Title: Pena-Yohai Initial Estimator for Robust S-Regression
Description: Deterministic Pena-Yohai initial estimator for robust S estimators
of regression. The procedure is described in detail in
Pena, D., & Yohai, V. (1999) <doi:10.2307/2670164>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pyinit versions 1.0.2 dated 2018-03-14 and 1.0.3 dated 2019-08-02
pyinit-1.0.2/pyinit/cleanup |only pyinit-1.0.2/pyinit/configure |only pyinit-1.0.2/pyinit/configure.ac |only pyinit-1.0.2/pyinit/configure.win |only pyinit-1.0.2/pyinit/src/Makevars.in |only pyinit-1.0.2/pyinit/src/autoconfig.h.in |only pyinit-1.0.2/pyinit/src/autoconfig.win.h |only pyinit-1.0.3/pyinit/DESCRIPTION | 10 +++---- pyinit-1.0.3/pyinit/MD5 | 20 +++++---------- pyinit-1.0.3/pyinit/NEWS.md | 3 ++ pyinit-1.0.3/pyinit/man/pyinit.Rd | 4 +-- pyinit-1.0.3/pyinit/src/Makevars |only pyinit-1.0.3/pyinit/src/config.h | 13 +-------- pyinit-1.0.3/pyinit/src/fastPY.c | 19 ++++++++------ pyinit-1.0.3/pyinit/src/mscale.c | 41 ++++++++++++++++++++++++++----- 15 files changed, 65 insertions(+), 45 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <http://data.neonscience.org>
or through the NEON Data API (see <http://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Christine Laney <claney@battelleecology.org>, Claire Lunch <clunch@battelleecology.org>
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.3.0 dated 2019-07-05 and 1.3.1 dated 2019-08-02
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/getVarsEddy.R | 6 ++++++ R/stackDataFiles.R | 8 ++++---- R/stackEddy.R | 6 ++++++ R/sysdata.rda |binary README.md | 8 ++++++++ 7 files changed, 36 insertions(+), 16 deletions(-)
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ
also has unique capabilities for comparing the compositional and thermodynamic
properties of different proteins.
Author: Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>),
R Core Team [ctb] (code derived from R's pmax())
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.3.2 dated 2019-04-21 and 1.3.3 dated 2019-08-02
DESCRIPTION | 8 MD5 | 195 +++++----- NAMESPACE | 3 R/add.obigt.R | 33 - R/affinity.R | 4 R/cgl.R | 6 R/diagram.R | 37 + R/equilibrate.R | 54 ++ R/examples.R | 6 R/hkf.R | 8 R/info.R | 21 - R/makeup.R | 16 R/mosaic.R | 49 +- R/nonideal.R | 24 - R/protein.info.R | 6 R/solubility.R | 90 +++- R/subcrt.R | 47 +- R/thermo.R | 3 R/util.affinity.R | 4 R/util.data.R | 84 ++-- R/util.formula.R | 17 R/util.legend.R |only R/util.units.R | 37 + demo/00Index | 1 demo/aluminum.R | 66 ++- demo/contour.R | 13 demo/copper.R | 4 demo/mosaic.R | 17 demo/revisit.R | 2 demo/saturation.R | 3 demo/sphalerite.R |only inst/CHECKLIST | 9 inst/CITATION | 16 inst/NEWS | 157 ++++++++ inst/doc/anintro.R | 105 +++-- inst/doc/anintro.Rmd | 161 ++++++-- inst/doc/anintro.html | 445 ++++++++++++++--------- inst/doc/eos-regress.Rmd | 1 inst/doc/eos-regress.html | 46 +- inst/doc/equilibrium.R | 2 inst/doc/equilibrium.Rnw | 2 inst/doc/equilibrium.pdf |binary inst/doc/hotspring.pdf |binary inst/doc/mklinks.sh | 4 inst/doc/obigt.Rmd | 2 inst/doc/obigt.html | 164 +++++--- inst/extdata/Berman/Got04_2004.csv |only inst/extdata/OBIGT/AS04.csv | 8 inst/extdata/OBIGT/AkDi.csv | 47 +- inst/extdata/OBIGT/Berman_cr.csv | 184 ++++----- inst/extdata/OBIGT/DEW_aq.csv | 400 ++++++++++----------- inst/extdata/OBIGT/H2O_aq.csv.xz |binary inst/extdata/OBIGT/OldAA.csv | 130 +++--- inst/extdata/OBIGT/SLOP98.csv | 340 +++++++++--------- inst/extdata/OBIGT/SUPCRT92.csv | 367 +++++++++---------- inst/extdata/OBIGT/biotic_aq.csv.xz |binary inst/extdata/OBIGT/inorganic_aq.csv.xz |binary inst/extdata/OBIGT/inorganic_cr.csv.xz |binary inst/extdata/OBIGT/inorganic_gas.csv.xz |binary inst/extdata/OBIGT/organic_aq.csv.xz |binary inst/extdata/OBIGT/organic_cr.csv.xz |binary inst/extdata/OBIGT/organic_gas.csv.xz |binary inst/extdata/OBIGT/organic_liq.csv.xz |binary inst/extdata/OBIGT/refs.csv | 5 inst/extdata/adds/LA19_test.csv |only inst/extdata/adds/obigt_check.csv | 604 +++++++++++++++++--------------- inst/extdata/protein/Sce.csv.xz |binary inst/extdata/thermo/stoich.csv.xz |binary man/add.obigt.Rd | 12 man/affinity.Rd | 20 - man/berman.Rd | 4 man/diagram.Rd | 74 ++- man/equilibrate.Rd | 29 + man/examples.Rd | 9 man/extdata.Rd | 6 man/mosaic.Rd | 20 - man/nonideal.Rd | 224 +++++++---- man/solubility.Rd | 8 man/thermo.Rd | 14 man/util.data.Rd | 4 man/util.expression.Rd | 2 man/util.formula.Rd | 8 man/util.legend.Rd |only man/util.units.Rd | 9 tests/testthat/test-DEW.R | 2 tests/testthat/test-berman.R | 2 tests/testthat/test-eos.R | 7 tests/testthat/test-ionize.aa.R | 4 tests/testthat/test-mosaic.R | 117 +++++- tests/testthat/test-nonideal.R | 44 ++ tests/testthat/test-solubility.R | 4 tests/testthat/test-util.data.R | 59 +++ tests/testthat/test-yeast.aa.R | 4 vignettes/anintro.Rmd | 161 ++++++-- vignettes/eos-regress.Rmd | 1 vignettes/equilibrium.Rnw | 2 vignettes/equilibrium.lyx | 2 vignettes/mklinks.sh | 4 vignettes/obigt.Rmd | 2 vignettes/obigt.bib | 505 ++++++++++++++------------ vignettes/vig.bib | 388 +++++++++++--------- 101 files changed, 3468 insertions(+), 2340 deletions(-)
Title: Comparative Methods for Phylogenetic Networks
Description: Analyze the phenotypic evolution of species
of hybrid origin on a phylogenetic network. This can detect a burst of variation
at the formation of a hybrid as well as an increase or decrease in trait
value at a hybridization event. Parameters are estimated by maximum
likelihood, and model averaging can be done automatically. Users need to
enter a comparative data set and a phylogenetic network.
Author: Dwueng-Chwuan Jhwueng [aut, cre],
Brian C. O'Meara [aut]
Maintainer: Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu>
Diff between BMhyb versions 1.5.2 dated 2017-10-07 and 2.1.5 dated 2019-08-02
BMhyb-1.5.2/BMhyb/README.md |only BMhyb-1.5.2/BMhyb/data/cichlid.RData |only BMhyb-1.5.2/BMhyb/data/nicotiana.RData |only BMhyb-1.5.2/BMhyb/man/AICc.Rd |only BMhyb-1.5.2/BMhyb/man/AdaptiveConfidenceIntervalSampling.Rd |only BMhyb-1.5.2/BMhyb/man/AdjustForDet.Rd |only BMhyb-1.5.2/BMhyb/man/AkaikeWeight.Rd |only BMhyb-1.5.2/BMhyb/man/AlterMatrixUsingDE.Rd |only BMhyb-1.5.2/BMhyb/man/AttachHybridsToDonor.Rd |only BMhyb-1.5.2/BMhyb/man/AttemptDeletionFix.Rd |only BMhyb-1.5.2/BMhyb/man/BMhybGrid.Rd |only BMhyb-1.5.2/BMhyb/man/BrissetteEtAlCorrection.Rd |only BMhyb-1.5.2/BMhyb/man/CalculateLikelihood.Rd |only BMhyb-1.5.2/BMhyb/man/ContourFromAdaptiveSampling.Rd |only BMhyb-1.5.2/BMhyb/man/ConvertExpm1.Rd |only BMhyb-1.5.2/BMhyb/man/ConvertLog1P.Rd |only BMhyb-1.5.2/BMhyb/man/ConvertVectorToMatrix.Rd |only BMhyb-1.5.2/BMhyb/man/DetPass.Rd |only BMhyb-1.5.2/BMhyb/man/GenerateRandomPositiveDefiniteMatrix.Rd |only BMhyb-1.5.2/BMhyb/man/GenerateRandomValues.Rd |only BMhyb-1.5.2/BMhyb/man/GenerateValues.Rd |only BMhyb-1.5.2/BMhyb/man/GetAncestor.Rd |only BMhyb-1.5.2/BMhyb/man/GetClade.Rd |only BMhyb-1.5.2/BMhyb/man/GetMeansModified.Rd |only BMhyb-1.5.2/BMhyb/man/GetVModified.Rd |only BMhyb-1.5.2/BMhyb/man/IsPositiveDefinite.Rd |only BMhyb-1.5.2/BMhyb/man/LumpIntoClades.Rd |only BMhyb-1.5.2/BMhyb/man/PlotAICRegion.Rd |only BMhyb-1.5.2/BMhyb/man/PlotConvexHull.Rd |only BMhyb-1.5.2/BMhyb/man/PlotNetwork.Rd |only BMhyb-1.5.2/BMhyb/man/PositiveDefiniteOptimizationFn.Rd |only BMhyb-1.5.2/BMhyb/man/SimulateTipData.Rd |only BMhyb-2.1.5/BMhyb/DESCRIPTION | 45 BMhyb-2.1.5/BMhyb/MD5 | 67 BMhyb-2.1.5/BMhyb/NAMESPACE | 31 BMhyb-2.1.5/BMhyb/NEWS.md |only BMhyb-2.1.5/BMhyb/R/bmhyb.r | 4265 ++++++---- BMhyb-2.1.5/BMhyb/R/data.R |only BMhyb-2.1.5/BMhyb/data/cichlid.rda |only BMhyb-2.1.5/BMhyb/data/nicotiana.rda |only BMhyb-2.1.5/BMhyb/man/AddHybridization.Rd |only BMhyb-2.1.5/BMhyb/man/BMhyb.Rd | 191 BMhyb-2.1.5/BMhyb/man/BMhybExhaustive.Rd |only BMhyb-2.1.5/BMhyb/man/ComputeLikelihood.Rd |only BMhyb-2.1.5/BMhyb/man/ComputeVCV.Rd |only BMhyb-2.1.5/BMhyb/man/ConvertEvonetToIgraphWithNodeNumbers.Rd |only BMhyb-2.1.5/BMhyb/man/CreateHybridlessEvonet.Rd |only BMhyb-2.1.5/BMhyb/man/GetConvexHull.Rd |only BMhyb-2.1.5/BMhyb/man/MergeExhaustiveForPlotting.Rd |only BMhyb-2.1.5/BMhyb/man/SimulateNetwork.Rd | 113 BMhyb-2.1.5/BMhyb/man/SimulateTips.Rd |only BMhyb-2.1.5/BMhyb/man/cichlid.Rd | 45 BMhyb-2.1.5/BMhyb/man/nicotiana.Rd | 40 BMhyb-2.1.5/BMhyb/man/plot.BMhybExhaustiveResult.Rd |only BMhyb-2.1.5/BMhyb/man/plot.BMhybResult.Rd |only BMhyb-2.1.5/BMhyb/man/print.BMhybExhaustiveResult.Rd |only BMhyb-2.1.5/BMhyb/man/print.BMhybResult.Rd |only BMhyb-2.1.5/BMhyb/man/summary.BMhybExhaustiveResult.Rd |only BMhyb-2.1.5/BMhyb/man/summary.BMhybResult.Rd |only BMhyb-2.1.5/BMhyb/tests/testthat/test_condition.R | 267 60 files changed, 3377 insertions(+), 1687 deletions(-)
Title: Easy Regression
Description: Performs analysis of regression in simple designs with quantitative treatments,
including mixed models and non linear models.
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>
Diff between easyreg versions 2.0 dated 2018-10-08 and 3.0 dated 2019-08-02
DESCRIPTION | 10 - MD5 | 26 +- NAMESPACE | 3 R/bl.R | 472 ++++++++++--------------------------------------- R/er1.R | 344 +++++++++++++++++++++++++++++------ R/er2.R | 151 ++++++--------- R/regplot.R | 33 ++- R/regtest.R | 137 ++++++++++++++ man/bl.Rd | 8 man/easyreg-package.Rd | 4 man/er1.Rd | 41 ++++ man/er2.Rd | 2 man/regplot.Rd | 36 +++ man/regtest.Rd | 8 14 files changed, 715 insertions(+), 560 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.8.0 dated 2019-06-28 and 0.8.4 dated 2019-08-02
DESCRIPTION | 11 MD5 | 49 - NEWS.md | 14 R/client.R | 4 R/httprequest.R | 4 R/response.R | 4 R/zzz.R | 2 README.md | 27 build/vignette.rds |binary inst/doc/async.Rmd | 18 inst/doc/async.html | 930 +++++++++++++---------------- inst/doc/best-practices-api-packages.Rmd | 16 inst/doc/best-practices-api-packages.html | 652 ++++++++------------ inst/doc/crul.Rmd | 18 inst/doc/crul.html | 962 +++++++++++++----------------- inst/doc/curl-options.Rmd | 18 inst/doc/curl-options.html | 802 +++++++++++-------------- inst/doc/how-to-use-crul.Rmd | 20 inst/doc/how-to-use-crul.html | 842 +++++++++++--------------- tests/fixtures |only tests/testthat/test-response.R | 41 + vignettes/async.Rmd | 18 vignettes/best-practices-api-packages.Rmd | 16 vignettes/crul.Rmd | 18 vignettes/curl-options.Rmd | 18 vignettes/how-to-use-crul.Rmd | 20 26 files changed, 2048 insertions(+), 2476 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>),
Carsten Schwemmer [ctb],
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.6.3 dated 2019-04-27 and 2.7.0 dated 2019-08-02
sjPlot-2.6.3/sjPlot/R/sjPlotStackFrequencies.R |only sjPlot-2.6.3/sjPlot/man/sjp.stackfrq.Rd |only sjPlot-2.6.3/sjPlot/man/sjt.stackfrq.Rd |only sjPlot-2.7.0/sjPlot/DESCRIPTION | 29 +- sjPlot-2.7.0/sjPlot/MD5 | 92 +++---- sjPlot-2.7.0/sjPlot/NAMESPACE | 9 sjPlot-2.7.0/sjPlot/NEWS.md | 191 +++----------- sjPlot-2.7.0/sjPlot/R/S3-methods.R | 2 sjPlot-2.7.0/sjPlot/R/helpfunctions.R | 2 sjPlot-2.7.0/sjPlot/R/html_print.R | 18 + sjPlot-2.7.0/sjPlot/R/plot_frq.R | 3 sjPlot-2.7.0/sjPlot/R/plot_likert.R | 75 ++++- sjPlot-2.7.0/sjPlot/R/plot_model.R | 5 sjPlot-2.7.0/sjPlot/R/plot_models.R | 17 - sjPlot-2.7.0/sjPlot/R/plot_point_estimates.R | 2 sjPlot-2.7.0/sjPlot/R/plot_stackfrq.R |only sjPlot-2.7.0/sjPlot/R/plot_type_est.R | 15 + sjPlot-2.7.0/sjPlot/R/plot_type_int.R | 4 sjPlot-2.7.0/sjPlot/R/sjTabItemAnalysis.R | 38 ++ sjPlot-2.7.0/sjPlot/R/sjTabSPSS.R | 47 ++- sjPlot-2.7.0/sjPlot/R/sjTabStackFrq.R | 134 ++-------- sjPlot-2.7.0/sjPlot/R/sjplot.R | 14 - sjPlot-2.7.0/sjPlot/R/tab_model.R | 119 ++++++--- sjPlot-2.7.0/sjPlot/R/tidiers.R | 16 + sjPlot-2.7.0/sjPlot/R/utils.R | 18 + sjPlot-2.7.0/sjPlot/README.md | 10 sjPlot-2.7.0/sjPlot/build/partial.rdb |binary sjPlot-2.7.0/sjPlot/build/vignette.rds |binary sjPlot-2.7.0/sjPlot/inst/doc/blackwhitefigures.html | 16 - sjPlot-2.7.0/sjPlot/inst/doc/custplot.html | 30 +- sjPlot-2.7.0/sjPlot/inst/doc/plot_interactions.html | 24 + sjPlot-2.7.0/sjPlot/inst/doc/plot_likert_scales.R |only sjPlot-2.7.0/sjPlot/inst/doc/plot_likert_scales.Rmd |only sjPlot-2.7.0/sjPlot/inst/doc/plot_likert_scales.html |only sjPlot-2.7.0/sjPlot/inst/doc/plot_marginal_effects.html | 30 +- sjPlot-2.7.0/sjPlot/inst/doc/plot_model_estimates.html | 38 +- sjPlot-2.7.0/sjPlot/inst/doc/sjtitemanalysis.html | 10 sjPlot-2.7.0/sjPlot/inst/doc/tab_bayes.R | 9 sjPlot-2.7.0/sjPlot/inst/doc/tab_bayes.Rmd | 13 sjPlot-2.7.0/sjPlot/inst/doc/tab_bayes.html | 210 +++++++--------- sjPlot-2.7.0/sjPlot/inst/doc/tab_mixed.html | 13 sjPlot-2.7.0/sjPlot/inst/doc/tab_model_estimates.html | 156 ++++------- sjPlot-2.7.0/sjPlot/inst/doc/table_css.html | 18 - sjPlot-2.7.0/sjPlot/man/plot_likert.Rd | 38 ++ sjPlot-2.7.0/sjPlot/man/plot_models.Rd | 17 + sjPlot-2.7.0/sjPlot/man/plot_stackfrq.Rd |only sjPlot-2.7.0/sjPlot/man/sjplot.Rd | 7 sjPlot-2.7.0/sjPlot/man/sjt.itemanalysis.Rd | 11 sjPlot-2.7.0/sjPlot/man/tab_model.Rd | 44 +-- sjPlot-2.7.0/sjPlot/man/tab_stackfrq.Rd |only sjPlot-2.7.0/sjPlot/vignettes/plot_likert_scales.Rmd |only sjPlot-2.7.0/sjPlot/vignettes/tab_bayes.Rmd | 13 52 files changed, 831 insertions(+), 726 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 1.0.3 dated 2019-04-26 and 1.0.4 dated 2019-08-02
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/BHSBVAR.R | 8 ++++---- build/vignette.rds |binary inst/doc/BHSBVAR.Rnw | 8 ++++---- inst/doc/BHSBVAR.pdf |binary man/BH_SBVAR.Rd | 8 ++++---- src/BHSBVAR.cpp | 6 ++++-- vignettes/BHSBVAR.Rnw | 8 ++++---- vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 13 files changed, 36 insertions(+), 34 deletions(-)
Title: Assessment of Data Trial Distributions According to the
Carlisle-Stouffer Method
Description: Assessment of the distributions of baseline continuous and categorical
variables in randomised trials. This method is based on the Carlisle-Stouffer
method with Monte Carlo simulations. It calculates p-values for each trial
baseline variable, as well as combined p-values for each trial - these p-values
measure how compatible are distributions of trials baseline variables with
random sampling. This package also allows for graphically plotting the
cumulative frequencies of computed p-values.
Please note that code was partly adapted from Carlisle JB, Loadsman JA.
(2017) <doi:10.1111/anae.13650>.
Author: Bernardo Sousa-Pinto [aut, cre],
Joao Julio Cerqueira [ctb],
Cristina Costa-Santos [ctb],
John B Carlisle [ctb],
John A Loadsman [ctb],
Armando Teixeira-Pinto [aut],
Hernani Goncalves [aut]
Maintainer: Bernardo Sousa-Pinto <bernardo@med.up.pt>
Diff between simdistr versions 1.0.0 dated 2018-07-02 and 1.0.1 dated 2019-08-02
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS.md |only R/CarlisleStouffer.R | 1 + 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Calculates the Minimum Sample Size Required for Developing a
Multivariable Prediction Model
Description: Computes the minimum sample size required for the development of a new multivariable prediction model using the criteria proposed by Riley et al. (2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate the minimum sample size for the development of models with continuous, binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi: 10.1002/sim.7992> lay out a series of criteria the sample size should meet. These aim to minimise the overfitting and to ensure precise estimation of key parameters in the prediction model.
Author: Joie Ensor [aut, cre],
Emma C. Martin [aut],
Richard D. Riley [aut]
Maintainer: Joie Ensor <j.ensor@keele.ac.uk>
Diff between pmsampsize versions 1.0.0 dated 2019-01-08 and 1.0.1 dated 2019-08-02
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NEWS.md | 8 +++++ R/pmsampsize.R | 8 ++++- R/pmsampsize_surv.R | 2 - man/pmsampsize.Rd | 9 +++++ tests/testthat/test_bin.R | 16 +++++----- tests/testthat/test_cont.R | 24 +++++++-------- tests/testthat/test_surv.R | 72 ++++++++++++++++++++++----------------------- 9 files changed, 93 insertions(+), 70 deletions(-)
Title: Elo Ratings
Description: A flexible framework for calculating Elo ratings and resulting
rankings of any two-team-per-matchup system (chess, sports leagues, 'Go',
etc.). This implementation is capable of evaluating a variety of matchups,
Elo rating updates, and win probabilities, all based on the basic Elo
rating system. It also includes methods to benchmark performance,
including logistic regression and Markov chain models.
Author: Ethan Heinzen [aut, cre]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between elo versions 1.1.0 dated 2019-01-21 and 2.0.0 dated 2019-08-02
elo-1.1.0/elo/R/auc.elo.run.R |only elo-1.1.0/elo/man/auc.elo.run.Rd |only elo-1.1.0/elo/tests/testthat/test_summary.elo.run.R |only elo-2.0.0/elo/DESCRIPTION | 11 elo-2.0.0/elo/MD5 | 89 +- elo-2.0.0/elo/NAMESPACE | 44 + elo-2.0.0/elo/NEWS.md | 50 + elo-2.0.0/elo/R/RcppExports.R | 8 elo-2.0.0/elo/R/auc.R |only elo-2.0.0/elo/R/elo.glm.R | 94 +- elo-2.0.0/elo/R/elo.markovchain.R |only elo-2.0.0/elo/R/elo.model.frame.R | 45 - elo-2.0.0/elo/R/elo.run.R | 8 elo-2.0.0/elo/R/elo.winpct.R |only elo-2.0.0/elo/R/favored.R |only elo-2.0.0/elo/R/fitted.R |only elo-2.0.0/elo/R/formula.specials.R | 47 + elo-2.0.0/elo/R/internal.functions.R | 105 ++ elo-2.0.0/elo/R/mov.R |only elo-2.0.0/elo/R/mse.R |only elo-2.0.0/elo/R/predict.elo.glm.R |only elo-2.0.0/elo/R/predict.elo.markovchain.R |only elo-2.0.0/elo/R/predict.elo.run.R | 22 elo-2.0.0/elo/R/predict.elo.winpct.R |only elo-2.0.0/elo/R/rank.teams.R |only elo-2.0.0/elo/R/score.R | 1 elo-2.0.0/elo/R/summary.elo.glm.R |only elo-2.0.0/elo/R/summary.elo.markovchain.R |only elo-2.0.0/elo/R/summary.elo.run.R | 35 elo-2.0.0/elo/R/summary.elo.winpct.R |only elo-2.0.0/elo/README.md | 4 elo-2.0.0/elo/build/vignette.rds |binary elo-2.0.0/elo/inst/doc/elo.R | 59 + elo-2.0.0/elo/inst/doc/elo.Rmd | 142 +++ elo-2.0.0/elo/inst/doc/elo.html | 741 +++++++++++++++++--- elo-2.0.0/elo/man/elo.auc.Rd |only elo-2.0.0/elo/man/elo.favored.Rd |only elo-2.0.0/elo/man/elo.fitted.Rd |only elo-2.0.0/elo/man/elo.glm.Rd | 43 - elo-2.0.0/elo/man/elo.markovchain.Rd |only elo-2.0.0/elo/man/elo.mov.Rd |only elo-2.0.0/elo/man/elo.mse.Rd |only elo-2.0.0/elo/man/elo.run.Rd | 4 elo-2.0.0/elo/man/elo.winpct.Rd |only elo-2.0.0/elo/man/formula.specials.Rd | 26 elo-2.0.0/elo/man/predict.elo.glm.Rd |only elo-2.0.0/elo/man/predict.elo.markovchain.Rd |only elo-2.0.0/elo/man/predict.elo.winpct.Rd |only elo-2.0.0/elo/man/rank.teams.Rd |only elo-2.0.0/elo/man/score.Rd | 3 elo-2.0.0/elo/man/summary.elo.glm.Rd |only elo-2.0.0/elo/man/summary.elo.markovchain.Rd |only elo-2.0.0/elo/man/summary.elo.run.Rd | 24 elo-2.0.0/elo/man/summary.elo.winpct.Rd |only elo-2.0.0/elo/src/RcppExports.cpp | 37 elo-2.0.0/elo/src/markovChain.cpp |only elo-2.0.0/elo/src/winPct.cpp |only elo-2.0.0/elo/tests/testthat/test_auxiliary.R |only elo-2.0.0/elo/tests/testthat/test_elo.glm.R |only elo-2.0.0/elo/tests/testthat/test_elo.markovchain.R |only elo-2.0.0/elo/tests/testthat/test_elo.model.frame.R | 37 elo-2.0.0/elo/tests/testthat/test_elo.team.R | 2 elo-2.0.0/elo/tests/testthat/test_elo.winpct.R |only elo-2.0.0/elo/vignettes/elo.Rmd | 142 +++ 64 files changed, 1549 insertions(+), 274 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-02 0.2.1
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@umontpellier.fr>
Diff between SpatialExtremes versions 2.0-7.1 dated 2019-07-21 and 2.0-7.2 dated 2019-08-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/header.h | 3 +++ 3 files changed, 8 insertions(+), 5 deletions(-)
More information about SpatialExtremes at CRAN
Permanent link
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] (The
development of this software package was supported by a research
grant from the National Institutes of Health/National Institute on
Aging, (Principal Investigators: Jarrod E. Dalton, PhD and Adam T.
Perzynski, PhD; Grant Number: 5R01AG055480-02). All of its contents
are solely the responsibility of the authors and do not necessarily
represent the official views of the NIH.)
Maintainer: Nik Krieger <nk@case.edu>
Diff between sociome versions 1.0.0 dated 2019-08-02 and 1.0.2 dated 2019-08-02
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 8 ++++++++ R/calculate_adi.R | 2 +- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Simple Colour Manipulation
Description: Functions for easily manipulating colours, creating colour scales and calculating colour distances.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between shades versions 1.3.1 dated 2019-01-07 and 1.4.0 dated 2019-08-02
DESCRIPTION | 10 - MD5 | 28 ++--- NEWS | 9 + R/properties.R | 11 +- R/shade.R | 18 ++- README.md | 9 + man/properties.Rd | 3 tests/testthat/test-50-missing.R |only tools/figures/addmix-1.svg | 2 tools/figures/dichromat-1.svg | 2 tools/figures/dichromat-2.svg | 2 tools/figures/ggplot-1.svg | 196 +++++++++++++++++++-------------------- tools/figures/missing-1.svg |only tools/figures/scales-1.svg | 196 +++++++++++++++++++-------------------- tools/figures/scales-2.svg | 196 +++++++++++++++++++-------------------- tools/figures/submix-1.svg | 2 16 files changed, 358 insertions(+), 326 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.7 dated 2019-04-29 and 8.8 dated 2019-08-02
forecast-8.7/forecast/tests/testthat/Rplots.pdf |only forecast-8.8/forecast/DESCRIPTION | 6 +- forecast-8.8/forecast/MD5 | 51 ++++++++++---------- forecast-8.8/forecast/NAMESPACE | 3 + forecast-8.8/forecast/NEWS.md | 6 ++ forecast-8.8/forecast/R/arima.R | 14 ++++- forecast-8.8/forecast/R/bootstrap.R | 21 ++++++-- forecast-8.8/forecast/R/clean.R | 25 ++++++---- forecast-8.8/forecast/R/ggplot.R | 4 - forecast-8.8/forecast/R/lm.R | 5 +- forecast-8.8/forecast/R/newarima2.R | 6 +- forecast-8.8/forecast/R/nnetar.R | 2 forecast-8.8/forecast/R/residuals.R | 4 + forecast-8.8/forecast/R/tscv.R | 2 forecast-8.8/forecast/build/vignette.rds |binary forecast-8.8/forecast/inst/doc/JSS2008.R | 20 ++++---- forecast-8.8/forecast/inst/doc/JSS2008.Rmd | 59 ++++++++---------------- forecast-8.8/forecast/inst/doc/JSS2008.pdf |binary forecast-8.8/forecast/man/autoplot.ts.Rd | 2 forecast-8.8/forecast/man/fitted.Arima.Rd | 1 forecast-8.8/forecast/man/forecast.Arima.Rd | 1 forecast-8.8/forecast/man/na.interp.Rd | 4 - forecast-8.8/forecast/man/residuals.forecast.Rd | 1 forecast-8.8/forecast/man/tsclean.Rd | 4 - forecast-8.8/forecast/vignettes/JSS2008.Rmd | 59 ++++++++---------------- forecast-8.8/forecast/vignettes/JSS2008_files |only 26 files changed, 156 insertions(+), 144 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>),
Martin Morgan [ctb],
Christine Stawitz [rev] (Christine reviewed the package for ropensci,
see <https://github.com/ropensci/software-review/issues/315>),
Carl Ganz [rev] (Carl reviewed the package for ropensci, see
<https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.2.4 dated 2019-07-21 and 1.2.5 dated 2019-08-02
UCSCXenaTools-1.2.4/UCSCXenaTools/R/workflow.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/DESCRIPTION | 28 UCSCXenaTools-1.2.5/UCSCXenaTools/MD5 | 52 - UCSCXenaTools-1.2.5/UCSCXenaTools/NAMESPACE | 15 UCSCXenaTools-1.2.5/UCSCXenaTools/NEWS.md | 12 UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaBrowse.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaDownload.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaFilter.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaGenerate.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaHub-class.R | 8 UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaPrepare.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaQuery.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaQueryProbeMap.R |only UCSCXenaTools-1.2.5/UCSCXenaTools/R/XenaScan.R | 38 - UCSCXenaTools-1.2.5/UCSCXenaTools/R/shiny.R | 50 - UCSCXenaTools-1.2.5/UCSCXenaTools/R/zzz.R | 4 UCSCXenaTools-1.2.5/UCSCXenaTools/README.md | 147 +--- UCSCXenaTools-1.2.5/UCSCXenaTools/build/vignette.rds |binary UCSCXenaTools-1.2.5/UCSCXenaTools/inst/doc/USCSXenaTools.R | 71 ++ UCSCXenaTools-1.2.5/UCSCXenaTools/inst/doc/USCSXenaTools.Rmd | 197 ++++++ UCSCXenaTools-1.2.5/UCSCXenaTools/inst/doc/USCSXenaTools.html | 309 +++++++++- UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaBrowse.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaDownload.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaFilter.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaGenerate.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaPrepare.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaQuery.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaQueryProbeMap.Rd | 2 UCSCXenaTools-1.2.5/UCSCXenaTools/man/XenaScan.Rd | 8 UCSCXenaTools-1.2.5/UCSCXenaTools/tests/testthat/test-basic-workflow.R | 4 UCSCXenaTools-1.2.5/UCSCXenaTools/vignettes/USCSXenaTools.Rmd | 197 ++++++ 31 files changed, 931 insertions(+), 223 deletions(-)
Title: An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Description: A suite of tools to allow you to download all
publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from
the 'Malaria Atlas Project' <https://map.ox.ac.uk/> servers as well as utility functions for plotting
the downloaded data.
Author: Daniel Pfeffer [aut] (<https://orcid.org/0000-0002-2204-3488>),
Tim Lucas [aut, cre] (<https://orcid.org/0000-0003-4694-8107>),
Daniel May [aut] (<https://orcid.org/0000-0003-0005-2452>),
Suzanne Keddie [aut] (<https://orcid.org/0000-0003-1254-7794>),
Jen Rozier [aut] (<https://orcid.org/0000-0002-2610-7557>),
Oliver Watson [aut] (<https://orcid.org/0000-0003-2374-0741>),
Harry Gibson [aut] (<https://orcid.org/0000-0001-6779-3250>),
Nick Golding [ctb],
David Smith [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between malariaAtlas versions 0.0.3 dated 2018-10-30 and 0.0.4 dated 2019-08-02
DESCRIPTION | 12 MD5 | 45 +- NAMESPACE | 1 R/autoplot.pr.points.R | 4 R/convertPrevalence.R | 6 R/fillDHScoordinates.R |only R/getPR.R | 10 R/getShp.R | 636 +++++++++++++++---------------- R/listRaster.R | 219 +++++----- README.md | 137 +++--- inst/doc/overview.html | 148 ++++--- man/figures/unnamed-chunk-11-1.png |binary man/figures/unnamed-chunk-12-1.png |binary man/figures/unnamed-chunk-15-1.png |binary man/figures/unnamed-chunk-16-1.png |binary man/figures/unnamed-chunk-19-1.png |binary man/figures/unnamed-chunk-20-1.png |binary man/figures/unnamed-chunk-22-1.png |binary man/figures/unnamed-chunk-23-1.png |binary man/figures/unnamed-chunk-24-1.png |binary man/fillDHSCoordinates.Rd |only man/getPR.Rd | 8 tests/testthat/test_extractRaster.R | 6 tests/testthat/test_fillDHScoordinates.R |only tests/testthat/test_getShp.R | 171 ++++---- 25 files changed, 728 insertions(+), 675 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters
heaped data, i.e. data which are rounded (to a possibly different degree
of coarseness). While this is mostly a minor problem in parametric density
estimation the bias can be very large for non-parametric methods such as kernel
density estimation. This package implements a partly Bayesian algorithm treating
the true unknown values as additional parameters and estimates the rounding
parameters to give a corrected kernel density estimate. It supports various
standard bandwidth selection methods. Varying rounding probabilities (depending
on the true value) and asymmetric rounding is estimable as well: Gross, M. and Rendtel, U. (2016) (<doi:10.1093/jssam/smw011>).
Additionally, bivariate non-parametric density estimation for rounded data, Gross, M. et al. (2016) (<doi:10.1111/rssa.12179>),
as well as data aggregated on areas is supported.
Author: Marcus Gross [aut, cre],
Kerstin Erfurth [ctb]
Maintainer: Marcus Gross <marcus.gross@inwt-statistics.de>
Diff between Kernelheaping versions 2.2.0 dated 2018-07-31 and 2.2.1 dated 2019-08-02
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/functions.R | 44 ++++++++++++++++++++++++++++++++------------ man/dbivr.Rd | 4 ++-- man/dheaping.Rd | 3 ++- man/dshapebivr.Rd | 4 ++-- man/dshapebivrProp.Rd | 4 ++-- man/sim.Kernelheaping.Rd | 4 ++-- man/toOtherShape.Rd | 6 +++--- 10 files changed, 60 insertions(+), 38 deletions(-)
Title: Flexible Gaussian Cluster Simulator
Description: Clustering is a central task in big data analyses and clusters are often Gaussian or near Gaussian. However, a flexible Gaussian cluster simulation tool with precise control over the size, variance, and spacing of the clusters in NXN dimensional space does not exist. This is why we created 'clusterlab'. The algorithm first creates X points equally spaced on the circumference of a circle in 2D space. These form the centers of each cluster to be simulated. Additional samples are added by adding Gaussian noise to each cluster center and concatenating the new sample co-ordinates. Then if the feature space is greater than 2D, the generated points are considered principal component scores and projected into N dimensional space using linear combinations using fixed eigenvectors. Through using vector rotations and scalar multiplication clusterlab can generate complex patterns of Gaussian clusters and outliers.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between clusterlab versions 0.0.2.6 dated 2019-01-22 and 0.0.2.7 dated 2019-08-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/introduction.Rmd | 6 +----- inst/doc/introduction.pdf |binary vignettes/introduction.Rmd | 6 +----- 6 files changed, 11 insertions(+), 19 deletions(-)
Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms
using adequate sample sizes for power and accuracy.
Author: Felipe Campelo [aut, cre],
Fernanda Takahashi [ctb],
Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <f.campelo@aston.ac.uk>
Diff between CAISEr versions 1.0.5 dated 2019-07-13 and 1.0.14 dated 2019-08-02
CAISEr-1.0.14/CAISEr/DESCRIPTION | 15 CAISEr-1.0.14/CAISEr/MD5 | 32 CAISEr-1.0.14/CAISEr/NAMESPACE | 1 CAISEr-1.0.14/CAISEr/NEWS.md | 10 CAISEr-1.0.14/CAISEr/R/calc_nreps.R | 1 CAISEr-1.0.14/CAISEr/R/onAttach.R |only CAISEr-1.0.14/CAISEr/R/plot_caiser.R |only CAISEr-1.0.14/CAISEr/R/plot_nreps.R | 7 CAISEr-1.0.14/CAISEr/R/run_experiment.R | 5 CAISEr-1.0.14/CAISEr/R/se_boot.R | 2 CAISEr-1.0.14/CAISEr/R/se_param.R | 2 CAISEr-1.0.14/CAISEr/R/summary_caiser.R | 2 CAISEr-1.0.14/CAISEr/README.md | 2 CAISEr-1.0.14/CAISEr/build/vignette.rds |binary CAISEr-1.0.14/CAISEr/inst/doc/Adapting_Algorithm_for_CAISEr.html | 600 ++++++---- CAISEr-1.0.14/CAISEr/man/calc_nreps.Rd | 1 CAISEr-1.0.14/CAISEr/man/plot.CAISEr.Rd |only CAISEr-1.0.14/CAISEr/man/run_experiment.Rd | 2 CAISEr-1.0.5/CAISEr/R/zzz.R |only 19 files changed, 452 insertions(+), 230 deletions(-)
Title: Two Arm Bayesian Clinical Trial Design with and Without
Historical Control Data
Description: A set of functions to help clinical trial researchers calculate power and sample size for two-arm Bayesian randomized clinical trials that do or do not incorporate historical control data. At some point during the design process, a clinical trial researcher who is designing a basic two-arm Bayesian randomized clinical trial needs to make decisions about power and sample size within the context of hypothesized treatment effects. Through simulation, the simple_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about treatment effect,control group characteristics, and outcome. If the clinical trial researcher has access to historical control data, then the researcher can design a two-arm Bayesian randomized clinical trial that incorporates the historical data. In such a case, the researcher needs to work through the potential consequences of historical and randomized control differences on trial characteristics, in addition to working through issues regarding power in the context of sample size, treatment effect size, and outcome. If a researcher designs a clinical trial that will incorporate historical control data, the researcher needs the randomized controls to be from the same population as the historical controls. What if this is not the case when the designed trial is implemented? During the design phase, the researcher needs to investigate the negative effects of possible historic/randomized control differences on power, type one error, and other trial characteristics. Using this information, the researcher should design the trial to mitigate these negative effects. Through simulation, the historic_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about historical and randomized control differences as well as treatment effects and outcomes. The results from historic_sim() and simple_sim() can be printed with print_table() and graphed with plot_table() methods. Outcomes considered are Gaussian, Poisson, Bernoulli, Lognormal, Weibull, and Piecewise Exponential.
Author: Barry Eggleston [cre, aut],
Doug Wilson [aut],
Becky McNeil [aut],
Joseph Ibrahim [aut],
Diane Catellier [fnd, rth, aut]
Maintainer: Barry Eggleston <beggleston@rti.org>
Diff between BayesCTDesign versions 0.5.0 dated 2018-08-14 and 0.6.0 dated 2019-08-02
DESCRIPTION | 8 MD5 | 47 NAMESPACE | 2 NEWS.md |only R/BayesCTDesigncode.R | 3151 ++++++++++++++++++++++++++++++++++--- R/BernoulliCode.R | 8 R/BernoulliErrorChecks.R | 36 R/GaussianCode.R | 4 R/GaussianErrorChecks.R | 30 R/GlobalErrorChecks.R | 440 ++++- R/LogNormalCode.R | 8 R/LogNormalErrorChecks.R | 50 R/PWECode.R | 8 R/PWEErrorChecks.R | 68 R/PoissonCode.R | 8 R/PoissonErrorChecks.R | 34 R/WeibullCode.R | 8 R/WeibullErrorChecks.R | 52 man/historic_sim.Rd | 96 - man/plot.bayes_ctd_array.Rd |only man/plot_table.Rd | 64 man/plot_table.bayes_ctd_array.Rd | 63 man/print.bayes_ctd_array.Rd |only man/print_table.Rd | 10 man/print_table.bayes_ctd_array.Rd | 10 man/simple_sim.Rd | 48 26 files changed, 3678 insertions(+), 575 deletions(-)
Title: Market Area Models for Retail and Service Locations
Description: Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package is a more user-friendly wrapper of the functions in the package 'MCI' (Wieland 2017) providing market area analysis using the Huff Model or the Multiplicative Competitive Interaction (MCI) Model. In 'MCI2', also a function for creating transport costs matrices is provided.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between MCI2 versions 1.1.1 dated 2019-01-03 and 1.1.2 dated 2019-08-02
DESCRIPTION | 8 +++---- MD5 | 40 +++++++++++++++++++------------------ NAMESPACE | 2 - R/huff.comp.R |only R/tcmat.create.R | 35 ++++++++++++++++++-------------- man/HaslachDistricts.Rd | 11 ++++++++-- man/HaslachStores.Rd | 10 ++++++--- man/HaslachSurvey.Rd | 4 ++- man/Haslach_coords_destinations.Rd | 4 +++ man/Haslach_coords_origins.Rd | 6 ++++- man/Haslach_tcmatAirline.Rd | 6 ++++- man/Haslach_tcmatDrvtime.Rd | 6 ++++- man/MCI2-package.Rd | 4 ++- man/huff.Rd | 2 + man/huff.comp.Rd |only man/huff.newdest.Rd | 2 + man/huff.updest.Rd | 2 + man/mci.Rd | 6 ++++- man/mci.sim.Rd | 4 ++- man/mcimat.create.Rd | 4 ++- man/rawdata.prep.Rd | 6 +++-- man/tcmat.create.Rd | 9 ++++++-- 22 files changed, 115 insertions(+), 56 deletions(-)
Title: Using R to Install Stuff on Windows OS (Such As: R, 'Rtools',
'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool),
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Tom Allard [ctb],
ChingChuan Chen [ctb],
Jonathan Hill [ctb],
Chan-Yub Park [ctb] (https://github.com/mrchypark),
Gerhard Nachtmann [ctb]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.21.3 dated 2019-06-09 and 0.22.0 dated 2019-08-02
ChangeLog | 146 ++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 15 ++--- MD5 | 16 ++--- NEWS | 12 ++++ NEWS.md | 12 ++++ R/install.R | 26 ++++++-- R/zzz.R | 3 - README.md | 65 +--------------------- man/install.Rtools.Rd | 2 9 files changed, 210 insertions(+), 87 deletions(-)
Title: Family of Lasso Regression
Description: Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan, and Han Liu
Maintainer: ORPHANED
Diff between flare versions 1.6.0.1 dated 2019-07-02 and 1.6.0.2 dated 2019-08-02
flare-1.6.0.1/flare/data/datalist |only flare-1.6.0.2/flare/DESCRIPTION | 12 +++++++----- flare-1.6.0.2/flare/MD5 | 13 ++++++------- flare-1.6.0.2/flare/build/vignette.rds |binary flare-1.6.0.2/flare/data/eyedata.rda |binary flare-1.6.0.2/flare/inst/doc/vignette.pdf |binary flare-1.6.0.2/flare/man/eyedata.Rd | 2 ++ flare-1.6.0.2/flare/man/sugm.plot.Rd | 2 ++ 8 files changed, 17 insertions(+), 12 deletions(-)
Title: Build 'data.table' Expressions with Data Manipulation Verbs
Description: A specialization of 'dplyr' data manipulation verbs that parse and build expressions
which are ultimately evaluated by 'data.table', letting it handle all optimizations. A set of
additional verbs is also provided to facilitate some common operations on a subset of the data.
Author: Alexis Sarda-Espinosa [cre, aut]
Maintainer: Alexis Sarda-Espinosa <alexis.sarda@gmail.com>
Diff between table.express versions 0.2.0 dated 2019-07-05 and 0.3.0 dated 2019-08-02
DESCRIPTION | 31 MD5 | 181 - NAMESPACE | 310 +- R/R6-EagerExprBuilder.R |only R/R6-ExprBuilder.R | 216 + R/UTILS-misc.R | 71 R/UTILS-nest_expr.R |only R/VERBS-anti_join.R | 30 R/VERBS-arrange.R | 10 R/VERBS-distinct.R | 58 R/VERBS-filter.R | 18 R/VERBS-filter_on.R | 54 R/VERBS-filter_sd.R | 54 R/VERBS-full_join.R | 10 R/VERBS-group_by.R | 8 R/VERBS-inner_join.R | 26 R/VERBS-joins.R | 12 R/VERBS-key_by.R | 12 R/VERBS-left_join.R | 47 R/VERBS-max_by.R |only R/VERBS-min_by.R |only R/VERBS-mutate.R | 22 R/VERBS-mutate_join.R | 30 R/VERBS-mutate_sd.R | 61 R/VERBS-order_by.R | 11 R/VERBS-right_join.R | 31 R/VERBS-select.R | 40 R/VERBS-semi_join.R | 87 R/VERBS-transmute.R | 39 R/VERBS-transmute_sd.R | 46 R/VERBS-where.R | 40 build/vignette.rds |binary inst/WORDLIST | 1 inst/_pkgdown.yml | 3 inst/doc/joins.Rmd | 109 - inst/doc/joins.html | 1507 ++++++------- inst/doc/table.express.Rmd | 327 +-- inst/doc/table.express.html | 1847 ++++++++--------- man/EagerExprBuilder.Rd |only man/ExprBuilder.Rd | 94 man/arrange-table.express.Rd | 47 man/chain.Rd | 60 man/distinct-table.express.Rd | 78 man/end_expr.Rd | 62 man/extrema_by.Rd |only man/filter-table.express.Rd | 55 man/filter_on.Rd | 105 man/filter_sd.Rd | 131 - man/frame_append.Rd | 52 man/group_by-table.express.Rd | 83 man/joins.Rd | 335 +-- man/key_by.Rd | 89 man/mutate-table.express.Rd | 97 man/mutate_sd.Rd | 139 - man/nest_expr.Rd |only man/order_by-table.express.Rd | 94 man/reexports.Rd | 106 man/select-table.express.Rd | 94 man/start_expr.Rd | 58 man/table.express-package.Rd | 275 +- man/transmute-table.express.Rd | 91 man/transmute_sd.Rd | 131 - man/where-table.express.Rd | 102 tests/testthat/acceptance/test-complex-flow.R | 226 ++ tests/testthat/acceptance/test-left-join-chain.R | 6 tests/testthat/integration/test-chain-joins.R | 22 tests/testthat/integration/test-chain-sd.R | 55 tests/testthat/integration/test-complex-filter_on.R | 20 tests/testthat/integration/test-complex-mutate_sd.R | 15 tests/testthat/integration/test-complex-mutations.R | 30 tests/testthat/integration/test-complex-transmute_sd.R | 15 tests/testthat/integration/test-sql-like.R | 26 tests/testthat/test-10-unit.R | 2 tests/testthat/unit/test-ExprBuilder.R | 72 tests/testthat/unit/test-anti_join.R | 20 tests/testthat/unit/test-arrange.R | 20 tests/testthat/unit/test-distinct.R | 31 tests/testthat/unit/test-filter.R | 33 tests/testthat/unit/test-filter_on.R | 36 tests/testthat/unit/test-filter_sd.R | 28 tests/testthat/unit/test-full_join.R | 10 tests/testthat/unit/test-group_by.R | 6 tests/testthat/unit/test-inner_join.R | 22 tests/testthat/unit/test-left_join.R | 14 tests/testthat/unit/test-max_by.R |only tests/testthat/unit/test-min_by.R |only tests/testthat/unit/test-mutate.R | 10 tests/testthat/unit/test-mutate_join.R | 15 tests/testthat/unit/test-mutate_sd.R | 39 tests/testthat/unit/test-right_join.R | 25 tests/testthat/unit/test-select.R | 10 tests/testthat/unit/test-semi_join.R | 39 tests/testthat/unit/test-transmute.R | 26 tests/testthat/unit/test-transmute_sd.R | 16 vignettes/joins.Rmd | 109 - vignettes/table.express.Rmd | 327 +-- 96 files changed, 5325 insertions(+), 3727 deletions(-)
Title: Calculates the Leaf Area Index (LAD) and Other Related Functions
Description: A set of functions for analyzing the structure
of forests based on the leaf area density (LAD) and leaf area index (LAI) measures
calculated from Airborne Laser Scanning (ALS), i.e., scanning lidar (Light Detection
and Ranging) data. The methodology is discussed and described in
Almeida et al. (2019) <doi:10.3390/rs11010092> and
Stark et al. (2012) <doi:10.1111/j.1461-0248.2012.01864.x>.
Author: Danilo Roberti Alves de Almeida [aut, cre]
(<https://orcid.org/0000-0002-8747-0085>),
Scott Christopher Stark [aut] (<https://orcid.org/0000-0002-1579-1648>),
Carlos Alberto Silva [aut] (<https://orcid.org/0000-0002-7844-3560>),
Caio Hamamura [aut] (<https://orcid.org/0000-0001-6149-5885>),
Ruben Valbuena [aut] (<https://orcid.org/0000-0003-0493-7581>)
Maintainer: Danilo Roberti Alves de Almeida <daniloflorestas@gmail.com>
Diff between leafR versions 0.2 dated 2019-06-23 and 0.3 dated 2019-08-02
DESCRIPTION | 14 +++-- MD5 | 9 ++- NAMESPACE | 3 + R/main.R | 152 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- man/FHD.Rd |only man/GC.Rd |only man/GS.Rd |only 7 files changed, 166 insertions(+), 12 deletions(-)
Title: Molecular Biology Visualization Tools for 'Shiny' Apps
Description: Interactive visualization of 'RDML' files via 'shiny' apps.
Package provides (1) PCR plate interface with ability to select
individual tubes and (2) amplification/melting plots with fast hiding and
highlighting individual curves.
Author: Konstantin A. Blagodatskikh [cre, aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between shinyMolBio versions 0.1 dated 2019-06-21 and 0.2 dated 2019-08-02
shinyMolBio-0.1/shinyMolBio/inst/pic |only shinyMolBio-0.2/shinyMolBio/CHANGELOG |only shinyMolBio-0.2/shinyMolBio/DESCRIPTION | 16 shinyMolBio-0.2/shinyMolBio/MD5 | 25 shinyMolBio-0.2/shinyMolBio/R/pcrPlate-input.R | 29 shinyMolBio-0.2/shinyMolBio/R/renderCurves.R | 20 shinyMolBio-0.2/shinyMolBio/README.md | 8 shinyMolBio-0.2/shinyMolBio/inst/css/pcrPlateInputStyle.css | 101 +- shinyMolBio-0.2/shinyMolBio/inst/js/pcrPlate-input-bindings.js | 380 +++++----- shinyMolBio-0.2/shinyMolBio/inst/js/renderCurves-bindings.js | 60 + shinyMolBio-0.2/shinyMolBio/inst/shiny-examples/pcrPlateInput/app.R | 92 +- shinyMolBio-0.2/shinyMolBio/man/pcrPlateInput.Rd | 3 shinyMolBio-0.2/shinyMolBio/man/updateCurves.Rd | 6 shinyMolBio-0.2/shinyMolBio/man/updatePcrPlateInput.Rd | 5 14 files changed, 472 insertions(+), 273 deletions(-)
Title: Wrapper of Python Library 'shap'
Description: Provides SHAP explanations of machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the Interpretable Machine Learning, there are more and more new ideas for explaining black-box models. One of the best known method for local explanations is SHapley Additive exPlanations (SHAP) introduced by Lundberg, S., et al., (2016) <arXiv:1705.07874> The SHAP method is used to calculate influences of variables on the particular observation. This method is based on Shapley values, a technique used in game theory. The R package 'shapper' is a port of the Python library 'shap'.
Author: Szymon Maksymiuk [aut, cre],
Alicja Gosiewska [aut],
Przemyslaw Biecek [aut],
Mateusz Staniak [ctb],
Michal Burdukiewicz [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between shapper versions 0.1.1 dated 2019-07-10 and 0.1.2 dated 2019-08-02
DESCRIPTION | 9 ++--- MD5 | 34 +++++++++++----------- NEWS.md | 6 +++ R/individual_variable_effect.R | 43 +++++++++++++++------------- R/install_shap.R | 3 + R/onLoad.R | 2 + R/plot_individual_variable_effect.R | 10 +++--- inst/doc/shapper_classification.R | 8 ++--- inst/doc/shapper_classification.Rmd | 21 ++++++------- inst/doc/shapper_classification.html | 16 +++++----- inst/doc/shapper_regression.R | 46 +++++++++++++++--------------- inst/doc/shapper_regression.Rmd | 50 ++++++++++++++++----------------- inst/doc/shapper_regression.html | 36 +++++++++++------------ man/individual_variable_effect.Rd | 15 ++++----- man/install_shap.Rd | 3 + man/plot.individual_variable_effect.Rd | 8 ++--- vignettes/shapper_classification.Rmd | 21 ++++++------- vignettes/shapper_regression.Rmd | 50 ++++++++++++++++----------------- 18 files changed, 195 insertions(+), 186 deletions(-)
More information about GeneralisedCovarianceMeasure at CRAN
Permanent link
Title: Embeddable Cairo Graphics Device Driver
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between cairoDevice versions 2.26 dated 2019-03-21 and 2.27 dated 2019-08-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/zzz.R | 9 +++++---- src/gtk.c | 25 ++++++++++++++----------- 4 files changed, 25 insertions(+), 21 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload of files.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Julien Barde [ctb] (<https://orcid.org/0000-0002-3519-6141>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.1 dated 2019-06-04 and 0.2 dated 2019-08-02
DESCRIPTION | 17 - MD5 | 23 - NAMESPACE | 2 NEWS.md |only R/ZenodoManager.R | 444 +++++++++++++++++++++++++++++- R/ZenodoRecord.R | 612 +++++++++++++++++++++++++++++++++++++++++- R/zen4R.R | 6 README.md | 75 ----- man/ZenodoManager.Rd | 57 +++ man/ZenodoRecord.Rd | 185 ++++++++++++ man/zen4R.Rd | 4 tests/testthat/test_funders.R |only tests/testthat/test_grants.R |only tests/testthat/test_records.R | 121 +++++++- 14 files changed, 1425 insertions(+), 121 deletions(-)
Title: 0-1 Test for Chaos
Description: Computes and visualize the results of the 0-1 test for chaos proposed
by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is
available in parallel for the independent values of parameter c. Additionally,
fast RQA is added to distinguish chaos from noise.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>
Diff between Chaos01 versions 1.1.1 dated 2018-02-14 and 1.2.0 dated 2019-08-02
DESCRIPTION | 13 +- MD5 | 31 +++--- NAMESPACE | 1 R/Kc_computation_C.R | 175 +++++++++++++++++++++++++++++++++++---- R/chaos01_plot.R | 158 ++++++++++++++++++++++++++++++++--- R/rqa_diag.R | 7 - R/rqa_plot.R | 2 R/rqa_seq.R | 7 - R/test_chaos01.R | 108 ++++++++++++++++-------- man/fast.rqa.Rd | 3 man/plot.chaos01.Rd | 20 +++- man/plot.chaos01.res.Rd | 2 man/plot.chaos01.rqa.sequence.Rd | 2 man/rqa.seq.Rd | 7 - man/testChaos01.Rd | 44 +++++++-- src/Chaos01_init.c | 2 src/myrollmean.c |only 17 files changed, 466 insertions(+), 116 deletions(-)
Title: Download and Prepare C14 Dates from Different Source Databases
Description: Query different C14 date databases and apply basic data cleaning, merging and calibration steps.
Author: Clemens Schmid [aut, cre, cph]
(<https://orcid.org/0000-0003-3448-5715>),
Dirk Seidensticker [aut] (<https://orcid.org/0000-0002-8155-7702>),
Daniel Knitter [aut] (<https://orcid.org/0000-0003-3014-4497>),
Martin Hinz [aut] (<https://orcid.org/0000-0002-9904-6548>),
David Matzig [aut] (<https://orcid.org/0000-0001-7349-5401>),
Wolfgang Hamer [aut] (<https://orcid.org/0000-0002-5943-5020>),
Kay Schmütz [aut],
Nils Mueller-Scheessel [ctb] (<https://orcid.org/0000-0001-7992-8722>)
Maintainer: Clemens Schmid <clemens@nevrome.de>
Diff between c14bazAAR versions 1.0.2 dated 2018-10-28 and 1.0.3 dated 2019-08-02
c14bazAAR-1.0.2/c14bazAAR/data/country_thesaurus.rda |only c14bazAAR-1.0.2/c14bazAAR/data/material_thesaurus.rda |only c14bazAAR-1.0.2/c14bazAAR/data/variable_reference.rda |only c14bazAAR-1.0.2/c14bazAAR/man/add_equality_group_number.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/add_or_replace_column_in_df.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/calibrate_to_probability_distribution.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/check_connection_to_url.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/check_if_columns_are_present.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/check_if_packages_are_available.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/circumference_calculator.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/clean_latlon.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/compare_and_combine_data_frame_values.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/country_thesaurus.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/determine_calage_from_probability_distribution.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/determine_dates_out_of_range_of_calcurve.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/digits_counter.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/dummy_func.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/find_correct_name_by_stringdist_comparison.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/find_lookup_decisions.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/generate_list_of_equality_partners.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/get_all_parser_functions.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/get_thesaurus.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/hdr.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/individual_precision.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/lookup_in_countrycode_codelist.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/lookup_in_thesaurus_table.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/material_thesaurus.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/print_lookup_decisions.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/stringify_data_frame.Rd |only c14bazAAR-1.0.2/c14bazAAR/man/variable_reference.Rd |only c14bazAAR-1.0.3/c14bazAAR/DESCRIPTION | 91 +++-- c14bazAAR-1.0.3/c14bazAAR/MD5 | 106 ++--- c14bazAAR-1.0.3/c14bazAAR/NAMESPACE | 2 c14bazAAR-1.0.3/c14bazAAR/NEWS.md |only c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_basic.R | 11 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_calibrate.R | 4 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_classify_material.R | 9 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_convert.R | 19 - c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_duplicates_mark.R | 72 +++ c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_duplicates_remove.R | 181 +++++++--- c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_enforce_types.R | 8 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_spatial_coordinate_precision.R | 17 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_spatial_determine_country_by_coordinate.R | 8 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_spatial_finalize_country_name.R | 4 c14bazAAR-1.0.3/c14bazAAR/R/c14_date_list_spatial_standardize_country_name.R | 11 c14bazAAR-1.0.3/c14bazAAR/R/data.R | 53 -- c14bazAAR-1.0.3/c14bazAAR/R/get_all_dates.R | 15 c14bazAAR-1.0.3/c14bazAAR/R/get_context.R | 8 c14bazAAR-1.0.3/c14bazAAR/R/get_eubar.R |only c14bazAAR-1.0.3/c14bazAAR/R/get_palmisano.R |only c14bazAAR-1.0.3/c14bazAAR/R/helpers_db_urls.R | 1 c14bazAAR-1.0.3/c14bazAAR/R/helpers_general.R | 42 ++ c14bazAAR-1.0.3/c14bazAAR/R/helpers_thesauri.R | 5 c14bazAAR-1.0.3/c14bazAAR/R/zzz.R | 2 c14bazAAR-1.0.3/c14bazAAR/README.md | 79 +++- c14bazAAR-1.0.3/c14bazAAR/build |only c14bazAAR-1.0.3/c14bazAAR/data/example_c14_date_list.rda |binary c14bazAAR-1.0.3/c14bazAAR/inst/doc |only c14bazAAR-1.0.3/c14bazAAR/man/as.sf.Rd | 8 c14bazAAR-1.0.3/c14bazAAR/man/c14_date_list.Rd | 5 c14bazAAR-1.0.3/c14bazAAR/man/c14bazAAR-package.Rd | 18 c14bazAAR-1.0.3/c14bazAAR/man/classify_material.Rd | 8 c14bazAAR-1.0.3/c14bazAAR/man/country_attribution.Rd | 4 c14bazAAR-1.0.3/c14bazAAR/man/db_getter.Rd | 18 c14bazAAR-1.0.3/c14bazAAR/man/duplicates.Rd | 82 +++- c14bazAAR-1.0.3/c14bazAAR/man/enforce_types.Rd | 6 c14bazAAR-1.0.3/c14bazAAR/man/example_c14_date_list.Rd | 2 c14bazAAR-1.0.3/c14bazAAR/tests/testthat/test_c14_date_list_convert.R | 9 c14bazAAR-1.0.3/c14bazAAR/tests/testthat/test_c14_date_list_country_attribution.R | 1 c14bazAAR-1.0.3/c14bazAAR/tests/testthat/test_c14_date_list_duplicates.R | 95 +++++ c14bazAAR-1.0.3/c14bazAAR/vignettes |only 71 files changed, 702 insertions(+), 302 deletions(-)
Title: Functions for the Lognormal Distribution
Description: The lognormal distribution
(Limpert et al. (2001) <doi:10.1641/0006-3568(2001)051%5B0341:lndats%5D2.0.co;2>)
can characterize uncertainty that is bounded by zero.
This package provides estimation of distribution parameters, computation of
moments and other basic statistics, and an approximation of the distribution
of the sum of several correlated lognormally distributed variables
(Lo 2013 <doi:10.12988/ams.2013.39511>).
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between lognorm versions 0.1.5 dated 2019-03-13 and 0.1.6 dated 2019-08-02
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 3 inst/doc/aggregateCorrelated.R | 59 ++++++ inst/doc/aggregateCorrelated.Rmd | 12 - inst/doc/aggregateCorrelated.html | 324 +++++++++++++++++++++++++++++++++++++- inst/doc/lognorm.html | 290 +++++++++++++++++++++++++++++----- inst/doc/lognormalSum.R | 3 inst/doc/lognormalSum.Rmd | 6 inst/doc/lognormalSum.html | 298 +++++++++++++++++++++++++++++----- vignettes/aggregateCorrelated.Rmd | 12 - vignettes/lognormalSum.Rmd | 6 12 files changed, 922 insertions(+), 121 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael Nelson [ctb],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-71 dated 2018-07-20 and 0.8-72 dated 2019-08-02
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 10 ++++++---- MD5 | 32 ++++++++++++++++---------------- R/dbf.R | 10 +++++----- R/octave.R | 11 ++++++----- R/read.dta.R | 14 +++++++------- R/read.epiinfo.R | 2 +- R/spss.R | 2 +- R/writeForeignCode.R | 14 +++++++------- R/writeForeignSAS.R | 22 +++++++++++----------- R/xport.R | 6 +++--- man/read.xport.Rd | 4 +++- tests/sas.R | 20 ++++++++++++++++++-- tests/spss.R | 5 +++-- tests/spss.Rout.save | 27 ++++++++++++++------------- tests/xport.R | 2 +- tests/xport.Rout.save | 21 +++++++++++++-------- 17 files changed, 136 insertions(+), 87 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.14.0 dated 2019-07-22 and 2.14.1 dated 2019-08-02
DESCRIPTION | 6 MD5 | 42 NEWS | 6 R/MultiSeries.R | 61 - R/StartAutopilot.R | 5 inst/doc/AdvancedTuning.html | 489 +++++---- inst/doc/AdvancedVignette.html | 1604 ++++++++---------------------- inst/doc/ComparingSubsets.html | 771 +++++++------- inst/doc/ComplianceDocumentation.html | 534 +++++---- inst/doc/DatetimePartitionedProjects.html | 589 ++++++----- inst/doc/IntroductionToDataRobot.html | 657 ++++++------ inst/doc/Multiclass.html | 869 +++++++--------- inst/doc/PartialDependence.html | 816 ++++++++------- inst/doc/PredictionExplanations.html | 1038 ++++++++++--------- inst/doc/RatingTables.html | 937 +++++++---------- inst/doc/TimeSeries.R | 6 inst/doc/TimeSeries.Rmd | 6 inst/doc/TimeSeries.html | 673 +++++++----- inst/doc/TrainingPredictions.html | 614 ++++++----- inst/doc/VariableImportance.html | 786 ++++++++------ man/RequestMultiSeriesDetection.Rd | 26 vignettes/TimeSeries.Rmd | 6 22 files changed, 5345 insertions(+), 5196 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-22 1.1-1
2013-11-19 1.0-2
2012-08-25 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-31 0.1.1
2019-05-24 0.1.0
Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre],
The Apache Software Foundation [aut, cph],
Julia Silge [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191),
David Gohel [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Diff between rtika versions 1.21 dated 2019-06-21 and 1.22 dated 2019-08-02
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++--------- NEWS.md | 9 +++++++ R/install_tika.R | 8 +++---- R/tika.R | 6 +++-- R/zzz.R | 2 - inst/doc/rtika_introduction.Rmd | 2 - inst/doc/rtika_introduction.html | 44 +++++++++++++++++++-------------------- man/install_tika.Rd | 8 +++---- man/tika.Rd | 5 ++-- vignettes/rtika_introduction.Rmd | 2 - 11 files changed, 61 insertions(+), 51 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Before reading this, execute BayesianFROC::fit_GUI() or BayesianFROC::fit_GUI_simple() or BayesianFROC::fit_GUI_dashboard(), then reader will understand this package without any explanation. Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis. See the vignettes for more details.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.1.4 dated 2019-07-03 and 0.1.5 dated 2019-08-02
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BayesianFROC-0.1.5/BayesianFROC/R/p_value_of_the_Bayesian_sense_for_chi_square_goodness_of_fit.R | 47 BayesianFROC-0.1.5/BayesianFROC/R/plot_curve_and_hit_rate_and_false_rate_simultaneously.R |only BayesianFROC-0.1.5/BayesianFROC/R/pnorm_or_qnorm.R |only BayesianFROC-0.1.5/BayesianFROC/R/sbc.R |only BayesianFROC-0.1.5/BayesianFROC/R/sbc_MRMC.R |only BayesianFROC-0.1.5/BayesianFROC/R/snippet_for_BayesianFROC.R | 47 BayesianFROC-0.1.5/BayesianFROC/R/stanfitExtended.R | 5 BayesianFROC-0.1.5/BayesianFROC/R/summarise_MRMC.R | 1 BayesianFROC-0.1.5/BayesianFROC/R/summary_EAP_CI_srsc.R | 2 BayesianFROC-0.1.5/BayesianFROC/R/the_row_number_of_logical_vector.R | 3 BayesianFROC-0.1.5/BayesianFROC/R/viewdata.R | 1 BayesianFROC-0.1.5/BayesianFROC/README.md | 671 +++- BayesianFROC-0.1.5/BayesianFROC/build/vignette.rds |binary BayesianFROC-0.1.5/BayesianFROC/data/dddddd.rda |only BayesianFROC-0.1.5/BayesianFROC/data/ddddddd.rda |only BayesianFROC-0.1.5/BayesianFROC/demo/demo_drawcurves_srsc.R | 4 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| 284 + BayesianFROC-0.1.5/BayesianFROC/inst/myapp/www |only BayesianFROC-0.1.5/BayesianFROC/inst/myappp |only BayesianFROC-0.1.5/BayesianFROC/man/Author_vs_classic_for_AUC.Rd | 3 BayesianFROC-0.1.5/BayesianFROC/man/Chi_square_goodness_of_fit_in_case_of_MRMC_Posterior_Mean.Rd | 3 BayesianFROC-0.1.5/BayesianFROC/man/Credible_Interval_for_curve.Rd | 8 BayesianFROC-0.1.5/BayesianFROC/man/DrawCurves_MRMC.Rd | 3 BayesianFROC-0.1.5/BayesianFROC/man/DrawCurves_MRMC_pairwise.Rd | 3 BayesianFROC-0.1.5/BayesianFROC/man/Draw_a_simulated_data_set.Rd | 8 BayesianFROC-0.1.5/BayesianFROC/man/Draw_a_simulated_data_set_and_Draw_posterior_samples.Rd | 8 BayesianFROC-0.1.5/BayesianFROC/man/Simulation_Based_Calibration_histogram.Rd | 8 BayesianFROC-0.1.5/BayesianFROC/man/Simulation_Based_Calibration_single_reader_single_modality_via_rstan_sbc.Rd |only BayesianFROC-0.1.5/BayesianFROC/man/Simulation_Based_Calibration_via_rstan_sbc_MRMC.Rd |only 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Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Hong Ooi [cre],
Microsoft Corporation [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between doParallel versions 1.0.14 dated 2018-09-24 and 1.0.15 dated 2019-08-02
DESCRIPTION | 17 MD5 | 30 - NAMESPACE | 14 NEWS | 86 ++-- build/vignette.rds |binary demo/00Index | 2 demo/sincParallel.R | 74 +-- inst/doc/gettingstartedParallel.R | 146 +++---- inst/doc/gettingstartedParallel.Rnw | 688 +++++++++++++++++------------------ inst/doc/gettingstartedParallel.pdf |binary inst/examples/bootParallel.R | 166 ++++---- inst/unitTests/options.R | 166 ++++---- inst/unitTests/runTestSuite.sh | 92 ++-- man/doParallel-package.Rd | 78 +-- man/registerDoParallel.Rd | 118 +++--- vignettes/gettingstartedParallel.Rnw | 688 +++++++++++++++++------------------ 16 files changed, 1181 insertions(+), 1184 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'QCA', 'DDIwR', and 'venn'.
Interprets and translates DNF - Disjunctive Normal Form expressions, for both
binary and multi-value crisp sets, and extracts information (set names, set
values) from those expressions. Other functions perform various other checks
if possibly numeric (even if all numbers reside in a character vector) and
coerce to numeric, or check if the numbers are whole. It also offers, among
many others, a highly flexible recoding function.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.2 dated 2019-05-19 and 0.3 dated 2019-08-02
DESCRIPTION | 8 - MD5 | 44 ++++---- R/asNumeric.R | 30 ----- R/brackets.R | 70 ++++++++---- R/checkMV.R | 46 +++----- R/checkSubset.R | 24 ---- R/combnk.R | 111 +++++++++----------- R/dashes.R | 26 ---- R/equality.R | 29 ----- R/isNegated.R | 30 ----- R/possibleNumeric.R | 50 ++++----- R/prettyTable.R | 37 +----- R/print.R | 28 ----- R/recode.R | 100 +++++++++++++----- R/sortExpressions.R | 46 ++------ R/string.R | 168 ++++++++++++++++++++++++++----- R/tildae.R | 32 +---- R/translate.R | 270 +++++++++++++++++++++++++++++++++++++++++++------- R/tryCatchWEM.R | 27 ----- R/wholeNumeric.R | 25 ---- inst/ChangeLog | 16 +- man/admisc.package.Rd | 100 +++++++++--------- man/numerics.Rd | 3 23 files changed, 729 insertions(+), 591 deletions(-)