Title: Stable Isotope Bayesian Ellipses in R
Description: Fits bi-variate ellipses to stable isotope data using Bayesian
inference with the aim being to describe and compare their isotopic
niche.
Author: Andrew Jackson and Andrew Parnell
Maintainer: Andrew Jackson <a.jackson@tcd.ie>
Diff between SIBER versions 2.1.0 dated 2017-02-22 and 2.1.2 dated 2017-03-15
SIBER-2.1.0/SIBER/R/hullarea.R |only SIBER-2.1.0/SIBER/R/laymanmetrics.R |only SIBER-2.1.2/SIBER/DESCRIPTION | 11 - SIBER-2.1.2/SIBER/MD5 | 66 +++++----- SIBER-2.1.2/SIBER/NEWS.md | 15 +- SIBER-2.1.2/SIBER/R/SIBER.R | 2 SIBER-2.1.2/SIBER/R/bayesianOverlap.R | 2 SIBER-2.1.2/SIBER/R/ellipseInOut.R | 2 SIBER-2.1.2/SIBER/R/hullArea.R |only SIBER-2.1.2/SIBER/R/laymanMetrics.R |only SIBER-2.1.2/SIBER/R/maxLikOverlap.R | 24 +++ SIBER-2.1.2/SIBER/R/plotGroupHulls.R | 3 SIBER-2.1.2/SIBER/R/plotSiberObject.R | 65 ++++++--- SIBER-2.1.2/SIBER/R/pointsToEllipsoid.R | 9 + SIBER-2.1.2/SIBER/build/vignette.rds |binary SIBER-2.1.2/SIBER/inst/doc/Customising-Plots-Manually.R | 3 SIBER-2.1.2/SIBER/inst/doc/Customising-Plots-Manually.Rmd | 5 SIBER-2.1.2/SIBER/inst/doc/Customising-Plots-Manually.html | 11 - SIBER-2.1.2/SIBER/inst/doc/Ellipse-Overlap.R | 16 +- SIBER-2.1.2/SIBER/inst/doc/Ellipse-Overlap.Rmd | 19 +- SIBER-2.1.2/SIBER/inst/doc/Ellipse-Overlap.html | 26 ++- SIBER-2.1.2/SIBER/inst/doc/Introduction-to-SIBER.R | 1 SIBER-2.1.2/SIBER/inst/doc/Introduction-to-SIBER.Rmd | 1 SIBER-2.1.2/SIBER/inst/doc/Introduction-to-SIBER.html | 12 - SIBER-2.1.2/SIBER/inst/doc/Points-Inside-Outside-Ellipse.html | 4 SIBER-2.1.2/SIBER/man/SIBER.Rd | 5 SIBER-2.1.2/SIBER/man/ellipseInOut.Rd | 2 SIBER-2.1.2/SIBER/man/hullArea.Rd | 2 SIBER-2.1.2/SIBER/man/laymanMetrics.Rd | 2 SIBER-2.1.2/SIBER/man/maxLikOverlap.Rd | 25 +++ SIBER-2.1.2/SIBER/man/plotGroupHulls.Rd | 4 SIBER-2.1.2/SIBER/man/plotSiberObject.Rd | 40 +++--- SIBER-2.1.2/SIBER/man/pointsToEllipsoid.Rd | 10 + SIBER-2.1.2/SIBER/vignettes/Customising-Plots-Manually.Rmd | 5 SIBER-2.1.2/SIBER/vignettes/Ellipse-Overlap.Rmd | 19 +- SIBER-2.1.2/SIBER/vignettes/Introduction-to-SIBER.Rmd | 1 36 files changed, 261 insertions(+), 151 deletions(-)
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 15.0-0.0 dated 2017-02-20 and 16.0-0.0 dated 2017-03-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/zzz.R | 2 +- data/sgptData_LONG.rda |binary inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/SGPdata-package.Rd | 4 ++-- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Q-Q and Manhattan Plots for GWAS Data
Description: Create Q-Q and manhattan plots for GWAS data from PLINK results.
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between qqman versions 0.1.2 dated 2014-09-25 and 0.1.4 dated 2017-03-15
DESCRIPTION | 14 ++++--- MD5 | 34 ++++++++++--------- NAMESPACE | 6 ++- NEWS.md |only R/manhattan.R | 48 +++++++++++++++++++++++---- R/qq.R | 4 ++ R/snpsOfInterest-data.R | 1 README.md | 4 +- build/vignette.rds |binary inst/doc/qqman.R | 6 +++ inst/doc/qqman.Rmd | 12 ++++++ inst/doc/qqman.html | 85 +++++++++++++++++++++++++++++++----------------- man/gwasResults.Rd | 4 +- man/manhattan.Rd | 34 +++++++++++-------- man/qq.Rd | 5 +- man/qqman.Rd | 4 +- man/snpsOfInterest.Rd | 6 +-- tools |only vignettes/qqman.Rmd | 12 ++++++ 19 files changed, 195 insertions(+), 84 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.4.3 dated 2016-09-19 and 0.5.0 dated 2017-03-15
DESCRIPTION | 10 MD5 | 24 + NAMESPACE | 8 R/MDMR-package.R | 63 +++- R/mdmr.R | 587 ++++++++++++++++++++++++++++++++++++++++++-- data/clustmdmrdata.RData |only inst/doc/mdmr-vignette.html | 26 - man/MDMR-package.Rd | 49 ++- man/X.clust.Rd |only man/Y.clust.Rd |only man/delta.Rd | 17 - man/mdmr.Rd | 16 - man/mixed.mdmr.Rd |only man/print.mixed.mdmr.Rd |only man/summary.mdmr.Rd | 7 man/summary.mixed.mdmr.Rd |only 16 files changed, 716 insertions(+), 91 deletions(-)
Title: Indoor Positioning Fingerprinting Toolset
Description: Algorithms and utility functions for indoor positioning using fingerprinting techniques.
These functions are designed for manipulation of RSSI (Received Signal Strength Intensity) data
sets, estimation of positions,comparison of the performance of different models, and graphical
visualization of data. Machine learning algorithms and methods such as k-nearest neighbors or
probabilistic fingerprinting are implemented in this package to perform analysis
and estimations over RSSI data sets.
Author: Emilio Sansano
Maintainer: Emilio Sansano <esansano@uji.es>
Diff between ipft versions 0.2.8 dated 2017-03-02 and 0.3.1 dated 2017-03-15
DESCRIPTION | 6 - MD5 | 22 +++-- NAMESPACE | 3 R/data.R | 20 +++++ R/ipft.R | 191 +++++++++++++++++++++++++++++++++++++++++----------- data/ipfpwap.rda |only man/ipfCluster.Rd | 7 + man/ipfEstbp.Rd |only man/ipfEstimate.Rd | 4 - man/ipfKnn.Rd | 4 - man/ipfProx.Rd |only man/ipfTransform.Rd | 8 +- man/ipfpwap.Rd |only src/ipf.cpp | 2 14 files changed, 204 insertions(+), 63 deletions(-)
Title: Tools for Electromyogram Signals (EMG) Analysis
Description: Data processing tools to compute the rectified, integrated and the averaged EMG. Routines for automatic detection of activation phases. A routine to compute and plot the ensemble average of the EMG. An EMG signal simulator for general purposes.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>
Diff between biosignalEMG versions 2.0.0 dated 2015-08-05 and 2.0.1 dated 2017-03-15
DESCRIPTION | 10 ++++---- MD5 | 50 +++++++++++++++++++++--------------------- NEWS | 5 ++++ R/onoff_bonato.R | 2 - R/onoff_singlethres.R | 12 ++++++---- man/as.emg.Rd | 2 - man/biosignalEMG-internal.Rd | 3 +- man/biosignalEMG-package.Rd | 4 +-- man/dcbiasremoval.Rd | 2 - man/eaemg.Rd | 2 - man/emg.Rd | 2 - man/envelope.Rd | 2 - man/extractchannel.Rd | 2 - man/highpass.Rd | 2 - man/iemg.Rd | 2 - man/integration.Rd | 2 - man/loadABF1.Rd | 2 - man/movingaverage.Rd | 2 - man/onoff_bonato.Rd | 2 - man/onoff_quality-measures.Rd | 2 - man/onoff_singlethres.Rd | 9 +++++-- man/print.summary.eaemg.Rd | 2 - man/print.summary.emg.Rd | 2 - man/rectification.Rd | 2 - man/syntheticemg.Rd | 2 - man/whitening.Rd | 2 - 26 files changed, 72 insertions(+), 59 deletions(-)
Title: Learning Sparse Bayesian Networks from High-Dimensional Data
Description: Fast methods for learning sparse Bayesian networks from high-dimensional data using sparse regularization, as described in as described in Aragam, Gu, and Zhou (2017) <https://arxiv.org/abs/1703.04025>. Designed to handle mixed experimental and observational data with thousands of variables with either continuous or discrete observations.
Author: Bryon Aragam [aut, cre]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebn versions 0.0.3 dated 2017-03-12 and 0.0.4 dated 2017-03-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 8 +++++++- R/zzz.R | 2 +- inst/CITATION | 24 ++++++++++++++---------- inst/doc/sparsebn-vignette.html | 26 +++++++++++++------------- tests/testthat/Rplots.pdf |binary 7 files changed, 46 insertions(+), 36 deletions(-)
Title: Plotting Methods for 'simmer'
Description: A set of plotting methods for 'simmer' trajectories and
simulations.
Author: Iñaki Ucar [aut, cph, cre],
Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer.plot versions 0.1.8 dated 2017-02-10 and 0.1.9 dated 2017-03-15
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/plot.trajectory.R | 33 +++++++++++++++++++++++++++++---- inst/doc/plot.simmer.html | 12 ++++++------ inst/doc/plot.trajectory.html | 4 ++-- man/plot.trajectory.Rd | 4 +++- tests/testthat/test-plot-trajectory.R | 27 +++++++++++++++++++++++++-- 8 files changed, 85 insertions(+), 26 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3.
Author: Jean-Romain Roussel [aut, cre, cph],
Martin Isenburg [cph] (Is the author of the LASlib and LASzip
libraries),
David Auty [ctb] (Reviewed the documentation),
Pierrick Marie [ctb] (Helped to compile LASlib code in R),
Florian De Boissieu [ctb] (Enable support of .lax file)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between rlas versions 1.1.0 dated 2017-02-05 and 1.1.1 dated 2017-03-15
DESCRIPTION | 10 +-- MD5 | 23 ++++---- NAMESPACE | 2 NEWS.md | 16 +++++- R/readLAS.r | 2 R/writeLAS.r | 70 +++++++++++++++++++-------- README.md | 2 src/LASlib/lasreader_las.cpp | 110 +++++++++++++++++++++---------------------- src/LASlib/laswriter_las.cpp | 33 ++++++------ src/LASzip/laszip.cpp | 3 - src/Makevars | 5 + src/Makevars.win | 5 + src/init.c |only 13 files changed, 162 insertions(+), 119 deletions(-)
Title: Markov Chain Monte Carlo for Potts Models
Description: It does Markov chain Monte Carlo (MCMC) simulation of Potts models
(Potts, 1952, <http://doi.org/10.1017/S0305004100027419>),
which are the multi-color generalization of Ising models
(so, as as special case, also simulates Ising models).
It uses the Swendsen-Wang algorithm (Swendsen and Wang, 1987,
<http://doi.org/10.1103/PhysRevLett.58.86>) so MCMC is fast.
It does maximum composite likelihood estimation of parameters
(Besag, 1975, <http://doi.org/10.2307/2987782>,
Lindsay, 1988, <http://doi.org/10.1090/conm/080>).
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif Johnson
<leif@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between potts versions 0.5-4 dated 2015-07-05 and 0.5-6 dated 2017-03-15
ChangeLog | 2 + DESCRIPTION | 23 ++++++++++----- MD5 | 19 ++++++------ NAMESPACE | 3 +- R/packPotts.R | 13 ++++---- R/potts.R | 18 +++++------- build/vignette.rds |binary inst/doc/cll.pdf |binary src/Makevars |only src/init.c | 36 ++++++++---------------- src/potts.c | 78 +++++++++++++++++++++++++++++------------------------ 11 files changed, 98 insertions(+), 94 deletions(-)
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sst, chla, ocean fronts & bathymetry). Recognized classes and formats include ncdf4, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer
Maintainer: Robert K. Bauer <robert.bauer@ird.fr>
Diff between oceanmap versions 0.0.3 dated 2017-03-08 and 0.0.4 dated 2017-03-15
oceanmap-0.0.3/oceanmap/data/region_definitions.bkp_old.rda |only oceanmap-0.0.4/oceanmap/ChangeLog | 4 oceanmap-0.0.4/oceanmap/DESCRIPTION | 8 oceanmap-0.0.4/oceanmap/MD5 | 63 +-- oceanmap-0.0.4/oceanmap/R/add.region.r | 37 +- oceanmap-0.0.4/oceanmap/R/cust.colorbar.r | 68 ++-- oceanmap-0.0.4/oceanmap/R/figure.r | 9 oceanmap-0.0.4/oceanmap/R/get.bathy.r | 31 + oceanmap-0.0.4/oceanmap/R/get.grid.res.r | 6 oceanmap-0.0.4/oceanmap/R/hidden.r | 78 ++-- oceanmap-0.0.4/oceanmap/R/plotmap.r | 105 +++--- oceanmap-0.0.4/oceanmap/R/regions.r | 2 oceanmap-0.0.4/oceanmap/R/set.colorbar.r | 24 + oceanmap-0.0.4/oceanmap/R/v.gz.r | 2 oceanmap-0.0.4/oceanmap/R/v.plot.r | 28 + oceanmap-0.0.4/oceanmap/R/v.r | 86 ++++- oceanmap-0.0.4/oceanmap/R/v.raster.r | 21 - oceanmap-0.0.4/oceanmap/data/parameter_definitions.rda |binary oceanmap-0.0.4/oceanmap/data/region_definitions.rda |binary oceanmap-0.0.4/oceanmap/inst/doc/oceanmap.pdf |binary oceanmap-0.0.4/oceanmap/inst/test_files/med4_aviso_sla_033d_7d_20020310_20020316.dt.upd.extrac.gz |only oceanmap-0.0.4/oceanmap/inst/test_files/medw4_modis_sst2_4km_1d_20020705_20020705.r2010.0.qual0.Rdata |only oceanmap-0.0.4/oceanmap/man/add.region.Rd | 4 oceanmap-0.0.4/oceanmap/man/cmap.Rd | 11 oceanmap-0.0.4/oceanmap/man/cust.colorbar.Rd | 7 oceanmap-0.0.4/oceanmap/man/figure.Rd | 15 oceanmap-0.0.4/oceanmap/man/get.bathy.Rd | 32 + oceanmap-0.0.4/oceanmap/man/nc2raster.Rd | 23 + oceanmap-0.0.4/oceanmap/man/oceanmap.Rd | 9 oceanmap-0.0.4/oceanmap/man/plotmap.Rd | 86 +++-- oceanmap-0.0.4/oceanmap/man/region_definitions.Rd | 8 oceanmap-0.0.4/oceanmap/man/set.colorbar.Rd | 65 +-- oceanmap-0.0.4/oceanmap/man/v.Rd | 166 +++++++--- oceanmap-0.0.4/oceanmap/man/worldmap.Rd | 5 34 files changed, 666 insertions(+), 337 deletions(-)
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test. The package is based on the publication of Ultsch, A., Thrun, M.C., Hansen-Goos, O., Lotsch, J. (2015) <DOI:10.3390/ijms161025897>.
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Florian Lerch, Jorn Lotsch, Alfred Ultsch
Maintainer: Florian Lerch <lerch@mathematik.uni-marburg.de>
Diff between AdaptGauss versions 1.2.4 dated 2016-06-30 and 1.3.3 dated 2017-03-15
DESCRIPTION | 17 +-- MD5 | 38 ++++---- NAMESPACE | 15 ++- R/AdaptGauss.R | 181 +++++++++++++++++----------------------- R/Bayes4Mixtures.R | 6 - R/Chi2testMixtures.R | 66 ++++++++------ R/EMGauss.R | 78 +++++++++++------ R/KStestMixtures.R | 15 +-- R/LikelihoodRatio4Mixtures.R | 10 +- R/PlotMixtures.R | 47 ++++++---- R/RandomLogGMM.R | 2 R/getOptGauss.R |only R/rsampleAdaptGauss.R |only man/AdaptGauss-package.Rd | 2 man/Chi2testMixtures.Rd | 8 - man/EMGauss.Rd | 5 - man/KStestMixtures.Rd | 3 man/LikelihoodRatio4Mixtures.Rd | 13 ++ man/ParetoDensityEstimation.Rd | 2 man/ParetoRadius.Rd | 2 man/PlotMixtures.Rd | 13 +- 21 files changed, 285 insertions(+), 238 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.1).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre],
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-31 dated 2017-01-23 and 0.4-32 dated 2017-03-15
CHANGELOG | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 44 ++++++++++++++++++++++---------------------- R/associators.R | 17 +++++++++++------ R/attributes.R | 16 ++++++++++------ R/classifiers.R | 17 +++++++++++------ R/clusterers.R | 17 +++++++++++------ R/converters.R | 14 ++++++++------ R/filters.R | 16 ++++++++++------ R/interfaces.R | 3 ++- R/stemmers.R | 7 ++++--- R/tokenizers.R | 7 ++++--- R/utils.R | 5 +++-- R/wow.R | 8 +++++++- R/wpm.R | 11 ++++++++++- R/zzz.R | 10 +++++----- inst/doc/RWeka.R | 26 +++++++++++++------------- inst/doc/RWeka.Rnw | 24 +++++++++++++++--------- inst/doc/RWeka.pdf |binary man/Weka_associators.Rd | 2 +- man/Weka_interfaces.Rd | 17 ++++++++++++----- vignettes/RWeka.Rnw | 24 +++++++++++++++--------- vignettes/RWeka.bib | 10 +++++----- 23 files changed, 187 insertions(+), 119 deletions(-)
Title: Simulate Probabilistic Long-Term Effects in Models with Temporal
Dependence
Description: Calculates and depicts probabilistic long-term effects
in binary models with temporal dependence variables. The package performs
two tasks. First, it calculates the change in the probability of the event
occurring given a change in a theoretical variable. Second, it calculates
the rolling difference in the future probability of the event for two
scenarios: one where the event occurred at a given time and one where the
event does not occur. The package is consistent with the recent movement to
depict meaningful and easy-to-interpret quantities of interest with the
requisite measures of uncertainty. It is the first to make it easy for
researchers to interpret short- and long-term effects of explanatory
variables in binary autoregressive models, which can have important
implications for the correct interpretation of these models.
Author: Christopher Gandrud [aut, cre],
Laron K. Williams [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between pltesim versions 0.1.1 dated 2017-02-23 and 0.1.2 dated 2017-03-15
DESCRIPTION | 23 +++++++++++++++++------ MD5 | 18 ++++++++++++------ NEWS | 11 +++++++++-- R/plot.plte.R | 6 ++++-- R/plte_builder.R | 5 +++++ README.md | 26 ++++++++++++-------------- man/figures |only man/plte_builder.Rd | 6 ++++++ 8 files changed, 65 insertions(+), 30 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation,
data tidying, and working with gene expression data.
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.12 dated 2017-01-22 and 0.1.13 dated 2017-03-15
DESCRIPTION | 12 +++--- MD5 | 88 ++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 4 ++ R/Cs.R |only man/Cs.Rd |only man/Mode.Rd | 1 man/Tcols.Rd | 1 man/Thist.Rd | 1 man/Tmisc.Rd | 1 man/Tpairs.Rd | 1 man/are_all_equal.Rd | 1 man/beep.Rd | 1 man/clean_names.Rd | 1 man/convert_to_NA.Rd | 1 man/corner.Rd | 1 man/counts2fpkm.Rd | 1 man/datename.Rd | 1 man/deseqresult2tbl.Rd | 1 man/dfsigfig.Rd | 1 man/dokuwiki.Rd | 1 man/ellipses.Rd | 1 man/fisherp.Rd | 1 man/gg_na.Rd | 1 man/gghues.Rd | 1 man/grapes-nin-grapes.Rd | 1 man/jsd.Rd | 1 man/lmp.Rd | 1 man/lowestnonzero.Rd | 1 man/lsa.Rd | 1 man/lsp.Rd | 1 man/nn.Rd | 1 man/o.Rd | 1 man/peek.Rd | 1 man/propmiss.Rd | 1 man/quartet.Rd | 1 man/read.cb.Rd | 1 man/registration.Rd | 1 man/remove_empty_cols.Rd | 1 man/remove_empty_rows.Rd | 1 man/rownames_to_symprobe.Rd | 1 man/saveit.Rd | 1 man/sicb.Rd | 1 man/strSort.Rd | 1 man/unfactor.Rd | 1 man/unrowname.Rd | 1 46 files changed, 56 insertions(+), 89 deletions(-)
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>
Diff between PopGenome versions 2.2.0 dated 2017-02-11 and 2.2.2 dated 2017-03-15
DESCRIPTION | 10 MD5 | 28 NAMESPACE | 3 NEWS | 10 build/vignette.rds |binary inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary inst/doc/Integration_of_new_Methods.pdf |binary inst/doc/Whole_genome_analyses_using_VCF_files.pdf | 961 +++++++++--------- src/Makevars | 5 src/Makevars.win | 4 src/PopGenome-win.def |only src/init.c |only src/tabix/bgzf.c | 135 +- src/tabix/bgzf.h | 13 src/tabix/bgzf_bak.c |only src/tabix/bgzf_bak.h |only src/whopgenome/whop_rsupport.h | 4 17 files changed, 603 insertions(+), 570 deletions(-)
Title: Dynamic Trees for Learning and Design
Description: Inference by sequential Monte Carlo for
dynamic tree regression and classification models
with hooks provided for sequential design and optimization,
fully online learning with drift, variable selection, and
sensitivity analysis of inputs. Illustrative
examples from the original dynamic trees paper are facilitated
by demos in the package; see demo(package="dynaTree").
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>, Matt A. Taddy <taddy@chicagobooth.edu> and Christoforos Anagnostopoulos <christoforos.anagnostopoulos06@imperial.ac.uk>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between dynaTree versions 1.2-9 dated 2016-06-06 and 1.2-10 dated 2017-03-15
ChangeLog | 7 +++++++ DESCRIPTION | 14 ++++++-------- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 2 +- man/alcX.dynaTree.Rd | 2 +- man/deletecloud.Rd | 2 +- man/dynaTree-class.Rd | 2 +- man/dynaTree-package.Rd | 2 +- man/dynaTree.Rd | 2 +- man/getBF.Rd | 2 +- man/plot.dynaTree.Rd | 2 +- man/predict.dynaTree.Rd | 2 +- man/rejuvenate.dynaTree.Rd | 2 +- man/relevance.dynaTree.Rd | 2 +- man/retire.dynaTree.Rd | 2 +- man/sens.dynaTree.Rd | 2 +- man/update.dynaTree.Rd | 2 +- man/varpropuse.Rd | 2 +- src/init.c |only src/particle.cc | 6 +++--- 20 files changed, 50 insertions(+), 44 deletions(-)
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Description: Complementary multivariate analysis to the Outlying Mean Index
analysis to explore niche shift of a community and biological constraint within an Euclidean space, with
graphical displays.
Author: Stephane Karasiewicz
Maintainer: Stephane Karasiewicz <stephane.karasiewicz@wanadoo.fr>
Diff between subniche versions 0.9.2 dated 2017-02-03 and 0.9.3 dated 2017-03-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/subniche.R | 24 ++++++++++++------------ man/sep.factor.row.Rd | 1 - man/subniche.Rd | 48 +++++++++++++++++++++++++++++------------------- 5 files changed, 50 insertions(+), 41 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo',
and several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.3-4 dated 2016-09-13 and 0.3-5 dated 2017-03-15
mitml-0.3-4/mitml/R/mitmlCast.R |only mitml-0.3-4/mitml/man/with.mitml.Rd |only mitml-0.3-5/mitml/DESCRIPTION | 12 +- mitml-0.3-5/mitml/MD5 | 57 +++++++----- mitml-0.3-5/mitml/NAMESPACE | 14 ++- mitml-0.3-5/mitml/NEWS | 31 ++++++ mitml-0.3-5/mitml/R/amelia2mitml.list.R |only mitml-0.3-5/mitml/R/c.mitml.list.R |only mitml-0.3-5/mitml/R/cbind.mitml.list.R |only mitml-0.3-5/mitml/R/internal-getCOEF.R | 25 ++++- mitml-0.3-5/mitml/R/internal-getVC.R | 132 ++++++++++++++++++++++------- mitml-0.3-5/mitml/R/mitmlComplete.R | 4 mitml-0.3-5/mitml/R/rbind.mitml.list.R |only mitml-0.3-5/mitml/R/sort.mitml.list.R |only mitml-0.3-5/mitml/R/subset.mitml.list.R |only mitml-0.3-5/mitml/R/testConstraints.R | 9 + mitml-0.3-5/mitml/R/testEstimates.R | 28 ++++-- mitml-0.3-5/mitml/R/testModels.R | 18 ++- mitml-0.3-5/mitml/R/within.mitml.list.R | 3 mitml-0.3-5/mitml/R/zzz.R | 2 mitml-0.3-5/mitml/README.md | 14 +-- mitml-0.3-5/mitml/build |only mitml-0.3-5/mitml/data/justice.rda |binary mitml-0.3-5/mitml/inst |only mitml-0.3-5/mitml/man/amelia2mitml.list.Rd |only mitml-0.3-5/mitml/man/c.mitml.list.Rd |only mitml-0.3-5/mitml/man/justice.Rd | 4 mitml-0.3-5/mitml/man/long2mitml.list.Rd | 3 mitml-0.3-5/mitml/man/mitml-package.Rd | 5 - mitml-0.3-5/mitml/man/sort.mitml.list.Rd |only mitml-0.3-5/mitml/man/subset.mitml.list.Rd |only mitml-0.3-5/mitml/man/testConstraints.Rd | 2 mitml-0.3-5/mitml/man/testEstimates.Rd | 2 mitml-0.3-5/mitml/man/testModels.Rd | 3 mitml-0.3-5/mitml/man/with.mitml.list.Rd |only mitml-0.3-5/mitml/vignettes |only 36 files changed, 279 insertions(+), 89 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 2.0.19 dated 2015-09-04 and 3.0.0 dated 2017-03-15
kohonen-2.0.19/kohonen/R/bdk.R |only kohonen-2.0.19/kohonen/R/topo.R |only kohonen-2.0.19/kohonen/inst/doc/kohonen-manual.pdf |only kohonen-2.0.19/kohonen/man/bdk.Rd |only kohonen-2.0.19/kohonen/man/som.Rd |only kohonen-2.0.19/kohonen/man/topo.error.Rd |only kohonen-2.0.19/kohonen/man/xyf.Rd |only kohonen-2.0.19/kohonen/src/bdk.c |only kohonen-2.0.19/kohonen/src/map.c |only kohonen-2.0.19/kohonen/src/som.c |only kohonen-2.0.19/kohonen/src/supersom.c |only kohonen-2.0.19/kohonen/src/xyf.c |only kohonen-3.0.0/kohonen/DESCRIPTION | 16 kohonen-3.0.0/kohonen/MD5 | 98 +- kohonen-3.0.0/kohonen/NAMESPACE | 15 kohonen-3.0.0/kohonen/NEWS | 20 kohonen-3.0.0/kohonen/R/Obsolete |only kohonen-3.0.0/kohonen/R/RcppExports.R |only kohonen-3.0.0/kohonen/R/check.data.R |only kohonen-3.0.0/kohonen/R/check.whatmap.R | 33 kohonen-3.0.0/kohonen/R/classvec2classmat.R | 4 kohonen-3.0.0/kohonen/R/expandMap.R |only kohonen-3.0.0/kohonen/R/getCodes.R |only kohonen-3.0.0/kohonen/R/getDistancePointers.R |only kohonen-3.0.0/kohonen/R/map.R | 186 +--- kohonen-3.0.0/kohonen/R/object.distances.R |only kohonen-3.0.0/kohonen/R/plot.kohonen.R | 508 ++++++----- kohonen-3.0.0/kohonen/R/predict.kohonen.R | 283 +++--- kohonen-3.0.0/kohonen/R/som.R | 72 - kohonen-3.0.0/kohonen/R/somgrid.R |only kohonen-3.0.0/kohonen/R/summary.R | 53 - kohonen-3.0.0/kohonen/R/supersom.R | 399 +++++--- kohonen-3.0.0/kohonen/R/unit.distances.R | 10 kohonen-3.0.0/kohonen/R/xyf.R | 126 -- kohonen-3.0.0/kohonen/build |only kohonen-3.0.0/kohonen/data/degelder.rda |only kohonen-3.0.0/kohonen/data/wines.rda |binary kohonen-3.0.0/kohonen/inst/doc/custom-distance-function.R |only kohonen-3.0.0/kohonen/inst/doc/custom-distance-function.Rmd |only kohonen-3.0.0/kohonen/inst/doc/custom-distance-function.html |only kohonen-3.0.0/kohonen/inst/doc/kohonen-manual_2007.pdf |only kohonen-3.0.0/kohonen/inst/doc/som-rgb-example.R |only kohonen-3.0.0/kohonen/inst/doc/som-rgb-example.Rmd |only kohonen-3.0.0/kohonen/inst/doc/som-rgb-example.html |only kohonen-3.0.0/kohonen/man/check.whatmap.Rd | 12 kohonen-3.0.0/kohonen/man/classvec2classmat.Rd | 13 kohonen-3.0.0/kohonen/man/degelder.Rd |only kohonen-3.0.0/kohonen/man/expandMap.Rd |only kohonen-3.0.0/kohonen/man/getCodes.Rd |only kohonen-3.0.0/kohonen/man/map.kohonen.Rd | 41 kohonen-3.0.0/kohonen/man/nir.Rd | 28 kohonen-3.0.0/kohonen/man/object.distances.Rd |only kohonen-3.0.0/kohonen/man/plot.kohonen.Rd | 82 - kohonen-3.0.0/kohonen/man/predict.kohonen.Rd | 218 ++-- kohonen-3.0.0/kohonen/man/summary.Rd | 5 kohonen-3.0.0/kohonen/man/supersom.Rd | 141 ++- kohonen-3.0.0/kohonen/man/unit.distances.Rd | 64 - kohonen-3.0.0/kohonen/man/wines.Rd | 5 kohonen-3.0.0/kohonen/src/Makevars |only kohonen-3.0.0/kohonen/src/RcppExports.cpp |only kohonen-3.0.0/kohonen/src/batch-supersom.cpp |only kohonen-3.0.0/kohonen/src/distance-functions.cpp |only kohonen-3.0.0/kohonen/src/distance-functions.h |only kohonen-3.0.0/kohonen/src/kohonen_init.c |only kohonen-3.0.0/kohonen/src/kohonen_types.h |only kohonen-3.0.0/kohonen/src/map.cpp |only kohonen-3.0.0/kohonen/src/neighbourhood-functions.cpp |only kohonen-3.0.0/kohonen/src/neighbourhood-functions.h |only kohonen-3.0.0/kohonen/src/pbatch-supersom.cpp |only kohonen-3.0.0/kohonen/src/supersom.cpp |only kohonen-3.0.0/kohonen/vignettes |only 71 files changed, 1255 insertions(+), 1177 deletions(-)
Title: Bibliometric and Co-Citation Analysis Tool
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>) and
Thomson Reuters' ISI Web of Knowledge (<http://www.webofknowledge.com/>) databases, performing bibliometric analysis
and building data matrices for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 1.4 dated 2017-01-24 and 1.5 dated 2017-03-15
DESCRIPTION | 10 - MD5 | 66 ++++----- NAMESPACE | 7 NEWS | 13 + R/Hindex.R | 23 ++- R/biblioAnalysis.R | 4 R/biblioNetwork.R | 26 --- R/conceptualStructure.R | 7 R/convert2df.R | 8 - R/histNetwork.R | 32 ---- R/histPlot.R | 12 + R/idByAuthor.R |only R/isi2df.R | 2 R/isibib2df.R | 2 R/keywordGrowth.R | 15 +- R/metaTagExtraction.R | 11 + R/networkPlot.R | 15 +- R/retrievalByAuthorID.R |only R/scopus2df.R | 2 R/summary.bibliometrix.R | 4 R/termExtraction.R | 1 build/vignette.rds |binary inst/doc/bibliometrix-vignette.R | 5 inst/doc/bibliometrix-vignette.Rmd | 7 inst/doc/bibliometrix-vignette.html | 262 +++++++++++++++++------------------- man/Hindex.Rd | 4 man/KeywordGrowth.Rd | 10 - man/biblioNetwork.Rd | 26 --- man/conceptualStructure.Rd | 6 man/histNetwork.Rd | 20 -- man/histPlot.Rd | 4 man/idByAuthor.Rd |only man/metaTagExtraction.Rd | 2 man/networkPlot.Rd | 7 man/retrievalByAuthorID.Rd |only vignettes/bibliometrix-vignette.Rmd | 7 36 files changed, 311 insertions(+), 309 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.3 dated 2017-02-01 and 0.2.3.1 dated 2017-03-15
DESCRIPTION | 8 +++--- MD5 | 55 +++++++++++++++++++++++----------------------- NAMESPACE | 2 - NEWS.md | 7 +++++ R/DoubleMetaphone.R | 2 - build/vignette.rds |binary inst/doc/Introduction.pdf |binary man/AddProbDup.Rd | 1 man/DataClean.Rd | 1 man/DisProbDup.Rd | 1 man/DoubleMetaphone.Rd | 2 - man/GN1000.Rd | 1 man/KWCounts.Rd | 1 man/KWIC.Rd | 1 man/MergeKW.Rd | 1 man/MergeProbDup.Rd | 1 man/PGRdup-package.Rd | 3 -- man/ParseProbDup.Rd | 1 man/ProbDup.Rd | 1 man/ReconstructProbDup.Rd | 1 man/ReviewProbDup.Rd | 1 man/SplitProbDup.Rd | 1 man/ValidatePrimKey.Rd | 1 man/ViewProbDup.Rd | 1 man/print.KWIC.Rd | 1 man/print.ProbDup.Rd | 1 man/read.genesys.Rd | 1 src/double_metaphone.h | 1 src/register.c |only 29 files changed, 44 insertions(+), 54 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between aster versions 0.9 dated 2017-03-12 and 0.9.1 dated 2017-03-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/init.c | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
Description: Test in mixed effects models. Attention is on mixed effects models
as implemented in the 'lme4' package. This package implements a parametric
bootstrap test and a Kenward Roger modification of F-tests for linear mixed
effects models and a parametric bootstrap test for generalized linear mixed
models.
Author: Ulrich Halekoh <uhalekoh@health.sdu.dk> Søren Højsgaard
<sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between pbkrtest versions 0.4-6 dated 2016-01-27 and 0.4-7 dated 2017-03-15
pbkrtest-0.4-6/pbkrtest/R/PB-anova.R |only pbkrtest-0.4-6/pbkrtest/data/beets.txt.gz |only pbkrtest-0.4-6/pbkrtest/data/budworm.txt.gz |only pbkrtest-0.4-6/pbkrtest/man/DATA-beets.Rd |only pbkrtest-0.4-6/pbkrtest/man/DATA-budworm.Rd |only pbkrtest-0.4-6/pbkrtest/man/KRmodcomp.Rd |only pbkrtest-0.4-6/pbkrtest/man/PBmodcomp.Rd |only pbkrtest-0.4-6/pbkrtest/man/PBrefdist.Rd |only pbkrtest-0.4-6/pbkrtest/man/getKR.Rd |only pbkrtest-0.4-6/pbkrtest/man/model2restrictionMatrix.Rd |only pbkrtest-0.4-6/pbkrtest/man/vcovAdj.Rd |only pbkrtest-0.4-7/pbkrtest/ChangeLog | 382 ++++---- pbkrtest-0.4-7/pbkrtest/DESCRIPTION | 28 pbkrtest-0.4-7/pbkrtest/MD5 | 64 - pbkrtest-0.4-7/pbkrtest/R/KR-linearAlgebra.R | 10 pbkrtest-0.4-7/pbkrtest/R/KR-modcomp.R | 220 +++- pbkrtest-0.4-7/pbkrtest/R/KR-vcovAdj.R | 69 + pbkrtest-0.4-7/pbkrtest/R/KR-vcovAdj16.R | 112 ++ pbkrtest-0.4-7/pbkrtest/R/PB-modcomp.R | 196 ++++ pbkrtest-0.4-7/pbkrtest/R/PB-refdist.R | 66 + pbkrtest-0.4-7/pbkrtest/R/PB-utils.R | 8 pbkrtest-0.4-7/pbkrtest/R/data-beets.R |only pbkrtest-0.4-7/pbkrtest/R/data-budworm.R |only pbkrtest-0.4-7/pbkrtest/R/getKR.R | 30 pbkrtest-0.4-7/pbkrtest/R/get_ddf_Lb.R | 159 ++- pbkrtest-0.4-7/pbkrtest/R/modelCoercion.R | 171 ++- pbkrtest-0.4-7/pbkrtest/R/pbkrtest-package.R |only pbkrtest-0.4-7/pbkrtest/R/zzz-PB-anova-not-used.R |only pbkrtest-0.4-7/pbkrtest/README.md |only pbkrtest-0.4-7/pbkrtest/build/vignette.rds |binary pbkrtest-0.4-7/pbkrtest/data/beets.RData |only pbkrtest-0.4-7/pbkrtest/data/budworm.RData |only pbkrtest-0.4-7/pbkrtest/inst/CITATION | 40 pbkrtest-0.4-7/pbkrtest/inst/doc/pbkrtest-introduction.Rnw | 530 ++++++------ pbkrtest-0.4-7/pbkrtest/inst/doc/pbkrtest-introduction.pdf |binary pbkrtest-0.4-7/pbkrtest/man/data-beets.Rd |only pbkrtest-0.4-7/pbkrtest/man/data-budworm.Rd |only pbkrtest-0.4-7/pbkrtest/man/get_ddf_Lb.Rd | 165 +-- pbkrtest-0.4-7/pbkrtest/man/getkr.Rd |only pbkrtest-0.4-7/pbkrtest/man/kr-modcomp.Rd |only pbkrtest-0.4-7/pbkrtest/man/kr-vcov.Rd |only pbkrtest-0.4-7/pbkrtest/man/model-coerce.Rd |only pbkrtest-0.4-7/pbkrtest/man/pb-modcomp.Rd |only pbkrtest-0.4-7/pbkrtest/man/pb-refdist.Rd |only pbkrtest-0.4-7/pbkrtest/man/pbkrtest-internal.Rd | 12 pbkrtest-0.4-7/pbkrtest/vignettes/pbkrtest-introduction.Rnw | 530 ++++++------ 46 files changed, 1734 insertions(+), 1058 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Lars Kotthoff [aut],
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut],
Mason Gallo [aut],
Jakob Bossek [ctb],
Erich Studerus [ctb],
Leonard Judt [ctb],
Tobias Kuehn [ctb],
Pascal Kerschke [ctb],
Florian Fendt [ctb],
Philipp Probst [ctb],
Xudong Sun [ctb],
Janek Thomas [ctb],
Bruno Vieira [ctb],
Laura Beggel [ctb],
Quay Au [ctb],
Martin Binder [ctb],
Florian Pfisterer [ctb],
Stefan Coors [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.10 dated 2017-02-07 and 2.11 dated 2017-03-15
mlr-2.10/mlr/R/RLearner_classif_avNNet.R |only mlr-2.10/mlr/R/RLearner_regr_avNNet.R |only mlr-2.10/mlr/R/isFailureModel.R |only mlr-2.10/mlr/tests/testthat/test_classif_avNNet.R |only mlr-2.10/mlr/tests/testthat/test_regr_avNNet.R |only mlr-2.11/mlr/DESCRIPTION | 58 mlr-2.11/mlr/MD5 | 682 +++++----- mlr-2.11/mlr/NAMESPACE | 70 - mlr-2.11/mlr/NEWS.md | 46 mlr-2.11/mlr/R/BaggingWrapper.R | 34 mlr-2.11/mlr/R/BaseWrapper.R | 7 mlr-2.11/mlr/R/BenchmarkResult_operators.R | 80 - mlr-2.11/mlr/R/ClassifTask.R | 13 mlr-2.11/mlr/R/ClusterTask.R | 8 mlr-2.11/mlr/R/ConstantClassWrapper.R | 2 mlr-2.11/mlr/R/CostSensClassifWrapper.R | 2 mlr-2.11/mlr/R/CostSensRegrWrapper.R | 23 mlr-2.11/mlr/R/CostSensTask.R | 12 mlr-2.11/mlr/R/CostSensWeightedPairsWrapper.R | 2 mlr-2.11/mlr/R/DummyFeaturesWrapper.R |only mlr-2.11/mlr/R/FailureModel.R | 10 mlr-2.11/mlr/R/FeatSelControl.R | 16 mlr-2.11/mlr/R/FeatSelControlExhaustive.R | 2 mlr-2.11/mlr/R/FeatSelControlGA.R | 2 mlr-2.11/mlr/R/FeatSelControlRandom.R | 2 mlr-2.11/mlr/R/FeatSelControlSequential.R | 2 mlr-2.11/mlr/R/Filter.R | 32 mlr-2.11/mlr/R/FilterWrapper.R | 14 mlr-2.11/mlr/R/HomogeneousEnsemble.R | 9 mlr-2.11/mlr/R/Impute.R | 15 mlr-2.11/mlr/R/ImputeMethods.R | 6 mlr-2.11/mlr/R/Learner_properties.R | 25 mlr-2.11/mlr/R/Measure.R | 1 mlr-2.11/mlr/R/Measure_properties.R |only mlr-2.11/mlr/R/ModelMultiplexer.R | 3 mlr-2.11/mlr/R/MulticlassWrapper.R | 27 mlr-2.11/mlr/R/MultilabelBinaryRelevanceWrapper.R | 24 mlr-2.11/mlr/R/MultilabelTask.R | 10 mlr-2.11/mlr/R/OptControl.R | 4 mlr-2.11/mlr/R/OverBaggingWrapper.R | 15 mlr-2.11/mlr/R/Prediction.R | 34 mlr-2.11/mlr/R/Prediction_operators.R | 15 mlr-2.11/mlr/R/RLearner.R | 2 mlr-2.11/mlr/R/RLearner_classif_C50.R | 21 mlr-2.11/mlr/R/RLearner_classif_bartMachine.R | 4 mlr-2.11/mlr/R/RLearner_classif_binomial.R | 7 mlr-2.11/mlr/R/RLearner_classif_blackboost.R | 2 mlr-2.11/mlr/R/RLearner_classif_cforest.R | 3 mlr-2.11/mlr/R/RLearner_classif_cvglmnet.R | 15 mlr-2.11/mlr/R/RLearner_classif_earth.R | 22 mlr-2.11/mlr/R/RLearner_classif_gamboost.R | 4 mlr-2.11/mlr/R/RLearner_classif_gbm.R | 2 mlr-2.11/mlr/R/RLearner_classif_glmboost.R | 4 mlr-2.11/mlr/R/RLearner_classif_glmnet.R | 17 mlr-2.11/mlr/R/RLearner_classif_h2ogbm.R | 2 mlr-2.11/mlr/R/RLearner_classif_kknn.R | 2 mlr-2.11/mlr/R/RLearner_classif_logreg.R | 11 mlr-2.11/mlr/R/RLearner_classif_multinom.R | 5 mlr-2.11/mlr/R/RLearner_classif_nnet.R | 5 mlr-2.11/mlr/R/RLearner_classif_plsdaCaret.R | 6 mlr-2.11/mlr/R/RLearner_classif_probit.R | 11 mlr-2.11/mlr/R/RLearner_classif_rFerns.R | 7 mlr-2.11/mlr/R/RLearner_classif_randomForest.R | 11 mlr-2.11/mlr/R/RLearner_classif_randomForestSRC.R | 12 mlr-2.11/mlr/R/RLearner_classif_ranger.R | 7 mlr-2.11/mlr/R/RLearner_classif_rda.R | 4 mlr-2.11/mlr/R/RLearner_classif_rknn.R | 4 mlr-2.11/mlr/R/RLearner_classif_xgboost.R | 14 mlr-2.11/mlr/R/RLearner_multilabel_cforest.R | 14 mlr-2.11/mlr/R/RLearner_regr_cforest.R | 16 mlr-2.11/mlr/R/RLearner_regr_cvglmnet.R | 13 mlr-2.11/mlr/R/RLearner_regr_earth.R | 3 mlr-2.11/mlr/R/RLearner_regr_gamboost.R | 4 mlr-2.11/mlr/R/RLearner_regr_glm.R | 5 mlr-2.11/mlr/R/RLearner_regr_glmnet.R | 12 mlr-2.11/mlr/R/RLearner_regr_kknn.R | 2 mlr-2.11/mlr/R/RLearner_regr_nnet.R | 5 mlr-2.11/mlr/R/RLearner_regr_randomForest.R | 178 +- mlr-2.11/mlr/R/RLearner_regr_randomForestSRC.R | 6 mlr-2.11/mlr/R/RLearner_regr_ranger.R | 7 mlr-2.11/mlr/R/RLearner_regr_xgboost.R | 6 mlr-2.11/mlr/R/RLearner_surv_cforest.R | 3 mlr-2.11/mlr/R/RLearner_surv_cvglmnet.R | 1 mlr-2.11/mlr/R/RLearner_surv_gamboost.R | 4 mlr-2.11/mlr/R/RLearner_surv_glmnet.R | 9 mlr-2.11/mlr/R/RLearner_surv_randomForestSRC.R | 7 mlr-2.11/mlr/R/RegrTask.R | 6 mlr-2.11/mlr/R/RemoveConstantFeaturesWrapper.R | 2 mlr-2.11/mlr/R/ResampleInstance.R | 2 mlr-2.11/mlr/R/ResamplePrediction.R | 2 mlr-2.11/mlr/R/ResampleResult.R | 10 mlr-2.11/mlr/R/ResampleResult_operators.R | 40 mlr-2.11/mlr/R/StackedLearner.R | 6 mlr-2.11/mlr/R/SurvTask.R | 8 mlr-2.11/mlr/R/Task.R | 7 mlr-2.11/mlr/R/TaskDesc.R | 22 mlr-2.11/mlr/R/Task_operators.R | 95 - mlr-2.11/mlr/R/TuneControl.R | 71 - mlr-2.11/mlr/R/TuneControlCMAES.R | 21 mlr-2.11/mlr/R/TuneControlDesign.R | 20 mlr-2.11/mlr/R/TuneControlGenSA.R | 20 mlr-2.11/mlr/R/TuneControlGrid.R | 18 mlr-2.11/mlr/R/TuneControlIrace.R | 27 mlr-2.11/mlr/R/TuneControlMBO.R | 74 - mlr-2.11/mlr/R/TuneControlRandom.R | 16 mlr-2.11/mlr/R/TuneMultiCritControl.R | 6 mlr-2.11/mlr/R/TuneMultiCritControlGrid.R | 8 mlr-2.11/mlr/R/TuneMultiCritControlNSGA2.R | 2 mlr-2.11/mlr/R/TuneMultiCritControlRandom.R | 2 mlr-2.11/mlr/R/TuneResult.R | 5 mlr-2.11/mlr/R/WeightedClassesWrapper.R | 4 mlr-2.11/mlr/R/WrappedModel.R | 28 mlr-2.11/mlr/R/batchmark.R |only mlr-2.11/mlr/R/benchmark.R | 51 mlr-2.11/mlr/R/benchmark_helpers.R |only mlr-2.11/mlr/R/calculateConfusionMatrix.R | 9 mlr-2.11/mlr/R/checkLearner.R | 6 mlr-2.11/mlr/R/checkLearnerBeforeTrain.R | 2 mlr-2.11/mlr/R/checkTaskSubset.R |only mlr-2.11/mlr/R/configureMlr.R | 29 mlr-2.11/mlr/R/createDummyFeatures.R | 9 mlr-2.11/mlr/R/evalOptimizationState.R | 29 mlr-2.11/mlr/R/generateFeatureImportance.R | 2 mlr-2.11/mlr/R/generateFilterValues.R | 27 mlr-2.11/mlr/R/generateLearningCurve.R | 2 mlr-2.11/mlr/R/generatePartialDependence.R | 17 mlr-2.11/mlr/R/getFeatureImportance.R | 2 mlr-2.11/mlr/R/getOOBPreds.R |only mlr-2.11/mlr/R/helpers.R | 22 mlr-2.11/mlr/R/listLearners.R | 22 mlr-2.11/mlr/R/listMeasures.R | 4 mlr-2.11/mlr/R/logFunOpt.R | 40 mlr-2.11/mlr/R/makeLearners.R | 2 mlr-2.11/mlr/R/measures.R | 97 + mlr-2.11/mlr/R/parallelization.R |only mlr-2.11/mlr/R/performance.R | 19 mlr-2.11/mlr/R/plotBMRBoxplots.R | 2 mlr-2.11/mlr/R/plotBMRRanksAsBarChart.R | 1 mlr-2.11/mlr/R/plotBMRSummary.R | 4 mlr-2.11/mlr/R/plotLearnerPrediction.R | 2 mlr-2.11/mlr/R/plotResiduals.R | 12 mlr-2.11/mlr/R/predict.R | 25 mlr-2.11/mlr/R/removeConstantFeatures.R | 2 mlr-2.11/mlr/R/resample.R | 42 mlr-2.11/mlr/R/selectFeatures.R | 3 mlr-2.11/mlr/R/selectFeaturesSequential.R | 2 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mlr-2.11/mlr/tests/testthat/test_base_SupervisedTask.R | 12 mlr-2.11/mlr/tests/testthat/test_base_TaskDesc.R | 14 mlr-2.11/mlr/tests/testthat/test_base_TuneWrapper.R | 2 mlr-2.11/mlr/tests/testthat/test_base_UnsupervisedTask.R | 6 mlr-2.11/mlr/tests/testthat/test_base_benchmark.R | 42 mlr-2.11/mlr/tests/testthat/test_base_blocking.R | 2 mlr-2.11/mlr/tests/testthat/test_base_calculateConfusionMatrix.R | 40 mlr-2.11/mlr/tests/testthat/test_base_checkTaskSubset.R |only mlr-2.11/mlr/tests/testthat/test_base_configureMlr.R | 4 mlr-2.11/mlr/tests/testthat/test_base_debugdump.R |only mlr-2.11/mlr/tests/testthat/test_base_generateFilterValuesData.R | 34 mlr-2.11/mlr/tests/testthat/test_base_generatePartialDependence.R | 9 mlr-2.11/mlr/tests/testthat/test_base_getOOBPreds.R |only mlr-2.11/mlr/tests/testthat/test_base_getTaskData.R | 2 mlr-2.11/mlr/tests/testthat/test_base_helpers.R | 24 mlr-2.11/mlr/tests/testthat/test_base_imbal_weightedclasses.R | 2 mlr-2.11/mlr/tests/testthat/test_base_impute.R | 12 mlr-2.11/mlr/tests/testthat/test_base_listLearners.R | 9 mlr-2.11/mlr/tests/testthat/test_base_measures.R | 114 + mlr-2.11/mlr/tests/testthat/test_base_orderedfactors.R | 2 mlr-2.11/mlr/tests/testthat/test_base_performance.R | 28 mlr-2.11/mlr/tests/testthat/test_base_plotBMRBoxplots.R | 9 mlr-2.11/mlr/tests/testthat/test_base_plotBMRRanksAsBarChart.R | 8 mlr-2.11/mlr/tests/testthat/test_base_plotBMRSummary.R | 9 mlr-2.11/mlr/tests/testthat/test_base_plotResiduals.R | 9 mlr-2.11/mlr/tests/testthat/test_base_plotViperCharts.R | 1 mlr-2.11/mlr/tests/testthat/test_base_predict.R | 8 mlr-2.11/mlr/tests/testthat/test_base_resample.R | 6 mlr-2.11/mlr/tests/testthat/test_base_resample_operators.R | 4 mlr-2.11/mlr/tests/testthat/test_base_simplifyMeasureNames.R |only mlr-2.11/mlr/tests/testthat/test_base_tuning.R | 12 mlr-2.11/mlr/tests/testthat/test_batchmark.R |only mlr-2.11/mlr/tests/testthat/test_classif_C50.R | 22 mlr-2.11/mlr/tests/testthat/test_classif_blackboost.R | 2 mlr-2.11/mlr/tests/testthat/test_classif_cvglmnet.R | 4 mlr-2.11/mlr/tests/testthat/test_classif_gbm.R | 2 mlr-2.11/mlr/tests/testthat/test_classif_glmnet.R | 9 mlr-2.11/mlr/tests/testthat/test_classif_plsdaCaret.R | 3 mlr-2.11/mlr/tests/testthat/test_learners_all_classif.R | 10 mlr-2.11/mlr/tests/testthat/test_learners_all_regr.R | 3 mlr-2.11/mlr/tests/testthat/test_learners_all_surv.R | 4 mlr-2.11/mlr/tests/testthat/test_learners_classiflabelswitch.R | 12 mlr-2.11/mlr/tests/testthat/test_parallel_all.R | 52 mlr-2.11/mlr/tests/testthat/test_regr_bgp.R | 10 mlr-2.11/mlr/tests/testthat/test_regr_bgpllm.R | 10 mlr-2.11/mlr/tests/testthat/test_regr_blm.R | 8 mlr-2.11/mlr/tests/testthat/test_regr_cvglmnet.R | 5 mlr-2.11/mlr/tests/testthat/test_regr_glmnet.R | 9 mlr-2.11/mlr/tests/testthat/test_regr_km.R | 10 mlr-2.11/mlr/tests/testthat/test_regr_laGP.R | 12 mlr-2.11/mlr/tests/testthat/test_regr_randomForest.R | 30 mlr-2.11/mlr/tests/testthat/test_regr_xgboost.R | 10 mlr-2.11/mlr/tests/testthat/test_stack.R | 2 mlr-2.11/mlr/tests/testthat/test_surv_glmnet.R | 5 mlr-2.11/mlr/tests/testthat/test_tuneParams.R | 57 mlr-2.11/mlr/tests/testthat/test_tune_ModelMultiplexer.R | 5 mlr-2.11/mlr/tests/testthat/test_tune_tuneMBO.R | 66 mlr-2.11/mlr/tests/testthat/test_tune_tuneParamsMultiCrit.R | 28 365 files changed, 3068 insertions(+), 1652 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph], Michael Hahsler [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.0.2 dated 2016-10-05 and 1.1.0 dated 2017-03-15
arulesCBA-1.0.2/arulesCBA/R/classifier.R |only arulesCBA-1.0.2/arulesCBA/man/classifier.Rd |only arulesCBA-1.0.2/arulesCBA/src/classify.c |only arulesCBA-1.1.0/arulesCBA/DESCRIPTION | 15 +- arulesCBA-1.1.0/arulesCBA/MD5 | 39 +++--- arulesCBA-1.1.0/arulesCBA/NAMESPACE | 5 arulesCBA-1.1.0/arulesCBA/R/CBA.R |only arulesCBA-1.1.0/arulesCBA/R/CBAInternal.R |only arulesCBA-1.1.0/arulesCBA/R/CBA_ruleset.R |only arulesCBA-1.1.0/arulesCBA/R/bCBA.R |only arulesCBA-1.1.0/arulesCBA/R/factorize.R |only arulesCBA-1.1.0/arulesCBA/R/predict.R | 135 ++++++++++++++++++---- arulesCBA-1.1.0/arulesCBA/R/print.R | 17 +- arulesCBA-1.1.0/arulesCBA/README.md | 11 + arulesCBA-1.1.0/arulesCBA/build/vignette.rds |binary arulesCBA-1.1.0/arulesCBA/inst/doc/arulesCBA.R | 4 arulesCBA-1.1.0/arulesCBA/inst/doc/arulesCBA.pdf |binary arulesCBA-1.1.0/arulesCBA/inst/doc/arulesCBA.rnw | 32 ++--- arulesCBA-1.1.0/arulesCBA/man/CBA.Rd |only arulesCBA-1.1.0/arulesCBA/man/CBA_ruleset.Rd |only arulesCBA-1.1.0/arulesCBA/man/predict.Rd | 16 +- arulesCBA-1.1.0/arulesCBA/man/rules.Rd | 5 arulesCBA-1.1.0/arulesCBA/src/cba.c |only arulesCBA-1.1.0/arulesCBA/src/dll.c |only arulesCBA-1.1.0/arulesCBA/src/weighted.c |only arulesCBA-1.1.0/arulesCBA/tests/testthat/tests.R | 14 -- arulesCBA-1.1.0/arulesCBA/vignettes/arulesCBA.rnw | 32 ++--- 27 files changed, 214 insertions(+), 111 deletions(-)
Title: Automatic Item Generator
Description: A collection of Automatic Item Generators used mainly for
psychological research. This package can generate linear syllogistic reasoning,
arithmetic and 2D/3D spatial reasoning items. It is recommended for research
purpose only.
Author: Bao Sheng Loe (Aiden)
Maintainer: Bao Sheng Loe (Aiden) <bsl28@cam.ac.uk>
Diff between AIG versions 0.1.2 dated 2017-03-05 and 0.1.3 dated 2017-03-15
DESCRIPTION | 15 ++++++++------ MD5 | 16 +++++++-------- R/lisy.R | 50 ++++++++++++++++++++++++++++++------------------ man/AIG.Rd | 2 - man/arith.Rd | 7 ++---- man/lisy.Rd | 7 ++---- man/spatial2d.Rd | 7 ++---- man/spatial3d.Rd | 7 ++---- man/spatial3d_mirror.Rd | 7 ++---- 9 files changed, 65 insertions(+), 53 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.9). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.9.0 dated 2016-08-20 and 0.3.2.9.1 dated 2017-03-15
ChangeLog | 19 +++++++++++ DESCRIPTION | 11 +++--- MD5 | 19 +++++------ NAMESPACE | 27 +++++++-------- R/fastLm.R | 4 +- README.md | 2 - build/vignette.rds |binary inst/NEWS.Rd | 10 +++++ inst/doc/RcppEigen-Introduction.pdf |binary inst/include/RcppEigenCholmod.h | 62 ++++++++++++++++++++++++------------ src/init.c |only 11 files changed, 103 insertions(+), 51 deletions(-)
Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Description: Enables researchers to sample redistricting plans from a pre-
specified target distribution using a Markov Chain Monte Carlo algorithm.
The package allows for the implementation of various constraints in the
redistricting process such as geographic compactness and population parity
requirements. The algorithm also can be used in combination with efficient
simulation methods such as simulated and parallel tempering algorithms. Tools
for analysis such as inverse probability reweighting and plotting functionality
are included. The package implements methods described in Fifield, Higgins, Imai
and Tarr (2016) ``A New Automated Redistricting Simulator Using Markov Chain
Monte Carlo,'' working paper available at <http://http://imai.princeton.edu/
research/files/redist.pdf>.
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr
<atarr@princeton.edu>, Michael Higgins <mikehiggins@k-state.edu>, and Kosuke
Imai <kimai@princeton.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>
Diff between redist versions 1.3 dated 2016-12-21 and 1.3-1 dated 2017-03-15
DESCRIPTION | 25 +- MD5 | 61 ++--- NAMESPACE | 63 ++--- R/RcppExports.R | 8 R/data.R |only R/enumerate.R | 64 ++++- R/redist-package.R |only R/redist.R | 529 +++++++++++++++++++++++++++++++++++++++------- R/redistMPI.R | 257 ++++++++++++++++++---- R/redist_findparams.R | 195 +++++++++++++--- R/rsg.R | 94 ++++++++ data/algdat.p10.rda |binary data/algdat.p20.rda |binary data/algdat.pfull.rda |binary man/algdat.p10.Rd | 59 +++-- man/algdat.p20.Rd | 59 +++-- man/algdat.pfull.Rd | 57 ++-- man/redist-package.Rd | 90 +++---- man/redist.combine.Rd | 105 +++++---- man/redist.combine.mpi.Rd | 109 +++++---- man/redist.diagplot.Rd | 75 +++--- man/redist.enumerate.Rd | 85 ++++--- man/redist.findparams.Rd | 100 +++++--- man/redist.ipw.Rd | 133 ++++++----- man/redist.mcmc.Rd | 194 ++++++++++------ man/redist.mcmc.mpi.Rd | 166 ++++++++------ man/redist.rsg.Rd | 143 ++++++------ man/redist.segcalc.Rd | 64 ++--- src/RcppExports.cpp | 20 + src/enumerate.cpp | 6 src/redist_init.c |only src/sw_mh_alg.cpp | 54 ++++ src/sw_mh_helper.cpp | 1 33 files changed, 1933 insertions(+), 883 deletions(-)
Title: Simulating from the Polya Posterior
Description: Simulate via Markov chain Monte Carlo (hit-and-run algorithm)
a Dirichlet distribution conditioned to satisfy a finite set of linear
equality and inequality constraints (hence to lie in a convex polytope
that is a subset of the unit simplex).
Author: Glen Meeden <glen@stat.umn.edu> and Radu Lazar
<lazar@stat.umn.edu> and Charles J. Geyer <charlie@stat.umn.edu>
Maintainer: Glen Meeden <glen@stat.umn.edu>
Diff between polyapost versions 1.4-2 dated 2015-07-08 and 1.4-3 dated 2017-03-15
polyapost |only 1 file changed
Title: Patterns and Statistical Differences Between Two Groups of
Strings
Description: Methods include converting series of event names to strings,
discovering common patterns in a group of strings, discovering "unique" patterns
when comparing two groups of strings as well as the number and starting position
of each "unique" pattern in each string, finding the transition matrix and information, and
statistically comparing the difference between two groups of strings.
Author: Hui (Tom) Tang, Norbert J. Pienta
Maintainer: Hui (Tom) Tang <htang2013@gmail.com>
Diff between GrpString versions 0.1.1 dated 2017-02-10 and 0.2.1 dated 2017-03-15
DESCRIPTION | 12 ++++++------ MD5 | 16 +++++++++------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/CommonPattern.R | 11 +---------- R/TransMx.R |only man/CommonPattern.Rd | 2 +- man/EveString.Rd | 2 +- man/TransInfo.Rd | 4 +++- man/TransMx.Rd |only 10 files changed, 29 insertions(+), 26 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl, Yan Yang, and Sharon Lohr
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.0-3 dated 2015-07-20 and 3.0-4 dated 2017-03-15
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS | 4 ++++ man/GPvam-package.Rd | 6 +++--- man/GPvam.Rd | 7 +++---- src/Makevars | 3 +-- src/Makevars.win | 6 +----- src/init.c |only 9 files changed, 26 insertions(+), 27 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.10.0 dated 2016-08-07 and 0.11.2 dated 2017-03-15
DESCRIPTION | 15 - MD5 | 124 ++++++---- NAMESPACE | 4 R/Convert_Simulated_Networks_To_Observed_Scale.R | 42 +++ R/Create_GERGM_Object_From_Formula.R | 21 + R/Data_Documentation.R |only R/Estimate_GERGM.R | 8 R/Estimate_Plot.R | 26 +- R/GERGM_Class.R | 2 R/GOF.R | 69 +++++- R/Log_Likelihood_and_MPLE_Objective.R | 9 R/MCMCMLE.R | 2 R/Package_Documentation.R | 12 - R/Prepare_Covariates.R | 12 - R/RcppExports.R | 14 - R/Run_MPLE.R | 26 ++ R/Simulate_GERGM.R | 10 R/Update_Lambda_Estimates.R | 72 ++++++ R/beta_model.R |only R/calculate_additional_GOF_statistics.R | 32 ++ R/calculate_network_statistics.R | 7 R/conditional_edge_prediction.R | 229 ++++++++++++++++---- R/conditional_edge_prediction_MSE.R |only R/conditional_edge_prediction_correlation_plot.R | 85 ++++++- R/draw_max_entry_conditional_uniform_corr.R |only R/gergm.R | 80 ++++-- R/hysteresis.R | 6 R/parallel_gergm.R | 39 ++- R/plot_network.R | 205 ++++++++++++----- R/prepare_parameter_estimate_data.R | 28 ++ R/selected_rows_functions.R | 5 R/simulate_networks.R | 92 ++++++-- R/single_gergm_specification.R | 2 R/zzz.R | 5 README.md | 87 ++++--- build |only data |only inst |only man/Estimate_Plot.Rd | 5 man/GOF.Rd | 6 man/Trace_Plot.Rd | 1 man/calculate_network_statistics.Rd | 5 man/conditional_edge_prediction.Rd | 7 man/conditional_edge_prediction_MSE.Rd |only man/conditional_edge_prediction_correlation_plot.Rd | 6 man/conditional_edge_prediction_plot.Rd | 1 man/covariate_data_2005.Rd |only man/find_example_simulated_network.Rd | 1 man/gergm.Rd | 44 ++- man/hysteresis.Rd | 7 man/hysteresis_plot.Rd | 1 man/lending_2005.Rd |only man/net_exports_2005.Rd |only man/parallel_gergm.Rd | 47 ++-- man/plot_network.Rd | 15 - man/simulate_networks.Rd | 40 +-- src/Extended_Metropolis_Hastings_Sampler.cpp | 227 +++++++++++++++++++ src/GERGM_init.c |only src/Makevars | 1 src/Makevars.win | 1 src/Metropolis_Hastings_Sampler.cpp |only src/RcppExports.cpp | 102 +++++--- tests/testthat/test_experimental_features.R | 52 ++++ tests/testthat/test_gergm.R | 1 tests/testthat/test_gergm_with_downweighting.R | 4 tests/testthat/test_hysteresis.R | 10 tests/testthat/test_node_subset_statistics.R | 2 vignettes |only 68 files changed, 1483 insertions(+), 473 deletions(-)
Title: Fuzzy Rank Tests and Confidence Intervals
Description: Does fuzzy tests and confidence intervals (following Geyer
and Meeden, Statistical Science, 2005, <doi:10.1214/088342305000000340>)
for sign test and Wilcoxon signed rank and rank sum tests.
Author: Charles J. Geyer <charlie@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between fuzzyRankTests versions 0.3-7 dated 2015-07-07 and 0.3-10 dated 2017-03-15
fuzzyRankTests-0.3-10/fuzzyRankTests/ChangeLog | 5 fuzzyRankTests-0.3-10/fuzzyRankTests/DESCRIPTION | 14 - fuzzyRankTests-0.3-10/fuzzyRankTests/MD5 | 44 ++--- fuzzyRankTests-0.3-10/fuzzyRankTests/NAMESPACE | 2 fuzzyRankTests-0.3-10/fuzzyRankTests/R/fuzzy.ranksum.test.R | 4 fuzzyRankTests-0.3-10/fuzzyRankTests/R/fuzzy.sign.test.R | 4 fuzzyRankTests-0.3-10/fuzzyRankTests/R/fuzzy.signrank.test.R | 4 fuzzyRankTests-0.3-10/fuzzyRankTests/src/Makevars |only fuzzyRankTests-0.3-10/fuzzyRankTests/src/init.c | 7 fuzzyRankTests-0.3-10/fuzzyRankTests/tests/ranksum.R | 2 fuzzyRankTests-0.3-10/fuzzyRankTests/tests/ranksum.Rout.save | 53 +++--- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/sign-ci.R | 7 fuzzyRankTests-0.3-10/fuzzyRankTests/tests/sign-ci.Rout.save | 31 +-- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/sign.R | 2 fuzzyRankTests-0.3-10/fuzzyRankTests/tests/sign.Rout.save | 10 - fuzzyRankTests-0.3-10/fuzzyRankTests/tests/signrank.R | 2 fuzzyRankTests-0.3-10/fuzzyRankTests/tests/signrank.Rout.save | 59 +++---- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/testc.R | 24 +-- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/testc.Rout.save | 79 ++++------ fuzzyRankTests-0.3-10/fuzzyRankTests/tests/testd.R | 14 - fuzzyRankTests-0.3-10/fuzzyRankTests/tests/testd.Rout.save | 71 ++++---- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/teste.R | 30 ++- fuzzyRankTests-0.3-10/fuzzyRankTests/tests/teste.Rout.save | 50 +++--- fuzzyRankTests-0.3-7/fuzzyRankTests/inst/doc/design.pdf |only 24 files changed, 260 insertions(+), 258 deletions(-)
More information about fuzzyRankTests at CRAN
Permanent link
Title: Data and Code Behind the Stories and Interactives at
'FiveThirtyEight'
Description: An R library that provides access to the code and data sets
published by FiveThirtyEight <https://github.com/fivethirtyeight/data>. Note
that while we received guidance from editors at 538, this package is not
officially published by 538.
Author: Albert Y. Kim [cre],
Chester Ismay [aut],
Jennifer Chunn [aut],
Andrew Flowers [ctb],
Jonathan Bouchet [ctb],
G. Elliott Morris [ctb],
Adam Spannbauer [ctb]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between fivethirtyeight versions 0.1.0 dated 2017-01-08 and 0.2.0 dated 2017-03-15
fivethirtyeight-0.1.0/fivethirtyeight/vignettes/datasets.csv |only fivethirtyeight-0.2.0/fivethirtyeight/DESCRIPTION | 32 fivethirtyeight-0.2.0/fivethirtyeight/MD5 | 191 +++-- fivethirtyeight-0.2.0/fivethirtyeight/NEWS.md | 13 fivethirtyeight-0.2.0/fivethirtyeight/R/data_albert.R | 358 +++++++--- fivethirtyeight-0.2.0/fivethirtyeight/R/data_chester.R | 53 + fivethirtyeight-0.2.0/fivethirtyeight/R/data_jen.R | 75 +- fivethirtyeight-0.2.0/fivethirtyeight/R/fivethirtyeight.R |only fivethirtyeight-0.2.0/fivethirtyeight/build/vignette.rds |binary fivethirtyeight-0.2.0/fivethirtyeight/data/college_all_ages.rda |binary fivethirtyeight-0.2.0/fivethirtyeight/data/college_grad_students.rda |only fivethirtyeight-0.2.0/fivethirtyeight/data/college_recent_grads.rda |only fivethirtyeight-0.2.0/fivethirtyeight/data/cousin_marriage.rda |only fivethirtyeight-0.2.0/fivethirtyeight/data/datalist | 6 fivethirtyeight-0.2.0/fivethirtyeight/data/hate_crimes.rda |only fivethirtyeight-0.2.0/fivethirtyeight/data/police_killings.rda |binary fivethirtyeight-0.2.0/fivethirtyeight/data/pres_2016_trail.rda |only fivethirtyeight-0.2.0/fivethirtyeight/data/riddler_castles.rda |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/NBA.R |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/NBA.Rmd |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/NBA.html |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/bechdel.R | 7 fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/bechdel.Rmd | 12 fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/bechdel.html | 11 fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/comics_gender.R |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/comics_gender.Rmd |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/comics_gender.html |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/fivethirtyeight.R | 16 fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/fivethirtyeight.Rmd | 20 fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/fivethirtyeight.html | 280 +++++-- fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/trump_twitter.R |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/trump_twitter.Rmd |only fivethirtyeight-0.2.0/fivethirtyeight/inst/doc/trump_twitter.html |only fivethirtyeight-0.2.0/fivethirtyeight/man/US_births_1994_2003.Rd | 11 fivethirtyeight-0.2.0/fivethirtyeight/man/US_births_2000_2014.Rd | 9 fivethirtyeight-0.2.0/fivethirtyeight/man/airline_safety.Rd | 27 fivethirtyeight-0.2.0/fivethirtyeight/man/avengers.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/bad_drivers.Rd | 5 fivethirtyeight-0.2.0/fivethirtyeight/man/bechdel.Rd | 21 fivethirtyeight-0.2.0/fivethirtyeight/man/biopics.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/bob_ross.Rd | 10 fivethirtyeight-0.2.0/fivethirtyeight/man/cand_events_20150114.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/cand_events_20150130.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/cand_state_20150114.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/cand_state_20150130.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/classic_rock_raw_data.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/classic_rock_song_list.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/college_all_ages.Rd | 12 fivethirtyeight-0.2.0/fivethirtyeight/man/college_grad_students.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/college_recent_grads.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/comic_characters.Rd | 9 fivethirtyeight-0.2.0/fivethirtyeight/man/comma_survey.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/congress_age.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/cousin_marriage.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/daily_show_guests.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/democratic_bench.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/drinks.Rd | 14 fivethirtyeight-0.2.0/fivethirtyeight/man/drug_use.Rd | 18 fivethirtyeight-0.2.0/fivethirtyeight/man/elo_blatter.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/endorsements.Rd | 7 fivethirtyeight-0.2.0/fivethirtyeight/man/fandango.Rd | 5 fivethirtyeight-0.2.0/fivethirtyeight/man/fifa_audience.Rd | 10 fivethirtyeight-0.2.0/fivethirtyeight/man/fivethirtyeight.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/flying.Rd | 37 - fivethirtyeight-0.2.0/fivethirtyeight/man/food_world_cup.Rd | 15 fivethirtyeight-0.2.0/fivethirtyeight/man/hate_crimes.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/hiphop_cand_lyrics.Rd | 5 fivethirtyeight-0.2.0/fivethirtyeight/man/hist_ncaa_bball_casts.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/hist_senate_preds.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/librarians.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/love_actually_adj.Rd | 29 fivethirtyeight-0.2.0/fivethirtyeight/man/love_actually_appearance.Rd | 37 - fivethirtyeight-0.2.0/fivethirtyeight/man/mad_men.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/male_flight_attend.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/mlb_as_play_talent.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/mlb_as_team_talent.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/murder_2015_final.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/murder_2016_prelim.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nba_draft_2015.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nba_tattoos.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nfl_fav_team.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nfl_suspensions.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nfltix_div_avgprice.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/nfltix_usa_avg.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/nflwr_aging_curve.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nflwr_hist.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/nutrition_pvalues.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/police_deaths.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/police_killings.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/police_locals.Rd | 13 fivethirtyeight-0.2.0/fivethirtyeight/man/pres_2016_trail.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/pres_commencement.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/pulitzer.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/riddler_castles.Rd |only fivethirtyeight-0.2.0/fivethirtyeight/man/san_andreas.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/senate_polls.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/steak_survey.Rd | 5 fivethirtyeight-0.2.0/fivethirtyeight/man/tarantino.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/tennis_events_time.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/tennis_players_time.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/tennis_serve_time.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/trump_news.Rd | 3 fivethirtyeight-0.2.0/fivethirtyeight/man/trump_twitter.Rd | 6 fivethirtyeight-0.2.0/fivethirtyeight/man/unisex_names.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/man/weather_check.Rd | 1 fivethirtyeight-0.2.0/fivethirtyeight/vignettes/NBA.Rmd |only fivethirtyeight-0.2.0/fivethirtyeight/vignettes/bechdel.Rmd | 12 fivethirtyeight-0.2.0/fivethirtyeight/vignettes/comics_gender.Rmd |only fivethirtyeight-0.2.0/fivethirtyeight/vignettes/fivethirtyeight.Rmd | 20 fivethirtyeight-0.2.0/fivethirtyeight/vignettes/trump_twitter.Rmd |only 110 files changed, 969 insertions(+), 504 deletions(-)
More information about fivethirtyeight at CRAN
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Title: Python Tools to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L Davis and Paul Gilbert.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.1 dated 2014-04-03 and 1.0.2 dated 2017-03-15
DESCRIPTION | 11 ++++---- MD5 | 16 ++++++------ NAMESPACE | 2 + NEWS | 6 +++- R/find_python_cmd.r | 6 ++-- man/can_find_python_cmd.Rd | 52 +++++++++++++++------------------------ man/find_python_cmd.Rd | 44 ++++++++++++++------------------- man/is_python_sufficient.Rd | 40 ++++++++++++++---------------- tests/testthat/test-findpython.r | 6 ++-- 9 files changed, 86 insertions(+), 97 deletions(-)