Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for Microsoft
PowerPoint and Excel. Functions extending package 'officer' are provided to
embed 'DrawingML' graphics into 'Microsoft PowerPoint' presentations and
'Microsoft Excel' workbooks.
Author: David Gohel [aut, cre],
Bob Rudis [ctb] (the javascript code used by function set_attr),
Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.2.3 dated 2020-01-26 and 0.2.4 dated 2020-02-17
rvg-0.2.3/rvg/man/ph_with_vg.Rd |only rvg-0.2.4/rvg/DESCRIPTION | 8 +++---- rvg-0.2.4/rvg/MD5 | 15 +++++++------ rvg-0.2.4/rvg/NEWS | 7 ++++++ rvg-0.2.4/rvg/R/defunct.R |only rvg-0.2.4/rvg/R/ph_with_vg.R | 40 +---------------------------------- rvg-0.2.4/rvg/inst/doc/overview.Rmd | 3 -- rvg-0.2.4/rvg/inst/doc/overview.html | 13 +++-------- rvg-0.2.4/rvg/man/rvg-defunct.Rd |only rvg-0.2.4/rvg/vignettes/overview.Rmd | 3 -- 10 files changed, 27 insertions(+), 62 deletions(-)
Title: Randomized Singular Value Decomposition
Description: Low-rank matrix decompositions are fundamental tools and widely used for data
analysis, dimension reduction, and data compression. Classically, highly accurate
deterministic matrix algorithms are used for this task. However, the emergence of
large-scale data has severely challenged our computational ability to analyze big data.
The concept of randomness has been demonstrated as an effective strategy to quickly produce
approximate answers to familiar problems such as the singular value decomposition (SVD).
The rsvd package provides several randomized matrix algorithms such as the randomized
singular value decomposition (rsvd), randomized principal component analysis (rpca),
randomized robust principal component analysis (rrpca), randomized interpolative
decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot
functions are provided.
Author: N. Benjamin Erichson [aut, cre]
Maintainer: N. Benjamin Erichson <erichson@berkeley.edu>
Diff between rsvd versions 1.0.2 dated 2019-07-29 and 1.0.3 dated 2020-02-17
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- R/ggcorplot.R | 2 -- R/ggscreeplot.R | 2 -- R/plots.R | 2 -- man/ggbiplot.Rd | 17 +++++++++++++---- man/ggcorplot.Rd | 14 +++++++++----- man/ggindplot.Rd | 13 ++++++++++--- man/ggscreeplot.Rd | 2 -- man/plot.rpca.Rd | 2 -- man/rid.Rd | 3 +-- man/rpca.Rd | 14 +++++++++++--- man/rrpca.Rd | 12 ++++++++++-- man/rsvd.Rd | 3 +-- 14 files changed, 74 insertions(+), 50 deletions(-)
Title: Parse 'NOAA' Integrated Surface Data Files
Description: Tools for parsing 'NOAA' Integrated Surface Data ('ISD') files,
described at <https://www.ncdc.noaa.gov/isd>. Data includes for example,
wind speed and direction, temperature, cloud data, sea level pressure,
and more. Includes data from approximately 35,000 stations worldwide,
though best coverage is in North America/Europe/Australia. Data is stored
as variable length ASCII character strings, with most fields optional.
Included are tools for parsing entire files, or individual lines of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between isdparser versions 0.3.0 dated 2018-10-23 and 0.4.0 dated 2020-02-17
isdparser-0.3.0/isdparser/inst/doc/isdparser_vignette.R |only isdparser-0.3.0/isdparser/inst/doc/isdparser_vignette.Rmd |only isdparser-0.3.0/isdparser/inst/doc/isdparser_vignette.html |only isdparser-0.3.0/isdparser/vignettes/isdparser_vignette.Rmd |only isdparser-0.4.0/isdparser/DESCRIPTION | 15 isdparser-0.4.0/isdparser/LICENSE | 2 isdparser-0.4.0/isdparser/MD5 | 71 ++-- isdparser-0.4.0/isdparser/NAMESPACE | 3 isdparser-0.4.0/isdparser/NEWS.md | 7 isdparser-0.4.0/isdparser/R/globals.R |only isdparser-0.4.0/isdparser/R/isd_parse_csv.R |only isdparser-0.4.0/isdparser/R/isd_parser.R | 2 isdparser-0.4.0/isdparser/R/isd_parser_line.R | 4 isdparser-0.4.0/isdparser/R/isdparser-package.R | 10 isdparser-0.4.0/isdparser/R/patterns_cloud_solar.R | 175 +++++----- isdparser-0.4.0/isdparser/R/patterns_ground_surface.R | 57 +-- isdparser-0.4.0/isdparser/R/patterns_hail.R | 4 isdparser-0.4.0/isdparser/R/patterns_marine.R | 91 ++--- isdparser-0.4.0/isdparser/R/patterns_network_metadata.R | 86 ++-- isdparser-0.4.0/isdparser/R/patterns_original_observation.R | 7 isdparser-0.4.0/isdparser/R/patterns_precipitation.R | 108 +++--- isdparser-0.4.0/isdparser/R/patterns_pressure.R | 61 ++- isdparser-0.4.0/isdparser/R/patterns_remarks.R | 3 isdparser-0.4.0/isdparser/R/patterns_runway_visual_range.R | 7 isdparser-0.4.0/isdparser/R/patterns_sea_surface_temp.R | 3 isdparser-0.4.0/isdparser/R/patterns_soil_temp.R | 13 isdparser-0.4.0/isdparser/R/patterns_temperature.R | 59 +-- isdparser-0.4.0/isdparser/R/patterns_unique_data.R | 115 +++--- isdparser-0.4.0/isdparser/R/patterns_weather_occurrence.R | 49 +- isdparser-0.4.0/isdparser/R/patterns_wind.R | 54 +-- isdparser-0.4.0/isdparser/R/zzz.R | 9 isdparser-0.4.0/isdparser/README.md | 111 +++--- isdparser-0.4.0/isdparser/build/vignette.rds |binary isdparser-0.4.0/isdparser/inst/doc/isdparser.Rmd |only isdparser-0.4.0/isdparser/inst/doc/isdparser.html |only isdparser-0.4.0/isdparser/inst/extdata/00702699999.csv |only isdparser-0.4.0/isdparser/man/isd_metadata.Rd | 3 isdparser-0.4.0/isdparser/man/isd_parse.Rd | 9 isdparser-0.4.0/isdparser/man/isd_parse_csv.Rd |only isdparser-0.4.0/isdparser/man/isd_parse_line.Rd | 2 isdparser-0.4.0/isdparser/tests/testthat/test-isd_parse_csv.R |only isdparser-0.4.0/isdparser/vignettes/isdparser.Rmd |only isdparser-0.4.0/isdparser/vignettes/isdparser.Rmd.og |only 43 files changed, 637 insertions(+), 503 deletions(-)
Title: Sample Size Estimation
Description: Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
Author: Thomas Fabbro [aut, cre]
Maintainer: Thomas Fabbro <thomas.fabbro@unibas.ch>
Diff between sse versions 0.7-15 dated 2019-12-10 and 0.7-16 dated 2020-02-17
ChangeLog | 6 ++++-- DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/examples.pdf |binary man/powCalc.Rd | 1 - 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Poisson Fixed Effects Robust
Description: Computation of robust standard errors of Poisson fixed effects
models, following Wooldridge (1999).
Author: Evan Wright [aut, cre]
Maintainer: Evan Wright <enwright@umich.edu>
Diff between poisFErobust versions 1.0.1 dated 2018-07-10 and 2.0.0 dated 2020-02-17
DESCRIPTION | 8 +++--- LICENSE | 2 - MD5 | 18 +++++++------- NEWS.md | 6 ++++ R/pois.fe.robust.R | 51 +++++++++++++++++++++++++++++------------- README.md | 2 - build/partial.rdb |binary man/pois.fe.robust.Rd | 24 ++++++++++++------- man/poisFErobust-package.Rd | 4 +-- tests/testthat/test_numeric.R | 19 ++++++++++++++- 10 files changed, 91 insertions(+), 43 deletions(-)
Title: Moments of Folded and Doubly Truncated Multivariate
Distributions
Description: It computes arbitrary products moments (mean vector and variance-covariance matrix), for some double truncated (and folded) multivariate distributions. These distributions belong to the family of selection elliptical distributions, which includes well known skewed distributions as the unified skew-t distribution (SUT) and its particular cases as the extended skew-t (EST), skew-t (ST) and the symmetric student-t (T) distribution. Analogous normal cases unified skew-normal (SUN), extended skew-normal (ESN), skew-normal (SN), and symmetric normal (N) are also included. Density, probabilities and random deviates are also offered for these members.
References used for this package:
Arellano-Valle, R. B. & Genton, M. G. (2005). On fundamental skew distributions. Journal of Multivariate Analysis, 96, 93-116.
Galarza C.E., Matos L.A., Dey D.K. & Lachos V.H. (2019) On Moments of Folded and Truncated Multivariate Extended Skew-Normal Distributions. Technical report. ID 19-14. University of Connecticut. <https://stat.uconn.edu/tech-reports-2019/>.
Author: Christian E. Galarza, Raymond Kan and Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between MomTrunc versions 5.69 dated 2020-01-24 and 5.71 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TT_mv_Hybrid.R | 10 +++++++--- build/partial.rdb |binary 4 files changed, 14 insertions(+), 10 deletions(-)
Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Description: Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetCleaner versions 1.1.3 dated 2019-12-01 and 1.1.4 dated 2020-02-17
DESCRIPTION | 13 +++++++------ MD5 | 23 +++++++++++++++++------ NEWS | 11 +++++++++++ R/correct.changes.R | 14 ++++++++++++++ R/qwerty.dist.R | 7 ++++++- R/spell.check.dictionary.R | 38 ++++++++++++++++++++++++-------------- build |only inst/doc |only man/qwerty.dist.Rd | 2 +- vignettes |only 10 files changed, 80 insertions(+), 28 deletions(-)
Title: Component-Wise MOEA/D Implementation
Description: Modular implementation of Multiobjective Evolutionary Algorithms
based on Decomposition (MOEA/D) [Zhang and Li (2007),
<DOI:10.1109/TEVC.2007.892759>] for quick assembling and
testing of new algorithmic components, as well as easy
replication of published MOEA/D proposals. The full framework is
documented in a paper published in the Journal of Statistical
Software [<doi:10.18637/jss.v092.i06>].
Author: Felipe Campelo [aut, cre],
Lucas Batista [com],
Claus Aranha [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>
Diff between MOEADr versions 1.1.0 dated 2017-10-24 and 1.1.1 dated 2020-02-17
DESCRIPTION | 19 MD5 | 220 ++++----- NAMESPACE | 1 NEWS.md | 9 R/check_stop_criteria.R | 8 R/constraint_none.R | 6 R/constraint_penalty.R | 6 R/constraint_vbr.R | 12 R/create_population.R | 6 R/decomposition_msld.R | 4 R/decomposition_sld.R | 4 R/decomposition_uniform.R | 6 R/define_neighborhood.R | 6 R/evaluate_population.R | 6 R/find_nondominated_points.R | 5 R/generate_weights.R | 6 R/ls_dvls.R | 6 R/ls_tpqa.R | 7 R/moead.R | 7 R/order_neigborhood.R | 6 R/perform_variation.R | 6 R/plot_moead.R | 6 R/preset_moead.R | 24 - R/print_moead.R | 6 R/print_progress.R | 6 R/sample_constraints.R | 6 R/scalarization_awt.R | 9 R/scalarization_ipbi.R | 9 R/scalarization_pbi.R | 9 R/scalarization_ws.R | 9 R/scalarization_wt.R | 8 R/scalarize_values.R | 6 R/scale_objectives.R | 6 R/stop_maxeval.R | 6 R/stop_maxiter.R | 6 R/stop_maxtime.R | 6 R/summary_moead.R | 5 R/update_population.R | 5 R/updt_best.R | 7 R/updt_restricted.R | 7 R/updt_standard.R | 6 R/variation_binrec.R | 6 R/variation_diffmut.R | 6 R/variation_localsearch.R | 5 R/variation_polymut.R | 11 R/variation_sbx.R | 4 R/variation_truncate.R | 6 README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/Basic_Usage.R | 14 inst/doc/Basic_Usage.Rmd | 2 inst/doc/Basic_Usage.html | 493 ++++++++++++++++----- inst/doc/Comparison_Usage.R | 12 inst/doc/Comparison_Usage.Rmd | 6 inst/doc/Comparison_Usage.html | 654 +++++++++++++++++++---------- inst/doc/Modification_Usage.R | 6 inst/doc/Modification_Usage.Rmd | 2 inst/doc/Modification_Usage.html | 398 ++++++++++++++--- inst/doc/problem-definition.R | 6 inst/doc/problem-definition.Rmd | 6 inst/doc/problem-definition.html | 506 ++++++++++++++++------ inst/doc/writing-functions-for-moeadr.Rmd | 2 inst/doc/writing-functions-for-moeadr.html | 210 ++++++++- man/box_constraints.Rd | 7 man/check_stop_criteria.Rd | 9 man/constraint_none.Rd | 11 man/constraint_penalty.Rd | 15 man/constraint_vbr.Rd | 39 - man/create_population.Rd | 9 man/decomposition_msld.Rd | 4 man/decomposition_sld.Rd | 4 man/decomposition_uniform.Rd | 4 man/define_neighborhood.Rd | 7 man/evaluate_population.Rd | 9 man/generate_weights.Rd | 7 man/ls_dvls.Rd | 28 - man/ls_tpqa.Rd | 25 - man/moead.Rd | 54 +- man/order_neighborhood.Rd | 11 man/perform_variation.Rd | 9 man/plot.moead.Rd | 22 man/preset_moead.Rd | 7 man/print.moead.Rd | 7 man/print_progress.Rd | 11 man/scalarization_awt.Rd | 8 man/scalarization_ipbi.Rd | 8 man/scalarization_pbi.Rd | 7 man/scalarization_ws.Rd | 7 man/scalarization_wt.Rd | 7 man/scalarize_values.Rd | 11 man/scale_objectives.Rd | 9 man/stop_maxeval.Rd | 9 man/stop_maxiter.Rd | 9 man/stop_maxtime.Rd | 9 man/summary.moead.Rd | 21 man/update_population.Rd | 11 man/updt_best.Rd | 13 man/updt_restricted.Rd | 9 man/updt_standard.Rd | 8 man/variation_binrec.Rd | 6 man/variation_diffmut.Rd | 6 man/variation_localsearch.Rd | 13 man/variation_polymut.Rd | 11 man/variation_sbx.Rd | 6 man/variation_truncate.Rd | 10 vignettes/Basic_Usage.Rmd | 2 vignettes/Comparison_Usage.Rmd | 6 vignettes/Modification_Usage.Rmd | 2 vignettes/problem-definition.Rmd | 6 vignettes/writing-functions-for-moeadr.Rmd | 2 112 files changed, 2520 insertions(+), 860 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between imager versions 0.41.2 dated 2019-01-23 and 0.42.1 dated 2020-02-17
imager-0.41.2/imager/README.md |only imager-0.41.2/imager/data/datalist |only imager-0.41.2/imager/inst/extdata/tennis_sif.mpeg |only imager-0.42.1/imager/DESCRIPTION | 31 imager-0.42.1/imager/MD5 | 164 imager-0.42.1/imager/NAMESPACE | 11 imager-0.42.1/imager/NEWS | 17 imager-0.42.1/imager/NEWS.md | 8 imager-0.42.1/imager/R/RcppExports.R | 4 imager-0.42.1/imager/R/basegraphics.R | 9 imager-0.42.1/imager/R/cimg_class.R | 26 imager-0.42.1/imager/R/conversions.R | 27 imager-0.42.1/imager/R/coordinates.R | 2 imager-0.42.1/imager/R/drawing.R | 2 imager-0.42.1/imager/R/filtering.R | 4 imager-0.42.1/imager/R/graphs.R | 2 imager-0.42.1/imager/R/imeval.R | 31 imager-0.42.1/imager/R/imgen.R | 13 imager-0.42.1/imager/R/inline.R | 2 imager-0.42.1/imager/R/interpolation.R | 22 imager-0.42.1/imager/R/loading.R | 9 imager-0.42.1/imager/R/pixset.R | 17 imager-0.42.1/imager/R/splitcombine.R | 43 imager-0.42.1/imager/R/utils-pipe.R |only imager-0.42.1/imager/R/utils.R | 149 imager-0.42.1/imager/build/vignette.rds |binary imager-0.42.1/imager/data/boats.rda |binary imager-0.42.1/imager/inst/doc/gettingstarted.R | 134 imager-0.42.1/imager/inst/doc/gettingstarted.Rmd | 59 imager-0.42.1/imager/inst/doc/gettingstarted.html | 1482 imager-0.42.1/imager/inst/doc/pixsets.R | 71 imager-0.42.1/imager/inst/doc/pixsets.Rmd | 6 imager-0.42.1/imager/inst/doc/pixsets.html | 1077 imager-0.42.1/imager/inst/extdata/coins.png |binary imager-0.42.1/imager/inst/extdata/parrots.png |binary imager-0.42.1/imager/inst/extdata/tennis_sif.mp4 |only imager-0.42.1/imager/inst/include/CImg.h |25778 ++++++------ imager-0.42.1/imager/inst/include/imager.h | 6 imager-0.42.1/imager/inst/include/plugins/inpaint.h | 66 imager-0.42.1/imager/inst/include/wrappers.h | 4 imager-0.42.1/imager/man/as.cimg.Rd | 3 imager-0.42.1/imager/man/as.cimg.function.Rd | 12 imager-0.42.1/imager/man/as.igraph.cimg.Rd | 2 imager-0.42.1/imager/man/as.raster.cimg.Rd | 11 imager-0.42.1/imager/man/blur_anisotropic.Rd | 16 imager-0.42.1/imager/man/bucketfill.Rd | 12 imager-0.42.1/imager/man/cimg.use.openmp.Rd | 2 imager-0.42.1/imager/man/diffusion_tensors.Rd | 10 imager-0.42.1/imager/man/displacement.Rd | 11 imager-0.42.1/imager/man/idply.Rd | 4 imager-0.42.1/imager/man/iiply.Rd | 2 imager-0.42.1/imager/man/ilply.Rd | 2 imager-0.42.1/imager/man/imager.Rd | 1 imager-0.42.1/imager/man/imappend.Rd | 4 imager-0.42.1/imager/man/imdirac.Rd | 4 imager-0.42.1/imager/man/imdraw.Rd | 2 imager-0.42.1/imager/man/imeval.Rd | 21 imager-0.42.1/imager/man/imfill.Rd | 2 imager-0.42.1/imager/man/imgradient.Rd | 2 imager-0.42.1/imager/man/iminfo.Rd | 2 imager-0.42.1/imager/man/implot.Rd | 2 imager-0.42.1/imager/man/imsharpen.Rd | 3 imager-0.42.1/imager/man/imshift.Rd | 10 imager-0.42.1/imager/man/imwarp.Rd | 16 imager-0.42.1/imager/man/isoblur.Rd | 4 imager-0.42.1/imager/man/liply.Rd | 2 imager-0.42.1/imager/man/load.video.Rd | 11 imager-0.42.1/imager/man/magick.Rd | 15 imager-0.42.1/imager/man/make.video.Rd | 10 imager-0.42.1/imager/man/mutate_plyr.Rd |only imager-0.42.1/imager/man/pad.Rd | 2 imager-0.42.1/imager/man/patchstat.Rd | 4 imager-0.42.1/imager/man/pipe.Rd |only imager-0.42.1/imager/man/plot.cimg.Rd | 25 imager-0.42.1/imager/man/px.remove_outer.Rd |only imager-0.42.1/imager/man/resize.Rd | 16 imager-0.42.1/imager/man/rm.alpha.Rd | 2 imager-0.42.1/imager/man/split_connected.Rd | 10 imager-0.42.1/imager/man/warp.Rd | 3 imager-0.42.1/imager/src/Makevars.in | 3 imager-0.42.1/imager/src/Makevars.win | 4 imager-0.42.1/imager/src/RcppExports.cpp | 9 imager-0.42.1/imager/src/hough.cpp | 2 imager-0.42.1/imager/src/utils.cpp | 7 imager-0.42.1/imager/tests/testthat/test_load_save_images.R |only imager-0.42.1/imager/tests/testthat/test_load_save_videos.R |only imager-0.42.1/imager/vignettes/gettingstarted.Rmd | 59 imager-0.42.1/imager/vignettes/pixsets.Rmd | 6 88 files changed, 16149 insertions(+), 13477 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between devtools versions 2.2.1 dated 2019-09-24 and 2.2.2 dated 2020-02-17
DESCRIPTION | 12 - MD5 | 101 ++++++------ NEWS.md | 36 ++++ R/build-readme.R | 2 R/build-site.R | 2 R/check-win.R | 8 - R/check.R | 12 + R/install.R | 33 ++-- R/lint.R | 2 R/package.R | 2 R/pkgbuild.R | 2 R/pkgload.R | 2 R/r-hub.R | 2 R/release.R | 29 +++ R/remotes.R | 8 - R/run-source.R | 4 R/show-news.R | 2 R/sitrep.R | 4 R/spell-check.R | 1 R/test.R | 36 ++-- inst/WORDLIST | 2 inst/doc/dependencies.Rmd | 19 ++ inst/doc/dependencies.html | 132 +++++++++------- inst/rstudio/addins.dcf | 5 man/build.Rd | 12 + man/build_vignettes.Rd | 14 + man/check.Rd | 64 +++++--- man/check_failures.Rd | 4 man/check_man.Rd | 4 man/check_rhub.Rd | 15 + man/check_win.Rd | 39 +++- man/create.Rd | 10 - man/devtools.Rd | 3 man/document.Rd | 5 man/install.Rd | 37 +++- man/install_deps.Rd | 45 +++-- man/lint.Rd | 2 man/load_all.Rd | 17 +- man/reexports.Rd | 6 man/release.Rd | 4 man/remote-reexports.Rd | 292 +++++++++++++++++++++++++------------ man/revdep.Rd | 10 - man/run_examples.Rd | 13 + man/submit_cran.Rd | 2 man/test.Rd | 22 ++ man/uninstall.Rd | 6 tests/testthat/test-install.R |only tests/testthat/test-test.R | 14 + tests/testthat/testTestWithFailure |only vignettes/dependencies.Rmd | 19 ++ 50 files changed, 765 insertions(+), 352 deletions(-)
Title: Functions for Computing Wavelet Filters, Wavelet Transforms and
Multiresolution Analyses
Description: Contains functions for computing and plotting
discrete wavelet transforms (DWT) and maximal overlap discrete
wavelet transforms (MODWT), as well as their inverses.
Additionally, it contains functionality for computing and
plotting wavelet transform filters that are used in the above
decompositions as well as multiresolution analyses.
Author: Eric Aldrich <ealdrich@gmail.com>
Maintainer: Eric Aldrich <ealdrich@gmail.com>
Diff between wavelets versions 0.3-0.1 dated 2019-01-27 and 0.3-0.2 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/extend.series.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Sparse Distance Weighted Discrimination
Description: Formulates a sparse distance weighted discrimination (SDWD) for high-dimensional classification and implements a very fast algorithm for computing its solution path with the L1, the elastic-net, and the adaptive elastic-net penalties.
Author: Boxiang Wang and Hui Zou
Maintainer: Boxiang Wang <boxiang-wang@uiowa.edu>
Diff between sdwd versions 1.0.2 dated 2015-08-05 and 1.0.3 dated 2020-02-17
sdwd-1.0.2/sdwd/ChangeLog |only sdwd-1.0.3/sdwd/DESCRIPTION | 10 - sdwd-1.0.3/sdwd/MD5 | 38 +++--- sdwd-1.0.3/sdwd/R/cv.sdwd.R | 71 +++++++---- sdwd-1.0.3/sdwd/R/p.sdwd.R | 13 +- sdwd-1.0.3/sdwd/R/utilities.R | 13 +- sdwd-1.0.3/sdwd/man/coef.cv.sdwd.Rd | 84 ++++++-------- sdwd-1.0.3/sdwd/man/coef.sdwd.Rd | 97 +++++++--------- sdwd-1.0.3/sdwd/man/colon.Rd | 3 sdwd-1.0.3/sdwd/man/cv.sdwd.Rd | 129 ++++++++++----------- sdwd-1.0.3/sdwd/man/plot.cv.sdwd.Rd | 80 ++++++------- sdwd-1.0.3/sdwd/man/plot.sdwd.Rd | 101 ++++++++-------- sdwd-1.0.3/sdwd/man/predict.cv.sdwd.Rd | 92 +++++++-------- sdwd-1.0.3/sdwd/man/predict.sdwd.Rd | 100 +++++++--------- sdwd-1.0.3/sdwd/man/print.sdwd.Rd | 92 +++++++-------- sdwd-1.0.3/sdwd/man/sdwd-internal.Rd | 96 ++++++++-------- sdwd-1.0.3/sdwd/man/sdwd-package.Rd | 121 ++++++++++---------- sdwd-1.0.3/sdwd/man/sdwd.Rd | 197 ++++++++++++++++----------------- sdwd-1.0.3/sdwd/src/auxiliary.f90 | 2 sdwd-1.0.3/sdwd/src/init.c |only sdwd-1.0.3/sdwd/src/sdwd.f90 | 136 +++++++++++----------- 21 files changed, 735 insertions(+), 740 deletions(-)
Title: Genome-Wide Structural Equation Modeling
Description: Melds genome-wide association tests with structural
equation modeling (SEM) using 'OpenMx'. This package contains
low-level C/C++ code to rapidly read genetic data encoded in U.K.
Biobank or 'plink' formats. Prebuilt modeling options include one and
two factor models. Alternately, analyses may utilize arbitrary,
user-provided SEMs. See Verhulst, Maes, & Neale (2017)
<doi:10.1007/s10519-017-9842-6> for details. An updated manuscript is
in preparation.
Author: Joshua N. Pritikin [aut, cre],
Bradley Verhulst [cph],
Gavin Band [cph],
Yann Collet [cph],
Facebook, Inc. [cph],
Yuta Mori [cph],
Shaun Purcell [cph],
Christopher Chang [cph],
Wojciech Mula [cph],
Kim Walisch [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between gwsem versions 0.1.14 dated 2020-02-17 and 0.1.15 dated 2020-02-17
DESCRIPTION | 81 +++++++++++------- MD5 | 58 +++++++----- NAMESPACE | 2 R/model.R | 22 ++++ R/package.R | 1 R/report.R | 3 build/gwsem.pdf |only inst/doc/growth.R | 32 +++---- inst/doc/growth.Rmd | 17 ++- inst/doc/growth.html | 135 +++++++++++++++++------------- man/GWAS.Rd | 1 man/buildItem.Rd | 2 man/buildOneFac.Rd | 1 man/buildOneFacRes.Rd | 1 man/buildTwoFac.Rd | 1 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-retired.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/isSuspicious.Rd | 1 man/loadResults.Rd | 1 man/loadSuspicious.Rd | 1 man/prepareComputePlan.Rd | 1 man/setupExogenousCovariates.Rd | 1 man/setupThresholds.Rd | 1 tests/testthat/test-formats.R | 30 ++---- tests/testthat/test-gxe.R | 33 ++++--- tools/test | 2 tools/travis/install-linux | 14 +-- vignettes/growth.Rmd | 17 ++- 35 files changed, 275 insertions(+), 184 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents.
Functions are provided to let users create tables, modify and format their content.
It extends package 'officer' that does not contain any feature for customized tabular reporting
and can be used within R markdown documents.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.5.7 dated 2020-02-03 and 0.5.8 dated 2020-02-17
flextable-0.5.7/flextable/inst/examples/demo_docx.Rmd |only flextable-0.5.7/flextable/inst/examples/demo_html.Rmd |only flextable-0.5.7/flextable/inst/examples/demo_pagedown.Rmd |only flextable-0.5.7/flextable/inst/examples/demo_pptx.Rmd |only flextable-0.5.7/flextable/man/format.flextable.Rd |only flextable-0.5.8/flextable/DESCRIPTION | 6 flextable-0.5.8/flextable/MD5 | 69 ++-- flextable-0.5.8/flextable/NAMESPACE | 3 flextable-0.5.8/flextable/NEWS | 20 + flextable-0.5.8/flextable/R/01_fpstruct.R | 19 - flextable-0.5.8/flextable/R/defunct.R |only flextable-0.5.8/flextable/R/deprecated.R | 59 +++- flextable-0.5.8/flextable/R/display.R | 66 ---- flextable-0.5.8/flextable/R/printers.R | 180 +++++++------ flextable-0.5.8/flextable/R/tabpart_add_rows.R | 4 flextable-0.5.8/flextable/R/tabpart_format.R | 2 flextable-0.5.8/flextable/README.md | 9 flextable-0.5.8/flextable/inst/doc/display.html | 2 flextable-0.5.8/flextable/inst/doc/format.html | 2 flextable-0.5.8/flextable/inst/doc/layout.html | 4 flextable-0.5.8/flextable/inst/doc/overview.html | 2 flextable-0.5.8/flextable/inst/doc/selectors.html | 2 flextable-0.5.8/flextable/inst/examples/rmd |only flextable-0.5.8/flextable/inst/web_1.0.0/tabwid.css | 2 flextable-0.5.8/flextable/man/as_raster.Rd | 1 flextable-0.5.8/flextable/man/display.Rd | 19 - flextable-0.5.8/flextable/man/docx_value.Rd | 30 +- flextable-0.5.8/flextable/man/flextable-defunct.Rd |only flextable-0.5.8/flextable/man/flextable_html_dependency.Rd |only flextable-0.5.8/flextable/man/htmltools_value.Rd | 11 flextable-0.5.8/flextable/man/knit_print.flextable.Rd | 41 ++ flextable-0.5.8/flextable/man/ph_with_flextable.Rd | 5 flextable-0.5.8/flextable/man/plot.flextable.Rd | 1 flextable-0.5.8/flextable/man/print.flextable.Rd | 1 flextable-0.5.8/flextable/man/save_as_docx.Rd | 1 flextable-0.5.8/flextable/man/save_as_html.Rd | 1 flextable-0.5.8/flextable/man/save_as_image.Rd | 1 flextable-0.5.8/flextable/man/save_as_pptx.Rd | 1 flextable-0.5.8/flextable/tests/testthat/test-errors.R | 12 39 files changed, 322 insertions(+), 254 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming
to complement existing R packages. The functionality includes among others
multidimensional compensatory and noncompensatory IRT models
(Reckase, 2009, <doi:10.1007/978-0-387-89976-3>),
MCMC for hierarchical IRT models and testlet models
(Fox, 2010, <doi:10.1007/978-1-4419-0742-4>),
NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>),
Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>;
Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>),
faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011,
<doi:10.1111/j.1745-3984.2011.00143.x>),
ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>),
DETECT statistic (Stout, Habing, Douglas & Kim, 1996,
<doi:10.1177/014662169602000403>), local structural equation modeling
(LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016,
<doi:10.1080/00273171.2016.1142856>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 3.8-11 dated 2020-02-15 and 3.9-4 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/RcppExports.R | 2 +- R/ccov_np_score_density.R | 9 +++++---- R/linking.haberman.R | 2 +- R/linking_haberman_als.R | 2 +- build/partial.rdb |binary inst/NEWS | 17 ++++++++++++----- src/RcppExports.cpp | 2 +- 9 files changed, 33 insertions(+), 25 deletions(-)
Title: Download, Edit and Include Wind and Sea Currents Data in
Ecological and Evolutionary Analysis
Description: Tools for download and manage surface wind and sea currents data from the Global Forecasting System <https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs> and to compute connectivity between locations.
Author: Javier Fernández-López [aut, cre],
Klaus Schliep [aut],
Yurena Arjona [aut]
Maintainer: Javier Fernández-López <jflopez.bio@gmail.com>
Diff between rWind versions 1.1.3 dated 2019-07-24 and 1.1.5 dated 2020-02-17
rWind-1.1.3/rWind/man/seaScud.dl.Rd |only rWind-1.1.5/rWind/DESCRIPTION | 12 - rWind-1.1.5/rWind/MD5 | 23 +-- rWind-1.1.5/rWind/NAMESPACE | 1 rWind-1.1.5/rWind/NEWS | 10 + rWind-1.1.5/rWind/R/rWind-package.R | 2 rWind-1.1.5/rWind/R/wind_functions2.R | 187 ++++--------------------- rWind-1.1.5/rWind/README.md | 5 rWind-1.1.5/rWind/inst/doc/Shortest_paths.html | 4 rWind-1.1.5/rWind/man/flow.dispersion.Rd | 2 rWind-1.1.5/rWind/man/flow.dispersion_int.Rd | 2 rWind-1.1.5/rWind/man/seaOscar.dl.Rd | 4 rWind-1.1.5/rWind/man/wind.dl.Rd | 5 13 files changed, 80 insertions(+), 177 deletions(-)
Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <http://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'. The vignette provides an update of the original paper <doi:10.18637/jss.v092.i04>.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 3.2.17 dated 2020-02-07 and 3.2.18 dated 2020-02-17
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS | 4 ++++ R/scala.R | 4 ++-- R/scalaConfig.R | 2 +- README.md | 16 ++++++++-------- inst/CITATION | 22 ++++++++++++++-------- inst/doc/rscala.pdf |binary inst/java/scala-2.11/rscala.jar |binary inst/java/scala-2.12/rscala.jar |binary inst/java/scala-2.13/rscala.jar |binary java/rscala-source.jar |binary man/scala.Rd | 4 ++-- man/scalaConfig.Rd | 2 +- 14 files changed, 50 insertions(+), 40 deletions(-)
Title: ROBustness in Network
Description: In network analysis, many community detection algorithms have been developed. However, their applications leave unaddressed one important question: the statistical validation of the results. robin (ROBustness In Network) is an R package for the validation of community detection. It has a double aim: to study the robustness of a community detection algorithm and to compare the robustness of different community detection algorithms on the same network. Reference in Annamaria Carissimo, Luisa Cutillo, Italia De Feis (2018) <doi:10.1016/j.csda.2017.10.006>.
Author: Valeria Policastro [aut, cre]
Maintainer: Valeria Policastro <valeria.policastro@gmail.com>
Diff between robin versions 0.99.1 dated 2019-10-24 and 1.0.0 dated 2020-02-17
robin-0.99.1/robin/README.md |only robin-1.0.0/robin/DESCRIPTION | 30 robin-1.0.0/robin/MD5 | 45 robin-1.0.0/robin/R/ROBIN.R | 2777 +++++++++--------- robin-1.0.0/robin/build/vignette.rds |binary robin-1.0.0/robin/inst/NEWS | 6 robin-1.0.0/robin/inst/doc/robin.R | 130 robin-1.0.0/robin/inst/doc/robin.Rmd | 382 +- robin-1.0.0/robin/inst/doc/robin.html | 3656 ++++++++++++------------- robin-1.0.0/robin/man/createITPSplineResult.Rd | 14 robin-1.0.0/robin/man/membershipCommunities.Rd | 24 robin-1.0.0/robin/man/methodCommunity.Rd | 29 robin-1.0.0/robin/man/plotComm.Rd | 4 robin-1.0.0/robin/man/plotGraph.Rd | 2 robin-1.0.0/robin/man/plotRobin.Rd | 15 robin-1.0.0/robin/man/prepGraph.Rd | 17 robin-1.0.0/robin/man/random.Rd | 2 robin-1.0.0/robin/man/rewireCompl.Rd | 20 robin-1.0.0/robin/man/robinAUC.Rd | 10 robin-1.0.0/robin/man/robinCompare.Rd | 39 robin-1.0.0/robin/man/robinFDATest.Rd | 17 robin-1.0.0/robin/man/robinGPTest.Rd | 2 robin-1.0.0/robin/man/robinRobust.Rd | 28 robin-1.0.0/robin/vignettes/robin.Rmd | 382 +- 24 files changed, 3851 insertions(+), 3780 deletions(-)
Title: Extracts Environmental Data from 'ERDDAP' Web Services
Description: Contains three functions that access
environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts
data along a trajectory for a given "radius" around the point. The
rxtracto_3D() function extracts data in a box. The rxtractogon() function
extracts data in a polygon. All of those three function use the 'rerddap' package
to extract the data, and should work with any 'ERDDAP' server.
There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddapXtracto versions 0.4.6 dated 2020-01-09 and 0.4.7 dated 2020-02-17
DESCRIPTION | 12 MD5 | 16 - NEWS.md | 7 R/rxtracto.R | 17 - inst/doc/UsingrerddapXtracto.R | 7 inst/doc/UsingrerddapXtracto.Rmd | 15 inst/doc/UsingrerddapXtracto.html | 598 +++++++++++++++++++------------------- man/rxtracto.Rd | 6 vignettes/UsingrerddapXtracto.Rmd | 15 9 files changed, 361 insertions(+), 332 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [aut, ctb, cre],
Stephen Lane [ctb],
Will Beasley [ctb],
Jeffrey Horner [ctb],
Will Gray [ctb],
Jeremy Stephens [ctb],
Marcus Lehr [ctb]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between redcapAPI versions 2.2 dated 2018-08-01 and 2.3 dated 2020-02-17
DESCRIPTION | 16 ++- MD5 | 82 ++++++++++---------- NAMESPACE | 3 R/checkbox_suffixes.R | 29 ++----- R/deleteRecords.R |only R/exportPDF.R | 2 R/exportRecords.R | 145 ++++++++++++++++++------------------ R/exportRecords_offline.R | 23 +++-- R/exportSurveyParticipants.R |only R/fieldToVar.R | 18 ++-- R/importFiles.R | 15 ++- R/importRecords.R | 3 R/makeRedcapFactor.R | 6 + R/parseBranchingLogic.R | 3 R/redcapAPI-pkg.R | 2 man/allocationTable.Rd | 75 ++++++++++++++---- man/deleteArms.Rd | 8 + man/deleteFiles.Rd | 12 ++ man/deleteRecords.Rd |only man/deprecated_redcapProjectInfo.Rd | 52 ++++++++++-- man/exportArms.Rd | 8 + man/exportBundle.Rd | 50 +++++++++--- man/exportEvents.Rd | 8 + man/exportFieldNames.Rd | 25 ++++-- man/exportFiles.Rd | 38 +++++++-- man/exportInstruments.Rd | 8 + man/exportMappings.Rd | 8 + man/exportMetaData.Rd | 11 +- man/exportNextRecordName.Rd | 7 + man/exportPdf.Rd | 40 +++++++-- man/exportProjectInformation.Rd | 8 + man/exportRecords.Rd | 86 ++++++++++++++++----- man/exportReports.Rd | 35 ++++++-- man/exportSurveyParticipants.Rd |only man/exportUsers.Rd | 14 ++- man/exportVersion.Rd | 3 man/fieldToVar.Rd | 9 +- man/genericApiCall.Rd | 32 ++++++- man/importArms.Rd | 12 +- man/importFiles.Rd | 49 +++++++++--- man/importRecords.Rd | 39 +++++++-- man/recodeCheck.Rd | 9 +- man/redcapAPI.Rd | 3 man/redcapConnection.Rd | 9 +- 44 files changed, 694 insertions(+), 311 deletions(-)
Title: Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap'
Package
Description: Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.
Author: Carson Sievert [aut],
Roy Mendelssohn [aut, ctb, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between plotdap versions 0.0.5 dated 2020-01-08 and 0.0.6 dated 2020-02-17
DESCRIPTION | 14 MD5 | 23 - NAMESPACE | 1 NEWS.md | 4 R/add_griddap.R | 12 R/add_tabledap.R | 28 + R/imports.R | 4 R/plotdap.R | 16 - inst/doc/using_plotdap.R | 20 - inst/doc/using_plotdap.Rmd | 15 - inst/doc/using_plotdap.html | 630 +++++++++++++++++++++----------------------- vignettes/overlay.png |only vignettes/using_plotdap.Rmd | 15 - 13 files changed, 409 insertions(+), 373 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>) and substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.7-6 dated 2019-12-15 and 3.8-9 dated 2020-02-17
DESCRIPTION | 8 ++-- MD5 | 63 ++++++++++++++++---------------- R/RcppExports.R | 2 - R/load.data.R | 13 +++++- R/subset_datlist.R | 4 +- R/subset_datlist_modify_factor_levels.R |only build/partial.rdb |binary data/data.allison.gssexp.rda |binary data/data.allison.hip.rda |binary data/data.allison.usnews.rda |binary data/data.enders.depression.rda |binary data/data.enders.eatingattitudes.rda |binary data/data.enders.employee.rda |binary data/data.graham.ex3.rda |binary data/data.graham.ex6.rda |binary data/data.graham.ex8a.rda |binary data/data.graham.ex8b.rda |binary data/data.graham.ex8c.rda |binary data/data.internet.rda |binary data/data.largescale.rda |binary data/data.ma01.rda |binary data/data.ma02.rda |binary data/data.ma03.rda |binary data/data.ma04.rda |binary data/data.ma05.rda |binary data/data.ma06.rda |binary data/data.ma07.rda |binary data/data.ma08.rda |binary data/data.smallscale.rda |binary inst/NEWS | 28 +++++++++----- man/jomo2datlist.Rd | 6 ++- man/mi.anova.Rd | 6 ++- src/RcppExports.cpp | 2 - 33 files changed, 77 insertions(+), 55 deletions(-)
Title: Label Attributes for Atomic Vectors
Description: Labels are a common construct in statistical software providing a
human readable description of a variable. While variable names are succinct,
quick to type, and follow a language's naming conventions, labels may
be more illustrative and may use plain text and spaces. R does not provide
native support for labels. Some packages, however, have made this feature
available. Most notably, the 'Hmisc' package provides labelling methods
for a number of different object. Due to design decisions, these methods
are not all exported, and so are unavailable for use in package development.
The 'labelVector' package supports labels for atomic vectors in a light-weight
design that is suitable for use in other packages.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between labelVector versions 0.1.0 dated 2018-07-28 and 0.1.1 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/get_label.R | 15 +++++++++++++-- R/set_label.R | 14 ++++++++++++-- build/vignette.rds |binary inst/doc/labelVector.R | 26 +++++++++++++------------- man/get_label.Rd | 8 +++++++- man/is_labelled.Rd | 1 - man/set_label.Rd | 5 ++++- 9 files changed, 61 insertions(+), 32 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut],
Manuel Oviedo de la Fuente [aut, cre],
Pedro Galeano [ctb],
Alicia Nieto [ctb],
Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Diff between fda.usc versions 2.0.1 dated 2019-12-16 and 2.0.2 dated 2020-02-17
DESCRIPTION | 8 MD5 | 96 +++--- NAMESPACE | 2 NEWS | 13 R/Descriptive.R | 6 R/S.np.R | 4 R/accuracy.R | 41 ++ R/classif.glm.R | 12 R/classif.gsam.R | 6 R/classif.kfold.R | 649 +++++++++++++++++++++++++++++++++++---------- R/fanova.onefactor.R | 2 R/fda.usc-package.R | 11 R/fdata.bootstrap.r | 172 ++++++++--- R/fdata2model.R | 2 R/fdata2pc.R | 6 R/flm.test.R | 2 R/fregre.bootstrap.r | 558 ++++++++++++++++++++++++++++++-------- R/fregre.igls.r | 6 R/fregre.plm.R | 2 R/kmeans.fd.R | 54 --- R/ldata.R | 51 +-- R/metric.dist.R | 567 --------------------------------------- R/metric.ldata.R |only R/plot.fdata.R | 161 ++++++----- R/predict.fregre.fd.r | 8 R/predict.fregre.glm.R | 29 +- R/predict.fregre.gls.r | 20 - R/predict.fregre.gsam.R | 59 +++- R/predict.fregre.lm.R | 65 +++- R/predict.fregre.plm.R | 6 R/summary.fdata.comp.r | 81 ++--- R/summary.fregre.fd.r | 364 +++---------------------- R/summary.fregre.gkam.R |only R/weights4class.R | 5 README.md | 7 man/S.np.Rd | 4 man/classif.glm.Rd | 3 man/classif.kfold.Rd | 28 - man/fda.usc-package.Rd | 11 man/fdata.bootstrap.Rd | 2 man/fregre.bootstrap.Rd | 3 man/kmeans.fd.Rd | 2 man/metric.dist.Rd | 3 man/metric.ldata.Rd | 8 man/plot.fdata.Rd | 14 man/predict.fregre.fd.Rd | 3 man/predict.fregre.lm.Rd | 5 man/summary.fdata.comp.Rd | 34 -- man/summary.fregre.fd.Rd | 6 man/summary.fregre.gkam.Rd | 18 - 50 files changed, 1651 insertions(+), 1568 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'; the package is
temporarily unavailable on the CRAN repository; formerly available versions
can be obtained from the archive), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'FCI' (fast causal inference),
'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.2.4 dated 2019-06-18 and 0.2.6.2 dated 2020-02-17
DESCRIPTION | 14 ++++++++------ MD5 | 24 ++++++++++++------------ R/getParentsStable.R | 1 - R/runFCI.R | 26 +++++++++++++++++++++----- R/runFCIPlus.R | 3 ++- R/runGES.R | 4 ++-- R/runGIES.R | 6 +++++- R/runPC.R | 12 +++++++++--- R/runRFCI.R | 27 +++++++++++++++++---------- man/getParents.Rd | 43 ++++++++++++++++++++++++++++--------------- man/getParentsStable.Rd | 34 ++++++++++++++++++++++------------ man/getRanking.Rd | 31 +++++++++++++++++++++---------- man/simulateInterventions.Rd | 19 ++++++++++++++++--- 13 files changed, 163 insertions(+), 81 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-31 dated 2019-01-09 and 1.0-32 dated 2020-02-17
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS | 11 ++++++++++- R/grmsd.R | 6 ++++-- R/newtargets.R | 2 +- R/varSelection.R | 6 +++--- R/yai.R | 4 ++-- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary man/grmsd.Rd | 3 ++- man/varSelection.Rd | 4 +++- src/yaImpute_init.c | 4 ++-- 13 files changed, 46 insertions(+), 32 deletions(-)
Title: Character String Processing Facilities
Description: Fast, correct, consistent, portable and convenient character
string/text processing in every locale and any native encoding.
Owing to the use of the 'ICU' (International Components for Unicode)
library, the package provides 'R' users with platform-independent functions
known to 'Java', 'Perl', 'Python', 'PHP' and 'Ruby' programmers. Available
features include: pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing and many more.
Author: Marek Gagolewski [aut, cre] (<https://orcid.org/0000-0003-0637-6028>),
Bartek Tartanus [ctb]
and other contributors (stringi source code);
IBM, Unicode, Inc. and other contributors (ICU4C source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.4.5 dated 2020-01-11 and 1.4.6 dated 2020-02-17
DESCRIPTION | 10 - MD5 | 208 +++++++++++++++++++-------------------- NEWS | 13 ++ R/join.R | 2 R/time_format.R | 3 configure.ac | 2 inst/CITATION | 4 man/oper_comparison.Rd | 31 +++-- man/oper_plus.Rd | 8 - man/stri_compare.Rd | 43 ++++---- man/stri_count.Rd | 9 - man/stri_count_boundaries.Rd | 59 ++++++----- man/stri_datetime_add.Rd | 31 +++-- man/stri_datetime_create.Rd | 32 +++--- man/stri_datetime_fields.Rd | 19 +-- man/stri_datetime_format.Rd | 40 ++++--- man/stri_datetime_fstr.Rd | 19 +-- man/stri_datetime_now.Rd | 19 +-- man/stri_datetime_symbols.Rd | 22 ++-- man/stri_detect.Rd | 37 +++++- man/stri_dup.Rd | 8 - man/stri_duplicated.Rd | 70 +++++++------ man/stri_enc_detect.Rd | 11 +- man/stri_enc_detect2.Rd | 42 ++++--- man/stri_enc_fromutf32.Rd | 12 +- man/stri_enc_info.Rd | 8 - man/stri_enc_isascii.Rd | 13 +- man/stri_enc_isutf16.Rd | 11 +- man/stri_enc_isutf8.Rd | 15 +- man/stri_enc_list.Rd | 8 - man/stri_enc_mark.Rd | 8 - man/stri_enc_set.Rd | 8 - man/stri_enc_toascii.Rd | 12 +- man/stri_enc_tonative.Rd | 12 +- man/stri_enc_toutf32.Rd | 12 +- man/stri_enc_toutf8.Rd | 12 +- man/stri_encode.Rd | 13 +- man/stri_escape_unicode.Rd | 5 man/stri_extract.Rd | 63 ++++++++--- man/stri_extract_boundaries.Rd | 78 ++++++++------ man/stri_flatten.Rd | 10 + man/stri_isempty.Rd | 8 - man/stri_join.Rd | 7 - man/stri_join_list.Rd | 7 - man/stri_length.Rd | 18 +-- man/stri_list2matrix.Rd | 7 - man/stri_locale_info.Rd | 7 - man/stri_locale_list.Rd | 7 - man/stri_locale_set.Rd | 7 - man/stri_locate.Rd | 64 ++++++++---- man/stri_locate_boundaries.Rd | 77 ++++++++------ man/stri_match.Rd | 39 +++++-- man/stri_na2empty.Rd | 7 - man/stri_numbytes.Rd | 10 + man/stri_opts_brkiter.Rd | 36 ++++-- man/stri_opts_collator.Rd | 52 ++++++--- man/stri_opts_fixed.Rd | 5 man/stri_opts_regex.Rd | 18 ++- man/stri_order.Rd | 35 +++--- man/stri_pad.Rd | 47 ++++++-- man/stri_rand_lipsum.Rd | 9 - man/stri_rand_shuffle.Rd | 5 man/stri_rand_strings.Rd | 5 man/stri_read_lines.Rd | 13 +- man/stri_read_raw.Rd | 5 man/stri_remove_empty.Rd | 7 - man/stri_replace.Rd | 92 +++++++++++------ man/stri_replace_na.Rd | 7 - man/stri_reverse.Rd | 4 man/stri_sort.Rd | 35 +++--- man/stri_split.Rd | 59 ++++++++--- man/stri_split_boundaries.Rd | 72 +++++++------ man/stri_split_lines.Rd | 25 ++-- man/stri_startsendswith.Rd | 14 +- man/stri_stats_general.Rd | 3 man/stri_stats_latex.Rd | 3 man/stri_sub.Rd | 6 - man/stri_sub_all.Rd | 6 - man/stri_subset.Rd | 33 ++++-- man/stri_timezone_info.Rd | 24 ++-- man/stri_timezone_list.Rd | 24 ++-- man/stri_timezone_set.Rd | 24 ++-- man/stri_trans_casemap.Rd | 66 ++++++------ man/stri_trans_char.Rd | 9 - man/stri_trans_general.Rd | 17 +-- man/stri_trans_list.Rd | 9 - man/stri_trans_nf.Rd | 13 +- man/stri_trim.Rd | 15 +- man/stri_unescape_unicode.Rd | 3 man/stri_unique.Rd | 37 +++--- man/stri_width.Rd | 10 + man/stri_wrap.Rd | 76 ++++++++------ man/stri_write_lines.Rd | 13 +- man/stringi-arguments.Rd | 19 +-- man/stringi-encoding.Rd | 50 +++++---- man/stringi-locale.Rd | 57 +++++----- man/stringi-package.Rd | 19 +-- man/stringi-search-boundaries.Rd | 68 ++++++------ man/stringi-search-charclass.Rd | 24 ++-- man/stringi-search-coll.Rd | 55 +++++----- man/stringi-search-fixed.Rd | 24 ++-- man/stringi-search-regex.Rd | 24 ++-- man/stringi-search.Rd | 118 ++++++++++++---------- src/stri_join.cpp | 18 +-- src/stri_prepare_arg.cpp | 11 +- 105 files changed, 1600 insertions(+), 1130 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.0.1.7 dated 2020-02-07 and 1.0.1.8 dated 2020-02-17
DESCRIPTION | 10 +++--- MD5 | 8 ++-- inst/CITATION | 82 ++++++++++++++++++++++++++++++-------------------- man/PAFit-package.Rd | 8 ++-- man/joint_estimate.rd | 3 + 5 files changed, 65 insertions(+), 46 deletions(-)
Title: Earth System History Variables
Description: The purpose of the 'chronosphere' project is to facilitate spatially explicit analyses of (paleo)environmental/ecological research. The package serves as a gateway to plate tectonic reconstructions, deep time global climate model results as well as fossil occurrence datasets such as the Paleobiology Database <https://www.paleobiodb.org/> and the PaleoReefs Database <https://www.paleo-reefs.pal.uni-erlangen.de/>. Environmental data stored on a remote server can be downloaded and imported directly to the R environment. Query functions to the GPlates <http://www.gplates.org/> desktop application or the GPlates Web Service <https://gws.gplates.org/> allow users to reconstruct coordinates, static plates, and Spatial objects. A wrapper class 'RasterArray' is implemented around the 'RasterLayer' class, allowing the organization of spatially explicit raster data in n-dimensional arrays. The project is developed under the umbrella of the DFG (Deutsche Forschungsgemeinschaft) Research Unit TERSANE2 (For 2332, TEmperature Related Stressors in ANcient Extinctions).
Author: Adam T. Kocsis, Nussaibah B. Raja
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between chronosphere versions 0.2.0 dated 2019-12-16 and 0.2.2 dated 2020-02-17
chronosphere-0.2.0/chronosphere/man/aggregate-RasterArray-method.Rd |only chronosphere-0.2.0/chronosphere/man/disaggregate-RasterArray-method.Rd |only chronosphere-0.2.2/chronosphere/DESCRIPTION | 12 chronosphere-0.2.2/chronosphere/MD5 | 136 +++--- chronosphere-0.2.2/chronosphere/NAMESPACE | 12 chronosphere-0.2.2/chronosphere/R/RasterArray-base.R | 8 chronosphere-0.2.2/chronosphere/R/RasterArray-combine.R | 4 chronosphere-0.2.2/chronosphere/R/RasterArray-raster.R | 25 - chronosphere-0.2.2/chronosphere/R/colours.R | 220 +++++++++- chronosphere-0.2.2/chronosphere/R/data.R | 8 chronosphere-0.2.2/chronosphere/R/fetching.R | 74 ++- chronosphere-0.2.2/chronosphere/R/inter.R | 4 chronosphere-0.2.2/chronosphere/R/platemodel.R | 8 chronosphere-0.2.2/chronosphere/R/plotting.R | 51 +- chronosphere-0.2.2/chronosphere/R/reconstruction.R | 7 chronosphere-0.2.2/chronosphere/R/utility.R | 35 + chronosphere-0.2.2/chronosphere/R/zzz.R |only chronosphere-0.2.2/chronosphere/build/vignette.rds |binary chronosphere-0.2.2/chronosphere/data/clim.RData |binary chronosphere-0.2.2/chronosphere/data/dems.RData |binary chronosphere-0.2.2/chronosphere/inst/NEWS.md | 35 + chronosphere-0.2.2/chronosphere/inst/doc/chronos.R | 4 chronosphere-0.2.2/chronosphere/inst/doc/chronos.Rmd | 4 chronosphere-0.2.2/chronosphere/inst/doc/chronos.pdf |binary chronosphere-0.2.2/chronosphere/man/adimatt.Rd | 1 chronosphere-0.2.2/chronosphere/man/aggregate.Rd |only chronosphere-0.2.2/chronosphere/man/apply-methods.Rd | 1 chronosphere-0.2.2/chronosphere/man/arraylength.Rd | 1 chronosphere-0.2.2/chronosphere/man/as.data.frame.RasterArray.Rd | 3 chronosphere-0.2.2/chronosphere/man/as.list-RasterArray-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/asRasterArray.Rd | 1 chronosphere-0.2.2/chronosphere/man/calc-RasterArray-function-method.Rd | 4 chronosphere-0.2.2/chronosphere/man/cellStats-RasterArray-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/chronosphere.Rd |only chronosphere-0.2.2/chronosphere/man/clim.Rd | 4 chronosphere-0.2.2/chronosphere/man/colnames.Rd | 1 chronosphere-0.2.2/chronosphere/man/combine.Rd | 1 chronosphere-0.2.2/chronosphere/man/crop-RasterArray-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/dataindex.Rd | 21 chronosphere-0.2.2/chronosphere/man/datasets.Rd |only chronosphere-0.2.2/chronosphere/man/dems.Rd | 4 chronosphere-0.2.2/chronosphere/man/dim-RasterArray-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/dimlayer.Rd | 1 chronosphere-0.2.2/chronosphere/man/dimnames.Rd | 1 chronosphere-0.2.2/chronosphere/man/disaggregate.Rd |only chronosphere-0.2.2/chronosphere/man/extract-RasterArray-data.frame-method.Rd | 4 chronosphere-0.2.2/chronosphere/man/extremeValues.Rd | 3 chronosphere-0.2.2/chronosphere/man/fetch.Rd | 29 - chronosphere-0.2.2/chronosphere/man/layers.Rd | 1 chronosphere-0.2.2/chronosphere/man/mapplot.Rd | 53 +- chronosphere-0.2.2/chronosphere/man/mask-RasterArray-methods.Rd | 78 ++- chronosphere-0.2.2/chronosphere/man/matchtime.Rd | 5 chronosphere-0.2.2/chronosphere/man/names.Rd | 1 chronosphere-0.2.2/chronosphere/man/ncell.Rd | 1 chronosphere-0.2.2/chronosphere/man/newbounds.Rd | 2 chronosphere-0.2.2/chronosphere/man/nums.Rd |only chronosphere-0.2.2/chronosphere/man/nvalues.Rd | 1 chronosphere-0.2.2/chronosphere/man/platemodel.Rd | 11 chronosphere-0.2.2/chronosphere/man/plot-RasterArray-missing-method.Rd | 7 chronosphere-0.2.2/chronosphere/man/projectRaster.Rd | 25 - chronosphere-0.2.2/chronosphere/man/proxy.Rd | 1 chronosphere-0.2.2/chronosphere/man/ramps.Rd | 34 + chronosphere-0.2.2/chronosphere/man/reconstruct.Rd | 47 +- chronosphere-0.2.2/chronosphere/man/replacementSingle.Rd | 1 chronosphere-0.2.2/chronosphere/man/res.Rd | 1 chronosphere-0.2.2/chronosphere/man/resample-RasterArray-ANY-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/rownames.Rd | 1 chronosphere-0.2.2/chronosphere/man/sub-RasterArray-ANY-ANY-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/sub-sub-RasterArray-ANY-ANY-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/sub-subset-RasterArray-ANY-ANY-method.Rd | 1 chronosphere-0.2.2/chronosphere/man/subset-RasterArray-method.Rd | 4 chronosphere-0.2.2/chronosphere/man/t-RasterArray-method.Rd | 1 chronosphere-0.2.2/chronosphere/vignettes/chronos.Rmd | 4 73 files changed, 680 insertions(+), 334 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families and a secure convergence algorithm.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.33 dated 2020-01-10 and 1.4.34 dated 2020-02-17
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- R/glmgam.R | 2 - R/mixedmodel.R | 2 - R/tweedief.R | 24 +++++++++++++-- inst/NEWS | 21 ++++++++++++- man/remlscorgamma.Rd | 65 +++++++++++++++++++++++++----------------- tests/statmod-Tests.R | 3 + tests/statmod-Tests.Rout.save | 14 ++++++--- 9 files changed, 107 insertions(+), 48 deletions(-)
Title: Tools for Comparing Text Messages Across Time and Media
Description: A collection of tools for measuring the similarity of text messages and tracing the flow of messages over
time and across media.
Author: Kasper Welbers & Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between RNewsflow versions 1.2.1 dated 2019-11-11 and 1.2.3 dated 2020-02-17
DESCRIPTION | 14 MD5 | 68 +- R/compare_documents.r | 20 R/data.r | 2 R/deprecated.r | 4 R/networks.r | 2 R/newsflow.r | 2 build/vignette.rds |binary data/rnewsflow_dfm.rda |binary inst/doc/RNewsflow.R | 48 - inst/doc/RNewsflow.Rmd | 3 inst/doc/RNewsflow.html | 1152 +++++++++++++++++++++++++-------------- man/as_document_network.Rd | 2 man/compare_documents.Rd | 42 + man/create_document_network.Rd | 9 man/create_queries.Rd | 19 man/delete.duplicates.Rd | 17 man/delete_duplicates.Rd | 16 man/directed.network.plot.Rd | 24 man/directed_network_plot.Rd | 24 man/document.network.Rd | 9 man/document.network.plot.Rd | 19 man/document_network_plot.Rd | 19 man/documents.compare.Rd | 19 man/hourdiff_range_thresholds.Rd | 10 man/network.aggregate.Rd | 15 man/network_aggregate.Rd | 15 man/newsflow.compare.Rd | 36 - man/newsflow_compare.Rd | 21 man/tcrossprod_sparse.Rd | 40 - man/term_char_sim.Rd | 16 man/term_innovation.Rd | 15 man/term_intersect.Rd | 3 man/term_union.Rd | 3 vignettes/RNewsflow.Rmd | 3 35 files changed, 1109 insertions(+), 602 deletions(-)
Title: Stan Models for the Paired Comparison Factor Model
Description: Provides convenience functions and pre-programmed Stan models
related to the paired comparison factor model. Its purpose is to make fitting
paired comparison data using Stan easy.
Author: Joshua N. Pritikin [aut, cre] (<https://orcid.org/0000-0002-9862-5484>),
Daniel C. Furr [ctb],
Trustees of Columbia University [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between pcFactorStan versions 1.3.0 dated 2020-01-19 and 1.4.0 dated 2020-02-17
DESCRIPTION | 6 +- MD5 | 22 +++---- inst/doc/manual.R | 111 +++++++++++++++++++++----------------- inst/doc/manual.Rmd | 72 +++++++++++++++++------- inst/doc/manual.html | 109 ++++++++++++++++++++----------------- src/stan_files/factor.stan | 15 +++-- src/stan_files/factor1.stan | 15 +++-- src/stan_files/factor1_ll.stan | 15 +++-- src/stan_files/factor_ll.stan | 15 +++-- tests/testthat/test-4likelihood.R | 2 tools/genStan | 15 +++-- vignettes/manual.Rmd | 72 +++++++++++++++++------- 12 files changed, 286 insertions(+), 183 deletions(-)
Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix?
How much ram is your current R session using? How much ram do you even have?
Learn the scintillating answer to these and many more such questions with
the 'memuse' package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [ctb] (FreeBSD improvements to meminfo),
Wei-Chen Chen [ctb] (Windows build fixes),
Dan Burgess [ctb] (donation of a Mac for development and testing)
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between memuse versions 4.0-0 dated 2017-11-10 and 4.1-0 dated 2020-02-17
ChangeLog | 4 +++ DESCRIPTION | 8 +++---- MD5 | 42 ++++++++++++++++++++-------------------- NAMESPACE | 1 R/accessors.r | 2 - R/howbig.r | 2 - R/sysinfo.r | 24 +++++++++++++++++----- README.md | 2 - man/accessors.Rd | 3 -- man/arithmetic.Rd | 1 man/comparators.Rd | 1 man/constructor.Rd | 28 ++++++++------------------ man/converters.Rd | 10 ++------- man/filesize.Rd | 5 +++- man/howbig.Rd | 15 +++++++++++--- man/howmany.Rd | 14 +++++++++++-- man/print-memuse.Rd | 11 +++++++--- man/sum-memuse-method.Rd | 1 man/swaps.Rd | 1 src/meminfo/src/os.h | 47 ++++++++++++++++++++++----------------------- src/meminfo/src/procinfo.c | 4 +-- src/meminfo/src/raminfo.c | 8 +++---- 22 files changed, 128 insertions(+), 106 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 1.0.8 dated 2019-10-23 and 1.2.5 dated 2020-02-17
DESCRIPTION | 8 +++--- MD5 | 46 +++++++++++++++++++-------------------- R/ancova.b.R | 22 +++++++++++++----- R/ancova.h.R | 14 +++++++++++ R/anova.h.R | 14 +++++++++++ R/anovaonew.b.R | 4 ++- R/conttables.b.R | 43 +++++++++++++++++++++++++++++++++++- R/corrmatrix.b.R | 7 +++++ R/corrmatrix.h.R | 26 +++++++++++++++++++++- R/linreg.b.R | 26 ++++++++++++++++------ R/linreg.h.R | 19 +++++++++++++++- R/logregbin.b.R | 10 ++++---- R/logregmulti.b.R | 2 - R/logregord.b.R | 8 +++--- inst/doc/new-syntax.R | 2 - man/ANOVA.Rd | 10 +++++--- man/ancova.Rd | 10 +++++--- man/corrMatrix.Rd | 8 ++++-- man/linReg.Rd | 20 ++++++++++------ tests/testthat/testlinreg.R | 28 +++++++++++++++++++++++ tests/testthat/testlogregbin.R | 3 +- tests/testthat/testlogregmulti.R | 4 ++- tests/testthat/testlogregord.R | 1 tests/testthat/testmancova.R | 1 24 files changed, 263 insertions(+), 73 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.7 dated 2020-01-07 and 0.1.8 dated 2020-02-17
DESCRIPTION | 8 MD5 | 118 +++++++--- NAMESPACE | 28 ++ R/helpers.R |only R/mghheader.R |only R/read_fs_annot.R | 4 R/read_fs_curv.R | 31 ++ R/read_fs_label.R | 2 R/read_fs_mgh.R | 305 +++++++++++++++++++++----- R/read_fs_patch.R |only R/read_fs_surface.R | 148 ++++++++++-- R/read_fs_weight.R |only R/read_nisurface.R |only R/write_fs_annot.R | 2 R/write_fs_curv.R | 2 R/write_fs_mgh.R | 108 +++++++-- R/write_fs_patch.R |only R/write_fs_surface.R | 65 +++++ R/write_fs_weight.R |only build/vignette.rds |binary inst/doc/freesurferformats.Rmd | 5 inst/doc/freesurferformats.html | 12 - inst/doc/freesurferformats_header.R |only inst/doc/freesurferformats_header.Rmd |only inst/doc/freesurferformats_header.html |only inst/extdata/lh.testsurface.asc |only inst/extdata/lh.tinysurface.asc |only inst/extdata/lh.tinysurface.gii |only man/faces.quad.to.tris.Rd |only man/faces.tris.to.quad.Rd |only man/filepath.ends.with.Rd |only man/fs.get.morph.file.ext.for.format.Rd | 7 man/fs.get.morph.file.format.from.filename.Rd | 7 man/fs.patch.Rd |only man/get.slice.orientation.Rd |only man/guess.filename.is.gzipped.Rd | 4 man/is.fs.volume.Rd |only man/mgh.is.conformed.Rd |only man/mghheader.crs.orientation.Rd |only man/mghheader.is.conformed.Rd |only man/mghheader.is.ras.valid.Rd |only man/mghheader.primary.slice.direction.Rd |only man/mghheader.ras2vox.Rd |only man/mghheader.ras2vox.tkreg.Rd |only man/mghheader.scanner2tkreg.Rd |only man/mghheader.tkreg2scanner.Rd |only man/mghheader.vox2ras.Rd |only man/mghheader.vox2ras.tkreg.Rd |only man/mghheader.vox2vox.Rd |only man/mri_dtype_numbytes.Rd |only man/print.fs.patch.Rd |only man/print.fs.volume.Rd |only man/read.fs.curv.Rd | 12 - man/read.fs.curv.asc.Rd |only man/read.fs.mgh.Rd | 14 - man/read.fs.morph.Rd | 4 man/read.fs.patch.Rd |only man/read.fs.patch.asc.Rd |only man/read.fs.surface.Rd | 16 - man/read.fs.surface.asc.Rd |only man/read.fs.weight.Rd |only man/read.fs.weight.asc.Rd |only man/read_nisurface.Rd |only man/read_nisurfacefile.Rd |only man/read_nisurfacefile.fsascii.Rd |only man/read_nisurfacefile.fsnative.Rd |only man/read_nisurfacefile.gifti.Rd |only man/readable.files.Rd |only man/translate.mri.dtype.Rd |only man/write.fs.curv.Rd | 6 man/write.fs.mgh.Rd | 13 - man/write.fs.morph.Rd | 6 man/write.fs.patch.Rd |only man/write.fs.surface.Rd | 10 man/write.fs.surface.asc.Rd |only man/write.fs.weight.Rd |only tests/testthat.R | 10 tests/testthat/test-mghheader.R |only tests/testthat/test-read-fs-mgh.R | 27 +- tests/testthat/test-read-fs-patch.R |only tests/testthat/test-read-fs-surface.R | 40 +++ tests/testthat/test-read-nisurface.R |only tests/testthat/test-write-fs-mgh.R | 87 +++++-- tests/testthat/test-write-fs-patch.R |only tests/testthat/test-write-fs-surface.R | 9 tests/testthat/test-write-fs-weight.R |only vignettes/freesurferformats.Rmd | 5 vignettes/freesurferformats_header.Rmd |only 88 files changed, 893 insertions(+), 222 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ
also has unique capabilities for comparing the compositional and thermodynamic
properties of different proteins.
Author: Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>),
R Core Team [ctb] (code derived from R's pmax())
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.3.4 dated 2019-12-15 and 1.3.5 dated 2020-02-17
DESCRIPTION | 8 - MD5 | 18 +- inst/NEWS | 6 inst/doc/anintro.html | 344 +++++++++++++++++++++++----------------------- inst/doc/eos-regress.html | 6 inst/doc/equilibrium.pdf |binary inst/doc/hotspring.pdf |binary inst/doc/obigt.html | 12 - man/add.protein.Rd | 1 vignettes/obigt.bib | 4 10 files changed, 202 insertions(+), 197 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>),
Alexander W. Friedrich [aut, ths]
(<https://orcid.org/0000-0003-4881-038X>),
Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>),
Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>),
Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>),
Judith M. Fonville [ctb],
Erwin E. A. Hassing [ctb],
Eric H. L. C. M. Hazenberg [ctb],
Annick Lenglet [ctb],
Bart C. Meijer [ctb],
Sofia Ny [ctb],
Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 0.9.0 dated 2019-11-29 and 1.0.0 dated 2020-02-17
AMR-0.9.0/AMR/R/mo_history.R |only AMR-0.9.0/AMR/inst/mo_history |only AMR-0.9.0/AMR/man/figures/clipboard_copy.png |only AMR-0.9.0/AMR/man/figures/clipboard_paste.png |only AMR-0.9.0/AMR/man/figures/clipboard_rsi.png |only AMR-0.9.0/AMR/man/figures/combi_therapy_2.png |only AMR-0.9.0/AMR/man/figures/combi_therapy_3.png |only AMR-0.9.0/AMR/man/figures/mic_example.png |only AMR-0.9.0/AMR/man/figures/mono_therapy.png |only AMR-0.9.0/AMR/man/figures/rsi_example1.png |only AMR-0.9.0/AMR/man/figures/rsi_example2.png |only AMR-0.9.0/AMR/man/figures/rsi_example3.png |only AMR-0.9.0/AMR/man/figures/rsi_example4.png |only AMR-1.0.0/AMR/DESCRIPTION | 15 AMR-1.0.0/AMR/MD5 | 308 ++-- AMR-1.0.0/AMR/NAMESPACE | 5 AMR-1.0.0/AMR/NEWS.md | 48 AMR-1.0.0/AMR/R/ab.R | 73 - AMR-1.0.0/AMR/R/ab_property.R | 62 AMR-1.0.0/AMR/R/age.R | 10 AMR-1.0.0/AMR/R/amr.R | 16 AMR-1.0.0/AMR/R/atc_online.R | 13 AMR-1.0.0/AMR/R/availability.R | 11 AMR-1.0.0/AMR/R/bug_drug_combinations.R | 9 AMR-1.0.0/AMR/R/catalogue_of_life.R | 19 AMR-1.0.0/AMR/R/count.R | 9 AMR-1.0.0/AMR/R/data.R | 67 AMR-1.0.0/AMR/R/deprecated.R | 11 AMR-1.0.0/AMR/R/disk.R | 43 AMR-1.0.0/AMR/R/eucast_rules.R | 30 AMR-1.0.0/AMR/R/extended.R | 9 AMR-1.0.0/AMR/R/filter_ab_class.R | 20 AMR-1.0.0/AMR/R/first_isolate.R | 8 AMR-1.0.0/AMR/R/freq.R | 14 AMR-1.0.0/AMR/R/g.test.R | 9 AMR-1.0.0/AMR/R/ggplot_rsi.R | 11 AMR-1.0.0/AMR/R/globals.R | 12 AMR-1.0.0/AMR/R/guess_ab_col.R | 13 AMR-1.0.0/AMR/R/join_microorganisms.R | 23 AMR-1.0.0/AMR/R/key_antibiotics.R | 9 AMR-1.0.0/AMR/R/kurtosis.R | 9 AMR-1.0.0/AMR/R/lifecycle.R |only AMR-1.0.0/AMR/R/like.R | 17 AMR-1.0.0/AMR/R/mdro.R | 13 AMR-1.0.0/AMR/R/mic.R | 11 AMR-1.0.0/AMR/R/misc.R | 62 AMR-1.0.0/AMR/R/mo.R | 587 +++----- AMR-1.0.0/AMR/R/mo_property.R | 70 - AMR-1.0.0/AMR/R/mo_source.R | 39 AMR-1.0.0/AMR/R/p_symbol.R | 9 AMR-1.0.0/AMR/R/proportion.R | 15 AMR-1.0.0/AMR/R/read.4d.R | 9 AMR-1.0.0/AMR/R/resistance_predict.R | 9 AMR-1.0.0/AMR/R/rsi.R | 94 - AMR-1.0.0/AMR/R/rsi_calc.R | 12 AMR-1.0.0/AMR/R/rsi_df.R | 8 AMR-1.0.0/AMR/R/skewness.R | 9 AMR-1.0.0/AMR/R/sysdata.rda |binary AMR-1.0.0/AMR/R/translate.R | 9 AMR-1.0.0/AMR/R/whocc.R | 8 AMR-1.0.0/AMR/R/zzz.R | 40 AMR-1.0.0/AMR/build/vignette.rds |binary AMR-1.0.0/AMR/data/antibiotics.rda |binary AMR-1.0.0/AMR/data/microorganisms.codes.rda |binary AMR-1.0.0/AMR/data/microorganisms.rda |binary AMR-1.0.0/AMR/data/rsi_translation.rda |binary AMR-1.0.0/AMR/inst/CITATION |only AMR-1.0.0/AMR/inst/doc/AMR.R | 7 AMR-1.0.0/AMR/inst/doc/AMR.Rmd | 23 AMR-1.0.0/AMR/inst/doc/AMR.html | 977 +++++++------- AMR-1.0.0/AMR/inst/doc/EUCAST.R | 27 AMR-1.0.0/AMR/inst/doc/EUCAST.Rmd | 36 AMR-1.0.0/AMR/inst/doc/EUCAST.html | 217 ++- AMR-1.0.0/AMR/inst/doc/MDR.html | 225 +-- AMR-1.0.0/AMR/inst/doc/WHONET.html | 85 - AMR-1.0.0/AMR/inst/doc/resistance_predict.html | 198 +- AMR-1.0.0/AMR/man/AMR-deprecated.Rd | 8 AMR-1.0.0/AMR/man/AMR.Rd | 8 AMR-1.0.0/AMR/man/WHOCC.Rd | 2 AMR-1.0.0/AMR/man/WHONET.Rd | 2 AMR-1.0.0/AMR/man/ab_property.Rd | 34 AMR-1.0.0/AMR/man/age.Rd | 10 AMR-1.0.0/AMR/man/age_groups.Rd | 10 AMR-1.0.0/AMR/man/antibiotics.Rd | 13 AMR-1.0.0/AMR/man/as.ab.Rd | 18 AMR-1.0.0/AMR/man/as.disk.Rd | 38 AMR-1.0.0/AMR/man/as.mic.Rd | 10 AMR-1.0.0/AMR/man/as.mo.Rd | 37 AMR-1.0.0/AMR/man/as.rsi.Rd | 69 AMR-1.0.0/AMR/man/atc_online.Rd | 8 AMR-1.0.0/AMR/man/availability.Rd | 12 AMR-1.0.0/AMR/man/bug_drug_combinations.Rd | 10 AMR-1.0.0/AMR/man/catalogue_of_life.Rd | 2 AMR-1.0.0/AMR/man/catalogue_of_life_version.Rd | 2 AMR-1.0.0/AMR/man/count.Rd | 14 AMR-1.0.0/AMR/man/eucast_rules.Rd | 13 AMR-1.0.0/AMR/man/example_isolates.Rd | 4 AMR-1.0.0/AMR/man/extended-functions.Rd | 10 AMR-1.0.0/AMR/man/figures/lifecycle_archived.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_dormant.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_experimental.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_maturing.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_questioning.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_retired.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_stable.svg |only AMR-1.0.0/AMR/man/figures/lifecycle_tidyverse.svg |only AMR-1.0.0/AMR/man/filter_ab_class.Rd | 10 AMR-1.0.0/AMR/man/first_isolate.Rd | 2 AMR-1.0.0/AMR/man/g.test.Rd | 8 AMR-1.0.0/AMR/man/ggplot_rsi.Rd | 8 AMR-1.0.0/AMR/man/guess_ab_col.Rd | 8 AMR-1.0.0/AMR/man/join.Rd | 10 AMR-1.0.0/AMR/man/key_antibiotics.Rd | 10 AMR-1.0.0/AMR/man/kurtosis.Rd | 8 AMR-1.0.0/AMR/man/lifecycle.Rd |only AMR-1.0.0/AMR/man/like.Rd | 18 AMR-1.0.0/AMR/man/mdro.Rd | 10 AMR-1.0.0/AMR/man/microorganisms.Rd | 12 AMR-1.0.0/AMR/man/microorganisms.codes.Rd | 6 AMR-1.0.0/AMR/man/microorganisms.old.Rd | 2 AMR-1.0.0/AMR/man/mo_property.Rd | 15 AMR-1.0.0/AMR/man/mo_source.Rd | 31 AMR-1.0.0/AMR/man/p_symbol.Rd | 8 AMR-1.0.0/AMR/man/proportion.Rd | 18 AMR-1.0.0/AMR/man/read.4D.Rd | 8 AMR-1.0.0/AMR/man/resistance_predict.Rd | 10 AMR-1.0.0/AMR/man/rsi_translation.Rd | 13 AMR-1.0.0/AMR/man/skewness.Rd | 8 AMR-1.0.0/AMR/man/translate.Rd | 10 AMR-1.0.0/AMR/tests/testthat.R | 8 AMR-1.0.0/AMR/tests/testthat/Rplots.pdf |binary AMR-1.0.0/AMR/tests/testthat/test-ab.R | 8 AMR-1.0.0/AMR/tests/testthat/test-ab_property.R | 12 AMR-1.0.0/AMR/tests/testthat/test-age.R | 8 AMR-1.0.0/AMR/tests/testthat/test-availability.R | 8 AMR-1.0.0/AMR/tests/testthat/test-bug_drug_combinations.R | 8 AMR-1.0.0/AMR/tests/testthat/test-count.R | 8 AMR-1.0.0/AMR/tests/testthat/test-data.R | 21 AMR-1.0.0/AMR/tests/testthat/test-deprecated.R | 8 AMR-1.0.0/AMR/tests/testthat/test-disk.R | 8 AMR-1.0.0/AMR/tests/testthat/test-eucast_rules.R | 8 AMR-1.0.0/AMR/tests/testthat/test-extended.R | 8 AMR-1.0.0/AMR/tests/testthat/test-filter_ab_class.R | 8 AMR-1.0.0/AMR/tests/testthat/test-first_isolate.R | 8 AMR-1.0.0/AMR/tests/testthat/test-freq.R | 8 AMR-1.0.0/AMR/tests/testthat/test-g.test.R | 8 AMR-1.0.0/AMR/tests/testthat/test-get_locale.R | 8 AMR-1.0.0/AMR/tests/testthat/test-ggplot_rsi.R | 10 AMR-1.0.0/AMR/tests/testthat/test-guess_ab_col.R | 8 AMR-1.0.0/AMR/tests/testthat/test-join_microorganisms.R | 8 AMR-1.0.0/AMR/tests/testthat/test-key_antibiotics.R | 8 AMR-1.0.0/AMR/tests/testthat/test-kurtosis.R | 8 AMR-1.0.0/AMR/tests/testthat/test-like.R | 8 AMR-1.0.0/AMR/tests/testthat/test-mdro.R | 8 AMR-1.0.0/AMR/tests/testthat/test-mic.R | 8 AMR-1.0.0/AMR/tests/testthat/test-misc.R | 8 AMR-1.0.0/AMR/tests/testthat/test-mo.R | 20 AMR-1.0.0/AMR/tests/testthat/test-mo_history.R | 8 AMR-1.0.0/AMR/tests/testthat/test-mo_property.R | 13 AMR-1.0.0/AMR/tests/testthat/test-p_symbol.R | 8 AMR-1.0.0/AMR/tests/testthat/test-proportion.R | 8 AMR-1.0.0/AMR/tests/testthat/test-read.4d.R | 8 AMR-1.0.0/AMR/tests/testthat/test-resistance_predict.R | 8 AMR-1.0.0/AMR/tests/testthat/test-rsi.R | 8 AMR-1.0.0/AMR/tests/testthat/test-skewness.R | 8 AMR-1.0.0/AMR/vignettes/AMR.Rmd | 23 AMR-1.0.0/AMR/vignettes/EUCAST.Rmd | 36 167 files changed, 2687 insertions(+), 1957 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super
Imposition by Translation And Rotation) growth curve models. SITAR is
a shape-invariant model with a regression B-spline mean curve and
subject-specific random effects on both the measurement and age
scales. The model was first described by Lindstrom (1995)
<doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole
et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole [aut, cre] (<https://orcid.org/0000-0001-5711-8200>)
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.1.1 dated 2019-03-12 and 1.1.2 dated 2020-02-17
DESCRIPTION | 13 MD5 | 98 +++-- NAMESPACE | 11 NEWS | 32 + R/LMS2z.R | 176 +++++----- R/apv_se.R | 98 +++-- R/cdc2000.R |only R/dfset.R | 19 - R/getPeakTrough.R | 111 ++++-- R/iotf.R |only R/pdLMS.R | 26 - R/plot.sitar.R | 107 ++---- R/predict.sitar.R | 2 R/sitar.R | 558 +++++++++++++++++++------------- R/sitarlib.R | 8 R/uk90.R | 10 R/ukwhopt.R | 48 +- R/ukwhoterm.R |only R/who06.R | 10 R/who0607.R |only build/vignette.rds |binary data/cdc2000.rda |only data/iotf.rda |only data/uk90.rda |binary data/ukwhopt.rda |binary data/ukwhoterm.rda |only data/who06.rda |binary data/who0607.rda |only inst/doc/Fitting_models_with_SITAR.R | 19 - inst/doc/Fitting_models_with_SITAR.Rmd | 3 inst/doc/Fitting_models_with_SITAR.html | 340 +++++++++++++++---- man/LMS2z.Rd | 69 ++- man/LMSfit.Rd | 13 man/anova.sitar.Rd | 12 man/apv_se.Rd | 18 - man/cdc2000.Rd |only man/dfpower.Rd | 11 man/dfset.Rd | 3 man/getPeakTrough.Rd | 46 +- man/iotf.Rd |only man/mplot.Rd | 3 man/pdLMS.Rd | 12 man/plot.sitar.Rd | 53 ++- man/plotclean.Rd | 11 man/predict.sitar.Rd | 13 man/recalib.Rd | 3 man/sitar.Rd | 42 +- man/summary.sitar.Rd | 3 man/timegap.Rd | 21 - man/uk90.Rd | 10 man/ukwhopt.Rd | 46 +- man/ukwhoterm.Rd |only man/velout.Rd | 3 man/who06.Rd | 10 man/who0607.Rd |only vignettes/Fitting_models_with_SITAR.Rmd | 3 56 files changed, 1363 insertions(+), 731 deletions(-)
Title: Global Triangular and Penta-Hexagonal Grids Based on Tessellated
Icosahedra
Description: Employs triangular tessellation to refine icosahedra
defined in 3d space. The procedures can be set to provide a grid with a
custom resolution. Both the primary triangular and their inverted penta-
hexagonal grids are available for implementation. Additional functions
are provided to position points (latitude-longitude data) on the grids,
to allow 2D and 3D plotting, use raster data and shapefiles.
Author: Adam T. Kocsis [aut, cre]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between icosa versions 0.9.81 dated 2017-04-18 and 0.10.0 dated 2020-02-17
icosa-0.10.0/icosa/DESCRIPTION | 29 +- icosa-0.10.0/icosa/MD5 | 169 +++++++------ icosa-0.10.0/icosa/NAMESPACE | 173 +++++++------ icosa-0.10.0/icosa/R/data-facelayer-basic.R |only icosa-0.10.0/icosa/R/data-facelayer-graphs.R |only icosa-0.10.0/icosa/R/data-facelayer-resample.R |only icosa-0.10.0/icosa/R/data-gridlayer-attributes.R |only icosa-0.10.0/icosa/R/data-gridlayer-basic.R |only icosa-0.10.0/icosa/R/data-gridlayer-groupgen.R |only icosa-0.10.0/icosa/R/data-gridlayer-subset.R |only icosa-0.10.0/icosa/R/data.R |only icosa-0.10.0/icosa/R/grid-attributes.R |only icosa-0.10.0/icosa/R/grid-build.R |only icosa-0.10.0/icosa/R/grid-graphs.R |only icosa-0.10.0/icosa/R/grid-lookup.R |only icosa-0.10.0/icosa/R/grid-move.R |only icosa-0.10.0/icosa/R/grid-resample.R |only icosa-0.10.0/icosa/R/grid-sp-lines.R |only icosa-0.10.0/icosa/R/grid-sp-polygons.R |only icosa-0.10.0/icosa/R/grid-subset.R |only icosa-0.10.0/icosa/R/plot-2d-facelayer.R |only icosa-0.10.0/icosa/R/plot-2d-grid.R |only icosa-0.10.0/icosa/R/plot-legend.R |only icosa-0.10.0/icosa/R/plot-rgl-facelayer.R |only icosa-0.10.0/icosa/R/plot-rgl-grid.R |only icosa-0.10.0/icosa/R/plot-rgl-sp3d.R |only icosa-0.10.0/icosa/R/plot-rgl-util.R |only icosa-0.10.0/icosa/R/utils-conversion.R |only icosa-0.10.0/icosa/R/utils-spherical.R |only icosa-0.10.0/icosa/R/utils-vectors.R |only icosa-0.10.0/icosa/R/zzz.R |only icosa-0.10.0/icosa/build/vignette.rds |binary icosa-0.10.0/icosa/data |only icosa-0.10.0/icosa/inst/NEWS.md |only icosa-0.10.0/icosa/inst/doc/icosa.R |only icosa-0.10.0/icosa/inst/doc/icosa.Rmd |only icosa-0.10.0/icosa/inst/doc/icosa.pdf |only icosa-0.10.0/icosa/inst/extdata/land_polygons_z1.dbf |only icosa-0.10.0/icosa/inst/extdata/land_polygons_z1.prj |only icosa-0.10.0/icosa/inst/extdata/land_polygons_z1.shp |only icosa-0.10.0/icosa/inst/extdata/land_polygons_z1.shx |only icosa-0.10.0/icosa/man/CarToPol.Rd | 76 +++-- icosa-0.10.0/icosa/man/PolToCar.Rd | 90 ++++--- icosa-0.10.0/icosa/man/SpLines.Rd |only icosa-0.10.0/icosa/man/SpPolygons.Rd |only icosa-0.10.0/icosa/man/arcdist.Rd | 72 ++--- icosa-0.10.0/icosa/man/arcdistmat.Rd | 94 +++---- icosa-0.10.0/icosa/man/arcpoints.Rd | 96 ++++--- icosa-0.10.0/icosa/man/cellocator.Rd |only icosa-0.10.0/icosa/man/centers.Rd |only icosa-0.10.0/icosa/man/chullsphere.Rd | 90 +++---- icosa-0.10.0/icosa/man/edgelength.Rd |only icosa-0.10.0/icosa/man/edges.Rd |only icosa-0.10.0/icosa/man/extract-methods.Rd |only icosa-0.10.0/icosa/man/facelayer-class.Rd | 43 +-- icosa-0.10.0/icosa/man/faces.Rd |only icosa-0.10.0/icosa/man/faces3d.Rd |only icosa-0.10.0/icosa/man/gridgraph.Rd |only icosa-0.10.0/icosa/man/gridlabs.Rd | 52 ++-- icosa-0.10.0/icosa/man/gridlabs3d.Rd |only icosa-0.10.0/icosa/man/guides3d.Rd | 109 ++++---- icosa-0.10.0/icosa/man/heatMapLegend.Rd | 104 ++++---- icosa-0.10.0/icosa/man/hexagrid-class.Rd | 166 ++++++------- icosa-0.10.0/icosa/man/icosa.Rd | 50 +-- icosa-0.10.0/icosa/man/length.Rd |only icosa-0.10.0/icosa/man/lines-methods.Rd | 41 +-- icosa-0.10.0/icosa/man/lines3d.Rd |only icosa-0.10.0/icosa/man/locate.Rd |only icosa-0.10.0/icosa/man/names.Rd |only icosa-0.10.0/icosa/man/newgraph.Rd |only icosa-0.10.0/icosa/man/newsp.Rd |only icosa-0.10.0/icosa/man/occupied.Rd | 75 ++--- icosa-0.10.0/icosa/man/orientation.Rd |only icosa-0.10.0/icosa/man/plot.Rd |only icosa-0.10.0/icosa/man/plot3d.Rd |only icosa-0.10.0/icosa/man/pos.Rd | 61 ++-- icosa-0.10.0/icosa/man/resample.Rd |only icosa-0.10.0/icosa/man/rotate.Rd |only icosa-0.10.0/icosa/man/rpsphere.Rd | 73 ++--- icosa-0.10.0/icosa/man/subset.Rd |only icosa-0.10.0/icosa/man/surfacearea.Rd |only icosa-0.10.0/icosa/man/surfacecentroid.Rd | 105 ++++---- icosa-0.10.0/icosa/man/tessguide.Rd |only icosa-0.10.0/icosa/man/translate.Rd |only icosa-0.10.0/icosa/man/trigrid-class.Rd | 202 +++++++-------- icosa-0.10.0/icosa/man/trishape.Rd |only icosa-0.10.0/icosa/man/values.Rd |only icosa-0.10.0/icosa/man/vertices.Rd |only icosa-0.10.0/icosa/man/vicinity.Rd |only icosa-0.10.0/icosa/src/PointInTetra.cpp | 2 icosa-0.10.0/icosa/src/RccpSource_.cpp | 74 +++++ icosa-0.10.0/icosa/src/RcppExports.cpp | 242 ++++++++++--------- icosa-0.10.0/icosa/src/init.c | 198 +++++++-------- icosa-0.10.0/icosa/vignettes/icosa.Rmd |only icosa-0.9.81/icosa/NEWS.md |only icosa-0.9.81/icosa/R/RcppExports.R |only icosa-0.9.81/icosa/R/application.R |only icosa-0.9.81/icosa/R/grids.r |only icosa-0.9.81/icosa/R/icosa.R |only icosa-0.9.81/icosa/R/layers.R |only icosa-0.9.81/icosa/R/sp2d.r |only icosa-0.9.81/icosa/R/sp3d.r |only icosa-0.9.81/icosa/R/utils.R |only icosa-0.9.81/icosa/inst/CITATION |only icosa-0.9.81/icosa/inst/doc/icosaIntroShort.R |only icosa-0.9.81/icosa/inst/doc/icosaIntroShort.Rmd |only icosa-0.9.81/icosa/inst/doc/icosaIntroShort.pdf |only icosa-0.9.81/icosa/inst/extdata/land_polygons_z3.dbf |only icosa-0.9.81/icosa/inst/extdata/land_polygons_z3.prj |only icosa-0.9.81/icosa/inst/extdata/land_polygons_z3.shp |only icosa-0.9.81/icosa/inst/extdata/land_polygons_z3.shx |only icosa-0.9.81/icosa/inst/extdata/prec1_1degree.grd |only icosa-0.9.81/icosa/inst/extdata/prec1_1degree.gri |only icosa-0.9.81/icosa/man/SpLines-methods.Rd |only icosa-0.9.81/icosa/man/SpPolygons-methods.Rd |only icosa-0.9.81/icosa/man/centers-methods.Rd |only icosa-0.9.81/icosa/man/edgelength-methods.Rd |only icosa-0.9.81/icosa/man/edgelength-trigrid-methods.Rd |only icosa-0.9.81/icosa/man/edges-methods.Rd |only icosa-0.9.81/icosa/man/faces-methods.Rd |only icosa-0.9.81/icosa/man/faces3d-methods.Rd |only icosa-0.9.81/icosa/man/gridgraph-methods.Rd |only icosa-0.9.81/icosa/man/gridlabs3d-methods.Rd |only icosa-0.9.81/icosa/man/length-methods.Rd |only icosa-0.9.81/icosa/man/lines3d-method.Rd |only icosa-0.9.81/icosa/man/lines3d-methods.Rd |only icosa-0.9.81/icosa/man/locate-methods.Rd |only icosa-0.9.81/icosa/man/names-methods.Rd |only icosa-0.9.81/icosa/man/newgraph-methods.Rd |only icosa-0.9.81/icosa/man/newsp-methods.Rd |only icosa-0.9.81/icosa/man/orientation-methods.Rd |only icosa-0.9.81/icosa/man/plot-methods.Rd |only icosa-0.9.81/icosa/man/plot3d-method.Rd |only icosa-0.9.81/icosa/man/plot3d-methods.Rd |only icosa-0.9.81/icosa/man/replace-methods.Rd |only icosa-0.9.81/icosa/man/resample-methods.Rd |only icosa-0.9.81/icosa/man/rotate-methods.Rd |only icosa-0.9.81/icosa/man/subset-methods.Rd |only icosa-0.9.81/icosa/man/surfacearea-methods.Rd |only icosa-0.9.81/icosa/man/translate-methods.Rd |only icosa-0.9.81/icosa/man/trishape-methods.Rd |only icosa-0.9.81/icosa/man/values-methods.Rd |only icosa-0.9.81/icosa/man/vertices-methods.Rd |only icosa-0.9.81/icosa/man/vicinity-methods.Rd |only icosa-0.9.81/icosa/vignettes/icosaIntroShort.Rmd |only 145 files changed, 1330 insertions(+), 1156 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018]. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>),
Felix Pape [ctb, ctr],
Tim Schreier [ctb, ctr],
Luis Winckelman [ctb, ctr],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 1.1.6 dated 2019-11-20 and 1.1.8 dated 2020-02-17
GeneralizedUmatrix-1.1.6/GeneralizedUmatrix/R/DefaultColorSequence.R |only GeneralizedUmatrix-1.1.6/GeneralizedUmatrix/man/addRowWiseC.Rd |only GeneralizedUmatrix-1.1.6/GeneralizedUmatrix/man/setdiffMatrix.Rd |only GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/DESCRIPTION | 18 GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/MD5 | 29 GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/NAMESPACE | 8 GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/R/GeneralizedUmatrix.R | 677 ++-- GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/R/NormalizeUmatrix.R |only GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/R/TopviewTopographicMap.R |only GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/R/plotTopographicMap.R | 842 ++--- GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/build/partial.rdb |binary GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.R | 58 GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.Rmd | 122 GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.html | 1538 +++++++++- GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/man/GeneralizedUmatrix.Rd | 184 - GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/man/NormalizeUmatrix.Rd |only GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/man/TopviewTopographicMap.Rd |only GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/man/plotTopographicMap.Rd | 196 - GeneralizedUmatrix-1.1.8/GeneralizedUmatrix/vignettes/GeneralizedUmatrix.Rmd | 122 19 files changed, 2506 insertions(+), 1288 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: An API for M-Estimation
Description: Provides a general, flexible framework for estimating parameters
and empirical sandwich variance estimator from a set of unbiased estimating
equations (i.e., M-estimation in the vein of Stefanski & Boos (2002)
<doi:10.1198/000313002753631330>). All examples from Stefanski & Boos (2002)
are published in the corresponding Journal of Statistical Software paper
<doi:10.18637/jss.v092.i02>. Also provides an API to compute finite-sample
variance corrections.
Author: Bradley Saul [aut, cre],
Brian Barkley [ctb]
Maintainer: Bradley Saul <bradleysaul@gmail.com>
Diff between geex versions 1.0.11 dated 2018-09-23 and 1.0.12 dated 2020-02-17
DESCRIPTION | 14 MD5 | 66 R/geex.R | 4 R/grab_psiFUN_funs.R | 3 build/vignette.rds |binary inst/CITATION |only inst/doc/v00_geex_intro.R | 26 inst/doc/v00_geex_intro.html | 289 +- inst/doc/v01_additional_examples.R | 60 inst/doc/v01_additional_examples.html | 435 ++-- inst/doc/v02_sandwich_comparison.R | 4 inst/doc/v02_sandwich_comparison.html | 127 - inst/doc/v03_root_solvers.R | 10 inst/doc/v03_root_solvers.html | 105 - inst/doc/v04_weights.R | 8 inst/doc/v04_weights.html | 159 - inst/doc/v05_finite_sample_corrections.R | 12 inst/doc/v05_finite_sample_corrections.html | 175 + inst/doc/v06_causal_example.R | 26 inst/doc/v06_causal_example.Rmd | 2 inst/doc/v06_causal_example.html | 428 ++-- inst/doc/v07_geex_design.R | 24 inst/doc/v07_geex_design.html | 2721 ++++++++++++++++++++++++++-- inst/v92i02.pdf |only man/coef-methods.Rd | 1 man/geex-package.Rd | 5 man/grab_meat_list-methods.Rd | 1 man/m_estimate.Rd | 19 man/nobs-methods.Rd | 1 man/roots-methods.Rd | 1 man/show-methods.Rd | 8 man/summary-methods.Rd | 1 man/vcov-methods.Rd | 1 man/weights-methods.Rd | 1 vignettes/v06_causal_example.Rmd | 2 35 files changed, 3726 insertions(+), 1013 deletions(-)
More information about arulesSequences at CRAN
Permanent link
More information about PHInfiniteEstimates at CRAN
Permanent link
Title: A Computer Program to Detect Markers Responding to Selection
Description: In the new era of population genomics, surveys of genetic polymorphism ("genome scans") offer the opportunity to distinguish locus-specific from genome wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DetSel has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations.
Author: Renaud Vitalis <renaud.vitalis@inrae.fr>.
Maintainer: Renaud Vitalis <renaud.vitalis@inrae.fr>
Diff between DetSel versions 1.0.3 dated 2019-05-14 and 1.0.4 dated 2020-02-17
ChangeLog | 4 +++ DESCRIPTION | 10 ++++----- MD5 | 27 ++++++++++++------------ NAMESPACE | 1 R/DetSel.R | 7 ++++++ man/DetSel.Rd | 2 - man/compute.p.values.Rd | 5 +++- man/draw.detsel.graphs.Rd | 5 +++- man/genepop.to.detsel.Rd | 6 ++++- man/make.example.files.Rd | 8 ++++++- man/read.data.Rd | 5 +++- man/remove.example.files.Rd |only man/run.detsel.Rd | 5 +++- src/GetData.c | 30 ++++++++++++++++++--------- src/SimulDiv.c | 48 ++++++++++++++++++++++++++++---------------- 15 files changed, 111 insertions(+), 52 deletions(-)
Title: Exact and Approximate Implementations of the Poisson Binomial
Distribution
Description: Implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006> and Biscarri et al. (2018) <doi:10.1016/j.csda.2018.01.007> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for the Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.0.1 dated 2020-02-05 and 1.0.2 dated 2020-02-17
PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Approximate.R |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Approximate.Rmd |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Approximate.html |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Exact.R |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Exact.Rmd |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Exact.html |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Rcpp.R |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Rcpp.Rmd |only PoissonBinomial-1.0.1/PoissonBinomial/inst/doc/Rcpp.html |only PoissonBinomial-1.0.1/PoissonBinomial/vignettes/Approximate.Rmd |only PoissonBinomial-1.0.1/PoissonBinomial/vignettes/Exact.Rmd |only PoissonBinomial-1.0.1/PoissonBinomial/vignettes/Rcpp.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/DESCRIPTION | 8 PoissonBinomial-1.0.2/PoissonBinomial/MD5 | 38 +- PoissonBinomial-1.0.2/PoissonBinomial/NEWS.md | 33 + PoissonBinomial-1.0.2/PoissonBinomial/build/vignette.rds |binary PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/intro.R |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/intro.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/intro.html |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_approx.R |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_approx.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_approx.html |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_exact.R |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_exact.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/proc_exact.html |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/use_with_rcpp.R |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/use_with_rcpp.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/inst/doc/use_with_rcpp.html |only PoissonBinomial-1.0.2/PoissonBinomial/src/Makevars.win | 173 +++++----- PoissonBinomial-1.0.2/PoissonBinomial/src/PoissonBinomial.cpp | 44 ++ PoissonBinomial-1.0.2/PoissonBinomial/vignettes/intro.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/vignettes/proc_approx.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/vignettes/proc_exact.Rmd |only PoissonBinomial-1.0.2/PoissonBinomial/vignettes/use_with_rcpp.Rmd |only 34 files changed, 173 insertions(+), 123 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.2.0 dated 2020-01-10 and 0.3.0 dated 2020-02-17
DESCRIPTION | 8 +-- MD5 | 36 ++++++++-------- NEWS.md | 13 ++++++ R/RcppExports.R | 9 ++-- R/fastpos.R | 49 ++++++++++++++++++++--- README.md | 44 ++++++++++---------- inst/doc/fastpos.R | 2 inst/doc/fastpos.Rmd | 2 inst/doc/fastpos.html | 66 +++++++++++++++---------------- man/create_pop.Rd | 4 + man/fastpos-package.Rd | 5 +- man/figures/README-unnamed-chunk-5-1.png |binary man/find_critical_pos.Rd | 7 +-- man/simulate_pos.Rd | 9 ++-- src/RcppExports.cpp | 8 +-- src/rcpparma.cpp | 19 +++++--- tests/testthat/cpos3.csv |only tests/testthat/cpos4.csv |only tests/testthat/test-fastpos.R | 6 +- vignettes/fastpos.Rmd | 2 20 files changed, 176 insertions(+), 113 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.19.0 dated 2019-12-06 and 1.0.0 dated 2020-02-17
DESCRIPTION | 12 +- MD5 | 141 ++++++++++++++++--------------- NAMESPACE | 6 + NEWS.md | 12 ++ R/abfit.R |only R/basis_set.R | 7 - R/fit_display.R | 45 +++++++++ R/fitting.R | 51 ++++++----- R/image_reg.R | 10 +- R/interactive_plotting.R | 81 +++++++++++------ R/mol_parameters.R | 159 ++++++++++++++++++++++++++++++++++- R/mrs_data_io.R | 7 + R/mrs_data_proc.R | 35 +++---- R/mrs_read_ima.R | 15 +++ R/mrs_read_lcm_raw.R |only R/mrs_read_list_data.R | 3 R/mrs_read_twix.R | 100 +++++++++++++++++++--- R/varpro_3_para.R | 7 - build/vignette.rds |binary inst/doc/spant-intro.R | 10 +- inst/doc/spant-intro.html | 25 ++--- man/abfit_opts.Rd |only man/align.Rd | 10 +- man/bbase.Rd |only man/calc_ed_from_lambda.Rd |only man/calc_spec_snr.Rd | 10 +- man/comb_coils.Rd | 3 man/comb_coils_fp_pc.Rd | 3 man/def_acq_paras.Rd | 9 + man/fit_amps.Rd | 3 man/fit_mrs.Rd | 19 +++- man/get_2d_psf.Rd | 3 man/get_mrsi_voi.Rd | 3 man/get_subset.Rd | 10 +- man/get_voxel.Rd | 3 man/hz.Rd |only man/image.mrs_data.Rd | 21 +++- man/int_spec.Rd | 3 man/mask_xy_mat.Rd | 3 man/mat2mrs_data.Rd | 3 man/mrs_data2vec.Rd | 3 man/norm_mrs.Rd | 3 man/ortho3.Rd | 30 +++++- man/ortho3_int.Rd | 11 +- man/peak_info.Rd | 9 + man/plot.fit_result.Rd | 24 ++++- man/plot.mrs_data.Rd | 26 ++++- man/plot_slice_fit_inter.Rd | 10 +- man/plot_slice_map.Rd | 16 ++- man/plot_slice_map_inter.Rd | 19 +++- man/rats.Rd | 10 +- man/read_ima_dyn_dir.Rd |only man/read_mrs.Rd | 14 ++- man/rep_mrs.Rd | 3 man/scale_amp_molar.Rd | 9 + man/sd.Rd | 4 man/seq_mega_press_ideal.Rd | 12 ++ man/seq_slaser_ideal.Rd | 3 man/set_def_acq_paras.Rd | 9 + man/sim_basis.Rd | 9 + man/sim_basis_1h_brain.Rd | 10 +- man/sim_basis_1h_brain_press.Rd | 9 + man/sim_basis_tqn.Rd | 9 + man/sim_brain_1h.Rd | 12 +- man/sim_mol.Rd | 12 ++ man/sim_noise.Rd | 11 +- man/sim_resonances.Rd | 11 +- man/stackplot.fit_result.Rd | 26 ++++- man/stackplot.mrs_data.Rd | 27 ++++- man/varpro_3_para_opts.Rd | 12 +- man/varpro_opts.Rd | 13 ++ man/vec2mrs_data.Rd | 10 +- tests/testthat/fit_res_varpro.rds |binary tests/testthat/fit_res_varpro_3p.rds |binary tests/testthat/test_fitting.R | 12 +- 75 files changed, 909 insertions(+), 321 deletions(-)
Title: Nonparametric Item Response Theory
Description: Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Author: Angelo Mazza, Antonio Punzo, Brian McGuire
Maintainer: Brian McGuire <mcguirebc@gmail.com>
Diff between KernSmoothIRT versions 6.3 dated 2020-02-11 and 6.4 dated 2020-02-17
DESCRIPTION | 6 +++--- MD5 | 9 ++++++--- R/ksIRT.R | 23 +++++++++++++++++------ data/BDI_1.rda |only data/HIV_1.rda |only data/Psych101_1.rda |only man/ksIRT.Rd | 6 +++++- 7 files changed, 31 insertions(+), 13 deletions(-)
Title: Kernel Approaches for Nonlinear Genetic Association Regression
Description: Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel (Friedrichs et al., 2017, <doi:10.1155/2017/6742763>).
Author: Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut],
Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb],
Heike Bickeboeller [ctb]
Maintainer: Juliane Manitz <r@manitz.org>
Diff between kangar00 versions 1.3 dated 2019-02-09 and 1.4 dated 2020-02-17
DESCRIPTION | 15 MD5 | 80 - NAMESPACE | 83 - R/GWASdata.r | 1184 ++++++++++++------------- R/data.R | 398 ++++---- R/get_network_matrix.r |only R/kernel.r | 1268 +++++++++++++-------------- R/lkmt.r | 590 ++++++------ R/pathway.r | 1088 +++++++++++------------ inst/CITATION | 186 +-- inst/extdata/geno.txt | 202 ++-- man/GWASdata-class.Rd | 186 +-- man/anno.Rd | 66 - man/calc_kernel.Rd | 210 ++-- man/gene_name_number-character-method.Rd | 52 - man/geno.Rd | 62 - man/get_ana-data.frame-method.Rd | 54 - man/get_anno-snp_info-pathway_info-method.Rd | 90 - man/get_network_matrix.Rd |only man/gwas.Rd | 62 - man/hsa04020.Rd | 52 - man/hsa04022_info.Rd | 54 - man/kangar00-package.Rd | 100 +- man/kernel-class.Rd | 130 +- man/lkmt-class.Rd | 152 +-- man/lkmt.net.kernel.hsa04020.Rd | 74 - man/lkmt_test.Rd | 178 +-- man/lowrank_kernel-class.Rd | 76 - man/make_psd-matrix-method.Rd | 92 - man/net.kernel.hsa04020.Rd | 68 - man/pathway-class.Rd | 378 ++++---- man/pathway_info-class.Rd | 118 +- man/pheno.Rd | 66 - man/read_geno-character-method.Rd | 94 +- man/rewire_network.Rd | 70 - man/rs10243170_info.Rd | 54 - man/set_names-matrix-method.Rd |only man/set_one-matrix-method.Rd |only man/snp_info-class.Rd | 130 +- tests/testthat.R | 8 tests/testthat/test_gwas.r | 74 - tests/testthat/test_kernel.r | 72 - tests/testthat/test_lkmt.r | 48 - 43 files changed, 3986 insertions(+), 3978 deletions(-)
Title: Explore Probability Distributions for Bivariate Temporal
Granularities
Description: Provides tools for systematically exploring large quantities of
temporal data across nonlinear temporal granularities
(deconstructions of time) by visualizing probability distributions.
Nonlinear time granularities can be circular, quasi-circular or
aperiodic. 'gravitas' computes nonlinear
single-order-up or multiple-order-up granularities, check the
feasibility of creating plots for any two nonlinear granularities
and recommend probability distributions plots for exploring
periodicity in the data.
Author: Sayani Gupta [aut, cre] (<https://orcid.org/0000-0003-0643-5358>),
Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>),
Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>),
Antony Unwin [aut] (<https://orcid.org/0000-0002-5841-5757>)
Maintainer: Sayani Gupta <gupta.sayani@gmail.com>
Diff between gravitas versions 0.1.0 dated 2019-11-05 and 0.1.2 dated 2020-02-17
DESCRIPTION | 22 ++++++++++++---------- MD5 | 38 ++++++++++++++++++++------------------ NEWS.md |only R/gran_advice.R | 1 - R/search_gran.R | 5 +---- R/temp_create_gran.R | 2 +- R/temp_search_gran.R | 2 +- README.md | 24 +++++++++++++----------- inst/doc/cricket.R | 19 ++++++++++--------- inst/doc/cricket.Rmd | 5 +++-- inst/doc/cricket.html | 34 +++++++++++++++++----------------- inst/doc/gravitas_vignette.R | 26 +++++++++++++------------- inst/doc/gravitas_vignette.html | 12 +++++------- man/create_gran.Rd | 19 ++++++++++++++----- man/figures/logo.png |only man/gran_obs.Rd | 2 -- man/harmony.Rd | 14 +++++++++++--- man/prob_plot.Rd | 17 +++++++++++++---- man/search_gran.Rd | 13 ++++++++++--- man/validate_gran.Rd | 15 ++++++++++----- vignettes/cricket.Rmd | 5 +++-- 21 files changed, 157 insertions(+), 118 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.0.4 dated 2019-12-02 and 1.0.5 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/jsPropensityGadget.R | 3 ++- build/vignette.rds |binary inst/doc/jsmodule.html | 4 ++-- 6 files changed, 20 insertions(+), 12 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis
of chemical toxicokinetics ("TK") as in Pearce et al. (2017)
<doi:10.18637/jss.v079.i04>. Chemical-specific in vitro
data have been obtained from relatively high throughput
experiments. Both physiologically-based ("PBTK") and empirical
(e.g., one compartment) "TK" models can be parameterized for
several hundred chemicals and multiple species. These models are
solved efficiently, often using compiled (C-based) code. A Monte
Carlo sampler is included for simulating biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and measurement limitations. Calibrated methods are included for
predicting tissue:plasma partition coefficients and volume of
distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (e.g., Tox21, ToxCast) to real-world exposures via
reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre] (<https://orcid.org/0000-0002-4024-534X>),
Robert Pearce [aut] (<https://orcid.org/0000-0003-3168-4049>),
Caroline Ring [aut] (<https://orcid.org/0000-0002-0463-1251>),
Greg Honda [aut] (<https://orcid.org/0000-0001-7713-9850>),
Mark Sfeir [aut],
Matt Linakis [aut] (<https://orcid.org/0000-0003-0526-2395>),
Jimena Davis [ctb],
James Sluka [ctb] (<https://orcid.org/0000-0002-5901-1404>),
Nisha Sipes [ctb] (<https://orcid.org/0000-0003-4203-6426>),
Barbara Wetmore [ctb],
Woodrow Setzer [ctb] (<https://orcid.org/0000-0002-6709-9186>)
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.10.1 dated 2019-09-10 and 2.0.0 dated 2020-02-17
httk-1.10.1/httk/R/3compPBPKmodel_inits.R |only httk-1.10.1/httk/R/calc_chem_stats.R |only httk-1.10.1/httk/R/calc_fu_hep.R |only httk-1.10.1/httk/R/calc_hepatic_clearance.R |only httk-1.10.1/httk/R/calc_ratioblood2plasma.R |only httk-1.10.1/httk/R/convert_httk.R |only httk-1.10.1/httk/R/draw_fup_clint.R |only httk-1.10.1/httk/R/get_httk_params.R |only httk-1.10.1/httk/R/get_invitropk_param.R |only httk-1.10.1/httk/R/httkpop.R |only httk-1.10.1/httk/R/httkpop_bio.R |only httk-1.10.1/httk/inst/doc/Honda_2019_updated_armitage.R |only httk-1.10.1/httk/inst/doc/Honda_2019_updated_armitage.Rmd |only httk-1.10.1/httk/inst/doc/Honda_2019_updated_armitage.html |only httk-1.10.1/httk/inst/doc/Pearce_2017_partitioning_plots.R |only httk-1.10.1/httk/inst/doc/Pearce_2017_partitioning_plots.Rmd |only httk-1.10.1/httk/inst/doc/Pearce_2017_partitioning_plots.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.html |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.R |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.Rmd |only httk-1.10.1/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.html |only httk-1.10.1/httk/inst/doc/Wambaugh_2018_Figures.R |only httk-1.10.1/httk/inst/doc/Wambaugh_2018_Figures.Rmd |only httk-1.10.1/httk/inst/doc/Wambaugh_2018_Figures.html |only httk-1.10.1/httk/inst/doc/Wambaugh_2019_figures.R |only httk-1.10.1/httk/inst/doc/Wambaugh_2019_figures.Rmd |only httk-1.10.1/httk/inst/doc/Wambaugh_2019_figures.html |only httk-1.10.1/httk/man/ToxCast2015subset.Rd |only httk-1.10.1/httk/man/calc_hepatic_clearance.Rd |only httk-1.10.1/httk/man/convert_httk.Rd |only httk-1.10.1/httk/man/draw_fup_clint.Rd |only httk-1.10.1/httk/man/get_httk_params.Rd |only httk-1.10.1/httk/man/httkpop_bio.Rd |only httk-1.10.1/httk/man/sipes2017.table.Rd |only httk-1.10.1/httk/vignettes/Honda_2019_updated_armitage.Rmd |only httk-1.10.1/httk/vignettes/Pearce_2017_partitioning_plots.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_age_dist.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_globalsensitivityplot.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_heightweight_splines_kde.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_hematocrit_splines.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_plot_css95.Rmd |only httk-1.10.1/httk/vignettes/Ring_2017_supplemental_vignette_serumcreat_splines_kde.Rmd |only httk-1.10.1/httk/vignettes/Wambaugh_2018_Figures.Rmd |only httk-1.10.1/httk/vignettes/Wambaugh_2019_figures.Rmd |only httk-2.0.0/httk/DESCRIPTION | 61 httk-2.0.0/httk/MD5 | 581 httk-2.0.0/httk/NAMESPACE | 28 httk-2.0.0/httk/NEWS | 35 httk-2.0.0/httk/R/Parameterize_gas_PBTK.R |only httk-2.0.0/httk/R/add_chemtable.R | 9 httk-2.0.0/httk/R/armitage.R | 2 httk-2.0.0/httk/R/available_rblood2plasma.R | 66 httk-2.0.0/httk/R/calc_analytic_css.R | 144 httk-2.0.0/httk/R/calc_analytic_css_1comp.R | 54 httk-2.0.0/httk/R/calc_analytic_css_3comp.R | 48 httk-2.0.0/httk/R/calc_analytic_css_3compss.R | 56 httk-2.0.0/httk/R/calc_analytic_css_pbtk.R | 43 httk-2.0.0/httk/R/calc_css.R | 241 httk-2.0.0/httk/R/calc_elimination_rate.R | 15 httk-2.0.0/httk/R/calc_hep_bioavailability.R |only httk-2.0.0/httk/R/calc_hep_clearance.R |only httk-2.0.0/httk/R/calc_hep_fu.R |only httk-2.0.0/httk/R/calc_krbc2pu.R |only httk-2.0.0/httk/R/calc_mc_css.R | 507 httk-2.0.0/httk/R/calc_mc_oral_equiv.R | 31 httk-2.0.0/httk/R/calc_mc_tk.R |only httk-2.0.0/httk/R/calc_rblood2plasma.R |only httk-2.0.0/httk/R/calc_stats.R | 236 httk-2.0.0/httk/R/calc_timecourse_peak.R | 2 httk-2.0.0/httk/R/calc_total_clearance.R | 11 httk-2.0.0/httk/R/calc_volume_of_distribution.R | 90 httk-2.0.0/httk/R/convert_httkpop_1comp.R |only httk-2.0.0/httk/R/create_mc_samples.R |only httk-2.0.0/httk/R/data.R | 924 httk-2.0.0/httk/R/export_pbtk_jarnac.R | 2 httk-2.0.0/httk/R/gen_age_height_weight.R | 5 httk-2.0.0/httk/R/gen_height_weight.R | 7 httk-2.0.0/httk/R/get_Wetmore_Oral_Equiv.R | 2 httk-2.0.0/httk/R/get_chem_id.R | 190 httk-2.0.0/httk/R/get_cheminfo.R | 239 httk-2.0.0/httk/R/get_invitroPK_param.R |only httk-2.0.0/httk/R/get_physchem_param.R | 212 httk-2.0.0/httk/R/get_rblood2plasma.R | 77 httk-2.0.0/httk/R/globals.R |only httk-2.0.0/httk/R/httk-package.R | 38 httk-2.0.0/httk/R/httkpop_biotophys_default.R |only httk-2.0.0/httk/R/httkpop_direct_resample.R | 6 httk-2.0.0/httk/R/httkpop_direct_resample_inner.R | 7 httk-2.0.0/httk/R/httkpop_generate.R | 22 httk-2.0.0/httk/R/httkpop_mc.R |only httk-2.0.0/httk/R/httkpop_virtual_indiv.R | 2 httk-2.0.0/httk/R/in.list.R | 8 httk-2.0.0/httk/R/inhalation_inits.R |only httk-2.0.0/httk/R/invitro_mc.R |only httk-2.0.0/httk/R/ionization_functions.R | 111 httk-2.0.0/httk/R/load_sipes2017.R | 52 httk-2.0.0/httk/R/lump_tissues.R | 191 httk-2.0.0/httk/R/modelinfo_1comp.R | 224 httk-2.0.0/httk/R/modelinfo_3comp.R | 316 httk-2.0.0/httk/R/modelinfo_3compss.R | 73 httk-2.0.0/httk/R/modelinfo_PBTK.R | 414 httk-2.0.0/httk/R/modelinfo_Schmitt.R | 113 httk-2.0.0/httk/R/modelinfo_gas_pbtk.R |only httk-2.0.0/httk/R/monte_carlo.R | 147 httk-2.0.0/httk/R/parameterize_1comp.R | 160 httk-2.0.0/httk/R/parameterize_3comp.R | 106 httk-2.0.0/httk/R/parameterize_pbtk.R | 276 httk-2.0.0/httk/R/parameterize_schmitt.R | 257 httk-2.0.0/httk/R/parameterize_steadystate.R | 241 httk-2.0.0/httk/R/predict_partitioning_schmitt.R | 69 httk-2.0.0/httk/R/propagate_invitrouv_1comp.R |only httk-2.0.0/httk/R/propagate_invitrouv_3comp.R |only httk-2.0.0/httk/R/propagate_invitrouv_pbtk.R |only httk-2.0.0/httk/R/r_left_censored_norm.R | 5 httk-2.0.0/httk/R/reset_httk.R |only httk-2.0.0/httk/R/scale_dosing.R |only httk-2.0.0/httk/R/solve_1comp.R | 447 httk-2.0.0/httk/R/solve_3comp.R | 451 httk-2.0.0/httk/R/solve_gas_pbtk.R |only httk-2.0.0/httk/R/solve_model.R |only httk-2.0.0/httk/R/solve_pbtk.R | 568 httk-2.0.0/httk/R/sysdata.rda |binary httk-2.0.0/httk/R/tissue_mass_functions.R | 328 httk-2.0.0/httk/R/tissue_masses_flows.R | 37 httk-2.0.0/httk/build/httk.pdf |23202 ++++++---- httk-2.0.0/httk/build/vignette.rds |binary httk-2.0.0/httk/data/Frank2018.RData |only httk-2.0.0/httk/data/Linakis2020.RData |only httk-2.0.0/httk/data/Tables.RData |binary httk-2.0.0/httk/data/armitage_input.RData |binary httk-2.0.0/httk/data/httkpop.RData |binary httk-2.0.0/httk/data/vignettes.RData |binary httk-2.0.0/httk/data/wambaugh2019.RData |binary httk-2.0.0/httk/data/well_param.RData |binary httk-2.0.0/httk/inst/CITATION |only httk-2.0.0/httk/inst/doc/Frank2018.R |only httk-2.0.0/httk/inst/doc/Frank2018.Rmd |only httk-2.0.0/httk/inst/doc/Frank2018.html |only httk-2.0.0/httk/inst/doc/Honda2019.R |only httk-2.0.0/httk/inst/doc/Honda2019.Rmd |only httk-2.0.0/httk/inst/doc/Honda2019.html |only httk-2.0.0/httk/inst/doc/LinakisSubmitted.R |only httk-2.0.0/httk/inst/doc/LinakisSubmitted.Rmd |only httk-2.0.0/httk/inst/doc/LinakisSubmitted.html |only httk-2.0.0/httk/inst/doc/Pearce2017.R |only httk-2.0.0/httk/inst/doc/Pearce2017.Rmd |only httk-2.0.0/httk/inst/doc/Pearce2017.html |only httk-2.0.0/httk/inst/doc/Ring_2017_vignette01_subpopulations.R | 94 httk-2.0.0/httk/inst/doc/Ring_2017_vignette01_subpopulations.Rmd | 8 httk-2.0.0/httk/inst/doc/Ring_2017_vignette01_subpopulations.html | 26 httk-2.0.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.R | 416 httk-2.0.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.Rmd | 18 httk-2.0.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 40 httk-2.0.0/httk/inst/doc/Ring_2017_vignette03_paper_fig2.R | 16 httk-2.0.0/httk/inst/doc/Ring_2017_vignette03_paper_fig2.Rmd | 14 httk-2.0.0/httk/inst/doc/Ring_2017_vignette03_paper_fig2.html | 26 httk-2.0.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.R | 42 httk-2.0.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.Rmd | 2 httk-2.0.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.html | 26 httk-2.0.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.R | 18 httk-2.0.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 2 httk-2.0.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 26 httk-2.0.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.R | 72 httk-2.0.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.Rmd | 2 httk-2.0.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.html | 26 httk-2.0.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.R | 12 httk-2.0.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.Rmd | 2 httk-2.0.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 26 httk-2.0.0/httk/inst/doc/Wambaugh2018.R |only httk-2.0.0/httk/inst/doc/Wambaugh2018.Rmd |only httk-2.0.0/httk/inst/doc/Wambaugh2018.html |only httk-2.0.0/httk/inst/doc/Wambaugh2019.R |only httk-2.0.0/httk/inst/doc/Wambaugh2019.Rmd |only httk-2.0.0/httk/inst/doc/Wambaugh2019.html |only httk-2.0.0/httk/man/EPA.ref.Rd |only httk-2.0.0/httk/man/Frank2018invivo.Rd |only httk-2.0.0/httk/man/Obach2008.Rd | 40 httk-2.0.0/httk/man/Tables.Rdata.stamp.Rd | 33 httk-2.0.0/httk/man/Wetmore.data.Rd | 90 httk-2.0.0/httk/man/Wetmore2012.Rd | 48 httk-2.0.0/httk/man/add_chemtable.Rd | 161 httk-2.0.0/httk/man/age_dist_smooth.Rd | 56 httk-2.0.0/httk/man/age_draw_smooth.Rd | 70 httk-2.0.0/httk/man/armitage_estimate_sarea.Rd | 76 httk-2.0.0/httk/man/armitage_eval.Rd | 192 httk-2.0.0/httk/man/armitage_input.Rd | 72 httk-2.0.0/httk/man/available_rblood2plasma.Rd | 114 httk-2.0.0/httk/man/blood_mass_correct.Rd | 68 httk-2.0.0/httk/man/blood_weight.Rd | 64 httk-2.0.0/httk/man/bmiage.Rd | 86 httk-2.0.0/httk/man/body_surface_area.Rd | 60 httk-2.0.0/httk/man/bone_mass_age.Rd | 74 httk-2.0.0/httk/man/brain_mass.Rd | 47 httk-2.0.0/httk/man/calc_analytic_css.Rd | 249 httk-2.0.0/httk/man/calc_analytic_css_1comp.Rd | 130 httk-2.0.0/httk/man/calc_analytic_css_3comp.Rd | 130 httk-2.0.0/httk/man/calc_analytic_css_3compss.Rd | 132 httk-2.0.0/httk/man/calc_analytic_css_pbtk.Rd | 130 httk-2.0.0/httk/man/calc_css.Rd | 304 httk-2.0.0/httk/man/calc_elimination_rate.Rd | 171 httk-2.0.0/httk/man/calc_hep_bioavailability.Rd |only httk-2.0.0/httk/man/calc_hep_clearance.Rd |only httk-2.0.0/httk/man/calc_hep_fu.Rd |only httk-2.0.0/httk/man/calc_ionization.Rd | 146 httk-2.0.0/httk/man/calc_krbc2pu.Rd |only httk-2.0.0/httk/man/calc_mc_css.Rd | 490 httk-2.0.0/httk/man/calc_mc_oral_equiv.Rd | 259 httk-2.0.0/httk/man/calc_mc_tk.Rd |only httk-2.0.0/httk/man/calc_rblood2plasma.Rd | 153 httk-2.0.0/httk/man/calc_stats.Rd | 214 httk-2.0.0/httk/man/calc_total_clearance.Rd | 137 httk-2.0.0/httk/man/calc_vdist.Rd | 160 httk-2.0.0/httk/man/chem.invivo.PK.aggregate.data.Rd | 48 httk-2.0.0/httk/man/chem.invivo.PK.data.Rd | 412 httk-2.0.0/httk/man/chem.invivo.PK.summary.data.Rd | 410 httk-2.0.0/httk/man/chem.lists.Rd | 76 httk-2.0.0/httk/man/chem.physical_and_invitro.data.Rd | 236 httk-2.0.0/httk/man/ckd_epi_eq.Rd | 74 httk-2.0.0/httk/man/concentration_data_Linakis2020.Rd |only httk-2.0.0/httk/man/convert_httkpop_1comp.Rd |only httk-2.0.0/httk/man/create_mc_samples.Rd |only httk-2.0.0/httk/man/estimate_gfr.Rd | 58 httk-2.0.0/httk/man/estimate_gfr_ped.Rd | 54 httk-2.0.0/httk/man/estimate_hematocrit.Rd | 58 httk-2.0.0/httk/man/export_pbtk_jarnac.Rd | 97 httk-2.0.0/httk/man/export_pbtk_sbml.Rd | 97 httk-2.0.0/httk/man/gen_age_height_weight.Rd | 136 httk-2.0.0/httk/man/gen_height_weight.Rd | 60 httk-2.0.0/httk/man/get_chem_id.Rd | 50 httk-2.0.0/httk/man/get_cheminfo.Rd | 190 httk-2.0.0/httk/man/get_gfr_category.Rd | 78 httk-2.0.0/httk/man/get_invitroPK_param.Rd |only httk-2.0.0/httk/man/get_lit_cheminfo.Rd | 126 httk-2.0.0/httk/man/get_lit_css.Rd | 162 httk-2.0.0/httk/man/get_lit_oral_equiv.Rd | 186 httk-2.0.0/httk/man/get_physchem_param.Rd | 64 httk-2.0.0/httk/man/get_rblood2plasma.Rd | 90 httk-2.0.0/httk/man/get_weight_class.Rd | 80 httk-2.0.0/httk/man/hematocrit_infants.Rd | 76 httk-2.0.0/httk/man/honda.ivive.Rd | 110 httk-2.0.0/httk/man/howgate.Rd | 34 httk-2.0.0/httk/man/httk-package.Rd | 103 httk-2.0.0/httk/man/httkpop.Rd | 88 httk-2.0.0/httk/man/httkpop_biotophys_default.Rd |only httk-2.0.0/httk/man/httkpop_direct_resample.Rd | 135 httk-2.0.0/httk/man/httkpop_direct_resample_inner.Rd | 123 httk-2.0.0/httk/man/httkpop_generate.Rd | 211 httk-2.0.0/httk/man/httkpop_mc.Rd |only httk-2.0.0/httk/man/httkpop_virtual_indiv.Rd | 137 httk-2.0.0/httk/man/in.list.Rd | 220 httk-2.0.0/httk/man/invitro_mc.Rd |only httk-2.0.0/httk/man/is.httk.Rd | 210 httk-2.0.0/httk/man/is_in_inclusive.Rd | 78 httk-2.0.0/httk/man/johnson.Rd | 37 httk-2.0.0/httk/man/kidney_mass_children.Rd | 56 httk-2.0.0/httk/man/liver_mass_children.Rd | 56 httk-2.0.0/httk/man/load_sipes2017.Rd | 94 httk-2.0.0/httk/man/lump_tissues.Rd | 135 httk-2.0.0/httk/man/lung_mass_children.Rd | 60 httk-2.0.0/httk/man/mcnally_dt.Rd | 76 httk-2.0.0/httk/man/metabolism_data_Linakis2020.Rd |only httk-2.0.0/httk/man/monte_carlo.Rd | 318 httk-2.0.0/httk/man/nhanes_mec_svy.Rd | 76 httk-2.0.0/httk/man/onlyp.Rd | 36 httk-2.0.0/httk/man/pancreas_mass_children.Rd | 56 httk-2.0.0/httk/man/parameterize_1comp.Rd | 187 httk-2.0.0/httk/man/parameterize_3comp.Rd | 202 httk-2.0.0/httk/man/parameterize_gas_pbtk.Rd |only httk-2.0.0/httk/man/parameterize_pbtk.Rd | 248 httk-2.0.0/httk/man/parameterize_schmitt.Rd | 154 httk-2.0.0/httk/man/parameterize_steadystate.Rd | 181 httk-2.0.0/httk/man/pc.data.Rd | 128 httk-2.0.0/httk/man/pharma.Rd | 50 httk-2.0.0/httk/man/physiology.data.Rd | 68 httk-2.0.0/httk/man/predict_partitioning_schmitt.Rd | 191 httk-2.0.0/httk/man/propagate_invitrouv_1comp.Rd |only httk-2.0.0/httk/man/propagate_invitrouv_3comp.Rd |only httk-2.0.0/httk/man/propagate_invitrouv_pbtk.Rd |only httk-2.0.0/httk/man/r_left_censored_norm.Rd | 59 httk-2.0.0/httk/man/reset_httk.Rd |only httk-2.0.0/httk/man/rfun.Rd | 56 httk-2.0.0/httk/man/scale_dosing.Rd |only httk-2.0.0/httk/man/sipes2017.Rd | 59 httk-2.0.0/httk/man/skeletal_muscle_mass.Rd | 76 httk-2.0.0/httk/man/skeletal_muscle_mass_children.Rd | 54 httk-2.0.0/httk/man/skin_mass_bosgra.Rd | 49 httk-2.0.0/httk/man/solve_1comp.Rd | 292 httk-2.0.0/httk/man/solve_3comp.Rd | 301 httk-2.0.0/httk/man/solve_gas_pbtk.Rd |only httk-2.0.0/httk/man/solve_model.Rd |only httk-2.0.0/httk/man/solve_pbtk.Rd | 349 httk-2.0.0/httk/man/spleen_mass_children.Rd | 60 httk-2.0.0/httk/man/spline_heightweight.Rd | 68 httk-2.0.0/httk/man/spline_hematocrit.Rd | 62 httk-2.0.0/httk/man/spline_serumcreat.Rd | 70 httk-2.0.0/httk/man/supptab1_Linakis2020.Rd |only httk-2.0.0/httk/man/supptab2_Linakis2020.Rd |only httk-2.0.0/httk/man/tissue.data.Rd | 92 httk-2.0.0/httk/man/tissue_masses_flows.Rd | 79 httk-2.0.0/httk/man/tissue_scale.Rd | 62 httk-2.0.0/httk/man/wambaugh2019.Rd | 120 httk-2.0.0/httk/man/wambaugh2019.nhanes.Rd | 77 httk-2.0.0/httk/man/wambaugh2019.raw.Rd | 196 httk-2.0.0/httk/man/wambaugh2019.seem3.Rd | 61 httk-2.0.0/httk/man/wambaugh2019.tox21.Rd |only httk-2.0.0/httk/man/well_param.Rd | 78 httk-2.0.0/httk/man/wfl.Rd | 76 httk-2.0.0/httk/src/init.c | 26 httk-2.0.0/httk/src/model1comp.c | 50 httk-2.0.0/httk/src/model3comp.c | 156 httk-2.0.0/httk/src/model_gas_pbtk.c |only httk-2.0.0/httk/tests/1comp_test.R | 6 httk-2.0.0/httk/tests/1comp_test.Rout.save | 244 httk-2.0.0/httk/tests/3comp_test.R | 6 httk-2.0.0/httk/tests/3comp_test.Rout.save | 238 httk-2.0.0/httk/tests/3compss_test.R | 4 httk-2.0.0/httk/tests/3compss_test.Rout.save | 11 httk-2.0.0/httk/tests/adddata_test.R | 39 httk-2.0.0/httk/tests/adddata_test.Rout.save | 128 httk-2.0.0/httk/tests/cheminfo_test.R | 3 httk-2.0.0/httk/tests/cheminfo_test.Rout.save | 16 httk-2.0.0/httk/tests/httk2.0_test.R |only httk-2.0.0/httk/tests/httk2.0_test.Rout.save |only httk-2.0.0/httk/tests/ivive_test.R | 6 httk-2.0.0/httk/tests/ivive_test.Rout.save | 9 httk-2.0.0/httk/tests/montecarlo_tests.R |only httk-2.0.0/httk/tests/montecarlo_tests.Rout.save |only httk-2.0.0/httk/tests/other_tests.R | 27 httk-2.0.0/httk/tests/other_tests.Rout.save | 149 httk-2.0.0/httk/tests/pbtk_test.R | 4 httk-2.0.0/httk/tests/pbtk_test.Rout.save | 238 httk-2.0.0/httk/tests/solve_gas_crude_test.R |only httk-2.0.0/httk/tests/solve_gas_crude_test.Rout.save |only httk-2.0.0/httk/vignettes/Frank2018.Rmd |only httk-2.0.0/httk/vignettes/Honda2019.Rmd |only httk-2.0.0/httk/vignettes/LinakisSubmitted.Rmd |only httk-2.0.0/httk/vignettes/Pearce2017.Rmd |only httk-2.0.0/httk/vignettes/Ring_2017_vignette01_subpopulations.Rmd | 8 httk-2.0.0/httk/vignettes/Ring_2017_vignette02_evalmodelsubpop.Rmd | 18 httk-2.0.0/httk/vignettes/Ring_2017_vignette03_paper_fig2.Rmd | 14 httk-2.0.0/httk/vignettes/Ring_2017_vignette04_paper_fig3.Rmd | 2 httk-2.0.0/httk/vignettes/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 2 httk-2.0.0/httk/vignettes/Ring_2017_vignette06_aerplotting.Rmd | 2 httk-2.0.0/httk/vignettes/Ring_2017_vignette_05a_virtualstudypops.Rmd | 2 httk-2.0.0/httk/vignettes/Wambaugh2018.Rmd |only httk-2.0.0/httk/vignettes/Wambaugh2019.Rmd |only 364 files changed, 27410 insertions(+), 20029 deletions(-)
Title: Compute Decision Interval and Average Run Length for CUSUM
Charts
Description: Computation of decision intervals (H) and average run lengths (ARL) for CUSUM charts.
Author: Douglas M. Hawkins, David H. Olwell, and Boxiang Wang
Maintainer: Boxiang Wang <boxiang-wang@uiowa.edu>
Diff between CUSUMdesign versions 1.1.3 dated 2016-05-19 and 1.1.4 dated 2020-02-17
DESCRIPTION | 10 +-- MD5 | 9 +-- man/getARL.Rd | 142 +++++++++++++++++++++++++-------------------------- man/getH.Rd | 160 +++++++++++++++++++++++++++++----------------------------- src/ANYSUBS.f | 37 ++++++++----- src/init.c |only 6 files changed, 185 insertions(+), 173 deletions(-)
Title: Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses
Description: Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.
Author: Gabriel Margarido [aut],
Marcelo Mollinari [aut],
Karl Broman [ctb],
Getulio Ferreira [ctb],
Rodrigo Amadeu [ctb],
Cristiane Taniguti [ctb, cre],
Augusto Garcia [aut, ctb]
Maintainer: Cristiane Taniguti <chtaniguti@usp.br>
Diff between onemap versions 2.1.2 dated 2020-02-12 and 2.1.3 dated 2020-02-17
DESCRIPTION | 17 MD5 | 102 R/add_marker.R | 2 R/combine_onemap.R | 4 R/compare.R | 103 R/cpp_utils.R | 2 R/create_dataset_bins.R | 6 R/draw_map.R | 6 R/draw_map2.R | 71 R/drop_marker.R | 2 R/find_bins.R | 2 R/get_info_2pt.R | 12 R/group.R | 9 R/group_seq.R | 10 R/make_seq.R | 206 - R/map.R | 11 R/marker_type.R | 4 R/mds_onemap.R | 5 R/onemap_read_vcfR.R | 20 R/order_seq.R | 2 R/phases.R | 2 R/rcd.R | 4 R/record.R | 4 R/rf_2pts.R | 12 R/rf_graph_table.R | 2 R/ripple_seq.R | 10 R/seriation.R | 4 R/test_segregation.R | 8 R/try_seq.R | 131 R/ug.R | 4 R/write_map.R | 8 inst/doc/Inbred_Based_Populations.R | 242 - inst/doc/Inbred_Based_Populations.html | 4367 +++++++++++++++------------------ inst/doc/Introduction_R.R | 54 inst/doc/Introduction_R.html | 447 --- inst/doc/Outcrossing_Populations.R | 278 +- inst/doc/Outcrossing_Populations.html | 4089 ++++++++++++++---------------- inst/doc/Overview.R | 2 inst/doc/Overview.html | 195 - man/draw_map.Rd | 10 man/draw_map2.Rd | 22 man/est_map_hmm_out.Rd | 3 man/group_seq.Rd | 10 man/make_seq.Rd | 3 man/mds_onemap.Rd | 17 man/onemap-internal.Rd | 11 man/onemap_read_vcfR.Rd | 9 man/order_seq.Rd | 14 man/rf_graph_table.Rd | 13 man/select_segreg.Rd | 3 man/vcf2raw.Rd | 11 man/write_onemap_raw.Rd | 8 52 files changed, 4998 insertions(+), 5595 deletions(-)
Title: An Ensemble Method for Interval-Censored Survival Data
Description: Implements the conditional inference forest approach
to modeling interval-censored survival data. It also provides
functions to tune the parameters and evaluate the model fit. See
Yao et al. (2019) <arXiv:1901.04599>.
Author: Weichi Yao [aut, cre],
Halina Frydman [aut],
Jeffrey S. Simonoff [aut]
Maintainer: Weichi Yao <wy635@stern.nyu.edu>
Diff between ICcforest versions 0.5.0 dated 2019-02-08 and 0.5.1 dated 2020-02-17
DESCRIPTION | 14 - MD5 | 16 - R/ICcforest.R | 5 R/sbrier_IC.R | 458 +++++++++++++++++++++++------------------------ R/tuneICRF.R | 3 man/ICcforest.Rd | 27 +- man/predict.ICcforest.Rd | 14 + man/sbrier_IC.Rd | 11 - man/tuneICRF.Rd | 28 +- 9 files changed, 299 insertions(+), 277 deletions(-)
Title: Perform Global Vector Autoregression Estimation and Inference
Description: Perform the estimation and inference of Global Vector Autoregression model (GVAR) of Pesaran, Schuermann and Weiner (2004) <DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and Smith (2007) <DOI:10.1002/jae.932>.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between GVARX versions 1.2 dated 2019-12-20 and 1.3 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/02GVAR_Xt.R | 36 +++++++++++++++++++++++------------- 3 files changed, 29 insertions(+), 19 deletions(-)
Title: Bayesian Latent Class Analysis
Description: Bayesian Latent Class Analysis using several different
methods.
Author: Arthur White [aut, cre] (Previous email address:
arthur.white@ucdconnect.ie),
Thomas Brendan Murphy [aut, ths]
Maintainer: Arthur White <arwhite@tcd.ie>
Diff between BayesLCA versions 1.7 dated 2015-04-10 and 1.8 dated 2020-02-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 5 ++++- R/blca.boot.R | 2 +- man/Alzheimer.Rd | 2 +- man/blca.boot.Rd | 8 ++++---- 6 files changed, 19 insertions(+), 16 deletions(-)