions(+), 2129 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal processes. The
models may include covariates and can be specified with familiar formula
syntax as in glm() and package 'flexsurv'. The methodology is described by
Kharrat et all (2019) <doi:10.18637/jss.v090.i13> (included as vignette
'Countr_guide' in the package).
Author: Tarak Kharrat [aut],
Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Countr versions 3.5.6 dated 2022-11-12 and 3.5.7 dated 2023-11-28
DESCRIPTION | 8 +++--- MD5 | 36 +++++++++++++++---------------- NAMESPACE | 4 ++- NEWS.md | 34 ++++++++++++++++++++--------- R/Countr-package.R | 25 +++++++++++++++++---- R/RcppExports.R | 3 -- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ComputationalPerformance.pdf |binary inst/doc/Countr_guide.pdf |binary inst/doc/ModelSelectionAndComparison.pdf |binary inst/doc/VarianceCovariance.pdf |binary inst/doc/exampleFertility.pdf |binary inst/doc/exampleFootball.pdf |binary man/dCount_dePril_bi.Rd | 2 - man/dCount_naive_bi.Rd | 2 - src/RcppExports.cpp | 33 ++++++++++++++++------------ src/conv_dePril.cpp | 1 src/conv_naive.cpp | 2 - 19 files changed, 90 insertions(+), 60 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] ,
Maximillian H.K. Hesselbarth [ctb] , get_unique_values, and rcpp_get_coma
functions),
Marco Sciaini [ctb] , get_unique_values, and rcpp_get_coma
functions),
Sebastian Hanss [ctb] , get_unique_values, and rcpp_get_coma
funct [...truncated...]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.9.4 dated 2023-04-04 and 0.9.5 dated 2023-11-28
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++-------- R/RcppExports.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/coma.R | 6 ++-- inst/doc/coma.html | 48 ++++++++++++++++++------------------ inst/doc/incoma.R | 6 ++-- inst/doc/incoma.html | 68 +++++++++++++++++++++++++-------------------------- inst/doc/wecoma.R | 6 ++-- inst/doc/wecoma.html | 62 +++++++++++++++++++++++----------------------- src/RcppExports.cpp | 52 +++++++++++++++++++-------------------- 12 files changed, 139 insertions(+), 139 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and a R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut, cre] ,
Mark Raasveldt [aut] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrochers [cph],
Victor Z [...truncated...]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>
Diff between duckdb versions 0.9.2 dated 2023-11-17 and 0.9.2-1 dated 2023-11-28
DESCRIPTION | 82 +++++++++++++++++++---------------------- MD5 | 4 +- inst/include/cpp11/protect.hpp | 2 - 3 files changed, 42 insertions(+), 46 deletions(-)
Title: Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Also offers fuzzy text search based on various string
distance measures. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. This package is built for speed and
runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
Author: Mark van der Loo [aut, cre] ,
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb],
Johannes Gruber [ctb],
Brian Ripley [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.10 dated 2022-11-07 and 0.9.12 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 8 ++++++++ README.md | 2 +- build/vignette.rds |binary inst/doc/RJournal_6_111-122-2014.pdf |binary inst/doc/stringdist_C-Cpp_api.pdf |binary src/Rstringdist.c | 14 +++++++------- src/qgram.c | 4 ++-- 9 files changed, 30 insertions(+), 22 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. It is designed as a generic yet powerful framework. The
architecture encloses a robust and fast simulation core written in 'C++' with
automatic monitoring capabilities. It provides a rich and flexible R API that
revolves around the concept of trajectory, a common path in the simulation
model for entities of the same type. Documentation about 'simmer' is provided
by several vignettes included in this package, via the paper by Ucar, Smeets
& Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar,
Hernández, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>);
see 'citation("simmer")' for details.
Author: Inaki Ucar [aut, cph, cre] ,
Bart Smeets [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between simmer versions 4.4.6.2 dated 2023-08-22 and 4.4.6.3 dated 2023-11-28
DESCRIPTION | 6 MD5 | 48 - NEWS.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/simmer-01-introduction.R | 14 inst/doc/simmer-01-introduction.html | 230 +++--- inst/doc/simmer-02-jss.R | 104 +- inst/doc/simmer-02-jss.pdf |binary inst/doc/simmer-03-trajectories.R | 6 inst/doc/simmer-03-trajectories.html | 264 +++--- inst/doc/simmer-04-bank-1.R | 16 inst/doc/simmer-04-bank-1.html | 1052 +++++++++++++-------------- inst/doc/simmer-04-bank-2.R | 22 inst/doc/simmer-04-bank-2.html | 1324 +++++++++++++++++------------------ inst/doc/simmer-05-simpy.R | 46 - inst/doc/simmer-05-simpy.html | 604 +++++++-------- inst/doc/simmer-06-queueing.R | 4 inst/doc/simmer-06-queueing.html | 398 +++++----- inst/doc/simmer-07-ctmc.R | 8 inst/doc/simmer-07-ctmc.html | 412 +++++----- inst/doc/simmer-08-philosophers.R | 10 inst/doc/simmer-08-philosophers.html | 168 ++-- inst/doc/simmer-aa-5G.html | 782 ++++++++++---------- inst/include/simmer/simulator_impl.h | 2 25 files changed, 2762 insertions(+), 2761 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for
fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or other 'DBI' drivers to connect to databases.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] ,
PostgreSQL Global Development Group [cph] ,
Oracle Inc. [cph] ,
Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 6.3.0 dated 2023-11-08 and 6.3.1 dated 2023-11-28
DESCRIPTION | 8 MD5 | 273 - NAMESPACE | 196 NEWS.md | 954 ++-- R/Andromeda.R | 726 +-- R/BulkLoad.R | 690 +-- R/Compression.R | 84 R/Connect.R | 1924 ++++---- R/CtasHack.R | 360 - R/DBI.R | 1612 +++---- R/DataHash.R | 530 +- R/DatabaseConnector.R | 162 R/DbiDateFunctions.R | 412 - R/Drivers.R | 406 - R/HelperFunctions.R | 280 - R/InsertTable.R | 966 ++-- R/ListTables.R | 364 - R/RStudio.R | 688 +-- R/Sql.R | 2166 +++++----- README.md | 254 - build/vignette.rds |binary inst/COPYRIGHTS | 132 inst/csv/jarChecksum.txt | 2 inst/csv/sqlReservedWords.csv | 964 ++-- inst/doc/Connecting.R | 134 inst/doc/Connecting.Rmd | 344 - inst/doc/Connecting.pdf |binary inst/doc/DbiAndDbplyr.R | 204 inst/doc/DbiAndDbplyr.Rmd | 370 - inst/doc/DbiAndDbplyr.pdf |binary inst/doc/Querying.R | 96 inst/doc/Querying.Rmd | 224 - inst/doc/Querying.pdf |binary inst/sql/sql_server/redshiftCopy.sql | 10 java/DatabaseConnector.jardesc | 32 java/org/ohdsi/databaseConnector/Authentication.java | 66 java/org/ohdsi/databaseConnector/BatchedInsert.java | 550 +- java/org/ohdsi/databaseConnector/BatchedQuery.java | 586 +- java/org/ohdsi/databaseConnector/Compression.java | 240 - java/org/ohdsi/databaseConnector/DebugBatchedQuery.java | 88 java/org/ohdsi/databaseConnector/DebugRtoSqlTranslation.java | 46 java/org/ohdsi/databaseConnector/JarChecksum.java | 92 java/org/ohdsi/databaseConnector/RFunctionToTranslate.java | 74 java/org/ohdsi/databaseConnector/RtoSqlTranslator.java | 260 - man/DatabaseConnector-package.Rd | 76 man/DatabaseConnectorDbiResult-class.Rd | 20 man/DatabaseConnectorDriver-class.Rd | 20 man/DatabaseConnectorDriver.Rd | 22 man/DatabaseConnectorJdbcResult-class.Rd | 20 man/assertTempEmulationSchemaSet.Rd | 54 man/computeDataHash.Rd | 68 man/connect.Rd | 472 +- man/createConnectionDetails.Rd | 446 +- man/createDbiConnectionDetails.Rd | 76 man/createZipFile.Rd | 48 man/dateAdd.Rd | 52 man/dateDiff.Rd | 52 man/dateFromParts.Rd | 52 man/day.Rd | 44 man/dbAppendTable-DatabaseConnectorConnection-character-method.Rd | 192 man/dbClearResult-DatabaseConnectorDbiResult-method.Rd | 84 man/dbClearResult-DatabaseConnectorJdbcResult-method.Rd | 84 man/dbColumnInfo-DatabaseConnectorDbiResult-method.Rd | 98 man/dbColumnInfo-DatabaseConnectorJdbcResult-method.Rd | 98 man/dbConnect-DatabaseConnectorDriver-method.Rd | 68 man/dbCreateTable-DatabaseConnectorConnection-method.Rd | 194 man/dbDisconnect-DatabaseConnectorConnection-method.Rd | 86 man/dbExecute-DatabaseConnectorConnection-character-method.Rd | 134 man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd | 132 man/dbFetch-DatabaseConnectorDbiResult-method.Rd | 118 man/dbFetch-DatabaseConnectorJdbcResult-method.Rd | 118 man/dbGetInfo-DatabaseConnectorConnection-method.Rd | 214 man/dbGetInfo-DatabaseConnectorDriver-method.Rd | 214 man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd | 148 man/dbGetRowCount-DatabaseConnectorDbiResult-method.Rd | 108 man/dbGetRowCount-DatabaseConnectorJdbcResult-method.Rd | 108 man/dbGetRowsAffected-DatabaseConnectorDbiResult-method.Rd | 92 man/dbGetRowsAffected-DatabaseConnectorJdbcResult-method.Rd | 92 man/dbGetStatement-DatabaseConnectorDbiResult-method.Rd | 82 man/dbGetStatement-DatabaseConnectorJdbcResult-method.Rd | 82 man/dbHasCompleted-DatabaseConnectorDbiResult-method.Rd | 90 man/dbHasCompleted-DatabaseConnectorJdbcResult-method.Rd | 90 man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd | 176 man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd | 176 man/dbListFields-DatabaseConnectorConnection-character-method.Rd | 140 man/dbListTables-DatabaseConnectorConnection-method.Rd | 136 man/dbReadTable-DatabaseConnectorConnection-character-method.Rd | 208 man/dbRemoveTable-DatabaseConnectorConnection-ANY-method.Rd | 154 man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd | 144 man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd | 144 man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd | 132 man/dbUnloadDriver-DatabaseConnectorDriver-method.Rd | 124 man/dbWriteTable-DatabaseConnectorConnection-ANY-method.Rd | 178 man/dbms.Rd | 60 man/disconnect.Rd | 56 man/downloadJdbcDrivers.Rd | 112 man/dropEmulatedTempTables.Rd | 56 man/eoMonth.Rd | 44 man/executeSql.Rd | 128 man/existsTable.Rd | 60 man/extractQueryTimes.Rd | 76 man/getAvailableJavaHeapSpace.Rd | 28 man/getTableNames.Rd | 60 man/inDatabaseSchema.Rd | 52 man/insertTable.Rd | 251 - man/isSqlReservedWord.Rd | 38 man/jdbcDrivers.Rd | 62 man/lowLevelExecuteSql.Rd | 34 man/lowLevelQuerySql.Rd | 80 man/lowLevelQuerySqlToAndromeda.Rd | 118 man/month.Rd | 44 man/querySql.Rd | 114 man/querySqlToAndromeda.Rd | 162 man/renderTranslateExecuteSql.Rd | 150 man/renderTranslateQueryApplyBatched.Rd | 220 - man/renderTranslateQuerySql.Rd | 140 man/renderTranslateQuerySqlToAndromeda.Rd | 178 man/requiresTempEmulation.Rd | 46 man/year.Rd | 44 tests/testthat.R | 14 tests/testthat/dbplyrTestFunction.R | 368 - tests/testthat/setup.R | 536 +- tests/testthat/test-BatchProcess.R | 50 tests/testthat/test-DBItest.R | 80 tests/testthat/test-compression.R | 42 tests/testthat/test-connection.R | 112 tests/testthat/test-connectionDetails.R | 24 tests/testthat/test-dataHash.R | 20 tests/testthat/test-dbplyr.R | 58 tests/testthat/test-fetchResults.R | 116 tests/testthat/test-getTableNames.R | 30 tests/testthat/test-insertTable.R | 282 - tests/testthat/test-isSqlReservedWord.R | 14 tests/testthat/test-sendUpdates.R | 40 tests/testthat/testthat-problems.rds |only vignettes/Connecting.Rmd | 344 - vignettes/DbiAndDbplyr.Rmd | 370 - vignettes/Querying.Rmd | 224 - 138 files changed, 14347 insertions(+), 14319 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Weighted Estimation in Cox Regression
Description: Implements weighted estimation in Cox regression as proposed by
Schemper, Wakounig and Heinze (Statistics in Medicine, 2009,
<doi:10.1002/sim.3623>) and as described in Dunkler, Ploner, Schemper and
Heinze (Journal of Statistical Software, 2018, <doi:10.18637/jss.v084.i02>).
Weighted Cox regression provides unbiased average hazard ratio
estimates also in case of non-proportional hazards.
Approximated generalized concordance probability an effect size measure for clear-cut
decisions can be obtained.
The package provides options to estimate time-dependent effects conveniently by
including interactions of covariates with arbitrary functions of time, with or without
making use of the weighting option.
Author: Daniela Dunkler [aut, cre],
Georg Heinze [aut],
Meinhard Ploner [aut]
Maintainer: Daniela Dunkler <daniela.dunkler@meduniwien.ac.at>
Diff between coxphw versions 4.0.2 dated 2020-06-22 and 4.0.3 dated 2023-11-28
DESCRIPTION | 13 MD5 | 36 README.md | 5 build/partial.rdb |binary build/vignette.rds |binary data/biofeedback.txt | 68 - inst/NEWS.Rd | 20 inst/doc/jss_2018_example_code.R | 12 inst/doc/jss_2018_example_code.html | 1596 ++++++++++++++++++------------------ man/concord.Rd | 2 man/coxphw-package.Rd | 6 man/coxphw.Rd | 2 man/coxphw.control.Rd | 4 man/gastric.Rd | 2 man/plot.coxphw.predict.Rd | 2 man/predict.coxphw.Rd | 4 man/wald.Rd | 6 src/coxphw.f90 | 3 tests/testthat/test_coxphw.R | 2 19 files changed, 917 insertions(+), 866 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.5.0 dated 2023-05-17 and 1.5.1 dated 2023-11-28
DESCRIPTION | 8 +++---- MD5 | 17 ++++++++-------- NEWS | 7 ++++++ inst/include/RNifti/NiftiImage.h | 10 ++++----- inst/include/RNifti/NiftiImage_impl.h | 34 ++++++++++++--------------------- inst/include/RNifti/NiftiImage_print.h | 6 ++--- src/main.cpp | 6 ----- src/niftilib/nifti1_io.c | 16 +++++++-------- src/niftilib/nifti2_io.c | 14 ++++++------- tests/testthat/Rplots.pdf |only 10 files changed, 57 insertions(+), 61 deletions(-)
Title: Individual-Level, Summary-Level and Single-Step Bayesian
Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
(1) fixed effects and coefficients of covariates,
(2) environmental random effects, and its corresponding variance,
(3) genetic variance,
(4) residual variance,
(5) heritability,
(6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
(7) SNP effect size,
(8) phenotype/genetic variance explained (PVE) for single or multiple SNPs,
(9) posterior probability of association of the genomic window (WPPA),
(10) posterior inclusive probability (PIP).
The functions are not limited, we will keep on going in enriching it with more features.
References: Meuwissen et al. (2001) <doi:10.1093/gene [...truncated...]
Author: Lilin Yin [aut, cre, cph],
Haohao Zhang [aut, cph],
Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>
Diff between hibayes versions 3.0.0 dated 2023-09-01 and 3.0.1 dated 2023-11-28
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 - R/bayes.r | 10 ++++++++-- R/sbayes.r | 10 ++++++++-- R/ssbayes.r | 10 ++++++++-- man/ibrm.Rd | 4 ++-- man/sbrm.Rd | 4 ++-- man/ssbrm.Rd | 4 ++-- src/read_bed.cpp | 4 ++-- src/tXXmat.cpp | 12 ++++++------ 11 files changed, 53 insertions(+), 36 deletions(-)
Title: CML and Bayesian Calibration of Multistage Tests
Description: Conditional Maximum Likelihood Calibration and data management of multistage tests.
Supports polytomous items and incomplete designs with linear as well as multistage tests.
Extended Nominal Response and Interaction models, DIF and profile analysis.
See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
Author: Timo Bechger [aut, cre],
Jesse Koops [aut],
Ivailo Partchev [aut],
Gunter Maris [aut],
Robert Zwitser [ctb]
Maintainer: Timo Bechger <tmbechger@gmail.com>
Diff between dexterMST versions 0.9.3 dated 2022-02-14 and 0.9.5 dated 2023-11-28
DESCRIPTION | 19 MD5 | 118 +- NAMESPACE | 121 +- NEWS | 81 - R/DIF.R | 420 +++---- R/RcppExports.R | 146 +- R/anon.R | 1023 ++++++++--------- R/data_selection.R | 820 +++++++------- R/database.R | 648 +++++------ R/design_plot.R | 406 +++---- R/dexter.R | 420 +++---- R/enorm.R | 476 ++++---- R/interaction.R | 458 +++---- R/misc.R | 378 +++--- R/mst.R | 1673 ++++++++++++++--------------- R/predicates.R | 1175 ++++++++++---------- R/profile_analysis.R | 208 +-- R/simMST.R | 164 +- R/suf_stats.R | 250 ++-- README.md | 263 ++-- build/vignette.rds |binary inst/doc/multistage_fundamentals.R | 540 ++++----- inst/doc/multistage_fundamentals.Rmd | 1036 +++++++++--------- inst/doc/multistage_fundamentals.html | 1955 +++++++++++++++++++++------------- inst/extdata/mst_sqlite.sql | 240 ++-- man/DIF_mst.Rd | 64 - man/add_item_properties_mst.Rd | 32 man/add_person_properties_mst.Rd | 34 man/add_response_data_mst.Rd | 88 - man/add_scoring_rules_mst.Rd | 34 man/alter_scoring_rules_mst.Rd | 36 man/close_mst_project.Rd | 28 man/create_mst_project.Rd | 34 man/create_mst_test.Rd | 227 ++- man/design_plot.Rd | 92 - man/dexterMST-package.Rd | 96 - man/fit_enorm_mst.Rd | 108 - man/fit_inter_mst.Rd | 36 man/get_booklets_mst.Rd | 58 - man/get_responses_mst.Rd | 50 man/import_from_dexter.Rd | 110 - man/mst_rules.Rd | 90 - man/open_mst_project.Rd | 28 man/plot.DIF_stats_mst.Rd | 46 man/plot.im_mst.Rd | 48 man/profile_tables_mst.Rd | 42 man/reexports.Rd | 36 man/sim_mst.Rd | 46 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 38 src/data.cpp | 18 src/elsym.cpp | 14 tests/testthat.R | 8 tests/testthat/test_calibration.R | 328 ++--- tests/testthat/test_inputs.R | 194 +-- tests/testthat/test_poly.R | 378 +++--- tests/testthat/test_profiles.R | 190 +-- vignettes/dexterMST.bib | 916 +++++++-------- vignettes/multistage_fundamentals.Rmd | 1036 +++++++++--------- 60 files changed, 9112 insertions(+), 8513 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem. It
features highly configurable search spaces via the 'paradox' package and
finds optimal hyperparameter configurations for any 'mlr3' learner.
'mlr3tuning' works with several optimization algorithms e.g. Random
Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and
Hyperband (in 'mlr3hyperband'). Moreover, it can automatically optimize
learners and estimate the performance of optimized models with nested
resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.19.1 dated 2023-11-20 and 0.19.2 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/zzz.R | 3 --- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Enhanced Foreign Function Interface Supporting Long Vectors
Description: Provides .C64(), which is an enhanced version of .C()
and .Fortran() from the foreign function interface. .C64() supports long
vectors, arguments of type 64-bit integer, and provides a mechanism to
avoid unnecessary copies of read-only and write-only arguments. This
makes it a convenient and fast interface to C/C++ and Fortran code.
Author: Kaspar Moesinger [aut],
Florian Gerber [aut] ,
Reinhard Furrer [cre, ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between dotCall64 versions 1.1-0 dated 2023-10-17 and 1.1-1 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 6 +++++- src/dotCall64.c | 7 +++++-- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized
large-N trials with the 'tricot' approach <https://climmob.net/>.
Developed by van Etten et al. (2019) <doi:10.1017/S0014479716000739>, it turns the
research paradigm on its head; instead of a few researchers designing complicated
trials to compare several technologies in search of the best solutions for the
target environment, it enables many participants to carry out reasonably simple
experiments that taken together can offer even more information. 'ClimMobTools'
enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between ClimMobTools versions 1.0 dated 2023-11-09 and 1.1 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/AAA-getDataCM.R | 5 ----- R/getProjectProgress.R | 1 - R/getProjectsCM.R | 3 --- R/internal_functions.R | 3 --- R/randomize.R | 48 +++++++++++++++++++++++++++++++++++++++++------- inst/doc/Overview.Rmd | 2 +- inst/doc/Overview.html | 16 ++++++++-------- man/ClimMobTools.Rd | 2 +- man/randomize.Rd | 33 ++++++++++++++++++++++++++++++++- vignettes/Overview.Rmd | 2 +- 13 files changed, 107 insertions(+), 47 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available mon [...truncated...]
Author: Michael Hoehle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Sabanes B [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.22.0 dated 2023-10-30 and 1.22.1 dated 2023-11-28
surveillance-1.22.0/surveillance/man/xtable.algoQV.Rd |only surveillance-1.22.1/surveillance/DESCRIPTION | 8 - surveillance-1.22.1/surveillance/MD5 | 51 ++++------ surveillance-1.22.1/surveillance/NEWS.md | 39 +++++-- surveillance-1.22.1/surveillance/R/hhh4.R | 13 +- surveillance-1.22.1/surveillance/R/pit.R | 9 - surveillance-1.22.1/surveillance/R/twinstim_methods.R | 2 surveillance-1.22.1/surveillance/build/partial.rdb |binary surveillance-1.22.1/surveillance/build/vignette.rds |binary surveillance-1.22.1/surveillance/demo/cost.R | 2 surveillance-1.22.1/surveillance/demo/fluBYBW.R | 5 surveillance-1.22.1/surveillance/demo/v77i11.R | 2 surveillance-1.22.1/surveillance/inst/doc/glrnb.pdf |binary surveillance-1.22.1/surveillance/inst/doc/hhh4.pdf |binary surveillance-1.22.1/surveillance/inst/doc/hhh4_spacetime.pdf |binary surveillance-1.22.1/surveillance/inst/doc/monitoringCounts.pdf |binary surveillance-1.22.1/surveillance/inst/doc/surveillance.pdf |binary surveillance-1.22.1/surveillance/inst/doc/twinSIR.pdf |binary surveillance-1.22.1/surveillance/inst/doc/twinstim.pdf |binary surveillance-1.22.1/surveillance/man/algo.quality.Rd | 21 +++- surveillance-1.22.1/surveillance/man/hhh4_validation.Rd | 1 surveillance-1.22.1/surveillance/man/knox.Rd | 4 surveillance-1.22.1/surveillance/man/toLatex.sts.Rd | 3 surveillance-1.22.1/surveillance/man/twinstim.Rd | 24 +--- surveillance-1.22.1/surveillance/man/twinstim_methods.Rd | 5 surveillance-1.22.1/surveillance/man/twinstim_simulation.Rd | 2 surveillance-1.22.1/surveillance/src/twins.cc | 6 - 27 files changed, 116 insertions(+), 81 deletions(-)
Title: EZ-to-Use Biplots
Description: Provides users with an EZ-to-use platform for representing data
with biplots. Currently principal component analysis (PCA) and canonical variate
analysis (CVA) biplots are included. This is accompanied by various formatting
options for the samples and axes. Alpha-bags and concentration ellipses
are included for visual enhancements and interpretation. For an extensive
discussion on the topic, see Gower, J.C., Lubbe, S. and le Roux, N.J.
(2011, ISBN: 978-0-470-01255-0) Understanding Biplots. Wiley: Chichester.
Author: Sugnet Lubbe [aut, cre] ,
Niel le Roux [aut] ,
Johane Nienkemper-Swanepoel [aut]
,
Raeesa Ganey [aut] ,
Carel van der Merwe [aut]
Maintainer: Sugnet Lubbe <muvisu@sun.ac.za>
Diff between biplotEZ versions 1.1.0 dated 2023-11-18 and 1.2.0 dated 2023-11-28
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 3 R/CVA.R | 42 ++-- R/PCA.R | 2 R/aesthetics.R | 17 + R/biplot.R | 166 ++++++++++++++++++ R/plotting.R | 214 ++++++++++++++++------- build/vignette.rds |binary inst/doc/Class_separation.R | 14 + inst/doc/Class_separation.Rmd | 118 ++++++++++++- inst/doc/Class_separation.html | 218 ++++++++++++++++++++++-- inst/doc/biplotEZ.R | 28 ++- inst/doc/biplotEZ.Rmd | 138 ++++++++++++++- inst/doc/biplotEZ.html | 370 ++++++++++++++++++++++++++++++----------- man/CVA.Rd | 11 + man/PCA.Rd | 1 man/fit.measures.Rd |only man/plot.biplot.Rd | 20 ++ man/summary.biplot.Rd |only vignettes/Class_separation.Rmd | 118 ++++++++++++- vignettes/biplotEZ.Rmd | 138 ++++++++++++++- 22 files changed, 1414 insertions(+), 252 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 4.1.3 dated 2023-06-15 and 4.1.4 dated 2023-11-28
DESCRIPTION | 14 - MD5 | 68 ++++---- NAMESPACE | 6 NEWS | 14 + R/Hindex.R | 2 R/convert2df.R | 42 +++-- R/couplingMap.R | 2 R/csvLens2df.R | 3 R/csvScopus2df.R | 4 R/dimensions2df.R | 27 +++ R/histNetwork.R | 345 +++++++++++++++++++++++++++++++++++------- R/histPlot.R | 13 - R/isi2df.R | 4 R/localCitations.R | 6 R/mergeDbSources.R | 1 R/missingData.R | 6 R/networkStat.R | 4 R/normalizeCItationScore.R | 2 R/sysdata.rda |binary R/zzz.R | 6 build/partial.rdb |binary data/bibtag.rda |binary data/countries.rda |binary data/customTheme.rda |binary data/logo.rda |binary data/stopwords.rda |binary inst/biblioshiny/libraries.R | 19 ++ inst/biblioshiny/server.R | 183 ++++++++++++---------- inst/biblioshiny/ui.R | 12 + inst/biblioshiny/utils.R | 293 +++++++++++++++++++++++++++++++---- man/convert2df.Rd | 20 +- man/couplingMap.Rd | 2 man/histNetwork.Rd | 13 - man/histPlot.Rd | 5 man/normalizeCitationScore.Rd | 2 35 files changed, 852 insertions(+), 266 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] . We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genom [...truncated...]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 9.1 dated 2023-09-02 and 9.3 dated 2023-11-28
ChangeLog | 4 + DESCRIPTION | 8 +- MD5 | 18 ++--- src/GenomeSequence.h | 2 src/PlinkInputFile.h | 5 + src/R_CPP_interface.cpp | 7 +- src/RangeList.h | 8 +- src/SingleChromosomeBCFIndex.cpp | 136 ++++++++++++++++++++++++--------------- src/SingleChromosomeVCFIndex.cpp | 42 +++++++++--- src/plink2genoLoader.cpp | 6 + 10 files changed, 159 insertions(+), 77 deletions(-)
Title: Sensory Data Analysis
Description: Statistical Methods to Analyse Sensory Data. SensoMineR: A package for sensory data analysis. S. Le and F. Husson (2008).
Author: Francois Husson, Sebastien Le, Marine Cadoret
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between SensoMineR versions 1.26 dated 2020-05-19 and 1.27 dated 2023-11-28
DESCRIPTION | 15 ++++------ MD5 | 68 +++++++++++++++++++++++------------------------ R/pmfa.R | 2 - data/hedochoc.rda |binary data/sensopanels.rda |binary man/IdMapConsumer.Rd | 2 - man/WordCountAna.Rd | 2 - man/averagetable.Rd | 2 - man/boxprod.Rd | 2 - man/cards.rd | 2 - man/carto.Rd | 2 - man/chocolates.Rd | 2 - man/compo.cocktail.Rd | 2 - man/cpa.Rd | 2 - man/cream_id.Rd | 2 - man/cream_signa.Rd | 2 - man/fahst.rd | 4 +- man/fasnt.rd | 6 ++-- man/fast.Rd | 8 ++--- man/hedo.cocktail.Rd | 2 - man/hsortplot.rd | 2 - man/nappesortplot.Rd | 4 +- man/napping.Rd | 2 - man/napping.don.Rd | 2 - man/napping.words.Rd | 2 - man/perfume.Rd | 2 - man/plot.WordCountAna.Rd | 2 - man/plot.fahst.rd | 2 - man/plot.fasnt.Rd | 2 - man/plot.fast.Rd | 2 - man/print.fahst.rd | 2 - man/print.fasnt.Rd | 2 - man/print.fast.Rd | 2 - man/sensochoc.Rd | 2 - man/smoothies.Rd | 2 - 35 files changed, 79 insertions(+), 80 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide methods
for automatically determining breaks and labels for axes and legends.
Author: Hadley Wickham [aut],
Thomas Lin Pedersen [cre, aut]
,
Dana Seidel [aut],
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between scales versions 1.2.1 dated 2022-08-19 and 1.3.0 dated 2023-11-28
scales-1.2.1/scales/R/bounds.r |only scales-1.2.1/scales/R/breaks.r |only scales-1.2.1/scales/R/colour-manip.r |only scales-1.2.1/scales/R/colour-mapping.r |only scales-1.2.1/scales/R/date-time.r |only scales-1.2.1/scales/R/documentation.r |only scales-1.2.1/scales/R/full-seq.r |only scales-1.2.1/scales/R/label-dollar.R |only scales-1.2.1/scales/R/label-number.r |only scales-1.2.1/scales/R/offset-by.r |only scales-1.2.1/scales/R/pal-area.r |only scales-1.2.1/scales/R/pal-brewer.r |only scales-1.2.1/scales/R/pal-dichromat.r |only scales-1.2.1/scales/R/pal-gradient.r |only scales-1.2.1/scales/R/pal-grey.r |only scales-1.2.1/scales/R/pal-hue.r |only scales-1.2.1/scales/R/pal-identity.r |only scales-1.2.1/scales/R/pal-linetype.r |only scales-1.2.1/scales/R/pal-manual.r |only scales-1.2.1/scales/R/pal-rescale.r |only scales-1.2.1/scales/R/pal-viridis.r |only scales-1.2.1/scales/R/range.r |only scales-1.2.1/scales/R/round-any.r |only scales-1.2.1/scales/R/scale-continuous.r |only scales-1.2.1/scales/R/scale-discrete.r |only scales-1.2.1/scales/R/trans-compose.R |only scales-1.2.1/scales/R/trans-date.r |only scales-1.2.1/scales/R/trans-numeric.r |only scales-1.2.1/scales/R/trans.r |only scales-1.2.1/scales/R/utils.r |only scales-1.2.1/scales/man/area_pal.Rd |only scales-1.2.1/scales/man/asn_trans.Rd |only scales-1.2.1/scales/man/atanh_trans.Rd |only scales-1.2.1/scales/man/boxcox_trans.Rd |only scales-1.2.1/scales/man/brewer_pal.Rd |only scales-1.2.1/scales/man/compose_trans.Rd |only scales-1.2.1/scales/man/date_trans.Rd |only scales-1.2.1/scales/man/dichromat_pal.Rd |only scales-1.2.1/scales/man/div_gradient_pal.Rd |only scales-1.2.1/scales/man/exp_trans.Rd |only scales-1.2.1/scales/man/gradient_n_pal.Rd |only scales-1.2.1/scales/man/grey_pal.Rd |only scales-1.2.1/scales/man/hms_trans.Rd |only scales-1.2.1/scales/man/hue_pal.Rd |only scales-1.2.1/scales/man/identity_pal.Rd |only scales-1.2.1/scales/man/identity_trans.Rd |only scales-1.2.1/scales/man/label_dollar.Rd |only scales-1.2.1/scales/man/linetype_pal.Rd |only scales-1.2.1/scales/man/log_trans.Rd |only scales-1.2.1/scales/man/manual_pal.Rd |only scales-1.2.1/scales/man/probability_trans.Rd |only scales-1.2.1/scales/man/reciprocal_trans.Rd |only scales-1.2.1/scales/man/rescale_pal.Rd |only scales-1.2.1/scales/man/reverse_trans.Rd |only scales-1.2.1/scales/man/seq_gradient_pal.Rd |only scales-1.2.1/scales/man/shape_pal.Rd |only scales-1.2.1/scales/man/sqrt_trans.Rd |only scales-1.2.1/scales/man/time_trans.Rd |only scales-1.2.1/scales/man/trans_new.Rd |only scales-1.2.1/scales/man/trans_range.Rd |only scales-1.2.1/scales/man/viridis_pal.Rd |only scales-1.2.1/scales/man/yj_trans.Rd |only scales-1.2.1/scales/tests/testthat/test-bounds.r |only scales-1.2.1/scales/tests/testthat/test-breaks-log.r |only scales-1.2.1/scales/tests/testthat/test-breaks.r |only scales-1.2.1/scales/tests/testthat/test-colour-manip.r |only scales-1.2.1/scales/tests/testthat/test-colour-mapping.r |only scales-1.2.1/scales/tests/testthat/test-full-seq.r |only scales-1.2.1/scales/tests/testthat/test-label-dollar.R |only scales-1.2.1/scales/tests/testthat/test-label-number.r |only scales-1.2.1/scales/tests/testthat/test-pal-hue.r |only scales-1.2.1/scales/tests/testthat/test-range.r |only scales-1.2.1/scales/tests/testthat/test-scale-continuous.r |only scales-1.2.1/scales/tests/testthat/test-scale-discrete.r |only scales-1.2.1/scales/tests/testthat/test-trans-date.r |only scales-1.2.1/scales/tests/testthat/test-trans-numeric.r |only scales-1.2.1/scales/tests/testthat/test-trans.r |only scales-1.3.0/scales/DESCRIPTION | 34 - scales-1.3.0/scales/LICENSE | 4 scales-1.3.0/scales/MD5 | 301 +++++----- scales-1.3.0/scales/NAMESPACE | 59 + scales-1.3.0/scales/NEWS.md | 53 + scales-1.3.0/scales/R/bounds.R |only scales-1.3.0/scales/R/breaks-retired.R | 6 scales-1.3.0/scales/R/breaks.R |only scales-1.3.0/scales/R/colour-manip.R |only scales-1.3.0/scales/R/colour-mapping.R |only scales-1.3.0/scales/R/colour-ramp.R | 2 scales-1.3.0/scales/R/date-time.R |only scales-1.3.0/scales/R/documentation.R |only scales-1.3.0/scales/R/full-seq.R |only scales-1.3.0/scales/R/label-bytes.R | 8 scales-1.3.0/scales/R/label-currency.R |only scales-1.3.0/scales/R/label-date.R | 27 scales-1.3.0/scales/R/label-number-si.R | 20 scales-1.3.0/scales/R/label-number.R |only scales-1.3.0/scales/R/label-ordinal.R | 2 scales-1.3.0/scales/R/label-percent.R | 1 scales-1.3.0/scales/R/label-pvalue.R | 2 scales-1.3.0/scales/R/labels-retired.R | 13 scales-1.3.0/scales/R/offset-by.R |only scales-1.3.0/scales/R/pal-area.R |only scales-1.3.0/scales/R/pal-brewer.R |only scales-1.3.0/scales/R/pal-dichromat.R |only scales-1.3.0/scales/R/pal-gradient.R |only scales-1.3.0/scales/R/pal-grey.R |only scales-1.3.0/scales/R/pal-hue.R |only scales-1.3.0/scales/R/pal-identity.R |only scales-1.3.0/scales/R/pal-linetype.R |only scales-1.3.0/scales/R/pal-manual.R |only scales-1.3.0/scales/R/pal-rescale.R |only scales-1.3.0/scales/R/pal-shape.r | 17 scales-1.3.0/scales/R/pal-viridis.R |only scales-1.3.0/scales/R/range.R |only scales-1.3.0/scales/R/round-any.R |only scales-1.3.0/scales/R/scale-continuous.R |only scales-1.3.0/scales/R/scale-discrete.R |only scales-1.3.0/scales/R/scales-package.R | 1 scales-1.3.0/scales/R/transform-compose.R |only scales-1.3.0/scales/R/transform-date.R |only scales-1.3.0/scales/R/transform-numeric.R |only scales-1.3.0/scales/R/transform.R |only scales-1.3.0/scales/R/utils.R |only scales-1.3.0/scales/README.md | 30 scales-1.3.0/scales/build/partial.rdb |binary scales-1.3.0/scales/man/Range.Rd | 2 scales-1.3.0/scales/man/alpha.Rd | 2 scales-1.3.0/scales/man/breaks_extended.Rd | 2 scales-1.3.0/scales/man/breaks_pretty.Rd | 2 scales-1.3.0/scales/man/breaks_timespan.Rd |only scales-1.3.0/scales/man/breaks_width.Rd | 2 scales-1.3.0/scales/man/col2hcl.Rd | 2 scales-1.3.0/scales/man/col_numeric.Rd | 2 scales-1.3.0/scales/man/comma.Rd | 13 scales-1.3.0/scales/man/cscale.Rd | 16 scales-1.3.0/scales/man/demo_continuous.Rd | 5 scales-1.3.0/scales/man/dollar_format.Rd | 28 scales-1.3.0/scales/man/dscale.Rd | 4 scales-1.3.0/scales/man/expand_range.Rd | 2 scales-1.3.0/scales/man/figures/README-labels-1.png |binary scales-1.3.0/scales/man/figures/README-transforms-1.png |binary scales-1.3.0/scales/man/figures/lifecycle-archived.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-defunct.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-deprecated.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-experimental.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-maturing.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-questioning.svg | 22 scales-1.3.0/scales/man/figures/lifecycle-soft-deprecated.svg |only scales-1.3.0/scales/man/figures/lifecycle-stable.svg | 30 scales-1.3.0/scales/man/figures/lifecycle-superseded.svg | 22 scales-1.3.0/scales/man/figures/logo.png |binary scales-1.3.0/scales/man/figures/logo.svg |only scales-1.3.0/scales/man/fullseq.Rd | 2 scales-1.3.0/scales/man/label_bytes.Rd | 48 + scales-1.3.0/scales/man/label_currency.Rd |only scales-1.3.0/scales/man/label_date.Rd | 53 + scales-1.3.0/scales/man/label_number.Rd | 13 scales-1.3.0/scales/man/label_number_auto.Rd | 2 scales-1.3.0/scales/man/label_number_si.Rd | 59 + scales-1.3.0/scales/man/label_ordinal.Rd | 52 + scales-1.3.0/scales/man/label_parse.Rd | 2 scales-1.3.0/scales/man/label_percent.Rd | 39 + scales-1.3.0/scales/man/label_pvalue.Rd | 2 scales-1.3.0/scales/man/label_scientific.Rd | 2 scales-1.3.0/scales/man/muted.Rd | 2 scales-1.3.0/scales/man/new_transform.Rd |only scales-1.3.0/scales/man/number.Rd | 16 scales-1.3.0/scales/man/oob.Rd | 2 scales-1.3.0/scales/man/pal_area.Rd |only scales-1.3.0/scales/man/pal_brewer.Rd |only scales-1.3.0/scales/man/pal_dichromat.Rd |only scales-1.3.0/scales/man/pal_div_gradient.Rd |only scales-1.3.0/scales/man/pal_gradient_n.Rd |only scales-1.3.0/scales/man/pal_grey.Rd |only scales-1.3.0/scales/man/pal_hue.Rd |only scales-1.3.0/scales/man/pal_identity.Rd |only scales-1.3.0/scales/man/pal_linetype.Rd |only scales-1.3.0/scales/man/pal_manual.Rd |only scales-1.3.0/scales/man/pal_rescale.Rd |only scales-1.3.0/scales/man/pal_seq_gradient.Rd |only scales-1.3.0/scales/man/pal_shape.Rd |only scales-1.3.0/scales/man/pal_viridis.Rd |only scales-1.3.0/scales/man/pretty_breaks.Rd | 2 scales-1.3.0/scales/man/rescale.Rd | 11 scales-1.3.0/scales/man/rescale_max.Rd | 2 scales-1.3.0/scales/man/rescale_mid.Rd | 8 scales-1.3.0/scales/man/rescale_none.Rd | 2 scales-1.3.0/scales/man/scales-package.Rd | 5 scales-1.3.0/scales/man/show_col.Rd | 10 scales-1.3.0/scales/man/train_continuous.Rd | 2 scales-1.3.0/scales/man/train_discrete.Rd | 6 scales-1.3.0/scales/man/transform_asinh.Rd |only scales-1.3.0/scales/man/transform_asn.Rd |only scales-1.3.0/scales/man/transform_atanh.Rd |only scales-1.3.0/scales/man/transform_boxcox.Rd |only scales-1.3.0/scales/man/transform_compose.Rd |only scales-1.3.0/scales/man/transform_date.Rd |only scales-1.3.0/scales/man/transform_exp.Rd |only scales-1.3.0/scales/man/transform_identity.Rd |only scales-1.3.0/scales/man/transform_log.Rd |only scales-1.3.0/scales/man/transform_probability.Rd |only scales-1.3.0/scales/man/transform_reciprocal.Rd |only scales-1.3.0/scales/man/transform_reverse.Rd |only scales-1.3.0/scales/man/transform_sqrt.Rd |only scales-1.3.0/scales/man/transform_time.Rd |only scales-1.3.0/scales/man/transform_timespan.Rd |only scales-1.3.0/scales/man/transform_yj.Rd |only scales-1.3.0/scales/man/trim_to_domain.Rd |only scales-1.3.0/scales/man/zero_range.Rd | 2 scales-1.3.0/scales/tests/testthat/_snaps/label-number.md | 5 scales-1.3.0/scales/tests/testthat/_snaps/trans-compose.md | 10 scales-1.3.0/scales/tests/testthat/_snaps/trans-date.md |only scales-1.3.0/scales/tests/testthat/_snaps/trans.md | 14 scales-1.3.0/scales/tests/testthat/test-bounds.R |only scales-1.3.0/scales/tests/testthat/test-breaks-log.R |only scales-1.3.0/scales/tests/testthat/test-breaks.R |only scales-1.3.0/scales/tests/testthat/test-colour-manip.R |only scales-1.3.0/scales/tests/testthat/test-colour-mapping.R |only scales-1.3.0/scales/tests/testthat/test-full-seq.R |only scales-1.3.0/scales/tests/testthat/test-label-currency.R |only scales-1.3.0/scales/tests/testthat/test-label-number-si.R | 6 scales-1.3.0/scales/tests/testthat/test-label-number.R |only scales-1.3.0/scales/tests/testthat/test-pal-hue.R |only scales-1.3.0/scales/tests/testthat/test-pal-manual.R | 8 scales-1.3.0/scales/tests/testthat/test-range.R |only scales-1.3.0/scales/tests/testthat/test-scale-continuous.R |only scales-1.3.0/scales/tests/testthat/test-scale-discrete.R |only scales-1.3.0/scales/tests/testthat/test-trans-compose.R | 29 scales-1.3.0/scales/tests/testthat/test-trans-date.R |only scales-1.3.0/scales/tests/testthat/test-trans-numeric.R |only scales-1.3.0/scales/tests/testthat/test-trans.R |only 231 files changed, 914 insertions(+), 348 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Romain Francois [ctb, cph] ,
Francesc Alted [ctb, cph] ,
Bryce Chamberlain [ctb] ,
Sal [...truncated...]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.5 dated 2023-02-22 and 0.25.6 dated 2023-11-28
ChangeLog | 6 DESCRIPTION | 10 MD5 | 34 +- R/RcppExports.R | 2 README.md | 28 - build/vignette.rds |binary configure | 686 +++++++++++++++++++++++++++++++++++++++++++- configure.ac | 36 +- data/starnames.rda |binary inst/doc/vignette.R | 32 ++ inst/doc/vignette.html | 25 - inst/doc/vignette.rmd | 52 ++- src/Makevars.in | 3 src/qs_common.h | 104 +++--- src/qs_functions.cpp | 32 +- tests/correctness_testing.R | 62 +++ tests/qattributes_testing.R | 63 +++- vignettes/vignette.rmd | 52 ++- 18 files changed, 1026 insertions(+), 201 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
More details can also be found in the corresponding article
<doi:10.18637/jss.v101.i06>.
Author: Stefan Lenz [aut, cre] ,
Harald Binder [aut, ths] ,
Angelo D'Ambrosio [ctb]
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 1.1.1 dated 2022-01-26 and 1.1.2 dated 2023-11-28
JuliaConnectoR-1.1.1/JuliaConnectoR/inst/examples/IndexedTables-Project/Manifest.toml |only JuliaConnectoR-1.1.1/JuliaConnectoR/inst/examples/IndexedTables-Project/Project.toml |only JuliaConnectoR-1.1.1/JuliaConnectoR/inst/examples/iris-example/project_1_6 |only JuliaConnectoR-1.1.2/JuliaConnectoR/DESCRIPTION | 6 - JuliaConnectoR-1.1.2/JuliaConnectoR/MD5 | 32 +++-- JuliaConnectoR-1.1.2/JuliaConnectoR/NAMESPACE | 5 JuliaConnectoR-1.1.2/JuliaConnectoR/R/connecting.R | 23 ++-- JuliaConnectoR-1.1.2/JuliaConnectoR/R/handling_dataframes.R | 12 +- JuliaConnectoR-1.1.2/JuliaConnectoR/inst/Julia/handling_dataframes.jl | 17 ++- JuliaConnectoR-1.1.2/JuliaConnectoR/inst/Julia/reading.jl | 18 ++- JuliaConnectoR-1.1.2/JuliaConnectoR/inst/examples/IndexedTables-Project/1_0 |only JuliaConnectoR-1.1.2/JuliaConnectoR/inst/examples/IndexedTables-Project/1_6 |only JuliaConnectoR-1.1.2/JuliaConnectoR/inst/examples/iris-example/iris-example.R | 18 +-- JuliaConnectoR-1.1.2/JuliaConnectoR/inst/examples/iris-example/iris-example.jl | 16 +- JuliaConnectoR-1.1.2/JuliaConnectoR/inst/examples/iris-example/project_1_9 |only JuliaConnectoR-1.1.2/JuliaConnectoR/man/as.data.frame.JuliaProxy.Rd | 12 +- JuliaConnectoR-1.1.2/JuliaConnectoR/tests/testthat.R | 5 JuliaConnectoR-1.1.2/JuliaConnectoR/tests/testthat/test.R | 55 ++++++---- 18 files changed, 131 insertions(+), 88 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: An Interface to IMF (International Monetary Fund) Data JSON API
Description: A straightforward interface for accessing the IMF
(International Monetary Fund) data JSON API,
available at <https://data.imf.org/>. This package offers direct access to
the primary API endpoints: Dataflow, DataStructure, and CompactData.
And, it provides an intuitive interface for exploring available
dimensions and attributes, as well as querying individual time-series datasets.
Additionally, the package implements a rate limit on API calls to reduce the
chances of exceeding service limits (limited to 10 calls every 5 seconds)
and encountering response errors.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between imf.data versions 0.1.2 dated 2023-11-23 and 0.1.3 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 +++++- R/methods.R | 21 +++++++++++---------- 4 files changed, 22 insertions(+), 17 deletions(-)
Title: Read and Write TIFF Images
Description: Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation.
Author: Simon Urbanek <Simon.Urbanek@r-project.org> [aut, cre],
Kent Johnson <kjohnson@akoyabio.com> [ctb]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between tiff versions 0.1-11 dated 2022-01-31 and 0.1-12 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 6 ++++++ src/Makevars.ucrt | 7 ++++++- src/common.c | 2 +- 5 files changed, 20 insertions(+), 9 deletions(-)
Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of
linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client
is included in this package as well.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-11 dated 2022-11-28 and 1.8-13 dated 2023-11-28
DESCRIPTION | 6 MD5 | 52 ++--- NEWS | 21 ++ R/conn.R | 3 R/zzz.R | 3 inst/java/REngine.jar |binary inst/java/Rserve.jar |binary man/ocap.Rd | 2 src/Makevars.in | 4 src/Makevars.win | 4 src/RSserver.c | 4 src/Rserv.c | 28 +- src/Rsrv.h | 4 src/bsdcmpt.h |only src/client/cxx/Rsrv.h | 4 src/client/java/Rserve/RConnection.java | 20 + src/client/java/Rserve/Rserve.jar |binary src/date.c |only src/http.c | 331 ++++++++++++++++++++++++++++---- src/proxy/date.c | 2 src/proxy/forward.c | 44 ++++ src/proxy/server.c | 2 src/proxy/tls.c | 4 src/proxy/websockets.c | 2 src/qap_encode.c | 2 src/standalone.c | 6 src/websockets.c | 4 src/winembed.c | 6 28 files changed, 452 insertions(+), 106 deletions(-)
Title: Client for Rserve
Description: Client for Rserve, allowing to connect to Rserve instances and issue commands.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between RSclient versions 0.7-9 dated 2022-11-29 and 0.7-10 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ src/Makevars.win | 6 +++++- src/cli.c | 4 ++-- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Fast Interactive Framework for Web Scripting Using R
Description: Infrastrcture for creating rich, dynamic web content using R scripts while maintaining very fast response time.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeffrey.horner@gmail.com>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between FastRWeb versions 1.2-0 dated 2021-11-03 and 1.2-1 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ src/Rcgi/Rconnection.cc | 7 ++++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Description: R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.6-1 dated 2023-08-17 and 1.6-2 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 9 +++++++++ src/Makevars.ucrt | 17 +++++++++++++++-- src/cairogd.h | 2 +- src/cairotalk.c | 4 ++-- 6 files changed, 35 insertions(+), 13 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.8 dated 2023-11-27 and 1.9.9 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 2 +- inst/include/dynamic_data.hpp | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Estimation for MVN and Student-t Data with Monotone Missingness
Description: Estimation of multivariate normal (MVN) and student-t data of
arbitrary dimension where the pattern of missing data is monotone.
See Pantaleo and Gramacy (2010) <arXiv:0907.2135>.
Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions fail,
the package can handle a nearly arbitrary amount of missing data.
The current version supports maximum likelihood inference and
a full Bayesian approach employing scale-mixtures for Gibbs sampling.
Monotone data augmentation extends this Bayesian approach to arbitrary
missingness patterns. A fully functional standalone interface to the
Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown),
Horseshoe (from Carvalho, Polson, & Scott), and ridge regression
with model selection via Reversible Jump, and student-t errors
(from Geweke) is also provided.
Author: Robert B. Gramacy <rbg@vt.edu>, with Fortran contributions from Cleve Moler as updated by Berwin A. Turlach
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between monomvn versions 1.9-18 dated 2023-08-21 and 1.9-19 dated 2023-11-28
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/blasso.cc | 6 +++--- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
fair-cut forest (Cortes (2021) <arXiv:2110:13402>),
robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>),
and customizable variations of them, for isolation-based outlier detection, clustered outlier detection,
distance or similarity approximation (Cortes (2019) <arXiv:1910.12362>),
isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting, and providing different metrics for
scoring anomalies based on isolation depth or density (Cortes (2021) <arXiv:2111.11639>).
Provides simp [...truncated...]
Author: David Cortes [aut, cre, cph],
Thibaut Goetghebuer-Planchon [cph] ,
David Blackman [cph] ,
Sebastiano Vigna [cph] ,
NumPy Developers [cph] ,
SciPy Developers [cph] ,
Enthought Inc [cph] ,
Stephen Moshier [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.5.24 dated 2023-11-19 and 0.5.24-1 dated 2023-11-28
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- src/Rwrapper.cpp | 8 +++++++- src/isotree.h | 17 ++++++++++++++--- 4 files changed, 28 insertions(+), 10 deletions(-)
Title: Fast Estimation of Time-Varying Infectious Disease Transmission
Rates
Description: Methods for estimating time-varying infectious disease
transmission rates from disease incidence time series, based on
discretizations of an SIR model, as analyzed in Jagan et al. (2020)
<doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.1.0 dated 2023-08-28 and 0.1.1 dated 2023-11-28
fastbeta-0.1.0/fastbeta/data/sir.e01.rda |only fastbeta-0.1.1/fastbeta/DESCRIPTION | 11 ++++++----- fastbeta-0.1.1/fastbeta/MD5 | 12 +++++++----- fastbeta-0.1.1/fastbeta/build/partial.rdb |binary fastbeta-0.1.1/fastbeta/data/sir.e01.R |only fastbeta-0.1.1/fastbeta/inst/NEWS.Rd |only fastbeta-0.1.1/fastbeta/inst/scripts/smallpox.R | 2 +- fastbeta-0.1.1/fastbeta/src/Makevars |only fastbeta-0.1.1/fastbeta/src/sir.c | 2 +- 9 files changed, 15 insertions(+), 12 deletions(-)
Title: Binary Causality Inference Framework
Description: A framework to infer causality on binary data using techniques in frequent pattern mining and estimation statistics. Given a set of individual vectors S={x} where x(i) is a realization value of binary variable i, the framework infers empirical causal relations of binary variables i,j from S in a form of causal graph G=(V,E) where V is a set of nodes representing binary variables and there is an edge from i to j in E if the variable i causes j. The framework determines dependency among variables as well as analyzing confounding factors before deciding whether i causes j. The publication of this package is at Chainarong Amornbunchornvej, Navaporn Surasvadi, Anon Plangprasopchok, and Suttipong Thajchayapong (2023) <doi:10.1016/j.heliyon.2023.e15947>.
Author: Chainarong Amornbunchornvej [aut, cre]
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between BiCausality versions 0.1.3 dated 2023-05-22 and 0.1.4 dated 2023-11-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 ++++- R/CausalGraphInferMainFunc.R | 2 +- R/bSCMDepndentGraphFastFunc.R | 2 -- inst/doc/BiCausality_demo.html | 2 +- man/CausalGraphInferMainFunc.Rd | 2 +- 7 files changed, 16 insertions(+), 15 deletions(-)
Title: Approximate Summation of Series
Description: Application of theoretical results which ensure that the summation
of an infinite discrete series is within an arbitrary margin of error of its
true value. The C code under the hood is shared through header files to allow
users to sum their own low level functions as well. Based on the paper by
Braden (1992) <doi: 10.2307/2324995>.
Author: Guido A. Moreira [cre, aut] ,
Luiz Max Carvalho [ctb]
Maintainer: Guido A. Moreira <guidoalber@gmail.com>
Diff between sumR versions 0.4.14 dated 2023-08-21 and 0.4.15 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/precompiled.Rd | 8 ++------ src/r_wrappers.c | 2 +- 4 files changed, 10 insertions(+), 14 deletions(-)
Title: Construct Consistent Time Series from Textual Data
Description: A rolling version of the Latent Dirichlet Allocation, see Rieger et al. (2021) <doi:10.18653/v1/2021.findings-emnlp.201>. By a sequential approach, it enables the construction of LDA-based time series of topics that are consistent with previous states of LDA models. After an initial modeling, updates can be computed efficiently, allowing for real-time monitoring and detection of events or structural breaks.
Author: Jonas Rieger [aut, cre]
Maintainer: Jonas Rieger <jonas.rieger@tu-dortmund.de>
Diff between rollinglda versions 0.1.2 dated 2022-10-01 and 0.1.3 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 2 +- src/ldagibbs.c | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-13 dated 2023-03-17 and 1.3-14 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/AAA.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary src/RandomForest.c | 4 ++-- tests/mob.Rout.save | 18 +++--------------- 10 files changed, 23 insertions(+), 31 deletions(-)
Title: Technical Trading Rules
Description: A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.
Author: Joshua Ulrich [cre, aut],
Ethan B. Smith [ctb]
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.24.3 dated 2021-12-12 and 0.24.4 dated 2023-11-28
TTR-0.24.3/TTR/CHANGES |only TTR-0.24.4/TTR/DESCRIPTION | 15 TTR-0.24.4/TTR/MD5 | 187 +++++----- TTR-0.24.4/TTR/NAMESPACE | 5 TTR-0.24.4/TTR/NEWS.md |only TTR-0.24.4/TTR/R/ADX.R | 90 ++-- TTR-0.24.4/TTR/R/ATR.R | 110 +++--- TTR-0.24.4/TTR/R/CCI.R | 78 ++-- TTR-0.24.4/TTR/R/CLV.R | 38 +- TTR-0.24.4/TTR/R/CMF.R | 54 +- TTR-0.24.4/TTR/R/CMO.R | 52 +- TTR-0.24.4/TTR/R/CTI.R | 2 TTR-0.24.4/TTR/R/DPO.R | 70 +-- TTR-0.24.4/TTR/R/DVI.R | 50 +- TTR-0.24.4/TTR/R/DonchianChannel.R | 78 ++-- TTR-0.24.4/TTR/R/EMV.R | 72 +-- TTR-0.24.4/TTR/R/GMMA.R | 66 +-- TTR-0.24.4/TTR/R/KST.R | 102 ++--- TTR-0.24.4/TTR/R/MACD.R | 136 +++---- TTR-0.24.4/TTR/R/MFI.R | 66 +-- TTR-0.24.4/TTR/R/MovingAverages.R | 344 ++++++++----------- TTR-0.24.4/TTR/R/OBV.R | 50 +- TTR-0.24.4/TTR/R/RSI.R | 120 +++--- TTR-0.24.4/TTR/R/SAR.R | 60 +-- TTR-0.24.4/TTR/R/SNR.R | 52 +- TTR-0.24.4/TTR/R/TDI.R | 80 ++-- TTR-0.24.4/TTR/R/TRIX.R | 92 ++--- TTR-0.24.4/TTR/R/TTR-package.R | 151 ++++---- TTR-0.24.4/TTR/R/TTRtools.R | 50 +- TTR-0.24.4/TTR/R/VHF.R | 52 +- TTR-0.24.4/TTR/R/WPR.R | 74 ++-- TTR-0.24.4/TTR/R/WebData.R | 218 ++++++------ TTR-0.24.4/TTR/R/ZigZag.R | 86 ++-- TTR-0.24.4/TTR/R/adjRatios.R | 50 +- TTR-0.24.4/TTR/R/aroon.R | 92 ++--- TTR-0.24.4/TTR/R/bollingerBands.R | 104 ++--- TTR-0.24.4/TTR/R/chaikinAD.R | 54 +- TTR-0.24.4/TTR/R/chaikinVolatility.R | 50 +- TTR-0.24.4/TTR/R/changes.R | 46 +- TTR-0.24.4/TTR/R/keltnerChannels.R | 118 +++--- TTR-0.24.4/TTR/R/percentRank.R | 84 ++-- TTR-0.24.4/TTR/R/priceBands.R | 100 ++--- TTR-0.24.4/TTR/R/rollFun.R | 42 +- TTR-0.24.4/TTR/R/runFun.R | 125 +++--- TTR-0.24.4/TTR/R/stochastics.R | 232 ++++++------ TTR-0.24.4/TTR/R/ultimateOscillator.R | 36 - TTR-0.24.4/TTR/R/volatility.R | 236 ++++++------- TTR-0.24.4/TTR/R/williamsAD.R | 48 +- TTR-0.24.4/TTR/README.md |only TTR-0.24.4/TTR/inst/unitTests/output.Oscillators.rda |binary TTR-0.24.4/TTR/inst/unitTests/runit.TTR.Misc.R | 5 TTR-0.24.4/TTR/inst/unitTests/runit.TTR.runFun.R | 29 + TTR-0.24.4/TTR/man/ADX.Rd | 16 TTR-0.24.4/TTR/man/ATR.Rd | 19 - TTR-0.24.4/TTR/man/CCI.Rd | 4 TTR-0.24.4/TTR/man/CLV.Rd | 4 TTR-0.24.4/TTR/man/CMF.Rd | 4 TTR-0.24.4/TTR/man/CMO.Rd | 16 TTR-0.24.4/TTR/man/DPO.Rd | 6 TTR-0.24.4/TTR/man/DVI.Rd | 4 TTR-0.24.4/TTR/man/DonchianChannel.Rd | 14 TTR-0.24.4/TTR/man/EMV.Rd | 12 TTR-0.24.4/TTR/man/GMMA.Rd | 4 TTR-0.24.4/TTR/man/KST.Rd | 8 TTR-0.24.4/TTR/man/MACD.Rd | 16 TTR-0.24.4/TTR/man/MFI.Rd | 4 TTR-0.24.4/TTR/man/MovingAverages.Rd | 81 +--- TTR-0.24.4/TTR/man/OBV.Rd | 4 TTR-0.24.4/TTR/man/RSI.Rd | 16 TTR-0.24.4/TTR/man/SAR.Rd | 4 TTR-0.24.4/TTR/man/SNR.Rd | 2 TTR-0.24.4/TTR/man/TDI.Rd | 12 TTR-0.24.4/TTR/man/TRIX.Rd | 8 TTR-0.24.4/TTR/man/TTR.Rd | 45 +- TTR-0.24.4/TTR/man/VHF.Rd | 8 TTR-0.24.4/TTR/man/WPR.Rd | 18 TTR-0.24.4/TTR/man/WebData.Rd | 50 +- TTR-0.24.4/TTR/man/ZigZag.Rd | 8 TTR-0.24.4/TTR/man/adjRatios.Rd | 22 - TTR-0.24.4/TTR/man/aroon.Rd | 16 TTR-0.24.4/TTR/man/bollingerBands.Rd | 24 - TTR-0.24.4/TTR/man/chaikinAD.Rd | 4 TTR-0.24.4/TTR/man/chaikinVolatility.Rd | 4 TTR-0.24.4/TTR/man/changes.Rd | 6 TTR-0.24.4/TTR/man/keltnerChannels.Rd | 8 TTR-0.24.4/TTR/man/priceBands.Rd | 14 TTR-0.24.4/TTR/man/rollFun.Rd | 8 TTR-0.24.4/TTR/man/runFun.Rd | 26 - TTR-0.24.4/TTR/man/stochastics.Rd | 42 +- TTR-0.24.4/TTR/man/ttrc.Rd | 4 TTR-0.24.4/TTR/man/volatility.Rd | 64 +-- TTR-0.24.4/TTR/man/williamsAD.Rd | 6 TTR-0.24.4/TTR/src/init.c | 4 TTR-0.24.4/TTR/src/moving_averages.c | 135 ++----- TTR-0.24.4/TTR/src/runfun.c | 71 ++- TTR-0.24.4/TTR/src/ttr.h | 1 96 files changed, 2493 insertions(+), 2504 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.5.4.1 dated 2023-07-23 and 0.5.5 dated 2023-11-28
svd-0.5.4.1/svd/src/propack/second.f |only svd-0.5.5/svd/DESCRIPTION | 6 +- svd-0.5.5/svd/MD5 | 11 ++-- svd-0.5.5/svd/src/Makevars | 3 - svd-0.5.5/svd/src/propack/dlansvd_irl.f | 74 ++++++++++++++++---------------- svd-0.5.5/svd/src/propack/propack_svd.c | 2 svd-0.5.5/svd/src/trlan/trlaux.c | 4 - 7 files changed, 49 insertions(+), 51 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
[...truncated...]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.21.10 dated 2023-11-07 and 2.21.11 dated 2023-11-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/MxMI.R | 21 +++++++++++---------- R/MxVersion.R | 2 +- build/OpenMx.pdf |binary build/stage23.rdb |binary inst/doc/deriv.html | 18 +++++++++--------- inst/doc/factor_analysis.html | 8 ++++---- inst/doc/reg_mimic.html | 10 +++++----- inst/doc/regularization.html | 2 +- man/mxMI.Rd | 4 ++-- src/omxAlgebraFitFunction.cpp | 2 +- 12 files changed, 49 insertions(+), 48 deletions(-)
Title: Dynamic Models with Regime-Switching
Description: Intensive longitudinal data have become increasingly prevalent in
various scientific disciplines. Many such data sets are noisy, multivariate,
and multi-subject in nature. The change functions may also be continuous,
or continuous but interspersed with periods of discontinuities (i.e.,
showing regime switches). The package 'dynr' (Dynamic Modeling in R) is an
R package that implements a set of computationally efficient algorithms for
handling a broad class of linear and nonlinear discrete- and continuous-time
models with regime-switching properties under the constraint of linear
Gaussian measurement functions. The discrete-time models can generally
take on the form of a state-space or difference equation model. The
continuous-time models are generally expressed as a set of ordinary or
stochastic differential equations. All estimation and computations are
performed in C, but users are provided with the option to specify the
model of interest via a set of simple and easy-to-learn model s [...truncated...]
Author: Lu Ou [aut],
Michael D. Hunter [aut, cre] ,
Sy-Miin Chow [aut] ,
Linying Ji [aut],
Meng Chen [aut],
Hui-Ju Hung [aut],
Jungmin Lee [aut],
Yanling Li [aut],
Jonathan Park [aut],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Benoit [...truncated...]
Maintainer: Michael D. Hunter <mike.dynr@gmail.com>
Diff between dynr versions 0.1.16-91 dated 2022-10-17 and 0.1.16-105 dated 2023-11-28
DESCRIPTION | 22 - MD5 | 38 +- R/dynrCook.R | 1 R/dynrFuncAddress.R | 36 +- R/dynrVersion.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/InstallationForDevelopers.Rnw | 410 +++++++++++++++-------------- inst/doc/InstallationForDevelopers.pdf |binary inst/doc/InstallationForUsers.Rnw | 286 ++++++++++---------- inst/doc/InstallationForUsers.pdf |binary inst/doc/LinearDiscreteTimeModels.pdf |binary inst/doc/NonlinearContinuousTimeModels.pdf |binary inst/doc/linearSDE.html | 180 ++++++------ src/brekfis.c | 6 src/ekf.c | 16 - src/slsqp.c | 2 vignettes/InstallationForDevelopers.Rnw | 410 +++++++++++++++-------------- vignettes/InstallationForUsers.Rnw | 286 ++++++++++---------- 20 files changed, 888 insertions(+), 809 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soil [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.0.1 dated 2023-09-06 and 2.0.2 dated 2023-11-28
DESCRIPTION | 6 MD5 | 111 ++- NAMESPACE | 2 NEWS.md | 11 R/SoilProfileCollection-methods.R | 2 R/SoilProfileCollection-operators.R | 4 R/aggregateColor.R | 61 +- R/bootstrapSoilTexture.R | 18 R/col2Munsell.R |only R/colorQuantiles.R | 81 +- R/estimateSoilColor.R | 18 R/evalMissingData.R | 222 +++++-- R/fillHzGaps.R | 15 R/generalize.hz.R | 8 R/groupedProfilePlot.R | 2 R/hzTransitionProbabilities.R | 43 - R/mixMunsell.R | 79 +- R/mostLikelyHzSequence.R | 1 R/munsell2rgb.R | 289 +++++---- R/plotColorMixture.R | 19 R/plotSPC.R | 4 R/profileInformationIndex.R | 353 +++++++++--- R/sketch-utils.R | 4 R/spec2Munsell.R | 8 R/warpHorizons.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 32 - inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 88 +- inst/doc/NCSP.html | 4 inst/doc/label-placement.R | 2 inst/doc/label-placement.html | 20 inst/doc/missing-data.R |only inst/doc/missing-data.Rmd |only inst/doc/missing-data.html |only man/SoilProfileCollection-plotting-methods.Rd | 1 man/aggregateColor.Rd | 2 man/bootstrapSoilTexture.Rd | 13 man/col2Munsell.Rd |only man/colorQuantiles.Rd | 9 man/doublebracket-set.Rd | 1 man/doublebracket.Rd | 3 man/estimateSoilColor.Rd | 2 man/evalMissingData.Rd | 111 ++- man/genhzTableToAdjMat.Rd |only man/hzTransitionProbabilities.Rd | 36 - man/mixMunsell.Rd | 10 man/plotColorQuantiles.Rd | 2 man/profileInformationIndex.Rd | 78 +- man/rgb2munsell.Rd | 2 man/spec2Munsell.Rd | 6 man/warpHorizons.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-aggregateColor.R | 11 tests/testthat/test-color-conversion.R | 124 ++-- tests/testthat/test-colorQuantiles.R | 23 tests/testthat/test-evalMissingData.R | 28 tests/testthat/test-mixMunsell.R | 2 tests/testthat/test-profileInformationIndex.R | 61 +- tests/testthat/test-spec2Munsell.R | 2 vignettes/missing-data.Rmd |only 61 files changed, 1248 insertions(+), 786 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-05 1.1.1
2019-01-31 1.1.0
2016-08-01 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-03 1.14.1
2018-11-28 1.3.4
2018-07-31 1.1.0
2018-03-07 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 2.2.14
2020-12-04 2.2.1
2019-07-05 2.0.10
2019-03-08 2.0.7
2018-11-29 2.0.4
2017-09-19 2.0.3
2017-05-11 2.0.1
2016-06-26 2.0.0
2015-06-10 1.9.4
2014-09-29 1.9.3
2014-07-16 1.9
2014-05-13 1.8
2013-10-22 1.7
2013-08-10 1.6
2013-06-15 1.5
2013-04-03 1.4
2012-12-13 1.3
2012-08-18 1.2
2012-08-15 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-27 2.5.3
2022-10-11 2.5.2
2022-07-19 2.5.1
2022-07-11 2.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-26 0.2.0
2019-03-13 0.1.10
2018-03-29 0.1.9
2017-07-19 0.1.5
2017-06-20 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-16 1.33
2022-03-04 1.31
2022-02-03 1.30
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-11 1.2.5
2021-12-22 1.2.4
2021-10-29 1.2.1
2021-07-22 1.1.0.4
2021-05-17 1.1.0.2
2021-05-12 1.1
2020-02-17 1.0.1.8
2020-02-07 1.0.1.7
2020-01-09 1.0.1.6
2019-12-20 1.0.1.5
2019-09-24 1.0.1.4
2019-04-11 1.0.1.2
2018-09-19 1.0.0.7
2018-08-28 1.0.0.6
2018-04-25 1.0.0.4
2018-02-05 1.0.0.3
2017-06-30 1.0.0.1
2017-06-14 1.0.0.0
2017-04-18 0.9.9.0
2017-04-17 0.9.8.8
2017-03-13 0.9.8.3
2017-03-12 0.9.8.2
2017-02-01 0.9.6
2017-01-31 0.9.5
2017-01-20 0.9.3
2016-10-18 0.8.7
2016-09-07 0.8.6
2016-07-05 0.7.9
2015-09-18 0.7.5
2015-03-27 0.7.2