Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Diff between plotROC versions 1.2 dated 2014-11-13 and 1.3 dated 2015-01-27
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 11 ++++---
LICENSE | 2 -
MD5 | 52 ++++++++++++++++++----------------
NAMESPACE | 2 -
NEWS | 8 +++++
R/calculate_roc.R | 63 ++++++++++++++++++++++++++++++------------
R/ggroc.R | 49 ++++++++++++++++++++------------
R/interactive_roc.R | 33 +++++++++++++---------
R/modCss.R | 2 -
R/modJs.R | 5 ++-
R/plot_journal_roc.R | 11 ++++---
build/vignette.rds |binary
inst/CITATION |only
inst/doc/examples.Rmd | 9 ++----
inst/doc/examples.html | 60 ++++++++++++++++++++--------------------
man/calculate_multi_roc.Rd | 15 +++++-----
man/calculate_roc.Rd | 17 ++++++-----
man/export_interactive_roc.Rd | 26 ++++++++++-------
man/ggroc.Rd | 22 +++++++++-----
man/modCss.Rd | 5 ++-
man/modJs.Rd | 10 ++++--
man/multi_ggroc.Rd | 23 ++++++++++-----
man/plot_interactive_roc.Rd | 7 ++--
man/plot_journal_roc.Rd | 10 +++---
man/shiny_plotROC.Rd | 3 +-
man/verify_d.Rd |only
tests |only
vignettes/examples.Rmd | 9 ++----
28 files changed, 272 insertions(+), 182 deletions(-)
Title: Tufte-style html document format for rmarkdown
Diff between tufterhandout versions 1.2 dated 2014-11-12 and 1.2.1 dated 2015-01-27
Description: Custom template and output formats for use with rmarkdown. Produce
Edward Tufte-style handouts in html formats with full support for rmarkdown
features
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 17 +++++++++--------
LICENSE | 4 ++--
MD5 | 25 ++++++++++++++-----------
NAMESPACE | 2 +-
NEWS | 5 +++++
R/html_tufte_handout.R | 14 +++++++++++++-
README.md | 8 ++++++++
build/vignette.rds |binary
inst/CITATION |only
inst/doc/example.Rmd | 7 +++++--
inst/doc/example.html | 27 ++++++++++++++++++++-------
man/html_tufte_handout.Rd | 3 ++-
tests |only
vignettes/example.Rmd | 7 +++++--
14 files changed, 84 insertions(+), 35 deletions(-)
Title: Detection of Outliers in Time Series
Diff between tsoutliers versions 0.5 dated 2015-01-25 and 0.6 dated 2015-01-27
Description: Detection of outliers in time series following the
Chen and Liu (1993) procedure. Innovative outliers, additive outliers,
level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
tsoutliers-0.5/tsoutliers/inst/CHANGES |only
tsoutliers-0.6/tsoutliers/DESCRIPTION | 8 ++---
tsoutliers-0.6/tsoutliers/MD5 | 22 +++++++--------
tsoutliers-0.6/tsoutliers/NEWS |only
tsoutliers-0.6/tsoutliers/R/locate-outliers.R | 4 +-
tsoutliers-0.6/tsoutliers/R/tso.R | 3 --
tsoutliers-0.6/tsoutliers/inst/doc/index.html | 10 +++---
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.R | 10 +++---
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.Rnw | 18 ++++++------
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.pdf |binary
tsoutliers-0.6/tsoutliers/man/locate-outliers.Rd | 2 -
tsoutliers-0.6/tsoutliers/man/tsoutliers.Rd | 6 ++--
tsoutliers-0.6/tsoutliers/vignettes/tsoutliers-intro.Rnw | 18 ++++++------
13 files changed, 50 insertions(+), 51 deletions(-)
Title: Read and Analyze PLEXOS Solutions from R
Diff between rplexos versions 0.11 dated 2014-12-16 and 0.12 dated 2015-01-27
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
NAMESPACE | 1 +
R/process_folder.R | 32 ++++++++++++++++++++------------
R/process_input.R |only
R/process_solution.R | 36 +++++++++++++++++++-----------------
README.md | 2 +-
build/vignette.rds |binary
man/process_folder.Rd | 23 ++++++++++++++++-------
src/process_xml.cpp | 30 +++++++++++++++++++-----------
10 files changed, 89 insertions(+), 60 deletions(-)
Title: Bayesian analysis of qRT-PCR data
Diff between MCMC.qpcr versions 1.1.3 dated 2014-04-13 and 1.1.5 dated 2015-01-27
Description: This package implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. Tutorial: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
DESCRIPTION | 10 +++++-----
MD5 | 12 +++++++-----
NAMESPACE | 1 +
R/HPDplotBygeneBygroup.R | 7 +++++--
R/trellisByGene.R |only
man/MCMC.qpcr-package.Rd | 4 ++--
man/getNormalizedData.Rd | 32 ++++++++++++++++++++++----------
man/trellisByGene.Rd |only
8 files changed, 42 insertions(+), 24 deletions(-)
Title: Functions for Ecdat
Diff between Ecfun versions 0.1-3 dated 2014-11-27 and 0.1-4 dated 2015-01-27
Description: Functions to update datasets in Ecdat and to create,
manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves
DESCRIPTION | 13 -
MD5 | 40 ++---
NAMESPACE | 3
R/BoxCox.R |only
R/matchName.R | 46 ++++--
R/matchName1.R | 117 +++++++++------
R/parseName.R | 21 +-
R/pmatch2.R | 15 +-
R/readCookPVI.R | 6
R/readUShouse.R | 289 ++++++++++++++++++++-------------------
R/subNonStandardCharacters.R | 106 +++++++-------
R/subNonStandardNames.R | 39 ++++-
man/BoxCox.Rd |only
man/grepNonStandardCharacters.Rd | 143 +++++++++----------
man/matchName.Rd | 112 ++++++++++-----
man/mergeUShouse.senate.Rd | 11 -
man/parseName.Rd | 27 +++
man/pmatch2.Rd | 16 ++
man/readUShouse.Rd | 230 +++++++++++++++----------------
man/subNonStandardCharacters.Rd | 251 +++++++++++++++++++--------------
man/subNonStandardNames.Rd | 78 ++++++++--
man/truncdist.Rd | 10 +
22 files changed, 939 insertions(+), 634 deletions(-)
Title: Constrained Inference for Linear Mixed Effects Models
Diff between CLME versions 2.0-1 dated 2014-12-05 and 2.0-2 dated 2015-01-27
Description: Constrained inference for linear mixed effects models using residual bootstrap methodology
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema
DESCRIPTION | 8 -
MD5 | 31 +++---
NEWS | 27 ++++-
R/clme.r | 5 -
R/clme_resids.r | 3
R/minque.r | 2
R/resid_boot.r | 2
R/shiny_clme.r | 167 ++++++++++++++++++++++++++++------
R/summary.clme.r | 5 -
R/utilities.r | 14 +-
inst/doc/clme_intro.R | 218 +++++++++++++++++++++++----------------------
inst/doc/clme_intro.Rnw | 183 +++++++++++++++++++------------------
inst/doc/clme_intro.pdf |binary
inst/doc/clme_vignette.pdf |only
man/minque.Rd | 3
man/shiny.clme.Rd | 92 +++++++++---------
vignettes/clme_intro.Rnw | 183 +++++++++++++++++++------------------
17 files changed, 545 insertions(+), 398 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.10-5 dated 2015-01-23 and 0.10-6 dated 2015-01-27
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NEWS | 5 +++++
inst/doc/cap-recap.pdf |binary
inst/doc/colext.pdf |binary
inst/doc/distsamp.pdf |binary
inst/doc/spp-dist.pdf |binary
inst/doc/unmarked.pdf |binary
src/nll_pcountOpen.cpp | 2 +-
9 files changed, 18 insertions(+), 13 deletions(-)
Title: Maximum Projection Designs
Diff between MaxPro versions 3.1-1 dated 2015-01-27 and 3.1-2 dated 2015-01-27
Description: Generate a maximum projection (MaxPro) design, a MaxPro Latin hypercube design or improve an initial design based on the MaxPro criterion. Details of the MaxPro criterion can be found in: Joseph, V. R., Gul, E., and Ba, S. (2015) "Maximum Projection Designs for Computer Experiments", Biometrika.
Author: Shan Ba and V. Roshan Joseph
Maintainer: Shan Ba
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
man/MaxPro-package.Rd | 6 +++---
man/MaxPro.Rd | 2 +-
man/MaxProImproveLHD.Rd | 6 +++---
man/MaxProLHD.Rd | 2 +-
src/MaxPro.cpp | 8 ++++----
7 files changed, 22 insertions(+), 22 deletions(-)
Title: TraMineR Extension
Diff between TraMineRextras versions 0.2.2 dated 2013-10-29 and 0.2.3 dated 2015-01-27
More information about TraMineRextras at CRAN
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard
DESCRIPTION | 15 +++++++--------
MD5 | 21 ++++++++++++---------
NAMESPACE | 8 ++++++--
R/seqedplot.R | 12 +++++++-----
R/seqgranularity.R | 19 +++++++++++++++++--
R/seqtabstocc.R |only
inst/CITATION |only
inst/NEWS | 18 +++++++++++++++++-
inst/NEWS.Rd | 13 +++++++++++++
man/createdatadiscrete.Rd | 8 ++++----
man/seqemlt.Rd | 45 ++++++++++++++++++++++++++-------------------
man/seqgranularity.Rd | 10 +++-------
man/seqtabstocc.Rd |only
13 files changed, 112 insertions(+), 57 deletions(-)
Permanent link
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Diff between TraMineR versions 1.8-8 dated 2014-01-14 and 1.8-9 dated 2015-01-27
Description: This is a toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard
DESCRIPTION | 14 ++--
MD5 | 52 ++++++++---------
NAMESPACE | 5 +
NEWS | 33 ++++++++++-
R/STS_to_TSE.R | 16 +++--
R/TraMineRInternal.R | 8 ++
R/dissmfacw.R | 2
R/seqpcplot.R | 67 ++++++++++++++++++----
R/seqpm.R | 4 -
build/vignette.rds |binary
data/ex1.rda |binary
data/ex2.rda |binary
data/famform.rda |binary
inst/CITATION | 16 +++--
inst/doc/TraMineR-state-sequence.R | 1
inst/doc/TraMineR-state-sequence.pdf |binary
man/TraMineR-package.Rd | 10 +--
man/TraMineRInternal.Rd | 12 ++--
man/dissmfac.Rd | 5 +
man/seqdef.Rd | 12 ++--
man/seqformat.Rd | 81 +++++++++------------------
man/seqlegend.Rd | 4 -
man/seqlogp.Rd | 10 +--
man/seqpcplot.Rd | 102 ++++++++++++++++++++++++++---------
man/seqplot.Rd | 50 ++++++++---------
man/seqpm.Rd | 9 +--
man/seqtrate.Rd | 2
27 files changed, 319 insertions(+), 196 deletions(-)
Title: Copy Number Estimation from Tumor Genome Sequencing Data
Diff between sequenza versions 2.1.0 dated 2014-10-08 and 2.1.1 dated 2015-01-27
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero
DESCRIPTION | 12 +++---
MD5 | 18 ++++-----
NEWS | 5 ++
R/next.R | 18 ++++++---
exec/sequenza-utils.py | 97 +++++++++++--------------------------------------
inst/CITATION | 9 +++-
inst/doc/sequenza.Rnw | 4 +-
inst/doc/sequenza.pdf |binary
man/VarScan2seqz.Rd | 3 +
vignettes/sequenza.Rnw | 4 +-
10 files changed, 69 insertions(+), 101 deletions(-)
Title: Single-Case Visual Analysis
Diff between SCVA versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27
Description: A package to make graphical representations of single case data and to transform graphical displays back to raw data. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCVA-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Single-Case Randomization Tests
Diff between SCRT versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27
Description: A package for designing single-case phase, alternation and multiple-baseline experiments, as well as for conducting randomization tests on data gathered by means of such designs.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCRT-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Single-Case Meta-Analysis
Diff between SCMA versions 1.1 dated 2014-01-13 and 1.1.1 dated 2015-01-27
Description: An R package for single-case meta-analysis.
Author: Isis Bulte
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCMA-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Rcmdr Plugin for Designing and Analyzing Single-case Experiments
Diff between RcmdrPlugin.SCDA versions 1.0 dated 2014-03-19 and 1.1 dated 2015-01-27
More information about RcmdrPlugin.SCDA at CRAN
Description: Provides a GUI for the SCVA, SCRT and SCMA packages. The package is written as an Rcmdr plugin.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 14
MD5 | 6
R/RcmdrPlugin.SCDA.R | 970 ++++++++++++++++------------------------
man/RcmdrPlugin.SCDA-package.Rd | 11
4 files changed, 420 insertions(+), 581 deletions(-)
Permanent link
Title: Quantile Regression for Linear Mixed-Effects Models
Diff between qrLMM versions 1.0-9 dated 2015-01-08 and 1.1 dated 2015-01-27
Description: Quantile regression (QR) for Linear
Mixed-Effects Models via the asymmetric Laplace distribution (ALD).
It uses the Stochastic Approximation of the EM (SAEM) algorithm for
deriving exact maximum likelihood estimates and full inference results
for the fixed-effects and variance components.
It also provides graphical summaries for assessing the algorithm
convergence and fitting results.
Author: Christian E. Galarza
Maintainer: Christian E. Galarza
DESCRIPTION | 8 ++++----
MD5 | 6 +++++-
data |only
man/Cholesterol.Rd |only
man/Orthodont.Rd |only
5 files changed, 9 insertions(+), 5 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-0 dated 2015-01-05 and 1.1-3 dated 2015-01-27
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
openair-1.1-0/openair/NEWS |only
openair-1.1-3/openair/DESCRIPTION | 14 ++--
openair-1.1-3/openair/MD5 | 75 +++++++++++++-------------
openair-1.1-3/openair/NAMESPACE | 1
openair-1.1-3/openair/R/GoogleMapsPlot.R | 3 +
openair-1.1-3/openair/R/TaylorDiagram.R | 28 ++++++---
openair-1.1-3/openair/R/TheilSen.R | 20 ++++--
openair-1.1-3/openair/R/calendarPlot.R | 18 +++++-
openair-1.1-3/openair/R/conditionalEval.R | 15 +++--
openair-1.1-3/openair/R/conditionalQuantile.R | 17 ++++-
openair-1.1-3/openair/R/corPlot.R | 13 +++-
openair-1.1-3/openair/R/kernelExceed.R | 9 ++-
openair-1.1-3/openair/R/linearRelation.R | 15 +++--
openair-1.1-3/openair/R/openair.generics.R | 3 -
openair-1.1-3/openair/R/percentileRose.R | 17 ++++-
openair-1.1-3/openair/R/polarAnnulus.R | 18 ++++--
openair-1.1-3/openair/R/polarCluster.R | 17 ++++-
openair-1.1-3/openair/R/polarFreq.R | 17 ++++-
openair-1.1-3/openair/R/polarPlot.R | 32 +++++++----
openair-1.1-3/openair/R/scatterPlot.R | 64 +++++++++++++---------
openair-1.1-3/openair/R/smoothTrend.R | 11 +++
openair-1.1-3/openair/R/summaryPlot.R | 18 ++++--
openair-1.1-3/openair/R/timePlot.R | 17 ++++-
openair-1.1-3/openair/R/timeProp.R | 11 +++
openair-1.1-3/openair/R/timeVariation.R | 18 ++++--
openair-1.1-3/openair/R/trajCluster.R | 11 +++
openair-1.1-3/openair/R/trajLevel.R | 27 +++++++--
openair-1.1-3/openair/R/trajPlot.R | 33 ++++++++++-
openair-1.1-3/openair/R/trendLevel.R | 35 +++++++-----
openair-1.1-3/openair/R/utilities.R | 7 ++
openair-1.1-3/openair/R/windRose.R | 12 +++-
openair-1.1-3/openair/README.md |only
openair-1.1-3/openair/inst/plume.png |only
openair-1.1-3/openair/inst/windRose.png |only
openair-1.1-3/openair/inst/windRosePM10.png |only
openair-1.1-3/openair/man/TaylorDiagram.Rd | 5 -
openair-1.1-3/openair/man/TheilSen.Rd | 2
openair-1.1-3/openair/man/scatterPlot.Rd | 9 ++-
openair-1.1-3/openair/man/trajLevel.Rd | 2
openair-1.1-3/openair/man/trajPlot.Rd | 2
openair-1.1-3/openair/src/rolling.cpp | 2
41 files changed, 434 insertions(+), 184 deletions(-)
Title: Draw Diagrams (mis)Representing the Results of Mass Spec
Experiments
Diff between msarc versions 1.4.3 dated 2014-12-04 and 1.4.5 dated 2015-01-27
Description: The output of an affinity-purification mass spectrometry
experiment is typically a list of proteins that were observed
in the experiment, identified by UniProt identifiers
(http://www.uniprot.org/). This package takes as input a list of
UniProt identifiers, and the associated Mascot scores from the
experiment (which indicate the likelihood that the protein has
been correctly identified), clusters them by gene ontology
category (http://geneontology.org/), then draws diagrams
showing the results in hierarchical clusters by category, with lines
for individual proteins representing the associated Mascot score.
The results are in general not publication-ready, but will rather
require editing via a graphics editor that can interpret SVG (scalable
vector graphics) format. As an alternative representation, the
package will also generate tag clouds based on the Mascot scores.
Author: Gord Brown, Hisham Mohammed
Maintainer: Gord Brown
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 6 +++---
R/cluster.R | 2 +-
R/plotter.R | 4 ++--
inst/doc/msarc.pdf |binary
6 files changed, 16 insertions(+), 16 deletions(-)
Title: Tools for Biostatistics, Public Policy, and Law
Diff between lawstat versions 2.4.1 dated 2013-12-16 and 2.5 dated 2015-01-27
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness,
measures of relative variability etc, the package contains new robust tests of symmetry,
omnibus and directional tests of normality, and their graphical counterparts such as
Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods
are illustrated by simulations and real-life examples from legal statistics, economics,
and biostatistics.
Author: (in alphabetical order)
Joseph L. Gastwirth
Maintainer: Vyacheslav Lyubchich
lawstat-2.4.1/lawstat/R/wavk.test.R |only
lawstat-2.4.1/lawstat/man/wavk.test.Rd |only
lawstat-2.5/lawstat/DESCRIPTION | 36 ++++++++++++++-------------------
lawstat-2.5/lawstat/MD5 | 6 +----
lawstat-2.5/lawstat/NAMESPACE | 4 ++-
5 files changed, 21 insertions(+), 25 deletions(-)
Title: Flux Estimation with Static Chamber Data
Diff between HMR versions 0.3.2 dated 2014-12-12 and 0.4.1 dated 2015-01-27
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen
Maintainer: Asger R. Pedersen
DESCRIPTION | 11 +++----
MD5 | 8 ++---
R/HMR.fit1.R | 67 +++++++++++++++++++++++++++++++++++-------
R/HMR.main.R | 92 ++++++++++++++++++++++++++++++++++++++++++++++-------------
man/HMR.Rd | 37 ++++++++++++++---------
5 files changed, 159 insertions(+), 56 deletions(-)
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 1.3.2 dated 2014-12-10 and 2.0 dated 2015-01-27
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
decompr-1.3.2/decompr/R/kung_fu.R |only
decompr-1.3.2/decompr/data/wiod2.rda |only
decompr-2.0/decompr/DESCRIPTION | 20
decompr-2.0/decompr/MD5 | 56 +
decompr-2.0/decompr/NAMESPACE | 16
decompr-2.0/decompr/NEWS | 198 +++---
decompr-2.0/decompr/R/decomp.R | 140 ++--
decompr-2.0/decompr/R/decompr.R | 130 ++--
decompr-2.0/decompr/R/leontief.R |only
decompr-2.0/decompr/R/load_tables.R | 97 +--
decompr-2.0/decompr/R/load_tables_vectors.R | 439 +++++++------
decompr-2.0/decompr/R/vertical_specialisation.R |only
decompr-2.0/decompr/R/wwz.R | 659 ++++++++++-----------
decompr-2.0/decompr/README.md | 134 ++--
decompr-2.0/decompr/data/leather.rda |only
decompr-2.0/decompr/data/wiod.rda |binary
decompr-2.0/decompr/inst/CITATION | 34 -
decompr-2.0/decompr/man/countries.Rd |only
decompr-2.0/decompr/man/decomp.Rd | 140 ++--
decompr-2.0/decompr/man/decompr.Rd | 41 -
decompr-2.0/decompr/man/final.Rd |only
decompr-2.0/decompr/man/final_demand.Rd | 27
decompr-2.0/decompr/man/industries.Rd |only
decompr-2.0/decompr/man/industry_names.Rd | 27
decompr-2.0/decompr/man/inter.Rd |only
decompr-2.0/decompr/man/intermediate_demand.Rd | 27
decompr-2.0/decompr/man/kung_fu.Rd | 79 +-
decompr-2.0/decompr/man/leontief.Rd |only
decompr-2.0/decompr/man/load_tables.Rd | 73 +-
decompr-2.0/decompr/man/load_tables_vectors.Rd | 101 +--
decompr-2.0/decompr/man/out.Rd |only
decompr-2.0/decompr/man/output.Rd | 27
decompr-2.0/decompr/man/region_names.Rd | 27
decompr-2.0/decompr/man/vertical_specialisation.Rd |only
decompr-2.0/decompr/man/wwz.Rd | 84 +-
35 files changed, 1351 insertions(+), 1225 deletions(-)
Title: Phenotypic Integration Index
Diff between PHENIX versions 1.0 dated 2014-10-24 and 1.1 dated 2015-01-27
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), a bootstrapping method to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
PHENIX-1.0/PHENIX/R/int.R |only
PHENIX-1.0/PHENIX/R/int.boot.R |only
PHENIX-1.0/PHENIX/R/intsc.R |only
PHENIX-1.0/PHENIX/R/intsc.boot.R |only
PHENIX-1.0/PHENIX/man/int.Rd |only
PHENIX-1.0/PHENIX/man/int.boot.Rd |only
PHENIX-1.0/PHENIX/man/intsc.Rd |only
PHENIX-1.0/PHENIX/man/intsc.boot.Rd |only
PHENIX-1.1/PHENIX/DESCRIPTION | 12 +++++-----
PHENIX-1.1/PHENIX/MD5 | 35 ++++++++++++++++++--------------
PHENIX-1.1/PHENIX/NAMESPACE | 3 +-
PHENIX-1.1/PHENIX/NEWS |only
PHENIX-1.1/PHENIX/R/cor.par.R | 12 ++++++----
PHENIX-1.1/PHENIX/R/pint.R |only
PHENIX-1.1/PHENIX/R/pint.boot.R |only
PHENIX-1.1/PHENIX/R/pint.p.R |only
PHENIX-1.1/PHENIX/R/pintsc.R |only
PHENIX-1.1/PHENIX/R/pintsc.boot.R |only
PHENIX-1.1/PHENIX/R/pintsc.p.R |only
PHENIX-1.1/PHENIX/man/PHENIX-package.Rd | 11 +++++-----
PHENIX-1.1/PHENIX/man/cor.par.Rd | 13 ++++++-----
PHENIX-1.1/PHENIX/man/paeonia.Rd | 8 +++----
PHENIX-1.1/PHENIX/man/pint.Rd |only
PHENIX-1.1/PHENIX/man/pint.boot.Rd |only
PHENIX-1.1/PHENIX/man/pint.p.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.boot.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.p.Rd |only
PHENIX-1.1/PHENIX/man/tussilago.Rd | 6 ++---
29 files changed, 55 insertions(+), 45 deletions(-)
Title: Analysis of Feedback in Time Series
Diff between FeedbackTS versions 1.3 dated 2015-01-05 and 1.3.1 dated 2015-01-27
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NAMESPACE | 6 ++++--
man/FeedbackTS-package.Rd | 6 +++---
man/KDD-class.Rd | 27 +++++++++++++++------------
man/KDD.yearly.average-class.Rd | 11 ++++++-----
man/KT.output-class.Rd | 22 ++++++++++++++--------
man/feedback.test.Rd | 5 ++---
8 files changed, 55 insertions(+), 44 deletions(-)
Title: Geographic data analysis and modeling
Diff between raster versions 2.3-12 dated 2014-10-18 and 2.3-24 dated 2015-01-27
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 11 +
DESCRIPTION | 14 +-
MD5 | 121 ++++++++---------
R/AAAClasses.R | 1
R/aggregate_sp.R | 2
R/buffer.R | 2
R/canProcessInMemory.R | 4
R/clump.R | 2
R/connection.R | 6
R/coverPolygons.R | 2
R/cropSpatial.R | 4
R/erase.R | 2
R/extractPoints.R | 25 ---
R/extractPoints_sp.R |only
R/extractPolygons.R | 16 +-
R/factor.R | 7 -
R/freq.R | 12 -
R/gdal.R | 2
R/getData.R | 4
R/gridDistance.R | 2
R/hillShade.R | 2
R/imageplot.R | 30 ----
R/indexReplace.R | 2
R/indexReplaceBrick.R | 6
R/intersect.R | 12 -
R/intersect_sp.R | 101 +++++++++++++-
R/isLonLat.R | 10 +
R/kml_multiple.R | 6
R/mean.R | 101 ++------------
R/multiCore.R | 2
R/netCDFtoRasterCD.R | 4
R/netCDFutil.R | 4
R/netCDFwriteCD.R | 99 +++++++-------
R/nsidcICE.R | 114 ++++++++--------
R/overlay.R | 2
R/plotCT.R | 2
R/plotRGB.R | 2
R/progressBar.R | 2
R/rasterFromFile.R | 2
R/rasterFromRasterFile.R | 2
R/rasterToPolygons.R | 2
R/rowMinMax.R | 5
R/sampleStratified.R | 5
R/select.R | 4
R/symdif.R | 2
R/tmpFile.R | 4
R/trim.R | 10 -
R/union_sp.R | 4
R/writeRaster.R | 2
R/zApply.R | 2
build/vignette.rds |binary
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/Raster-classes.Rd | 1
man/extract.Rd | 25 ++-
man/getData.Rd | 17 ++
man/interpolate.Rd | 5
man/intersect.Rd | 10 -
man/raster.Rd | 326 ++++++++++++++++++++++++-----------------------
src/dist_util.c | 2
src/edge.c | 2
62 files changed, 594 insertions(+), 578 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.55 dated 2015-01-14 and 3.0.59 dated 2015-01-27
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
RandomFields-3.0.55/RandomFields/src/Covariance.h |only
RandomFields-3.0.59/RandomFields/DESCRIPTION | 8
RandomFields-3.0.59/RandomFields/MD5 | 253
RandomFields-3.0.59/RandomFields/NAMESPACE | 66
RandomFields-3.0.59/RandomFields/R/Class.R | 23
RandomFields-3.0.59/RandomFields/R/Crossvalidation.R | 2
RandomFields-3.0.59/RandomFields/R/Methods-aux.R | 144
RandomFields-3.0.59/RandomFields/R/QMath.R |only
RandomFields-3.0.59/RandomFields/R/RC_GLOBALS.R | 4
RandomFields-3.0.59/RandomFields/R/RCauto.R | 46
RandomFields-3.0.59/RandomFields/R/RFempvario-Methods-plots.R | 10
RandomFields-3.0.59/RandomFields/R/RFempvario.R | 104
RandomFields-3.0.59/RandomFields/R/RFgui.R | 32
RandomFields-3.0.59/RandomFields/R/RMmodels-Methods-plots.R | 176
RandomFields-3.0.59/RandomFields/R/RMmodels.R | 4333 +++++++---
RandomFields-3.0.59/RandomFields/R/RMmodelsConvenience.R | 17
RandomFields-3.0.59/RandomFields/R/RMmodelsSpecial.R | 2
RandomFields-3.0.59/RandomFields/R/auxiliary.R | 276
RandomFields-3.0.59/RandomFields/R/basic.fctns.R |only
RandomFields-3.0.59/RandomFields/R/convert.R | 377
RandomFields-3.0.59/RandomFields/R/convert_new.R | 291
RandomFields-3.0.59/RandomFields/R/fitgauss.R | 13
RandomFields-3.0.59/RandomFields/R/generatemodels.R | 319
RandomFields-3.0.59/RandomFields/R/getNset.R | 184
RandomFields-3.0.59/RandomFields/R/internal_use.R | 583 -
RandomFields-3.0.59/RandomFields/R/kriging.R | 753 -
RandomFields-3.0.59/RandomFields/R/obsolete.R | 17
RandomFields-3.0.59/RandomFields/R/rf.R | 291
RandomFields-3.0.59/RandomFields/R/zzz.R |only
RandomFields-3.0.59/RandomFields/inst/CITATION | 40
RandomFields-3.0.59/RandomFields/man/CoordinateSystems.Rd | 5
RandomFields-3.0.59/RandomFields/man/MajorRevisions.Rd | 14
RandomFields-3.0.59/RandomFields/man/QMath.Rd |only
RandomFields-3.0.59/RandomFields/man/RC.Rd | 4
RandomFields-3.0.59/RandomFields/man/RF.Rd | 17
RandomFields-3.0.59/RandomFields/man/RFcov.Rd | 3
RandomFields-3.0.59/RandomFields/man/RFcrossvalidate.Rd | 3
RandomFields-3.0.59/RandomFields/man/RFempVariog-class.Rd | 4
RandomFields-3.0.59/RandomFields/man/RFempiricalvariogram.Rd | 5
RandomFields-3.0.59/RandomFields/man/RFfit-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFfit.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFformula.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFgetModelNames.Rd | 8
RandomFields-3.0.59/RandomFields/man/RFgridDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFinterpolate.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFoptions.Rd | 15
RandomFields-3.0.59/RandomFields/man/RFpointsDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFratiotest.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulate.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulate.more.examples.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulateAdvanced.Rd | 20
RandomFields-3.0.59/RandomFields/man/RFsp-class.Rd | 4
RandomFields-3.0.59/RandomFields/man/RFsp2conventional.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFspatialGridDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFspatialPointsDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMconstant.Rd | 35
RandomFields-3.0.59/RandomFields/man/RMcovariate.Rd |only
RandomFields-3.0.59/RandomFields/man/RMdelay.Rd | 9
RandomFields-3.0.59/RandomFields/man/RMfix.Rd |only
RandomFields-3.0.59/RandomFields/man/RMgennsst.Rd |only
RandomFields-3.0.59/RandomFields/man/RMgneiting.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMiaco.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmatrix.Rd | 9
RandomFields-3.0.59/RandomFields/man/RMmodel-class.Rd | 34
RandomFields-3.0.59/RandomFields/man/RMmodel.Rd | 6
RandomFields-3.0.59/RandomFields/man/RMmodelExt-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmodelgenerator-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmodelsAdvanced.Rd | 17
RandomFields-3.0.59/RandomFields/man/RMmodelsAuxiliary.Rd | 4
RandomFields-3.0.59/RandomFields/man/RMmodelsSphere.Rd | 7
RandomFields-3.0.59/RandomFields/man/RMmodelsTailcorrelation.Rd | 1
RandomFields-3.0.59/RandomFields/man/RMmult.Rd | 3
RandomFields-3.0.59/RandomFields/man/RMnsst.Rd | 3
RandomFields-3.0.59/RandomFields/man/RMplus.Rd | 1
RandomFields-3.0.59/RandomFields/man/RMprod.Rd |only
RandomFields-3.0.59/RandomFields/man/RMsum.Rd |only
RandomFields-3.0.59/RandomFields/man/RMtrafo.Rd | 16
RandomFields-3.0.59/RandomFields/man/RMtrend.Rd | 12
RandomFields-3.0.59/RandomFields/man/RP.Rd | 2
RandomFields-3.0.59/RandomFields/man/RR.Rd | 5
RandomFields-3.0.59/RandomFields/man/RandomFields.Rd | 17
RandomFields-3.0.59/RandomFields/man/conventional2RFspDataFrame.Rd | 3
RandomFields-3.0.59/RandomFields/man/internal.Rd | 5
RandomFields-3.0.59/RandomFields/man/papers.Rd | 12
RandomFields-3.0.59/RandomFields/man/papers.jss14.Rd | 15
RandomFields-3.0.59/RandomFields/man/soil.Rd | 4
RandomFields-3.0.59/RandomFields/src/AutoRandomFields.cc | 20
RandomFields-3.0.59/RandomFields/src/AutoRandomFields.h | 40
RandomFields-3.0.59/RandomFields/src/Brown.cc | 199
RandomFields-3.0.59/RandomFields/src/Coordinate_systems.cc | 248
RandomFields-3.0.59/RandomFields/src/Coordinate_systems.h |only
RandomFields-3.0.59/RandomFields/src/D.H.cc | 10
RandomFields-3.0.59/RandomFields/src/Gneiting.cc | 257
RandomFields-3.0.59/RandomFields/src/Huetchen.cc | 41
RandomFields-3.0.59/RandomFields/src/InternalCov.cc | 478 -
RandomFields-3.0.59/RandomFields/src/KeyInfo.cc | 151
RandomFields-3.0.59/RandomFields/src/MLE.cc | 126
RandomFields-3.0.59/RandomFields/src/Operator.h |only
RandomFields-3.0.59/RandomFields/src/PoissonPolygon.cc | 32
RandomFields-3.0.59/RandomFields/src/Primitive.cc | 945 +-
RandomFields-3.0.59/RandomFields/src/QMath.cc |only
RandomFields-3.0.59/RandomFields/src/RF.h | 176
RandomFields-3.0.59/RandomFields/src/RandomFields.h | 5
RandomFields-3.0.59/RandomFields/src/Specific.cc | 6
RandomFields-3.0.59/RandomFields/src/Xempvario.cc | 7
RandomFields-3.0.59/RandomFields/src/auxiliary.cc | 43
RandomFields-3.0.59/RandomFields/src/avltr_modified.cc | 2
RandomFields-3.0.59/RandomFields/src/basic.h | 3
RandomFields-3.0.59/RandomFields/src/circulant.cc | 88
RandomFields-3.0.59/RandomFields/src/direct.cc | 36
RandomFields-3.0.59/RandomFields/src/empvario.cc | 4
RandomFields-3.0.59/RandomFields/src/extremes.cc | 51
RandomFields-3.0.59/RandomFields/src/families.cc | 6
RandomFields-3.0.59/RandomFields/src/fftVario.cc | 5
RandomFields-3.0.59/RandomFields/src/gauss.cc | 71
RandomFields-3.0.59/RandomFields/src/getNset.cc | 565 -
RandomFields-3.0.59/RandomFields/src/hilfsdateien.cc | 2
RandomFields-3.0.59/RandomFields/src/hyperplan.cc | 26
RandomFields-3.0.59/RandomFields/src/initNerror.cc | 471 -
RandomFields-3.0.59/RandomFields/src/kriging.cc | 52
RandomFields-3.0.59/RandomFields/src/nugget.cc | 12
RandomFields-3.0.59/RandomFields/src/operator.cc | 220
RandomFields-3.0.59/RandomFields/src/plusmalS.cc | 523 -
RandomFields-3.0.59/RandomFields/src/primitive.h | 47
RandomFields-3.0.59/RandomFields/src/rf_interfaces.cc | 387
RandomFields-3.0.59/RandomFields/src/sequential.cc | 30
RandomFields-3.0.59/RandomFields/src/shape_processes.h | 2
RandomFields-3.0.59/RandomFields/src/spectral.cc | 7
RandomFields-3.0.59/RandomFields/src/startGetNset.cc | 125
RandomFields-3.0.59/RandomFields/src/tbm.cc | 28
RandomFields-3.0.59/RandomFields/src/trend.cc | 58
RandomFields-3.0.59/RandomFields/src/userinterfaces.cc | 90
RandomFields-3.0.59/RandomFields/src/variogramAndCo.cc | 388
RandomFields-3.0.59/RandomFields/src/variogramAndCo.h | 163
134 files changed, 8627 insertions(+), 6337 deletions(-)
Title: Permutations and Mallows Distributions
Diff between PerMallows versions 1.7 dated 2014-09-15 and 1.8 dated 2015-01-27
Description: Includes functions to work with the Mallows, Generalized Mallows and Weighted Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances and the random generation of permutations.
Author: Ekhine Irurozki
Maintainer: Ekhine Irurozki
DESCRIPTION | 10
MD5 | 129 ++++++------
R/PerMallows.R | 86 +++++---
man/compose.Rd | 3
man/count.derangements.Rd | 3
man/count.perms.cycles.Rd | 3
man/count.perms.distance.Rd | 3
man/count.perms.fixed.points.Rd | 3
man/count.perms.unfixed.points.gtet.Rd | 3
man/cycle2str.Rd | 3
man/cycles2permutation.Rd | 3
man/data.apa.Rd | 3
man/data.order.Rd | 3
man/decomposition2permutation.Rd | 3
man/dgmm.Rd | 3
man/distance.Rd | 3
man/dmm.Rd | 3
man/expectation.gmm.Rd | 3
man/expectation.mm.Rd | 3
man/freq.matrix.Rd | 3
man/generate.aux.files.Rd | 3
man/identity.permutation.Rd | 3
man/insert.at.Rd | 3
man/inverse.permutation.Rd | 3
man/inversion.at.Rd | 3
man/is.permutation.Rd | 7
man/lgmm.Rd | 3
man/lgmm.theta.Rd | 3
man/lmm.Rd | 3
man/lmm.theta.Rd | 3
man/marginal.Rd | 3
man/maxi.dist.Rd |only
man/order.ratings.Rd | 3
man/perm.sample.med.Rd | 3
man/perm.sample.small.Rd | 3
man/permutation2cycles.Rd | 3
man/permutation2decomposition.Rd | 3
man/permutations.of.Rd | 3
man/r.derangement.Rd | 3
man/r.dist.d.Rd | 3
man/r.perms.cycles.Rd | 3
man/read.permutation.file.Rd | 3
man/rgmm.Rd | 3
man/rmm.Rd | 3
man/runif.permutation.Rd | 3
man/swap.Rd | 3
src/Cayley.cpp | 345 ++++++++++++---------------------
src/Cayley.h | 50 +++-
src/Ferrers_diagram.cpp | 6
src/Ferrers_diagram.h | 7
src/Generic.cpp | 113 ++--------
src/Generic.h | 18 -
src/Hamming.cpp | 201 ++-----------------
src/Hamming.h | 48 ++--
src/Kendall.cpp | 71 +++---
src/Kendall.h | 2
src/Lap.h | 2
src/Newton_raphson.cpp | 45 +---
src/Newton_raphson.h | 3
src/Ulam.cpp | 145 ++-----------
src/Ulam.h | 51 +---
src/Ulam_disk.cpp | 270 ++++++++++++++++---------
src/Ulam_disk.h | 47 ++--
src/Wrapper.cpp | 9
src/main.cpp | 86 ++++++--
vignettes/PerMallows.tex | 204 +++++++++----------
66 files changed, 943 insertions(+), 1135 deletions(-)
Title: Classification, Regression and Feature Evaluation
Diff between CORElearn versions 0.9.44 dated 2014-12-24 and 0.9.45 dated 2015-01-27
Description: The package is a port of stand-alone C++ software to R.
It contains several machine learning model learning techniques in classification and regression,
for example classification and regression trees with optional constructive induction and models in the leafs,
random forests, kNN, naive Bayes, and locally weighted regression.
It is especially strong in feature evaluation where it contains several variants of Relief
algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM.
Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja"
ChangeLog | 1
DESCRIPTION | 18 -
MD5 | 139 +++----
NAMESPACE | 37 +-
R/Rinterface.R | 74 ++--
R/rfVisualize.R | 14
man/CORElearn-package.Rd | 6
man/CoreModel.Rd | 6
man/attrEval.Rd | 6
man/classPrototypes.Rd | 2
man/destroyModels.Rd | 2
man/display.CoreModel.Rd |only
man/getCoreModel.Rd | 2
man/getRpartModel.Rd | 26 -
man/modelEval.Rd | 16
man/ordDataGen.Rd | 2
man/ordEval.Rd | 2
man/plot.CoreModel.Rd | 41 +-
man/plot.ordEval.Rd | 7
man/predict.CoreModel.Rd | 2
man/rfOutliers.Rd | 2
man/saveRF.Rd | 10
src/Rconvert.cpp | 21 -
src/Rfront.cpp | 85 ++--
src/Rfront.h | 21 +
src/binarize.cpp | 26 -
src/binarizeReg.cpp | 28 -
src/binnode.h | 4
src/binnodeReg.h | 5
src/c45read.cpp | 2
src/c45read.h | 8
src/calibrate.cpp | 8
src/calibrate.h | 2
src/constrct.cpp | 8
src/constrct.h | 17
src/constrctReg.cpp | 6
src/constrctReg.h | 17
src/contain.h | 4
src/dataStore.cpp | 19 -
src/dataStore.h | 10
src/estCommon.cpp | 38 +-
src/estimator.cpp | 42 +-
src/estimatorReg.cpp | 22 -
src/expr.cpp | 12
src/expr.h | 6
src/exprReg.cpp | 8
src/exprReg.h | 10
src/frontend.cpp | 18 -
src/ftree.cpp | 44 --
src/ftree.h | 14
src/general.h | 2
src/kdtree.cpp | 26 -
src/kdtree.h | 7
src/modelReg.cpp | 2
src/mstring.cpp | 8
src/mstring.h | 1
src/printUtil.cpp | 4
src/regtree.cpp | 45 --
src/regtree.h | 159 ++++----
src/relieff.cpp | 2
src/rfUtil.cpp | 1
src/rfVisual.cpp | 8
src/rndforest.cpp | 10
src/rndforest.h | 2
src/rrelieff.cpp | 6
src/treenode.cpp | 18 -
src/treenodeReg.cpp | 18 -
src/trutil.cpp | 279 +++++++++------
src/trutilReg.cpp | 842 +++++++++++++++++++++++++----------------------
src/utils.cpp | 2
src/utils.h | 11
71 files changed, 1303 insertions(+), 1070 deletions(-)
Title: Univariate and Multivariate Spatial-temporal Modeling
Diff between spBayes versions 0.3-8 dated 2013-11-15 and 0.3-9 dated 2015-01-27
Description: Fits univariate and multivariate spatio-temporal
models with Markov chain Monte Carlo (MCMC).
Author: Andrew O. Finley
Maintainer: Andrew O. Finley
DESCRIPTION | 10 +++++-----
MD5 | 27 ++++++++++++++-------------
NAMESPACE | 2 ++
inst/CITATION |only
inst/ChangeLog | 6 ++++++
man/spDynLM.Rd | 4 ++++
man/spGLM.Rd | 8 +++++++-
man/spLM.Rd | 4 ++++
man/spMisalignGLM.Rd | 2 ++
man/spMisalignLM.Rd | 2 ++
man/spMvGLM.Rd | 4 ++++
man/spMvLM.Rd | 4 ++++
man/spPredict.Rd | 4 ++++
man/spRecover.Rd | 4 ++++
src/spMisalign.cpp | 2 +-
15 files changed, 63 insertions(+), 20 deletions(-)
Title: Multidimensional Scaling in R: SMACOF.
Diff between smacof versions 1.5-0 dated 2014-06-23 and 1.6-2 dated 2015-01-27
Description: This package provides the following approaches of multidimensional
scaling (MDS) based on stress minimization by means of majorization
(smacof): Simple smacof (basic MDS) on symmetric dissimilarity matrices,
smacof for rectangular matrices (unfolding models), smacof with constraints
on the configuration, three-way smacof for individual differences
(including constraints for idioscal, indscal, and identity), and spherical
smacof (primal and dual algorithm). The MDS type can be ratio, interval, ordinal manner
(including primary, secondary, and tertiary approaches for tie handling), and msplines.
Jackknife and permutation tests are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Ingwer Borg [ctb], Patrick
J. F. Groenen [aut]
Maintainer: Patrick Mair
smacof-1.5-0/smacof/inst/doc |only
smacof-1.6-2/smacof/DESCRIPTION | 19 +++++-----
smacof-1.6-2/smacof/MD5 | 54 ++++++++++---------------------
smacof-1.6-2/smacof/NAMESPACE | 4 ++
smacof-1.6-2/smacof/R/idioscal.R |only
smacof-1.6-2/smacof/R/indscal.R |only
smacof-1.6-2/smacof/R/mds.R |only
smacof-1.6-2/smacof/R/plot.smacof.R | 8 ++--
smacof-1.6-2/smacof/R/plot.smacofID.r | 8 ++--
smacof-1.6-2/smacof/R/plot.smacofJK.R | 4 +-
smacof-1.6-2/smacof/R/plot.smacofR.R | 4 +-
smacof-1.6-2/smacof/R/print.smacofB.R | 2 -
smacof-1.6-2/smacof/R/smacofIndDiff.R | 26 ++++----------
smacof-1.6-2/smacof/R/smacofRect.R | 17 +++++----
smacof-1.6-2/smacof/R/smacofSym.R | 2 -
smacof-1.6-2/smacof/R/unfolding.R |only
smacof-1.6-2/smacof/inst/NEWS.Rd | 7 ++++
smacof-1.6-2/smacof/man/smacofIndDiff.Rd | 29 ++++++++++++++--
smacof-1.6-2/smacof/man/smacofRect.Rd | 14 +++-----
smacof-1.6-2/smacof/man/smacofSym.Rd | 18 ++++++----
20 files changed, 114 insertions(+), 102 deletions(-)
Title: Relative Distribution Methods
Diff between reldist versions 1.6-3 dated 2014-08-20 and 1.6-4 dated 2015-01-27
Description: R functions for the comparison of distributions.
This includes nonparametric estimation of the relative distribution
PDF and CDF and numerical summaries as described in
"Relative Distribution Methods in the Social Sciences"
by Mark S. Handcock and Martina Morris,
Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789
Author: Mark S. Handcock
Maintainer: Mark S. Handcock
DESCRIPTION | 10 +++++-----
LICENSE | 2 +-
MD5 | 20 ++++++++++----------
R/bgk_kde.R | 7 +++++--
R/reldist.R | 33 +++++++++++++++++++++++++++------
R/wtd.quantile.R | 2 +-
inst/CITATION | 6 +++---
man/gini.Rd | 4 ++--
man/precipitation.Rd | 2 +-
man/reldist.Rd | 24 +++++++++++++++---------
tests/FigSM.R | 3 ++-
11 files changed, 72 insertions(+), 41 deletions(-)
More information about quantification at CRAN
Permanent link
Title: Metric Unfolding
Diff between munfold versions 0.3-1 dated 2013-01-05 and 0.3-3 dated 2015-01-27
Description: This package provides Schoeneman's algorithm for metric
multidimensional unfolding and Procrustes rotation of unfolding results.
Author: Martin Elff
Maintainer: Martin Elff
DESCRIPTION | 18 ++++++++++--------
MD5 | 9 +++++----
NAMESPACE | 30 +++++++++++++++---------------
R/Unfold.R | 4 ++--
R/schoenemann.R | 5 ++---
inst |only
6 files changed, 34 insertions(+), 32 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Diff between icd9 versions 0.5 dated 2014-07-21 and 1.0 dated 2015-01-27
Description: Calculate comorbidities, and perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey
icd9-0.5/icd9/NEWS |only
icd9-0.5/icd9/data/elixhauserComorbid.RData |only
icd9-0.5/icd9/data/quanElixhauserComorbid.RData |only
icd9-0.5/icd9/inst/doc/icd9.Rnw |only
icd9-0.5/icd9/inst/extdata/ICD9_E_Charlson.sas.txt |only
icd9-0.5/icd9/inst/extdata/ccs_multi_pr_tool_2014.csv |only
icd9-0.5/icd9/inst/extdata/comoanaly2012-2013.txt |only
icd9-0.5/icd9/man/allIsNumeric.Rd |only
icd9-0.5/icd9/man/appendZeroToNine.Rd |only
icd9-0.5/icd9/man/asCharacterNoWarn.Rd |only
icd9-0.5/icd9/man/asNumericNoWarn.Rd |only
icd9-0.5/icd9/man/elixhauserComorbid.Rd |only
icd9-0.5/icd9/man/elixhauserComorbidNames.Rd |only
icd9-0.5/icd9/man/grapes-nin-grapes.Rd |only
icd9-0.5/icd9/man/icd9ChildrenDecimal.Rd |only
icd9-0.5/icd9/man/icd9ChildrenShort.Rd |only
icd9-0.5/icd9/man/icd9Comorbidities.Rd |only
icd9-0.5/icd9/man/icd9CondenseToExplain.Rd |only
icd9-0.5/icd9/man/icd9CondenseToMajor.Rd |only
icd9-0.5/icd9/man/icd9DecimalToParts.Rd |only
icd9-0.5/icd9/man/icd9DecimalToShort.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeDecimal.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeMajor.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeShort.Rd |only
icd9-0.5/icd9/man/icd9GetMajor.Rd |only
icd9-0.5/icd9/man/icd9InvalidActions.Rd |only
icd9-0.5/icd9/man/icd9InvalidDecimal.Rd |only
icd9-0.5/icd9/man/icd9IsVE.Rd |only
icd9-0.5/icd9/man/icd9ParentMinor.Rd |only
icd9-0.5/icd9/man/icd9PartsRecompose.Rd |only
icd9-0.5/icd9/man/icd9Real.Rd |only
icd9-0.5/icd9/man/icd9ShortToDecimal.Rd |only
icd9-0.5/icd9/man/icd9ShortToParts.Rd |only
icd9-0.5/icd9/man/icd9SortShort.Rd |only
icd9-0.5/icd9/man/icd9SubsequentMinors.Rd |only
icd9-0.5/icd9/man/icd9Valid.Rd |only
icd9-0.5/icd9/man/icd9ValidDecimal.Rd |only
icd9-0.5/icd9/man/icd9ValidMajor.Rd |only
icd9-0.5/icd9/man/icd9ValidMapping.Rd |only
icd9-0.5/icd9/man/icd9ValidNaWarnStop.Rd |only
icd9-0.5/icd9/man/icd9ValidShort.Rd |only
icd9-0.5/icd9/man/icd9WarnStopMessage.Rd |only
icd9-0.5/icd9/man/parseElixhauser.Rd |only
icd9-0.5/icd9/man/parseQuanElixhauser.Rd |only
icd9-0.5/icd9/man/quanElixhauserComorbid.Rd |only
icd9-0.5/icd9/man/saveSourceTreeData.Rd |only
icd9-0.5/icd9/man/spawnReferenceChildren.Rd |only
icd9-0.5/icd9/man/stopIfInvalidIcd9.Rd |only
icd9-0.5/icd9/man/strip.Rd |only
icd9-0.5/icd9/man/trim.Rd |only
icd9-0.5/icd9/tests/testthat/test-comorbid.R |only
icd9-0.5/icd9/tests/testthat/test-convert.R |only
icd9-0.5/icd9/tests/testthat/test-explain.R |only
icd9-0.5/icd9/tests/testthat/test-icd9.R |only
icd9-0.5/icd9/tests/testthat/test-ranges.R |only
icd9-0.5/icd9/tests/testthat/test-sas.R |only
icd9-0.5/icd9/tests/testthat/test-validation.R |only
icd9-0.5/icd9/vignettes/icd9-concordance.tex |only
icd9-0.5/icd9/vignettes/icd9.Rnw |only
icd9-1.0/icd9/DESCRIPTION | 40 -
icd9-1.0/icd9/MD5 | 238 +++----
icd9-1.0/icd9/NAMESPACE | 85 +-
icd9-1.0/icd9/R/RcppExports.R |only
icd9-1.0/icd9/R/RcppExportsShim.R |only
icd9-1.0/icd9/R/benchmark.R | 166 ++++-
icd9-1.0/icd9/R/comorbid.R | 492 +++++++--------
icd9-1.0/icd9/R/convert.R | 374 ++++--------
icd9-1.0/icd9/R/datadocs.R | 66 +-
icd9-1.0/icd9/R/explain.R | 378 ++++++------
icd9-1.0/icd9/R/filter.R |only
icd9-1.0/icd9/R/icd9-package.R | 124 ++-
icd9-1.0/icd9/R/manip.R | 149 ----
icd9-1.0/icd9/R/old.R |only
icd9-1.0/icd9/R/parse.R | 468 +++++++++------
icd9-1.0/icd9/R/ranges.R | 561 ++++--------------
icd9-1.0/icd9/R/sas.R | 96 +--
icd9-1.0/icd9/R/score.R |only
icd9-1.0/icd9/R/sysdata.rda |only
icd9-1.0/icd9/R/util.R | 242 +++----
icd9-1.0/icd9/R/valid.R | 460 +++++---------
icd9-1.0/icd9/R/zzz.R | 19
icd9-1.0/icd9/README.md | 122 ++-
icd9-1.0/icd9/build/vignette.rds |binary
icd9-1.0/icd9/data/ahrqComorbid.RData |binary
icd9-1.0/icd9/data/ahrqComorbidAll.RData |binary
icd9-1.0/icd9/data/elixComorbid.RData |only
icd9-1.0/icd9/data/icd9Chapters.RData |binary
icd9-1.0/icd9/data/icd9ChaptersMajor.RData |binary
icd9-1.0/icd9/data/icd9ChaptersSub.RData |binary
icd9-1.0/icd9/data/icd9Hierarchy.RData |binary
icd9-1.0/icd9/data/mappingNames.rda |binary
icd9-1.0/icd9/data/quanDeyoComorbid.RData |binary
icd9-1.0/icd9/data/quanElixComorbid.RData |only
icd9-1.0/icd9/inst/COPYING |only
icd9-1.0/icd9/inst/COPYRIGHTS |only
icd9-1.0/icd9/inst/doc/icd9.R | 244 ++++---
icd9-1.0/icd9/inst/doc/icd9.pdf |binary
icd9-1.0/icd9/inst/doc/introduction.R |only
icd9-1.0/icd9/inst/doc/introduction.Rmd |only
icd9-1.0/icd9/inst/doc/introduction.html |only
icd9-1.0/icd9/inst/extdata/ICD9_E_Charlson.sas |only
icd9-1.0/icd9/inst/extdata/ICD9_E_Elixhauser.sas |only
icd9-1.0/icd9/inst/include |only
icd9-1.0/icd9/man/ahrqComorbid.Rd | 5
icd9-1.0/icd9/man/ahrqComorbidAll.Rd | 6
icd9-1.0/icd9/man/convert.Rd |only
icd9-1.0/icd9/man/elixComorbid.Rd |only
icd9-1.0/icd9/man/elixComorbidNames.Rd |only
icd9-1.0/icd9/man/icd9-package.Rd | 123 ++-
icd9-1.0/icd9/man/icd9AddLeadingZeroes.Rd | 70 --
icd9-1.0/icd9/man/icd9Benchmark.Rd | 4
icd9-1.0/icd9/man/icd9Chapters.Rd | 8
icd9-1.0/icd9/man/icd9ChaptersToMap.Rd | 23
icd9-1.0/icd9/man/icd9Charlson.Rd |only
icd9-1.0/icd9/man/icd9Children.Rd |only
icd9-1.0/icd9/man/icd9Comorbid.Rd |only
icd9-1.0/icd9/man/icd9Condense.Rd |only
icd9-1.0/icd9/man/icd9Count.Rd |only
icd9-1.0/icd9/man/icd9DiffComorbid.Rd |only
icd9-1.0/icd9/man/icd9DropLeadingZeroes.Rd | 71 --
icd9-1.0/icd9/man/icd9ExpandMinor.Rd | 44 -
icd9-1.0/icd9/man/icd9ExpandRange.Rd |only
icd9-1.0/icd9/man/icd9Explain.Rd | 61 +
icd9-1.0/icd9/man/icd9ExtractAlphaNumeric.Rd | 6
icd9-1.0/icd9/man/icd9FilterInvalid.Rd |only
icd9-1.0/icd9/man/icd9FilterPoa.Rd | 39 -
icd9-1.0/icd9/man/icd9FilterValid.Rd |only
icd9-1.0/icd9/man/icd9GenerateSysData.Rd |only
icd9-1.0/icd9/man/icd9GetChapters.Rd | 12
icd9-1.0/icd9/man/icd9GetValid.Rd |only
icd9-1.0/icd9/man/icd9GuessIsShort.Rd | 5
icd9-1.0/icd9/man/icd9Hierarchy.Rd | 3
icd9-1.0/icd9/man/icd9InReferenceCode.Rd | 45 -
icd9-1.0/icd9/man/icd9Is.Rd |only
icd9-1.0/icd9/man/icd9IsReal.Rd |only
icd9-1.0/icd9/man/icd9IsValid.Rd |only
icd9-1.0/icd9/man/icd9IsValidMapping.Rd |only
icd9-1.0/icd9/man/icd9LongToWide.Rd |only
icd9-1.0/icd9/man/icd9ParseAndSaveMappings.Rd | 7
icd9-1.0/icd9/man/icd9PoaChoices.Rd | 3
icd9-1.0/icd9/man/icd9Sort.Rd |only
icd9-1.0/icd9/man/icd9WideToLong.Rd |only
icd9-1.0/icd9/man/logicalToBinary.Rd | 16
icd9-1.0/icd9/man/parseAhrqSas.Rd | 8
icd9-1.0/icd9/man/parseElix.Rd |only
icd9-1.0/icd9/man/parseIcd9Chapters.Rd | 24
icd9-1.0/icd9/man/parseIcd9Descriptions.Rd | 6
icd9-1.0/icd9/man/parseQuanDeyoSas.Rd | 12
icd9-1.0/icd9/man/parseQuanElix.Rd |only
icd9-1.0/icd9/man/quanDeyoComorbid.Rd | 5
icd9-1.0/icd9/man/quanElixComorbid.Rd |only
icd9-1.0/icd9/man/read.zip.url.Rd | 3
icd9-1.0/icd9/man/sasDropOtherAssignment.Rd | 12
icd9-1.0/icd9/man/sasExtractLetStrings.Rd | 11
icd9-1.0/icd9/man/sasFormatExtract.Rd | 12
icd9-1.0/icd9/man/sasParseAssignments.Rd | 6
icd9-1.0/icd9/man/strMultiMatch.Rd | 15
icd9-1.0/icd9/src |only
icd9-1.0/icd9/tests/testthat/helper-base.R |only
icd9-1.0/icd9/tests/testthat/test-fast-convert.R |only
icd9-1.0/icd9/tests/testthat/test-fast-explain.R |only
icd9-1.0/icd9/tests/testthat/test-fast-icd9.R |only
icd9-1.0/icd9/tests/testthat/test-fast-ranges.R |only
icd9-1.0/icd9/tests/testthat/test-fast-reshape.R |only
icd9-1.0/icd9/tests/testthat/test-fast-sas.R |only
icd9-1.0/icd9/tests/testthat/test-fast-score.R |only
icd9-1.0/icd9/tests/testthat/test-fast-valid.R |only
icd9-1.0/icd9/tests/testthat/test-is.R |only
icd9-1.0/icd9/tests/testthat/test-slow-comorbid.R |only
icd9-1.0/icd9/tests/testthat/test-slow-score.R |only
icd9-1.0/icd9/tests/testthat/test-util.R | 55 +
icd9-1.0/icd9/vignettes/introduction.Rmd |only
172 files changed, 2489 insertions(+), 2555 deletions(-)
Title: Export grid Graphics as SVG
Diff between gridSVG versions 1.4-2 dated 2014-12-16 and 1.4-3 dated 2015-01-27
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/gridsvg.R | 38 ++++++++++++++++++++++++--------------
R/svg.R | 11 +++++++----
inst/NEWS.Rd | 14 ++++++++++++++
inst/doc/animation.pdf |binary
inst/doc/extensibility.pdf |binary
inst/doc/gridSVG.pdf |binary
8 files changed, 57 insertions(+), 30 deletions(-)
Title: Analysis and Modeling for Geostatistical Count Data
Diff between geoCount versions 1.131209 dated 2013-12-09 and 1.150120 dated 2015-01-27
Description: This package provides a variety of functions to analyze and model geostatistical count data with generalized linear spatial models, including
1) simulate and visualize the data;
2) posterior sampling with robust MCMC algorithms (in serial or parallel way);
3) perform prediction for unsampled locations;
4) conduct Bayesian model checking procedure to evaluate the goodness of fitting;
5) conduct transformed residual checking procedure.
In the package, seamlessly embedded C++ programs and parallel computing techniques are implemented to speed up the computing processes.
Author: Liang Jing
Maintainer: Liang Jing
DESCRIPTION | 13
MD5 | 13
NAMESPACE | 1
R/checkingTRC.R | 248 ++++++------
R/runMCMC.R | 822 +++++++++++++++++++++----------------------
inst/CITATION |only
inst/doc/geoCount_HowtoUse.R | 598 +++++++++++++++----------------
src/Makevars | 8
8 files changed, 868 insertions(+), 835 deletions(-)