Title: The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Description: Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Author: Fumio Ishioka
Maintainer: Fumio Ishioka <fishioka@okayama-u.ac.jp>
Diff between echelon versions 0.1.0 dated 2020-01-09 and 0.2.0 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 35 ++++++++++++++++++----------------- NEWS.md |only R/e.echebin.r | 4 ++-- R/e.echelon.r | 1 - R/e.echepoi.r | 4 ++-- R/e.scan.pop.r | 3 ++- man/e.cluster.decision.Rd | 4 ++-- man/e.cluster.dendrogram.Rd | 12 ++++++------ man/e.cluster.map.Rd | 18 +++++++++--------- man/e.dendrogram.Rd | 38 +++++++++++++++++++------------------- man/e.dendrogram.axis.Rd | 18 +++++++++--------- man/e.main.Rd | 6 +++--- man/e.monte.bin.Rd | 12 ++++++------ man/e.monte.poi.Rd | 14 +++++++------- man/e.profile.Rd | 6 +++--- man/e.scan.Rd | 12 ++++++------ man/e.scan.pop.Rd | 14 +++++++------- man/nlimb.Rd | 4 ++-- 19 files changed, 107 insertions(+), 106 deletions(-)
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the
'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the
circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain
from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit
of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age).
The statistics relate only to events on public roads that were reported
to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See
the Department for Transport website
<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more
information on these datasets.
The package is described in a paper in the Journal of Open Source Software
(Lovelace et al. 2019) <doi:10.21105/joss.01181>.
See
Gilardi et al. (2022) <doi [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Malcolm Morgan [aut] ,
Layik Hama [aut] ,
Mark Padgham [aut] ,
David Ranzolin [rev],
Adam Sparks [rev, ctb] ,
Ivo Wengraf [ctb],
RAC Foundation [fnd]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 3.0.2 dated 2023-11-04 and 3.0.3 dated 2024-02-08
DESCRIPTION | 8 MD5 | 39 - NEWS.md | 6 R/data.R | 2 R/dl.R | 8 R/format.R | 2 R/read.R | 4 R/utils.R | 3 build/vignette.rds |binary inst/doc/blog.html | 4 inst/doc/stats19-training.R | 154 +++--- inst/doc/stats19-training.html | 297 +++++------ inst/doc/stats19.R | 318 ++++++------ inst/doc/stats19.html | 1050 ++--------------------------------------- man/accidents_sample.Rd | 4 man/check_input_file.Rd | 4 man/dl_stats19.Rd | 8 man/find_file_name.Rd | 3 man/format_collisions.Rd | 5 man/get_stats19.Rd | 4 vignettes/packages.bib |only 21 files changed, 485 insertions(+), 1438 deletions(-)
Title: Simultaneous Non-Gaussian Component Analysis
Description: Implementation of SING algorithm to extract joint and individual non-Gaussian components from two datasets. SING uses an objective function that maximizes the skewness and kurtosis of latent components with a penalty to enhance the similarity between subject scores. Unlike other existing methods, SING does not use PCA for dimension reduction, but rather uses non-Gaussianity, which can improve feature extraction. Benjamin B.Risk, Irina Gaynanova (2021) <doi:10.1214/21-AOAS1466>.
Author: Liangkang Wang [aut, cre] ,
Irina Gaynanova [aut] ,
Benjamin Risk [aut]
Maintainer: Liangkang Wang <liangkang_wang@brown.edu>
Diff between singR versions 0.1.1 dated 2022-09-12 and 0.1.2 dated 2024-02-08
DESCRIPTION | 16 - MD5 | 16 - R/singR.R | 6 build/vignette.rds |binary inst/CITATION | 23 - inst/doc/singR-tutorial.R | 6 inst/doc/singR-tutorial.html | 681 +++++++++++++++++++++++++++++-------------- src/Makevars | 1 src/Makevars.win | 1 9 files changed, 499 insertions(+), 251 deletions(-)
Title: Robust Gaussian Stochastic Process Emulation
Description: Robust parameter estimation and prediction of Gaussian stochastic
process emulators. It allows for robust parameter estimation and prediction using
Gaussian stochastic process emulator. It also implements the parallel partial
Gaussian stochastic process emulator for computer model with massive outputs
See the reference: Mengyang Gu and Jim Berger, 2016, Annals of Applied Statistics;
Mengyang Gu, Xiaojing Wang and Jim Berger, 2018, Annals of Statistics.
Author: Mengyang Gu [aut, cre],
Jesus Palomo [aut],
James Berger [aut]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between RobustGaSP versions 0.6.5 dated 2022-06-01 and 0.6.6 dated 2024-02-08
CHANGELOG | 5 +++ DESCRIPTION | 6 ++-- MD5 | 36 ++++++++++++------------- R/ppgasp.R | 6 ++-- R/rgasp.R | 8 +++-- build/partial.rdb |binary man/Sample.rgasp.Rd | 3 -- man/findInertInputs.Rd | 2 - man/generate_predictive_mean_cov.Rd | 3 -- man/neg_log_marginal_post_approx_ref.Rd | 5 +-- man/neg_log_marginal_post_approx_ref_ppgasp.Rd | 7 ++-- man/neg_log_marginal_post_ref_ppgasp.Rd | 5 +-- man/ppgasp.Rd | 2 - man/pred_rgasp.Rd | 3 -- man/predict.ppgasp.Rd | 2 - man/rgasp.Rd | 2 - man/separable_kernel.Rd | 2 - man/separable_multi_kernel.Rd | 2 - src/functions.cpp | 8 ++++- 19 files changed, 56 insertions(+), 51 deletions(-)
Title: Moments and Distributions of Ratios of Quadratic Forms Using
Recursion
Description: Evaluates moments of ratios (and products) of quadratic forms
in normal variables, specifically using recursive algorithms developed by
Bao and Kan (2013) <doi:10.1016/j.jmva.2013.03.002> and Hillier et al.
(2014) <doi:10.1017/S0266466613000364>. Also provides distribution,
quantile, and probability density functions of simple ratios of quadratic
forms in normal variables with several algorithms. Originally developed as
a supplement to Watanabe (2023) <doi:10.1007/s00285-023-01930-8> for
evaluating average evolvability measures in evolutionary quantitative
genetics, but can be used for a broader class of statistics. Generating
functions for these moments are also closely related to the top-order zonal
and invariant polynomials of matrix arguments.
Author: Junya Watanabe [aut, cre, cph]
,
Patrick Alken [cph] ,
Brian Gough [cph] ,
Pavel Holoborodko [cph] ,
Gerard Jungman [cph] ,
Reid Priedhorsky [cph] ,
Free Software Foundation, Inc. [cph]
Maintainer: Junya Watanabe <Junya.Watanabe@uab.cat>
Diff between qfratio versions 1.1.0 dated 2023-10-02 and 1.1.1 dated 2024-02-08
DESCRIPTION | 34 - MD5 | 67 +-- NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 15 R/dist_funs.R | 288 +++++++++++-- R/dk_funs.R | 2 R/methods_qfrm.R | 20 R/qfratio-package.R | 68 ++- R/ratio_fun.R | 75 +-- R/utils.R | 158 +++++++ README.md | 20 build/partial.rdb |binary build/vignette.rds |binary inst/doc/qfratio.R | 8 inst/doc/qfratio.html | 46 +- inst/doc/qfratio_distr.R | 18 inst/doc/qfratio_distr.Rmd | 63 ++- inst/doc/qfratio_distr.html | 836 +++++++++++++++++++++------------------- man/a1_pk.Rd | 2 man/gsl_wrap.Rd |only man/new_qfrm.Rd | 20 man/pqfr.Rd | 110 +++-- man/qfmrm.Rd | 18 man/qfratio-package.Rd | 20 man/qfrm.Rd | 46 +- man/qfrm_cpp.Rd | 12 man/range_qfr.Rd |only src/RcppExports.cpp | 29 + src/gsl_wrap.cpp |only src/scripts/SOURCES_QFRATIO.mkf | 1 tests/testthat/test_distr.R | 152 +++---- tests/testthat/test_ratio.R | 116 ++--- tests/testthat/test_ratio_cpp.R | 64 --- vignettes/bibliography.bib | 2 vignettes/qfratio_distr.Rmd | 63 ++- 36 files changed, 1500 insertions(+), 880 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface from within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating time spent and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Matthew Fidler [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.0.8 dated 2024-02-07 and 0.0.10 dated 2024-02-08
NMsim-0.0.10/NMsim/DESCRIPTION | 6 NMsim-0.0.10/NMsim/MD5 | 141 ++-------- NMsim-0.0.10/NMsim/NAMESPACE | 14 NMsim-0.0.10/NMsim/NEWS.md | 12 NMsim-0.0.10/NMsim/R/NMreadSim.R | 19 - NMsim-0.0.10/NMsim/R/NMsim.R | 18 - NMsim-0.0.10/NMsim/R/NMsimModTab_utils.R |only NMsim-0.0.10/NMsim/man/NMsim.Rd | 8 NMsim-0.0.10/NMsim/man/NMsimModTabOperations.Rd |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/NMsim_xgxr021_sd1_NMreadSim_paths.rds |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/NMsim_xgxr021_sd1_NMreadSim_paths_res.fst |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/NMsim_xgxr025_sd1_NMreadSim_paths.rds |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/NMsim_xgxr025_sd1_paths.rds |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/xgxr021_sd1_NMreadSim |only NMsim-0.0.10/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1.mod | 18 - NMsim-0.0.10/NMsim/tests/testthat/testOutput/xgxr025_sd1_NMreadSim |only NMsim-0.0.10/NMsim/tests/testthat/testReference/NMsim_01.rds |binary NMsim-0.0.10/NMsim/tests/testthat/test_NMreadSim.R |only NMsim-0.0.10/NMsim/tests/testthat/test_NMsim.R | 52 ++- NMsim-0.0.8/NMsim/R/NMsimModels_utils.R |only NMsim-0.0.8/NMsim/man/NMsimModelsOperations.Rd |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMdata_backup |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_01_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_02_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_03_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_04_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_05_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_06_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_07_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_08_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_09_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10.ext |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10.lst |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10.mod |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10.xml |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10_1.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_10_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_2.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_3.tab |only NMsim-0.0.8/NMsim/tests/testthat/testOutput/xgxr025_sd1/NMsim_xgxr025_sd1_input.rds |only NMsim-0.0.8/NMsim/tests/testthat/testReference/NMsim_02.rds |only NMsim-0.0.8/NMsim/tests/testthat/testReference/NMsim_03.rds |only NMsim-0.0.8/NMsim/tests/testthat/testReference/NMsim_05.rds |only NMsim-0.0.8/NMsim/tests/testthat/testReference/NMsim_06.rds |only 113 files changed, 115 insertions(+), 173 deletions(-)
Title: Multiple Counting Process Structure for Survival Analysis
Description: Counting process structure is fundamental to model time varying covariates.
This package restructures dataframes in the counting process format for one or more variables.
F. W. Dekker, et al. (2008) <doi:10.1038/ki.2008.328>.
Author: Elia Gonzato [aut, cre, cph]
Maintainer: Elia Gonzato <elia.gonzato@outlook.it>
Diff between mtvc versions 1.0.0 dated 2024-02-05 and 1.1.0 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 10 +++++++--- R/data.R | 9 ++++----- R/mtvc.R | 2 +- man/mtvc.Rd | 2 +- man/simwide.Rd | 14 ++++++-------- 7 files changed, 29 insertions(+), 28 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metR versions 0.14.1 dated 2023-10-30 and 0.15.0 dated 2024-02-08
DESCRIPTION | 12 MD5 | 58 - NAMESPACE | 5 NEWS.md | 20 R/FitWave.R | 36 - R/geom_arrow.R | 3 R/geom_contour_fill.R | 4 R/geom_contour_tanaka.R | 6 R/guide_colorstrip.R | 124 ++- R/guide_vector.R | 24 R/scale-unbinned.R | 98 -- R/stat_contour2.r | 69 +- R/stat_contour_fill.R | 146 +++- R/textContourGrob.R | 29 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.R | 71 +- inst/doc/Visualization-tools.Rmd | 87 +- inst/doc/Visualization-tools.html | 1282 +++++++++++++------------------------- inst/doc/Working-with-data.Rmd | 4 inst/doc/Working-with-data.html | 1008 ++++++++++------------------- man/geom_contour2.Rd | 15 man/geom_contour_fill.Rd | 17 man/geom_contour_tanaka.Rd | 15 man/guide_colourstrip.Rd | 1 man/waves.Rd | 36 - tests/testthat/Rplots.pdf |binary vignettes/Visualization-tools.Rmd | 87 +- vignettes/Working-with-data.Rmd | 4 30 files changed, 1449 insertions(+), 1818 deletions(-)
Title: Individual Based Model Population Simulation
Description: Simulation of the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs) <doi:10.48550/arXiv.2303.06183>.
The package enables users to simulate population evolution, in which individuals are characterized by their age and some characteristics, and the population is modified by different types of events, including births/arrivals, death/exit events, or changes of characteristics. The frequency at which an event can occur to an individual can depend on their age and characteristics, but also on the characteristics of other individuals (interactions).
Such models have a wide range of applications. For instance, IBMs can be used for simulating the evolution of a heterogeneous insurance portfolio with selection or for validating mortality forecasts.
This package overcomes the limitations of time-consuming IBMs simulations by implementing new efficient algorithms based on thinning methods, which are compiled using the 'Rcpp' package while provid [...truncated...]
Author: Daphne Giorgi [aut, cre],
Sarah Kaakai [aut],
Vincent Lemaire [aut]
Maintainer: Daphne Giorgi <daphne.giorgi@sorbonne-universite.fr>
Diff between IBMPopSim versions 0.4.3 dated 2023-01-07 and 1.0.0 dated 2024-02-08
IBMPopSim-0.4.3/IBMPopSim/man/plot_population.Rd |only IBMPopSim-0.4.3/IBMPopSim/man/plot_pyramid.Rd |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_birth_intensities-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_compo_fem-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_compo_fem2-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_compo_fem2-2.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_death_rate-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_df-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_pyramids-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hpIMD_pyramids-2.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_birth_distrib-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_death_rate_1-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_intensities-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_log_death-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_pop_init-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_pop_init_1e6-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_pyramid_50-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_pyramids-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/hp_pyramids2-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_LeeCarter_risk1-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_cohort-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_evol_mortality-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_forecast-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_mortality_rates-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_pyr_group-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/insur_pyramid-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/main_plot_30-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/main_prob_subgroup1-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/plot_piecewise-1.pdf |only IBMPopSim-0.4.3/IBMPopSim/vignettes/plot_stepfun-1.pdf |only IBMPopSim-1.0.0/IBMPopSim/DESCRIPTION | 19 IBMPopSim-1.0.0/IBMPopSim/MD5 | 224 + IBMPopSim-1.0.0/IBMPopSim/NAMESPACE | 21 IBMPopSim-1.0.0/IBMPopSim/NEWS.md | 20 IBMPopSim-1.0.0/IBMPopSim/R/RcppExports.R | 16 IBMPopSim-1.0.0/IBMPopSim/R/data.R | 6 IBMPopSim-1.0.0/IBMPopSim/R/events.R | 40 IBMPopSim-1.0.0/IBMPopSim/R/model.R | 379 ++- IBMPopSim-1.0.0/IBMPopSim/R/popsim.R | 102 IBMPopSim-1.0.0/IBMPopSim/R/pyramid.R | 205 + IBMPopSim-1.0.0/IBMPopSim/R/utils.R | 145 - IBMPopSim-1.0.0/IBMPopSim/README.md | 14 IBMPopSim-1.0.0/IBMPopSim/build/vignette.rds |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim.R | 13 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim.Rmd | 1203 ++-------- IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_cpp.R | 8 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_cpp.Rmd | 45 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_cpp.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop.R | 36 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop.Rmd | 249 +- IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop_IMD.R | 31 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop_IMD.Rmd | 239 + IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_human_pop_IMD.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_insurance_portfolio.R | 28 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_insurance_portfolio.Rmd | 139 - IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_insurance_portfolio.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_interaction.R | 8 IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_interaction.Rmd | 144 - IBMPopSim-1.0.0/IBMPopSim/inst/doc/IBMPopSim_interaction.pdf |binary IBMPopSim-1.0.0/IBMPopSim/inst/include/popsim_template.cpp | 4 IBMPopSim-1.0.0/IBMPopSim/man/EW_popIMD_14.Rd | 2 IBMPopSim-1.0.0/IBMPopSim/man/add_characteristic.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/add_characteristic.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/age_pyramid.Rd | 21 IBMPopSim-1.0.0/IBMPopSim/man/age_pyramid.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/age_pyramids.Rd | 13 IBMPopSim-1.0.0/IBMPopSim/man/age_pyramids.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/assertEvents.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/assertPopulation.Rd | 2 IBMPopSim-1.0.0/IBMPopSim/man/compatibility_chars_events.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/compatibility_pop_model.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/death_table.Rd | 8 IBMPopSim-1.0.0/IBMPopSim/man/exposure_table.Rd | 6 IBMPopSim-1.0.0/IBMPopSim/man/fragments/cpp.Rmd | 7 IBMPopSim-1.0.0/IBMPopSim/man/fragments/cpp.html |only IBMPopSim-1.0.0/IBMPopSim/man/fragments/installation.Rmd | 19 IBMPopSim-1.0.0/IBMPopSim/man/fragments/installation.html |only IBMPopSim-1.0.0/IBMPopSim/man/fragments/installation.pdf |only IBMPopSim-1.0.0/IBMPopSim/man/fragments/quick_model.Rmd | 2 IBMPopSim-1.0.0/IBMPopSim/man/get_characteristics.Rd | 17 IBMPopSim-1.0.0/IBMPopSim/man/get_characteristics.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/id_complete.Rd | 4 IBMPopSim-1.0.0/IBMPopSim/man/mk_event_individual.Rd | 2 IBMPopSim-1.0.0/IBMPopSim/man/mk_event_inhomogeneous_poisson.Rd | 2 IBMPopSim-1.0.0/IBMPopSim/man/mk_event_interaction.Rd | 2 IBMPopSim-1.0.0/IBMPopSim/man/mk_event_poisson.Rd | 4 IBMPopSim-1.0.0/IBMPopSim/man/mk_model.Rd | 5 IBMPopSim-1.0.0/IBMPopSim/man/plot.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/plot.pyramid.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/popsample.Rd | 14 IBMPopSim-1.0.0/IBMPopSim/man/popsample.pyramid.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/popsim.Rd | 20 IBMPopSim-1.0.0/IBMPopSim/man/population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/population_alive.Rd | 20 IBMPopSim-1.0.0/IBMPopSim/man/population_alive.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/print.event.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/print.model.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/print.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/pyramid.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/summary.event.Rd | 4 IBMPopSim-1.0.0/IBMPopSim/man/summary.logs.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/summary.model.Rd | 4 IBMPopSim-1.0.0/IBMPopSim/man/summary.population.Rd |only IBMPopSim-1.0.0/IBMPopSim/man/summary.simulation_output.Rd |only IBMPopSim-1.0.0/IBMPopSim/src/RcppExports.cpp | 16 IBMPopSim-1.0.0/IBMPopSim/src/rcpp_tables.cpp | 32 IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim.Rmd | 1203 ++-------- IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim.Rmd.orig | 658 ++--- IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim.bib | 9 IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_cpp.Rmd | 45 IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_cpp.Rmd.orig | 6 IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_human_pop.Rmd | 249 +- IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_human_pop.Rmd.orig | 136 - IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_human_pop_IMD.Rmd | 239 + IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_human_pop_IMD.Rmd.orig | 121 - IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_insurance_portfolio.Rmd | 139 - IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_insurance_portfolio.Rmd.orig | 145 - IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_interaction.Rmd | 144 - IBMPopSim-1.0.0/IBMPopSim/vignettes/IBMPopSim_interaction.Rmd.orig | 60 IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_birth_intensities-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_compo_fem-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_compo_fem2-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_compo_fem2-2.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_death_rate-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_df-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hpIMD_pyramids-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_birth_distrib-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_death_rate_1-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_intensities-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_log_death-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_pop_init-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_pop_init_1e6-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_pyramid_50-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_pyramids-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/hp_pyramids2-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_LeeCarter_risk1-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_cohort-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_evol_mortality-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_forecast-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_mortality_rates-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_pyr_group-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/insur_pyramid-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/inter_output-1.png |binary IBMPopSim-1.0.0/IBMPopSim/vignettes/inter_output2-1.png |binary IBMPopSim-1.0.0/IBMPopSim/vignettes/inter_output3-1.png |binary IBMPopSim-1.0.0/IBMPopSim/vignettes/inter_pyramid-1.png |binary IBMPopSim-1.0.0/IBMPopSim/vignettes/main_plot_30-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/main_prob_subgroup1-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/plot_piecewise-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/plot_stepfun-1.png |only IBMPopSim-1.0.0/IBMPopSim/vignettes/precompile.R | 32 153 files changed, 3226 insertions(+), 3524 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) to estimate and compare performances between these models is used to describe model performances.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default.
When fitting not a relaxed lasso model but an elastic-net model, then the R-packages 'nestedcv' <https://cran.r-project.org/package=ne [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-1 dated 2024-01-08 and 0.4-2 dated 2024-02-08
glmnetr-0.4-1/glmnetr/R/RandomForest_231230.R |only glmnetr-0.4-1/glmnetr/R/ann_tab_cv_231230.R |only glmnetr-0.4-1/glmnetr/R/cv.glmnetr_230508.R |only glmnetr-0.4-1/glmnetr/R/cv.stepreg_230218.R |only glmnetr-0.4-1/glmnetr/R/nested.glmnetr_231230.R |only glmnetr-0.4-1/glmnetr/R/summary.nested.glmnetr_231230.R |only glmnetr-0.4-1/glmnetr/R/xgbm_tuned_230606.R |only glmnetr-0.4-1/glmnetr/inst/doc/An_Overview_of_glmnetr_231230.pdf |only glmnetr-0.4-1/glmnetr/inst/doc/An_Overview_of_glmnetr_231230.pdf.asis |only glmnetr-0.4-1/glmnetr/inst/doc/Using_ann_tab_cv_231230.pdf |only glmnetr-0.4-1/glmnetr/inst/doc/Using_ann_tab_cv_231230.pdf.asis |only glmnetr-0.4-1/glmnetr/inst/doc/Using_stepreg_231230.pdf |only glmnetr-0.4-1/glmnetr/inst/doc/Using_stepreg_231230.pdf.asis |only glmnetr-0.4-1/glmnetr/man/glmnetr.foldid.Rd |only glmnetr-0.4-1/glmnetr/vignettes/An_Overview_of_glmnetr_231230.Rmd |only glmnetr-0.4-1/glmnetr/vignettes/An_Overview_of_glmnetr_231230.pdf.asis |only glmnetr-0.4-1/glmnetr/vignettes/Using_ann_tab_cv_231230.Rmd |only glmnetr-0.4-1/glmnetr/vignettes/Using_ann_tab_cv_231230.pdf.asis |only glmnetr-0.4-1/glmnetr/vignettes/Using_stepreg_231230.Rmd |only glmnetr-0.4-1/glmnetr/vignettes/Using_stepreg_231230.pdf.asis |only glmnetr-0.4-2/glmnetr/DESCRIPTION | 12 - glmnetr-0.4-2/glmnetr/MD5 | 110 +++++----- glmnetr-0.4-2/glmnetr/NAMESPACE | 5 glmnetr-0.4-2/glmnetr/R/RandomForest_240202.R |only glmnetr-0.4-2/glmnetr/R/ann_tab_cv_240202.R |only glmnetr-0.4-2/glmnetr/R/cv.glmnetr_240202.R |only glmnetr-0.4-2/glmnetr/R/cv.stepreg_240202.R |only glmnetr-0.4-2/glmnetr/R/nested.glmnetr_240202.R |only glmnetr-0.4-2/glmnetr/R/summary.nested.glmnetr_240202.R |only glmnetr-0.4-2/glmnetr/R/xgbm_tuned_240202.R |only glmnetr-0.4-2/glmnetr/build/vignette.rds |binary glmnetr-0.4-2/glmnetr/inst/doc/An_Overview_of_glmnetr_240202.pdf |only glmnetr-0.4-2/glmnetr/inst/doc/An_Overview_of_glmnetr_240202.pdf.asis |only glmnetr-0.4-2/glmnetr/inst/doc/Using_ann_tab_cv_240202.pdf |only glmnetr-0.4-2/glmnetr/inst/doc/Using_ann_tab_cv_240202.pdf.asis |only glmnetr-0.4-2/glmnetr/inst/doc/Using_stepreg_240202.pdf |only glmnetr-0.4-2/glmnetr/inst/doc/Using_stepreg_240202.pdf.asis |only glmnetr-0.4-2/glmnetr/man/ann_tab_cv.Rd | 2 glmnetr-0.4-2/glmnetr/man/ann_tab_cv_best.Rd | 2 glmnetr-0.4-2/glmnetr/man/bsint.Rd | 2 glmnetr-0.4-2/glmnetr/man/calceloss.Rd | 2 glmnetr-0.4-2/glmnetr/man/cox.sat.dev.Rd | 2 glmnetr-0.4-2/glmnetr/man/cv.glmnetr.Rd | 10 glmnetr-0.4-2/glmnetr/man/cv.stepreg.Rd | 16 + glmnetr-0.4-2/glmnetr/man/diff_time.Rd | 2 glmnetr-0.4-2/glmnetr/man/diff_time1.Rd | 2 glmnetr-0.4-2/glmnetr/man/dtstndrz.Rd | 2 glmnetr-0.4-2/glmnetr/man/factor.foldid.Rd | 2 glmnetr-0.4-2/glmnetr/man/get.foldid.Rd |only glmnetr-0.4-2/glmnetr/man/glmnetr.Rd | 2 glmnetr-0.4-2/glmnetr/man/glmnetr.compcv.Rd | 8 glmnetr-0.4-2/glmnetr/man/glmnetr.compcv0.Rd | 14 - glmnetr-0.4-2/glmnetr/man/glmnetr.simdata.Rd | 2 glmnetr-0.4-2/glmnetr/man/glmnetr_devratio.Rd | 2 glmnetr-0.4-2/glmnetr/man/glmnetrll_1fold.Rd | 2 glmnetr-0.4-2/glmnetr/man/nested.glmnetr.Rd | 72 ++++-- glmnetr-0.4-2/glmnetr/man/predict.cv.stepreg.Rd | 2 glmnetr-0.4-2/glmnetr/man/predict.nested.glmnetr.Rd | 2 glmnetr-0.4-2/glmnetr/man/prednn_tl.Rd | 2 glmnetr-0.4-2/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.4-2/glmnetr/man/print.rf_tune.Rd | 2 glmnetr-0.4-2/glmnetr/man/rf_tune.Rd | 9 glmnetr-0.4-2/glmnetr/man/summary.cv.stepreg.Rd | 2 glmnetr-0.4-2/glmnetr/man/summary.nested.glmnetr.Rd | 7 glmnetr-0.4-2/glmnetr/man/summary.rf_tune.Rd | 2 glmnetr-0.4-2/glmnetr/man/wtlast.Rd | 2 glmnetr-0.4-2/glmnetr/man/wtmiddle.Rd | 2 glmnetr-0.4-2/glmnetr/man/wtzero.Rd | 2 glmnetr-0.4-2/glmnetr/man/xgb.simple.Rd | 17 + glmnetr-0.4-2/glmnetr/man/xgb.tuned.Rd | 17 + glmnetr-0.4-2/glmnetr/vignettes/An_Overview_of_glmnetr_240202.Rmd |only glmnetr-0.4-2/glmnetr/vignettes/An_Overview_of_glmnetr_240202.pdf.asis |only glmnetr-0.4-2/glmnetr/vignettes/Using_ann_tab_cv_240202.Rmd |only glmnetr-0.4-2/glmnetr/vignettes/Using_ann_tab_cv_240202.pdf.asis |only glmnetr-0.4-2/glmnetr/vignettes/Using_stepreg_240202.Rmd |only glmnetr-0.4-2/glmnetr/vignettes/Using_stepreg_240202.pdf.asis |only 76 files changed, 207 insertions(+), 136 deletions(-)
Title: Additional Geometries and Stats for 'ggplot2'
Description: An (aspirational) collection of additional geometries and
statistics for 'ggplot2'.
Author: Markus Doering [aut, cre, cph]
Maintainer: Markus Doering <m4rkus.doering@gmail.com>
Diff between ggpointless versions 0.0.3 dated 2022-08-25 and 0.1.0 dated 2024-02-08
ggpointless-0.0.3/ggpointless/man/operator.Rd |only ggpointless-0.0.3/ggpointless/tests/testthat/test-operator.R |only ggpointless-0.0.3/ggpointless/vignettes/man |only ggpointless-0.1.0/ggpointless/DESCRIPTION | 35 ggpointless-0.1.0/ggpointless/MD5 | 113 - ggpointless-0.1.0/ggpointless/NAMESPACE | 6 ggpointless-0.1.0/ggpointless/NEWS.md | 28 ggpointless-0.1.0/ggpointless/R/geom-catenary.R |only ggpointless-0.1.0/ggpointless/R/geom-chaikin.R | 131 - ggpointless-0.1.0/ggpointless/R/geom-lexis.R | 130 - ggpointless-0.1.0/ggpointless/R/geom-pointless.R | 1 ggpointless-0.1.0/ggpointless/R/ggpointless-package.R | 3 ggpointless-0.1.0/ggpointless/R/legend-draw.R | 12 ggpointless-0.1.0/ggpointless/R/stat-catenary.R |only ggpointless-0.1.0/ggpointless/R/stat-lexis.R | 2 ggpointless-0.1.0/ggpointless/R/stat_chaikin.R |only ggpointless-0.1.0/ggpointless/R/utils.R | 12 ggpointless-0.1.0/ggpointless/README.md | 68 ggpointless-0.1.0/ggpointless/build/vignette.rds |binary ggpointless-0.1.0/ggpointless/inst/WORDLIST |only ggpointless-0.1.0/ggpointless/inst/doc/examples.R | 6 ggpointless-0.1.0/ggpointless/inst/doc/examples.Rmd | 2 ggpointless-0.1.0/ggpointless/inst/doc/examples.html | 738 +++++----- ggpointless-0.1.0/ggpointless/inst/doc/ggpointless.R | 32 ggpointless-0.1.0/ggpointless/inst/doc/ggpointless.Rmd | 55 ggpointless-0.1.0/ggpointless/inst/doc/ggpointless.html | 501 +++--- ggpointless-0.1.0/ggpointless/man/draw_key_lexis.Rd | 4 ggpointless-0.1.0/ggpointless/man/figures/README-geom-catenary-1.png |only ggpointless-0.1.0/ggpointless/man/figures/README-geom-chaikin-1.png |binary ggpointless-0.1.0/ggpointless/man/figures/README-geom-lexis-1.png |binary ggpointless-0.1.0/ggpointless/man/figures/README-hello-world-1.png |binary ggpointless-0.1.0/ggpointless/man/figures/logo.png |binary ggpointless-0.1.0/ggpointless/man/geom_catenary.Rd |only ggpointless-0.1.0/ggpointless/man/geom_chaikin.Rd | 20 ggpointless-0.1.0/ggpointless/man/geom_lexis.Rd | 15 ggpointless-0.1.0/ggpointless/man/geom_pointless.Rd | 14 ggpointless-0.1.0/ggpointless/man/ggpointless-ggproto.Rd | 7 ggpointless-0.1.0/ggpointless/man/ggpointless-package.Rd | 8 ggpointless-0.1.0/ggpointless/tests/spelling.R |only ggpointless-0.1.0/ggpointless/tests/testthat.R | 8 ggpointless-0.1.0/ggpointless/tests/testthat/Rplots.pdf |binary ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/geom-catenary |only ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/geom-chaikin/readme-geom-chaikin-example.svg | 8 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/geom-lexis/different-point-shape.svg | 28 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/geom-lexis/no-horizontal-segments.svg | 34 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/geom-lexis/readme-geom-lexis-example.svg | 8 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/legend-draw/lexis-key-glyphs.svg | 18 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/legend-draw/point-show-false.svg | 4 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/legend-draw/point-show-true.svg | 8 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/legend-draw/pointrange-and-lexis-key-glyphs.svg | 36 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/stat-chaikin/cut-corners-1-time.svg | 2 ggpointless-0.1.0/ggpointless/tests/testthat/_snaps/stat-lexis/points-can-be-squares.svg | 28 ggpointless-0.1.0/ggpointless/tests/testthat/test-debme.R |only ggpointless-0.1.0/ggpointless/tests/testthat/test-geom-catenary.R |only ggpointless-0.1.0/ggpointless/tests/testthat/test-geom-lexis.R | 4 ggpointless-0.1.0/ggpointless/tests/testthat/test-getCatenaryParameter.R |only ggpointless-0.1.0/ggpointless/tests/testthat/test-legend-draw.R | 2 ggpointless-0.1.0/ggpointless/tests/testthat/test-stat-lexis.R | 2 ggpointless-0.1.0/ggpointless/vignettes/examples.Rmd | 2 ggpointless-0.1.0/ggpointless/vignettes/ggpointless.Rmd | 55 60 files changed, 1149 insertions(+), 1041 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 3.1.2 dated 2023-09-25 and 3.1.3 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/stsm_data_checks.R | 8 ++++---- R/stsm_detect_frequency.R | 14 +++++++------- R/stsm_estimate.R | 12 ++++++------ R/stsm_ssm.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary man/stsm_estimate.Rd | 12 ++++++------ man/stsm_ssm.Rd | 2 +- 11 files changed, 46 insertions(+), 40 deletions(-)
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling
Algorithms for 'nimble'
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes two versions of Hamiltonian Monte Carlo (HMC) No-U-Turn (NUTS) sampling, and (under development) Langevin samplers. The `NUTS_classic` sampler implements the original HMC-NUTS algorithm as described in Hoffman and Gelman (2014) <arXiv:1111.4246>. The `NUTS` sampler is a modern version of HMC-NUTS sampling matching the HMC sampler available in version 2.32.2 of Stan (Stan Development Team, 2023). In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling.
Author: Daniel Turek [aut, cre],
Perry de Valpine [aut],
Christopher Paciorek [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleHMC versions 0.2.0 dated 2023-09-11 and 0.2.1 dated 2024-02-08
DESCRIPTION | 11 +- MD5 | 10 +- R/HMC_samplers.R | 99 ++++++++++++++------ inst/NEWS.md | 14 ++ tests/testthat/test-HMC.R | 205 ++++++++++++++++++++++++++++++++++++++++--- tests/testthat/test-tuning.R | 21 +--- 6 files changed, 290 insertions(+), 70 deletions(-)
Title: 'Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)'
Description: Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Author: Christoph Hofer [cre],
Rene Locher [aut],
Andreas Ruckstuhl [ctb]
Maintainer: Christoph Hofer <christoph.hofer@zhaw.ch>
Diff between IDPmisc versions 1.1.20 dated 2020-01-21 and 1.1.21 dated 2024-02-08
IDPmisc-1.1.20/IDPmisc/R/plot.page.R |only IDPmisc-1.1.21/IDPmisc/ChangeLog | 916 +++++++++---------- IDPmisc-1.1.21/IDPmisc/DESCRIPTION | 20 IDPmisc-1.1.21/IDPmisc/MD5 | 170 +-- IDPmisc-1.1.21/IDPmisc/NAMESPACE | 80 - IDPmisc-1.1.21/IDPmisc/R/Arrows.R | 114 +- IDPmisc-1.1.21/IDPmisc/R/IDPcolorRamp.R | 148 +-- IDPmisc-1.1.21/IDPmisc/R/Image.R | 114 +- IDPmisc-1.1.21/IDPmisc/R/LegendAndTitle.R | 90 - IDPmisc-1.1.21/IDPmisc/R/NaRV.omit.R | 64 - IDPmisc-1.1.21/IDPmisc/R/Td.R | 58 - IDPmisc-1.1.21/IDPmisc/R/Td.aw.R | 72 - IDPmisc-1.1.21/IDPmisc/R/Tf.ai.R | 70 - IDPmisc-1.1.21/IDPmisc/R/cart2clock.R | 34 IDPmisc-1.1.21/IDPmisc/R/clock2cart.R | 38 IDPmisc-1.1.21/IDPmisc/R/col2hsv.R | 14 IDPmisc-1.1.21/IDPmisc/R/data.sheet.R | 28 IDPmisc-1.1.21/IDPmisc/R/draw.leg.R | 1220 +++++++++++++------------- IDPmisc-1.1.21/IDPmisc/R/general.control.R | 108 +- IDPmisc-1.1.21/IDPmisc/R/getXY.R | 78 - IDPmisc-1.1.21/IDPmisc/R/grid.control.R | 104 +- IDPmisc-1.1.21/IDPmisc/R/griddat.R | 338 +++---- IDPmisc-1.1.21/IDPmisc/R/hr.R | 14 IDPmisc-1.1.21/IDPmisc/R/ilagplot.R | 240 ++--- IDPmisc-1.1.21/IDPmisc/R/inf.omit.R | 10 IDPmisc-1.1.21/IDPmisc/R/ipairs.R | 434 ++++----- IDPmisc-1.1.21/IDPmisc/R/ipanel.smooth.R | 32 IDPmisc-1.1.21/IDPmisc/R/iplot.R | 356 +++---- IDPmisc-1.1.21/IDPmisc/R/iplotLegend.R | 84 - IDPmisc-1.1.21/IDPmisc/R/iplotMain.R | 28 IDPmisc-1.1.21/IDPmisc/R/itermplot.R | 332 +++---- IDPmisc-1.1.21/IDPmisc/R/key.control.R | 34 IDPmisc-1.1.21/IDPmisc/R/longtsPlot.R | 436 ++++----- IDPmisc-1.1.21/IDPmisc/R/ok.R | 24 IDPmisc-1.1.21/IDPmisc/R/plot.rose.R | 610 ++++++------- IDPmisc-1.1.21/IDPmisc/R/plotPage.R |only IDPmisc-1.1.21/IDPmisc/R/plotdat.R | 62 - IDPmisc-1.1.21/IDPmisc/R/poster.plot.R | 106 +- IDPmisc-1.1.21/IDPmisc/R/pw.R | 24 IDPmisc-1.1.21/IDPmisc/R/pw.ai.R | 20 IDPmisc-1.1.21/IDPmisc/R/pw.aw.R | 20 IDPmisc-1.1.21/IDPmisc/R/rfbaseline.R | 228 ++-- IDPmisc-1.1.21/IDPmisc/R/rose.R | 320 +++--- IDPmisc-1.1.21/IDPmisc/R/rose.grob.R | 238 ++--- IDPmisc-1.1.21/IDPmisc/R/segments.circle.R | 68 - IDPmisc-1.1.21/IDPmisc/R/showColors.R | 62 - IDPmisc-1.1.21/IDPmisc/R/title.control.R | 32 IDPmisc-1.1.21/IDPmisc/R/val.rose.R | 51 - IDPmisc-1.1.21/IDPmisc/R/zoom.R | 140 +- IDPmisc-1.1.21/IDPmisc/R/zzz.R | 31 IDPmisc-1.1.21/IDPmisc/data/MS.rda |binary IDPmisc-1.1.21/IDPmisc/man/Arrows.Rd | 198 ++-- IDPmisc-1.1.21/IDPmisc/man/IDPcolorRamp.Rd | 162 +-- IDPmisc-1.1.21/IDPmisc/man/IDPmisc-package.Rd | 86 - IDPmisc-1.1.21/IDPmisc/man/Image.Rd | 170 +-- IDPmisc-1.1.21/IDPmisc/man/MS.Rd | 90 - IDPmisc-1.1.21/IDPmisc/man/NaRV.omit.Rd | 108 +- IDPmisc-1.1.21/IDPmisc/man/cart2clock.Rd | 106 +- IDPmisc-1.1.21/IDPmisc/man/clock2cart.Rd | 96 +- IDPmisc-1.1.21/IDPmisc/man/col2hsv.Rd | 72 - IDPmisc-1.1.21/IDPmisc/man/data.sheet.Rd | 60 - IDPmisc-1.1.21/IDPmisc/man/draw.leg.Rd | 388 ++++---- IDPmisc-1.1.21/IDPmisc/man/general.control.Rd | 162 +-- IDPmisc-1.1.21/IDPmisc/man/getXY.Rd | 124 +- IDPmisc-1.1.21/IDPmisc/man/grid.control.Rd | 148 +-- IDPmisc-1.1.21/IDPmisc/man/humidity.Rd | 182 +-- IDPmisc-1.1.21/IDPmisc/man/ilagplot.Rd | 204 ++-- IDPmisc-1.1.21/IDPmisc/man/ipairs.Rd | 265 ++--- IDPmisc-1.1.21/IDPmisc/man/ipanel.smooth.Rd | 130 +- IDPmisc-1.1.21/IDPmisc/man/iplot.Rd | 230 ++-- IDPmisc-1.1.21/IDPmisc/man/iplotLegend.Rd | 92 - IDPmisc-1.1.21/IDPmisc/man/itermplot.Rd | 238 ++--- IDPmisc-1.1.21/IDPmisc/man/key.control.Rd | 80 - IDPmisc-1.1.21/IDPmisc/man/longtsPlot.Rd | 388 ++++---- IDPmisc-1.1.21/IDPmisc/man/ok.Rd | 54 - IDPmisc-1.1.21/IDPmisc/man/peaks.Rd | 178 +-- IDPmisc-1.1.21/IDPmisc/man/pkg-internal.Rd | 109 +- IDPmisc-1.1.21/IDPmisc/man/plot.rose.Rd | 426 ++++----- IDPmisc-1.1.21/IDPmisc/man/poster.plot.Rd | 118 +- IDPmisc-1.1.21/IDPmisc/man/rfbaseline.Rd | 190 ++-- IDPmisc-1.1.21/IDPmisc/man/rfbaselineScale.Rd | 50 - IDPmisc-1.1.21/IDPmisc/man/rose-class.Rd | 92 - IDPmisc-1.1.21/IDPmisc/man/rose.Rd | 244 ++--- IDPmisc-1.1.21/IDPmisc/man/showColors.Rd | 96 +- IDPmisc-1.1.21/IDPmisc/man/title.control.Rd | 74 - IDPmisc-1.1.21/IDPmisc/man/zoom.Rd | 96 +- IDPmisc-1.1.21/IDPmisc/src/init.c | 2 87 files changed, 6709 insertions(+), 6713 deletions(-)
Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between ggnewscale versions 0.4.9 dated 2023-05-25 and 0.4.10 dated 2024-02-08
DESCRIPTION | 9 - MD5 | 16 - NEWS.md | 2 R/new-scale.R | 47 ++++- README.md | 255 +++++++++++++++++++++++-------- man/figures/README-unnamed-chunk-3-1.png |binary man/ggnewscale-package.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-newscale.R | 5 9 files changed, 255 insertions(+), 80 deletions(-)
Title: Multiple Testing Procedures with Adaptation for Discrete Tests
Description: Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
Author: Sebastian Doehler [aut, ctb],
Florian Junge [aut, ctb, cre],
Guillermo Durand [aut, ctb],
Etienne Roquain [ctb],
Christina Kihn [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteFDR versions 1.3.6 dated 2021-09-03 and 1.3.7 dated 2024-02-08
DiscreteFDR-1.3.6/DiscreteFDR/R/DiscreteFDR.R |only DiscreteFDR-1.3.7/DiscreteFDR/DESCRIPTION | 32 DiscreteFDR-1.3.7/DiscreteFDR/MD5 | 73 DiscreteFDR-1.3.7/DiscreteFDR/NAMESPACE | 2 DiscreteFDR-1.3.7/DiscreteFDR/NEWS.md | 17 DiscreteFDR-1.3.7/DiscreteFDR/R/Aux_fun.R | 148 - DiscreteFDR-1.3.7/DiscreteFDR/R/DBR_fun.R | 95 - DiscreteFDR-1.3.7/DiscreteFDR/R/DiscreteFDR-package.R |only DiscreteFDR-1.3.7/DiscreteFDR/R/RcppExports.R | 158 - DiscreteFDR-1.3.7/DiscreteFDR/R/amnesia.R | 36 DiscreteFDR-1.3.7/DiscreteFDR/R/discreteBH_fun.R | 131 - DiscreteFDR-1.3.7/DiscreteFDR/R/fast_appli.R | 164 - DiscreteFDR-1.3.7/DiscreteFDR/R/plot_funs.R | 71 DiscreteFDR-1.3.7/DiscreteFDR/R/print_funs.R | 48 DiscreteFDR-1.3.7/DiscreteFDR/R/summary_funs.R | 78 DiscreteFDR-1.3.7/DiscreteFDR/R/support.R | 172 + DiscreteFDR-1.3.7/DiscreteFDR/build/partial.rdb |binary DiscreteFDR-1.3.7/DiscreteFDR/build/vignette.rds |binary DiscreteFDR-1.3.7/DiscreteFDR/inst/doc/DiscreteFDR.Rmd | 2 DiscreteFDR-1.3.7/DiscreteFDR/inst/doc/DiscreteFDR.html | 1097 ++++++++---- DiscreteFDR-1.3.7/DiscreteFDR/man/DBR.Rd | 22 DiscreteFDR-1.3.7/DiscreteFDR/man/DiscreteFDR.Rd | 77 DiscreteFDR-1.3.7/DiscreteFDR/man/amnesia.Rd | 31 DiscreteFDR-1.3.7/DiscreteFDR/man/discrete.BH.Rd | 30 DiscreteFDR-1.3.7/DiscreteFDR/man/fast.Discrete.Rd | 41 DiscreteFDR-1.3.7/DiscreteFDR/man/figures |only DiscreteFDR-1.3.7/DiscreteFDR/man/fisher.pvalues.support.Rd | 105 - DiscreteFDR-1.3.7/DiscreteFDR/man/hist.DiscreteFDR.Rd | 13 DiscreteFDR-1.3.7/DiscreteFDR/man/kernel.Rd | 227 +- DiscreteFDR-1.3.7/DiscreteFDR/man/match.pvals.Rd | 33 DiscreteFDR-1.3.7/DiscreteFDR/man/plot.DiscreteFDR.Rd | 19 DiscreteFDR-1.3.7/DiscreteFDR/man/print.DiscreteFDR.Rd | 5 DiscreteFDR-1.3.7/DiscreteFDR/man/summary.DiscreteFDR.Rd | 9 DiscreteFDR-1.3.7/DiscreteFDR/src/kernel_fun.cpp | 166 - DiscreteFDR-1.3.7/DiscreteFDR/vignettes/DiscreteFDR.Rmd | 2 35 files changed, 1843 insertions(+), 1261 deletions(-)
Title: A Fast Algorithm to Factorize High-Dimensional Tensor Product
Matrices
Description: Here we provide tools for the computation and factorization of high-dimensional
tensor products that are formed by smaller matrices. The methods are based on
properties of Kronecker products (Searle 1982, p. 265, ISBN-10: 0470009616).
We evaluated this methodology by benchmark testing and illustrated its use in
Gaussian Linear Models ('Lopez-Cruz et al., 2024') <doi:10.1093/g3journal/jkae001>.
Author: Marco Lopez-Cruz [aut, cre],
Gustavo de los Campos [aut],
Paulino Perez-Rodriguez [aut]
Maintainer: Marco Lopez-Cruz <lopezcru@msu.edu>
Diff between tensorEVD versions 0.1.0 dated 2023-11-14 and 0.1.1 dated 2024-02-08
tensorEVD-0.1.0/tensorEVD/inst/md |only tensorEVD-0.1.1/tensorEVD/DESCRIPTION | 21 tensorEVD-0.1.1/tensorEVD/MD5 | 58 tensorEVD-0.1.1/tensorEVD/NEWS.md |only tensorEVD-0.1.1/tensorEVD/R/Hadamard.R | 131 tensorEVD-0.1.1/tensorEVD/R/Kronecker.R | 29 tensorEVD-0.1.1/tensorEVD/R/Kronecker_cov.R | 57 tensorEVD-0.1.1/tensorEVD/R/tensorEVD.R | 59 tensorEVD-0.1.1/tensorEVD/build/vignette.rds |binary tensorEVD-0.1.1/tensorEVD/inst/doc/hadamard.R |only tensorEVD-0.1.1/tensorEVD/inst/doc/hadamard.html |only tensorEVD-0.1.1/tensorEVD/inst/doc/kronecker.R |only tensorEVD-0.1.1/tensorEVD/inst/doc/kronecker.html |only tensorEVD-0.1.1/tensorEVD/inst/doc/tensorEVD-documentation.R |only tensorEVD-0.1.1/tensorEVD/inst/doc/tensorEVD-documentation.html | 1776 ++++- tensorEVD-0.1.1/tensorEVD/inst/doc/tensorEVD.R |only tensorEVD-0.1.1/tensorEVD/inst/doc/tensorEVD.html |only tensorEVD-0.1.1/tensorEVD/inst/extdata/results_simulation.txt | 2972 +++++++--- tensorEVD-0.1.1/tensorEVD/man/hadamard.Rd | 21 tensorEVD-0.1.1/tensorEVD/man/kronecker.Rd | 18 tensorEVD-0.1.1/tensorEVD/man/kronecker_covariance.Rd | 19 tensorEVD-0.1.1/tensorEVD/man/tensorEVD.Rd | 33 tensorEVD-0.1.1/tensorEVD/src/c_hadamard.c | 46 tensorEVD-0.1.1/tensorEVD/src/c_kronecker_cov.c | 42 tensorEVD-0.1.1/tensorEVD/src/c_tensor_evd.c | 5 tensorEVD-0.1.1/tensorEVD/src/init.c | 8 tensorEVD-0.1.1/tensorEVD/src/tensorEVD.h | 3 tensorEVD-0.1.1/tensorEVD/src/utils.c | 58 tensorEVD-0.1.1/tensorEVD/vignettes/fig_hadamard_bm1.png |only tensorEVD-0.1.1/tensorEVD/vignettes/fig_kronecker_bm1.png |only tensorEVD-0.1.1/tensorEVD/vignettes/fig_kronecker_bm2.png |only tensorEVD-0.1.1/tensorEVD/vignettes/hadamard.Rmd |only tensorEVD-0.1.1/tensorEVD/vignettes/kronecker.Rmd |only tensorEVD-0.1.1/tensorEVD/vignettes/style.css | 12 tensorEVD-0.1.1/tensorEVD/vignettes/tensorEVD-documentation.Rmd | 362 - tensorEVD-0.1.1/tensorEVD/vignettes/tensorEVD.Rmd |only 36 files changed, 3961 insertions(+), 1769 deletions(-)
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the
Web Service methods provided by the National 'Phenology' Network
(<https://usanpn.org/>), which includes data on various life history
events that occur at specific times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
David LeBauer [ctb],
Eric R Scott [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.7.0 dated 2024-01-24 and 1.2.8.0 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/zzz.R | 2 +- inst/doc/III_individual_phenometrics.html | 2 +- inst/doc/II_status_intensity.html | 2 +- inst/doc/IV_site_phenometrics.html | 2 +- inst/doc/I_introduction.html | 2 +- inst/doc/VIII_data_cleaning.html | 2 +- inst/doc/VII_combine_raster_point.html | 2 +- inst/doc/VI_geospatial.html | 2 +- inst/doc/V_magnitude_phenometrics.html | 2 +- tests/testthat/test-npn-geoserver.R | 6 +++--- tests/testthat/test-npn-get-species.R | 2 +- 14 files changed, 36 insertions(+), 29 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent tria [...truncated...]
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] ,
Julia Romanowska [ctb] ,
Oivind Skare [ctb]
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.3.0 dated 2022-05-20 and 7.3.1 dated 2024-02-08
DESCRIPTION | 12 - MD5 | 136 +++++++++++----------- NAMESPACE | 5 R/JohnsonFit.R | 2 R/coef.haptable.hapSlide.R | 2 R/f.convert.matrix.ff.R | 1 R/f.create.snp.names.R | 7 - R/f.data.R | 16 ++ R/f.data.ready.R | 8 + R/f.get.gen.data.cols.R | 1 R/f.prep.data.parallel.R | 4 R/f.sel.markers.R | 20 ++- R/genDataGetPart.R | 46 +++++-- R/genDataPreprocess.R | 21 +++ R/genDataRead.R | 27 ++++ R/haplin.R | 32 ++++- R/haplinStrat.R | 15 ++ R/plot.haplinSlide.R | 14 +- R/print.HWE.test.R | 2 R/print.haplin.ready.R | 8 - R/print.haplinStrat.R | 12 - R/print.info.R | 4 R/showGen.R | 10 + R/summary.haplinStrat.R | 2 build/vignette.rds |binary inst/doc/A_Haplin_intro_installation.Rmd | 4 inst/doc/A_Haplin_intro_installation.html | 26 ++-- inst/doc/B_Reading_data.html | 19 ++- inst/doc/C_Running_Haplin.R | 2 inst/doc/C_Running_Haplin.html | 183 +++++++++++++++--------------- inst/doc/D_Running_Haplin_on_cluster.html | 17 +- inst/doc/E_hapRelEff.R | 85 +++++++++---- inst/doc/E_hapRelEff.Rmd | 104 ++++++++++------- inst/doc/E_hapRelEff.html | 136 ++++++++++++++-------- man/cbindFiles.Rd | 2 man/convertPed.Rd | 4 man/f.convert.matrix.ff.Rd | 5 man/f.create.snp.names.Rd | 6 man/genDataGetPart.Rd | 2 man/genDataPreprocess.Rd | 4 man/genDataRead.Rd | 4 man/gxe.Rd | 2 man/hapPower.Rd | 4 man/hapPowerAsymp.Rd | 2 man/hapRelEff.Rd | 2 man/hapRun.Rd | 4 man/hapSim.Rd | 6 man/haplin.Rd | 4 man/haplinSlide.Rd | 4 man/haplinStrat.Rd | 4 man/haptable.Rd | 2 man/lineByLine.Rd | 2 man/output.Rd | 2 man/pJohnson.Rd | 1 man/pQQ.Rd | 2 man/pedToHaplin.Rd | 5 man/plot.haplin.Rd | 4 man/plot.haptable.Rd | 2 man/print.haplin.Rd | 2 man/print.summary.haplin.Rd | 2 man/rbindFiles.Rd | 2 man/snpPos.Rd | 2 man/snpPower.Rd | 2 man/snpSampleSize.Rd | 2 man/suest.Rd | 2 man/summary.haplin.Rd | 2 man/toDataFrame.Rd | 2 vignettes/A_Haplin_intro_installation.Rmd | 4 vignettes/E_hapRelEff.Rmd | 104 ++++++++++------- 69 files changed, 762 insertions(+), 426 deletions(-)
More information about OnomasticDiversity at CRAN
Permanent link
Title: A Fast 'WHATWG' Compliant URL Parser
Description: A wrapper for 'ada-url', a 'WHATWG' compliant and fast URL parser written in modern 'C++'. Also contains auxiliary functions such as a public suffix extractor.
Author: David Schoch [aut, cre] ,
Chung-hong Chan [aut] ,
Yagiz Nizipli [ctb, cph] ,
Daniel Lemire [ctb, cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between adaR versions 0.3.1 dated 2023-11-16 and 0.3.2 dated 2024-02-08
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 4 README.md | 30 +- build/vignette.rds |binary src/ada/ada.cpp | 441 +++++++++++++++++++++----------------------- src/ada/ada.h | 16 - src/adaR.cpp | 55 ++--- src/adaR.h | 2 tests/testthat/test-clear.R | 5 tests/testthat/test-get.R | 16 + tests/testthat/test-parse.R | 55 +++-- tests/testthat/test-set.R | 6 13 files changed, 349 insertions(+), 313 deletions(-)
Title: Scalable Gaussian-Process Approximations
Description: Fast scalable Gaussian process approximations, particularly well suited to spatial (aerial, remote-sensed) and environmental data, described in more detail in Katzfuss and Guinness (2017) <arXiv:1708.06302>. Package also contains a fast implementation of the incomplete Cholesky decomposition (IC0), based on Schaefer et al. (2019) <arXiv:1706.02205> and MaxMin ordering proposed in Guinness (2018) <arXiv:1609.05372>.
Author: Matthias Katzfuss [aut],
Marcin Jurek [aut, cre],
Daniel Zilber [aut],
Wenlong Gong [aut],
Joe Guinness [ctb],
Jingjie Zhang [ctb],
Florian Schaefer [ctb]
Maintainer: Marcin Jurek <marcinjurek1988@gmail.com>
Diff between GPvecchia versions 0.1.4 dated 2022-10-24 and 0.1.6 dated 2024-02-08
GPvecchia-0.1.4/GPvecchia/tests/testthat/test-maxmin.r |only GPvecchia-0.1.6/GPvecchia/DESCRIPTION | 13 GPvecchia-0.1.6/GPvecchia/MD5 | 49 GPvecchia-0.1.6/GPvecchia/NEWS.md | 12 GPvecchia-0.1.6/GPvecchia/R/GPvecchia.R | 3 GPvecchia-0.1.6/GPvecchia/R/ordering_functions.R | 2 GPvecchia-0.1.6/GPvecchia/README.md | 5 GPvecchia-0.1.6/GPvecchia/build/vignette.rds |binary GPvecchia-0.1.6/GPvecchia/inst/doc/GPvecchia_vignette.R | 2 GPvecchia-0.1.6/GPvecchia/inst/doc/GPvecchia_vignette.html | 816 +++++----- GPvecchia-0.1.6/GPvecchia/man/GPvecchia.Rd | 1 GPvecchia-0.1.6/GPvecchia/man/order_coordinate.Rd | 2 GPvecchia-0.1.6/GPvecchia/src/Esqe.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/Esqe.h | 2 GPvecchia-0.1.6/GPvecchia/src/Makevars | 2 GPvecchia-0.1.6/GPvecchia/src/Makevars.win | 2 GPvecchia-0.1.6/GPvecchia/src/Matern.cpp | 27 GPvecchia-0.1.6/GPvecchia/src/Matern.h | 6 GPvecchia-0.1.6/GPvecchia/src/MaxMin.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/U_NZentries.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/dist.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/dist.h | 2 GPvecchia-0.1.6/GPvecchia/src/fastTree.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/ic0.cpp | 2 GPvecchia-0.1.6/GPvecchia/src/ic0.h | 2 GPvecchia-0.1.6/GPvecchia/tests/testthat/test-MaternFun.r |only GPvecchia-0.1.6/GPvecchia/tests/testthat/test-createL-HVecchia.r |only 27 files changed, 503 insertions(+), 457 deletions(-)
Title: Measuring the Power in Voting Systems
Description: This R package allows the determination of some distributions of
the voters' power when passing laws in weighted voting situations.
Author: Livino M. Armijos-Toro [aut, cre],
Jose M. Alonso-Meijide [aut],
Manuel A. Mosquera [aut],
Alejandro Saavedra-Nieves [aut]
Maintainer: Livino M. Armijos-Toro <livinoa@gmail.com>
Diff between powerindexR versions 1.0.3 dated 2023-07-18 and 1.5 dated 2024-02-08
powerindexR-1.0.3/powerindexR/R/numero.coalition.R |only powerindexR-1.5/powerindexR/DESCRIPTION | 16 - powerindexR-1.5/powerindexR/MD5 | 36 +-- powerindexR-1.5/powerindexR/NAMESPACE | 5 powerindexR-1.5/powerindexR/R/MWC.R | 31 ++ powerindexR-1.5/powerindexR/R/QMWC.R | 35 ++- powerindexR-1.5/powerindexR/R/binary.digit.R |only powerindexR-1.5/powerindexR/R/check.subset.R | 2 powerindexR-1.5/powerindexR/R/coalition.R |only powerindexR-1.5/powerindexR/R/id.coalition.R |only powerindexR-1.5/powerindexR/R/multiply1.R | 2 powerindexR-1.5/powerindexR/R/multiply2.R | 8 powerindexR-1.5/powerindexR/R/pi.banzhaf.R | 56 +++- powerindexR-1.5/powerindexR/R/pi.colomermartinez.R | 127 +++++------ powerindexR-1.5/powerindexR/R/pi.johnston.R | 148 +++++-------- powerindexR-1.5/powerindexR/R/pi.johnstoncolomermartinez.R | 148 +++++-------- powerindexR-1.5/powerindexR/R/pi.shapley.R | 37 ++- powerindexR-1.5/powerindexR/R/powerindex.R | 13 - powerindexR-1.5/powerindexR/build/partial.rdb |binary powerindexR-1.5/powerindexR/man/pi.banzhaf.Rd | 7 powerindexR-1.5/powerindexR/man/pi.shapley.Rd | 7 21 files changed, 366 insertions(+), 312 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.41 dated 2023-11-01 and 0.42 dated 2024-02-08
DESCRIPTION | 8 LICENSE | 2 MD5 | 44 ++- NAMESPACE | 7 NEWS.md | 18 + R/cran.R | 4 R/knitr.R |only R/packages.R | 2 R/record.R |only R/revcheck.R | 65 +++-- R/string.R | 75 +++++ R/utils.R | 47 ++- R/yaml.R | 58 +++- build/vignette.rds |binary inst/doc/xfun.html | 532 +++++++----------------------------------- inst/resources |only man/csv_options.Rd |only man/decimal_dot.Rd |only man/divide_chunk.Rd |only man/isFALSE.Rd | 7 man/record.Rd |only man/split_source.Rd | 21 + man/yaml_body.Rd | 4 man/yaml_load.Rd | 18 + tests/test-cran/test-knitr.R |only tests/test-cran/test-string.R | 8 tests/test-cran/test-yaml.R |only 27 files changed, 396 insertions(+), 524 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [ctb] ,
Xintong Li [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 0.5.1 dated 2023-11-21 and 0.6.0 dated 2024-02-08
PatientProfiles-0.5.1/PatientProfiles/R/addAttributes.R |only PatientProfiles-0.5.1/PatientProfiles/man/addAttributes.Rd |only PatientProfiles-0.5.1/PatientProfiles/man/getConceptName.Rd |only PatientProfiles-0.5.1/PatientProfiles/man/getEndName.Rd |only PatientProfiles-0.5.1/PatientProfiles/man/getSourceConceptName.Rd |only PatientProfiles-0.5.1/PatientProfiles/man/getStartName.Rd |only PatientProfiles-0.5.1/PatientProfiles/man/suppressCounts.Rd |only PatientProfiles-0.6.0/PatientProfiles/DESCRIPTION | 20 PatientProfiles-0.6.0/PatientProfiles/MD5 | 152 +-- PatientProfiles-0.6.0/PatientProfiles/NAMESPACE | 18 PatientProfiles-0.6.0/PatientProfiles/R/addCategories.R | 32 PatientProfiles-0.6.0/PatientProfiles/R/addCohortIntersect.R | 358 +------ PatientProfiles-0.6.0/PatientProfiles/R/addConceptIntersect.R | 73 + PatientProfiles-0.6.0/PatientProfiles/R/addDateOfBirth.R | 8 PatientProfiles-0.6.0/PatientProfiles/R/addDemographics.R | 223 +--- PatientProfiles-0.6.0/PatientProfiles/R/addIntersect.R | 227 ++-- PatientProfiles-0.6.0/PatientProfiles/R/addTableIntersect.R |only PatientProfiles-0.6.0/PatientProfiles/R/checks.R | 97 +- PatientProfiles-0.6.0/PatientProfiles/R/formats.R | 2 PatientProfiles-0.6.0/PatientProfiles/R/formattedTables.R |only PatientProfiles-0.6.0/PatientProfiles/R/gtResult.R | 43 PatientProfiles-0.6.0/PatientProfiles/R/mockPatientProfiles.R | 146 --- PatientProfiles-0.6.0/PatientProfiles/R/summariseCharacteristics.R | 466 +++++----- PatientProfiles-0.6.0/PatientProfiles/R/summariseLargeScaleCharacteristics.R | 217 ++-- PatientProfiles-0.6.0/PatientProfiles/R/summariseResult.R | 145 +-- PatientProfiles-0.6.0/PatientProfiles/R/sysdata.rda |binary PatientProfiles-0.6.0/PatientProfiles/R/tidyTables.R |only PatientProfiles-0.6.0/PatientProfiles/R/utilities.R |only PatientProfiles-0.6.0/PatientProfiles/inst/doc/addCohortIntersections.R | 39 PatientProfiles-0.6.0/PatientProfiles/inst/doc/addCohortIntersections.Rmd | 41 PatientProfiles-0.6.0/PatientProfiles/inst/doc/addCohortIntersections.html | 68 - PatientProfiles-0.6.0/PatientProfiles/inst/doc/addPatientCharacteristics.R | 11 PatientProfiles-0.6.0/PatientProfiles/inst/doc/addPatientCharacteristics.html | 94 +- PatientProfiles-0.6.0/PatientProfiles/inst/doc/addPatientCharacteristics.rmd | 11 PatientProfiles-0.6.0/PatientProfiles/man/addAge.Rd | 35 PatientProfiles-0.6.0/PatientProfiles/man/addCategories.Rd | 25 PatientProfiles-0.6.0/PatientProfiles/man/addCdmName.Rd | 4 PatientProfiles-0.6.0/PatientProfiles/man/addCohortIntersect.Rd | 59 - PatientProfiles-0.6.0/PatientProfiles/man/addCohortIntersectCount.Rd | 62 - PatientProfiles-0.6.0/PatientProfiles/man/addCohortIntersectDate.Rd | 62 - PatientProfiles-0.6.0/PatientProfiles/man/addCohortIntersectDays.Rd | 62 - PatientProfiles-0.6.0/PatientProfiles/man/addCohortIntersectFlag.Rd | 59 - PatientProfiles-0.6.0/PatientProfiles/man/addCohortName.Rd | 2 PatientProfiles-0.6.0/PatientProfiles/man/addConceptIntersect.Rd | 2 PatientProfiles-0.6.0/PatientProfiles/man/addDateOfBirth.Rd | 4 PatientProfiles-0.6.0/PatientProfiles/man/addDemographics.Rd | 13 PatientProfiles-0.6.0/PatientProfiles/man/addFutureObservation.Rd | 48 - PatientProfiles-0.6.0/PatientProfiles/man/addInObservation.Rd | 9 PatientProfiles-0.6.0/PatientProfiles/man/addIntersect.Rd | 9 PatientProfiles-0.6.0/PatientProfiles/man/addLargeScaleCharacteristics.Rd | 14 PatientProfiles-0.6.0/PatientProfiles/man/addPriorObservation.Rd | 48 - PatientProfiles-0.6.0/PatientProfiles/man/addSex.Rd | 66 - PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersect.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersectCount.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersectDate.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersectDays.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersectField.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/addTableIntersectFlag.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/endDateColumn.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/formatCharacteristics.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/gtCharacteristics.Rd | 10 PatientProfiles-0.6.0/PatientProfiles/man/gtResult.Rd | 26 PatientProfiles-0.6.0/PatientProfiles/man/sourceConceptIdColumn.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/standardConceptIdColumn.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/startDateColumn.Rd |only PatientProfiles-0.6.0/PatientProfiles/man/summariseCharacteristics.Rd | 15 PatientProfiles-0.6.0/PatientProfiles/man/summariseLargeScaleCharacteristics.Rd | 20 PatientProfiles-0.6.0/PatientProfiles/man/summariseResult.Rd | 7 PatientProfiles-0.6.0/PatientProfiles/man/tidyCharacteristics.Rd |only PatientProfiles-0.6.0/PatientProfiles/tests/manual/test-sqltest.R | 17 PatientProfiles-0.6.0/PatientProfiles/tests/testthat/setup.R | 6 PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addAttributes.R | 36 PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addCategories.R | 16 PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addCohortIntersect.R | 113 +- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addConceptIntersect.R |only PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addDemographics.R | 404 +++++--- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addFutureObservation.R | 112 +- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addInObservation.R | 47 - PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addIntersect.R | 363 +++---- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addPriorObservation.R | 123 -- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-addSex.R | 38 PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-checks.R | 140 ++- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-mockPatientProfiles.R | 77 - PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-summariseCharacteristics.R | 271 ++--- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-summariseLargeScaleCharacteristics.R | 72 + PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-summariseResult.R | 199 +--- PatientProfiles-0.6.0/PatientProfiles/tests/testthat/test-tableSummary.R | 7 PatientProfiles-0.6.0/PatientProfiles/vignettes/addCohortIntersections.Rmd | 41 PatientProfiles-0.6.0/PatientProfiles/vignettes/addPatientCharacteristics.rmd | 11 89 files changed, 2396 insertions(+), 2849 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Description: Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>
Diff between NMF versions 0.26 dated 2023-03-20 and 0.27 dated 2024-02-08
DESCRIPTION | 12 ++++++------ MD5 | 27 ++++++++++++++------------- NAMESPACE | 4 ++-- R/NMFSet-class.R | 24 +++++++++++++++--------- R/colorcode.R | 2 +- R/options.R | 3 ++- R/rnmf.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/NMF-vignette.pdf |binary inst/doc/consensus.pdf |binary inst/doc/heatmaps.pdf |binary man/aggregate.measure.Rd |only man/ccSpec.Rd | 2 +- man/rnmf.Rd | 2 +- 15 files changed, 44 insertions(+), 36 deletions(-)
Title: Run Multiverse Style Analyses
Description: Run the same analysis over a range of arbitrary data processing
decisions. 'multitool' provides an interface for creating alternative
analysis pipelines and turning them into a grid of all possible pipelines.
Using this grid as a blueprint, you can model your data across all possible
pipelines and summarize the results.
Author: Ethan Young [aut, cre, cph] ,
Stefan Vermeent [aut]
Maintainer: Ethan Young <young.ethan.scott@gmail.com>
Diff between multitool versions 0.1.3 dated 2023-10-25 and 0.1.4 dated 2024-02-08
DESCRIPTION | 12 +- MD5 | 32 +++--- NEWS.md | 8 + R/utils.R | 24 ++-- R/visualize-pipeline.R | 2 build/vignette.rds |binary inst/doc/create-your-blueprint.R | 18 +-- inst/doc/create-your-blueprint.Rmd | 24 ++-- inst/doc/create-your-blueprint.html | 77 ++++++-------- inst/doc/multitool-nomenclature.html | 4 inst/doc/run-your-pipeline.Rmd | 4 inst/doc/run-your-pipeline.html | 176 +++++++++++++++++----------------- inst/doc/validate-your-blueprint.html | 4 man/create_blueprint_graph.Rd | 2 man/multitool-package.Rd | 2 vignettes/create-your-blueprint.Rmd | 24 ++-- vignettes/run-your-pipeline.Rmd | 4 17 files changed, 211 insertions(+), 206 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.5.3 dated 2023-12-09 and 5.5.5 dated 2024-02-08
huxtable-5.5.3/huxtable/tests/testthat/404.html |only huxtable-5.5.5/huxtable/DESCRIPTION | 6 huxtable-5.5.5/huxtable/MD5 | 45 - huxtable-5.5.5/huxtable/NEWS.md | 8 huxtable-5.5.5/huxtable/R/aaa-utils.R | 36 + huxtable-5.5.5/huxtable/R/knitr.R | 1 huxtable-5.5.5/huxtable/R/mapping-functions.R | 3 huxtable-5.5.5/huxtable/R/package-docs.R | 29 + huxtable-5.5.5/huxtable/build/vignette.rds |binary huxtable-5.5.5/huxtable/inst/doc/design-principles.html | 4 huxtable-5.5.5/huxtable/inst/doc/huxreg.html | 4 huxtable-5.5.5/huxtable/inst/doc/huxtable.R | 19 huxtable-5.5.5/huxtable/inst/doc/huxtable.Rmd | 5 huxtable-5.5.5/huxtable/inst/doc/huxtable.pdf |binary huxtable-5.5.5/huxtable/inst/doc/themes.html | 4 huxtable-5.5.5/huxtable/man/huxtable-FAQ.Rd | 29 + huxtable-5.5.5/huxtable/man/huxtable-news.Rd | 13 huxtable-5.5.5/huxtable/tests/testthat/quarto-test-tex-labels-out.pdf |only huxtable-5.5.5/huxtable/tests/testthat/quarto-test-tex-labels.qmd |only huxtable-5.5.5/huxtable/tests/testthat/quarto-test.aux |only huxtable-5.5.5/huxtable/tests/testthat/quarto-test.log |only huxtable-5.5.5/huxtable/tests/testthat/quarto-test.qmd | 1 huxtable-5.5.5/huxtable/tests/testthat/table-tester-2.log | 264 ++++------ huxtable-5.5.5/huxtable/tests/testthat/test-mapping-functions.R | 10 huxtable-5.5.5/huxtable/tests/testthat/test-yy-end-to-end.R | 29 - huxtable-5.5.5/huxtable/vignettes/huxtable.Rmd | 3 26 files changed, 318 insertions(+), 195 deletions(-)
Title: MEREC - Method Based on the Removal Effects of Criteria
Description: Implementation of the MEthod based on the Removal Effects of Criteria - MEREC- a new objective weighting method for determining criteria weights for Multiple Criteria Decision Making problems, created by Mehdi Keshavarz-Ghorabaee (2021) <doi:10.3390/sym13040525>. Given a decision matrix, the function return the Merec´s weight vector and all intermediate matrix/vectors used to calculate it.
Author: Lucas Sebastiao de Paula [aut, cre]
,
Bernardo Silva [ctb] ,
Marcos Santos [ctb]
Maintainer: Lucas Sebastiao de Paula <lucas@ime.eb.br>
Diff between rmerec versions 0.1.0 dated 2023-12-01 and 0.1.1 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/merec.R | 5 ++++- 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Linear Model Weights
Description: Computes the implied weights of linear regression models for estimating
average causal effects and provides diagnostics based on these weights. These
diagnostics rely on the analyses in Chattopadhyay and Zubizarreta (2023)
<doi:10.1093/biomet/asac058> where
several regression estimators are represented as weighting estimators, in connection
to inverse probability weighting. 'lmw' provides tools to diagnose
representativeness, balance, extrapolation, and influence for these models,
clarifying the target population of inference. Tools are also available to
simplify estimating treatment effects for specific target populations of interest.
Author: Ambarish Chattopadhyay [aut] ,
Noah Greifer [aut, cre] ,
Jose Zubizarreta [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between lmw versions 0.0.1 dated 2023-03-14 and 0.0.2 dated 2024-02-08
DESCRIPTION | 17 + MD5 | 52 ++--- NAMESPACE | 1 NEWS.md | 21 ++ R/aux_functions.R | 68 ++++--- R/get_X.R | 59 +++--- R/get_w.R | 50 +++-- R/influence.lmw.R | 16 - R/input_processing.R | 285 ++++++++++++++++--------------- R/lmw.R | 15 - R/lmw_est.R | 20 +- R/lmw_est_aipw.R | 18 - R/lmw_est_iv.R | 22 +- R/lmw_iv.R | 13 - R/plot.lmw.R | 55 +++-- R/plot.lmw_est.R | 5 R/plot.summary.lmw.R | 24 +- R/summary.lmw.R | 128 +++++++------ R/summary.lmw_est.R | 18 + build/partial.rdb |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/lmw-package.Rd | 3 man/lmw.Rd | 7 man/lmw_iv.Rd | 3 man/plot.lmw.Rd | 10 - 27 files changed, 522 insertions(+), 388 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings mat [...truncated...]
Author: Niels Waller [aut, cre],
Justin Kracht [ctb],
Jeff Jones [ctb],
Casey Giordano [ctb],
Hoang V. Nguyen [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 2.4.2 dated 2024-01-23 and 2.4.3 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + R/alphaR.R |only inst/CITATION | 2 +- man/alphaR.Rd |only 6 files changed, 11 insertions(+), 8 deletions(-)
Title: Random Effects Meta-Analysis for Correlated Test Statistics
Description: Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
Author: Gabriel Hoffman [aut, cre]
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Diff between remaCor versions 0.0.16 dated 2023-06-21 and 0.0.18 dated 2024-02-08
DESCRIPTION | 8 +++--- MD5 | 34 +++++++++++++++++++---------- NEWS.md | 9 +++++++ R/LS.R | 12 ++++------ R/LS_empirical_pvalue.R | 12 +++++++--- R/LS_test.R |only R/RE2C.R | 18 +++++++-------- TODO |only build/partial.rdb |binary inst/doc/remaCor.html | 56 ++++++++++++++++++++++++------------------------ man/LS.Rd | 9 +++---- man/LS.empirical.Rd | 2 - man/RE2C.Rd | 18 +++++++-------- src/Makevars.win | 2 - vignettes/remaCor_cache |only 15 files changed, 102 insertions(+), 78 deletions(-)
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'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.6.6.1 dated 2023-12-04 and 0.12.8.0.0 dated 2024-02-08
RcppArmadillo-0.12.6.6.1/RcppArmadillo/inst/include/RcppArmadilloAs.h |only RcppArmadillo-0.12.6.6.1/RcppArmadillo/inst/include/RcppArmadilloConfig.h |only RcppArmadillo-0.12.6.6.1/RcppArmadillo/inst/include/RcppArmadilloForward.h |only RcppArmadillo-0.12.6.6.1/RcppArmadillo/inst/include/RcppArmadilloSugar.h |only RcppArmadillo-0.12.6.6.1/RcppArmadillo/inst/include/RcppArmadilloWrap.h |only RcppArmadillo-0.12.8.0.0/RcppArmadillo/ChangeLog | 31 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.12.8.0.0/RcppArmadillo/MD5 | 67 +- RcppArmadillo-0.12.8.0.0/RcppArmadillo/R/init.R | 2 RcppArmadillo-0.12.8.0.0/RcppArmadillo/configure | 18 RcppArmadillo-0.12.8.0.0/RcppArmadillo/configure.ac | 4 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/NEWS.Rd | 26 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo | 2 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 4 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 4 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 7 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/compiler_check.hpp | 10 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 4 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 168 ++++--- RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 4 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 1 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 3 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 240 +++++++++- RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 42 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_shift.hpp | 35 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_meat.hpp | 15 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/op_rank_meat.hpp | 19 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/op_shift_meat.hpp | 2 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 55 -- RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_bones.hpp | 11 RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp | 27 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_shift_bones.hpp |only RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_shift_meat.hpp |only RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 39 + RcppArmadillo-0.12.8.0.0/RcppArmadillo/inst/tinytest/test_misc.R | 9 38 files changed, 676 insertions(+), 187 deletions(-)
Title: Hard and Soft Cluster Validity Indices
Description: Algorithms for checking the accuracy of a clustering result with known classes, computing cluster validity indices, and generating plots for comparing them.
The package is compatible with K-means, fuzzy C means, EM clustering, and hierarchical clustering (single, average, and complete linkage).
The details of the indices in this package can be found in:
C. Alok. (2010) <https://hdl.handle.net/10603/93443>,
J. C. Bezdek, M. Moshtaghi, T. Runkler, C. Leckie (2016) <doi:10.1109/TFUZZ.2016.2540063>,
T. Calinski, J. Harabasz (1974) <doi:10.1080/03610927408827101>,
C. H. Chou, M. C. Su, E. Lai (2004) <doi:10.1007/s10044-004-0218-1>,
D. L. Davies, D. W. Bouldin (1979) <doi:10.1109/TPAMI.1979.4766909>,
J. C. Dunn (1973) <doi:10.1080/01969727308546046>,
F. Haouas, Z. Ben Dhiaf, A. Hammouda, B. Solaiman (2017) <doi:10.1109/FUZZ-IEEE.2017.8015651>,
M. Kim, R. S. Ramakrishna (2005) <doi:10.1016/j.patrec.2005.04.007>,
S. H. Kwon (1998) <doi:10.1049 [...truncated...]
Author: Nathakhun Wiroonsri [cre, aut]
,
Onthada Preedasawakul [aut]
Maintainer: Nathakhun Wiroonsri <nathakhun.wir@kmutt.ac.th>
Diff between UniversalCVI versions 1.1.0 dated 2023-11-08 and 1.1.1 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/AccClust.R | 8 ++++++++ R/FzzyCVIs.R | 2 +- R/KWON2.IDX.R | 2 +- man/WP.IDX.Rd | 4 ++-- 7 files changed, 25 insertions(+), 13 deletions(-)
Title: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over
Time
Description: Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.
Author: Matheus Lima Araujo [aut, cre, cph]
,
Luiz Gabriel Souza e Souza Ferreira [aut]
,
Gabriel Nakamura [aut] ,
Marco Tulio Pacheco Coelho [aut]
,
Thiago Fernando Rangel [aut]
Maintainer: Matheus Lima Araujo <matheusaraujolima@live.com>
Diff between treesliceR versions 1.0.0 dated 2023-12-18 and 1.0.1 dated 2024-02-08
treesliceR-1.0.0/treesliceR/data/pass_asb.rda |only treesliceR-1.0.0/treesliceR/man/pass_asb.Rd |only treesliceR-1.0.1/treesliceR/DESCRIPTION | 6 treesliceR-1.0.1/treesliceR/MD5 | 86 +++++----- treesliceR-1.0.1/treesliceR/NEWS.md | 8 treesliceR-1.0.1/treesliceR/R/CpB.R | 41 +++- treesliceR-1.0.1/treesliceR/R/CpB_RW.R | 39 +++- treesliceR-1.0.1/treesliceR/R/CpD.R | 8 treesliceR-1.0.1/treesliceR/R/CpE.R | 8 treesliceR-1.0.1/treesliceR/R/CpR_sensitivity.R | 52 ++---- treesliceR-1.0.1/treesliceR/R/data_description.R | 14 - treesliceR-1.0.1/treesliceR/R/phylo_pieces.R | 16 - treesliceR-1.0.1/treesliceR/R/r_phylo.R | 72 +++++--- treesliceR-1.0.1/treesliceR/R/squeeze_int.R | 32 +-- treesliceR-1.0.1/treesliceR/R/squeeze_root.R | 12 - treesliceR-1.0.1/treesliceR/R/squeeze_tips.R | 14 - treesliceR-1.0.1/treesliceR/README.md | 8 treesliceR-1.0.1/treesliceR/data/AU_adj.rda |only treesliceR-1.0.1/treesliceR/inst/doc/Intro-treesliceR.R | 6 treesliceR-1.0.1/treesliceR/inst/doc/Intro-treesliceR.Rmd | 8 treesliceR-1.0.1/treesliceR/inst/doc/Intro-treesliceR.html | 8 treesliceR-1.0.1/treesliceR/inst/doc/Passeriformes-diversification.R | 14 - treesliceR-1.0.1/treesliceR/inst/doc/Passeriformes-diversification.Rmd | 16 - treesliceR-1.0.1/treesliceR/inst/doc/Passeriformes-diversification.html | 50 +++-- treesliceR-1.0.1/treesliceR/man/AU_adj.Rd |only treesliceR-1.0.1/treesliceR/man/CpB.Rd | 17 + treesliceR-1.0.1/treesliceR/man/CpB_RW.Rd | 17 + treesliceR-1.0.1/treesliceR/man/CpD.Rd | 4 treesliceR-1.0.1/treesliceR/man/CpE.Rd | 4 treesliceR-1.0.1/treesliceR/man/CpR_sensitivity.Rd | 6 treesliceR-1.0.1/treesliceR/man/phylo_pieces.Rd | 6 treesliceR-1.0.1/treesliceR/man/r_phylo.Rd | 21 +- treesliceR-1.0.1/treesliceR/man/squeeze_int.Rd | 4 treesliceR-1.0.1/treesliceR/man/squeeze_root.Rd | 4 treesliceR-1.0.1/treesliceR/man/squeeze_tips.Rd | 4 treesliceR-1.0.1/treesliceR/tests/testthat/test-CpB.R | 26 +-- treesliceR-1.0.1/treesliceR/tests/testthat/test-CpB_RW.R | 14 - treesliceR-1.0.1/treesliceR/tests/testthat/test-CpD.R | 2 treesliceR-1.0.1/treesliceR/tests/testthat/test-CpE.R | 2 treesliceR-1.0.1/treesliceR/tests/testthat/test-CpR_sensitivity.R | 17 + treesliceR-1.0.1/treesliceR/tests/testthat/test-r_phylo.R | 37 +--- treesliceR-1.0.1/treesliceR/tests/testthat/test-squeeze_int.R | 2 treesliceR-1.0.1/treesliceR/tests/testthat/test-squeeze_root.R | 4 treesliceR-1.0.1/treesliceR/tests/testthat/test-squeeze_tips.R | 4 treesliceR-1.0.1/treesliceR/vignettes/Intro-treesliceR.Rmd | 8 treesliceR-1.0.1/treesliceR/vignettes/Passeriformes-diversification.Rmd | 16 - 46 files changed, 404 insertions(+), 333 deletions(-)
Title: Taxonomic Monographs Tools
Description: Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, identification keys (dichotomous and interactive), and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology histograms and distributional and diversity maps are also available.
Author: Marcelo Reginato
Maintainer: Marcelo Reginato <reginatobio@yahoo.com.br>
Diff between monographaR versions 1.3.0 dated 2024-01-10 and 1.3.1 dated 2024-02-08
DESCRIPTION | 16 +-- MD5 | 45 +++++++--- NAMESPACE | 12 +- R/codeGap.R |only R/codeMatrix.R |only R/dichoKey.R | 186 +++++++++++++++++++++++------------------- R/dichoKey.app.R |only R/interactiveKey.R | 28 +++++- R/interactiveKeyLabels.R | 14 ++- build/vignette.rds |binary data/keyCode.rda |binary data/monographaR_examples.rda |binary inst/doc/keys.R |only inst/doc/keys.Rmd |only inst/doc/keys.html |only inst/doc/tutorial.Rmd | 2 man/codeGap.Rd |only man/codeMatrix.Rd |only man/dataKey.Rd | 3 man/dichoKey.Rd | 2 man/dichoKey.app.Rd |only man/interactiveKey.Rd | 111 ++++++++++++------------- man/monographaR-package.Rd | 11 +- vignettes/keys.Rmd |only vignettes/png |only vignettes/tutorial.Rmd | 2 26 files changed, 250 insertions(+), 182 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: An implementation of split-population duration regression models.
Unlike regular duration models, split-population duration models are
mixture models that accommodate the presence of a sub-population that is
not at risk for failure, e.g. cancer patients who have been cured by
treatment. This package implements Weibull and Loglogistic forms for the
duration component, and focuses on data with time-varying covariates.
These models were originally formulated in Boag (1949) and Berkson and Gage
(1952), and extended in Schmidt and Witte (1989).
Author: Andreas Beger [aut, cre] ,
Daina Chiba [aut] ,
Daniel W. Hill, Jr. [aut],
Nils W. Metternich [aut] ,
Shahryar Minhas [aut],
Michael D. Ward [aut, cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.17.1 dated 2018-05-06 and 0.17.2 dated 2024-02-08
spduration-0.17.1/spduration/src/Makevars |only spduration-0.17.2/spduration/DESCRIPTION | 35 spduration-0.17.2/spduration/MD5 | 82 spduration-0.17.2/spduration/NAMESPACE | 1 spduration-0.17.2/spduration/NEWS.md | 54 spduration-0.17.2/spduration/R/accessors.spdur.R | 16 spduration-0.17.2/spduration/R/add_duration.R | 61 spduration-0.17.2/spduration/R/attempt_date.R | 10 spduration-0.17.2/spduration/R/data-docs.R | 2 spduration-0.17.2/spduration/R/plot.spdur.R | 6 spduration-0.17.2/spduration/R/spdur.R | 5 spduration-0.17.2/spduration/R/spduration-package.R | 11 spduration-0.17.2/spduration/R/summary.spdur.R | 3 spduration-0.17.2/spduration/README.md | 38 spduration-0.17.2/spduration/build/vignette.rds |binary spduration-0.17.2/spduration/inst/doc/introduction.R | 30 spduration-0.17.2/spduration/inst/doc/introduction.Rmd | 2 spduration-0.17.2/spduration/inst/doc/introduction.html | 1319 +++++++--- spduration-0.17.2/spduration/man/accessors.Rd | 6 spduration-0.17.2/spduration/man/add_duration.Rd | 12 spduration-0.17.2/spduration/man/bscoup.Rd | 8 spduration-0.17.2/spduration/man/coups.Rd | 6 spduration-0.17.2/spduration/man/expand.call.Rd | 8 spduration-0.17.2/spduration/man/figures/README-unnamed-chunk-2-1.png |binary spduration-0.17.2/spduration/man/figures/logo.png |only spduration-0.17.2/spduration/man/forecast.spdur.Rd | 9 spduration-0.17.2/spduration/man/hazard.Rd | 10 spduration-0.17.2/spduration/man/model.coups.Rd | 4 spduration-0.17.2/spduration/man/plot_hazard.Rd | 3 spduration-0.17.2/spduration/man/predict.spdur.Rd | 10 spduration-0.17.2/spduration/man/sepplot.Rd | 18 spduration-0.17.2/spduration/man/spdur.Rd | 16 spduration-0.17.2/spduration/man/spduration.Rd | 28 spduration-0.17.2/spduration/src/Makevars.win | 3 spduration-0.17.2/spduration/src/RcppExports.cpp | 5 spduration-0.17.2/spduration/tests/testthat.R | 4 spduration-0.17.2/spduration/tests/testthat/test-summary-spdur.R |only spduration-0.17.2/spduration/tests/testthat/test_accessors.R |only spduration-0.17.2/spduration/tests/testthat/test_add_duration.R | 40 spduration-0.17.2/spduration/tests/testthat/test_plotting.R | 2 spduration-0.17.2/spduration/tests/testthat/test_predict.spdur.R | 2 spduration-0.17.2/spduration/tests/testthat/test_spdur.R | 31 spduration-0.17.2/spduration/vignettes/introduction.Rmd | 2 spduration-0.17.2/spduration/vignettes/spdur.bib | 2 44 files changed, 1401 insertions(+), 503 deletions(-)
Title: Snow Profile Alignment, Aggregation, and Clustering
Description: Snow profiles describe the vertical (1D) stratigraphy of layered
snow with different layer characteristics, such as grain type, hardness,
deposition date, and many more. Hence, they represent a data format similar
to multivariate time series containing categorical, ordinal, and numerical
data types. Use this package to align snow profiles by matching their
individual layers based on Dynamic Time Warping (DTW). The aligned profiles
can then be assessed with an independent, global similarity measure that is
geared towards avalanche hazard assessment. Finally, through exploiting data
aggregation and clustering methods, the similarity measure provides the
foundation for grouping and summarizing snow profiles according to similar
hazard conditions. In particular, this package allows for averaging large
numbers of snow profiles with DTW Barycenter Averaging and thereby
facilitates the computation of individual layer distributions and summary
statistics that are relevant for avalanche forecas [...truncated...]
Author: Florian Herla [aut, cre],
Pascal Haegeli [aut],
Simon Horton [aut],
Paul Billecocq [aut],
SFU Avalanche Research Program [fnd]
Maintainer: Florian Herla <fherla@sfu.ca>
Diff between sarp.snowprofile.alignment versions 1.2.1 dated 2022-08-07 and 1.2.2 dated 2024-02-08
DESCRIPTION | 14 +-- MD5 | 37 ++++---- NAMESPACE | 1 NEWS.md | 6 + R/averageSP.R | 2 R/averageSPalongSeason.R | 29 ++++-- R/concat.R |only R/dbaSP.R | 10 +- R/medoidSP.R | 10 +- R/warpSP.R | 1 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 53 +++++------ inst/doc/averaging.html | 137 +++++++++++++++--------------- inst/doc/technical-details.html | 125 ++++++++++++++------------- inst/doc/workflow.html | 125 ++++++++++++++------------- man/averageSP.Rd | 8 - man/averageSPalongSeason.Rd | 2 man/concat_avgSP_timeseries.Rd |only man/medoidSP.Rd | 2 man/sarp.snowprofile.alignment-package.Rd | 2 21 files changed, 309 insertions(+), 255 deletions(-)
More information about sarp.snowprofile.alignment at CRAN
Permanent link
Title: The 'shiny' App for Test Analysis and Visualization
Description: This application enables exploratory factor analysis, confirmatory factor analysis, classical measurement theory analysis, unidimensional item response theory, multidimensional item response theory, and continuous item response model analysis, through the 'shiny' interactive interface. It also facilitates the visualization of the results. Users can easily download the analysis results from the interactive interface. Additionally, users can download a concise report about items and test quality on the interactive interface.
Author: Youxiang Jiang [cre, aut] ,
Hongbo Wen [ctb, ths]
Maintainer: Youxiang Jiang <jiangyouxiang34@163.com>
Diff between TestAnaAPP versions 0.1.5 dated 2024-01-09 and 0.1.8 dated 2024-02-08
DESCRIPTION | 6 +-- MD5 | 12 +++---- R/run_app.R | 1 R/server.R | 59 +++++++++++++++++++------------------- R/ui.R | 6 +-- inst/rmd/IRT_Analysis_Report.Rmd | 12 ++++--- inst/rmd/MIRT_Analysis_Report.Rmd | 25 ++++++++++------ 7 files changed, 66 insertions(+), 55 deletions(-)
Title: Pearson Distribution System
Description: Implementation of the Pearson distribution system, including full
support for the (d,p,q,r)-family of functions for probability distributions
and fitting via method of moments and maximum likelihood method.
Author: Martin Becker [aut, cre] ,
Stefan Kloessner [aut] ,
Joel Heinrich [ctb]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between PearsonDS versions 1.3.0 dated 2023-08-12 and 1.3.1 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 8 ++++++++ configure.win | 4 +++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: 'Fitbit' Visualizations
Description: Connection to the 'Fitbit' Web API <https://dev.fitbit.com/build/reference/web-api/> by including 'ggplot2' Visualizations, 'Leaflet' and 3-dimensional 'Rayshader' Maps. The 3-dimensional 'Rayshader' Map requires the installation of the 'CopernicusDEM' R package which includes the 30- and 90-meter elevation data.
Author: Lampros Mouselimis [aut, cre]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fitbitViz versions 1.0.5 dated 2023-01-06 and 1.0.6 dated 2024-02-08
DESCRIPTION | 10 MD5 | 16 NEWS.md | 5 R/fitbit_utils.R | 9 README.md | 268 - build/vignette.rds |binary inst/doc/fitbit_viz.R | 38 inst/doc/fitbit_viz.html | 8227 +++++++++++++++++++++++++++++++++++++++++++++-- man/plot_data_type.Rd | 15 9 files changed, 8051 insertions(+), 537 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Edward Burn [aut, cre] ,
Kim Lopez [aut] ,
Marti Catala [ctb] ,
Xintong Li [ctb] ,
Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortSurvival versions 0.2.5 dated 2023-12-07 and 0.3.0 dated 2024-02-08
DESCRIPTION | 16 MD5 | 98 NAMESPACE | 1 R/CohortSurvival-package.R | 16 R/addCohortSurvival.R | 531 +-- R/benchmarkCohortSurvival.R | 1047 +++--- R/estimateSurvival.R | 2780 ++++++++-------- R/generateDeathCohort.R | 59 R/inputValidation.R | 258 - R/mockMGUS2cdm.R | 386 +- R/plotSurvival.R | 562 +-- R/recordAttrition.R | 130 R/summariseSurvivalParticipants.R | 38 R/suppressSurvivalCounts.R | 122 R/survivalSummary.R | 70 R/utils-pipe.R | 28 R/utils-tidy-eval.R | 216 - R/utils.R | 281 + README.md | 13 inst/doc/a01_Single_event_of_interest.R | 4 inst/doc/a01_Single_event_of_interest.Rmd | 4 inst/doc/a01_Single_event_of_interest.html | 229 - inst/doc/a02_Competing_risk_survival.R | 8 inst/doc/a02_Competing_risk_survival.Rmd | 8 inst/doc/a02_Competing_risk_survival.html | 235 - man/CohortSurvival-package.Rd | 6 man/addCohortSurvival.Rd | 17 man/benchmarkCohortSurvival.Rd | 13 man/estimateCompetingRiskSurvival.Rd | 12 man/estimateSingleEventSurvival.Rd | 12 man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/generateDeathCohortSet.Rd | 51 man/pipe.Rd | 40 man/reexports.Rd | 32 man/splitNameLevel.Rd |only man/tidyeval.Rd | 202 - man/uniteNameLevel.Rd |only tests/testthat.R | 24 tests/testthat/test-addCohortSurvival.R | 487 +- tests/testthat/test-benchmarkCohortSurvival.R | 173 - tests/testthat/test-estimateSurvival.R | 3392 +++++++++++--------- tests/testthat/test-generateDeathCohort.R | 453 ++ tests/testthat/test-mockMGUS2cdm.R | 26 tests/testthat/test-plotSurvival.R | 314 - tests/testthat/test-summariseSurvivalParticipants.R | 30 tests/testthat/test-survivalSummary.R | 34 vignettes/a01_Single_event_of_interest.Rmd | 4 vignettes/a02_Competing_risk_survival.Rmd | 8 51 files changed, 6888 insertions(+), 5582 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Air Quality Data of Switzerland for One Year in 30 Min
Resolution
Description: Ozone, NOx (= Sum of nitrogen monoxide and nitrogen dioxide), nitrogen monoxide, ambient temperature, dew point, wind speed and wind direction at 3 sites around lake of Lucerne in Central Switzerland in 30 min time resolution for year 2004.
Author: Christoph Hofer [cre],
Rene Locher [aut]
Maintainer: Christoph Hofer <christoph.hofer@zhaw.ch>
Diff between SwissAir versions 1.1.5 dated 2018-10-02 and 1.1.6 dated 2024-02-08
ChangeLog | 126 ++++++++--------- DESCRIPTION | 15 +- MD5 | 10 - NAMESPACE | 16 +- data/AirQual.rda |binary man/AirQual.Rd | 386 +++++++++++++++++++++++++++---------------------------- 6 files changed, 278 insertions(+), 275 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.8.1 dated 2024-01-15 and 0.9.0 dated 2024-02-08
slendr-0.8.1/slendr/R/cli-runners.R |only slendr-0.9.0/slendr/DESCRIPTION | 10 slendr-0.9.0/slendr/MD5 | 162 - slendr-0.9.0/slendr/NEWS.md | 20 slendr-0.9.0/slendr/R/compilation.R | 16 slendr-0.9.0/slendr/R/engines.R | 76 slendr-0.9.0/slendr/R/interface.R | 2 slendr-0.9.0/slendr/R/tree-sequences.R | 8 slendr-0.9.0/slendr/R/utils.R | 16 slendr-0.9.0/slendr/R/zzz.R | 26 slendr-0.9.0/slendr/inst/doc/vignette-00-installation.Rmd | 112 + slendr-0.9.0/slendr/inst/doc/vignette-00-installation.html | 148 + slendr-0.9.0/slendr/inst/doc/vignette-01-tutorial.R | 12 slendr-0.9.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 2 slendr-0.9.0/slendr/inst/doc/vignette-01-tutorial.html | 359 +-- slendr-0.9.0/slendr/inst/doc/vignette-02-grid-model.R | 14 slendr-0.9.0/slendr/inst/doc/vignette-02-grid-model.Rmd | 2 slendr-0.9.0/slendr/inst/doc/vignette-02-grid-model.html | 491 ++--- slendr-0.9.0/slendr/inst/doc/vignette-03-interactions.R | 6 slendr-0.9.0/slendr/inst/doc/vignette-03-interactions.Rmd | 4 slendr-0.9.0/slendr/inst/doc/vignette-03-interactions.html | 201 +- slendr-0.9.0/slendr/inst/doc/vignette-04-nonspatial-models.R | 12 slendr-0.9.0/slendr/inst/doc/vignette-04-nonspatial-models.Rmd | 6 slendr-0.9.0/slendr/inst/doc/vignette-04-nonspatial-models.html | 179 - slendr-0.9.0/slendr/inst/doc/vignette-05-tree-sequences.R | 26 slendr-0.9.0/slendr/inst/doc/vignette-05-tree-sequences.Rmd | 6 slendr-0.9.0/slendr/inst/doc/vignette-05-tree-sequences.html | 459 ++--- slendr-0.9.0/slendr/inst/doc/vignette-06-locations.R | 30 slendr-0.9.0/slendr/inst/doc/vignette-06-locations.Rmd | 2 slendr-0.9.0/slendr/inst/doc/vignette-06-locations.html | 663 +++---- slendr-0.9.0/slendr/inst/doc/vignette-07-backends.R | 12 slendr-0.9.0/slendr/inst/doc/vignette-07-backends.Rmd | 2 slendr-0.9.0/slendr/inst/doc/vignette-07-backends.html | 607 +++--- slendr-0.9.0/slendr/inst/doc/vignette-08-nonslendr-tskit.R | 37 slendr-0.9.0/slendr/inst/doc/vignette-08-nonslendr-tskit.Rmd | 27 slendr-0.9.0/slendr/inst/doc/vignette-08-nonslendr-tskit.html | 367 ++-- slendr-0.9.0/slendr/inst/doc/vignette-09-paper.R | 46 slendr-0.9.0/slendr/inst/doc/vignette-09-paper.Rmd | 14 slendr-0.9.0/slendr/inst/doc/vignette-09-paper.html | 901 +++++----- slendr-0.9.0/slendr/inst/doc/vignette-10-tracts.R | 12 slendr-0.9.0/slendr/inst/doc/vignette-10-tracts.Rmd | 11 slendr-0.9.0/slendr/inst/doc/vignette-10-tracts.html | 592 +++--- slendr-0.9.0/slendr/inst/extdata/models/introgression/checksums.tsv | 18 slendr-0.9.0/slendr/inst/extdata/models/introgression/script.py | 4 slendr-0.9.0/slendr/inst/extdata/models/introgression/script.slim | 7 slendr-0.9.0/slendr/inst/extdata/models/introgression_msprime.trees |binary slendr-0.9.0/slendr/inst/extdata/models/introgression_slim.trees |binary slendr-0.9.0/slendr/inst/extdata/models/msprime.trees |binary slendr-0.9.0/slendr/inst/scripts/__pycache__/script.cpython-312.pyc |only slendr-0.9.0/slendr/inst/scripts/script.slim | 5 slendr-0.9.0/slendr/man/msprime.Rd | 3 slendr-0.9.0/slendr/man/slendr.Rd | 2 slendr-0.9.0/slendr/man/slim.Rd | 8 slendr-0.9.0/slendr/man/ts_mutate.Rd | 4 slendr-0.9.0/slendr/man/ts_recapitate.Rd | 4 slendr-0.9.0/slendr/tests/testthat/afs_Windows.tsv.gz |only slendr-0.9.0/slendr/tests/testthat/distances.tsv.gz |binary slendr-0.9.0/slendr/tests/testthat/f4_Windows.tsv.gz |only slendr-0.9.0/slendr/tests/testthat/f4ratio_Windows.tsv.gz |only slendr-0.9.0/slendr/tests/testthat/helper-functions.R | 2 slendr-0.9.0/slendr/tests/testthat/test-ibd-squashing.R | 2 slendr-0.9.0/slendr/tests/testthat/test-interaction-changes.R | 1 slendr-0.9.0/slendr/tests/testthat/test-msprime-geneflow.R | 8 slendr-0.9.0/slendr/tests/testthat/test-msprime.R | 1 slendr-0.9.0/slendr/tests/testthat/test-nonserialized.R | 1 slendr-0.9.0/slendr/tests/testthat/test-population.R | 3 slendr-0.9.0/slendr/tests/testthat/test-pure-msprime-vs-slendr.R | 4 slendr-0.9.0/slendr/tests/testthat/test-pure-slim-vs-slendr.R | 11 slendr-0.9.0/slendr/tests/testthat/test-simulation-runs.R | 11 slendr-0.9.0/slendr/tests/testthat/test-time-direction.R | 4 slendr-0.9.0/slendr/tests/testthat/test-ts-pure-nonspatial.R | 13 slendr-0.9.0/slendr/tests/testthat/test-ts-pure-spatial.R | 5 slendr-0.9.0/slendr/tests/testthat/test-ts.R | 1 slendr-0.9.0/slendr/vignettes/images/original_ex4.png |only slendr-0.9.0/slendr/vignettes/vignette-00-installation.Rmd | 112 + slendr-0.9.0/slendr/vignettes/vignette-01-tutorial.Rmd | 2 slendr-0.9.0/slendr/vignettes/vignette-02-grid-model.Rmd | 2 slendr-0.9.0/slendr/vignettes/vignette-03-interactions.Rmd | 4 slendr-0.9.0/slendr/vignettes/vignette-04-nonspatial-models.Rmd | 6 slendr-0.9.0/slendr/vignettes/vignette-05-tree-sequences.Rmd | 6 slendr-0.9.0/slendr/vignettes/vignette-06-locations.Rmd | 2 slendr-0.9.0/slendr/vignettes/vignette-07-backends.Rmd | 2 slendr-0.9.0/slendr/vignettes/vignette-08-nonslendr-tskit.Rmd | 27 slendr-0.9.0/slendr/vignettes/vignette-09-paper.Rmd | 14 slendr-0.9.0/slendr/vignettes/vignette-10-tracts.Rmd | 11 85 files changed, 3192 insertions(+), 2816 deletions(-)
Title: Download Data from Mexico's Air Quality Information System
Description: Easy-to-use functions for downloading air quality data from
the Mexican National Air Quality Information System (SINAICA). Allows
you to query pollution and meteorological parameters from more than a
hundred monitoring stations located throughout Mexico. See
<https://sinaica.inecc.gob.mx> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between rsinaica versions 0.6.1 dated 2019-02-04 and 1.0.0 dated 2024-02-08
rsinaica-0.6.1/rsinaica/R/rsinaica.R |only rsinaica-0.6.1/rsinaica/man/dot-increase_month.Rd |only rsinaica-0.6.1/rsinaica/man/dot-recode_sinaica_units.Rd |only rsinaica-0.6.1/rsinaica/man/rsinaica.Rd |only rsinaica-1.0.0/rsinaica/DESCRIPTION | 30 +-- rsinaica-1.0.0/rsinaica/MD5 | 44 ++--- rsinaica-1.0.0/rsinaica/NAMESPACE | 2 rsinaica-1.0.0/rsinaica/NEWS.md | 4 rsinaica-1.0.0/rsinaica/R/rsinaica-package.R |only rsinaica-1.0.0/rsinaica/R/sinaica_param_data.R | 77 ++++----- rsinaica-1.0.0/rsinaica/R/sinaica_station_data.R | 80 +++++----- rsinaica-1.0.0/rsinaica/R/sinaica_station_params_and_dates.R | 26 +-- rsinaica-1.0.0/rsinaica/R/utils.R | 2 rsinaica-1.0.0/rsinaica/data/stations_sinaica.rda |binary rsinaica-1.0.0/rsinaica/man/figures/README-unnamed-chunk-3-1.png |binary rsinaica-1.0.0/rsinaica/man/figures/README-unnamed-chunk-6-1.png |binary rsinaica-1.0.0/rsinaica/man/params_sinaica.Rd | 6 rsinaica-1.0.0/rsinaica/man/rsinaica-package.Rd |only rsinaica-1.0.0/rsinaica/man/sinaica_param_data.Rd | 71 ++++---- rsinaica-1.0.0/rsinaica/man/sinaica_station_data.Rd | 76 +++++---- rsinaica-1.0.0/rsinaica/man/sinaica_station_dates.Rd | 6 rsinaica-1.0.0/rsinaica/man/sinaica_station_params.Rd | 6 rsinaica-1.0.0/rsinaica/man/stations_sinaica.Rd | 6 rsinaica-1.0.0/rsinaica/tests/testthat/test-sinaica_param_data.R | 14 - rsinaica-1.0.0/rsinaica/tests/testthat/test-sinaica_params_and_dates.R | 6 rsinaica-1.0.0/rsinaica/tests/testthat/test-sinaica_station_data.R | 24 +-- 26 files changed, 252 insertions(+), 228 deletions(-)
Title: Bayesian Probit Choice Modeling
Description: Bayes estimation of probit choice models, both in the cross-sectional and
panel setting. The package can analyze binary, multivariate, ordered, and
ranked choices, and places a special focus on modeling heterogeneity of
choice behavior among deciders. The main functionality includes model
fitting via Markov chain Monte Carlo methods, tools for convergence
diagnostic, choice data simulation, in-sample and out-of-sample choice
prediction, and model selection using information criteria and Bayes
factors. The latent class model extension facilitates preference-based
decider classification, where the number of latent classes can be inferred
via the Dirichlet process or a weight-based updating scheme. This allows for
flexible modeling of choice behavior without the need to impose structural
constraints. For a reference on the method see Oelschlaeger and Bauer (2021)
<https://trid.trb.org/view/1759753>.
Author: Lennart Oelschlaeger [aut, cre]
,
Dietmar Bauer [aut] ,
Sebastian Buescher [ctb],
Manuel Batram [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.1.2 dated 2022-11-06 and 1.1.3 dated 2024-02-08
RprobitB-1.1.2/RprobitB/R/RprobitB_package.R |only RprobitB-1.1.2/RprobitB/R/datasets.R |only RprobitB-1.1.2/RprobitB/R/utils.R |only RprobitB-1.1.2/RprobitB/data/choice_berserk.rda |only RprobitB-1.1.2/RprobitB/man/M.Rd |only RprobitB-1.1.2/RprobitB/man/RprobitB.Rd |only RprobitB-1.1.2/RprobitB/man/choice_berserk.Rd |only RprobitB-1.1.2/RprobitB/man/delta.Rd |only RprobitB-1.1.2/RprobitB/man/figures/logo.pdf |only RprobitB-1.1.2/RprobitB/man/figures/logo.svg |only RprobitB-1.1.2/RprobitB/man/is_covariance_matrix.Rd |only RprobitB-1.1.2/RprobitB/man/permutations.Rd |only RprobitB-1.1.2/RprobitB/man/pprint.Rd |only RprobitB-1.1.2/RprobitB/tests/testthat/_snaps/utils.md |only RprobitB-1.1.2/RprobitB/tests/testthat/test-utils.R |only RprobitB-1.1.2/RprobitB/vignettes/flowchart.png |only RprobitB-1.1.2/RprobitB/vignettes/ref.bib |only RprobitB-1.1.3/RprobitB/DESCRIPTION | 20 RprobitB-1.1.3/RprobitB/MD5 | 177 RprobitB-1.1.3/RprobitB/NAMESPACE | 14 RprobitB-1.1.3/RprobitB/NEWS.md | 6 RprobitB-1.1.3/RprobitB/R/R_hat.R |only RprobitB-1.1.3/RprobitB/R/RcppExports.R | 3 RprobitB-1.1.3/RprobitB/R/RprobitB-package.R |only RprobitB-1.1.3/RprobitB/R/data.R |only RprobitB-1.1.3/RprobitB/R/data_management.R | 701 - RprobitB-1.1.3/RprobitB/R/model_evaluation.R | 252 RprobitB-1.1.3/RprobitB/R/model_fitting.R | 3760 +++--- RprobitB-1.1.3/RprobitB/R/model_selection.R | 353 RprobitB-1.1.3/RprobitB/R/plot.R | 1190 +- RprobitB-1.1.3/RprobitB/README.md | 94 RprobitB-1.1.3/RprobitB/build/partial.rdb |only RprobitB-1.1.3/RprobitB/build/vignette.rds |binary RprobitB-1.1.3/RprobitB/data/train_choice.rda |only RprobitB-1.1.3/RprobitB/inst/REFERENCES.bib |only RprobitB-1.1.3/RprobitB/inst/doc/RprobitB.Rmd | 72 RprobitB-1.1.3/RprobitB/inst/doc/RprobitB.html | 45 RprobitB-1.1.3/RprobitB/inst/doc/v01_model_definition.R | 34 RprobitB-1.1.3/RprobitB/inst/doc/v01_model_definition.Rmd | 228 RprobitB-1.1.3/RprobitB/inst/doc/v01_model_definition.html | 338 RprobitB-1.1.3/RprobitB/inst/doc/v02_choice_data.R | 53 RprobitB-1.1.3/RprobitB/inst/doc/v02_choice_data.Rmd | 531 RprobitB-1.1.3/RprobitB/inst/doc/v02_choice_data.html | 388 RprobitB-1.1.3/RprobitB/inst/doc/v03_model_fitting.R | 58 RprobitB-1.1.3/RprobitB/inst/doc/v03_model_fitting.Rmd | 539 RprobitB-1.1.3/RprobitB/inst/doc/v03_model_fitting.html | 323 RprobitB-1.1.3/RprobitB/inst/doc/v04_modeling_heterogeneity.R | 54 RprobitB-1.1.3/RprobitB/inst/doc/v04_modeling_heterogeneity.Rmd | 408 RprobitB-1.1.3/RprobitB/inst/doc/v04_modeling_heterogeneity.html | 392 RprobitB-1.1.3/RprobitB/inst/doc/v05_choice_prediction.R | 64 RprobitB-1.1.3/RprobitB/inst/doc/v05_choice_prediction.Rmd | 238 RprobitB-1.1.3/RprobitB/inst/doc/v05_choice_prediction.html | 300 RprobitB-1.1.3/RprobitB/inst/doc/v06_model_selection.R | 40 RprobitB-1.1.3/RprobitB/inst/doc/v06_model_selection.Rmd | 387 RprobitB-1.1.3/RprobitB/inst/doc/v06_model_selection.html | 321 RprobitB-1.1.3/RprobitB/man/R_hat.Rd | 3 RprobitB-1.1.3/RprobitB/man/RprobitB-package.Rd |only RprobitB-1.1.3/RprobitB/man/RprobitB_fit.Rd | 5 RprobitB-1.1.3/RprobitB/man/RprobitB_latent_classes.Rd | 3 RprobitB-1.1.3/RprobitB/man/RprobitB_normalization.Rd | 19 RprobitB-1.1.3/RprobitB/man/as_cov_names.Rd | 4 RprobitB-1.1.3/RprobitB/man/check_form.Rd | 6 RprobitB-1.1.3/RprobitB/man/create_labels_b.Rd | 2 RprobitB-1.1.3/RprobitB/man/create_labels_s.Rd | 2 RprobitB-1.1.3/RprobitB/man/create_lagged_cov.Rd | 11 RprobitB-1.1.3/RprobitB/man/figures/README-coef-1.png |binary RprobitB-1.1.3/RprobitB/man/figures/logo.png |binary RprobitB-1.1.3/RprobitB/man/parameter_labels.Rd | 4 RprobitB-1.1.3/RprobitB/man/plot.RprobitB_data.Rd | 12 RprobitB-1.1.3/RprobitB/man/plot_acf.Rd | 5 RprobitB-1.1.3/RprobitB/man/plot_class_allocation.Rd | 8 RprobitB-1.1.3/RprobitB/man/plot_class_seq.Rd |only RprobitB-1.1.3/RprobitB/man/plot_mixture_contour.Rd | 8 RprobitB-1.1.3/RprobitB/man/plot_mixture_marginal.Rd | 8 RprobitB-1.1.3/RprobitB/man/plot_trace.Rd |only RprobitB-1.1.3/RprobitB/man/predict.RprobitB_fit.Rd | 2 RprobitB-1.1.3/RprobitB/man/preference_flip.Rd | 40 RprobitB-1.1.3/RprobitB/man/prepare_data.Rd | 9 RprobitB-1.1.3/RprobitB/man/simulate_choices.Rd | 4 RprobitB-1.1.3/RprobitB/man/train_choice.Rd |only RprobitB-1.1.3/RprobitB/man/undiff_Sigma.Rd | 7 RprobitB-1.1.3/RprobitB/man/update_s.Rd | 2 RprobitB-1.1.3/RprobitB/src/Makevars | 6 RprobitB-1.1.3/RprobitB/src/Makevars.win | 6 RprobitB-1.1.3/RprobitB/src/gibbs.cpp | 3 RprobitB-1.1.3/RprobitB/tests/testthat.R | 8 RprobitB-1.1.3/RprobitB/tests/testthat/R_hat.R |only RprobitB-1.1.3/RprobitB/tests/testthat/_snaps/data_management.md | 19 RprobitB-1.1.3/RprobitB/tests/testthat/_snaps/model_evaluation.md | 5860 +++++----- RprobitB-1.1.3/RprobitB/tests/testthat/test-data_management.R | 14 RprobitB-1.1.3/RprobitB/tests/testthat/test-model_evaluation.R | 12 RprobitB-1.1.3/RprobitB/tests/testthat/test-model_fitting.R | 16 RprobitB-1.1.3/RprobitB/tests/testthat/test-model_selection.R | 12 RprobitB-1.1.3/RprobitB/vignettes/RprobitB.Rmd | 72 RprobitB-1.1.3/RprobitB/vignettes/img/flowchart.png |only RprobitB-1.1.3/RprobitB/vignettes/img/plot-acf-model-train-1.png |only RprobitB-1.1.3/RprobitB/vignettes/img/plot-coef-model-train-1.png |only RprobitB-1.1.3/RprobitB/vignettes/img/plot-trace-model-train-1.png |only RprobitB-1.1.3/RprobitB/vignettes/img/roc-example-1.png |binary RprobitB-1.1.3/RprobitB/vignettes/img/summary-train-choice-data-1.png |only RprobitB-1.1.3/RprobitB/vignettes/v01_model_definition.Rmd | 228 RprobitB-1.1.3/RprobitB/vignettes/v02_choice_data.Rmd | 531 RprobitB-1.1.3/RprobitB/vignettes/v03_model_fitting.Rmd | 539 RprobitB-1.1.3/RprobitB/vignettes/v04_modeling_heterogeneity.Rmd | 408 RprobitB-1.1.3/RprobitB/vignettes/v05_choice_prediction.Rmd | 238 RprobitB-1.1.3/RprobitB/vignettes/v06_model_selection.Rmd | 387 106 files changed, 9973 insertions(+), 9933 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Manuel Munoz Marquez [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ct [...truncated...]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.9-1 dated 2023-09-28 and 2.9-2 dated 2024-02-08
Rcmdr-2.9-1/Rcmdr/inst/doc/Commander-ru.pdf |only Rcmdr-2.9-1/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |only Rcmdr-2.9-1/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr-ko.pdf |only Rcmdr-2.9-2/Rcmdr/DESCRIPTION | 8 Rcmdr-2.9-2/Rcmdr/MD5 | 19 Rcmdr-2.9-2/Rcmdr/NEWS | 362 +++++----- Rcmdr-2.9-2/Rcmdr/R/data-menu.R | 324 ++++---- Rcmdr-2.9-2/Rcmdr/R/statistics-means-menu.R | 358 ++++----- Rcmdr-2.9-2/Rcmdr/build/vignette.rds |binary Rcmdr-2.9-2/Rcmdr/inst/doc/Empezando-con-Rcmdr-es.pdf |binary Rcmdr-2.9-2/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary Rcmdr-2.9-2/Rcmdr/man/Rcmdr.Utilities.Rd | 184 ++--- 12 files changed, 623 insertions(+), 632 deletions(-)
Title: Visualise the Path to a Stopping Point in Qualitative Interviews
Based on Novel Codes
Description: In semi-structured interviews that use the 'framework' method, it
is not always clear how refinements to interview questions affect the
decision of when to stop interviews. The trend of 'novel' and 'duplicate'
interview codes (novel codes are information that other interviewees have
not previously mentioned) provides insight into the richness of qualitative
information. This package provides tools to visualise when refinements occur
and how that affects the trends of novel and duplicate codes. These
visualisations, when used progressively as new interviews are finished, can
help the researcher to decide on a stopping point for their interviews.
Author: Kam Wong [aut, cph] ,
Desi Quintans [cre, aut, cph]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between novelqualcodes versions 0.13.0 dated 2023-09-11 and 0.13.1 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- README.md | 14 +++++++++++--- build/vignette.rds |binary inst/doc/guided-tour.R | 2 +- inst/doc/guided-tour.Rmd | 8 +++++--- inst/doc/guided-tour.html | 17 ++++++++++++----- vignettes/guided-tour.Rmd | 8 +++++--- 8 files changed, 45 insertions(+), 26 deletions(-)
More information about novelqualcodes at CRAN
Permanent link
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.3.0 dated 2023-12-04 and 1.4.0 dated 2024-02-08
DESCRIPTION | 6 - MD5 | 45 +++++++------ NEWS.md | 36 +++++++++++ R/Aaaa.R | 3 R/class_ev.R | 3 R/class_mrgmod.R | 43 +++++++++++++ R/compile.R | 1 R/events.R | 92 +++++++++++++++------------- R/model_include.R | 4 - R/modspec.R | 19 +++++ R/mread.R | 4 + R/param.R | 5 - R/print.R | 2 inst/WORDLIST | 1 inst/base/databox_cpp.h | 7 ++ inst/base/modelheader.h | 5 - inst/base/mrgsolv.h | 3 inst/base/mrgsolve-evtools-regimen.h |only inst/base/mrgsolve-evtools.h | 67 +++++++++++++++++++- man/ev.Rd | 68 +++++++++++--------- man/param.Rd | 5 - src/devtran.cpp | 8 +- tests/testthat/test-ev.R | 30 ++++++++- tests/testthat/test-modspec.R | 114 ++++++++++++++++++++++++++++++++++- 24 files changed, 450 insertions(+), 121 deletions(-)
Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre] ,
Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.6.1 dated 2024-01-22 and 3.6.2 dated 2024-02-08
DESCRIPTION | 12 MD5 | 92 - NAMESPACE | 13 R/DBgetEvalid.R | 7 R/DBgetPlots.R | 3 R/DBgetXY.R | 7 R/check.estdata.R | 23 R/check.popdataCHNG.R | 25 R/check.popdataP2VEG.R | 329 +++-- R/check.popdataPLT.R | 672 +++++----- R/check.rowcol.R | 1316 +++++++++++++-------- R/check.tree.R | 1 R/datLUTclass.R | 3 R/datLUTnm.R | 22 R/datLUTspp.R | 73 - R/datSumTree.R | 22 R/datSumTreeDom.R | 90 + R/est.outtabs.R | 28 R/modGBarea.R | 11 R/modGBchng.R | 2 R/modGBp2veg.R | 16 R/modGBpop.R | 11 R/modGBratio.R | 33 R/modGBtree.R | 37 R/modMAarea.R | 2 R/modMApop.R | 11 R/modMAratio.R | 56 R/modMAtree.R | 2 R/modSAarea.R | 1 R/modSApop.R | 11 R/modSAtree.R | 1 R/popTableIDs.R | 2 R/popTables.R | 3 R/spClassifyRast.R | 77 - inst/doc/FIESTA_tutorial_GB.R | 1 inst/doc/FIESTA_tutorial_GB.Rmd | 1 inst/doc/FIESTA_tutorial_GB.html | 2352 +++++++++++++++++++------------------- inst/doc/FIESTA_tutorial_MA.html | 615 ++++----- inst/doc/FIESTA_tutorial_PB.html | 22 inst/doc/FIESTA_tutorial_SA.html | 218 +-- inst/doc/FIESTA_tutorial_dat.html | 326 ++--- man/FIESTA-package.Rd | 9 man/popTableIDs.Rd | 3 man/popTables.Rd | 4 man/ref_estvar.Rd | 2 man/spClassifyRast.Rd | 6 vignettes/FIESTA_tutorial_GB.Rmd | 1 47 files changed, 3648 insertions(+), 2926 deletions(-)
Title: Economic Statistics System of the Bank of Korea
Description: API wrapper to download statistical information from the Economic
Statistics System (ECOS) of the Bank of Korea
<https://ecos.bok.or.kr/api/#/>.
Author: Seokhoon Joo [aut, cre],
Jaehyun Joo [ctb]
Maintainer: Seokhoon Joo <seokhoonj@gmail.com>
Diff between ecos versions 0.1.5 dated 2023-08-07 and 0.1.6 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 8 ++++++++ R/statSearch.R | 4 ++-- README.md | 7 +++++-- man/figures |only 6 files changed, 23 insertions(+), 11 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and only
adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019) <doi:10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre] ,
Guillem Rigaill [aut],
Nathalie Vialaneix [aut] ,
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.6.8 dated 2024-01-13 and 0.6.9 dated 2024-02-08
adjclust-0.6.8/adjclust/R/zzzz.R |only adjclust-0.6.9/adjclust/DESCRIPTION | 33 adjclust-0.6.9/adjclust/MD5 | 85 +- adjclust-0.6.9/adjclust/NEWS.md | 8 adjclust-0.6.9/adjclust/R/RcppExports.R | 24 adjclust-0.6.9/adjclust/R/adjclust.R | 75 + adjclust-0.6.9/adjclust/R/hicClust.R | 2 adjclust-0.6.9/adjclust/R/plotSim.R | 13 adjclust-0.6.9/adjclust/R/snpClust.R | 2 adjclust-0.6.9/adjclust/inst/doc/hicClust.R | 4 adjclust-0.6.9/adjclust/inst/doc/hicClust.Rmd | 6 adjclust-0.6.9/adjclust/inst/doc/hicClust.html | 271 +++---- adjclust-0.6.9/adjclust/inst/doc/notesCHAC.html | 385 +++------- adjclust-0.6.9/adjclust/inst/doc/snpClust.R | 4 adjclust-0.6.9/adjclust/inst/doc/snpClust.Rmd | 5 adjclust-0.6.9/adjclust/inst/doc/snpClust.html | 273 +++---- adjclust-0.6.9/adjclust/man/adjClust.Rd | 17 adjclust-0.6.9/adjclust/man/hicClust.Rd | 2 adjclust-0.6.9/adjclust/man/snpClust.Rd | 2 adjclust-0.6.9/adjclust/src/Makevars | 2 adjclust-0.6.9/adjclust/src/Makevars.win | 2 adjclust-0.6.9/adjclust/src/RcppExports.cpp | 66 - adjclust-0.6.9/adjclust/src/adjClustFast.cpp | 118 --- adjclust-0.6.9/adjclust/src/mainFunctions.c | 4 adjclust-0.6.9/adjclust/tests/testthat.R | 2 adjclust-0.6.9/adjclust/tests/testthat/test_adjClust.R | 21 adjclust-0.6.9/adjclust/tests/testthat/test_adjclust_equivalentTo_hclust.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_adjclust_equivalentTo_rioja.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_ascendingCompatibility.R | 3 adjclust-0.6.9/adjclust/tests/testthat/test_chac.R | 3 adjclust-0.6.9/adjclust/tests/testthat/test_correct.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_corrected_plot.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_cuttree.R | 3 adjclust-0.6.9/adjclust/tests/testthat/test_dense_sparse_comparison.R | 3 adjclust-0.6.9/adjclust/tests/testthat/test_final_height.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_hicClust.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_modify.R | 4 adjclust-0.6.9/adjclust/tests/testthat/test_plotSim.R | 6 adjclust-0.6.9/adjclust/tests/testthat/test_similarity_equivalentTo_dissimilarity.R | 3 adjclust-0.6.9/adjclust/tests/testthat/test_snpClust.R | 1 adjclust-0.6.9/adjclust/tests/testthat/test_snpClust_NA-in-LD.R | 5 adjclust-0.6.9/adjclust/tests/testthat/test_warning_with_decreasing_height_plots.R | 5 adjclust-0.6.9/adjclust/vignettes/hicClust.Rmd | 6 adjclust-0.6.9/adjclust/vignettes/snpClust.Rmd | 5 44 files changed, 539 insertions(+), 940 deletions(-)
Title: Weighted BACON Algorithms
Description: The BACON algorithms are methods for multivariate outlier
nomination (detection) and robust linear regression by Billor, Hadi,
and Velleman (2000) <doi:10.1016/S0167-9473(99)00101-2>. The extension
to weighted problems is due to Beguin and Hulliger (2008)
<https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X200800110616>; see
also <doi:10.21105/joss.03238>.
Author: Tobias Schoch [aut, cre] ,
R-core [cph]
Maintainer: Tobias Schoch <tobias.schoch@gmail.com>
Diff between wbacon versions 0.6 dated 2021-11-04 and 0.6-1 dated 2024-02-08
wbacon-0.6-1/wbacon/.Rinstignore | 54 wbacon-0.6-1/wbacon/DESCRIPTION | 10 wbacon-0.6-1/wbacon/MD5 | 76 wbacon-0.6-1/wbacon/NAMESPACE | 90 wbacon-0.6-1/wbacon/R/median_w.R | 8 wbacon-0.6-1/wbacon/R/plot_wbaconlm.R | 390 +-- wbacon-0.6-1/wbacon/R/plot_wbaconmv.R | 209 - wbacon-0.6-1/wbacon/R/predict_wbaconlm.R | 34 wbacon-0.6-1/wbacon/R/quantile_w.R | 102 wbacon-0.6-1/wbacon/R/wbacon.R | 287 +- wbacon-0.6-1/wbacon/R/wbacon_reg.R | 363 +-- wbacon-0.6-1/wbacon/build/partial.rdb |binary wbacon-0.6-1/wbacon/build/vignette.rds |binary wbacon-0.6-1/wbacon/data |only wbacon-0.6-1/wbacon/inst/CITATION | 19 wbacon-0.6-1/wbacon/inst/NEWS.Rd | 119 wbacon-0.6-1/wbacon/inst/doc/doc_c_functions.pdf |binary wbacon-0.6-1/wbacon/inst/doc/methods.pdf |binary wbacon-0.6-1/wbacon/inst/doc/wbacon.R | 141 - wbacon-0.6-1/wbacon/inst/doc/wbacon.Rmd | 798 +++--- wbacon-0.6-1/wbacon/inst/doc/wbacon.html | 2760 +++++++++++++++-------- wbacon-0.6-1/wbacon/inst/paper/paper.bib | 320 +- wbacon-0.6-1/wbacon/inst/paper/paper.md | 350 +- wbacon-0.6-1/wbacon/inst/varia/Dockerfile |only wbacon-0.6-1/wbacon/inst/varia/_make_pkg.R | 183 - wbacon-0.6-1/wbacon/man/is_outlier.Rd | 62 wbacon-0.6-1/wbacon/man/median_w.Rd | 54 wbacon-0.6-1/wbacon/man/philips.Rd |only wbacon-0.6-1/wbacon/man/plot_wbaconlm.Rd | 171 - wbacon-0.6-1/wbacon/man/plot_wbaconmv.Rd | 148 - wbacon-0.6-1/wbacon/man/predict_wbaconlm.Rd | 114 wbacon-0.6-1/wbacon/man/quantile_w.Rd | 89 wbacon-0.6-1/wbacon/man/wbacon-package.Rd | 70 wbacon-0.6-1/wbacon/man/wbacon.Rd | 298 +- wbacon-0.6-1/wbacon/man/wbacon_reg.Rd | 324 +- wbacon-0.6-1/wbacon/src/init.c |only wbacon-0.6-1/wbacon/src/wbacon.c | 5 wbacon-0.6-1/wbacon/src/wquantile.c | 18 wbacon-0.6-1/wbacon/tests/test_wbacon.R | 193 - wbacon-0.6-1/wbacon/tests/test_wbacon_reg.R | 134 - wbacon-0.6-1/wbacon/vignettes/fluent.css |only wbacon-0.6-1/wbacon/vignettes/wbacon.Rmd | 798 +++--- wbacon-0.6/wbacon/src/wbacon_init.c |only 43 files changed, 5093 insertions(+), 3698 deletions(-)
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.3.1 dated 2024-01-30 and 1.3.2 dated 2024-02-08
DESCRIPTION | 7 +++---- MD5 | 15 ++++++++------- R/sysdata.rda |binary R/toxEval.R | 9 +++++++-- inst/doc/Chemical_names.html | 2 +- inst/doc/Introduction.html | 4 ++-- inst/doc/PrepareData.html | 2 +- inst/shiny/www/footer.html |only man/end_point_info.Rd | 2 +- 9 files changed, 23 insertions(+), 18 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data
exploration, by creating them, manipulating them, and adding color
helpers to highlight important informations (differences from totals,
comparisons between lines or columns, contributions to variance, margins
of error, etc.). All functions are pipe-friendly and render data frames
which can be easily manipulated. In the same time, time-taking operations
are done with 'data.table' to go faster with big dataframes. Tables can
be exported to 'Excel' and in html with formats and colors.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between tabxplor versions 1.1.1 dated 2024-01-22 and 1.1.2 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/fmt_class.R | 2 +- R/tab_classes.R | 6 ++++-- README.md | 2 +- man/tab_kable.Rd | 5 ++++- 7 files changed, 29 insertions(+), 14 deletions(-)
Title: Mann-Kendall Test, Seasonal and Regional Kendall Tests
Description: Contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.
Author: Aldo Marchetto
Maintainer: Aldo Marchetto <aldo.marchetto@cnr.it>
Diff between rkt versions 1.6 dated 2021-03-29 and 1.7 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/print.rkt.Rd | 10 +++++----- man/rkt-package.Rd | 33 ++++++++++++++++----------------- man/rkt.Rd | 9 ++++----- 5 files changed, 33 insertions(+), 35 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
This method draws from the simulation framework used in the Gelman and Hill (2007) textbook:
Data Analysis Using Regression and Multilevel/Hierarchical Models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut],
Alex Whitworth [ctb]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between merTools versions 0.6.1 dated 2023-03-20 and 0.6.2 dated 2024-02-08
merTools-0.6.1/merTools/man/merTools.Rd |only merTools-0.6.2/merTools/DESCRIPTION | 10 merTools-0.6.2/merTools/MD5 | 71 merTools-0.6.2/merTools/NEWS.md | 6 merTools-0.6.2/merTools/R/helpers.R | 2 merTools-0.6.2/merTools/R/merData.R | 2 merTools-0.6.2/merTools/R/merFastDisplay.R | 2 merTools-0.6.2/merTools/R/merTools-package.r | 7 merTools-0.6.2/merTools/README.md | 145 - merTools-0.6.2/merTools/build/vignette.rds |binary merTools-0.6.2/merTools/inst/doc/Using_predictInterval.html | 418 +-- merTools-0.6.2/merTools/inst/doc/imputation.html | 1274 +++++----- merTools-0.6.2/merTools/inst/doc/marginal_effects.html | 60 merTools-0.6.2/merTools/inst/doc/merToolsIntro.html | 450 +-- merTools-0.6.2/merTools/man/buildModelMatrix.Rd | 2 merTools-0.6.2/merTools/man/figures/README_FEsimPlot-1.png |binary merTools-0.6.2/merTools/man/figures/README_reImpactplot-1.png |binary merTools-0.6.2/merTools/man/figures/README_reSimplot-1.png |binary merTools-0.6.2/merTools/man/figures/README_substImpactPredict-1.png |binary merTools-0.6.2/merTools/man/figures/README_unnamed-chunk-14-1.png |binary merTools-0.6.2/merTools/man/figures/README_unnamed-chunk-7-1.png |binary merTools-0.6.2/merTools/man/figures/README_unnamed-chunk-8-1.png |binary merTools-0.6.2/merTools/man/findFormFuns.Rd | 2 merTools-0.6.2/merTools/man/merTools-package.Rd |only merTools-0.6.2/merTools/tests/testthat/_snaps |only merTools-0.6.2/merTools/tests/testthat/test-REmargins.R | 2 merTools-0.6.2/merTools/tests/testthat/test-expectedRank.R | 1 merTools-0.6.2/merTools/tests/testthat/test-helpers.R | 68 merTools-0.6.2/merTools/tests/testthat/test-merData.R | 102 merTools-0.6.2/merTools/tests/testthat/test-merExtract.R | 37 merTools-0.6.2/merTools/tests/testthat/test-merModList.R | 45 merTools-0.6.2/merTools/tests/testthat/test-plots.R | 48 merTools-0.6.2/merTools/tests/testthat/test-predict.R | 836 ------ merTools-0.6.2/merTools/tests/testthat/test-predict1.R |only merTools-0.6.2/merTools/tests/testthat/test-predict2.R |only merTools-0.6.2/merTools/tests/testthat/test-predict3.R |only merTools-0.6.2/merTools/tests/testthat/test-predict4.R |only merTools-0.6.2/merTools/tests/testthat/test-seeds.R | 13 merTools-0.6.2/merTools/tests/testthat/test-subboot.R | 16 merTools-0.6.2/merTools/tests/testthat/test-substEff.R | 26 40 files changed, 1491 insertions(+), 2154 deletions(-)
Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2',
facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre]
,
Baptiste Auguie [ctb] ,
Shaun Jackman [ctb] ,
Hadley Wickham [ctb] ,
Winston Chang [ctb]
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>
Diff between lemon versions 0.4.7 dated 2023-11-07 and 0.4.9 dated 2024-02-08
DESCRIPTION | 6 MD5 | 28 - R/facet-rep-lab.r | 48 +- R/facet-wrap.r | 9 R/geom-pointline.r | 31 - R/ggplot2.r | 5 inst/doc/capped-axes.html | 137 ++++---- inst/doc/facet-rep-labels.html | 8 inst/doc/geoms.html | 4 inst/doc/gtable_show_lemonade.html | 14 inst/doc/legends.html | 48 +- inst/doc/lemon_print.html | 4 man/remove_labels_from_axis.Rd | 4 tests/testthat/_snaps/facet/facet-rep-grid-spacing.svg | 158 ++++----- tests/testthat/_snaps/facet/facet-rep-wrap-spacing.svg | 286 ++++++++--------- 15 files changed, 406 insertions(+), 384 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-27 0.3.2
2017-11-17 0.3.1
2017-08-02 0.3.0
2016-12-09 0.2.0
2016-01-09 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-22 0.7.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-23 4.5.4
2023-02-17 4.5.3
2023-01-08 4.5.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-24 0.6.0
2023-05-24 0.5.1
2022-08-29 0.5.0
2022-03-02 0.4.2
2022-02-04 0.4.1
2022-01-18 0.4.0
2021-03-18 0.3.0
2021-01-09 0.2.1
2020-12-04 0.2.0
2020-06-30 0.1.3
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.5.1 dated 2023-11-13 and 0.5.2 dated 2024-02-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/initializeLogging.R | 3 ++- inst/doc/error-handling.html | 12 ++++++------ inst/doc/logging.html | 32 ++++++++++++++++---------------- 6 files changed, 37 insertions(+), 31 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Load Data for Analysis System
Description: Provides a framework to load text and excel files through a 'shiny' graphical interface. It allows renaming, transforming, ordering and removing variables. It includes basic exploratory methods such as the mean, median, mode, normality test, histogram and correlation.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [aut],
Joseline Quiros [aut]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between loadeR versions 1.1.6 dated 2023-03-27 and 1.1.8 dated 2024-02-08
DESCRIPTION | 14 +++++----- MD5 | 54 +++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 4 ++ R/loadeR.R | 9 ++---- R/mod_acercade.R | 2 - R/mod_carga_datos.R | 4 +- R/mod_correlacion.R | 4 +- R/mod_dispersion.R | 4 +- R/mod_distribuciones.R | 5 ++- R/mod_distribuciones_fct.R | 26 ------------------ R/mod_distribuciones_utils.R | 15 ++++++++-- R/mod_normal.R | 4 +- R/mod_r_numerico.R | 4 +- inst/golem-config.yml | 2 - man/loadeR.Rd | 14 ++++++++-- man/mod_carga_datos_server.Rd | 2 - man/mod_carga_datos_ui.Rd | 2 - man/mod_correlacion_server.Rd | 2 - man/mod_correlacion_ui.Rd | 2 - man/mod_dispersion_server.Rd | 2 - man/mod_dispersion_ui.Rd | 2 - man/mod_distribuciones_server.Rd | 2 - man/mod_distribuciones_ui.Rd | 2 - man/mod_normal_server.Rd | 2 - man/mod_normal_ui.Rd | 2 - man/mod_r_numerico_server.Rd | 2 - man/mod_r_numerico_ui.Rd | 2 - 28 files changed, 94 insertions(+), 96 deletions(-)
Title: Cluster-Based Permutation Analysis for Densely Sampled Time Data
Description: An implementation of fast cluster-based permutation analysis
(CPA) for densely-sampled time data developed in Maris & Oostenveld,
2007 <doi:10.1016/j.jneumeth.2007.03.024>. Supports (generalized,
mixed-effects) regression models for the calculation of timewise
statistics. Provides both a wholesale and a piecemeal interface to the
CPA procedure with an emphasis on interpretability and diagnostics.
Integrates 'Julia' libraries 'MixedModels.jl' and 'GLM.jl' for
performance improvements, with additional functionalities for
interfacing with 'Julia' from 'R' powered by the 'JuliaConnectoR'
package.
Author: June Choe [aut, cre, cph]
Maintainer: June Choe <jchoe001@gmail.com>
Diff between jlmerclusterperm versions 1.1.0 dated 2023-10-07 and 1.1.1 dated 2024-02-08
DESCRIPTION | 6 MD5 | 24 +- NEWS.md | 10 + R/aaa.R | 313 ++++++++++++++++++------------------ R/jlmer.R | 230 +++++++++++++------------- R/jlmer_spec.R | 17 + R/permute_timewise_statistics.R | 342 ++++++++++++++++++++-------------------- README.md | 4 inst/doc/jlmerclusterperm.Rmd | 156 +++++++++--------- inst/doc/jlmerclusterperm.html | 3 man/jlmer.Rd | 2 man/to_jlmer.Rd | 2 vignettes/jlmerclusterperm.Rmd | 156 +++++++++--------- 13 files changed, 641 insertions(+), 624 deletions(-)
More information about jlmerclusterperm at CRAN
Permanent link
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Samra Goumri [aut],
Zauad Shahreer Abeer [aut],
Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.4.3 dated 2024-01-10 and 1.4.4 dated 2024-02-08
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- R/edit-data-utils.R | 7 +++++++ R/edit-data.R | 9 ++++++++- build/vignette.rds |binary inst/doc/i18n.html | 2 +- inst/i18n/fr.csv | 2 +- man/edit-data.Rd | 7 +++++++ 9 files changed, 42 insertions(+), 16 deletions(-)
Title: Silly Putty Clustering
Description: Implements a simple, novel clustering algorithm based on
optimizing the silhouette width. See <doi:10.1101/2023.11.07.566055>
for details.
Author: Kevin R. Coombes, Dwayne Tally
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between SillyPutty versions 0.3.2 dated 2023-11-08 and 0.4.1 dated 2024-02-08
DESCRIPTION | 11 - MD5 | 10 - NAMESPACE | 4 NEWS | 37 +++++ R/03-HCSP.R |only inst/doc/SillyPuttyVignette.html | 262 +++++++++++++++++++++++++++------------ man/05-HCSP.Rd |only 7 files changed, 232 insertions(+), 92 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<https://CRAN.R-project.org/package=mirai> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 0.8.0 dated 2024-01-09 and 0.9.0 dated 2024-02-08
crew-0.8.0/crew/tests/local.R |only crew-0.9.0/crew/DESCRIPTION | 14 crew-0.9.0/crew/MD5 | 59 - crew-0.9.0/crew/NAMESPACE | 2 crew-0.9.0/crew/NEWS.md | 11 crew-0.9.0/crew/R/crew_assert.R | 2 crew-0.9.0/crew/R/crew_controller.R | 414 ++++++++--- crew-0.9.0/crew/R/crew_controller_group.R | 306 +++++++- crew-0.9.0/crew/R/crew_launcher.R | 17 crew-0.9.0/crew/R/crew_monitor_local.R | 4 crew-0.9.0/crew/R/crew_package.R | 3 crew-0.9.0/crew/R/utils_mirai.R | 41 - crew-0.9.0/crew/R/utils_promises.R |only crew-0.9.0/crew/build/vignette.rds |binary crew-0.9.0/crew/inst/WORDLIST | 2 crew-0.9.0/crew/inst/doc/introduction.R | 22 crew-0.9.0/crew/inst/doc/introduction.Rmd | 37 - crew-0.9.0/crew/inst/doc/introduction.html | 108 ++ crew-0.9.0/crew/inst/doc/promises.R |only crew-0.9.0/crew/inst/doc/promises.Rmd |only crew-0.9.0/crew/inst/doc/promises.html |only crew-0.9.0/crew/man/crew-package.Rd | 1 crew-0.9.0/crew/man/crew_class_controller.Rd | 378 +++++++++- crew-0.9.0/crew/man/crew_class_controller_group.Rd | 443 +++++++++++- crew-0.9.0/crew/man/crew_class_launcher.Rd | 4 crew-0.9.0/crew/tests/interactive |only crew-0.9.0/crew/tests/local/test-backlog_crash.R |only crew-0.9.0/crew/tests/local/test-map.R | 14 crew-0.9.0/crew/tests/testthat/test-crew_controller.R | 419 +++++++++++ crew-0.9.0/crew/tests/testthat/test-crew_controller_group.R | 279 +++++++ crew-0.9.0/crew/tests/testthat/test-crew_controller_local.R | 275 ------- crew-0.9.0/crew/tests/testthat/test-crew_monitor_local.R | 1 crew-0.9.0/crew/vignettes/introduction.Rmd | 37 - crew-0.9.0/crew/vignettes/promises.Rmd |only 34 files changed, 2367 insertions(+), 526 deletions(-)