Title: Mapping of a Categorical Variable in a Panel Dataset
Description: There are offered automatic methods to map a categorical variable according to a specific encoding across different time points.
The main rule is to replicate the observation if it could be assign to a few categories.
Then using simple frequencies or statistical methods to approximate probabilities of being assign to each of them.
This algorithm was invented and implemented in the paper by (Nasinski, Majchrowska and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>).
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between cat2cat versions 0.1.7 dated 2020-11-29 and 0.2.0 dated 2020-12-08
cat2cat-0.1.7/cat2cat/man/cross_cat2cat.Rd |only cat2cat-0.1.7/cat2cat/man/prune_cat2cat.Rd |only cat2cat-0.2.0/cat2cat/DESCRIPTION | 8 cat2cat-0.2.0/cat2cat/MD5 | 36 ++- cat2cat-0.2.0/cat2cat/NAMESPACE | 10 - cat2cat-0.2.0/cat2cat/NEWS.md | 15 + cat2cat-0.2.0/cat2cat/R/cat2cat.R | 16 - cat2cat-0.2.0/cat2cat/R/cat2cat_agg.R | 14 - cat2cat-0.2.0/cat2cat/R/lms.R | 13 - cat2cat-0.2.0/cat2cat/R/plot_cat2cat.R |only cat2cat-0.2.0/cat2cat/build/vignette.rds |binary cat2cat-0.2.0/cat2cat/inst/doc/Introduction.R | 33 +++ cat2cat-0.2.0/cat2cat/inst/doc/Introduction.Rmd | 54 +++-- cat2cat-0.2.0/cat2cat/inst/doc/Introduction.html | 155 ++++++++++++---- cat2cat-0.2.0/cat2cat/man/cross_c2c.Rd |only cat2cat-0.2.0/cat2cat/man/plot_c2c.Rd |only cat2cat-0.2.0/cat2cat/man/prune_c2c.Rd |only cat2cat-0.2.0/cat2cat/man/summary_c2c.Rd | 4 cat2cat-0.2.0/cat2cat/tests/testthat/test-cat2cat.R | 8 cat2cat-0.2.0/cat2cat/tests/testthat/test-cat2cat_agg.R | 8 cat2cat-0.2.0/cat2cat/tests/testthat/test-lms.R |only cat2cat-0.2.0/cat2cat/tests/testthat/test-plot.R |only cat2cat-0.2.0/cat2cat/vignettes/Introduction.Rmd | 54 +++-- 23 files changed, 304 insertions(+), 124 deletions(-)
Title: Easy Plotting of Periodic Data with 'ggplot2'
Description: Implements methods to plot periodic data in any arbitrary range on the fly.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between ggperiodic versions 1.0.0 dated 2019-03-12 and 1.0.1 dated 2020-12-08
ggperiodic-1.0.0/ggperiodic/tests/figs |only ggperiodic-1.0.1/ggperiodic/DESCRIPTION | 11 ggperiodic-1.0.1/ggperiodic/MD5 | 19 ggperiodic-1.0.1/ggperiodic/NEWS.md | 4 ggperiodic-1.0.1/ggperiodic/build/vignette.rds |binary ggperiodic-1.0.1/ggperiodic/inst/doc/wraping-around-ggplot2.R | 14 ggperiodic-1.0.1/ggperiodic/inst/doc/wraping-around-ggplot2.html | 194 ++++++---- ggperiodic-1.0.1/ggperiodic/man/ggperiodic.Rd | 4 ggperiodic-1.0.1/ggperiodic/tests/testthat/test-fortify.R | 4 9 files changed, 159 insertions(+), 91 deletions(-)
Title: Wrapper Functions for 'Freesurfer'
Description: Wrapper functions that interface with 'Freesurfer'
<https://surfer.nmr.mgh.harvard.edu/>, a powerful and
commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with
'Freesurfer' completely in R, where you pass R objects of class 'nifti',
implemented by package 'oro.nifti', and the function executes an 'Freesurfer'
command and returns an R object of class 'nifti' or necessary output.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>),
Athanasia Mo Mowinckel [ctb] (<https://orcid.org/0000-0002-5756-0223>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between freesurfer versions 1.6.7 dated 2020-03-30 and 1.6.8 dated 2020-12-08
DESCRIPTION | 11 - MD5 | 50 +++--- NEWS.md | 6 R/fs_setup.R | 31 +++- R/mnc2nii.R | 2 R/mri_convert.R | 2 R/mri_deface.R | 15 +- R/mri_info.R | 2 R/mri_mask.R | 2 R/mris_euler_number.R | 2 R/nii2mnc.R | 2 R/read_fs_table.R | 2 build/vignette.rds |binary inst/doc/exploring_included_data.R | 23 ++- inst/doc/exploring_included_data.Rmd | 23 ++- inst/doc/exploring_included_data.html | 245 ++++++++++++++++++++-------------- man/have_fs.Rd | 4 man/mnc2nii.Rd | 2 man/mri_convert.Rd | 2 man/mri_deface.Rd | 15 +- man/mri_info.Rd | 2 man/mri_mask.Rd | 2 man/mris_euler_number.Rd | 2 man/nii2mnc.Rd | 2 man/read_fs_table.Rd | 2 vignettes/exploring_included_data.Rmd | 23 ++- 26 files changed, 312 insertions(+), 162 deletions(-)
Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between survParamSim versions 0.1.3 dated 2020-11-24 and 0.1.4 dated 2020-12-08
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS.md | 16 +++++++++++++++- README.md | 4 +++- man/figures/README-hr_pi-1.png |binary man/figures/README-km_pi_group-1.png |binary tests/testthat/helper-utils.R |only tests/testthat/test-calc_km_pi.R | 10 +++++----- 8 files changed, 33 insertions(+), 16 deletions(-)
Title: Simulating Plays and Drives in the NFL
Description: The intent here is to enable the simulation of plays/drives and
evaluate game-play strategies in the National Football League (NFL).
Built-in strategies include going for it on fourth down and varying the
proportion of passing/rushing plays during a drive. The user should be
familiar with nflscrapR data before trying to write his/her own
strategies. This work is inspired by a blog post by Mike Lopez,
currently the Director of Data and Analytics at the NFL, Lopez (2019) <https://statsbylopez.netlify.app/post/resampling-nfl-drives/>.
Author: Ryan Elmore [cre, aut] (<https://orcid.org/0000-0002-0092-4532>),
Ben Williams [aut] (<https://orcid.org/0000-0001-8474-5066>),
Will Palmquist [aut] (<https://orcid.org/0000-0002-6100-0923>)
Maintainer: Ryan Elmore <Ryan.Elmore@du.edu>
Diff between NFLSimulatoR versions 0.2 dated 2020-12-01 and 0.2.1 dated 2020-12-08
DESCRIPTION | 6 +-- MD5 | 20 +++++------ NEWS.md | 9 +++++ R/down_distance_updater.R | 65 ++++++++++++++++--------------------- R/download_nflfastR_data.R | 3 + R/prep_pbp_data.R | 12 +++--- R/sample_fourth_down_strategy.R | 22 ++++++------ README.md | 15 +++++++- man/download_nflfastR_data.Rd | 2 - man/prep_pbp_data.Rd | 4 +- man/sample_fourth_down_strategy.Rd | 8 ++-- 11 files changed, 92 insertions(+), 74 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible framework for
statistical inference of a broad class of time series and other data. KFAS
includes computationally efficient functions for Kalman filtering, smoothing,
forecasting, and simulation of multivariate exponential family state space models,
with observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.4.0 dated 2020-12-07 and 1.4.1 dated 2020-12-08
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/KFAS.pdf |binary src/declarations.h | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-14 0.4.9
2019-10-02 0.4.4
2018-03-06 0.2.4
2017-10-13 0.2.2
2017-09-15 0.2.0
2017-04-01 0.1.0
Title: Stable and Interpretable RUle Set
Description: A regression and classification algorithm based on random forests, which takes the form of a short list of rules. SIRUS combines the simplicity of decision trees with a predictivity close to random forests. The core aggregation principle of random forests is kept, but instead of aggregating predictions, SIRUS aggregates the forest structure: the most frequent nodes of the forest are selected to form a stable rule ensemble model. The algorithm is fully described in the following articles: Benard C., Biau G., da Veiga S., Scornet E. (2019) <arXiv:1908.06852> for classification, and Benard C., Biau G., da Veiga S., Scornet E. (2020) <arXiv:2004.14841> for regression. This R package is a fork from the project ranger (<https://github.com/imbs-hl/ranger>).
Author: Clement Benard [aut, cre], Marvin N. Wright [ctb, cph]
Maintainer: Clement Benard <clement.benard5@gmail.com>
Diff between sirus versions 0.2.1 dated 2020-01-20 and 0.3.1 dated 2020-12-08
DESCRIPTION | 18 - MD5 | 24 +- NAMESPACE | 32 +-- R/sirus.R | 463 ++++++++++++++++++++++++++++++--------------------- R/sirus_utility.R | 239 ++++++++++++++++---------- man/sirus.cv.Rd | 174 +++++++++++-------- man/sirus.fit.Rd | 208 ++++++++++++++-------- man/sirus.plot.cv.Rd | 86 ++++----- man/sirus.predict.Rd | 72 +++---- man/sirus.print.Rd | 70 +++---- src/DataSparse.cpp |only src/DataSparse.h |only src/RcppExports.cpp | 1 tests/testthat.R | 8 14 files changed, 825 insertions(+), 570 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and robustness analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.23.0 dated 2020-11-28 and 1.23.1 dated 2020-12-08
DESCRIPTION | 6 MD5 | 8 NEWS | 5 R/sensiHSIC.R | 23 - R/sobolshap_knn.R | 1003 ++++++++++++++++++++++++++---------------------------- 5 files changed, 526 insertions(+), 519 deletions(-)
Title: Robust Bootstrap Forecast Densities for GARCH Models
Description: Bootstrap forecast densities for GARCH (Generalized Autoregressive Conditional Heteroskedastic) returns and volatilities using the robust residual-based bootstrap procedure of Trucios, Hotta and Ruiz (2017) <DOI:10.1080/00949655.2017.1359601>.
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Diff between RobGARCHBoot versions 1.1.0 dated 2020-11-24 and 1.1.1 dated 2020-12-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/RobGARCHBootParallel.R | 4 ++-- man/RobGARCHBootParallel.Rd | 5 ++++- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman [aut, cre],
Christopher Chang [ctb],
Xavi Puig [ctb],
Jan Wigginton [ctb],
Leonardo Ortoleva [ctb],
William R. Engels [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.6.7 dated 2020-09-20 and 1.6.9 dated 2020-12-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/HardyWeinberg.Rnw | 2 +- inst/doc/HardyWeinberg.pdf |binary man/HardyWeinberg-package.Rd | 4 ++-- src/HWxChromosomal.cpp | 30 +++++++++++++++--------------- vignettes/HardyWeinberg.Rnw | 2 +- 7 files changed, 29 insertions(+), 29 deletions(-)
Title: Stability Measures for Feature Selection
Description: An implementation of many measures for the
assessment of the stability of feature selection. Both simple measures
and measures which take into account the similarities between features
are available, see Bommert et al. (2017) <doi:10.1155/2017/7907163>.
Author: Andrea Bommert [aut, cre] (<https://orcid.org/0000-0002-1005-9351>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Andrea Bommert <bommert@statistik.tu-dortmund.de>
Diff between stabm versions 1.1.3 dated 2020-11-09 and 1.1.4 dated 2020-12-08
DESCRIPTION | 6 +-- MD5 | 56 ++++++++++++++++++------------------ NAMESPACE | 1 R/bibentries.R | 26 +++++++++------- R/list_stability_measures.R | 2 + R/stability_functions_adjusted.R | 47 ++++++++++++++---------------- R/stability_functions_corrected.R | 18 +++++------ R/stability_functions_uncorrected.R | 14 ++++----- build/partial.rdb |binary inst/doc/stabm.Rmd | 2 - inst/doc/stabm.pdf |binary man/listStabilityMeasures.Rd | 3 + man/stabilityDavis.Rd | 11 +++---- man/stabilityDice.Rd | 9 +++-- man/stabilityIntersectionCount.Rd | 4 +- man/stabilityIntersectionGreedy.Rd | 6 +-- man/stabilityIntersectionMBM.Rd | 10 +++--- man/stabilityIntersectionMean.Rd | 6 +-- man/stabilityJaccard.Rd | 9 +++-- man/stabilityKappa.Rd | 7 +--- man/stabilityLustgarten.Rd | 9 +++-- man/stabilityNovovicova.Rd | 9 +++-- man/stabilityOchiai.Rd | 9 +++-- man/stabilityPhi.Rd | 9 +++-- man/stabilitySechidis.Rd | 2 - man/stabilitySomol.Rd | 13 ++++---- man/stabilityYu.Rd | 3 + man/stabilityZucknick.Rd | 12 +++---- vignettes/stabm.Rmd | 2 - 29 files changed, 161 insertions(+), 144 deletions(-)
Title: Create Japanese Administration Area and Office Maps
Description: Utilizing the data that Japanese administration area provided
by the National Land Numerical Information download service (<https://nlftp.mlit.go.jp/ksj/index.html>).
This package provide map data is based on the Digital Map 25000 (Map Image) published
by Geospatial Information Authority of Japan (Approval No.603FY2017 information usage <https://www.gsi.go.jp>).
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Geospatial Information Authority of Japan [dtc] (This package data
sets, National Land numerical information by the Geographical
Survey Institute with the approval of Geographical Survey Institute
Head (Approval No.603FY2017 information usage))
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpndistrict versions 0.3.8 dated 2020-11-27 and 0.3.9 dated 2020-12-08
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 2 ++ R/city_name_table.R | 2 +- man/find_jis_code.Rd | 9 +++++++++ man/jpn_admins.Rd | 2 ++ 7 files changed, 27 insertions(+), 13 deletions(-)
Title: Data Language Engine for 'knitr' / 'rmarkdown'
Description: Implements a data language engine for incorporating data directly in
'rmarkdown' documents so that they can be made completely standalone.
Author: David M. Kaplan [aut, cre, cph]
(<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000)
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>
Diff between knitrdata versions 0.6.0 dated 2020-12-02 and 0.6.1 dated 2020-12-08
knitrdata-0.6.0/knitrdata/man/insert_data_chunk_dialog.Rd |only knitrdata-0.6.1/knitrdata/DESCRIPTION | 7 knitrdata-0.6.1/knitrdata/MD5 | 25 - knitrdata-0.6.1/knitrdata/NEWS.md | 6 knitrdata-0.6.1/knitrdata/R/rstudio_addins.R | 181 +++++----- knitrdata-0.6.1/knitrdata/inst/doc/data_language_engine_vignette.Rmd | 6 knitrdata-0.6.1/knitrdata/inst/doc/data_language_engine_vignette.html | 10 knitrdata-0.6.1/knitrdata/man/create_chunk.Rd | 1 knitrdata-0.6.1/knitrdata/man/create_data_chunk_dialog.Rd | 50 +- knitrdata-0.6.1/knitrdata/man/insert_data_chunk_template.Rd | 12 knitrdata-0.6.1/knitrdata/man/list_rmd_chunks.Rd | 1 knitrdata-0.6.1/knitrdata/man/remove_chunks_dialog.Rd | 6 knitrdata-0.6.1/knitrdata/tests/test.md5sum_chunks.R | 1 knitrdata-0.6.1/knitrdata/vignettes/data_language_engine_vignette.Rmd | 6 14 files changed, 178 insertions(+), 134 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.11.0 dated 2020-11-24 and 0.11.1 dated 2020-12-08
insight-0.11.0/insight/tests/testthat/test-felm.R |only insight-0.11.1/insight/DESCRIPTION | 22 +- insight-0.11.1/insight/MD5 | 103 ++++----- insight-0.11.1/insight/NAMESPACE | 2 insight-0.11.1/insight/NEWS.md | 66 ++++-- insight-0.11.1/insight/R/compute_variances.R | 6 insight-0.11.1/insight/R/export_table.R | 62 ++++- insight-0.11.1/insight/R/find_formula.R | 24 +- insight-0.11.1/insight/R/find_parameters.R | 8 insight-0.11.1/insight/R/find_random.R | 31 +- insight-0.11.1/insight/R/find_smooth.R |only insight-0.11.1/insight/R/find_statistic.R | 3 insight-0.11.1/insight/R/format_rope.R | 5 insight-0.11.1/insight/R/format_table.R | 47 ++-- insight-0.11.1/insight/R/get_data.R | 110 ++++++---- insight-0.11.1/insight/R/get_parameters.R | 18 + insight-0.11.1/insight/R/get_predictors.R | 7 insight-0.11.1/insight/R/get_statistic.R | 3 insight-0.11.1/insight/R/get_variances.R | 16 - insight-0.11.1/insight/R/helper_functions.R | 1 insight-0.11.1/insight/R/is_model.R | 3 insight-0.11.1/insight/R/standardize_names.R | 6 insight-0.11.1/insight/R/utils_get_data.R | 22 +- insight-0.11.1/insight/R/utils_model_info.R | 4 insight-0.11.1/insight/build/partial.rdb |binary insight-0.11.1/insight/inst/WORDLIST | 1 insight-0.11.1/insight/man/export_table.Rd | 29 ++ insight-0.11.1/insight/man/find_parameters.Rd | 11 - insight-0.11.1/insight/man/find_random.Rd | 31 +- insight-0.11.1/insight/man/find_smooth.Rd |only insight-0.11.1/insight/man/format_rope.Rd | 4 insight-0.11.1/insight/man/get_data.Rd | 26 +- insight-0.11.1/insight/man/get_predictors.Rd | 4 insight-0.11.1/insight/man/get_variance.Rd | 7 insight-0.11.1/insight/man/parameters_table.Rd | 3 insight-0.11.1/insight/tests/spelling.R | 9 insight-0.11.1/insight/tests/testthat/test-backticks.R | 1 insight-0.11.1/insight/tests/testthat/test-bigglm.R | 1 insight-0.11.1/insight/tests/testthat/test-censReg.R | 1 insight-0.11.1/insight/tests/testthat/test-cgam.R | 1 insight-0.11.1/insight/tests/testthat/test-clean_names.R | 1 insight-0.11.1/insight/tests/testthat/test-clm.R | 1 insight-0.11.1/insight/tests/testthat/test-clm2.R | 1 insight-0.11.1/insight/tests/testthat/test-clmm.R | 1 insight-0.11.1/insight/tests/testthat/test-coxme.R | 1 insight-0.11.1/insight/tests/testthat/test-coxph.R | 1 insight-0.11.1/insight/tests/testthat/test-crch.R | 1 insight-0.11.1/insight/tests/testthat/test-find_smooth.R |only insight-0.11.1/insight/tests/testthat/test-get_data.R | 2 insight-0.11.1/insight/tests/testthat/test-glmmTMB.R | 10 insight-0.11.1/insight/tests/testthat/test-ivreg.R | 4 insight-0.11.1/insight/tests/testthat/test-ivreg_AER.R | 1 insight-0.11.1/insight/tests/testthat/test-metaBMA.R |only insight-0.11.1/insight/tests/testthat/test-offset.R | 35 +-- insight-0.11.1/insight/tests/testthat/test-standardize_names.R | 14 - 55 files changed, 497 insertions(+), 274 deletions(-)
Title: Estimate Causal Effects with Borrowing Between Data Sources
Description: Estimate population average treatment effects from a primary data source
with borrowing from supplemental sources. Causal estimation is done with either a
Bayesian linear model or with Bayesian additive regression trees (BART) to adjust
for confounding. Borrowing is done with multisource exchangeability models (MEMs). For
information on BART, see Chipman, George, & McCulloch (2010) <doi:10.1214/09-AOAS285>.
For information on MEMs, see Kaizer, Koopmeiners, &
Hobbs (2018) <doi:10.1093/biostatistics/kxx031>.
Author: Jeffrey A. Boatman [aut, cre],
David M. Vock [aut],
Joseph S. Koopmeiners [aut]
Maintainer: Jeffrey A. Boatman <jeffrey.boatman@gmail.com>
Diff between borrowr versions 0.1.1 dated 2019-10-30 and 0.2.0 dated 2020-12-08
DESCRIPTION | 12 MD5 | 34 - NAMESPACE | 35 - R/RcppExports.R | 22 R/bayes_lm.R | 418 +++++++++++------- R/credint.R |only R/fit_mems.R | 3 R/pate.R | 711 +++++++++++++++--------------- R/utils.R | 6 R/wbart.R | 246 +++++----- README.md | 23 build/vignette.rds |binary inst/doc/borrowr-package.R | 82 +-- inst/doc/borrowr-package.Rmd | 182 +++---- inst/doc/borrowr-package.html | 972 +++++++++++++++++++++--------------------- man/adapt.Rd | 66 +- man/credint.Rd |only man/pate.Rd | 315 +++++++------ vignettes/borrowr-package.Rmd | 182 +++---- 19 files changed, 1744 insertions(+), 1565 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-13 0.2.0
2017-05-16 0.1.3
2016-09-11 0.1.1
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>,
chapter 6.
Author: Mark van der Loo [cre, aut] (<https://orcid.org/0000-0002-9807-4686>),
Edwin de Jonge [aut] (<https://orcid.org/0000-0002-6580-4718>),
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.9.3 dated 2019-12-16 and 1.0.1 dated 2020-12-08
validate-0.9.3/validate/R/barplot.R |only validate-0.9.3/validate/inst/doc/indicators.R |only validate-0.9.3/validate/inst/doc/indicators.Rmd |only validate-0.9.3/validate/inst/doc/indicators.html |only validate-0.9.3/validate/inst/doc/introduction.R |only validate-0.9.3/validate/inst/doc/introduction.Rmd |only validate-0.9.3/validate/inst/doc/introduction.html |only validate-0.9.3/validate/inst/doc/rule_files.R |only validate-0.9.3/validate/inst/doc/rule_files.Rmd |only validate-0.9.3/validate/inst/doc/rule_files.html |only validate-0.9.3/validate/inst/tinytest/test_gh_issue_91.R |only validate-0.9.3/validate/inst/tinytest/test_gh_issue_92.R |only validate-0.9.3/validate/inst/tinytest/test_gh_issue_98.R |only validate-0.9.3/validate/vignettes/indicators.Rmd |only validate-0.9.3/validate/vignettes/introduction.Rmd |only validate-0.9.3/validate/vignettes/rule_files.Rmd |only validate-1.0.1/validate/DESCRIPTION | 20 - validate-1.0.1/validate/MD5 | 141 +++++++------ validate-1.0.1/validate/NAMESPACE | 35 +++ validate-1.0.1/validate/NEWS | 47 ++++ validate-1.0.1/validate/R/confrontation.R | 74 +++++- validate-1.0.1/validate/R/expressionset.R | 6 validate-1.0.1/validate/R/genericrules.R |only validate-1.0.1/validate/R/indicator.R | 67 +++++- validate-1.0.1/validate/R/parse.R | 17 + validate-1.0.1/validate/R/plot.R |only validate-1.0.1/validate/R/retailers.R | 86 +++++++ validate-1.0.1/validate/R/rule.R | 2 validate-1.0.1/validate/R/syntax.R | 40 ++- validate-1.0.1/validate/R/utils.R | 83 +++++++ validate-1.0.1/validate/R/validate_pkg.R | 5 validate-1.0.1/validate/R/validator.R | 2 validate-1.0.1/validate/build/vignette.rds |binary validate-1.0.1/validate/data/nace_rev2.csv.gz |only validate-1.0.1/validate/data/samplonomy.RData |only validate-1.0.1/validate/inst/doc/JSS_3483.pdf |binary validate-1.0.1/validate/inst/doc/cookbook.R |only validate-1.0.1/validate/inst/doc/cookbook.Rmd |only validate-1.0.1/validate/inst/doc/cookbook.html |only validate-1.0.1/validate/inst/tinytest/test_genericrules.R |only validate-1.0.1/validate/inst/tinytest/test_gh_issue_091.R |only validate-1.0.1/validate/inst/tinytest/test_gh_issue_092.R |only validate-1.0.1/validate/inst/tinytest/test_gh_issue_098.R |only validate-1.0.1/validate/inst/tinytest/test_gh_issue_116.R |only validate-1.0.1/validate/inst/tinytest/test_indicator.R | 26 ++ validate-1.0.1/validate/inst/tinytest/test_methods.R | 8 validate-1.0.1/validate/inst/tinytest/test_parse.R | 5 validate-1.0.1/validate/inst/tinytest/test_syntax.R | 7 validate-1.0.1/validate/inst/tinytest/test_utils.R | 36 +++ validate-1.0.1/validate/man/add_indicators.Rd |only validate-1.0.1/validate/man/aggregate-validation-method.Rd | 1 validate-1.0.1/validate/man/all-validation-method.Rd | 1 validate-1.0.1/validate/man/any-validation-method.Rd | 1 validate-1.0.1/validate/man/barplot-validation-method.Rd | 3 validate-1.0.1/validate/man/check_that.Rd | 1 validate-1.0.1/validate/man/compare.Rd | 1 validate-1.0.1/validate/man/confront.Rd | 1 validate-1.0.1/validate/man/contains_exactly.Rd |only validate-1.0.1/validate/man/do_by.Rd |only validate-1.0.1/validate/man/event.Rd | 1 validate-1.0.1/validate/man/exists_any.Rd | 12 - validate-1.0.1/validate/man/field_format.Rd |only validate-1.0.1/validate/man/field_length.Rd |only validate-1.0.1/validate/man/hb.Rd |only validate-1.0.1/validate/man/hierarchy.Rd |only validate-1.0.1/validate/man/in_range.Rd |only validate-1.0.1/validate/man/indicator-class.Rd | 6 validate-1.0.1/validate/man/indicator.Rd | 9 validate-1.0.1/validate/man/is_complete.Rd | 7 validate-1.0.1/validate/man/is_linear_sequence.Rd |only validate-1.0.1/validate/man/is_unique.Rd | 14 + validate-1.0.1/validate/man/lbj_cells-class.Rd | 4 validate-1.0.1/validate/man/nace_rev2.Rd |only validate-1.0.1/validate/man/names.Rd | 23 ++ validate-1.0.1/validate/man/number_format.Rd |only validate-1.0.1/validate/man/part_whole_relation.Rd |only validate-1.0.1/validate/man/plot-validation-method.Rd | 39 +++ validate-1.0.1/validate/man/retailers.Rd | 10 validate-1.0.1/validate/man/rx.Rd |only validate-1.0.1/validate/man/samplonomy.Rd |only validate-1.0.1/validate/man/satisfying.Rd |only validate-1.0.1/validate/man/sort-validation-method.Rd | 1 validate-1.0.1/validate/man/syntax.Rd | 2 validate-1.0.1/validate/man/validate-summary.Rd | 1 validate-1.0.1/validate/man/validate.Rd | 7 validate-1.0.1/validate/man/validation-class.Rd | 1 validate-1.0.1/validate/man/values.Rd | 1 validate-1.0.1/validate/tests/testthat |only validate-1.0.1/validate/vignettes/chunk_opts.R |only validate-1.0.1/validate/vignettes/clean_supermarkets.R |only validate-1.0.1/validate/vignettes/clean_supermarkets2.R |only validate-1.0.1/validate/vignettes/cookbook.Rmd |only validate-1.0.1/validate/vignettes/fig |only validate-1.0.1/validate/vignettes/jss3483.pdf |binary validate-1.0.1/validate/vignettes/myrules.R |only validate-1.0.1/validate/vignettes/myrules.yaml |only 96 files changed, 698 insertions(+), 156 deletions(-)
Title: Multilingual Stopword Lists
Description: Provides multiple sources of stopwords, for use in text analysis and natural language processing.
Author: Kenneth Benoit [aut, cre],
David Muhr [aut],
Kohei Watanabe [aut]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between stopwords versions 2.0 dated 2020-04-14 and 2.1 dated 2020-12-08
DESCRIPTION | 8 +- LICENSE | 4 - MD5 | 33 ++++---- NEWS.md | 11 ++ R/data.r | 37 +++++++-- R/stopwords-options.R | 3 README.md | 150 ++++++++++++++++++++-------------------- build |only data/data_stopwords_ancient.rda |binary data/data_stopwords_marimo.rda |binary data/data_stopwords_perseus.rda |only inst/WORDLIST | 25 +++--- man/data_stopwords_ancient.Rd | 18 +++- man/data_stopwords_marimo.Rd | 2 man/data_stopwords_misc.Rd | 2 man/data_stopwords_perseus.Rd |only man/data_stopwords_smart.Rd | 2 man/data_stopwords_snowball.Rd | 2 tests/testthat/test-stopwords.R | 6 + 19 files changed, 175 insertions(+), 128 deletions(-)
Title: Expressions and Dataframes with Statistical Details
Description: Statistical processing backend for 'ggstatsplot',
this package creates expressions with details from statistical tests.
It can additionally return dataframes with these results, which also
make these functions a more pipe-friendly way to do statistical
analysis. Currently, it supports only the most common types of
statistical tests: parametric, nonparametric, robust, and Bayesian
versions of t-test/ANOVA, correlation analyses, contingency table
analysis, and meta-analysis.
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 0.6.1 dated 2020-12-01 and 0.6.2 dated 2020-12-08
DESCRIPTION | 13 +- MD5 | 56 ++++----- NAMESPACE | 5 NEWS.md | 16 ++ R/helpers_anova.R | 72 +++--------- R/helpers_contingency_tabs.R | 15 +- R/helpers_correlation.R | 13 -- R/helpers_miscellaneous.R | 11 + R/helpers_t_onesample.R | 43 +++---- R/helpers_t_test.R | 46 +++---- README.md | 6 - inst/doc/stats_details.html | 4 man/expr_anova_nonparametric.Rd | 7 - man/expr_anova_robust.Rd | 7 - man/expr_contingency_tab.Rd | 2 man/figures/README-corr-1.png |binary man/reexports.Rd | 2 tests/testthat/test-expr_anova_nonparametric.R | 17 +- tests/testthat/test-expr_anova_parametric.R | 131 ++++++++++------------ tests/testthat/test-expr_anova_robust.R | 13 -- tests/testthat/test-expr_contingency_tab.R | 26 ++-- tests/testthat/test-expr_corr_test.R | 8 - tests/testthat/test-expr_meta_random_parametric.R | 2 tests/testthat/test-expr_meta_random_robust.R | 2 tests/testthat/test-expr_t_nonparametric.R | 7 - tests/testthat/test-expr_t_onesample.R | 25 +--- tests/testthat/test-expr_t_parametric.R | 15 +- tests/testthat/test-expr_t_robust.R | 20 +-- tests/testthat/test-expr_templates.R | 6 - 29 files changed, 268 insertions(+), 322 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Staged Event Trees
Description: Creates and fits staged event tree probability models,
which are probabilistic graphical models capable of representing
asymmetric conditional independence statements
for categorical variables.
Includes functions to create, plot and fit staged
event trees from data, as well as many efficient structure
learning algorithms.
References:
Collazo R. A., Görgen C. and Smith J. Q.
(2018, ISBN:9781498729604).
Görgen C., Bigatti A., Riccomagno E. and Smith J. Q. (2018)
<arXiv:1705.09457>.
Thwaites P. A., Smith, J. Q. (2017) <arXiv:1510.00186>.
Barclay L. M., Hutton J. L. and Smith J. Q. (2013)
<doi:10.1016/j.ijar.2013.05.006>.
Smith J. Q. and Anderson P. E. (2008)
<doi:10.1016/j.artint.2007.05.004>.
Author: Gherardo Varando [aut, cre] (<https://orcid.org/0000-0002-6708-1103>),
Federico Carli [aut],
Manuele Leonelli [aut] (<https://orcid.org/0000-0002-2562-5192>),
Eva Riccomagno [aut]
Maintainer: Gherardo Varando <gherardo.varando@gmail.com>
Diff between stagedtrees versions 2.0.0 dated 2020-10-29 and 2.0.1 dated 2020-12-08
DESCRIPTION | 6 +- MD5 | 18 +++--- NEWS.md | 4 + R/2-plot-functions.R | 4 + README.md | 88 +++++++++++++++--------------- man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary 10 files changed, 65 insertions(+), 55 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized maximum likelihood estimators for precision matrices and supporting functions to employ these estimators in a graphical modeling setting. For details see van Wieringen & Peeters (2016) <doi:10.1016/j.csda.2016.05.012> and associated publications.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.2.3 dated 2020-08-28 and 2.2.4 dated 2020-12-08
rags2ridges-2.2.3/rags2ridges/man/armaRidgeP.Rd |only rags2ridges-2.2.4/rags2ridges/DESCRIPTION | 8 rags2ridges-2.2.4/rags2ridges/MD5 | 148 rags2ridges-2.2.4/rags2ridges/NAMESPACE | 174 rags2ridges-2.2.4/rags2ridges/R/RcppExports.R | 300 - rags2ridges-2.2.4/rags2ridges/R/rags2ridges-package.R |only rags2ridges-2.2.4/rags2ridges/R/rags2ridges.R | 2889 +++++++--- rags2ridges-2.2.4/rags2ridges/R/rags2ridgesDepr.R | 275 rags2ridges-2.2.4/rags2ridges/R/rags2ridgesFused.R | 1459 +++-- rags2ridges-2.2.4/rags2ridges/R/rags2ridgesVariants.r | 505 + rags2ridges-2.2.4/rags2ridges/R/ridgeP-methods.R |only rags2ridges-2.2.4/rags2ridges/README.md | 4 rags2ridges-2.2.4/rags2ridges/inst/NEWS.Rd | 10 rags2ridges-2.2.4/rags2ridges/man/ADdata.Rd | 44 rags2ridges-2.2.4/rags2ridges/man/CNplot.Rd | 253 rags2ridges-2.2.4/rags2ridges/man/Communities.Rd | 160 rags2ridges-2.2.4/rags2ridges/man/DiffGraph.Rd | 168 rags2ridges-2.2.4/rags2ridges/man/GGMblockNullPenalty.Rd | 133 rags2ridges-2.2.4/rags2ridges/man/GGMblockTest.Rd | 190 rags2ridges-2.2.4/rags2ridges/man/GGMmutualInfo.Rd | 44 rags2ridges-2.2.4/rags2ridges/man/GGMnetworkStats.Rd | 97 rags2ridges-2.2.4/rags2ridges/man/GGMnetworkStats.fused.Rd | 37 rags2ridges-2.2.4/rags2ridges/man/GGMpathStats.Rd | 326 - rags2ridges-2.2.4/rags2ridges/man/GGMpathStats.fused.Rd | 40 rags2ridges-2.2.4/rags2ridges/man/KLdiv.Rd | 112 rags2ridges-2.2.4/rags2ridges/man/KLdiv.fused.Rd | 83 rags2ridges-2.2.4/rags2ridges/man/NLL.Rd | 54 rags2ridges-2.2.4/rags2ridges/man/Ugraph.Rd | 270 rags2ridges-2.2.4/rags2ridges/man/Union.Rd | 50 rags2ridges-2.2.4/rags2ridges/man/adjacentMat.Rd | 37 rags2ridges-2.2.4/rags2ridges/man/conditionNumberPlot.Rd | 138 rags2ridges-2.2.4/rags2ridges/man/covML.Rd | 51 rags2ridges-2.2.4/rags2ridges/man/covMLknown.Rd | 91 rags2ridges-2.2.4/rags2ridges/man/createS.Rd | 199 rags2ridges-2.2.4/rags2ridges/man/default.penalty.Rd | 120 rags2ridges-2.2.4/rags2ridges/man/default.target.Rd | 110 rags2ridges-2.2.4/rags2ridges/man/default.target.fused.Rd | 65 rags2ridges-2.2.4/rags2ridges/man/dot-armaRidgeP.Rd |only rags2ridges-2.2.4/rags2ridges/man/edgeHeat.Rd | 117 rags2ridges-2.2.4/rags2ridges/man/evaluateS.Rd | 67 rags2ridges-2.2.4/rags2ridges/man/evaluateSfit.Rd | 97 rags2ridges-2.2.4/rags2ridges/man/fullMontyS.Rd | 141 rags2ridges-2.2.4/rags2ridges/man/fused.test.Rd | 98 rags2ridges-2.2.4/rags2ridges/man/getKEGGPathway.Rd | 61 rags2ridges-2.2.4/rags2ridges/man/is.Xlist.Rd | 66 rags2ridges-2.2.4/rags2ridges/man/isSymmetricPD.Rd | 60 rags2ridges-2.2.4/rags2ridges/man/kegg.target.Rd | 101 rags2ridges-2.2.4/rags2ridges/man/loss.Rd | 100 rags2ridges-2.2.4/rags2ridges/man/momentS.Rd | 52 rags2ridges-2.2.4/rags2ridges/man/optPenalty.LOOCV.Rd | 157 rags2ridges-2.2.4/rags2ridges/man/optPenalty.LOOCVauto.Rd | 137 rags2ridges-2.2.4/rags2ridges/man/optPenalty.aLOOCV.Rd | 199 rags2ridges-2.2.4/rags2ridges/man/optPenalty.fused.Rd | 288 rags2ridges-2.2.4/rags2ridges/man/optPenalty.kCV.Rd | 164 rags2ridges-2.2.4/rags2ridges/man/optPenalty.kCVauto.Rd | 143 rags2ridges-2.2.4/rags2ridges/man/optPenaltyPchordal.Rd | 116 rags2ridges-2.2.4/rags2ridges/man/pcor.Rd | 48 rags2ridges-2.2.4/rags2ridges/man/plot.ptest.Rd | 67 rags2ridges-2.2.4/rags2ridges/man/pooledS.Rd | 68 rags2ridges-2.2.4/rags2ridges/man/print.optPenaltyFusedGrid.Rd | 74 rags2ridges-2.2.4/rags2ridges/man/print.ptest.Rd | 57 rags2ridges-2.2.4/rags2ridges/man/pruneMatrix.Rd | 24 rags2ridges-2.2.4/rags2ridges/man/rags2ridges-package.Rd | 251 rags2ridges-2.2.4/rags2ridges/man/ridgeP.Rd | 188 rags2ridges-2.2.4/rags2ridges/man/ridgeP.fused.Rd | 166 rags2ridges-2.2.4/rags2ridges/man/ridgePathS.Rd | 140 rags2ridges-2.2.4/rags2ridges/man/ridgePchordal.Rd | 212 rags2ridges-2.2.4/rags2ridges/man/ridgePsign.Rd | 90 rags2ridges-2.2.4/rags2ridges/man/ridgeS.Rd | 50 rags2ridges-2.2.4/rags2ridges/man/rmvnormal.Rd | 37 rags2ridges-2.2.4/rags2ridges/man/sparsify.Rd | 155 rags2ridges-2.2.4/rags2ridges/man/sparsify.fused.Rd | 45 rags2ridges-2.2.4/rags2ridges/man/support4ridgeP.Rd | 81 rags2ridges-2.2.4/rags2ridges/man/symm.Rd | 36 rags2ridges-2.2.4/rags2ridges/src/rags2ridges.cpp | 264 rags2ridges-2.2.4/rags2ridges/tests/testthat/helper-P_alt_ref.R |only rags2ridges-2.2.4/rags2ridges/tests/testthat/helper-P_archII_ref.R |only rags2ridges-2.2.4/rags2ridges/tests/testthat/helper-P_archI_ref.R |only rags2ridges-2.2.4/rags2ridges/tests/testthat/test-ridgeP.R |only 79 files changed, 8565 insertions(+), 4296 deletions(-)
Title: Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Description: Fit survival data and perform dynamic prediction under joint frailty-copula models for tumour progression and death.
Likelihood-based methods are employed for estimating model parameters, where the baseline hazard functions are modeled by the cubic M-spline or the Weibull model.
The methods are applicable for meta-analytic data containing individual-patient information from several studies.
Survival outcomes need information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
Methodologies were published in
Emura et al. (2017) <doi:10.1177/0962280215604510>, Emura et al. (2018) <doi:10.1177/0962280216688032>,
Emura et al. (2020) <doi:10.1177/0962280219892295>, Shinohara et al. (2020) <doi:10.1080/03610918.2020.1855449>
and Wu et al. (2020) <doi:10.1007/s00180-020-00977-1>.
See also the book of Emura et al. (2019) <doi:10.1007/978-981-13-3516-7>.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 3.9 dated 2020-11-04 and 3.10 dated 2020-12-08
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- R/condCox.reg.R | 7 ++++--- man/F.window.Weibull.Rd | 3 +++ man/F.windows.Weibull.Rd | 3 +++ man/condCox.reg.Rd | 4 +++- man/dataOvarian.Rd | 7 ++++--- man/joint.Cox-package.Rd | 12 ++++++++---- 8 files changed, 38 insertions(+), 23 deletions(-)
Title: Markov Models for Health Economic Evaluations
Description: An implementation of the modelling and reporting features described
in reference textbook and guidelines (Briggs, Andrew, et al. Decision
Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011;
Siebert, U. et al. State-Transition Modeling. Medical Decision Making
32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis,
heterogeneity analysis, time dependency on state-time and model-time
(semi-Markov and non-homogeneous Markov models), etc.
Author: Kevin Zarca [aut, cre],
Antoine Filipovic-Pierucci [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb],
Jordan Amdahl [ctb],
Yonatan Carranza Alarcon [ctb],
Vince Daniels [ctb]
Maintainer: Kevin Zarca <kevin.zarca@gmail.com>
Diff between heemod versions 0.13.0 dated 2020-05-11 and 0.14.0 dated 2020-12-08
DESCRIPTION | 8 MD5 | 121 +++--- NEWS.md | 8 R/correct_counts.R | 6 R/resamp_eval.R | 4 R/run_model_define.R | 9 R/strategy_eval.R | 13 R/tabular_input.R | 9 README.md | 4 build/vignette.rds |binary inst/doc/a_introduction.html | 200 +++++++---- inst/doc/b_time_dependency.html | 140 +++++-- inst/doc/c_homogeneous.Rmd | 2 inst/doc/c_homogeneous.html | 314 ++++++++++------- inst/doc/d_non_homogeneous.html | 388 +++++++++++++-------- inst/doc/e_probabilistic.html | 426 ++++++++++++++---------- inst/doc/f_sensitivity.html | 184 +++++++--- inst/doc/g_heterogeneity.R | 2 inst/doc/g_heterogeneity.Rmd | 2 inst/doc/g_heterogeneity.html | 290 ++++++++++------ inst/doc/h_tabular.html | 147 ++++++-- inst/doc/i_reproduction.R | 4 inst/doc/i_reproduction.Rmd | 6 inst/doc/i_reproduction.html | 585 ++++++++++++++++++--------------- inst/doc/j_survival.html | 374 ++++++++++++--------- inst/doc/k_calibration.R | 2 inst/doc/k_calibration.Rmd | 2 inst/doc/k_calibration.html | 168 ++++++--- inst/tabular/thr/THR_options.csv | 4 inst/tabular/thr/THR_options_2core.csv | 2 inst/tabular/thr/output |only man/calibrate_model.Rd | 4 man/cluster.Rd | 2 man/create_states_from_tabular.Rd | 4 man/define_parameters.Rd | 2 man/eval_resample.Rd | 2 man/reexports.Rd | 2 man/run_model.Rd | 8 man/run_model_tabular.Rd | 5 man/run_psa.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_calibration.R | 4 tests/testthat/test_dmhee.R | 4 tests/testthat/test_heterogeneity.R | 4 tests/testthat/test_matrix.R | 2 tests/testthat/test_model.R | 26 - tests/testthat/test_probabilistic.R | 4 tests/testthat/test_run_model.R | 14 tests/testthat/test_sensitivity.R | 2 tests/testthat/test_starting_values.R | 7 tests/testthat/test_tabular_input.R | 6 vignettes/c_homogeneous.Rmd | 2 vignettes/g_heterogeneity.Rmd | 2 vignettes/i_reproduction.Rmd | 6 vignettes/k_calibration.Rmd | 2 55 files changed, 2173 insertions(+), 1367 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word' and 'Microsoft PowerPoint'
documents from 'R Markdown'. Functions are provided to let users create tables, modify and format
their content. It also extends package 'officer' that does not contain any feature for customized
tabular reporting.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb],
Michael Barrowman [ctb] (inline footnotes),
Atsushi Yasumoto [ctb] (support for bookdown cross reference)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.6.0 dated 2020-12-01 and 0.6.1 dated 2020-12-08
flextable-0.6.0/flextable/R/defunct.R |only flextable-0.6.0/flextable/inst/web_1.0.0/tabwid.js |only flextable-0.6.0/flextable/man/docx_value.Rd |only flextable-0.6.0/flextable/man/flextable-defunct.Rd |only flextable-0.6.1/flextable/DESCRIPTION | 10 flextable-0.6.1/flextable/MD5 | 44 flextable-0.6.1/flextable/NAMESPACE | 8 flextable-0.6.1/flextable/NEWS.md | 18 flextable-0.6.1/flextable/R/chunk_images.R | 4 flextable-0.6.1/flextable/R/formatters.R | 79 flextable-0.6.1/flextable/R/html_str.R | 39 flextable-0.6.1/flextable/R/latex_chunks.R | 3 flextable-0.6.1/flextable/R/latex_str.R | 2 flextable-0.6.1/flextable/R/printers.R | 97 flextable-0.6.1/flextable/inst/doc/display.html | 864 +++++ flextable-0.6.1/flextable/inst/doc/format.html | 1512 +++++++++- flextable-0.6.1/flextable/inst/doc/layout.html | 1188 +++++++ flextable-0.6.1/flextable/inst/doc/overview.html | 378 ++ flextable-0.6.1/flextable/inst/doc/selectors.html | 486 ++- flextable-0.6.1/flextable/inst/examples/rmd/captions_example.Rmd | 2 flextable-0.6.1/flextable/inst/flextablelogo.svg | 48 flextable-0.6.1/flextable/inst/web_1.0.0/tabwid.css | 59 flextable-0.6.1/flextable/man/figures/logo.png |binary flextable-0.6.1/flextable/man/knit_print.flextable.Rd | 11 flextable-0.6.1/flextable/tests/testthat/test-text.R | 8 25 files changed, 4362 insertions(+), 498 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb],
Xianying Tan [ctb],
Rick Saporta [ctb],
Otto Seiskari [ctb],
Xianghui Dong [ctb],
Michel Lang [ctb],
Watal Iwasaki [ctb],
Seth Wenchel [ctb],
Karl Broman [ctb],
Tobias Schmidt [ctb],
David Arenburg [ctb],
Ethan Smith [ctb],
Francois Cocquemas [ctb],
Matthieu Gomez [ctb],
Philippe Chataignon [ctb],
Nello Blaser [ctb],
Dmitry Selivanov [ctb],
Andrey Riabushenko [ctb],
Cheng Lee [ctb],
Declan Groves [ctb],
Daniel Possenriede [ctb],
Felipe Parages [ctb],
Denes Toth [ctb],
Mus Yaramaz-David [ctb],
Ayappan Perumal [ctb],
James Sams [ctb],
Martin Morgan [ctb],
Michael Quinn [ctb],
@javrucebo [ctb],
@marc-outins [ctb],
Roy Storey [ctb],
Manish Saraswat [ctb],
Morgan Jacob [ctb],
Michael Schubmehl [ctb],
Davis Vaughan [ctb],
Toby Hocking [ctb],
Leonardo Silvestri [ctb],
Tyson Barrett [ctb],
Jim Hester [ctb],
Anthony Damico [ctb],
Sebastian Freundt [ctb],
David Simons [ctb],
Elliott Sales de Andrade [ctb],
Cole Miller [ctb],
Jens Peder Meldgaard [ctb],
Vaclav Tlapak [ctb],
Kevin Ushey [ctb],
Dirk Eddelbuettel [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.13.2 dated 2020-10-19 and 1.13.4 dated 2020-12-08
DESCRIPTION | 12 MD5 | 80 NAMESPACE | 10 NEWS.md | 382 ---- R/data.table.R | 10 R/test.data.table.R | 4 README.md | 5 configure | 5 inst/doc/datatable-benchmarking.html | 297 +-- inst/doc/datatable-faq.html | 881 +++++----- inst/doc/datatable-importing.html | 289 +-- inst/doc/datatable-intro.html | 987 ++++++------ inst/doc/datatable-keys-fast-subset.html | 713 ++++---- inst/doc/datatable-reference-semantics.html | 603 +++---- inst/doc/datatable-reshape.html | 567 +++--- inst/doc/datatable-sd-usage.html | 848 +++++----- inst/doc/datatable-secondary-indices-and-auto-indexing.html | 529 +++--- inst/po/en@quot/LC_MESSAGES/R-data.table.mo |binary inst/po/en@quot/LC_MESSAGES/data.table.mo |binary inst/po/zh_CN/LC_MESSAGES/data.table.mo |binary inst/tests/other.Rraw.bz2 |binary inst/tests/tests-DESCRIPTION | 2 inst/tests/tests.Rraw.bz2 |binary man/fread.Rd | 5 man/fwrite.Rd | 2 po/R-data.table.pot | 4 po/data.table.pot | 748 +++++---- po/zh_CN.po | 819 +++++---- src/Makevars.in | 2 src/assign.c | 2 src/data.table.h | 2 src/fifelse.c | 42 src/forder.c | 4 src/fsort.c | 189 +- src/fwrite.c | 70 src/init.c | 10 src/myomp.h | 9 src/nafill.c | 2 src/openmp-utils.c | 2 src/snprintf.c | 39 src/utils.c | 7 41 files changed, 4234 insertions(+), 3948 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 1.2-3 dated 2020-10-14 and 1.2-4 dated 2020-12-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plotEstimator.R | 23 ++++++++++++++--------- inst/doc/BayesSUR.pdf |binary man/plotEstimator.Rd | 14 +++++++------- 5 files changed, 29 insertions(+), 24 deletions(-)
Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including likelihood ratios
for relationship testing, general relatedness inference, marker simulation, and
power analysis. General computation of exclusion powers is based on Egeland et
al. (2014) <doi:10.1016/j.fsigen.2013.05.001>. Several functions deal
specifically with family reunion cases, implementing and developing ideas from
Kling et al. (2017) <doi:10.1016/j.fsigen.2017.08.006>. A novelty of 'forrel'
is the ability to model background inbreeding in forensic pedigree computations.
This can have significant impact in applications, as exemplified in Vigeland
and Egeland (2019) <doi:10.1016/j.fsigss.2019.10.175>. 'forrel' is part of the
ped suite, a collection of packages for pedigree analysis. In particular,
'forrel' imports 'pedtools' for creating and manipulating pedigrees and markers,
'pedprobr' for likelihood computations, and 'pedmut' for mutation modelling.
Pedigree data may be created from scratch, or loaded from text files. Data
import from the 'Familias' software (Egeland et al. (2000)
<doi:10.1016/S0379-0738(00)00147-X>) is supported.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>),
Egeland Thore [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between forrel versions 1.1.0 dated 2020-11-13 and 1.2.0 dated 2020-12-08
DESCRIPTION | 10 MD5 | 68 +++--- NAMESPACE | 3 NEWS.md | 24 +- R/MPPsims.R | 6 R/exclusionPower.R | 40 +-- R/ibdEstim.R | 46 ++-- R/kappaBootstrap.R |only R/kinshipLR.R | 45 +++- R/markerSim.R | 4 R/missingPersonEP.R | 37 +-- R/missingPersonIP.R | 4 R/missingPersonPlot.R | 14 - R/pairwiseSim.R | 60 +++-- R/randomPersonEP.R |only R/utils.R | 2 build/partial.rdb |binary man/Familias2ped.Rd | 160 +++++++------- man/MPPsims.Rd | 264 ++++++++++++------------ man/exclusionPower.Rd | 363 ++++++++++++++++----------------- man/ibdEstim.Rd | 215 +++++++++---------- man/kappaBootstrap.Rd |only man/kinshipLR.Rd | 23 +- man/markerSimParametric.Rd | 169 +++++++-------- man/missingPersonEP.Rd | 28 +- man/missingPersonIP.Rd | 4 man/missingPersonLR.Rd | 134 ++++++------ man/missingPersonPlot.Rd | 4 man/profileSimParametric.Rd | 96 ++++---- man/randomPersonEP.Rd |only tests/testthat/test-exclusion.R | 1 tests/testthat/test-familias.R | 1 tests/testthat/test-inbred-founders.R | 1 tests/testthat/test-kinshipLR-merlin.R | 6 tests/testthat/test-kinshipLR.R | 1 tests/testthat/test-sims.R | 1 tests/testthat/test-utils.R | 2 37 files changed, 947 insertions(+), 889 deletions(-)
Title: Tidy Wrapper for 'BayesFactor' Package
Description: Provides helper functions that make it easy to run
'BayesFactor' package tests on a data which is in a tidy format.
Additionally, it provides a more consistent syntax and by default
returns a dataframe with rich details. These functions can also return
expressions containing results from Bayes Factor tests that can then
be displayed on custom plots. Posterior estimation is carried out using
the 'bayestestR' package.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between tidyBF versions 0.4.0 dated 2020-10-30 and 0.4.2 dated 2020-12-08
tidyBF-0.4.0/tidyBF/R/bf_oneway_anova.R |only tidyBF-0.4.0/tidyBF/man/bf_oneway_anova.Rd |only tidyBF-0.4.0/tidyBF/man/meta_data_check.Rd |only tidyBF-0.4.2/tidyBF/DESCRIPTION | 19 +- tidyBF-0.4.2/tidyBF/MD5 | 58 +++--- tidyBF-0.4.2/tidyBF/NAMESPACE | 14 - tidyBF-0.4.2/tidyBF/NEWS.md | 37 ++-- tidyBF-0.4.2/tidyBF/R/bf_contingency_tab.R | 67 ++----- tidyBF-0.4.2/tidyBF/R/bf_corr_test.R | 8 tidyBF-0.4.2/tidyBF/R/bf_expr_template.R | 5 tidyBF-0.4.2/tidyBF/R/bf_meta_random.R | 20 -- tidyBF-0.4.2/tidyBF/R/bf_ttest.R | 100 ++++++++--- tidyBF-0.4.2/tidyBF/R/global_vars.R | 3 tidyBF-0.4.2/tidyBF/R/helpers_bf_tests.R | 63 +----- tidyBF-0.4.2/tidyBF/R/reexports.R | 18 - tidyBF-0.4.2/tidyBF/README.md | 71 +++++-- tidyBF-0.4.2/tidyBF/inst/CITATION | 1 tidyBF-0.4.2/tidyBF/man/bf_contingency_tab.Rd | 10 - tidyBF-0.4.2/tidyBF/man/bf_corr_test.Rd | 10 - tidyBF-0.4.2/tidyBF/man/bf_expr_template.Rd | 8 tidyBF-0.4.2/tidyBF/man/bf_extractor.Rd | 10 - tidyBF-0.4.2/tidyBF/man/bf_meta_random.Rd | 26 -- tidyBF-0.4.2/tidyBF/man/bf_ttest.Rd | 59 +++++- tidyBF-0.4.2/tidyBF/man/figures/README-expr_plot5-1.png |binary tidyBF-0.4.2/tidyBF/man/reexports.Rd | 8 tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_contingency_tab.R | 38 +++- tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_corr_test.R | 2 tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_extractor.R | 4 tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_meta_random.R | 16 - tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_oneway_anova.R | 51 ----- tidyBF-0.4.2/tidyBF/tests/testthat/test-bf_ttest.R | 8 tidyBF-0.4.2/tidyBF/tests/testthat/test-loop_execution.R |only 32 files changed, 365 insertions(+), 369 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see support list of insight; Lüdecke,
Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), this package
implements features like bootstrapping or simulating of parameters and
models, feature reduction (feature extraction and variable selection)
as well as functions to describe data and variable characteristics
(e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Søren Højsgaard [aut],
Zen J. Lau [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.10.0 dated 2020-12-01 and 0.10.1 dated 2020-12-08
DESCRIPTION | 21 MD5 | 131 +++--- NAMESPACE | 1 NEWS.md | 18 R/ci.R | 2 R/ci_betwithin.R | 20 R/cluster_analysis.R | 4 R/dof.R | 2 R/extract_parameters.R | 181 +++++++- R/format.R | 5 R/format_p_adjust.R |only R/get_scores.R | 108 ++--- R/model_parameters.BFBayesFactor.R | 2 R/model_parameters.aov.R | 21 R/model_parameters.bayesian.R | 20 R/model_parameters.emmGrid.R | 4 R/model_parameters.gam.R | 10 R/model_parameters.htest.R | 10 R/model_parameters.lavaan.R | 6 R/model_parameters.lqmm.R | 12 R/model_parameters.multinom.R | 37 + R/model_parameters.zeroinfl.R | 30 - R/model_parameters_default.R | 40 + R/model_parameters_mixed.R | 60 +- R/p_value.R | 4 R/print.parameters_model.R | 146 ++++-- R/print_md.R | 29 + R/utils_model_parameters.R | 13 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 10 inst/doc/demean.R | 13 inst/doc/demean.Rmd | 13 inst/doc/demean.html | 493 +++++++++++------------ inst/doc/efa_cfa.html | 116 ++--- inst/doc/model_parameters.html | 338 +++++++-------- inst/doc/model_parameters_formatting.html | 86 ++-- inst/doc/model_parameters_mice.html | 102 ++-- inst/doc/model_parameters_robust.html | 150 +++--- inst/doc/model_parameters_standardized.html | 48 +- inst/doc/parameters_reduction.html | 46 +- inst/doc/parameters_selection.html | 44 +- man/check_kmo.Rd | 76 +-- man/check_sphericity.Rd | 64 +- man/cluster_discrimination.Rd | 60 +- man/display.parameters_model.Rd | 286 ++++++------- man/format_p_adjust.Rd |only man/get_scores.Rd | 88 ++-- man/model_parameters.aov.Rd | 4 man/model_parameters.merMod.Rd | 1 man/model_parameters.mlm.Rd | 13 man/p_value.DirichletRegModel.Rd | 60 +- man/p_value.poissonmfx.Rd | 88 ++-- man/p_value_kenward.Rd | 126 ++--- man/p_value_ml1.Rd | 154 +++---- man/p_value_satterthwaite.Rd | 122 ++--- man/random_parameters.Rd | 112 ++--- man/reexports.Rd | 2 man/smoothness.Rd | 68 +-- tests/spelling.R | 9 tests/testthat/test-lavaan.R | 2 tests/testthat/test-mlm.R |only tests/testthat/test-model_parameters.aov_es_ci.R | 16 tests/testthat/test-model_parameters.glm.R | 8 tests/testthat/test-model_parameters.hurdle.R | 24 - tests/testthat/test-model_parameters.maov.R | 36 - tests/testthat/test-parameters_type-2.R | 162 +++---- vignettes/demean.Rmd | 13 68 files changed, 2150 insertions(+), 1840 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'broomExtra', 'ggstatsplot', 'groupedstats',
'pairwiseComparisons', 'statsExpressions', and 'tidyBF'.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 5.0.0 dated 2020-12-07 and 5.0.1 dated 2020-12-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 8 ++++++++ NEWS.md | 5 +++++ R/reexports.R | 18 ++++++++++++++++++ man/reexports.Rd | 6 ++++++ 6 files changed, 46 insertions(+), 9 deletions(-)
Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Create, visualize, manipulate, and analyze bipartite mineral-chemistry
networks for set of focal element(s) across deep-time on Earth. The method is
described in Spielman and Moore (2020) <doi:10.3389/feart.2020.585087>.
Author: Stephanie J. Spielman [aut, cre]
(<https://orcid.org/0000-0002-9090-4788>)
Maintainer: Stephanie J. Spielman <spielman@rowan.edu>
Diff between dragon versions 1.0.5 dated 2020-11-05 and 1.1.0 dated 2020-12-08
dragon-1.0.5/dragon/inst/testdata/edges_by_redox.csv.zip |only dragon-1.0.5/dragon/inst/testdata/graph_by_redox.igraph |only dragon-1.0.5/dragon/inst/testdata/locality_info.csv.zip |only dragon-1.0.5/dragon/inst/testdata/nodes_by_redox.csv.zip |only dragon-1.0.5/dragon/inst/testdata/styled_edges.csv.zip |only dragon-1.0.5/dragon/inst/testdata/styled_nodes.csv.zip |only dragon-1.0.5/dragon/inst/testdata/true_mineral_nodes.csv.zip |only dragon-1.1.0/dragon/DESCRIPTION | 8 dragon-1.1.0/dragon/MD5 | 61 +- dragon-1.1.0/dragon/R/app_server.R | 22 dragon-1.1.0/dragon/R/app_ui.R | 45 + dragon-1.1.0/dragon/R/fct_build-network.R | 127 +++-- dragon-1.1.0/dragon/R/fct_build-shiny-tables.R | 6 dragon-1.1.0/dragon/R/fct_prepare-med-data.R | 16 dragon-1.1.0/dragon/R/fct_timeline.R | 2 dragon-1.1.0/dragon/R/sysdata.rda |binary dragon-1.1.0/dragon/R/utils_definitions.R | 2 dragon-1.1.0/dragon/R/utils_globals.R | 6 dragon-1.1.0/dragon/R/utils_names.R | 10 dragon-1.1.0/dragon/R/utils_ui-choices.R | 32 + dragon-1.1.0/dragon/README.md | 24 dragon-1.1.0/dragon/inst/doc/dragon.R | 2 dragon-1.1.0/dragon/inst/doc/dragon.Rmd | 7 dragon-1.1.0/dragon/inst/doc/dragon.html | 16 dragon-1.1.0/dragon/inst/testdata/prepare_testdata.R | 117 +--- dragon-1.1.0/dragon/man/initialize_network.Rd | 10 dragon-1.1.0/dragon/tests/testthat/edges_by_redox.csv.zip |only dragon-1.1.0/dragon/tests/testthat/graph_by_redox.igraph |only dragon-1.1.0/dragon/tests/testthat/locality_info.csv.zip |only dragon-1.1.0/dragon/tests/testthat/nodes_by_redox.csv.zip |only dragon-1.1.0/dragon/tests/testthat/setup_network-style.R |only dragon-1.1.0/dragon/tests/testthat/setup_test-settings.R | 125 +---- dragon-1.1.0/dragon/tests/testthat/styled_edges.csv.zip |only dragon-1.1.0/dragon/tests/testthat/styled_nodes.csv.zip |only dragon-1.1.0/dragon/tests/testthat/test_build-network.R | 247 +++++++++- dragon-1.1.0/dragon/tests/testthat/test_build-shiny-tables.R | 8 dragon-1.1.0/dragon/tests/testthat/true_mineral_nodes.csv.zip |only dragon-1.1.0/dragon/vignettes/dragon.Rmd | 7 dragon-1.1.0/dragon/vignettes/dragon.bib | 4 39 files changed, 583 insertions(+), 321 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Paul Bailey [aut, cre], Claire Kelley [aut], Trang Nguyen [aut], Huade Huo [aut], Christian Kjeldsen [ctb] (tests with TIMSS data).
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.1.5 dated 2020-09-09 and 3.1.6 dated 2020-12-08
DESCRIPTION | 10 - MD5 | 22 ++-- NAMESPACE | 1 R/adaptiveQuad.R | 60 ++++++----- R/helpers.R | 12 +- build/vignette.rds |binary inst/NEWS.Rd | 12 ++ inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary man/mix.Rd | 21 +++ man/waldTest.Rd | 3 tests/testthat/test-1-main.R | 14 +- 12 files changed, 97 insertions(+), 58 deletions(-)
Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening
Services
Description: Allows using two URL shortening services, which also provide
expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth2) and 'is.gd' (no API key).
Author: John Malc [aut, cre] (@dmpe),
Andrea Dodet [ctb] (@andodet),
Stephen Synchronicity [ctb] (@yogat3ch)
Maintainer: John Malc <cincenko@outlook.com>
Diff between urlshorteneR versions 1.3.0 dated 2020-09-08 and 1.4.3 dated 2020-12-08
DESCRIPTION | 24 - MD5 | 119 ++--- NAMESPACE | 1 NEWS | 5 R/ApiKey.R | 55 +- R/bitly_bsd.R | 2 R/bitly_camp.R | 16 R/bitly_custom_links.R | 8 R/bitly_groups.R | 246 +++++------ R/bitly_links.R | 28 - R/bitly_orgs.R | 6 R/bitly_user_app_info.R | 22 README.md | 27 - build/vignette.rds |binary inst/doc/Tutorial.Rmd | 2 inst/doc/Tutorial.html | 311 ++------------ man/bitly_add_cust_bitlink.Rd | 2 man/bitly_auth.Rd | 10 man/bitly_bsds.Rd | 2 man/bitly_create_bitlink.Rd | 4 man/bitly_create_campaigns.Rd | 2 man/bitly_create_channel.Rd | 2 man/bitly_expand_link.Rd | 2 man/bitly_rate_limits.Rd |only man/bitly_retrieve_bitlink.Rd | 2 man/bitly_retrieve_bitlinks_by_groups.Rd | 8 man/bitly_retrieve_campaign.Rd | 2 man/bitly_retrieve_campaigns.Rd | 2 man/bitly_retrieve_channel.Rd | 2 man/bitly_retrieve_channels.Rd | 2 man/bitly_retrieve_clicks.Rd | 4 man/bitly_retrieve_clicks_summary.Rd | 4 man/bitly_retrieve_cust_bitlink.Rd | 2 man/bitly_retrieve_destination_metrics.Rd | 2 man/bitly_retrieve_group.Rd | 2 man/bitly_retrieve_group_click_metrics_by_countries.Rd | 2 man/bitly_retrieve_group_click_metrics_by_ref_networks.Rd | 2 man/bitly_retrieve_group_pref.Rd | 2 man/bitly_retrieve_group_shorten_counts.Rd | 2 man/bitly_retrieve_groups.Rd | 4 man/bitly_retrieve_links_grouped.Rd | 8 man/bitly_retrieve_metrics_by_countries.Rd | 4 man/bitly_retrieve_metrics_by_referrers.Rd | 4 man/bitly_retrieve_metrics_by_referrers_by_domain.Rd | 6 man/bitly_retrieve_org.Rd | 2 man/bitly_retrieve_org_shorten_counts.Rd | 2 man/bitly_retrieve_orgs.Rd | 2 man/bitly_retrieve_sorted_bitlinks_by_groups.Rd | 4 man/bitly_retrieve_sorted_links.Rd | 6 man/bitly_retrieve_tags.Rd | 2 man/bitly_shorten_link.Rd | 2 man/bitly_update_bitlink.Rd | 2 man/bitly_update_campaign.Rd | 2 man/bitly_update_channel.Rd | 2 man/bitly_update_cust_bitlink.Rd | 2 man/bitly_update_group.Rd | 4 man/bitly_update_group_pref.Rd | 2 man/bitly_update_user.Rd | 2 man/bitly_user_info.Rd | 2 man/bitly_user_metrics_referring_domains.Rd | 6 vignettes/Tutorial.Rmd | 2 61 files changed, 431 insertions(+), 577 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.13.0 dated 2019-04-18 and 2.14.0 dated 2020-12-08
DESCRIPTION | 14 +--- MD5 | 28 ++++---- NAMESPACE | 5 - NEWS | 14 +++- R/FullNameInterface.R | 4 - R/GenericDataFile.R | 2 R/GenericDataFileSet.PARALLEL.R | 8 -- R/TabularTextFile.R | 2 inst/WORDLIST | 101 +++++++++++++++++++++++++++++++ man/ChecksumFileSet.Rd | 2 man/GenericTabularFileSet.Rd | 2 man/RDataFileSet.Rd | 2 man/RdsFileSet.Rd | 2 man/TabularTextFileSet.Rd | 2 man/dsApplyInPairs.GenericDataFileSet.Rd | 22 ------ 15 files changed, 148 insertions(+), 62 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' and 'mlr3proba'
with interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Quay Au [aut] (<https://orcid.org/0000-0002-5252-8902>),
Stefan Coors [aut] (<https://orcid.org/0000-0002-7465-2146>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.4.2 dated 2020-11-11 and 0.4.3 dated 2020-12-08
DESCRIPTION | 11 - MD5 | 139 ++++++++++--------- NAMESPACE | 2 NEWS.md | 19 +- R/LearnerClassifCVGlmnet.R | 9 - R/LearnerClassifGlmnet.R | 8 - R/LearnerClassifKKNN.R | 2 R/LearnerClassifLDA.R | 4 R/LearnerClassifLogReg.R | 9 + R/LearnerClassifMultinom.R | 4 R/LearnerClassifNaiveBayes.R | 4 R/LearnerClassifNnet.R |only R/LearnerClassifQDA.R | 4 R/LearnerClassifRanger.R | 4 R/LearnerClassifSVM.R | 7 - R/LearnerClassifXgboost.R | 4 R/LearnerRegrCVGlmnet.R | 6 R/LearnerRegrGlmnet.R | 8 - R/LearnerRegrKKNN.R | 2 R/LearnerRegrKM.R | 2 R/LearnerRegrLM.R | 4 R/LearnerRegrRanger.R | 4 R/LearnerRegrSVM.R | 7 - R/LearnerRegrXgboost.R | 4 R/LearnerSurvCVGlmnet.R | 6 R/LearnerSurvGlmnet.R | 8 - R/LearnerSurvRanger.R | 20 -- R/LearnerSurvXgboost.R | 4 R/bibentries.R | 209 ++++++++++++++++-------------- R/zzz.R | 8 - README.md | 1 build/partial.rdb |binary man/mlr_learners_classif.cv_glmnet.Rd | 3 man/mlr_learners_classif.glmnet.Rd | 2 man/mlr_learners_classif.kknn.Rd | 10 - man/mlr_learners_classif.log_reg.Rd | 13 + man/mlr_learners_classif.nnet.Rd |only man/mlr_learners_classif.ranger.Rd | 9 - man/mlr_learners_classif.svm.Rd | 3 man/mlr_learners_regr.cv_glmnet.Rd | 2 man/mlr_learners_regr.glmnet.Rd | 4 man/mlr_learners_regr.kknn.Rd | 10 - man/mlr_learners_regr.ranger.Rd | 9 - man/mlr_learners_regr.svm.Rd | 3 man/mlr_learners_surv.cv_glmnet.Rd | 2 man/mlr_learners_surv.glmnet.Rd | 4 man/mlr_learners_surv.ranger.Rd | 9 - tests/testthat/test_classif_cv_glmnet.R | 2 tests/testthat/test_classif_glmnet.R | 2 tests/testthat/test_classif_kknn.R | 4 tests/testthat/test_classif_lda.R | 2 tests/testthat/test_classif_log_reg.R | 2 tests/testthat/test_classif_multinom.R | 2 tests/testthat/test_classif_naive_bayes.R | 2 tests/testthat/test_classif_nnet.R |only tests/testthat/test_classif_qda.R | 2 tests/testthat/test_classif_ranger.R | 2 tests/testthat/test_classif_svm.R | 2 tests/testthat/test_classif_xgboost.R | 2 tests/testthat/test_register.R | 2 tests/testthat/test_regr_cv_glmnet.R | 2 tests/testthat/test_regr_glmnet.R | 2 tests/testthat/test_regr_kknn.R | 4 tests/testthat/test_regr_km.R | 2 tests/testthat/test_regr_lm.R | 2 tests/testthat/test_regr_ranger.R | 2 tests/testthat/test_regr_svm.R | 2 tests/testthat/test_regr_xgboost.R | 2 tests/testthat/test_surv_cv_glmnet.R | 2 tests/testthat/test_surv_glmnet.R | 2 tests/testthat/test_surv_ranger.R | 17 +- tests/testthat/test_surv_xgboost.R | 13 - 72 files changed, 346 insertions(+), 338 deletions(-)
Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods,
statistical summaries and graphics functions for the analysing tidy time
series data. The package name 'feasts' is an acronym comprising of its key
features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Di Cook [ctb],
Thiyanga Talagala [ctb] (Correlation features),
Leanne Chhay [ctb] (Guerrero's method)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between feasts versions 0.1.5 dated 2020-08-27 and 0.1.6 dated 2020-12-08
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 16 + R/acf.R | 2 R/features.R | 2 R/graphics.R | 22 +- R/utils.R | 4 inst/doc/feasts.html | 445 ++++++++++++++++----------------------------------- man/unitroot.Rd | 2 9 files changed, 193 insertions(+), 322 deletions(-)
Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks.
'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
This package offers an R interface to work with it.
It is designed to be distributed and efficient with the following advantages:
1. Faster training speed and higher efficiency.
2. Lower memory usage.
3. Better accuracy.
4. Parallel learning supported.
5. Capable of handling large-scale data.
In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple machines.
Author: Guolin Ke [aut, cre],
Damien Soukhavong [aut],
James Lamb [aut],
Qi Meng [aut],
Thomas Finley [aut],
Taifeng Wang [aut],
Wei Chen [aut],
Weidong Ma [aut],
Qiwei Ye [aut],
Tie-Yan Liu [aut],
Yachen Yan [ctb],
Microsoft Corporation [cph],
Dropbox, Inc. [cph],
Jay Loden [cph],
Dave Daeschler [cph],
Giampaolo Rodola [cph],
IBM Corporation [ctb]
Maintainer: Guolin Ke <guolin.ke@microsoft.com>
Diff between lightgbm versions 3.1.0 dated 2020-11-18 and 3.1.1 dated 2020-12-08
lightgbm-3.1.0/lightgbm/src/application/application.cpp |only lightgbm-3.1.0/lightgbm/src/include/LightGBM/application.h |only lightgbm-3.1.1/lightgbm/DESCRIPTION | 8 lightgbm-3.1.1/lightgbm/MD5 | 68 +-- lightgbm-3.1.1/lightgbm/R/callback.R | 2 lightgbm-3.1.1/lightgbm/R/lgb.Booster.R | 40 + lightgbm-3.1.1/lightgbm/R/lgb.Dataset.R | 137 +++--- lightgbm-3.1.1/lightgbm/R/lgb.Predictor.R | 8 lightgbm-3.1.1/lightgbm/R/lgb.convert_with_rules.R | 8 lightgbm-3.1.1/lightgbm/R/lgb.cv.R | 89 ++-- lightgbm-3.1.1/lightgbm/R/lgb.importance.R | 6 lightgbm-3.1.1/lightgbm/R/lgb.interprete.R | 28 - lightgbm-3.1.1/lightgbm/R/lgb.model.dt.tree.R | 21 lightgbm-3.1.1/lightgbm/R/lgb.plot.interpretation.R | 6 lightgbm-3.1.1/lightgbm/R/lgb.train.R | 19 lightgbm-3.1.1/lightgbm/R/lightgbm.R | 2 lightgbm-3.1.1/lightgbm/R/utils.R | 16 lightgbm-3.1.1/lightgbm/README.md | 159 +------ lightgbm-3.1.1/lightgbm/configure | 18 lightgbm-3.1.1/lightgbm/configure.ac | 2 lightgbm-3.1.1/lightgbm/src/Makevars.in | 1 lightgbm-3.1.1/lightgbm/src/Makevars.win.in | 1 lightgbm-3.1.1/lightgbm/src/boosting/gbdt.cpp | 2 lightgbm-3.1.1/lightgbm/src/c_api.cpp | 215 +++------- lightgbm-3.1.1/lightgbm/src/include/LightGBM/dataset_loader.h | 2 lightgbm-3.1.1/lightgbm/src/include/LightGBM/feature_group.h | 59 ++ lightgbm-3.1.1/lightgbm/src/include/LightGBM/train_share_states.h | 3 lightgbm-3.1.1/lightgbm/src/include/LightGBM/utils/threading.h | 18 lightgbm-3.1.1/lightgbm/src/io/dataset.cpp | 22 - lightgbm-3.1.1/lightgbm/src/io/dataset_loader.cpp | 42 + lightgbm-3.1.1/lightgbm/src/io/train_share_states.cpp | 5 lightgbm-3.1.1/lightgbm/src/objective/binary_objective.hpp | 12 lightgbm-3.1.1/lightgbm/src/objective/regression_objective.hpp | 11 lightgbm-3.1.1/lightgbm/src/objective/xentropy_objective.hpp | 28 - lightgbm-3.1.1/lightgbm/tests/testthat/test_dataset.R | 60 ++ lightgbm-3.1.1/lightgbm/tests/testthat/test_learning_to_rank.R | 8 36 files changed, 577 insertions(+), 549 deletions(-)
Title: Keep Track of User-Defined Environment Names
Description: Set of functions to keep track and find objects in user-defined environments
by identifying environments by name --which cannot be retrieved with the built-in function environmentName().
The package also provides functionality to obtain simplified information about function calling chains
and to get an object's memory address.
Author: Daniel Mastropietro
Maintainer: Daniel Mastropietro <mastropi@uwalumni.com>
Diff between envnames versions 0.4.0 dated 2019-01-04 and 0.4.1 dated 2020-12-08
DESCRIPTION | 21 - MD5 | 94 ++--- build/vignette.rds |binary inst/doc/envnames.R | 94 ++--- inst/doc/envnames.Rmd | 7 inst/doc/envnames.pdf |binary man/address.Rd | 34 +- man/check_environment.Rd | 58 +-- man/check_object_exists.Rd | 68 ++-- man/check_object_with_path.Rd | 96 +++--- man/clean_up_matching_environments.Rd | 64 ++-- man/collapse_root_and_member.Rd | 56 +-- man/crawl_envs.Rd | 102 +++--- man/crawl_envs_in_env.Rd | 38 +- man/destandardize_env_name.Rd | 44 +- man/environment_name.Rd | 262 ++++++++-------- man/extract_root_and_last_member.Rd | 46 +- man/get_env_names.Rd | 182 +++++------ man/get_environment_name.Rd | 42 +- man/get_envs_in_env.Rd | 78 ++-- man/get_fun_calling.Rd | 98 +++--- man/get_fun_calling_chain.Rd | 94 ++--- man/get_fun_env.Rd | 116 +++---- man/get_fun_name.Rd | 74 ++-- man/get_namespace_addresses.Rd | 34 +- man/get_namespace_names.Rd | 42 +- man/get_obj_address.Rd | 231 +++++++------- man/get_obj_addresses_from_obj_names.Rd | 54 +-- man/get_obj_name.Rd | 288 +++++++++--------- man/get_obj_value.Rd | 240 +++++++-------- man/get_objects_in_package.Rd | 38 +- man/get_searchpath_environment_addresses.Rd | 32 +- man/get_user_environment_names_in_env.Rd | 38 +- man/get_user_environment_names_in_search_path.Rd | 42 +- man/get_user_environments_in_user_envs_recursively.Rd | 56 +-- man/is_logical.Rd | 50 +-- man/is_memory_address.Rd | 62 +-- man/is_null_or_na.Rd | 42 +- man/is_string.Rd | 44 +- man/obj_find.Rd | 260 ++++++++-------- man/parse_memory_address.Rd | 48 +-- man/reset_option_warn.Rd | 28 - man/set_option_warn_to_nowarning.Rd | 32 +- man/standardize_env_name.Rd | 52 +-- man/testenv.Rd | 26 - man/unlist_with_names.Rd | 40 +- tests/testthat/test-obj_find.r | 68 +++- vignettes/envnames.Rmd | 7 48 files changed, 1842 insertions(+), 1780 deletions(-)
Title: Analyze Group Patterns using Graph Theory in Educational
Settings
Description: Analyzes group patterns using discourse analysis data with graph theory mathematics. Takes the order of which individuals talk and converts it to a network edge and weight list. Returns the density, centrality, centralization, and subgroup information for each group. Based on the analytical framework laid out in Chai et al. (2019) <doi:10.1187/cbe.18-11-0222>.
Author: Albert Chai [aut],
Andrew Lee [aut],
Joshua Le [aut, cre],
Katherine Ly [ctb],
Kevin Banh [ctb],
Priya Pahal [ctb],
Stanley Lo [aut]
Maintainer: Joshua Le <jpl038@ucsd.edu>
Diff between discourseGT versions 1.1.1 dated 2020-10-29 and 1.1.2 dated 2020-12-08
discourseGT-1.1.1/discourseGT/R/graphicalPlot.R |only discourseGT-1.1.1/discourseGT/R/plotGraphs.R |only discourseGT-1.1.1/discourseGT/R/plotGraphs2.R |only discourseGT-1.1.1/discourseGT/man/graphicalPlot.Rd |only discourseGT-1.1.1/discourseGT/man/plotGraphs.Rd |only discourseGT-1.1.1/discourseGT/man/plotGraphs2.Rd |only discourseGT-1.1.2/discourseGT/DESCRIPTION | 8 ++--- discourseGT-1.1.2/discourseGT/MD5 | 22 +++++++------- discourseGT-1.1.2/discourseGT/R/basicPlot.R |only discourseGT-1.1.2/discourseGT/R/plot1Att.R |only discourseGT-1.1.2/discourseGT/R/plot2Att.R |only discourseGT-1.1.2/discourseGT/R/subgroupsNetAnalysis.R | 2 - discourseGT-1.1.2/discourseGT/R/writeData.R | 2 - discourseGT-1.1.2/discourseGT/man/basicPlot.Rd |only discourseGT-1.1.2/discourseGT/man/plot1Att.Rd |only discourseGT-1.1.2/discourseGT/man/plot2Att.Rd |only discourseGT-1.1.2/discourseGT/man/subgroupsNetAnalysis.Rd | 2 - discourseGT-1.1.2/discourseGT/man/writeData.Rd | 2 - 18 files changed, 19 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-25 0.1-1
2020-11-23 0.1-0