Title: Prepare Reproducible Example Code via the Clipboard
Description: Convenience wrapper that uses the 'rmarkdown' package to render
small snippets of code to target formats that include both code and output.
The goal is to encourage the sharing of small, reproducible, and runnable
examples on code-oriented websites, such as <https://stackoverflow.com> and
<https://github.com>, or in email. The user's clipboard is the default source
of input code and the default target for rendered output. 'reprex' also
extracts clean, runnable R code from various common formats, such as
copy/paste from an R session.
Author: Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>),
David Robinson [aut],
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between reprex versions 0.1.2 dated 2018-01-26 and 0.2.0 dated 2018-06-22
reprex-0.1.2/reprex/tests/testthat/foo.R |only reprex-0.1.2/reprex/tests/testthat/test-roundtrips.R |only reprex-0.2.0/reprex/DESCRIPTION | 59 - reprex-0.2.0/reprex/LICENSE | 4 reprex-0.2.0/reprex/MD5 | 80 + reprex-0.2.0/reprex/NAMESPACE | 3 reprex-0.2.0/reprex/NEWS.md | 58 + reprex-0.2.0/reprex/R/ensure.R | 24 reprex-0.2.0/reprex/R/filepaths.R |only reprex-0.2.0/reprex/R/optionally.R |only reprex-0.2.0/reprex/R/reprex-addin.R | 176 ++-- reprex-0.2.0/reprex/R/reprex-undo.R | 192 +++- reprex-0.2.0/reprex/R/reprex.R | 407 +++++----- reprex-0.2.0/reprex/R/stringify_expression.R | 97 +- reprex-0.2.0/reprex/R/utils-interactivity.R |only reprex-0.2.0/reprex/R/utils.R | 155 +-- reprex-0.2.0/reprex/R/whisker.R | 50 + reprex-0.2.0/reprex/R/zzz.R |only reprex-0.2.0/reprex/README.md | 226 +---- reprex-0.2.0/reprex/build |only reprex-0.2.0/reprex/inst/addins |only reprex-0.2.0/reprex/inst/doc |only reprex-0.2.0/reprex/inst/rstudio/addins.dcf | 7 reprex-0.2.0/reprex/inst/templates/REPREX.R | 44 - reprex-0.2.0/reprex/man/figures |only reprex-0.2.0/reprex/man/opt.Rd |only reprex-0.2.0/reprex/man/reprex.Rd | 158 ++- reprex-0.2.0/reprex/man/reprex_addin.Rd | 36 reprex-0.2.0/reprex/man/un-reprex.Rd | 115 +- reprex-0.2.0/reprex/tests/testthat.R | 4 reprex-0.2.0/reprex/tests/testthat/expressions.rds |only reprex-0.2.0/reprex/tests/testthat/helper.R | 24 reprex-0.2.0/reprex/tests/testthat/reference |only reprex-0.2.0/reprex/tests/testthat/test-env.R | 15 reprex-0.2.0/reprex/tests/testthat/test-input.R | 87 +- reprex-0.2.0/reprex/tests/testthat/test-knitr-options.R | 35 reprex-0.2.0/reprex/tests/testthat/test-optionally.R |only reprex-0.2.0/reprex/tests/testthat/test-outfiles.R | 65 - reprex-0.2.0/reprex/tests/testthat/test-pandoc.R |only reprex-0.2.0/reprex/tests/testthat/test-reprex.R |only reprex-0.2.0/reprex/tests/testthat/test-session-info.R | 19 reprex-0.2.0/reprex/tests/testthat/test-stdout-stderr.R |only reprex-0.2.0/reprex/tests/testthat/test-stringify-expression.R | 167 ++-- reprex-0.2.0/reprex/tests/testthat/test-styler.R |only reprex-0.2.0/reprex/tests/testthat/test-tidyverse.R |only reprex-0.2.0/reprex/tests/testthat/test-undo.R |only reprex-0.2.0/reprex/tests/testthat/test-utils.R |only reprex-0.2.0/reprex/tests/testthat/test-venues.R | 45 - reprex-0.2.0/reprex/vignettes |only 49 files changed, 1401 insertions(+), 951 deletions(-)
Title: Efficient Estimation of Grouped Survival Models Using the Exact
Likelihood Function
Description: These 'Rcpp'-based functions compute the efficient score statistics for grouped time-to-event data (Prentice and Gloeckler, 1978), with the optional inclusion of baseline covariates. Functions for estimating the parameter of interest and nuisance parameters, including baseline hazards, using maximum likelihood are also provided. A parallel set of functions allow for the incorporation of family structure of related individuals (e.g., trios). Note that the current implementation of the frailty model (Ripatti and Palmgren, 2000) is sensitive to departures from model assumptions, and should be considered experimental. For these data, the exact proportional-hazards-model-based likelihood is computed by evaluating multiple variable integration. The integration is accomplished using the 'Cuba' library (Hahn, 2005), and the source files are included in this package. The maximization process is carried out using Brent's algorithm, with the C++ code file from John Burkardt and John Denker (Brent, 2002).
Author: Jiaxing Lin [aut],
Alexander Sibley [aut],
Tracy Truong [aut],
Kouros Owzar [aut],
Zhiguo Li [aut],
Yu Jiang [ctb],
Janice McCarthy [ctb],
Andrew Allen [ctb]
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Diff between groupedSurv versions 1.0.1 dated 2018-05-15 and 1.0.2 dated 2018-06-22
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS | 6 ++++++ R/betaEst.R | 27 ++++++++++++++------------- R/groupedSurv.R | 10 ++++++++-- R/thetaEst.R | 3 ++- inst/doc/groupedSurv.R | 26 +++++++++++++++++--------- inst/doc/groupedSurv.Rnw | 22 +++++++++++++++++++--- inst/doc/groupedSurv.pdf |binary man/betaEst.Rd | 2 +- man/geneStat.Rd | 4 ++-- man/groupedSurv-package.Rd | 4 ++-- man/groupedSurv.Rd | 2 +- man/thetaEst.Rd | 2 +- src/helper_EF.h | 15 ++++++++------- src/helper_NF.h | 14 ++++++++------ vignettes/groupedSurv.Rnw | 22 +++++++++++++++++++--- 17 files changed, 129 insertions(+), 72 deletions(-)
Title: Chronological Bayesian Models Integrating Optically Stimulated
Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and 14C age estimate. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.
Author: Claire Christophe [aut],
Anne Philippe [aut, cre],
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Guillaume Guerin [aut] (<https://orcid.org/0000-0001-6298-5579>)
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between BayLum versions 0.1.1 dated 2017-09-07 and 0.1.2 dated 2018-06-22
BayLum-0.1.1/BayLum/NEWS |only BayLum-0.1.1/BayLum/R/Concat_DataFile.R |only BayLum-0.1.1/BayLum/R/MCMC_plot.R |only BayLum-0.1.1/BayLum/man/Concat_DataFile.Rd |only BayLum-0.1.1/BayLum/man/MCMC_plot.Rd |only BayLum-0.1.2/BayLum/DESCRIPTION | 25 BayLum-0.1.2/BayLum/MD5 | 79 - BayLum-0.1.2/BayLum/NAMESPACE | 3 BayLum-0.1.2/BayLum/NEWS.md |only BayLum-0.1.2/BayLum/R/AgeC14_Computation.R | 128 + BayLum-0.1.2/BayLum/R/AgeS_Computation.R | 137 +- BayLum-0.1.2/BayLum/R/Age_Computation.R | 104 + BayLum-0.1.2/BayLum/R/Age_OSLC14.R | 164 +- BayLum-0.1.2/BayLum/R/BayLum-package.R | 21 BayLum-0.1.2/BayLum/R/Generate_DataFile.R | 124 + BayLum-0.1.2/BayLum/R/Generate_DataFile_MG.R | 84 - BayLum-0.1.2/BayLum/R/LT_RegenDose.R | 104 + BayLum-0.1.2/BayLum/R/Palaeodose_Computation.R | 72 - BayLum-0.1.2/BayLum/R/SCMatrix.R | 2 BayLum-0.1.2/BayLum/R/SC_Ordered.R | 36 BayLum-0.1.2/BayLum/R/ScatterSamples.R | 21 BayLum-0.1.2/BayLum/R/combine_DataFiles.R |only BayLum-0.1.2/BayLum/R/plot_MCMC.R |only BayLum-0.1.2/BayLum/build/vignette.rds |binary BayLum-0.1.2/BayLum/data/AtmosphericNorth_CalC14.RData |binary BayLum-0.1.2/BayLum/data/AtmosphericSouth_CalC14.RData |binary BayLum-0.1.2/BayLum/data/Marine_CalC14.RData |binary BayLum-0.1.2/BayLum/inst/CITATION |only BayLum-0.1.2/BayLum/inst/doc/BayLum.html | 1154 ++++++++++++----- BayLum-0.1.2/BayLum/inst/extdata/samp2 |only BayLum-0.1.2/BayLum/man/AgeC14_Computation.Rd | 33 BayLum-0.1.2/BayLum/man/AgeS_Computation.Rd | 57 BayLum-0.1.2/BayLum/man/Age_Computation.Rd | 31 BayLum-0.1.2/BayLum/man/Age_OSLC14.Rd | 38 BayLum-0.1.2/BayLum/man/BayLum-package.Rd | 20 BayLum-0.1.2/BayLum/man/Generate_DataFile.Rd | 132 + BayLum-0.1.2/BayLum/man/Generate_DataFile_MG.Rd | 126 + BayLum-0.1.2/BayLum/man/LT_RegenDose.Rd | 32 BayLum-0.1.2/BayLum/man/Palaeodose_Computation.Rd | 17 BayLum-0.1.2/BayLum/man/SC_Ordered.Rd | 21 BayLum-0.1.2/BayLum/man/combine_DataFiles.Rd |only BayLum-0.1.2/BayLum/man/plot_MCMC.Rd |only BayLum-0.1.2/BayLum/tests |only BayLum-0.1.2/BayLum/vignettes/BayLum.Rmd | 539 ++++--- 44 files changed, 2220 insertions(+), 1084 deletions(-)
Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation.
The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup.
The diagram may show thousands of them. The position of the dot in the diagram is determined by the
sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The
sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore,
the diagram shows the line of no effect and the overall study results. For small subgroups, which
are found on the left side of the plot, larger random deviations from the mean study effect are expected,
while for larger subgroups only small deviations from the study mean can be expected to be chance findings.
So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a
kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups.
Author: Bodo Kirsch, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Diff between subscreen versions 0.2.2 dated 2017-07-19 and 1.0.0 dated 2018-06-22
DESCRIPTION | 27 +++++--- MD5 | 15 ++-- NEWS.md |only R/subscreen.R | 3 R/subscreencalc.R | 146 +++++++++++++++++++---------------------------- R/subscreenshow.R | 97 ++++++++++++++++++++++--------- man/subscreen-package.Rd | 8 -- man/subscreencalc.Rd | 48 +++++++++++---- man/subscreenshow.Rd | 16 +++-- 9 files changed, 208 insertions(+), 152 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression as described for example
in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>
Diff between sdcTable versions 0.22.8 dated 2017-07-29 and 0.23 dated 2018-06-22
sdcTable-0.22.8/sdcTable/inst/doc/sdcTable.Rnw |only sdcTable-0.22.8/sdcTable/inst/doc/sdcTable.pdf |only sdcTable-0.22.8/sdcTable/vignettes/overview.eps |only sdcTable-0.22.8/sdcTable/vignettes/sdcTable.Rnw |only sdcTable-0.23/sdcTable/DESCRIPTION | 16 - sdcTable-0.23/sdcTable/MD5 | 44 +-- sdcTable-0.23/sdcTable/NAMESPACE | 35 +-- sdcTable-0.23/sdcTable/R/classes.r | 25 -- sdcTable-0.23/sdcTable/R/export_functions.r | 201 ++++++++--------- sdcTable-0.23/sdcTable/R/manage_hiers.R |only sdcTable-0.23/sdcTable/R/methods_class_sdcProblem.r | 32 +- sdcTable-0.23/sdcTable/R/methods_multiple_classes.r | 41 +-- sdcTable-0.23/sdcTable/build/vignette.rds |binary sdcTable-0.23/sdcTable/data/microData1.RData |binary sdcTable-0.23/sdcTable/data/microData2.RData |binary sdcTable-0.23/sdcTable/data/problem.RData |binary sdcTable-0.23/sdcTable/data/problemWithSupps.RData |binary sdcTable-0.23/sdcTable/data/protectedData.RData |binary sdcTable-0.23/sdcTable/inst/doc/sdcTable.R | 233 ++++++-------------- sdcTable-0.23/sdcTable/inst/doc/sdcTable.html |only sdcTable-0.23/sdcTable/inst/doc/sdcTable.rmd |only sdcTable-0.23/sdcTable/man/getInfo.Rd | 8 sdcTable-0.23/sdcTable/man/makeProblem.Rd | 41 +-- sdcTable-0.23/sdcTable/man/manage_hierarchies.Rd |only sdcTable-0.23/sdcTable/src/suppMultDimTable.cpp | 3 sdcTable-0.23/sdcTable/vignettes/overview.png |only sdcTable-0.23/sdcTable/vignettes/sdcTable.rmd |only sdcTable-0.23/sdcTable/vignettes/workDat.RData |binary 28 files changed, 289 insertions(+), 390 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut],
Jakob Schwalb-Willmann [aut],
Robert J. Hijmans [ctb]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.2.1 dated 2018-04-09 and 0.2.3 dated 2018-06-22
RStoolbox-0.2.1/RStoolbox/tests/testthat/test-0.R |only RStoolbox-0.2.3/RStoolbox/DESCRIPTION | 6 RStoolbox-0.2.3/RStoolbox/MD5 | 38 - RStoolbox-0.2.3/RStoolbox/NEWS | 12 RStoolbox-0.2.3/RStoolbox/R/ggRGB.R | 30 + RStoolbox-0.2.3/RStoolbox/R/readEE.R | 8 RStoolbox-0.2.3/RStoolbox/R/saveRSTBX.R | 7 RStoolbox-0.2.3/RStoolbox/R/sysdata.rda |binary RStoolbox-0.2.3/RStoolbox/R/tasseledCap.R | 19 RStoolbox-0.2.3/RStoolbox/man/readEE.Rd | 2 RStoolbox-0.2.3/RStoolbox/man/saveRSTBX.Rd | 7 RStoolbox-0.2.3/RStoolbox/man/tasseledCap.Rd | 17 RStoolbox-0.2.3/RStoolbox/tests/testthat/Rplots.pdf |only RStoolbox-0.2.3/RStoolbox/tests/testthat/test-classifyQA.R | 2 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-fCover.R | 9 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-radCor.R | 7 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-spectralIndices.R | 2 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-superClass.R | 208 +++++----- RStoolbox-0.2.3/RStoolbox/tests/testthat/test-topCor.R | 8 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-unsuperClass.R | 1 RStoolbox-0.2.3/RStoolbox/tests/testthat/test-validateMap.R | 24 - 21 files changed, 227 insertions(+), 180 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation for non-local and some conjugate priors. Bayes factors for regression and mixtures. Routines to sample, evaluate prior densities, distributions and quantiles.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 2.1.1 dated 2018-05-08 and 2.1.2 dated 2018-06-22
ChangeLog | 7 +++ DESCRIPTION | 8 +-- MD5 | 40 +++++++++---------- NAMESPACE | 2 R/bms_ortho.R | 96 +++++++++++++++++++++++++++++++++++++--------- R/modelSelection.R | 54 +++++++++++++++----------- R/msPriorSpec.R | 22 ++++++++-- R/normaliwish.R | 97 ++++++++++++++++++++++++++++++++++++++++++++++- R/pmomLM.R | 19 +++++---- R/rmom.R | 1 inst/doc/mombf.Rnw | 5 +- inst/doc/mombf.pdf |binary man/modelSelection.Rd | 6 ++ man/msPriorSpec-class.Rd | 29 ++++++++++++-- man/postModeOrtho.Rd | 13 ++++-- src/cstat.cpp | 19 +++++++++ src/cstat.h | 2 src/modelSel.cpp | 33 +++++++++++---- src/modelSel.h | 6 ++ vignettes/mombf.Rnw | 5 +- vignettes/references.bib | 33 +++++++++++++++ 21 files changed, 399 insertions(+), 98 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard %dopar% loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.6.6 dated 2017-04-10 and 1.7.1 dated 2018-06-22
doRNG-1.6.6/doRNG/inst/doc/doRNG-unitTests.R |only doRNG-1.6.6/doRNG/inst/doc/doRNG-unitTests.Rnw |only doRNG-1.6.6/doRNG/inst/doc/doRNG-unitTests.pdf |only doRNG-1.6.6/doRNG/inst/unitTests |only doRNG-1.6.6/doRNG/man/doRNG.Rd |only doRNG-1.6.6/doRNG/tests/doRUnit.R |only doRNG-1.6.6/doRNG/vignettes/doRNG-unitTests.Rnw |only doRNG-1.7.1/doRNG/DESCRIPTION | 20 ++++----- doRNG-1.7.1/doRNG/MD5 | 32 ++++++--------- doRNG-1.7.1/doRNG/NEWS | 12 +++++ doRNG-1.7.1/doRNG/R/doRNG-package.R | 9 ---- doRNG-1.7.1/doRNG/R/doRNG.R | 50 ++++++++++++------------ doRNG-1.7.1/doRNG/build/vignette.rds |binary doRNG-1.7.1/doRNG/demo/doRNG.R | 46 ++++++++++++---------- doRNG-1.7.1/doRNG/inst/REFERENCES.bib | 2 doRNG-1.7.1/doRNG/inst/doc/doRNG.pdf |binary doRNG-1.7.1/doRNG/man/doRNG-package.Rd | 16 ++----- doRNG-1.7.1/doRNG/man/grapes-dorng-grapes.Rd |only doRNG-1.7.1/doRNG/man/infoDoRNG.Rd | 9 ++-- doRNG-1.7.1/doRNG/tests/testthat |only doRNG-1.7.1/doRNG/tests/testthat.R |only 21 files changed, 99 insertions(+), 97 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <http://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre],
Jonathan Keane [aut],
Gordon Shotwell [aut]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.22.0 dated 2018-05-02 and 1.23.0 dated 2018-06-22
crunch-1.22.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/apidocs-as_selected-tabbook.json |only crunch-1.22.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/apidocs-ca-mr-tabbook.json |only crunch-1.22.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/apidocs-mr-ca-tabbook.json |only crunch-1.22.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/tabbook-array-result.json |only crunch-1.22.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/tabbook-result.json |only crunch-1.22.0/crunch/inst/doc/datasets.R |only crunch-1.22.0/crunch/inst/doc/datasets.Rmd |only crunch-1.22.0/crunch/inst/doc/datasets.html |only crunch-1.22.0/crunch/inst/doc/getting-started.R |only crunch-1.22.0/crunch/inst/doc/getting-started.Rmd |only crunch-1.22.0/crunch/inst/doc/getting-started.html |only crunch-1.22.0/crunch/tests/testthat/cubes |only crunch-1.22.0/crunch/tests/testthat/test-cube-with-array-selected-array.R |only crunch-1.22.0/crunch/vignettes/datasets.Rmd |only crunch-1.22.0/crunch/vignettes/getting-started.Rmd |only crunch-1.23.0/crunch/DESCRIPTION | 44 crunch-1.23.0/crunch/MD5 | 369 crunch-1.23.0/crunch/NAMESPACE | 4 crunch-1.23.0/crunch/R/AllGenerics.R | 15 crunch-1.23.0/crunch/R/R-to-variable.R | 18 crunch-1.23.0/crunch/R/SO-survey.R |only crunch-1.23.0/crunch/R/add-variable.R | 18 crunch-1.23.0/crunch/R/append-dataset.R | 29 crunch-1.23.0/crunch/R/as-data-frame.R | 11 crunch-1.23.0/crunch/R/change-category-id.R | 70 crunch-1.23.0/crunch/R/crunch.R | 2 crunch-1.23.0/crunch/R/cube-dims.R | 133 crunch-1.23.0/crunch/R/cube-residuals.R | 24 crunch-1.23.0/crunch/R/cube-result.R | 96 crunch-1.23.0/crunch/R/cube-subset.R | 36 crunch-1.23.0/crunch/R/cube-transforms.R | 273 crunch-1.23.0/crunch/R/dataset-stream.R | 2 crunch-1.23.0/crunch/R/dataset.R | 3 crunch-1.23.0/crunch/R/expressions.R | 1 crunch-1.23.0/crunch/R/folders.R | 3 crunch-1.23.0/crunch/R/fork-and-merge.R | 73 crunch-1.23.0/crunch/R/formula.R | 8 crunch-1.23.0/crunch/R/join-dataset.R | 36 crunch-1.23.0/crunch/R/make-array.R | 20 crunch-1.23.0/crunch/R/misc.R | 34 crunch-1.23.0/crunch/R/multitables.R | 10 crunch-1.23.0/crunch/R/new-dataset.R | 2 crunch-1.23.0/crunch/R/ordering.R | 52 crunch-1.23.0/crunch/R/pretty-print.R | 6 crunch-1.23.0/crunch/R/search.R | 7 crunch-1.23.0/crunch/R/shoji-catalog.R | 24 crunch-1.23.0/crunch/R/show.R | 8 crunch-1.23.0/crunch/R/summary-insertions.R | 10 crunch-1.23.0/crunch/R/tab-book.R | 23 crunch-1.23.0/crunch/R/transform-calculate.R | 30 crunch-1.23.0/crunch/R/tuple.R | 2 crunch-1.23.0/crunch/R/user.R | 2 crunch-1.23.0/crunch/R/variable-delete.R | 2 crunch-1.23.0/crunch/R/variable.R | 23 crunch-1.23.0/crunch/R/zcl.R | 16 crunch-1.23.0/crunch/build/vignette.rds |binary crunch-1.23.0/crunch/data |only crunch-1.23.0/crunch/inst/WORDLIST | 161 crunch-1.23.0/crunch/inst/app.crunch.io/api/datasets/1/exclusion-58db30-PATCH.json |only crunch-1.23.0/crunch/inst/app.crunch.io/api/datasets/1/multitables/apidocs-tabbook.json |11488 ++++++---- 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crunch-1.23.0/crunch/man/changeCategoryID.Rd | 18 crunch-1.23.0/crunch/man/crunch.Rd | 2 crunch-1.23.0/crunch/man/dataset-reference.Rd |only crunch-1.23.0/crunch/man/describe.Rd | 10 crunch-1.23.0/crunch/man/forkDataset.Rd | 30 crunch-1.23.0/crunch/man/getDimTypes.Rd |only crunch-1.23.0/crunch/man/hasFunction.Rd |only crunch-1.23.0/crunch/man/joinDatasets.Rd | 19 crunch-1.23.0/crunch/man/makeArrayGadget.Rd |only crunch-1.23.0/crunch/man/mergeFork.Rd | 47 crunch-1.23.0/crunch/man/tuple-methods.Rd | 3 crunch-1.23.0/crunch/man/user-email.Rd |only crunch-1.23.0/crunch/tests/testthat/app.crunch.io/api/datasets/1 |only crunch-1.23.0/crunch/tests/testthat/dataset-fixtures/apidocs.json | 4 crunch-1.23.0/crunch/tests/testthat/dataset-fixtures/apidocs2.json | 8 crunch-1.23.0/crunch/tests/testthat/dataset-fixtures/test_ds.rds |binary crunch-1.23.0/crunch/tests/testthat/helper.R | 1 crunch-1.23.0/crunch/tests/testthat/test-add-variable.R | 39 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crunch-1.23.0/crunch/tests/testthat/test-misc.R | 45 crunch-1.23.0/crunch/tests/testthat/test-multitables.R | 45 crunch-1.23.0/crunch/tests/testthat/test-pretty-print.R | 16 crunch-1.23.0/crunch/tests/testthat/test-projects.R | 21 crunch-1.23.0/crunch/tests/testthat/test-search.R | 7 crunch-1.23.0/crunch/tests/testthat/test-variable-catalog.R | 13 crunch-1.23.0/crunch/tests/testthat/test-variable-delete.R | 5 crunch-1.23.0/crunch/tests/testthat/test-variable-order.R | 13 crunch-1.23.0/crunch/tests/testthat/test-variable-transforms.R | 60 crunch-1.23.0/crunch/tests/testthat/test-zcl.R | 29 crunch-1.23.0/crunch/vignettes/array-variables.Rmd | 2 crunch-1.23.0/crunch/vignettes/crunch |only crunch-1.23.0/crunch/vignettes/crunch.Rmd |only crunch-1.23.0/crunch/vignettes/fork-and-merge |only crunch-1.23.0/crunch/vignettes/fork-and-merge.Rmd |only crunch-1.23.0/crunch/vignettes/images/WantWorkMRReodered.png |only crunch-1.23.0/crunch/vignettes/images/crunch-companySize-screen.png |only 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Title: Analysis of R Code for Reproducible Research and Code
Comprehension
Description: Tools for analyzing R expressions
or blocks of code and determining the dependencies between them.
It focuses on R scripts, but can be used on the bodies of functions.
There are many facilities including the ability to summarize or get a high-level
view of code, determining dependencies between variables, code improvement
suggestions.
Author: Duncan Temple Lang, Roger Peng, Deborah Nolan, Gabriel Becker
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between CodeDepends versions 0.5-3 dated 2017-05-29 and 0.6.0 dated 2018-06-22
DESCRIPTION | 12 - MD5 | 29 +- NAMESPACE | 10 R/callGraph.R | 115 ++++++++-- R/codeDepends.R | 60 ++++- R/functionHandlers.R | 475 +++++++++++++++++++++++++++++++-------------- R/separateBlocks.R | 2 R/sideEffects.R | 6 build/vignette.rds |binary inst/doc/intro.html | 27 +- inst/unitTests/rcppfun.cpp |only man/findWhenUnneeded.Rd | 9 man/handlers.Rd | 35 ++- man/makeCallGraph.Rd | 11 - tests/draw.R | 7 tests/inputs.R | 52 ++++ 16 files changed, 619 insertions(+), 231 deletions(-)
Title: Data to Accompany Applied Linear Regression 3rd Edition
Description: Data files and a few functions used in the textbook S. Weisberg (2005),
'Applied Linear Regression,' 3rd edition, Wiley are presented.
This package depends on the car package. Many functions formerly
in alr3 have been renamed and now reside in car.
Data files have been lightly modified to make some data columns row labels. Many
of these files are also in the newer alr4 package.
Author: Sanford Weisberg <sandy@umn.edu>
Maintainer: Sanford Weisberg <sandy@umn.edu>
Diff between alr3 versions 2.0.7 dated 2018-04-11 and 2.0.8 dated 2018-06-22
alr3-2.0.7/alr3/man/alr3-package.Rd |only alr3-2.0.8/alr3/DESCRIPTION | 19 alr3-2.0.8/alr3/MD5 | 5 alr3-2.0.8/alr3/R/alr3.R | 743 +++++++++++++++++------------------- 4 files changed, 382 insertions(+), 385 deletions(-)
Title: Displays Palette of 5 Colors
Description: Displays palette of 5 colors based on photos depicting the unique
and vibrant culture of Punjab in Northern India. Since Punjab translates
to ``Land of 5 Rivers'' there are 5 colors per palette. If users need
more than 5 colors, they can merge 2 to 3 palettes to create their own
color-combination, or they can cherry-pick their own custom colors.
Users can view up to 3 palettes together. Users can also list all the
palette choices. And last but not least, users can see the photo that
inspired a particular palette.
Author: Sonia Ahluwalia [aut, cre]
Maintainer: Sonia Ahluwalia <sonia.bhar.ahluwalia@gmail.com>
Diff between RanglaPunjab versions 1.1.1 dated 2018-05-28 and 2.3.1 dated 2018-06-22
RanglaPunjab-1.1.1/RanglaPunjab/inst/img/sohnimaliwal.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/DESCRIPTION | 26 - RanglaPunjab-2.3.1/RanglaPunjab/MD5 | 33 - RanglaPunjab-2.3.1/RanglaPunjab/NAMESPACE | 2 RanglaPunjab-2.3.1/RanglaPunjab/R/RanglaPunjab.R | 247 ++++++++-- RanglaPunjab-2.3.1/RanglaPunjab/build |only RanglaPunjab-2.3.1/RanglaPunjab/inst/doc |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/amritsarilassi.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/amritsaripedewalilassi.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/biryanirice.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/haveli.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/haveli2.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/kulfi.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/inst/img/sohnimahiwal.jpg |only RanglaPunjab-2.3.1/RanglaPunjab/man/CherryPickPalette.Rd |only RanglaPunjab-2.3.1/RanglaPunjab/man/ListPalette.Rd | 7 RanglaPunjab-2.3.1/RanglaPunjab/man/MergePalette.Rd | 16 RanglaPunjab-2.3.1/RanglaPunjab/man/PaintPalette.Rd | 9 RanglaPunjab-2.3.1/RanglaPunjab/man/RanglaPunjab.Rd | 6 RanglaPunjab-2.3.1/RanglaPunjab/man/ShowPalettePhoto.Rd | 6 RanglaPunjab-2.3.1/RanglaPunjab/vignettes |only 21 files changed, 275 insertions(+), 77 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>
Diff between wallace versions 1.0.4 dated 2018-02-12 and 1.0.5 dated 2018-06-22
DESCRIPTION | 12 MD5 | 171 +- NAMESPACE | 12 NEWS.md | 15 R/run_wallace.R | 34 R/wallace-package.R | 84 - README.md | 108 - inst/shiny/Rmd/gtext_comp1.Rmd | 36 inst/shiny/Rmd/gtext_comp1.html |only inst/shiny/Rmd/gtext_comp1_dbOccs.Rmd | 52 inst/shiny/Rmd/gtext_comp1_userOccs.Rmd | 28 inst/shiny/Rmd/gtext_comp2.Rmd | 28 inst/shiny/Rmd/gtext_comp2_removeByID.Rmd | 38 inst/shiny/Rmd/gtext_comp2_selectOccsOnMap.Rmd | 42 inst/shiny/Rmd/gtext_comp2_spatialThin.Rmd | 64 inst/shiny/Rmd/gtext_comp3.Rmd | 54 inst/shiny/Rmd/gtext_comp3_userEnvs.Rmd | 62 inst/shiny/Rmd/gtext_comp3_worldclim.Rmd | 80 - inst/shiny/Rmd/gtext_comp4.Rmd | 36 inst/shiny/Rmd/gtext_comp4_backg.Rmd | 72 - inst/shiny/Rmd/gtext_comp4_userBg.Rmd | 26 inst/shiny/Rmd/gtext_comp5.Rmd | 36 inst/shiny/Rmd/gtext_comp5_nonspatial.Rmd | 48 inst/shiny/Rmd/gtext_comp5_spatial.Rmd | 40 inst/shiny/Rmd/gtext_comp6.Rmd | 108 - inst/shiny/Rmd/gtext_comp6_bioclim.Rmd | 48 inst/shiny/Rmd/gtext_comp6_maxent.Rmd | 98 - inst/shiny/Rmd/gtext_comp7.Rmd | 32 inst/shiny/Rmd/gtext_comp7_bcPlots.Rmd | 44 inst/shiny/Rmd/gtext_comp7_map.Rmd | 56 inst/shiny/Rmd/gtext_comp7_mxEvalPlots.Rmd | 48 inst/shiny/Rmd/gtext_comp7_respCurves.Rmd | 44 inst/shiny/Rmd/gtext_comp8.Rmd | 32 inst/shiny/Rmd/gtext_comp8_mess.Rmd | 52 inst/shiny/Rmd/gtext_comp8_pjArea.Rmd | 50 inst/shiny/Rmd/gtext_comp8_pjTime.Rmd | 54 inst/shiny/Rmd/text_about.Rmd | 52 inst/shiny/Rmd/text_intro.Rmd | 6 inst/shiny/Rmd/text_intro_tab.Rmd | 92 - inst/shiny/Rmd/text_sessionCode.Rmd | 34 inst/shiny/Rmd/userReport.Rmd | 962 ++++++------- inst/shiny/css/styles.css | 166 +- inst/shiny/funcs/functions.R | 1083 +++++++-------- inst/shiny/js/scroll.js | 28 inst/shiny/modules/mod_c1_queryDB.R | 345 ++-- inst/shiny/modules/mod_c1_userOccs.R | 112 - inst/shiny/modules/mod_c2_removeByID.R | 66 inst/shiny/modules/mod_c2_selectOccs.R | 89 - inst/shiny/modules/mod_c2_thinOccs.R | 92 - inst/shiny/modules/mod_c3_userEnvs.R | 82 - inst/shiny/modules/mod_c3_worldclim.R | 128 - inst/shiny/modules/mod_c4_bgExtent.R | 132 - inst/shiny/modules/mod_c4_bgMskSamplePts.R | 78 - inst/shiny/modules/mod_c4_userBgExtent.R | 152 +- inst/shiny/modules/mod_c5_partitionNonSpat.R | 89 - inst/shiny/modules/mod_c5_partitionSpat.R | 122 - inst/shiny/modules/mod_c6_bioclim.R | 74 - inst/shiny/modules/mod_c6_maxent.R | 185 +- inst/shiny/modules/mod_c7_bcPlots.R | 78 - inst/shiny/modules/mod_c7_mapPreds.R | 86 - inst/shiny/modules/mod_c7_mapPredsMaxent.R | 152 +- inst/shiny/modules/mod_c7_mxEvalPlots.R | 86 - inst/shiny/modules/mod_c7_respPlots.R | 78 - inst/shiny/modules/mod_c8_envSimilarity.R | 81 - inst/shiny/modules/mod_c8_projectArea.R | 104 - inst/shiny/modules/mod_c8_projectTime.R | 242 +-- inst/shiny/modules/mod_threshPred.R | 88 - inst/shiny/server.R | 1767 ++++++++++++------------- inst/shiny/ui.R | 800 +++++------ man/run_wallace.Rd | 46 man/wallace-package.Rd | 100 - tests/README.txt | 38 tests/testthat.R | 18 tests/testthat/run_test.R | 32 tests/testthat/run_wallace.R | 14 tests/testthat/test-basic.r | 76 - tests/testthat/test-c1-Occ_Data.R | 152 +- tests/testthat/test-c2-Process_Occs.R | 190 +- tests/testthat/test-c3-Env_Data.R | 180 +- tests/testthat/test-c4-Process_Envs.R | 204 +- tests/testthat/test-c5-Partition_Occs.R | 42 tests/testthat/test-c6-Model.R | 181 +- tests/testthat/test-c7-Visualize.R | 216 +-- tests/testthat/test-c8-Project.R | 250 +-- tests/testthat/test-controls.R | 30 tests/testthat/test-functions.R | 84 - tests/testthat/test-workflow.R | 944 ++++++------- 87 files changed, 6246 insertions(+), 6126 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.2-1 dated 2018-04-23 and 0.2-2 dated 2018-06-22
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/internal.R | 1 + build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/tram.pdf |binary man/Coxph.Rd | 5 +++++ tests/Coxph-Ex.Rout.save | 18 +++++++++--------- 8 files changed, 35 insertions(+), 21 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-0 dated 2018-03-08 and 1.0-1 dated 2018-06-22
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.R | 6 +++--- inst/doc/mlt.Rnw | 6 +++--- inst/doc/mlt.pdf |binary tests/GBSG2.Rout.save | 12 ++++++------ tests/faithful.Rout.save | 4 ++-- tests/timedep_covar.Rout.save | 6 +++--- tests/udist-Ex.Rout.save | 4 ++-- vignettes/mlt.Rnw | 6 +++--- 11 files changed, 44 insertions(+), 37 deletions(-)
Title: The Spike-and-Slab LASSO
Description: Efficient coordinate ascent algorithm for fitting regularization paths for linear models penalized by Spike-and-Slab LASSO. Rockova and George (2018) <doi:10.1080/01621459.2016.1260469>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gmoran@wharton.upenn.edu>
Diff between SSLASSO versions 0.0-1 dated 2017-09-21 and 1.1 dated 2018-06-22
DESCRIPTION | 12 ++++---- MD5 | 10 +++---- R/SSLASSO.R | 71 +++++++++++++++++++++++----------------------------- man/SSLASSO.Rd | 16 +++++------ man/plot.SSLASSO.Rd | 2 - src/SSL_gaussian.c | 24 ++++++++++------- 6 files changed, 67 insertions(+), 68 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.3-2 dated 2018-06-08 and 1.3-3 dated 2018-06-22
ChangeLog | 19 ++ DESCRIPTION | 14 +- MD5 | 21 +-- configure | 267 ++++++++++++++++++++-------------------- configure.ac | 4 inst/ChangeLog | 19 ++ inst/README | 44 +++--- inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/m4 |only src/gdal-bindings.cpp | 9 - src/ogr_proj.cpp | 3 12 files changed, 226 insertions(+), 176 deletions(-)
Title: A Set of Tools for Calculating Spatial Synchrony Between
Tree-Ring Chronologies
Description: Provides functions for the calculation and plotting of synchrony in
tree growth from tree-ring width chronologies (TRW index). It combines
variance-covariance (VCOV) mixed modelling with functions that quantify
the degree to which the TRW chronologies contain a common temporal
signal. It also implements temporal trends in spatial synchrony using a
moving window. These methods can also be used with other kind of ecological
variables that have temporal autocorrelation corrected.
Author: Josu G. Alday, Tatiana A. Shestakova, Victor Resco de Dios, Jordi Voltas
Maintainer: Josu G. Alday <josucham@gmail.com>
Diff between DendroSync versions 0.1.0 dated 2017-05-22 and 0.1.1 dated 2018-06-22
DESCRIPTION | 8 +++--- MD5 | 9 +++--- NEWS.md |only R/sync.plot.R | 67 +++++++++++++++++++++++++++++++--------------------- R/sync.trend.plot.R | 44 +++++++++++++++++++++++----------- README.md | 4 +-- 6 files changed, 82 insertions(+), 50 deletions(-)
Title: Copula Mixed Effect Models for Multivariate Meta-Analysis of
Diagnostic Test Accuracy Studies
Description: It has functions to implement the copula mixed models for multivariate meta-analysis of diagnostic test accuracy studies.
Author: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Diff between CopulaREMADA versions 1.0 dated 2016-09-13 and 1.1 dated 2018-06-22
DESCRIPTION | 18 ++++++------- INDEX | 3 ++ MD5 | 58 +++++++++++++++++++++++++++----------------- NAMESPACE | 7 +++-- R/MLest-4variate.R |only R/dvinesim.R |only R/pcondcop.R |only build |only data/arthritis.rda |only data/mgrid15.rda |only data/mgrid30.rda |only data/mgrid50.rda |only man/CT.Rd | 2 - man/CopulaREMADA-package.Rd |only man/CopulaREMADA.Rd | 4 +-- man/LAG.Rd | 2 - man/MRI.Rd | 2 - man/OGT.Rd | 2 - man/SROC.Rd | 4 +-- man/VineCopulaREMADA.Rd | 9 +++--- man/Vuong.Rd | 4 +-- man/arthritis.Rd |only man/betaDG.Rd | 6 ++-- man/cvinesim.Rd | 8 +++--- man/dcop.Rd | 2 - man/dvinesim.Rd |only man/hybridCopulaREMADA.Rd | 8 +++--- man/mgrid.Rd |only man/pcondcop.Rd |only man/qcondcop.Rd | 2 - man/quadVineCopulaREMADA.Rd |only man/rCopulaREMADA.Rd | 2 - man/rVineCopulaREMADA.Rd | 9 +++--- man/rcop.Rd | 2 - man/tau2par.Rd | 2 - man/telomerase.Rd | 2 - man/vineVuong.Rd | 11 +++----- 37 files changed, 93 insertions(+), 76 deletions(-)
Title: Bayesian Multi-Plate High-Throughput Screening of Compounds
Description: Can be used for joint identification of candidate compound hits from multiple assays, in drug discovery. This package implements the framework of I. D. Shterev, D. B. Dunson, C. Chan and G. D. Sempowski. "Bayesian Multi-Plate High-Throughput Screening of Compounds", Scientific Reports 8 (1), 9551. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.
Author: Ivo D. Shterev [aut, cre],
David B. Dunson [aut],
Cliburn Chan [aut],
Gregory D. Sempowski [aut]
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between BHTSpack versions 0.3 dated 2018-06-14 and 0.4 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/CITATION | 14 +++++++------- inst/doc/BHTSpackManual.pdf |binary vignettes/BHTSpackBibl.bib | 5 ++++- 6 files changed, 20 insertions(+), 17 deletions(-)
Title: Discriminating Well Surveyed Spatial Units from Exhaustive
Biodiversity Databases
Description: It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user or polygons. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.
Author: Cástor Guisande González and Jorge M. Lobo
Maintainer: Cástor Guisande González <castor@uvigo.es>
Diff between KnowBR versions 1.7 dated 2018-04-10 and 1.8 dated 2018-06-22
DESCRIPTION | 6 +-- MD5 | 22 +++++++------- R/KnowB.R | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++-- R/KnowBPolygon.R | 27 +++++++++++++---- R/MapCell.R | 5 +-- R/MapPolygon.R | 14 ++++----- man/KnowB.Rd | 18 +++++------ man/KnowBPolygon.Rd | 11 +++---- man/MapCell.Rd | 12 +++---- man/MapPolygon.Rd | 17 +++++------ man/figures/F2.jpg |binary man/figures/F3.jpg |binary 12 files changed, 150 insertions(+), 61 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.3.2.2 dated 2018-05-06 and 0.3.3 dated 2018-06-22
ChangeLog | 9 DESCRIPTION | 8 MD5 | 40 - NAMESPACE | 3 NEWS.md | 7 R/configr.R | 2 R/help.R |only R/read.R | 16 R/utils.R | 4 README.md | 19 inst/doc/configr.R | 13 inst/doc/configr.Rmd | 42 + inst/doc/configr.html | 1343 ++++++++++++++++++++---------------------- inst/doc/filetypes.Rmd | 11 inst/doc/filetypes.html | 466 ++++++-------- inst/extdata/complex.toml |only inst/extdata/help.toml |only man/config.help.Rd |only man/str2config.Rd |only tests/testthat/test_b_read.R | 11 tests/testthat/test_k_parse.R | 6 tests/testthat/test_n_help.R |only vignettes/configr.Rmd | 42 + vignettes/filetypes.Rmd | 11 24 files changed, 1068 insertions(+), 985 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront
data with them and analyze or visualize the results. The package supports
rules that are per-field, in-record, cross-record or cross-dataset. Rules
can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut],
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.2.4 dated 2018-03-28 and 0.2.5 dated 2018-06-22
validate-0.2.4/validate/man/nofun.Rd |only validate-0.2.5/validate/DESCRIPTION | 7 validate-0.2.5/validate/MD5 | 41 ++--- validate-0.2.5/validate/NAMESPACE | 1 validate-0.2.5/validate/NEWS | 8 + validate-0.2.5/validate/R/confrontation.R | 2 validate-0.2.5/validate/R/functions.R | 159 ++++---------------- validate-0.2.5/validate/R/parse.R | 35 ---- validate-0.2.5/validate/R/validator.R | 2 validate-0.2.5/validate/build/vignette.rds |binary validate-0.2.5/validate/inst/doc/indicators.html | 12 - validate-0.2.5/validate/inst/doc/introduction.R | 3 validate-0.2.5/validate/inst/doc/introduction.Rmd | 27 +++ validate-0.2.5/validate/inst/doc/introduction.html | 57 +++++-- validate-0.2.5/validate/inst/doc/rule_files.Rmd | 2 validate-0.2.5/validate/inst/doc/rule_files.html | 7 validate-0.2.5/validate/man/indicator.Rd | 9 - validate-0.2.5/validate/man/syntax.Rd | 50 +++++- validate-0.2.5/validate/tests/testthat/testParse.R | 11 - validate-0.2.5/validate/tests/testthat/testSyntax.R | 40 ----- validate-0.2.5/validate/vignettes/introduction.Rmd | 27 +++ validate-0.2.5/validate/vignettes/rule_files.Rmd | 2 22 files changed, 234 insertions(+), 268 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb]
(<https://orcid.org/0000-0002-0705-1287>),
Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.2.7 dated 2018-05-30 and 0.3.0 dated 2018-06-22
heatwaveR-0.2.7/heatwaveR/src/rle2_char.cpp |only heatwaveR-0.2.7/heatwaveR/src/rle2_num.cpp |only heatwaveR-0.3.0/heatwaveR/DESCRIPTION | 19 heatwaveR-0.3.0/heatwaveR/MD5 | 72 - heatwaveR-0.3.0/heatwaveR/NAMESPACE | 1 heatwaveR-0.3.0/heatwaveR/NEWS.md | 33 heatwaveR-0.3.0/heatwaveR/R/RcppExports.R | 8 heatwaveR-0.3.0/heatwaveR/R/detect_event.R | 75 - heatwaveR-0.3.0/heatwaveR/R/exceedance.R | 66 - heatwaveR-0.3.0/heatwaveR/R/geoms.R | 2 heatwaveR-0.3.0/heatwaveR/R/graph_functions.R | 4 heatwaveR-0.3.0/heatwaveR/R/make_whole.R | 10 heatwaveR-0.3.0/heatwaveR/R/make_whole_fast.R | 17 heatwaveR-0.3.0/heatwaveR/R/proto_event.R | 103 + heatwaveR-0.3.0/heatwaveR/R/ts2clm.R | 16 heatwaveR-0.3.0/heatwaveR/README.md | 45 heatwaveR-0.3.0/heatwaveR/build/vignette.rds |binary heatwaveR-0.3.0/heatwaveR/inst/doc/OISST_preparation.R | 6 heatwaveR-0.3.0/heatwaveR/inst/doc/OISST_preparation.Rmd | 6 heatwaveR-0.3.0/heatwaveR/inst/doc/OISST_preparation.html | 580 +++------- heatwaveR-0.3.0/heatwaveR/inst/doc/complex_clims.R |only heatwaveR-0.3.0/heatwaveR/inst/doc/complex_clims.Rmd |only heatwaveR-0.3.0/heatwaveR/inst/doc/complex_clims.html |only heatwaveR-0.3.0/heatwaveR/inst/doc/gridded_event_detection.html | 499 +++----- heatwaveR-0.3.0/heatwaveR/man/detect_event.Rd | 22 heatwaveR-0.3.0/heatwaveR/man/geom_flame.Rd | 2 heatwaveR-0.3.0/heatwaveR/man/heatwaveR-package.Rd | 2 heatwaveR-0.3.0/heatwaveR/man/make_whole.Rd | 9 heatwaveR-0.3.0/heatwaveR/man/make_whole_fast.Rd | 12 heatwaveR-0.3.0/heatwaveR/man/proto_event.Rd | 10 heatwaveR-0.3.0/heatwaveR/src/RcppExports.cpp | 24 heatwaveR-0.3.0/heatwaveR/tests/testthat/test-detect_event.R | 14 heatwaveR-0.3.0/heatwaveR/tests/testthat/test-exceedance.R | 18 heatwaveR-0.3.0/heatwaveR/tests/testthat/test-graph_functions.R | 7 heatwaveR-0.3.0/heatwaveR/tests/testthat/test-proto_event.R | 33 heatwaveR-0.3.0/heatwaveR/tests/testthat/test-ts2clm.R | 13 heatwaveR-0.3.0/heatwaveR/vignettes/OISST_preparation.Rmd | 6 heatwaveR-0.3.0/heatwaveR/vignettes/bibliography.bib | 93 + heatwaveR-0.3.0/heatwaveR/vignettes/complex_clims.Rmd |only heatwaveR-0.3.0/heatwaveR/vignettes/logo.png |binary 40 files changed, 860 insertions(+), 967 deletions(-)
Title: Graphical Integrated Text Mining Solution
Description: An 'R Commander' plug-in providing an integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, vocabulary tables, terms
co-occurrences and documents similarity measures, time series analysis,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files, 'Twitter' queries,
as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between RcmdrPlugin.temis versions 0.7.9 dated 2017-07-11 and 0.7.10 dated 2018-06-22
RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/DESCRIPTION | 8 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/MD5 | 34 +-- RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/NEWS | 8 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/common.R | 4 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/dictionary.R | 11 - RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/importCorpus.R | 2 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/showCorpusCa.R | 18 +- RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/tablelist.R | 12 - RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/R/termCooc.R | 87 ++++++---- RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/inst/po/fr/LC_MESSAGES/R-RcmdrPlugin.temis.mo |binary RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/man/cooccurrentTerms.rd |only RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/man/importCorpusDlg.rd | 4 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/man/specificTermsDlg.rd | 2 RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/man/termCoocDlg.rd | 32 +++ RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/po/R-RcmdrPlugin.temis.pot | 22 ++ RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/po/R-fr.po | 28 ++- RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/po/R-sl.po | 16 - RcmdrPlugin.temis-0.7.10/RcmdrPlugin.temis/tests/RJournal.R | 3 RcmdrPlugin.temis-0.7.9/RcmdrPlugin.temis/man/termChisqDist.rd |only 19 files changed, 197 insertions(+), 94 deletions(-)
More information about RcmdrPlugin.temis at CRAN
Permanent link
Title: Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Description: Helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich. We use this package mainly for prototyping,
teaching, and having fun with proteomics data. But it can also be
used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>),
Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>),
Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
Diff between protViz versions 0.2.45 dated 2017-11-17 and 0.3.1 dated 2018-06-22
protViz-0.2.45/protViz/inst/shiny-examples/atuth |only protViz-0.2.45/protViz/vignettes/graphics/protViz-concordance.tex |only protViz-0.3.1/protViz/DESCRIPTION | 17 - protViz-0.3.1/protViz/MD5 | 75 ++-- protViz-0.3.1/protViz/R/mascot.R | 33 ++ protViz-0.3.1/protViz/R/pepxml.R |only protViz-0.3.1/protViz/R/ssrc.R | 14 protViz-0.3.1/protViz/R/sysdata.rda |binary protViz-0.3.1/protViz/README.md | 4 protViz-0.3.1/protViz/build/vignette.rds |binary protViz-0.3.1/protViz/data/AA.RData |binary protViz-0.3.1/protViz/data/HexNAc.RData |binary protViz-0.3.1/protViz/data/averagine.RData |binary protViz-0.3.1/protViz/data/fetuinLFQ.RData |binary protViz-0.3.1/protViz/data/iRTpeptides.RData |binary protViz-0.3.1/protViz/data/iTRAQ.RData |binary protViz-0.3.1/protViz/data/msms.RData |binary protViz-0.3.1/protViz/data/pgLFQfeature.RData |binary protViz-0.3.1/protViz/data/pgLFQprot.RData |binary protViz-0.3.1/protViz/data/pressureProfile.RData |binary protViz-0.3.1/protViz/exec/protViz_mascot2XML.bash |only protViz-0.3.1/protViz/exec/protViz_mgf2RData.pl | 4 protViz-0.3.1/protViz/inst/NEWS.Rd | 8 protViz-0.3.1/protViz/inst/doc/PTM_MarkerFinder.R | 20 - protViz-0.3.1/protViz/inst/doc/PTM_MarkerFinder.Rnw | 5 protViz-0.3.1/protViz/inst/doc/PTM_MarkerFinder.pdf |binary protViz-0.3.1/protViz/inst/doc/poster.R | 10 protViz-0.3.1/protViz/inst/doc/poster.Rnw | 29 - protViz-0.3.1/protViz/inst/doc/poster.pdf |binary protViz-0.3.1/protViz/inst/doc/protViz.R | 82 ++--- protViz-0.3.1/protViz/inst/doc/protViz.Rnw | 160 +++++----- protViz-0.3.1/protViz/inst/doc/protViz.pdf |binary protViz-0.3.1/protViz/man/AA.Rd | 33 +- protViz-0.3.1/protViz/man/fasta.Rd | 6 protViz-0.3.1/protViz/man/fetuinLFQ.Rd | 4 protViz-0.3.1/protViz/man/findNN.Rd | 56 ++- protViz-0.3.1/protViz/vignettes/PTM_MarkerFinder.Rnw | 5 protViz-0.3.1/protViz/vignettes/poster.Rnw | 29 - protViz-0.3.1/protViz/vignettes/protViz.Rnw | 160 +++++----- protViz-0.3.1/protViz/vignettes/protViz.bib | 26 + 40 files changed, 469 insertions(+), 311 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.0-1 dated 2018-04-20 and 1.0-2 dated 2018-06-22
DESCRIPTION | 8 +-- MD5 | 40 +++++++++---------- R/R.R | 2 R/distr.R | 18 ++++++-- R/dpq_etc.R | 6 +- R/loglik.R | 57 +++++++++++++++------------ R/methods.R | 10 ++-- R/mlt.R | 17 ++++++-- build/partial.rdb |binary inst/NEWS.Rd | 13 ++++++ tests/2sample.Rout.save | 4 - tests/Cox-Ex.Rout.save | 14 +++--- tests/bugfixes.R | 8 +++ tests/bugfixes.Rout.save | 30 +++++++++----- tests/dpq-Ex.Rout.save | 92 ++++++++++++++++++++------------------------- tests/glm-Ex.Rout.save | 10 ++-- tests/lm-Ex.Rout.save | 4 - tests/polr-Ex.Rout.save | 6 +- tests/predict-Ex.Rout.save | 4 - tests/subset.Rout.save | 4 - tests/surv-Ex.Rout.save | 13 ++---- 21 files changed, 200 insertions(+), 160 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.8 dated 2017-05-29 and 1.7.9 dated 2018-06-22
lcmm-1.7.8/lcmm/R/firstlib.R |only lcmm-1.7.8/lcmm/man/plot.lcmm.Rd |only lcmm-1.7.8/lcmm/man/standardMethods.Rd |only lcmm-1.7.9/lcmm/DESCRIPTION | 9 lcmm-1.7.9/lcmm/MD5 | 232 +-- lcmm-1.7.9/lcmm/NAMESPACE | 249 ++- lcmm-1.7.9/lcmm/NEWS | 347 ++--- lcmm-1.7.9/lcmm/R/Contlcmm.R | 17 lcmm-1.7.9/lcmm/R/Diffepoce.R | 85 + lcmm-1.7.9/lcmm/R/ForInternalUse.R |only lcmm-1.7.9/lcmm/R/Jointlcmm.R | 504 +++++++- lcmm-1.7.9/lcmm/R/Ordlcmm.R | 15 lcmm-1.7.9/lcmm/R/VarCov.Jointlcmm.R | 4 lcmm-1.7.9/lcmm/R/VarCov.hlme.R | 76 - lcmm-1.7.9/lcmm/R/VarCov.lcmm.R | 5 lcmm-1.7.9/lcmm/R/VarCov.multlcmm.R | 5 lcmm-1.7.9/lcmm/R/VarCovRE.Jointlcmm.R | 4 lcmm-1.7.9/lcmm/R/VarCovRE.hlme.R | 329 ++--- lcmm-1.7.9/lcmm/R/VarCovRE.lcmm.R | 4 lcmm-1.7.9/lcmm/R/VarCovRE.multlcmm.R | 4 lcmm-1.7.9/lcmm/R/VarExpl.Jointlcmm.R | 15 lcmm-1.7.9/lcmm/R/VarExpl.hlme.R | 58 lcmm-1.7.9/lcmm/R/VarExpl.lcmm.R | 16 lcmm-1.7.9/lcmm/R/VarExpl.multlcmm.R | 16 lcmm-1.7.9/lcmm/R/WaldMult.R | 371 +++-- lcmm-1.7.9/lcmm/R/cuminc.R | 30 lcmm-1.7.9/lcmm/R/data_hlme.R |only lcmm-1.7.9/lcmm/R/data_lcmm.R |only lcmm-1.7.9/lcmm/R/dynpred.R | 125 + lcmm-1.7.9/lcmm/R/epoce.R | 118 + lcmm-1.7.9/lcmm/R/estimates.Jointlcmm.R | 3 lcmm-1.7.9/lcmm/R/estimates.hlme.R | 97 - lcmm-1.7.9/lcmm/R/estimates.lcmm.R | 4 lcmm-1.7.9/lcmm/R/estimates.multlcmm.R | 4 lcmm-1.7.9/lcmm/R/fitY.Jointlcmm.R | 37 lcmm-1.7.9/lcmm/R/fitY.lcmm.R | 14 lcmm-1.7.9/lcmm/R/fitY.multlcmm.R | 16 lcmm-1.7.9/lcmm/R/gridsearch.R | 57 lcmm-1.7.9/lcmm/R/hlme.R | 299 ++++ lcmm-1.7.9/lcmm/R/lcmm-package.R |only lcmm-1.7.9/lcmm/R/lcmm.R | 1125 ++++++++++++----- lcmm-1.7.9/lcmm/R/multlcmm.R | 363 +++++ lcmm-1.7.9/lcmm/R/paquid.R |only lcmm-1.7.9/lcmm/R/plot.Diffepoce.R | 2 lcmm-1.7.9/lcmm/R/plot.R | 218 +++ lcmm-1.7.9/lcmm/R/plot.cuminc.R | 31 lcmm-1.7.9/lcmm/R/plot.dynpred.R | 59 lcmm-1.7.9/lcmm/R/plot.epoce.R | 41 lcmm-1.7.9/lcmm/R/plot.predictL.R | 5 lcmm-1.7.9/lcmm/R/plot.predictY.R | 77 + lcmm-1.7.9/lcmm/R/plot.predictYcond.R |only lcmm-1.7.9/lcmm/R/plot.predictlink.R | 2 lcmm-1.7.9/lcmm/R/plotbaselinerisk.R | 20 lcmm-1.7.9/lcmm/R/plotfit.R | 68 - lcmm-1.7.9/lcmm/R/postprob.Jointlcmm.R | 5 lcmm-1.7.9/lcmm/R/postprob.hlme.R | 58 lcmm-1.7.9/lcmm/R/postprob.lcmm.R | 4 lcmm-1.7.9/lcmm/R/postprob.multlcmm.R | 5 lcmm-1.7.9/lcmm/R/predictL.Jointlcmm.R | 12 lcmm-1.7.9/lcmm/R/predictL.lcmm.R | 979 ++++++++------- lcmm-1.7.9/lcmm/R/predictL.multlcmm.R | 13 lcmm-1.7.9/lcmm/R/predictY.Jointlcmm.R | 18 lcmm-1.7.9/lcmm/R/predictY.hlme.R | 16 lcmm-1.7.9/lcmm/R/predictY.lcmm.R | 1886 ++++++++++++++++-------------- lcmm-1.7.9/lcmm/R/predictY.multlcmm.R | 17 lcmm-1.7.9/lcmm/R/predictYcond.R |only lcmm-1.7.9/lcmm/R/predictlink.Jointlcmm.R | 3 lcmm-1.7.9/lcmm/R/predictlink.lcmm.R | 3 lcmm-1.7.9/lcmm/R/predictlink.multlcmm.R | 508 ++++---- lcmm-1.7.9/lcmm/R/print.Diffepoce.R | 2 lcmm-1.7.9/lcmm/R/print.Jointlcmm.R | 2 lcmm-1.7.9/lcmm/R/print.epoce.R | 2 lcmm-1.7.9/lcmm/R/print.hlme.R | 2 lcmm-1.7.9/lcmm/R/print.lcmm.R | 174 +- lcmm-1.7.9/lcmm/R/print.multlcmm.R | 2 lcmm-1.7.9/lcmm/R/standardMethods.R | 90 + lcmm-1.7.9/lcmm/R/summary.Diffepoce.R | 2 lcmm-1.7.9/lcmm/R/summary.Jointlcmm.R | 32 lcmm-1.7.9/lcmm/R/summary.epoce.R | 2 lcmm-1.7.9/lcmm/R/summary.hlme.R | 24 lcmm-1.7.9/lcmm/R/summary.lcmm.R | 728 ++++++----- lcmm-1.7.9/lcmm/R/summary.multlcmm.R | 30 lcmm-1.7.9/lcmm/R/summarytable.R | 59 lcmm-1.7.9/lcmm/THANKS | 2 lcmm-1.7.9/lcmm/man/Diffepoce.Rd | 180 +- lcmm-1.7.9/lcmm/man/ForInternalUse.Rd | 14 lcmm-1.7.9/lcmm/man/Jointlcmm.Rd | 613 ++++++--- lcmm-1.7.9/lcmm/man/StandardMethods.Rd |only lcmm-1.7.9/lcmm/man/VarCov.Rd | 41 lcmm-1.7.9/lcmm/man/VarCovRE.Rd | 37 lcmm-1.7.9/lcmm/man/VarExpl.Rd | 63 - lcmm-1.7.9/lcmm/man/WaldMult.Rd | 57 lcmm-1.7.9/lcmm/man/cuminc.Rd | 65 - lcmm-1.7.9/lcmm/man/data_hlme.Rd | 37 lcmm-1.7.9/lcmm/man/data_lcmm.Rd | 66 - lcmm-1.7.9/lcmm/man/dynpred.Rd | 161 +- lcmm-1.7.9/lcmm/man/epoce.Rd | 209 ++- lcmm-1.7.9/lcmm/man/estimates.Rd | 75 - lcmm-1.7.9/lcmm/man/fitY.Rd | 49 lcmm-1.7.9/lcmm/man/gridsearch.Rd | 71 - lcmm-1.7.9/lcmm/man/hlme.Rd | 398 +++--- lcmm-1.7.9/lcmm/man/lcmm-package.Rd | 121 + lcmm-1.7.9/lcmm/man/lcmm.Rd | 598 +++++---- lcmm-1.7.9/lcmm/man/multlcmm.Rd | 537 +++++--- lcmm-1.7.9/lcmm/man/paquid.Rd | 67 - lcmm-1.7.9/lcmm/man/plot.Rd |only lcmm-1.7.9/lcmm/man/plot.cuminc.Rd | 74 - lcmm-1.7.9/lcmm/man/plot.dynpred.Rd | 71 - lcmm-1.7.9/lcmm/man/plot.pred.accuracy.Rd | 65 - lcmm-1.7.9/lcmm/man/plot.predict.Rd | 100 - lcmm-1.7.9/lcmm/man/postprob.Rd | 89 - lcmm-1.7.9/lcmm/man/predictL.Rd | 99 - lcmm-1.7.9/lcmm/man/predictY.Rd | 269 ++-- lcmm-1.7.9/lcmm/man/predictYcond.Rd |only lcmm-1.7.9/lcmm/man/predictlink.Rd | 91 - lcmm-1.7.9/lcmm/man/print.lcmm.Rd | 48 lcmm-1.7.9/lcmm/man/summary.lcmm.Rd | 56 lcmm-1.7.9/lcmm/man/summarytable.Rd | 48 lcmm-1.7.9/lcmm/src/Makevars | 3 lcmm-1.7.9/lcmm/src/hetmixOrd.f90 | 4 lcmm-1.7.9/lcmm/src/hetmixlin.f90 | 2 lcmm-1.7.9/lcmm/src/init.c | 1 lcmm-1.7.9/lcmm/src/lcmm.h | 15 lcmm-1.7.9/lcmm/src/predictYcond.f90 |only 124 files changed, 9166 insertions(+), 5188 deletions(-)
Title: Conditionally Unbiased Bounded Influence Estimates
Description: Conditionally unbiased bounded influence estimates as described in
Kuensch et al. (1989) <doi:10.1080/01621459.1989.10478791> in three special cases of
the generalized linear model: Bernoulli, Binomial, and Poisson distributed responses.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Diff between robcbi versions 1.1.1 dated 2018-05-09 and 1.1-2 dated 2018-06-22
DESCRIPTION | 15 ++++++++------- MD5 | 4 ++-- man/robcbi-package.Rd | 9 +++++---- 3 files changed, 15 insertions(+), 13 deletions(-)
Title: Moving Sum Based Procedures for Changes in the Mean
Description: Implementations of MOSUM-based statistical procedures and algorithms for detecting multiple changes in the mean. This comprises the MOSUM procedure for estimating multiple mean changes from Eichinger and Kirch (2018) <doi:10.3150/16-BEJ887> and the multiscale algorithmic extensions from Cho and Kirch (2018+).
Author: Alexander Meier [aut],
Haeran Cho [aut, cre],
Claudia Kirch [aut]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>
Diff between mosum versions 1.1 dated 2018-04-05 and 1.2.0 dated 2018-06-22
mosum-1.1/mosum/R/mosumCpts.R |only mosum-1.1/mosum/R/mosumTest.R |only mosum-1.1/mosum/R/multiscaleGrid.R |only mosum-1.1/mosum/R/multiscaleMosum_bottomUp.R |only mosum-1.1/mosum/R/multiscaleMosum_merging.R |only mosum-1.1/mosum/R/persp3D_multiscaleMosum.R |only mosum-1.1/mosum/R/piecewiseStationary.R |only mosum-1.1/mosum/R/piecewiseStationary_modelSignals.R |only mosum-1.1/mosum/man/cpts.bootstrap.Rd |only mosum-1.1/mosum/man/mosum.cpts.Rd |only mosum-1.1/mosum/man/mosum.cpts.bootstrap.Rd |only mosum-1.1/mosum/man/mosum.criticalValue.Rd |only mosum-1.1/mosum/man/mosum.test.Rd |only mosum-1.1/mosum/man/multiscale.bottomUp.cpts.Rd |only mosum-1.1/mosum/man/multiscale.cpts.Rd |only mosum-1.1/mosum/man/multiscale.cpts.bootstrap.Rd |only mosum-1.1/mosum/man/piecewiseStationary_signal.Rd |only mosum-1.1/mosum/man/piecewiseStationary_timeSeries.Rd |only mosum-1.1/mosum/man/plot.mosum.Rd |only mosum-1.1/mosum/src/registerDynamicSymbol.c |only mosum-1.2.0/mosum/DESCRIPTION | 20 mosum-1.2.0/mosum/MD5 | 105 ++-- mosum-1.2.0/mosum/NAMESPACE | 25 - mosum-1.2.0/mosum/R/RcppExports.R | 2 mosum-1.2.0/mosum/R/bandwidth.R |only mosum-1.2.0/mosum/R/bootstrap.R | 181 ++++---- mosum-1.2.0/mosum/R/bottom_up.R |only mosum-1.2.0/mosum/R/local_prune.R |only mosum-1.2.0/mosum/R/mosum.R | 375 +++++++++-------- mosum-1.2.0/mosum/R/mosum_stat.R |only mosum-1.2.0/mosum/R/mosum_test.R |only mosum-1.2.0/mosum/R/persp3D.R |only mosum-1.2.0/mosum/R/test_data.R |only mosum-1.2.0/mosum/R/test_models.R |only mosum-1.2.0/mosum/inst/tests/testAbsoluteBandwidth.R | 61 +- mosum-1.2.0/mosum/inst/tests/testBootstrap.R | 28 - mosum-1.2.0/mosum/inst/tests/testMosumCpts.R | 31 - mosum-1.2.0/mosum/inst/tests/testMosumStatistic.R | 22 mosum-1.2.0/mosum/inst/tests/testMultiscale.R | 145 +++--- mosum-1.2.0/mosum/inst/tests/testMultiscale_bottomUp.R | 14 mosum-1.2.0/mosum/inst/tests/testThresholds.R | 24 - mosum-1.2.0/mosum/man/bandwidths.default.Rd | 2 mosum-1.2.0/mosum/man/confint.mosum.cpts.Rd |only mosum-1.2.0/mosum/man/confint.multiscale.cpts.Rd |only mosum-1.2.0/mosum/man/cpts_bootstrap.Rd | 2 mosum-1.2.0/mosum/man/dup.merge.Rd | 8 mosum-1.2.0/mosum/man/modelSignal.blocks.Rd | 8 mosum-1.2.0/mosum/man/modelSignal.fms.Rd | 8 mosum-1.2.0/mosum/man/modelSignal.mix.Rd | 8 mosum-1.2.0/mosum/man/modelSignal.stairs10.Rd | 8 mosum-1.2.0/mosum/man/modelSignal.teeth10.Rd | 8 mosum-1.2.0/mosum/man/mosum.Rd | 103 ++-- mosum-1.2.0/mosum/man/mosum.asymptoticA.Rd | 4 mosum-1.2.0/mosum/man/mosum.asymptoticB.Rd | 2 mosum-1.2.0/mosum/man/mosum.pValue.Rd | 3 mosum-1.2.0/mosum/man/mosum.stat.Rd |only mosum-1.2.0/mosum/man/mosumCriticalValue.Rd |only mosum-1.2.0/mosum/man/multiscale.bottomUp.Rd |only mosum-1.2.0/mosum/man/multiscale.grid.Rd | 13 mosum-1.2.0/mosum/man/multiscale.localPrune.Rd |only mosum-1.2.0/mosum/man/persp3D.multiscaleMosum.Rd | 66 +- mosum-1.2.0/mosum/man/plot.mosum.cpts.Rd | 13 mosum-1.2.0/mosum/man/plot.mosum.stat.Rd |only mosum-1.2.0/mosum/man/plot.multiscale.cpts.Rd | 25 - mosum-1.2.0/mosum/man/print.mosum.cpts.Rd |only mosum-1.2.0/mosum/man/print.multiscale.cpts.Rd |only mosum-1.2.0/mosum/man/rolling_sum.Rd | 4 mosum-1.2.0/mosum/man/summary.mosum.cpts.Rd |only mosum-1.2.0/mosum/man/summary.multiscale.cpts.Rd |only mosum-1.2.0/mosum/man/testData.Rd |only mosum-1.2.0/mosum/man/testSignal.Rd |only mosum-1.2.0/mosum/src/bootstrap.cpp | 6 mosum-1.2.0/mosum/src/exhaust_bic.cpp | 4 mosum-1.2.0/mosum/src/mosum_util.cpp | 2 74 files changed, 722 insertions(+), 608 deletions(-)
Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall, David C. Woods & Maria Adamou
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>
Diff between acebayes versions 1.4.1 dated 2017-07-13 and 1.5 dated 2018-06-22
acebayes-1.4.1/acebayes/man/efficiency.Rd |only acebayes-1.5/acebayes/DESCRIPTION | 10 acebayes-1.5/acebayes/MD5 | 36 acebayes-1.5/acebayes/NAMESPACE | 15 acebayes-1.5/acebayes/R/acebayes.R | 4812 ++++++++++++++------------ acebayes-1.5/acebayes/R/sysdata.rda |binary acebayes-1.5/acebayes/build/vignette.rds |binary acebayes-1.5/acebayes/inst/doc/acebayes.pdf |binary acebayes-1.5/acebayes/man/ace.Rd | 53 acebayes-1.5/acebayes/man/acebayes-package.Rd | 29 acebayes-1.5/acebayes/man/aceglm.Rd | 52 acebayes-1.5/acebayes/man/acenlm.Rd | 43 acebayes-1.5/acebayes/man/aceobjects.Rd | 23 acebayes-1.5/acebayes/man/assess.Rd |only acebayes-1.5/acebayes/man/assessobjects.Rd |only acebayes-1.5/acebayes/man/overstallwoods.Rd | 4 acebayes-1.5/acebayes/man/plot.ace.Rd | 18 acebayes-1.5/acebayes/man/plot.assess.Rd |only acebayes-1.5/acebayes/man/utilities.Rd | 4 acebayes-1.5/acebayes/src/Makevars | 15 acebayes-1.5/acebayes/src/Makevars.win | 14 21 files changed, 2980 insertions(+), 2148 deletions(-)
Title: Estimating Asset Correlations from Default Data
Description: Functions for the estimation of intra- and inter-cohort correlations in the Vasicek credit portfolio model. For intra-cohort correlations, the package covers the two method of moments estimators of Gordy (2000) <doi:10.1016/S0378-4266(99)00054-0>, the method of moments estimator of Lucas (1995) <http://jfi.iijournals.com/content/4/4/76> and a Binomial approximation extension of this approach. Moreover, the maximum likelihood estimators of Gordy and Heitfield (2010) <http://elsa.berkeley.edu/~mcfadden/e242_f03/heitfield.pdf> and Duellmann and Gehde-Trapp (2004) <http://hdl.handle.net/10419/19729> are implemented. For inter-cohort correlations, the method of moments estimator of Bluhm and Overbeck (2003) <doi:10.1007/978-3-642-59365-9_2>/Bams et al. (2016) <https://ssrn.com/abstract=2676595> is provided and the maximum likelihood estimators comprise the approaches of Gordy and Heitfield (2010)/Kalkbrener and Onwunta (2010) <ISBN: 978-1906348250> and Pfeuffer et al. (2018). Bootstrap and Jackknife procedures for bias correction are included as well as the method of moments estimator of Frei and Wunsch (2018) <doi:10.21314/JCR.2017.231> for auto-correlated time series.
Author: Maximilian Nagl [aut,cre], Yevhen Havrylenko [aut], Marius Pfeuffer [aut], Kevin Jakob [aut], Matthias Fischer [aut], Daniel Roesch [aut]
Maintainer: Maximilian Nagl <maximilian.nagl@ur.de>
Diff between AssetCorr versions 1.0.0 dated 2018-06-06 and 1.0.1 dated 2018-06-22
DESCRIPTION | 14 MD5 | 69 ++-- NAMESPACE | 8 R/analyze_AssetCorr.R |only R/interALL.R |only R/interCMM.R | 76 ---- R/interCopula.R | 48 --- R/interCov.R | 456 +++++++++++++---------------- R/interJDP.R | 514 ++++++++++++++------------------- R/interMLE.R | 52 --- R/intraALL.R | 10 R/intraAMLE.R | 370 +++++++++++------------ R/intraAMM.R | 305 +++++++++---------- R/intraBeta.R |only R/intraCMM.R | 368 +++++++++++------------ R/intraFMM.R | 298 +++++++++---------- R/intraJDP1.R | 70 ---- R/intraJDP2.R | 71 ---- R/intraMLE.R | 568 ++++++++++++++++-------------------- R/intraMode.R |only build/partial.rdb |binary inst/NEWS.Rd | 44 ++ inst/REFERENCES.bib.sav |only inst/doc/AssetCorr_vignette.R | 38 ++ inst/doc/AssetCorr_vignette.Rmd | 445 +++++++++++++++------------- inst/doc/AssetCorr_vignette.html | 606 ++++++++++++++++++++++++++------------- man/AssetCorr-package.Rd | 2 man/analyze_AssetCorr.Rd |only man/interALL.Rd |only man/intraALL.Rd | 14 man/intraAMLE.Rd | 5 man/intraAMM.Rd | 5 man/intraBeta.Rd |only man/intraCMM.Rd | 5 man/intraFMM.Rd | 5 man/intraJDP1.Rd | 5 man/intraJDP2.Rd | 5 man/intraMLE.Rd | 5 man/intraMode.Rd |only vignettes/AssetCorr_vignette.Rmd | 445 +++++++++++++++------------- 40 files changed, 2448 insertions(+), 2478 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between statnet.common versions 4.1.2 dated 2018-06-05 and 4.1.4 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/formula.utilities.R | 8 +++++--- R/mcmc-utils.R | 9 +++++++-- build/statnet.common.pdf |binary inst/CITATION | 4 ++-- man/mcmc-utilities.Rd | 9 +++++++-- 7 files changed, 31 insertions(+), 19 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Bayesian Isotonic Regression with Bernstein Polynomials
Description: Provides functions for fitting Bayesian monotonic regression models to data.
Author: S. McKay Curtis <s.mckay.curtis@gmail.com>
Maintainer: S. McKay Curtis <s.mckay.curtis@gmail.com>
Diff between bisoreg versions 1.4 dated 2015-03-19 and 1.5 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 7 ++++++- NEWS | 6 ++++++ R/loess.wrapper.R | 36 +++++++++++++++++++----------------- man/bisoreg-package.Rd | 13 +------------ man/bisoreg.Rd | 5 +++-- src/bisoreg_init.c |only 8 files changed, 46 insertions(+), 42 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster,
Brendan McArdle, Ben Stevenson, Chris Wild
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.1-26 dated 2017-12-07 and 3.1-27 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/pairs20x.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Continuous Analog of a Binomial Distribution
Description: Implementation of the d/p/q/r family of functions for a continuous analog to the standard discrete binomial with continuous size parameter and continuous support with x in [0, size + 1], following Ilienko (2013) <arXiv:1303.5990>.
Author: Dan Dalthorp
Maintainer: Dan Dalthorp <ddalthorp@usgs.gov>
Diff between cbinom versions 1.1 dated 2018-06-10 and 1.2 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/cbinom.cpp | 3 +++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Create Plots from MCMC Output
Description: Functions for convenient plotting and viewing of MCMC output.
Author: S. McKay Curtis [aut, cre],
Ilya Goldin [ctb],
Evangelos Evangelou [ctb],
'sumtxt' from GitHub [ctb]
Maintainer: S. McKay Curtis <s.mckay.curtis@gmail.com>
Diff between mcmcplots versions 0.4.2 dated 2015-03-19 and 0.4.3 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 7 +++++++ NEWS | 3 +++ man/mcmcplots-package.Rd | 11 ----------- 5 files changed, 18 insertions(+), 19 deletions(-)
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.4.3 dated 2018-03-04 and 0.4.4 dated 2018-06-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/sticker.R | 14 ++++++++------ README.md | 41 +++++++++++++++++++++++++++++++++++++++-- man/theme_sticker.Rd | 4 +++- 6 files changed, 60 insertions(+), 18 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 6.1.0 dated 2017-08-12 and 6.2.0 dated 2018-06-22
DESCRIPTION | 12 - LICENSE | 2 MD5 | 26 +-- R/Delaporte.R | 66 ++++----- README.md | 2 build/partial.rdb |binary inst/NEWS.Rd | 11 + man/Delaporte-package.Rd | 4 man/Delaporte.Rd | 9 - src/delaporte.f95 | 315 ++++++++++++++++++++++++-------------------- src/lgamma.f95 | 74 +++++----- src/utils.f95 | 57 ++++--- src/utils_and_wrappers.c | 82 ++++++----- tests/testthat/test-delap.r | 44 +++++- 14 files changed, 407 insertions(+), 297 deletions(-)