Title: Two-Level Normal Independent Sampling Estimation
Description: Functions for two level normal models as described in Everson and Morris (2000). J. R. Statist. Soc. B, 62 prt 2, pp.399--412.
Author: S-PLUS original by Phil Everson; R port by Roger D. Peng <rpeng@jhsph.edu>
Maintainer: Roger D. Peng <rpeng@jhsph.edu>
Diff between tlnise versions 2.0 dated 2013-05-24 and 2.0-2 dated 2016-10-12
DESCRIPTION | 20 ++++++++------------ MD5 | 8 ++++---- NAMESPACE | 4 +++- R/internal.R | 6 ++---- inst/CITATION | 2 +- 5 files changed, 18 insertions(+), 22 deletions(-)
Title: Exploring Genomic Relations for Precision Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.3 dated 2016-08-26 and 1.0.4 dated 2016-10-12
XGR-1.0.3/XGR/data/datalist |only XGR-1.0.4/XGR/DESCRIPTION | 12 - XGR-1.0.4/XGR/MD5 | 163 ++++++++++++------------ XGR-1.0.4/XGR/NAMESPACE | 4 XGR-1.0.4/XGR/R/xCircos.r | 96 +++++++++----- XGR-1.0.4/XGR/R/xConverter.r | 7 - XGR-1.0.4/XGR/R/xEnrichConciser.r | 2 XGR-1.0.4/XGR/R/xEnricher.r | 4 XGR-1.0.4/XGR/R/xEnricherGenes.r | 10 - XGR-1.0.4/XGR/R/xEnricherYours.r | 12 + XGR-1.0.4/XGR/R/xGRviaGeneAnno.r | 4 XGR-1.0.4/XGR/R/xGRviaGenomicAnno.r | 139 +++++++++++++++------ XGR-1.0.4/XGR/R/xGRviaGenomicAnnoAdv.r | 141 +++++++++++++++------ XGR-1.0.4/XGR/R/xRDataLoader.r | 13 + XGR-1.0.4/XGR/R/xSM2DF.r |only XGR-1.0.4/XGR/R/xSNP2GeneScores.r | 6 XGR-1.0.4/XGR/R/xSNP2nGenes.r | 82 ++---------- XGR-1.0.4/XGR/R/xSNPlocations.r |only XGR-1.0.4/XGR/R/xSNPscores.r | 20 +-- XGR-1.0.4/XGR/R/xSocialiser.r | 6 XGR-1.0.4/XGR/R/xSocialiserGenes.r | 6 XGR-1.0.4/XGR/R/xSocialiserSNPs.r | 8 + XGR-1.0.4/XGR/R/xSparseMatrix.r | 2 XGR-1.0.4/XGR/R/xSubneterSNPs.r | 7 - XGR-1.0.4/XGR/data/ImmunoBase.RData |binary XGR-1.0.4/XGR/data/JKscience_TS2A.RData |binary XGR-1.0.4/XGR/inst/NEWS | 10 + XGR-1.0.4/XGR/inst/xCircos.html | 39 ++++- XGR-1.0.4/XGR/inst/xDAGanno.html | 2 XGR-1.0.4/XGR/inst/xDAGsim.html | 6 XGR-1.0.4/XGR/inst/xEnrichCompare.html | 2 XGR-1.0.4/XGR/inst/xEnrichConciser.html | 2 XGR-1.0.4/XGR/inst/xEnrichDAGplotAdv.html | 2 XGR-1.0.4/XGR/inst/xEnricher.html | 2 XGR-1.0.4/XGR/inst/xEnricherGenes.html | 48 +++---- XGR-1.0.4/XGR/inst/xEnricherYours.html | 2 XGR-1.0.4/XGR/inst/xGRviaGeneAnno.html | 49 +++---- XGR-1.0.4/XGR/inst/xGRviaGenomicAnno.html | 173 +++++++++++++++++++++++++- XGR-1.0.4/XGR/inst/xGRviaGenomicAnnoAdv.html | 177 ++++++++++++++++++++++++++- XGR-1.0.4/XGR/inst/xRDataLoader.html | 8 - XGR-1.0.4/XGR/inst/xSM2DF.html |only XGR-1.0.4/XGR/inst/xSNP2GeneScores.html | 8 - XGR-1.0.4/XGR/inst/xSNP2nGenes.html | 12 + XGR-1.0.4/XGR/inst/xSNPlocations.html |only XGR-1.0.4/XGR/inst/xSNPscores.html | 4 XGR-1.0.4/XGR/inst/xSubneterSNPs.html | 30 ++-- XGR-1.0.4/XGR/man/xCircos.Rd | 41 ++++-- XGR-1.0.4/XGR/man/xConverter.Rd | 2 XGR-1.0.4/XGR/man/xDAGanno.Rd | 4 XGR-1.0.4/XGR/man/xDAGsim.Rd | 8 - XGR-1.0.4/XGR/man/xEnrichBarplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichCompare.Rd | 4 XGR-1.0.4/XGR/man/xEnrichConciser.Rd | 6 XGR-1.0.4/XGR/man/xEnrichDAGplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichDAGplotAdv.Rd | 4 XGR-1.0.4/XGR/man/xEnrichNetplot.Rd | 2 XGR-1.0.4/XGR/man/xEnrichViewer.Rd | 2 XGR-1.0.4/XGR/man/xEnricher.Rd | 4 XGR-1.0.4/XGR/man/xEnricherGenes.Rd | 50 +++---- XGR-1.0.4/XGR/man/xEnricherSNPs.Rd | 2 XGR-1.0.4/XGR/man/xEnricherYours.Rd | 4 XGR-1.0.4/XGR/man/xFunArgs.Rd | 2 XGR-1.0.4/XGR/man/xGRsampling.Rd | 2 XGR-1.0.4/XGR/man/xGRviaGeneAnno.Rd | 51 +++---- XGR-1.0.4/XGR/man/xGRviaGenomicAnno.Rd | 125 ++++++++++++++++++- XGR-1.0.4/XGR/man/xGRviaGenomicAnnoAdv.Rd | 129 ++++++++++++++++++- XGR-1.0.4/XGR/man/xLiftOver.Rd | 2 XGR-1.0.4/XGR/man/xRDataLoader.Rd | 10 - XGR-1.0.4/XGR/man/xRd2HTML.Rd | 2 XGR-1.0.4/XGR/man/xRdWrap.Rd | 2 XGR-1.0.4/XGR/man/xSM2DF.Rd |only XGR-1.0.4/XGR/man/xSNP2GeneScores.Rd | 10 - XGR-1.0.4/XGR/man/xSNP2nGenes.Rd | 14 +- XGR-1.0.4/XGR/man/xSNPlocations.Rd |only XGR-1.0.4/XGR/man/xSNPscores.Rd | 4 XGR-1.0.4/XGR/man/xSocialiser.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserDAGplot.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserDAGplotAdv.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserGenes.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserNetplot.Rd | 2 XGR-1.0.4/XGR/man/xSocialiserSNPs.Rd | 2 XGR-1.0.4/XGR/man/xSparseMatrix.Rd | 2 XGR-1.0.4/XGR/man/xSubneterGenes.Rd | 2 XGR-1.0.4/XGR/man/xSubneterSNPs.Rd | 32 ++-- XGR-1.0.4/XGR/man/xVisKernels.Rd | 2 XGR-1.0.4/XGR/man/xVisNet.Rd | 2 86 files changed, 1329 insertions(+), 533 deletions(-)
Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.3.0 dated 2016-08-18 and 1.4.0 dated 2016-10-12
umx-1.3.0/umx/man/getOpenMx.Rd |only umx-1.4.0/umx/DESCRIPTION | 8 umx-1.4.0/umx/MD5 | 141 +++---- umx-1.4.0/umx/NAMESPACE | 5 umx-1.4.0/umx/NEWS | 14 umx-1.4.0/umx/R/build_run_modify.r | 524 ++++++++++++++++----------- umx-1.4.0/umx/R/deprecated.r | 5 umx-1.4.0/umx/R/fit_and_reporting.r | 275 ++++++++------ umx-1.4.0/umx/R/misc_and_utility.r | 67 ++- umx-1.4.0/umx/R/xmu.r | 30 + umx-1.4.0/umx/man/RMSEA.MxModel.Rd | 2 umx-1.4.0/umx/man/RMSEA.Rd | 2 umx-1.4.0/umx/man/RMSEA.summary.mxmodel.Rd | 2 umx-1.4.0/umx/man/confint.MxModel.Rd | 2 umx-1.4.0/umx/man/extractAIC.MxModel.Rd | 2 umx-1.4.0/umx/man/install.OpenMx.Rd |only umx-1.4.0/umx/man/loadings.Rd | 2 umx-1.4.0/umx/man/logLik.Rd | 2 umx-1.4.0/umx/man/plot.MxModel.Rd | 30 + umx-1.4.0/umx/man/residuals.MxModel.Rd | 2 umx-1.4.0/umx/man/umx-deprecated.Rd | 4 umx-1.4.0/umx/man/umx.Rd | 21 - umx-1.4.0/umx/man/umxACE.Rd | 70 ++- umx-1.4.0/umx/man/umxACESexLim.Rd | 11 umx-1.4.0/umx/man/umxACEcov.Rd | 17 umx-1.4.0/umx/man/umxCF_SexLim.Rd | 11 umx-1.4.0/umx/man/umxCI.Rd | 3 umx-1.4.0/umx/man/umxCI_boot.Rd | 2 umx-1.4.0/umx/man/umxCP.Rd | 11 umx-1.4.0/umx/man/umxCompare.Rd | 3 umx-1.4.0/umx/man/umxDiagnose.Rd | 8 umx-1.4.0/umx/man/umxEquate.Rd | 6 umx-1.4.0/umx/man/umxExpCov.Rd | 10 umx-1.4.0/umx/man/umxExpMeans.Rd | 3 umx-1.4.0/umx/man/umxFactor.Rd | 2 umx-1.4.0/umx/man/umxFitIndices.Rd | 40 +- umx-1.4.0/umx/man/umxGxE.Rd | 11 umx-1.4.0/umx/man/umxGxE_window.Rd | 11 umx-1.4.0/umx/man/umxIP.Rd | 11 umx-1.4.0/umx/man/umxJiggle.Rd | 2 umx-1.4.0/umx/man/umxLabel.Rd | 8 umx-1.4.0/umx/man/umxLatent.Rd | 8 umx-1.4.0/umx/man/umxMatrix.Rd |only umx-1.4.0/umx/man/umxModify.Rd | 6 umx-1.4.0/umx/man/umxPath.Rd | 12 umx-1.4.0/umx/man/umxPlotACE.Rd | 16 umx-1.4.0/umx/man/umxPlotACEcov.Rd | 20 - umx-1.4.0/umx/man/umxPlotCP.Rd | 32 + umx-1.4.0/umx/man/umxPlotGxE.Rd | 32 + umx-1.4.0/umx/man/umxPlotIP.Rd | 30 + umx-1.4.0/umx/man/umxRAM.Rd | 6 umx-1.4.0/umx/man/umxRAM2Ordinal.Rd | 6 umx-1.4.0/umx/man/umxRun.Rd | 6 umx-1.4.0/umx/man/umxSummary.MxModel.Rd | 4 umx-1.4.0/umx/man/umxSummaryACE.Rd | 16 umx-1.4.0/umx/man/umxSummaryACEcov.Rd | 17 umx-1.4.0/umx/man/umxSummaryCP.Rd | 14 umx-1.4.0/umx/man/umxSummaryGxE.Rd | 14 umx-1.4.0/umx/man/umxSummaryIP.Rd | 14 umx-1.4.0/umx/man/umxThresholdMatrix.Rd | 7 umx-1.4.0/umx/man/umxValues.Rd | 7 umx-1.4.0/umx/man/umx_drop_ok.Rd | 2 umx-1.4.0/umx/man/umx_fix_first_loadings.Rd | 7 umx-1.4.0/umx/man/umx_fix_latents.Rd | 7 umx-1.4.0/umx/man/umx_get_options.Rd | 2 umx-1.4.0/umx/man/umx_make_TwinData.Rd | 14 umx-1.4.0/umx/man/umx_make_sql_from_excel.Rd | 1 umx-1.4.0/umx/man/umx_pad.Rd | 2 umx-1.4.0/umx/man/umx_rename.Rd | 2 umx-1.4.0/umx/man/umx_standardize_RAM.Rd | 2 umx-1.4.0/umx/man/umx_time.Rd | 11 umx-1.4.0/umx/man/xmu_dot_make_paths.Rd | 4 umx-1.4.0/umx/man/xmu_dot_make_residuals.Rd | 6 73 files changed, 1068 insertions(+), 639 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://www.synbreed.tum.de>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-29 dated 2016-01-18 and 0.11-41 dated 2016-10-12
synbreed-0.11-29/synbreed/vignettes/IntroSyn.pdf |only synbreed-0.11-41/synbreed/DESCRIPTION | 16 synbreed-0.11-41/synbreed/MD5 | 52 synbreed-0.11-41/synbreed/R/LD.r | 101 synbreed-0.11-41/synbreed/R/LDDist.r | 43 synbreed-0.11-41/synbreed/R/codeGeno.r | 1490 +++++------ synbreed-0.11-41/synbreed/R/discard.markers.r | 4 synbreed-0.11-41/synbreed/R/kinship.r | 15 synbreed-0.11-41/synbreed/R/manhattanPlot.r | 23 synbreed-0.11-41/synbreed/R/plot.relationshipMatrix.r | 187 + synbreed-0.11-41/synbreed/R/read.write.vcf.r | 4 synbreed-0.11-41/synbreed/build |only synbreed-0.11-41/synbreed/inst/doc |only synbreed-0.11-41/synbreed/java/COPYRIGHTS | 4 synbreed-0.11-41/synbreed/man/LDDist.Rd | 3 synbreed-0.11-41/synbreed/man/codeGeno.Rd | 15 synbreed-0.11-41/synbreed/man/discard.individuals.Rd | 2 synbreed-0.11-41/synbreed/man/discard.markers.Rd | 2 synbreed-0.11-41/synbreed/man/manhattanPlot.Rd | 7 synbreed-0.11-41/synbreed/man/plot.relationshipMatrix.Rd | 18 synbreed-0.11-41/synbreed/vignettes/IntroSyn.Rnw |only synbreed-0.11-41/synbreed/vignettes/IntroSyn.tex | 1766 +++++++------- synbreed-0.11-41/synbreed/vignettes/figs/cattleHist.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapCattle.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapMaize.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/genMapMice.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/maizeHist.pdf |binary synbreed-0.11-41/synbreed/vignettes/figs/miceHist.pdf |binary 28 files changed, 1957 insertions(+), 1795 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.46-1 dated 2016-07-08 and 1.47-0 dated 2016-10-12
spatstat-1.46-1/spatstat/man/circumradius.Rd |only spatstat-1.46-1/spatstat/tests/testsAtoN.R |only spatstat-1.46-1/spatstat/tests/testsPtoZ.R |only spatstat-1.47-0/spatstat/DESCRIPTION | 19 spatstat-1.47-0/spatstat/MD5 | 339 +++++++------ spatstat-1.47-0/spatstat/NAMESPACE | 86 +++ spatstat-1.47-0/spatstat/NEWS | 267 ++++++++++ spatstat-1.47-0/spatstat/R/Fest.R | 5 spatstat-1.47-0/spatstat/R/First.R | 3 spatstat-1.47-0/spatstat/R/Hest.R | 1 spatstat-1.47-0/spatstat/R/Jest.R | 24 spatstat-1.47-0/spatstat/R/Kest.R | 4 spatstat-1.47-0/spatstat/R/Kmeasure.R | 22 spatstat-1.47-0/spatstat/R/addvar.R | 2 spatstat-1.47-0/spatstat/R/bc.R |only spatstat-1.47-0/spatstat/R/boundingcircle.R |only spatstat-1.47-0/spatstat/R/breakpts.R | 5 spatstat-1.47-0/spatstat/R/bw.ppl.R | 17 spatstat-1.47-0/spatstat/R/clusterinfo.R | 24 spatstat-1.47-0/spatstat/R/density.lpp.R | 4 spatstat-1.47-0/spatstat/R/density.ppp.R | 121 +++- spatstat-1.47-0/spatstat/R/disc.R | 8 spatstat-1.47-0/spatstat/R/dummy.R | 9 spatstat-1.47-0/spatstat/R/edgeRipley.R | 8 spatstat-1.47-0/spatstat/R/eval.fv.R | 6 spatstat-1.47-0/spatstat/R/fardist.R | 12 spatstat-1.47-0/spatstat/R/fitted.ppm.R | 3 spatstat-1.47-0/spatstat/R/fv.R | 29 - spatstat-1.47-0/spatstat/R/geyer.R | 14 spatstat-1.47-0/spatstat/R/hierpair.family.R | 2 spatstat-1.47-0/spatstat/R/images.R | 6 spatstat-1.47-0/spatstat/R/intensity.R | 6 spatstat-1.47-0/spatstat/R/kernel2d.R |only spatstat-1.47-0/spatstat/R/kppm.R | 6 spatstat-1.47-0/spatstat/R/leverage.R | 6 spatstat-1.47-0/spatstat/R/linalg.R | 106 ++-- spatstat-1.47-0/spatstat/R/linearK.R | 35 - spatstat-1.47-0/spatstat/R/linearKmulti.R | 32 - spatstat-1.47-0/spatstat/R/lineardisc.R | 49 + spatstat-1.47-0/spatstat/R/linearpcf.R | 36 - spatstat-1.47-0/spatstat/R/linearpcfmulti.R | 36 - spatstat-1.47-0/spatstat/R/linequad.R | 142 +++-- spatstat-1.47-0/spatstat/R/linfun.R | 23 spatstat-1.47-0/spatstat/R/linim.R | 65 ++ spatstat-1.47-0/spatstat/R/linnet.R | 72 ++ spatstat-1.47-0/spatstat/R/lintess.R | 10 spatstat-1.47-0/spatstat/R/lpp.R | 8 spatstat-1.47-0/spatstat/R/lppm.R | 4 spatstat-1.47-0/spatstat/R/mincontrast.R | 6 spatstat-1.47-0/spatstat/R/minkowski.R | 61 +- spatstat-1.47-0/spatstat/R/morphology.R | 15 spatstat-1.47-0/spatstat/R/nnfunlpp.R | 18 spatstat-1.47-0/spatstat/R/options.R | 24 spatstat-1.47-0/spatstat/R/otherpackages.R |only spatstat-1.47-0/spatstat/R/pairwise.family.R | 2 spatstat-1.47-0/spatstat/R/parres.R | 4 spatstat-1.47-0/spatstat/R/pcfinhom.R | 10 spatstat-1.47-0/spatstat/R/pcfmulti.R | 13 spatstat-1.47-0/spatstat/R/pcfmulti.inhom.R | 13 spatstat-1.47-0/spatstat/R/persp.im.R | 42 - spatstat-1.47-0/spatstat/R/pixellate.R | 16 spatstat-1.47-0/spatstat/R/plot.fv.R | 5 spatstat-1.47-0/spatstat/R/plot.im.R | 35 + spatstat-1.47-0/spatstat/R/plot.owin.R | 5 spatstat-1.47-0/spatstat/R/plot.ppp.R | 33 - spatstat-1.47-0/spatstat/R/plot3d.R | 48 + spatstat-1.47-0/spatstat/R/pool.R | 26 - spatstat-1.47-0/spatstat/R/pp3.R | 22 spatstat-1.47-0/spatstat/R/psp.R | 7 spatstat-1.47-0/spatstat/R/quadratcount.R | 14 spatstat-1.47-0/spatstat/R/rLGCP.R | 13 spatstat-1.47-0/spatstat/R/random.R | 55 +- spatstat-1.47-0/spatstat/R/relrisk.R | 4 spatstat-1.47-0/spatstat/R/relrisk.ppm.R | 2 spatstat-1.47-0/spatstat/R/resid4plot.R | 2 spatstat-1.47-0/spatstat/R/resolve.defaults.R | 21 spatstat-1.47-0/spatstat/R/rho2hat.R | 2 spatstat-1.47-0/spatstat/R/rhohat.R | 8 spatstat-1.47-0/spatstat/R/rmh.default.R | 39 + spatstat-1.47-0/spatstat/R/rmh.ppm.R | 7 spatstat-1.47-0/spatstat/R/smooth.ppp.R | 102 +++- spatstat-1.47-0/spatstat/R/sparse3Darray.R | 52 +- spatstat-1.47-0/spatstat/R/sparselinalg.R | 2 spatstat-1.47-0/spatstat/R/summary.im.R | 11 spatstat-1.47-0/spatstat/R/summary.quad.R | 103 ++-- spatstat-1.47-0/spatstat/R/superimpose.R | 17 spatstat-1.47-0/spatstat/R/symbolmap.R | 85 ++- spatstat-1.47-0/spatstat/R/tapplysum.R |only spatstat-1.47-0/spatstat/R/terse.R | 92 ++- spatstat-1.47-0/spatstat/R/treebranches.R | 12 spatstat-1.47-0/spatstat/R/units.R | 38 + spatstat-1.47-0/spatstat/R/util.R | 120 +--- spatstat-1.47-0/spatstat/R/vcov.ppm.R | 4 spatstat-1.47-0/spatstat/R/weightedStats.R |only spatstat-1.47-0/spatstat/R/window.R | 5 spatstat-1.47-0/spatstat/R/wingeom.R | 66 +- spatstat-1.47-0/spatstat/data/chicago.rda |binary spatstat-1.47-0/spatstat/data/dendrite.rda |binary spatstat-1.47-0/spatstat/data/simplenet.rda |binary spatstat-1.47-0/spatstat/data/spiders.rda |binary spatstat-1.47-0/spatstat/demo/spatstat.R | 2 spatstat-1.47-0/spatstat/inst/doc/BEGINNER.txt | 15 spatstat-1.47-0/spatstat/inst/doc/datasets.R | 131 ++--- spatstat-1.47-0/spatstat/inst/doc/datasets.Rnw | 1 spatstat-1.47-0/spatstat/inst/doc/datasets.pdf |binary spatstat-1.47-0/spatstat/inst/doc/getstart.pdf |binary spatstat-1.47-0/spatstat/inst/doc/replicated.pdf |binary spatstat-1.47-0/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.47-0/spatstat/inst/doc/updates.R | 13 spatstat-1.47-0/spatstat/inst/doc/updates.Rnw | 245 ++++++++- spatstat-1.47-0/spatstat/inst/doc/updates.pdf |binary spatstat-1.47-0/spatstat/man/Extract.linim.Rd |only spatstat-1.47-0/spatstat/man/Kinhom.Rd | 17 spatstat-1.47-0/spatstat/man/MinkowskiSum.Rd | 18 spatstat-1.47-0/spatstat/man/Smooth.ppp.Rd | 3 spatstat-1.47-0/spatstat/man/anyNA.im.Rd |only spatstat-1.47-0/spatstat/man/applynbd.Rd | 11 spatstat-1.47-0/spatstat/man/as.linnet.linim.Rd | 15 spatstat-1.47-0/spatstat/man/as.linnet.psp.Rd | 4 spatstat-1.47-0/spatstat/man/bc.ppm.Rd |only spatstat-1.47-0/spatstat/man/boundingcircle.Rd |only spatstat-1.47-0/spatstat/man/bw.ppl.Rd | 6 spatstat-1.47-0/spatstat/man/density.ppp.Rd | 73 ++ spatstat-1.47-0/spatstat/man/diameter.linnet.Rd | 23 spatstat-1.47-0/spatstat/man/dilation.Rd | 3 spatstat-1.47-0/spatstat/man/discs.Rd | 26 - spatstat-1.47-0/spatstat/man/eval.fv.Rd | 18 spatstat-1.47-0/spatstat/man/grow.rectangle.Rd | 21 spatstat-1.47-0/spatstat/man/improve.kppm.Rd | 7 spatstat-1.47-0/spatstat/man/invoke.symbolmap.Rd | 2 spatstat-1.47-0/spatstat/man/kppm.Rd | 23 spatstat-1.47-0/spatstat/man/laslett.Rd | 3 spatstat-1.47-0/spatstat/man/lengths.psp.Rd | 12 spatstat-1.47-0/spatstat/man/lgcp.estK.Rd | 20 spatstat-1.47-0/spatstat/man/lgcp.estpcf.Rd | 13 spatstat-1.47-0/spatstat/man/linearKinhom.Rd | 51 +- spatstat-1.47-0/spatstat/man/linearpcfinhom.Rd | 7 spatstat-1.47-0/spatstat/man/linequad.Rd |only spatstat-1.47-0/spatstat/man/linfun.Rd | 3 spatstat-1.47-0/spatstat/man/linim.Rd | 4 spatstat-1.47-0/spatstat/man/lintess.Rd | 2 spatstat-1.47-0/spatstat/man/lppm.Rd | 13 spatstat-1.47-0/spatstat/man/mean.im.Rd | 1 spatstat-1.47-0/spatstat/man/mean.linim.Rd |only spatstat-1.47-0/spatstat/man/methods.linfun.Rd | 13 spatstat-1.47-0/spatstat/man/nnfun.lpp.Rd | 8 spatstat-1.47-0/spatstat/man/plot.im.Rd | 35 + spatstat-1.47-0/spatstat/man/plot.pp3.Rd | 26 - spatstat-1.47-0/spatstat/man/plot.ppp.Rd | 11 spatstat-1.47-0/spatstat/man/ppm.Rd | 5 spatstat-1.47-0/spatstat/man/ppm.ppp.Rd | 53 ++ spatstat-1.47-0/spatstat/man/rLGCP.Rd | 34 - spatstat-1.47-0/spatstat/man/rSSI.Rd | 23 spatstat-1.47-0/spatstat/man/rcellnumber.Rd | 25 spatstat-1.47-0/spatstat/man/rescale.Rd | 18 spatstat-1.47-0/spatstat/man/rex.Rd |only spatstat-1.47-0/spatstat/man/rhohat.Rd | 15 spatstat-1.47-0/spatstat/man/rmh.default.Rd | 25 spatstat-1.47-0/spatstat/man/rmh.ppm.Rd | 20 spatstat-1.47-0/spatstat/man/simulate.kppm.Rd | 7 spatstat-1.47-0/spatstat/man/spatstat-deprecated.Rd | 11 spatstat-1.47-0/spatstat/man/spatstat-internal.Rd | 64 ++ spatstat-1.47-0/spatstat/man/spatstat-package.Rd | 8 spatstat-1.47-0/spatstat/man/summary.im.Rd | 6 spatstat-1.47-0/spatstat/man/summary.kppm.Rd | 20 spatstat-1.47-0/spatstat/man/sumouter.Rd | 20 spatstat-1.47-0/spatstat/man/symbolmap.Rd | 15 spatstat-1.47-0/spatstat/man/weighted.median.Rd |only spatstat-1.47-0/spatstat/src/linalg.c | 79 +++ spatstat-1.47-0/spatstat/src/lineardisc.c | 26 - spatstat-1.47-0/spatstat/src/linearradius.c |only spatstat-1.47-0/spatstat/src/linequad.c | 510 -------------------- spatstat-1.47-0/spatstat/src/linequad.h |only spatstat-1.47-0/spatstat/src/ply.c |only spatstat-1.47-0/spatstat/src/ply.h |only spatstat-1.47-0/spatstat/tests/testsAtoF.R |only spatstat-1.47-0/spatstat/tests/testsGtoK.R |only spatstat-1.47-0/spatstat/tests/testsLtoM.R |only spatstat-1.47-0/spatstat/tests/testsNtoP.R |only spatstat-1.47-0/spatstat/tests/testsQtoR.R |only spatstat-1.47-0/spatstat/tests/testsStoZ.R |only spatstat-1.47-0/spatstat/vignettes/datasets.Rnw | 1 spatstat-1.47-0/spatstat/vignettes/packagesizes.txt | 1 spatstat-1.47-0/spatstat/vignettes/updates.Rnw | 245 ++++++++- 184 files changed, 3300 insertions(+), 1787 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification arose from verifying high-resolution forecasts, where coarser-resolution models generally are favored even when a human forecaster finds the higher-resolution model to be considerably better. Most newly proposed methods, which largely come from image analysis, computer vision, and similar, are available, with more on the way.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.4 dated 2016-02-22 and 0.5 dated 2016-10-12
DESCRIPTION | 9 MD5 | 35 +- R/FeatureFinder.R | 64 ++--- R/Features.R | 619 ++++++++++++++++++++++++++------------------------- R/Fint2d.R | 135 +++++++---- R/LocMeasures.R | 184 ++++++++++----- R/MergeForce.R | 1 R/craer.R | 40 ++- R/deltamm.R | 118 +++++---- R/minboundmatch.R | 24 - R/plot.matched.R |only R/rigider.R | 43 ++- man/craer.Rd | 3 man/deltamm.Rd | 19 + man/locmeasures2d.Rd | 22 - man/locperf.Rd | 14 - man/minboundmatch.Rd | 28 ++ man/rigider.Rd | 13 - man/saller.Rd | 2 19 files changed, 795 insertions(+), 578 deletions(-)
Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication
of infectious diseases from surveillance time series. Also provides support
for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Diff between spaero versions 0.1.1 dated 2016-05-22 and 0.2.0 dated 2016-10-12
DESCRIPTION | 11 - MD5 | 26 ++-- NEWS.md | 30 ++++- R/analysis.R | 163 +++++++++++++++------------- R/simulation.R | 103 ++++++++++------- build/vignette.rds |binary inst/doc/spaero-introduction.Rmd | 11 + inst/doc/spaero-introduction.pdf |binary man/create_simulator.Rd | 21 ++- man/get_stats.Rd | 38 +++--- src/transition_rates.c | 33 +++++ tests/testthat/test-simulator.R | 136 +++++++++++------------ tests/testthat/test-stats.R | 221 +++++++++++++++++++------------------- vignettes/spaero-introduction.Rmd | 9 + 14 files changed, 455 insertions(+), 347 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb],
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb],
Amandine Gasc [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.0.4 dated 2016-07-11 and 2.0.5 dated 2016-10-12
DESCRIPTION | 8 - MD5 | 32 +++--- NEWS | 17 +++ R/seewave.r | 198 +++++++++++++++++++++--------------------- inst/doc/seewave_IO.pdf |binary inst/doc/seewave_analysis.pdf |binary man/ACI.Rd | 2 man/AR.Rd | 2 man/NDSI.Rd | 16 +-- man/bwfilter.Rd | 2 man/dBscale.Rd | 2 man/ffilter.Rd | 2 man/fma.Rd | 6 - man/fund.Rd | 2 man/seewave.package.Rd | 4 man/smoothw.Rd | 2 man/zc.Rd | 2 17 files changed, 159 insertions(+), 138 deletions(-)
Title: Integrated Taxonomic Information System Client
Description: An interface to the Integrated Taxonomic Information System ('ITIS')
(<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST
'API' methods (<https://www.itis.gov/ws_description.html>), as well as the
'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between ritis versions 0.5.0 dated 2016-06-22 and 0.5.4 dated 2016-10-12
DESCRIPTION | 15 +++++------ MD5 | 24 +++++++++--------- NEWS.md | 9 ++++++ R/search_common.R | 2 - R/zzz.R | 4 +-- README.md | 52 ++++++++++++++++++--------------------- inst/doc/ritis_vignette.Rmd | 51 ++++++++++++++++++-------------------- inst/doc/ritis_vignette.html | 49 +++++++++++++++++------------------- inst/vign/ritis_vignette.Rmd | 4 +-- inst/vign/ritis_vignette.md | 51 ++++++++++++++++++-------------------- man/search_common.Rd | 2 - tests/testthat/test-itis_facet.R | 2 - vignettes/ritis_vignette.Rmd | 51 ++++++++++++++++++-------------------- 13 files changed, 155 insertions(+), 161 deletions(-)
Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models
and providing an interface to Partial Least Squares Regression and Linear and
Quadratic Discriminant analysis. Several statistical summaries are extended,
predictions are offered for additional types of analyses, and extra plots, tests
and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between RcmdrPlugin.NMBU versions 1.8.6 dated 2016-08-27 and 1.8.7 dated 2016-10-12
DESCRIPTION | 17 +++++++++---- MD5 | 14 +++++------ NAMESPACE | 3 +- R/NMBU.GUI.Data.R | 56 +++++++++++++++++++++++----------------------- R/NMBU.GUI.Models.R | 37 +++++++++++++++++++++++------- R/NMBU.RcmdrPlugin.NMBU.R | 3 ++ R/NMBU.Utilities.R | 7 +++++ inst/etc/menus.txt | 5 ---- 8 files changed, 87 insertions(+), 55 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.2.2 dated 2016-09-24 and 0.2.3 dated 2016-10-12
DESCRIPTION | 10 MD5 | 25 + R/RcppExports.R | 56 ++- R/momentS.r |only R/ridgeVAR1.r | 12 inst/NEWS.Rd | 9 inst/include |only man/momentS.Rd |only man/ragt2ridges-package.Rd | 2 man/ridgeVAR1.Rd | 2 man/sparsifyVAR1.Rd | 2 src/RcppExports.cpp | 665 ++++++++++++++++++++++++++++++++++----------- src/defaultTarget.h |only src/rags2ridges.h |only src/ragt2ridges.cpp | 437 ----------------------------- src/ridgePchordal.h |only 16 files changed, 586 insertions(+), 634 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9 dated 2016-07-27 and 0.9.1 dated 2016-10-12
DESCRIPTION | 8 ++-- MD5 | 12 +++---- R/lda_from_pls.R | 10 ++++- R/shaving.R | 84 ++++++++++++++++++++++++++++++++++++++----------- inst/CITATION | 2 - man/lda_from_pls_cv.Rd | 4 +- man/shaving.Rd | 12 +++++-- 7 files changed, 98 insertions(+), 34 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and
'ScaLAPACK' numerical libraries. This enables R to utilize
distributed linear algebra for codes written in the 'SPMD' fashion.
This interface is deliberately low-level and mimics the style of
the native libraries it wraps. For a much higher level way of
managing distributed matrices, see the 'pbdDMAT' package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdBASE versions 0.4-3 dated 2016-01-24 and 0.4-5 dated 2016-10-12
pbdBASE-0.4-3/pbdBASE/build |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyev.Rd |only pbdBASE-0.4-3/pbdBASE/src/base/linalg/auxil.f90 |only pbdBASE-0.4-3/pbdBASE/src/base/utils/scale.f90 |only pbdBASE-0.4-3/pbdBASE/src/utils/test.c |only pbdBASE-0.4-5/pbdBASE/ChangeLog | 14 ++ pbdBASE-0.4-5/pbdBASE/DESCRIPTION | 31 ++--- pbdBASE-0.4-5/pbdBASE/MD5 | 70 +++++------ pbdBASE-0.4-5/pbdBASE/NAMESPACE | 5 pbdBASE-0.4-5/pbdBASE/R/base_mpi_blacs.r | 5 pbdBASE-0.4-5/pbdBASE/R/base_scalapack.r | 31 ++--- pbdBASE-0.4-5/pbdBASE/R/get_conf.r | 2 pbdBASE-0.4-5/pbdBASE/R/pbdBASE-package.r | 3 pbdBASE-0.4-5/pbdBASE/R/redist.r |only pbdBASE-0.4-5/pbdBASE/README.md | 31 ++--- pbdBASE-0.4-5/pbdBASE/inst/CITATION | 28 ++-- pbdBASE-0.4-5/pbdBASE/inst/RNACI/RNACI.h | 127 +++++++++------------ pbdBASE-0.4-5/pbdBASE/inst/doc/pbdBASE-guide.Rnw | 2 pbdBASE-0.4-5/pbdBASE/inst/doc/pbdBASE-guide.pdf |binary pbdBASE-0.4-5/pbdBASE/man/base.redist.Rd |only pbdBASE-0.4-5/pbdBASE/man/base.rpdsyevr.Rd |only pbdBASE-0.4-5/pbdBASE/man/gridexit.Rd | 3 pbdBASE-0.4-5/pbdBASE/src/Makevars.in | 10 - pbdBASE-0.4-5/pbdBASE/src/Makevars.win | 6 pbdBASE-0.4-5/pbdBASE/src/base/expm/matexp.c | 13 -- pbdBASE-0.4-5/pbdBASE/src/base/linalg/linalg.h | 9 + pbdBASE-0.4-5/pbdBASE/src/base/linalg/norms.f90 |only pbdBASE-0.4-5/pbdBASE/src/base/stats/stats.h | 7 + pbdBASE-0.4-5/pbdBASE/src/base/utils/redist.c |only pbdBASE-0.4-5/pbdBASE/src/base/utils/scale.c |only pbdBASE-0.4-5/pbdBASE/src/base/utils/utils.h | 12 + pbdBASE-0.4-5/pbdBASE/src/base_lm.c | 1 pbdBASE-0.4-5/pbdBASE/src/base_p_matexp.c | 7 - pbdBASE-0.4-5/pbdBASE/src/base_putil.c | 7 - pbdBASE-0.4-5/pbdBASE/src/base_scalapack.c | 125 ++++++++++++-------- pbdBASE-0.4-5/pbdBASE/src/comm_utils.c | 19 +-- pbdBASE-0.4-5/pbdBASE/src/export_blacs/pkg_Bdef.h | 13 +- pbdBASE-0.4-5/pbdBASE/src/export_blacs/pkg_tools.c | 1 pbdBASE-0.4-5/pbdBASE/src/pbdBASE.h | 2 pbdBASE-0.4-5/pbdBASE/src/redist.c |only pbdBASE-0.4-5/pbdBASE/src/scalapack.h | 20 +++ pbdBASE-0.4-5/pbdBASE/vignettes/pbdBASE-guide.Rnw | 2 42 files changed, 344 insertions(+), 262 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it makes possible to create and manipulate multivariate
network data with different formats, and there are effective ways available to treat multiple
networks with routines that combine algebraic systems like the partially ordered semigroup or
the semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. It also provides an algebraic approach for two-mode networks
through Galois derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.1 dated 2016-09-14 and 2.2 dated 2016-10-12
DESCRIPTION | 8 +- MD5 | 26 +++---- R/bnd.R | 9 +- R/jnt.R | 20 +++-- R/read.srt.R | 148 +++++++++++++++++++++--------------------- R/rel.sys.R | 36 +++++++--- R/zbind.R | 42 +++++++---- inst/CHANGELOG | 16 ++++ inst/doc/TwoModeNetworks.Rnw | 66 ++++++++---------- inst/doc/TwoModeNetworks.pdf |binary inst/doc/TwoModeNetworks.r | 43 +++++++----- man/multiplex-package.Rd | 4 - man/read.srt.Rd | 30 +++----- vignettes/TwoModeNetworks.Rnw | 66 ++++++++---------- 14 files changed, 278 insertions(+), 236 deletions(-)
Title: An Interactive Visualisation of Meta-Analysis as a Physical
Weighing Machine
Description: An interactive application to visualise meta-analysis data as a
physical weighing machine. The interface is based on the Shiny web application
framework, though can be run locally and with the user's own data.
Author: Jack Bowden <j.bowden@bristol.ac.uk> (conception), Christopher Jackson
<chris.jackson@mrc-bsu.cam.ac.uk> (programming)
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between MetaAnalyser versions 0.2 dated 2016-08-10 and 0.2.1 dated 2016-10-12
DESCRIPTION | 16 ++++++++++------ MD5 | 13 +++++++------ NAMESPACE | 2 +- inst/CITATION | 2 +- inst/NEWS |only man/MetaAnalyser.Rd | 3 ++- man/metasumm.Rd | 2 +- man/resd_dsl.Rd | 3 ++- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Tools for Two-Dimensional Monte-Carlo Simulations
Description: A complete framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-Order Monte-Carlo simulations. Also includes various distributions (pert, triangular, Bernoulli, empirical discrete and continuous).
Author: Regis Pouillot [aut, cre],
Marie-Laure Delignette-Muller [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Regis Pouillot <rpouillot@yahoo.fr>
Diff between mc2d versions 0.1-16 dated 2016-02-15 and 0.1-17 dated 2016-10-12
DESCRIPTION | 12 ++--- MD5 | 18 ++++---- R/betagen.R | 39 +++++++++---------- R/pert.R | 92 ++++++++++++++++++++++++--------------------- R/triang.R | 74 ++++++++++++++++++++++-------------- build/vignette.rds |binary data/ec.rda |binary inst/NEWS | 7 +++ inst/doc/docmcEnglish.pdf |binary inst/doc/mc2dLmEnglish.pdf |binary 10 files changed, 137 insertions(+), 105 deletions(-)
Title: Matrix Correlation Coefficients
Description: Computation and visualization of matrix correlation coefficients.
The main method is the Similarity of Matrices Index, while various related
measures like r1, r2, r3, r4, Yanai's GCD, RV, RV2 and adjusted RV are included
for comparison.
Author: Kristian Hovde Liland [aut, cre],
Tormod Næs [ctb],
Ulf Geir Indahl [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nofima.no>
Diff between MatrixCorrelation versions 0.8.1 dated 2016-04-25 and 0.9 dated 2016-10-12
DESCRIPTION | 12 ++++++------ MD5 | 19 +++++++++++-------- NAMESPACE | 2 ++ R/PMI.R |only R/RV.R | 17 +++++++++-------- R/RcppExports.R | 6 +++++- R/allCorrelations.R | 5 +++-- man/PSI.Rd |only man/RV.Rd | 2 +- man/allCorrelations.Rd | 4 ++-- src/RV2cpp.cpp |only src/RcppExports.cpp | 30 +++++++++++++++++++++--------- 12 files changed, 60 insertions(+), 37 deletions(-)
More information about MatrixCorrelation at CRAN
Permanent link
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Author: Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, and David A. MacIntyre
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 0.0.1 dated 2014-11-25 and 1.0 dated 2016-10-12
KODAMA-0.0.1/KODAMA/R/KODAMA.R |only KODAMA-0.0.1/KODAMA/R/simulated.R |only KODAMA-0.0.1/KODAMA/man/KNN.CV.Rd |only KODAMA-0.0.1/KODAMA/man/PCA.CA.KNN.CV.Rd |only KODAMA-0.0.1/KODAMA/man/PLS.SVM.CV.Rd |only KODAMA-0.0.1/KODAMA/man/classprob.Rd |only KODAMA-0.0.1/KODAMA/man/core.Rd |only KODAMA-0.0.1/KODAMA/man/kfold.Rd |only KODAMA-0.0.1/KODAMA/man/knn.dist.Rd |only KODAMA-0.0.1/KODAMA/man/knn.predict.Rd |only KODAMA-0.0.1/KODAMA/man/knn.probability.Rd |only KODAMA-0.0.1/KODAMA/man/majority.Rd |only KODAMA-1.0/KODAMA/DESCRIPTION | 21 +- KODAMA-1.0/KODAMA/MD5 | 102 ++++++++--- KODAMA-1.0/KODAMA/NAMESPACE | 28 ++- KODAMA-1.0/KODAMA/R/KOD.R |only KODAMA-1.0/KODAMA/R/RcppExports.R |only KODAMA-1.0/KODAMA/R/datasets.R |only KODAMA-1.0/KODAMA/R/preprocessing.R | 260 +++++++++++++++-------------- KODAMA-1.0/KODAMA/build |only KODAMA-1.0/KODAMA/data/lymphoma.RData |binary KODAMA-1.0/KODAMA/inst |only KODAMA-1.0/KODAMA/man/KODAMA.Rd | 222 ++++++++++++------------ KODAMA-1.0/KODAMA/man/MetRef.Rd | 90 +++++----- KODAMA-1.0/KODAMA/man/USA.Rd | 94 +++++----- KODAMA-1.0/KODAMA/man/core_cpp.Rd |only KODAMA-1.0/KODAMA/man/dinisurface.Rd | 81 ++++----- KODAMA-1.0/KODAMA/man/floyd.Rd |only KODAMA-1.0/KODAMA/man/helicoid.Rd | 81 ++++----- KODAMA-1.0/KODAMA/man/k.test.Rd |only KODAMA-1.0/KODAMA/man/knn.double.cv.Rd |only KODAMA-1.0/KODAMA/man/knn.kodama.Rd |only KODAMA-1.0/KODAMA/man/loads.Rd |only KODAMA-1.0/KODAMA/man/lymphoma.Rd | 103 ++++++----- KODAMA-1.0/KODAMA/man/mcplot.Rd |only KODAMA-1.0/KODAMA/man/normalization.Rd | 123 +++++++------ KODAMA-1.0/KODAMA/man/pls.double.cv.Rd |only KODAMA-1.0/KODAMA/man/pls.kodama.Rd |only KODAMA-1.0/KODAMA/man/scaling.Rd | 114 +++++++----- KODAMA-1.0/KODAMA/man/spirals.Rd | 100 +++++------ KODAMA-1.0/KODAMA/man/swissroll.Rd | 106 ++++++----- KODAMA-1.0/KODAMA/man/transformy.Rd | 83 +++++---- KODAMA-1.0/KODAMA/src |only KODAMA-1.0/KODAMA/vignettes |only 44 files changed, 891 insertions(+), 717 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified
values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.2.4 dated 2016-08-30 and 0.2.5 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/helpers.R | 9 ++++----- build/vignette.rds |binary inst/doc/getting_started.Rmd | 2 +- inst/doc/getting_started.html | 6 +++--- vignettes/getting_started.Rmd | 2 +- 7 files changed, 19 insertions(+), 20 deletions(-)
Title: Collection of Tools for Genomic Data Analysis
Description: A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools versions 0.2.1 dated 2016-10-07 and 0.2.2 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/importGFF3.R | 15 +++++++++++++-- build/vignette.rds |binary data/annotTrack.rda |binary data/geneEXP.rda |binary data/genotData.rda |binary data/mdrExample.rda |binary data/phenoData.rda |binary inst/doc/GenomicTools-Vignette.pdf |binary man/GenomicTools-package.Rd | 4 ++-- 12 files changed, 31 insertions(+), 20 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 7.2 dated 2016-09-09 and 7.3 dated 2016-10-12
ChangeLog | 5 DESCRIPTION | 6 MD5 | 40 +- NAMESPACE | 3 R/arfima.R | 62 +-- R/etsforecast.R | 1 R/fitBATS.R | 808 ++++++++++++++++++++---------------------- R/fitTBATS.R | 800 ++++++++++++++++++++--------------------- R/forecastBATS.R | 30 - R/forecastTBATS.R | 36 - R/getResponse.R | 50 +- R/ggplot.R | 10 R/naive.R | 3 R/nnetar.R | 51 ++ R/simulate.R | 191 +++++++-- README.md | 1 man/forecast.nnetar.Rd |only man/nnetar.Rd | 16 man/simulate.Rd | 12 tests/testthat/Rplots.pdf |only tests/testthat/test-bats.R | 2 tests/testthat/test-hfitted.R | 25 - 22 files changed, 1148 insertions(+), 1004 deletions(-)
Title: Ecological Niche in R and GRASS
Description: A set of tools for the analysis of ecological niche of species and calculation of habitat suitability maps.
Author: Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes Gonzalez-Wanguemert
Maintainer: Fernando Garcia Canovas <fcgarcia@ualg.pt>
Diff between ENiRG versions 1.0 dated 2016-05-05 and 1.0.1 dated 2016-10-12
ChangeLog | 16 +++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/enirg.R | 2 +- inst/CITATION | 11 +++++------ man/ENiRG-package.Rd | 8 ++++---- man/apis.enirg.Rd | 4 ++-- man/enirg.Rd | 6 +++++- 8 files changed, 43 insertions(+), 26 deletions(-)
Title: Functions and Data for the Second Edition of "Data Mining with
R"
Description: Functions and data accompanying the second edition of the book "Data Mining with R, learning with case studies" by Luis Torgo, published by CRC Press.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between DMwR2 versions 0.0.1 dated 2016-09-09 and 0.0.2 dated 2016-10-12
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 2 +- 4 files changed, 11 insertions(+), 8 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 1.1-6 dated 2015-07-22 and 1.1-7 dated 2016-10-12
DESCRIPTION | 13 +++-- MD5 | 128 ++++++++++++++++++++++++++-------------------------- R/colormap.R | 45 +++++++++--------- 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/colormap.Rd | 8 +-- 65 files changed, 99 insertions(+), 95 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
Scripts for an easy application of the functions are provided at the CM SAF homepage
(http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.6.1 dated 2016-01-28 and 1.7.0 dated 2016-10-12
DESCRIPTION | 12 ++--- MD5 | 116 ++++++++++++++++++++++++++++++--------------------- NAMESPACE | 14 +++++- R/box_mergetime.R | 8 +++ R/cmsaf.add.R | 2 R/cmsaf.addc.R | 2 R/cmsaf.div.R | 2 R/cmsaf.divc.R | 2 R/cmsaf.mul.R | 2 R/cmsaf.mulc.R | 2 R/cmsaf.sub.R | 2 R/cmsaf.subc.R | 2 R/dayrange.R | 2 R/divdpm.R | 2 R/extract.period.R | 8 +++ R/fldmax.R | 11 +++- R/fldmean.R | 6 +- R/fldmin.R | 8 +++ R/levbox_mergetime.R | 14 ++++-- R/mon.anomaly.R | 29 ++++++++++-- R/monmax.R |only R/monmean.R | 2 R/monmin.R |only R/monsd.R |only R/monsum.R | 54 +++++++++++------------ R/muldpm.R | 2 R/multimonmean.R | 4 - R/multimonsum.R | 4 - R/ncinfo.R | 5 +- R/remapbil.R | 24 ++++++---- R/seas.anomaly.R | 25 ++++++++++ R/seasmean.R | 4 - R/sellonlatbox.R | 8 +++ R/selmon.R | 8 +++ R/selperiod.R | 8 +++ R/selpoint.R | 14 ++++-- R/seltime.R | 8 +++ R/selyear.R | 8 +++ R/timmax.R |only R/timmean.R | 2 R/timmin.R |only R/timsd.R |only R/trend.R | 2 R/wfldmean.R | 2 R/year.anomaly.R | 25 ++++++++++ R/yearmean.R | 2 R/yearsum.R | 2 R/ymonmax.R |only R/ymonmean.R | 4 - R/ymonmin.R |only R/ymonsd.R |only R/ymonsum.R | 2 R/yseasmax.R |only R/yseasmean.R | 4 - R/yseasmin.R |only R/yseassd.R |only man/cmsaf-package.Rd | 4 - man/monmax.Rd |only man/monmin.Rd |only man/monsd.Rd |only man/ncinfo.Rd | 3 - man/selperiod.Rd | 2 man/timmax.Rd |only man/timmin.Rd |only man/timsd.Rd |only man/ymonmax.Rd |only man/ymonmin.Rd |only man/ymonsd.Rd |only man/yseasmax.Rd |only man/yseasmin.Rd |only man/yseassd.Rd |only 71 files changed, 323 insertions(+), 155 deletions(-)
Title: Exact Binary Sequential Designs and Analysis
Description: For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.
Author: Jenn Kirk, Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between binseqtest versions 1.0.1 dated 2015-07-02 and 1.0.2 dated 2016-10-12
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/ExactBinarySequentialDesigns.pdf |binary man/binseqtest-package.Rd | 2 +- 7 files changed, 16 insertions(+), 12 deletions(-)
Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>
Diff between mpr versions 1.0.3 dated 2016-09-21 and 1.0.4 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mpr-internal.R | 4 ++++ R/mpr.R | 16 ++++++++-------- R/stepmpr.R | 4 ++-- R/update.mpr.R | 2 +- 6 files changed, 24 insertions(+), 20 deletions(-)
Title: a Bunch of Structure and Sequence Analysis
Description: Reads and plots placements obtained using pplacer/guppy (see http://matsen.fhcrc.org/pplacer/ for details). Read PDB file (protein 3D structure file).
Author: pierre lefeuvre
Maintainer: pierre lefeuvre <pierre.lefeuvre@cirad.fr>
Diff between BoSSA versions 1.2 dated 2010-01-26 and 2.0 dated 2016-10-12
BoSSA-1.2/BoSSA/R/AccNumb.R |only BoSSA-1.2/BoSSA/R/FastaSorter.R |only BoSSA-1.2/BoSSA/R/InfoFasta.R |only BoSSA-1.2/BoSSA/R/InfoGB.R |only BoSSA-1.2/BoSSA/R/InfoGenBank.R |only BoSSA-1.2/BoSSA/R/InfoSeq.R |only BoSSA-1.2/BoSSA/R/TaxoGB.r |only BoSSA-1.2/BoSSA/R/blast.R |only BoSSA-1.2/BoSSA/R/distGPS.R |only BoSSA-1.2/BoSSA/R/getGB.R |only BoSSA-1.2/BoSSA/R/grpPhylogeo.R |only BoSSA-1.2/BoSSA/R/outBLAST.R |only BoSSA-1.2/BoSSA/R/read.PDB.R |only BoSSA-1.2/BoSSA/R/rename.R |only BoSSA-1.2/BoSSA/R/sortBLAST.R |only BoSSA-1.2/BoSSA/R/submitBLAST.R |only BoSSA-1.2/BoSSA/man/FastaSorter.Rd |only BoSSA-1.2/BoSSA/man/InfoGenBank.Rd |only BoSSA-1.2/BoSSA/man/TaxoGB.Rd |only BoSSA-1.2/BoSSA/man/blast.Rd |only BoSSA-1.2/BoSSA/man/distGPS.Rd |only BoSSA-1.2/BoSSA/man/grpPhylogeo.Rd |only BoSSA-1.2/BoSSA/man/read.PDB.Rd |only BoSSA-2.0/BoSSA/DESCRIPTION | 24 ++++++++++-------------- BoSSA-2.0/BoSSA/MD5 |only BoSSA-2.0/BoSSA/NAMESPACE | 25 ++++++++++++++----------- BoSSA-2.0/BoSSA/R/get_edge.R |only BoSSA-2.0/BoSSA/R/pplace_to_matrix.R |only BoSSA-2.0/BoSSA/R/pplace_to_table.R |only BoSSA-2.0/BoSSA/R/pplace_tree.R |only BoSSA-2.0/BoSSA/R/read_jplace.R |only BoSSA-2.0/BoSSA/R/read_pdb.R |only BoSSA-2.0/BoSSA/R/read_sqlite.R |only BoSSA-2.0/BoSSA/R/sub_pplace.R |only BoSSA-2.0/BoSSA/build |only BoSSA-2.0/BoSSA/data |only BoSSA-2.0/BoSSA/inst |only BoSSA-2.0/BoSSA/man/BoSSA-package.Rd |only BoSSA-2.0/BoSSA/man/pplace.Rd |only BoSSA-2.0/BoSSA/man/pplace_to_matrix.Rd |only BoSSA-2.0/BoSSA/man/pplace_to_table.Rd |only BoSSA-2.0/BoSSA/man/pplace_tree.Rd |only BoSSA-2.0/BoSSA/man/read_pdb.Rd |only BoSSA-2.0/BoSSA/man/read_sqlite.Rd |only BoSSA-2.0/BoSSA/man/sub_pplace.Rd |only 45 files changed, 24 insertions(+), 25 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model
selection and estimation in high-dimensional statistical models. Through this
publicly available package, we provide a unified environment to carry out
variable selection using iterative sure independence screening (SIS) and all
of its variants in generalized linear models and the Cox proportional hazards
model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao
Wu
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between SIS versions 0.8-1 dated 2016-08-13 and 0.8-3 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/standardize.R | 3 ++- inst |only man/standardize.Rd | 3 ++- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes
from <http://bootswatch.com/>, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans and Roboto fonts),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinythemes versions 1.1 dated 2016-09-19 and 1.1.1 dated 2016-10-12
DESCRIPTION | 12 ++-- MD5 | 13 ++--- NAMESPACE | 4 + NEWS.md | 5 + R/shinytheme.R | 132 +++++++++++++++++++++++++++++++++++++++++++++++---- README.md | 63 ++++++++++++++++-------- man/shinytheme.Rd | 2 man/themeSelector.Rd |only 8 files changed, 187 insertions(+), 44 deletions(-)
Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between red versions 0.1.1 dated 2016-09-28 and 0.1.2 dated 2016-10-12
DESCRIPTION | 8 +-- MD5 | 8 +-- R/red.R | 146 ++++++++++++++++++++++++++++---------------------------- man/map.easy.Rd | 4 - man/map.sdm.Rd | 10 ++- 5 files changed, 90 insertions(+), 86 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.0 dated 2016-10-03 and 2.3.1 dated 2016-10-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SSURGO_FUNCTIONS.R | 1 + inst/CITATION | 4 ++-- man/FedData-package.Rd | 4 ++-- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Group Sequential Design Class for Clinical Trials
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
Author: David A Schoenfeld, PhD and Hui Zheng, PhD
Maintainer: "Hui Zheng, PhD" <hzheng1@mgh.harvard.edu>
Diff between seqmon versions 0.2 dated 2007-10-22 and 2.1 dated 2016-10-12
seqmon-0.2/seqmon/INDEX |only seqmon-0.2/seqmon/R/seqmon.R |only seqmon-0.2/seqmon/gen.R |only seqmon-0.2/seqmon/seqmon.R |only seqmon-2.1/seqmon/DESCRIPTION | 27 ++-- seqmon-2.1/seqmon/LICENSE |only seqmon-2.1/seqmon/MD5 |only seqmon-2.1/seqmon/NAMESPACE |only seqmon-2.1/seqmon/R/sequential_design_class.R |only seqmon-2.1/seqmon/man/alphaspend.Rd |only seqmon-2.1/seqmon/man/alphaspendf.Rd |only seqmon-2.1/seqmon/man/betaspend.Rd |only seqmon-2.1/seqmon/man/betaspendf.Rd |only seqmon-2.1/seqmon/man/calcBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/calcBoundaries.Rd |only seqmon-2.1/seqmon/man/curtail.Rd |only seqmon-2.1/seqmon/man/curtailDesign-methods.Rd |only seqmon-2.1/seqmon/man/curtailDesign.Rd |only seqmon-2.1/seqmon/man/getProbabilities-methods.Rd |only seqmon-2.1/seqmon/man/getProbabilities.Rd |only seqmon-2.1/seqmon/man/plotBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/plotBoundaries.Rd |only seqmon-2.1/seqmon/man/printSummary-methods.Rd |only seqmon-2.1/seqmon/man/printSummary.Rd |only seqmon-2.1/seqmon/man/seqmon-package.Rd |only seqmon-2.1/seqmon/man/seqmon.Rd | 100 +++++++----------- seqmon-2.1/seqmon/man/sequential.design-class.Rd |only seqmon-2.1/seqmon/man/sequential.design.Rd |only seqmon-2.1/seqmon/man/setAlphaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setAlphaspendfString.Rd |only seqmon-2.1/seqmon/man/setBaseAlphaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBaseAlphaspendf.Rd |only seqmon-2.1/seqmon/man/setBaseBetaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBaseBetaspendf.Rd |only seqmon-2.1/seqmon/man/setBetaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setBetaspendfString.Rd |only seqmon-2.1/seqmon/man/setCurrentLook-methods.Rd |only seqmon-2.1/seqmon/man/setCurrentLook.Rd |only seqmon-2.1/seqmon/man/setDatestamp-methods.Rd |only seqmon-2.1/seqmon/man/setDatestamp.Rd |only seqmon-2.1/seqmon/man/setNoncentrality-methods.Rd |only seqmon-2.1/seqmon/man/setNoncentrality.Rd |only seqmon-2.1/seqmon/man/setTimes-methods.Rd |only seqmon-2.1/seqmon/man/setTimes.Rd |only seqmon-2.1/seqmon/man/updateDesign-methods.Rd |only seqmon-2.1/seqmon/man/updateDesign.Rd |only 46 files changed, 55 insertions(+), 72 deletions(-)