Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package 'CDVine' are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler, Thomas Nagler, Tobias Erhardt
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>
Diff between VineCopula versions 1.5 dated 2015-06-05 and 1.6 dated 2015-07-22
VineCopula-1.5/VineCopula/tests/TRUEadditonalExampleRuns.Rout.save |only VineCopula-1.6/VineCopula/DESCRIPTION | 11 VineCopula-1.6/VineCopula/MD5 | 29 VineCopula-1.6/VineCopula/NAMESPACE | 9 VineCopula-1.6/VineCopula/R/BiCopCDF.r | 6 VineCopula-1.6/VineCopula/R/ClaytonGumbelCopula.R | 870 +++---- VineCopula-1.6/VineCopula/R/RVineMLE.R | 954 +++---- VineCopula-1.6/VineCopula/R/RVineStructureSelect.r | 1226 +++++----- VineCopula-1.6/VineCopula/R/RVineTreePlot.r | 90 VineCopula-1.6/VineCopula/inst/ChangeLog | 13 VineCopula-1.6/VineCopula/man/BiCopGofTest.Rd | 4 VineCopula-1.6/VineCopula/man/RVineTreePlot.Rd | 3 VineCopula-1.6/VineCopula/man/VineCopula-package.Rd | 6 VineCopula-1.6/VineCopula/src/hfunc.c | 2 VineCopula-1.6/VineCopula/tests/Examples/VineCopula-Ex.Rout.save | 45 VineCopula-1.6/VineCopula/tests/additonalExampleRuns.Rout.save | 4 16 files changed, 1684 insertions(+), 1588 deletions(-)
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson
Maintainer: John Lawson <lawson@byu.edu>
Diff between daewr versions 1.1-4 dated 2014-12-17 and 1.1-6 dated 2015-07-22
DESCRIPTION | 17 ++---- MD5 | 130 ++++++++++++++++++++++++++-------------------------- NAMESPACE | 24 ++++----- R/Tukey1df.R | 2 data/Apo.rda |binary data/BPmonitor.rda |binary data/Bdish.rda |binary data/Bff.rda |binary data/BoxM.rda |binary data/COdata.rda |binary data/MPV.rda |binary data/Naph.rda |binary data/SPMPV.rda |binary data/Smotor.rda |binary data/Tet.rda |binary data/Treb.rda |binary data/antifungal.rda |binary data/apple.rda |binary data/arso.rda |binary data/augm.rda |binary data/bha.rda |binary data/bioequiv.rda |binary data/bioeqv.rda |binary data/blood.rda |binary data/bread.rda |binary data/cake.rda |binary data/cement.rda |binary data/chem.rda |binary data/chipman.rda |binary data/cont.rda |binary data/cpipe.rda |binary data/culture.rda |binary data/dairy.rda |binary data/drug.rda |binary data/eptaxr.rda |binary data/eptaxs2.rda |binary data/eptaxyb.rda |binary data/gagerr.rda |binary data/gear.rda |binary data/hardwood.rda |binary data/inject.rda |binary data/pastry.rda |binary data/pest.rda |binary data/pesticide.rda |binary data/plasma.rda |binary data/polvdat.rda |binary data/polymer.rda |binary data/prodstd.rda |binary data/qsar.rda |binary data/rcb.rda |binary data/residue.rda |binary data/rubber.rda |binary data/sausage.rda |binary data/soup.rda |binary data/soupmx.rda |binary data/splitPdes.rda |binary data/strung.rda |binary data/strungtile.rda |binary data/sugarbeet.rda |binary data/taste.rda |binary data/teach.rda |binary data/tile.rda |binary data/virus.rda |binary data/volt.rda |binary data/web.rda |binary man/Tukey1df.Rd | 2 66 files changed, 85 insertions(+), 90 deletions(-)
Title: Semiparametric Bivariate Regression Models
Description: Routine for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.4 dated 2015-06-11 and 3.5 dated 2015-07-22
ChangeLog | 7 DESCRIPTION | 11 MD5 | 55 +++- NAMESPACE | 16 + R/AT.r | 457 +++++++++++++++++++++++++++++++++++----- R/BiCDF.r | 6 R/OR.r |only R/RR.r |only R/SemiParBIVProbit.r | 26 +- R/copgHs2.r |only R/prev.r | 127 ++++++++++- R/print.AT.r | 8 R/print.OR.r |only R/print.RR.r |only R/resp.check.R | 5 R/summary.SemiParBIVProbit.r | 29 +- data |only man/AT.Rd | 47 ++-- man/OR.Rd |only man/RR.Rd |only man/SemiParBIVProbit-package.Rd | 4 man/SemiParBIVProbit.Rd | 110 ++++++--- man/SemiParBIVProbitObject.Rd | 2 man/copgHs2.Rd |only man/hiv.Rd |only man/logLik.SemiParBIVProbit.Rd | 2 man/mb.Rd | 5 man/meps.Rd |only man/plot.SemiParBIVProbit.Rd | 3 man/prev.Rd | 16 - man/print.OR.Rd |only man/print.RR.Rd |only man/resp.check.Rd | 4 man/war.Rd |only 34 files changed, 758 insertions(+), 182 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.7 dated 2015-07-10 and 0.8 dated 2015-07-22
DESCRIPTION | 8 MD5 | 44 NAMESPACE | 3 R/auxilaryfunctions.R | 2348 ++++++++++++++++++++++------------------- R/boral.jags.R | 343 +++-- inst/NEWS.Rd | 84 - man/boral-package.Rd | 12 man/boral.Rd | 214 ++- man/calc.condlogLik.Rd | 31 man/calc.logLik.lv0.Rd | 27 man/calc.marglogLik.Rd | 40 man/create.life.Rd | 73 - man/fitted.boral.Rd | 2 man/get.enviro.cor.Rd | 6 man/get.hpdintervals.Rd | 15 man/get.measures.Rd | 31 man/get.more.measures.Rd | 7 man/get.residual.cor.Rd | 10 man/lvsplot.Rd | 9 man/make.jagsboralmodel.Rd | 56 man/make.jagsboralnullmodel.Rd | 54 man/plot.boral.Rd | 2 man/summary.boral.Rd | 2 23 files changed, 1971 insertions(+), 1450 deletions(-)
Title: Analysis of Habitat Selection by Animals
Description: A collection of tools for the analysis of habitat selection by animals.
Author: Clement Calenge, contributions from Mathieu Basille, Stephane Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitat versions 1.8.17 dated 2015-03-27 and 1.8.18 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 4 ++++ src/tests.c | 2 +- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: PPI and Gaussian Network Construction from Transcriptomic
Analysis Results Integrating a Multilevel Factor
Description: A toolbox for a construction of protein-protein interaction networks through the 'STRING' application programming interface, and an inference of Gaussian networks through 'SIMoNe' and 'WGCNA' approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active 'Cytoscape' session.
Author: Emmanuel Chaplais, Henri-Jean Garchon
Maintainer: Emmanuel Chaplais <emmanuel.chaplais@inserm.fr>
Diff between stringgaussnet versions 1.0 dated 2015-06-16 and 1.1 dated 2015-07-22
stringgaussnet-1.0/stringgaussnet/build/partial.rdb |only stringgaussnet-1.1/stringgaussnet/DESCRIPTION | 15 ++-- stringgaussnet-1.1/stringgaussnet/MD5 | 34 ++++++---- stringgaussnet-1.1/stringgaussnet/NAMESPACE | 4 + stringgaussnet-1.1/stringgaussnet/R/convertAliases.R | 1 stringgaussnet-1.1/stringgaussnet/R/getSTRINGNet.R | 2 stringgaussnet-1.1/stringgaussnet/R/plot.WGCNANet.R | 2 stringgaussnet-1.1/stringgaussnet/R/print.SIMoNeNet.R | 2 stringgaussnet-1.1/stringgaussnet/R/saveCytoscapeSession.R | 2 stringgaussnet-1.1/stringgaussnet/build/vignette.rds |only stringgaussnet-1.1/stringgaussnet/data/SpASamples.rda |binary stringgaussnet-1.1/stringgaussnet/inst |only stringgaussnet-1.1/stringgaussnet/man/SpASamples.Rd | 1 stringgaussnet-1.1/stringgaussnet/man/getSTRINGNet.Rd | 2 stringgaussnet-1.1/stringgaussnet/man/stringgaussnet-package.Rd | 30 ++------ stringgaussnet-1.1/stringgaussnet/vignettes |only 16 files changed, 50 insertions(+), 45 deletions(-)
More information about stringgaussnet at CRAN
Permanent link
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb],
Martin Maechler [ctb],
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-2 dated 2014-12-18 and 1.0-3 dated 2015-07-22
DESCRIPTION | 12 ++-- MD5 | 24 ++++----- NAMESPACE | 5 +- R/mvt.R | 106 ++++++++++++++++--------------------------- build/vignette.rds |binary inst/CITATION | 2 inst/NEWS | 9 +++ inst/doc/MVT_Rnews.pdf |binary man/pmvt.Rd | 1 man/qmvnorm.Rd | 19 +++---- man/qmvt.Rd | 43 ++++++++++------- tests/bugfix-tests.R | 17 ++++++ tests/bugfix-tests.Rout.save | 68 ++++++++++++++++++++------- 13 files changed, 175 insertions(+), 131 deletions(-)
Title: Hybrid Hierarchical Clustering
Description: Hybrid hierarchical clustering via mutual clusters. A mutual cluster is a set of points closer to each other than to all other points. Mutual clusters are used to enrich top-down hierarchical clustering.
Author: Hugh Chipman, Rob Tibshirani, with tsvq code originally from Trevor Hastie
Maintainer: Hugh Chipman <hugh.chipman@acadiau.ca>
Diff between hybridHclust versions 1.0-4 dated 2011-08-12 and 1.0-5 dated 2015-07-22
DESCRIPTION | 19 +++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 5 ++++- data/sorlielabels.RData |binary demo/hybridHclust.R | 2 +- man/hybridHclust.Rd | 1 - man/mutualCluster.Rd | 1 - man/print.mutualCluster.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Data for "GAMs: An Introduction with R"
Description: Data sets and scripts used in the book "Generalized
Additive Models: An Introduction with R", Wood (2006) CRC.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamair versions 0.0-8 dated 2012-03-27 and 0.0-9 dated 2015-07-22
gamair-0.0-8/gamair/changelog |only gamair-0.0-9/gamair/ChangeLog |only gamair-0.0-9/gamair/DESCRIPTION | 7 ++++--- gamair-0.0-9/gamair/MD5 | 12 ++++++------ gamair-0.0-9/gamair/man/cairo.Rd | 2 +- gamair-0.0-9/gamair/man/chl.Rd | 2 +- gamair-0.0-9/gamair/man/co2s.Rd | 2 +- gamair-0.0-9/gamair/man/engine.Rd | 5 +++-- 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Tools to Deal with Raster Maps
Description: A collection of tools to deal with raster maps.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatMA versions 0.3.9 dated 2015-03-27 and 0.3.10 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 4 +++- src/tests.c | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Analysis of Animal Movements
Description: A collection of tools for the analysis of animal movements.
Author: Clement Calenge, contributions from Stephane Dray and Manuela Royer
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatLT versions 0.3.19 dated 2015-03-29 and 0.3.20 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ inst/doc/adehabitatLT.pdf |binary src/tests.c | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Analysis of Habitat Selection by Animals
Description: A collection of tools for the analysis of habitat selection.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatHS versions 0.3.11 dated 2015-03-27 and 0.3.12 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 3 +++ src/tests.c | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Home Range Estimation
Description: A collection of tools for the estimation of animals home range.
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatHR versions 0.4.13 dated 2015-03-27 and 0.4.14 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ R/BRB.r | 4 +++- src/tests.c | 12 ++++++++---- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Ancona "Politecnica delle Marche")
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.1 dated 2015-06-07 and 1.2 dated 2015-07-22
DESCRIPTION | 12 ++--- MD5 | 22 ++++----- NAMESPACE | 4 + R/cquad_basic.R | 33 ++++++++----- R/cquad_equ.R | 26 +++++++--- R/cquad_ext.R | 121 ++++++++++++--------------------------------------- R/cquad_pseudo.R | 12 ++--- R/summary.cquad.R | 2 man/cquad-package.Rd | 4 - man/cquad_basic.Rd | 1 man/cquad_equ.Rd | 1 man/cquad_ext.Rd | 1 12 files changed, 102 insertions(+), 137 deletions(-)
More information about PlotPrjNetworks at CRAN
Permanent link
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov <valentin.todorov@chello.at>,
Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Tobias Verbeke <tobias.verbeke@openanalytics.eu>,
Manuel Koller <mkoller@ispm.unibe.ch>,
Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-4 dated 2015-06-10 and 0.92-5 dated 2015-07-22
DESCRIPTION | 10 ++-- MD5 | 58 ++++++++++++++-------------- NAMESPACE | 10 ++-- R/MTestimador2.R | 8 ++- R/glmrob.R | 5 -- R/lmrob.MM.R | 1 R/lmrob.R | 82 ++++++++++++++++++++-------------------- R/nlrob.R | 17 +++++++- TODO | 2 inst/NEWS.Rd | 23 ++++++++++- inst/doc/estimating.functions.R | 2 inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary man/radarImage.Rd | 1 man/summary.lmrob.Rd | 18 +++++--- tests/NAcoef.R | 25 ++++++++---- tests/NAcoef.Rout.save | 50 ++++++++++-------------- tests/binom-ni-small.Rout.save | 14 +++--- tests/glmrob-1.R | 13 ++---- tests/lmrob-psifns.R | 7 --- tests/lmrob-psifns.Rout.save | 19 +++------ tests/poisson-ex.R | 39 +++++++++++++++---- vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 30 files changed, 230 insertions(+), 174 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Author: Francois Michonneau [aut, cre],
Ben Bolker [aut],
Mark Holder [aut],
Paul Lewis [aut],
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.4.0 dated 2015-07-09 and 0.6.0 dated 2015-07-22
rncl-0.4.0/rncl/src/ancestors.c |only rncl-0.4.0/rncl/src/descendants.c |only rncl-0.4.0/rncl/src/phyloXX.c |only rncl-0.4.0/rncl/src/reorderBinary.c |only rncl-0.4.0/rncl/src/reorderRobust.c |only rncl-0.6.0/rncl/DESCRIPTION | 10 +- rncl-0.6.0/rncl/MD5 | 28 +++---- rncl-0.6.0/rncl/NAMESPACE | 1 rncl-0.6.0/rncl/R/collapse_singles.R |only rncl-0.6.0/rncl/R/rncl-package.R | 1 rncl-0.6.0/rncl/R/rncl.R | 60 +++++++--------- rncl-0.6.0/rncl/README.md | 15 ++-- rncl-0.6.0/rncl/inst/nexusfiles/test_empty.nex |only rncl-0.6.0/rncl/inst/nexusfiles/test_subset_alltaxa.nex |only rncl-0.6.0/rncl/inst/nexusfiles/test_subset_taxa.nex | 5 - rncl-0.6.0/rncl/man/read_nexus_phylo.Rd | 2 rncl-0.6.0/rncl/man/rncl.Rd | 14 +-- rncl-0.6.0/rncl/src/GetNCL.cpp | 59 ++++++++++++--- rncl-0.6.0/rncl/tests/testthat/test.rncl.R | 48 ++++++++++++ 19 files changed, 155 insertions(+), 88 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.3 dated 2015-02-23 and 1.4 dated 2015-07-22
RJSDMX-1.3/RJSDMX/man/geCodes.Rd |only RJSDMX-1.4/RJSDMX/DESCRIPTION | 6 RJSDMX-1.4/RJSDMX/MD5 | 31 +- RJSDMX-1.4/RJSDMX/NAMESPACE | 1 RJSDMX-1.4/RJSDMX/R/SdmxClient.R | 256 +++++++++++++++++++++--- RJSDMX-1.4/RJSDMX/R/TSConverter.R | 56 +++-- RJSDMX-1.4/RJSDMX/inst/java/SDMX.jar |binary RJSDMX-1.4/RJSDMX/man/addProvider.Rd | 62 ++--- RJSDMX-1.4/RJSDMX/man/getCodes.Rd |only RJSDMX-1.4/RJSDMX/man/getDSDIdentifier.Rd | 48 +--- RJSDMX-1.4/RJSDMX/man/getDimensions.Rd | 45 +--- RJSDMX-1.4/RJSDMX/man/getFlows.Rd | 77 +++---- RJSDMX-1.4/RJSDMX/man/getProviders.Rd | 55 +---- RJSDMX-1.4/RJSDMX/man/getSDMX.Rd | 80 +++---- RJSDMX-1.4/RJSDMX/man/getTimeSeries.Rd | 59 ++--- RJSDMX-1.4/RJSDMX/man/getTimeSeriesRevisions.Rd |only RJSDMX-1.4/RJSDMX/man/sdmxHelp.Rd | 63 ++--- RJSDMX-1.4/RJSDMX/man/sdmxdf.Rd | 75 +++---- 18 files changed, 518 insertions(+), 396 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram
visualization for the structure of RDML object.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between RDML versions 0.8-4 dated 2015-04-21 and 0.9-1 dated 2015-07-22
RDML-0.8-4/RDML/R/names.RDML.R |only RDML-0.8-4/RDML/man/RDML.class.Rd |only RDML-0.8-4/RDML/man/merge-method.Rd |only RDML-0.8-4/RDML/man/names.RDML.Rd |only RDML-0.9-1/RDML/CHANGELOG | 3 RDML-0.9-1/RDML/DESCRIPTION | 18 RDML-0.9-1/RDML/MD5 | 96 +- RDML-0.9-1/RDML/NAMESPACE | 73 + RDML-0.9-1/RDML/R/RDML.AsDendrogram.R | 32 RDML-0.9-1/RDML/R/RDML.AsTable.R | 39 RDML-0.9-1/RDML/R/RDML.GetFData.R | 118 -- RDML-0.9-1/RDML/R/RDML.Merge.R | 56 - RDML-0.9-1/RDML/R/RDML.R | 562 ++----------- RDML-0.9-1/RDML/R/RDML.SetFData.R | 130 ++- RDML-0.9-1/RDML/R/RDML.asserts.R | 233 +++-- RDML-0.9-1/RDML/R/RDML.init.R | 840 ++++++++++---------- RDML-0.9-1/RDML/R/RDML.types.R |only RDML-0.9-1/RDML/R/functional_wrappers.R |only RDML-0.9-1/RDML/README.md | 4 RDML-0.9-1/RDML/build |only RDML-0.9-1/RDML/inst/doc |only RDML-0.9-1/RDML/man/AsDendrogram-function.Rd |only RDML-0.9-1/RDML/man/GetFData-function.Rd |only RDML-0.9-1/RDML/man/MergeRDMLs.Rd |only RDML-0.9-1/RDML/man/RDML.Rd |only RDML-0.9-1/RDML/man/adpsType.Rd |only RDML-0.9-1/RDML/man/annotationType.Rd |only RDML-0.9-1/RDML/man/asdendrogram-method.Rd | 61 - RDML-0.9-1/RDML/man/astable-function.Rd |only RDML-0.9-1/RDML/man/astable-method.Rd | 155 +-- RDML-0.9-1/RDML/man/baseTemperatureType.Rd |only RDML-0.9-1/RDML/man/cdnaSynthesisMethodType.Rd |only RDML-0.9-1/RDML/man/commercialAssayType.Rd |only RDML-0.9-1/RDML/man/cqDetectionMethodType.Rd |only RDML-0.9-1/RDML/man/dataCollectionSoftwareType.Rd |only RDML-0.9-1/RDML/man/dataType.Rd |only RDML-0.9-1/RDML/man/documentationType.Rd |only RDML-0.9-1/RDML/man/dyeType.Rd |only RDML-0.9-1/RDML/man/enumType.Rd |only RDML-0.9-1/RDML/man/experimentType.Rd |only RDML-0.9-1/RDML/man/experimenterType.Rd |only RDML-0.9-1/RDML/man/getfdata-method.Rd | 109 +- RDML-0.9-1/RDML/man/gradientType.Rd |only RDML-0.9-1/RDML/man/idReferencesType.Rd |only RDML-0.9-1/RDML/man/idType.Rd |only RDML-0.9-1/RDML/man/labelFormatType.Rd |only RDML-0.9-1/RDML/man/lidOpenType.Rd |only RDML-0.9-1/RDML/man/loopType.Rd |only RDML-0.9-1/RDML/man/mdpsType.Rd |only RDML-0.9-1/RDML/man/measureType.Rd |only RDML-0.9-1/RDML/man/new-method.Rd | 80 - RDML-0.9-1/RDML/man/nucleotideType.Rd |only RDML-0.9-1/RDML/man/oligoType.Rd |only RDML-0.9-1/RDML/man/pauseType.Rd |only RDML-0.9-1/RDML/man/pcrFormatType.Rd |only RDML-0.9-1/RDML/man/primingMethodType.Rd |only RDML-0.9-1/RDML/man/quantityType.Rd |only RDML-0.9-1/RDML/man/quantityUnitType.Rd |only RDML-0.9-1/RDML/man/rdmlBaseType.Rd |only RDML-0.9-1/RDML/man/rdmlIdType.Rd |only RDML-0.9-1/RDML/man/reactIdType.Rd |only RDML-0.9-1/RDML/man/reactType.Rd |only RDML-0.9-1/RDML/man/runType.Rd |only RDML-0.9-1/RDML/man/sampleType.Rd |only RDML-0.9-1/RDML/man/sampleTypeType.Rd |only RDML-0.9-1/RDML/man/sequencesType.Rd |only RDML-0.9-1/RDML/man/setfdata-function.Rd |only RDML-0.9-1/RDML/man/setfdata-method.Rd | 105 +- RDML-0.9-1/RDML/man/stepType.Rd |only RDML-0.9-1/RDML/man/targetType.Rd |only RDML-0.9-1/RDML/man/targetTypeType.Rd |only RDML-0.9-1/RDML/man/temperatureType.Rd |only RDML-0.9-1/RDML/man/templateQuantityType.Rd |only RDML-0.9-1/RDML/man/thermalCyclingConditionsType.Rd |only RDML-0.9-1/RDML/man/xRefType.Rd |only RDML-0.9-1/RDML/vignettes |only 76 files changed, 1342 insertions(+), 1372 deletions(-)
Title: Distance Sampling Analyses
Description: Analysis of distance sampling data collected on line transect surveys. Estimates distance-based detection functions and abundances.
Author: Trent McDonald [cre, aut],
Ryan Nielson [aut],
Jason Carlisle [aut],
Ben Augustine [ctb],
James Griswald [ctb],
Joel Reynolds [ctb],
Pham Quang [ctb],
Earl Becker [ctb],
Aaron Christ [ctb],
Brook Russelland [ctb],
Patrick McKann [ctb]
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between Rdistance versions 1.2.2 dated 2015-04-22 and 1.3.2 dated 2015-07-22
DESCRIPTION | 13 +-- MD5 | 64 ++++++++------- NAMESPACE | 5 + R/F.abund.estim.r | 98 ++++++++++++++---------- R/F.automated.CDA.r | 13 +-- R/F.start.limits.r | 2 R/zzz.R | 4 build/vignette.rds |binary data/sparrow.detections.rda |binary data/sparrow.transects.rda |binary inst/doc/Rdistance_BeginnerTutorial.R | 9 +- inst/doc/Rdistance_BeginnerTutorial.Rmd | 21 ++--- inst/doc/Rdistance_BeginnerTutorial.pdf |binary inst/doc/Rdistance_CustomDetectionFunction.R | 6 - inst/doc/Rdistance_CustomDetectionFunction.Rmd | 11 +- inst/doc/Rdistance_CustomDetectionFunction.pdf |binary inst/doc/Rdistance_ModelingAbundance.R |only inst/doc/Rdistance_ModelingAbundance.Rmd |only inst/doc/Rdistance_ModelingAbundance.pdf |only man/AIC.dfunc.Rd | 8 - man/ESW.Rd | 8 - man/F.abund.estim.Rd | 31 +++---- man/F.automated.CDA.Rd | 20 +--- man/F.dfunc.estim.Rd | 10 -- man/Gamma.like.Rd | 14 ++- man/coef.dfunc.Rd | 8 - man/perp.dists.Rd | 2 man/print.abund.Rd | 20 +++- man/print.dfunc.Rd | 15 ++- man/sparrow.detections.Rd | 4 man/sparrow.transects.Rd | 7 - man/uniform.like.Rd | 19 ++-- vignettes/Rdistance_BeginnerTutorial.Rmd | 21 ++--- vignettes/Rdistance_CustomDetectionFunction.Rmd | 11 +- vignettes/Rdistance_ModelingAbundance.Rmd |only 35 files changed, 232 insertions(+), 212 deletions(-)
Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between nadiv versions 2.14.0 dated 2015-07-03 and 2.14.1 dated 2015-07-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/makeAinv.R | 11 ++++++++--- man/makeAinv.Rd | 2 +- man/nadiv-package.Rd | 4 ++-- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multi-variate clustering (MVC), cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 1.2.1 dated 2015-05-24 and 1.2.2 dated 2015-07-22
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 6 +++++- R/HiClimR.R | 17 ++++++++++++----- R/coarseR.R | 3 ++- R/fastCor.R | 3 ++- R/geogMask.R | 3 ++- R/grid2D.R | 3 ++- R/minSigCor.R | 3 ++- R/validClimR.R | 3 ++- README.md | 11 ++++++++++- inst/CITATION | 2 +- src/HiClimR.f90 | 1 + 13 files changed, 58 insertions(+), 31 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
0xdata team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.0.0.22 dated 2015-06-14 and 3.0.0.30 dated 2015-07-22
h2o-3.0.0.22/h2o/man/as.matrix.h2o.Rd |only h2o-3.0.0.22/h2o/man/cut.H2OFrame.Rd |only h2o-3.0.0.22/h2o/man/median-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/quantile.Rd |only h2o-3.0.0.22/h2o/man/transform.H2OFrame.Rd |only h2o-3.0.0.30/h2o/DESCRIPTION | 8 h2o-3.0.0.30/h2o/MD5 | 168 ++++++------ h2o-3.0.0.30/h2o/NAMESPACE | 24 + h2o-3.0.0.30/h2o/R/classes.R | 4 h2o-3.0.0.30/h2o/R/communication.R | 12 h2o-3.0.0.30/h2o/R/connection.R | 2 h2o-3.0.0.30/h2o/R/deeplearning.R | 26 + h2o-3.0.0.30/h2o/R/export.R | 16 - h2o-3.0.0.30/h2o/R/frame.R | 294 ++++++++++++++-------- h2o-3.0.0.30/h2o/R/gbm.R | 28 +- h2o-3.0.0.30/h2o/R/glrm.R | 12 h2o-3.0.0.30/h2o/R/import.R | 28 +- h2o-3.0.0.30/h2o/R/kvstore.R | 44 --- h2o-3.0.0.30/h2o/R/logging.R | 13 h2o-3.0.0.30/h2o/R/models.R | 84 +++++- h2o-3.0.0.30/h2o/R/parse.R | 12 h2o-3.0.0.30/h2o/R/pca.R | 14 - h2o-3.0.0.30/h2o/R/randomforest.R | 26 + h2o-3.0.0.30/h2o/R/shim.R | 8 h2o-3.0.0.30/h2o/R/svd.R | 2 h2o-3.0.0.30/h2o/inst/buildnum.txt | 2 h2o-3.0.0.30/h2o/man/apply-H2OFrame-method.Rd | 2 h2o-3.0.0.30/h2o/man/as.data.frame.H2OFrame.Rd | 2 h2o-3.0.0.30/h2o/man/as.factor-H2OFrame-method.Rd | 2 h2o-3.0.0.30/h2o/man/h2o-package.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.anomaly.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.anyFactor.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.auc.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.biases.Rd |only h2o-3.0.0.30/h2o/man/h2o.cbind.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.centroid_stats.Rd |only h2o-3.0.0.30/h2o/man/h2o.clearLog.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.clusterStatus.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.colnames.Rd | 9 h2o-3.0.0.30/h2o/man/h2o.confusionMatrix.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.cut.Rd |only h2o-3.0.0.30/h2o/man/h2o.ddply.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.deepfeatures.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.deeplearning.Rd | 14 - h2o-3.0.0.30/h2o/man/h2o.dim.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.downloadCSV.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.download_pojo.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.exportHDFS.Rd | 10 h2o-3.0.0.30/h2o/man/h2o.gbm.Rd | 13 h2o-3.0.0.30/h2o/man/h2o.getModel.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.giniCoef.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.glrm.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.head.Rd | 11 h2o-3.0.0.30/h2o/man/h2o.ifelse.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.importFile.Rd | 14 - h2o-3.0.0.30/h2o/man/h2o.impute.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.insertMissingValues.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.interaction.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.length.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.levels.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.loadModel.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.ls.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.match.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.mean.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.median.Rd |only h2o-3.0.0.30/h2o/man/h2o.merge.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.metric.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.mse.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.nrow.Rd | 7 h2o-3.0.0.30/h2o/man/h2o.parseRaw.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.parseSetup.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.performance.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.prcomp.Rd | 13 h2o-3.0.0.30/h2o/man/h2o.quantile.Rd |only h2o-3.0.0.30/h2o/man/h2o.r2.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.randomForest.Rd | 9 h2o-3.0.0.30/h2o/man/h2o.rbind.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.removeAll.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.runif.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.scale.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.sd.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.setLevel.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.splitFrame.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.startLogging.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.stopLogging.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.subset.Rd |only h2o-3.0.0.30/h2o/man/h2o.summary.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.table.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.transform.Rd |only h2o-3.0.0.30/h2o/man/h2o.var.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.weights.Rd |only h2o-3.0.0.30/h2o/man/zzz.Rd |only 92 files changed, 742 insertions(+), 324 deletions(-)
Title: Various R Programming Tools for Model Fitting
Description: Various R programming tools for model fitting.
Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
Johnson. Contributions from Randall C. Johnson are Copyright
(2005) SAIC-Frederick, Inc. Funded by the Intramural Research
Program, of the NIH, National Cancer Institute, Center for
Cancer Research under NCI Contract NO1-CO-12400.
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gmodels versions 2.15.4.1 dated 2013-09-21 and 2.16.2 dated 2015-07-22
ChangeLog | 769 +++++++++++++++++++--------------------------------- DESCRIPTION | 20 - MD5 | 32 +- NAMESPACE | 23 + NEWS | 51 +++ R/ci.R | 83 +++-- R/est.mer.R | 96 +++--- R/estimable.R | 142 +++++---- R/estimable.mlm.R | 24 - R/fit.contrast.R | 163 +++++------ R/to.est.R | 19 - inst/ChangeLog | 769 +++++++++++++++++++--------------------------------- inst/NEWS | 51 +++ man/ci.Rd | 58 ++- man/estimable.Rd | 42 +- man/fit.contrast.Rd | 28 - tests |only 17 files changed, 1052 insertions(+), 1318 deletions(-)
Title: Fitting Mixed Models with Known Covariance Structures
Description: The main functions are 'emmreml', and 'emmremlMultiKernel'. 'emmreml' solves a mixed model with known covariance structure using the 'EMMA' algorithm. 'emmremlMultiKernel' is a wrapper for 'emmreml' to handle multiple random components with known covariance structures. The function 'emmremlMultivariate' solves a multivariate gaussian mixed model with known covariance structure using the 'ECM' algorithm.
Author: Deniz Akdemir, Okeke Uche Godfrey
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between EMMREML versions 3.0 dated 2015-03-31 and 3.1 dated 2015-07-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 7 +++++++ R/emmreml.R | 8 +++++--- R/emmremlMultiKernel.R | 6 +++--- R/emmremlMultivariate.R | 7 ++----- man/EMMREML-package.Rd | 4 ++-- man/emmreml.Rd | 2 +- man/emmremlMultiKernel.Rd | 3 ++- man/emmremlMultivariate.Rd | 5 ++--- 10 files changed, 38 insertions(+), 32 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Various actuarial science functionalities, mostly in the
fields of loss distributions, risk theory (including ruin theory),
simulation of compound hierarchical models and credibility theory.
The package also features 17 probability laws commonly used in
insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 1.1-9 dated 2015-07-07 and 1.1-10 dated 2015-07-22
DESCRIPTION | 10 +++---- MD5 | 20 +++++++------- R/cm.R | 2 - R/hierarc.R | 63 +++++++++++++++++++++++++---------------------- inst/NEWS.Rd | 17 ++++++++++-- inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.pdf |binary inst/doc/lossdist.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary 11 files changed, 64 insertions(+), 48 deletions(-)