Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Diff between markophylo versions 1.0.2 dated 2015-08-31 and 1.0.3 dated 2015-11-05
DESCRIPTION | 22 +++-- MD5 | 24 +++-- NAMESPACE | 6 - NEWS | 12 ++ R/custom-general14.R | 85 ++++++++++++++------ inst/CITATION |only inst/doc/estimaterates.R | 30 +++++-- inst/doc/estimaterates.Rmd | 59 +++++++++++--- inst/doc/estimaterates.html | 179 +++++++++++++++++++++++++------------------- man/estimaterates.Rd | 4 man/markophylo-package.Rd | 6 - man/patterns.Rd |only man/plottree.Rd | 4 vignettes/estimaterates.Rmd | 59 +++++++++++--- 14 files changed, 327 insertions(+), 163 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.18 dated 2015-10-07 and 0.5.20 dated 2015-11-05
vtreat-0.5.18/vtreat/man/getNewVarNames.Rd |only vtreat-0.5.18/vtreat/tests/testthat/testRareCases.R |only vtreat-0.5.20/vtreat/DESCRIPTION | 8 vtreat-0.5.20/vtreat/MD5 | 22 - vtreat-0.5.20/vtreat/NAMESPACE | 2 vtreat-0.5.20/vtreat/R/vtreat.R | 269 +++++++++++++------- vtreat-0.5.20/vtreat/README.md | 2 vtreat-0.5.20/vtreat/man/designTreatmentsC.Rd | 6 vtreat-0.5.20/vtreat/man/designTreatmentsN.Rd | 6 vtreat-0.5.20/vtreat/man/designTreatmentsZ.Rd |only vtreat-0.5.20/vtreat/man/prepare.Rd | 4 vtreat-0.5.20/vtreat/man/vtreat-package.Rd | 4 vtreat-0.5.20/vtreat/tests/testthat/testNoY.R |only vtreat-0.5.20/vtreat/vignettes/vtreatOverfit.Rmd | 7 14 files changed, 216 insertions(+), 114 deletions(-)
Title: Survival Prediction by Joint Analysis of Microarray Gene
Expression Data
Description: Microarray gene expression data can be analyzed individually or jointly using merging methods or meta-analysis to predict patients' survival and risk assessment.
Author: Haleh Yasrebi
Maintainer: Haleh Yasrebi<hyasrebi@yahoo.com>
Diff between survJamda versions 1.1.3 dated 2015-05-02 and 1.1.4 dated 2015-11-05
DESCRIPTION | 8 ++-- MD5 | 76 ++++++++++++++++++++------------------ NAMESPACE | 9 ++++ R/calPerformance.auc.plot.R | 6 ++- R/calPerformance.merge.indep.R | 5 +- R/calPerformance.meta.R | 2 - R/calPerformance.single.indep.R | 3 + R/comb.surv.censor.R | 6 +-- R/compute.combat.R | 4 +- R/cross.val.combat.R | 4 +- R/cross.val.surv.R | 5 +- R/det.batchID.R | 2 - R/det.set.ind.R | 15 +------ R/eval.subset.R | 4 +- R/featureselection.R | 1 R/main.merge.indep.valid.R | 8 ++-- R/main.process.R | 13 +++--- R/plot.roc.curves.R |only R/plot.time.dep.R |only R/plotROC.R | 20 ++-------- R/pred.time.indep.valid.R | 8 ++-- R/prepcombat.R | 10 ++--- R/prepzscore1.R | 7 +-- R/prepzscore2.R | 1 R/splitMerged.auc.plot.R | 7 +-- R/splitMerged.indep.R | 14 +++---- R/splitZscore2.auc.plot.R | 4 +- R/splitZscore2.merge.indep.R | 5 +- inst/doc/survJamda.pdf |binary man/calPerformance.auc.plot.Rd | 9 +++- man/calPerformance.merge.indep.Rd | 6 +-- man/main.process.Rd | 10 +++-- man/plot.roc.curves.Rd |only man/plot.time.dep.Rd |only man/plotROC.Rd | 11 +++-- man/pred.time.indep.valid.Rd | 6 ++- man/splitMerged.auc.plot.Rd | 4 +- man/splitMerged.indep.Rd | 10 ++--- man/splitZscore2.auc.plot.Rd | 5 ++ man/splitZscore2.merge.indep.Rd | 5 ++ man/survJamda-package.Rd | 11 +++-- 41 files changed, 172 insertions(+), 152 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.0-23 dated 2015-08-16 and 1.0-25 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 4 ++-- inst/NEWS | 10 ++++++++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.11 dated 2015-08-26 and 0.0.12 dated 2015-11-05
DESCRIPTION | 11 - MD5 | 31 ++-- NAMESPACE | 7 - R/UTA.R | 16 ++ R/UTADIS.R | 18 ++ R/UTASTAR.R | 15 ++ R/additiveValueFunctionElicitation.R | 2 R/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R | 23 +++ R/plotAlternativesValuesPreorder.R |only R/weightedSum.R | 70 +++++------ man/UTA.Rd | 42 ++---- man/UTASTAR.Rd | 10 - man/applyPiecewiseLinearValueFunctionsOnPerformanceTable.Rd | 10 - man/assignAlternativesToCategoriesByThresholds.Rd | 3 man/plotAlternativesValuesPreorder.Rd |only tests/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R | 2 tests/assignAlternativesToCategoriesByThresholds.R | 2 tests/plotAlternativesValuesPreorder.R |only 18 files changed, 156 insertions(+), 106 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 0.1 dated 2015-07-22 and 0.3 dated 2015-11-05
imputeTS-0.1/imputeTS/R/int.precheck.R |only imputeTS-0.1/imputeTS/man/precheck.Rd |only imputeTS-0.3/imputeTS/DESCRIPTION | 12 ++++--- imputeTS-0.3/imputeTS/MD5 | 42 +++++++++++++++++--------- imputeTS-0.3/imputeTS/NAMESPACE | 11 ++++++ imputeTS-0.3/imputeTS/NEWS | 17 ++++++++++ imputeTS-0.3/imputeTS/R/data.heating.R |only imputeTS-0.3/imputeTS/R/data.nh4.R |only imputeTS-0.3/imputeTS/R/imputeTS-package.R |only imputeTS-0.3/imputeTS/R/int.algoInterface.R |only imputeTS-0.3/imputeTS/R/int.preCheck.R |only imputeTS-0.3/imputeTS/R/na.replace.R | 2 - imputeTS-0.3/imputeTS/R/na.seadec.R |only imputeTS-0.3/imputeTS/R/na.seasplit.R |only imputeTS-0.3/imputeTS/R/vis.differences.R |only imputeTS-0.3/imputeTS/data |only imputeTS-0.3/imputeTS/inst/TODO | 18 +++++++++-- imputeTS-0.3/imputeTS/man/heating.Rd |only imputeTS-0.3/imputeTS/man/imputeTS-package.Rd |only imputeTS-0.3/imputeTS/man/na.interpolation.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.locf.Rd | 11 +++--- imputeTS-0.3/imputeTS/man/na.mean.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.random.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.remove.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.replace.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.seadec.Rd |only imputeTS-0.3/imputeTS/man/na.seasplit.Rd |only imputeTS-0.3/imputeTS/man/nh4.Rd |only imputeTS-0.3/imputeTS/man/vis.differences.Rd |only 29 files changed, 111 insertions(+), 47 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2.2 dated 2015-10-21 and 2.3 dated 2015-11-05
pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.R |only pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.Rd |only pcnetmeta-2.3/pcnetmeta/DESCRIPTION | 12 ++++---- pcnetmeta-2.3/pcnetmeta/MD5 | 32 +++++++++++------------ pcnetmeta-2.3/pcnetmeta/NAMESPACE | 4 +- pcnetmeta-2.3/pcnetmeta/R/absolute.plot.R | 9 +++++- pcnetmeta-2.3/pcnetmeta/R/contrast.plot.R | 10 +++++-- pcnetmeta-2.3/pcnetmeta/R/nma.ab.bin.R |only pcnetmeta-2.3/pcnetmeta/R/nma.ab.cont.R | 25 ++++++++++++----- pcnetmeta-2.3/pcnetmeta/R/nma.ab.followup.R | 9 +++++- pcnetmeta-2.3/pcnetmeta/R/nma.ab.py.R | 8 +++++ pcnetmeta-2.3/pcnetmeta/man/absolute.plot.Rd | 10 +++++-- pcnetmeta-2.3/pcnetmeta/man/contrast.plot.Rd | 12 +++++--- pcnetmeta-2.3/pcnetmeta/man/nma.ab.bin.Rd |only pcnetmeta-2.3/pcnetmeta/man/nma.ab.cont.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/nma.ab.followup.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/nma.ab.py.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/pcnetmeta-package.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/rank.prob.Rd | 4 +- 19 files changed, 92 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-02 0.5
2014-09-07 0.4
2014-08-26 0.3
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 0.94-3 dated 2015-08-26 and 0.94-4 dated 2015-11-05
DESCRIPTION | 10 - MD5 | 15 +- NAMESPACE | 1 R/RSAGA-core.R | 9 - R/RSAGA-modules.R | 257 +++++++++++++++++++++++++++++++++++++++--- R/RSAGA-package.R | 2 inst/doc/RSAGA-landslides.pdf |binary man/RSAGA-package.Rd | 2 man/rsaga.pisr2.Rd |only 9 files changed, 262 insertions(+), 34 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.4 dated 2015-08-22 and 3.3.6 dated 2015-11-05
DESCRIPTION | 14 - MD5 | 67 ++++----- NAMESPACE | 5 NEWS | 47 ++++++ R/ANOVA.R | 190 ++++++++++++++++++++++---- R/ANOVAz1.R | 265 ++++++++++++++++++++++--------------- R/ANOVAz2.R | 331 +++++++++++++++++++++++++++++------------------ R/Logit.R | 35 ++++ R/Read.R | 82 ++++++++--- R/Regression.R | 50 ++----- R/ScatterPlot.R | 4 R/anova.zknitr.R |only R/details.R | 9 - R/logit.z4Pred.R | 2 R/plt.zmain.R | 17 -- R/print.outall.r | 2 R/reg.z1anvBasic.R | 7 R/reg.z1bckBasic.R | 10 - R/reg.z1modelBasic.R | 2 R/reg.z2Relations.R | 21 +- R/reg.z3resfitResidual.R | 2 R/reg.z4Pred.R | 2 R/reg.z5Plot.R | 51 +++---- R/reg.zknitr.R | 14 - R/ttest.R | 4 R/ttp2zgraph.R | 3 R/zzz.R | 67 ++++++--- man/ANOVA.Rd | 51 ++++++- man/BoxPlot.Rd | 2 man/Density.Rd | 2 man/Histogram.Rd | 2 man/Logit.Rd | 2 man/Read.Rd | 7 man/Regression.Rd | 18 -- man/ScatterPlot.Rd | 15 -- 35 files changed, 904 insertions(+), 498 deletions(-)
Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet'
software.
Author: Emily Beylerian [cre, aut],
Kirk Li [ctb],
Samuel Jenness [ctb],
Martina Morris [ctb]
Maintainer: Emily Beylerian <ebey@uw.edu>
Diff between statnetWeb versions 0.3.6 dated 2015-08-21 and 0.4.0 dated 2015-11-05
DESCRIPTION | 15 +-- MD5 | 24 ++--- NAMESPACE | 4 R/run_sw.R | 1 R/statnetWeb-package.R | 2 README.md | 45 +-------- inst/shiny/global.R | 40 ++++++-- inst/shiny/server.R | 213 ++++++++++++++++++++++++++++++++++++++++------- inst/shiny/ui.R | 43 +++++++-- inst/shiny/www/alert.js | 9 + inst/shiny/www/style.css | 10 +- man/run_sw.Rd | 4 man/statnetWeb.Rd | 2 13 files changed, 299 insertions(+), 113 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.4.11 dated 2015-08-18 and 1.4.12 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 2 +- R/CDCabove.R | 4 +++- R/CDCbelow.R | 5 +++-- R/Effectsize.R | 25 +++++++++++++++++++++++++ R/RobustCDCabove.R | 7 ++++++- R/RobustCDCbelow.R | 5 ++++- R/meanES.R |only man/meanES.Rd |only 10 files changed, 55 insertions(+), 17 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.2 dated 2015-10-27 and 1.7.3 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/build.dist.struct.R | 11 +++++++---- R/rcbalance.R | 4 +++- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab. Thus they
are available to the user as a script file or as an aide for the user to
learn R or to copy-and-paste directly into R itself.
Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (Author of original print.summary.nnet),
Jose Magana [ctb] (Contributed the ggpairs plots.)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 3.5.0 dated 2015-07-14 and 4.0.0 dated 2015-11-05
rattle-3.5.0/rattle/R/pam.R |only rattle-3.5.0/rattle/inst/etc/rattle.ui.140722 |only rattle-3.5.0/rattle/inst/etc/rattle.ui.150207 |only rattle-4.0.0/rattle/DESCRIPTION | 35 rattle-4.0.0/rattle/MD5 | 69 - rattle-4.0.0/rattle/NAMESPACE | 5 rattle-4.0.0/rattle/R/acquireAuditData.R | 12 rattle-4.0.0/rattle/R/appendLibLog.R |only rattle-4.0.0/rattle/R/binning.R | 12 rattle-4.0.0/rattle/R/data.R | 91 + rattle-4.0.0/rattle/R/evaluate.R | 56 - rattle-4.0.0/rattle/R/executeBoxPlot2.R |only rattle-4.0.0/rattle/R/executeHistPlot2.R | 99 +- rattle-4.0.0/rattle/R/executePairsPlotSelect2.R |only rattle-4.0.0/rattle/R/explore.R | 300 +----- rattle-4.0.0/rattle/R/fancyRpartPlot.R | 41 rattle-4.0.0/rattle/R/hclust.R | 28 rattle-4.0.0/rattle/R/help.R | 8 rattle-4.0.0/rattle/R/kmeans.R | 21 rattle-4.0.0/rattle/R/log.R | 24 rattle-4.0.0/rattle/R/rattle.R | 36 rattle-4.0.0/rattle/R/rattleInfo.R | 20 rattle-4.0.0/rattle/R/riskchart.R | 6 rattle-4.0.0/rattle/R/rpart.R | 9 rattle-4.0.0/rattle/build/vignette.rds |binary rattle-4.0.0/rattle/data/locationsAUS.RData |binary rattle-4.0.0/rattle/data/weather.RData |binary rattle-4.0.0/rattle/data/weatherAUS.RData |binary rattle-4.0.0/rattle/inst/NEWS | 88 + rattle-4.0.0/rattle/inst/doc/rattle.R | 8 rattle-4.0.0/rattle/inst/doc/rattle.Rnw | 23 rattle-4.0.0/rattle/inst/doc/rattle.pdf |binary rattle-4.0.0/rattle/inst/etc/ConnectRlogo.png |only rattle-4.0.0/rattle/inst/etc/rattle.ui | 1187 +++++++++++------------- rattle-4.0.0/rattle/inst/etc/tooltips.xml | 3 rattle-4.0.0/rattle/man/fancyRpartPlot.Rd | 11 rattle-4.0.0/rattle/man/internal.Rd | 1 rattle-4.0.0/rattle/man/riskchart.Rd | 10 rattle-4.0.0/rattle/vignettes/rattle.Rnw | 23 39 files changed, 1133 insertions(+), 1093 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.10 dated 2015-07-10 and 0.0.12 dated 2015-11-05
DESCRIPTION | 8 - MD5 | 18 +-- inst/include/Error_utils.h | 40 ++++---- inst/include/Solve.h | 2 inst/include/utils.h | 3 src/Error_utils.h | 40 ++++---- src/RFutils.cc | 2 src/Solve.h | 2 src/solve.cc | 223 ++++++++++++++++++++++++++++----------------- src/utils.h | 3 10 files changed, 204 insertions(+), 137 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.1 dated 2015-07-25 and 3.1.3 dated 2015-11-05
DESCRIPTION | 6 MD5 | 48 +++--- NAMESPACE | 8 - R/Methods-aux.R | 6 R/RFgui.R | 231 +++++++++++++------------------- R/convert.R | 7 R/fitgauss.R | 310 +++++++++++++++++++++---------------------- R/internal_use.R | 1 R/rf-plots.R | 40 +---- man/RFgridDataFrame-class.Rd | 2 man/RFgui.Rd | 7 src/MLE.cc | 7 src/Primitive.cc | 2 src/RF.h | 9 - src/direct.cc | 9 - src/error.h | 11 - src/gausslikeli.cc | 117 +++++++++++++--- src/getNset.cc | 5 src/hyperplan.cc | 10 - src/initNerror.cc | 12 - src/nugget.cc | 9 - src/plusmalS.cc | 12 + src/sequential.cc | 10 - src/trend.cc | 2 src/variogramAndCo.cc | 7 25 files changed, 452 insertions(+), 436 deletions(-)
Title: Permutation Significance for Random Forests
Description: Estimate False Discovery Rates (FDRs) for importance metrics from random forest runs.
Author: Ankur Chakravarthy
Maintainer: Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>
Diff between pRF versions 1.0 dated 2015-03-03 and 1.1 dated 2015-11-05
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/AC_pRF.R | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.6 dated 2015-11-03 and 0.4.6-1 dated 2015-11-05
DESCRIPTION | 8 +- MD5 | 69 +++++++++++---------- NAMESPACE | 2 R/bundle.R | 19 ++++-- R/utils.R | 18 +++++ inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 man/appDependencies.Rd | 9 +- man/bundle.Rd | 9 ++ man/clean.Rd | 2 man/disable.Rd | 2 man/init.Rd | 2 man/install.Rd | 2 man/install_github.Rd | 10 +-- man/install_local.Rd | 2 man/migrate.Rd | 2 man/packify.Rd | 2 man/packrat-external.Rd | 2 man/packrat-mode.Rd | 2 man/packrat-options.Rd | 2 man/packrat.Rd | 3 man/repos_create.Rd | 2 man/repos_upload.Rd | 2 man/repository-management.Rd | 4 - man/restore.Rd | 2 man/search_path.Rd | 2 man/snapshot.Rd | 10 +-- man/snapshotImpl.Rd | 10 +-- man/status.Rd | 2 man/unbundle.Rd | 2 man/unused_packages.Rd | 2 tests/testthat/helper-bundle.R |only tests/testthat/test-bundle.R | 98 ++++++++----------------------- tests/testthat/test-downloader.R | 4 + tests/testthat/test-hash.R | 8 ++ tests/testthat/test-local-repositories.R | 5 - 36 files changed, 158 insertions(+), 166 deletions(-)
Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity
score analysis for multilevel, or clustered, data.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between multilevelPSA versions 1.2.2 dated 2014-11-25 and 1.2.3 dated 2015-11-05
DESCRIPTION | 13 ++-- MD5 | 92 ++++++++++++++++----------------- NAMESPACE | 18 ++++++ NEWS | 6 ++ R/mlpsa.logistic.R | 2 R/multilevelPSA-package.R | 3 + R/plot.mlpsa.circ.R | 65 +++++++++++------------ R/plot.mlpsa.distribution.R | 15 +++-- R/xtable.mlpsa.r | 6 +- README.md | 10 ++- man/align.plots.Rd | 3 - man/as.data.frame.covariate.balance.Rd | 3 - man/covariate.balance.Rd | 3 - man/covariateBalance.Rd | 25 ++++---- man/cv.trans.psa.Rd | 13 ++-- man/difftable.plot.Rd | 3 - man/geom_rug_alt.Rd | 3 - man/getPropensityScores.Rd | 3 - man/getStrata.Rd | 3 - man/is.mlpsa.Rd | 3 - man/loess.plot.Rd | 11 ++- man/lsos.Rd | 7 +- man/missing.plot.Rd | 3 - man/mlpsa.Rd | 11 ++- man/mlpsa.circ.plot.Rd | 13 ++-- man/mlpsa.ctree.Rd | 5 + man/mlpsa.difference.plot.Rd | 9 +-- man/mlpsa.distribution.plot.Rd | 7 +- man/mlpsa.logistic.Rd | 3 - man/multilevelPSA-package.Rd | 7 +- man/pisa.colnames.Rd | 3 - man/pisa.countries.Rd | 3 - man/pisa.psa.cols.Rd | 3 - man/pisana.Rd | 7 +- man/plot.covariate.balance.Rd | 3 - man/plot.mlpsa.Rd | 11 ++- man/plot.psrange.Rd | 3 - man/print.covariate.balance.Rd | 3 - man/print.mlpsa.Rd | 3 - man/print.psrange.Rd | 3 - man/print.xmlpsa.Rd | 3 - man/psrange.Rd | 7 +- man/summary.mlpsa.Rd | 3 - man/summary.psrange.Rd | 3 - man/tree.plot.Rd | 5 + man/xtable.mlpsa.Rd | 9 ++- man/zeroGrob.Rd | 3 - 47 files changed, 259 insertions(+), 184 deletions(-)
Title: Linear Parametric Models Applied to Hydrological Series
Description: Apply Univariate Long Memory Models,
Multivariate Short Memory Models To Hydrological Dataset.
Author: Corrado Tallerini [aut, cre],
Salvatore Grimaldi [aut]
Maintainer: Corrado Tallerini <corrado.tallerini@vodafone.it>
Diff between LPM versions 2.5 dated 2015-07-08 and 2.6 dated 2015-11-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++---- NAMESPACE | 2 +- R/IDFcurve.R |only build/partial.rdb |binary data/Hourly.rainfall.series.rda |only man/Hourly.rainfall.series.Rd |only man/IDFcurve.Rd |only man/restrict.Rd | 7 +++++++ 9 files changed, 21 insertions(+), 10 deletions(-)
Title: Multiresolution Kriging Based on Markov Random Fields
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. An extension of this
version over previous ones ( < 5.4 ) is the support for different
geometries besides a rectangular domain.
One benefit of the LatticeKrig model/approach
is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 5.4 dated 2015-10-22 and 5.4-1 dated 2015-11-05
DESCRIPTION | 8 +- MD5 | 44 ++++++------ R/LKrig.precision.R | 7 +- R/LKrigNormalizeBasis.R | 3 R/Radial.basis.R | 2 R/Tensor.basis.R | 2 man/LKrig.Rd | 2 man/LKrig.basis.Rd | 15 ++++ man/LatticeKrig.Rd | 11 +-- man/gridList-class.Rd | 119 +++++++++++++++++------------------ tests/LKrig.FindNorm.test.Rout.save | 6 - tests/LKrig.basis.test.R | 4 - tests/LKrig.basis.test.Rout.save | 6 - tests/LKrig.lnPLike.test.R | 4 - tests/LKrig.lnPlike.test.Rout.save | 6 - tests/LKrig.nullspace.test.Rout.save | 6 - tests/LKrig.precision.test.R | 18 ++--- tests/LKrig.precision.test.Rout.save | 6 - tests/LKrig.se.test.Rout.save | 6 - tests/LKrig.test.3D.Rout.save | 6 - tests/LKrig.test.R | 6 - tests/LKrig.test.Rout.save | 6 - tests/LKrig.test.inverse.R | 6 - 23 files changed, 158 insertions(+), 141 deletions(-)
Title: Read and Preprocess Fluorescence Excitation-Emission Matrix
(EEM) Data
Description: Read raw EEM data and prepares them for further analysis.
Author: Vipavee Trivittayasil
Maintainer: Vipavee Trivittayasil <vipavee.tri@gmail.com>
Diff between EEM versions 1.0.1 dated 2015-08-05 and 1.0.4 dated 2015-11-05
EEM-1.0.1/EEM/README.md |only EEM-1.0.4/EEM/DESCRIPTION | 12 +-- EEM-1.0.4/EEM/MD5 | 31 ++++----- EEM-1.0.4/EEM/R/EEM.R | 2 EEM-1.0.4/EEM/R/drawEEM.R | 116 +++++++++++++++++++++-------------- EEM-1.0.4/EEM/R/findLocalMax.R | 6 + EEM-1.0.4/EEM/R/plotScore.R | 22 +++--- EEM-1.0.4/EEM/R/plotScorem.R | 8 +- EEM-1.0.4/EEM/inst/doc/vignette.R | 10 +-- EEM-1.0.4/EEM/inst/doc/vignette.Rmd | 12 +-- EEM-1.0.4/EEM/inst/doc/vignette.html | 19 +++-- EEM-1.0.4/EEM/man/EEM.Rd | 2 EEM-1.0.4/EEM/man/drawEEM.Rd | 47 +++++++------- EEM-1.0.4/EEM/man/findLocalMax.Rd | 2 EEM-1.0.4/EEM/man/plotScore.Rd | 10 +-- EEM-1.0.4/EEM/man/plotScorem.Rd | 4 - EEM-1.0.4/EEM/vignettes/vignette.Rmd | 12 +-- 17 files changed, 171 insertions(+), 144 deletions(-)
Title: Double Generalized Linear Models
Description: Model fitting and evaluation tools for double generalized linear models (DGLMs).
This class of models uses one generalized linear model (GLM) to fit the specified response and
a second GLM to fit the deviance of the first model.
Author: Peter K Dunn <pdunn2@usc.edu.au> and Gordon K Smyth
Maintainer: Robert Corty <robert_corty@med.unc.edu>
Diff between dglm versions 1.8.1 dated 2014-11-07 and 1.8.2 dated 2015-11-05
dglm-1.8.1/dglm/R/dglmall.R |only dglm-1.8.2/dglm/DESCRIPTION | 16 +++++++++------- dglm-1.8.2/dglm/MD5 | 15 +++++++++++---- dglm-1.8.2/dglm/NAMESPACE | 5 +++++ dglm-1.8.2/dglm/R/anova.dglm.R |only dglm-1.8.2/dglm/R/dglm.R |only dglm-1.8.2/dglm/R/dglm.constant.R |only dglm-1.8.2/dglm/R/dglm.control.R |only dglm-1.8.2/dglm/R/print.summary.dglm.R |only dglm-1.8.2/dglm/R/summary.dglm.R |only dglm-1.8.2/dglm/man/dglm.Rd | 2 +- dglm-1.8.2/dglm/tests |only 12 files changed, 26 insertions(+), 12 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.8.2 dated 2015-09-28 and 0.8.3 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/LoadAPSIMouts.R | 21 ++++++++++++++------- R/MetFunctions.R | 49 ++++++++++++++++++++++++++++++++++--------------- README.md | 7 +++++++ man/checkMet.Rd | 4 ++++ man/loadApsim.Rd | 12 +++++++----- man/prepareMet.Rd | 22 ++++++++++++++++------ 8 files changed, 93 insertions(+), 44 deletions(-)