Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium,
deemed D-statistics, for pairs of loci. Beissinger et al. (2016) <doi:10.1038/hdy.2015.81>.
Author: Paul F. Petrowski <pfpetrowski@mail.missouri.edu> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@mail.missouri.edu>
Diff between ohtadstats versions 1.1.1 dated 2018-05-27 and 1.2.1 dated 2018-08-14
DESCRIPTION | 13 +++++++------ MD5 | 13 ++++++++----- NAMESPACE | 1 + R/determinejob.R |only R/dparallel.R |only R/dstat.R | 2 +- R/dwrapper.R | 2 +- man/dparallel.Rd |only man/dwrapper.Rd | 2 +- 9 files changed, 19 insertions(+), 14 deletions(-)
Title: Interface to the Search API for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search API (<http://api.plos.org/>) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.8.2 dated 2018-07-19 and 0.8.4 dated 2018-08-14
DESCRIPTION | 14 +- MD5 | 53 ++++----- NEWS.md | 12 ++ R/searchplos.R | 18 +-- README.md | 78 +++++++------- inst/doc/facethighlight.Rmd | 48 ++++---- inst/doc/facethighlight.html | 52 ++++----- inst/doc/rplos_vignette.Rmd | 42 +++---- inst/doc/rplos_vignette.html | 46 ++++---- inst/vign/facethighlight.md | 48 ++++---- inst/vign/figure/plosword1plot-1.png |binary inst/vign/figure/throughtime1-1.png |binary inst/vign/rplos_vignette.md | 42 +++---- man/facetplos.Rd | 13 +- man/highplos.Rd | 15 +- man/plosabstract.Rd | 22 +++ man/plosauthor.Rd | 22 +++ man/plosfigtabcaps.Rd | 22 +++ man/plossubject.Rd | 22 +++ man/plostitle.Rd | 16 ++ man/plosviews.Rd | 3 man/rplos.Rd | 1 man/searchplos.Rd | 22 +++ tests/fixtures/vcr_cassettes/searchplos_large_numbers.yml |only tests/testthat/test-searchplos.R | 26 +++- tools/unnamed-chunk-21-1.png |binary vignettes/facethighlight.Rmd | 48 ++++---- vignettes/rplos_vignette.Rmd | 42 +++---- 28 files changed, 418 insertions(+), 309 deletions(-)
Title: Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests
Description: Implements the Lilliefors-corrected Kolmogorov-Smirnov test for use
in goodness-of-fit tests, suitable when population parameters are unknown and
must be estimated by sample statistics. P-values are estimated by simulation.
Can be used with a variety of continuous distributions, including normal,
lognormal, univariate mixtures of normals, uniform, loguniform, exponential,
gamma, and Weibull distributions. Functions to generate random numbers and
calculate density, distribution, and quantile functions are provided for use
with the log uniform and mixture distributions.
Author: Phil Novack-Gottshall, Steve C. Wang
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>
Diff between KScorrect versions 1.2.3 dated 2018-03-04 and 1.2.4 dated 2018-08-14
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 3 +++ R/LcKS.R | 10 +++++----- 4 files changed, 17 insertions(+), 14 deletions(-)
Title: Joint Analysis and Imputation of Incomplete Data
Description: Provides joint analysis and imputation of linear regression models,
generalized linear regression models or linear mixed models with incomplete
(covariate) data in the Bayesian framework.
The package performs some preprocessing of the data and creates a 'JAGS'
model, which will then automatically be passed to 'JAGS'
<http://mcmc-jags.sourceforge.net> with the help of
the package 'rjags'.
It also provides summary and plotting functions for the output.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>
Diff between JointAI versions 0.2.0 dated 2018-07-05 and 0.3.0 dated 2018-08-14
DESCRIPTION | 22 +- MD5 | 120 ++++++++----- NAMESPACE | 4 NEWS.md | 41 ++++ R/JointAI.R | 78 ++++++++ R/JointAIObject.R | 36 ++-- R/NHANES.R |only R/add_samples.R | 29 ++- R/convergence_criteria.R | 73 +++----- R/datasets.R | 6 R/divide_matrices.R | 119 +++++++------ R/get_MIdat.R | 34 ++- R/get_data_list.R | 48 +++-- R/get_imp_method.R | 17 + R/get_inits.R | 4 R/get_params.R | 49 +++-- R/get_refs.R | 111 +++++++++++- R/helpfunctions.R | 282 ++++++++++++++++++++------------ R/helpfunctions_impmodels.R | 194 ++++++++++++++-------- R/helpfunctions_post.R | 125 +++++++++----- R/impmodels_binary.R | 2 R/impmodels_continuous.R | 386 ++++++++++++++++++++++++++++---------------- R/impmodels_multinomial.R | 4 R/impmodels_ordinal.R | 6 R/md_pattern.R | 196 ++++++++++++++++------ R/model_imp.R | 180 +++++++++++++------- R/plots.R | 360 ++++++++++++++++++++++++++++++----------- R/predict.R | 19 +- R/print_functions.R |only R/simLong.R |only R/summary.JointAI.R | 68 +++---- build |only data/NHANES.RData |only data/simLong.RData |only data/simWide.RData |only inst |only man/GR_crit.Rd | 32 ++- man/JointAI.Rd | 47 ++++- man/JointAIObject.Rd | 36 ++-- man/MC_error.Rd | 31 ++- man/NHANES.Rd |only man/add_samples.Rd | 29 ++- man/default_hyperpars.Rd | 44 ++--- man/densplot.Rd | 64 +++++-- man/get_MIdat.Rd | 30 ++- man/get_imp_meth.Rd | 11 - man/list_impmodels.Rd |only man/longDF.Rd | 4 man/md_pattern.Rd | 39 ++-- man/model_imp.Rd | 111 +++++++----- man/parameters.Rd |only man/plot_all.Rd |only man/predDF.Rd | 11 - man/predict.JointAI.Rd | 10 - man/set_refcat.Rd |only man/sharedParams.Rd |only man/simLong.Rd |only man/sim_data.Rd | 7 man/summary.JointAI.Rd | 38 ++-- man/traceplot.Rd | 57 ++++-- man/wideDF.Rd | 2 vignettes |only 62 files changed, 2166 insertions(+), 1050 deletions(-)
Title: Import/Export Routines for 'MALDIquant'
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from 'MALDIquant'
objects.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>),
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.11.1 dated 2017-12-04 and 0.11.5 dated 2018-08-14
DESCRIPTION | 18 +++++---- MD5 | 59 +++++++++++++++--------------- NEWS | 31 +++++++++++++++ R/export-methods.R | 2 - R/import-functions.R | 2 - R/mzMl-functions.R | 13 +++--- R/parseMzMl.R | 2 - build/vignette.rds |binary inst/doc/MALDIquantForeign-intro.pdf |binary man/MALDIquantForeign-package.Rd | 7 +-- man/MALDIquantForeign-parallel.Rd | 7 +-- man/base64-encode.Rd | 7 +-- man/export-methods.Rd | 9 ++-- man/exportImzMl-methods.Rd | 9 ++-- man/exportMsd-methods.Rd | 9 ++-- man/exportMzMl-methods.Rd | 11 ++--- man/exportTab-methods.Rd | 13 +++--- man/import-functions.Rd | 12 +++--- man/importAnalyze-functions.Rd | 7 +-- man/importBrukerFlex-functions.Rd | 7 +-- man/importCdf-functions.Rd | 7 +-- man/importCiphergenXml-functions.Rd | 7 +-- man/importImzMl-functions.Rd | 7 +-- man/importMsd-functions.Rd | 7 +-- man/importMzMl-functions.Rd | 9 ++-- man/importMzXml-functions.Rd | 7 +-- man/importTab-functions.Rd | 11 ++--- man/supportedFileFormats-functions.Rd | 7 +-- tests/testthat/test_exportImzMl-methods.R | 4 +- tests/testthat/test_exportMzMl-methods.R | 2 - tests/testthat/test_mzMl-functions.R |only 31 files changed, 154 insertions(+), 139 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to <https://www.quandl.com/docs/api>. For more help on the package itself go to <https://www.quandl.com/help/r>.
Author: Raymond McTaggart [aut, cre],
Gergely Daroczi [aut],
Clement Leung [aut],
Quandl Inc. [cph]
Maintainer: Raymond McTaggart <ray@quandl.com>
Diff between Quandl versions 2.8.0 dated 2016-04-23 and 2.9.1 dated 2018-08-14
ChangeLog | 7 + DESCRIPTION | 16 +-- LICENSE | 2 MD5 | 42 ++++----- R/Quandl.R | 123 +++++++++++++-------------- R/Quandlapi.R | 32 +++---- R/Quandlconfig.R | 8 - R/Quandldatabase.R | 10 +- R/Quandldatatable.R | 34 +++---- man/Quandl.Rd | 4 man/Quandl.api_key.Rd | 1 man/Quandl.auth.Rd | 1 man/Quandl.database.bulk_download_to_file.Rd | 1 man/Quandl.database.bulk_download_url.Rd | 1 man/Quandl.dataset.get.Rd | 1 man/Quandl.datatable.Rd | 5 - man/Quandl.search.Rd | 1 man/metaData.Rd | 1 man/quandl.api.Rd | 5 - tests/testthat/test-api.r | 2 tests/testthat/test-datatable-helper.r | 30 ++++++ tests/testthat/test-datatable.r | 17 +++ 22 files changed, 196 insertions(+), 148 deletions(-)
Title: Transforms Input Data from a PMML Perspective
Description: Allows for data to be transformed before using it to construct models. Builds structures to allow functions in the PMML package to
output transformation details in addition to the model in the resulting PMML file. The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.
Author: Tridivesh Jena, Wen Ching Lin, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>
Diff between pmmlTransformations versions 1.3.1 dated 2017-02-27 and 1.3.2 dated 2018-08-14
DESCRIPTION | 20 MD5 | 10 build/vignette.rds |binary inst/ChangeLog | 5 inst/doc/FunctionXform.html | 1180 ++++++++++++++----------------------- man/pmmlTransformations-package.Rd | 14 6 files changed, 476 insertions(+), 753 deletions(-)
More information about pmmlTransformations at CRAN
Permanent link
Title: A High-Level R Interface for Neural Nets
Description: Adds a high-level interface for 'keras' neural nets. kms() fits neural net and accepts R formulas to aid data munging and hyperparameter selection. kms() can optionally accept a compiled keras_sequential_model() from 'keras'.
kms() accepts a number of parameters (like loss and optimizer) and splits the data into (optionally sparse) test and training matrices. kms() facilitates setting advanced hyperparameters (e.g., regularization). kms() returns a single object with predictions, a confusion matrix, and function call details.
Author: Pete Mohanty [aut, cre]
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>
Diff between kerasformula versions 1.0.0 dated 2018-05-06 and 1.5.0 dated 2018-08-14
DESCRIPTION | 13 +- MD5 | 22 +-- NAMESPACE | 7 + R/confusion.R | 2 R/kms.R | 259 +++++++++++++++++++++++++++++---------------- R/predict.R | 13 +- build/vignette.rds |binary inst/doc/kerasformula.R | 21 +-- inst/doc/kerasformula.Rmd | 28 +--- inst/doc/kerasformula.html | 27 +--- man/kms.Rd | 55 +++++++-- vignettes/kerasformula.Rmd | 28 +--- 12 files changed, 289 insertions(+), 186 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests
(parametric, non-parametric, or robust) included in the plots themselves. It is targeted primarily at
behavioral sciences community to provide a one-line code to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots, histograms) or categorical (pie charts) data.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.0.4 dated 2018-07-05 and 0.0.5 dated 2018-08-14
ggstatsplot-0.0.4/ggstatsplot/inst/doc/theme_mprl.R |only ggstatsplot-0.0.4/ggstatsplot/inst/doc/theme_mprl.Rmd |only ggstatsplot-0.0.4/ggstatsplot/inst/doc/theme_mprl.html |only ggstatsplot-0.0.4/ggstatsplot/vignettes/theme_mprl.Rmd |only ggstatsplot-0.0.5/ggstatsplot/DESCRIPTION | 28 ggstatsplot-0.0.5/ggstatsplot/MD5 | 195 +-- ggstatsplot-0.0.5/ggstatsplot/NAMESPACE | 6 ggstatsplot-0.0.5/ggstatsplot/NEWS.md | 32 ggstatsplot-0.0.5/ggstatsplot/R/combine_plots.R | 61 - ggstatsplot-0.0.5/ggstatsplot/R/data.R | 4 ggstatsplot-0.0.5/ggstatsplot/R/ggbetweenstats.R | 303 +++-- ggstatsplot-0.0.5/ggstatsplot/R/ggcoefstats.R | 440 +++++--- ggstatsplot-0.0.5/ggstatsplot/R/ggcorrmat.R | 145 +- ggstatsplot-0.0.5/ggstatsplot/R/gghistostats.R | 192 ++- ggstatsplot-0.0.5/ggstatsplot/R/ggpiestats.R | 389 +++---- ggstatsplot-0.0.5/ggstatsplot/R/ggscatterstats.R | 145 +- ggstatsplot-0.0.5/ggstatsplot/R/ggstatsplot-package.R | 53 - ggstatsplot-0.0.5/ggstatsplot/R/global_vars.R | 7 ggstatsplot-0.0.5/ggstatsplot/R/grouped_ggbetweenstats.R | 68 - ggstatsplot-0.0.5/ggstatsplot/R/grouped_ggcorrmat.R | 25 ggstatsplot-0.0.5/ggstatsplot/R/grouped_gghistostats.R | 17 ggstatsplot-0.0.5/ggstatsplot/R/grouped_ggpiestats.R | 162 +-- ggstatsplot-0.0.5/ggstatsplot/R/grouped_ggscatterstats.R | 51 ggstatsplot-0.0.5/ggstatsplot/R/helpers_effsize_ci.R | 263 ++--- ggstatsplot-0.0.5/ggstatsplot/R/helpers_labeller.R |only ggstatsplot-0.0.5/ggstatsplot/R/helpers_messages.R | 18 ggstatsplot-0.0.5/ggstatsplot/R/helpers_stats.R | 91 - ggstatsplot-0.0.5/ggstatsplot/R/helpers_textresults.R |only ggstatsplot-0.0.5/ggstatsplot/R/theme_mprl.R | 26 ggstatsplot-0.0.5/ggstatsplot/README.md | 198 ++- ggstatsplot-0.0.5/ggstatsplot/build/vignette.rds |binary ggstatsplot-0.0.5/ggstatsplot/inst/WORDLIST | 11 ggstatsplot-0.0.5/ggstatsplot/inst/doc/combine_plots.R | 85 + ggstatsplot-0.0.5/ggstatsplot/inst/doc/combine_plots.Rmd | 126 ++ ggstatsplot-0.0.5/ggstatsplot/inst/doc/combine_plots.html | 130 ++ ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggbetweenstats.R | 4 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggbetweenstats.Rmd | 12 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggbetweenstats.html | 86 - ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggcoefstats.R | 282 +++++ ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggcoefstats.Rmd | 386 +++++++ ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggcoefstats.html | 525 ++++++++-- ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggcorrmat.Rmd | 6 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggcorrmat.html | 36 ggstatsplot-0.0.5/ggstatsplot/inst/doc/gghistostats.R | 4 ggstatsplot-0.0.5/ggstatsplot/inst/doc/gghistostats.Rmd | 7 ggstatsplot-0.0.5/ggstatsplot/inst/doc/gghistostats.html | 28 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggpiestats.R | 24 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggpiestats.Rmd | 35 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggpiestats.html | 47 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggscatterstats.R | 6 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggscatterstats.Rmd | 12 ggstatsplot-0.0.5/ggstatsplot/inst/doc/ggscatterstats.html | 28 ggstatsplot-0.0.5/ggstatsplot/inst/doc/theme_ggstatsplot.R |only ggstatsplot-0.0.5/ggstatsplot/inst/doc/theme_ggstatsplot.Rmd |only ggstatsplot-0.0.5/ggstatsplot/inst/doc/theme_ggstatsplot.html |only ggstatsplot-0.0.5/ggstatsplot/man/Titanic_full.Rd | 1 ggstatsplot-0.0.5/ggstatsplot/man/chisq_v_ci.Rd | 14 ggstatsplot-0.0.5/ggstatsplot/man/combine_plots.Rd | 67 - ggstatsplot-0.0.5/ggstatsplot/man/cor_tets_ci.Rd | 15 ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggbetweenstats1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggbetweenstats2-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggcoefstats1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggcoefstats2-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggcoefstats3-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggcorrmat1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-gghistostats1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-gghistostats2-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggpiestats1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggpiestats2-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggpiestats3-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggpiestats4-1.png |only ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggscatterstats1-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/figures/README-ggscatterstats2-1.png |binary ggstatsplot-0.0.5/ggstatsplot/man/ggbetweenstats.Rd | 64 - ggstatsplot-0.0.5/ggstatsplot/man/ggcoefstats.Rd | 55 - ggstatsplot-0.0.5/ggstatsplot/man/ggcorrmat.Rd | 23 ggstatsplot-0.0.5/ggstatsplot/man/gghistostats.Rd | 47 ggstatsplot-0.0.5/ggstatsplot/man/ggpiestats.Rd | 29 ggstatsplot-0.0.5/ggstatsplot/man/ggscatterstats.Rd | 39 ggstatsplot-0.0.5/ggstatsplot/man/ggstatsplot-package.Rd | 34 ggstatsplot-0.0.5/ggstatsplot/man/grouped_ggbetweenstats.Rd | 96 + ggstatsplot-0.0.5/ggstatsplot/man/grouped_ggcorrmat.Rd | 65 - ggstatsplot-0.0.5/ggstatsplot/man/grouped_gghistostats.Rd | 62 - ggstatsplot-0.0.5/ggstatsplot/man/grouped_ggpiestats.Rd | 55 - ggstatsplot-0.0.5/ggstatsplot/man/grouped_ggscatterstats.Rd | 68 - ggstatsplot-0.0.5/ggstatsplot/man/intent_morality.Rd | 1 ggstatsplot-0.0.5/ggstatsplot/man/lm_effsize_ci.Rd | 17 ggstatsplot-0.0.5/ggstatsplot/man/movies_long.Rd | 1 ggstatsplot-0.0.5/ggstatsplot/man/movies_wide.Rd | 1 ggstatsplot-0.0.5/ggstatsplot/man/robcor_ci.Rd | 12 ggstatsplot-0.0.5/ggstatsplot/man/t1way_ci.Rd | 15 ggstatsplot-0.0.5/ggstatsplot/man/theme_ggstatsplot.Rd |only ggstatsplot-0.0.5/ggstatsplot/man/theme_mprl.Rd | 6 ggstatsplot-0.0.5/ggstatsplot/man/tz_labeller.Rd |only ggstatsplot-0.0.5/ggstatsplot/man/untable.Rd | 4 ggstatsplot-0.0.5/ggstatsplot/tests/spelling.R | 4 ggstatsplot-0.0.5/ggstatsplot/tests/testthat/test_ggbetweenstats.R | 7 ggstatsplot-0.0.5/ggstatsplot/vignettes/combine_plots.Rmd | 126 ++ ggstatsplot-0.0.5/ggstatsplot/vignettes/ggbetweenstats.Rmd | 12 ggstatsplot-0.0.5/ggstatsplot/vignettes/ggcoefstats.Rmd | 386 +++++++ ggstatsplot-0.0.5/ggstatsplot/vignettes/ggcorrmat.Rmd | 6 ggstatsplot-0.0.5/ggstatsplot/vignettes/gghistostats.Rmd | 7 ggstatsplot-0.0.5/ggstatsplot/vignettes/ggpiestats.Rmd | 35 ggstatsplot-0.0.5/ggstatsplot/vignettes/ggscatterstats.Rmd | 12 ggstatsplot-0.0.5/ggstatsplot/vignettes/theme_ggstatsplot.Rmd |only 105 files changed, 4233 insertions(+), 1952 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. The model is fit using adaptive quadrature.
Author: Paul Bailey, Claire Kelley, Trang Nguyen, Huade Huo.
Maintainer: Claire Kelley <ckelley@air.org>
Diff between WeMix versions 1.0.2 dated 2018-04-10 and 2.0.0 dated 2018-08-14
WeMix-1.0.2/WeMix/README.md |only WeMix-1.0.2/WeMix/inst/doc/WeightedMixedModels.html |only WeMix-2.0.0/WeMix/DESCRIPTION | 16 WeMix-2.0.0/WeMix/MD5 | 38 - WeMix-2.0.0/WeMix/NAMESPACE | 9 WeMix-2.0.0/WeMix/R/adaptiveQuad.R | 479 ++++++++++++-------- WeMix-2.0.0/WeMix/R/drv.R | 331 ++++++++++++- WeMix-2.0.0/WeMix/R/lnl.R | 29 - WeMix-2.0.0/WeMix/R/weMix-package.R | 12 WeMix-2.0.0/WeMix/build/vignette.rds |binary WeMix-2.0.0/WeMix/inst/NEWS.Rd |only WeMix-2.0.0/WeMix/inst/doc/WeightedMixedModels.R | 43 + WeMix-2.0.0/WeMix/inst/doc/WeightedMixedModels.Rmd | 148 +++++- WeMix-2.0.0/WeMix/inst/doc/WeightedMixedModels.pdf |only WeMix-2.0.0/WeMix/man/WeMix-package.Rd | 12 WeMix-2.0.0/WeMix/man/calc_lin_lnl_quad_fast.Rd | 4 WeMix-2.0.0/WeMix/man/mix.Rd | 97 ++-- WeMix-2.0.0/WeMix/src/Makevars.win | 2 WeMix-2.0.0/WeMix/src/calc_lin_lnl_quad_fast.cpp | 2 WeMix-2.0.0/WeMix/tests/testthat/Examples.smcl |only WeMix-2.0.0/WeMix/tests/testthat/test-0-main.R | 125 ++--- WeMix-2.0.0/WeMix/tests/testthat_tests.R |only WeMix-2.0.0/WeMix/vignettes/WeightedMixedModels.Rmd | 148 +++++- 23 files changed, 1120 insertions(+), 375 deletions(-)
Title: Calculates and Analyzes the Proliferative Index
Description: Provides functions for calculating and analyzing the proliferative
index (PI) from an RNA-seq dataset. As described in Ramaker & Lasseigne,
et al. bioRxiv, 2016 <doi:10.1101/063057>.
Author: Brittany Lasseigne [aut, cre],
Ryne Ramaker [aut]
Maintainer: Brittany Lasseigne <brittany.lasseigne@gmail.com>
Diff between ProliferativeIndex versions 1.0.0 dated 2017-02-16 and 1.0.1 dated 2018-08-14
DESCRIPTION | 8 +- MD5 | 30 ++++----- R/calculatePI.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/ProliferativeIndexVignette.R | 3 inst/doc/ProliferativeIndexVignette.Rmd | 3 inst/doc/ProliferativeIndexVignette.html | 103 ++++++++++++++++++++----------- man/calculatePI.Rd | 1 man/compareModeltoPI.Rd | 1 man/comparePI.Rd | 1 man/exReadDataObj.Rd | 1 man/exVSTPI.Rd | 1 man/readDataForPI.Rd | 1 man/vstTCGA_ACCData_sub.Rd | 1 vignettes/ProliferativeIndexVignette.Rmd | 3 16 files changed, 90 insertions(+), 71 deletions(-)
More information about ProliferativeIndex at CRAN
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Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 1.13.2 dated 2018-04-27 and 2.0.0 dated 2018-08-14
rcompanion-1.13.2/rcompanion/R/rcompanion-package.r |only rcompanion-2.0.0/rcompanion/DESCRIPTION | 16 rcompanion-2.0.0/rcompanion/MD5 | 172 +++++----- rcompanion-2.0.0/rcompanion/NAMESPACE | 10 rcompanion-2.0.0/rcompanion/R/epsilonSquared.r | 10 rcompanion-2.0.0/rcompanion/R/freemanTheta.r | 23 - rcompanion-2.0.0/rcompanion/R/groupwiseHuber.r | 4 rcompanion-2.0.0/rcompanion/R/groupwiseMedian.r | 12 rcompanion-2.0.0/rcompanion/R/groupwiseSum.r | 11 rcompanion-2.0.0/rcompanion/R/nagelkerke.r | 2 rcompanion-2.0.0/rcompanion/R/nagelkerkeHermite.r | 122 ------- rcompanion-2.0.0/rcompanion/R/nominalSymmetryTest.r | 4 rcompanion-2.0.0/rcompanion/R/pairwiseDifferences.r | 138 -------- rcompanion-2.0.0/rcompanion/R/pairwiseMcnemar.r | 8 rcompanion-2.0.0/rcompanion/R/pairwiseMedianMatrix.r | 17 rcompanion-2.0.0/rcompanion/R/pairwiseMedianTest.r | 18 - rcompanion-2.0.0/rcompanion/R/pairwiseNominalIndependence.r | 8 rcompanion-2.0.0/rcompanion/R/pairwiseNominalMatrix.r | 6 rcompanion-2.0.0/rcompanion/R/pairwiseOrdinalIndependence.r | 4 rcompanion-2.0.0/rcompanion/R/pairwiseOrdinalMatrix.r | 121 ------- rcompanion-2.0.0/rcompanion/R/pairwiseOrdinalPairedMatrix.r | 133 ------- rcompanion-2.0.0/rcompanion/R/pairwiseOrdinalPairedTest.r | 120 ------ rcompanion-2.0.0/rcompanion/R/pairwiseOrdinalTest.r | 109 ------ rcompanion-2.0.0/rcompanion/R/pairwisePercentileTest.r | 2 rcompanion-2.0.0/rcompanion/R/pairwisePermutationMatrix.r | 4 rcompanion-2.0.0/rcompanion/R/pairwisePermutationSymmetry.r | 4 rcompanion-2.0.0/rcompanion/R/pairwisePermutationSymmetryMatrix.r | 4 rcompanion-2.0.0/rcompanion/R/pairwisePermutationTest.r | 4 rcompanion-2.0.0/rcompanion/R/pairwiseRobustMatrix.r | 120 ------ rcompanion-2.0.0/rcompanion/R/pairwiseRobustTest.r | 112 ------ rcompanion-2.0.0/rcompanion/R/pairwiseSignMatrix.r | 4 rcompanion-2.0.0/rcompanion/R/pairwiseSignTest.r | 4 rcompanion-2.0.0/rcompanion/R/rcompanion.R |only rcompanion-2.0.0/rcompanion/man/accuracy.Rd | 4 rcompanion-2.0.0/rcompanion/man/cateNelson.Rd | 11 rcompanion-2.0.0/rcompanion/man/cldList.Rd | 12 rcompanion-2.0.0/rcompanion/man/cohenG.Rd | 4 rcompanion-2.0.0/rcompanion/man/cohenH.Rd | 4 rcompanion-2.0.0/rcompanion/man/cohenW.Rd | 4 rcompanion-2.0.0/rcompanion/man/compareGLM.Rd | 4 rcompanion-2.0.0/rcompanion/man/compareLM.Rd | 4 rcompanion-2.0.0/rcompanion/man/cramerV.Rd | 4 rcompanion-2.0.0/rcompanion/man/cramerVFit.Rd | 4 rcompanion-2.0.0/rcompanion/man/epsilonSquared.Rd | 9 rcompanion-2.0.0/rcompanion/man/freemanTheta.Rd | 27 - rcompanion-2.0.0/rcompanion/man/fullPTable.Rd | 4 rcompanion-2.0.0/rcompanion/man/groupwiseCMH.Rd | 8 rcompanion-2.0.0/rcompanion/man/groupwiseGeometric.Rd | 4 rcompanion-2.0.0/rcompanion/man/groupwiseHuber.Rd | 12 rcompanion-2.0.0/rcompanion/man/groupwiseMean.Rd | 12 rcompanion-2.0.0/rcompanion/man/groupwiseMedian.Rd | 25 - rcompanion-2.0.0/rcompanion/man/groupwisePercentile.Rd | 4 rcompanion-2.0.0/rcompanion/man/groupwiseSum.Rd | 14 rcompanion-2.0.0/rcompanion/man/nagelkerke.Rd | 6 rcompanion-2.0.0/rcompanion/man/nagelkerkeHermite.Rd | 56 --- rcompanion-2.0.0/rcompanion/man/nominalSymmetryTest.Rd | 8 rcompanion-2.0.0/rcompanion/man/pairwiseDifferences.Rd | 81 ---- rcompanion-2.0.0/rcompanion/man/pairwiseMcnemar.Rd | 10 rcompanion-2.0.0/rcompanion/man/pairwiseMedianMatrix.Rd | 17 rcompanion-2.0.0/rcompanion/man/pairwiseMedianTest.Rd | 15 rcompanion-2.0.0/rcompanion/man/pairwiseModelAnova.Rd | 4 rcompanion-2.0.0/rcompanion/man/pairwiseNominalIndependence.Rd | 12 rcompanion-2.0.0/rcompanion/man/pairwiseNominalMatrix.Rd | 15 rcompanion-2.0.0/rcompanion/man/pairwiseOrdinalIndependence.Rd | 8 rcompanion-2.0.0/rcompanion/man/pairwiseOrdinalMatrix.Rd | 81 ---- rcompanion-2.0.0/rcompanion/man/pairwiseOrdinalPairedMatrix.Rd | 97 ----- rcompanion-2.0.0/rcompanion/man/pairwiseOrdinalPairedTest.Rd | 89 ----- rcompanion-2.0.0/rcompanion/man/pairwiseOrdinalTest.Rd | 79 ---- rcompanion-2.0.0/rcompanion/man/pairwisePercentileTest.Rd | 10 rcompanion-2.0.0/rcompanion/man/pairwisePermutationMatrix.Rd | 8 rcompanion-2.0.0/rcompanion/man/pairwisePermutationSymmetry.Rd | 8 rcompanion-2.0.0/rcompanion/man/pairwisePermutationSymmetryMatrix.Rd | 12 rcompanion-2.0.0/rcompanion/man/pairwisePermutationTest.Rd | 12 rcompanion-2.0.0/rcompanion/man/pairwiseRobustMatrix.Rd | 82 ---- rcompanion-2.0.0/rcompanion/man/pairwiseRobustTest.Rd | 78 ---- rcompanion-2.0.0/rcompanion/man/pairwiseSignMatrix.Rd | 8 rcompanion-2.0.0/rcompanion/man/pairwiseSignTest.Rd | 8 rcompanion-2.0.0/rcompanion/man/percentileTest.Rd | 4 rcompanion-2.0.0/rcompanion/man/plotDensityHistogram.Rd | 4 rcompanion-2.0.0/rcompanion/man/plotNormalDensity.Rd | 4 rcompanion-2.0.0/rcompanion/man/plotNormalHistogram.Rd | 4 rcompanion-2.0.0/rcompanion/man/plotPredy.Rd | 11 rcompanion-2.0.0/rcompanion/man/rcompanion-package.Rd | 48 +- rcompanion-2.0.0/rcompanion/man/scheirerRayHare.Rd | 4 rcompanion-2.0.0/rcompanion/man/transformTukey.Rd | 8 rcompanion-2.0.0/rcompanion/man/wilcoxonOneSampleR.Rd | 4 rcompanion-2.0.0/rcompanion/man/wilcoxonPairedR.Rd | 4 rcompanion-2.0.0/rcompanion/man/wilcoxonR.Rd | 4 88 files changed, 471 insertions(+), 1932 deletions(-)
Title: Convert Strings into any Case
Description: A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.
Author: Malte Grosser [aut, cre]
Maintainer: Malte Grosser <malte.grosser@gmail.com>
Diff between snakecase versions 0.9.1 dated 2018-03-25 and 0.9.2 dated 2018-08-14
DESCRIPTION | 10 - MD5 | 35 ++-- NAMESPACE | 1 NEWS.md | 7 R/caseconverters.R | 101 ++++++++++---- R/relevant.R |only R/replace_special_characters_internal.R | 37 ++++- R/to_any_case.R | 119 ++++++++++------ R/to_parsed_case_internal.R | 9 + build/vignette.rds |binary inst/doc/caseconverters.Rmd | 2 inst/doc/caseconverters.html | 6 man/caseconverter.Rd | 64 +++++--- man/relevant.Rd |only man/replace_special_characters_internal.Rd | 6 man/to_any_case.Rd | 23 +-- man/to_parsed_case_internal.Rd | 5 tests/testthat/test-to_any_case.R | 207 ++++++++++++++++++++++++++++- tests/testthat/test-to_sentence_case.R |only vignettes/caseconverters.Rmd | 2 20 files changed, 488 insertions(+), 146 deletions(-)
Title: Analyses for Distance-Sampling and Abundance Estimation
Description: Distance-sampling is a popular method for abundance estimation in
ecology. This package contains functions and associated routines to analyze
distance-sampling data collected on point or line transects.
It accommodates line and point transect analyses
in one routine
that accepts a regression-like formula object. Abundance routines
perform automated bootstrapping and automated detection-function
selection. Overall (study area) and site-level (transect or point)
abundance estimates are
available. A large suite of classical, parametric detection functions are
included. Some uncommon (e.g., Gamma, negative exponential)
detection functions are also included and users can define
their own custom detection functions if needed. One form of
non-parametric smoothed distance function is included.
The help files and vignettes have been
vetted by multiple authors and tested in multiple workshop
settings.
Author: c(
person("Trent", "McDonald", email="tmcdonald@west-inc.com", role=c("cre","aut")),
person("Ryan", "Nielson", email="rnielson@west-inc.com", role=c("aut")),
person("Jason", "Carlisle", email="jcarlisle@west-inc.com", role=c("aut")),
person("Aidan", "McDonald", email="aidan@mcdcentral.org", role=c("aut")),
person("Ben", "Augustine", email="", role=c("ctb")),
person("James", "Griswald", email="", role=c("ctb")),
person("Joel", "Reynolds", email="", role=c("ctb")),
person("Pham", "Quang", email="", role=c("ctb")),
person("Earl", "Becker", email="", role=c("ctb")),
person("Aaron", "Christ", email="", role=c("ctb")),
person("Brook", "Russelland", email="", role=c("ctb")),
person("Patrick", "McKann", email="", role=c("ctb")),
person("Lacey", "Jeroue", email="", role=c("ctb")),
person("Hoffman", "Abigail", email="", role=c("ctb")),
person("Kleinsausser", "Michael", email="", role=c("ctb"))
)
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between Rdistance versions 1.3.2 dated 2015-07-22 and 2.1.1 dated 2018-08-14
Rdistance-1.3.2/Rdistance/R/ESW.r |only Rdistance-1.3.2/Rdistance/R/F.abund.estim.r |only Rdistance-1.3.2/Rdistance/R/F.automated.CDA.r |only Rdistance-1.3.2/Rdistance/R/F.dfunc.estim.R |only Rdistance-1.3.2/Rdistance/R/F.double.obs.prob.r |only Rdistance-1.3.2/Rdistance/R/F.gx.estim.r |only Rdistance-1.3.2/Rdistance/R/F.maximize.g.r |only Rdistance-1.3.2/Rdistance/R/F.nLL.r |only Rdistance-1.3.2/Rdistance/R/F.start.limits.r |only Rdistance-1.3.2/Rdistance/R/Gamma.like.r |only Rdistance-1.3.2/Rdistance/R/coef.dfunc.r |only Rdistance-1.3.2/Rdistance/R/perp.dists.R |only Rdistance-1.3.2/Rdistance/R/plot.dfunc.r |only Rdistance-1.3.2/Rdistance/R/print.abund.r |only Rdistance-1.3.2/Rdistance/R/print.dfunc.r |only Rdistance-1.3.2/Rdistance/R/simple.expansion.r |only Rdistance-1.3.2/Rdistance/data/sparrow.detections.rda |only Rdistance-1.3.2/Rdistance/data/sparrow.transects.rda |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_BeginnerTutorial.R |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_BeginnerTutorial.Rmd |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_BeginnerTutorial.pdf |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_ModelingAbundance.R |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_ModelingAbundance.Rmd |only Rdistance-1.3.2/Rdistance/inst/doc/Rdistance_ModelingAbundance.pdf |only Rdistance-1.3.2/Rdistance/man/F.abund.estim.Rd |only Rdistance-1.3.2/Rdistance/man/F.automated.CDA.Rd |only Rdistance-1.3.2/Rdistance/man/F.dfunc.estim.Rd |only Rdistance-1.3.2/Rdistance/man/perp.dists.Rd |only Rdistance-1.3.2/Rdistance/man/sparrow.detections.Rd |only Rdistance-1.3.2/Rdistance/man/sparrow.transects.Rd |only Rdistance-1.3.2/Rdistance/vignettes/Rdistance_BeginnerTutorial.Rmd |only Rdistance-1.3.2/Rdistance/vignettes/Rdistance_ModelingAbundance.Rmd |only Rdistance-2.1.1/Rdistance/DESCRIPTION | 56 - Rdistance-2.1.1/Rdistance/MD5 | 164 ++-- Rdistance-2.1.1/Rdistance/NAMESPACE | 67 + Rdistance-2.1.1/Rdistance/R/AIC.dfunc.R | 78 ++ Rdistance-2.1.1/Rdistance/R/EDR.R |only Rdistance-2.1.1/Rdistance/R/ESW.R |only Rdistance-2.1.1/Rdistance/R/F.double.obs.prob.R |only Rdistance-2.1.1/Rdistance/R/F.gx.estim.R |only Rdistance-2.1.1/Rdistance/R/F.maximize.g.R |only Rdistance-2.1.1/Rdistance/R/F.nLL.R |only Rdistance-2.1.1/Rdistance/R/F.start.limits.R |only Rdistance-2.1.1/Rdistance/R/Gamma.like.R |only Rdistance-2.1.1/Rdistance/R/Rdistance-package.R |only Rdistance-2.1.1/Rdistance/R/RdistanceControls.R |only Rdistance-2.1.1/Rdistance/R/abundEstim.R |only Rdistance-2.1.1/Rdistance/R/autoDistSamp.R |only Rdistance-2.1.1/Rdistance/R/coef.dfunc.R |only Rdistance-2.1.1/Rdistance/R/cosine.expansion.R | 34 + Rdistance-2.1.1/Rdistance/R/dfuncEstim.R |only Rdistance-2.1.1/Rdistance/R/dfuncSmu.R |only Rdistance-2.1.1/Rdistance/R/effectiveDistance.R |only Rdistance-2.1.1/Rdistance/R/estimateN.R |only Rdistance-2.1.1/Rdistance/R/getDfuncModelFrame.R |only Rdistance-2.1.1/Rdistance/R/halfnorm.like.R | 255 +++++-- Rdistance-2.1.1/Rdistance/R/hazrate.like.R | 197 ++++- Rdistance-2.1.1/Rdistance/R/hermite.expansion.R | 33 Rdistance-2.1.1/Rdistance/R/integration.constant.R | 230 ++++++ Rdistance-2.1.1/Rdistance/R/likeParamNames.R |only Rdistance-2.1.1/Rdistance/R/negexp.like.R | 140 ++-- Rdistance-2.1.1/Rdistance/R/perpDists.R |only Rdistance-2.1.1/Rdistance/R/plot.dfunc.R |only Rdistance-2.1.1/Rdistance/R/predict.dfunc.R |only Rdistance-2.1.1/Rdistance/R/print.abund.R |only Rdistance-2.1.1/Rdistance/R/print.dfunc.R |only Rdistance-2.1.1/Rdistance/R/secondDeriv.R |only Rdistance-2.1.1/Rdistance/R/simple.expansion.R |only Rdistance-2.1.1/Rdistance/R/smu.like.R |only Rdistance-2.1.1/Rdistance/R/sparrowDetectionData.R |only Rdistance-2.1.1/Rdistance/R/sparrowSiteData.R |only Rdistance-2.1.1/Rdistance/R/thrasherDetectionData.R |only Rdistance-2.1.1/Rdistance/R/thrasherSiteData.R |only Rdistance-2.1.1/Rdistance/R/uniform.like.R | 226 +++++- Rdistance-2.1.1/Rdistance/R/zzz.R | 5 Rdistance-2.1.1/Rdistance/build/vignette.rds |binary Rdistance-2.1.1/Rdistance/data/sparrowDetectionData.rda |only Rdistance-2.1.1/Rdistance/data/sparrowSiteData.rda |only Rdistance-2.1.1/Rdistance/data/thrasherDetectionData.rda |only Rdistance-2.1.1/Rdistance/data/thrasherSiteData.rda |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerLineTransectCovar.R |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerLineTransectCovar.Rmd |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerLineTransectCovar.pdf |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerPointTransects.R |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerPointTransects.Rmd |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_BeginnerPointTransects.pdf |only Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_CustomDetectionFunction.R | 14 Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_CustomDetectionFunction.Rmd | 36 - Rdistance-2.1.1/Rdistance/inst/doc/Rdistance_CustomDetectionFunction.pdf |binary Rdistance-2.1.1/Rdistance/man/AIC.dfunc.Rd | 132 +-- Rdistance-2.1.1/Rdistance/man/EDR.Rd |only Rdistance-2.1.1/Rdistance/man/ESW.Rd | 154 ++-- Rdistance-2.1.1/Rdistance/man/F.double.obs.prob.Rd | 96 +- Rdistance-2.1.1/Rdistance/man/F.gx.estim.Rd | 172 ++--- Rdistance-2.1.1/Rdistance/man/F.maximize.g.Rd | 48 - Rdistance-2.1.1/Rdistance/man/F.nLL.Rd | 111 +-- Rdistance-2.1.1/Rdistance/man/F.start.limits.Rd | 139 +--- Rdistance-2.1.1/Rdistance/man/Gamma.like.Rd | 140 +--- Rdistance-2.1.1/Rdistance/man/Rdistance-package.Rd | 157 +++- Rdistance-2.1.1/Rdistance/man/RdistanceControls.Rd |only Rdistance-2.1.1/Rdistance/man/abundEstim.Rd |only Rdistance-2.1.1/Rdistance/man/autoDistSamp.Rd |only Rdistance-2.1.1/Rdistance/man/coef.dfunc.Rd | 64 - Rdistance-2.1.1/Rdistance/man/cosine.expansion.Rd | 94 +- Rdistance-2.1.1/Rdistance/man/dfuncEstim.Rd |only Rdistance-2.1.1/Rdistance/man/dfuncSmu.Rd |only Rdistance-2.1.1/Rdistance/man/effectiveDistance.Rd |only Rdistance-2.1.1/Rdistance/man/estimateN.Rd |only Rdistance-2.1.1/Rdistance/man/getDfuncModelFrame.Rd |only Rdistance-2.1.1/Rdistance/man/halfnorm.like.Rd |only Rdistance-2.1.1/Rdistance/man/hazrate.like.Rd |only Rdistance-2.1.1/Rdistance/man/hermite.expansion.Rd | 91 +- Rdistance-2.1.1/Rdistance/man/integration.constant.Rd | 130 ++- Rdistance-2.1.1/Rdistance/man/likeParamNames.Rd |only Rdistance-2.1.1/Rdistance/man/nexexp.like.Rd |only Rdistance-2.1.1/Rdistance/man/perpDists.Rd |only Rdistance-2.1.1/Rdistance/man/plot.dfunc.Rd | 226 ++++-- Rdistance-2.1.1/Rdistance/man/predict.dfunc.Rd |only Rdistance-2.1.1/Rdistance/man/print.abund.Rd | 82 +- Rdistance-2.1.1/Rdistance/man/print.dfunc.Rd | 96 +- Rdistance-2.1.1/Rdistance/man/secondDeriv.Rd |only Rdistance-2.1.1/Rdistance/man/simple.expansion.Rd | 88 -- Rdistance-2.1.1/Rdistance/man/smu.like.Rd |only Rdistance-2.1.1/Rdistance/man/sparrowDetectionData.Rd |only Rdistance-2.1.1/Rdistance/man/sparrowSiteData.Rd |only Rdistance-2.1.1/Rdistance/man/thrasherDetectionData.Rd |only Rdistance-2.1.1/Rdistance/man/thrasherSiteData.Rd |only Rdistance-2.1.1/Rdistance/man/uniform.like.Rd | 336 ++++------ Rdistance-2.1.1/Rdistance/vignettes/Rdistance_BeginnerLineTransectCovar.Rmd |only Rdistance-2.1.1/Rdistance/vignettes/Rdistance_BeginnerPointTransects.Rmd |only Rdistance-2.1.1/Rdistance/vignettes/Rdistance_CustomDetectionFunction.Rmd | 36 - 131 files changed, 2387 insertions(+), 1540 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Laura J. Graham [ctb] (<https://orcid.org/0000-0002-1057-3721>),
Kimberly A. With [ctb] (<https://orcid.org/0000-0001-5570-1515>),
Jeffrey Hollister [ctb] (<https://orcid.org/0000-0002-3611-7281>),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 0.1.0 dated 2018-08-11 and 0.1.1 dated 2018-08-14
DESCRIPTION | 7 MD5 | 102 ++--- NAMESPACE | 1 NEWS.md | 6 R/data.R | 330 ++++++++--------- R/get_adjacencies.R | 2 R/get_circumscribingcircle.R | 136 +++---- R/get_nearestneighbour.R | 158 ++++---- R/get_patches.R | 324 ++++++++--------- R/landscapemetrics-package.R | 118 +++--- R/lsm_c_contig_mn.R | 230 ++++++------ R/lsm_c_contig_sd.R | 232 ++++++------ R/lsm_c_iji.R | 248 ++++++------- R/lsm_c_te.R | 4 R/lsm_l_iji.R | 272 +++++++------- R/lsm_l_pr.R | 158 ++++---- R/lsm_l_rpr.R | 4 R/lsm_p_core.R | 11 R/lsm_p_ncore.R | 12 R/lsm_p_perim.R | 2 R/pad_raster.R | 35 + R/show_correlation.R | 476 ++++++++++++------------- inst/doc/getstarted.Rmd | 296 +++++++-------- inst/doc/getstarted.html | 18 man/lsm_l_rpr.Rd | 3 man/pad_raster.Rd | 12 src/get_adjacency.cpp | 2 tests/testthat/test-calculate-metrics.R | 64 +-- tests/testthat/test-get-adjacencies.R | 60 +-- tests/testthat/test-get-circumscribungcircle.R | 40 +- tests/testthat/test-get-nearestneighbour.R | 36 - tests/testthat/test-get-patches.R | 32 - tests/testthat/test-lsm-c-contig-cv.R | 82 ++-- tests/testthat/test-lsm-c-enn-cv.R | 78 ++-- tests/testthat/test-lsm-c-frac-cv.R | 84 ++-- tests/testthat/test-lsm-c-iji.R | 60 +-- tests/testthat/test-lsm-c-pafrac.R | 60 +-- tests/testthat/test-lsm-c-shape-cv.R | 82 ++-- tests/testthat/test-lsm-l-ai.R | 58 +-- tests/testthat/test-lsm-l-cohesion.R | 56 +- tests/testthat/test-lsm-l-condent.R | 44 +- tests/testthat/test-lsm-l-contag.R | 56 +- tests/testthat/test-lsm-l-contig-cv.R | 78 ++-- tests/testthat/test-lsm-l-ent.R | 44 +- tests/testthat/test-lsm-l-joinent.R | 44 +- tests/testthat/test-lsm-l-mutinf.R | 44 +- tests/testthat/test-lsm-l-shape-cv.R | 78 ++-- tests/testthat/test-lsm-p-nca.R | 60 +-- tests/testthat/test-lsm-p-perim.R | 70 +-- tests/testthat/test-show-correlation.R | 42 +- tests/testthat/test-show-patches.R | 14 vignettes/getstarted.Rmd | 296 +++++++-------- 52 files changed, 2448 insertions(+), 2413 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.3.10 dated 2017-01-28 and 3.4.8 dated 2018-08-14
phreeqc-3.3.10/phreeqc/LICENSE |only phreeqc-3.4.8/phreeqc/DESCRIPTION | 16 phreeqc-3.4.8/phreeqc/LICENSE.note |only phreeqc-3.4.8/phreeqc/MD5 | 257 phreeqc-3.4.8/phreeqc/NAMESPACE | 2 phreeqc-3.4.8/phreeqc/R/phreeqc.R | 103 phreeqc-3.4.8/phreeqc/data/databases.rda |binary phreeqc-3.4.8/phreeqc/data/examples.rda |binary phreeqc-3.4.8/phreeqc/man/Amm.dat.Rd | 14 phreeqc-3.4.8/phreeqc/man/ColdChem.dat.Rd |only phreeqc-3.4.8/phreeqc/man/ex1.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex10.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex11.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex12.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex13.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex14.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex15.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex15.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/ex16.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex17.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex18.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex19.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex2.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex20.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex21.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex22.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex3.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex4.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex5.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex6.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex7.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex8.Rd | 1 phreeqc-3.4.8/phreeqc/man/ex9.Rd | 1 phreeqc-3.4.8/phreeqc/man/iso.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/llnl.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/minteq.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/minteq.v4.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/phrAccumulateLine.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrClearAccumulatedLines.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetAccumulatedLines.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetComponentList.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetDumpFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetDumpFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetDumpStrings.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetDumpStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetErrorFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetErrorFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetErrorStrings.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetErrorStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetLogFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetLogFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetLogStrings.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetLogStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetOutputFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetOutputFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetOutputStrings.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetOutputStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetSelectedOutput.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetSelectedOutputFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrGetWarningStrings.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrLoadDatabase.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrLoadDatabaseString.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrRunAccumulated.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrRunFile.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrRunString.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetDumpFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetDumpFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetDumpStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetErrorFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetErrorFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetErrorStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetLogFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetLogFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetLogStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetOutputFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetOutputFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetOutputStringsOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetSelectedOutputFileName.Rd | 1 phreeqc-3.4.8/phreeqc/man/phrSetSelectedOutputFileOn.Rd | 1 phreeqc-3.4.8/phreeqc/man/phreeqc-package.Rd | 11 phreeqc-3.4.8/phreeqc/man/phreeqc.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/pitzer.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/sit.dat.Rd | 10 phreeqc-3.4.8/phreeqc/man/wateq4f.dat.Rd | 10 phreeqc-3.4.8/phreeqc/src/IPhreeqc.cpp | 10 phreeqc-3.4.8/phreeqc/src/IPhreeqc.h | 2 phreeqc-3.4.8/phreeqc/src/IPhreeqchpp.h | 20 phreeqc-3.4.8/phreeqc/src/R.cpp | 56 phreeqc-3.4.8/phreeqc/src/Version.h | 8 phreeqc-3.4.8/phreeqc/src/phreeqcpp/GasPhase.h | 3 phreeqc-3.4.8/phreeqc/src/phreeqcpp/ISolution.cpp | 1 phreeqc-3.4.8/phreeqc/src/phreeqcpp/ISolution.h | 3 phreeqc-3.4.8/phreeqc/src/phreeqcpp/PBasic.cpp | 131 phreeqc-3.4.8/phreeqc/src/phreeqcpp/PBasic.h | 11 phreeqc-3.4.8/phreeqc/src/phreeqcpp/PHRQ_io.cpp | 13 phreeqc-3.4.8/phreeqc/src/phreeqcpp/PPassemblage.cpp | 17 phreeqc-3.4.8/phreeqc/src/phreeqcpp/PPassemblage.h | 2 phreeqc-3.4.8/phreeqc/src/phreeqcpp/Phreeqc.cpp | 275 phreeqc-3.4.8/phreeqc/src/phreeqcpp/Phreeqc.h | 34 phreeqc-3.4.8/phreeqc/src/phreeqcpp/SelectedOutput.cpp | 2 phreeqc-3.4.8/phreeqc/src/phreeqcpp/SelectedOutput.h | 7 phreeqc-3.4.8/phreeqc/src/phreeqcpp/Solution.cpp | 24 phreeqc-3.4.8/phreeqc/src/phreeqcpp/Solution.h | 3 phreeqc-3.4.8/phreeqc/src/phreeqcpp/SolutionIsotope.cpp | 4 phreeqc-3.4.8/phreeqc/src/phreeqcpp/SurfaceCharge.h | 5 phreeqc-3.4.8/phreeqc/src/phreeqcpp/basicsubs.cpp | 275 phreeqc-3.4.8/phreeqc/src/phreeqcpp/cl1.cpp | 2 phreeqc-3.4.8/phreeqc/src/phreeqcpp/cvode.cpp | 2 phreeqc-3.4.8/phreeqc/src/phreeqcpp/gases.cpp | 21 phreeqc-3.4.8/phreeqc/src/phreeqcpp/global_structures.h | 53 phreeqc-3.4.8/phreeqc/src/phreeqcpp/integrate.cpp | 72 phreeqc-3.4.8/phreeqc/src/phreeqcpp/inverse.cpp | 188 phreeqc-3.4.8/phreeqc/src/phreeqcpp/isotopes.cpp | 12 phreeqc-3.4.8/phreeqc/src/phreeqcpp/kinetics.cpp | 30 phreeqc-3.4.8/phreeqc/src/phreeqcpp/mainsubs.cpp | 87 phreeqc-3.4.8/phreeqc/src/phreeqcpp/model.cpp | 216 phreeqc-3.4.8/phreeqc/src/phreeqcpp/parse.cpp | 6 phreeqc-3.4.8/phreeqc/src/phreeqcpp/pitzer.cpp | 135 phreeqc-3.4.8/phreeqc/src/phreeqcpp/pitzer_structures.cpp | 2 phreeqc-3.4.8/phreeqc/src/phreeqcpp/prep.cpp | 170 phreeqc-3.4.8/phreeqc/src/phreeqcpp/print.cpp | 160 phreeqc-3.4.8/phreeqc/src/phreeqcpp/read.cpp | 153 phreeqc-3.4.8/phreeqc/src/phreeqcpp/readtr.cpp | 443 - phreeqc-3.4.8/phreeqc/src/phreeqcpp/sit.cpp | 25 phreeqc-3.4.8/phreeqc/src/phreeqcpp/spread.cpp | 82 phreeqc-3.4.8/phreeqc/src/phreeqcpp/step.cpp | 15 phreeqc-3.4.8/phreeqc/src/phreeqcpp/structures.cpp | 18 phreeqc-3.4.8/phreeqc/src/phreeqcpp/tidy.cpp | 56 phreeqc-3.4.8/phreeqc/src/phreeqcpp/transport.cpp | 4257 ++++++++------ phreeqc-3.4.8/phreeqc/src/phreeqcpp/utilities.cpp | 13 phreeqc-3.4.8/phreeqc/src/thread.h | 2 131 files changed, 4815 insertions(+), 2868 deletions(-)
Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and exposte it to OGC CSW.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geonapi versions 0.1-0 dated 2018-04-27 and 0.2-0 dated 2018-08-14
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- R/GNManager.R | 53 +++++++++++++++++++----------- R/GNUtils.R | 69 +++++++++++++++++++++++++--------------- R/geonapi.R | 4 +- README.md | 6 ++- man/GNUtils.Rd | 2 - man/geonapi.Rd | 4 +- tests/testthat/test_GNManager.R | 4 -- 9 files changed, 101 insertions(+), 65 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.2.2 dated 2018-01-25 and 1.2.3 dated 2018-08-14
DESCRIPTION | 10 +- MD5 | 26 ++--- NEWS.md | 4 R/print.rpsftm.R | 2 R/summary.rpsftm.R | 2 build/vignette.rds |binary inst/doc/rpsftm_vignette.html | 44 +++++----- man/est_eqn.Rd | 3 man/print.summary.coxph.Rd | 4 man/print.summary.survreg.Rd | 3 tests/testthat/test_rpsftm.R | 22 +++++ vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-7-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-9-1.png |binary 14 files changed, 74 insertions(+), 46 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.1.3 dated 2018-04-13 and 1.1.4 dated 2018-08-14
DESCRIPTION | 14 - MD5 | 495 ++++++++++++++++++++----------------- NAMESPACE | 29 ++ R/ClassMethod-XGR.r | 143 ++++++++++ R/xAggregate.r | 67 ++++- R/xBiheatmap.r | 2 R/xBiproject.r |only R/xCheckParallel.r | 2 R/xCircos.r | 4 R/xColormap.r | 2 R/xCombineNet.r | 4 R/xConverter.r | 1 R/xCorrelation.r | 2 R/xCrosstalk.r | 2 R/xDAGpropagate.r | 2 R/xDAGsim.r | 2 R/xDefineEQTL.r |only R/xDefineGenomicAnno.r |only R/xDefineHIC.r |only R/xDefineNet.r | 10 R/xDefineOntology.r |only R/xEnrichBarplot.r | 14 - R/xEnrichCompare.r | 2 R/xEnrichDAGplot.r | 2 R/xEnrichDAGplotAdv.r | 2 R/xEnrichForest.r | 4 R/xEnrichHeatmap.r | 2 R/xEnrichLadder.r | 89 +++++- R/xEnrichMatrix.r | 4 R/xEnrichNetplot.r | 2 R/xEnrichTreemap.r | 2 R/xEnricher.r | 9 R/xEnricherGenes.r | 108 +------- R/xEnricherGenesAdv.r | 6 R/xEnricherSNPs.r | 2 R/xEnricherYours.r | 2 R/xGGnetwork.r | 2 R/xGR.r | 81 ++++-- R/xGR2GeneScores.r | 2 R/xGR2nGenes.r | 2 R/xGR2xGeneAnno.r | 6 R/xGR2xGeneAnnoAdv.r | 6 R/xGR2xGeneScores.r | 2 R/xGR2xGenes.r | 12 R/xGR2xNet.r | 2 R/xGRcse.r | 2 R/xGRkaryogram.r |only R/xGRmanhattan.r |only R/xGRoverlap.r | 31 +- R/xGRsampling.r | 2 R/xGRscores.r | 2 R/xGRsep.r | 2 R/xGRsort.r | 10 R/xGRtrack.r | 286 ++++++++++++++++----- R/xGRviaGeneAnno.r | 6 R/xGRviaGeneAnnoAdv.r | 6 R/xGRviaGenomicAnno.r | 221 +--------------- R/xGRviaGenomicAnnoAdv.r | 214 ---------------- R/xGScore.r | 10 R/xGScoreAdv.r | 140 ---------- R/xGraphML.r | 2 R/xHEB.r | 3 R/xHeatmap.r | 58 ++-- R/xLDblock.r |only R/xLDenricher.r |only R/xLDsampling.r |only R/xLiftOver.r | 2 R/xOBOcode.r | 2 R/xPCHiCplot.r |only R/xPolarBar.r | 2 R/xPolarDot.r | 2 R/xRDataLoader.r | 26 + R/xRPS.r |only R/xRWenricher.r |only R/xRWkernel.r |only R/xRepurpose.r |only R/xSM2DF.r | 2 R/xSNP2GeneScores.r | 4 R/xSNP2nGenes.r | 4 R/xSNPlocations.r | 4 R/xSNPscores.r | 4 R/xSimplifyNet.r | 4 R/xSocialiser.r | 2 R/xSocialiserGenes.r | 4 R/xSocialiserSNPs.r | 4 R/xSubneterGR.r | 2 R/xSubneterGenes.r | 124 ++++++++- R/xSubneterSNPs.r | 4 R/xVisInterp.r | 2 R/xVisInterpAnimate.r | 2 R/xVisKernels.r | 2 R/xVolcano.r | 2 data/ImmunoBase.RData |binary inst/DR.html |only inst/NEWS | 24 + inst/aOnto.html |only inst/bLD.html |only inst/cPath.html | 2 inst/eTerm.html | 2 inst/ls_eTerm.html | 2 inst/mSeed.html | 2 inst/xAggregate.html | 27 +- inst/xBiheatmap.html | 2 inst/xBiproject.html |only inst/xCircos.html | 8 inst/xCombineNet.html | 2 inst/xCorrelation.html | 2 inst/xCrosstalk.html | 2 inst/xDAGpropagate.html | 2 inst/xDAGsim.html | 2 inst/xDefineEQTL.html |only inst/xDefineGenomicAnno.html |only inst/xDefineHIC.html |only inst/xDefineNet.html | 15 - inst/xDefineOntology.html |only inst/xEnrichBarplot.html | 2 inst/xEnrichCompare.html | 2 inst/xEnrichDAGplot.html | 2 inst/xEnrichDAGplotAdv.html | 2 inst/xEnrichForest.html | 2 inst/xEnrichHeatmap.html | 2 inst/xEnrichLadder.html | 88 ++++++ inst/xEnrichMatrix.html | 4 inst/xEnrichNetplot.html | 2 inst/xEnrichTreemap.html | 2 inst/xEnricherGenes.html | 63 ---- inst/xEnricherGenesAdv.html | 62 ---- inst/xEnricherSNPs.html | 2 inst/xEnricherYours.html | 2 inst/xGGnetwork.html | 2 inst/xGR.html | 20 + inst/xGR2GeneScores.html | 2 inst/xGR2nGenes.html | 2 inst/xGR2xGeneAnno.html | 76 ----- inst/xGR2xGeneAnnoAdv.html | 62 ---- inst/xGR2xGeneScores.html | 2 inst/xGR2xGenes.html | 2 inst/xGR2xNet.html | 2 inst/xGRcse.html | 2 inst/xGRkaryogram.html |only inst/xGRmanhattan.html |only inst/xGRoverlap.html | 8 inst/xGRsampling.html | 2 inst/xGRscores.html | 2 inst/xGRsep.html | 2 inst/xGRsort.html | 2 inst/xGRtrack.html | 71 ++++- inst/xGRviaGeneAnno.html | 62 ---- inst/xGRviaGeneAnnoAdv.html | 83 +----- inst/xGRviaGenomicAnno.html | 543 ----------------------------------------- inst/xGRviaGenomicAnnoAdv.html | 529 --------------------------------------- inst/xGScore.html | 4 inst/xGScoreAdv.html | 516 -------------------------------------- inst/xGraphML.html | 2 inst/xHEB.html | 2 inst/xHeatmap.html | 2 inst/xLDblock.html |only inst/xLDenricher.html |only inst/xLDsampling.html |only inst/xLiftOver.html | 2 inst/xOBOcode.html | 2 inst/xPCHiCplot.html |only inst/xPolarBar.html | 2 inst/xPolarDot.html | 2 inst/xRDataLoader.html | 2 inst/xRPS.html |only inst/xRWenricher.html |only inst/xRWkernel.html |only inst/xRepurpose.html |only inst/xSM2DF.html | 2 inst/xSNP2GeneScores.html | 6 inst/xSNP2nGenes.html | 9 inst/xSNPlocations.html | 8 inst/xSNPscores.html | 4 inst/xSimplifyNet.html | 2 inst/xSocialiser.html | 2 inst/xSocialiserGenes.html | 4 inst/xSocialiserSNPs.html | 4 inst/xSubneterGR.html | 2 inst/xSubneterGenes.html | 41 ++- inst/xSubneterSNPs.html | 6 inst/xVisInterp.html | 2 inst/xVisInterpAnimate.html | 2 inst/xVolcano.html | 2 man/DR.Rd |only man/aOnto.Rd |only man/bLD.Rd |only man/cPath.Rd | 2 man/eTerm.Rd | 2 man/ls_eTerm.Rd | 2 man/mSeed.Rd | 2 man/xAggregate.Rd | 21 + man/xBiheatmap.Rd | 2 man/xBiproject.Rd |only man/xCircos.Rd | 8 man/xCombineNet.Rd | 2 man/xCorrelation.Rd | 2 man/xCrosstalk.Rd | 2 man/xDAGpropagate.Rd | 2 man/xDAGsim.Rd | 2 man/xDefineEQTL.Rd |only man/xDefineGenomicAnno.Rd |only man/xDefineHIC.Rd |only man/xDefineNet.Rd | 15 - man/xDefineOntology.Rd |only man/xEnrichBarplot.Rd | 2 man/xEnrichCompare.Rd | 2 man/xEnrichDAGplot.Rd | 2 man/xEnrichDAGplotAdv.Rd | 2 man/xEnrichForest.Rd | 2 man/xEnrichHeatmap.Rd | 2 man/xEnrichLadder.Rd | 76 +++++ man/xEnrichMatrix.Rd | 4 man/xEnrichNetplot.Rd | 2 man/xEnrichTreemap.Rd | 2 man/xEnricherGenes.Rd | 63 ---- man/xEnricherGenesAdv.Rd | 62 ---- man/xEnricherSNPs.Rd | 2 man/xEnricherYours.Rd | 2 man/xGGnetwork.Rd | 2 man/xGR.Rd | 14 - man/xGR2GeneScores.Rd | 2 man/xGR2nGenes.Rd | 2 man/xGR2xGeneAnno.Rd | 76 ----- man/xGR2xGeneAnnoAdv.Rd | 62 ---- man/xGR2xGeneScores.Rd | 2 man/xGR2xGenes.Rd | 2 man/xGR2xNet.Rd | 2 man/xGRcse.Rd | 2 man/xGRkaryogram.Rd |only man/xGRmanhattan.Rd |only man/xGRoverlap.Rd | 8 man/xGRsampling.Rd | 2 man/xGRscores.Rd | 2 man/xGRsep.Rd | 2 man/xGRsort.Rd | 2 man/xGRtrack.Rd | 63 +++- man/xGRviaGeneAnno.Rd | 62 ---- man/xGRviaGeneAnnoAdv.Rd | 83 +----- man/xGRviaGenomicAnno.Rd | 370 --------------------------- man/xGRviaGenomicAnnoAdv.Rd | 362 --------------------------- man/xGScore.Rd | 4 man/xGScoreAdv.Rd | 353 -------------------------- man/xGraphML.Rd | 2 man/xHEB.Rd | 2 man/xHeatmap.Rd | 2 man/xLDblock.Rd |only man/xLDenricher.Rd |only man/xLDsampling.Rd |only man/xLiftOver.Rd | 2 man/xOBOcode.Rd | 2 man/xPCHiCplot.Rd |only man/xPolarBar.Rd | 2 man/xPolarDot.Rd | 2 man/xRDataLoader.Rd | 2 man/xRPS.Rd |only man/xRWenricher.Rd |only man/xRWkernel.Rd |only man/xRepurpose.Rd |only man/xSM2DF.Rd | 2 man/xSNP2GeneScores.Rd | 6 man/xSNP2nGenes.Rd | 9 man/xSNPlocations.Rd | 8 man/xSNPscores.Rd | 4 man/xSimplifyNet.Rd | 2 man/xSocialiser.Rd | 2 man/xSocialiserGenes.Rd | 4 man/xSocialiserSNPs.Rd | 4 man/xSubneterGR.Rd | 2 man/xSubneterGenes.Rd | 33 ++ man/xSubneterSNPs.Rd | 6 man/xVisInterp.Rd | 2 man/xVisInterpAnimate.Rd | 2 man/xVolcano.Rd | 2 274 files changed, 1987 insertions(+), 4669 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise
performed manually. This includes setting up unit testing, test
coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between usethis versions 1.3.0 dated 2018-02-24 and 1.4.0 dated 2018-08-14
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Title: Improved Predictors
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems
as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut],
Torsten Hothorn [aut, cre],
Brian D. Ripley [ctb],
Terry Therneau [ctb],
Beth Atkinson [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between ipred versions 0.9-6 dated 2017-03-01 and 0.9-7 dated 2018-08-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/sbrier.R | 7 ++++++- build/vignette.rds |binary inst/NEWS | 5 +++++ inst/doc/ipred-examples.pdf |binary tests/Examples/ipred-Ex.Rout.save | 17 +++++++++++++---- 7 files changed, 34 insertions(+), 15 deletions(-)
Title: Adjusting for Optimism in 'glmnet' Regression using
Bootstrapping
Description: Main objective of a predictive model is to provide accurated predictions of a new observations.
Unfortunately we don't know how well the model performs. In addition, at the current era of omic
data where p >> n, is not reasonable applying internal validation using data-splitting. Under this
background a good method to assessing model performance is applying internal bootstrap validation
(Harrell Jr, Frank E (2015) <doi:10.1007/978-1-4757-3462-1>.) This package provides bootstrap validation
for the linear, logistic, multinomial and cox 'glmnet' models as well as lm and glm models.
Author: Antonio Jose Canada Martinez
Maintainer: Antonio Jose Canada Martinez <ancamar2@gmail.com>
Diff between BootValidation versions 0.1.5 dated 2018-05-18 and 0.1.65 dated 2018-08-14
DESCRIPTION | 8 INDEX |only MD5 | 23 +- NAMESPACE | 12 + R/parallel_vboot.R | 530 ++++++++++++++++++++++++++++++++++++--------------- README.md | 6 man/plot.bootVal.Rd |only man/print.bootVal.Rd |only man/vboot.Rd | 16 - man/vboot.coxnet.Rd | 21 +- man/vboot.elnet.Rd | 23 +- man/vboot.glm.Rd |only man/vboot.lm.Rd |only man/vboot.lognet.Rd | 23 +- man/vboot.multnet.Rd | 21 +- 15 files changed, 469 insertions(+), 214 deletions(-)
More information about BootValidation at CRAN
Permanent link
Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method and spatially correlated Poisson sampling (for spatially balanced sampling) are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included.
Author: Anton Grafström, Jonathan Lisic
Maintainer: Anton Grafström <anton.grafstrom@gmail.com>
Diff between BalancedSampling versions 1.5.2 dated 2016-07-04 and 1.5.3 dated 2018-08-14
BalancedSampling-1.5.2/BalancedSampling/man/flightphase.Rd |only BalancedSampling-1.5.3/BalancedSampling/DESCRIPTION | 8 BalancedSampling-1.5.3/BalancedSampling/MD5 | 12 BalancedSampling-1.5.3/BalancedSampling/R/RcppExports.R | 34 +- BalancedSampling-1.5.3/BalancedSampling/R/hlpm.R |only BalancedSampling-1.5.3/BalancedSampling/man/flightphase.rd |only BalancedSampling-1.5.3/BalancedSampling/man/hlpm.Rd |only BalancedSampling-1.5.3/BalancedSampling/man/lpm2_kdtree.Rd | 3 BalancedSampling-1.5.3/BalancedSampling/src/RcppExports.cpp | 190 ++++++------ 9 files changed, 139 insertions(+), 108 deletions(-)
More information about BalancedSampling at CRAN
Permanent link
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Andreas Alfons, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Kamil Barton, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Romain Francois, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Christopher Jackson, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Henric Nilsson, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Nathan Russell, Nick Sabbe, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Karline Soetaert, Werner A. Stahel, Alec Stephenson, Mark Stevenson, Matthias Templ, Terry Therneau, Yves Tille, Adrian Trapletti, Joshua Ulrich, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Hadley Wickham, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.24 dated 2018-03-19 and 0.99.25 dated 2018-08-14
DESCRIPTION | 12 - MD5 | 81 ++++++----- NAMESPACE | 26 ++- NEWS | 83 +++++++++-- R/Desc.R | 179 ++++++++++++++++++++++--- R/DescTools.r | 278 +++++++++++++++++++++++++++++++++++----- R/LinMod.R | 35 ++++- R/SpecialPlots.r | 24 +++ R/StatsAndCIs.r | 175 ++++++++++++++++++++++++- inst/doc/DescToolsCompanion.pdf |binary man/AddMonthsYM.Rd | 3 man/Assocs.Rd | 2 man/Between.Rd | 16 +- man/BreslowDayTest.Rd | 191 +++++++++++++-------------- man/CountCompCases.Rd | 4 man/DescTools-package.Rd | 43 ++++-- man/GeomSn.Rd |only man/GoodmanKruskalGamma.Rd | 2 man/HotellingsT.Rd | 4 man/KendallTauB.Rd | 4 man/Label.Rd | 8 + man/NPV.Rd | 22 ++- man/OddsRatio.Rd | 65 +++++---- man/PMT.Rd |only man/Phrase.Rd | 6 man/PlotBag.Rd | 7 - man/PlotCashFlow.Rd |only man/PlotCorr.Rd | 41 +++++ man/PlotMiss.Rd | 4 man/PlotMultiDens.Rd | 2 man/PoissonCI.Rd | 26 ++- man/SLN.Rd |only man/SomersDelta.Rd | 2 man/StrVal.Rd | 8 - man/StuartTauC.Rd | 2 man/ToWrd.Rd | 24 +-- man/TwoGroups.Rd |only man/UnirootAll.Rd |only man/VIF.Rd | 3 man/VarCI.Rd | 36 ++++- man/Winsorize.Rd | 3 man/WrdPageBreak.Rd |only man/XLGetRange.Rd | 6 man/XLView.Rd | 6 man/d.countries.Rd | 6 45 files changed, 1092 insertions(+), 347 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR)
of microbial isolates, by using new S3 classes and applying EUCAST expert rules
on antibiograms according to Leclercq (2013)
<doi:10.1111/j.1469-0691.2011.03703.x>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, rev] (<https://orcid.org/0000-0001-5809-5995>),
Erwin E.A. Hassing [ctb],
Corinna Glasner [ths] (<https://orcid.org/0000-0003-1241-1328>),
Alex W. Friedrich [ths] (<https://orcid.org/0000-0003-4881-038X>),
Bhanu Sinha [ths] (<https://orcid.org/0000-0003-1634-0010>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 0.2.0 dated 2018-05-06 and 0.3.0 dated 2018-08-14
AMR-0.2.0/AMR/R/first_isolates.R |only AMR-0.2.0/AMR/R/join.R |only AMR-0.2.0/AMR/R/print.R |only AMR-0.2.0/AMR/R/rsi_analysis.R |only AMR-0.2.0/AMR/man/figures/rsi_example.png |only AMR-0.2.0/AMR/man/guess_bactid.Rd |only AMR-0.2.0/AMR/man/print.Rd |only AMR-0.2.0/AMR/man/rsi_predict.Rd |only AMR-0.2.0/AMR/tests/testthat/test-first_isolates.R |only AMR-0.2.0/AMR/tests/testthat/test-joins.R |only AMR-0.2.0/AMR/tests/testthat/test-print.R |only AMR-0.2.0/AMR/tests/testthat/test-rsi_analysis.R |only AMR-0.3.0/AMR/DESCRIPTION | 50 - AMR-0.3.0/AMR/MD5 | 137 ++- AMR-0.3.0/AMR/NAMESPACE | 105 ++ AMR-0.3.0/AMR/NEWS.md | 78 + AMR-0.3.0/AMR/R/abname.R |only AMR-0.3.0/AMR/R/atc.R | 382 ++------- AMR-0.3.0/AMR/R/bactid.R |only AMR-0.3.0/AMR/R/classes.R | 110 +- AMR-0.3.0/AMR/R/clipboard.R |only AMR-0.3.0/AMR/R/data.R | 41 - AMR-0.3.0/AMR/R/eucast.R | 142 ++- AMR-0.3.0/AMR/R/first_isolate.R |only AMR-0.3.0/AMR/R/freq.R | 628 +++++++++++----- AMR-0.3.0/AMR/R/g.test.R |only AMR-0.3.0/AMR/R/ggplot_rsi.R |only AMR-0.3.0/AMR/R/globals.R | 38 AMR-0.3.0/AMR/R/join_microorganisms.R |only AMR-0.3.0/AMR/R/key_antibiotics.R |only AMR-0.3.0/AMR/R/kurtosis.R |only AMR-0.3.0/AMR/R/like.R |only AMR-0.3.0/AMR/R/misc.R | 161 +++- AMR-0.3.0/AMR/R/n_rsi.R |only AMR-0.3.0/AMR/R/p.symbol.R |only AMR-0.3.0/AMR/R/portion.R |only AMR-0.3.0/AMR/R/resistance_predict.R |only AMR-0.3.0/AMR/R/rsi.R |only AMR-0.3.0/AMR/R/skewness.R |only AMR-0.3.0/AMR/README.md | 448 ++++++----- AMR-0.3.0/AMR/build |only AMR-0.3.0/AMR/data/antibiotics.rda |binary AMR-0.3.0/AMR/data/microorganisms.rda |binary AMR-0.3.0/AMR/data/microorganisms.umcg.rda |binary AMR-0.3.0/AMR/data/septic_patients.rda |binary AMR-0.3.0/AMR/inst |only AMR-0.3.0/AMR/man/EUCAST.Rd | 101 ++ AMR-0.3.0/AMR/man/abname.Rd | 21 AMR-0.3.0/AMR/man/as.bactid.Rd |only AMR-0.3.0/AMR/man/as.mic.Rd | 12 AMR-0.3.0/AMR/man/as.rsi.Rd | 10 AMR-0.3.0/AMR/man/atc_property.Rd | 34 AMR-0.3.0/AMR/man/clipboard.Rd |only AMR-0.3.0/AMR/man/figures/clipboard_copy.png |only AMR-0.3.0/AMR/man/figures/clipboard_paste.png |only AMR-0.3.0/AMR/man/figures/clipboard_rsi.png |only AMR-0.3.0/AMR/man/figures/rsi_example1.png |only AMR-0.3.0/AMR/man/figures/rsi_example2.png |only AMR-0.3.0/AMR/man/figures/rsi_example3.png |only AMR-0.3.0/AMR/man/figures/rsi_example4.png |only AMR-0.3.0/AMR/man/first_isolate.Rd | 60 + AMR-0.3.0/AMR/man/freq.Rd | 134 ++- AMR-0.3.0/AMR/man/g.test.Rd |only AMR-0.3.0/AMR/man/ggplot_rsi.Rd |only AMR-0.3.0/AMR/man/join.Rd | 2 AMR-0.3.0/AMR/man/key_antibiotics.Rd | 105 ++ AMR-0.3.0/AMR/man/kurtosis.Rd |only AMR-0.3.0/AMR/man/like.Rd | 35 AMR-0.3.0/AMR/man/microorganisms.Rd | 7 AMR-0.3.0/AMR/man/microorganisms.umcg.Rd | 3 AMR-0.3.0/AMR/man/n_rsi.Rd |only AMR-0.3.0/AMR/man/p.symbol.Rd |only AMR-0.3.0/AMR/man/portion.Rd |only AMR-0.3.0/AMR/man/ratio.Rd |only AMR-0.3.0/AMR/man/resistance_predict.Rd |only AMR-0.3.0/AMR/man/rsi.Rd | 93 -- AMR-0.3.0/AMR/man/septic_patients.Rd | 25 AMR-0.3.0/AMR/man/skewness.Rd |only AMR-0.3.0/AMR/tests/testthat/Rplots.pdf |binary AMR-0.3.0/AMR/tests/testthat/test-abname.R |only AMR-0.3.0/AMR/tests/testthat/test-atc.R | 42 - AMR-0.3.0/AMR/tests/testthat/test-bactid.R |only AMR-0.3.0/AMR/tests/testthat/test-classes.R | 4 AMR-0.3.0/AMR/tests/testthat/test-clipboard.R |only AMR-0.3.0/AMR/tests/testthat/test-eucast.R | 34 AMR-0.3.0/AMR/tests/testthat/test-first_isolate.R |only AMR-0.3.0/AMR/tests/testthat/test-freq.R | 93 +- AMR-0.3.0/AMR/tests/testthat/test-g.test.R |only AMR-0.3.0/AMR/tests/testthat/test-ggplot_rsi.R |only AMR-0.3.0/AMR/tests/testthat/test-join_microorganisms.R |only AMR-0.3.0/AMR/tests/testthat/test-key_antibiotics.R |only AMR-0.3.0/AMR/tests/testthat/test-kurtosis.R |only AMR-0.3.0/AMR/tests/testthat/test-like.R |only AMR-0.3.0/AMR/tests/testthat/test-mdro.R | 3 AMR-0.3.0/AMR/tests/testthat/test-misc.R | 12 AMR-0.3.0/AMR/tests/testthat/test-p.symbol.R |only AMR-0.3.0/AMR/tests/testthat/test-portion.R |only AMR-0.3.0/AMR/tests/testthat/test-skewness.R |only AMR-0.3.0/AMR/vignettes |only 99 files changed, 2034 insertions(+), 1116 deletions(-)
Title: Fit Projected 2D Profiles to Galaxy Images
Description: Get data / Define model / ??? / Profit! 'ProFit' is a Bayesian galaxy fitting tool that uses a fast 'C++' image generation library and a flexible interface to a large number of likelihood samplers.
Author: Aaron Robotham, Dan Taranu, Rodrigo Tobar
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between ProFit versions 1.2.1 dated 2018-08-03 and 1.2.3 dated 2018-08-14
DESCRIPTION | 8 - MD5 | 30 +++--- build/partial.rdb |binary inst/doc/ProFit-Galaxy-Fit-Example.html | 8 - inst/doc/ProFit-Isophotal-Ellipses.html | 4 inst/doc/ProFit-Make-Model-Image.html | 16 +-- inst/doc/ProFit-OpenCL-OpenMP.html | 4 inst/doc/ProFit-PSF-Convolution-Can-Be-Convoluted.html | 4 inst/doc/ProFit-PSF-Fit-Example.html | 4 inst/doc/ProFit-Sigma-Maps.html | 76 ++++++++--------- inst/doc/ProFit-The-Full-Monty.html | 4 man/ProFit-package.Rd | 4 src/libprofit/VERSION | 2 src/libprofit/profit/fft_impl.h | 23 ----- src/libprofit/src/fft.cpp | 32 +++++-- src/r_profit.cpp | 44 +++++++++ 16 files changed, 152 insertions(+), 111 deletions(-)
Title: Analysis of Multivariate Data and Repeated Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures
and general MANOVA designs that do neither assume multivariate normality nor
covariance homogeneity, i.e., the procedures are applicable for a wide range
of general multivariate factorial designs. Furthermore, post-hoc comparisons
are provided for the multivariate analyses.
Friedrich, S., Konietschke, F. and Pauly, M. (2018) <arXiv:1801.08002>.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@alumni.uni-ulm.de>
Diff between MANOVA.RM versions 0.2.1 dated 2017-09-29 and 0.3.1 dated 2018-08-14
DESCRIPTION | 21 +- MD5 | 71 ++++---- NAMESPACE | 3 R/Data.R | 18 +- R/MANOVA-function.R | 105 ++++++++---- R/MANOVA.RM-package.R | 14 - R/MANOVA_Statistics.R | 244 +++++++++++++--------------- R/MANOVA_simCI.R |only R/MANOVAwide-function.R | 140 +++++++++------- R/RM-function.R | 42 +++- R/RM_Statistics.R | 29 +-- R/RM_Statistics_oneway.R | 2 R/RM_Statistics_subplot.R | 2 R/confint_MANOVA.R | 12 - R/hypo_matrix_MANOVA.R | 13 - R/plot_helper_fct.R | 18 +- R/utility_functions.R | 85 ++++++++- build/vignette.rds |binary inst/NEWS.md | 25 ++ inst/doc/Introduction_to_MANOVA.RM.R | 38 ++++ inst/doc/Introduction_to_MANOVA.RM.Rmd | 154 +++++++++++++---- inst/doc/Introduction_to_MANOVA.RM.html | 278 ++++++++++++++++++++++++-------- man/EEG.Rd | 7 man/EEGwide.Rd | 7 man/GUI.MANOVA.Rd | 1 man/GUI.MANOVAwide.Rd | 1 man/GUI.RM.Rd | 1 man/MANOVA.Rd | 17 + man/MANOVA.wide.Rd | 5 man/MANOVARM.Rd | 16 - man/RM.Rd | 17 - man/conf.reg.Rd | 7 man/o2cons.Rd | 5 man/plot.RM.Rd |only man/print.MANOVA.Rd |only man/print.RM.Rd |only man/simCI.Rd |only man/summary.MANOVA.Rd |only man/summary.RM.Rd |only vignettes/Introduction_to_MANOVA.RM.Rmd | 154 +++++++++++++---- 40 files changed, 1042 insertions(+), 510 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.1.0 dated 2018-03-16 and 1.2.0 dated 2018-08-14
DESCRIPTION | 10 - MD5 | 48 +++--- R/align.R | 5 R/aphid.R | 2 R/data.R | 2 R/plot.R | 6 R/read.R | 4 R/train.R | 339 +++++++++++++++++++++++++------------------ R/write.R | 9 - README.md | 16 +- build/vignette.rds |binary inst/CITATION | 5 inst/doc/aphid-vignette.html | 62 ++++--- man/align.Rd | 45 +++-- man/aphid.Rd | 2 man/derivePHMM.Rd | 54 +++--- man/generate.Rd | 3 man/map.Rd | 6 man/plot.PHMM.Rd | 6 man/posterior.Rd | 3 man/readPHMM.Rd | 2 man/substitution.Rd | 2 man/train.Rd | 8 - man/weight.Rd | 4 man/writePHMM.Rd | 12 - 25 files changed, 379 insertions(+), 276 deletions(-)
Title: Power Analysis for Longitudinal Multilevel Models
Description: Calculate power for the 'time x treatment' effect
in two- and three-level multilevel longitudinal studies with missing data.
Both the third-level factor (e.g. therapists, schools, or physicians),
and the second-level factor (e.g. subjects), can be assigned random slopes.
Studies with partially nested designs, unequal cluster sizes,
unequal allocation to treatment arms, and different dropout patterns
per treatment are supported. For all designs power can be
calculated both analytically and via simulations. The analytical
calculations extends the method described in Galbraith et al. (2002)
<doi:10.1016/S0197-2456(02)00205-2>, to three-level models.
Additionally, the simulation tools provides flexible ways to investigate
bias, Type I errors and the consequences of model misspecification.
Author: Kristoffer Magnusson [aut, cre]
Maintainer: Kristoffer Magnusson <hello@kristoffer.email>
Diff between powerlmm versions 0.3.0 dated 2018-04-17 and 0.4.0 dated 2018-08-14
DESCRIPTION | 8 MD5 | 72 + NAMESPACE | 9 NEWS.md | 28 R/VPC.r | 15 R/helpers.R | 14 R/power.R | 3 R/setup.R | 40 - R/simulate.R | 1101 ++++++++++++++++++++++------ R/simulate_model_selection.R |only README.md | 103 ++ build/vignette.rds |binary inst/doc/simulations.R | 425 ++++++++-- inst/doc/simulations.Rmd | 372 ++++++++- inst/doc/simulations.html | 554 ++++++++++++-- inst/doc/technical.pdf |binary inst/doc/three-level.html | 34 inst/doc/two-level.html | 10 inst/shiny_powerlmm/server.r | 9 inst/shiny_powerlmm/ui.r | 7 man/as.data.frame.plcp_multi_sim_summary.Rd |only man/get_power.Rd | 4 man/get_power_table.Rd | 4 man/print.plcp_multi.Rd | 4 man/print.plcp_multi_sim_summary.Rd | 14 man/print.plcp_sim.Rd | 3 man/print.plcp_sim_formula.Rd |only man/print.plcp_sim_summary.Rd | 5 man/sim_formula.Rd |only man/sim_formula_compare.Rd |only man/simulate.plcp.Rd | 69 - man/study_parameters.Rd | 8 man/summary.plcp_multi_sim.Rd | 29 man/summary.plcp_sim.Rd | 51 + man/transform_to_posttest.Rd |only tests/testthat.R | 1 tests/testthat/tests.simulate_LRT.R |only tests/testthat/tests.simulation.R | 191 ++-- tests/testthat/tests.simulation_formula.R |only tests/testthat/tests.simulation_multi.R | 60 + vignettes/simulations.Rmd | 372 ++++++++- 41 files changed, 2958 insertions(+), 661 deletions(-)
Title: Filter Methods for Parameter Estimation in Linear Regression
Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear regressions, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods.
Author: Christian Llano Robayo [aut, cre],
Nazrul Shaikh [aut]
Maintainer: Christian Llano Robayo <cxl985@miami.edu>
Diff between LMfilteR versions 0.1.1 dated 2017-10-12 and 0.1.2 dated 2018-08-14
DESCRIPTION | 12 - MD5 | 12 - NAMESPACE | 7 NEWS.md | 16 +- R/PF_lm.R | 434 +++++++++++++++++++++++++++++--------------------------- R/PF_lm_ss.R |only man/PF_lm.Rd | 222 ++++++++++++++++------------ man/PF_lm_ss.Rd |only 8 files changed, 384 insertions(+), 319 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 3.3.0 dated 2018-06-24 and 3.4.0 dated 2018-08-14
cobalt-3.3.0/cobalt/man/bal.tab.list.Rd |only cobalt-3.4.0/cobalt/DESCRIPTION | 10 cobalt-3.4.0/cobalt/MD5 | 71 cobalt-3.4.0/cobalt/NAMESPACE | 8 cobalt-3.4.0/cobalt/NEWS.md | 18 cobalt-3.4.0/cobalt/R/bal.plot.R | 171 + cobalt-3.4.0/cobalt/R/bal.tab.R | 500 +++- cobalt-3.4.0/cobalt/R/functions_for_processing.R | 393 +-- cobalt-3.4.0/cobalt/R/love.plot.R | 96 cobalt-3.4.0/cobalt/R/print.bal.tab.R | 2 cobalt-3.4.0/cobalt/R/utilities.R | 97 cobalt-3.4.0/cobalt/R/x2base.R | 1171 +++++++++- cobalt-3.4.0/cobalt/README.md | 32 cobalt-3.4.0/cobalt/build/partial.rdb |binary cobalt-3.4.0/cobalt/build/vignette.rds |binary cobalt-3.4.0/cobalt/inst/doc/cobalt_A0_basic_use.R | 26 cobalt-3.4.0/cobalt/inst/doc/cobalt_A0_basic_use.Rmd | 46 cobalt-3.4.0/cobalt/inst/doc/cobalt_A0_basic_use.html | 541 ++-- cobalt-3.4.0/cobalt/inst/doc/cobalt_A1_other_packages.R | 46 cobalt-3.4.0/cobalt/inst/doc/cobalt_A1_other_packages.Rmd | 83 cobalt-3.4.0/cobalt/inst/doc/cobalt_A1_other_packages.html | 155 - cobalt-3.4.0/cobalt/inst/doc/cobalt_A2_cluster_imp.html | 274 +- cobalt-3.4.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.R | 8 cobalt-3.4.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.Rmd | 16 cobalt-3.4.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.html | 116 cobalt-3.4.0/cobalt/inst/figures/README-unnamed-chunk-3-1.png |binary cobalt-3.4.0/cobalt/inst/figures/README-unnamed-chunk-3-2.png |binary cobalt-3.4.0/cobalt/inst/figures/README-unnamed-chunk-3-3.png |only cobalt-3.4.0/cobalt/inst/figures/README-unnamed-chunk-4-1.png |binary cobalt-3.4.0/cobalt/man/bal.plot.Rd | 33 cobalt-3.4.0/cobalt/man/bal.tab.Rd | 8 cobalt-3.4.0/cobalt/man/bal.tab.default.Rd |only cobalt-3.4.0/cobalt/man/bal.tab.df.formula.Rd | 20 cobalt-3.4.0/cobalt/man/bal.tab.time.list.Rd |only cobalt-3.4.0/cobalt/man/love.plot.Rd | 27 cobalt-3.4.0/cobalt/man/var.names.Rd |only cobalt-3.4.0/cobalt/vignettes/cobalt_A0_basic_use.Rmd | 46 cobalt-3.4.0/cobalt/vignettes/cobalt_A1_other_packages.Rmd | 83 cobalt-3.4.0/cobalt/vignettes/cobalt_A3_longitudinal_treat.Rmd | 16 39 files changed, 2839 insertions(+), 1274 deletions(-)