Title: A Seamless Integration of 'Eviews' and R
Description: It allows running 'EViews'(<https://eviews.com>) program from R, R Markdown and Quarto documents. 'EViews' (Econometric Views) is a statistical software for Econometric analysis. This package integrates 'EViews' and R and also serves as an 'EViews' Knit-Engine for 'knitr' package. Write all your 'EViews' commands in R, R Markdown or Quarto documents.
Author: Sagiru Mati [aut, cre]
Maintainer: Sagiru Mati <smati@smati.com.ng>
Diff between EviewsR versions 0.1.2 dated 2022-05-01 and 0.1.3 dated 2022-08-09
EviewsR-0.1.2/EviewsR/demo/export.R |only EviewsR-0.1.2/EviewsR/demo/import.R |only EviewsR-0.1.2/EviewsR/inst/examples/R-files/export.R |only EviewsR-0.1.2/EviewsR/inst/examples/R-files/import.R |only EviewsR-0.1.2/EviewsR/vignettes/tools |only EviewsR-0.1.3/EviewsR/DESCRIPTION | 10 EviewsR-0.1.3/EviewsR/MD5 | 178 +- EviewsR-0.1.3/EviewsR/NAMESPACE | 13 EviewsR-0.1.3/EviewsR/NEWS.md | 29 EviewsR-0.1.3/EviewsR/R/create_object.R | 67 EviewsR-0.1.3/EviewsR/R/eng_eviews.R | 521 +++++++ EviewsR-0.1.3/EviewsR/R/eviews_graph.R | 349 +++-- EviewsR-0.1.3/EviewsR/R/eviews_import.R | 77 - EviewsR-0.1.3/EviewsR/R/eviews_pagesave.R | 42 EviewsR-0.1.3/EviewsR/R/eviews_wfcreate.R | 65 EviewsR-0.1.3/EviewsR/R/eviews_wfsave.R | 45 EviewsR-0.1.3/EviewsR/R/exec_commands.R | 55 EviewsR-0.1.3/EviewsR/R/export.R | 5 EviewsR-0.1.3/EviewsR/R/export_dataframe.R |only EviewsR-0.1.3/EviewsR/R/import.R | 40 EviewsR-0.1.3/EviewsR/R/import_equation.R |only EviewsR-0.1.3/EviewsR/R/import_graph.R |only EviewsR-0.1.3/EviewsR/R/import_kable.R |only EviewsR-0.1.3/EviewsR/R/import_series.R |only EviewsR-0.1.3/EviewsR/R/import_table.R | 136 + EviewsR-0.1.3/EviewsR/R/import_workfile.R |only EviewsR-0.1.3/EviewsR/R/rwalk.R | 78 - EviewsR-0.1.3/EviewsR/R/set_eviews_path.R | 9 EviewsR-0.1.3/EviewsR/R/utils.R | 93 + EviewsR-0.1.3/EviewsR/README.md | 686 +++++++--- EviewsR-0.1.3/EviewsR/build/vignette.rds |binary EviewsR-0.1.3/EviewsR/demo/00Index | 10 EviewsR-0.1.3/EviewsR/demo/create_object.R | 8 EviewsR-0.1.3/EviewsR/demo/eviews_graph.R | 14 EviewsR-0.1.3/EviewsR/demo/eviews_import.R | 9 EviewsR-0.1.3/EviewsR/demo/eviews_pagesave.R | 2 EviewsR-0.1.3/EviewsR/demo/eviews_wfcreate.R | 9 EviewsR-0.1.3/EviewsR/demo/eviews_wfsave.R | 2 EviewsR-0.1.3/EviewsR/demo/exec_commands.R | 21 EviewsR-0.1.3/EviewsR/demo/export_dataframe.R |only EviewsR-0.1.3/EviewsR/demo/import_equation.R |only EviewsR-0.1.3/EviewsR/demo/import_graph.R |only EviewsR-0.1.3/EviewsR/demo/import_kable.R |only EviewsR-0.1.3/EviewsR/demo/import_series.R |only EviewsR-0.1.3/EviewsR/demo/import_table.R | 22 EviewsR-0.1.3/EviewsR/demo/import_workfile.R |only EviewsR-0.1.3/EviewsR/demo/rwalk.R | 24 EviewsR-0.1.3/EviewsR/inst/EVIEWS/EviewsR.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/EviewsR1.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/EviewsRLogo.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/EviewsR_hex.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/Eviewsr_test.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/UNTITLED.wf1 |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/eviews.pdf |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/eviews.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/eviews1.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/eviews_logo.jpg |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/hexcode.R |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/x_graph.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/y_graph.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/z_graph.png |only EviewsR-0.1.3/EviewsR/inst/EVIEWS/zyx.png |only EviewsR-0.1.3/EviewsR/inst/doc/EviewsR.R | 180 ++ EviewsR-0.1.3/EviewsR/inst/doc/EviewsR.Rmd | 447 +++++- EviewsR-0.1.3/EviewsR/inst/doc/EviewsR.html | 379 +++-- EviewsR-0.1.3/EviewsR/inst/eng_eviews.R |only EviewsR-0.1.3/EviewsR/inst/examples/EviewsR.Rmd | 458 +++++- EviewsR-0.1.3/EviewsR/inst/examples/EviewsR.pdf |only EviewsR-0.1.3/EviewsR/inst/examples/EviewsR.qmd |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/create_object.R | 8 EviewsR-0.1.3/EviewsR/inst/examples/R-files/eviews_graph.R | 14 EviewsR-0.1.3/EviewsR/inst/examples/R-files/eviews_import.R | 9 EviewsR-0.1.3/EviewsR/inst/examples/R-files/eviews_pagesave.R | 2 EviewsR-0.1.3/EviewsR/inst/examples/R-files/eviews_wfcreate.R | 9 EviewsR-0.1.3/EviewsR/inst/examples/R-files/eviews_wfsave.R | 2 EviewsR-0.1.3/EviewsR/inst/examples/R-files/exec_commands.R | 21 EviewsR-0.1.3/EviewsR/inst/examples/R-files/export_dataframe.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_equation.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_graph.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_kable.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_series.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_table.R | 22 EviewsR-0.1.3/EviewsR/inst/examples/R-files/import_workfile.R |only EviewsR-0.1.3/EviewsR/inst/examples/R-files/rwalk.R | 24 EviewsR-0.1.3/EviewsR/inst/figures |only EviewsR-0.1.3/EviewsR/inst/rmarkdown/templates/EviewsR/skeleton/skeleton.Rmd | 509 +++---- EviewsR-0.1.3/EviewsR/man/EviewsR-package.Rd | 8 EviewsR-0.1.3/EviewsR/man/create_object.Rd | 56 EviewsR-0.1.3/EviewsR/man/eng_eviews.Rd | 17 EviewsR-0.1.3/EviewsR/man/eviews_graph.Rd | 71 - EviewsR-0.1.3/EviewsR/man/eviews_import.Rd | 54 EviewsR-0.1.3/EviewsR/man/eviews_pagesave.Rd | 46 EviewsR-0.1.3/EviewsR/man/eviews_wfcreate.Rd | 41 EviewsR-0.1.3/EviewsR/man/eviews_wfsave.Rd | 46 EviewsR-0.1.3/EviewsR/man/exec_commands.Rd | 43 EviewsR-0.1.3/EviewsR/man/export.Rd | 24 EviewsR-0.1.3/EviewsR/man/export_dataframe.Rd |only EviewsR-0.1.3/EviewsR/man/import.Rd | 42 EviewsR-0.1.3/EviewsR/man/import_equation.Rd |only EviewsR-0.1.3/EviewsR/man/import_graph.Rd |only EviewsR-0.1.3/EviewsR/man/import_kable.Rd |only EviewsR-0.1.3/EviewsR/man/import_series.Rd |only EviewsR-0.1.3/EviewsR/man/import_table.Rd | 139 -- EviewsR-0.1.3/EviewsR/man/import_workfile.Rd |only EviewsR-0.1.3/EviewsR/man/rwalk.Rd | 57 EviewsR-0.1.3/EviewsR/man/set_eviews_path.Rd | 12 EviewsR-0.1.3/EviewsR/vignettes/EviewsR.Rmd | 447 +++++- 107 files changed, 4162 insertions(+), 1644 deletions(-)
Title: Create Codebooks from Data Frames
Description: Quickly and easily create codebooks (i.e. data dictionaries) directly from a data frame.
Author: Brad Cannell [aut, cre, cph]
Maintainer: Brad Cannell <brad.cannell@gmail.com>
Diff between codebookr versions 0.1.4 dated 2022-07-18 and 0.1.5 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/cb_summary_stats_few_cats.R | 2 +- R/cb_summary_stats_time.R | 7 ++++--- R/cb_theme_col_attr.R | 2 +- R/codebook.R | 1 + README.md | 13 ++++++++++--- 9 files changed, 38 insertions(+), 20 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Romain Francois [ctb, cph] ,
Francesc Alted [ctb, cph] ,
Bryce Chamberlain [ctb] ,
Sal [...truncated...]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.3 dated 2022-02-22 and 0.25.4 dated 2022-08-09
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 1 + R/qs-package.R | 1 + R/zzz.R | 2 +- README.md | 3 --- build/vignette.rds |binary data/starnames.rda |binary inst/doc/vignette.R | 3 --- inst/doc/vignette.html | 8 +++----- inst/doc/vignette.rmd | 3 --- src/qs_common.h | 12 +++++++++--- src/qs_deserialize_common.h | 29 +++++++++++++++++++---------- src/qs_serialize_common.h | 6 +++--- vignettes/vignette.rmd | 3 --- 16 files changed, 61 insertions(+), 54 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] ,
Alessandro Gasparini [ctb] ,
Benjie Gillam [ctb],
Claus Thorn Ekstroem [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Deo Salil [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] ,
Inaki Ucar [ctb] ,
John Little [ctb],
Joselyn Ch [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.25 dated 2022-06-13 and 0.26 dated 2022-08-09
DESCRIPTION | 8 +++++--- MD5 | 8 ++++---- R/utils.R | 4 ++-- build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/js/data-uri.js | 4 ++-- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Wrapper for the 'Intro.js' Library
Description: A wrapper for the 'Intro.js' library (For more info: <https://introjs.com/>).
This package makes it easy to include step-by-step introductions, and clickable hints in a 'Shiny'
application. It supports both static introductions in the UI, and programmatic introductions from
the server-side.
Author: Carl Ganz [aut, cre],
Afshin Mehrabani [ctb, cph]
Maintainer: Carl Ganz <carlganz@gmail.com>
Diff between rintrojs versions 0.3.0 dated 2021-06-06 and 0.3.2 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 14 +++++++++++++- R/introjs.R | 2 +- README.md | 17 ++++++----------- inst/javascript/rintro.js | 4 ++-- tests/testthat/test_introBox.R | 15 ++++++--------- 7 files changed, 38 insertions(+), 34 deletions(-)
Title: Creates Valid HTML5 Strings
Description: Generates valid HTML tag strings for HTML5 elements documented by Mozilla.
Attributes are passed as named lists, with names being the attribute name and values being the attribute value.
Attribute values are automatically double-quoted. To declare a DOCTYPE, wrap html() with function doctype().
Mozilla's documentation for HTML5 is available here: <https://developer.mozilla.org/en-US/docs/Web/HTML/Element>.
Elements marked as obsolete are not included.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between html5 versions 1.0.0 dated 2022-06-22 and 1.0.1 dated 2022-08-09
DESCRIPTION | 6 +-- MD5 | 4 +- R/html5.R | 110 ++++++++++++++++++++++++++++++++++++++---------------------- 3 files changed, 76 insertions(+), 44 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp],
A [...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-7 dated 2021-10-18 and 0.7-8 dated 2022-08-09
DESCRIPTION | 13 +- MD5 | 42 ++++---- NAMESPACE | 1 R/determine.subgroups.R | 2 R/gimme.R | 30 +++-- R/indSEM.R | 11 +- R/indiv.search.ms.R | 4 R/prune.paths.R | 2 R/return.zs.R | 23 ++-- R/search.paths.ms.R | 2 R/setup.R | 7 - R/simulateData.R |only R/subgroupStage.R | 2 build/vignette.rds |binary data/HRFsim.rda |binary data/ms.fit.rda |binary data/simData.rda |binary data/simDataLV.rda |binary data/ts.rda |binary inst/doc/gimme_vignette.html | 219 +++++++++++++++++++++++++++++-------------- man/gimmeSEM.Rd | 13 +- man/return.zs.Rd | 5 man/simulateVAR.Rd |only 23 files changed, 240 insertions(+), 136 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
SpryMedia Limited [ctb, cph] ,
Brian Reavis [ctb, cph] ,
Leon Gersen [ctb, cph] ,
Bartek Szopka [ct [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.23 dated 2022-05-10 and 0.24 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/datatables.R | 3 +++ R/utils.R | 19 +++++++++++++++++++ build/vignette.rds |binary inst/doc/DT.html | 11 ++++++----- inst/htmlwidgets/datatables.js | 3 ++- 7 files changed, 40 insertions(+), 16 deletions(-)
Title: Bayesian Change-Point Detection and Time Series Decomposition
Description: Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications include its use to identify regime shifts in ecological data, map forest disturbance and land degradation from satellite imagery, detect market trends in economic data, pinpoint anomaly and extreme events in climate data, and unravel system dynamics in biological data. Details on BEAST are reported in Zhao et al. (2019) <doi:10.1016/j.rse.2019.04.034>.
Author: Kaiguang Zhao [aut, cre],
Tongxi Hu [aut],
Yang Li [aut],
Jack Dongarra [ctb],
Cleve Moler [ctb]
Maintainer: Kaiguang Zhao <zhao.1423@osu.edu>
Diff between Rbeast versions 0.9.4 dated 2022-05-18 and 0.9.5 dated 2022-08-09
Rbeast-0.9.4/Rbeast/NEWS |only Rbeast-0.9.5/Rbeast/DESCRIPTION | 8 Rbeast-0.9.5/Rbeast/MD5 | 83 Rbeast-0.9.5/Rbeast/NEWS.md |only Rbeast-0.9.5/Rbeast/R/beast.R | 4 Rbeast-0.9.5/Rbeast/R/geeLandsat.R | 2 Rbeast-0.9.5/Rbeast/R/plot.beast.R | 31 Rbeast-0.9.5/Rbeast/inst/CITATION |only Rbeast-0.9.5/Rbeast/man/beast.Rd | 52 Rbeast-0.9.5/Rbeast/man/beast123.Rd | 84 Rbeast-0.9.5/Rbeast/man/plot.beast.Rd | 4 Rbeast-0.9.5/Rbeast/src/abc_000_macro.h | 8 Rbeast-0.9.5/Rbeast/src/abc_common.c | 3 Rbeast-0.9.5/Rbeast/src/abc_ide_util.c | 172 - Rbeast-0.9.5/Rbeast/src/abc_ide_util.h | 3 Rbeast-0.9.5/Rbeast/src/abc_mat.c | 30 Rbeast-0.9.5/Rbeast/src/abc_mat.h | 3 Rbeast-0.9.5/Rbeast/src/abc_math_avx.c | 3 Rbeast-0.9.5/Rbeast/src/abc_mcmc.c | 1 Rbeast-0.9.5/Rbeast/src/abc_mcmc.h | 4 Rbeast-0.9.5/Rbeast/src/abc_mem.c | 64 Rbeast-0.9.5/Rbeast/src/abc_mem.h | 6 Rbeast-0.9.5/Rbeast/src/abc_vec.c | 21 Rbeast-0.9.5/Rbeast/src/abc_vec.h | 7 Rbeast-0.9.5/Rbeast/src/abc_vec_avx2.c | 80 Rbeast-0.9.5/Rbeast/src/abc_vec_avx512.c | 80 Rbeast-0.9.5/Rbeast/src/abc_vec_generic.c | 71 Rbeast-0.9.5/Rbeast/src/beastv2_COREV4.c | 131 Rbeast-0.9.5/Rbeast/src/beastv2_COREV4_gui.c | 1697 +++++------- Rbeast-0.9.5/Rbeast/src/beastv2_COREV4_mthrd.c | 131 Rbeast-0.9.5/Rbeast/src/beastv2_basis_allocinitmem.c | 47 Rbeast-0.9.5/Rbeast/src/beastv2_basis_gensegment.c | 3 Rbeast-0.9.5/Rbeast/src/beastv2_basis_updateKsKe_prec0123.c | 3 Rbeast-0.9.5/Rbeast/src/beastv2_func.h | 23 Rbeast-0.9.5/Rbeast/src/beastv2_func_q.c | 10 Rbeast-0.9.5/Rbeast/src/beastv2_header.h | 21 Rbeast-0.9.5/Rbeast/src/beastv2_header_solaris.h | 24 Rbeast-0.9.5/Rbeast/src/beastv2_io_in_args.c | 2 Rbeast-0.9.5/Rbeast/src/beastv2_io_out_allocmem_q.c | 249 - Rbeast-0.9.5/Rbeast/src/beastv2_model_allocinit.h | 1 Rbeast-0.9.5/Rbeast/src/beastv2_model_allocinit_q.c | 126 Rbeast-0.9.5/Rbeast/src/beastv2_prior_precfunc.c | 86 Rbeast-0.9.5/Rbeast/src/beastv2_prior_precfunc.h | 1 Rbeast-0.9.5/Rbeast/src/beastv2_xxyy_allocmem_q.c | 13 44 files changed, 1816 insertions(+), 1576 deletions(-)
Title: Population Downscaling
Description: Downscaling of population data obtained
by census surveys using areal interpolation. Given a
set of source zone polygons such as
census tracts or city blocks alongside with population counts and a
target zone of incogruent yet superimposed polygon features (such as
individual buildings) populR transforms population counts from the
former to the latter using Areal Weighting and Volume Weighting
Interpolation methods.
Author: Marios Batsaris
Maintainer: Marios Batsaris <m.batsaris@aegean.gr>
Diff between populR versions 0.1.5 dated 2022-07-11 and 0.1.6 dated 2022-08-09
populR-0.1.5/populR/R/pp_rmse.R |only populR-0.1.5/populR/man/pp_rmse.Rd |only populR-0.1.5/populR/tests/testthat/test-pp_rmse.R |only populR-0.1.6/populR/DESCRIPTION | 20 +++-- populR-0.1.6/populR/MD5 | 39 ++++++----- populR-0.1.6/populR/NAMESPACE | 2 populR-0.1.6/populR/R/pp_compare.R |only populR-0.1.6/populR/R/pp_estimate.R | 44 +++++++----- populR-0.1.6/populR/R/pp_round.R | 63 +++++++++--------- populR-0.1.6/populR/R/src.R | 6 - populR-0.1.6/populR/R/trg.R | 14 ++-- populR-0.1.6/populR/build |only populR-0.1.6/populR/data/trg.rda |binary populR-0.1.6/populR/inst/doc |only populR-0.1.6/populR/man/pp_compare.Rd |only populR-0.1.6/populR/man/pp_estimate.Rd | 34 ++++++--- populR-0.1.6/populR/man/pp_round.Rd | 17 ++-- populR-0.1.6/populR/man/src.Rd | 6 - populR-0.1.6/populR/man/trg.Rd | 14 ++-- populR-0.1.6/populR/tests/testthat/Rplots.pdf |binary populR-0.1.6/populR/tests/testthat/test-pp_compare.R |only populR-0.1.6/populR/tests/testthat/test-pp_estimate.R | 22 +++--- populR-0.1.6/populR/tests/testthat/test-pp_round.R | 20 ++--- populR-0.1.6/populR/vignettes |only 24 files changed, 165 insertions(+), 136 deletions(-)
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods,
such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
databases and clonotype tracking in vaccination and cancer studies. A successor to our
previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Author: Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [aut],
Eugene Rumynskiy [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut],
Maria Samokhina [aut],
Anna Lorenc [ctb],
Daniel J. Moore [ctb],
Victor Greiff [ctb],
ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <support@immunomind.io>
Diff between immunarch versions 0.6.9 dated 2022-05-30 and 0.7.0 dated 2022-08-09
DESCRIPTION | 14 - MD5 | 95 +++++----- NAMESPACE | 20 ++ R/align_lineage.R | 123 ++++++++------ R/distance.R | 2 R/germline.R | 252 ++++++++++++++++++++++------- R/immunr_data_format.R | 7 R/io-parsers.R | 6 R/io-utility.R | 12 - R/kmers.R | 16 - R/phylip.R | 269 ++++++++++++++++++++++++++----- R/seqCluster.R | 2 R/somatic_hypermutation.R |only R/tools.R | 54 +++++- R/vis.R | 110 +++++++++++- README.md | 44 ++--- data/bcrdata.rda |binary inst/doc/v1_introduction.Rmd | 32 +-- inst/doc/v1_introduction.html | 36 ++-- inst/doc/v2_data.R | 4 inst/doc/v2_data.Rmd | 42 ++-- inst/doc/v2_data.html | 44 ++--- man/bunch_translate.Rd | 4 man/getKmers.Rd | 10 - man/repAlignLineage.Rd | 34 ++- man/repClonalFamily.Rd | 19 +- man/repGermline.Rd | 46 +++-- man/repSomaticHypermutation.Rd |only man/seqCluster.Rd | 1 man/seqDist.Rd | 1 man/split_to_kmers.Rd | 6 man/vis.Rd | 4 man/vis.clonal_family.Rd |only man/vis.clonal_family_tree.Rd |only man/vis.step_failure_ignored.Rd |only vignettes/v1_introduction.Rmd | 32 +-- vignettes/v2_data.Rmd | 42 ++-- vignettes/web_only/BCRpipeline.Rmd |only vignettes/web_only/clustering.Rmd |only vignettes/web_only/load_10x.Rmd | 6 vignettes/web_only/load_mixcr.Rmd | 16 - vignettes/web_only/repFilter_v3.Rmd | 12 - vignettes/web_only/v10_prop.Rmd | 4 vignettes/web_only/v11_db.Rmd | 26 +- vignettes/web_only/v21_singlecell.Rmd | 6 vignettes/web_only/v3_basic_analysis.Rmd | 34 +-- vignettes/web_only/v4_overlap.Rmd | 4 vignettes/web_only/v5_gene_usage.Rmd | 4 vignettes/web_only/v6_diversity.Rmd | 8 vignettes/web_only/v7_fixvis.Rmd | 4 vignettes/web_only/v8_tracking.Rmd | 20 +- vignettes/web_only/v9_kmers.Rmd | 24 +- 52 files changed, 1053 insertions(+), 498 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] ,
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevičius [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.15 dated 2022-02-18 and 0.16 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NEWS.md | 5 +++++ R/graphics.r | 12 +++++++----- README.md | 6 +++++- tests/testthat/ggplot-empty-1.r |only tests/testthat/ggplot-empty-2.r |only tests/testthat/test-graphics.r | 8 ++++++++ 8 files changed, 36 insertions(+), 15 deletions(-)
Title: Estimation of Time Varying Reproduction Numbers and Restored
Incidence Curves Using Variational Techniques
Description: Estimation, by inverting a renewal equation,
of time-varying reproduction numbers and restored incidence curves with
festive days and weekly biases corrected as described in
Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and
Alvarez et al. (2022) <doi:10.3390/biology11040540>. EpiInvert can manage
daily incidence data and weekly aggregated incidence data. This version of the
package also includes EpiInvertForecast, a learning method for the short time
forecast of the restored incidence curve.
Author: Luis Alvarez [aut, cre] ,
Jean-David Morel [ctb] ,
Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>
Diff between EpiInvert versions 0.1.1 dated 2022-05-20 and 0.2.0 dated 2022-08-09
DESCRIPTION | 11 +- MD5 | 42 ++++---- NAMESPACE | 16 +-- NEWS.md | 12 ++ R/EpiInvert.R | 144 +++++++++++++++++++++++++++++ R/RcppExports.R | 8 + R/data.R | 33 ++++++ R/plot.R | 95 ++++++++++++++++++- R/select_params.R | 3 README.md | 11 +- data/festives.rda |binary data/incidence_weekly_aggregated.rda |only data/restored_incidence_database.rda |only man/EpiInvert.Rd | 7 + man/EpiInvertForecast.Rd |only man/EpiInvertForecast_plot.Rd |only man/figures/README-fig1-1.png |binary man/incidence_weekly_aggregated.Rd |only man/restored_incidence_database.Rd |only src/EpiInvertCore_q_variable.cpp | 154 ++++++++++++++++++++++++++++---- src/EpiInvertCore_q_variable.h | 18 +++ src/EpiInvert_main.cpp | 71 ++++++++++++++ src/RcppExports.cpp | 24 ++++ src/utilities.cpp | 16 +++ tests/testthat/test-USA_parametric_si.R | 13 ++ 25 files changed, 604 insertions(+), 74 deletions(-)
Title: Collective Matrix Factorization
Description: Collective matrix factorization (CMF) finds joint low-rank
representations for a collection of matrices with shared row or column
entities. This code learns a variational Bayesian approximation for CMF,
supporting multiple likelihood potentials and missing data, while
identifying both factors shared by multiple matrices and factors private
for each matrix. For further details on the method see
Klami et al. (2014) <arXiv:1312.5921>.
The package can also be used to learn Bayesian canonical correlation
analysis (CCA) and group factor analysis (GFA) models, both of which are
special cases of CMF. This is likely to be useful for people looking for
CCA and GFA solutions supporting missing data and non-Gaussian likelihoods.
See Klami et al. (2013) <https://research.cs.aalto.fi/pml/online-papers/klami13a.pdf>
and Virtanen et al. (2012) <http://proceedings.mlr.press/v22/virtanen12.html>
for details on Bayesian CCA and GFA, respectively.
Author: Arto Klami [aut],
Lauri Vaere [aut],
Felix Held [ctb, cre]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between CMF versions 1.0.2 dated 2020-03-13 and 1.0.3 dated 2022-08-09
CMF-1.0.2/CMF/R/RcppExports.R |only CMF-1.0.2/CMF/src/RcppExports.cpp |only CMF-1.0.3/CMF/DESCRIPTION | 23 CMF-1.0.3/CMF/MD5 | 27 CMF-1.0.3/CMF/NAMESPACE | 2 CMF-1.0.3/CMF/R/CMF.R | 1054 +++++++++++++++++------------- CMF-1.0.3/CMF/R/cpp11.R |only CMF-1.0.3/CMF/README.md |only CMF-1.0.3/CMF/man/CMF-package.Rd | 126 +-- CMF-1.0.3/CMF/man/CMF.Rd | 67 - CMF-1.0.3/CMF/man/getCMFopts.Rd | 61 - CMF-1.0.3/CMF/man/matrix_to_triplets.Rd | 12 CMF-1.0.3/CMF/man/p_check_sparsity.Rd |only CMF-1.0.3/CMF/man/p_gradUsparseWrapper.Rd |only CMF-1.0.3/CMF/man/predictCMF.Rd | 11 CMF-1.0.3/CMF/man/triplets_to_matrix.Rd | 10 CMF-1.0.3/CMF/src/cpp11.cpp |only CMF-1.0.3/CMF/src/helper.cpp | 268 ++++--- 18 files changed, 919 insertions(+), 742 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clift [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.27 dated 2022-06-14 and 0.28 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/utils.R | 2 -- build/vignette.rds |binary inst/resources/gitbook/css/style.css | 10 ++++------ inst/resources/gitbook/js/plugin-clipboard.js | 6 +++++- inst/templates/bs4_book.html | 2 +- inst/templates/gitbook.html | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.10 dated 2022-05-10 and 1.11 dated 2022-08-09
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- R/check.R | 10 +++++ R/hugo.R | 92 ++++++++++++++++++++++++++---------------------- R/render.R | 3 + R/serve.R | 27 ++++++-------- R/utils.R | 8 ---- inst/scripts/new_post.R | 6 --- man/hugo_cmd.Rd | 20 +++++----- 9 files changed, 99 insertions(+), 91 deletions(-)
Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an
Rd file to a list, create the 'roxygen' documentation and update the original
R script (e.g. the one containing the definition of the function)
accordingly. This package also provides utilities that can help developers
build packages using 'roxygen' more easily. The 'formatR' package can be used
to reformat the R code in the examples sections so that the code will be
more readable.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between Rd2roxygen versions 1.13 dated 2022-03-02 and 1.14 dated 2022-08-09
DESCRIPTION | 8 - MD5 | 12 - NEWS.md | 4 R/rd2roxygen.R | 4 build/vignette.rds |binary inst/doc/Rd2roxygen.html | 298 ++++++++++++++++++++++++++++++++++++++++++++--- man/parse_file.Rd | 2 7 files changed, 297 insertions(+), 31 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb], Shaobo Li [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 2.3 dated 2022-03-22 and 3.0 dated 2022-08-09
rqPen-2.3/rqPen/man/LASSO.fit.Rd |only rqPen-2.3/rqPen/man/LASSO.fit.nonpen.Rd |only rqPen-2.3/rqPen/man/QICD.group.Rd |only rqPen-2.3/rqPen/man/QICD.master.Rd |only rqPen-2.3/rqPen/man/check.Rd |only rqPen-2.3/rqPen/man/getRho.Rd |only rqPen-2.3/rqPen/man/get_coef_pen.Rd |only rqPen-2.3/rqPen/man/groupMultLambda.Rd |only rqPen-2.3/rqPen/man/group_derivs.Rd |only rqPen-2.3/rqPen/man/lasso.Rd |only rqPen-2.3/rqPen/man/mcp.Rd |only rqPen-2.3/rqPen/man/mcp_deriv.Rd |only rqPen-2.3/rqPen/man/model_eval.Rd |only rqPen-2.3/rqPen/man/nonzero.Rd |only rqPen-2.3/rqPen/man/nonzero.cv.rq.group.pen.Rd |only rqPen-2.3/rqPen/man/pos_part.Rd |only rqPen-2.3/rqPen/man/qaSIS.Rd |only rqPen-2.3/rqPen/man/qbic.Rd |only rqPen-2.3/rqPen/man/randomly_assign.Rd |only rqPen-2.3/rqPen/man/rq.group.lin.prog.Rd |only rqPen-2.3/rqPen/man/rq.lasso.fit.mult.Rd |only rqPen-2.3/rqPen/man/rqPen-package.Rd |only rqPen-2.3/rqPen/man/scad.Rd |only rqPen-2.3/rqPen/man/scad_deriv.Rd |only rqPen-2.3/rqPen/man/square.Rd |only rqPen-2.3/rqPen/man/transform_coefs.Rd |only rqPen-3.0/rqPen/DESCRIPTION | 22 rqPen-3.0/rqPen/MD5 | 100 - rqPen-3.0/rqPen/NAMESPACE | 115 - rqPen-3.0/rqPen/NEWS | 21 rqPen-3.0/rqPen/R/QICD_functions.R | 52 rqPen-3.0/rqPen/R/mainFunctions.R | 1891 ++++++++++++++++++++++-- rqPen-3.0/rqPen/R/rqPen.R |only rqPen-3.0/rqPen/R/workHorse.R | 1350 ++++++++++++++--- rqPen-3.0/rqPen/README.md |only rqPen-3.0/rqPen/build |only rqPen-3.0/rqPen/inst |only rqPen-3.0/rqPen/man/QICD.Rd | 106 - rqPen-3.0/rqPen/man/QICD.nonpen.Rd | 101 - rqPen-3.0/rqPen/man/beta_plots.Rd | 64 rqPen-3.0/rqPen/man/bytau.plot.Rd |only rqPen-3.0/rqPen/man/bytau.plot.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/bytau.plot.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/coef.cv.rq.group.pen.Rd | 47 rqPen-3.0/rqPen/man/coef.cv.rq.pen.Rd | 48 rqPen-3.0/rqPen/man/coef.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/coef.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/cv.rq.group.pen.Rd | 146 + rqPen-3.0/rqPen/man/cv.rq.pen.Rd | 143 + rqPen-3.0/rqPen/man/cv_plots.Rd | 52 rqPen-3.0/rqPen/man/plot.cv.rq.group.pen.Rd | 25 rqPen-3.0/rqPen/man/plot.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/plot.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/predict.cv.rq.pen.Rd | 29 rqPen-3.0/rqPen/man/predict.qic.select.Rd |only rqPen-3.0/rqPen/man/predict.rq.pen.Rd | 26 rqPen-3.0/rqPen/man/predict.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/predict.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/print.cv.rq.pen.Rd | 28 rqPen-3.0/rqPen/man/print.qic.select.Rd |only rqPen-3.0/rqPen/man/print.rq.pen.Rd | 24 rqPen-3.0/rqPen/man/print.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/print.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/qic.Rd |only rqPen-3.0/rqPen/man/qic.select.Rd |only rqPen-3.0/rqPen/man/qic.select.rq.pen.seq.Rd |only rqPen-3.0/rqPen/man/qic.select.rq.pen.seq.cv.Rd |only rqPen-3.0/rqPen/man/rq.group.fit.Rd | 114 - rqPen-3.0/rqPen/man/rq.group.pen.Rd |only rqPen-3.0/rqPen/man/rq.group.pen.cv.Rd |only rqPen-3.0/rqPen/man/rq.lasso.fit.Rd | 121 - rqPen-3.0/rqPen/man/rq.nc.fit.Rd | 139 + rqPen-3.0/rqPen/man/rq.pen.Rd |only rqPen-3.0/rqPen/man/rq.pen.cv.Rd |only rqPen-3.0/rqPen/man/rqPen.Rd |only rqPen-3.0/rqPen/src/QCD.cpp | 46 76 files changed, 3890 insertions(+), 920 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 ML framework with spatio-temporal resampling
methods to account for the presence of spatiotemporal autocorrelation
(STAC) in predictor variables. STAC may cause highly biased
performance estimates in cross-validation if ignored.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.0.1 dated 2022-06-22 and 2.0.2 dated 2022-08-09
DESCRIPTION | 8 MD5 | 142 ++-- NAMESPACE | 1 NEWS.md | 10 R/TaskClassifST.R | 56 + R/TaskRegrST.R | 47 + R/as_task_classif_st.R | 23 R/as_task_regr_st.R | 23 R/autoplot.R | 18 R/autoplot_spcv_cstf.R | 8 R/bibentries.R | 2 R/helper.R | 35 + R/zzz.R | 57 + README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mlr3spatiotempcv.R | 14 inst/doc/mlr3spatiotempcv.Rmd | 112 +-- inst/doc/mlr3spatiotempcv.html | 300 +++++----- inst/doc/spatiotemp-viz.html | 111 +-- inst/references.bib | 2 man/TaskClassifST.Rd | 54 + man/TaskRegrST.Rd | 46 - man/as_task_classif_st.Rd | 5 man/as_task_regr_st.Rd | 5 man/autoplot.ResamplingCV.Rd | 2 man/autoplot.ResamplingCustomCV.Rd | 2 man/autoplot.ResamplingSpCVBlock.Rd | 2 man/autoplot.ResamplingSpCVBuffer.Rd | 2 man/autoplot.ResamplingSpCVCoords.Rd | 2 man/autoplot.ResamplingSpCVDisc.Rd | 2 man/autoplot.ResamplingSpCVEnv.Rd | 2 man/autoplot.ResamplingSpCVTiles.Rd | 2 man/autoplot.ResamplingSptCVCluto.Rd | 2 man/autoplot.ResamplingSptCVCstf.Rd | 2 man/mlr3spatiotempcv-package.Rd | 4 man/mlr_resamplings_repeated_spcv_block.Rd | 10 man/mlr_resamplings_repeated_spcv_coords.Rd | 10 man/mlr_resamplings_repeated_spcv_disc.Rd | 10 man/mlr_resamplings_repeated_spcv_env.Rd | 10 man/mlr_resamplings_repeated_spcv_tiles.Rd | 10 man/mlr_resamplings_repeated_sptcv_cluto.Rd | 12 man/mlr_resamplings_repeated_sptcv_cstf.Rd | 12 man/mlr_resamplings_spcv_block.Rd | 10 man/mlr_resamplings_spcv_buffer.Rd | 10 man/mlr_resamplings_spcv_coords.Rd | 10 man/mlr_resamplings_spcv_disc.Rd | 10 man/mlr_resamplings_spcv_env.Rd | 10 man/mlr_resamplings_spcv_tiles.Rd | 10 man/mlr_resamplings_sptcv_cluto.Rd | 12 man/mlr_resamplings_sptcv_cstf.Rd | 10 tests/testthat/_snaps/2-autoplot/repsptcvcstf-2d-space-var-fold-1-2-rep-2.svg | 112 +-- tests/testthat/_snaps/2-autoplot/repsptcvcstf-2d-space-var-fold-1-rep-2.svg | 100 +-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-all-test-sets.svg | 88 +- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1-2.svg | 210 +++---- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1.svg | 140 ++-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-all-test-sets.svg | 88 +- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2-rep-2.svg | 72 +- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2-sample-fold-n.svg | 240 ++++---- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2.svg | 270 ++++----- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-rep-2.svg | 100 +-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-sample-fold-n.svg | 140 ++-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1.svg | 130 ++-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-sample-fold-n.svg | 80 +- tests/testthat/helper.R | 126 ---- tests/testthat/test-1-autoplot.R | 1 tests/testthat/test-ResamplingRepeatedSptCVCstf.R | 36 - tests/testthat/test-ResamplingSptCVCstf.R | 36 - tests/testthat/test-TaskClassifST.R | 28 tests/testthat/test-TaskRegrST.R | 14 tests/testthat/test-mlr3pipelines-graph-integration.R | 6 vignettes/mlr3spatiotempcv.Rmd | 112 +-- 72 files changed, 1732 insertions(+), 1658 deletions(-)
More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 1.0.4 dated 2021-12-05 and 1.0.5 dated 2022-08-09
DESCRIPTION | 10 MD5 | 57 - NAMESPACE | 1 NEWS.md | 13 R/ff_permute.R | 14 R/finalfit.R | 528 ++++++--------- R/finalfit_internal_functions.R | 56 + R/fit2df.R | 2 R/or_plot.R | 2 R/summaryfactorlist.R | 73 +- README.md | 1 inst/doc/all_tables_examples.R | 25 inst/doc/all_tables_examples.Rmd | 51 + inst/doc/all_tables_examples.html | 1280 +++++++++++++++++++------------------- inst/doc/bootstrap.html | 23 inst/doc/data_prep.html | 4 inst/doc/export.html | 1 inst/doc/finalfit.html | 1 inst/doc/missing.R | 18 inst/doc/missing.Rmd | 18 inst/doc/missing.html | 171 ++--- inst/doc/survival.html | 9 man/ff_parse_formula.Rd |only man/finalfit.Rd | 16 man/fit2df.Rd | 1 man/format_n_percent.Rd | 4 man/rm_empty_block.Rd | 3 man/summary_factorlist.Rd | 18 vignettes/all_tables_examples.Rmd | 51 + vignettes/missing.Rmd | 18 30 files changed, 1308 insertions(+), 1161 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 1.2.0 dated 2022-07-23 and 1.3.0 dated 2022-08-09
BranchGLM-1.2.0/BranchGLM/src/ParVariableSelection.cpp |only BranchGLM-1.3.0/BranchGLM/DESCRIPTION | 6 BranchGLM-1.3.0/BranchGLM/MD5 | 42 - BranchGLM-1.3.0/BranchGLM/NAMESPACE | 1 BranchGLM-1.3.0/BranchGLM/R/BranchGLM.R | 13 BranchGLM-1.3.0/BranchGLM/R/RcppExports.R | 20 BranchGLM-1.3.0/BranchGLM/R/VariableSelection.R | 63 +- BranchGLM-1.3.0/BranchGLM/build/vignette.rds |binary BranchGLM-1.3.0/BranchGLM/inst/doc/BranchGLM-Vignette.Rmd | 9 BranchGLM-1.3.0/BranchGLM/inst/doc/BranchGLM-Vignette.html | 180 +++---- BranchGLM-1.3.0/BranchGLM/man/BranchGLM.Rd | 13 BranchGLM-1.3.0/BranchGLM/man/VariableSelection.Rd | 19 BranchGLM-1.3.0/BranchGLM/man/predict.BranchGLMVS.Rd |only BranchGLM-1.3.0/BranchGLM/src/BranchAndBound.cpp |only BranchGLM-1.3.0/BranchGLM/src/BranchGLMHelpers.cpp | 247 ++++++--- BranchGLM-1.3.0/BranchGLM/src/BranchGLMHelpers.h | 10 BranchGLM-1.3.0/BranchGLM/src/ParBranchGLMHelpers.cpp | 331 ++++++++----- BranchGLM-1.3.0/BranchGLM/src/ParBranchGLMHelpers.h | 48 - BranchGLM-1.3.0/BranchGLM/src/RcppExports.cpp | 114 +++- BranchGLM-1.3.0/BranchGLM/src/StepwiseMethods.cpp |only BranchGLM-1.3.0/BranchGLM/src/VariableSelection.cpp | 76 ++ BranchGLM-1.3.0/BranchGLM/src/VariableSelection.h | 19 BranchGLM-1.3.0/BranchGLM/tests/testthat/test-BranchGLM.R | 14 BranchGLM-1.3.0/BranchGLM/vignettes/BranchGLM-Vignette.Rmd | 9 24 files changed, 790 insertions(+), 444 deletions(-)
Title: Simulate the Extent of Host Switching by Consumers
Description: Using a simulation-based approach, the 'HostSwitch' package provides functions to investigate host switches by consumers.
The individual-based model is based on the concept of ecological fitting.
The mockup model is published by Araujo et al. 2015. Understanding Host-Switching by Ecological Fitting (<doi:10.1371/journal.pone.0139225>).
The package provides an R-friendly and modified version of this model which can be applied to different consumer-resource scenarios.
Author: Valeria Trivellone [aut] ,
Sabrina B.L. Araujo [aut] ,
Bernd Panassiti [cre, aut]
Maintainer: Bernd Panassiti <bernd.panassiti@gmail.com>
Diff between HostSwitch versions 0.1.1 dated 2022-05-24 and 0.1.2 dated 2022-08-09
DESCRIPTION | 23 MD5 | 51 - NAMESPACE | 6 NEWS.md | 7 R/HostSwitch.R | 418 +++++---- R/ShinyPlots.R | 65 - R/helper_functions.R | 61 - R/parli.R | 194 ++-- R/plots.R | 137 +-- R/startup.R | 5 R/testHostSwitch.R | 475 +++++------ README.md |only inst/doc/HostSwitch.R | 3 inst/doc/HostSwitch.Rmd | 304 +++---- inst/doc/HostSwitch.html | 53 - inst/tinytest |only man/check_valid_parameters.Rd |only man/parli.Rd | 107 +- man/plotHostSwitch.Rd | 4 man/shinyHostSwitch.Rd | 19 man/simHostSwitch.Rd | 122 +- man/summaryHostSwitch.Rd | 2 man/survivalProbability.Rd | 33 man/testHostSwitch.Rd | 38 tests |only vignettes/HostSwitch.Rmd | 304 +++---- vignettes/HostSwitch_files/figure-html/unnamed-chunk-6-1.png |binary vignettes/HostSwitch_files/figure-html/unnamed-chunk-7-1.png |only 28 files changed, 1393 insertions(+), 1038 deletions(-)
Title: Handy File and String Manipulation
Description: This started out as a package for file and string
manipulation. Since then, the 'fs' and 'strex' packages emerged,
offering functionality previously given by this package (but it's done
better in these new ones). Those packages have hence almost pushed
'filesstrings' into extinction. However, it still has a small number
of unique, handy file manipulation functions which can be seen in the
vignette. One example is a function to remove spaces from all file
names in a directory.
Author: Rory Nolan [aut, cre, cph] ,
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 3.2.2 dated 2021-04-18 and 3.2.3 dated 2022-08-09
DESCRIPTION | 27 ++++------- MD5 | 18 +++---- NEWS.md | 12 +++-- README.md | 10 +--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 19 +++----- inst/doc/files.html | 97 +++++++++++++++++++++++++++---------------- man/nth_number_after_mth.Rd | 7 --- man/nth_number_before_mth.Rd | 7 --- 10 files changed, 106 insertions(+), 91 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.1 dated 2022-05-20 and 0.8.2 dated 2022-08-09
correlation-0.8.1/correlation/R/backports.R |only correlation-0.8.1/correlation/tests/spelling.R |only correlation-0.8.2/correlation/DESCRIPTION | 21 - correlation-0.8.2/correlation/MD5 | 60 +- correlation-0.8.2/correlation/NEWS.md | 4 correlation-0.8.2/correlation/R/cor_test.R | 3 correlation-0.8.2/correlation/R/cor_test_biserial.R | 1 correlation-0.8.2/correlation/R/cor_text.R | 13 correlation-0.8.2/correlation/R/cor_to_cov.R | 1 correlation-0.8.2/correlation/R/cor_to_p.R | 1 correlation-0.8.2/correlation/R/cor_to_spcor.R | 2 correlation-0.8.2/correlation/R/correlation.R | 1 correlation-0.8.2/correlation/R/matrix_inverse.R | 1 correlation-0.8.2/correlation/R/methods.easycorrelation.R | 1 correlation-0.8.2/correlation/R/methods_format.R | 3 correlation-0.8.2/correlation/R/utils_clean_data.R | 2 correlation-0.8.2/correlation/R/visualisation_recipe.cor_test.R | 1 correlation-0.8.2/correlation/R/visualisation_recipe.easycormatrix.R | 8 correlation-0.8.2/correlation/README.md | 34 - correlation-0.8.2/correlation/build/vignette.rds |binary correlation-0.8.2/correlation/inst/doc/multilevel.Rmd | 2 correlation-0.8.2/correlation/inst/doc/multilevel.html | 128 +++--- correlation-0.8.2/correlation/inst/doc/types.R | 31 - correlation-0.8.2/correlation/inst/doc/types.Rmd | 33 - correlation-0.8.2/correlation/inst/doc/types.html | 204 +++++----- correlation-0.8.2/correlation/man/figures/README-12-1.png |binary correlation-0.8.2/correlation/man/figures/README-7-1.png |binary correlation-0.8.2/correlation/man/figures/README-corr-1.png |binary correlation-0.8.2/correlation/tests/testthat/test-display_print_matrix.R | 1 correlation-0.8.2/correlation/vignettes/bibliography.bib | 26 + correlation-0.8.2/correlation/vignettes/multilevel.Rmd | 2 correlation-0.8.2/correlation/vignettes/types.Rmd | 33 - 32 files changed, 326 insertions(+), 291 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.14.1 dated 2022-07-12 and 0.15.0 dated 2022-08-09
tiledb-0.14.1/tiledb/R/batchedQuery.R |only tiledb-0.15.0/tiledb/DESCRIPTION | 8 - tiledb-0.15.0/tiledb/MD5 | 54 +++++----- tiledb-0.15.0/tiledb/NAMESPACE | 1 tiledb-0.15.0/tiledb/NEWS.md | 21 ++++ tiledb-0.15.0/tiledb/R/Attribute.R | 2 tiledb-0.15.0/tiledb/R/BatchedQuery.R |only tiledb-0.15.0/tiledb/R/DataFrame.R | 61 ++++++++---- tiledb-0.15.0/tiledb/R/Dim.R | 11 +- tiledb-0.15.0/tiledb/R/QueryCondition.R | 25 +++- tiledb-0.15.0/tiledb/R/TileDBArray.R | 6 - tiledb-0.15.0/tiledb/R/zzz.R | 14 ++ tiledb-0.15.0/tiledb/configure | 18 +-- tiledb-0.15.0/tiledb/configure.ac | 2 tiledb-0.15.0/tiledb/inst/examples/quickstart_dense_memfs.R | 7 - tiledb-0.15.0/tiledb/inst/tinytest/test_group.R | 29 +++-- tiledb-0.15.0/tiledb/inst/tinytest/test_querycondition.R | 7 + tiledb-0.15.0/tiledb/inst/tinytest/test_timetravel.R | 38 ------- tiledb-0.15.0/tiledb/man/completedBatched.Rd | 2 tiledb-0.15.0/tiledb/man/createBatched.Rd | 2 tiledb-0.15.0/tiledb/man/fetchBatched.Rd | 2 tiledb-0.15.0/tiledb/man/fromDataFrame.Rd | 14 ++ tiledb-0.15.0/tiledb/man/parse_query_condition.Rd | 21 +++- tiledb-0.15.0/tiledb/man/statusBatched.Rd | 2 tiledb-0.15.0/tiledb/man/tiledb_attr.Rd | 2 tiledb-0.15.0/tiledb/man/tiledb_dim.Rd | 11 +- tiledb-0.15.0/tiledb/man/tiledb_filter.Rd | 1 tiledb-0.15.0/tiledb/src/libtiledb.cpp | 1 tiledb-0.15.0/tiledb/tools/tiledbVersion.txt | 4 29 files changed, 231 insertions(+), 135 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, and implicitly supports parallel processing.
For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.8 dated 2021-12-08 and 2.9 dated 2022-08-09
DESCRIPTION | 8 ++--- MD5 | 35 +++++++++++++----------- NEWS.md | 5 +++ R/Attach.R | 11 ++++++- R/SimBoot.R | 11 ++++++- R/analysis.R | 4 +- R/runSimulation.R | 17 ++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Catch_errors.html | 45 ++++++++++++++++++------------- inst/doc/Fixed_obj_fun.html | 14 ++++++--- inst/doc/MultipleAnalyses.html | 31 ++++++++++++--------- inst/doc/Parallel-computing.html | 8 ++++- inst/doc/Saving-results.html | 32 ++++++++++++---------- inst/doc/SimDesign-intro.html | 56 +++++++++++++++++++++------------------ man/Attach.Rd | 7 ++++ man/runSimulation.Rd | 4 ++ tests/tests/mpi |only 18 files changed, 174 insertions(+), 114 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-47 dated 2022-01-27 and 3.1-49 dated 2022-08-09
DESCRIPTION | 8 - MD5 | 115 ++++++++------ NAMESPACE | 12 + NEWS | 46 +++++ R/InsertVerticalPanels.R |only R/ResizeEtc.R | 6 R/ToBW.likert.R |only R/ancovaplot.R | 10 - R/do.formula.trellis.xysplom.R | 12 - R/intxplot.R | 2 R/latex.array.R | 65 ++++++-- R/likert.R | 10 - R/likert.formula.R | 2 R/likertWeighted.R | 180 +++++++++++++++-------- R/likertWeighted47.R |only R/residual.plots.R | 14 - build/partial.rdb |binary inst/CITATION | 8 - man/EmphasizeVerticalPanels.Rd |only man/HH.package.Rd | 5 man/HHscriptnames.Rd | 2 man/InsertVerticalPanels.Rd |only man/NormalAndT.Rd | 2 man/NormalAndTplot.Rd | 2 man/ToBW.likert.Rd |only man/X.residuals.Rd | 2 man/ancova-class.Rd | 2 man/ancova.Rd | 2 man/ancovaplot.Rd | 2 man/arma.loop.Rd | 2 man/as.multicomp.Rd | 2 man/bivariateNormal.Rd | 2 man/cp.Rd | 2 man/datasets.Rd | 2 man/hov.Rd | 2 man/interaction2wt.Rd | 2 man/ladder.Rd | 2 man/latex.array.Rd | 27 +++ man/likertWeighted.Rd | 315 ++++++++++++++++++----------------------- man/likertWeighted47.Rd |only man/lm.case.Rd | 2 man/mmc.Rd | 2 man/mmc.mean.Rd | 2 man/multicomp.order.Rd | 2 man/multicomp.reverse.Rd | 2 man/odds.ratio.Rd | 2 man/orthog.complete.Rd | 2 man/panel.cartesian.Rd | 2 man/panel.interaction2wt.Rd | 2 man/pdf.latex.Rd |only man/plot.hov.Rd | 2 man/plot.mmc.multicomp.Rd | 2 man/plot.multicomp.Rd | 2 man/positioned-class.Rd | 2 man/regr1.plot.Rd | 2 man/regr2.plot.Rd | 2 man/resid.squares.Rd | 2 man/residual.plots.Rd | 2 man/rowPcts.Rd | 11 - man/toCQxR.Rd |only man/tsdiagplot.Rd | 2 man/vif.Rd | 2 man/xysplom.Rd | 2 63 files changed, 537 insertions(+), 381 deletions(-)
Title: Get and Show Personal 'Google Scholar' Profile
Description: Provides functions to get personal 'Google Scholar'
profile data from web API and show it in table or figure format.
Author: Shixiang Wang [aut, cre]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between tinyscholar versions 0.1.6 dated 2022-07-04 and 0.1.7 dated 2022-08-09
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 4 R/utils-tidy-eval.R | 2 build/vignette.rds |binary inst/doc/tinyscholar.R | 4 inst/doc/tinyscholar.Rmd | 4 inst/doc/tinyscholar.html | 373 ++++++++++++++++++++++++---------------------- man/tidyeval.Rd | 2 vignettes/tinyscholar.Rmd | 4 10 files changed, 223 insertions(+), 194 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide substitution,
copy number alteration, etc. are the major force for cancer
initialization and development. Due to the specificity of molecular
lesions caused by genomic alterations, we can generate characteristic
alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021)
<DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al.
(2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al.
(2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to
extract, analyze and visualize signatures from genomic alteration
records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] ,
Ziyu Tao [aut] ,
Huimin Li [aut] ,
Tao Wu [aut] ,
Xue-Song Liu [aut, ctb] ,
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.1.5 dated 2022-06-30 and 2.1.6 dated 2022-08-09
DESCRIPTION | 6 +- MD5 | 12 ++-- NEWS.md | 4 + R/utils-tidy-eval.R | 2 inst/doc/cnsignature.html | 128 +++++++++++++++++++++++----------------------- inst/doc/sigminer.html | 4 - man/tidyeval.Rd | 2 7 files changed, 81 insertions(+), 77 deletions(-)
Title: Functions for Optimal Matching
Description: Distance based bipartite matching using minimum cost flow, oriented
to matching of treatment and control groups in observational studies (Hansen
and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to
generate distances from generalised linear models (propensity score
matching), formulas giving variables on which to limit matched distances,
stratified or exact matching directives, or calipers, alone or in
combination.
Author: Ben Hansen [aut],
Mark Fredrickson [aut],
Josh Errickson [cre, aut],
Josh Buckner [aut],
Adam Rauh [ctb]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between optmatch versions 0.10.3 dated 2022-05-16 and 0.10.4 dated 2022-08-09
DESCRIPTION | 12 - MD5 | 46 ++-- NAMESPACE | 1 NEWS.md | 17 + R/InfinitySparseMatrix.R | 17 + R/match_on.R | 37 +-- R/scores.R | 2 build/vignette.rds |binary inst/doc/fullmatch-vignette.R | 79 +++++--- inst/doc/fullmatch-vignette.Rmd | 95 ++++++--- inst/doc/fullmatch-vignette.html | 94 ++------- inst/doc/matching-from-foreign-software.html | 4 inst/doc/matching-within-subgroups.html | 4 man/dbind.Rd | 6 man/match_on-methods.Rd | 2 man/scores.Rd | 2 tests/testthat/test.CBPS.R | 49 ++-- tests/testthat/test.InfinitySparseMatrix.R | 266 ++++++++++++++------------- tests/testthat/test.fill.NAs.R | 3 tests/testthat/test.mahal-dist.R | 20 +- tests/testthat/test.match_on.R | 6 tests/testthat/test.rank.mahal.R | 19 + tests/testthat/test.utilities.R | 4 vignettes/fullmatch-vignette.Rmd | 95 ++++++--- 24 files changed, 501 insertions(+), 379 deletions(-)
Title: Retrieve Data from the Census APIs
Description: A wrapper for the U.S. Census Bureau APIs that returns data frames of
Census data and metadata. Available datasets include the
Decennial Census, American Community Survey, Small Area Health Insurance Estimates,
Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
Author: Hannah Recht [aut, cre]
Maintainer: Hannah Recht <censusapi.rstats@gmail.com>
Diff between censusapi versions 0.7.1 dated 2020-10-14 and 0.8.0 dated 2022-08-09
censusapi-0.7.1/censusapi/build |only censusapi-0.7.1/censusapi/inst |only censusapi-0.7.1/censusapi/vignettes |only censusapi-0.8.0/censusapi/DESCRIPTION | 14 - censusapi-0.8.0/censusapi/MD5 | 28 -- censusapi-0.8.0/censusapi/NEWS.md | 47 +++- censusapi-0.8.0/censusapi/R/getcensus_functions.R | 226 +++++++++++--------- censusapi-0.8.0/censusapi/R/makevar_functions.R | 20 - censusapi-0.8.0/censusapi/R/metadata_functions.R | 226 ++++++++++++++++---- censusapi-0.8.0/censusapi/README.md | 120 ---------- censusapi-0.8.0/censusapi/man/getCensus.Rd | 103 +++++---- censusapi-0.8.0/censusapi/man/getFunction.Rd | 4 censusapi-0.8.0/censusapi/man/listCensusApis.Rd | 7 censusapi-0.8.0/censusapi/man/listCensusMetadata.Rd | 83 ++++++- censusapi-0.8.0/censusapi/man/makeVarlist.Rd | 6 15 files changed, 545 insertions(+), 339 deletions(-)
Title: An Automated Cell Type Annotation Tool for Single-Cell
RNA-Sequencing Data
Description: An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Li Xing, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.
Author: Xiangling Ji [aut],
Danielle Tsao [aut],
Kailun Bai [ctb],
Min Tsao [aut],
Li Xing [aut],
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Diff between scAnnotate versions 0.0.2 dated 2022-08-08 and 0.0.3 dated 2022-08-09
DESCRIPTION | 10 ++++++---- MD5 | 2 +- 2 files changed, 7 insertions(+), 5 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions:
<https://nrfa.ceh.ac.uk/costs-terms-and-conditions>).
The package contains R wrappers to the UK NRFA data temporary-API. There are
functions to retrieve stations falling in a bounding box, to generate a map
and extracting time series and general information. The package is fully
described in Vitolo et al (2016) "rnrfa: An R package to Retrieve, Filter and
Visualize Data from the UK National River Flow Archive"
<https://journal.r-project.org/archive/2016/RJ-2016-036/RJ-2016-036.pdf>.
Author: Ilaria Prosdocimi [ctb, cre] ,
Claudia Vitolo [aut] ,
Matthew Fry [ctb] ,
Wouter Buytaert [ctb] ,
Michael Spencer [ctb] ,
Tobias Gauster [ctb]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between rnrfa versions 2.0.4 dated 2021-02-15 and 2.0.6 dated 2022-08-09
DESCRIPTION | 45 - MD5 | 52 - NAMESPACE | 101 +-- NEWS.md | 205 +++--- R/catalogue.R | 268 ++++---- R/gdf.R | 76 +- R/get_ts.R | 242 +++----- R/internals.R | 366 ++++++------ R/osg_parse.R | 261 ++++---- R/plot_rain_flow.R | 160 ++--- R/plot_trend.R | 176 +++-- R/rnrfa-package.R | 58 - R/seasonal_averages.R | 82 +- README.md | 240 ++++--- build/vignette.rds |binary inst/doc/rnrfa-vignette.R | 304 +++++----- inst/doc/rnrfa-vignette.Rmd | 606 ++++++++++---------- inst/doc/rnrfa-vignette.html | 1206 +++++++++++++++++++++------------------- man/gdf.Rd | 83 +- man/get_ts.Rd | 145 ++-- man/osg_parse.Rd | 79 +- man/plot_trend.Rd | 71 +- tests/testthat.R | 18 tests/testthat/test-gdf.R | 56 - tests/testthat/test-get_ts.R | 162 ++--- tests/testthat/test-osg_parse.R | 168 ++--- vignettes/rnrfa-vignette.Rmd | 606 ++++++++++---------- 27 files changed, 3002 insertions(+), 2834 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word' and 'Microsoft PowerPoint'
documents from 'R Markdown'. Functions are provided to let users create tables, modify and format
their content. It also extends package 'officer' that does not contain any feature for customized
tabular reporting.
Author: David Gohel [aut, cre],
Clementine Jager [ctb],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] ,
Titouan Robert [ctb],
Michael Barrowman [ctb] ,
Atsushi Yasumoto [ctb] ,
Paul Julian [ctb] ,
Sean Browning [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.7.2 dated 2022-06-12 and 0.7.3 dated 2022-08-09
DESCRIPTION | 14 +++---- MD5 | 60 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 30 +++++++++++++++ R/as_flextable_tabulator.R | 14 ++++++- R/chunk_images.R | 55 +++++++++++++++++++-------- R/clintables.R |only R/docx_str.R | 10 ++++- R/flextable.R | 9 +++- R/footnote.R | 8 ++++ R/html_str.R | 13 +++++- R/merge_flextable.R | 14 +++---- R/pptx_str.R | 26 ++++++++----- R/printers.R | 15 +++++++ R/styles.R | 42 +++++---------------- R/tabpart_tools.R | 75 +++++++++++++++++++++++++++++++------ R/themes.R | 4 ++ README.md | 2 - build/vignette.rds |binary inst/web_1.1.0/scrool.css | 3 + inst/web_1.1.0/tabwid.css | 3 + man/as_flextable.tabulator.Rd | 5 ++ man/as_image.Rd | 42 ++++++++++++--------- man/figures/fig_as_image_1.png |binary man/rotate.Rd | 6 ++- man/save_as_pptx.Rd | 11 +++++ man/set_caption.Rd | 6 ++- man/shift_table.Rd |only man/tabulator.Rd | 4 +- tests/testthat/test-dimensions.R | 17 ++++++++ tests/testthat/test-misc.R | 78 ++++++++++++++++++++++++++++++++++----- tests/testthat/test-styles.R | 31 +++++++++++++++ 32 files changed, 442 insertions(+), 156 deletions(-)
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and
Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] ,
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 3.1.0 dated 2022-07-01 and 3.1.1 dated 2022-08-09
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NEWS.md | 8 +++++ inst/doc/EmpiricalCiCalibrationVignette.pdf |binary inst/doc/EmpiricalMaxSprtCalibrationVignette.R | 31 ++++++++++++---------- inst/doc/EmpiricalMaxSprtCalibrationVignette.Rmd | 31 ++++++++++++---------- inst/doc/EmpiricalMaxSprtCalibrationVignette.pdf |binary inst/doc/EmpiricalPCalibrationVignette.pdf |binary tests/testthat/test-critical-values.R | 3 +- vignettes/EmpiricalMaxSprtCalibrationVignette.Rmd | 31 ++++++++++++---------- 10 files changed, 74 insertions(+), 56 deletions(-)
More information about EmpiricalCalibration at CRAN
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Title: Calibration Bands
Description: Package to assess the calibration of probabilistic classifiers using confidence bands for monotonic functions. Besides testing the classical goodness-of-fit null hypothesis of perfect calibration, the confidence bands calculated within that package facilitate inverted goodness-of-fit tests whose rejection allows for a sought-after conclusion of a sufficiently well-calibrated model. The package creates flexible graphical tools to perform these tests. For construction details see also Dimitriadis, Dümbgen, Henzi, Puke, Ziegel (2022) <arXiv:2203.04065>.
Author: Timo Dimitriadis [aut],
Alexander Henzi [aut],
Marius Puke [aut, cre]
Maintainer: Marius Puke <marius.puke@uni-hohenheim.de>
Diff between calibrationband versions 0.1.0 dated 2022-08-09 and 0.2.1 dated 2022-08-09
DESCRIPTION | 9 +++++---- MD5 | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-)
More information about calibrationband at CRAN
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Title: Analyze Bioassays and Probit Graphs
Description: A robust framework for analyzing mortality data from bioassays for one or several strains/lines/populations.
Author: Piyal Karunarathne [aut, cre] ,
Pascal Milesi [aut] ,
Pierrick Labbe [aut]
Maintainer: Piyal Karunarathne <piyalkarumail@yahoo.com>
Diff between BioRssay versions 1.0.0 dated 2022-05-26 and 1.1.0 dated 2022-08-09
DESCRIPTION | 9 +- MD5 | 22 ++--- NEWS.md | 12 ++ R/plots.R | 101 +++++++++++++++++++++++ R/ratios.R | 20 ++-- README.md | 18 +++- inst/doc/BioRssay.R | 12 ++ inst/doc/BioRssay.Rmd | 19 +++- inst/doc/BioRssay.html | 211 +++++++++++++++++++++++++------------------------ man/model.signif.Rd | 2 man/resist.ratio.Rd | 6 - vignettes/BioRssay.Rmd | 19 +++- 12 files changed, 309 insertions(+), 142 deletions(-)
Title: Pathway Based Tumor Mutational Burden
Description: A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.
Author: Junwei Han [aut, cre, cph],
Xiangmei Li [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between pathwayTMB versions 0.1.2 dated 2022-05-18 and 0.1.3 dated 2022-08-09
DESCRIPTION | 6 +- MD5 | 28 ++++++------ R/main.R | 96 +++++++++++++++++++++----------------------- R/visualization.R | 24 +++++------ data/mut_matrix.rda |binary inst/doc/pathwayTMB.Rmd | 9 +--- inst/doc/pathwayTMB.html | 32 ++++++-------- man/GenePathwayOncoplots.Rd | 4 - man/get_final_signature.Rd | 4 + man/get_mut_matrix.Rd | 12 ++--- man/mut_matrix.Rd | 2 man/plotKMcurves.Rd | 8 +-- man/plotMutInteract.Rd | 8 +-- man/plotROC.Rd | 4 - vignettes/pathwayTMB.Rmd | 9 +--- 15 files changed, 120 insertions(+), 126 deletions(-)
More information about SurfaceReconstruction at CRAN
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Title: Be Nice on the Web
Description: Be responsible when scraping data from websites by following polite principles: introduce yourself, ask for permission, take slowly and never ask twice.
Author: Dmytro Perepolkin [aut, cre]
Maintainer: Dmytro Perepolkin <dperepolkin@gmail.com>
Diff between polite versions 0.1.1 dated 2019-11-30 and 0.1.2 dated 2022-08-09
DESCRIPTION | 18 - MD5 | 43 ++- NAMESPACE | 10 NEWS.md | 22 + R/bow.R | 22 + R/formals.R |only R/html.R | 2 R/nod.R | 3 R/politely.R |only R/rip.R | 2 R/scrape.R | 52 ---- R/utils.R | 57 ++++ README.md | 367 ++++++++++++++++++++++++++++-- inst/templates/polite_template.R | 88 ++++++- man/bow.Rd | 14 - man/figures/README-unnamed-chunk-10-1.png |only man/guess_basename.Rd |only man/html_attrs_dfr.Rd | 9 man/nullcoalesce.Rd | 4 man/politely.Rd |only man/rip.Rd | 10 man/scrape.Rd | 20 + tests/testthat/test-scrape.R |only tests/testthat/test_bow.R | 32 ++ tests/testthat/test_nod.R | 6 tests/testthat/testthat-problems.rds |only 26 files changed, 628 insertions(+), 153 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. 'dsims' repeatedly generates
instances of a user defined population within a given survey region. It then
generates realisations of a survey design and simulates the detection process.
The data are then analysed so that the results can be compared for accuracy
and precision across all replications. This process allows users to optimise
survey designs for their specific set of survey conditions. The effects of
uncertainty in population distribution or parameters can be investigated
under a number of simulations so that users can be confident that they have
achieved a robust survey design before deploying vessels into the field. The
distance sampling designs used in this package from 'dssd' are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13:
978-0199225873). General distance sampling methods are detailed in Introduction
to Distance Sampling: Estimating Abundance of Biological Populations, Buckland
et. al. (2004, ISBN-13: 978-0198509271). Find out more about estimating
animal/plant abundance with distance sampling at <http://distancesampling.org/>.
Author: Laura Marshall [aut, cre],
Thomas Len [ctb]
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between dsims versions 0.2.3 dated 2022-06-15 and 1.0.0 dated 2022-08-09
dsims-0.2.3/dsims/R/rtpois.R |only dsims-0.2.3/dsims/man/rtpois.Rd |only dsims-0.2.3/dsims/tests/testthat/test-BasicLine.R |only dsims-1.0.0/dsims/DESCRIPTION | 19 - dsims-1.0.0/dsims/MD5 | 70 ++-- dsims-1.0.0/dsims/NAMESPACE | 6 dsims-1.0.0/dsims/NEWS | 70 ++-- dsims-1.0.0/dsims/R/AICc.R | 6 dsims-1.0.0/dsims/R/DS.Analysis.R | 125 ++++++- dsims-1.0.0/dsims/R/Detectability.R | 2 dsims-1.0.0/dsims/R/Simulation.R | 92 ++++- dsims-1.0.0/dsims/R/Survey.LT.R | 1 dsims-1.0.0/dsims/R/Survey.PT.R | 1 dsims-1.0.0/dsims/R/Survey.R | 68 +++- dsims-1.0.0/dsims/R/accumulate.warnings.R | 2 dsims-1.0.0/dsims/R/add.covariate.values.R | 2 dsims-1.0.0/dsims/R/add.summary.results.R | 2 dsims-1.0.0/dsims/R/check.covariates.R | 4 dsims-1.0.0/dsims/R/get.covered.area.lines.R |only dsims-1.0.0/dsims/R/get.covered.area.points.R |only dsims-1.0.0/dsims/R/message.handler.R | 2 dsims-1.0.0/dsims/R/process.dist.shapes.R |only dsims-1.0.0/dsims/R/read.line.transects.R |only dsims-1.0.0/dsims/R/read.point.transects.R |only dsims-1.0.0/dsims/R/read.seg.transects.R |only dsims-1.0.0/dsims/R/run.simulation.R | 46 +- dsims-1.0.0/dsims/R/rztpois.R |only dsims-1.0.0/dsims/R/single.sim.loop.R | 95 +++-- dsims-1.0.0/dsims/R/store.dht.results.R | 3 dsims-1.0.0/dsims/build/vignette.rds |binary dsims-1.0.0/dsims/inst/doc/GettingStarted.html | 10 dsims-1.0.0/dsims/man/analyse.data-methods.Rd | 8 dsims-1.0.0/dsims/man/histogram.N.ests-methods.Rd | 7 dsims-1.0.0/dsims/man/plot-methods.Rd | 14 dsims-1.0.0/dsims/man/run.simulation-methods.Rd | 8 dsims-1.0.0/dsims/man/run.survey-methods.Rd | 5 dsims-1.0.0/dsims/man/rztpois.Rd |only dsims-1.0.0/dsims/tests/testthat/test-ProblemCases.R | 16 dsims-1.0.0/dsims/tests/testthat/test-check_AnalysisOptions.R | 32 + dsims-1.0.0/dsims/tests/testthat/test-check_ExtremeCases.R |only dsims-1.0.0/dsims/tests/testthat/test-check_IndividualCovariates.R | 164 ++++++++++ dsims-1.0.0/dsims/tests/testthat/test-check_Other.R |only dsims-1.0.0/dsims/tests/testthat/test-check_ReadInTransects.R |only 43 files changed, 672 insertions(+), 208 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.3-1 dated 2022-03-03 and 3.4-0 dated 2022-08-09
survival-3.3-1/survival/noweb/cnew.Rnw |only survival-3.3-1/survival/noweb/cnew2.Rnw |only survival-3.3-1/survival/noweb/tmerge.Rnw.orig |only survival-3.3-1/survival/tests/aareg2.R |only survival-3.3-1/survival/tests/brier.R |only survival-3.3-1/survival/vignettes/temp |only survival-3.4-0/survival/DESCRIPTION | 8 survival-3.4-0/survival/MD5 | 253 +++--- survival-3.4-0/survival/NAMESPACE | 5 survival-3.4-0/survival/R/anova.coxphlist.R | 2 survival-3.4-0/survival/R/basehaz.R | 2 survival-3.4-0/survival/R/concordance.R | 51 - survival-3.4-0/survival/R/cox.zph.R | 5 survival-3.4-0/survival/R/coxph.R | 64 + survival-3.4-0/survival/R/coxph.getdata.R | 14 survival-3.4-0/survival/R/drop.special.R | 3 survival-3.4-0/survival/R/model.matrix.coxph.R | 4 survival-3.4-0/survival/R/nsk.R | 22 survival-3.4-0/survival/R/parsecovar.R | 24 survival-3.4-0/survival/R/predict.coxph.R | 6 survival-3.4-0/survival/R/predict.coxphms.R | 2 survival-3.4-0/survival/R/print.summary.survfitms.R | 2 survival-3.4-0/survival/R/residuals.coxph.R | 9 survival-3.4-0/survival/R/stacker.R | 4 survival-3.4-0/survival/R/survSplit.R | 2 survival-3.4-0/survival/R/survdiff.R | 7 survival-3.4-0/survival/R/survexp.R | 2 survival-3.4-0/survival/R/survfit.coxphms.R | 162 ++- survival-3.4-0/survival/R/survfitCI.R | 23 survival-3.4-0/survival/R/survfitKM.R | 8 survival-3.4-0/survival/R/xtras.R | 3 survival-3.4-0/survival/build/vignette.rds |binary survival-3.4-0/survival/inst/NEWS.Rd | 22 survival-3.4-0/survival/inst/doc/adjcurve.pdf |binary survival-3.4-0/survival/inst/doc/approximate.pdf |binary survival-3.4-0/survival/inst/doc/compete.R | 6 survival-3.4-0/survival/inst/doc/compete.Rnw | 6 survival-3.4-0/survival/inst/doc/compete.pdf |binary survival-3.4-0/survival/inst/doc/concordance.pdf |binary survival-3.4-0/survival/inst/doc/discrim.pdf |binary survival-3.4-0/survival/inst/doc/multi.pdf |binary survival-3.4-0/survival/inst/doc/other.pdf |binary survival-3.4-0/survival/inst/doc/population.pdf |binary survival-3.4-0/survival/inst/doc/splines.R | 2 survival-3.4-0/survival/inst/doc/splines.Rnw | 2 survival-3.4-0/survival/inst/doc/splines.pdf |binary survival-3.4-0/survival/inst/doc/survival.pdf |binary survival-3.4-0/survival/inst/doc/tiedtimes.pdf |binary survival-3.4-0/survival/inst/doc/timedep.R | 6 survival-3.4-0/survival/inst/doc/timedep.Rnw | 6 survival-3.4-0/survival/inst/doc/timedep.pdf |binary survival-3.4-0/survival/inst/doc/validate.pdf |binary survival-3.4-0/survival/man/agreg.fit.Rd | 2 survival-3.4-0/survival/man/basehaz.Rd | 10 survival-3.4-0/survival/man/concordance.Rd | 43 - survival-3.4-0/survival/man/coxph.Rd | 10 survival-3.4-0/survival/man/coxph.object.Rd | 18 survival-3.4-0/survival/man/coxphms.object.Rd |only survival-3.4-0/survival/man/pseudo.Rd | 20 survival-3.4-0/survival/man/rotterdam.Rd | 2 survival-3.4-0/survival/man/rttright.Rd | 15 survival-3.4-0/survival/man/summary.coxph.Rd | 2 survival-3.4-0/survival/man/survdiff.Rd | 4 survival-3.4-0/survival/man/survfit.coxph.Rd | 4 survival-3.4-0/survival/man/survfit.formula.Rd | 6 survival-3.4-0/survival/man/tcut.Rd | 32 survival-3.4-0/survival/noweb/cch.Rnw |only survival-3.4-0/survival/noweb/code.nw | 450 ++++++----- survival-3.4-0/survival/noweb/code.toc | 77 - survival-3.4-0/survival/noweb/concordance.Rnw | 51 - survival-3.4-0/survival/noweb/coxph.Rnw | 93 +- survival-3.4-0/survival/noweb/coxsurv2.Rnw | 6 survival-3.4-0/survival/noweb/coxsurv3.Rnw | 184 ++-- survival-3.4-0/survival/noweb/coxsurv3.save |only survival-3.4-0/survival/noweb/coxsurv3.save2 |only survival-3.4-0/survival/noweb/msurv.rwt |only survival-3.4-0/survival/noweb/msurv.save |only survival-3.4-0/survival/noweb/msurvnew |only survival-3.4-0/survival/noweb/noweb.sty | 2 survival-3.4-0/survival/noweb/parse.Rnw | 24 survival-3.4-0/survival/noweb/predict.coxph.Rnw | 10 survival-3.4-0/survival/noweb/residuals.survfit.Rnw | 44 - survival-3.4-0/survival/noweb/survexp.Rnw | 2 survival-3.4-0/survival/noweb/survfit.riskwt |only survival-3.4-0/survival/noweb/survfit.save |only survival-3.4-0/survival/noweb/survfitCI.Rnw | 23 survival-3.4-0/survival/noweb/survfitCI.riskwt |only survival-3.4-0/survival/noweb/survfitCI.save |only survival-3.4-0/survival/noweb/survfitKM.Rnw | 8 survival-3.4-0/survival/noweb/yates2new.Rnw |only survival-3.4-0/survival/noweb/zph.Rnw | 5 survival-3.4-0/survival/src/agexact.c | 12 survival-3.4-0/survival/src/agfit5.c | 26 survival-3.4-0/survival/src/agmart.c | 4 survival-3.4-0/survival/src/agmart3.c | 8 survival-3.4-0/survival/src/agsurv3.c | 10 survival-3.4-0/survival/src/agsurv4.c | 4 survival-3.4-0/survival/src/agsurv5.c | 2 survival-3.4-0/survival/src/collapse.c | 2 survival-3.4-0/survival/src/coxdetail.c | 6 survival-3.4-0/survival/src/coxfit5.c | 26 survival-3.4-0/survival/src/coxmart.c | 6 survival-3.4-0/survival/src/coxmart2.c | 6 survival-3.4-0/survival/src/coxph_wtest.c | 2 survival-3.4-0/survival/src/coxscho.c | 6 survival-3.4-0/survival/src/coxsurv2.c | 17 survival-3.4-0/survival/src/pyears1.c | 10 survival-3.4-0/survival/src/pyears2.c | 6 survival-3.4-0/survival/src/pystep.c | 2 survival-3.4-0/survival/src/survConcordance.c | 8 survival-3.4-0/survival/src/survS.h | 2 survival-3.4-0/survival/src/survdiff2.c | 6 survival-3.4-0/survival/src/survfit4.c | 2 survival-3.4-0/survival/src/survpenal.c | 2 survival-3.4-0/survival/src/survproto.h | 146 +-- survival-3.4-0/survival/src/survreg6.c | 6 survival-3.4-0/survival/src/survreg7.c | 6 survival-3.4-0/survival/src/survregc1.c | 4 survival-3.4-0/survival/src/survregc2.c | 4 survival-3.4-0/survival/tests/Examples/survival-Ex.Rout.save | 162 +-- survival-3.4-0/survival/tests/aareg.Rout.save | 95 -- survival-3.4-0/survival/tests/coxsurv6.R |only survival-3.4-0/survival/tests/coxsurv6.Rout.save |only survival-3.4-0/survival/tests/dropspecial.R |only survival-3.4-0/survival/tests/fr_simple.R | 10 survival-3.4-0/survival/tests/fr_simple.Rout.save | 24 survival-3.4-0/survival/tests/mstrata.R | 24 survival-3.4-0/survival/tests/mstrata.Rout.save | 31 survival-3.4-0/survival/tests/multi2.R | 71 - survival-3.4-0/survival/tests/multi2.Rout.save | 90 +- survival-3.4-0/survival/tests/multi3.R |only survival-3.4-0/survival/tests/multi3.Rout.save |only survival-3.4-0/survival/tests/multistate.R | 1 survival-3.4-0/survival/tests/multistate.Rout.save | 8 survival-3.4-0/survival/tests/plot1.pdf |only survival-3.4-0/survival/tests/yates0.Rout.save | 8 survival-3.4-0/survival/vignettes/.install_extras |only survival-3.4-0/survival/vignettes/compete.Rnw | 6 survival-3.4-0/survival/vignettes/splines.Rnw | 2 survival-3.4-0/survival/vignettes/timedep.Rnw | 6 140 files changed, 1492 insertions(+), 1271 deletions(-)
Title: Visualize Data on Spirals
Description: It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart.
It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high
resolution. 2. It is efficient for time series data to reveal periodic patterns.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between spiralize versions 1.0.5 dated 2022-02-05 and 1.0.6 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/graphics.R | 46 +++++++++++++++++++++++++++++++++++----------- R/initialize.R | 36 ++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/spiralize.html | 5 +++-- man/spiral_horizon.Rd | 4 +++- 8 files changed, 80 insertions(+), 37 deletions(-)
Title: Analyze Dependency Heaviness of R Packages
Description: A new metric named 'dependency heaviness' is proposed that measures the number
of additional dependency packages that a parent package brings to its child package
and are unique to the dependency packages imported by all other parents.
The dependency heaviness analysis is visualized by a customized heatmap.
The package is described in <doi:10.1093/bioinformatics/btac449>.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between pkgndep versions 1.1.4 dated 2022-06-09 and 1.1.5 dated 2022-08-09
DESCRIPTION | 11 ++++--- MD5 | 15 +++++----- R/global.R | 2 - R/plot.R | 2 - R/stat.R | 11 +++++-- inst/CITATION |only inst/doc/pkgndep.html | 61 +++++++++++++++++++++--------------------- man/heaviness.Rd | 3 +- tests/testthat/test_pkgndep.R | 31 ++++++++++++--------- 9 files changed, 75 insertions(+), 61 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro [aut] ,
Douglas Bates [aut] ,
Saikat DebRoy [ctb] ,
Deepayan Sarkar [ctb] ,
EISPACK authors [ctb] ,
Siem Heisterkamp [ctb] ,
Bert Van Willigen [ctb] ,
Johannes Ranke [ctb] ),
R Core Team [aut, cre]
Maintainer: R Core Team <R-core@R-project.org>
Diff between nlme versions 3.1-158 dated 2022-06-15 and 3.1-159 dated 2022-08-09
ChangeLog | 15 +++++++++++- DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- R/gnls.R | 50 ++++++++++++++++++----------------------- build/partial.rdb |binary inst/scripts/ch01.R | 2 - inst/scripts/runme.R | 4 +++ man/gls.Rd | 4 +++ man/lme.Rd | 4 +++ src/nlme.c | 24 ++++++++++--------- tests/extras/scripts.Rout.save | 4 +-- tests/gls.R | 19 +++++++++++++++ 12 files changed, 98 insertions(+), 58 deletions(-)
More information about calibrationband at CRAN
Permanent link
Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.6.9 dated 2022-04-26 and 1.7.0 dated 2022-08-09
dispRity-1.6.9/dispRity/man/combine.subsets.Rd |only dispRity-1.6.9/dispRity/man/extract.dispRity.Rd |only dispRity-1.6.9/dispRity/man/fill.dispRity.Rd |only dispRity-1.6.9/dispRity/man/matrix.dispRity.Rd |only dispRity-1.6.9/dispRity/man/n.subsets.Rd |only dispRity-1.6.9/dispRity/man/size.subsets.Rd |only dispRity-1.7.0/dispRity/DESCRIPTION | 20 dispRity-1.7.0/dispRity/MD5 | 144 + dispRity-1.7.0/dispRity/NAMESPACE | 19 dispRity-1.7.0/dispRity/NEWS.md | 41 dispRity-1.7.0/dispRity/R/MCMCglmm.subsets.R |only dispRity-1.7.0/dispRity/R/MCMCglmm.subsets_fun.R |only dispRity-1.7.0/dispRity/R/MCMCglmm.utilities.R |only dispRity-1.7.0/dispRity/R/MCMCglmm.utilities_fun.R |only dispRity-1.7.0/dispRity/R/as.covar.R |only dispRity-1.7.0/dispRity/R/as.covar_fun.R |only dispRity-1.7.0/dispRity/R/char.diff.R | 11 dispRity-1.7.0/dispRity/R/covar.plot.R |only dispRity-1.7.0/dispRity/R/covar.plot_fun.R |only dispRity-1.7.0/dispRity/R/covar.utilities.R |only dispRity-1.7.0/dispRity/R/covar.utilities_fun.R |only dispRity-1.7.0/dispRity/R/custom.subsets.R | 4 dispRity-1.7.0/dispRity/R/custom.subsets_fun.R | 7 dispRity-1.7.0/dispRity/R/dispRity-package.R | 73 dispRity-1.7.0/dispRity/R/dispRity.R | 82 - dispRity-1.7.0/dispRity/R/dispRity.covar.projections.R |only dispRity-1.7.0/dispRity/R/dispRity.covar.projections_fun.R |only dispRity-1.7.0/dispRity/R/dispRity.fast.R |only dispRity-1.7.0/dispRity/R/dispRity.metric.R | 271 ++- dispRity-1.7.0/dispRity/R/dispRity.utilities.R | 736 ++++------ dispRity-1.7.0/dispRity/R/dispRity.utilities_fun.R | 21 dispRity-1.7.0/dispRity/R/dispRity_fun.R | 101 + dispRity-1.7.0/dispRity/R/geomorph.ordination.R | 4 dispRity-1.7.0/dispRity/R/make.metric.R | 20 dispRity-1.7.0/dispRity/R/match.tip.edge.R |only dispRity-1.7.0/dispRity/R/model.test.sim.R | 6 dispRity-1.7.0/dispRity/R/model.test_fun.R | 8 dispRity-1.7.0/dispRity/R/multi.ace_fun.R | 2 dispRity-1.7.0/dispRity/R/pair.plot.R | 2 dispRity-1.7.0/dispRity/R/plot.dispRity.R | 52 dispRity-1.7.0/dispRity/R/plot.dispRity_fun.R | 398 +++-- dispRity-1.7.0/dispRity/R/print.dispRity.R | 39 dispRity-1.7.0/dispRity/R/randtest.dispRity.R | 2 dispRity-1.7.0/dispRity/R/sanitizing.R | 2 dispRity-1.7.0/dispRity/R/sequential.test.R |only dispRity-1.7.0/dispRity/R/sequential.test_fun.R |only dispRity-1.7.0/dispRity/R/summary.dispRity.R | 13 dispRity-1.7.0/dispRity/R/test.dispRity.R | 4 dispRity-1.7.0/dispRity/R/test.metric.R | 20 dispRity-1.7.0/dispRity/R/test.metric_fun.R | 92 - dispRity-1.7.0/dispRity/R/tree.age.R | 8 dispRity-1.7.0/dispRity/R/zzz.R | 2 dispRity-1.7.0/dispRity/build |only dispRity-1.7.0/dispRity/data/BeckLee_ages.rda |binary dispRity-1.7.0/dispRity/data/BeckLee_disparity.rda |binary dispRity-1.7.0/dispRity/data/BeckLee_mat50.rda |binary dispRity-1.7.0/dispRity/data/BeckLee_mat99.rda |binary dispRity-1.7.0/dispRity/data/BeckLee_tree.rda |binary dispRity-1.7.0/dispRity/data/charadriiformes.rda |only dispRity-1.7.0/dispRity/data/datalist | 1 dispRity-1.7.0/dispRity/data/demo_data.rda |binary dispRity-1.7.0/dispRity/data/disparity.rda |binary dispRity-1.7.0/dispRity/inst/CITATION | 27 dispRity-1.7.0/dispRity/inst/References.bib | 48 dispRity-1.7.0/dispRity/inst/vignettes/Projection_analysis.Rmd |only dispRity-1.7.0/dispRity/man/MCMCglmm.subsets.Rd |only dispRity-1.7.0/dispRity/man/MCMCglmm.utilities.Rd |only dispRity-1.7.0/dispRity/man/add.tree.Rd | 4 dispRity-1.7.0/dispRity/man/as.covar.Rd |only dispRity-1.7.0/dispRity/man/char.diff.Rd | 10 dispRity-1.7.0/dispRity/man/charadriiformes.Rd |only dispRity-1.7.0/dispRity/man/covar.plot.Rd |only dispRity-1.7.0/dispRity/man/covar.utilities.Rd |only dispRity-1.7.0/dispRity/man/custom.subsets.Rd | 2 dispRity-1.7.0/dispRity/man/demo_data.Rd | 2 dispRity-1.7.0/dispRity/man/dispRity-package.Rd | 2 dispRity-1.7.0/dispRity/man/dispRity.Rd | 4 dispRity-1.7.0/dispRity/man/dispRity.covar.projections.Rd |only dispRity-1.7.0/dispRity/man/dispRity.fast.Rd |only dispRity-1.7.0/dispRity/man/dispRity.metric.Rd | 49 dispRity-1.7.0/dispRity/man/geomorph.ordination.Rd | 4 dispRity-1.7.0/dispRity/man/get.matrix.Rd |only dispRity-1.7.0/dispRity/man/get.subsets.Rd | 48 dispRity-1.7.0/dispRity/man/make.dispRity.Rd | 13 dispRity-1.7.0/dispRity/man/make.metric.Rd | 5 dispRity-1.7.0/dispRity/man/match.tip.edge.Rd |only dispRity-1.7.0/dispRity/man/model.test.sim.Rd | 6 dispRity-1.7.0/dispRity/man/plot.dispRity.Rd | 12 dispRity-1.7.0/dispRity/man/sort.dispRity.Rd | 2 dispRity-1.7.0/dispRity/man/tree.age.Rd | 6 dispRity-1.7.0/dispRity/src/char.diff.c |only 91 files changed, 1563 insertions(+), 886 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn [aut, cre] ,
Jed Wing [ctb],
Steve Weston [ctb],
Andre Williams [ctb],
Chris Keefer [ctb],
Allan Engelhardt [ctb],
Tony Cooper [ctb],
Zachary Mayer [ctb],
Brenton Kenkel [ctb],
R Core Team [ctb],
Michael Benesty [ctb],
Reynald Lescarbeau [ct [...truncated...]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-92 dated 2022-04-19 and 6.0-93 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/prec_rec.R | 5 +++++ R/safs.R | 5 +++-- R/selectByFilter.R | 2 +- R/specificity.R | 21 ++++++++++++--------- R/train.default.R | 27 ++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 ++++++++- inst/models/models.RData |binary man/safs.Rd | 3 ++- man/sensitivity.Rd | 14 +++++++++++++- src/caret.c | 3 +++ 14 files changed, 78 insertions(+), 45 deletions(-)
Title: The Bayesian Spatial Bradley--Terry Model
Description: An implementation of the Bayesian Spatial Bradley--Terry (BSBT) model. It can be used to investigate data sets where judges compared different spatial areas. It constructs a network to describe how the areas are connected, and then places a correlated prior distribution on the quality parameter for each area, based on the network. The package includes MCMC algorithms to estimate the quality parameters. The methodology is published in Seymour et. al. (2020) <arXiv:2010.14128>.
Author: Rowland Seymour [aut, cre] ,
James Briant [aut],
Yichi Zhang [aut]
Maintainer: Rowland Seymour <rowland.seymour@nottingham.ac.uk>
Diff between BSBT versions 1.2.0 dated 2021-12-21 and 1.2.1 dated 2022-08-09
DESCRIPTION | 17 - MD5 | 20 - NEWS.md | 5 R/constrained_covariance_functions.R | 4 R/mcmc_functions.R | 1 build/vignette.rds |binary data/forcedmarriage.comparisons.rda |only inst/doc/BSBT_example.html | 288 ++++++++++++++++++- inst/doc/vulnerability_in_dar.html | 341 ++++++++++++++++++++--- man/constrained_adjacency_covariance_function.Rd | 2 man/constrained_covariance_function.Rd | 2 man/forcedmarriage.comparisons.Rd |only 12 files changed, 611 insertions(+), 69 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for sensitivity analysis of model outputs (factor screening, global sensitivity analysis and robustness analysis), as well as for interpretability of machine learning models. Most of the functions have to be applied on scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Margot Herin, Marouane Il Idrissi, Loic Le G [...truncated...]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.27.0 dated 2021-10-20 and 1.27.1 dated 2022-08-09
sensitivity-1.27.0/sensitivity/R/emvd.R |only sensitivity-1.27.0/sensitivity/man/emvd.Rd |only sensitivity-1.27.1/sensitivity/DESCRIPTION | 8 sensitivity-1.27.1/sensitivity/MD5 | 40 sensitivity-1.27.1/sensitivity/NAMESPACE | 6 sensitivity-1.27.1/sensitivity/NEWS | 14 sensitivity-1.27.1/sensitivity/R/base.R | 3 sensitivity-1.27.1/sensitivity/R/nodeggplot.R | 6 sensitivity-1.27.1/sensitivity/R/nodeplot.R | 6 sensitivity-1.27.1/sensitivity/R/parameterSets.R | 10 sensitivity-1.27.1/sensitivity/R/pme.R | 56 sensitivity-1.27.1/sensitivity/R/pmvd.R |only sensitivity-1.27.1/sensitivity/R/shapleysobol_knn.R | 28 sensitivity-1.27.1/sensitivity/R/sobolrec.R | 816 +++++++------- sensitivity-1.27.1/sensitivity/man/lmg.Rd | 15 sensitivity-1.27.1/sensitivity/man/morris.Rd | 4 sensitivity-1.27.1/sensitivity/man/pcc.Rd | 7 sensitivity-1.27.1/sensitivity/man/pme.Rd | 23 sensitivity-1.27.1/sensitivity/man/pmvd.Rd |only sensitivity-1.27.1/sensitivity/man/sensitivity-package.Rd | 16 sensitivity-1.27.1/sensitivity/man/shapleysobol_knn.Rd | 14 sensitivity-1.27.1/sensitivity/man/sobolshap_knn.Rd | 3 sensitivity-1.27.1/sensitivity/man/src.Rd | 7 23 files changed, 570 insertions(+), 512 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: Guangchuang Yu [aut, cre] ,
James Keirstead [aut],
Gregory Jefferis [aut] ,
Gordon Getzinger [ctb],
Jorge Cimentada [ctb],
Max Czapanskiy [ctb],
Dominique Makowski [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 0.2.3 dated 2022-06-23 and 0.2.4 dated 2022-08-09
DESCRIPTION | 8 - MD5 | 29 ++- NAMESPACE | 6 NEWS.md | 6 R/predict.r | 12 + R/publications.r | 256 ++++++++++++++++++++++++++++++++++- R/scholar.r | 14 + R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/scholar.html | 98 ++++++------- man/get_article_scholar_url.Rd |only man/get_publication_abstract.Rd |only man/get_publication_data_extended.Rd |only man/get_publication_date.Rd |only man/get_publication_url.Rd |only man/predict_h_index.Rd | 6 tests/testthat/test-scholar.R | 30 +++- 18 files changed, 382 insertions(+), 85 deletions(-)
Title: Import XY-Data into R
Description: Provides access to the 'xylib' C library for to import xy
data from powder diffraction, spectroscopy and other experimental methods.
Author: Sebastian Kreutzer [aut, trl, cre]
,
Johannes Friedrich [aut] ,
RLum Team [ctb],
Marcin Wojdyr [cph] ,
Peng Zhang [cph]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between rxylib versions 0.2.7 dated 2022-02-20 and 0.2.8 dated 2022-08-09
DESCRIPTION | 22 +++++------ MD5 | 44 +++++++++++----------- NEWS.md | 73 ++------------------------------------ R/convert_xy2TKA.R | 17 ++++---- R/read_xyData.R | 25 +++---------- R/rxylib.R | 6 ++- README.md | 7 ++- inst/include/xylib/cache.h | 19 +++------ inst/include/xylib/canberra_mca.h | 1 inst/include/xylib/util.h | 11 ----- man/convert_xy2TKA.Rd | 6 +-- man/read_xyData.Rd | 5 +- man/rxylib-package.Rd | 6 ++- src/xylib/bruker_raw.cpp | 7 ++- src/xylib/bruker_spc.cpp | 2 - src/xylib/cache.cpp | 4 +- src/xylib/canberra_cnf.cpp | 11 ++--- src/xylib/canberra_mca.cpp | 7 --- src/xylib/csv.cpp | 2 - src/xylib/util.cpp | 6 +-- src/xylib/xrdml.cpp | 3 + src/xylib/xylib.cpp | 4 +- tests/testthat/test_read_xyData.R | 5 +- 23 files changed, 102 insertions(+), 191 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Paul Nulty [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
William Lowe [aut] ,
Christian Mueller [ctb],
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 3.2.1 dated 2022-03-01 and 3.2.2 dated 2022-08-09
DESCRIPTION | 8 - MD5 | 59 ++++---- NAMESPACE | 1 NEWS.md | 9 + R/dfm-methods.R | 2 R/dfm_lookup.R | 2 R/dictionaries.R | 120 ++++++++++------- R/fcm.R | 4 R/object-builder.R | 1 R/object2fixed.R | 2 R/phrases.R | 6 R/tokens_chunk.R | 3 R/tokens_select.R | 16 +- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/quickstart.html | 224 ++++++++++++++++++++++++-------- man/dfm_lookup.Rd | 2 man/flatten_dictionary.Rd | 53 +++---- man/flatten_list.Rd |only man/tokens_select.Rd | 8 - src/tokens_select_mt.cpp | 15 -- tests/testthat/test-collocations.R | 11 - tests/testthat/test-default-methods.R | 4 tests/testthat/test-dictionaries.R | 60 ++++++++ tests/testthat/test-fcm.R | 31 ++++ tests/testthat/test-object-builders.R | 10 + tests/testthat/test-object-robustness.R | 16 ++ tests/testthat/test-phrases.R | 21 +-- tests/testthat/test-tokens_chunk.R | 19 +- tests/testthat/test-tokens_select.R | 48 ++++++ 31 files changed, 540 insertions(+), 217 deletions(-)
Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Description: Functions for the input/output and visualization of
medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI'
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [aut],
Karsten Tabelow [ctb],
Jon Clayden [ctb],
John Muschelli [aut]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.nifti versions 0.11.2 dated 2022-06-10 and 0.11.3 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/plot.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 5.3.0 dated 2022-06-24 and 5.4.2 dated 2022-08-09
lefko3-5.3.0/lefko3/NEWS |only lefko3-5.3.0/lefko3/man/lambda3.lefkoMat.Rd |only lefko3-5.3.0/lefko3/man/lambda3.matrix.Rd |only lefko3-5.3.0/lefko3/src/matsndyn.cpp |only lefko3-5.4.2/lefko3/DESCRIPTION | 10 lefko3-5.4.2/lefko3/MD5 | 132 - lefko3-5.4.2/lefko3/NAMESPACE | 2 lefko3-5.4.2/lefko3/NEWS.md |only lefko3-5.4.2/lefko3/R/RcppExports.R | 1595 +++++++++++++---------- lefko3-5.4.2/lefko3/R/data.R | 137 + lefko3-5.4.2/lefko3/R/datamanag.R | 12 lefko3-5.4.2/lefko3/R/errorchecks.R | 5 lefko3-5.4.2/lefko3/R/modelselection.R | 3 lefko3-5.4.2/lefko3/R/popchar.R | 315 ---- lefko3-5.4.2/lefko3/R/popdyn.R | 421 ------ lefko3-5.4.2/lefko3/build/vignette.rds |binary lefko3-5.4.2/lefko3/data/anthyllis.rda |only lefko3-5.4.2/lefko3/inst/doc/Chapter2.Rmd | 176 +- lefko3-5.4.2/lefko3/inst/doc/Chapter2.html | 238 +-- lefko3-5.4.2/lefko3/inst/doc/Chapter6.Rmd | 68 lefko3-5.4.2/lefko3/inst/doc/Chapter6.html | 321 ++-- lefko3-5.4.2/lefko3/inst/doc/Chapter8.Rmd | 132 - lefko3-5.4.2/lefko3/inst/doc/Chapter8.html | 387 ++--- lefko3-5.4.2/lefko3/inst/doc/Chapter9.Rmd | 24 lefko3-5.4.2/lefko3/inst/doc/Chapter9.html | 73 - lefko3-5.4.2/lefko3/man/actualstage3.Rd | 35 lefko3-5.4.2/lefko3/man/anthyllis.Rd |only lefko3-5.4.2/lefko3/man/cypvert.Rd | 86 + lefko3-5.4.2/lefko3/man/density_vr.Rd | 2 lefko3-5.4.2/lefko3/man/f_projection3.Rd | 10 lefko3-5.4.2/lefko3/man/hist_null.Rd | 12 lefko3-5.4.2/lefko3/man/lambda3.Rd | 46 lefko3-5.4.2/lefko3/man/lmean.Rd | 4 lefko3-5.4.2/lefko3/man/modelsearch.Rd | 3 lefko3-5.4.2/lefko3/man/projection3.Rd | 13 lefko3-5.4.2/lefko3/src/LefkoUtils.cpp |only lefko3-5.4.2/lefko3/src/LefkoUtils.h |only lefko3-5.4.2/lefko3/src/MatsNProj.cpp |only lefko3-5.4.2/lefko3/src/PopChar.cpp |only lefko3-5.4.2/lefko3/src/PopDyn2.cpp |only lefko3-5.4.2/lefko3/src/RcppExports.cpp | 277 +-- lefko3-5.4.2/lefko3/vignettes/Ch2.26-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch2.27-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch2.28-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch2.38-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch2.39-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.12-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.13-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.16-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.18-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.21-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.22-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch6.5-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.12-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.15-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.16-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.17-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.20-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.21-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.25-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.26-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch8.7-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch9.10-1.png |binary lefko3-5.4.2/lefko3/vignettes/Ch9.11-1.png |binary lefko3-5.4.2/lefko3/vignettes/Chapter2.Rmd | 176 +- lefko3-5.4.2/lefko3/vignettes/Chapter2.Rmd.orig | 23 lefko3-5.4.2/lefko3/vignettes/Chapter6.Rmd | 68 lefko3-5.4.2/lefko3/vignettes/Chapter6.Rmd.orig | 23 lefko3-5.4.2/lefko3/vignettes/Chapter8.Rmd | 132 - lefko3-5.4.2/lefko3/vignettes/Chapter8.Rmd.orig | 51 lefko3-5.4.2/lefko3/vignettes/Chapter9.Rmd | 24 lefko3-5.4.2/lefko3/vignettes/Chapter9.Rmd.orig | 12 lefko3-5.4.2/lefko3/vignettes/Lefko3Tutorial.bib | 84 + 73 files changed, 2495 insertions(+), 2637 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.5.6 dated 2022-05-19 and 0.5.7 dated 2022-08-09
inti-0.5.6/inti/R/figure2rmd.R |only inti-0.5.6/inti/R/gdoc2rmd.R |only inti-0.5.6/inti/R/table2rmd.R |only inti-0.5.6/inti/man/figure2rmd.Rd |only inti-0.5.6/inti/man/gdoc2rmd.Rd |only inti-0.5.6/inti/man/table2rmd.Rd |only inti-0.5.7/inti/DESCRIPTION | 10 inti-0.5.7/inti/MD5 | 62 ++--- inti-0.5.7/inti/NAMESPACE | 6 inti-0.5.7/inti/NEWS.md | 15 + inti-0.5.7/inti/R/H2cal.R | 4 inti-0.5.7/inti/R/figure2qmd.R |only inti-0.5.7/inti/R/gdoc2qmd.R |only inti-0.5.7/inti/R/jc_tombola.R | 100 +++++--- inti-0.5.7/inti/R/outliers_remove.R | 16 + inti-0.5.7/inti/R/plot_raw.R | 13 - inti-0.5.7/inti/R/split_folder.R | 3 inti-0.5.7/inti/R/table2qmd.R |only inti-0.5.7/inti/R/yupana_mvr.R | 112 +++++----- inti-0.5.7/inti/build/partial.rdb |binary inti-0.5.7/inti/build/vignette.rds |binary inti-0.5.7/inti/inst/doc/apps.html | 8 inti-0.5.7/inti/inst/doc/heritability.html | 38 +-- inti-0.5.7/inti/inst/doc/rticles.html | 2 inti-0.5.7/inti/inst/doc/tarpuy.html | 2 inti-0.5.7/inti/inst/doc/yupana.html | 14 - inti-0.5.7/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 inti-0.5.7/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 6 inti-0.5.7/inti/inst/yupana/server.R | 67 +---- inti-0.5.7/inti/inst/yupana/ui.R | 4 inti-0.5.7/inti/man/figure2qmd.Rd |only inti-0.5.7/inti/man/figures/logo.png |binary inti-0.5.7/inti/man/gdoc2qmd.Rd |only inti-0.5.7/inti/man/jc_tombola.Rd | 21 - inti-0.5.7/inti/man/outliers_remove.Rd | 11 inti-0.5.7/inti/man/plot_raw.Rd | 5 inti-0.5.7/inti/man/table2qmd.Rd |only inti-0.5.7/inti/man/yupana_mvr.Rd | 26 -- 38 files changed, 283 insertions(+), 268 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<http://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess,
S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview
of the field.
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.2.7 dated 2022-01-26 and 0.2.8 dated 2022-08-09
apollo-0.2.7/apollo/R/output |only apollo-0.2.8/apollo/DESCRIPTION | 8 apollo-0.2.8/apollo/MD5 | 159 - apollo-0.2.8/apollo/NAMESPACE | 7 apollo-0.2.8/apollo/R/RcppExports.R | 78 apollo-0.2.8/apollo/R/apollo_basTest.R | 11 apollo-0.2.8/apollo/R/apollo_choiceAnalysis.R | 8 apollo-0.2.8/apollo/R/apollo_classAlloc.R | 2 apollo-0.2.8/apollo/R/apollo_cnl.R | 637 +++--- apollo-0.2.8/apollo/R/apollo_combineResults.R | 4 apollo-0.2.8/apollo/R/apollo_conditionals.R | 79 apollo-0.2.8/apollo/R/apollo_dVdB.R | 158 - apollo-0.2.8/apollo/R/apollo_dVdB2.R |only apollo-0.2.8/apollo/R/apollo_deltaMethod.R | 18 apollo-0.2.8/apollo/R/apollo_dft.R | 50 apollo-0.2.8/apollo/R/apollo_diagnostics.R | 2 apollo-0.2.8/apollo/R/apollo_el.R | 47 apollo-0.2.8/apollo/R/apollo_estimate.R | 1689 +++++++++-------- apollo-0.2.8/apollo/R/apollo_estimateHB.R | 862 +++++--- apollo-0.2.8/apollo/R/apollo_fmnl.R | 46 apollo-0.2.8/apollo/R/apollo_insertFunc.R | 865 ++++---- apollo-0.2.8/apollo/R/apollo_insertQuotes.R |only apollo-0.2.8/apollo/R/apollo_lc.R | 71 apollo-0.2.8/apollo/R/apollo_lcConditionals.R | 138 - apollo-0.2.8/apollo/R/apollo_lcEM.R | 1092 +++++------ apollo-0.2.8/apollo/R/apollo_longToWide.R |only apollo-0.2.8/apollo/R/apollo_makeCluster.R | 474 ++-- apollo-0.2.8/apollo/R/apollo_makeGrad.R | 415 ++-- apollo-0.2.8/apollo/R/apollo_makeLogLike.R | 561 ++--- apollo-0.2.8/apollo/R/apollo_mdcev.R | 45 apollo-0.2.8/apollo/R/apollo_mdcnev.R | 1010 +++++----- apollo-0.2.8/apollo/R/apollo_mixConditionals.R |only apollo-0.2.8/apollo/R/apollo_mixUnconditionals.R |only apollo-0.2.8/apollo/R/apollo_mnl.R | 788 ++++---- apollo-0.2.8/apollo/R/apollo_modeChoiceData.R | 4 apollo-0.2.8/apollo/R/apollo_modelOutput.R | 181 + apollo-0.2.8/apollo/R/apollo_modifyUserDefFunc.R |only apollo-0.2.8/apollo/R/apollo_nl.R | 647 +++--- apollo-0.2.8/apollo/R/apollo_normalDensity.R | 69 apollo-0.2.8/apollo/R/apollo_ol.R | 600 +++--- apollo-0.2.8/apollo/R/apollo_op.R | 602 +++--- apollo-0.2.8/apollo/R/apollo_outOfSample.R | 712 ++++--- apollo-0.2.8/apollo/R/apollo_panelProd.R | 263 +- apollo-0.2.8/apollo/R/apollo_prediction.R | 53 apollo-0.2.8/apollo/R/apollo_prepareProb.R | 2 apollo-0.2.8/apollo/R/apollo_preprocess.R | 25 apollo-0.2.8/apollo/R/apollo_print.R | 1 apollo-0.2.8/apollo/R/apollo_rrm.R |only apollo-0.2.8/apollo/R/apollo_saveOutput.R | 497 ++--- apollo-0.2.8/apollo/R/apollo_speedTest.R | 2 apollo-0.2.8/apollo/R/apollo_unconditionals.R | 69 apollo-0.2.8/apollo/R/apollo_validate.R | 605 +++--- apollo-0.2.8/apollo/R/apollo_validateData.R | 146 - apollo-0.2.8/apollo/R/apollo_validateHBControl.R | 3 apollo-0.2.8/apollo/R/apollo_validateInputs.R | 4 apollo-0.2.8/apollo/R/apollo_varcov.R | 2 apollo-0.2.8/apollo/R/apollo_weighting.R | 31 apollo-0.2.8/apollo/R/apollo_writeF12.R | 202 +- apollo-0.2.8/apollo/R/onAttach.R | 62 apollo-0.2.8/apollo/build/vignette.rds |binary apollo-0.2.8/apollo/data/apollo_drugChoiceData.RData |binary apollo-0.2.8/apollo/data/apollo_modeChoiceData.RData |binary apollo-0.2.8/apollo/inst/doc/apollofirstexample.R | 620 +++--- apollo-0.2.8/apollo/inst/doc/apollofirstexample.html | 1840 ++++++++++--------- apollo-0.2.8/apollo/man/apollo_bootstrap.Rd | 4 apollo-0.2.8/apollo/man/apollo_choiceAnalysis.Rd | 2 apollo-0.2.8/apollo/man/apollo_conditionals.Rd | 18 apollo-0.2.8/apollo/man/apollo_dVdB.Rd | 2 apollo-0.2.8/apollo/man/apollo_dVdB2.Rd |only apollo-0.2.8/apollo/man/apollo_deltaMethod.Rd | 1 apollo-0.2.8/apollo/man/apollo_estimate.Rd | 2 apollo-0.2.8/apollo/man/apollo_insertRRMQuotes.Rd |only apollo-0.2.8/apollo/man/apollo_lcConditionals.Rd | 2 apollo-0.2.8/apollo/man/apollo_longToWide.Rd |only apollo-0.2.8/apollo/man/apollo_mixConditionals.Rd |only apollo-0.2.8/apollo/man/apollo_mixUnconditionals.Rd |only apollo-0.2.8/apollo/man/apollo_modeChoiceData.Rd | 4 apollo-0.2.8/apollo/man/apollo_modifyUserDefFunc.Rd |only apollo-0.2.8/apollo/man/apollo_ol.Rd | 2 apollo-0.2.8/apollo/man/apollo_op.Rd | 2 apollo-0.2.8/apollo/man/apollo_outOfSample.Rd | 164 + apollo-0.2.8/apollo/man/apollo_rrm.Rd |only apollo-0.2.8/apollo/man/apollo_unconditionals.Rd | 23 apollo-0.2.8/apollo/man/apollo_validateData.Rd | 10 apollo-0.2.8/apollo/man/apollo_validateHBControl.Rd | 1 apollo-0.2.8/apollo/man/apollo_validateInputs.Rd | 4 apollo-0.2.8/apollo/man/apollo_writeF12.Rd | 2 apollo-0.2.8/apollo/src/RcppExports.cpp | 5 88 files changed, 9069 insertions(+), 7745 deletions(-)
Title: Time Series for Data Science
Description: Accompanies the texts Time Series for Data Science with R by Woodward, Sadler and Robertson & Applied Time Series Analysis with R, 2nd edition by Woodward, Gray, and Elliott. It is helpful for data analysis and for time series instruction.
Author: Wayne Woodward
Maintainer: Bivin Sadler <bsadler@smu.edu>
Diff between tswge versions 1.0.0 dated 2016-12-05 and 2.0.0 dated 2022-08-09
DESCRIPTION | 18 +- MD5 | 150 ++++++++++++---- NAMESPACE | 29 ++- R/aic.ar.wge.R |only R/aic.burg.wge.R |only R/aic.wge.R | 9 - R/aic5.ar.wge.R |only R/aic5.wge.R | 7 R/artrans.wge.R | 2 R/butterworth.wge.R | 4 R/co.wge.R |only R/est.ar.wge.R | 47 ++--- R/est.arma.wge.R | 5 R/expsmooth.wge.R |only R/factor.comp.wge.R | 4 R/factor.wge.R | 58 +++++- R/fore.arima.wge.R |only R/fore.arma.wge.R | 80 +++++---- R/fore.aruma.wge.R | 317 +++++++++++++++++++---------------- R/fore.sigplusnoise.wge.R | 373 +++++++++++++++++++++--------------------- R/gen.arima.wge.R | 65 +++++-- R/gen.arma.wge.R | 28 ++- R/gen.aruma.wge.R | 2 R/gen.sigplusnoise.wge.R | 68 ++----- R/ma.pred.wge.R |only R/ma.smooth.wge.R |only R/mult.wge.R | 106 ++++++----- R/pacfts.wge.R |only R/pi.weights.wge.R |only R/plotts.sample.wge.R | 130 ++++++++------ R/plotts.true.wge.R | 86 +++++++-- R/plotts.wge.R | 88 ++++++--- R/psi.weights.wge.R | 4 R/roll.win.rmse.nn.wge.R |only R/roll.win.rmse.wge.R |only R/sample.spec.wge.R |only R/slr.wge.R |only R/true.arma.aut.wge.R | 6 R/true.arma.spec.wge.R | 6 R/unit.circle.wge.R |only R/wbg.boot.wge.R |only data/Bsales.rda |only data/MedDays.rda |only data/NAICS.rda |only data/NSA.rda |only data/bitcoin.rda |only data/cardiac.rda |only data/dfw.2011.rda |only data/dfw.mon.rda |only data/dfw.yr.rda |only data/dow.annual.rda |only data/dow1985.rda |only data/global2020.rda |only data/linearchirp.rda |only data/ozona.rda |only data/rate.rda |only data/sunspot2.0.month.rda |only data/sunspot2.0.rda |only data/tesla.rda |only data/tx.unemp.adj.rda |only data/tx.unemp.unadj.rda |only data/us.retail.rda |only data/uspop.rda |only data/wtcrude2020.rda |only data/yellowcab.precleaned.rda |only man/Bsales.Rd |only man/MedDays.Rd |only man/NAICS.Rd |only man/NSA.Rd |only man/aic.ar.wge.Rd |only man/aic.burg.wge.Rd |only man/aic5.ar.wge.Rd |only man/bitcoin.Rd |only man/cardiac.Rd |only man/co.wge.Rd |only man/dfw.2011.Rd |only man/dfw.mon.Rd |only man/dfw.yr.Rd |only man/dow.annual.Rd |only man/dow1985.Rd |only man/est.ar.wge.Rd | 55 +++--- man/expsmooth.wge.Rd |only man/factor.wge.Rd | 31 +-- man/fore.arima.wge.Rd |only man/fore.arma.wge.Rd | 6 man/fore.aruma.wge.Rd | 87 +++++---- man/fore.sigplusnoise.wge.Rd | 67 +++---- man/gen.arima.wge.Rd | 4 man/gen.arma.wge.Rd | 5 man/global2020.Rd |only man/linearchirp.Rd |only man/ma.pred.wge.Rd |only man/ma.smooth.wge.Rd |only man/ozona.Rd |only man/pacfts.wge.Rd |only man/pi.weights.wge.Rd |only man/plotts.sample.wge.Rd | 50 +++-- man/plotts.true.wge.Rd | 5 man/plotts.wge.Rd | 42 +++- man/psi.weights.wge.Rd | 32 +-- man/rate.Rd |only man/roll.win.rmse.nn.wge.Rd |only man/roll.win.rmse.wge.Rd |only man/sample.spec.wge.Rd |only man/slr.wge.Rd |only man/sunspot2.0.Rd |only man/sunspot2.0.month.Rd |only man/tesla.Rd |only man/tx.unemp.adj.Rd |only man/tx.unemp.unadj.Rd |only man/unit.circle.wge.Rd |only man/us.retail.Rd |only man/uspop.Rd |only man/wbg.boot.wge.Rd |only man/wtcrude2020.Rd |only man/yellowcab.precleaned.Rd |only 116 files changed, 1216 insertions(+), 860 deletions(-)
Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for
Stochastic Differential Equations With R Examples, ISBN
978-0-387-75838-1, Springer, NY.
Author: Stefano Maria Iacus
Maintainer: Stefano Maria Iacus <siacus@iq.harvard.edu>
Diff between sde versions 2.0.15 dated 2016-04-13 and 2.0.18 dated 2022-08-09
DESCRIPTION | 9 ++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 2 +- NEWS |only build/partial.rdb |only build/vignette.rds |binary inst/doc/sde.errata.pdf |binary man/MOdist.Rd | 2 +- man/quotes.Rd | 2 +- man/sdeDiv.Rd | 2 +- src/sde.sim.c | 21 +++++++++++++-------- 11 files changed, 31 insertions(+), 25 deletions(-)
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, least-cost corridors, least-cost networks using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 1.6 dated 2022-03-18 and 1.7 dated 2022-08-09
DESCRIPTION | 12 +-- MD5 | 32 +++++----- NAMESPACE | 2 NEWS.md | 16 +++-- R/movealloc.R | 19 +++++- R/movebound.R | 27 +++++++- R/movecomp.R | 17 +++-- R/movecorr.R | 33 ++++++++-- R/movecost.R | 171 ++++++++++++++++++++++++++++++++++++++++++------------- R/movenetw.R | 162 ++++++++++++++++++++++++++++++++++++++++++---------- README.md | 7 +- man/movealloc.Rd | 5 + man/movebound.Rd | 11 +++ man/movecomp.Rd | 11 +++ man/movecorr.Rd | 11 +++ man/movecost.Rd | 106 +++++++++++++++++++++++++--------- man/movenetw.Rd | 46 ++++++++++---- 17 files changed, 530 insertions(+), 158 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Proposes a new file format ('gson') for storing gene set and related information, and provides read, write and other utilities to process this file format.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.0.6 dated 2022-06-06 and 0.0.7 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md |only R/00-AllClasses.R | 11 +++++++---- R/IO.R | 9 +++++++-- R/gson.R | 6 ++++-- man/GSON-class.Rd | 2 ++ man/gson.Rd | 3 +++ 8 files changed, 34 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-14 1.1.1
2022-06-28 1.0.0
Title: Hybrid Forecasting Model Based on STL Decomposition and ELM
Description: Univariate time series forecasting with STL decomposition based Extreme Learning Machine hybrid model. For method details see Xiong T, Li C, Bao Y (2018). <doi:10.1016/j.neucom.2017.11.053>.
Author: Girish Kumar Jha [aut, cre],
Ronit Jaiswal [aut, ctb],
Kapil Choudhary [ctb],
Rajeev Ranjan Kumar [ctb]
Maintainer: Girish Kumar Jha <girish.stat@gmail.com>
Diff between stlELM versions 0.1.0 dated 2021-02-22 and 0.1.1 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/STLELM.R | 3 ++- data/Data_potato.rda |binary man/Data_potato.Rd | 10 +++++----- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'.
This package provides a Database Interface 'DBI' compliant
driver for 'R' to access 'PostgreSQL' database systems.
In order to build and install this package from source, 'PostgreSQL'
itself must be present your system to provide 'PostgreSQL' functionality
via its libraries and header files. These files are provided as
'postgresql-devel' package under some Linux distributions.
On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga , Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Diff between RPostgreSQL versions 0.7-3 dated 2021-10-22 and 0.7-4 dated 2022-08-09
DESCRIPTION | 8 - MD5 | 20 +-- R/PostgreSQLSupport.R | 2 configure.ac | 9 + man/dbConnect-methods.Rd | 6 - src/RS-DBI.c | 242 +++++++++++++++++++++----------------------- src/RS-DBI.h | 76 ++++++------- src/RS-PostgreSQL.c | 135 ++++++++++++------------ src/RS-pgsql-getResult.c | 6 - src/RS-pgsql-pqexec.c | 6 - src/RS-pgsql-pqexecparams.c | 12 +- 11 files changed, 266 insertions(+), 256 deletions(-)
Title: Inspection, Comparison and Visualisation of Data Frames
Description: A collection of utilities for columnwise summary, comparison and visualisation of data frames. Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.
Author: Alastair Rushworth [aut, cre],
David Wilkins [ctb]
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Diff between inspectdf versions 0.0.11 dated 2021-04-02 and 0.0.12 dated 2022-08-09
DESCRIPTION | 12 - MD5 | 42 ++--- NAMESPACE | 9 + NEWS.md | 11 + R/check_factors.R | 2 R/get_df_names.R | 4 R/inspect_mem.R | 10 - R/inspect_num.R | 159 ++++++++++++------- R/inspect_types.R | 14 - R/palletes.R | 7 R/plot_cat.R | 154 +++++++++--------- R/plot_cor.R | 30 +++ R/plot_imb.R | 36 +++- R/plot_mem.R | 27 ++- R/plot_na.R | 37 +++- R/plot_num.R | 431 ++++++++++++++++++++++++++++++++++++++++------------ R/plot_types.R | 56 ++++-- R/prop_value.R | 10 - R/show_plot.R | 264 ++++++++++--------------------- R/zzz.R | 15 + man/show_plot.Rd | 79 ++++----- src/RcppExports.cpp | 5 22 files changed, 871 insertions(+), 543 deletions(-)
Title: Ensemble Empirical Mode Decomposition and Its Variant Based ELM
Model
Description: Forecasting univariate time series with different decomposition based Extreme Learning Machine models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>, Parida M, Behera MK, Nayak N (2018). <doi:10.1109/ICSESP.2018.8376723>.
Author: Girish Kumar Jha [aut, cre],
Kapil Choudhary [aut, ctb],
Rajeev Ranjan Kumar [ctb],
Ronit Jaiswal [ctb]
Maintainer: Girish Kumar Jha <girish.stat@gmail.com>
Diff between EEMDelm versions 0.1.0 dated 2021-01-14 and 0.1.1 dated 2022-08-09
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-18 0.1
Title: Fast Computation of Latent Correlations for Mixed Data
Description: The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated),
comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation.
The estimation is based on latent copula Gaussian models.
For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017).
For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <arXiv:1809.06255>.
For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>.
For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.
Author: Mingze Huang [aut, cre] ,
Grace Yoon [aut] ,
Christian Müller [aut] ,
Irina Gaynanova [aut]
Maintainer: Mingze Huang <mingzehuang@gmail.com>
Diff between latentcor versions 1.2.1 dated 2022-06-07 and 2.0.0 dated 2022-08-09
DESCRIPTION | 23 ++--- MD5 | 48 +++++++---- NAMESPACE | 53 +++++++----- NEWS.md | 4 R/evaluation.R |only R/internal.R | 5 - R/interpolant.R |only R/interpolation.R |only R/ipol.R |only R/latentcor.R | 2 R/multilinear.R |only R/sysdata.rda |only R/tools.R |only README.md | 6 + inst/doc/latentcor.R | 2 inst/doc/latentcor.Rmd | 3 inst/doc/latentcor.html | 117 +++++++++++++-------------- inst/doc/latentcor_math.Rmd | 2 inst/doc/latentcor_math.html | 80 +++++++++--------- man/evaluation.Rd |only man/examples/latentcor_ex.R | 20 ++-- man/interpolant.Rd |only man/interpolation.Rd |only man/ipol.Rd |only man/latentcor.Rd | 22 ++--- man/mlappx.real.Rd |only src |only tests/testthat/test_latentcor.R | 170 ++++++++++++++++++++-------------------- vignettes/latentcor.Rmd | 3 vignettes/latentcor_math.Rmd | 2 30 files changed, 300 insertions(+), 262 deletions(-)
Title: Optimum Block Length
Description: Obtain optimum block from Non-overlapping Block Bootstrap method.
Author: Daniel James [cre, aut],
Ayinde Kayode [aut]
Maintainer: Daniel James <futathesis@gmail.com>
Diff between OBL versions 0.1.0 dated 2022-06-28 and 0.2.0 dated 2022-08-09
DESCRIPTION | 8 ++--- MD5 | 20 ++++++++------ NAMESPACE | 13 ++++++--- NEWS.md |only R/autoboot.R | 30 +++++++++------------ R/blockplot.R |only inst/doc/OBL.R | 18 +++++++++++- inst/doc/OBL.Rmd | 29 ++++++++++++++++++-- inst/doc/OBL.html | 56 ++++++++++++++++++++++++++++++---------- man/This.Rd | 25 ++++++++++++++++- man/figures |only vignettes/OBL.Rmd | 29 ++++++++++++++++++-- vignettes/measurement_scale.PNG |only 13 files changed, 172 insertions(+), 56 deletions(-)