Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] ,
Alessandro Gasparini [ctb] ,
Benjie Gillam [ctb],
Claus Thorn Ekstroem [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] ,
Inaki Ucar [ctb] ,
John Little [ctb],
Joselyn Ch [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.24 dated 2022-04-26 and 0.25 dated 2022-06-13
DESCRIPTION | 10 +++++---- MD5 | 8 ++++--- R/utils.R | 14 ++++++++----- inst/rmarkdown/templates/xaringan/resources/js/data-uri.js | 2 - inst/rmarkdown/templates/xaringan/resources/wic-fonts.css |only inst/rmarkdown/templates/xaringan/resources/wic.css |only 6 files changed, 21 insertions(+), 13 deletions(-)
Title: Comparing Restricted Mean Survival Time
Description: Performs two-sample comparisons using the restricted mean survival time (RMST) as a summary measure of the survival time distribution. Three kinds of between-group contrast metrics (i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It performs an ANCOVA-type covariate adjustment as well as unadjusted analyses for those measures.
Author: Hajime Uno, Lu Tian, Miki Horiguchi, Angel Cronin, Chakib Battioui, James Bell
Maintainer: Hajime Uno <huno@jimmy.harvard.edu>
Diff between survRM2 versions 1.0-3 dated 2020-06-13 and 1.0-4 dated 2022-06-13
DESCRIPTION | 11 MD5 | 17 - NEWS.md | 5 R/rmst2.R | 32 + R/survRM2-package.R | 4 README.md |only build/vignette.rds |binary inst/doc/survRM2-vignette3-2.html | 609 +++++++++++++++++++++++++++++++------- man/rmst2.Rd | 24 + man/survRM2-package.Rd | 4 10 files changed, 577 insertions(+), 129 deletions(-)
Title: Distance Sampling Survey Design
Description: Creates survey designs for distance sampling surveys. These
designs can be assessed for various effort and coverage statistics.
Once the user is satisfied with the design characteristics they can
generate a set of transects to use in their distance sampling survey.
Many of the designs implemented in this R package were first made
available in our 'Distance' for Windows software and are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008,
ISBN-13: 978-0199225873). Find out more about estimating animal/plant
abundance with distance sampling at <http://distancesampling.org/>.
Author: Laura Marshall [aut, cre],
Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dssd versions 0.3.2 dated 2022-05-31 and 0.3.3 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 7 +++++++ inst/doc/GettingStarted.html | 6 +++--- inst/doc/MultiStrataVignette.html | 4 ++-- tests/testthat/test-check_SegDesign.R | 16 +++------------- tests/testthat/test-x_seed_tests.R | 12 ++++++++++++ 7 files changed, 36 insertions(+), 27 deletions(-)
Title: Design-Based Inference in Vector Generalised Linear Models
Description: Provides inference based on the survey package for the wide range of parametric models in the 'VGAM' package.
Author: Thomas Lumley
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between svyVGAM versions 1.0 dated 2021-03-05 and 1.1 dated 2022-06-13
DESCRIPTION | 6 MD5 | 16 - R/svgam.R | 8 build/vignette.rds |binary inst/doc/theory.html | 237 ++++---------------- inst/doc/zeroinfl.R | 5 inst/doc/zeroinfl.Rmd | 15 - inst/doc/zeroinfl.html | 580 ++++++++++++++++--------------------------------- vignettes/zeroinfl.Rmd | 15 - 9 files changed, 287 insertions(+), 595 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.26.0 dated 2022-05-23 and 1.26.1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.2 dated 2022-05-18 and 1.3 dated 2022-06-13
DESCRIPTION | 12 +++---- MD5 | 8 ++--- R/UFAx_workflow.R | 60 +++++++++++++++++++------------------- inst/extdata/UFAx_parameters.xlsx |binary man/UFAx_workflow.Rd | 7 +++- 5 files changed, 45 insertions(+), 42 deletions(-)
Title: Portfolio Allocation and Risk Management Applications
Description: Provision of a set of models and methods for use in the allocation and management of capital in financial portfolios.
Author: Alexios Galanos [aut, cre],
Bernhard Pfaff [ctb],
Miguel Sousa Lobo [ctb] ,
Lieven Vandenberghe [ctb] ,
Stephen Boyd [ctb] ,
Herve Lebret [ctb]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between parma versions 1.5-3 dated 2016-08-25 and 1.6 dated 2022-06-13
parma-1.5-3/parma/README.md |only parma-1.5-3/parma/inst/doc/Portfolio_Optimization_in_parma.Rnw |only parma-1.5-3/parma/vignettes/Portfolio_Optimization_in_parma.Rnw |only parma-1.5-3/parma/vignettes/Portfolio_Optimization_in_parma.tex |only parma-1.5-3/parma/vignettes/frontier.png |only parma-1.5-3/parma/vignettes/frontier.tex |only parma-1.5-3/parma/vignettes/lpmutility.png |only parma-1.5-3/parma/vignettes/lpmutility.tex |only parma-1.5-3/parma/vignettes/lpnlp1.tex |only parma-1.5-3/parma/vignettes/lpnlp2.tex |only parma-1.5-3/parma/vignettes/mam.png |only parma-1.5-3/parma/vignettes/mam.tex |only parma-1.5-3/parma/vignettes/parma.tex |only parma-1.5-3/parma/vignettes/parmabib.bib |only parma-1.5-3/parma/vignettes/riskcompare.tex |only parma-1.5-3/parma/vignettes/solvers.tex |only parma-1.6/parma/Changelog | 20 +- parma-1.6/parma/DESCRIPTION | 18 +- parma-1.6/parma/MD5 | 88 ++++------ parma-1.6/parma/NAMESPACE | 2 parma-1.6/parma/R/p-GNLP.R | 4 parma-1.6/parma/R/p-LP.R | 56 +++--- parma-1.6/parma/R/p-MILP.R | 8 parma-1.6/parma/R/p-NLP.R | 4 parma-1.6/parma/R/p-QP.R | 6 parma-1.6/parma/R/p-SOCP.R | 6 parma-1.6/parma/R/p-Utility.R | 4 parma-1.6/parma/R/p-classes.R | 6 parma-1.6/parma/R/p-cmaes.R | 6 parma-1.6/parma/R/p-constraints.R | 6 parma-1.6/parma/R/p-fun.R | 4 parma-1.6/parma/R/p-main.R | 6 parma-1.6/parma/R/p-methods.R | 4 parma-1.6/parma/R/p-timeseries.R | 6 parma-1.6/parma/R/zzz.R | 8 parma-1.6/parma/build/vignette.rds |binary parma-1.6/parma/inst/CITATION | 4 parma-1.6/parma/inst/COPYRIGHTS | 4 parma-1.6/parma/inst/doc/Portfolio_Optimization_in_parma.pdf |binary parma-1.6/parma/inst/doc/Portfolio_Optimization_in_parma.pdf.asis |only parma-1.6/parma/inst/parma.tests/parma.tests.R | 6 parma-1.6/parma/man/cmaes-solver.Rd | 6 parma-1.6/parma/man/constraints.Rd | 4 parma-1.6/parma/man/parma-package.Rd | 11 - parma-1.6/parma/man/parmaPort-class.Rd | 4 parma-1.6/parma/man/parmaSpec-class.Rd | 2 parma-1.6/parma/man/parmafrontier-methods.Rd | 4 parma-1.6/parma/man/parmasolve-methods.Rd | 6 parma-1.6/parma/man/parmaspec-methods.Rd | 4 parma-1.6/parma/man/parmautility-methods.Rd | 6 parma-1.6/parma/man/riskfun.Rd | 4 parma-1.6/parma/src/Makevars | 1 parma-1.6/parma/src/Makevars.win |only parma-1.6/parma/src/init.c |only parma-1.6/parma/vignettes/Portfolio_Optimization_in_parma.pdf.asis |only 55 files changed, 160 insertions(+), 168 deletions(-)
Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Author: Zankrut Goyani [aut, cre, cph],
Alok Shrivasatva [aut]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>
Diff between selection.index versions 1.1.3 dated 2021-09-25 and 1.1.4 dated 2022-06-13
selection.index-1.1.3/selection.index/R/sel.index.R |only selection.index-1.1.3/selection.index/R/sel.score.rank.R |only selection.index-1.1.3/selection.index/man/sel.index.Rd |only selection.index-1.1.3/selection.index/man/sel.score.rank.Rd |only selection.index-1.1.3/selection.index/tests/testthat/test-sel.index.R |only selection.index-1.1.3/selection.index/tests/testthat/test-sel.score.rank.R |only selection.index-1.1.4/selection.index/DESCRIPTION | 29 selection.index-1.1.4/selection.index/MD5 | 66 selection.index-1.1.4/selection.index/NAMESPACE | 21 selection.index-1.1.4/selection.index/NEWS.md | 37 selection.index-1.1.4/selection.index/R/comb.indices.R | 98 - selection.index-1.1.4/selection.index/R/gen.advance.R | 42 selection.index-1.1.4/selection.index/R/gen.varcov.R | 120 - selection.index-1.1.4/selection.index/R/phen.varcov.R | 122 - selection.index-1.1.4/selection.index/R/rcomb.indices.R | 126 - selection.index-1.1.4/selection.index/R/seldata.R | 42 selection.index-1.1.4/selection.index/R/weight.R | 28 selection.index-1.1.4/selection.index/R/weight.mat.R | 28 selection.index-1.1.4/selection.index/README.md | 299 ++-- selection.index-1.1.4/selection.index/build/vignette.rds |binary selection.index-1.1.4/selection.index/inst/doc/Examples.R | 85 - selection.index-1.1.4/selection.index/inst/doc/Examples.Rmd | 157 -- selection.index-1.1.4/selection.index/inst/doc/Examples.html | 724 ++++++---- selection.index-1.1.4/selection.index/man/comb.indices.Rd | 68 selection.index-1.1.4/selection.index/man/gen.advance.Rd | 52 selection.index-1.1.4/selection.index/man/gen.varcov.Rd | 48 selection.index-1.1.4/selection.index/man/phen.varcov.Rd | 48 selection.index-1.1.4/selection.index/man/rcomb.indices.Rd | 72 selection.index-1.1.4/selection.index/man/seldata.Rd | 58 selection.index-1.1.4/selection.index/man/weight.Rd | 44 selection.index-1.1.4/selection.index/man/weight.mat.Rd | 40 selection.index-1.1.4/selection.index/tests/testthat.R | 8 selection.index-1.1.4/selection.index/tests/testthat/test-comb.indices.R | 12 selection.index-1.1.4/selection.index/tests/testthat/test-gen.advance.R | 18 selection.index-1.1.4/selection.index/tests/testthat/test-genphen.R | 14 selection.index-1.1.4/selection.index/tests/testthat/test-rcomb.indices.R | 12 selection.index-1.1.4/selection.index/vignettes/Examples.Rmd | 157 -- 37 files changed, 1375 insertions(+), 1300 deletions(-)
More information about selection.index at CRAN
Permanent link
Title: S3 Methods Simplified
Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.methodsS3 versions 1.8.1 dated 2020-08-26 and 1.8.2 dated 2022-06-13
R.methodsS3-1.8.1/R.methodsS3/NEWS |only R.methodsS3-1.8.2/R.methodsS3/DESCRIPTION | 6 ++-- R.methodsS3-1.8.2/R.methodsS3/MD5 | 22 +++++++-------- R.methodsS3-1.8.2/R.methodsS3/NEWS.md |only R.methodsS3-1.8.2/R.methodsS3/R/000.R | 9 ++++-- R.methodsS3-1.8.2/R.methodsS3/R/010.setGenericS3.R | 13 ++++---- R.methodsS3-1.8.2/R.methodsS3/R/030.setMethodS3.R | 16 ++++++---- R.methodsS3-1.8.2/R.methodsS3/R/999.package.R | 4 +- R.methodsS3-1.8.2/R.methodsS3/R/throw.default.R | 10 ++++-- R.methodsS3-1.8.2/R.methodsS3/R/zzz.R | 9 ++++++ R.methodsS3-1.8.2/R.methodsS3/man/R.methodsS3-package.Rd | 5 +-- R.methodsS3-1.8.2/R.methodsS3/man/setMethodS3.Rd | 5 ++- R.methodsS3-1.8.2/R.methodsS3/man/throw.Rd | 10 ++++-- 13 files changed, 67 insertions(+), 42 deletions(-)
Title: PWIGLS for Two-Level Multivariate and Multilevel Linear Models
Description: Estimates two-level multilevel linear model and two-level multivariate linear multilevel model with weights following Probability Weighted Iterative Generalised Least Squares approach. For details see Veiga et al.(2014) <doi:10.1111/rssc.12020>.
Author: Alinne Veiga [aut, cre] ,
Joao Messa [aut, trl, com]
Maintainer: Alinne Veiga <alinne.veiga@ibge.gov.br>
Diff between pwlmm versions 1.1.0 dated 2022-05-10 and 1.1.1 dated 2022-06-13
DESCRIPTION | 6 +-- MD5 | 18 ++++----- R/RcppExports.R | 20 +++++----- R/pwigls2.R | 88 ++++++++++++++++++++++++------------------------ R/wmlmm.R | 62 ++++++++++++++++----------------- inst/doc/pwlmm.Rmd | 19 +--------- inst/doc/pwlmm.html | 12 +----- src/RcppExports.cpp | 52 ++++++++++++++-------------- src/rcppeigen_messa.cpp | 54 ++++++++++++++--------------- vignettes/pwlmm.Rmd | 19 +--------- 10 files changed, 159 insertions(+), 191 deletions(-)
Title: Simulate Evapotranspiration and Soil Moisture with the SVAT
Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation
atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran.
The model simulates daily transpiration, interception, soil and snow evaporation,
streamflow and soil water fluxes through a soil profile covered with vegetation,
as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003)
<doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions
for model set up, execution and parallelization provides easy access to plot-level SVAT
simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre]
,
Volodymyr Trotsiuk [aut] ,
Klaus Hammel [aut],
Martin Kennel [aut],
Anthony Federer [aut],
Robert Nuske [ctb] ,
Bavarian State Institute of Forestry [cph, fnd],
Northwest German Forest Research Institute [cph, fnd]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>
Diff between LWFBrook90R versions 0.4.5 dated 2021-11-30 and 0.5.0 dated 2022-06-13
LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/intro_LWFB90.R |only LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/intro_LWFB90.Rmd |only LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/intro_LWFB90.html |only LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/multiruns.R |only LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/multiruns.Rmd |only LWFBrook90R-0.4.5/LWFBrook90R/inst/doc/multiruns.html |only LWFBrook90R-0.4.5/LWFBrook90R/vignettes/intro_LWFB90.Rmd |only LWFBrook90R-0.4.5/LWFBrook90R/vignettes/multiruns.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/DESCRIPTION | 13 LWFBrook90R-0.5.0/LWFBrook90R/MD5 | 68 +- LWFBrook90R-0.5.0/LWFBrook90R/NAMESPACE | 1 LWFBrook90R-0.5.0/LWFBrook90R/NEWS.md | 69 +- LWFBrook90R-0.5.0/LWFBrook90R/R/mrunLWFB90.R | 4 LWFBrook90R-0.5.0/LWFBrook90R/R/msiterunLWFB90.R | 4 LWFBrook90R-0.5.0/LWFBrook90R/R/process_outputs.R |only LWFBrook90R-0.5.0/LWFBrook90R/R/r_lwfbrook90.R | 7 LWFBrook90R-0.5.0/LWFBrook90R/R/runLWFB90.R | 282 +--------- LWFBrook90R-0.5.0/LWFBrook90R/R/sysdata.rda |binary LWFBrook90R-0.5.0/LWFBrook90R/README.md | 25 LWFBrook90R-0.5.0/LWFBrook90R/build/vignette.rds |binary LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBook90R-1-Intro.R |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBook90R-1-Intro.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBook90R-1-Intro.html |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.R |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-2-Options_Param.html |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-3-Multiruns.R |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-3-Multiruns.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-3-Multiruns.html |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-4-Multisite-Runs.R |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-4-Multisite-Runs.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/inst/doc/LWFBrook90R-4-Multisite-Runs.html |only LWFBrook90R-0.5.0/LWFBrook90R/inst/examples/run_multi_LWFB90-help.R | 16 LWFBrook90R-0.5.0/LWFBrook90R/man/figures/README-unnamed-chunk-5-1.png |binary LWFBrook90R-0.5.0/LWFBrook90R/man/process_outputs_LWFB90.Rd |only LWFBrook90R-0.5.0/LWFBrook90R/man/run_LWFB90.Rd | 87 +-- LWFBrook90R-0.5.0/LWFBrook90R/man/run_multi_LWFB90.Rd | 16 LWFBrook90R-0.5.0/LWFBrook90R/src/md_brook90.f95 | 71 +- LWFBrook90R-0.5.0/LWFBrook90R/src/output_day.h | 77 +- LWFBrook90R-0.5.0/LWFBrook90R/src/output_layer_pint.h |only LWFBrook90R-0.5.0/LWFBrook90R/src/output_pint.h |only LWFBrook90R-0.5.0/LWFBrook90R/src/skeleton.c | 29 - LWFBrook90R-0.5.0/LWFBrook90R/tests/testthat/test-msiterunLWFB90.R | 35 - LWFBrook90R-0.5.0/LWFBrook90R/tests/testthat/test-options.R | 4 LWFBrook90R-0.5.0/LWFBrook90R/tests/testthat/test-runLWFB90.R | 121 ++-- LWFBrook90R-0.5.0/LWFBrook90R/vignettes/LWFBook90R-1-Intro.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/vignettes/LWFBrook90R-2-Options_Param.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/vignettes/LWFBrook90R-3-Multiruns.Rmd |only LWFBrook90R-0.5.0/LWFBrook90R/vignettes/LWFBrook90R-4-Multisite-Runs.Rmd |only 49 files changed, 394 insertions(+), 535 deletions(-)
Title: A 'Linter' for R Code
Description: Checks adherence to a given style, syntax errors and possible semantic issues.
Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text',
'Atom' and 'Visual Studio Code'.
Author: Jim Hester [aut, cre],
Florent Angly [aut] ,
Russ Hyde [aut],
Michael Chirico [aut],
Kun Ren [aut],
Alexander Rosenstock [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 2.0.1 dated 2020-02-19 and 3.0.0 dated 2022-06-13
lintr-2.0.1/lintr/R/equals_na_lintr.R |only lintr-2.0.1/lintr/R/function_left_parentheses.R |only lintr-2.0.1/lintr/R/semicolon_terminator_linter.R |only lintr-2.0.1/lintr/man/Lint.Rd |only lintr-2.0.1/lintr/man/lint_dir.Rd |only lintr-2.0.1/lintr/man/lint_file.Rd |only lintr-2.0.1/lintr/man/lint_package.Rd |only lintr-2.0.1/lintr/man/lintr-deprecated.Rd |only lintr-2.0.1/lintr/man/lintr.Rd |only lintr-2.0.1/lintr/man/with_defaults.Rd |only lintr-2.0.1/lintr/tests/testthat/test-deprecated.R |only lintr-2.0.1/lintr/tests/testthat/test-semicolon_terminator_linter.R |only lintr-3.0.0/lintr/DESCRIPTION | 101 - lintr-3.0.0/lintr/MD5 | 520 ++++-- lintr-3.0.0/lintr/NAMESPACE | 65 lintr-3.0.0/lintr/NEWS.md | 351 ++++ lintr-3.0.0/lintr/R/T_and_F_symbol_linter.R | 84 - lintr-3.0.0/lintr/R/aaa.R | 29 lintr-3.0.0/lintr/R/actions.R | 44 lintr-3.0.0/lintr/R/addins.R | 16 lintr-3.0.0/lintr/R/any_duplicated_linter.R |only lintr-3.0.0/lintr/R/any_is_na_linter.R |only lintr-3.0.0/lintr/R/assignment_linter.R | 59 lintr-3.0.0/lintr/R/backport_linter.R |only lintr-3.0.0/lintr/R/brace_linter.R |only lintr-3.0.0/lintr/R/cache.R | 85 - lintr-3.0.0/lintr/R/class_equals_linter.R |only lintr-3.0.0/lintr/R/closed_curly_linter.R | 106 - lintr-3.0.0/lintr/R/commas_linter.R | 128 - lintr-3.0.0/lintr/R/comment_linters.R | 114 - lintr-3.0.0/lintr/R/comments.R | 98 - lintr-3.0.0/lintr/R/condition_message_linter.R |only lintr-3.0.0/lintr/R/conjunct_test_linter.R |only lintr-3.0.0/lintr/R/consecutive_stopifnot_linter.R |only lintr-3.0.0/lintr/R/cyclocomp_linter.R | 48 lintr-3.0.0/lintr/R/declared_functions.R | 19 lintr-3.0.0/lintr/R/deprecated.R | 97 - lintr-3.0.0/lintr/R/duplicate_argument_linter.R |only lintr-3.0.0/lintr/R/equals_na_linter.R |only lintr-3.0.0/lintr/R/exclude.R | 360 +++- lintr-3.0.0/lintr/R/expect_comparison_linter.R |only lintr-3.0.0/lintr/R/expect_identical_linter.R |only lintr-3.0.0/lintr/R/expect_length_linter.R |only lintr-3.0.0/lintr/R/expect_lint.R | 70 lintr-3.0.0/lintr/R/expect_named_linter.R |only lintr-3.0.0/lintr/R/expect_not_linter.R |only lintr-3.0.0/lintr/R/expect_null_linter.R |only lintr-3.0.0/lintr/R/expect_s3_class_linter.R |only lintr-3.0.0/lintr/R/expect_true_false_linter.R |only lintr-3.0.0/lintr/R/expect_type_linter.R |only lintr-3.0.0/lintr/R/extract.R | 99 - lintr-3.0.0/lintr/R/extraction_operator_linter.R | 83 lintr-3.0.0/lintr/R/fixed_regex_linter.R |only lintr-3.0.0/lintr/R/function_left_parentheses_linter.R |only lintr-3.0.0/lintr/R/get_source_expressions.R | 839 ++++++---- lintr-3.0.0/lintr/R/ids_with_token.R | 41 lintr-3.0.0/lintr/R/ifelse_censor_linter.R |only lintr-3.0.0/lintr/R/implicit_integer_linter.R | 48 lintr-3.0.0/lintr/R/infix_spaces_linter.R | 202 +- lintr-3.0.0/lintr/R/inner_combine_linter.R |only lintr-3.0.0/lintr/R/is_lint_level.R |only lintr-3.0.0/lintr/R/line_length_linter.R | 53 lintr-3.0.0/lintr/R/lint.R | 549 ++++-- lintr-3.0.0/lintr/R/linter_tag_docs.R |only lintr-3.0.0/lintr/R/linter_tags.R |only lintr-3.0.0/lintr/R/literal_coercion_linter.R |only lintr-3.0.0/lintr/R/make_linter_from_regex.R |only lintr-3.0.0/lintr/R/methods.R | 87 - lintr-3.0.0/lintr/R/missing_argument_linter.R |only lintr-3.0.0/lintr/R/missing_package_linter.R |only lintr-3.0.0/lintr/R/namespace.R | 86 - lintr-3.0.0/lintr/R/namespace_linter.R |only lintr-3.0.0/lintr/R/nested_ifelse_linter.R |only lintr-3.0.0/lintr/R/no_tab_linter.R | 48 lintr-3.0.0/lintr/R/numeric_leading_zero_linter.R |only lintr-3.0.0/lintr/R/object_name_linters.R | 405 +--- lintr-3.0.0/lintr/R/object_usage_linter.R | 370 ++-- lintr-3.0.0/lintr/R/open_curly_linter.R | 113 - lintr-3.0.0/lintr/R/outer_negation_linter.R |only lintr-3.0.0/lintr/R/package_hooks_linter.R |only lintr-3.0.0/lintr/R/paren_body_linter.R |only lintr-3.0.0/lintr/R/paren_brace_linter.R | 66 lintr-3.0.0/lintr/R/paste_linter.R |only lintr-3.0.0/lintr/R/path_linters.R | 135 - lintr-3.0.0/lintr/R/pipe_call_linter.R |only lintr-3.0.0/lintr/R/pipe_continuation_linter.R | 95 - lintr-3.0.0/lintr/R/redundant_ifelse_linter.R |only lintr-3.0.0/lintr/R/regex_subset_linter.R |only lintr-3.0.0/lintr/R/semicolon_linter.R |only lintr-3.0.0/lintr/R/seq_linter.R | 94 - lintr-3.0.0/lintr/R/settings.R | 69 lintr-3.0.0/lintr/R/single_quotes_linter.R | 53 lintr-3.0.0/lintr/R/spaces_inside_linter.R | 119 - lintr-3.0.0/lintr/R/spaces_left_parentheses_linter.R | 100 - lintr-3.0.0/lintr/R/sprintf_linter.R |only lintr-3.0.0/lintr/R/string_boundary_linter.R |only lintr-3.0.0/lintr/R/strings_as_factors_linter.R |only lintr-3.0.0/lintr/R/system_file_linter.R |only lintr-3.0.0/lintr/R/trailing_blank_lines_linter.R | 53 lintr-3.0.0/lintr/R/trailing_whitespace_linter.R | 77 lintr-3.0.0/lintr/R/tree-utils.R | 102 - lintr-3.0.0/lintr/R/undesirable_function_linter.R | 91 - lintr-3.0.0/lintr/R/undesirable_operator_linter.R | 101 - lintr-3.0.0/lintr/R/unneeded_concatenation_linter.R | 158 - lintr-3.0.0/lintr/R/unreachable_code_linter.R |only lintr-3.0.0/lintr/R/unused_import_linter.R |only lintr-3.0.0/lintr/R/use_lintr.R |only lintr-3.0.0/lintr/R/utils.R | 261 +-- lintr-3.0.0/lintr/R/vector_logic_linter.R |only lintr-3.0.0/lintr/R/with.R |only lintr-3.0.0/lintr/R/with_id.R | 15 lintr-3.0.0/lintr/R/xml_nodes_to_lints.R |only lintr-3.0.0/lintr/R/xp_utils.R |only lintr-3.0.0/lintr/R/yoda_test_linter.R |only lintr-3.0.0/lintr/R/zzz.R | 363 ++-- lintr-3.0.0/lintr/README.md | 283 --- lintr-3.0.0/lintr/build/lintr.pdf |binary lintr-3.0.0/lintr/build/vignette.rds |binary lintr-3.0.0/lintr/inst/doc/continuous-integration.R |only lintr-3.0.0/lintr/inst/doc/continuous-integration.Rmd |only lintr-3.0.0/lintr/inst/doc/continuous-integration.html |only lintr-3.0.0/lintr/inst/doc/creating_linters.Rmd | 292 ++- lintr-3.0.0/lintr/inst/doc/creating_linters.html | 223 +- lintr-3.0.0/lintr/inst/doc/editors.R |only lintr-3.0.0/lintr/inst/doc/editors.Rmd |only lintr-3.0.0/lintr/inst/doc/editors.html |only lintr-3.0.0/lintr/inst/doc/lintr.R |only lintr-3.0.0/lintr/inst/doc/lintr.Rmd |only lintr-3.0.0/lintr/inst/doc/lintr.html |only lintr-3.0.0/lintr/inst/example/complexity.R | 14 lintr-3.0.0/lintr/inst/lintr |only lintr-3.0.0/lintr/man/Linter.Rd |only lintr-3.0.0/lintr/man/T_and_F_symbol_linter.Rd |only lintr-3.0.0/lintr/man/absolute_path_linter.Rd |only lintr-3.0.0/lintr/man/any_duplicated_linter.Rd |only lintr-3.0.0/lintr/man/any_is_na_linter.Rd |only lintr-3.0.0/lintr/man/assignment_linter.Rd |only lintr-3.0.0/lintr/man/available_linters.Rd |only lintr-3.0.0/lintr/man/backport_linter.Rd |only lintr-3.0.0/lintr/man/best_practices_linters.Rd |only lintr-3.0.0/lintr/man/brace_linter.Rd |only lintr-3.0.0/lintr/man/checkstyle_output.Rd | 3 lintr-3.0.0/lintr/man/class_equals_linter.Rd |only lintr-3.0.0/lintr/man/clear_cache.Rd | 6 lintr-3.0.0/lintr/man/closed_curly_linter.Rd |only lintr-3.0.0/lintr/man/commas_linter.Rd |only lintr-3.0.0/lintr/man/commented_code_linter.Rd |only lintr-3.0.0/lintr/man/common_mistakes_linters.Rd |only lintr-3.0.0/lintr/man/condition_message_linter.Rd |only lintr-3.0.0/lintr/man/configurable_linters.Rd |only lintr-3.0.0/lintr/man/conjunct_test_linter.Rd |only lintr-3.0.0/lintr/man/consecutive_stopifnot_linter.Rd |only lintr-3.0.0/lintr/man/consistency_linters.Rd |only lintr-3.0.0/lintr/man/correctness_linters.Rd |only lintr-3.0.0/lintr/man/cyclocomp_linter.Rd |only lintr-3.0.0/lintr/man/default_linters.Rd | 43 lintr-3.0.0/lintr/man/default_settings.Rd | 6 lintr-3.0.0/lintr/man/default_undesirable_functions.Rd | 60 lintr-3.0.0/lintr/man/deprecated_linters.Rd |only lintr-3.0.0/lintr/man/duplicate_argument_linter.Rd |only lintr-3.0.0/lintr/man/efficiency_linters.Rd |only lintr-3.0.0/lintr/man/equals_na_linter.Rd |only lintr-3.0.0/lintr/man/exclude.Rd | 19 lintr-3.0.0/lintr/man/executing_linters.Rd |only lintr-3.0.0/lintr/man/expect_comparison_linter.Rd |only lintr-3.0.0/lintr/man/expect_identical_linter.Rd |only lintr-3.0.0/lintr/man/expect_length_linter.Rd |only lintr-3.0.0/lintr/man/expect_lint.Rd | 30 lintr-3.0.0/lintr/man/expect_lint_free.Rd | 2 lintr-3.0.0/lintr/man/expect_named_linter.Rd |only lintr-3.0.0/lintr/man/expect_not_linter.Rd |only lintr-3.0.0/lintr/man/expect_null_linter.Rd |only lintr-3.0.0/lintr/man/expect_s3_class_linter.Rd |only lintr-3.0.0/lintr/man/expect_s4_class_linter.Rd |only lintr-3.0.0/lintr/man/expect_true_false_linter.Rd |only lintr-3.0.0/lintr/man/expect_type_linter.Rd |only lintr-3.0.0/lintr/man/extraction_operator_linter.Rd |only lintr-3.0.0/lintr/man/figures |only lintr-3.0.0/lintr/man/fixed_regex_linter.Rd |only lintr-3.0.0/lintr/man/function_left_parentheses_linter.Rd |only lintr-3.0.0/lintr/man/get_source_expressions.Rd | 54 lintr-3.0.0/lintr/man/ids_with_token.Rd | 39 lintr-3.0.0/lintr/man/ifelse_censor_linter.Rd |only lintr-3.0.0/lintr/man/implicit_integer_linter.Rd |only lintr-3.0.0/lintr/man/infix_spaces_linter.Rd |only lintr-3.0.0/lintr/man/inner_combine_linter.Rd |only lintr-3.0.0/lintr/man/is_lint_level.Rd |only lintr-3.0.0/lintr/man/line_length_linter.Rd |only lintr-3.0.0/lintr/man/lint-s3.Rd |only lintr-3.0.0/lintr/man/lint.Rd |only lintr-3.0.0/lintr/man/linters.Rd | 341 +--- lintr-3.0.0/lintr/man/linters_with_defaults.Rd |only lintr-3.0.0/lintr/man/linters_with_tags.Rd |only lintr-3.0.0/lintr/man/lintr-package.Rd |only lintr-3.0.0/lintr/man/literal_coercion_linter.Rd |only lintr-3.0.0/lintr/man/missing_argument_linter.Rd |only lintr-3.0.0/lintr/man/missing_package_linter.Rd |only lintr-3.0.0/lintr/man/modify_defaults.Rd |only lintr-3.0.0/lintr/man/namespace_linter.Rd |only lintr-3.0.0/lintr/man/nested_ifelse_linter.Rd |only lintr-3.0.0/lintr/man/no_tab_linter.Rd |only lintr-3.0.0/lintr/man/nonportable_path_linter.Rd |only lintr-3.0.0/lintr/man/normalize_exclusions.Rd |only lintr-3.0.0/lintr/man/numeric_leading_zero_linter.Rd |only lintr-3.0.0/lintr/man/object_length_linter.Rd |only lintr-3.0.0/lintr/man/object_name_linter.Rd |only lintr-3.0.0/lintr/man/object_usage_linter.Rd |only lintr-3.0.0/lintr/man/open_curly_linter.Rd |only lintr-3.0.0/lintr/man/outer_negation_linter.Rd |only lintr-3.0.0/lintr/man/package_development_linters.Rd |only lintr-3.0.0/lintr/man/package_hooks_linter.Rd |only lintr-3.0.0/lintr/man/paren_body_linter.Rd |only lintr-3.0.0/lintr/man/paren_brace_linter.Rd |only lintr-3.0.0/lintr/man/parse_exclusions.Rd | 18 lintr-3.0.0/lintr/man/paste_linter.Rd |only lintr-3.0.0/lintr/man/pipe_call_linter.Rd |only lintr-3.0.0/lintr/man/pipe_continuation_linter.Rd |only lintr-3.0.0/lintr/man/read_settings.Rd | 14 lintr-3.0.0/lintr/man/readability_linters.Rd |only lintr-3.0.0/lintr/man/redundant_ifelse_linter.Rd |only lintr-3.0.0/lintr/man/regex_subset_linter.Rd |only lintr-3.0.0/lintr/man/robustness_linters.Rd |only lintr-3.0.0/lintr/man/semicolon_linter.Rd |only lintr-3.0.0/lintr/man/seq_linter.Rd |only lintr-3.0.0/lintr/man/single_quotes_linter.Rd |only lintr-3.0.0/lintr/man/spaces_inside_linter.Rd |only lintr-3.0.0/lintr/man/spaces_left_parentheses_linter.Rd |only lintr-3.0.0/lintr/man/sprintf_linter.Rd |only lintr-3.0.0/lintr/man/string_boundary_linter.Rd |only lintr-3.0.0/lintr/man/strings_as_factors_linter.Rd |only lintr-3.0.0/lintr/man/style_linters.Rd |only lintr-3.0.0/lintr/man/system_file_linter.Rd |only lintr-3.0.0/lintr/man/todo_comment_linter.Rd |only lintr-3.0.0/lintr/man/trailing_blank_lines_linter.Rd |only lintr-3.0.0/lintr/man/trailing_whitespace_linter.Rd |only lintr-3.0.0/lintr/man/undesirable_function_linter.Rd |only lintr-3.0.0/lintr/man/undesirable_operator_linter.Rd |only lintr-3.0.0/lintr/man/unneeded_concatenation_linter.Rd |only lintr-3.0.0/lintr/man/unreachable_code_linter.Rd |only lintr-3.0.0/lintr/man/unused_import_linter.Rd |only lintr-3.0.0/lintr/man/use_lintr.Rd |only lintr-3.0.0/lintr/man/vector_logic_linter.Rd |only lintr-3.0.0/lintr/man/xml_nodes_to_lints.Rd |only lintr-3.0.0/lintr/man/yoda_test_linter.Rd |only lintr-3.0.0/lintr/tests/testthat/checkstyle.xml | 2 lintr-3.0.0/lintr/tests/testthat/default_linter_testcode.R | 21 lintr-3.0.0/lintr/tests/testthat/dummy_packages |only lintr-3.0.0/lintr/tests/testthat/dummy_projects |only lintr-3.0.0/lintr/tests/testthat/exclusions-test | 6 lintr-3.0.0/lintr/tests/testthat/helper.R | 48 lintr-3.0.0/lintr/tests/testthat/knitr_formats/test.Rmd | 11 lintr-3.0.0/lintr/tests/testthat/knitr_malformed |only lintr-3.0.0/lintr/tests/testthat/test-T_and_F_symbol_linter.R | 54 lintr-3.0.0/lintr/tests/testthat/test-absolute_path_linter.R | 114 - lintr-3.0.0/lintr/tests/testthat/test-any_duplicated_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-any_is_na_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-assignment_linter.R | 67 lintr-3.0.0/lintr/tests/testthat/test-backport_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-brace_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-cache.R | 469 +++-- lintr-3.0.0/lintr/tests/testthat/test-checkstyle_output.R | 13 lintr-3.0.0/lintr/tests/testthat/test-ci.R |only lintr-3.0.0/lintr/tests/testthat/test-class_equals_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-closed_curly_linter.R | 62 lintr-3.0.0/lintr/tests/testthat/test-commas_linter.R | 86 - lintr-3.0.0/lintr/tests/testthat/test-commented_code_linter.R | 32 lintr-3.0.0/lintr/tests/testthat/test-comments.R | 65 lintr-3.0.0/lintr/tests/testthat/test-condition_message_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-conjunct_test_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-consecutive_stopifnot_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-cyclocomp_linter.R | 10 lintr-3.0.0/lintr/tests/testthat/test-defaults.R | 56 lintr-3.0.0/lintr/tests/testthat/test-dir_linters.R |only lintr-3.0.0/lintr/tests/testthat/test-duplicate_argument_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-equals_na_linter.R | 46 lintr-3.0.0/lintr/tests/testthat/test-error.R | 64 lintr-3.0.0/lintr/tests/testthat/test-exclusions.R | 253 --- lintr-3.0.0/lintr/tests/testthat/test-expect_comparison_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_identical_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_length_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_lint.R | 30 lintr-3.0.0/lintr/tests/testthat/test-expect_named_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_not_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_null_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_s3_class_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_true_false_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-expect_type_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-extraction_operator_linter.R | 32 lintr-3.0.0/lintr/tests/testthat/test-fixed_regex_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-function_left_parentheses_linter.R | 102 - lintr-3.0.0/lintr/tests/testthat/test-get_source_expressions.R | 276 +++ lintr-3.0.0/lintr/tests/testthat/test-ids_with_token.R |only lintr-3.0.0/lintr/tests/testthat/test-ifelse_censor_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-implicit_integer_linter.R | 35 lintr-3.0.0/lintr/tests/testthat/test-infix_spaces_linter.R | 155 + lintr-3.0.0/lintr/tests/testthat/test-inner_combine_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-is_lint_level.R |only lintr-3.0.0/lintr/tests/testthat/test-knitr_formats.R | 159 + lintr-3.0.0/lintr/tests/testthat/test-line_length_linter.R | 71 lintr-3.0.0/lintr/tests/testthat/test-lint_file.R |only lintr-3.0.0/lintr/tests/testthat/test-lint_package.R |only lintr-3.0.0/lintr/tests/testthat/test-linter_tags.R |only lintr-3.0.0/lintr/tests/testthat/test-literal_coercion_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-make_linter_from_regex.R |only lintr-3.0.0/lintr/tests/testthat/test-methods.R | 136 + lintr-3.0.0/lintr/tests/testthat/test-missing_argument_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-missing_package_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-namespace.R |only lintr-3.0.0/lintr/tests/testthat/test-namespace_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-nested_ifelse_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-no_tab_linter.R | 33 lintr-3.0.0/lintr/tests/testthat/test-nonportable_path_linter.R | 7 lintr-3.0.0/lintr/tests/testthat/test-normalize_exclusions.R |only lintr-3.0.0/lintr/tests/testthat/test-numeric_leading_zero_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-object_length_linter.R | 54 lintr-3.0.0/lintr/tests/testthat/test-object_name_linter.R | 157 + lintr-3.0.0/lintr/tests/testthat/test-object_usage_linter.R | 476 ++++- lintr-3.0.0/lintr/tests/testthat/test-open_curly_linter.R | 124 + lintr-3.0.0/lintr/tests/testthat/test-outer_negation_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-package_hooks_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-paren_body_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-paren_brace_linter.R | 45 lintr-3.0.0/lintr/tests/testthat/test-parse_exclusions.R |only lintr-3.0.0/lintr/tests/testthat/test-paste_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-pipe_call_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-pipe_continuation_linter.R | 31 lintr-3.0.0/lintr/tests/testthat/test-redundant_ifelse_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-regex_subset_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-rstudio_markers.R | 188 +- lintr-3.0.0/lintr/tests/testthat/test-semicolon_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-seq_linter.R | 98 - lintr-3.0.0/lintr/tests/testthat/test-settings.R | 103 + lintr-3.0.0/lintr/tests/testthat/test-single_quotes_linter.R | 59 lintr-3.0.0/lintr/tests/testthat/test-spaces_inside_linter.R | 152 + lintr-3.0.0/lintr/tests/testthat/test-spaces_left_parentheses_linter.R | 138 - lintr-3.0.0/lintr/tests/testthat/test-sprintf_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-string_boundary_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-strings_as_factors_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-system_file_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-todo_comment_linter.R | 12 lintr-3.0.0/lintr/tests/testthat/test-trailing_blank_lines_linter.R | 81 lintr-3.0.0/lintr/tests/testthat/test-trailing_whitespace_linter.R | 78 lintr-3.0.0/lintr/tests/testthat/test-undesirable_function_linter.R | 62 lintr-3.0.0/lintr/tests/testthat/test-undesirable_operator_linter.R | 45 lintr-3.0.0/lintr/tests/testthat/test-unneeded_concatenation_linter.R | 100 - lintr-3.0.0/lintr/tests/testthat/test-unreachable_code_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-unused_import_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-use_lintr.R |only lintr-3.0.0/lintr/tests/testthat/test-vector_logic_linter.R |only lintr-3.0.0/lintr/tests/testthat/test-with.R |only lintr-3.0.0/lintr/tests/testthat/test-with_id.R |only lintr-3.0.0/lintr/tests/testthat/test-xml_nodes_to_lints.R |only lintr-3.0.0/lintr/tests/testthat/test-yoda_test_linter.R |only lintr-3.0.0/lintr/vignettes/atom.png |only lintr-3.0.0/lintr/vignettes/continuous-integration.Rmd |only lintr-3.0.0/lintr/vignettes/creating_linters.Rmd | 292 ++- lintr-3.0.0/lintr/vignettes/editors.Rmd |only lintr-3.0.0/lintr/vignettes/emacs-still.gif |only lintr-3.0.0/lintr/vignettes/lintr.Rmd |only lintr-3.0.0/lintr/vignettes/rstudio.png |only lintr-3.0.0/lintr/vignettes/sublime-still.gif |only lintr-3.0.0/lintr/vignettes/vim-syntastic-still.gif |only lintr-3.0.0/lintr/vignettes/vim-syntastic.gif |only lintr-3.0.0/lintr/vignettes/vscode.png |only 364 files changed, 8565 insertions(+), 5061 deletions(-)
Title: Working with 'LimeSurvey' Surveys and Responses
Description: 'LimeSurvey' is Free/Libre Open Source Software for
the development and administrations of online studies, using
sophisticated tailoring capabilities to support multiple study
designs (see <https://www.limesurvey.org>). This package supports
programmatic creation of surveys that can then be imported into
'LimeSurvey', as well as user friendly import of responses from
'LimeSurvey' studies.
Author: Gjalt-Jorn Peters [aut, cre] ,
Andrew Heiss [aut]
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Diff between limonaid versions 0.1.4 dated 2022-06-08 and 0.1.5 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-ls_read_tsv.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Excess Mass Calculation and Plots
Description: Implementation of a function which calculates the empirical excess mass
for given \eqn{\lambda} and given maximal number of modes (excessm()). Offering
powerful plot features to visualize empirical excess mass (exmplot()). This
includes the possibility of drawing several plots (with different maximal
number of modes / cut off values) in a single graph.
Author: Marc-Daniel Mildenberger
Maintainer: Marc-Daniel Mildenberger <mildenberger.stat@web.de>
Diff between ExcessMass versions 1.0 dated 2017-05-16 and 1.0.1 dated 2022-06-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/ExcessMass-package.Rd | 7 ++++--- man/exmsilhouette.Rd | 8 ++++---- 4 files changed, 15 insertions(+), 14 deletions(-)
Title: Calibrating Parameters for the Samejima's Continuous IRT Model
Description: Estimates item and person parameters for the Samejima's Continuous Response Model (CRM), computes item fit residual statistics, draws empirical 3D item category response curves, draws theoretical 3D item category response curves, and generates data under the CRM for simulation studies.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <cen.zop@gmail.com>
Diff between EstCRM versions 1.4 dated 2015-07-13 and 1.5 dated 2022-06-13
DESCRIPTION | 12 - MD5 | 20 +- NEWS | 6 R/fitCRM.R | 2 man/EstCRM-package.Rd | 6 man/EstCRMitem.Rd | 111 ++++++------ man/EstCRMperson.Rd | 77 ++++---- man/bootCRM.Rd | 50 ++--- man/fitCRM.Rd | 70 +++---- man/plotCRM.Rd | 36 ++-- man/simCRM.Rd | 438 +++++++++++++++++++++++++------------------------- 11 files changed, 416 insertions(+), 412 deletions(-)
Title: Equations to 'XML'
Description: Provides function to transform latex math expressions
into format 'HTML' or 'Office Open XML Math'. The 'XML'
result can then be included in 'HTML', 'Microsoft Word'
documents or 'Microsoft PowerPoint' presentations by using
a 'Markdown' document or the R package 'officer'.
Author: David Gohel [aut, cre],
ArData [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between equatags versions 0.1.1 dated 2021-08-04 and 0.2.0 dated 2022-06-13
equatags-0.1.1/equatags/inst/mathjax-node |only equatags-0.1.1/equatags/man/figures |only equatags-0.1.1/equatags/man/mathjax_install.Rd |only equatags-0.2.0/equatags/DESCRIPTION | 16 +-- equatags-0.2.0/equatags/MD5 | 24 +---- equatags-0.2.0/equatags/NAMESPACE | 6 - equatags-0.2.0/equatags/NEWS.md | 4 equatags-0.2.0/equatags/R/mathjax_node_setup.R | 105 +++-------------------- equatags-0.2.0/equatags/R/write_mathjax.R | 99 ++++----------------- equatags-0.2.0/equatags/README.md | 103 +++++----------------- equatags-0.2.0/equatags/man/mathjax_available.Rd | 7 - equatags-0.2.0/equatags/man/mathjax_uninstall.Rd | 16 +-- equatags-0.2.0/equatags/man/transform_mathjax.Rd | 29 ++---- 13 files changed, 107 insertions(+), 302 deletions(-)
Title: Dynamic Trees for Learning and Design
Description: Inference by sequential Monte Carlo for
dynamic tree regression and classification models
with hooks provided for sequential design and optimization,
fully online learning with drift, variable selection, and
sensitivity analysis of inputs. Illustrative
examples from the original dynamic trees paper
(Gramacy, Taddy & Polson (2011); <doi:10.1198/jasa.2011.ap09769>) are facilitated
by demos in the package; see demo(package="dynaTree").
Author: Robert B. Gramacy <rbg@vt.edu>, Matt A. Taddy and Christoforos Anagnostopoulos
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between dynaTree versions 1.2-12 dated 2022-04-01 and 1.2-13 dated 2022-06-13
ChangeLog | 6 +++ DESCRIPTION | 10 ++--- MD5 | 10 ++--- man/dynaTree.Rd | 31 ++++++++------- man/sens.dynaTree.Rd | 101 +++++++++++++++++++++++++-------------------------- src/rhelp.h | 2 - 6 files changed, 84 insertions(+), 76 deletions(-)
Title: Finding Convergence Clubs
Description: Functions for clustering regions that form convergence clubs, according to the definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>. A package description is available in Sichera and Pizzuto (2019).
Author: Roberto Sichera [aut, cre, cph],
Pietro Pizzuto [aut]
Maintainer: Roberto Sichera <rob.sichera@gmail.com>
Diff between ConvergenceClubs versions 2.2.1 dated 2019-11-20 and 2.2.4 dated 2022-06-13
DESCRIPTION | 12 - MD5 | 42 ++-- NAMESPACE | 3 R/computeH.R | 132 ++++++------ R/countryGDP.R | 102 ++++----- R/dim.convergence.clubs.R | 40 +-- R/estimateMod.R | 4 R/findClubs.R | 2 R/mergeClubs.R | 422 ++++++++++++++++++++--------------------- R/mergeDivergent.R | 328 +++++++++++++++---------------- R/plot.convergence.clubs.R | 34 ++- R/transition_paths.R |only R/utils.R | 38 +-- README.md | 13 - inst/CITATION | 28 +- man/GDP.Rd | 4 man/axis_marks.Rd | 28 +- man/filteredGDP.Rd | 4 man/findClubs.Rd | 4 man/plot.convergence.clubs.Rd | 4 man/print.convergence.clubs.Rd | 30 +- man/print_table.Rd | 32 +-- man/transition_paths.Rd |only 23 files changed, 667 insertions(+), 639 deletions(-)
More information about ConvergenceClubs at CRAN
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Title: Bayesian Model for CACE Analysis
Description: Performs CACE (Complier Average Causal Effect analysis) on either a single study or meta-analysis of datasets with binary outcomes, using either complete or incomplete noncompliance information. Our package implements the Bayesian methods proposed in Zhou et al. (2019) <doi:10.1111/biom.13028>, which introduces a Bayesian hierarchical model for estimating CACE in meta-analysis of clinical trials with noncompliance, and Zhou et al. (2021) <doi:10.1080/01621459.2021.1900859>, with an application example on Epidural Analgesia.
Author: Jinhui Yang [aut, cre] ,
Jincheng Zhou [aut] ,
James Hodges [ctb],
Haitao Chu [ctb]
Maintainer: Jinhui Yang <james.yangjinhui@gmail.com>
Diff between BayesCACE versions 1.2 dated 2022-01-06 and 1.2.1 dated 2022-06-13
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 1 + R/cace.meta.c.R | 5 ++--- R/cace.meta.ic.R | 5 ++--- R/cace.study.R | 5 ++--- R/plt.cacebayes.R | 47 +++++++++++++++++++++++++---------------------- R/plt.forest.R | 14 +++++++------- build/partial.rdb |binary man/cace.meta.c.Rd | 2 +- man/cace.meta.ic.Rd | 2 +- man/cace.study.Rd | 2 +- man/plt.acf.Rd | 4 ++-- man/plt.density.Rd | 4 ++-- man/plt.forest.Rd | 4 ++-- man/plt.trace.Rd | 4 ++-- 16 files changed, 70 insertions(+), 69 deletions(-)
Title: Spatial Point Patterns Analysis
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function (Ripley B. D. (1977) <doi:10.1111/j.2517-6161.1977.tb01615.x>), for univariate,
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
statistical significance based on Monte Carlo simulations.
Author: Raphael Pelissier [aut], Francois Goreau [aut], Philippe Verley [ctb, cre]
Maintainer: Raphael Pelissier <raphael.pelissier@ird.fr>
Diff between ads versions 1.5-5 dated 2021-03-16 and 1.5-6 dated 2022-06-13
DESCRIPTION | 19 +++++++------------ MD5 | 26 +++++++++++++------------- R/util.R | 2 +- man/internal.Rd | 2 +- man/k12fun.Rd | 4 ++-- man/kdfun.Rd | 4 ++-- man/kfun.Rd | 4 ++-- man/kmfun.Rd | 4 ++-- man/kp.fun.Rd | 4 ++-- man/kpqfun.Rd | 4 ++-- man/krfun.Rd | 4 ++-- man/ksfun.Rd | 4 ++-- man/triangulate.Rd | 7 ------- src/triangulate.h | 2 +- 14 files changed, 39 insertions(+), 51 deletions(-)
Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including
a new adaptation of a technique based on ranks which can guarantee
normally distributed transformed data if there are no ties: ordered
quantile normalization (ORQ). ORQ normalization combines a rank-mapping
approach with a shifted logit approximation that allows
the transformation to work on data outside the original domain. It is
also able to handle new data within the original domain via linear
interpolation. The package is built to estimate the best normalizing
transformation for a vector consistently and accurately. It implements
the Box-Cox transformation, the Yeo-Johnson transformation, three types
of Lambert WxF transformations, and the ordered quantile normalization
transformation. It estimates the normalization efficacy of other
commonly used transformations, and it allows users to specify
custom transformations or normalization statistics. Finally, functionality
can be integrated into a machine learning workflow via recipes.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between bestNormalize versions 1.8.2 dated 2021-09-16 and 1.8.3 dated 2022-06-13
DESCRIPTION | 14 MD5 | 38 - NAMESPACE | 4 NEWS.md | 5 R/bestNormalize.R | 2 R/step_best_normalize.R | 10 R/step_orderNorm.R | 14 README.md | 5 build/vignette.rds |binary inst/doc/bestNormalize.Rmd | 2 inst/doc/bestNormalize.html | 777 +++++++++++++++++++++++------------- inst/doc/customization.Rmd | 2 inst/doc/customization.html | 308 +++++++------- man/bestNormalize-package.Rd | 2 man/bestNormalize.Rd | 2 man/step_orderNorm.Rd | 2 tests/testthat/test_bn_parallel.R | 6 tests/testthat/test_print_methods.R | 13 vignettes/bestNormalize.Rmd | 2 vignettes/customization.Rmd | 2 20 files changed, 746 insertions(+), 464 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Includes, among others, specific functions such as state survival plots, position-wise group-typical states, dynamic sequence indicators, and dissimilarities between event sequences. Also includes contributions by non-members of the TraMineR team such as the relative frequency plot and methods for polyadic data.
Author: Gilbert Ritschard [aut, cre, ths, cph]
,
Matthias Studer [aut] ,
Reto Buergin [aut] ,
Tim Liao [ctb] ,
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.6.3 dated 2022-01-19 and 0.6.4 dated 2022-06-13
DESCRIPTION | 18 ++++++++++-------- MD5 | 22 +++++++++++----------- R/seqindic-dyn.R | 2 +- R/seqplot-rf.R | 22 ++++++++++++++++++---- R/seqsplot.R | 14 +++++--------- build/partial.rdb |binary inst/NEWS | 14 +++++++++++++- inst/NEWS.Rd | 23 ++++++++++++++++++++++- man/TraMineRextras-package.Rd | 22 ++++++++++++++++++++-- man/seqplot-rf.Rd | 12 ++++++++---- man/seqsamm.Rd | 18 +++++++++--------- man/seqtabstocc.Rd | 6 +++--- 12 files changed, 120 insertions(+), 53 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: A Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 2.1 dated 2022-03-14 and 2.2 dated 2022-06-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 10 ++++++++-- R/setup_C.R | 4 ++-- build/partial.rdb |binary man/Tinflex-package.Rd | 4 ++-- man/Tinflex.setup.Rd | 5 +++-- 7 files changed, 25 insertions(+), 18 deletions(-)
Title: Resampling Functions
Description: Bootstrap, permutation tests, and jackknife,
featuring easy-to-use syntax.
Author: Tim Hesterberg
Maintainer: Tim Hesterberg <timhesterberg@gmail.com>
Diff between resample versions 0.4 dated 2015-04-12 and 0.6 dated 2022-06-13
resample-0.4/resample/R/limits.R |only resample-0.4/resample/man/limits.percentile.Rd |only resample-0.6/resample/DESCRIPTION | 11 +-- resample-0.6/resample/MD5 | 55 ++++++++--------- resample-0.6/resample/NAMESPACE | 10 +-- resample-0.6/resample/R/MakeFunction.R | 8 +- resample-0.6/resample/R/bootstrap.R | 6 - resample-0.6/resample/R/bootstrap2.R | 6 - resample-0.6/resample/R/confidence.R |only resample-0.6/resample/R/jackknife.R | 4 - resample-0.6/resample/R/permutationTest.R | 6 - resample-0.6/resample/R/permutationTest2.R | 10 ++- resample-0.6/resample/R/resample.R | 7 +- resample-0.6/resample/R/samplers.R | 2 resample-0.6/resample/inst/doc/ChangeLog.txt | 35 ++++++++++ resample-0.6/resample/inst/doc/bootstrapComparison.txt |only resample-0.6/resample/man/ExpandProbs.Rd | 4 - resample-0.6/resample/man/IfElse.Rd | 2 resample-0.6/resample/man/Quantile.Rd | 2 resample-0.6/resample/man/bootstrap.Rd | 4 - resample-0.6/resample/man/cat0.Rd | 2 resample-0.6/resample/man/colVars.Rd | 4 - resample-0.6/resample/man/confidence.Rd |only resample-0.6/resample/man/deprecated.Rd | 38 +++++------ resample-0.6/resample/man/jackknife.Rd | 4 - resample-0.6/resample/man/print.resample.Rd | 4 - resample-0.6/resample/man/resample-data.Rd | 4 - resample-0.6/resample/man/resample-package.Rd | 52 +++++----------- resample-0.6/resample/man/resample.Rd | 4 - resample-0.6/resample/man/samp.bootstrap.Rd | 4 - resample-0.6/resample/tests/permutationTest2.t | 17 ++++- 31 files changed, 173 insertions(+), 132 deletions(-)
Title: Tools for Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter, Practical Tools for Designing and Weighting Survey Samples (2nd edition, 2018). Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.2.6 dated 2022-03-20 and 1.2.7 dated 2022-06-13
DESCRIPTION | 8 MD5 | 40 +- R/NRFUopt.R | 3 R/clusOpt2.R | 54 +- build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Singlestage-samsize.pdf |binary inst/doc/Varcomps-multistage.pdf |binary man/NRFUopt.Rd | 1 vignettes/Singlestage-samsize.html | 569 +++++++++++++++++++++++++--- vignettes/Varcomps-multistage.html | 729 +++++++++++++++++++++++++++++++------ 21 files changed, 1177 insertions(+), 227 deletions(-)
Title: Fast Cross-Validation for Multi-Penalty Ridge Regression
Description: Multi-penalty linear, logistic and cox ridge regression, including estimation of the penalty parameters by efficient (repeated) cross-validation and marginal likelihood maximization. Multiple high-dimensional data types that require penalization are allowed, as well as unpenalized variables. Paired and preferential data types can be specified. See Van de Wiel et al. (2021), <arXiv:2005.09301>.
Author: Mark A. van de Wiel
Maintainer: Mark A. van de Wiel <mark.vdwiel@amsterdamumc.nl>
Diff between multiridge versions 1.9 dated 2021-06-15 and 1.11 dated 2022-06-13
DESCRIPTION | 10 +-- MD5 | 20 +++---- NAMESPACE | 2 R/MultiLambdaCVfun.R | 135 ++++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/CVscore.Rd | 2 man/doubleCV.Rd | 2 man/fastCV2.Rd | 6 +- man/mlikCV.Rd | 4 - man/optLambdas.Rd | 2 man/optLambdasWrap.Rd | 2 11 files changed, 97 insertions(+), 88 deletions(-)
Title: Migration Indices
Description: Calculate various indices, like Crude Migration Rate,
different Gini indices or the Coefficient of Variation among others, to
show the (un)equality of migration.
Author: Lajos Balint <balint@demografia.hu> and Gergely Daroczi
<daroczig@rapporter.net>
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between migration.indices versions 0.3.0 dated 2013-10-07 and 0.3.1 dated 2022-06-13
DESCRIPTION | 17 ++---- MD5 | 78 ++++++++++++++-------------- NAMESPACE | 18 ++++++ NEWS | 5 + R/acv.R | 2 R/crude.R | 2 R/gini.R | 8 ++ R/graph.R | 13 +++- R/migration.indices.R | 2 R/others.R | 29 ++++++++++ README.md |only data/migration.hyp.rda |binary inst/CITATION | 4 - man/check.migration.matrix.Rd | 17 ++---- man/migration.acv.Rd | 27 +++------ man/migration.acv.in.Rd | 25 +++----- man/migration.acv.out.Rd | 25 +++----- man/migration.cmr.Rd | 25 +++----- man/migration.connectivity.Rd | 28 +++------- man/migration.cv.in.Rd | 28 +++------- man/migration.cv.out.Rd | 28 +++------- man/migration.effectiveness.Rd | 27 +++------ man/migration.field.diagram.Rd | 40 ++++++-------- man/migration.gini.Rd | 68 +++++++++--------------- man/migration.gini.col.Rd | 29 ++++------ man/migration.gini.col.standardized.Rd | 34 ++++-------- man/migration.gini.exchange.Rd | 30 ++++------ man/migration.gini.exchange.standardized.Rd | 37 +++++-------- man/migration.gini.in.Rd | 44 +++++---------- man/migration.gini.out.Rd | 44 +++++---------- man/migration.gini.row.Rd | 29 ++++------ man/migration.gini.row.standardized.Rd | 34 ++++-------- man/migration.gini.total.Rd | 48 +++++------------ man/migration.hyp.Rd | 20 +++---- man/migration.indices.Rd | 9 +-- man/migration.inequality.Rd | 27 +++------ man/migration.rate.Rd |only man/migration.weighted.gini.in.Rd | 32 +++-------- man/migration.weighted.gini.mean.Rd | 37 ++++--------- man/migration.weighted.gini.out.Rd | 36 ++++-------- man/migration.world.Rd | 18 +++--- 41 files changed, 442 insertions(+), 582 deletions(-)
More information about migration.indices at CRAN
Permanent link
Title: Calculate Lunar Phase & Distance, Seasons and Related
Environmental Factors
Description: Provides functions to calculate lunar and other related
environmental covariates.
Author: Emmanuel Lazaridis [aut, cre]
Maintainer: Emmanuel Lazaridis <emmanuel@strategicarrow.com>
Diff between lunar versions 0.1-04 dated 2014-09-08 and 0.2-1 dated 2022-06-13
DESCRIPTION | 21 +++++------ MD5 | 34 +++++++++--------- NAMESPACE | 2 - R/lunar-package.R | 5 +- R/lunar.package.R | 76 ++++++++++++++++++++++++++--------------- inst/CITATION | 11 ++--- man/lunar-package.Rd | 15 +++++--- man/lunar.4phases.Rd | 9 ++-- man/lunar.8phases.Rd | 9 ++-- man/lunar.distance.Rd | 10 ++--- man/lunar.distance.mean.Rd | 16 +++++--- man/lunar.distances.Rd | 9 ++-- man/lunar.illumination.Rd | 12 +++--- man/lunar.illumination.mean.Rd | 16 +++++--- man/lunar.metric.mean.Rd | 17 +++++---- man/lunar.phase.Rd | 16 ++++---- man/terrestrial.season.Rd | 22 +++++++++-- man/terrestrial.seasons.Rd | 9 ++-- 18 files changed, 185 insertions(+), 124 deletions(-)
Title: Locally Stationary Two-Dimensional Wavelet Process Estimation
Scheme
Description: Estimates two-dimensional local wavelet spectra.
Author: Idris Eckley [aut, cre],
Guy Nason [aut],
Sarah Taylor [ctb],
Matthew Nunes [ctb]
Maintainer: Idris Eckley <i.eckley@lancaster.ac.uk>
Diff between LS2W versions 1.3.4 dated 2018-05-23 and 1.3.5 dated 2022-06-13
DESCRIPTION | 11 +++--- MD5 | 80 +++++++++++++++++++++++++------------------------- NAMESPACE | 1 R/specplot.R | 2 - inst/CITATION | 4 +- man/A.Rd | 4 +- man/A2name.Rd | 3 + man/AvBasis.wst2D.Rd | 3 + man/D1Amat.Rd | 3 + man/D2ACW.Rd | 3 + man/D2ACWmat.Rd | 3 + man/D2Amat.Rd | 9 +++-- man/D2autoplot.Rd | 3 + man/DWEnv.Rd | 4 +- man/Haar2MA.diag.Rd | 3 + man/Haar2MA.horiz.Rd | 3 + man/Haar2MA.vert.Rd | 3 + man/HaarMontage.Rd | 3 + man/LS2W-package.Rd | 4 +- man/LS2Wsim.Rd | 3 + man/LS2Wsim.cddews.Rd | 3 + man/Phi1Dname.Rd | 3 + man/PhiJ.Rd | 3 + man/Psi1Dname.Rd | 3 + man/Psi2Dname.Rd | 3 + man/PsiJ.Rd | 3 + man/cddews.Rd | 3 + man/cdtoimwd.Rd | 3 + man/convert.imwd.Rd | 3 + man/example.ls2w.Rd | 3 + man/getdata.Rd | 3 + man/imwd.Rd | 3 + man/imwr.imwd.rd | 3 + man/packetj.Rd | 3 + man/print.cddews.Rd | 3 + man/sample.stats.Rd | 3 + man/specplot.Rd | 3 + man/summary.cddews.Rd | 3 + man/threshold.imwd.Rd | 3 + src/functionsIE.c | 31 +++++++++++-------- src/testit.c | 3 - 41 files changed, 173 insertions(+), 70 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamas Nepusz <ntamas@gmail.com>
Diff between igraph versions 1.3.1 dated 2022-04-20 and 1.3.2 dated 2022-06-13
DESCRIPTION | 6 MD5 | 126 +++++++++--------- NEWS.md | 28 +++- R/centrality.R | 32 ++-- R/coloring.R | 3 R/community.R | 61 +++++++- R/games.R | 2 R/iterators.R | 4 R/plot.shapes.R | 62 --------- R/scg.R | 32 ++-- build/partial.rdb |binary inst/NEWS.md | 28 +++- man/betweenness.Rd | 6 man/closeness.Rd | 20 +- man/cluster_leiden.Rd | 52 ++++++- man/cluster_louvain.Rd | 3 man/greedy_vertex_coloring.Rd | 3 man/harmonic_centrality.Rd | 2 man/modularity.igraph.Rd | 2 man/sample_sbm.Rd | 2 man/scg.Rd | 16 +- man/scg_group.Rd | 16 +- man/shapes.Rd | 62 --------- src/core/community/edge_betweenness.c | 5 src/core/community/fast_modularity.c | 8 + src/core/community/label_propagation.c | 11 + src/core/community/leading_eigenvector.c | 14 +- src/core/community/leiden.c | 12 + src/core/community/walktrap/walktrap.cpp | 7 + src/core/core/printing.c | 4 src/core/core/psumtree.c | 9 + src/core/games/barabasi.c | 48 ++++--- src/core/games/citations.c | 16 ++ src/core/games/recent_degree.c | 16 ++ src/core/graph/cattributes.c | 22 +-- src/core/hrg/hrg.cc | 6 src/core/hrg/hrg_types.cc | 4 src/core/io/dl-parser.c | 144 ++++++++++----------- src/core/io/dl-parser.h | 4 src/core/io/dl-parser.y | 1 src/core/io/dot.c | 28 ++-- src/core/io/edgelist.c | 3 src/core/io/gml-parser.c | 62 ++++----- src/core/io/gml-parser.h | 4 src/core/io/gml-parser.y | 1 src/core/io/graphml.c | 15 -- src/core/io/lgl-parser.c | 30 ++-- src/core/io/lgl-parser.h | 4 src/core/io/lgl-parser.y | 3 src/core/io/ncol-parser.c | 24 +-- src/core/io/ncol-parser.h | 4 src/core/io/ncol-parser.y | 1 src/core/io/pajek-parser.c | 212 +++++++++++++++---------------- src/core/io/pajek-parser.h | 4 src/core/io/pajek-parser.y | 1 src/core/layout/fruchterman_reingold.c | 185 ++++++++++++--------------- src/core/layout/kamada_kawai.c | 118 ++++++----------- src/core/layout/layout_internal.h | 13 + src/core/layout/layout_random.c | 186 +++++++++++++++++++++++++++ src/core/operators/rewire.c | 8 - src/core/random/random.c | 16 +- src/rinterface.c | 16 ++ tests/testthat/test_layout.fr.R | 7 - tests/testthat/test_layout.kk.R | 57 ++++---- 64 files changed, 1103 insertions(+), 798 deletions(-)
Title: United Formula Annotation (UFA) for HRMS Data Processing
Description: A pipeline to annotate peaklists from the IDSL.IPA package with molecular formula using an isotopic profile matching approach. The IDSL.UFA pipeline is especially beneficial when MS/MS data are not available. The IDSL.UFA package has functions to process user-defined adduct formulas.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFA versions 1.3 dated 2022-06-07 and 1.4 dated 2022-06-13
DESCRIPTION | 10 +- MD5 | 14 +-- R/UFA_profile_visualizer.R | 10 -- R/UFA_score_function_optimization_xlsxAnalyzer.R | 2 R/UFA_xlsxAnalyzer.R | 2 R/aligned_molecular_formula_annotator.R | 97 ++++++----------------- R/zero_score_function.R | 8 - build/partial.rdb |binary 8 files changed, 48 insertions(+), 95 deletions(-)
Title: Holistic Generalized Linear Models
Description: Holistic generalized linear models (HGLMs) extend generalized linear models (GLMs) by enabling the possibility to add further constraints to the model. The 'holiglm' package simplifies estimating HGLMs using convex optimization.
Author: Benjamin Schwendinger [aut, cre],
Florian Schwendinger [aut],
Laura Vana [aut]
Maintainer: Benjamin Schwendinger <benjaminschwe@gmail.com>
Diff between holiglm versions 0.2 dated 2022-06-08 and 0.2.1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/constraints.R | 1 + R/hglm.R | 4 ++-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: An Efficient C/C++ Toolset for R
Description: Accelerated computation for some basic R functions.
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer <bastianxpfeifer@gmail.com>
Diff between BASIX versions 1.1 dated 2013-10-24 and 1.2 dated 2022-06-13
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++-------- NAMESPACE | 4 +++- README.md |only src/C_get_sfreqh_C.c | 9 ++++++--- src/CompareVEK.c | 9 ++++++--- src/combnapply_C.c | 5 +++-- src/find_windowC.c | 23 ++++++++++++++--------- src/init.c |only src/my_match_C.c | 16 ++++++++++------ src/my_unique_C.c | 7 ++++--- 11 files changed, 63 insertions(+), 42 deletions(-)
Title: Flexible Relative Survival Analysis
Description: Package for parametric relative survival analyses. It allows to model non-linear and
non-proportional effects and both non proportional and non linear effects, using splines (B-spline and truncated power basis), Weighted Cumulative Index of Exposure effect, with correction model for
the life table. Both non proportional and non linear effects are described in
Remontet, L. et al. (2007) <doi:10.1002/sim.2656> and
Mahboubi, A. et al. (2011) <doi:10.1002/sim.4208>.
Permanent link
Title: Continuous Associated Kernel Estimation
Description: Continuous smoothing of probability density function on a compact or semi-infinite support is performed using four continuous associated kernels: extended beta, gamma, lognormal and reciprocal inverse Gaussian. The cross-validation technique is also implemented for bandwidth selection.
Author: W. E. Wansouwe, F. G. Libengue and C. C. Kokonendji
Maintainer: W. E. Wansouwe <ericwansouwe@gmail.com>
Diff between Conake versions 1.0 dated 2015-03-01 and 1.0.1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 2 ++ R/simp_int.R | 2 +- 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Compute the Biweight Mean Vector and Covariance & Correlation
Matrice
Description: Compute multivariate location, scale, and correlation
estimates based on Tukey's biweight M-estimator.
Author: Jo Hardin <jo.hardin@pomona.edu>
Maintainer: Jo Hardin <jo.hardin@pomona.edu>
Diff between biwt versions 1.0 dated 2009-08-28 and 1.0.1 dated 2022-06-13
DESCRIPTION | 15 ++++++++------- MD5 |only NAMESPACE |only 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Associated Kernel Estimations
Description: Continuous and discrete (count or categorical) estimation of density, probability mass function (p.m.f.) and regression functions are performed using associated kernels. The cross-validation technique and the local Bayesian procedure are also implemented for bandwidth selection.
Author: W. E. Wansouwe, S. M. Some and C. C. Kokonendji
Maintainer: W. E. Wansouwe <ericwansouwe@gmail.com>
Diff between Ake versions 1.0 dated 2015-03-29 and 1.0.1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 7 ++----- R/simp_int.R | 2 +- data/milk.rda |binary 5 files changed, 10 insertions(+), 13 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut], Muhammed Ali Yilmaz [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 2.6 dated 2021-03-15 and 2.7 dated 2022-06-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/boxcoxfr.R | 3 +-- R/boxcoxlm.R | 3 +-- R/boxcoxmeta.R | 3 +-- R/boxcoxnc.R | 3 +-- man/boxcoxfr.Rd | 4 ++-- 7 files changed, 16 insertions(+), 20 deletions(-)
Title: Estimate Structured Additive Regression Models with 'BayesX'
Description: An R interface to estimate structured additive regression (STAR) models with 'BayesX'.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between R2BayesX versions 1.1-1.1 dated 2021-10-19 and 1.1-3 dated 2022-06-13
DESCRIPTION | 12 ++-- MD5 | 96 ++++++++++++++++++------------------ R/bayesx.construct.ps.smooth.spec.R | 4 - R/bayesx_logfile.R | 2 R/colorlegend.R | 8 ++- R/find.smooth.random.R | 2 R/interp2.R | 20 +------ R/parse.bayesx.input.R | 8 +-- R/plot3d.R | 2 R/plotmap.R | 2 R/read.bayesx.model.output.R | 5 + R/residuals.bayesx.R | 2 R/s4class.R | 4 + R/sliceplot.R | 2 R/write.bayesx.input.R | 2 R/write.term.info.R | 2 data/BeechBnd.rda |binary data/BeechGra.rda |binary data/FantasyBnd.rda |binary data/ForestHealth.rda |binary data/GAMart.rda |binary data/GermanyBnd.rda |binary data/MunichBnd.rda |binary data/ZambiaBnd.rda |binary data/ZambiaNutrition.rda |binary inst/CITATION | 8 +-- man/BeechBnd.Rd | 2 man/BeechGra.Rd | 2 man/ForestHealth.Rd | 4 - man/GermanyBnd.Rd | 2 man/MunichBnd.Rd | 2 man/R2BayesX-package.Rd | 4 - man/ZambiaBnd.Rd | 2 man/ZambiaNutrition.Rd | 2 man/bayesx.Rd | 8 +-- man/bayesx.control.Rd | 8 +-- man/bnd2gra.Rd | 2 man/nbAndGraConversion.Rd | 4 - man/plot3d.Rd | 19 +------ man/plotmap.Rd | 19 +------ man/read.bnd.Rd | 2 man/read.gra.Rd | 2 man/shp2bnd.Rd | 2 man/sliceplot.Rd | 19 +------ man/spAndBndConversion.Rd | 4 - man/write.bnd.Rd | 2 man/write.gra.Rd | 2 src/R2BayesX_functions.c | 2 src/R2BayesX_init.c | 18 +++++- 49 files changed, 145 insertions(+), 169 deletions(-)
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes ('asc', 'chr'),
- convert character vector to ASCII representation ('ASCIIfy'),
- apply title capitalization rules to a character vector ('capwords').
Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley and CRAN team
Maintainer: ORPHANED
Diff between gtools versions 3.9.2.1 dated 2022-05-23 and 3.9.2.2 dated 2022-06-13
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/checkRVersion.R | 18 ++++++++++++++---- tests/test_setTCPNoDelay.R | 3 ++- 4 files changed, 25 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-08 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-01 1.1
2014-12-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-19 1.2
2014-05-02 1.1.2
2013-12-07 1.1.1
2013-01-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-11 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-21 1.1
2012-03-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-30 1.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-22 0.2.0
2015-05-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-27 2.0
2013-03-15 1.0
2013-03-15 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-08 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-20 1.2.2
2014-05-27 1.2
2014-01-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-27 1.0.3
2015-03-29 1.0.1
2014-11-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-09 1.1.8
2013-03-05 1.1.5
2013-02-10 1.1.3
2013-02-08 1.1.2
2012-11-14 1.1.0
2012-10-04 1.0.2
2012-09-06 1.0
2012-06-26 0.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-02 1.0-2
2013-11-24 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-30 1.2.2
2014-05-29 1.2.1
2014-01-09 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-02 1.0.1
2013-07-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-12 1.2
2013-08-14 1.1
2012-04-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-01 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-12 1.03-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-06 0.5.0
2013-08-14 0.4.2
2013-07-08 0.4.1
2012-10-31 0.3.0
2012-02-16 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-22 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-07 1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-13 1.0
Title: Plotting Tool for Brain Atlases
Description: Contains 'ggplot2' geom for plotting brain atlases using
simple features. The largest component of the package is the data
for the two built-in atlases. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre]
,
Didac Vidal-Pineiro [aut]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 1.6.4 dated 2021-09-03 and 1.6.5 dated 2022-06-13
DESCRIPTION | 16 MD5 | 42 +- NAMESPACE | 1 NEWS.md | 17 R/ggseg-package.R | 5 R/layer-brain.R | 2 R/position-brain.R | 62 +-- R/read_freesurfer.R | 6 README.md | 5 build/vignette.rds |binary data/aseg.rda |binary inst/WORDLIST | 1 inst/doc/externalData.html | 310 +++++++++++++++-- inst/doc/freesurfer_files.html | 277 ++++++++++++++- inst/doc/ggseg.R | 19 + inst/doc/ggseg.Rmd | 35 + inst/doc/ggseg.html | 378 ++++++++++++++++++--- man/ggseg.Rd | 4 man/read_atlas_files.Rd | 2 man/read_freesurfer_stats.Rd | 2 tests/testthat/_snaps/ggseg/ggseg-aseg-stacked.svg | 78 ++-- vignettes/ggseg.Rmd | 35 + 22 files changed, 1075 insertions(+), 222 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-12 0.2.1
2014-08-04 0.1.0
2014-06-16 0.0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-04 0.7-1
2013-07-19 0.7-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-01 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-16 0.3
2012-01-12 0.2
2011-06-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-01-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-03 1.1
2012-11-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-13 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-26 0.6
2011-10-06 0.5
2009-07-23 0.4
2006-08-11 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-14 0.9-1
2014-04-24 0.9
2014-01-31 0.8.2
2013-09-12 0.6.32
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-20 0.3-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-13 0.99.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-26 1.2
Title: Custom Components for Shiny Applications
Description: Provides useful UI components and input widgets for 'Shiny' applications.
The offered components allow to apply non-standard operations and view to your
'Shiny' application, but also help to overcome common performance issues.
Author: Krystian Igras [cre, aut]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyGizmo versions 0.1 dated 2022-04-27 and 0.2 dated 2022-06-13
DESCRIPTION | 9 +++++---- MD5 | 31 +++++++++++++++++++------------ NAMESPACE | 3 +++ NEWS.md | 8 +++++++- R/conditionalJS.R |only R/pickCheckbox.R | 2 +- R/textArea.R | 2 +- R/uiModal.R | 6 +++--- R/valueButton.R | 35 ++++++++++++++++++++++++++++------- README.md | 23 ++++++++++++++++------- inst/www/conditionaljs.css |only inst/www/conditionaljs.js |only man/conditionalJS.Rd |only man/figures/condjs.gif |only man/jsCalls.Rd |only man/js_calls.Rd |only man/modalDialogUI.Rd | 2 +- man/pickCheckboxInput.Rd | 2 +- man/textArea.Rd | 2 +- man/valueButton.Rd | 7 +++++-- 20 files changed, 91 insertions(+), 41 deletions(-)
Title: Reading FRE Corporate Data of Public Traded Companies from B3
Description: Reads corporate data such as board composition and compensation for companies traded at B3,
the Brazilian exchange <https://www.b3.com.br/>. All data is downloaded and imported from the ftp site <http://dados.cvm.gov.br/dados/CIA_ABERTA/DOC/FRE/>.
Author: Marcelo Perlin [aut, cre],
Guilherme Kirch [aut]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetFREData versions 0.7 dated 2021-09-03 and 0.8.1 dated 2022-06-13
DESCRIPTION | 15 - MD5 | 23 +- NEWS.md | 9 + R/fct_download_file.R | 2 R/fct_get_fre_ftp_contents.R | 3 R/fct_get_info_companies.R | 45 ----- README.md | 4 build/vignette.rds |binary inst/doc/GetFREData-vignette-introduction.Rmd | 2 inst/doc/GetFREData-vignette-introduction.html | 207 ++++++++++++++++++++++++- tests/testthat/test-fredata.R | 25 ++- tests/testthat/test-get-info-companies.R |only vignettes/GetFREData-vignette-introduction.Rmd | 2 13 files changed, 257 insertions(+), 80 deletions(-)
Title: Finding the DNA and Protein Sequences of Any Genomic or
Proteomic Loci
Description: Using the DNA sequence and gene annotation files provided in
'ENSEMBL' <https://www.ensembl.org/index.html>,
the functions implemented in the package try to find the DNA sequences and
protein sequences of any given genomic loci, and to find the genomic coordinates
and protein sequences of any given protein locations, which are the frequent
tasks in the analysis of genomic and proteomic data.
Author: Yaoyong Li
Maintainer: Yaoyong Li<liyaoyong85@gmail.com>
Diff between geno2proteo versions 0.0.5 dated 2022-02-10 and 0.0.6 dated 2022-06-13
DESCRIPTION | 8 +-- MD5 | 22 +++++----- NEWS | 14 ++++++ R/proteinLocsToProteinSeq.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/geno2proteoIntroduction.R | 5 -- inst/doc/geno2proteoIntroduction.Rnw | 22 ++++++---- inst/doc/geno2proteoIntroduction.pdf |binary inst/extdata/transId_pfamDomainStartEnd_chr16_Zdomains_22examples_proteinID.txt | 1 man/generatingCDSaaFile.Rd | 4 - vignettes/geno2proteoIntroduction.Rnw | 22 ++++++---- 12 files changed, 65 insertions(+), 34 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic,
and programmer friendly through a flexible and parsimonious syntax.
It is well integrated with base R, 'dplyr' / (grouped) 'tibble',
'data.table', 'sf', 'plm' (panel-series and data frames), and
non-destructively handles other matrix or data frame based classes (like
'ts', 'xts' / 'zoo', 'tsibble', ...)
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values/rows,
factor generation and interactions. Fast and flexible functions for data
manipulation, data object conversions, and memory efficient R programming.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function, weighted
and parallelized data aggregation.
(3) Advanced transformations: Fast row/column arithmetic, (grouped) replacing
and sweeping out of statistics (by reference), (grouped, weighted) scaling/standardizing,
(higher-dimensional) between (averaging) and (quasi-)within (demeaning) transformations,
linear prediction, model fitting and testing exclusion restrictions.
(4) Advanced time-computations: Fast and flexible indexed time series and panel data classes.
Fast (sequences of) lags/leads, and (lagged/leaded, iterated, quasi-, log-)
differences and (compounded) growth rates on (irregular) time series and panels.
Multivariate auto-, partial- and cross-correlation functions for panel data.
Panel data to (ts-)array conversions.
(5) List processing: Recursive list search, splitting,
extraction/subsetting, apply, and generalized row-binding / unlisting to data frame.
(6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed)
summary statistics and descriptive tools.
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [ [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.8.4 dated 2022-06-08 and 1.8.5 dated 2022-06-13
DESCRIPTION | 6 MD5 | 156 ++++++++++----------- NEWS.md | 7 R/fhdbetween_fhdwithin.R | 2 R/fsubset_ftransform.R | 53 +------ R/recode_replace.R | 2 R/small_helper.R | 31 +--- inst/doc/collapse_documentation.html | 4 man/BY.Rd | 4 man/GRP.Rd | 4 man/TRA.Rd | 6 man/across.Rd | 8 - man/collap.Rd | 4 man/collapse-package.Rd | 12 - man/fast-statistical-functions.Rd | 2 man/fdiff.Rd | 3 man/flag.Rd | 4 man/fmean.Rd | 4 man/fmedian.Rd | 4 man/fmin_fmax.Rd | 4 man/fndistinct.Rd | 4 man/fnobs.Rd | 4 man/fnth.Rd | 4 man/fprod.Rd | 4 man/fscale.Rd | 4 man/fsum.Rd | 4 man/fsummarise.Rd | 5 man/ftransform.Rd | 8 - man/fvar_fsd.Rd | 4 man/indexing.Rd | 8 - man/qtab.Rd | 4 src/fmean.c | 5 src/fmode.c | 6 src/fndistinct.c | 4 src/fnth_fmedian.cpp | 6 src/fprod.c | 10 - src/fsum.c | 4 src/kit_dup.c | 19 +- tests/testthat/test-BY.R | 2 tests/testthat/test-GRP.R | 9 - tests/testthat/test-TRA.R | 2 tests/testthat/test-attribute-handling.R | 2 tests/testthat/test-collap.R | 2 tests/testthat/test-dapply.R | 2 tests/testthat/test-data.table.R | 8 - tests/testthat/test-fHDbetween-fHDwithin-HDB-HDW.R | 8 - tests/testthat/test-fNobs-fNdistinct.R | 1 tests/testthat/test-fbetween-fwithin-B-W.R | 2 tests/testthat/test-fcumsum.R | 10 + tests/testthat/test-fdiff-fgrowth-D-G.R | 1 tests/testthat/test-ffirst-flast.R | 1 tests/testthat/test-flag-L-F.R | 2 tests/testthat/test-flm-fFtest.R | 2 tests/testthat/test-fmean.R | 2 tests/testthat/test-fmedian.R | 2 tests/testthat/test-fmin-fmax.R | 2 tests/testthat/test-fmode.R | 2 tests/testthat/test-fprod.R | 6 tests/testthat/test-fscale-STD.R | 2 tests/testthat/test-fsubset-ftransform.R | 2 tests/testthat/test-fsum.R | 2 tests/testthat/test-fvar-fsd.R | 2 tests/testthat/test-indexing.R | 10 + tests/testthat/test-list-processing.R | 9 - tests/testthat/test-misc.R | 4 tests/testthat/test-miscellaneous-issues.R | 6 tests/testthat/test-psmat-psacf.R | 2 tests/testthat/test-qsu.R | 2 tests/testthat/test-qtab.R | 2 tests/testthat/test-quick-conversion.R | 7 tests/testthat/test-recode-replace.R | 2 tests/testthat/test-roworder-colorder-rename.R | 6 tests/testthat/test-select-replace-vars.R | 2 tests/testthat/test-seqid-groupid.R | 2 tests/testthat/test-setop.R | 8 - tests/testthat/test-sf.R | 6 tests/testthat/test-splitting.R | 2 tests/testthat/test-varying.R | 9 - tests/testthat/test-whichv.R | 8 + 79 files changed, 339 insertions(+), 251 deletions(-)
Title: Stable and Interpretable RUle Set
Description: A regression and classification algorithm based on random forests, which takes the form of a short list of rules. SIRUS combines the simplicity of decision trees with a predictivity close to random forests. The core aggregation principle of random forests is kept, but instead of aggregating predictions, SIRUS aggregates the forest structure: the most frequent nodes of the forest are selected to form a stable rule ensemble model. The algorithm is fully described in the following articles: Benard C., Biau G., da Veiga S., Scornet E. (2021), Electron. J. Statist., 15:427-505 <DOI:10.1214/20-EJS1792> for classification, and Benard C., Biau G., da Veiga S., Scornet E. (2021), AISTATS, PMLR 130:937-945 <http://proceedings.mlr.press/v130/benard21a>, for regression. This R package is a fork from the project ranger (<https://github.com/imbs-hl/ranger>).
Author: Clement Benard [aut, cre], Marvin N. Wright [ctb, cph]
Maintainer: Clement Benard <clement.benard5@gmail.com>
Diff between sirus versions 0.3.2 dated 2021-02-22 and 0.3.3 dated 2022-06-13
DESCRIPTION | 16 ++++++++-------- MD5 | 22 +++++++++++----------- R/RcppExports.R | 38 +++++++++++++++++++------------------- R/ranger.R | 4 ++-- R/sirus.R | 28 +++++++++++++++++----------- R/sirus_utility.R | 14 +++++++++----- README.md | 14 +++++++------- build/partial.rdb |binary man/sirus.cv.Rd | 8 ++++---- man/sirus.fit.Rd | 6 +++--- src/Forest.cpp | 2 +- src/RcppExports.cpp | 5 +++++ 12 files changed, 86 insertions(+), 71 deletions(-)
Title: Robust Small Area Estimation
Description: Methods to fit robust alternatives to commonly used models used in
Small Area Estimation. The methods here used are based on best linear
unbiased predictions and linear mixed models. At this time available models
include area level models incorporating spatial and temporal correlation in
the random effects.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between saeRobust versions 0.2.0 dated 2018-03-27 and 0.3.0 dated 2022-06-13
DESCRIPTION | 11 MD5 | 46 +- NEWS | 20 - R/NAMESPACE.R | 15 R/bootstrap.R | 55 +-- R/correlation.R | 30 - R/rfh.R | 72 ++-- R/update.R | 14 build/vignette.rds |binary inst/doc/fixedPoint.R | 10 inst/doc/fixedPoint.html | 410 +++++++++++++++++++++---- man/bootstrap.Rd | 4 man/correlation.Rd | 9 man/fit.Rd | 36 +- man/mse.Rd | 3 man/rfh.Rd | 3 man/update.Rd | 1 src/RcppExports.cpp | 5 tests/testthat/test-bootstrap.R | 32 - tests/testthat/test-fit.R | 25 - tests/testthat/test-print.R | 11 tests/testthat/test-rfh.R | 4 tests/testthat/test-robustObjectiveFunctions.R | 1 tests/testthat/verify-print-rfh-1.out |only tests/testthat/verify-print-rfh-2.out |only 25 files changed, 570 insertions(+), 247 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 0.3.4 dated 2022-06-05 and 0.3.4-1 dated 2022-06-13
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- R/backend-dbplyr__duckdb_connection.R | 13 +--------- man/backend-duckdb.Rd | 13 +--------- src/duckdb/src/include/duckdb/common/exception_format_value.hpp | 4 +-- src/duckdb/src/parallel/executor.cpp | 3 -- tests/testthat/test_arrow.R | 12 ++++----- 7 files changed, 21 insertions(+), 42 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 1.1.0 dated 2022-06-08 and 1.1.1 dated 2022-06-13
DESCRIPTION | 6 +- MD5 | 20 ++++---- R/BranchGLM.R | 59 +++++++++++++++++--------- R/VariableSelection.R | 90 ++++++++++++++++++++++++---------------- man/BranchGLM.Rd | 12 +++-- man/predict.BranchGLM.Rd | 1 src/BranchGLMHelpers.cpp | 64 ++++++++++------------------ src/BranchGLMHelpers.h | 2 src/ParBranchGLMHelpers.cpp | 28 ++++++------ src/ParVariableSelection.cpp | 4 - tests/testthat/test-BranchGLM.R | 21 ++++++++- 11 files changed, 173 insertions(+), 134 deletions(-)
Title: Riskset ROC Curve Estimation from Censored Survival Data
Description: Compute time-dependent Incident/dynamic accuracy measures
(ROC curve, AUC, integrated AUC )from censored survival data
under proportional or non-proportional hazard assumption of
Heagerty & Zheng (Biometrics, Vol 61 No 1, 2005, PP 92-105).
Author: Patrick J. Heagerty <heagerty@u.washington.edu>, packaging by
Paramita Saha-Chaudhuri <paramita.sahachaudhuri.work@gmail.com>
Maintainer: Paramita Saha-Chaudhuri
<paramita.sahachaudhuri.work@gmail.com>
Diff between risksetROC versions 1.0.4 dated 2012-09-26 and 1.0.4.1 dated 2022-06-13
DESCRIPTION | 16 +++++++--------- MD5 | 6 +++--- NAMESPACE | 3 +++ data/pbc.RData |binary 4 files changed, 13 insertions(+), 12 deletions(-)
Title: Simple Methods for Calculating and Backtesting Value at Risk and
Expected Shortfall
Description: Enables the user to calculate Value at Risk (VaR)
and Expected Shortfall (ES) by means of various types of historical
simulation. Currently plain-, age-, volatility-weighted- and filtered
historical simulation are implemented in this package. Volatility weighting
can be carried out via an exponentially weighted moving average model
(EWMA) or other GARCH-type models. The performance can be assessed via
Traffic Light Test, Coverage Tests and Loss Functions. The methods of the
package are described in Gurrola-Perez, P. and Murphy, D. (2015)
<https://EconPapers.repec.org/RePEc:boe:boeewp:0525> as well as McNeil, J.,
Frey, R., and Embrechts, P. (2015) <https://ideas.repec.org/b/pup/pbooks/10496.html>.
Author: Sebastian Letmathe [aut, cre]
Maintainer: Sebastian Letmathe <sebastian.letmathe@uni-paderborn.de>
Diff between quarks versions 1.1.0 dated 2022-03-30 and 1.1.1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/cvgtest.R | 39 +++++++++++++++------------------------ R/lossfun.R | 24 ++++++++++++------------ R/plop.R | 2 +- R/print.quarks.R | 26 ++++++++++++++++++++++++-- R/rollcast.R | 5 +++-- README.md | 43 +++++++++++++++++++++++++------------------ man/cvgtest.Rd | 44 +++++++++++++++++++++----------------------- man/lossfun.Rd | 8 ++++---- man/plop.Rd | 2 +- 12 files changed, 124 insertions(+), 101 deletions(-)
Title: Simulation of Legal Exemption System for European Cartel Law
Description: Monte Carlo simulations of a game-theoretic model for the
legal exemption system of the European cartel law are implemented
in order to estimate the (mean) deterrent effect of this system.
The input and output parameters of the simulated cartel
opportunities can be visualized by three-dimensional projections.
A description of the model is given in Moritz et al. (2018)
<doi:10.1515/bejeap-2017-0235>.
Author: Martin Becker [aut, cre]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between SimEUCartelLaw versions 1.0.2 dated 2022-03-29 and 1.0.3 dated 2022-06-13
SimEUCartelLaw-1.0.2/SimEUCartelLaw/man/RglPlot.Rd |only SimEUCartelLaw-1.0.3/SimEUCartelLaw/DESCRIPTION | 10 - SimEUCartelLaw-1.0.3/SimEUCartelLaw/MD5 | 11 -- SimEUCartelLaw-1.0.3/SimEUCartelLaw/NAMESPACE | 5 SimEUCartelLaw-1.0.3/SimEUCartelLaw/R/SimEUCartelLaw-package.r | 1 SimEUCartelLaw-1.0.3/SimEUCartelLaw/R/SimEUCartelLaw.r | 53 ---------- SimEUCartelLaw-1.0.3/SimEUCartelLaw/man/SimEUCartelLawpackage.Rd | 7 - 7 files changed, 13 insertions(+), 74 deletions(-)
More information about SimEUCartelLaw at CRAN
Permanent link
Title: Stratigraphic Tree Analysis for Palaeontology
Description: Functions for the stratigraphic analysis of phylogenetic trees.
Author: Mark A. Bell [aut, cph],
Graeme T. Lloyd [aut, cre, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Diff between strap versions 1.4 dated 2014-11-05 and 1.6-0 dated 2022-06-13
strap-1.4/strap/R/strap-internal.R |only strap-1.6-0/strap/CHANGELOG | 18 strap-1.6-0/strap/DESCRIPTION | 24 strap-1.6-0/strap/MD5 | 40 - strap-1.6-0/strap/NAMESPACE | 23 strap-1.6-0/strap/R/DateNodeHedman.R |only strap-1.6-0/strap/R/DatePhylo.R | 75 + strap-1.6-0/strap/R/DatePhyloHedman.R |only strap-1.6-0/strap/R/FindDescendants.R | 51 - strap-1.6-0/strap/R/StratPhyloCongruence.R | 994 +++++++++++--------------- strap-1.6-0/strap/R/geoscalePhylo.R | 848 ++++++++++++---------- strap-1.6-0/strap/R/geoscalePhylo.mod.R |only strap-1.6-0/strap/R/strap-package.R |only strap-1.6-0/strap/README.md |only strap-1.6-0/strap/inst |only strap-1.6-0/strap/man/Asaphidae.Rd | 19 strap-1.6-0/strap/man/DateNodeHedman.Rd |only strap-1.6-0/strap/man/DatePhylo.Rd | 64 - strap-1.6-0/strap/man/DatePhyloHedman.Rd |only strap-1.6-0/strap/man/Dipnoi.Rd | 19 strap-1.6-0/strap/man/FindDescendants.Rd | 37 strap-1.6-0/strap/man/StratPhyloCongruence.Rd | 210 +++-- strap-1.6-0/strap/man/UKzones.Rd | 25 strap-1.6-0/strap/man/geoscalePhylo.Rd | 273 ++++--- strap-1.6-0/strap/man/geoscalePhylo.mod.Rd |only strap-1.6-0/strap/man/strap-package.Rd | 47 - 26 files changed, 1517 insertions(+), 1250 deletions(-)
Title: A Collection of Models that Employ a Product Partition
Distribution as a Prior on Partitions
Description: Provides a suite of functions that fit models that use PPM type priors for partitions.
Models include hierarchical Gaussian and probit ordinal models with a (covariate
dependent) PPM. If a covariate dependent product partition model is selected,
then all the options detailed in Page, G.L.; Quintana, F.A. (2018)
<doi:10.1007/s11222-017-9777-z> are available. If covariate values are missing,
then the approach detailed in Page, G.L.; Quintana, F.A.; Mueller, P (2020)
<doi:10.1080/10618600.2021.1999824> is employed. Also included in the package is
a function that fits a Gaussian likelihood spatial product partition model that is
detailed in Page, G.L.; Quintana, F.A. (2016) <doi:10.1214/15-BA971>, and
multivariate change point models that are detailed in Quinlan, J.J.; Page, G.L.;
Castro, L.M. (2021) <arXiv:2201.07830>.
Author: Garritt L. Page [aut, cre, cph],
Jose J. Quinlan [aut, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between ppmSuite versions 0.2.2 dated 2022-05-31 and 0.2.3 dated 2022-06-13
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- R/ordinal_ppmx.R | 2 - R/ppmx.R | 2 - src/Rutil.c | 7 +++--- src/gaussian.ppmx.c | 49 ++++++++++++++++++++++++++++++++++---------- src/gaussian.ppmx.missing.c | 49 ++++++++++++++++++++++++++++++-------------- src/ordinal.ppmx.c | 2 - src/ordinal.ppmx.missing.c | 2 - 9 files changed, 91 insertions(+), 44 deletions(-)
More information about PlatformDesign at CRAN
Permanent link
Title: Multiple Imputation for Proteomics
Description: A framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) <arxiv:2108.07086>. It is dedicated to dealing with multiple imputation for proteomics.
Author: Marie Chion [aut] ,
Christine Carapito [aut] ,
Frederic Bertrand [cre, aut] ,
Gordon Smyth [ctb],
Davis McCarthy [ctb],
Helene Borges [ctb],
Thomas Burger [ctb],
Quentin Giai-Gianetto [ctb],
Samuel Wieczorek [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between mi4p versions 0.9 dated 2022-03-25 and 1.0 dated 2022-06-13
DESCRIPTION | 13 MD5 | 68 - NEWS.md | 5 R/check.conditions.R | 13 R/check.design.R | 14 R/datasets.R | 33 R/mi4limma.R | 44 R/mi4p-package.R | 29 R/multi_impute.R | 54 - R/rubin1_all.R | 12 R/rubin1_one.R | 12 R/rubin2_all.R | 2 R/rubin2bt_all.R | 3 R/rubin2bt_one.R | 3 R/rubin2wt_all.R | 3 R/rubin2wt_one.R | 3 R/within_variance_comp_emmeans.R | 3 README.md | 1468 ++---------------------------- data/datalist | 1 data/mm_peptides.RData |only inst/doc/Intromi4p.html | 77 + man/check.conditions.Rd | 10 man/check.design.Rd | 11 man/figures/README-unnamed-chunk-24-1.png |only man/figures/README-unnamed-chunk-25-1.png |only man/mi4limma.Rd | 38 man/mi4p-package.Rd | 28 man/mm_peptides.Rd |only man/multi.impute.Rd | 51 - man/rubin1.all.Rd | 12 man/rubin1.one.Rd | 11 man/rubin2.all.Rd | 3 man/rubin2bt.all.Rd | 3 man/rubin2bt.one.Rd | 3 man/rubin2wt.all.Rd | 3 man/rubin2wt.one.Rd | 3 man/within_variance_comp_emmeans.Rd | 3 37 files changed, 570 insertions(+), 1469 deletions(-)
Title: Umbrella Review Package for R
Description: A comprehensive range of facilities to perform umbrella reviews with stratification of the evidence in R. The package accomplishes this aim by building on three core functions that: (i) automatically perform all required calculations in an umbrella review (including but not limited to meta-analyses), (ii) stratify evidence according to various classification criteria, and (iii) generate a visual representation of the results. Note that if you are not familiar with R, the core features of this package are available from a web browser (<https://www.metaumbrella.org/>).
Author: Corentin J Gosling [aut, cre],
Aleix Solanes [aut],
Paolo Fusar-Poli [aut],
Joaquim Radua [aut]
Maintainer: Corentin J Gosling <cgosling@parisnanterre.fr>
Diff between metaumbrella versions 1.0.4 dated 2022-06-09 and 1.0.5 dated 2022-06-13
DESCRIPTION | 6 - MD5 | 60 +++++------ NEWS.md | 9 + R/add_evidence.R | 4 R/check_data.R | 6 - R/esb_test.R | 3 R/functions_format_dataset.R | 4 R/functions_summary.R | 14 +- R/metaumbrella.R | 4 R/umbrella.R | 9 - README.md | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/calculations-details.Rmd | 39 ++++--- inst/doc/calculations-details.html | 81 ++++++++------ inst/doc/conduct-umbrella.Rmd | 6 - inst/doc/conduct-umbrella.html | 62 +++++------ inst/doc/format-dataset.Rmd | 2 inst/doc/format-dataset.html | 28 ++--- inst/doc/generate-forest.R | 8 - inst/doc/generate-forest.Rmd | 12 +- inst/doc/generate-forest.html | 25 ++-- man/add.evidence.Rd | 4 man/metaumbrella-package.Rd | 4 man/summary.umbrella.Rd | 4 tests/testthat/test-functions_meta.R | 190 ++++++++--------------------------- tests/testthat/test-umbrella.R | 34 ++++++ vignettes/calculations-details.Rmd | 39 ++++--- vignettes/conduct-umbrella.Rmd | 6 - vignettes/format-dataset.Rmd | 2 vignettes/generate-forest.Rmd | 12 +- 31 files changed, 332 insertions(+), 351 deletions(-)
Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs 12C/13C isotope pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms and total ion chromatograms.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 1.6 dated 2022-06-07 and 1.7 dated 2022-06-13
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- R/mzRTindexer.R |only R/sample_rt_corrector.R | 1 + build/partial.rdb |binary inst/CITATION | 2 +- man/mzRTindexer.Rd |only 7 files changed, 12 insertions(+), 9 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution. A Shiny app is also available.
Author: Jarrett D. Phillips [aut, cre],
Steven H. French [ctb], Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.6 dated 2022-05-26 and 1.0.6-1 dated 2022-06-13
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/zzz.R | 3 +-- build/partial.rdb |binary inst/shiny/HACSim-RShiny-App-master/rsconnect |only man/envr.Rd | 2 +- man/sim.seqs.Rd | 11 +++++++---- 7 files changed, 18 insertions(+), 15 deletions(-)
Title: 'Rstudio' Addin for Version Control and Assignment Management
using Git
Description: An 'Rstudio' addin for version control that allows users to clone
repositories, create and delete branches, and sync forks on GitHub, GitLab, etc.
Furthermore, the addin uses the GitLab API to allow instructors to create
forks and merge requests for all students/teams with one click of a button.
Author: Vincent Nijs [aut, cre],
Sanjiv Erat [aut]
Maintainer: Vincent Nijs <vnijs@ucsd.edu>
Diff between gitgadget versions 0.6.9 dated 2022-05-02 and 0.7.0 dated 2022-06-13
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 7 R/git.R | 6 README.md | 10 inst/app/components/branch.R | 10 inst/app/components/intro.R | 10 inst/app/components/sync.R | 10 inst/app/gitgadget_ui.R | 6 inst/doc/gitgadget.html | 440 ++++++++++++++++++++++++++++++++++++++----- 10 files changed, 447 insertions(+), 78 deletions(-)
Title: Creating Demographic Table
Description: Functions for creating demographic table with
simple summary statistics, with optional
comparison(s) over one or more groups. Numeric
variables are summarized in means, standard
deviations, medians, inter-quartile-ranges (IQR),
skewness, Shapiro-Wilk normality test and ranges,
and compared using two-sample t-test, Wilcoxon test,
ANOVA and/or Kruskal-Wallis test. Logical and
factor variables are summarized in counts and
percentages and compared using chi-squared test
and/or Fisher's exact test.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.1.3 dated 2022-06-03 and 0.1.4 dated 2022-06-13
DESCRIPTION | 32 ++++++++++++++++++-------------- MD5 | 6 +++--- NEWS.md | 2 ++ R/DemographicTable.R | 6 ++++-- 4 files changed, 27 insertions(+), 19 deletions(-)
More information about DemographicTable at CRAN
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-30 0.2.2