Title: Scalable Exact Algorithm for Large-Scale Set-Based
Gene-Environment Interaction Tests
Description: The explosion of biobank data offers immediate opportunities for
gene-environment (GxE) interaction studies of complex diseases because of the
large sample sizes and rich collection in genetic and non-genetic information.
However, the extremely large sample size also introduces new computational
challenges in GxE assessment, especially for set-based GxE variance component (VC)
tests, a widely used strategy to boost overall GxE signals and to evaluate the
joint GxE effect of multiple variants from a biologically meaningful unit
(e.g., gene).
We present 'SEAGLE', a Scalable Exact AlGorithm for Large-scale Set-based
GxE tests, to permit GxE VC test scalable to biobank data. 'SEAGLE' employs modern
matrix computations to achieve the same “exact” results as the original GxE VC
tests, and does not impose additional assumptions nor relies on approximations.
'SEAGLE' can easily accommodate sample sizes in the order of 10^5, is implementable
on standard laptops, and does not require specialized equipment.
The accompanying manuscript for this package can be found at Chi, Ipsen, Hsiao,
Lin, Wang, Lee, Lu, and Tzeng. (2021+) <arXiv:2105.03228>.
Author: Jocelyn Chi [aut, cre],
Ilse Ipsen [aut],
Jung-Ying Tzeng [aut]
Maintainer: Jocelyn Chi <jocetchi@gmail.com>
Diff between SEAGLE versions 1.0.0 dated 2021-06-07 and 1.0.1 dated 2021-11-05
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- README.md | 16 +++++++++++----- build/vignette.rds |binary data/cosihap.RData |binary inst/CITATION | 15 ++++++++++----- inst/doc/example4.Rmd | 2 +- inst/doc/example4.html | 2 +- vignettes/example4.Rmd | 2 +- 9 files changed, 37 insertions(+), 25 deletions(-)
Title: Efficient and Doubly Robust Population Size Estimation
Description: Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.
Author: Manjari Das [aut, cre] (<https://orcid.org/0000-0002-6781-6368>),
Edward H. Kennedy [aut] (<https://orcid.org/0000-0002-1510-8175>)
Maintainer: Manjari Das <manjari8d@gmail.com>
Diff between drpop versions 0.0.2 dated 2021-10-25 and 0.0.3 dated 2021-11-05
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/popsize.R | 9 ++++----- R/popsize_cond.R | 6 +++--- R/qhat_estimation_functions.R | 26 +++++++++++++------------- man/popsize.Rd | 6 +++--- man/popsize_cond.Rd | 6 +++--- man/qhat_gam.Rd | 2 +- man/qhat_logit.Rd | 2 +- man/qhat_mlogit.Rd | 2 +- man/qhat_ranger.Rd | 2 +- man/qhat_rangerlogit.Rd | 2 +- man/qhat_sl.Rd | 4 ++-- 14 files changed, 57 insertions(+), 51 deletions(-)
Title: A Shiny App for the 'fdapace' Package
Description: Shiny app for the 'fdapace' package.
Author: Camden Possinger [cre, aut]
Maintainer: Camden Possinger <cpossinger@ucdavis.edu>
Diff between fdapaceShiny versions 1.0.1 dated 2021-09-26 and 1.0.3 dated 2021-11-05
DESCRIPTION | 13 ++++++------- MD5 | 14 +++++++------- NEWS.md | 4 ++-- R/app_server.R | 2 +- R/mod_FCR_model_box.R | 2 +- R/mod_FPCA_model_box.R | 4 ++-- R/mod_global_options.R | 4 ++-- build/vignette.rds |binary 8 files changed, 21 insertions(+), 22 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <sebastian.calonico@columbia.edu>, Matias D. Cattaneo <cattaneo@princeton.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@princeton.edu>
Maintainer: Sebastian Calonico <sebastian.calonico@columbia.edu>
Diff between rdrobust versions 1.0.6 dated 2021-09-02 and 1.0.7 dated 2021-11-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rdrobust.R | 16 ++++++++-------- man/rdrobust-package.Rd | 4 ++-- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Udunits-2 Bindings for R
Description: Provides simple bindings to Unidata's udunits library.
Author: James Hiebert <hiebert@uvic.ca>
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between udunits2 versions 0.13 dated 2016-11-17 and 0.13.1 dated 2021-11-05
DESCRIPTION | 6 MD5 | 6 configure | 2439 +++++++++++++++++++++++++++++------------------------------ configure.ac | 5 4 files changed, 1242 insertions(+), 1214 deletions(-)
Title: A Shiny-Based Application for Extracting Forest Information from
LiDAR Data
Description: Set of tools implemented into a shiny-based application for extracting and analyzing individual tree forest attributes from LiDAR (Light Detection and Ranging) data.
Author: Carlos Alberto Silva [aut, cre, cph],
Andrew Hudak [aut],
Lee Vierling [aut],
Ruben Valbuena [aut],
Adrian Cardil [aut],
Midhun Mohan [aut],
Danilo Roberti Alves de Almeida [aut],
Eben North Broadbent [aut],
Angelica Zambrano [aut],
Ben Wilkinson [aut],
Ajay Sharma [aut],
Jason Drake [aut],
Paul Medley [aut],
Jason Vogel [aut],
Gabriel Prata [aut],
Jeff Atkins [aut],
Caio Hamamura [aut],
Carine Klauberg [aut]
Maintainer: Carlos Alberto Silva <carlos_engflorestal@outlook.com>
Diff between treetop versions 0.0.1 dated 2021-03-02 and 0.0.3 dated 2021-11-05
DESCRIPTION | 20 MD5 | 17 NAMESPACE | 81 - R/launchApp.R | 104 - R/zzz.R | 26 README.md |only build/partial.rdb |binary inst/app/server.r | 2427 +++++++++++++++++++++---------------------- inst/app/ui.r | 849 +++++++-------- inst/extdata/Eglin_plot1.asc | 6 10 files changed, 1764 insertions(+), 1766 deletions(-)
Title: Control the Number of Threads on 'BLAS'
Description: Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS', 'ACML', 'BLIS' and 'MKL').
And possible to control the number of threads in 'OpenMP'.
Get a number of logical cores and physical cores if feasible.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama <nakama@ki.rim.or.jp>
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
Diff between RhpcBLASctl versions 0.21-247 dated 2021-09-04 and 0.21-247.1 dated 2021-11-05
DESCRIPTION | 6 MD5 | 8 configure | 2435 ++++++++++++++++++++++++++++---------------------------- configure.ac | 8 src/config.h.in | 48 + 5 files changed, 1279 insertions(+), 1226 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] (Yann Collet is the author of the bundled zstd,
lz4 and xxHash code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library),
Bryce Chamberlain [ctb] (qsavem and qload functions)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.1 dated 2021-07-25 and 0.25.1.1 dated 2021-11-05
DESCRIPTION | 6 MD5 | 12 build/vignette.rds |binary configure | 718 ++++++++++++++++++++++++++----------------------- configure.ac | 23 - data/starnames.rda |binary inst/doc/vignette.html | 144 +++++---- 7 files changed, 488 insertions(+), 415 deletions(-)
Title: Interface for FAME Time Series Database
Description: Read and write FAME databases.
Author: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Maintainer: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Diff between fame versions 2.21 dated 2015-07-12 and 2.21.1 dated 2021-11-05
DESCRIPTION | 6 MD5 | 6 configure | 3170 ++++++++++++++++++++++++++++++++++++----------------------- configure.ac | 5 4 files changed, 1967 insertions(+), 1220 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-14 0.3-1
2020-02-28 0.3-0
2020-02-01 0.2-9
2020-01-12 0.2-8
2019-12-13 0.2-7
2019-06-24 0.2-6
2019-04-08 0.2-5
2018-04-05 0.2-4
2018-01-05 0.2-3
2016-09-25 0.2-2
2016-01-22 0.2-1
2014-12-24 0.2-0
2014-05-31 0.1-9
2014-03-11 0.1-8
2014-01-27 0.1-7
2013-07-05 0.1-6
2013-03-12 0.1-5
2013-02-15 0.1-4
2013-01-01 0.1-3
2012-12-20 0.1-2
2012-11-30 0.1-1
2012-10-13 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-23 2.5-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-02 0.4
Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: The goal of the 'SwimmeR' package is to provide means of acquiring, and then analyzing, data from swimming (and diving) competitions. To that end 'SwimmeR' allows results to be read in from .html sources, like 'Hy-Tek' real time results pages, '.pdf' files, 'ISL' results, 'Omega' results, and (on a development basis) '.hy3' files. Once read in, 'SwimmeR' can convert swimming times (performances) between the computationally useful format of seconds reported to the '100ths' place (e.g. 95.37), and the conventional reporting format (1:35.37) used in the swimming community. 'SwimmeR' can also score meets in a variety of formats with user defined point values, convert times between courses ('LCM', 'SCM', 'SCY') and draw single elimination brackets, as well as providing a suite of tools for working cleaning swimming data. This is a developmental package, not yet mature.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between SwimmeR versions 0.12.0 dated 2021-08-14 and 0.13.0 dated 2021-11-05
SwimmeR-0.12.0/SwimmeR/R/Read_Results.R |only SwimmeR-0.12.0/SwimmeR/R/format_as_seconds.R |only SwimmeR-0.12.0/SwimmeR/R/samms_parse.R |only SwimmeR-0.12.0/SwimmeR/man/samms_parse.Rd |only SwimmeR-0.12.0/SwimmeR/tests/testthat/test-Course_Convert.R |only SwimmeR-0.13.0/SwimmeR/DESCRIPTION | 6 SwimmeR-0.13.0/SwimmeR/LICENSE | 4 SwimmeR-0.13.0/SwimmeR/MD5 | 266 SwimmeR-0.13.0/SwimmeR/NAMESPACE | 192 SwimmeR-0.13.0/SwimmeR/NEWS.md | 359 SwimmeR-0.13.0/SwimmeR/R/ISL_event_parse.R | 130 SwimmeR-0.13.0/SwimmeR/R/ISL_splits_parse.R | 392 SwimmeR-0.13.0/SwimmeR/R/ISL_swim_parse.R | 874 - SwimmeR-0.13.0/SwimmeR/R/King200Breast.R | 28 SwimmeR-0.13.0/SwimmeR/R/Swim_Parse.R | 1287 - SwimmeR-0.13.0/SwimmeR/R/SwimmeR-defunct.R |only SwimmeR-0.13.0/SwimmeR/R/SwimmeR-deprecated.R | 16 SwimmeR-0.13.0/SwimmeR/R/add_row_numbers.R | 38 SwimmeR-0.13.0/SwimmeR/R/coalesce_many.R |only SwimmeR-0.13.0/SwimmeR/R/collect_relay_swimmers.R | 280 SwimmeR-0.13.0/SwimmeR/R/correcting_splits.R | 262 SwimmeR-0.13.0/SwimmeR/R/course_conversions.R | 648 SwimmeR-0.13.0/SwimmeR/R/deprec_collect_relay_swimmers.R | 250 SwimmeR-0.13.0/SwimmeR/R/deprec_swim_parse.R | 3050 ++-- SwimmeR-0.13.0/SwimmeR/R/discard_errors.R | 92 SwimmeR-0.13.0/SwimmeR/R/dive_place.R | 80 SwimmeR-0.13.0/SwimmeR/R/draw_bracket.R | 648 SwimmeR-0.13.0/SwimmeR/R/event_parse.R | 183 SwimmeR-0.13.0/SwimmeR/R/fill_down.R | 38 SwimmeR-0.13.0/SwimmeR/R/fill_left.R | 54 SwimmeR-0.13.0/SwimmeR/R/fold.R | 62 SwimmeR-0.13.0/SwimmeR/R/format_age.R | 116 SwimmeR-0.13.0/SwimmeR/R/format_results.R | 108 SwimmeR-0.13.0/SwimmeR/R/get_mode.R | 104 SwimmeR-0.13.0/SwimmeR/R/globals.R | 217 SwimmeR-0.13.0/SwimmeR/R/hy3_parse.R | 1054 - SwimmeR-0.13.0/SwimmeR/R/hy3_places.R | 150 SwimmeR-0.13.0/SwimmeR/R/hy3_times.R | 158 SwimmeR-0.13.0/SwimmeR/R/hytek_swim_parse.R |only SwimmeR-0.13.0/SwimmeR/R/interleave_results.R | 70 SwimmeR-0.13.0/SwimmeR/R/is_link_broken.R | 44 SwimmeR-0.13.0/SwimmeR/R/lines_sort.R | 153 SwimmeR-0.13.0/SwimmeR/R/list_transform.R | 40 SwimmeR-0.13.0/SwimmeR/R/mmss_format.R | 54 SwimmeR-0.13.0/SwimmeR/R/na_pad.R |only SwimmeR-0.13.0/SwimmeR/R/name_reorder.R | 218 SwimmeR-0.13.0/SwimmeR/R/not_in.R | 46 SwimmeR-0.13.0/SwimmeR/R/omega_collect_relay_swimmers.R | 321 SwimmeR-0.13.0/SwimmeR/R/omega_heat_parse.R | 161 SwimmeR-0.13.0/SwimmeR/R/omega_splits_parse_relays.R | 466 SwimmeR-0.13.0/SwimmeR/R/omega_splits_rename.R | 50 SwimmeR-0.13.0/SwimmeR/R/omega_swim_parse.R | 2197 +-- SwimmeR-0.13.0/SwimmeR/R/reaction_times_parse.R | 149 SwimmeR-0.13.0/SwimmeR/R/read_results.R |only SwimmeR-0.13.0/SwimmeR/R/results_score.R | 760 - SwimmeR-0.13.0/SwimmeR/R/samms_swim_parse.R |only SwimmeR-0.13.0/SwimmeR/R/sec_format.R |only SwimmeR-0.13.0/SwimmeR/R/splash_collect_relay_swimmers.R |only SwimmeR-0.13.0/SwimmeR/R/splash_collect_splits.R |only SwimmeR-0.13.0/SwimmeR/R/splash_determine_indent_length.R |only SwimmeR-0.13.0/SwimmeR/R/splash_splits_parse.R |only SwimmeR-0.13.0/SwimmeR/R/splash_splits_parse_relays.R |only SwimmeR-0.13.0/SwimmeR/R/splash_swim_parse.R |only SwimmeR-0.13.0/SwimmeR/R/splits_parse.R | 573 SwimmeR-0.13.0/SwimmeR/R/splits_reform.R | 80 SwimmeR-0.13.0/SwimmeR/R/splits_to_cumulative.R | 340 SwimmeR-0.13.0/SwimmeR/R/splits_to_lap.R | 364 SwimmeR-0.13.0/SwimmeR/R/swim_place.R | 68 SwimmeR-0.13.0/SwimmeR/R/tie_rescore.R | 80 SwimmeR-0.13.0/SwimmeR/R/undo_interleave.R |only SwimmeR-0.13.0/SwimmeR/R/utils-pipe.R | 22 SwimmeR-0.13.0/SwimmeR/README.md | 379 SwimmeR-0.13.0/SwimmeR/build/vignette.rds |binary SwimmeR-0.13.0/SwimmeR/inst/CITATION | 26 SwimmeR-0.13.0/SwimmeR/inst/doc/SwimmeR.R | 350 SwimmeR-0.13.0/SwimmeR/inst/doc/SwimmeR.Rmd | 674 SwimmeR-0.13.0/SwimmeR/inst/doc/SwimmeR.html | 1221 - SwimmeR-0.13.0/SwimmeR/man/King200Breast.Rd | 38 SwimmeR-0.13.0/SwimmeR/man/Read_Results.Rd | 68 SwimmeR-0.13.0/SwimmeR/man/Swim_Parse.Rd | 194 SwimmeR-0.13.0/SwimmeR/man/SwimmeR-defunct.Rd |only SwimmeR-0.13.0/SwimmeR/man/SwimmeR-deprecated.Rd | 5 SwimmeR-0.13.0/SwimmeR/man/add_row_numbers.Rd | 44 SwimmeR-0.13.0/SwimmeR/man/coalesce_many.Rd |only SwimmeR-0.13.0/SwimmeR/man/coalesce_many_helper.Rd |only SwimmeR-0.13.0/SwimmeR/man/collect_relay_swimmers.Rd | 40 SwimmeR-0.13.0/SwimmeR/man/collect_relay_swimmers_omega.Rd | 6 SwimmeR-0.13.0/SwimmeR/man/collect_relay_swimmers_splash.Rd |only SwimmeR-0.13.0/SwimmeR/man/course_convert.Rd | 98 SwimmeR-0.13.0/SwimmeR/man/course_convert_DF.Rd | 86 SwimmeR-0.13.0/SwimmeR/man/course_convert_helper.Rd |only SwimmeR-0.13.0/SwimmeR/man/determine_indent_length_splash.Rd |only SwimmeR-0.13.0/SwimmeR/man/discard_errors.Rd | 78 SwimmeR-0.13.0/SwimmeR/man/dive_place.Rd | 52 SwimmeR-0.13.0/SwimmeR/man/draw_bracket.Rd | 138 SwimmeR-0.13.0/SwimmeR/man/event_parse.Rd | 50 SwimmeR-0.13.0/SwimmeR/man/event_parse_ISL.Rd | 50 SwimmeR-0.13.0/SwimmeR/man/fill_down.Rd | 40 SwimmeR-0.13.0/SwimmeR/man/fill_left.Rd | 46 SwimmeR-0.13.0/SwimmeR/man/fold.Rd | 50 SwimmeR-0.13.0/SwimmeR/man/format_results.Rd | 50 SwimmeR-0.13.0/SwimmeR/man/get_mode.Rd | 92 SwimmeR-0.13.0/SwimmeR/man/grapes-notin-grapes.Rd | 56 SwimmeR-0.13.0/SwimmeR/man/hy3_places.Rd | 50 SwimmeR-0.13.0/SwimmeR/man/hy3_times.Rd | 44 SwimmeR-0.13.0/SwimmeR/man/interleave_results.Rd | 60 SwimmeR-0.13.0/SwimmeR/man/is_link_broken.Rd | 42 SwimmeR-0.13.0/SwimmeR/man/lines_sort.Rd | 60 SwimmeR-0.13.0/SwimmeR/man/list_transform.Rd | 48 SwimmeR-0.13.0/SwimmeR/man/mmss_format.Rd | 62 SwimmeR-0.13.0/SwimmeR/man/na_pad.Rd |only SwimmeR-0.13.0/SwimmeR/man/pipe.Rd | 24 SwimmeR-0.13.0/SwimmeR/man/read_results_flag.Rd | 40 SwimmeR-0.13.0/SwimmeR/man/results_score.Rd | 180 SwimmeR-0.13.0/SwimmeR/man/sec_format.Rd | 64 SwimmeR-0.13.0/SwimmeR/man/sec_format_helper.Rd | 34 SwimmeR-0.13.0/SwimmeR/man/splash_collect_splits.Rd |only SwimmeR-0.13.0/SwimmeR/man/splits_parse.Rd | 57 SwimmeR-0.13.0/SwimmeR/man/splits_parse_ISL.Rd | 48 SwimmeR-0.13.0/SwimmeR/man/splits_parse_omega_relays.Rd | 3 SwimmeR-0.13.0/SwimmeR/man/splits_parse_splash.Rd |only SwimmeR-0.13.0/SwimmeR/man/splits_parse_splash_helper_1.Rd |only SwimmeR-0.13.0/SwimmeR/man/splits_parse_splash_helper_2.Rd |only SwimmeR-0.13.0/SwimmeR/man/splits_parse_splash_relays.Rd |only SwimmeR-0.13.0/SwimmeR/man/splits_reform.Rd | 54 SwimmeR-0.13.0/SwimmeR/man/swim_parse_ISL.Rd | 86 SwimmeR-0.13.0/SwimmeR/man/swim_parse_hytek.Rd |only SwimmeR-0.13.0/SwimmeR/man/swim_parse_old.Rd | 162 SwimmeR-0.13.0/SwimmeR/man/swim_parse_omega.Rd | 4 SwimmeR-0.13.0/SwimmeR/man/swim_parse_samms.Rd |only SwimmeR-0.13.0/SwimmeR/man/swim_parse_splash.Rd |only SwimmeR-0.13.0/SwimmeR/man/swim_place.Rd | 52 SwimmeR-0.13.0/SwimmeR/man/tie_rescore.Rd | 54 SwimmeR-0.13.0/SwimmeR/man/undo_interleave.Rd |only SwimmeR-0.13.0/SwimmeR/tests/testthat.R | 8 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-ISL.R | 7950 +++++------ SwimmeR-0.13.0/SwimmeR/tests/testthat/test-age_format.R | 20 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-course_convert.R |only SwimmeR-0.13.0/SwimmeR/tests/testthat/test-format_splits.R | 486 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-get_mode.R | 20 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-hy3_parse.R | 26 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-omega.R | 5669 ++++--- SwimmeR-0.13.0/SwimmeR/tests/testthat/test-reaction_times.R | 1266 - SwimmeR-0.13.0/SwimmeR/tests/testthat/test-read_results.R | 68 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-relay_swimmers.R | 100 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-results_score.R | 178 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-samms.R | 100 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-sec_format.R |only SwimmeR-0.13.0/SwimmeR/tests/testthat/test-splash.R |only SwimmeR-0.13.0/SwimmeR/tests/testthat/test-splits.R | 356 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-swim_parse.R | 672 SwimmeR-0.13.0/SwimmeR/tests/testthat/test-swim_parse_old.R | 336 SwimmeR-0.13.0/SwimmeR/vignettes/SwimmeR.Rmd | 674 153 files changed, 20028 insertions(+), 20462 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.3.2 dated 2021-10-20 and 0.3.3 dated 2021-11-05
DESCRIPTION | 8 ++-- MD5 | 11 +++--- NEWS.md | 7 ++-- R/methods-fix_region.R | 52 +++++++++++++++++++------------ inst/doc/nigeria-maps.html | 20 +++++------ tests/testthat/data/mispelt-lga.rds |only tests/testthat/test-methods-fix_region.R | 22 +++++++++++-- 7 files changed, 77 insertions(+), 43 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to where the current file is,
print strings with rich formats and colors);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of regression models and other results
(to R Console and MS Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.7.2 dated 2021-06-21 and 0.7.3 dated 2021-11-05
DESCRIPTION | 10 ++-- MD5 | 26 +++++------ NEWS.md | 6 ++ R/bruceR.R | 23 ++++++---- R/bruceR_stats_01_basic.R | 60 ++++++++++++++++++-------- R/bruceR_stats_03_manova.R | 4 - R/bruceR_stats_05_advance.R | 98 +++++++++++++++++++++++++++++++++++++------- README.md | 8 +-- build/partial.rdb |binary man/MANOVA.Rd | 4 - man/PROCESS.Rd | 1 man/granger_causality.Rd | 8 ++- man/granger_test.Rd | 19 +++++--- man/lavaan_summary.Rd | 5 +- 14 files changed, 193 insertions(+), 79 deletions(-)
Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Peter Kochunov [aut, cph],
Si Gao [aut, cre],
Kathryn Hatch [aut],
Fatima Talib [aut]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Diff between RVIpkg versions 0.2.6 dated 2021-07-29 and 0.2.8 dated 2021-11-05
DESCRIPTION | 19 ++++++++++++------- MD5 | 28 ++++++++++++++-------------- R/EP.GM.R | 6 +++++- R/EP.Subcortical.R | 6 +++++- R/EP.WM.R | 32 ++++++++++++++++++-------------- R/RVI_func.R | 46 +++++++++++++++++++--------------------------- R/sysdata.rda |binary build/partial.rdb |binary data/EP.GM.rda |binary data/EP.Subcortical.rda |binary data/EP.WM.rda |binary man/EP.GM.Rd | 6 +++++- man/EP.Subcortical.Rd | 6 +++++- man/EP.WM.Rd | 6 +++++- man/RVI_func.Rd | 32 ++++++++++++++------------------ 15 files changed, 102 insertions(+), 85 deletions(-)
Title: Classification Based MCAR Test
Description: Implementation of a KL-based (Kullback-Leibler) test for MCAR (Missing Completely At Random) in the context of missing data as introduced in Michel et al. (2021) <arXiv:2109.10150>.
Author: Meta-Lina Spohn [aut, cre],
Loris Michel [aut],
Jeffrey Naef [aut]
Maintainer: Meta-Lina Spohn <metalina.spohn@stat.math.ethz.ch>
Diff between PKLMtest versions 1.0.0 dated 2021-10-12 and 1.0.1 dated 2021-11-05
DESCRIPTION | 25 ++++++++++++++---- MD5 | 4 +- R/PKLMtest.R | 80 ++++++++++++++++++++++++++++++++++------------------------- 3 files changed, 68 insertions(+), 41 deletions(-)
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models,
and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint,
Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or
'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
Joachim Gassen [ctb] (<https://orcid.org/0000-0003-4364-2911>),
Nathan Eastwood [ctb],
Nick Huntington-Klein [ctb] (<https://orcid.org/0000-0002-7352-3991>),
Moritz Schwarz [ctb] (<https://orcid.org/0000-0003-0340-3780>),
Benjamin Elbers [ctb] (0000-0001-5392-3448),
Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.9.3 dated 2021-11-02 and 0.9.4 dated 2021-11-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/utils_rounding.R | 6 ++++++ README.md | 1 + build/modelsummary.pdf |binary tests/testthat/_snaps/rounding.md | 35 ++++++++++++++++++++++++++++++++--- tests/testthat/test-rounding.R | 10 ++++++++++ 8 files changed, 63 insertions(+), 13 deletions(-)
Title: R-Based Visualization Techniques for Task-Based Applications
Description: Performance analysis workflow that combines the power of the R
language (and the tidyverse realm) and many auxiliary tools to
provide a consistent, flexible, extensible, fast, and versatile
framework for the performance analysis of task-based applications
that run on top of the StarPU runtime (with its MPI (Message
Passing Interface) layer for multi-node support). Its goal is to
provide a fruitful prototypical environment to conduct performance
analysis hypothesis-checking for task-based applications that run
on heterogeneous (multi-GPU, multi-core) multi-node HPC
(High-performance computing) platforms.
Author: Lucas Mello Schnorr [aut, ths]
(<https://orcid.org/0000-0003-4828-9942>),
Vinicius Garcia Pinto [aut] (<https://orcid.org/0000-0002-6845-9358>),
Lucas Leandro Nesi [aut, cre] (<https://orcid.org/0000-0001-8874-1839>),
Marcelo Cogo Miletto [aut] (<https://orcid.org/0000-0002-1191-3863>),
Guilherme Alles [ctb],
Arnaud Legrand [ctb],
Luka Stanisic [ctb],
Rémy Drouilhet [ctb]
Maintainer: Lucas Leandro Nesi <lucas.nesi@inf.ufrgs.br>
Diff between starvz versions 0.6.0 dated 2021-10-16 and 0.7.0 dated 2021-11-05
starvz-0.6.0/starvz/src/lastest.cpp |only starvz-0.7.0/starvz/DESCRIPTION | 12 - starvz-0.7.0/starvz/MD5 | 33 ++-- starvz-0.7.0/starvz/NAMESPACE | 5 starvz-0.7.0/starvz/R/RcppExports.R | 4 starvz-0.7.0/starvz/R/phase1.R | 167 ---------------------- starvz-0.7.0/starvz/R/phase1_outlier.R |only starvz-0.7.0/starvz/R/phase1_parse_csv.R | 131 +++++++++-------- starvz-0.7.0/starvz/R/phase2_config.R | 2 starvz-0.7.0/starvz/R/phase2_mpi.R | 7 starvz-0.7.0/starvz/R/phase2_states_chart.R | 4 starvz-0.7.0/starvz/R/phase2_util.R | 6 starvz-0.7.0/starvz/R/read_functions.R | 2 starvz-0.7.0/starvz/R/starvz_data.R | 3 starvz-0.7.0/starvz/R/write_functions.R | 3 starvz-0.7.0/starvz/inst/etc/default.yaml | 2 starvz-0.7.0/starvz/inst/tools/phase1-workflow.sh | 2 starvz-0.7.0/starvz/src/RcppExports.cpp | 10 - starvz-0.7.0/starvz/src/last.cpp |only 19 files changed, 125 insertions(+), 268 deletions(-)
More information about fractalRegression at CRAN
Permanent link
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed
model described in Signorelli et al. (2021,
<doi:10.1177/1471082X20936017>). Likelihood approximation based on
adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre, cph]
(<https://orcid.org/0000-0002-8102-3356>),
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between ptmixed versions 1.0.3 dated 2021-03-02 and 1.1.0 dated 2021-11-05
ptmixed-1.0.3/ptmixed/inst/NEWS.md |only ptmixed-1.1.0/ptmixed/DESCRIPTION | 8 - ptmixed-1.1.0/ptmixed/MD5 | 64 +++++----- ptmixed-1.1.0/ptmixed/R/df1.R | 4 ptmixed-1.1.0/ptmixed/R/loglik.R | 4 ptmixed-1.1.0/ptmixed/R/makespaghetti.R | 11 + ptmixed-1.1.0/ptmixed/R/nbglm.R | 4 ptmixed-1.1.0/ptmixed/R/nbmixed.R | 4 ptmixed-1.1.0/ptmixed/R/pmf.R | 4 ptmixed-1.1.0/ptmixed/R/ptglm.R | 4 ptmixed-1.1.0/ptmixed/R/ptmixed.R | 4 ptmixed-1.1.0/ptmixed/R/ranef.R | 4 ptmixed-1.1.0/ptmixed/R/simulate_ptglmm.R | 4 ptmixed-1.1.0/ptmixed/R/summary-ptglm.R | 4 ptmixed-1.1.0/ptmixed/R/summary-ptglmm.R | 4 ptmixed-1.1.0/ptmixed/R/wald-test.R | 4 ptmixed-1.1.0/ptmixed/inst/CITATION | 15 +- ptmixed-1.1.0/ptmixed/inst/NEWS.Rmd |only ptmixed-1.1.0/ptmixed/inst/doc/Overview_functionalities_ptmixed.Rmd | 6 ptmixed-1.1.0/ptmixed/inst/doc/Overview_functionalities_ptmixed.html | 6 ptmixed-1.1.0/ptmixed/man/df1.Rd | 4 ptmixed-1.1.0/ptmixed/man/loglik.pt.1re.Rd | 4 ptmixed-1.1.0/ptmixed/man/make.spaghetti.Rd | 4 ptmixed-1.1.0/ptmixed/man/nbglm.Rd | 4 ptmixed-1.1.0/ptmixed/man/nbmixed.Rd | 4 ptmixed-1.1.0/ptmixed/man/pmf.Rd | 4 ptmixed-1.1.0/ptmixed/man/ptglm.Rd | 4 ptmixed-1.1.0/ptmixed/man/ptmixed.Rd | 4 ptmixed-1.1.0/ptmixed/man/ranef.Rd | 4 ptmixed-1.1.0/ptmixed/man/simulate_ptglmm.Rd | 4 ptmixed-1.1.0/ptmixed/man/summary.ptglm.Rd | 4 ptmixed-1.1.0/ptmixed/man/summary.ptglmm.Rd | 4 ptmixed-1.1.0/ptmixed/man/wald.test.Rd | 4 ptmixed-1.1.0/ptmixed/vignettes/Overview_functionalities_ptmixed.Rmd | 6 34 files changed, 113 insertions(+), 103 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre],
Ignacio García Jurado [aut],
Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 1.4.0 dated 2021-07-08 and 1.4.3 dated 2021-11-05
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/function_pert_calendario.R | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Author: Krzysztof Bartoszek [cre, aut],
Jesualdo Fuentes-Gonzalez [ctb],
Jason Pienaar [ctb],
John Clarke [ctb]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.6.5 dated 2021-06-03 and 2.7 dated 2021-11-05
mvSLOUCH-2.6.5/mvSLOUCH/R/from_matrixcalc_1_0_3_matrixcalculations.R |only mvSLOUCH-2.7/mvSLOUCH/DESCRIPTION | 32 ++-- mvSLOUCH-2.7/mvSLOUCH/MD5 | 73 +++++----- mvSLOUCH-2.7/mvSLOUCH/NAMESPACE | 3 mvSLOUCH-2.7/mvSLOUCH/R/OUphylregression.R |only mvSLOUCH-2.7/mvSLOUCH/R/PhyloSDEestim.R | 10 - mvSLOUCH-2.7/mvSLOUCH/R/calls_to_matrixcalc.R |only mvSLOUCH-2.7/mvSLOUCH/R/evolmodelest.R | 4 mvSLOUCH-2.7/mvSLOUCH/R/loglik.R | 21 ++ mvSLOUCH-2.7/mvSLOUCH/R/modelparamstransform.R | 1 mvSLOUCH-2.7/mvSLOUCH/R/phylgls.R | 6 mvSLOUCH-2.7/mvSLOUCH/R/precalcs.R | 4 mvSLOUCH-2.7/mvSLOUCH/R/regimes.R | 2 mvSLOUCH-2.7/mvSLOUCH/R/sdemeanphyl.R |only mvSLOUCH-2.7/mvSLOUCH/R/sdemoments.R | 9 - mvSLOUCH-2.7/mvSLOUCH/R/simulVasicekproc.R | 6 mvSLOUCH-2.7/mvSLOUCH/R/simulVasicekprocphyl.R | 1 mvSLOUCH-2.7/mvSLOUCH/R/simulclustphyl.R | 2 mvSLOUCH-2.7/mvSLOUCH/R/wrappers.R | 33 +++- mvSLOUCH-2.7/mvSLOUCH/build/vignette.rds |binary mvSLOUCH-2.7/mvSLOUCH/inst/doc/mvSLOUCH_Carnivorans.Rmd | 7 mvSLOUCH-2.7/mvSLOUCH/inst/doc/mvSLOUCH_Carnivorans.html | 19 -- mvSLOUCH-2.7/mvSLOUCH/man/BrownianMotionModel.Rd | 13 - mvSLOUCH-2.7/mvSLOUCH/man/OU_RSS.Rd |only mvSLOUCH-2.7/mvSLOUCH/man/OU_phylreg.Rd |only mvSLOUCH-2.7/mvSLOUCH/man/OU_xVz.Rd |only mvSLOUCH-2.7/mvSLOUCH/man/SummarizeBM.Rd | 4 mvSLOUCH-2.7/mvSLOUCH/man/SummarizeMVSLOUCH.Rd | 7 mvSLOUCH-2.7/mvSLOUCH/man/SummarizeOUCH.Rd | 5 mvSLOUCH-2.7/mvSLOUCH/man/estimate.evolutionary.model.Rd | 35 +++- mvSLOUCH-2.7/mvSLOUCH/man/mvSLOUCH-internal.Rd | 16 ++ mvSLOUCH-2.7/mvSLOUCH/man/mvSLOUCH-package.Rd | 12 - mvSLOUCH-2.7/mvSLOUCH/man/mvslouchModel.Rd | 37 +++-- mvSLOUCH-2.7/mvSLOUCH/man/ouchModel.Rd | 22 ++- mvSLOUCH-2.7/mvSLOUCH/man/parametric.bootstrap.Rd | 25 ++- mvSLOUCH-2.7/mvSLOUCH/man/simulBMProcPhylTree.Rd | 2 mvSLOUCH-2.7/mvSLOUCH/man/simulMVSLOUCHProcPhylTree.Rd | 2 mvSLOUCH-2.7/mvSLOUCH/man/simulOUCHProcPhylTree.Rd | 2 mvSLOUCH-2.7/mvSLOUCH/man/simulate_clustered_phylogeny.Rd | 6 mvSLOUCH-2.7/mvSLOUCH/vignettes/Carnivora_mvSLOUCH_objects.RData |binary mvSLOUCH-2.7/mvSLOUCH/vignettes/mvSLOUCH_Carnivorans.Rmd | 7 41 files changed, 287 insertions(+), 141 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-23 0.5.0
2021-06-22 0.4.0
2020-09-26 0.3.0
2018-05-06 0.1.5
Title: Permutation Conditional Random Tests
Description: It provides functions to perform permutation conditional random one-sample and two-samples t-tests in a multivariate framework.
Author: Angela Andreella [aut, cre] (Main author,
<https://orcid.org/0000-0002-1141-3041>)
Maintainer: Angela Andreella <angela.andreella@unipd.it>
Diff between pecora versions 0.1.0 dated 2021-10-07 and 0.1.1 dated 2021-11-05
pecora-0.1.0/pecora/man/rowVariance.Rd |only pecora-0.1.1/pecora/DESCRIPTION | 6 - pecora-0.1.1/pecora/MD5 | 25 ++++--- pecora-0.1.1/pecora/NAMESPACE | 1 pecora-0.1.1/pecora/NEWS.md | 9 ++ pecora-0.1.1/pecora/R/oneSample.R | 83 +++++++------------------ pecora-0.1.1/pecora/R/pecora-package.R |only pecora-0.1.1/pecora/R/t2p.R |only pecora-0.1.1/pecora/R/twoSamples.R | 98 +++++++++++------------------- pecora-0.1.1/pecora/R/utils.R | 14 +--- pecora-0.1.1/pecora/man/oneSample.Rd | 27 ++------ pecora-0.1.1/pecora/man/pecora-package.Rd |only pecora-0.1.1/pecora/man/t2p.Rd |only pecora-0.1.1/pecora/man/twoSamples.Rd | 30 +++------ pecora-0.1.1/pecora/src/permGroup.cpp | 2 pecora-0.1.1/pecora/src/signFlip.cpp | 1 16 files changed, 109 insertions(+), 187 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey [aut, cre] (<https://orcid.org/0000-0002-7522-3677>)
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.5 dated 2021-09-22 and 1.6 dated 2021-11-05
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 8 +++++++- R/sumz.R | 12 ++++++++---- build/metap.pdf |binary build/partial.rdb |binary data/dat.metap.rda |binary inst/doc/compare.R | 2 +- inst/doc/compare.Rnw | 2 +- inst/doc/compare.pdf |binary inst/doc/metap.R | 2 +- inst/doc/metap.Rnw | 8 ++++++-- inst/doc/metap.pdf |binary man/dat.metap.Rd | 25 ++++++++++++++++++++----- man/logitp.Rd | 2 +- man/macros/macros.Rd | 1 + man/plotp.Rd | 2 +- man/sumlog.Rd | 4 ++-- man/sumz.Rd | 6 ++++-- man/wilkinsonp.Rd | 2 +- vignettes/compare.Rnw | 2 +- vignettes/metap.Rnw | 8 ++++++-- 22 files changed, 86 insertions(+), 50 deletions(-)
Title: Basic Finance; NPV/IRR/Annuities/Bond-Pricing; Black Scholes
Description: Implements the basic financial analysis
functions similar to (but not identical to) what
is available in most spreadsheet software. This
includes finding the IRR and NPV of regularly
spaced cash flows and annuities. Bond pricing and
YTM calculations are included. In addition, Black
Scholes option pricing and Greeks are also
provided.
Author: Jayanth Varma [aut, cre]
Maintainer: Jayanth Varma <jrvarma@iima.ac.in>
Diff between jrvFinance versions 1.4.2 dated 2021-04-18 and 1.4.3 dated 2021-11-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/annuity.R | 2 +- build/vignette.rds |binary inst/doc/jrvFinance-demo.html | 23 ++++++++++++++++++++--- 6 files changed, 34 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-07 1.7
2019-09-24 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-20 0.1.11
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Armadillo requires a C++11 compiler.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.10.7.0.0 dated 2021-09-30 and 0.10.7.3.0 dated 2021-11-05
ChangeLog | 22 +++++++ DESCRIPTION | 8 +- MD5 | 42 +++++++------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary configure | 18 +++--- configure.ac | 6 +- inst/NEWS.Rd | 29 +++++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Mat_bones.hpp | 8 +- inst/include/armadillo_bits/Mat_meat.hpp | 16 ++--- inst/include/armadillo_bits/SpMat_meat.hpp | 5 - inst/include/armadillo_bits/SpSubview_meat.hpp | 14 ++-- inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_check.hpp | 2 inst/include/armadillo_bits/op_flip_meat.hpp | 68 ++++++++++++++++++++--- inst/include/armadillo_bits/op_pinv_meat.hpp | 39 +++++++++++++ inst/include/armadillo_bits/op_reverse_meat.hpp | 70 ++++++++++++++++-------- inst/include/armadillo_bits/subview_bones.hpp | 12 ++-- inst/include/armadillo_bits/subview_meat.hpp | 39 +++++++++++++ 22 files changed, 303 insertions(+), 99 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] (<https://orcid.org/0000-0002-6589-301X>),
Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Michael Fop [ctb] (<https://orcid.org/0000-0003-3936-2757>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.4.7 dated 2020-11-20 and 5.4.8 dated 2021-11-05
DESCRIPTION | 13 MD5 | 183 ++-- NAMESPACE | 2 NEWS.md | 14 R/bootstrap.R | 5 R/clustCombi.R | 6 R/densityMclust.R | 92 +- R/gmmhd.R | 20 R/graphics.R | 7 R/mbahc.R | 105 +- R/mclust.R | 74 + R/mclustda.R | 210 +++-- R/mclustdr.R | 169 ++-- R/mclustssc.R | 4 R/util.R | 12 R/weights.R | 29 build/vignette.rds |binary inst/CITATION | 2 inst/doc/mclust.R | 19 inst/doc/mclust.Rmd | 28 inst/doc/mclust.html | 1362 ++++++++++++++++------------------ man/Baudry_etal_2010_JCGS_examples.Rd | 2 man/EuroUnemployment.Rd | 2 man/GvHD.Rd | 2 man/MclustBootstrap.Rd | 2 man/MclustDA.Rd | 2 man/MclustDR.Rd | 26 man/MclustDRsubsel.Rd | 4 man/acidity.Rd | 3 man/bic.Rd | 2 man/cdens.Rd | 22 man/cdensE.Rd | 2 man/classPriorProbs.Rd | 2 man/clustCombi.Rd | 4 man/combiPlot.Rd | 2 man/combiTree.Rd | 2 man/coordProj.Rd | 2 man/cross.Rd | 2 man/cvMclustDA.Rd | 98 +- man/decomp2sigma.Rd | 2 man/dens.Rd | 24 man/densityMclust.Rd | 18 man/densityMclust.diagnostic.Rd | 2 man/diabetes.Rd | 2 man/dupPartition.Rd |only man/em.Rd | 2 man/emE.Rd | 2 man/entPlot.Rd | 2 man/estep.Rd | 2 man/estepE.Rd | 2 man/gmmhd.Rd | 2 man/hc.Rd | 80 + man/hcE.Rd | 21 man/hclass.Rd | 2 man/imputeData.Rd | 2 man/imputePairs.Rd | 2 man/logLik.Mclust.Rd | 2 man/logLik.MclustDA.Rd | 2 man/mclust-internal.Rd | 4 man/mclust-package.Rd | 19 man/mclust.options.Rd | 27 man/mclust1Dplot.Rd | 2 man/mclust2Dplot.Rd | 2 man/mclustBIC.Rd | 5 man/mclustBICupdate.Rd | 2 man/mclustBootstrapLRT.Rd | 2 man/mclustICL.Rd | 2 man/mclustLoglik.Rd | 2 man/me.Rd | 2 man/me.weighted.Rd | 19 man/mstep.Rd | 2 man/mstepE.Rd | 2 man/mvnX.Rd | 2 man/plot.Mclust.Rd | 2 man/plot.MclustBoostrap.Rd | 2 man/plot.MclustDA.Rd | 2 man/plot.MclustDR.Rd | 5 man/plot.clustCombi.Rd | 2 man/plot.densityMclust.Rd | 7 man/plot.mclustBIC.Rd | 2 man/plot.mclustICL.Rd | 2 man/predict.MclustDA.Rd | 2 man/predict.MclustSSC.Rd | 2 man/predict.densityMclust.Rd | 2 man/randProj.Rd | 2 man/sim.Rd | 4 man/simE.Rd | 2 man/summary.MclustBootstrap.Rd | 2 man/surfacePlot.Rd | 4 man/thyroid.Rd | 3 man/wdbc.Rd | 3 vignettes/mclust.Rmd | 28 vignettes/vignette.css | 39 93 files changed, 1578 insertions(+), 1341 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-10 0.15
2016-02-23 0.14.9
2016-01-31 0.14.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-22 0.9.10
2020-11-21 0.9.9
2020-06-19 0.9.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-19 1.2
2017-06-29 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-04 0.21-247
2019-10-03 0.19-276
2018-07-24 0.18-204
2018-07-05 0.18-185
2018-01-11 0.18-12
2017-12-19 0.17-353
2015-09-01 0.15-244
2015-06-25 0.15-176
2015-05-28 0.15-147
2015-05-26 0.15-146
2015-05-25 0.15-145
2014-09-19 0.14-261
2014-09-12 0.14-256
2014-03-22 0.14-78
2014-03-13 0.14-72
2014-03-12 0.14-71
2013-12-09 0.13-343.05
2013-12-06 0.13-340.18
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-30 0.1-3
2016-01-24 0.1-2
2014-05-19 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-16 0.4-0
2016-09-23 0.3-1
2016-01-25 0.3-0
2014-05-26 0.2-3
2014-03-11 0.2-2
2014-02-03 0.2-1
2013-09-29 0.2-0
2013-08-01 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 1.1.0
2017-05-03 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-02 1.0.0
2020-02-11 0.1.2
2018-05-14 0.1.1
2018-01-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-16 0.1.16-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-06 0.2-1
2018-02-01 0.2-0
2017-01-01 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-08 0.1.5
2016-12-25 0.1.4
2016-12-22 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-22 1.0.0-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-21 1.4.0
2019-06-21 1.3.6
2017-01-31 1.3.3
2016-11-21 1.3.2
2015-11-30 1.3.1
2014-07-28 1.2.11
2013-05-23 1.2.9
2013-01-23 1.2.6
2012-12-19 1.2.4
2012-10-01 1.2.3
2012-04-24 1.2.2
2012-03-15 1.2.1
2011-08-24 1.1.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 0.5-3
2020-02-02 0.5-2
2020-01-30 0.5-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-20 2.0.1
2020-03-10 2.0.0
2020-02-27 1.0.3
2019-12-05 1.0.2
2019-11-29 1.0.1
2019-11-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-13 0.2-1
2019-11-28 0.1-9
2019-11-20 0.1-8
2019-06-05 0.1-7
2017-05-14 0.1-6
2016-12-21 0.1-5
2013-07-03 0.1-4
2013-07-02 0.1-3
2013-06-24 0.1-2
2013-06-04 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-19 0.1.4
2019-12-05 0.1.3
2017-02-20 0.1.2
2017-02-06 0.1.1
2016-12-19 0.1.0
2016-11-03 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-13 0.1-1
2018-04-26 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-24 1.1.0
2016-07-25 1.0.1
2016-07-20 1.0
Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of
linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client
is included in this package as well.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-8 dated 2021-11-03 and 1.8-9 dated 2021-11-05
Rserve-1.8-8/Rserve/src/rsio.c |only Rserve-1.8-8/Rserve/src/rsio.h |only Rserve-1.8-9/Rserve/DESCRIPTION | 6 Rserve-1.8-9/Rserve/MD5 | 40 +-- Rserve-1.8-9/Rserve/NEWS | 4 Rserve-1.8-9/Rserve/configure | 226 +++++++++++++++++- Rserve-1.8-9/Rserve/configure.ac | 2 Rserve-1.8-9/Rserve/inst/java/REngine.jar |binary Rserve-1.8-9/Rserve/inst/java/Rserve.jar |binary Rserve-1.8-9/Rserve/src/Makevars.in | 4 Rserve-1.8-9/Rserve/src/Makevars.win | 4 Rserve-1.8-9/Rserve/src/Rserv.c | 18 - Rserve-1.8-9/Rserve/src/Rsrv.h | 18 + Rserve-1.8-9/Rserve/src/client/cxx/Rsrv.h | 18 + Rserve-1.8-9/Rserve/src/client/java/Rserve/Rserve.jar |binary Rserve-1.8-9/Rserve/src/config.h.in | 3 Rserve-1.8-9/Rserve/src/proxy/date.c | 37 ++ Rserve-1.8-9/Rserve/src/proxy/forward.c | 30 +- Rserve-1.8-9/Rserve/src/proxy/rscript.c | 3 Rserve-1.8-9/Rserve/src/qap_decode.c | 27 +- Rserve-1.8-9/Rserve/src/qap_encode.c | 83 ++++-- Rserve-1.8-9/Rserve/src/ulog.c | 4 22 files changed, 421 insertions(+), 106 deletions(-)
Title: Read and Write TIFF Images
Description: Functions to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors, including native image representation.
Author: Simon Urbanek <Simon.Urbanek@r-project.org> [aut, cre],
Kent Johnson <kjohnson@akoyabio.com> [ctb]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between tiff versions 0.1-8 dated 2021-03-31 and 0.1-10 dated 2021-11-05
DESCRIPTION | 6 MD5 | 12 NEWS | 9 configure | 2523 +++++++++++++++++++++++++++++------------------------------ configure.ac | 2 src/read.c | 30 src/write.c | 9 7 files changed, 1313 insertions(+), 1278 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-18 0.4.0
2021-08-19 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-21 1.0.5
2021-05-28 1.0.4
2021-04-18 1.0.3
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>),
Miquel de Caceres [ctb] (<https://orcid.org/0000-0001-7132-2080>),
Aitor Ameztegui [ctb] (<https://orcid.org/0000-0003-2006-1559>)
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.0.2 dated 2021-10-25 and 0.0.3 dated 2021-11-05
DESCRIPTION | 11 +++++----- MD5 | 39 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 7 ++++++ R/get_data.R | 11 ++++++++++ R/services_options.R | 2 - R/utils.R | 16 +++++++++++--- R/zzz.R |only README.md | 36 +++++++++++++++++++-------------- inst/doc/aemet.html | 4 +-- inst/doc/meteocat.Rmd | 2 - inst/doc/meteocat.html | 4 +-- man/get_meteo_from.Rd | 8 +++++++ man/get_stations_info_from.Rd | 8 +++++++ man/services_options.Rd | 2 - tests/testthat/test-aemet.R | 13 +++++------- tests/testthat/test-meteocat.R | 19 ++++++++--------- tests/testthat/test-meteoclimatic.R | 3 -- tests/testthat/test-meteogalicia.R | 25 +++++++++++------------ tests/testthat/test-riaa.R | 13 +++++++----- vignettes/meteocat.Rmd | 2 - 21 files changed, 138 insertions(+), 88 deletions(-)
Title: Scalable Geographically Weighted Regression
Description: Fast and regularized version of GWR for large dataset, detailed in Murakami, Tsutsumida, Yoshida, Nakaya, and Lu (2019) <arXiv:1905.00266>.
Author: Daisuke Murakami[cre,aut], Narumasa Tsutsumida[ctb], Takahiro Yoshida[ctb], Tomoki Nakaya[ctb], Lu Binbin[ctb]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between scgwr versions 0.1.2-1 dated 2020-08-07 and 0.1.2-2 dated 2021-11-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 7 +++---- R/scgwr.R | 2 +- man/scgwr_p.Rd | 2 +- 5 files changed, 14 insertions(+), 15 deletions(-)
Title: Scelestial: Steiner Tree Based Single-Cell Lineage Tree
Inference
Description: Scelestial infers a lineage tree from single-cell DNA mutation matrix.
It generates a tree with approximately maximum parsimony through
a Steiner tree approximation algorithm.
Author: Mohammad Hadi Foroughmand Araabi [aut, cre],
Sama Goliaei [aut, ctb],
Alice McHardy [ctb]
Maintainer: Mohammad Hadi Foroughmand Araabi <foroughmand@gmail.com>
Diff between RScelestial versions 1.0.1 dated 2020-03-23 and 1.0.2 dated 2021-11-05
DESCRIPTION | 13 MD5 | 25 - NEWS.md |only R/Li-data.R | 2 R/scelestial.R | 54 +- build/vignette.rds |binary inst/doc/RScelestial-vignette.html | 680 ++++++++++++------------------- man/Li.Rd | 2 man/as.mutation.matrix.Rd | 3 man/as.ten.state.matrix.Rd | 3 man/as.ten.state.matrix.from.node.seq.Rd | 3 src/scelestial.cc | 20 src/scelestial.h | 414 ++---------------- src/synthesis.h | 169 ++++--- 14 files changed, 474 insertions(+), 914 deletions(-)
Title: Read/Write, Transform, and Summarize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Features include reading/writing all 'BIOM' formats, rarefaction, alpha
diversity, beta diversity (including 'UniFrac'), summarizing counts by
taxonomic level, and sample subsetting. Standalone functions for
reading, writing, and subsetting phylogenetic trees are also provided.
All CPU intensive operations are encoded in C with multi-thread support.
Author: Daniel P. Smith [aut, cre, cph]
(<https://orcid.org/0000-0002-2479-2044>)
Maintainer: Daniel P. Smith <dansmith@orst.edu>
Diff between rbiom versions 1.0.2 dated 2020-05-29 and 1.0.3 dated 2021-11-05
DESCRIPTION | 14 - MD5 | 9 NAMESPACE | 1 NEWS.md |only R/write.biom.r | 645 +++++++++++++++++++++++++--------------------------- src/RcppExports.cpp | 5 6 files changed, 338 insertions(+), 336 deletions(-)
Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre] (0000-0001-9788-3628)
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.4.0 dated 2021-10-22 and 0.4.1 dated 2021-11-05
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 571 +++++++++++++++++++------------------- R/detail.R | 31 +- R/paste.R | 3 R/struct.R | 2 README.md | 34 +- man/detail.Rd | 8 man/struct.Rd | 2 tests/testthat/test-detail.R | 17 + tests/testthat/test-paste.R | 18 - tests/testthat/test-system-file.R | 5 12 files changed, 378 insertions(+), 343 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert [aut, cre] (<https://orcid.org/0000-0002-6862-5221>)
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.8.95.1 dated 2020-07-13 and 0.8.95.2 dated 2021-11-05
DESCRIPTION | 7 MD5 | 22 - build/vignette.rds |binary configure | 26 - inst/doc/quickstart.Rmd | 2 inst/doc/quickstart.html | 414 +++++++--------------------- inst/doc/technicaldocs.html | 400 +++++++-------------------- inst/doc/userguide.Rmd | 4 inst/doc/userguide.html | 634 +++++++++++++++---------------------------- tests/testthat/test-4-qsys.r | 2 vignettes/quickstart.Rmd | 2 vignettes/userguide.Rmd | 4 12 files changed, 474 insertions(+), 1043 deletions(-)