Title: Wavelet Routines for Global and Local Multiple Correlation
Description: Wavelet routines that calculate single sets of
wavelet multiple correlations (WMC) and cross-correlations (WMCC)
out of n variables.
They can later be plotted in single graphs, as an alternative to trying
to make sense out of several sets of wavelet correlations or
wavelet cross-correlations.
The code is based on the calculation, at each wavelet scale, of the
square root of the coefficient of determination in a linear combination
of variables for which such coefficient of determination is a maximum.
The code provided here is based on the wave.correlation routine in
Brandon Whitcher's waveslim R package Version: 1.6.4, which in turn is
based on wavelet methodology developed in Percival and Walden (2000) <DOI:10.1017/CBO9780511841040>;
Gençay, Selçuk and Whitcher (2002) <DOI:10.1016/B978-012279670-8.50013-6> and others.
Version 2 incorporates wavelet local multiple correlations (WLMC).
These are like the previous global WMC but consisting in one
single set of multiscale correlations along time. That is, at each time
t, they are calculated by letting a window of weighted wavelet
coefficients around t move along time. Six weight functions are provided.
Namely, the uniform window, Cleveland's tricube window, Epanechnikov's
parabolic window, Bartlett's triangular window and Wendland's truncated
power window and the Gaussian window.
Version 2.2 incorporates an auxiliary function that calculates local
multiple correlations (LMC). They are calculated by letting move along time
a window of weighted time series values around t. Any of the six weight
functions mentioned above can be used.
Author: Javier Fernandez-Macho [aut, cre]
Maintainer: Javier Fernandez-Macho <javier.fernandezmacho@ehu.es>
Diff between wavemulcor versions 2.1.0 dated 2017-07-03 and 2.2.1 dated 2018-06-08
wavemulcor-2.1.0/wavemulcor/man/wavemulcor-package.Rd |only wavemulcor-2.2.1/wavemulcor/DESCRIPTION | 25 +++++----- wavemulcor-2.2.1/wavemulcor/MD5 | 15 +++--- wavemulcor-2.2.1/wavemulcor/NAMESPACE | 3 - wavemulcor-2.2.1/wavemulcor/NEWS | 15 ++---- wavemulcor-2.2.1/wavemulcor/R/local.multiple.correlation.R |only wavemulcor-2.2.1/wavemulcor/man/local.multiple.correlation.Rd |only wavemulcor-2.2.1/wavemulcor/man/wave.local.multiple.correlation.Rd | 8 +-- wavemulcor-2.2.1/wavemulcor/man/wave.multiple.correlation.Rd | 2 wavemulcor-2.2.1/wavemulcor/man/wave.multiple.cross.correlation.Rd | 2 10 files changed, 34 insertions(+), 36 deletions(-)
Title: Utilities for Delaying Function Execution
Description: Executes arbitrary R or C functions some time after the current
time, after the R execution stack has emptied.
Author: Joe Cheng [aut, cre],
RStudio [cph],
Marcus Geelnard [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/),
Evan Nemerson [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between later versions 0.7.2 dated 2018-05-01 and 0.7.3 dated 2018-06-08
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 4 ++++ src/interrupt.h |only src/later.cpp | 25 ++++++++++++++++--------- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Bayesian Analysis of Change Point Problems
Description: Provides an implementation of the Barry and Hartigan (1993) product
partition model for the normal errors change point problem using Markov Chain
Monte Carlo. It also extends the methodology to regression models on a connected
graph (Wang and Emerson, 2015); this allows estimation of change point models
with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0,
is currently not implemented.
Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
Maintainer: Xiaofei Wang <xiaofei.wang@yale.edu>
Diff between bcp versions 4.0.1 dated 2018-04-11 and 4.0.2 dated 2018-06-08
DESCRIPTION | 8 +- MD5 | 14 ++-- R/bcp.R | 5 + src/Cbcp.cpp | 169 +++++++++++++++++++++++++------------------------- src/CbcpM.cpp | 74 ++++++++++++--------- src/HelperVariables.h | 33 +++++---- src/MCMC.h | 152 ++++++++++++++++++++++---------------------- src/Makevars | 25 ------- 8 files changed, 236 insertions(+), 244 deletions(-)
Title: Additional Functions for Retrieving, Organizing, and Analyzing
Estuary Monitoring Data
Description: Additional tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System <http://cdmo.baruch.sc.edu/>. These tools
address common challenges associated with continuous time series data
for environmental decision making, and are intended for use in annual reporting activities.
Author: Julie Padilla [aut, cre],
Marcus Beck [ctb],
Bob Rudis [ctb]
Maintainer: Julie Padilla <jpadilla@limno.com>
Diff between SWMPrExtension versions 0.3.14 dated 2018-05-12 and 0.3.15 dated 2018-06-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 15 +++++++++------ R/threshold_percentile_plot.R | 12 +++++++----- man/threshold_percentile_plot.Rd | 2 +- 5 files changed, 24 insertions(+), 19 deletions(-)
More information about SWMPrExtension at CRAN
Permanent link
Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models
using partial dependence plots and other techniques.
Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.4.0 dated 2018-06-01 and 3.4.1 dated 2018-06-08
plotmo-3.4.0/plotmo/inst/slowtests/README.R |only plotmo-3.4.1/plotmo/DESCRIPTION | 12 plotmo-3.4.1/plotmo/MD5 | 70 plotmo-3.4.1/plotmo/NEWS | 18 plotmo-3.4.1/plotmo/R/caret.R | 70 plotmo-3.4.1/plotmo/R/check.index.R | 19 plotmo-3.4.1/plotmo/R/gbm.R | 2 plotmo-3.4.1/plotmo/R/lib.R | 21 plotmo-3.4.1/plotmo/R/meta.R | 10 plotmo-3.4.1/plotmo/R/methods.R | 12 plotmo-3.4.1/plotmo/R/mlr.R | 152 plotmo-3.4.1/plotmo/R/partdep.R | 4 plotmo-3.4.1/plotmo/R/plotmo.R | 51 plotmo-3.4.1/plotmo/R/predict.R | 1 plotmo-3.4.1/plotmo/R/prolog.R | 2 plotmo-3.4.1/plotmo/R/residuals.R | 6 plotmo-3.4.1/plotmo/R/rpart.R | 4 plotmo-3.4.1/plotmo/R/type.R | 84 plotmo-3.4.1/plotmo/R/w1.R | 287 plotmo-3.4.1/plotmo/inst/doc/modguide.pdf |binary plotmo-3.4.1/plotmo/inst/doc/plotmo-notes.pdf | 3810 +++++------- plotmo-3.4.1/plotmo/inst/doc/plotres-notes.pdf | 41 plotmo-3.4.1/plotmo/inst/slowtests/README.txt | 18 plotmo-3.4.1/plotmo/inst/slowtests/make.README.figs.R |only plotmo-3.4.1/plotmo/inst/slowtests/test.caret.Rout.save | 6 plotmo-3.4.1/plotmo/inst/slowtests/test.gbm.R | 7 plotmo-3.4.1/plotmo/inst/slowtests/test.gbm.Rout.save | 9 plotmo-3.4.1/plotmo/inst/slowtests/test.glmnet.Rout.save | 17 plotmo-3.4.1/plotmo/inst/slowtests/test.mlr.R | 290 plotmo-3.4.1/plotmo/inst/slowtests/test.mlr.Rout.save | 732 +- plotmo-3.4.1/plotmo/inst/slowtests/test.non.earth.R | 4 plotmo-3.4.1/plotmo/inst/slowtests/test.non.earth.Rout.save | 25 plotmo-3.4.1/plotmo/inst/slowtests/test.plotmo.R | 2 plotmo-3.4.1/plotmo/inst/slowtests/test.plotmo.Rout.save | 36 plotmo-3.4.1/plotmo/inst/slowtests/test.plotmo.x.Rout.save | 168 plotmo-3.4.1/plotmo/inst/slowtests/test.plotmo3.Rout.save | 12 plotmo-3.4.1/plotmo/man/plotmo.misc.Rd | 4 37 files changed, 3364 insertions(+), 2642 deletions(-)
Title: Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre],
Paola Rondon-Villarreal [aut, ths],
Rodrigo Torres [aut, ths],
J. Sebastian Paez [ctb]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between Peptides versions 2.3 dated 2018-03-18 and 2.4 dated 2018-06-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 3 +++ R/aaCheck.R | 10 +++++++--- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Fitting Density Ratio Classes
Description: Fits Density Ratio Classes to elicited
probability-quantile points or intervals.
Author: Simon L. Rinderknecht and Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Diff between fitDRC versions 1.1 dated 2014-01-01 and 1.1.1 dated 2018-06-08
DESCRIPTION | 10 MD5 | 8 NAMESPACE | 54 R/fitDRC.r | 4769 +++++++++++++++++++++++++------------------------- man/fitDRC-package.Rd | 4 5 files changed, 2447 insertions(+), 2398 deletions(-)
Title: Fast Pseudo Random Number Generators
Description: Several fast random number generators are provided as C++
header only libraries: The PCG family by O'Neill (2014
<https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as
Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018
<arXiv:1805.01407>). In addition fast functions for generating random
numbers according to a uniform, normal and exponential distribution
are included. The latter two use the Ziggurat algorithm originally
proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>).
These functions are exported to R and as a C++ interface and are
enabled for use with the 64 bit version of the Mersenne-Twister by
Matsumoto and Nishimura (1998 <doi:10.1145/272991.272995>), the
default 64 bit generator from the PCG family as well as Xoroshiro128+
and Xoshiro256+.
Author: Ralf Stubner [aut, cre],
daqana GmbH [cph],
David Blackman [ctb],
Melissa O'Neill [ctb],
Sebastiano Vigna [ctb]
Maintainer: Ralf Stubner <ralf.stubner@daqana.com>
Diff between dqrng versions 0.0.3 dated 2018-05-14 and 0.0.4 dated 2018-06-08
dqrng-0.0.3/dqrng/man/dqrng.Rd |only dqrng-0.0.4/dqrng/.aspell |only dqrng-0.0.4/dqrng/DESCRIPTION | 6 +- dqrng-0.0.4/dqrng/MD5 | 33 +++++++----- dqrng-0.0.4/dqrng/NEWS.md | 10 +++ dqrng-0.0.4/dqrng/R/RcppExports.R | 9 +-- dqrng-0.0.4/dqrng/R/dqrng-package.R | 52 ------------------- dqrng-0.0.4/dqrng/R/dqset.seed.R | 49 +++++++++++++++++- dqrng-0.0.4/dqrng/README.md | 5 + dqrng-0.0.4/dqrng/build/vignette.rds |binary dqrng-0.0.4/dqrng/inst/doc/dqrng.html | 22 ++++---- dqrng-0.0.4/dqrng/inst/doc/parallel.R |only dqrng-0.0.4/dqrng/inst/doc/parallel.Rmd |only dqrng-0.0.4/dqrng/inst/doc/parallel.html |only dqrng-0.0.4/dqrng/inst/include/dqrng_distribution.h | 4 - dqrng-0.0.4/dqrng/inst/include/dqrng_generator.h | 13 ++++ dqrng-0.0.4/dqrng/inst/include/xoshiro.h | 54 ++++++++++++++++++++ dqrng-0.0.4/dqrng/man/dqrng-functions.Rd |only dqrng-0.0.4/dqrng/man/dqrng-package.Rd |only dqrng-0.0.4/dqrng/src/dqrng.cpp | 11 +--- dqrng-0.0.4/dqrng/tests/testthat/test-generators.R | 9 +++ dqrng-0.0.4/dqrng/vignettes/parallel.Rmd |only 22 files changed, 180 insertions(+), 97 deletions(-)
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa.
Author: Alex Couture-Beil <rjson_pkg@mofo.ca>
Maintainer: Alex Couture-Beil <rjson_pkg@mofo.ca>
Diff between rjson versions 0.2.19 dated 2018-05-18 and 0.2.20 dated 2018-06-08
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ R/json.R | 4 +-- inst/doc/json_rpc_server.pdf |binary man/toJSON.Rd | 3 +- src/dump.cpp | 46 ++++++++++++++++++++++++++++++++----------- src/funcs.h | 2 - 7 files changed, 49 insertions(+), 24 deletions(-)
Title: Item Based Collaborative Filtering for Multi-Trait and
Multi-Environment Data
Description: Implements the item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.
Author: Francisco Javier Luna-Vazquez [aut, cre],
Osval Antonio Montesinos-Lopez [aut],
Abelardo Montesinos-Lopez [aut],
Jose Crossa [aut]
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Diff between IBCF.MTME versions 1.2-5 dated 2018-02-22 and 1.3-2 dated 2018-06-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/CrossValidation.R | 1 - R/IBCF.R | 4 ++-- R/IBCFYear.R | 43 ++++++++++++++++++++++--------------------- R/Title.R | 6 +++--- man/IBCF.Years.Rd | 6 ++++-- 8 files changed, 49 insertions(+), 40 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph],
Raphaël Leblois [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.1.7 dated 2017-11-03 and 1.1.25 dated 2018-06-08
DESCRIPTION | 15 +-- MD5 | 94 +++++++++++++--------- NAMESPACE | 5 - R/CKrigcoefs.R | 43 +++++++--- R/LRTfn.R | 19 +++- R/addtoedges.R | 3 R/buildFONKgpointls.R | 26 +++++- R/calc1DCIs.R | 39 +++++++-- R/calc1Dprofiles.R | 48 +++++++++++ R/calc2D3Dplots.R | 3 R/calcGCV.R | 2 R/calcLRTs.R | 2 R/calcProfileLR.R | 4 R/calcProfileOK.R | 2 R/calcgridRelProfile.R | 181 +++++++++++++++++++++++--------------------- R/canonize.R | 39 ++++++++- R/coresWrapper.R | 148 +++++++++++++++++------------------ R/findglobalMLE.R | 6 + R/formatName.R | 17 +++- R/fromFONKtoanyspace.R | 4 R/generateInitpts.R | 2 R/gridfn.R | 32 ++++++- R/predict.surface.redef.R | 3 R/profile.R | 6 - R/profileFn.R | 2 R/provideCovFnParams.R | 1 R/providefullhull.R | 23 +++++ R/prune_by_dist.R | 12 -- R/resetCHull.R | 20 +++- R/rhull.R | 6 - R/selectFn.R | 2 R/subHullWrapper.R | 14 ++- R/toNMratioFromCanonical.R |only R/tofullKrigingspace.R | 50 +++++++++++- R/tom1overmuFromCanonical.R |only R/tom2overmuFromCanonical.R |only R/tomratioFromCanonical.R |only R/writeFinalInfo.R | 8 + inst/NEWS.Rd | 21 ++++- man/blackbox-internal.Rd | 12 +- man/options.Rd | 10 +- src/Krigmain.cpp | 2 tests/test-all.R | 29 ++++++- tests/tests_private |only 44 files changed, 650 insertions(+), 305 deletions(-)
Title: Genetic Analysis Package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gap versions 1.1-21 dated 2018-01-24 and 1.1-22 dated 2018-06-08
gap-1.1-21/gap/inst/tests/OpenMx |only gap-1.1-21/gap/inst/tests/R/MR.R |only gap-1.1-21/gap/inst/tests/R/R2.R |only gap-1.1-21/gap/inst/tests/R/test_data.rda |only gap-1.1-21/gap/inst/tests/h2 |only gap-1.1-21/gap/inst/tests/haplo.stats |only gap-1.1-21/gap/inst/tests/klem |only gap-1.1-21/gap/inst/tests/misc |only gap-1.1-21/gap/inst/tests/no |only gap-1.1-21/gap/inst/tests/references.txt |only gap-1.1-22/gap/ChangeLog | 5 ++ gap-1.1-22/gap/DESCRIPTION | 10 ++-- gap-1.1-22/gap/MD5 | 67 ++++++++++------------------ gap-1.1-22/gap/R/pbsize.R | 4 - gap-1.1-22/gap/inst/doc/gap.R | 20 ++++---- gap-1.1-22/gap/inst/doc/gap.Rnw | 10 ---- gap-1.1-22/gap/inst/doc/gap.pdf |binary gap-1.1-22/gap/inst/doc/h2.pdf |binary gap-1.1-22/gap/inst/doc/jss.pdf |binary gap-1.1-22/gap/inst/doc/pedtodot.pdf |binary gap-1.1-22/gap/inst/doc/rnews.pdf |binary gap-1.1-22/gap/inst/tests/C |only gap-1.1-22/gap/inst/tests/R/ACE.R |only gap-1.1-22/gap/inst/tests/R/PD.R |only gap-1.1-22/gap/inst/tests/R/SH2B1.R |only gap-1.1-22/gap/inst/tests/R/SH2B1.txt |only gap-1.1-22/gap/inst/tests/README.txt | 29 ++---------- gap-1.1-22/gap/man/gap-package.Rd | 2 gap-1.1-22/gap/man/masize.Rd | 2 gap-1.1-22/gap/src/pfc.f | 14 ++--- gap-1.1-22/gap/src/pfc.sim.f | 2 gap-1.1-22/gap/vignettes/figures/ESplot.pdf |binary gap-1.1-22/gap/vignettes/figures/lukas.pdf |binary gap-1.1-22/gap/vignettes/figures/qqunif.pdf |binary gap-1.1-22/gap/vignettes/gap.Rnw | 10 ---- 35 files changed, 66 insertions(+), 109 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 5.0-8 dated 2018-04-30 and 5.1-0 dated 2018-06-08
gamlss-5.0-8/gamlss/man/gamlss.package.Rd |only gamlss-5.1-0/gamlss/DESCRIPTION | 8 ++++---- gamlss-5.1-0/gamlss/MD5 | 16 +++++++++------- gamlss-5.1-0/gamlss/NAMESPACE | 3 ++- gamlss-5.1-0/gamlss/R/DropAddStepGAIC-Parallel.R | 2 ++ gamlss-5.1-0/gamlss/R/chooseDistParallel.R | 23 ++++++++++++++--------- gamlss-5.1-0/gamlss/R/gamlss.R | 6 +++++- gamlss-5.1-0/gamlss/build |only gamlss-5.1-0/gamlss/inst/doc/NEWS.txt | 4 ++-- gamlss-5.1-0/gamlss/man/gamlss-package.Rd |only gamlss-5.1-0/gamlss/man/numeric.deriv.Rd |only 11 files changed, 38 insertions(+), 24 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Bill Venables [ctb],
Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.6 dated 2018-03-20 and 1.7 dated 2018-06-08
BART-1.6/BART/src/latent.cpp |only BART-1.6/BART/src/latent.h |only BART-1.6/BART/src/rand_draws.cpp |only BART-1.6/BART/src/rand_draws.h |only BART-1.6/BART/src/randomkit.cpp |only BART-1.6/BART/src/randomkit.h |only BART-1.6/BART/vignettes/time-to-event.pdfsync |only BART-1.7/BART/DESCRIPTION | 19 BART-1.7/BART/MD5 | 295 +++++++------ BART-1.7/BART/NAMESPACE | 14 BART-1.7/BART/NEWS | 40 + BART-1.7/BART/R/crisk.bart.R | 106 +++-- BART-1.7/BART/R/crisk.pre.bart.R | 2 BART-1.7/BART/R/crisk2.bart.R |only BART-1.7/BART/R/draw_lambda.R |only BART-1.7/BART/R/draw_lambda_i.R |only BART-1.7/BART/R/draw_z.R |only BART-1.7/BART/R/gbart.R |only BART-1.7/BART/R/lbart.R | 11 BART-1.7/BART/R/mbart.R | 41 + BART-1.7/BART/R/mc.crisk.bart.R | 118 +++-- BART-1.7/BART/R/mc.crisk.pwbart.R | 43 +- BART-1.7/BART/R/mc.crisk2.bart.R |only BART-1.7/BART/R/mc.crisk2.pwbart.R |only BART-1.7/BART/R/mc.gbart.R |only BART-1.7/BART/R/mc.lbart.R | 21 BART-1.7/BART/R/mc.mbart.R | 34 + BART-1.7/BART/R/mc.pbart.R | 35 + BART-1.7/BART/R/mc.recur.bart.R | 81 ++- BART-1.7/BART/R/mc.surv.bart.R | 90 ++-- BART-1.7/BART/R/mc.wbart.R | 30 + BART-1.7/BART/R/pbart.R | 14 BART-1.7/BART/R/predict.crisk2bart.R |only BART-1.7/BART/R/predict.criskbart.R | 17 BART-1.7/BART/R/predict.crskmbart.R |only BART-1.7/BART/R/predict.lbart.R | 1 BART-1.7/BART/R/predict.mbart.R | 48 +- BART-1.7/BART/R/predict.pbart.R | 2 BART-1.7/BART/R/predict.recurbart.R | 2 BART-1.7/BART/R/predict.survbart.R | 4 BART-1.7/BART/R/predict.wbart.R | 2 BART-1.7/BART/R/r_lefttruncnorm.R |only BART-1.7/BART/R/recur.bart.R | 74 ++- BART-1.7/BART/R/recur.pre.bart.R | 4 BART-1.7/BART/R/rs.wbart.R |only BART-1.7/BART/R/rtnorm.R |only BART-1.7/BART/R/rtnorm_reject.R |only BART-1.7/BART/R/surv.bart.R | 74 ++- BART-1.7/BART/R/surv.pre.bart.R | 9 BART-1.7/BART/R/wbart.R | 8 BART-1.7/BART/build/vignette.rds |binary BART-1.7/BART/cleanup | 15 BART-1.7/BART/cleanup.win | 15 BART-1.7/BART/data/ACTG175.rda |binary BART-1.7/BART/data/arq.rda |binary BART-1.7/BART/data/bladder.rda |binary BART-1.7/BART/data/lung.rda |binary BART-1.7/BART/data/transplant.rda |binary BART-1.7/BART/data/xdm20.test.rda |binary BART-1.7/BART/data/xdm20.train.rda |binary BART-1.7/BART/data/ydm20.test.rda |binary BART-1.7/BART/data/ydm20.train.rda |binary BART-1.7/BART/demo/00Index | 9 BART-1.7/BART/demo/aids.itr.lbart.R | 79 ++- BART-1.7/BART/demo/aids.itr.pbart.R | 74 +-- BART-1.7/BART/demo/bladder.recur.bart.R | 6 BART-1.7/BART/demo/concord.surv.bart.R | 2 BART-1.7/BART/demo/cube.lbart.R |only BART-1.7/BART/demo/cube.mbart.R |only BART-1.7/BART/demo/cube.pbart.R | 1 BART-1.7/BART/demo/geweke.pbart2.R | 5 BART-1.7/BART/demo/inform.alt.gbart.R |only BART-1.7/BART/demo/inform.null.gbart.R |only BART-1.7/BART/demo/liver.crisk.bart.R | 47 ++ BART-1.7/BART/demo/liver.crisk2.bart.R |only BART-1.7/BART/demo/lung.surv.bart.R | 4 BART-1.7/BART/demo/nhanes.pbart1.R | 32 - BART-1.7/BART/demo/nhanes.pbart2.R | 24 - BART-1.7/BART/demo/test.draw_lambda_i.R |only BART-1.7/BART/demo/test.rtnorm.R |only BART-1.7/BART/inst/cxx-ex/bart.cpp | 43 -- BART-1.7/BART/inst/cxx-ex/bart.h | 11 BART-1.7/BART/inst/cxx-ex/bartfuns.cpp | 55 ++ BART-1.7/BART/inst/cxx-ex/bartfuns.h | 9 BART-1.7/BART/inst/cxx-ex/clbart.cpp | 31 + BART-1.7/BART/inst/cxx-ex/cmbart.cpp | 94 +++- BART-1.7/BART/inst/cxx-ex/cpbart.cpp | 9 BART-1.7/BART/inst/cxx-ex/cwbart.cpp | 4 BART-1.7/BART/inst/cxx-ex/heterbart.cpp | 6 BART-1.7/BART/inst/cxx-ex/latent.cpp | 24 + BART-1.7/BART/inst/cxx-ex/latent.h | 8 BART-1.7/BART/inst/cxx-ex/lmain.cpp | 3 BART-1.7/BART/inst/cxx-ex/pmain.cpp | 3 BART-1.7/BART/inst/cxx-ex/rand_draws.cpp | 15 BART-1.7/BART/inst/cxx-ex/rand_draws.h | 6 BART-1.7/BART/inst/cxx-ex/rn.h | 218 ++++------ BART-1.7/BART/inst/cxx-ex/rtnorm.cpp | 17 BART-1.7/BART/inst/cxx-ex/rtnorm.h | 9 BART-1.7/BART/inst/cxx-ex/wmain.cpp | 2 BART-1.7/BART/inst/doc/bincat.Rnw | 38 + BART-1.7/BART/inst/doc/bincat.pdf |binary BART-1.7/BART/inst/doc/computing.Rnw | 5 BART-1.7/BART/inst/doc/computing.pdf |binary BART-1.7/BART/inst/doc/cont1.Rnw | 4 BART-1.7/BART/inst/doc/cont1.pdf |binary BART-1.7/BART/inst/doc/cont2.pdf |binary BART-1.7/BART/inst/doc/hwbart.pdf |binary BART-1.7/BART/inst/doc/time-to-event.Rnw | 39 + BART-1.7/BART/inst/doc/time-to-event.pdf |binary BART-1.7/BART/inst/include |only BART-1.7/BART/man/BART-package.Rd | 52 -- BART-1.7/BART/man/crisk.bart.Rd | 339 ++++++++-------- BART-1.7/BART/man/crisk2.bart.Rd |only BART-1.7/BART/man/draw_lambda_i.Rd |only BART-1.7/BART/man/gbart.Rd |only BART-1.7/BART/man/lbart.Rd | 25 - BART-1.7/BART/man/mbart.Rd | 121 +++-- BART-1.7/BART/man/mc.crisk.pwbart.Rd | 100 ++-- BART-1.7/BART/man/mc.crisk2.pwbart.Rd |only BART-1.7/BART/man/mc.lbart.Rd | 12 BART-1.7/BART/man/mc.mbart.Rd | 138 +++--- BART-1.7/BART/man/mc.pbart.Rd | 44 +- BART-1.7/BART/man/mc.wbart.Rd | 42 + BART-1.7/BART/man/pbart.Rd | 36 - BART-1.7/BART/man/predict.crisk2bart.Rd |only BART-1.7/BART/man/predict.criskbart.Rd | 91 +++- BART-1.7/BART/man/recur.bart.Rd | 117 +++-- BART-1.7/BART/man/rtnorm.Rd |only BART-1.7/BART/man/surv.bart.Rd | 124 +++-- BART-1.7/BART/man/wbart.Rd | 15 BART-1.7/BART/src/bart.cpp | 43 -- BART-1.7/BART/src/bart.h | 11 BART-1.7/BART/src/bartfuns.cpp | 55 ++ BART-1.7/BART/src/bartfuns.h | 9 BART-1.7/BART/src/cgbart.cpp |only BART-1.7/BART/src/clbart.cpp | 31 + BART-1.7/BART/src/cmbart.cpp | 94 +++- BART-1.7/BART/src/cpbart.cpp | 9 BART-1.7/BART/src/cwbart.cpp | 4 BART-1.7/BART/src/heterbart.cpp | 6 BART-1.7/BART/src/init.c | 12 BART-1.7/BART/src/lambda.cpp |only BART-1.7/BART/src/lambda.h |only BART-1.7/BART/src/rn.h | 218 ++++------ BART-1.7/BART/src/rn.h.bad |only BART-1.7/BART/src/rtnorm.cpp | 17 BART-1.7/BART/src/rtnorm.h | 9 BART-1.7/BART/vignettes/bincat.Rnw | 38 + BART-1.7/BART/vignettes/computing.Rnw | 5 BART-1.7/BART/vignettes/cont1.Rnw | 4 BART-1.7/BART/vignettes/figures/RI-B6-Pl.pdf |binary BART-1.7/BART/vignettes/figures/RI-Th-B6.pdf |binary BART-1.7/BART/vignettes/figures/RI-Th-Pl.pdf |binary BART-1.7/BART/vignettes/figures/clbp.pdf |binary BART-1.7/BART/vignettes/figures/geweke-pbart2-100.pdf |binary BART-1.7/BART/vignettes/figures/geweke-pbart2-1000.pdf |binary BART-1.7/BART/vignettes/figures/geweke-pbart2-10000.pdf |binary BART-1.7/BART/vignettes/figures/liver-BART.pdf |binary BART-1.7/BART/vignettes/figures/lung.pdf |binary BART-1.7/BART/vignettes/figures/neck.pdf |binary BART-1.7/BART/vignettes/references.bib | 24 + BART-1.7/BART/vignettes/time-to-event.Rnw | 39 + 162 files changed, 2462 insertions(+), 1627 deletions(-)
Title: Calculator of Understandability Metrics for BPMN
Description: Calculate several understandability metrics of BPMN models. BPMN stands for business process modelling notation and is a language for expressing business processes into business process diagrams. Examples of these understandability metrics are: average connector degree, maximum connector degree, sequentiality, cyclicity, diameter, depth, token split, control flow complexity, connector mismatch, connector heterogeneity, separability, structuredness and cross connectivity. See R documentation and paper on metric implementation included in this package for more information concerning the metrics.
Author: Jonas Lieben
Maintainer: Jonas Lieben <jonas.lieben@uhasselt.be>
Diff between understandBPMN versions 1.0.0 dated 2018-03-14 and 1.1.0 dated 2018-06-08
DESCRIPTION | 10 MD5 | 87 +-- NAMESPACE | 15 NEWS.md |only R/Behavioral_profile.R |only R/Create_path_log.R | 9 R/UnderstandBPMN.R | 4 R/helper.R | 244 +++++++++ R/metrics.R | 627 +++++++++++++++++-------- R/sysdata.rda |only README.md | 3 inst/sysdata.rda |only man/activity_multiple_times_executed.Rd |only man/activity_names_repetitions.Rd |only man/avg_connector_degree.Rd | 6 man/calculate_metrics.Rd | 9 man/coefficient_network_connectivity.Rd | 6 man/connectivity_level_between_pools.Rd | 6 man/connector_heterogeneity.Rd | 6 man/connector_mismatch.Rd | 6 man/control_flow_complexity.Rd | 6 man/create_path_and_repetition_log.Rd | 6 man/cross_connectivity.Rd | 20 man/cyclicity.Rd | 18 man/cyclomatic_metric.Rd |only man/density_process_model.Rd | 6 man/depth.Rd | 18 man/diameter.Rd | 18 man/direct_parallel_relations.Rd |only man/filtered_path_log_parallel.Rd |only man/max_connector_degree.Rd | 6 man/n_data_objects.Rd | 6 man/n_duplicate_tasks.Rd | 6 man/n_empty_sequence_flows.Rd | 6 man/n_message_flows.Rd | 6 man/n_pools.Rd | 6 man/n_swimlanes.Rd | 6 man/separability.Rd | 18 man/sequentiality.Rd | 6 man/size_process_model.Rd | 6 man/some_traces_without_activity.Rd |only man/structuredness.Rd | 19 man/token_split.Rd | 6 man/traces_contain_relation.Rd |only src/create_path_log.cpp | 89 ++- tests/testthat/diagram_behavioral_profile.bpmn | 58 +- tests/testthat/paper_diagram_simple.bpmn | 4 tests/testthat/testHelper.R | 10 tests/testthat/testMetrics.R | 150 +++-- tests/testthat/testPathLog.R | 17 50 files changed, 1077 insertions(+), 478 deletions(-)
More information about understandBPMN at CRAN
Permanent link
Title: Multi-Objective Parameter Tuning for Classifiers
Description: Generic methods for parameter tuning of classification algorithms using multiple scoring functions.
Author: Christoph Müssel, Ludwig Lausser, Hans Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between TunePareto versions 2.4 dated 2014-03-31 and 2.5 dated 2018-06-08
DESCRIPTION | 12 ++-- MD5 | 19 +++---- NAMESPACE | 120 +++++++++++++++++++++++----------------------- R/classifiers.R | 2 R/helpers.R | 14 ++--- R/tunePareto.R | 22 +++----- R/visualizations.R | 6 -- inst/NEWS.Rd | 12 ++++ man/TunePareto-package.Rd | 4 - src/TunePareto.c | 2 src/TunePareto_init.c |only 11 files changed, 112 insertions(+), 101 deletions(-)
Title: IRT Equating Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods (Battauz M. (2013) <doi:10.1007/s11336-012-9316-y>, Battauz M. (2015) <doi:10.18637/jss.v068.i07>).
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 2.0-4 dated 2017-11-02 and 2.0-5 dated 2018-06-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/functions.r | 4 +++- build/vignette.rds |binary inst/NEWS | 4 ++-- inst/doc/equateIRT_paper.pdf |binary inst/doc/equateIRT_tutorial.html | 2 +- man/equateIRT-package.Rd | 4 ++-- 8 files changed, 19 insertions(+), 17 deletions(-)
Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models (Pearl, 2000, Chapter 5) <ISBN:978-0-521-89560-6>, where each factor of the joint probability distribution is a distributed-lag linear regression model (Judge et al., 1985, Chapters 9-10) <ISBN: 978-0-471-89530-5>. DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 2.2 dated 2018-03-03 and 2.3 dated 2018-06-08
DESCRIPTION | 8 MD5 | 37 +-- NAMESPACE | 3 R/dlsem.r | 502 ++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/dlsem_vignette.R | 33 +- inst/doc/dlsem_vignette.Rnw | 101 ++++---- inst/doc/dlsem_vignette.pdf |binary man/as.graphNEL.Rd |only man/auto.lagPlot.Rd | 6 man/causalEff.Rd | 8 man/dlsem-package.Rd | 4 man/dlsem.Rd | 41 +-- man/isIndep.Rd | 4 man/lagPlot.Rd | 6 man/unirootTest.Rd | 19 - vignettes/dlsem_vignette.Rnw | 101 ++++---- vignettes/figures/lagsh1a.pdf |binary vignettes/figures/lagsh1b.pdf |binary vignettes/figures/lagsh1c.pdf |binary 20 files changed, 434 insertions(+), 439 deletions(-)
Title: Interface with Google BigQuery with Shiny Compatibility
Description: Interface with 'Google BigQuery',
see <https://cloud.google.com/bigquery/> for more information.
This package uses 'googleAuthR' so is compatible with similar packages,
including 'Google Cloud Storage' (<https://cloud.google.com/storage/>) for result extracts.
Author: Mark Edmondson [aut, cre],
Hadley Wickham [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between bigQueryR versions 0.3.2 dated 2017-10-23 and 0.4.0 dated 2018-06-08
bigQueryR-0.3.2/bigQueryR/man/bq_get_global_dataset.Rd |only bigQueryR-0.3.2/bigQueryR/man/bq_get_global_project.Rd |only bigQueryR-0.3.2/bigQueryR/man/bq_global_dataset.Rd |only bigQueryR-0.3.2/bigQueryR/man/bq_global_project.Rd |only bigQueryR-0.4.0/bigQueryR/DESCRIPTION | 13 - bigQueryR-0.4.0/bigQueryR/MD5 | 70 ++++---- bigQueryR-0.4.0/bigQueryR/NAMESPACE | 12 + bigQueryR-0.4.0/bigQueryR/NEWS.md | 17 + bigQueryR-0.4.0/bigQueryR/R/auth.R | 26 +- bigQueryR-0.4.0/bigQueryR/R/fastBqDownload.R |only bigQueryR-0.4.0/bigQueryR/R/globals.R | 56 ++++-- bigQueryR-0.4.0/bigQueryR/R/jobs.R | 24 ++ bigQueryR-0.4.0/bigQueryR/R/listBigQuery.R | 2 bigQueryR-0.4.0/bigQueryR/R/options.R | 2 bigQueryR-0.4.0/bigQueryR/R/partition.R | 39 ++-- bigQueryR-0.4.0/bigQueryR/R/print_methods.R | 4 bigQueryR-0.4.0/bigQueryR/R/query.R | 18 +- bigQueryR-0.4.0/bigQueryR/R/tables.R | 83 ++++++++- bigQueryR-0.4.0/bigQueryR/R/uploadData.R | 139 ++++++++++++---- bigQueryR-0.4.0/bigQueryR/build/vignette.rds |binary bigQueryR-0.4.0/bigQueryR/inst/client.json |only bigQueryR-0.4.0/bigQueryR/inst/doc/bigQueryR.html | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_auth.Rd | 7 bigQueryR-0.4.0/bigQueryR/man/bqr_copy_table.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_create_table.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_delete_table.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_download_query.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_get_global_dataset.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_get_global_project.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_get_job.Rd | 6 bigQueryR-0.4.0/bigQueryR/man/bqr_global_dataset.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_global_project.Rd |only bigQueryR-0.4.0/bigQueryR/man/bqr_list_datasets.Rd | 2 bigQueryR-0.4.0/bigQueryR/man/bqr_list_jobs.Rd | 2 bigQueryR-0.4.0/bigQueryR/man/bqr_list_tables.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_partition.Rd | 22 +- bigQueryR-0.4.0/bigQueryR/man/bqr_query.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_query_asynch.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_table_data.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_table_meta.Rd | 4 bigQueryR-0.4.0/bigQueryR/man/bqr_upload_data.Rd | 23 ++ bigQueryR-0.4.0/bigQueryR/tests |only 42 files changed, 433 insertions(+), 166 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. This package is built for speed and
runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.5.0 dated 2018-06-07 and 0.9.5.1 dated 2018-06-08
stringdist-0.9.5.0/stringdist/src/stringdist_pkg.h |only stringdist-0.9.5.1/stringdist/DESCRIPTION | 10 stringdist-0.9.5.1/stringdist/MD5 | 17 - stringdist-0.9.5.1/stringdist/NEWS | 3 stringdist-0.9.5.1/stringdist/inst/doc/loo2014stringdist.pdf |binary stringdist-0.9.5.1/stringdist/inst/doc/stringdist_api.pdf |binary stringdist-0.9.5.1/stringdist/inst/include/stringdist_api.h | 141 ++++++----- stringdist-0.9.5.1/stringdist/src/R_register_native.c | 1 stringdist-0.9.5.1/stringdist/src/Rstringdist.c | 2 stringdist-0.9.5.1/stringdist/src/stringdist.c | 2 10 files changed, 98 insertions(+), 78 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-27 dated 2018-06-01 and 0.3-28 dated 2018-06-08
ChangeLog | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 14 +++++----- configure | 18 +++++++------- inst/ChangeLog | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 - src/rgeos.c | 4 +-- src/rgeos_geos2R.c | 68 +++++++++++++++++++++++++++++++++++------------------ 8 files changed, 200 insertions(+), 46 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: JJ Allaire [aut, cre],
Kevin Ushey [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between reticulate versions 1.7 dated 2018-04-28 and 1.8 dated 2018-06-08
DESCRIPTION | 8 MD5 | 64 ++- NAMESPACE | 9 NEWS.md | 23 + R/conversion.R | 61 ++- R/help.R | 12 R/knitr-engine.R | 39 -- R/package.R | 3 R/python-dict.R |only R/python.R | 235 +++++++++++--- R/repl.R | 24 - R/source.R | 11 inst/doc/package.Rmd | 2 inst/doc/package.html | 3 inst/doc/python_packages.Rmd | 2 inst/doc/python_packages.html | 3 inst/doc/r_markdown.Rmd | 2 inst/doc/r_markdown.html | 2 inst/python/rpytools/__pycache__/generator.cpython-36.pyc |binary man/py_del_item.Rd |only man/py_get_item.Rd |only man/py_set_item.Rd |only src/libpython.h | 15 src/python.cpp | 152 +++++---- tests/testthat/resources/eng-reticulate-example.Rmd | 25 - tests/testthat/resources/eng-reticulate-example.html | 27 + tests/testthat/test-help-handlers.R | 4 tests/testthat/test-python-dict.R | 26 + tests/testthat/test-python-knitr-engine.R | 7 tests/testthat/test-python-numpy.R | 7 tests/testthat/test-python-pandas.R | 35 +- tests/testthat/test-python-scipy-sparse-matrix.R | 1 vignettes/package.Rmd | 2 vignettes/python_packages.Rmd | 2 vignettes/r_markdown.Rmd | 2 35 files changed, 547 insertions(+), 261 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut],
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
Norbert Mercier [ctb],
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb],
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [ctb],
Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>),
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.8.4 dated 2018-04-20 and 0.8.5 dated 2018-06-08
DESCRIPTION | 12 - MD5 | 252 +++++++++++------------ NEWS | 37 +++ R/Luminescence-package.R | 4 R/analyse_Al2O3C_CrossTalk.R | 8 R/analyse_Al2O3C_ITC.R | 12 - R/analyse_Al2O3C_Measurement.R | 105 +++++++-- R/analyse_SAR.CWOSL.R | 2 R/analyse_baSAR.R | 183 ++++++++++++---- R/methods_RLum.R | 2 inst/NEWS.Rd | 49 ++++ inst/doc/HowTo_analyse_Al2O3.html | 78 ++++--- man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/GitHub-API.Rd | 2 man/Luminescence-package.Rd | 4 man/PSL2Risoe.BINfileData.Rd | 2 man/RLum-class.Rd | 2 man/RLum.Analysis-class.Rd | 2 man/RLum.Data.Curve-class.Rd | 2 man/RLum.Data.Image-class.Rd | 2 man/RLum.Data.Spectrum-class.Rd | 2 man/RLum.Results-class.Rd | 2 man/Risoe.BINfileData-class.Rd | 2 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 12 - man/analyse_Al2O3C_ITC.Rd | 16 - man/analyse_Al2O3C_Measurement.Rd | 38 ++- man/analyse_FadingMeasurement.Rd | 4 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 4 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 31 +- man/analyse_pIRIRSequence.Rd | 2 man/analyse_portableOSL.Rd | 2 man/app_RLum.Rd | 2 man/apply_CosmicRayRemoval.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Kars2008.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxRatio.Rd | 2 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/convert_Activity2Concentration.Rd | 2 man/convert_BIN2CSV.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 2 man/convert_RLum2Risoe.BINfileData.Rd | 4 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_LMCurve.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 2 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 4 man/methods_RLum.Rd | 2 man/model_LuminescenceSignals.Rd | 2 man/names_RLum.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_NRt.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_RadialPlot.Rd | 2 man/plot_Risoe.BINfileData.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 2 man/read_Daybreak2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 2 man/structure_RLum.Rd | 2 man/template_DRAC.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/write_R2BIN.Rd | 2 man/write_RLum2CSV.Rd | 2 tests/testthat/test_analyse_Al2O3C_Measurement.R | 6 vignettes/HowTo_analyse_Al2O3.Rmd | 10 127 files changed, 687 insertions(+), 398 deletions(-)
Title: Daten, Beispiele und Funktionen zu 'Large-Scale Assessment mit
R'
Description: Dieses R-Paket stellt Zusatzmaterial in Form von Daten, Funktionen
und R-Hilfe-Seiten für den Herausgeberband Breit, S. und Schreiner,
C. (Hrsg.). (2016). "Large-Scale Assessment mit R: Methodische Grundlagen
der österreichischen Bildungsstandardüberprüfung." Wien: facultas.
(ISBN: 978-3-7089-1343-8, <https://www.bifie.at/node/3770>) zur
Verfügung.
Author: Thomas Kiefer [aut, cre],
Alexander Robitzsch [aut],
Matthias Trendtel [aut],
Robert Fellinger [aut]
Maintainer: Thomas Kiefer <t.kiefer@bifie.at>
Diff between LSAmitR versions 1.0-1 dated 2018-01-19 and 1.0-2 dated 2018-06-08
LSAmitR-1.0-1/LSAmitR/man/LSAmitR-package.Rd |only LSAmitR-1.0-2/LSAmitR/DESCRIPTION | 16 +++++++++------- LSAmitR-1.0-2/LSAmitR/MD5 | 7 ++++--- LSAmitR-1.0-2/LSAmitR/build |only LSAmitR-1.0-2/LSAmitR/inst/NEWS | 13 +++++++++++-- LSAmitR-1.0-2/LSAmitR/man/LSAmitR-package_20180608.Rd |only 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.2.2 dated 2018-03-21 and 1.2.3 dated 2018-06-08
DESCRIPTION | 8 ++--- MD5 | 38 ++++++++++++------------- NAMESPACE | 2 + NEWS.md | 17 +++++++++++ R/copy.R | 16 +++++++++- R/create.R | 9 +++--- R/file.R | 8 ++--- R/fs_path.R | 10 ++++++ R/path.R | 6 ++-- R/utils.R | 8 +++-- README.md | 67 ++++++++++++++++++++++++++------------------- man/create.Rd | 6 ++-- man/file_chmod.Rd | 4 +- man/path_math.Rd | 2 - src/Makevars | 5 ++- src/file.cc | 8 ++--- src/path.cc | 2 - tests/testthat/test-copy.R | 31 ++++++++++++++++++++ tests/testthat/test-file.R | 26 +++-------------- tests/testthat/test-path.R | 6 ++++ 20 files changed, 180 insertions(+), 99 deletions(-)
Title: Genome Interval Arithmetic in R
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Author: Jay Hesselberth [aut, cre] (<https://orcid.org/0000-0002-6299-179X>),
Kent Riemondy [aut] (<https://orcid.org/0000-0003-0750-1273>)
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.4.0 dated 2018-01-25 and 0.4.1 dated 2018-06-08
DESCRIPTION | 16 LICENSE | 2 MD5 | 57 +- NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 4 R/bed_partition.r |only R/tbls.r | 15 README.md | 168 +------ build/vignette.rds |binary inst/doc/valr.R | 1 inst/doc/valr.Rmd | 1 inst/doc/valr.html | 730 +++++++++++++++++++------------ man/as.tbl_interval.Rd | 15 man/bed_cluster.Rd | 3 man/bed_complement.Rd | 3 man/bed_flank.Rd | 3 man/bed_merge.Rd | 3 man/bed_partition.Rd |only man/bed_shift.Rd | 3 man/bed_slop.Rd | 3 man/figures/README-intersect_glyph-1.png |binary src/RcppExports.cpp | 12 src/init.c | 36 - src/makewindows.cpp | 6 src/partition.cpp |only tests/testthat/test_partition.r |only vignettes/img |only vignettes/valr.Rmd | 1 29 files changed, 632 insertions(+), 457 deletions(-)
Title: Composite-Likelihood Based Analysis of Random Fields
Description: A set of procedures for the analysis of Random Fields using likelihood and non-standard likelihood methods is provided. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood inference is emerging as a useful tool for mitigating such computational problems. This methodology shows satisfactory results when compared with other techniques such as the tapering method. Moreover, composite likelihood (and related quantities) have some useful properties similar to those of the standard likelihood.
Author: Simone Padoan[aut, cre] <simone.padoan@unibocconi.it>, Moreno Bevilacqua[aut] <moreno.bevilacqua@uv.cl>
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between CompRandFld versions 1.0.3-4 dated 2015-02-01 and 1.0.3-5 dated 2018-06-08
DESCRIPTION | 15 ++++++++------- MD5 | 11 ++++++----- NAMESPACE | 16 ++++++++++++++-- R/Likelihood.r | 2 +- data/irishwinds.rda |binary data/usrain.rda |binary src/registerDynamicSymbol.c |only 7 files changed, 29 insertions(+), 15 deletions(-)
Title: Time-Course Gene Set Analysis
Description: Implementation of Time-course Gene Set Analysis (TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre],
Damien Chimits [aut],
Anthony Devaux [aut]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between TcGSA versions 0.10.5 dated 2017-05-03 and 0.11.1 dated 2018-06-08
TcGSA-0.10.5/TcGSA/NEWS |only TcGSA-0.10.5/TcGSA/R/rmixchisq.R |only TcGSA-0.10.5/TcGSA/README |only TcGSA-0.10.5/TcGSA/man/rmixchisq.Rd |only TcGSA-0.11.1/TcGSA/DESCRIPTION | 25 +++-- TcGSA-0.11.1/TcGSA/MD5 | 85 +++++++++-------- TcGSA-0.11.1/TcGSA/NAMESPACE | 7 + TcGSA-0.11.1/TcGSA/NEWS.md |only TcGSA-0.11.1/TcGSA/R/TcGSA-internal.R | 4 TcGSA-0.11.1/TcGSA/R/TcGSA-package.R | 6 - TcGSA-0.11.1/TcGSA/R/TcGSA.LR.R | 14 +- TcGSA-0.11.1/TcGSA/R/TcGSA.LR.parallel.R | 18 +-- TcGSA-0.11.1/TcGSA/R/TcGSA.dataLME.R | 2 TcGSA-0.11.1/TcGSA/R/chisqmix.R |only TcGSA-0.11.1/TcGSA/R/clustTrend.R | 32 +++--- TcGSA-0.11.1/TcGSA/R/multtest.TcGSA.R | 138 ++++++++++++++++++---------- TcGSA-0.11.1/TcGSA/R/plot.TcGSA.R | 38 ++++--- TcGSA-0.11.1/TcGSA/R/plot1GS.R | 57 ++++++----- TcGSA-0.11.1/TcGSA/R/plotFit.GS.R | 13 +- TcGSA-0.11.1/TcGSA/R/plotMultipleGS.R |only TcGSA-0.11.1/TcGSA/R/plotPat.1GS.R | 11 +- TcGSA-0.11.1/TcGSA/R/plotPat.TcGSA.R | 58 +++++------ TcGSA-0.11.1/TcGSA/R/plotSelect.GS.R | 12 +- TcGSA-0.11.1/TcGSA/R/pval_simu.R | 4 TcGSA-0.11.1/TcGSA/R/signifLRT.TcGSA.R | 20 ++-- TcGSA-0.11.1/TcGSA/R/summary.TcGSA.R | 10 +- TcGSA-0.11.1/TcGSA/README.md |only TcGSA-0.11.1/TcGSA/build |only TcGSA-0.11.1/TcGSA/inst/CITATION | 2 TcGSA-0.11.1/TcGSA/inst/doc |only TcGSA-0.11.1/TcGSA/man/TcGSA-internal.Rd | 4 TcGSA-0.11.1/TcGSA/man/TcGSA-package.Rd | 6 - TcGSA-0.11.1/TcGSA/man/TcGSA.LR.Rd | 8 - TcGSA-0.11.1/TcGSA/man/TcGSA.LR.parallel.Rd | 10 +- TcGSA-0.11.1/TcGSA/man/chisqmix.Rd |only TcGSA-0.11.1/TcGSA/man/clustTrend.Rd | 30 +++--- TcGSA-0.11.1/TcGSA/man/data_simu_TcGSA.Rd | 4 TcGSA-0.11.1/TcGSA/man/multtest.TcGSA.Rd | 12 +- TcGSA-0.11.1/TcGSA/man/plot.TcGSA.Rd | 34 +++--- TcGSA-0.11.1/TcGSA/man/plot1GS.Rd | 46 +++++---- TcGSA-0.11.1/TcGSA/man/plotFit.GS.Rd | 13 +- TcGSA-0.11.1/TcGSA/man/plotMultipleGS.Rd |only TcGSA-0.11.1/TcGSA/man/plotPat.1GS.Rd | 11 +- TcGSA-0.11.1/TcGSA/man/plotPat.TcGSA.Rd | 50 +++++----- TcGSA-0.11.1/TcGSA/man/plotSelect.GS.Rd | 12 +- TcGSA-0.11.1/TcGSA/man/pval_simu.Rd | 4 TcGSA-0.11.1/TcGSA/man/signifLRT.TcGSA.Rd | 16 +-- TcGSA-0.11.1/TcGSA/man/summary.TcGSA.Rd | 10 +- TcGSA-0.11.1/TcGSA/vignettes |only 49 files changed, 452 insertions(+), 374 deletions(-)
Title: 'pinp' is not 'PNAS'
Description: A 'PNAS'-alike style for 'rmarkdown', derived from the
'Proceedings of the National Academy of Sciences of the United States
of America' ('PNAS', see <https://www.pnas.org>) 'LaTeX' style, and
adapted for use with 'markdown' and 'pandoc'.
Author: Dirk Eddelbuettel and James Balamuta
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pinp versions 0.0.4 dated 2017-11-04 and 0.0.5 dated 2018-06-08
ChangeLog | 6 +++++ DESCRIPTION | 8 +++---- MD5 | 15 +++++++------ build/vignette.rds |binary inst/NEWS.Rd | 8 +++++++ inst/doc/pinp.Rmd | 60 ++++++++++------------------------------------------- inst/doc/pinp.pdf |binary vignettes/bib.tex |only vignettes/pinp.Rmd | 60 ++++++++++------------------------------------------- 9 files changed, 50 insertions(+), 107 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.4.1 dated 2016-09-18 and 1.4.2 dated 2018-06-08
DESCRIPTION | 14 +- MD5 | 28 ++-- R/GetMap.R | 14 +- R/GetMapTiles.R | 19 ++ R/LatLon2XY.centered.R | 2 R/PlotOnMapTiles.R | 43 +++--- R/SpatialToPBS.R | 16 +- R/qbbox.R | 4 data/NYleukemia.rda |binary data/columbus.rda |binary data/incidents.rda |binary data/pennLC.rda |binary man/GetMap.Rd | 317 ++++++++++++++++++++++++++++++++----------------- man/GetMapTiles.Rd | 15 ++ man/PlotOnMapTiles.Rd | 5 15 files changed, 316 insertions(+), 161 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects at the mean or average marginal effects from
statistical models and returns the result as tidy data frames. These
data frames are ready to use with the 'ggplot2'-package.
Marginal effects can be calculated for many different models. Interaction
terms, splines and polynomial terms are also supported. The two main
functions are ggpredict() and ggaverage(), however, there are
some convenient wrapper-functions especially for polynomials or
interactions. There is a generic plot()-method to plot the results
using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.3.3 dated 2018-05-06 and 0.3.4 dated 2018-06-08
DESCRIPTION | 21 - MD5 | 55 +-- NAMESPACE | 3 NEWS.md | 16 R/efc.R | 2 R/ggeffect.R | 2 R/ggpredict.R | 49 +- R/plot.R | 53 ++ R/predictions.R | 39 +- R/utils_expand_data_to_grid.R | 6 R/utils_parse_vars_arguments.R | 24 + README.md | 16 data/efc.RData |binary data/efc_test.RData |only inst/CITATION | 18 - inst/doc/marginaleffects.R | 10 inst/doc/marginaleffects.Rmd | 18 - inst/doc/marginaleffects.html | 735 ++++++++++++++++------------------------- man/efc.Rd | 1 man/figures/logo.png |binary man/ggeffect.Rd | 23 - man/ggpredict.Rd | 23 - man/plot.Rd | 13 tests |only vignettes/marginaleffects.Rmd | 18 - 25 files changed, 598 insertions(+), 547 deletions(-)
Title: Bivariate Residual Plots with Simulation Polygons
Description: Generates bivariate residual plots with simulation polygons for any diagnostics and bivariate model from which functions to extract the desired diagnostics, simulate new data and refit the models are available.
Author: Rafael de Andrade Moral [aut, cre],
John Hinde [aut],
Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Diff between bivrp versions 1.0 dated 2016-12-16 and 1.1 dated 2018-06-08
DESCRIPTION | 12 +++-- MD5 | 18 ++++---- R/bivrp-internal.R | 13 +++--- R/bivrp.R | 6 +- R/plot.bivrp.R | 26 ++++++++---- R/polygon-operations.R | 25 +++++++++++- build/partial.rdb |binary man/bivrp.Rd | 93 +++++++++++++++++++++++----------------------- man/plot.bivrp.Rd | 6 +- man/polygon-operations.Rd | 12 +++-- 10 files changed, 125 insertions(+), 86 deletions(-)
Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of
Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>,
<DOI:10.1037/10409-008>. Penalized maximum likelihood
estimation and Markov Chain Monte Carlo estimation are
also provided, see Luedtke, Robitzsch and Wagner (2017)
<DOI:10.1037/met0000155>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between STARTS versions 0.3-24 dated 2018-03-21 and 0.4-24 dated 2018-06-08
DESCRIPTION | 10 MD5 | 72 ++-- R/coef.starts_uni.R | 2 R/logLik.starts_uni.R | 10 R/plot.starts_uni.R | 6 R/starts_cov.R | 8 R/starts_deprecated.R | 8 R/starts_estimate_description.R | 40 +- R/starts_estimate_model_fit.R | 34 - R/starts_estimate_model_fit_rmsea.R | 14 R/starts_estimate_model_fit_srmr.R | 12 R/starts_ic_add.R | 14 R/starts_sim1dim.R | 10 R/starts_summary_print_computation_time.R | 8 R/starts_summary_print_ic.R | 8 R/starts_uni_cov.R | 46 +- R/starts_uni_cov_pars.R | 16 R/starts_uni_estimate.R | 304 ++++++++--------- R/starts_uni_estimate_prepare_fitting.R | 68 +-- R/starts_uni_estimate_prepare_fitting_prior_model.R | 40 +- R/starts_uni_estimate_prepare_fitting_prior_variance.R | 8 R/starts_uni_estimate_proc.R | 137 ++++--- R/starts_uni_estimate_proc_modify_suff_stat.R | 36 +- R/starts_uni_estimate_variance_proportions_mcmc.R | 10 R/starts_uni_estimate_variance_proportions_pml.R | 50 +- R/starts_uni_sim.R | 48 +- R/starts_vector_with_names.R | 4 R/summary.starts_uni.R | 181 ++++------ R/summary_starts_uni_print_model_fit.R |only R/vcov.starts_uni.R | 2 R/zzz.R | 18 - README.md | 5 data/data.starts02.rda |only data/datalist | 1 inst/NEWS | 20 + man/STARTS-package.Rd | 7 man/data.starts.Rd | 33 + man/starts_uni.Rd | 42 +- 38 files changed, 698 insertions(+), 634 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]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.3-1 dated 2018-06-03 and 1.3-2 dated 2018-06-08
ChangeLog | 29 +++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- LICENSE.note | 22 +++++++++++++++++++++- MD5 | 18 +++++++++--------- configure | 18 +++++++++--------- inst/ChangeLog | 29 +++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 +- inst/doc/OGR_shape_encoding.pdf |binary src/gdal-bindings.cpp | 28 ++++++++++++++++------------ src/ogrsource.cpp | 10 +++++----- 10 files changed, 123 insertions(+), 41 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.3.0 dated 2018-06-07 and 0.3.1 dated 2018-06-08
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 13 +++++++++++++ R/impute_below.R | 2 -- inst/doc/getting-started-w-naniar.html | 6 +++--- inst/doc/naniar-visualisation.html | 4 ++-- inst/doc/replace-with-na.html | 4 ++-- man/figures/README-facet-by-month-1.png |binary man/figures/README-geom-miss-point-1.png |binary man/figures/README-gg-miss-span-1.png |binary man/figures/README-regular-geom-point-1.png |binary man/figures/README-shadow-impute-1.png |binary man/figures/README-shadow-w-ggplot-1.png |binary man/figures/README-upset-plot-1.png |binary 14 files changed, 37 insertions(+), 26 deletions(-)
Title: Multi-Objective Optimization for Collecting Cluster Alternatives
Description: Provides methods to analyze cluster alternatives based on multi-objective optimization of cluster validation indices. For details see Kraus et al. (2011) <doi:10.1007/s00180-011-0244-6>.
Author: Johann Kraus <johann.kraus@uni-ulm.de>
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between MOCCA versions 1.2 dated 2012-12-24 and 1.3 dated 2018-06-08
DESCRIPTION | 17 ++++++++--------- MD5 | 6 +++--- NAMESPACE | 2 +- man/MOCCA-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 15 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa [cre],
Stephane Jankowski [aut]
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2.5 dated 2016-10-20 and 1.2.6 dated 2018-06-08
MultNonParam-1.2.5/MultNonParam/R/functions.R |only MultNonParam-1.2.5/MultNonParam/R/zzz.r |only MultNonParam-1.2.5/MultNonParam/data/prostate.data.txt.gz |only MultNonParam-1.2.5/MultNonParam/data/sotiriou.data.txt.gz |only MultNonParam-1.2.5/MultNonParam/inst/probest.R |only MultNonParam-1.2.5/MultNonParam/inst/temp.csv |only MultNonParam-1.2.5/MultNonParam/man/prostate.data.Rd |only MultNonParam-1.2.5/MultNonParam/man/sotiriou.data.Rd |only MultNonParam-1.2.5/MultNonParam/man/wilding.Rd |only MultNonParam-1.2.6/MultNonParam/DESCRIPTION | 25 MultNonParam-1.2.6/MultNonParam/MD5 | 70 MultNonParam-1.2.6/MultNonParam/NAMESPACE | 36 MultNonParam-1.2.6/MultNonParam/R/MultNonParam.R |only MultNonParam-1.2.6/MultNonParam/R/aov.P.R | 14 MultNonParam-1.2.6/MultNonParam/R/betatest.R |only MultNonParam-1.2.6/MultNonParam/R/dmannwhitney.R |only MultNonParam-1.2.6/MultNonParam/R/higgins.fisher.kruskal.test.R | 16 MultNonParam-1.2.6/MultNonParam/R/mood.median.test.R | 13 MultNonParam-1.2.6/MultNonParam/R/page.test.unbalanced.R | 4 MultNonParam-1.2.6/MultNonParam/R/probest.R | 103 - MultNonParam-1.2.6/MultNonParam/R/prostate.R |only MultNonParam-1.2.6/MultNonParam/R/sensativity.plot.R |only MultNonParam-1.2.6/MultNonParam/R/sotiriou.R |only MultNonParam-1.2.6/MultNonParam/R/symscorestat.R | 23 MultNonParam-1.2.6/MultNonParam/R/testve.R |only MultNonParam-1.2.6/MultNonParam/R/tukey.kruskal.test.R | 16 MultNonParam-1.2.6/MultNonParam/R/util.jplot.R |only MultNonParam-1.2.6/MultNonParam/data/prostate.RData |only MultNonParam-1.2.6/MultNonParam/data/sotiriou.RData |only MultNonParam-1.2.6/MultNonParam/man/MultNonParam-package.Rd | 53 MultNonParam-1.2.6/MultNonParam/man/aov.P.Rd | 62 MultNonParam-1.2.6/MultNonParam/man/betatest.Rd | 45 MultNonParam-1.2.6/MultNonParam/man/dmannwhitney.Rd | 41 MultNonParam-1.2.6/MultNonParam/man/higgins.fisher.kruskal.test.Rd | 60 MultNonParam-1.2.6/MultNonParam/man/mood.median.test.Rd |only MultNonParam-1.2.6/MultNonParam/man/page.test.unbalanced.Rd | 1 MultNonParam-1.2.6/MultNonParam/man/probest.Rd | 111 - MultNonParam-1.2.6/MultNonParam/man/prostate.Rd |only MultNonParam-1.2.6/MultNonParam/man/sensitivity.plot.Rd | 50 MultNonParam-1.2.6/MultNonParam/man/sotiriou.Rd |only MultNonParam-1.2.6/MultNonParam/man/symscorestat.Rd | 66 MultNonParam-1.2.6/MultNonParam/man/testve.Rd | 87 - MultNonParam-1.2.6/MultNonParam/man/tukey.kruskal.test.Rd | 57 MultNonParam-1.2.6/MultNonParam/man/util.jplot.Rd | 51 MultNonParam-1.2.6/MultNonParam/src/aovp.f90 | 765 ++++------ MultNonParam-1.2.6/MultNonParam/src/init.c |only MultNonParam-1.2.6/MultNonParam/src/nextp.f90 |only MultNonParam-1.2.6/MultNonParam/src/probest.f90 | 10 48 files changed, 894 insertions(+), 885 deletions(-)
Title: Ellipse Summary Plot of Quantiles
Description: Correlation chart of two set (x and y) of data.
Using Quantiles. Visualize the effect of factor.
Author: Shinichiro Tomizono
Maintainer: Shinichiro Tomizono <cowares@gmail.com>
Diff between elliplot versions 1.1.1 dated 2013-09-29 and 1.2.0 dated 2018-06-08
DESCRIPTION | 9 +++++---- MD5 | 7 ++++--- NAMESPACE | 10 +++++++++- build |only man/elliplot-package.Rd | 20 ++++++++------------ 5 files changed, 26 insertions(+), 20 deletions(-)
Title: Beads Summary Plot of Ranges
Description: Visualize one-factor data frame.
Beads plot consists of diamonds of each factor of each data series.
A diamond indicates average and range.
Look over a data frame with many numeric columns and a factor column.
Author: Shinichiro Tomizono
Maintainer: Shinichiro Tomizono <cowares@gmail.com>
Diff between diaplt versions 1.2.1 dated 2013-11-13 and 1.3.0 dated 2018-06-08
DESCRIPTION | 9 +++++---- MD5 | 7 ++++--- NAMESPACE | 10 +++++++++- build |only man/diaplt-package.Rd | 22 ++++++++-------------- 5 files changed, 26 insertions(+), 22 deletions(-)
Title: Double Box Plot for Two-Axes Correlation
Description: Correlation chart of two set (x and y) of data.
Using Quartiles with boxplot style.
Visualize the effect of factor.
Author: Shinichiro Tomizono
Maintainer: Shinichiro Tomizono <cowares@gmail.com>
Diff between boxplotdbl versions 1.2.2 dated 2013-11-24 and 1.3.0 dated 2018-06-08
DESCRIPTION | 9 +++++---- MD5 | 7 ++++--- NAMESPACE | 10 +++++++++- build |only man/boxplotdbl-package.Rd | 23 ++++++++--------------- 5 files changed, 26 insertions(+), 23 deletions(-)