Title: Import and Analyse Ego-Centered Network Data
Description: Tools for importing, analyzing and visualizing ego-centered
network data. Supports several data formats, including the export formats of
'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the
intuitive visualization of ego-centered networks is provided. Also included
are procedures for creating and visualizing Clustered Graphs
(Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Author: Till Krenz [aut, cre],
Pavel N. Krivitsky [aut],
Raffaele Vacca [aut],
Michal Bojanowski [aut] ,
Markus Gamper [ctb],
Andreas Herz [aut],
Christopher McCarty [ctb]
Maintainer: Till Krenz <egor@tillt.net>
Diff between egor versions 1.22.1 dated 2022-01-14 and 1.22.5 dated 2022-05-13
egor-1.22.1/egor/R/egor_doc.R |only egor-1.22.1/egor/man/egor-package-doc.Rd |only egor-1.22.5/egor/DESCRIPTION | 8 egor-1.22.5/egor/MD5 | 54 egor-1.22.5/egor/NEWS.md | 11 egor-1.22.5/egor/R/as_egor.R | 6 egor-1.22.5/egor/R/composition.R | 8 egor-1.22.5/egor/R/egor-package.R |only egor-1.22.5/egor/R/gss2004.R | 4 egor-1.22.5/egor/R/read.egonet.R | 37 egor-1.22.5/egor/inst/check_and_release.R | 7 egor-1.22.5/egor/inst/create_example_data.R | 20 egor-1.22.5/egor/inst/doc/egor_allbus.html | 290 +++- egor-1.22.5/egor/inst/doc/qualtrics.html | 397 ++++- egor-1.22.5/egor/inst/doc/using_egor.html | 313 +++- egor-1.22.5/egor/inst/extdata/alters_8.csv | 1154 +--------------- egor-1.22.5/egor/inst/extdata/alters_8_wide.csv | 146 -- egor-1.22.5/egor/inst/extdata/egos_8.csv | 146 -- egor-1.22.5/egor/inst/extdata/one_file_8.csv | 146 -- egor-1.22.5/egor/man/alts_diversity_count.Rd | 4 egor-1.22.5/egor/man/comp_ply.Rd | 4 egor-1.22.5/egor/man/egor-package.Rd |only egor-1.22.5/egor/man/gss2004.Rd | 2 egor-1.22.5/egor/man/onefile_to_egor.Rd | 12 egor-1.22.5/egor/man/twofiles_to_egor.Rd | 18 egor-1.22.5/egor/tests/testthat/test-clustered_graphs.R | 1 egor-1.22.5/egor/tests/testthat/test-ei.R | 8 egor-1.22.5/egor/tests/testthat/test-onefile_to_egor.R | 14 egor-1.22.5/egor/tests/testthat/test-read.R | 26 egor-1.22.5/egor/tests/testthat/test-twofiles_to_egor.R | 36 30 files changed, 1244 insertions(+), 1628 deletions(-)
Title: Standardizing Physiological Composite Risk Endpoints
Description: Provides a number of functions to
simplify and automate the scoring, comparison, and evaluation of
different ways of creating composites of data. It is particularly
aimed at facilitating the creation of physiological composites of
metabolic syndrome symptom score (MetSSS) and allostatic load (AL).
Provides a wrapper to calculate the MetSSS on new data using the
Healthy Hearts formula.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between pscore versions 0.1-2 dated 2015-06-24 and 0.4.0 dated 2022-05-13
pscore-0.1-2/pscore/man/distanceScores.Rd |only pscore-0.1-2/pscore/man/winsorizor.Rd |only pscore-0.4.0/pscore/DESCRIPTION | 37 - pscore-0.4.0/pscore/MD5 | 49 + pscore-0.4.0/pscore/NAMESPACE | 20 pscore-0.4.0/pscore/NEWS |only pscore-0.4.0/pscore/R/MetSSS.R |only pscore-0.4.0/pscore/R/MetSSS_model.R |only pscore-0.4.0/pscore/R/classes.R |only pscore-0.4.0/pscore/R/composite.R | 638 +++++++++++------------- pscore-0.4.0/pscore/R/methods.R |only pscore-0.4.0/pscore/R/misc.R | 88 +-- pscore-0.4.0/pscore/R/onLoad.R |only pscore-0.4.0/pscore/R/predictions.R |only pscore-0.4.0/pscore/build |only pscore-0.4.0/pscore/data/MetSSS_model.rda |only pscore-0.4.0/pscore/inst |only pscore-0.4.0/pscore/man/BioDB.Rd | 7 pscore-0.4.0/pscore/man/CompositeData-class.Rd |only pscore-0.4.0/pscore/man/CompositeData.Rd |only pscore-0.4.0/pscore/man/CompositeReady-class.Rd |only pscore-0.4.0/pscore/man/CompositeReady.Rd |only pscore-0.4.0/pscore/man/MetSSS.Rd |only pscore-0.4.0/pscore/man/MetSSS_model.Rd |only pscore-0.4.0/pscore/man/Scores.Rd |only pscore-0.4.0/pscore/man/dropData.Rd |only pscore-0.4.0/pscore/man/factorComposite.Rd | 86 ++- pscore-0.4.0/pscore/man/ldensity.Rd | 5 pscore-0.4.0/pscore/man/mahalanobisComposite.Rd | 81 +-- pscore-0.4.0/pscore/man/predictCS.Rd |only pscore-0.4.0/pscore/man/prepareComposite.Rd | 87 ++- pscore-0.4.0/pscore/man/preparePredict.Rd |only pscore-0.4.0/pscore/man/sumComposite.Rd | 91 +-- pscore-0.4.0/pscore/tests |only pscore-0.4.0/pscore/vignettes |only 35 files changed, 616 insertions(+), 573 deletions(-)
Title: Genetic Analysis Package
Description: As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18.
<doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it contains functions for
sample size calculations of both population-based and family-based designs, probability
of familial disease aggregation, kinship calculation, statistics in linkage analysis,
and association analysis involving genetic markers including haplotype analysis with or
without environmental covariates. Over years, the package has been developed in-between
many projects hence also in line with the name (gap).
Author: Jing Hua Zhao [aut, cre] ,
Kurt Hornik [ctb],
Brian Ripley [ctb],
Uwe Liggs [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gap versions 1.2.3-1 dated 2021-04-21 and 1.2.3-6 dated 2022-05-13
gap-1.2.3-1/gap/data/OPG.rda |only gap-1.2.3-1/gap/data/PD.rda |only gap-1.2.3-1/gap/data/aldh2.rda |only gap-1.2.3-1/gap/data/apoeapoc.rda |only gap-1.2.3-1/gap/data/cf.RData |only gap-1.2.3-1/gap/data/cnv.rda |only gap-1.2.3-1/gap/data/crohn.RData |only gap-1.2.3-1/gap/data/fa.RData |only gap-1.2.3-1/gap/data/fsnps.RData |only gap-1.2.3-1/gap/data/hla.rda |only gap-1.2.3-1/gap/data/inf1.rda |only gap-1.2.3-1/gap/data/jma.cojo.rda |only gap-1.2.3-1/gap/data/l51.rda |only gap-1.2.3-1/gap/data/lukas.rda |only gap-1.2.3-1/gap/data/mao.RData |only gap-1.2.3-1/gap/data/meyer.rda |only gap-1.2.3-1/gap/data/mfblong.rda |only gap-1.2.3-1/gap/data/nep499.RData |only gap-1.2.3-1/gap/inst/doc/gap.Rnw |only gap-1.2.3-1/gap/inst/doc/gap.pdf |only gap-1.2.3-1/gap/man/h2.Rd |only gap-1.2.3-1/gap/vignettes/figures |only gap-1.2.3-1/gap/vignettes/gap.Rnw |only gap-1.2.3-1/gap/vignettes/pedigrees |only gap-1.2.3-1/gap/vignettes/results |only gap-1.2.3-6/gap/ChangeLog | 48 + gap-1.2.3-6/gap/DESCRIPTION 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gap-1.2.3-6/gap/R/gc.lambda.R |only gap-1.2.3-6/gap/R/gcontrol.R | 58 + gap-1.2.3-6/gap/R/gcontrol2.R | 39 + gap-1.2.3-6/gap/R/gcp.R | 52 + gap-1.2.3-6/gap/R/genecounting.R | 90 ++ gap-1.2.3-6/gap/R/get_b_se.R |only gap-1.2.3-6/gap/R/get_pve_se.R |only gap-1.2.3-6/gap/R/get_sdy.R |only gap-1.2.3-6/gap/R/gif.R | 65 + gap-1.2.3-6/gap/R/gsmr.R |only gap-1.2.3-6/gap/R/h2.R | 76 ++ gap-1.2.3-6/gap/R/h2.jags.R | 50 + gap-1.2.3-6/gap/R/h2G.R |only gap-1.2.3-6/gap/R/h2GE.R |only gap-1.2.3-6/gap/R/h2l.R |only gap-1.2.3-6/gap/R/hap.R | 76 ++ gap-1.2.3-6/gap/R/hap.em.R | 60 + gap-1.2.3-6/gap/R/hap.score.R | 78 ++ gap-1.2.3-6/gap/R/htr.R | 62 + gap-1.2.3-6/gap/R/hwe.R | 56 + gap-1.2.3-6/gap/R/hwe.cc.R | 62 + gap-1.2.3-6/gap/R/hwe.hardy.R | 90 ++ gap-1.2.3-6/gap/R/hwe.jags.R | 96 ++ gap-1.2.3-6/gap/R/invnormal.R |only gap-1.2.3-6/gap/R/kin.morgan.R | 46 + gap-1.2.3-6/gap/R/log10p.R |only gap-1.2.3-6/gap/R/log10pvalue.R |only gap-1.2.3-6/gap/R/logp.R |only gap-1.2.3-6/gap/R/makeped.R | 55 + 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Title: Textual Data Analysis Package Used by the TXM Software
Description: Statistical exploration of textual corpora using several methods
from French 'Textometrie' (new name of 'Lexicometrie') and French 'Data Analysis' schools.
It includes methods for exploring irregularity of distribution of lexicon features across
text sets or parts of texts (Specificity analysis); multi-dimensional exploration (Factorial analysis), etc.
Those methods are used in the TXM software.
Author: Sylvain Loiseau, Lise Vaudor, Matthieu Decorde, Serge Heiden
Maintainer: Matthieu Decorde <matthieu.decorde@ens-lyon.fr>
Diff between textometry versions 0.1.4 dated 2015-01-09 and 0.1.5 dated 2022-05-13
DESCRIPTION | 9 +++++---- MD5 | 12 +++++++----- NAMESPACE | 3 +++ NEWS.md |only README.md |only data/bfm.rda |binary data/robespierre.rda |binary inst/CITATION | 4 ++-- 8 files changed, 17 insertions(+), 11 deletions(-)
Title: Design of the Best Phage Cocktail
Description: There are 4 possible methods: "ExhaustiveSearch"; "ExhaustivePhi"; "ClusteringSearch"; and "ClusteringPhi".
"ExhaustiveSearch"--> gives you the best phage cocktail from a phage-bacteria
infection network. It checks different phage cocktail sizes from 1 to 7 and
only stops before if it lyses all bacteria. Other option is when users have
decided not to obtain a phage cocktail size higher than a limit value.
"ExhaustivePhi"--> firstly, it finds Phi out. Phi is a formula
indicating the necessary phage cocktail size. Phi needs nestedness temperature
and fill, which are internally calculated. This function will only look for the
best combination (phage cocktail) with a Phi size.
"ClusteringSearch"--> firstly, an agglomerative hierarchical clustering using
Ward's algorithm is calculated for phages. They will be clustered according to
bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in
order to select 1 phage per cluster. Using the phages selected during the
clustering, it checks different phage cocktail sizes from 1 to 7 and only stops
before if it lyses all bacteria. Other option is when users have decided not to
obtain a phage cocktail size higher than a limit value.
"ClusteringPhi"--> firstly, an agglomerative hierarchical clustering using Ward's
algorithm is calculated for phages. They will be clustered according to bacteria
lysed by them. PhageCocktail() chooses how many clusters are needed in order to
select 1 phage per cluster. Once the function has one phage per cluster, it
calculates Phi. If the number of clusters is less than Phi number, it will be
changed to obtain, as minimum, this quantity of candidates (phages). Then, it
calculates the best combination of Phi phages using those selected during the
clustering with Ward algorithm.
If you use PhageCocktail, please cite it as:
"PhageCocktail: An R Package to Design Phage Cocktails from Experimental
Phage-Bacteria Infection Networks". María Victoria Díaz-Galián, Miguel A.
Vega-Rodríguez, Felipe Molina. Computer Methods and Programs in Biomedicine,
221, 106865, Elsevier Ireland, Clare, Ireland, 2022, pp. 1-9, ISSN: 0169-2607.
<doi:10.1016/j.cmpb.2022.106865>.
Author: Maria Victoria Diaz-Galian [aut, cre]
,
Miguel A. Vega-Rodriguez [aut]
,
Felipe Molina [aut]
Maintainer: Maria Victoria Diaz-Galian <mvdiazgalian@unex.es>
Diff between PhageCocktail versions 1.0.2 dated 2022-05-10 and 1.0.3 dated 2022-05-13
DESCRIPTION | 12 ++--- MD5 | 6 +- build/partial.rdb |binary man/PhageCocktail.Rd | 113 ++++++++++++++++++++++++++++----------------------- 4 files changed, 72 insertions(+), 59 deletions(-)
Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision
trees and forests to Structural Equation Models (SEM). SEM trees hierarchically
split empirical data into homogeneous groups each sharing similar data patterns
with respect to a SEM by recursively selecting optimal predictors of these
differences. SEM forests are an extension of SEM trees. They are ensembles of
SEM trees each built on a random sample of the original data. By aggregating
over a forest, we obtain measures of variable importance that are more robust
than measures from single trees. A description of the method was published by
Brandmaier, von Oertzen, McArdle, & Lindenberger (2013) <doi:10.1037/a0030001>
and Arnold, Voelkle, & Brandmaier (2020) <doi:10.3389/fpsyg.2020.564403>.
Author: Andreas M. Brandmaier [aut, cre],
John J. Prindle [aut],
Manuel Arnold [aut],
Caspar J. Van Lissa [aut]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
Diff between semtree versions 0.9.17 dated 2021-07-30 and 0.9.18 dated 2022-05-13
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Title: Utilities for Scoring and Assessing Predictions
Description: Provides a collection of metrics and proper scoring rules
(Tilmann Gneiting & Adrian E Raftery (2007)
<doi:10.1198/016214506000001437>, Jordan, A., Krüger, F., & Lerch, S. (2019)
<doi:10.18637/jss.v090.i12>) within a consistent framework for
evaluation, comparison and visualisation of forecasts.
In addition to proper scoring rules, functions are provided to assess
bias, sharpness and calibration
(Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind
M. Eggo, W. John Edmunds (2019) <doi:10.1371/journal.pcbi.1006785>) of
forecasts.
Several types of predictions (e.g. binary, discrete, continuous) which may
come in different formats (e.g. forecasts represented by predictive samples
or by quantiles of the predictive distribution) can be evaluated.
Scoring metrics can be used either through a convenient data.frame format,
or can be applied as individual functions in a vector / matrix format.
All functionality has been implemented with a focus on performance and is
robustly tested.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Sebastian Funk [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 0.1.7.2 dated 2021-07-21 and 1.0.0 dated 2022-05-13
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Title: Functions for Optimal Matching
Description: Distance based bipartite matching using minimum cost flow, oriented
to matching of treatment and control groups in observational studies (Hansen
and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to
generate distances from generalised linear models (propensity score
matching), formulas giving variables on which to limit matched distances,
stratified or exact matching directives, or calipers, alone or in
combination.
Author: Ben Hansen [aut],
Mark Fredrickson [aut],
Josh Errickson [cre, aut],
Josh Buckner [aut],
Adam Rauh [ctb]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between optmatch versions 0.10.0 dated 2022-03-15 and 0.10.1 dated 2022-05-13
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Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov
models. These include processing of tracking data, fitting hidden Markov models
to movement data, visualization of data and fitted model, decoding of the state
process...
Author: Theo Michelot, Roland Langrock, Toby Patterson, Brett McClintock, Eric Rexstad
Maintainer: Theo Michelot <tm75@st-andrews.ac.uk>
Diff between moveHMM versions 1.7 dated 2019-05-19 and 1.8 dated 2022-05-13
moveHMM-1.7/moveHMM/tests/testthat/test_plot_moveData.R |only moveHMM-1.7/moveHMM/vignettes/plotSat.pdf |only moveHMM-1.8/moveHMM/DESCRIPTION | 10 moveHMM-1.8/moveHMM/MD5 | 127 +-- moveHMM-1.8/moveHMM/NAMESPACE | 3 moveHMM-1.8/moveHMM/R/allProbs.R | 2 moveHMM-1.8/moveHMM/R/fitHMM.R | 64 + moveHMM-1.8/moveHMM/R/getPlotData.R |only moveHMM-1.8/moveHMM/R/nLogLike.R | 4 moveHMM-1.8/moveHMM/R/plotStationary.R | 106 -- moveHMM-1.8/moveHMM/R/plot_moveData.R | 123 +- moveHMM-1.8/moveHMM/R/plot_moveHMM.R | 580 +++----------- moveHMM-1.8/moveHMM/R/predictStationary.R |only moveHMM-1.8/moveHMM/R/predictTPM.R |only moveHMM-1.8/moveHMM/R/prepData.R | 11 moveHMM-1.8/moveHMM/R/pseudoRes.R | 5 moveHMM-1.8/moveHMM/R/stationary.R | 5 moveHMM-1.8/moveHMM/R/utils.R |only moveHMM-1.8/moveHMM/R/viterbi.R | 12 moveHMM-1.8/moveHMM/README.md | 13 moveHMM-1.8/moveHMM/build/vignette.rds |binary moveHMM-1.8/moveHMM/data/haggis_data.RData |only moveHMM-1.8/moveHMM/inst/doc/moveHMM-custom-plots.R | 16 moveHMM-1.8/moveHMM/inst/doc/moveHMM-custom-plots.pdf |binary moveHMM-1.8/moveHMM/inst/doc/moveHMM-example.R |only moveHMM-1.8/moveHMM/inst/doc/moveHMM-example.Rmd |only moveHMM-1.8/moveHMM/inst/doc/moveHMM-example.pdf |only moveHMM-1.8/moveHMM/inst/doc/moveHMM-guide.R | 61 - moveHMM-1.8/moveHMM/inst/doc/moveHMM-guide.Rnw | 158 +-- moveHMM-1.8/moveHMM/inst/doc/moveHMM-guide.pdf |binary moveHMM-1.8/moveHMM/inst/doc/moveHMM-starting-values.R | 26 moveHMM-1.8/moveHMM/inst/doc/moveHMM-starting-values.Rnw | 32 moveHMM-1.8/moveHMM/inst/doc/moveHMM-starting-values.pdf |binary moveHMM-1.8/moveHMM/man/allProbs.Rd | 13 moveHMM-1.8/moveHMM/man/fitHMM.Rd | 48 - moveHMM-1.8/moveHMM/man/getPalette.Rd |only moveHMM-1.8/moveHMM/man/getPlotData.Rd |only moveHMM-1.8/moveHMM/man/haggis_data.Rd |only moveHMM-1.8/moveHMM/man/nLogLike.Rd | 17 moveHMM-1.8/moveHMM/man/nLogLike_rcpp.Rd | 17 moveHMM-1.8/moveHMM/man/plot.moveData.Rd | 3 moveHMM-1.8/moveHMM/man/plot.moveHMM.Rd | 28 moveHMM-1.8/moveHMM/man/plotSat.Rd | 17 moveHMM-1.8/moveHMM/man/predictStationary.Rd |only moveHMM-1.8/moveHMM/man/predictTPM.Rd |only moveHMM-1.8/moveHMM/man/prepData.Rd | 11 moveHMM-1.8/moveHMM/man/simData.Rd | 20 moveHMM-1.8/moveHMM/man/stationary.Rd | 5 moveHMM-1.8/moveHMM/man/viterbi.Rd | 4 moveHMM-1.8/moveHMM/src/RcppExports.cpp | 5 moveHMM-1.8/moveHMM/src/densities.h | 11 moveHMM-1.8/moveHMM/tests/testthat/test_CI.R | 18 moveHMM-1.8/moveHMM/tests/testthat/test_allProbs.R | 40 moveHMM-1.8/moveHMM/tests/testthat/test_densities.R | 42 - moveHMM-1.8/moveHMM/tests/testthat/test_fitHMM.R | 118 +- moveHMM-1.8/moveHMM/tests/testthat/test_logAlpha.R | 12 moveHMM-1.8/moveHMM/tests/testthat/test_moveData.R | 32 moveHMM-1.8/moveHMM/tests/testthat/test_moveHMM.R | 46 - moveHMM-1.8/moveHMM/tests/testthat/test_n2w.R | 36 moveHMM-1.8/moveHMM/tests/testthat/test_nLogLike.R | 102 +- moveHMM-1.8/moveHMM/tests/testthat/test_parDef.R | 30 moveHMM-1.8/moveHMM/tests/testthat/test_prepData.R | 46 - moveHMM-1.8/moveHMM/tests/testthat/test_simData.R | 93 +- moveHMM-1.8/moveHMM/tests/testthat/test_stateProbs.R | 4 moveHMM-1.8/moveHMM/tests/testthat/test_trMatrix_rcpp.R | 20 moveHMM-1.8/moveHMM/tests/testthat/test_turnAngle.R | 16 moveHMM-1.8/moveHMM/tests/testthat/test_viterbi.R | 2 moveHMM-1.8/moveHMM/tests/testthat/test_w2n.R | 56 - moveHMM-1.8/moveHMM/vignettes/haggis.jpg |only moveHMM-1.8/moveHMM/vignettes/moveHMM-example.Rmd |only moveHMM-1.8/moveHMM/vignettes/moveHMM-guide.Rnw | 158 +-- moveHMM-1.8/moveHMM/vignettes/moveHMM-starting-values.Rnw | 32 moveHMM-1.8/moveHMM/vignettes/refs.bib | 77 + 73 files changed, 1142 insertions(+), 1395 deletions(-)
Title: Interface Tools for LSD Simulation Results Files
Description: Interfaces R with LSD simulation models. Reads object-oriented data in results files (.res[.gz]) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallel threads of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre]
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
Diff between LSDinterface versions 1.2.0 dated 2022-02-27 and 1.2.1 dated 2022-05-13
DESCRIPTION | 12 +- MD5 | 20 ++-- R/files.R | 34 ++++++-- R/info.R | 197 +++++++++++++++++++++++++++++++++++++---------- R/read_mult.R | 33 +++++++ R/read_sngl.R | 44 ++++++++-- R/select.R | 63 ++++++++++++--- R/vars.R | 41 +++++++++ build/partial.rdb |binary man/info.distance.lsd.Rd | 21 +++-- man/info.stats.lsd.Rd | 10 +- 11 files changed, 384 insertions(+), 91 deletions(-)
Title: Tools for HLA Data
Description: A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
Author: Joan Zhang [aut, cre],
Aileen Johnson [aut],
Christian P Larsen [cph, aut]
Maintainer: Joan Zhang <joan.zhang@emory.edu>
Diff between hlaR versions 0.1.2 dated 2022-02-01 and 0.1.3 dated 2022-05-13
hlaR-0.1.2/hlaR/R/func-for-haplotype.R |only hlaR-0.1.2/hlaR/man/FuncForCompHaplo.Rd |only hlaR-0.1.3/hlaR/DESCRIPTION | 14 hlaR-0.1.3/hlaR/MD5 | 28 - hlaR-0.1.3/hlaR/NAMESPACE | 1 hlaR-0.1.3/hlaR/R/allele-haplotype.R | 383 ++++++++++++------------- hlaR-0.1.3/hlaR/R/eplet-MHC-I.R | 97 +++++- hlaR-0.1.3/hlaR/R/eplet-MHC-II.R | 241 ++++++++++++--- hlaR-0.1.3/hlaR/R/globals.R | 3 hlaR-0.1.3/hlaR/R/utils.R |only hlaR-0.1.3/hlaR/inst/doc/allele-haplotype.html | 96 ++++-- hlaR-0.1.3/hlaR/inst/doc/eplet-mm.R | 1 hlaR-0.1.3/hlaR/inst/doc/eplet-mm.Rmd | 3 hlaR-0.1.3/hlaR/inst/doc/eplet-mm.html | 197 ++++++++---- hlaR-0.1.3/hlaR/man/CalEpletMHCII.Rd | 2 hlaR-0.1.3/hlaR/man/utils.Rd |only hlaR-0.1.3/hlaR/vignettes/eplet-mm.Rmd | 3 17 files changed, 693 insertions(+), 376 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.1 dated 2022-05-06 and 0.1.2 dated 2022-05-13
DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/LDS |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp1.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp10.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp11.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp12.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp14.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp2.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp3.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp4.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp5.6.7.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp7.power.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp8.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/inst/example/chp9.R |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp1.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp12.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp2.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp3.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp4.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp567.Rd |only DanielBiostatistics10th-0.1.1/DanielBiostatistics10th/man/Chp7power.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/DESCRIPTION | 11 DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/MD5 | 84 ++--- DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/NAMESPACE | 3 DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/NEWS.md | 6 DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/DanielBiostatistics10th.R | 6 DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/Gosset_Welch.R | 18 - DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp1.R | 18 - DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp12.R | 46 ++- DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp2.R | 56 +++ DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp3.R | 96 +++--- DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp4.R | 25 - DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp5.6.7.R | 143 ++++------ DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/R/chp7.power.R | 45 +-- DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter1.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter10.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter11.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter12.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter14.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter2.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter3.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter4.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter5.6.7.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter7.power.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter8.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/Chapter9.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_C09.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_C10.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_C11.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_C12.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_C13.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_chp6.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_chp7.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LDS_chp8.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/inst/example/LargeData_Chapter2_NCBIRTH800.R |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter01.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter02.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter03.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter04.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter05to07.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter07_power.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Chapter12.Rd |only DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/DanielBiostatistics10th-package.Rd | 5 DanielBiostatistics10th-0.1.2/DanielBiostatistics10th/man/Gosset_Welch.Rd | 15 - 63 files changed, 333 insertions(+), 244 deletions(-)
More information about DanielBiostatistics10th at CRAN
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Title: Tools for Modeling Bumblebee Colony Growth and Decline
Description: Bumblebee colonies grow during worker production, then decline after switching to production of reproductive individuals (drones and gynes). This package provides tools for modeling and visualizing this pattern by identifying a switchpoint with a growth rate before and a decline rate after the switchpoint. The mathematical models fit by bumbl are described in Crone and Williams (2016) <doi:10.1111/ele.12581>.
Author: Eric R. Scott [aut, cre]
Maintainer: Eric R. Scott <scottericr@gmail.com>
Diff between bumbl versions 1.0.1 dated 2021-08-25 and 1.0.2 dated 2022-05-13
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 5 R/colony-growth.R | 11 + R/data.R | 50 ++++++- R/simulate.R | 22 ++- README.md | 9 - data/test_df.rda |only inst/CITATION | 2 inst/doc/bumbl.html | 299 ++++++++++++++++++++++++++++++++++++++++---- man/bombus.Rd | 23 ++- man/brkpt.Rd | 13 + man/bumbl.Rd | 5 man/test_df.Rd |only tests/testthat/test-brkpt.R | 42 ++---- tests/testthat/test-bumbl.R | 161 +++++++++++------------ 16 files changed, 506 insertions(+), 172 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre]
,
Joao Bazzo [ctb]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Diff between vein versions 0.9.5 dated 2022-02-06 and 0.9.6 dated 2022-05-13
DESCRIPTION | 10 MD5 | 208 ++++++------- NAMESPACE | 1 NEWS.md | 10 R/EmissionFactors.R | 6 R/EmissionFactorsList.R | 2 R/Emissions.R | 6 R/EmissionsArray.R | 4 R/EmissionsList.R | 2 R/Evaporative.R | 2 R/Speed.R | 14 R/Vehicles.R | 4 R/add_lkm.R | 4 R/celsius.R | 2 R/cold_mileage.R | 6 R/colplot.R | 1 R/dmonth.R |only R/ef_china.R | 8 R/ef_eea.R | 65 +++- R/ef_evap.R | 4 R/ef_hdv_speed.R | 2 R/ef_ldv_cold.R | 2 R/ef_ldv_speed.R | 40 +- R/ef_nitro.R | 2 R/emis.R | 19 - R/emis_chem.R | 2 R/emis_cold.R | 12 R/emis_cold_td.R | 10 R/emis_det.R | 6 R/emis_evap.R | 580 +++++++++++++++++++------------------- R/emis_evap2.R | 36 +- R/emis_grid.R | 6 R/emis_hot_td.R | 20 - R/emis_order.R | 11 R/emis_paved.R | 2 R/emis_post.R | 11 R/emis_source.R | 4 R/emis_to_streets.R | 2 R/emis_wear.R | 2 R/emis_wrf.R | 2 R/fuel_corr.R | 4 R/get_project.R | 48 ++- R/grid_emis.R | 10 R/hot_soak.R | 4 R/invcop.R | 2 R/inventory.R | 14 R/long_to_wide.R | 2 R/make_grid.R | 69 ++-- R/moves_rpsy_source.R | 2 R/moves_speed.R | 2 R/my_age.R | 16 - R/net.R | 4 R/netspeed.R | 2 R/pc_cold.R | 2 R/profiles.R | 2 R/running_losses.R | 6 R/speciate.R | 8 R/split_emis.R | 2 R/sysdata.rda |binary R/to_latex.R | 1 R/vkm.R | 2 R/wide_to_long.R | 2 build/vignette.rds |binary data/decoder.rda |binary inst/doc/basics.html | 210 +++++++++++++ man/EmissionFactors.Rd | 2 man/EmissionFactorsList.Rd | 2 man/Emissions.Rd | 2 man/EmissionsArray.Rd | 4 man/Speed.Rd | 10 man/colplot.Rd | 6 man/dmonth.Rd |only man/ef_eea.Rd | 64 ++-- man/emis_cold.Rd | 8 man/emis_det.Rd | 2 man/emis_evap.Rd | 14 man/emis_evap2.Rd | 36 +- man/emis_grid.Rd | 4 man/emis_hot_td.Rd | 12 man/emis_order.Rd | 9 man/emis_paved.Rd | 2 man/emis_post.Rd | 4 man/emis_source.Rd | 4 man/emis_wear.Rd | 2 man/figures/unnamed-chunk-7-1.png |binary man/fuel_corr.Rd | 4 man/get_project.Rd | 6 man/grid_emis.Rd | 8 man/invcop.Rd | 2 man/inventory.Rd | 14 man/moves_rpsy_sf.Rd | 2 man/my_age.Rd | 12 man/net.Rd | 4 man/netspeed.Rd | 2 man/pc_cold.Rd | 2 man/profiles.Rd | 2 man/running_losses-deprecated.Rd | 8 man/speciate.Rd | 4 man/to_latex.Rd | 6 man/vein-deprecated.Rd | 6 man/vkm.Rd | 2 man/wide_to_long.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-dmonth.R |only tests/testthat/test-ef_eea.R |only tests/testthat/test-emis.R | 10 tests/testthat/test-make_grid.R | 2 107 files changed, 1081 insertions(+), 752 deletions(-)
Title: A Unifying API for Calling the 'Unity' '3D' Video Game Engine
Description: Functions for the creation and manipulation of scenes and objects
within the 'Unity' '3D' video game engine (<https://unity.com/>). Specific
focuses include the creation and import of terrain data and 'GameObjects' as
well as scene management.
Author: Michael Mahoney [aut, cre] ,
Will Jones [rev] for rOpenSci,
see <https://github.com/ropensci/software-review/issues/521>),
Tan Tran [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/521>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between unifir versions 0.2.0 dated 2022-05-04 and 0.2.1 dated 2022-05-13
DESCRIPTION | 8 +-- MD5 | 28 ++++++------- NEWS.md | 7 +++ R/add_asset.R | 10 +--- R/add_light.R | 8 --- R/scene_management.R | 11 ----- README.md | 31 +++++++++++++- inst/CITATION | 23 +++++----- inst/WORDLIST | 6 ++ inst/doc/unifir-dev-guide.R | 3 - inst/doc/unifir-dev-guide.Rmd | 3 - inst/doc/unifir-dev-guide.html | 59 ++++++++++++---------------- man/unifir-package.Rd | 2 tests/testthat/test-associate_coordinates.R | 4 + vignettes/unifir-dev-guide.Rmd | 3 - 15 files changed, 116 insertions(+), 90 deletions(-)
Title: Group-Adaptive Elastic Net Penalised Generalised Linear Models
Description: Fit linear and logistic regression models penalised with group-adaptive elastic net penalties.
The group penalties correspond to groups of covariates defined by a co-data group set.
The method accommodates inclusion of unpenalised covariates and overlapping groups.
See Van Nee et al. (2021) <arXiv:2101.03875>.
Author: Mirrelijn M. van Nee [aut, cre],
Tim van de Brug [aut],
Mark A. van de Wiel [aut]
Maintainer: Mirrelijn M. van Nee <m.vannee@amsterdamumc.nl>
Diff between squeezy versions 1.1 dated 2022-03-22 and 1.1-1 dated 2022-05-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/squeezy.R | 3 ++- build/partial.rdb |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Integrative Immunoinformatics for Mycobacterial Diseases in R
Platform
Description: The mycobacrvR package contains utilities to provide detailed information for B cell and T cell epitopes for predicted adhesins from various servers such as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB. Please refer the URL below to download data files (data_mycobacrvR.zip) used in functions of this package.
Author: Deepika Kulshreshtha, Rupanjali Chaudhuri, Surabhi Seth, S. Ramachandran
Maintainer: S. Ramachandran<ramu@igib.in>
Diff between mycobacrvR versions 1.0 dated 2013-12-26 and 1.1 dated 2022-05-13
DESCRIPTION | 16 ++-- MD5 | 30 ++++----- NAMESPACE | 1 R/abcpred_nmer.R | 109 +++++++++++++++++++--------------- R/bcepred_nmer.R | 102 ++++++++++++++++++------------- R/bimas_nmer.R | 124 ++++++++++++++++++++++++-------------- R/iedb_arb_mhci_nmer.R | 123 +++++++++++++++++++++++--------------- R/iedb_arb_mhcii_nmer.R | 123 +++++++++++++++++++++++--------------- R/iedb_consensus_mhci_nmer.R | 125 ++++++++++++++++++++++++--------------- R/iedb_consensus_mhcii_nmer.R | 124 ++++++++++++++++++++++++-------------- R/netmhcNN_nmer.R | 124 ++++++++++++++++++++++++-------------- R/netmhcWT_nmer.R | 124 ++++++++++++++++++++++++-------------- R/propred_nmer.R | 124 ++++++++++++++++++++++++-------------- man/iedb_arb_mhcii_nmer.Rd | 2 man/iedb_consensus_mhci_nmer.Rd | 2 man/iedb_consensus_mhcii_nmer.Rd | 2 16 files changed, 766 insertions(+), 489 deletions(-)
Title: Flexible Co-Data Learning for High-Dimensional Prediction
Description: Fit linear, logistic and Cox survival regression models penalised with adaptive multi-group ridge penalties.
The multi-group penalties correspond to groups of covariates defined by (multiple) co-data sources.
Group hyperparameters are estimated with an empirical Bayes method of moments, penalised with an extra level of hyper shrinkage.
Various types of hyper shrinkage may be used for various co-data.
Co-data may be continuous or categorical.
The method accommodates inclusion of unpenalised covariates, posterior selection of covariates and multiple data types.
The model fit is used to predict for new samples.
The name 'ecpc' stands for Empirical Bayes, Co-data learnt, Prediction and Covariate selection.
See Van Nee et al. (2020) <arXiv:2005.04010>.
Author: Mirrelijn M. van Nee [aut, cre],
Lodewyk F.A. Wessels [aut],
Mark A. van de Wiel [aut]
Maintainer: Mirrelijn M. van Nee <m.vannee@amsterdamumc.nl>
Diff between ecpc versions 3.0 dated 2022-03-22 and 3.1 dated 2022-05-13
DESCRIPTION | 14 MD5 | 17 NAMESPACE | 14 R/ecpc.R | 901 +++++++++++++++++++++++++++++++++++++++------------- R/ecpc_methods.R |only build/partial.rdb |binary man/coef.ecpc.Rd |only man/ecpc.Rd | 63 +++ man/plot.ecpc.Rd |only man/postSelect.Rd | 17 man/predict.ecpc.Rd |only man/print.ecpc.Rd |only 12 files changed, 780 insertions(+), 246 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays,
fit multiple functions.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.21.2 dated 2022-03-14 and 1.21.14 dated 2022-05-13
DESCRIPTION | 8 +- MD5 | 42 ++++++----- NAMESPACE | 4 + R/funnelPlot.R | 1 R/linReg.R | 4 - R/openFile.R | 14 ++- R/openPDF.R | 14 +++ R/runRversions.R |only R/tableColVal.R | 13 ++- R/tmessage.R |only R/traceCall.R | 66 ++++++++++-------- build/vignette.rds |binary inst/doc/berryFunctions.R | 13 +++ inst/doc/berryFunctions.Rmd | 20 +++++ inst/doc/berryFunctions.html | 157 ++++++++++++++++++++++++------------------- man/funnelPlot.Rd | 1 man/linReg.Rd | 3 man/openFile.Rd | 3 man/openPDF.Rd | 12 +-- man/runRversions.Rd |only man/tableColVal.Rd | 11 ++- man/tmessage.Rd |only man/traceCall.Rd | 19 +++-- vignettes/berryFunctions.Rmd | 20 +++++ 24 files changed, 276 insertions(+), 149 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and
the second edition of "Numerical Methods and Optimization
in Finance" by M. Gilli, D. Maringer and E. Schumann
(2019, ISBN:978-0128150658). The package provides
implementations of optimisation heuristics (Differential
Evolution, Genetic Algorithms, Particle Swarm
Optimisation, Simulated Annealing and Threshold
Accepting), and other optimisation tools, such as grid
search and greedy search. There are also functions for
the valuation of financial instruments such as bonds and
options, for portfolio selection and functions that help
with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 2.5-0 dated 2021-10-20 and 2.5-1 dated 2022-05-13
DESCRIPTION | 8 - MD5 | 42 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSqueens.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/portfolio.R | 58 +++++--- inst/doc/portfolio.Rnw | 44 ++++-- inst/doc/portfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/tinytest/test_portfolio.R | 259 ++++++++++++++++++++-------------------- inst/unitTests/test_results.txt | 20 +-- man/mvFrontier.Rd | 17 +- man/randomReturns.Rd | 26 ++-- man/trackingPortfolio.Rd | 36 ++--- vignettes/portfolio.Rnw | 44 ++++-- 22 files changed, 300 insertions(+), 254 deletions(-)
Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative) related inputs and outputs.
Converts data files to and from SPSS, Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between DDIwR versions 0.10 dated 2022-04-20 and 0.11 dated 2022-05-13
DESCRIPTION | 12 +- MD5 | 31 ++--- NAMESPACE | 2 R/cleanup.R | 4 R/collectMetadata.R | 4 R/convert.R | 42 ++++--- R/exportDDI.R | 267 ++++++++++++++++++++++++++++---------------------- R/getMetadata.R | 49 ++++++--- R/onAttach.R | 1 R/replaceTicks.R |only R/setupfile.R | 35 +++--- R/writeMetadata.R | 2 inst/ChangeLog | 42 ++++--- man/DDIwR_internal.Rd | 1 man/DDIwR_package.Rd | 4 man/exportDDI.Rd | 25 ++-- man/getMetadata.Rd | 5 17 files changed, 297 insertions(+), 229 deletions(-)
Title: Generative Art with 'ggplot2'
Description: Provides algorithms for creating artworks in the 'ggplot2' language that incorporate some form of randomness.
Author: Koen Derks [aut, cre]
Maintainer: Koen Derks <koen-derks@hotmail.com>
Diff between aRtsy versions 0.1.7 dated 2022-04-10 and 0.1.8 dated 2022-05-13
DESCRIPTION | 10 MD5 | 149 +- NAMESPACE | 71 - NEWS.md | 166 +- R/RcppExports.R | 4 R/canvas_ant.R | 170 +- R/canvas_blacklight.R | 114 +- R/canvas_chladni.R | 144 +- R/canvas_circlemap.R | 132 +- R/canvas_cobweb.R | 180 +-- R/canvas_collatz.R | 166 +- R/canvas_diamonds.R | 184 +-- R/canvas_flow.R | 244 ++-- R/canvas_forest.R | 132 +- R/canvas_function.R | 192 +-- R/canvas_gemstone.R | 114 +- R/canvas_mandelbrot.R | 164 +- R/canvas_maze.R | 260 ++-- R/canvas_mosaic.R | 132 +- R/canvas_nebula.R | 112 - R/canvas_petri.R | 206 +-- R/canvas_phyllotaxis.R | 122 +- R/canvas_planet.R | 250 ++-- R/canvas_polylines.R | 132 +- R/canvas_recaman.R | 200 +-- R/canvas_ribbons.R | 170 +- R/canvas_segments.R | 144 +- R/canvas_splits.R |only R/canvas_squares.R | 140 +- R/canvas_stripes.R | 124 +- R/canvas_strokes.R | 152 +- R/canvas_turmite.R | 170 +- R/canvas_watercolors.R | 188 +-- R/colorPalette.R | 352 +++--- R/internal.R | 240 ++-- R/saveCanvas.R | 78 - R/theme_canvas.R | 108 - R/zzz.R | 46 README.md | 1255 +++++++++++----------- inst/CITATION | 18 man/aRtsy.Rd | 70 - man/canvas_ant.Rd | 96 - man/canvas_blacklight.Rd | 82 - man/canvas_chladni.Rd | 96 - man/canvas_circlemap.Rd | 98 - man/canvas_cobweb.Rd | 82 - man/canvas_collatz.Rd | 96 - man/canvas_diamonds.Rd | 94 - man/canvas_flow.Rd | 130 +- man/canvas_forest.Rd | 82 - man/canvas_function.Rd | 106 - man/canvas_gemstone.Rd | 82 - man/canvas_mandelbrot.Rd | 98 - man/canvas_maze.Rd | 92 - man/canvas_mosaic.Rd | 82 - man/canvas_nebula.Rd | 80 - man/canvas_petri.Rd | 102 - man/canvas_phyllotaxis.Rd | 100 - man/canvas_planet.Rd | 136 +- man/canvas_polylines.Rd | 90 - man/canvas_recaman.Rd | 110 - man/canvas_ribbons.Rd | 76 - man/canvas_segments.Rd | 90 - man/canvas_splits.Rd |only man/canvas_squares.Rd | 90 - man/canvas_stripes.Rd | 80 - man/canvas_strokes.Rd | 90 - man/canvas_turmite.Rd | 102 - man/canvas_watercolors.Rd | 92 - man/colorPalette.Rd | 66 - man/figures/colors.svg | 2042 ++++++++++++++++++------------------ man/saveCanvas.Rd | 60 - man/theme_canvas.Rd | 52 src/RcppExports.cpp | 19 src/canvas_splits.cpp |only tests/testthat.R | 8 tests/testthat/test-all-paintings.R | 370 +++--- 77 files changed, 6117 insertions(+), 6059 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. Reference: Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut],
Ken Kellner [cre, aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
Ariel Muldoon [ctb], [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between unmarked versions 1.2.3 dated 2022-04-26 and 1.2.5 dated 2022-05-13
unmarked-1.2.3/unmarked/inst/doc/cap-recap.Rnw |only unmarked-1.2.3/unmarked/inst/doc/cap-recap.pdf |only unmarked-1.2.3/unmarked/inst/doc/colext.R |only unmarked-1.2.3/unmarked/inst/doc/colext.Rnw |only unmarked-1.2.3/unmarked/inst/doc/colext.pdf |only unmarked-1.2.3/unmarked/inst/doc/distsamp.Rnw |only unmarked-1.2.3/unmarked/inst/doc/distsamp.pdf |only unmarked-1.2.3/unmarked/inst/doc/occuMulti.R |only unmarked-1.2.3/unmarked/inst/doc/occuMulti.Rnw |only unmarked-1.2.3/unmarked/inst/doc/occuMulti.pdf |only unmarked-1.2.3/unmarked/inst/doc/powerAnalysis.Rnw |only unmarked-1.2.3/unmarked/inst/doc/powerAnalysis.pdf |only unmarked-1.2.3/unmarked/inst/doc/random-effects.R |only unmarked-1.2.3/unmarked/inst/doc/random-effects.Rnw |only unmarked-1.2.3/unmarked/inst/doc/random-effects.pdf |only unmarked-1.2.3/unmarked/inst/doc/simulate.Rnw |only unmarked-1.2.3/unmarked/inst/doc/simulate.pdf |only unmarked-1.2.3/unmarked/inst/doc/spp-dist.Rnw |only unmarked-1.2.3/unmarked/inst/doc/spp-dist.pdf |only unmarked-1.2.3/unmarked/inst/doc/unmarked.Rnw |only unmarked-1.2.3/unmarked/inst/doc/unmarked.pdf |only unmarked-1.2.3/unmarked/vignettes/cap-recap.Rnw |only unmarked-1.2.3/unmarked/vignettes/colext-cov.pdf |only unmarked-1.2.3/unmarked/vignettes/colext-gof.pdf |only unmarked-1.2.3/unmarked/vignettes/colext-yearlysim.pdf |only unmarked-1.2.3/unmarked/vignettes/colext.Rnw |only unmarked-1.2.3/unmarked/vignettes/distsamp.Rnw |only unmarked-1.2.3/unmarked/vignettes/ecology.bst |only unmarked-1.2.3/unmarked/vignettes/occuMulti.Rnw |only unmarked-1.2.3/unmarked/vignettes/powerAnalysis.Rnw |only unmarked-1.2.3/unmarked/vignettes/random-effects.Rnw |only unmarked-1.2.3/unmarked/vignettes/simulate.Rnw |only unmarked-1.2.3/unmarked/vignettes/spp-dist-psi2.pdf |only unmarked-1.2.3/unmarked/vignettes/spp-dist.Rnw |only unmarked-1.2.3/unmarked/vignettes/unmarked.Rnw |only unmarked-1.2.5/unmarked/DESCRIPTION | 23 +- unmarked-1.2.5/unmarked/MD5 | 83 ++++------ unmarked-1.2.5/unmarked/NEWS.md | 6 unmarked-1.2.5/unmarked/build/vignette.rds |binary unmarked-1.2.5/unmarked/inst/doc/cap-recap.R | 135 ++++++----------- unmarked-1.2.5/unmarked/inst/doc/cap-recap.Rmd |only unmarked-1.2.5/unmarked/inst/doc/cap-recap.html |only unmarked-1.2.5/unmarked/inst/doc/distsamp.R | 75 +-------- unmarked-1.2.5/unmarked/inst/doc/distsamp.Rmd |only unmarked-1.2.5/unmarked/inst/doc/distsamp.html |only unmarked-1.2.5/unmarked/inst/doc/powerAnalysis.R | 135 +++-------------- unmarked-1.2.5/unmarked/inst/doc/powerAnalysis.Rmd |only unmarked-1.2.5/unmarked/inst/doc/powerAnalysis.html |only unmarked-1.2.5/unmarked/inst/doc/simulate.R | 121 ++------------- unmarked-1.2.5/unmarked/inst/doc/simulate.Rmd |only unmarked-1.2.5/unmarked/inst/doc/simulate.html |only unmarked-1.2.5/unmarked/inst/doc/spp-dist.R | 133 +++++----------- unmarked-1.2.5/unmarked/inst/doc/spp-dist.Rmd |only unmarked-1.2.5/unmarked/inst/doc/spp-dist.html |only unmarked-1.2.5/unmarked/inst/doc/unmarked.R | 97 ++++-------- unmarked-1.2.5/unmarked/inst/doc/unmarked.Rmd |only unmarked-1.2.5/unmarked/inst/doc/unmarked.html |only unmarked-1.2.5/unmarked/man/cruz.Rd | 2 unmarked-1.2.5/unmarked/vignettes/cap-recap.Rmd |only unmarked-1.2.5/unmarked/vignettes/colext-data-1.png |only unmarked-1.2.5/unmarked/vignettes/colext-est-1.png |only unmarked-1.2.5/unmarked/vignettes/colext-gof-1.png |only unmarked-1.2.5/unmarked/vignettes/colext-pred-1.png |only unmarked-1.2.5/unmarked/vignettes/colext.R |only unmarked-1.2.5/unmarked/vignettes/colext.Rmd.orig |only unmarked-1.2.5/unmarked/vignettes/colext.html |only unmarked-1.2.5/unmarked/vignettes/distsamp.Rmd |only unmarked-1.2.5/unmarked/vignettes/ecology.csl |only unmarked-1.2.5/unmarked/vignettes/powerAnalysis.Rmd |only unmarked-1.2.5/unmarked/vignettes/simulate.Rmd |only unmarked-1.2.5/unmarked/vignettes/spp-dist.Rmd |only unmarked-1.2.5/unmarked/vignettes/unmarked.Rmd |only unmarked-1.2.5/unmarked/vignettes/unmarked.bib | 106 +++++++++++++ 73 files changed, 353 insertions(+), 563 deletions(-)
More information about terminaldigits at CRAN
Permanent link
Title: Extreme Value Analysis for Circular Data
Description: General functions for performing extreme value analysis on a circular
domain as part of the statistical methodology in the paper by Konzen, E.,
Neves, C., and Jonathan, P. (2021). Modeling nonstationary extremes of storm severity: Comparing parametric and semiparametric inference. Environmetrics, 32(4), e2667.
Author: Evandro Konzen
Maintainer: Evandro Konzen <circularev.r@gmail.com>
Diff between circularEV versions 0.1.0 dated 2021-01-21 and 0.1.1 dated 2022-05-13
DESCRIPTION | 14 ++++++-------- MD5 | 24 ++++++++++++------------ R/LocalEstim.R | 2 +- R/SplineML.R | 2 +- R/ThrSelection.R | 2 +- inst/doc/localMethods.R | 26 +++++++++++++------------- inst/doc/localMethods.html | 38 ++++++++++++++++++++++++++------------ inst/doc/splineML.R | 28 ++++++++++++++-------------- inst/doc/splineML.html | 38 ++++++++++++++++++++++++++------------ man/LocalEstim.Rd | 2 +- man/SplineML.Rd | 2 +- man/ThrSelection.Rd | 2 +- man/circularEV-package.Rd | 4 +--- 13 files changed, 104 insertions(+), 80 deletions(-)
Title: Simple Image Viewer for R Using the 'tcltk' Package
Description: A 'Tcl/Tk' Graphical User Interface (GUI) to display images than can be zoomed and panned using the mouse and keyboard shortcuts. 'tkImgR' read and write different image formats (PPM/PGM, PNG and GIF) using the standard 'Tcl/Tk' distribution (>=8.6), but other formats (JPEG, TIFF, CR2) can be handled using the 'tkImg' package for 'Tcl/Tk'.
Author: Filipe Campelo [aut, cre]
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Diff between tkImgR versions 0.0.1 dated 2022-05-02 and 0.0.5 dated 2022-05-13
tkImgR-0.0.1/tkImgR/tests/testthat.R |only tkImgR-0.0.5/tkImgR/DESCRIPTION | 17 ++-- tkImgR-0.0.5/tkImgR/MD5 | 19 ++-- tkImgR-0.0.5/tkImgR/R/functions.R | 104 +++++++++++++++++++++----- tkImgR-0.0.5/tkImgR/R/tkcanvasCommands.R | 26 ++++++ tkImgR-0.0.5/tkImgR/R/tkimageCommands.R | 86 +++++++++++++++++---- tkImgR-0.0.5/tkImgR/R/zzz.R | 2 tkImgR-0.0.5/tkImgR/man/tkImShow.Rd | 25 +++++- tkImgR-0.0.5/tkImgR/man/tkcanvasCommands.Rd | 27 ++++++ tkImgR-0.0.5/tkImgR/man/tkimageCommands.Rd | 74 ++++++++++++++++-- tkImgR-0.0.5/tkImgR/tests/testthat/testthat.R | 52 +++++++++++-- 11 files changed, 362 insertions(+), 70 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut] ,
Scott Chamberlain [aut] ,
Hilmar Lapp [aut] ,
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.4.6 dated 2022-02-08 and 2.4.7 dated 2022-05-13
DESCRIPTION | 8 MD5 | 45 ++--- NEWS.md | 7 R/add_characters.R | 8 R/add_trees.R | 4 R/classes.R | 2 R/nexml_add.R | 7 R/nexml_write.R | 30 --- R/utils.R | 11 + README.md | 4 build/vignette.rds |binary inst/doc/S4.html | 263 +++++++++++++++++++++++++++++-- inst/doc/intro.html | 266 +++++++++++++++++++++++++++++-- inst/doc/metadata.html | 303 +++++++++++++++++++++++++++++++++--- inst/doc/simmap.html | 326 +++++++++++++++++++++++++++++++++++---- inst/doc/sparql.html | 248 ++++++++++++++++++++++++++++- man/add_characters.Rd | 5 man/add_trees.Rd | 5 man/nexml_add.Rd | 6 man/nexml_write.Rd | 30 --- tests/testthat/Rplots.pdf |only tests/testthat/helper-RNeXML.R | 1 tests/testthat/test_global_ids.R | 5 tests/testthat/test_publish.R | 1 24 files changed, 1362 insertions(+), 223 deletions(-)
Title: Computing Envelope Estimators
Description: Provides a general routine, envMU, which allows estimation of the M envelope of span(U) given root n consistent estimators of M and U. The routine envMU does not presume a model. This package implements response envelopes, partial response envelopes, envelopes in the predictor space, heteroscedastic envelopes, simultaneous envelopes, scaled response envelopes, scaled envelopes in the predictor space, groupwise envelopes, weighted envelopes, envelopes in logistic regression and envelopes in Poisson regression. For each of these model-based routines the package provides inference tools including bootstrap, cross validation, estimation and prediction, hypothesis testing on coefficients are included except for weighted envelopes. Tools for selection of dimension include AIC, BIC and likelihood ratio testing. Background is available at Cook, R. D., Forzani, L. and Su, Z. (2016) <doi:10.1016/j.jmva.2016.05.006>. Optimization is based on a clockwise coordinate descent algorithm.
Author: Minji Lee, Zhihua Su
Maintainer: Minji Lee <minjilee101@gmail.com>
Diff between Renvlp versions 3.0 dated 2021-09-11 and 3.1 dated 2022-05-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/envMU.R | 15 ++++++++++++--- man/Renvlp.Rd | 6 +++--- man/stenv.Rd | 2 +- 5 files changed, 25 insertions(+), 16 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models and generalized linear and additive multilevel models (see Piironen,
Paasiniemi and Vehtari, 2020, <doi:10.1214/20-EJS1711>; Catalina, Bürkner
and Vehtari, 2020, <arXiv:2010.06994>). The package is compatible with the
'rstanarm' and 'brms' packages, but other reference models can also be used.
See the documentation as well as the package vignette for more information
and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb]
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between projpred versions 2.1.1 dated 2022-04-03 and 2.1.2 dated 2022-05-13
DESCRIPTION | 8 MD5 | 63 +++--- NEWS.md | 22 ++ R/cv_varsel.R | 47 ++-- R/divergence_minimizers.R | 50 +++-- R/formula.R | 36 --- R/methods.R | 58 ++--- R/misc.R | 6 R/project.R | 6 R/refmodel.R | 90 ++++----- R/search.R | 9 R/varsel.R | 91 ++++++--- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/projpred.R | 164 ++++++++-------- inst/doc/projpred.Rmd | 20 -- inst/doc/projpred.html | 358 +++++++++++++++++++++---------------- man/cv_varsel.Rd | 42 +++- man/figures |only man/plot.vsel.Rd | 2 man/refmodel-init-get.Rd | 22 +- man/summary.vsel.Rd | 2 man/varsel.Rd | 42 +++- tests/testthat/helpers/testers.R | 166 ++++++++++------- tests/testthat/setup.R | 329 +++++++++++++++++++++------------- tests/testthat/test_datafit.R | 14 + tests/testthat/test_formula.R | 68 ++++++- tests/testthat/test_methods_vsel.R | 6 tests/testthat/test_proj_pred.R | 16 - tests/testthat/test_refmodel.R | 80 +++----- tests/testthat/test_varsel.R | 127 +++++++++---- vignettes/projpred.Rmd | 20 -- 33 files changed, 1180 insertions(+), 786 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the
Oceanographic literature. This package is discussed extensively by
Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Author: Dan Kelley [aut, cre] ,
Clark Richards [aut] ,
Chantelle Layton [ctb]
coauthor),
British Geological Survey [ctb, cph]
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 1.7-2 dated 2022-03-22 and 1.7-3 dated 2022-05-13
oce-1.7-2/oce/inst/extdata/test_met_vsn1.csv |only oce-1.7-2/oce/inst/extdata/test_met_vsn2.csv |only oce-1.7-2/oce/inst/extdata/test_met_vsn3.csv |only oce-1.7-2/oce/inst/extdata/test_met_xml2.xml |only oce-1.7-2/oce/man/figures/oce-demo-1.png |only oce-1.7-2/oce/man/figures/oce-demo-2.png |only oce-1.7-2/oce/man/figures/oce-demo-3.png |only oce-1.7-2/oce/man/figures/oce-demo-4.png |only oce-1.7-2/oce/man/figures/oce-demo-5.png |only oce-1.7-2/oce/man/figures/oce-demo-6.png |only oce-1.7-2/oce/man/test_met_csv1.csv.Rd |only oce-1.7-2/oce/man/test_met_csv2.csv.Rd |only oce-1.7-2/oce/man/test_met_xml2.xml.Rd |only oce-1.7-2/oce/tests/testthat/test_local_adp.R |only oce-1.7-2/oce/tests/testthat/test_local_adv.R |only oce-1.7-2/oce/tests/testthat/test_local_cm.R |only oce-1.7-2/oce/tests/testthat/test_local_coastline.R |only oce-1.7-2/oce/tests/testthat/test_local_ctd.R |only oce-1.7-2/oce/tests/testthat/test_local_gps.R |only oce-1.7-2/oce/tests/testthat/test_local_index.R |only oce-1.7-2/oce/tests/testthat/test_local_lobo.R |only oce-1.7-2/oce/tests/testthat/test_local_odf.R |only oce-1.7-2/oce/tests/testthat/test_local_plotProfile.R |only oce-1.7-2/oce/tests/testthat/test_local_satellite.R |only oce-1.7-2/oce/tests/testthat/test_local_section.R |only oce-1.7-2/oce/tests/testthat/test_met.R |only oce-1.7-3/oce/DESCRIPTION | 6 oce-1.7-3/oce/MD5 | 406 +- oce-1.7-3/oce/NAMESPACE | 4 oce-1.7-3/oce/NEWS.md | 13 oce-1.7-3/oce/R/AllClass.R | 3 oce-1.7-3/oce/R/adp.R | 2 oce-1.7-3/oce/R/adp.nortek.R | 28 oce-1.7-3/oce/R/air.R | 2 oce-1.7-3/oce/R/argo.R | 40 oce-1.7-3/oce/R/argo.copernicus.R |only oce-1.7-3/oce/R/coastline.R | 9 oce-1.7-3/oce/R/colors.R | 13 oce-1.7-3/oce/R/ctd.R | 167 - oce-1.7-3/oce/R/ctd.aml.R | 3 oce-1.7-3/oce/R/ctd.odv.R | 4 oce-1.7-3/oce/R/ctd.sbe.R | 4 oce-1.7-3/oce/R/ctd.ssda.R |only oce-1.7-3/oce/R/ctd.woce.R | 6 oce-1.7-3/oce/R/echosounder.R | 2 oce-1.7-3/oce/R/extdata.R | 71 oce-1.7-3/oce/R/gps.R | 8 oce-1.7-3/oce/R/imagep.R | 7 oce-1.7-3/oce/R/index.R | 2 oce-1.7-3/oce/R/landsat.R | 4 oce-1.7-3/oce/R/map.R | 30 oce-1.7-3/oce/R/met.R | 392 +- oce-1.7-3/oce/R/misc.R | 10 oce-1.7-3/oce/R/oce.R | 35 oce-1.7-3/oce/R/odf.R | 434 +-- oce-1.7-3/oce/R/rsk.R | 2 oce-1.7-3/oce/R/section.R | 2167 +++++++-------- oce-1.7-3/oce/R/sw.R | 243 + oce-1.7-3/oce/R/topo.R | 31 oce-1.7-3/oce/build/partial.rdb |binary oce-1.7-3/oce/build/vignette.rds |binary oce-1.7-3/oce/inst/WORDLIST | 6 oce-1.7-3/oce/inst/doc/A_oce.Rmd | 2 oce-1.7-3/oce/inst/doc/A_oce.html | 59 oce-1.7-3/oce/inst/doc/B_ctd.html | 17 oce-1.7-3/oce/inst/doc/C_adp.html | 26 oce-1.7-3/oce/inst/doc/D_map_projections.Rmd | 10 oce-1.7-3/oce/inst/doc/D_map_projections.html | 68 oce-1.7-3/oce/inst/doc/E_flags.Rmd | 2 oce-1.7-3/oce/inst/doc/E_flags.html | 44 oce-1.7-3/oce/inst/doc/F_subclassing.Rmd | 2 oce-1.7-3/oce/inst/doc/F_subclassing.html | 45 oce-1.7-3/oce/inst/extdata/ctd_ssda.csv |only oce-1.7-3/oce/man/CTD_BCD2014666_008_1_DN.ODF.gz.Rd | 5 oce-1.7-3/oce/man/GMTOffsetFromTz.Rd | 2 oce-1.7-3/oce/man/addSpine.Rd | 15 oce-1.7-3/oce/man/adp_rdi.000.Rd | 3 oce-1.7-3/oce/man/airRho.Rd | 2 oce-1.7-3/oce/man/argo-class.Rd | 1 oce-1.7-3/oce/man/argo.Rd | 1 oce-1.7-3/oce/man/argoGrid.Rd | 1 oce-1.7-3/oce/man/argoNames2oceNames.Rd | 5 oce-1.7-3/oce/man/as.argo.Rd | 1 oce-1.7-3/oce/man/as.ctd.Rd | 2 oce-1.7-3/oce/man/as.met.Rd | 7 oce-1.7-3/oce/man/beamToXyzAdp.Rd | 2 oce-1.7-3/oce/man/cnvName2oceName.Rd | 4 oce-1.7-3/oce/man/coastlineWorld.Rd | 2 oce-1.7-3/oce/man/colormapGMT.Rd | 9 oce-1.7-3/oce/man/ctd-class.Rd | 4 oce-1.7-3/oce/man/ctd.Rd | 2 oce-1.7-3/oce/man/ctd.cnv.Rd | 5 oce-1.7-3/oce/man/ctdDecimate.Rd | 2 oce-1.7-3/oce/man/ctdFindProfiles.Rd | 2 oce-1.7-3/oce/man/ctdRaw.Rd | 2 oce-1.7-3/oce/man/ctdRepair.Rd | 2 oce-1.7-3/oce/man/ctdTrim.Rd | 2 oce-1.7-3/oce/man/ctd_aml.csv.Rd | 5 oce-1.7-3/oce/man/d200321-001.ctd.Rd | 5 oce-1.7-3/oce/man/d201211_0011.cnv.Rd | 5 oce-1.7-3/oce/man/decodeHeaderNortek.Rd | 2 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oce-1.7-3/oce/man/oceColorsCDOM.Rd | 4 oce-1.7-3/oce/man/oceColorsChlorophyll.Rd | 4 oce-1.7-3/oce/man/oceColorsDensity.Rd | 4 oce-1.7-3/oce/man/oceColorsFreesurface.Rd | 4 oce-1.7-3/oce/man/oceColorsOxygen.Rd | 4 oce-1.7-3/oce/man/oceColorsPAR.Rd | 4 oce-1.7-3/oce/man/oceColorsPhase.Rd | 4 oce-1.7-3/oce/man/oceColorsSalinity.Rd | 4 oce-1.7-3/oce/man/oceColorsTemperature.Rd | 4 oce-1.7-3/oce/man/oceColorsTurbidity.Rd | 4 oce-1.7-3/oce/man/oceColorsTurbo.Rd | 2 oce-1.7-3/oce/man/oceColorsVelocity.Rd | 4 oce-1.7-3/oce/man/oceColorsVorticity.Rd | 4 oce-1.7-3/oce/man/oceNames2whpNames.Rd | 4 oce-1.7-3/oce/man/oceUnits2whpUnits.Rd | 4 oce-1.7-3/oce/man/ocecolors.Rd | 2 oce-1.7-3/oce/man/plot-argo-method.Rd | 3 oce-1.7-3/oce/man/plot-ctd-method.Rd | 3 oce-1.7-3/oce/man/plot-met-method.Rd | 5 oce-1.7-3/oce/man/plot-section-method.Rd | 96 oce-1.7-3/oce/man/plotProfile.Rd | 4 oce-1.7-3/oce/man/plotScan.Rd | 2 oce-1.7-3/oce/man/plotTS.Rd | 29 oce-1.7-3/oce/man/read.adp.nortek.Rd | 4 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oce-1.7-3/oce/man/read.section.Rd | 2 oce-1.7-3/oce/man/read.topo.Rd | 1 oce-1.7-3/oce/man/rsk.Rd | 2 oce-1.7-3/oce/man/section-class.Rd | 2 oce-1.7-3/oce/man/section.Rd | 20 oce-1.7-3/oce/man/sectionGrid.Rd | 20 oce-1.7-3/oce/man/sectionSmooth.Rd | 1 oce-1.7-3/oce/man/sectionSort.Rd | 17 oce-1.7-3/oce/man/setFlags-ctd-method.Rd | 2 oce-1.7-3/oce/man/sub-sub-argo-method.Rd | 1 oce-1.7-3/oce/man/sub-sub-ctd-method.Rd | 2 oce-1.7-3/oce/man/sub-sub-met-method.Rd | 5 oce-1.7-3/oce/man/sub-sub-section-method.Rd | 6 oce-1.7-3/oce/man/sub-subset-argo-method.Rd | 1 oce-1.7-3/oce/man/sub-subset-ctd-method.Rd | 2 oce-1.7-3/oce/man/sub-subset-met-method.Rd | 5 oce-1.7-3/oce/man/subset-argo-method.Rd | 1 oce-1.7-3/oce/man/subset-ctd-method.Rd | 2 oce-1.7-3/oce/man/subset-met-method.Rd | 5 oce-1.7-3/oce/man/subset-section-method.Rd | 2 oce-1.7-3/oce/man/summary-argo-method.Rd | 1 oce-1.7-3/oce/man/summary-ctd-method.Rd | 2 oce-1.7-3/oce/man/summary-met-method.Rd | 5 oce-1.7-3/oce/man/swSigma0.Rd | 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oce-1.7-3/oce/vignettes/F_subclassing.Rmd | 2 220 files changed, 2899 insertions(+), 2790 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 Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [aut, ctb]
,
Alex Hayes [rev]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.17.0 dated 2022-03-29 and 0.17.1 dated 2022-05-13
DESCRIPTION | 27 - MD5 | 200 +++++------ NAMESPACE | 22 + NEWS.md | 33 + R/check_if_installed.R | 11 R/clean_parameters.R | 48 ++ R/ellipsis_info.R | 2 R/export_table.R | 48 ++ R/find_formula.R | 6 R/find_offset.R | 5 R/find_parameters.R | 14 R/find_parameters_other.R | 38 ++ R/find_predictors.R | 22 + R/find_statistic.R | 10 R/find_variables.R | 26 - R/format_message.R | 3 R/get_data.R | 167 +++------ R/get_df.R | 31 + R/get_loglikelihood.R | 60 +-- R/get_modelmatrix.R | 64 +++ R/get_parameters.R | 4 R/get_parameters_others.R | 57 +++ R/get_predicted.R | 53 ++- R/get_predicted_args.R | 15 R/get_predicted_bayesian.R | 11 R/get_predicted_ci.R | 77 ++-- R/get_predicted_gam.R | 1 R/get_predicted_mixed.R | 10 R/get_predicted_other.R | 1 R/get_predicted_se.R | 153 +------- R/get_statistic.R | 54 +++ R/get_varcov.R | 404 +++++++++++++++++------ R/get_varcov_sandwich.R |only R/is_mixed_model.R | 5 R/is_model.R | 7 R/is_model_supported.R | 15 R/model_info.R | 5 R/n_obs.R | 6 R/standardize_names.R | 5 R/text_remove_backticks.R | 9 R/utils_compact.R | 4 R/utils_get_data.R | 36 +- README.md | 177 ++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/display.html | 432 +++++++++++++++++++------ inst/doc/export.html | 250 +++++++++++++- inst/doc/insight.html | 384 ++++++++++++++++++++-- man/check_if_installed.Rd | 9 man/find_offset.Rd | 72 ++-- man/find_parameters.Rd | 26 + man/find_predictors.Rd | 26 + man/find_smooth.Rd | 54 +-- man/find_transformation.Rd | 74 ++-- man/find_variables.Rd | 31 + man/fish.Rd | 20 - man/format_message.Rd | 2 man/format_pd.Rd | 56 +-- man/get_data.Rd | 105 +----- man/get_parameters.Rd | 26 + man/get_predicted.Rd | 169 ++++----- man/get_predicted_ci.Rd |only man/get_varcov.Rd | 85 +++- man/has_intercept.Rd | 68 +-- man/is_gam_model.Rd | 68 +-- man/is_mixed_model.Rd | 58 +-- man/trim_ws.Rd | 94 ++--- tests/testthat/test-BayesFactorBF.R | 18 - tests/testthat/test-Gam2.R | 4 tests/testthat/test-afex_aov.R | 52 +-- tests/testthat/test-all_models_equal.R | 3 tests/testthat/test-backticks.R | 25 + tests/testthat/test-betabin.R | 5 tests/testthat/test-betareg.R | 35 ++ tests/testthat/test-bife.R | 11 tests/testthat/test-bigglm.R | 4 tests/testthat/test-blmer.R | 8 tests/testthat/test-censReg.R | 17 tests/testthat/test-cgam.R | 4 tests/testthat/test-coxph.R | 3 tests/testthat/test-cpglmm.R | 2 tests/testthat/test-ellipses_info.R | 6 tests/testthat/test-feis.R | 6 tests/testthat/test-find_predictor_nested_re.R | 2 tests/testthat/test-find_terms.R | 2 tests/testthat/test-fixest.R | 25 + tests/testthat/test-formatting.R | 9 tests/testthat/test-gamm.R | 4 tests/testthat/test-gamm4.R | 2 tests/testthat/test-gbm.R | 2 tests/testthat/test-geeglm.R | 5 tests/testthat/test-get_data.R | 22 - tests/testthat/test-get_modelmatrix-estimatr.R |only tests/testthat/test-get_predicted-iv.R |only tests/testthat/test-get_predicted.R | 4 tests/testthat/test-get_varcov.R |only tests/testthat/test-iv_robust.R | 29 + tests/testthat/test-lmer.R | 39 ++ tests/testthat/test-marginaleffects.R | 4 tests/testthat/test-mhurdle.R |only tests/testthat/test-rms.R | 29 + tests/testthat/test-standardize_names.R | 12 tests/testthat/test-zeroinfl.R | 20 + 104 files changed, 3101 insertions(+), 1376 deletions(-)
Title: Learning Graphical Models with Hubs
Description: Implements the hub graphical lasso and hub covariance graph proposal by Tan, KM., London, P., Mohan, K., Lee, S-I., Fazel, M., and Witten, D. (2014). Learning graphical models with hubs. Journal of Machine Learning Research 15(Oct):3297-3331.
Author: Kean Ming Tan
Maintainer: Kean Ming Tan <keanming@umich.edu>
Diff between hglasso versions 1.2 dated 2014-08-09 and 1.3 dated 2022-05-13
hglasso-1.2/hglasso/R/hglasso-internal.R |only hglasso-1.3/hglasso/DESCRIPTION | 14 +++++++------- hglasso-1.3/hglasso/MD5 | 11 +++++------ hglasso-1.3/hglasso/NAMESPACE | 7 +++++-- hglasso-1.3/hglasso/R/Functions.R | 2 +- hglasso-1.3/hglasso/man/hglasso-package.Rd | 2 +- hglasso-1.3/hglasso/man/summary.hglasso.Rd | 2 +- 7 files changed, 20 insertions(+), 18 deletions(-)
Title: Maximum Penalized Likelihood Estimation with Extended Lasso
Penalty
Description: Estimates coefficients of extended LASSO penalized linear regression and generalized linear models. Currently lasso and elastic net penalized linear regression and generalized linear models are considered. This package currently utilizes an accurate approximation of L1 penalty and then a modified Jacobi algorithm to estimate the coefficients. There is provision for plotting of the solutions and predictions of coefficients at given values of lambda. This package also contains functions for cross validation to select a suitable lambda value given the data. Also provides a function for estimation in fused lasso penalized linear regression. For more details, see Mandal, B. N.(2014). Computational methods for L1 penalized GLM model fitting, unpublished report submitted to Macquarie University, NSW, Australia.
Author: B N Mandal <mandal.stat@gmail.com> and Jun Ma <jun.ma@mq.edu.au>
Maintainer: B N Mandal <mandal.stat@gmail.com>
Diff between extlasso versions 0.2 dated 2014-08-19 and 0.3 dated 2022-05-13
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- NAMESPACE | 4 +++- 3 files changed, 12 insertions(+), 10 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Author: Olivier Broennimann [cre, aut, ctb],
Valeria Di Cola [aut, ctb],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Daniel Scherrer [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Heidi Mod [ctb],
Julien Potti [...truncated...]
Maintainer: Olivier Broennimann <olivier.broennimann@unil.ch>
Diff between ecospat versions 3.2.1 dated 2022-01-07 and 3.2.2 dated 2022-05-13
DESCRIPTION | 14 ++- MD5 | 47 ++++++------ NAMESPACE | 8 +- NEWS | 19 ++++- R/ecospat.CCV.R | 20 ++--- R/ecospat.ESM.EnsembleEvaluation.R |only R/ecospat.ESM.R | 129 +++++++++++++++++++--------------- R/ecospat.ESM.responsePlot.R | 31 ++++---- R/ecospat.ESM.threshold.R | 2 R/ecospat.boyce.R | 4 - R/ecospat.makeDataFrame.R | 13 +-- R/ecospat.nichePOSNB.R | 46 ++++++------ R/ecospat.nichedynamic.R | 11 ++ build/partial.rdb |binary inst/doc/vignette_ecospat_package.pdf |binary man/ecospat.ESM.EnsembleEvaluation.Rd |only man/ecospat.ESM.EnsembleModeling.Rd | 65 ----------------- man/ecospat.ESM.EnsembleProjection.Rd | 63 ---------------- man/ecospat.ESM.Modeling.Rd | 57 ++++++++------- man/ecospat.ESM.Projection.Rd | 65 +---------------- man/ecospat.ESM.VarContrib.Rd | 52 +------------ man/ecospat.ESM.responsePlot.Rd | 44 ----------- man/ecospat.ESM.threshold.Rd | 45 ----------- man/ecospat.nicheNBmean.Rd |only man/ecospat.nichePOSNB.Rd | 21 +++-- man/ecospat.testNichePOSNB.Rd | 2 26 files changed, 267 insertions(+), 491 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'Roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 7.1.2 dated 2021-09-08 and 7.2.0 dated 2022-05-13
roxygen2-7.1.2/roxygen2/tests/testthat/description-example.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/description-example_2.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/helper-pkg.R |only roxygen2-7.1.2/roxygen2/tests/testthat/markdown-code-errors.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/roxygen-block-3-warnings.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-block-print.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-markdown-table.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-format-r4.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-format.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-import.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-package-author.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-usage-wrap-new.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-object-usage-wrap-old.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examples-dontrun-escape-2.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examples-dontrun-escape.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examples-interleave.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examplesIf.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-inherit-dots-inherit.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-inherit-dots-multi.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-inherit-dots.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-inherit-link.txt |only roxygen2-7.2.0/roxygen2/DESCRIPTION | 55 roxygen2-7.2.0/roxygen2/MD5 | 279 ++- roxygen2-7.2.0/roxygen2/NAMESPACE | 2 roxygen2-7.2.0/roxygen2/NEWS.md | 74 + roxygen2-7.2.0/roxygen2/R/block.R | 11 roxygen2-7.2.0/roxygen2/R/collate.R | 8 roxygen2-7.2.0/roxygen2/R/field.R | 2 roxygen2-7.2.0/roxygen2/R/load.R | 6 roxygen2-7.2.0/roxygen2/R/markdown-escaping.R | 3 roxygen2-7.2.0/roxygen2/R/markdown-link.R | 13 roxygen2-7.2.0/roxygen2/R/markdown-state.R | 19 roxygen2-7.2.0/roxygen2/R/markdown.R | 74 - roxygen2-7.2.0/roxygen2/R/namespace.R | 52 roxygen2-7.2.0/roxygen2/R/object-defaults.R | 77 - roxygen2-7.2.0/roxygen2/R/object-from-call.R | 7 roxygen2-7.2.0/roxygen2/R/object-import.R | 43 roxygen2-7.2.0/roxygen2/R/object-package.R | 53 roxygen2-7.2.0/roxygen2/R/object-r6.R | 29 roxygen2-7.2.0/roxygen2/R/package_files.R | 2 roxygen2-7.2.0/roxygen2/R/rd-describe-in.R | 8 roxygen2-7.2.0/roxygen2/R/rd-examples.R | 11 roxygen2-7.2.0/roxygen2/R/rd-family.R | 3 roxygen2-7.2.0/roxygen2/R/rd-find-link-files.R | 21 roxygen2-7.2.0/roxygen2/R/rd-include-rmd.R | 8 roxygen2-7.2.0/roxygen2/R/rd-inherit.R | 219 +-- roxygen2-7.2.0/roxygen2/R/rd-markdown.R | 16 roxygen2-7.2.0/roxygen2/R/rd-r6.R | 97 - roxygen2-7.2.0/roxygen2/R/rd-raw.R | 14 roxygen2-7.2.0/roxygen2/R/rd-section.R | 6 roxygen2-7.2.0/roxygen2/R/rd-template.R | 4 roxygen2-7.2.0/roxygen2/R/rd-usage.R | 2 roxygen2-7.2.0/roxygen2/R/rd.R | 15 roxygen2-7.2.0/roxygen2/R/roclet.R | 2 roxygen2-7.2.0/roxygen2/R/roxygenize-setup.R |only roxygen2-7.2.0/roxygen2/R/roxygenize.R | 36 roxygen2-7.2.0/roxygen2/R/safety.R | 53 roxygen2-7.2.0/roxygen2/R/select-args.R | 32 roxygen2-7.2.0/roxygen2/R/tag-parser.R | 142 +- roxygen2-7.2.0/roxygen2/R/tag.R | 52 roxygen2-7.2.0/roxygen2/R/topic.R | 5 roxygen2-7.2.0/roxygen2/R/topics.R | 5 roxygen2-7.2.0/roxygen2/R/utils-io.R | 4 roxygen2-7.2.0/roxygen2/R/utils-rd.R | 46 roxygen2-7.2.0/roxygen2/R/utils.R | 26 roxygen2-7.2.0/roxygen2/R/vignette.R | 6 roxygen2-7.2.0/roxygen2/README.md | 2 roxygen2-7.2.0/roxygen2/build/vignette.rds |binary roxygen2-7.2.0/roxygen2/inst/doc/extending.Rmd | 34 roxygen2-7.2.0/roxygen2/inst/doc/extending.html | 354 ++++- roxygen2-7.2.0/roxygen2/inst/doc/namespace.R | 40 roxygen2-7.2.0/roxygen2/inst/doc/namespace.Rmd | 117 + roxygen2-7.2.0/roxygen2/inst/doc/namespace.html | 502 ++++++- roxygen2-7.2.0/roxygen2/inst/doc/rd-formatting.R | 120 + roxygen2-7.2.0/roxygen2/inst/doc/rd-formatting.Rmd | 231 ++- roxygen2-7.2.0/roxygen2/inst/doc/rd-formatting.html | 707 ++++++++-- roxygen2-7.2.0/roxygen2/inst/doc/rd.Rmd | 498 +++---- roxygen2-7.2.0/roxygen2/inst/doc/rd.html | 675 ++++++++- roxygen2-7.2.0/roxygen2/inst/doc/roxygen2.Rmd | 12 roxygen2-7.2.0/roxygen2/inst/doc/roxygen2.html | 290 +++- roxygen2-7.2.0/roxygen2/man/RoxyTopic.Rd | 72 - roxygen2-7.2.0/roxygen2/man/load.Rd | 6 roxygen2-7.2.0/roxygen2/man/load_options.Rd | 12 roxygen2-7.2.0/roxygen2/man/markdown_pass1.Rd | 30 roxygen2-7.2.0/roxygen2/man/roxy_tag.Rd | 8 roxygen2-7.2.0/roxygen2/man/roxygen2-package.Rd | 10 roxygen2-7.2.0/roxygen2/src/cpp11.cpp | 14 roxygen2-7.2.0/roxygen2/src/parser2.cpp | 15 roxygen2-7.2.0/roxygen2/src/wrapUsage.cpp | 3 roxygen2-7.2.0/roxygen2/tests/testthat.R | 6 roxygen2-7.2.0/roxygen2/tests/testthat/_snaps |only roxygen2-7.2.0/roxygen2/tests/testthat/empty/DESCRIPTION | 1 roxygen2-7.2.0/roxygen2/tests/testthat/helper-test.R | 16 roxygen2-7.2.0/roxygen2/tests/testthat/roxygen-block-3-A.Rd | 24 roxygen2-7.2.0/roxygen2/tests/testthat/roxygen-block-3-B.Rd | 34 roxygen2-7.2.0/roxygen2/tests/testthat/roxygen-block-3-C.Rd | 36 roxygen2-7.2.0/roxygen2/tests/testthat/test-block.R | 33 roxygen2-7.2.0/roxygen2/tests/testthat/test-collate.R | 48 roxygen2-7.2.0/roxygen2/tests/testthat/test-load.R | 2 roxygen2-7.2.0/roxygen2/tests/testthat/test-markdown-code.R | 151 +- roxygen2-7.2.0/roxygen2/tests/testthat/test-markdown-link.R | 29 roxygen2-7.2.0/roxygen2/tests/testthat/test-markdown-state.R | 45 roxygen2-7.2.0/roxygen2/tests/testthat/test-markdown.R | 78 - roxygen2-7.2.0/roxygen2/tests/testthat/test-namespace.R | 136 + roxygen2-7.2.0/roxygen2/tests/testthat/test-object-defaults.R | 27 roxygen2-7.2.0/roxygen2/tests/testthat/test-object-format.R | 9 roxygen2-7.2.0/roxygen2/tests/testthat/test-object-from-call.R | 25 roxygen2-7.2.0/roxygen2/tests/testthat/test-object-import.R | 34 roxygen2-7.2.0/roxygen2/tests/testthat/test-object-package.R | 60 roxygen2-7.2.0/roxygen2/tests/testthat/test-object-r6.R |only roxygen2-7.2.0/roxygen2/tests/testthat/test-package_files.R | 19 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-describe-in.R | 37 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-examples.R | 30 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-find-link-files.R |only roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-include-rmd.R | 20 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-inherit.R | 195 ++ roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-markdown-escaping.R | 2 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-markdown.R | 29 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-r6.R | 39 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-raw.R | 31 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-section.R | 5 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-template.R | 8 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd-usage.R | 20 roxygen2-7.2.0/roxygen2/tests/testthat/test-rd.R | 107 - roxygen2-7.2.0/roxygen2/tests/testthat/test-roxygenize-setup.R |only roxygen2-7.2.0/roxygen2/tests/testthat/test-safety.R | 6 roxygen2-7.2.0/roxygen2/tests/testthat/test-select-args.R | 12 roxygen2-7.2.0/roxygen2/tests/testthat/test-tag-parser.R |only roxygen2-7.2.0/roxygen2/tests/testthat/test-tag.R | 10 roxygen2-7.2.0/roxygen2/tests/testthat/test-tokenize.R | 20 roxygen2-7.2.0/roxygen2/tests/testthat/test-topics.R |only roxygen2-7.2.0/roxygen2/tests/testthat/test-utils-io.R | 74 - roxygen2-7.2.0/roxygen2/tests/testthat/test-utils-rd.R | 14 roxygen2-7.2.0/roxygen2/tests/testthat/test-utils.R | 34 roxygen2-7.2.0/roxygen2/tests/testthat/testNamespace/DESCRIPTION | 2 roxygen2-7.2.0/roxygen2/tests/testthat/testNonASCII/R/a.r | 1 roxygen2-7.2.0/roxygen2/vignettes/extending.Rmd | 34 roxygen2-7.2.0/roxygen2/vignettes/namespace.Rmd | 117 + roxygen2-7.2.0/roxygen2/vignettes/rd-formatting.Rmd | 231 ++- roxygen2-7.2.0/roxygen2/vignettes/rd.Rmd | 498 +++---- roxygen2-7.2.0/roxygen2/vignettes/roxygen2.Rmd | 12 141 files changed, 5283 insertions(+), 2512 deletions(-)
Title: Pipeline Tools Inspired by 'GNU Make'
Description: A suite of tools for transforming an existing workflow into a
self-documenting pipeline with very minimal upfront costs. Segments of
the pipeline are specified in much the same way a 'Make' rule is, by
declaring an executable recipe (which might be an R script), along
with the corresponding targets and dependencies. When the entire
pipeline is run through, only those recipes that need to be executed
will be. Meanwhile, execution metadata is captured behind the scenes
for later inspection.
Author: Kinto Behr [aut, cre, cph]
Maintainer: Kinto Behr <kinto.behr@gmail.com>
Diff between makepipe versions 0.1.0 dated 2021-11-23 and 0.2.0 dated 2022-05-13
makepipe-0.1.0/makepipe/man/figures/README-example_pipeline.png |only makepipe-0.2.0/makepipe/DESCRIPTION | 11 makepipe-0.2.0/makepipe/MD5 | 45 - makepipe-0.2.0/makepipe/NAMESPACE | 1 makepipe-0.2.0/makepipe/NEWS.md | 155 +--- makepipe-0.2.0/makepipe/R/Pipeline.R | 384 ++++++++-- makepipe-0.2.0/makepipe/R/Segment.R | 13 makepipe-0.2.0/makepipe/R/make.R | 27 makepipe-0.2.0/makepipe/R/out_of_date.R | 79 +- makepipe-0.2.0/makepipe/R/params.R | 2 makepipe-0.2.0/makepipe/R/utils.R | 69 + makepipe-0.2.0/makepipe/README.md | 75 + makepipe-0.2.0/makepipe/inst/doc/makepipe.html | 196 +++++ makepipe-0.2.0/makepipe/man/Pipeline.Rd | 135 +++ makepipe-0.2.0/makepipe/man/figures/pipeline_nomnoml_outofdate.png |only makepipe-0.2.0/makepipe/man/figures/pipeline_nomnoml_uptodate.png |only makepipe-0.2.0/makepipe/man/figures/pipeline_visnetwork_outofdate.png |only makepipe-0.2.0/makepipe/man/figures/pipeline_visnetwork_uptodate.png |only makepipe-0.2.0/makepipe/man/make_params.Rd | 3 makepipe-0.2.0/makepipe/man/make_with_recipe.Rd | 8 makepipe-0.2.0/makepipe/man/make_with_source.Rd | 8 makepipe-0.2.0/makepipe/man/pipeline-accessors.Rd | 14 makepipe-0.2.0/makepipe/man/pipeline-vis.Rd | 39 - makepipe-0.2.0/makepipe/tests/testthat/_snaps/Pipeline |only makepipe-0.2.0/makepipe/tests/testthat/test-Pipeline.R | 62 + makepipe-0.2.0/makepipe/tests/testthat/test-make.R | 42 - makepipe-0.2.0/makepipe/tests/testthat/test-utils.R |only 27 files changed, 1102 insertions(+), 266 deletions(-)
Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents
according to Geneva Graduate Institute conventions and regulations.
The most common use is for writing and compiling theses or thesis
chapters, as drafts or for examination with correct preamble formatting.
However, the package also offers users to create HTML presentation
slides with 'xaringan', complete problem sets, format posters, and,
for course instructors, prepare a syllabus.
The package includes additional functions for institutional color palettes,
an institutional 'ggplot' theme, a function for counting manuscript words,
and a bibliographical analysis toolkit.
Author: James Hollway [aut, cre, cph] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between iheiddown versions 0.9.2 dated 2022-05-06 and 0.9.3 dated 2022-05-13
DESCRIPTION | 8 MD5 | 22 NEWS.md | 7 R/bibstats.R | 16 build/vignette.rds |binary inst/doc/poster.html | 276 ++++++- inst/doc/presentations.html | 387 ++++++++-- inst/doc/problemset.html | 267 ++++++ inst/doc/syllabus.html | 261 ++++++ inst/doc/thesis.html | 352 ++++++++- inst/rmarkdown/templates/iheiddown_poster/resources/template.html | 12 tests/testthat/test-countwords.R | 1 12 files changed, 1441 insertions(+), 168 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 0.9.12 dated 2022-02-12 and 1.0 dated 2022-05-13
survivoR-0.9.12/survivoR/data/challenges.rda |only survivoR-0.9.12/survivoR/man/challenges.Rd |only survivoR-1.0/survivoR/DESCRIPTION | 17 survivoR-1.0/survivoR/MD5 | 64 + survivoR-1.0/survivoR/NEWS.md | 24 survivoR-1.0/survivoR/R/datasets.R | 190 +++-- survivoR-1.0/survivoR/README.md | 594 +++++++++++------- survivoR-1.0/survivoR/data/advantage_details.rda |only survivoR-1.0/survivoR/data/advantage_movement.rda |only survivoR-1.0/survivoR/data/boot-mapping.rda |only survivoR-1.0/survivoR/data/castaway_details.rda |binary survivoR-1.0/survivoR/data/castaways.rda |binary survivoR-1.0/survivoR/data/challenge_description.rda |binary survivoR-1.0/survivoR/data/challenge_results.rda |binary survivoR-1.0/survivoR/data/confessionals.rda |binary survivoR-1.0/survivoR/data/jury-votes.rda |binary survivoR-1.0/survivoR/data/season-palettes.rda |binary survivoR-1.0/survivoR/data/season-summary.rda |binary survivoR-1.0/survivoR/data/tribe-colours.rda |binary survivoR-1.0/survivoR/data/tribe-mapping.rda |binary survivoR-1.0/survivoR/data/viewers.rda |binary survivoR-1.0/survivoR/data/vote-history.rda |binary survivoR-1.0/survivoR/man/advantage_details.Rd |only survivoR-1.0/survivoR/man/advantage_movement.Rd |only survivoR-1.0/survivoR/man/boot_mapping.Rd |only survivoR-1.0/survivoR/man/castaway_details.Rd | 2 survivoR-1.0/survivoR/man/castaways.Rd | 10 survivoR-1.0/survivoR/man/challenge_results.Rd | 2 survivoR-1.0/survivoR/man/confessionals.Rd | 19 survivoR-1.0/survivoR/man/hidden_idols.Rd | 8 survivoR-1.0/survivoR/man/jury_votes.Rd | 4 survivoR-1.0/survivoR/man/season_summary.Rd | 2 survivoR-1.0/survivoR/man/tribe_colours.Rd | 2 survivoR-1.0/survivoR/man/tribe_mapping.Rd | 10 survivoR-1.0/survivoR/man/viewers.Rd | 2 survivoR-1.0/survivoR/man/vote_history.Rd | 9 survivoR-1.0/survivoR/tests/testthat/test-castaways.R | 16 37 files changed, 634 insertions(+), 341 deletions(-)
Title: Assign Treatments, Power Calculations, Balances, Impact
Evaluation of Experiments
Description: Assists in the whole process of designing and evaluating Randomized Control Trials.
Robust treatment assignment by strata/blocks, that handles misfits;
Power calculations of the minimum detectable treatment effect or minimum populations;
Balance tables of T-test of covariates;
Balance Regression: (treatment ~ all x variables) with F-test of null model;
Impact_evaluation: Impact evaluation regressions. This function
gives you the option to include control_vars, fixed effect variables,
cluster variables (for robust SE), multiple endogenous variables and
multiple heterogeneous variables (to test treatment effect heterogeneity)
summary_statistics: Function that creates a summary statistics table with statistics
rank observations in n groups: Creates a factor variable with n groups. Each group has
a min and max label attach to each category.
Athey, Susan, and Guido W. Imbens (2017) <arXiv:1607.00698>.
Author: Isidoro Garcia-Urquieta [aut, cre]
Maintainer: Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>
Diff between RCT versions 1.1.1 dated 2021-08-02 and 1.1.2 dated 2022-05-13
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 5 R/impact_eval.R | 4 README.md | 1 build/vignette.rds |binary inst/doc/my-vignette.html | 199 +++++++++++++++++++++++++++----------- tests/testthat/test_impact_eval.R | 22 +++- 8 files changed, 183 insertions(+), 70 deletions(-)
Title: Translation Layer from MATLAB to R
Description: Allows users familiar with MATLAB to use MATLAB-named functions in
R. Several basic MATLAB functions are written in this package to mimic the
behavior of their original counterparts, with more to come as this package
grows.
Author: Waldir Leoncio [aut, cre]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between matlab2r versions 1.1.0 dated 2022-04-13 and 1.1.1 dated 2022-05-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/matlab2r.R | 7 ++----- R/setdiff.R | 1 + man/isspace.Rd | 2 +- 5 files changed, 12 insertions(+), 14 deletions(-)
Title: Regularization for Semiparametric Additive Hazards Regression
Description: Computationally efficient procedures for regularized
estimation with the semiparametric additive hazards regression
model.
Author: Anders Gorst-Rasmussen <agorstras@gmail.com>
Maintainer: Anders Gorst-Rasmussen <agorstras@gmail.com>
Diff between ahaz versions 1.14 dated 2013-06-03 and 1.15 dated 2022-05-13
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NAMESPACE | 6 ++++++ R/helpers.R | 4 ++-- inst/CITATION | 4 ++-- man/ahazpen.Rd | 4 ++-- src/ahaz.c | 18 +++++++++++++++--- 7 files changed, 40 insertions(+), 22 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-18 1.0.1
2019-06-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-08 0.1.0
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] ,
Chester Ismay [aut] ,
Andrew Bray [ctb] ,
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] ,
Will Hopper [ctb] ,
Benjamin S. Baumer [ctb] ,
Marium Tapal [ctb] ,
Wayne Ndlovu [ctb],
Catherine Peppers [ctb],
Annah Mutaya [ctb],
A [...truncated...]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.5.3 dated 2022-01-20 and 0.5.4 dated 2022-05-13
moderndive-0.5.3/moderndive/vignettes/kaggle.png |only moderndive-0.5.3/moderndive/vignettes/leaderboard_orig.png |only moderndive-0.5.4/moderndive/DESCRIPTION | 84 ++ moderndive-0.5.4/moderndive/MD5 | 45 + moderndive-0.5.4/moderndive/NEWS.md | 20 moderndive-0.5.4/moderndive/R/datasets.R | 303 ++++++++++ moderndive-0.5.4/moderndive/build/partial.rdb |only moderndive-0.5.4/moderndive/data/amazon_books.rda |only moderndive-0.5.4/moderndive/data/avocados.rda |only moderndive-0.5.4/moderndive/data/babies.rda |only moderndive-0.5.4/moderndive/data/coffee_ratings.rda |only moderndive-0.5.4/moderndive/data/early_january_weather.rda |only moderndive-0.5.4/moderndive/data/ev_charging.rda |only moderndive-0.5.4/moderndive/data/ipf_lifts.rda |only moderndive-0.5.4/moderndive/data/ma_traffic_2020_vs_2019.rda |only moderndive-0.5.4/moderndive/data/mario_kart_auction.rda |only moderndive-0.5.4/moderndive/data/mass_traffic_2020.rda |only moderndive-0.5.4/moderndive/data/saratoga_houses.rda |only moderndive-0.5.4/moderndive/inst/doc/moderndive.R | 2 moderndive-0.5.4/moderndive/inst/doc/moderndive.Rmd | 4 moderndive-0.5.4/moderndive/inst/doc/moderndive.html | 9 moderndive-0.5.4/moderndive/man/amazon_books.Rd |only moderndive-0.5.4/moderndive/man/avocados.Rd |only moderndive-0.5.4/moderndive/man/babies.Rd |only moderndive-0.5.4/moderndive/man/coffee_ratings.Rd |only moderndive-0.5.4/moderndive/man/early_january_weather.Rd |only moderndive-0.5.4/moderndive/man/ev_charging.Rd |only moderndive-0.5.4/moderndive/man/figures/kaggle.jpeg |only moderndive-0.5.4/moderndive/man/figures/leaderboard_orig.jpeg |only moderndive-0.5.4/moderndive/man/ipf_lifts.Rd |only moderndive-0.5.4/moderndive/man/ma_traffic_2020_vs_2019.Rd |only moderndive-0.5.4/moderndive/man/mario_kart_auction.Rd |only moderndive-0.5.4/moderndive/man/mass_traffic_2020.Rd |only moderndive-0.5.4/moderndive/man/saratoga_houses.Rd |only moderndive-0.5.4/moderndive/vignettes/kaggle.jpeg |only moderndive-0.5.4/moderndive/vignettes/leaderboard_orig.jpeg |only moderndive-0.5.4/moderndive/vignettes/moderndive.Rmd | 4 moderndive-0.5.4/moderndive/vignettes/paper.html | 15 38 files changed, 453 insertions(+), 33 deletions(-)