Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation.
The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup.
The diagram may show thousands of them. The position of the dot in the diagram is determined by the
sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The
sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore,
the diagram shows the line of no effect and the overall study results. For small subgroups, which
are found on the left side of the plot, larger random deviations from the mean study effect are expected,
while for larger subgroups only small deviations from the study mean can be expected to be chance findings.
So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a
kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups.
This approach was presented in Muysers (2020) <doi:10.1007/s43441-019-00082-6> and referenced in Ballarini (2020) <doi:10.1002/pst.2012>.
New to version 3 is the Automatic Screening of one- or MUlti-factorial Subgroups (ASMUS) for documentation of the structured review of subgroup findings.
Author: Bodo Kirsch, Steffen Jeske, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Diff between subscreen versions 2.0.1 dated 2019-01-07 and 3.0.0 dated 2020-07-30
subscreen-2.0.1/subscreen/inst/shiny-app/subscreen/scresults.rds |only subscreen-2.0.1/subscreen/inst/shiny-app/subscreen/scrimportance.rds |only subscreen-3.0.0/subscreen/DESCRIPTION | 15 subscreen-3.0.0/subscreen/MD5 | 30 subscreen-3.0.0/subscreen/NAMESPACE | 18 subscreen-3.0.0/subscreen/NEWS.md | 69 subscreen-3.0.0/subscreen/R/subscreencalc.R | 695 subscreen-3.0.0/subscreen/R/subscreenshow.R | 54 subscreen-3.0.0/subscreen/R/subscreenvi.R | 87 subscreen-3.0.0/subscreen/R/zzz.R |only subscreen-3.0.0/subscreen/build/vignette.rds |binary subscreen-3.0.0/subscreen/inst/doc/subscreen.html | 403 subscreen-3.0.0/subscreen/inst/doc/subscreen.rmd | 138 subscreen-3.0.0/subscreen/inst/shiny-app/subscreen/app.R | 8271 +++++++--- subscreen-3.0.0/subscreen/inst/www |only subscreen-3.0.0/subscreen/man/subscreencalc.Rd | 72 subscreen-3.0.0/subscreen/man/subscreenshow.Rd | 9 subscreen-3.0.0/subscreen/vignettes/subscreen.rmd | 138 18 files changed, 6770 insertions(+), 3229 deletions(-)
Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly
Unrelated Regression (usually called SUR) models, with spatial structure, by maximum
likelihood and three-stage least squares. The package estimates the
most common spatial specifications, that is, SUR with Spatial Lag of
X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM),
SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM),
SUR with Spatial Durbin Error Model (called SUR-SDEM),
SUR with Spatial Autoregressive terms and Spatial Autoregressive
Disturbances (called SUR-SARAR), SUR-SARAR with Spatial Lag of X
regressors (called SUR-GNM) and SUR with Spatially Independent Model (called SUR-SIM).
The methodology of these models can be found in next references
Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443>
Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut],
Fernando A Lopez [aut],
Roman Minguez [aut, cre],
Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between spsur versions 1.0.1.3 dated 2020-04-07 and 1.0.1.4 dated 2020-07-30
spsur-1.0.1.3/spsur/R/lrtestspsur.R |only spsur-1.0.1.3/spsur/demo/demo_lrtestspsur.R |only spsur-1.0.1.3/spsur/inst/doc/vig1.R |only spsur-1.0.1.3/spsur/inst/doc/vig1.Rmd |only spsur-1.0.1.3/spsur/inst/doc/vig1.html |only spsur-1.0.1.3/spsur/inst/doc/vig2.R |only spsur-1.0.1.3/spsur/inst/doc/vig2.Rmd |only spsur-1.0.1.3/spsur/inst/doc/vig2.html |only spsur-1.0.1.3/spsur/man/lrtestspsur.Rd |only spsur-1.0.1.3/spsur/vignettes/fig21_qgeom_usa.png |only spsur-1.0.1.3/spsur/vignettes/fig22_qmap_usa.png |only spsur-1.0.1.3/spsur/vignettes/fig23_qreslm_usa.png |only spsur-1.0.1.3/spsur/vignettes/fig31_qressim_usa.png |only spsur-1.0.1.3/spsur/vignettes/vig1.Rmd |only spsur-1.0.1.3/spsur/vignettes/vig2.Rmd |only spsur-1.0.1.4/spsur/DESCRIPTION | 23 spsur-1.0.1.4/spsur/MD5 | 107 +-- spsur-1.0.1.4/spsur/NAMESPACE | 11 spsur-1.0.1.4/spsur/R/X_restr.R | 18 spsur-1.0.1.4/spsur/R/aux_functions.R | 6 spsur-1.0.1.4/spsur/R/datasets.R | 54 + spsur-1.0.1.4/spsur/R/dgp_spSUR.R | 135 ++-- spsur-1.0.1.4/spsur/R/fit_spsur_3sls.R | 2 spsur-1.0.1.4/spsur/R/get_data_spsur.R | 74 ++ spsur-1.0.1.4/spsur/R/impactspsur.R | 193 +++--- spsur-1.0.1.4/spsur/R/lmtestspsur.R | 231 +++---- spsur-1.0.1.4/spsur/R/lr_betas.R | 119 +--- spsur-1.0.1.4/spsur/R/methods_spsur.R | 384 +++++++++---- spsur-1.0.1.4/spsur/R/spSUR-package.R | 29 spsur-1.0.1.4/spsur/R/spsur3sls.R | 122 +++- spsur-1.0.1.4/spsur/R/spsurml.R | 363 ++++++++---- spsur-1.0.1.4/spsur/R/spsurtime.R | 73 +- spsur-1.0.1.4/spsur/R/summary.spsur.R | 2 spsur-1.0.1.4/spsur/R/wald_betas.R | 90 +-- spsur-1.0.1.4/spsur/R/wald_deltas.R | 331 +++++------ spsur-1.0.1.4/spsur/build/vignette.rds |binary spsur-1.0.1.4/spsur/data/spain.covid.RData |only spsur-1.0.1.4/spsur/demo/00Index | 2 spsur-1.0.1.4/spsur/demo/demo_methods_spsur.R |only spsur-1.0.1.4/spsur/demo/demo_spsur3sls.R | 27 spsur-1.0.1.4/spsur/demo/demo_spsurml.R | 104 +++ spsur-1.0.1.4/spsur/inst/doc/Vignette_User_Guide.Rmd |only spsur-1.0.1.4/spsur/inst/doc/Vignette_User_Guide.html |only spsur-1.0.1.4/spsur/inst/doc/spsur-vs-spatialreg.Rmd |only spsur-1.0.1.4/spsur/inst/doc/spsur-vs-spatialreg.html |only spsur-1.0.1.4/spsur/man/dgp_spsur.Rd | 135 ++-- spsur-1.0.1.4/spsur/man/impactspsur.Rd | 187 +++--- spsur-1.0.1.4/spsur/man/lmtestspsur.Rd | 113 ++- spsur-1.0.1.4/spsur/man/lr_betas.Rd | 117 +-- spsur-1.0.1.4/spsur/man/methods_spsur.Rd | 74 ++ spsur-1.0.1.4/spsur/man/spain.covid.Rd |only spsur-1.0.1.4/spsur/man/spain.covid.sf.Rd |only spsur-1.0.1.4/spsur/man/spsur-package.Rd | 22 spsur-1.0.1.4/spsur/man/spsur3sls.Rd | 74 +- spsur-1.0.1.4/spsur/man/spsurml.Rd | 315 +++++++--- spsur-1.0.1.4/spsur/man/spsurtime.Rd | 72 +- spsur-1.0.1.4/spsur/man/wald_betas.Rd | 88 +- spsur-1.0.1.4/spsur/man/wald_deltas.Rd | 73 +- spsur-1.0.1.4/spsur/vignettes/Vignette_User_Guide.Rmd |only spsur-1.0.1.4/spsur/vignettes/bibliosure.bib | 62 -- spsur-1.0.1.4/spsur/vignettes/plotgeom-1.png |only spsur-1.0.1.4/spsur/vignettes/quantilemap-1.png |only spsur-1.0.1.4/spsur/vignettes/residualquantilemap-1.png |only spsur-1.0.1.4/spsur/vignettes/residualsurquantilemap-1.png |only spsur-1.0.1.4/spsur/vignettes/spsur-vs-spatialreg.Rmd |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-2-1.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-2-2.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-2-3.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-4-1.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-5-1.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-6-1.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-7-1.png |only spsur-1.0.1.4/spsur/vignettes/unnamed-chunk-8-1.png |only 73 files changed, 2353 insertions(+), 1479 deletions(-)
Title: Binarize Images for Enhancing Optical Character Recognition
Description: Improve optical character recognition by binarizing images. The package focuses primarily on local adaptive thresholding algorithms.
In English, this means that it has the ability to turn a color or gray scale image into a black and white image. This is particularly useful
as a preprocessing step for optical character recognition or handwritten text recognition.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital
Humanities [cph] (R wrapper),
Brandon M. Petty [ctb, cph] (Files in src/Doxa)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>
Diff between image.binarization versions 0.1.0 dated 2020-07-27 and 0.1.1 dated 2020-07-30
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS.md |only R/image_binarization.R | 1 + README.md | 1 + man/image_binarization.Rd | 1 + src/Doxa/Parameters.hpp | 9 ++++++++- src/Makevars | 2 +- 8 files changed, 22 insertions(+), 11 deletions(-)
More information about image.binarization at CRAN
Permanent link
More information about assertive.reflection at CRAN
Permanent link
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.9.0 dated 2019-11-06 and 1.0.0 dated 2020-07-30
crul-0.9.0/crul/R/delete-requests.R |only crul-0.9.0/crul/R/post-requests.R |only crul-0.9.0/crul/inst/doc/best-practices-api-packages.R |only crul-0.9.0/crul/man/delete-requests.Rd |only crul-0.9.0/crul/man/post-requests.Rd |only crul-1.0.0/crul/DESCRIPTION | 13 crul-1.0.0/crul/LICENSE | 2 crul-1.0.0/crul/MD5 | 149 +- crul-1.0.0/crul/NAMESPACE | 3 crul-1.0.0/crul/NEWS.md | 27 crul-1.0.0/crul/R/async-queue.R |only crul-1.0.0/crul/R/async.R | 115 + crul-1.0.0/crul/R/asyncvaried.R | 88 - crul-1.0.0/crul/R/client.R | 230 +-- crul-1.0.0/crul/R/crul-package.r | 8 crul-1.0.0/crul/R/curl-options.R | 10 crul-1.0.0/crul/R/curl_options.R | 40 crul-1.0.0/crul/R/httprequest.R | 110 + crul-1.0.0/crul/R/ok.R | 99 + crul-1.0.0/crul/R/ok_utils.R |only crul-1.0.0/crul/R/paginator.R | 168 +- crul-1.0.0/crul/R/response.R | 114 - crul-1.0.0/crul/R/set.R | 25 crul-1.0.0/crul/R/upload.R | 16 crul-1.0.0/crul/R/verbs.R | 44 crul-1.0.0/crul/R/zzz.R | 12 crul-1.0.0/crul/README.md | 349 ----- crul-1.0.0/crul/build/vignette.rds |binary crul-1.0.0/crul/inst/doc/async.Rmd | 80 - crul-1.0.0/crul/inst/doc/async.html | 394 +++--- crul-1.0.0/crul/inst/doc/best-practices-api-packages.Rmd | 61 crul-1.0.0/crul/inst/doc/best-practices-api-packages.html | 186 +-- crul-1.0.0/crul/inst/doc/choosing-a-client.Rmd |only crul-1.0.0/crul/inst/doc/choosing-a-client.html |only crul-1.0.0/crul/inst/doc/crul.Rmd | 134 +- crul-1.0.0/crul/inst/doc/crul.html | 441 +++---- crul-1.0.0/crul/inst/doc/curl-options.Rmd | 14 crul-1.0.0/crul/inst/doc/curl-options.html | 272 ++-- crul-1.0.0/crul/inst/doc/how-to-use-crul.Rmd | 39 crul-1.0.0/crul/inst/doc/how-to-use-crul.html | 317 ++--- crul-1.0.0/crul/man/Async.Rd | 429 ++++++ crul-1.0.0/crul/man/AsyncQueue.Rd |only crul-1.0.0/crul/man/AsyncVaried.Rd | 248 +++- crul-1.0.0/crul/man/HttpClient.Rd | 678 +++++++++-- crul-1.0.0/crul/man/HttpRequest.Rd | 445 ++++++- crul-1.0.0/crul/man/HttpResponse.Rd | 290 +++- crul-1.0.0/crul/man/Paginator.Rd | 545 +++++++- crul-1.0.0/crul/man/crul-options.Rd | 21 crul-1.0.0/crul/man/crul-package.Rd | 6 crul-1.0.0/crul/man/curl-options.Rd | 10 crul-1.0.0/crul/man/curl_verbose.Rd |only crul-1.0.0/crul/man/figures |only crul-1.0.0/crul/man/handle.Rd | 2 crul-1.0.0/crul/man/hooks.Rd | 6 crul-1.0.0/crul/man/ok.Rd | 71 + crul-1.0.0/crul/man/upload.Rd | 18 crul-1.0.0/crul/man/verb-DELETE.Rd | 20 crul-1.0.0/crul/man/verb-GET.Rd | 9 crul-1.0.0/crul/man/verb-HEAD.Rd | 9 crul-1.0.0/crul/man/verb-PATCH.Rd | 9 crul-1.0.0/crul/man/verb-POST.Rd | 42 crul-1.0.0/crul/man/verb-PUT.Rd | 9 crul-1.0.0/crul/man/writing-options.Rd | 2 crul-1.0.0/crul/tests/testthat/test-async.R | 5 crul-1.0.0/crul/tests/testthat/test-asyncqueue.R |only crul-1.0.0/crul/tests/testthat/test-auth.R | 8 crul-1.0.0/crul/tests/testthat/test-client-status.R | 8 crul-1.0.0/crul/tests/testthat/test-client.R | 4 crul-1.0.0/crul/tests/testthat/test-curl_verbose.R |only crul-1.0.0/crul/tests/testthat/test-handle.R | 4 crul-1.0.0/crul/tests/testthat/test-ok.R | 32 crul-1.0.0/crul/tests/testthat/test-proxies.R | 6 crul-1.0.0/crul/tests/testthat/test-request.R | 17 crul-1.0.0/crul/tests/testthat/test-retry.R | 2 crul-1.0.0/crul/vignettes/async.Rmd | 80 - crul-1.0.0/crul/vignettes/async.Rmd.og |only crul-1.0.0/crul/vignettes/best-practices-api-packages.Rmd | 61 crul-1.0.0/crul/vignettes/best-practices-api-packages.Rmd.og |only crul-1.0.0/crul/vignettes/choosing-a-client.Rmd |only crul-1.0.0/crul/vignettes/choosing-a-client.Rmd.og |only crul-1.0.0/crul/vignettes/crul.Rmd | 134 +- crul-1.0.0/crul/vignettes/crul.Rmd.og |only crul-1.0.0/crul/vignettes/curl-options.Rmd | 14 crul-1.0.0/crul/vignettes/curl-options.Rmd.og |only crul-1.0.0/crul/vignettes/how-to-use-crul.Rmd | 39 crul-1.0.0/crul/vignettes/how-to-use-crul.Rmd.og |only 86 files changed, 4511 insertions(+), 2332 deletions(-)
Title: Sequential Multiple Assignment Randomized Trial and Adaptive
Randomization
Description: Primary data analysis for sequential multiple assignment randomization trial (SMART) and calibration tools for clinical trial planning purposes. \n
The methods used for this package include: \n
(1) Likelihood-based global test (hypothesis test, power calculation) by in Zhong X., Cheng, B., Qian M., Cheung Y.K. (2019) <doi: 10.1016/j.cct.2019.105830>. \n
(2) IPWE-based global test (hypotehsis test, power calculation) by Ogbagaber S.B., Karp J., Wahed A.S. (2016) <doi:10.1002/sim.6747>. \n
(3) G estimates (pairwise comparison, power calculation) by Lavori R., Dawson P.W. (2012) <doi: 10.1093/biostatistics/kxr016>. \n
(4) IPW estimates (pairwise comparison, power calculation) by Murphy S.A. (2005) <doi: 10.1002/sim.2022>. \n
(5) SAMRT with adaptive randomization by Cheung Y.K. (2015) <doi: 10.1111/biom.12258>.
Author: Tony Zhong <xiaobo.zhong@mountsinai.org> \n
Xinru Wang <xw2676@cumc.columbia.edu> \n
Bin Cheng <bc2159@cumc.columbia.edu> \n
Ying Kuen Cheung <yc632@cumc.columbia.edu>
Maintainer: Tony Zhong <xiaobo.zhong@mountsinai.org>
Diff between SMARTAR versions 1.0.0 dated 2019-11-05 and 1.1.0 dated 2020-07-30
SMARTAR-1.0.0/SMARTAR/R/seqplot.R |only SMARTAR-1.1.0/SMARTAR/DESCRIPTION | 35 SMARTAR-1.1.0/SMARTAR/LICENSE |only SMARTAR-1.1.0/SMARTAR/MD5 | 84 - SMARTAR-1.1.0/SMARTAR/NAMESPACE | 6 SMARTAR-1.1.0/SMARTAR/NEWS.md |only SMARTAR-1.1.0/SMARTAR/R/SMARTAR.R |only SMARTAR-1.1.0/SMARTAR/R/atsci.R | 33 SMARTAR-1.1.0/SMARTAR/R/atsciplot.R | 203 +++- SMARTAR-1.1.0/SMARTAR/R/atsmeans.R | 411 +++++--- SMARTAR-1.1.0/SMARTAR/R/atsscan.R | 314 +++--- SMARTAR-1.1.0/SMARTAR/R/cv.R | 92 + SMARTAR-1.1.0/SMARTAR/R/ddplot.R | 571 ++++++----- SMARTAR-1.1.0/SMARTAR/R/ecov.R | 1517 +++++++++++++++++++----------- SMARTAR-1.1.0/SMARTAR/R/em.R | 133 +- SMARTAR-1.1.0/SMARTAR/R/evcmat.R | 51 - SMARTAR-1.1.0/SMARTAR/R/gemean.R | 262 +++-- SMARTAR-1.1.0/SMARTAR/R/getag.R | 25 SMARTAR-1.1.0/SMARTAR/R/getcmat.R | 28 SMARTAR-1.1.0/SMARTAR/R/getdf.R | 187 ++- SMARTAR-1.1.0/SMARTAR/R/getncp.R | 58 - SMARTAR-1.1.0/SMARTAR/R/markats.R | 166 +-- SMARTAR-1.1.0/SMARTAR/R/memean.R | 25 SMARTAR-1.1.0/SMARTAR/R/nstage.R | 21 SMARTAR-1.1.0/SMARTAR/R/overlap.R | 83 - SMARTAR-1.1.0/SMARTAR/R/pwtest.R | 77 - SMARTAR-1.1.0/SMARTAR/R/seqmeans.R | 290 +++-- SMARTAR-1.1.0/SMARTAR/R/seqplots.R |only SMARTAR-1.1.0/SMARTAR/R/seqscan.R | 233 ++-- SMARTAR-1.1.0/SMARTAR/R/smartest.R | 222 ++-- SMARTAR-1.1.0/SMARTAR/R/smartsize.R | 148 +- SMARTAR-1.1.0/SMARTAR/R/summary.myclass.R |only SMARTAR-1.1.0/SMARTAR/R/tcov.R | 1412 +++++++++++++++++++-------- SMARTAR-1.1.0/SMARTAR/R/tumat.R | 298 +++-- SMARTAR-1.1.0/SMARTAR/R/tvmat.R | 111 +- SMARTAR-1.1.0/SMARTAR/R/weight.R | 236 ++-- SMARTAR-1.1.0/SMARTAR/R/x2test.R | 47 SMARTAR-1.1.0/SMARTAR/README.md |only SMARTAR-1.1.0/SMARTAR/build |only SMARTAR-1.1.0/SMARTAR/inst |only SMARTAR-1.1.0/SMARTAR/man/SMARTAR.Rd |only SMARTAR-1.1.0/SMARTAR/man/atsmeans.Rd | 189 ++- SMARTAR-1.1.0/SMARTAR/man/getncp.Rd | 18 SMARTAR-1.1.0/SMARTAR/man/seqmeans.Rd | 145 +- SMARTAR-1.1.0/SMARTAR/man/smartest.Rd | 155 +-- SMARTAR-1.1.0/SMARTAR/man/smartsize.Rd | 108 +- SMARTAR-1.1.0/SMARTAR/man/summary.Rd |only SMARTAR-1.1.0/SMARTAR/vignettes |only 48 files changed, 4982 insertions(+), 3012 deletions(-)
Title: Assertions to Check Properties of Dates and Times
Description: A set of predicates and assertions for checking the properties of
dates and times. This is mainly for use by other package developers who
want to include run-time testing features in their own packages. End-users
will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.datetimes versions 0.0-2 dated 2016-05-10 and 0.0-3 dated 2020-07-30
DESCRIPTION | 15 - MD5 | 22 +- NEWS | 5 R/assert-is-date-string.R | 92 +++++----- R/assert-is-time.R | 298 +++++++++++++++++------------------ R/imports.R | 18 +- R/is-date-string.R | 78 ++++----- R/is-time.R | 221 +++++++++++-------------- README.md | 85 +++++---- man/is_date_string.Rd | 107 ++++++------ man/is_in_past.Rd | 226 ++++++++++++++------------ tests/testthat/test-is-date-string.R | 28 +-- 12 files changed, 602 insertions(+), 593 deletions(-)
More information about assertive.datetimes at CRAN
Permanent link
Title: Methods for Missing Data
Description: Supply functions for the creation and handling of
missing data as well as tools to evaluate missing data methods. Nearly
all possibilities of generating missing data discussed by Santos et.
al (2019) <doi:10.1109/ACCESS.2019.2891360> and some additional are
implemented. Functions are supplied to compare parameter estimates
and imputed values to true values to evaluate missing data methods.
Evaluations of these types are done, for example, by Cetin-Berber et
al. (2019) <doi:10.1177/0013164418805532> and Kim et al. (2005)
<doi:10.1093/bioinformatics/bth499>.
Author: Tobias Rockel [aut, cre]
Maintainer: Tobias Rockel <Rockel.To@gmail.com>
Diff between missMethods versions 0.1.0 dated 2020-04-01 and 0.2.0 dated 2020-07-30
DESCRIPTION | 37 - MD5 | 162 ++++--- NAMESPACE | 8 NEWS.md | 27 + R/apply_imputation.R | 36 - R/delete_1_to_x.R | 141 +++--- R/delete_MCAR.R | 66 +-- R/delete_censoring.R | 92 ++-- R/delete_one_group.R | 74 ++- R/delete_rank.R | 47 +- R/evaluate_imputation_parameters.R | 97 ++-- R/evaluate_imputed_values.R | 87 ++- R/evaluate_parameters.R | 28 - R/impute_EM.R |only R/impute_LS_adaptive.R |only R/impute_LS_array.R |only R/impute_LS_combined.R |only R/impute_LS_gene.R |only R/impute_expected_values.R |only R/impute_in_classes.R |only R/impute_location_parameter.R | 30 - R/impute_sRHD.R | 30 - R/median.R | 15 R/utils-delete.R | 145 +++--- R/utils-docu.R | 38 + R/utils-evaluation.R | 11 R/utils-md-pattern.R | 38 - R/utils.R | 83 +++ README.md | 34 - build/vignette.rds |binary inst/WORDLIST | 18 inst/doc/Generating-missing-values.R | 10 inst/doc/Generating-missing-values.Rmd | 50 +- inst/doc/Generating-missing-values.html | 157 ++++++- man/apply_imputation.Rd | 170 +++---- man/delete_MAR_1_to_x.Rd | 395 +++++++++--------- man/delete_MAR_censoring.Rd | 244 +++++------ man/delete_MAR_one_group.Rd | 283 ++++++------ man/delete_MAR_rank.Rd | 162 +++---- man/delete_MCAR.Rd | 155 +++---- man/delete_MNAR_1_to_x.Rd | 162 +++---- man/delete_MNAR_censoring.Rd | 109 ++-- man/delete_MNAR_one_group.Rd | 144 +++--- man/delete_MNAR_rank.Rd | 96 ++-- man/evaluate_imputation_parameters.Rd | 91 ++-- man/evaluate_imputed_values.Rd | 243 +++++------ man/evaluate_parameters.Rd | 106 ++-- man/impute_EM.Rd |only man/impute_LS_adaptive.Rd |only man/impute_LS_array.Rd |only man/impute_LS_combined.Rd |only man/impute_LS_gene.Rd |only man/impute_expected_values.Rd |only man/impute_hot_deck_in_classes.Rd |only man/impute_in_classes.Rd |only man/impute_mean.Rd | 154 +++---- man/impute_median.Rd | 130 ++--- man/impute_mode.Rd | 98 ++-- man/impute_sRHD.Rd | 164 +++---- man/median.factor.Rd | 15 tests/testthat.R | 1 tests/testthat/datasets |only tests/testthat/helper-datasets.R | 54 +- tests/testthat/test-EM-impute.txt |only tests/testthat/test-LSimpute_documentation.txt |only tests/testthat/test-MNAR_documentation.txt |only tests/testthat/test-apply_imputation.R | 136 +++--- tests/testthat/test-delete_1_to_x.R | 149 +++--- tests/testthat/test-delete_MCAR.R | 19 tests/testthat/test-delete_censoring.R | 97 ++-- tests/testthat/test-delete_one_group.R | 158 ++++--- tests/testthat/test-delete_rank.R | 44 +- tests/testthat/test-evaluate_imputation_parameters.R | 351 ++++++++------- tests/testthat/test-evaluate_imputed_values.R | 4 tests/testthat/test-evaluate_parameters.R | 10 tests/testthat/test-imputation_functions_data_types.R |only tests/testthat/test-impute_EM.R |only tests/testthat/test-impute_LS_adaptive-verbosity.txt |only tests/testthat/test-impute_LS_adaptive.R |only tests/testthat/test-impute_LS_array-verbosity.txt |only tests/testthat/test-impute_LS_array.R |only tests/testthat/test-impute_LS_combined-verbosity.txt |only tests/testthat/test-impute_LS_combined.R |only tests/testthat/test-impute_LS_gene.R |only tests/testthat/test-impute_expected_values.R |only tests/testthat/test-impute_in_classes.R |only tests/testthat/test-impute_methods_by_simulation.R |only tests/testthat/test-impute_sRHD.R | 91 ++-- tests/testthat/test-utils-delete.R | 72 +-- tests/testthat/test-utils-docu.R |only tests/testthat/test-utils-evaluation.R | 8 tests/testthat/test-utils-md-pattern.R | 9 tests/testthat/test-utils.R | 75 +++ vignettes/Generating-missing-values.Rmd | 50 +- vignettes/bibliography.bibtex |only 95 files changed, 3295 insertions(+), 2515 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.2.2 dated 2020-07-22 and 1.2.3 dated 2020-07-30
DESCRIPTION | 7 ++-- MD5 | 17 +++++----- NEWS.md | 6 +++ R/cran_flavors.R | 6 +-- inst/WORDLIST |only inst/doc/foghorn.html | 53 +++++++++++++++++---------------- man/cran_details.Rd | 6 +-- man/cran_results.Rd | 6 +-- man/n_cran_flavors.Rd | 4 +- tests/testthat/test-n_cran_platforms.R | 2 - 10 files changed, 58 insertions(+), 49 deletions(-)
Title: Convert R Graphics to Flash Animations
Description: Using the 'Ming' library
<http://www.libming.org/> to create Flash animations.
Users can either use the 'SWF' device swf() to generate 'SWF' file
directly through plotting functions like plot() and lines(),
or convert images of other formats ('SVG', 'PNG', 'JPEG') into 'SWF'.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between R2SWF versions 0.9-3 dated 2020-05-09 and 0.9-4 dated 2020-07-30
DESCRIPTION | 8 +++---- MD5 | 8 +++---- inst/NEWS.Rd | 9 ++++++++ src/swfDevice.c | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- src/swfDevice.h | 49 +++++++++++++++++++++++++++----------------- 5 files changed, 107 insertions(+), 28 deletions(-)
Title: Integrative Differential Network Analysis in Genomics
Description: Fits covariate dependent partial correlation matrices for integrative models to identify differential networks between two groups. The methods are described in Class et. al., (2018) <doi:10.1093/bioinformatics/btx750> and Ha et. al., (2015) <doi:10.1093/bioinformatics/btv406>.
Author: Caleb A. Class <cclass@butler.edu>, Min Jin Ha <mjha@mdanderson.org>
Maintainer: Caleb A. Class <cclass@butler.edu>
Diff between iDINGO versions 1.0.3 dated 2019-09-06 and 1.0.4 dated 2020-07-30
DESCRIPTION | 14 +-- MD5 | 28 +++---- NEWS.md | 4 + R/Greg.em.R | 154 +++++++++++++++++++++---------------------- R/Sigmax.R | 24 +++--- R/dingo.R | 184 ++++++++++++++++++++++++++-------------------------- R/extendedBIC.R | 12 +-- R/scaledMat.R | 8 +- R/scoring.boot.R | 124 +++++++++++++++++------------------ R/trans.Fisher.R | 10 +- man/Greg.em.Rd | 140 +++++++++++++++++++-------------------- man/Sigmax.Rd | 132 ++++++++++++++++++------------------- man/extendedBIC.Rd | 106 ++++++++++++++--------------- man/scaledMat.Rd | 42 +++++------ man/trans.Fisher.Rd | 42 +++++------ 15 files changed, 514 insertions(+), 510 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>),
Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>),
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>),
Matthew E Watts [aut],
Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>),
Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>),
Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 5.0.1 dated 2020-05-15 and 5.0.2 dated 2020-07-30
DESCRIPTION | 23 MD5 | 514 NAMESPACE | 2 R/ArrayParameter-proto.R | 56 R/Collection-proto.R | 52 R/ConservationModifier-proto.R | 90 R/ConservationProblem-proto.R | 224 R/Constraint-proto.R | 8 R/Decision-proto.R | 8 R/Id.R | 6 R/MiscParameter-proto.R | 34 R/Objective-proto.R | 6 R/OptimizationProblem-methods.R | 52 R/OptimizationProblem-proto.R | 82 R/Parameter-proto.R | 36 R/Parameters-proto.R | 48 R/Penalty-proto.R | 8 R/Portfolio-proto.R | 28 R/RcppExports.R | 4 R/ScalarParameter-proto.R | 46 R/Solver-proto.R | 52 R/Target-proto.R | 6 R/add_absolute_targets.R | 28 R/add_binary_decisions.R | 20 R/add_boundary_penalties.R | 94 R/add_connectivity_penalties.R | 99 R/add_contiguity_constraints.R | 72 R/add_cuts_portfolio.R | 33 R/add_default_decisions.R | 8 R/add_default_portfolio.R | 6 R/add_default_solver.R | 12 R/add_extra_portfolio.R | 10 R/add_feature_contiguity_constraints.R | 105 R/add_feature_weights.R | 40 R/add_gap_portfolio.R | 22 R/add_gurobi_solver.R | 52 R/add_linear_penalties.R |only R/add_locked_in_constraints.R | 72 R/add_locked_out_constraints.R | 18 R/add_loglinear_targets.R | 77 R/add_lpsymphony_solver.R | 12 R/add_mandatory_allocation_constraints.R | 15 R/add_manual_bounded_constraints.R | 26 R/add_manual_locked_constraints.R | 34 R/add_manual_targets.R | 58 R/add_max_cover_objective.R | 47 R/add_max_features_objective.R | 30 R/add_max_phylo_div_objective.R | 41 R/add_max_phylo_end_objective.R | 39 R/add_max_utility_objective.R | 31 R/add_min_set_objective.R | 20 R/add_min_shortfall_objective.R | 20 R/add_neighbor_contraints.R | 83 R/add_proportion_decisions.R | 8 R/add_relative_targets.R | 12 R/add_rsymphony_solver.R | 24 R/add_semicontinuous_decisions.R | 20 R/add_shuffle_portfolio.R | 18 R/add_top_portfolio.R | 14 R/adjacency_matrix.R | 32 R/binary_stack.R | 18 R/boundary_matrix.R | 47 R/branch_matrix.R | 6 R/category_layer.R | 14 R/category_vector.R | 22 R/compile.R | 40 R/connectivity_matrix.R | 177 R/constraints.R | 32 R/data.R | 115 R/decisions.R | 34 R/deprecated.R | 20 R/distribute_load.R | 12 R/fast_extract.R | 38 R/feature_abundances.R | 56 R/feature_names.R | 6 R/feature_representation.R | 92 R/ferrier_score.R | 54 R/internal.R | 82 R/intersecting_units.R | 18 R/irreplaceability.R | 26 R/loglinear_interpolation.R | 20 R/magrittr-operators.R | 12 R/marxan_boundary_data_to_matrix.R | 30 R/marxan_problem.R | 115 R/misc.R | 4 R/new_optimization_problem.R | 6 R/number_of_features.R | 6 R/number_of_planning_units.R | 6 R/number_of_total_units.R | 6 R/number_of_zones.R | 6 R/objectives.R | 32 R/package.R | 34 R/parameters.R | 84 R/penalties.R | 44 R/portfolios.R | 38 R/pproto.R | 12 R/predefined_optimization_problem.R | 38 R/presolve_check.R | 23 R/print.R | 2 R/problem.R | 207 R/proximity_matrix.R | 24 R/rarity_weighted_richness.R | 78 R/replacement_cost.R | 92 R/rij_matrix.R | 30 R/run_calculations.R | 14 R/show.R | 2 R/simulate.R | 34 R/solve.R | 135 R/solvers.R | 28 R/targets.R | 24 R/tbl_df.R | 12 R/waiver.R | 8 R/zone_names.R | 4 R/zones.R | 56 README.md | 14 build/vignette.rds |binary inst/doc/gurobi_installation.html | 26 inst/doc/prioritizr.Rmd | 100 inst/doc/prioritizr.html | 391 inst/doc/publication_record.Rmd | 7 inst/doc/publication_record.html | 23 inst/doc/saltspring.Rmd | 58 inst/doc/saltspring.html | 248 inst/doc/tasmania.Rmd | 2 inst/doc/tasmania.html |27531 +++++++++++++++++++++++- inst/doc/zones.html | 16 man/ArrayParameter-class.Rd | 24 man/Collection-class.Rd | 24 man/ConservationModifier-class.Rd | 46 man/ConservationProblem-class.Rd | 136 man/Constraint-class.Rd | 6 man/Decision-class.Rd | 6 man/MiscParameter-class.Rd | 16 man/Objective-class.Rd | 4 man/OptimizationProblem-class.Rd | 16 man/OptimizationProblem-methods.Rd | 30 man/Parameter-class.Rd | 10 man/Parameters-class.Rd | 16 man/Penalty-class.Rd | 6 man/Portfolio-class.Rd | 12 man/ScalarParameter-class.Rd | 20 man/Solver-class.Rd | 30 man/Target-class.Rd | 6 man/add_absolute_targets.Rd | 104 man/add_binary_decisions.Rd | 26 man/add_boundary_penalties.Rd | 128 man/add_connectivity_penalties.Rd | 169 man/add_contiguity_constraints.Rd | 96 man/add_cuts_portfolio.Rd | 40 man/add_default_decisions.Rd | 8 man/add_default_solver.Rd | 16 man/add_extra_portfolio.Rd | 18 man/add_feature_contiguity_constraints.Rd | 142 man/add_feature_weights.Rd | 76 man/add_gap_portfolio.Rd | 26 man/add_gurobi_solver.Rd | 30 man/add_linear_penalties.Rd |only man/add_locked_in_constraints.Rd | 134 man/add_locked_out_constraints.Rd | 134 man/add_loglinear_targets.Rd | 77 man/add_lsymphony_solver.Rd | 30 man/add_mandatory_allocation_constraints.Rd | 40 man/add_manual_bounded_constraints.Rd | 44 man/add_manual_locked_constraints.Rd | 52 man/add_manual_targets.Rd | 86 man/add_max_cover_objective.Rd | 110 man/add_max_features_objective.Rd | 86 man/add_max_phylo_div_objective.Rd | 135 man/add_max_phylo_end_objective.Rd | 137 man/add_max_utility_objective.Rd | 81 man/add_min_set_objective.Rd | 62 man/add_min_shortfall_objective.Rd | 76 man/add_neighbor_constraints.Rd | 120 man/add_proportion_decisions.Rd | 26 man/add_relative_targets.Rd | 106 man/add_rsymphony_solver.Rd | 24 man/add_semicontinuous_decisions.Rd | 36 man/add_shuffle_portfolio.Rd | 24 man/add_top_portfolio.Rd | 24 man/adjacency_matrix.Rd | 46 man/array_parameters.Rd | 20 man/as.Rd | 2 man/as.list.Rd | 4 man/binary_stack.Rd | 20 man/boundary_matrix.Rd | 49 man/branch_matrix.Rd | 10 man/category_layer.Rd | 18 man/category_vector.Rd | 14 man/compile.Rd | 26 man/connectivity_matrix.Rd | 173 man/constraints.Rd | 96 man/decisions.Rd | 68 man/distribute_load.Rd | 6 man/fast_extract.Rd | 32 man/feature_abundances.Rd | 90 man/feature_names.Rd | 3 man/feature_representation.Rd | 138 man/ferrier_score.Rd | 60 man/figures/README-boundary_penalties-1.png |binary man/figures/README-contiguity_constraints-1.png |binary man/figures/README-locked_in_constraints-1.png |binary man/figures/README-minimal_solution-1.png |binary man/figures/README-replacement_cost-1.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/intersecting_units.Rd | 16 man/irreplaceability.Rd | 46 man/loglinear_interpolation.Rd | 8 man/marxan_boundary_data_to_matrix.Rd | 12 man/marxan_problem.Rd | 137 man/matrix_parameters.Rd | 2 man/misc_parameter.Rd | 2 man/new_id.Rd | 4 man/new_optimization_problem.Rd | 6 man/new_waiver.Rd | 2 man/number_of_features.Rd | 4 man/number_of_planning_units.Rd | 4 man/number_of_total_units.Rd | 4 man/number_of_zones.Rd | 4 man/objectives.Rd | 54 man/parameters.Rd | 6 man/penalties.Rd | 74 man/pipe.Rd | 7 man/portfolios.Rd | 80 man/predefined_optimization_problem.Rd | 44 man/presolve_check.Rd | 180 man/print.Rd | 2 man/prioritizr-deprecated.Rd | 18 man/prioritizr.Rd | 60 man/problem.Rd | 333 man/proximity_matrix.Rd | 27 man/rarity_weighted_richness.Rd | 100 man/replacement_cost.Rd | 142 man/rij_matrix.Rd | 32 man/run_calculations.Rd | 12 man/scalar_parameters.Rd | 22 man/show.Rd | 2 man/sim_data.Rd | 159 man/simulate_cost.Rd | 15 man/simulate_data.Rd | 17 man/simulate_species.Rd | 13 man/solve.Rd | 160 man/solvers.Rd | 68 man/targets.Rd | 32 man/tee.Rd | 7 man/tibble-methods.Rd | 18 man/zone_names.Rd | 2 man/zones.Rd | 86 src/RcppExports.cpp | 13 src/init.c | 2 src/rcpp_apply_linear_penalties.cpp |only tests/testthat/test_add_feature_weights.R | 22 tests/testthat/test_add_linear_penalties.R |only tests/testthat/test_feature_representation.R | 11 tests/testthat/test_rij_matrix.R | 35 vignettes/prioritizr.Rmd | 100 vignettes/publication_record.Rmd | 7 vignettes/saltspring.Rmd | 58 vignettes/tasmania.Rmd | 2 260 files changed, 33474 insertions(+), 5933 deletions(-)
Title: Providing Interactive Interpretations and Explanations of
Statistical Results
Description: Allows to provide live interpretations and explanations of statistical
functions in R. These interpretations and explanations are shown when the explained function
is called by the user. They can interact with the values of the explained function's actual
results to offer relevant, meaningful insights. The 'xplain' interpretations and explanations
are based on an easy-to-use XML format that allows to include R code to interact with the
returns of the explained function.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between xplain versions 0.2.1 dated 2018-05-02 and 0.2.2 dated 2020-07-30
DESCRIPTION | 20 ++++++++------ MD5 | 15 ++++++---- R/xplain.r | 70 +++++++++++++++++++++++++++++++++++++------------ README.md |only inst |only man/xplain-package.Rd | 4 +- man/xplain.Rd | 6 ++-- man/xplain.getcall.Rd | 8 +++-- man/xplain.overview.Rd | 9 +++--- 9 files changed, 90 insertions(+), 42 deletions(-)
Title: Co-Tucker3 Analysis of Two Sequences of Matrices
Description: Provides a function called COTUCKER3() (Co-Inertia Analysis
+ Tucker3 method) which performs a Co-Tucker3 analysis of two sequences of
matrices, as well as other functions called PCA() (Principal Component Analysis)
and BGA() (Between-Groups Analysis), which perform analysis of one matrix,
COIA() (Co-Inertia Analysis), which performs analysis of two matrices, PTA()
(Partial Triadic Analysis), STATIS(), STATISDUAL() and TUCKER3(), which perform analysis of a sequence
of matrices, and BGCOIA() (Between-Groups Co-Inertia Analysis), STATICO()
(STATIS method + Co-Inertia Analysis), COSTATIS() (Co-Inertia Analysis + STATIS
method), which also perform analysis of two sequences of matrices.
Author: Miguel Rodriguez-Rosa <miguel_rosa90@usal.es> [aut, cre]
Maintainer: Miguel Rodriguez-Rosa <miguel_rosa90@usal.es>
Diff between KTensorGraphs versions 0.2 dated 2019-10-01 and 1.0 dated 2020-07-30
KTensorGraphs-0.2/KTensorGraphs/R |only KTensorGraphs-1.0/KTensorGraphs/DESCRIPTION | 10 +++++----- KTensorGraphs-1.0/KTensorGraphs/MD5 | 5 ++--- KTensorGraphs-1.0/KTensorGraphs/man/cotucker3.Rd | 10 ++++++++-- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not unlike
data.frames and import/export filters for csv files.
ff objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and virtual
attributes. ff objects have well-defined hybrid copying semantics,
which gives rise to certain performance improvements through
virtualization. ff objects can be stored and reopened across R
sessions. ff files can be shared by multiple ff R objects
(using different data en/de-coding schemes) in the same process
or from multiple R processes to exploit parallelism. A wide choice of
finalizer options allows to work with 'permanent' files as well as
creating/removing 'temporary' ff files completely transparent to the
user. On certain OS/Filesystem combinations, creating the ff files
works without notable delay thanks to using sparse file allocation.
Several access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve good
performance even with large datasets, for example virtual matrix
transpose without touching a single byte on disk. Further, to reduce
disk I/O, 'logicals' and non-standard data types get stored native and
compact on binary flat files i.e. logicals take up exactly 2 bits to
represent TRUE, FALSE and NA.
Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and ram
objects and support for batch processing on ff objects (e.g. as.ram,
as.ff, ffapply). ff interfaces closely with functionality from package
'bit': chunked looping, fast bit operations and coercions between
different objects that can store subscript information ('bit',
'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows
to work interactively with selections of large datasets and quickly
modify selection criteria.
Further high-performance enhancements can be made available upon request.
Author: Daniel Adler [aut],
Christian Gläser [aut],
Oleg Nenadic [aut],
Jens Oehlschlägel [aut, cre],
Martijn Schuemie [aut],
Walter Zucchini [aut]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 2.2-14.2 dated 2020-04-16 and 4.0.2 dated 2020-07-30
ff-2.2-14.2/ff/inst/ANNOUNCEMENT-2.0.txt |only ff-2.2-14.2/ff/inst/ANNOUNCEMENT-2.1.2.txt |only ff-2.2-14.2/ff/inst/ANNOUNCEMENT-2.1.txt |only ff-2.2-14.2/ff/inst/ANNOUNCEMENT-2.2.txt |only ff-2.2-14.2/ff/inst/README_devel.txt |only ff-2.2-14.2/ff/man/chunk.bit.rd |only ff-2.2-14.2/ff/man/clone.rd |only ff-2.2-14.2/ff/man/dimnames.ff_array.rd |only ff-4.0.2/ff/DESCRIPTION | 31 ff-4.0.2/ff/LICENSE | 2 ff-4.0.2/ff/MD5 | 298 - ff-4.0.2/ff/NAMESPACE | 259 ff-4.0.2/ff/NEWS | 1068 ++-- ff-4.0.2/ff/R/CFUN.R | 4 ff-4.0.2/ff/R/array.R | 86 ff-4.0.2/ff/R/as.ff.R | 12 ff-4.0.2/ff/R/bigsample.R | 4 ff-4.0.2/ff/R/ff.R | 1145 ++-- ff-4.0.2/ff/R/ffapply.R | 30 ff-4.0.2/ff/R/ffbit.R | 158 ff-4.0.2/ff/R/ffcsv.R | 442 - ff-4.0.2/ff/R/ffdf.R | 93 ff-4.0.2/ff/R/fffactor.R | 6 ff-4.0.2/ff/R/ffreturn.R | 30 ff-4.0.2/ff/R/ffsave.R | 18 ff-4.0.2/ff/R/fileresize.R | 4 ff-4.0.2/ff/R/fileutil.R | 4 ff-4.0.2/ff/R/generics.R | 16 ff-4.0.2/ff/R/getpagesize.R | 4 ff-4.0.2/ff/R/hi.R | 170 ff-4.0.2/ff/R/ordermerge.R | 7454 ++++++++++++++-------------- ff-4.0.2/ff/R/util.R | 10 ff-4.0.2/ff/R/vmode.R | 28 ff-4.0.2/ff/R/vt.R | 4 ff-4.0.2/ff/R/zzz.R | 413 - ff-4.0.2/ff/exec/prebuild.sh | 34 ff-4.0.2/ff/inst/doc |only ff-4.0.2/ff/man/CFUN.rd | 2 ff-4.0.2/ff/man/Extract.ff.rd | 8 ff-4.0.2/ff/man/Extract.ffdf.rd | 2 ff-4.0.2/ff/man/LimWarn.rd | 21 ff-4.0.2/ff/man/add.rd | 4 ff-4.0.2/ff/man/array2vector.rd | 2 ff-4.0.2/ff/man/arrayIndex2vectorIndex.rd | 4 ff-4.0.2/ff/man/as.ff.bit.rd | 6 ff-4.0.2/ff/man/as.ff.rd | 2 ff-4.0.2/ff/man/as.ffdf.rd | 2 ff-4.0.2/ff/man/as.hi.rd | 18 ff-4.0.2/ff/man/as.integer.hi.rd | 2 ff-4.0.2/ff/man/as.vmode.rd | 2 ff-4.0.2/ff/man/bigsample.rd | 2 ff-4.0.2/ff/man/chunk.ffdf.rd | 11 ff-4.0.2/ff/man/clone.ff.rd |only ff-4.0.2/ff/man/clone.ffdf.rd | 2 ff-4.0.2/ff/man/close.ff.rd | 2 ff-4.0.2/ff/man/delete.rd | 4 ff-4.0.2/ff/man/dim.ff.rd | 8 ff-4.0.2/ff/man/dimnames.ff.rd |only ff-4.0.2/ff/man/dimnames.ffdf.rd | 2 ff-4.0.2/ff/man/dimorderCompatible.rd | 2 ff-4.0.2/ff/man/dummy.dimnames.rd | 2 ff-4.0.2/ff/man/ff.rd | 58 ff-4.0.2/ff/man/ffapply.rd | 6 ff-4.0.2/ff/man/ffconform.rd | 4 ff-4.0.2/ff/man/ffdf.rd | 16 ff-4.0.2/ff/man/ffdfindexget.rd | 162 ff-4.0.2/ff/man/ffdfsort.rd | 120 ff-4.0.2/ff/man/ffdrop.rd | 2 ff-4.0.2/ff/man/ffindexget.rd | 158 ff-4.0.2/ff/man/ffindexorder.rd | 152 ff-4.0.2/ff/man/ffinfo.rd | 4 ff-4.0.2/ff/man/ffload.rd | 4 ff-4.0.2/ff/man/fforder.rd | 194 ff-4.0.2/ff/man/ffreturn.rd | 2 ff-4.0.2/ff/man/ffsave.rd | 4 ff-4.0.2/ff/man/ffsort.rd | 184 ff-4.0.2/ff/man/ffsuitable.rd | 2 ff-4.0.2/ff/man/ffxtensions.rd | 2 ff-4.0.2/ff/man/file.resize.rd | 2 ff-4.0.2/ff/man/filename.rd | 2 ff-4.0.2/ff/man/finalize.rd | 4 ff-4.0.2/ff/man/finalizer.rd | 12 ff-4.0.2/ff/man/fixdiag.rd | 2 ff-4.0.2/ff/man/geterror.ff.rd | 2 ff-4.0.2/ff/man/getpagesize.rd | 2 ff-4.0.2/ff/man/getset.ff.rd | 2 ff-4.0.2/ff/man/hi.rd | 8 ff-4.0.2/ff/man/hiparse.rd | 4 ff-4.0.2/ff/man/is.ff.rd | 2 ff-4.0.2/ff/man/is.ffdf.rd | 2 ff-4.0.2/ff/man/is.open.rd | 2 ff-4.0.2/ff/man/is.readonly.rd | 2 ff-4.0.2/ff/man/is.sorted.rd | 8 ff-4.0.2/ff/man/length.ff.rd | 4 ff-4.0.2/ff/man/length.ffdf.rd | 2 ff-4.0.2/ff/man/length.hi.rd | 32 ff-4.0.2/ff/man/levels.ff.rd | 2 ff-4.0.2/ff/man/matcomb.rd | 2 ff-4.0.2/ff/man/matprint.rd | 2 ff-4.0.2/ff/man/maxffmode.rd | 2 ff-4.0.2/ff/man/maxlength.rd | 2 ff-4.0.2/ff/man/mismatch.rd | 2 ff-4.0.2/ff/man/na.count.rd | 6 ff-4.0.2/ff/man/names.ff.rd | 6 ff-4.0.2/ff/man/nrowAssign.rd | 8 ff-4.0.2/ff/man/open.ff.rd | 2 ff-4.0.2/ff/man/pagesize.rd | 2 ff-4.0.2/ff/man/physical.ff.rd | 4 ff-4.0.2/ff/man/physical.ffdf.rd | 4 ff-4.0.2/ff/man/print.ff.rd | 2 ff-4.0.2/ff/man/ram2ffcode.rd | 4 ff-4.0.2/ff/man/ramattribs.rd | 6 ff-4.0.2/ff/man/ramorder.default.rd | 260 ff-4.0.2/ff/man/ramsort.default.rd | 228 ff-4.0.2/ff/man/read.table.ffdf.rd | 321 - ff-4.0.2/ff/man/readwrite.ff.rd | 2 ff-4.0.2/ff/man/regtest.fforder.rd | 612 +- ff-4.0.2/ff/man/repnam.rd | 4 ff-4.0.2/ff/man/sortLevels.rd | 4 ff-4.0.2/ff/man/splitPathFile.rd | 2 ff-4.0.2/ff/man/swap.rd | 2 ff-4.0.2/ff/man/symmIndex2vectorIndex.rd | 4 ff-4.0.2/ff/man/symmetric.rd | 2 ff-4.0.2/ff/man/unclass_-.rd | 2 ff-4.0.2/ff/man/undim.rd | 2 ff-4.0.2/ff/man/unsort.rd | 6 ff-4.0.2/ff/man/update.ff.rd | 2 ff-4.0.2/ff/man/vecprint.rd | 2 ff-4.0.2/ff/man/vector.vmode.rd | 2 ff-4.0.2/ff/man/vector2array.rd | 2 ff-4.0.2/ff/man/vectorIndex2arrayIndex.rd | 4 ff-4.0.2/ff/man/vmode.ffdf.rd | 2 ff-4.0.2/ff/man/vmode.rd | 2 ff-4.0.2/ff/man/vt.rd | 2 ff-4.0.2/ff/man/vw.rd | 4 ff-4.0.2/ff/man/write.table.ffdf.rd | 4 ff-4.0.2/ff/src/Array.hpp | 5 ff-4.0.2/ff/src/MMapFileMapping.cpp | 23 ff-4.0.2/ff/src/MMapFileMapping.hpp | 10 ff-4.0.2/ff/src/Win32FileMapping.cpp | 12 ff-4.0.2/ff/src/Win32FileMapping.hpp | 4 ff-4.0.2/ff/src/config.h | 6 ff-4.0.2/ff/src/ff.cpp | 51 ff-4.0.2/ff/src/ff.h | 4 ff-4.0.2/ff/src/ordermerge.c | 2 ff-4.0.2/ff/src/r_ff.c | 106 ff-4.0.2/ff/src/r_ff.h | 6 ff-4.0.2/ff/src/r_ff_addgetset.h | 2 ff-4.0.2/ff/src/r_ff_makevmodes.h | 2 ff-4.0.2/ff/src/r_ff_methoddeclaration.h | 2 ff-4.0.2/ff/src/r_ff_methodswitch.h | 2 ff-4.0.2/ff/src/utk_file_allocate_fseek.cpp | 19 ff-4.0.2/ff/tests |only 153 files changed, 7517 insertions(+), 7377 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlägel [aut, cre], Leonardo Silvestri [ctb]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit64 versions 0.9-7.1 dated 2020-07-15 and 4.0.2 dated 2020-07-30
bit64-0.9-7.1/bit64/inst/ANNOUNCEMENT-0.8.txt |only bit64-0.9-7.1/bit64/inst/ANNOUNCEMENT-0.9-Details.txt |only bit64-0.9-7.1/bit64/inst/ANNOUNCEMENT-0.9.txt |only bit64-0.9-7.1/bit64/inst/README_devel.txt |only bit64-0.9-7.1/bit64/src/Makevars |only bit64-0.9-7.1/bit64/src/Makevars.win |only bit64-4.0.2/bit64/DESCRIPTION | 21 bit64-4.0.2/bit64/MD5 | 78 - bit64-4.0.2/bit64/NAMESPACE | 1121 ++++++++--------- bit64-4.0.2/bit64/NEWS | 86 + bit64-4.0.2/bit64/R/cache.R | 19 bit64-4.0.2/bit64/R/hash64.R | 193 ++- bit64-4.0.2/bit64/R/highlevel64.R | 10 bit64-4.0.2/bit64/R/integer64.R | 768 ++++++++---- bit64-4.0.2/bit64/R/patch64.R | 332 ++--- bit64-4.0.2/bit64/R/sort64.R | 3 bit64-4.0.2/bit64/R/sortuse64.R | 1145 ++++++++---------- bit64-4.0.2/bit64/R/zzz.R | 6 bit64-4.0.2/bit64/data/benchmark64.data.rda |binary bit64-4.0.2/bit64/data/optimizer64.data.rda |binary bit64-4.0.2/bit64/exec/prebuild.sh | 34 bit64-4.0.2/bit64/inst/doc |only bit64-4.0.2/bit64/man/all.equal.integer64.rd |only bit64-4.0.2/bit64/man/as.character.integer64.rd | 7 bit64-4.0.2/bit64/man/as.integer64.character.rd | 29 bit64-4.0.2/bit64/man/bit64-package.rd | 7 bit64-4.0.2/bit64/man/bit64S3.rd | 228 +-- bit64-4.0.2/bit64/man/cache.rd | 7 bit64-4.0.2/bit64/man/extract.replace.integer64.rd | 7 bit64-4.0.2/bit64/man/format.integer64.rd | 8 bit64-4.0.2/bit64/man/hashmap.rd | 2 bit64-4.0.2/bit64/man/qtile.rd | 1 bit64-4.0.2/bit64/man/ramsort.integer64.rd | 2 bit64-4.0.2/bit64/man/runif64.rd |only bit64-4.0.2/bit64/man/sortnut.rd | 318 ++-- bit64-4.0.2/bit64/man/sum.integer64.rd | 3 bit64-4.0.2/bit64/src/cache.c | 3 bit64-4.0.2/bit64/src/hash64.c | 16 bit64-4.0.2/bit64/src/init.c | 21 bit64-4.0.2/bit64/src/integer64.c | 84 + bit64-4.0.2/bit64/src/integer64.h | 1 bit64-4.0.2/bit64/src/sort64.c | 7 bit64-4.0.2/bit64/src/sortuse64.c | 14 43 files changed, 2650 insertions(+), 1931 deletions(-)
Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Jens Oehlschlägel [aut, cre], Brian Ripley [ctb]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 1.1-15.2 dated 2020-02-10 and 4.0.3 dated 2020-07-30
bit-1.1-15.2/bit/exec |only bit-1.1-15.2/bit/inst/ANNOUNCEMENT-1.0.txt |only bit-1.1-15.2/bit/inst/README_devel.txt |only bit-1.1-15.2/bit/man/Extract.rd |only bit-1.1-15.2/bit/man/LogicBit.rd |only bit-1.1-15.2/bit/man/Summary.rd |only bit-1.1-15.2/bit/man/as.bit.rd |only bit-1.1-15.2/bit/man/as.bitwhich.rd |only bit-1.1-15.2/bit/man/as.logical.bit.rd |only bit-1.1-15.2/bit/man/as.which.rd |only bit-1.1-15.2/bit/man/bbatch.rd |only bit-1.1-15.2/bit/man/bit-package.rd |only bit-1.1-15.2/bit/man/bit_init.rd |only bit-1.1-15.2/bit/man/bitwhich.rd |only bit-1.1-15.2/bit/man/c.bit.rd |only bit-1.1-15.2/bit/man/chunk.rd |only bit-1.1-15.2/bit/man/clone.rd |only bit-1.1-15.2/bit/man/intrle.rd |only bit-1.1-15.2/bit/man/is.bit.rd |only bit-1.1-15.2/bit/man/is.sorted.rd |only bit-1.1-15.2/bit/man/length.bit.rd |only bit-1.1-15.2/bit/man/physical.rd |only bit-1.1-15.2/bit/man/ramsort.rd |only bit-1.1-15.2/bit/man/regtest.bit.rd |only bit-1.1-15.2/bit/man/repeat.time.rd |only bit-1.1-15.2/bit/man/repfromto.rd |only bit-1.1-15.2/bit/man/ri.rd |only bit-1.1-15.2/bit/man/rlepack.rd |only bit-1.1-15.2/bit/man/setattributes.rd |only bit-1.1-15.2/bit/man/unattr.rd |only bit-1.1-15.2/bit/man/vecseq.rd |only bit-4.0.3/bit/DESCRIPTION | 54 bit-4.0.3/bit/MD5 | 162 bit-4.0.3/bit/NAMESPACE | 585 +-- bit-4.0.3/bit/NEWS | 146 bit-4.0.3/bit/R/attrutil.R | 303 - bit-4.0.3/bit/R/bit-package.R |only bit-4.0.3/bit/R/bit.R | 4518 ++++++++++++++------------- bit-4.0.3/bit/R/bitsort.R |only bit-4.0.3/bit/R/chunkutil.R | 460 +- bit-4.0.3/bit/R/clone.R | 101 bit-4.0.3/bit/R/generics.R | 564 ++- bit-4.0.3/bit/R/integerutil.R |only bit-4.0.3/bit/R/merge.R |only bit-4.0.3/bit/R/rle.R | 228 - bit-4.0.3/bit/R/timeutil.R | 63 bit-4.0.3/bit/R/zzz.R | 32 bit-4.0.3/bit/build |only bit-4.0.3/bit/inst/doc |only bit-4.0.3/bit/man/CoercionToStandard.Rd |only bit-4.0.3/bit/man/Extract.Rd |only bit-4.0.3/bit/man/Metadata.Rd |only bit-4.0.3/bit/man/PhysVirt.Rd |only bit-4.0.3/bit/man/Sorting.Rd |only bit-4.0.3/bit/man/Summaries.Rd |only bit-4.0.3/bit/man/as.bit.Rd |only bit-4.0.3/bit/man/as.bitwhich.Rd |only bit-4.0.3/bit/man/as.booltype.Rd |only bit-4.0.3/bit/man/as.character.bit.Rd |only bit-4.0.3/bit/man/as.character.bitwhich.Rd |only bit-4.0.3/bit/man/as.ri.Rd |only bit-4.0.3/bit/man/as.which.Rd |only bit-4.0.3/bit/man/bbatch.Rd |only bit-4.0.3/bit/man/bit-package.Rd |only bit-4.0.3/bit/man/bit.Rd |only bit-4.0.3/bit/man/bit_in.Rd |only bit-4.0.3/bit/man/bit_init.Rd |only bit-4.0.3/bit/man/bit_rangediff.Rd |only bit-4.0.3/bit/man/bit_setops.Rd |only bit-4.0.3/bit/man/bit_sort.Rd |only bit-4.0.3/bit/man/bit_sort_unique.Rd |only bit-4.0.3/bit/man/bit_unidup.Rd |only bit-4.0.3/bit/man/bitsort.Rd |only bit-4.0.3/bit/man/bitwhich.Rd |only bit-4.0.3/bit/man/bitwhich_representation.Rd |only bit-4.0.3/bit/man/booltype.Rd |only bit-4.0.3/bit/man/booltypes.Rd |only bit-4.0.3/bit/man/c.booltype.Rd |only bit-4.0.3/bit/man/chunk.Rd |only bit-4.0.3/bit/man/chunks.Rd |only bit-4.0.3/bit/man/clone.Rd |only bit-4.0.3/bit/man/copy.Rd |only bit-4.0.3/bit/man/countsort.Rd |only bit-4.0.3/bit/man/firstNA.Rd |only bit-4.0.3/bit/man/get_length.Rd |only bit-4.0.3/bit/man/getsetattr.Rd |only bit-4.0.3/bit/man/in.bitwhich.Rd |only bit-4.0.3/bit/man/intrle.Rd |only bit-4.0.3/bit/man/is.booltype.Rd |only bit-4.0.3/bit/man/is.na.bit.Rd |only bit-4.0.3/bit/man/length.bit.Rd |only bit-4.0.3/bit/man/maxindex.Rd |only bit-4.0.3/bit/man/merge_rev.Rd |only bit-4.0.3/bit/man/print.bit.Rd |only bit-4.0.3/bit/man/print.bitwhich.Rd |only bit-4.0.3/bit/man/quicksort2.Rd |only bit-4.0.3/bit/man/quicksort3.Rd |only bit-4.0.3/bit/man/range_na.Rd |only bit-4.0.3/bit/man/range_nanozero.Rd |only bit-4.0.3/bit/man/range_sortna.Rd |only bit-4.0.3/bit/man/rep.booltype.Rd |only bit-4.0.3/bit/man/repeat.time.Rd |only bit-4.0.3/bit/man/repfromto.Rd |only bit-4.0.3/bit/man/rev.booltype.Rd |only bit-4.0.3/bit/man/reverse.Rd |only bit-4.0.3/bit/man/ri.Rd |only bit-4.0.3/bit/man/rlepack.Rd |only bit-4.0.3/bit/man/still.identical.Rd |only bit-4.0.3/bit/man/str.bit.Rd |only bit-4.0.3/bit/man/str.bitwhich.Rd |only bit-4.0.3/bit/man/symdiff.Rd |only bit-4.0.3/bit/man/unattr.Rd |only bit-4.0.3/bit/man/vecseq.Rd |only bit-4.0.3/bit/man/xor.Rd |only bit-4.0.3/bit/src/Makevars |only bit-4.0.3/bit/src/attrutil.c | 4 bit-4.0.3/bit/src/bit.c | 2949 +++++++++++++++-- bit-4.0.3/bit/src/chunkutil.c | 4 bit-4.0.3/bit/src/clone.c | 62 bit-4.0.3/bit/src/init.c | 192 - bit-4.0.3/bit/src/integerutil.c |only bit-4.0.3/bit/src/merge.c |only bit-4.0.3/bit/src/merge.c.h |only bit-4.0.3/bit/src/merge.h |only bit-4.0.3/bit/src/range.c.h |only bit-4.0.3/bit/src/rle.c | 138 bit-4.0.3/bit/src/sort.c |only bit-4.0.3/bit/src/sort.h |only bit-4.0.3/bit/tests |only bit-4.0.3/bit/vignettes |only 130 files changed, 6872 insertions(+), 3693 deletions(-)
More information about OpenRepGrid.ic at CRAN
Permanent link
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre],
Thomas Lumley [ctb],
Tomasz Żółtak [ctb],
Ben Schneider [aut, ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.3.10 dated 2020-05-26 and 0.4.0 dated 2020-07-30
DESCRIPTION | 19 +- MD5 | 48 ++--- NAMESPACE | 2 NEWS.md | 7 R/group-by.r | 6 R/manip.r | 33 ++- R/srvyr.r | 9 - R/summarise.r | 110 +++++++++++-- R/survey_count_tally.R | 27 --- R/survey_statistics.r | 64 ++++++- R/survey_statistics_helpers.R | 9 - build/vignette.rds |binary inst/doc/extending-srvyr.html | 26 ++- inst/doc/srvyr-database.html | 256 ++++++++++++++++--------------- inst/doc/srvyr-vs-survey.R | 4 inst/doc/srvyr-vs-survey.Rmd | 4 inst/doc/srvyr-vs-survey.html | 198 +++++++++++++---------- man/summarise.Rd | 5 tests/testthat/test_as_survey_twophase.r | 12 + tests/testthat/test_dplyr_verbs.R | 160 +++++++++++++++++++ tests/testthat/test_filter.R | 116 ++++++++++++++ tests/testthat/test_survey_count_tally.R | 91 +++++++++++ tests/testthat/test_survey_mean_factor.r | 107 ++++++++++++ tests/testthat/test_survey_statistics.r | 75 +++++++-- vignettes/srvyr-vs-survey.Rmd | 4 25 files changed, 1049 insertions(+), 343 deletions(-)
Title: Client for the Comprehensive Knowledge Archive Network ('CKAN')
API
Description: Client for 'CKAN' API (<https://ckan.org/>). Includes interface
to 'CKAN' 'APIs' for search, list, show for packages, organizations, and
resources. In addition, provides an interface to the 'datastore' API.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Imanuel Costigan [aut],
Wush Wu [aut] (<https://orcid.org/0000-0001-5180-0567>),
Florian Mayer [aut] (<https://orcid.org/0000-0003-4269-4242>),
Sharla Gelfand [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between ckanr versions 0.4.0 dated 2019-10-11 and 0.5.0 dated 2020-07-30
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Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames
for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with
visible chromatids (when not circular).
Supports micrometers, cM and Mb or any unit. Two styles of centromeres are available: triangular and rounded;
and six styles of marks: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow, downArrow;
its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in
concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964)
<doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999)
<doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes
by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.15.3 dated 2020-07-02 and 1.16.1 dated 2020-07-30
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Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modeling mutations in pedigrees with
marker data, as used e.g. in likelihood computations with microsatellite data.
Implemented models include proportional and stepwise models, as well as random
models for experimental work, and custom models allowing the user to apply any
valid mutation matrix. Allele lumping is done following the lumpability criteria
of Kemeny and Snell (1976), ISBN:0387901922.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedmut versions 0.1.0 dated 2019-10-01 and 0.2.0 dated 2020-07-30
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-17 0.3-5.1
2016-12-30 0.3-5
2016-05-10 0.3-4
2016-03-29 0.3-3
2016-03-08 0.3-2
2015-10-08 0.3-1
2015-07-15 0.3-0
2015-06-24 0.2-6
2015-03-24 0.2-4
2015-02-04 0.2-1
2013-10-13 0.1-8
2013-01-05 0.1-7
2012-05-29 0.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-17 0.0-4.1
2016-12-30 0.0-4
2016-03-29 0.0-3
2016-03-06 0.0-2
2015-10-06 0.0-1
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>), substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>), and features
for the generation of synthetic datasets
(Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>;
Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>),
Simon Grund [aut] (<https://orcid.org/0000-0002-1290-8986>),
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.9-14 dated 2020-05-09 and 3.10-28 dated 2020-07-30
DESCRIPTION | 20 +++--- MD5 | 87 ++++++++++++++++------------ NAMESPACE | 5 + R/ANSI_create_table.R | 51 +++++++++------- R/ANSI_create_table_check_variable_values.R |only R/RcppExports.R | 2 R/mice.impute.constant.R |only R/mice.impute.imputeR.cFun.R | 3 R/mice.impute.imputeR.lmFun.R | 3 R/mice.impute.synthpop.R |only R/mice_imputation_get_states.R | 9 ++ R/mice_imputation_linear_model_main.R | 2 R/syn.constant.R |only R/syn.formula.R |only R/syn.mice.R |only R/syn_mice.R |only R/syn_mice_catch_arguments.R |only R/syn_mice_completed_datasets.R |only R/syn_mice_create_argument_list.R |only R/syn_mice_create_design_matrix.R |only build/partial.rdb |binary data/data.allison.gssexp.rda |binary data/data.allison.hip.rda |binary data/data.allison.usnews.rda |binary data/data.enders.depression.rda |binary data/data.enders.eatingattitudes.rda |binary data/data.enders.employee.rda |binary data/data.graham.ex3.rda |binary data/data.graham.ex6.rda |binary data/data.graham.ex8a.rda |binary data/data.graham.ex8b.rda |binary data/data.graham.ex8c.rda |binary data/data.internet.rda |binary data/data.largescale.rda |binary data/data.ma01.rda |binary data/data.ma02.rda |binary data/data.ma03.rda |binary data/data.ma04.rda |binary data/data.ma05.rda |binary data/data.ma06.rda |binary data/data.ma07.rda |binary data/data.ma08.rda |binary data/data.smallscale.rda |binary inst/NEWS | 19 ++++++ man/mice.impute.constant.Rd |only man/mice.impute.synthpop.Rd |only man/miceadds-package.Rd | 23 +++++++ man/miceadds-utilities.Rd | 4 - man/syn.constant.Rd |only man/syn.formula.Rd |only man/syn.mice.Rd |only man/syn_mice.Rd |only src/RcppExports.cpp | 2 53 files changed, 157 insertions(+), 73 deletions(-)
Title: Graphical Independence Networks
Description: Probability propagation in graphical independence networks, also
known as Bayesian networks or probabilistic expert systems. Documentation
of the package is provided in vignettes included in the package and in
the paper by Højsgaard (2012, <doi:10.18637/jss.v046.i10>).
See 'citation("gRain")' for details.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRain versions 1.3-5 dated 2020-06-14 and 1.3-6 dated 2020-07-30
DESCRIPTION | 13 +++++++---- MD5 | 28 ++++++++++++------------- NEWS | 16 ++++++++++++++ R/evidence-joint.R | 6 ++--- R/evidence.R | 3 +- R/querygrain.R | 3 +- inst/CITATION | 1 inst/doc/grain-intro.R | 20 ++++++++--------- inst/doc/grain-intro.Rnw | 24 ++++++++++----------- inst/doc/grain-intro.pdf |binary man/grain-simulate.Rd | 1 man/grain_jevidence.Rd | 6 ++--- vignettes/figures/grain-chest-LS-1.pdf |binary vignettes/figures/grain-unnamed-chunk-33-1.pdf |binary vignettes/grain-intro.Rnw | 24 ++++++++++----------- 15 files changed, 83 insertions(+), 62 deletions(-)
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 3.0.4 dated 2020-06-07 and 3.0.5 dated 2020-07-30
DESCRIPTION | 16 +- MD5 | 54 ++++----- NAMESPACE | 25 ++++ NEWS.md | 9 + R/CCAMLRGIS.R | 5 R/CCAMLRGIS_DataDescription.R | 2 R/add_labels.R | 2 R/assign_areas.r | 44 ++++++- R/create.R | 124 ++++++++++++++++------ R/get_depths.R | 27 +++- R/load.R | 6 - README.md | 6 - build/vignette.rds |binary inst/doc/CCAMLRGIS.R | 68 ++++++------ inst/doc/CCAMLRGIS.Rmd | 66 +++++------ inst/doc/CCAMLRGIS.html | 84 +++++++++------ man/Coast.Rd | 54 ++++----- man/assign_areas.Rd | 165 +++++++++++++++-------------- man/create_Lines.Rd | 232 +++++++++++++++++++++--------------------- man/create_Points.Rd | 182 +++++++++++++++++--------------- man/create_PolyGrids.Rd | 224 +++++++++++++++++++++------------------- man/create_Polys.Rd | 196 ++++++++++++++++++----------------- man/create_Stations.Rd | 222 ++++++++++++++++++++-------------------- man/get_depths.Rd | 163 +++++++++++++++-------------- man/load_Coastline.Rd | 74 ++++++------- man/load_MPAs.Rd | 74 ++++++------- man/load_SSRUs.Rd | 74 ++++++------- vignettes/CCAMLRGIS.Rmd | 66 +++++------ 28 files changed, 1226 insertions(+), 1038 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA). Data is obtained from Protected Planet
<http://protectedplanet.net>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 1.0.2 dated 2020-04-15 and 1.0.3 dated 2020-07-30
DESCRIPTION | 10 +- MD5 | 46 ++++----- NEWS.md | 23 +++- R/geo.R | 26 +++-- R/internal.R | 28 ++--- R/package.R | 14 +- R/wdpa_clean.R | 112 +++++++++++------------ R/wdpa_fetch.R | 54 +++++------ R/wdpa_read.R | 24 +++- R/wdpa_url.R | 20 ++-- README.md | 46 ++++----- build/vignette.rds |binary inst/doc/wdpar.Rmd | 7 - inst/doc/wdpar.html | 105 ++++++++++----------- man/figures/README-readme-map-1.png |binary man/st_erase_overlaps.Rd | 16 +-- man/wdpa_clean.Rd | 174 ++++++++++++++++++------------------ man/wdpa_fetch.Rd | 24 ++-- man/wdpa_read.Rd | 10 +- man/wdpa_url.Rd | 4 man/wdpar.Rd | 6 - tests/testthat/test_internal.R | 6 + tests/testthat/test_wdpa_clean.R | 3 vignettes/wdpar.Rmd | 7 - 24 files changed, 398 insertions(+), 367 deletions(-)
Title: Robust Backfitting
Description: A robust backfitting algorithm for additive models based on (robust) local polynomial
kernel smoothers. It includes both bounded and re-descending (kernel) M-estimators, and
it computes predictions for points outside the training set if desired. See
Boente, Martinez and Salibian-Barrera (2017) <doi:10.1080/10485252.2017.1369077> for
details.
Author: Matias Salibian-Barrera [aut, cre],
Alejandra Martinez [aut]
Maintainer: Matias Salibian-Barrera <matias@stat.ubc.ca>
Diff between RBF versions 1.0.0 dated 2019-06-14 and 2.0.1 dated 2020-07-30
RBF-1.0.0/RBF/man/backf.l2.cv.Rd |only RBF-1.0.0/RBF/man/backf.rob.cv.Rd |only RBF-2.0.1/RBF/DESCRIPTION | 12 RBF-2.0.1/RBF/MD5 | 32 RBF-2.0.1/RBF/NAMESPACE | 39 RBF-2.0.1/RBF/R/RBF-fn.R | 1779 +++++++++++++++++-------------- RBF-2.0.1/RBF/man/RBF-package.Rd | 56 RBF-2.0.1/RBF/man/backf.cl.Rd | 122 +- RBF-2.0.1/RBF/man/backf.rob.Rd | 146 +- RBF-2.0.1/RBF/man/deviance.backf.Rd |only RBF-2.0.1/RBF/man/fitted.values.backf.Rd |only RBF-2.0.1/RBF/man/formula.backf.Rd |only RBF-2.0.1/RBF/man/k.epan.Rd | 58 - RBF-2.0.1/RBF/man/plot.backf.Rd | 66 - RBF-2.0.1/RBF/man/predict.backf.Rd | 50 RBF-2.0.1/RBF/man/print.backf.Rd |only RBF-2.0.1/RBF/man/psi.huber.Rd | 60 - RBF-2.0.1/RBF/man/psi.tukey.Rd | 60 - RBF-2.0.1/RBF/man/residuals.backf.Rd | 48 RBF-2.0.1/RBF/man/summary.backf.Rd | 56 20 files changed, 1426 insertions(+), 1158 deletions(-)
Title: Visualize Species Occurrence Data
Description: Utilities for visualizing species occurrence data. Includes
functions to visualize occurrence data from 'spocc', 'rgbif',
and other packages. Mapping options included for base R plots, 'ggplot2',
'ggmap', 'leaflet' and 'GitHub' 'gists'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between mapr versions 0.4.0 dated 2018-03-21 and 0.5.0 dated 2020-07-30
mapr-0.4.0/mapr/inst/doc/mapr_vignette.Rmd |only mapr-0.4.0/mapr/inst/doc/mapr_vignette.html |only mapr-0.4.0/mapr/man/map_ggmap.Rd |only mapr-0.4.0/mapr/tests/testthat/test-map_ggmap.R |only mapr-0.4.0/mapr/vignettes/img |only mapr-0.4.0/mapr/vignettes/mapr_vignette.Rmd |only mapr-0.5.0/mapr/DESCRIPTION | 21 +- mapr-0.5.0/mapr/LICENSE | 2 mapr-0.5.0/mapr/MD5 | 74 ++++----- mapr-0.5.0/mapr/NAMESPACE | 10 - mapr-0.5.0/mapr/NEWS.md | 24 +++ mapr-0.5.0/mapr/R/hull.R | 2 mapr-0.5.0/mapr/R/map_ggmap.R | 192 ------------------------ mapr-0.5.0/mapr/R/map_ggplot.R | 67 ++++---- mapr-0.5.0/mapr/R/map_gist.R | 34 ++-- mapr-0.5.0/mapr/R/map_leaflet.R | 54 +++--- mapr-0.5.0/mapr/R/map_plot.R | 35 +++- mapr-0.5.0/mapr/R/mapr-package.R | 41 ++--- mapr-0.5.0/mapr/R/zzz.r | 24 +++ mapr-0.5.0/mapr/README.md | 91 +---------- mapr-0.5.0/mapr/build/vignette.rds |binary mapr-0.5.0/mapr/data/gbif_eg1.rda |binary mapr-0.5.0/mapr/data/occdat_eg1.rda |binary mapr-0.5.0/mapr/inst/doc/mapr.Rmd |only mapr-0.5.0/mapr/inst/doc/mapr.html |only mapr-0.5.0/mapr/man/figures |only mapr-0.5.0/mapr/man/gbif_eg1.Rd | 9 - mapr-0.5.0/mapr/man/hull.Rd | 2 mapr-0.5.0/mapr/man/map_ggmap-defunct.Rd |only mapr-0.5.0/mapr/man/map_ggplot.Rd | 32 ++-- mapr-0.5.0/mapr/man/map_gist.Rd | 26 ++- mapr-0.5.0/mapr/man/map_leaflet.Rd | 28 ++- mapr-0.5.0/mapr/man/map_plot.Rd | 30 ++- mapr-0.5.0/mapr/man/mapr-package.Rd | 3 mapr-0.5.0/mapr/man/occdat_eg1.Rd | 9 - mapr-0.5.0/mapr/man/style_geojson.Rd | 12 + mapr-0.5.0/mapr/tests/testthat/spocc_df_1.rda |only mapr-0.5.0/mapr/tests/testthat/test-map_gist.R | 2 mapr-0.5.0/mapr/tests/testthat/test-utils.R |only mapr-0.5.0/mapr/vignettes/mapr.Rmd |only mapr-0.5.0/mapr/vignettes/mapr.Rmd.og |only 41 files changed, 367 insertions(+), 457 deletions(-)