Title: A Soil Survey Toolkit
Diff between sharpshootR versions 0.6-3 dated 2014-05-06 and 0.7-2 dated 2015-02-19
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: USDA-NRCS Soil Survey Staff
Maintainer: Dylan Beaudette
DESCRIPTION | 24 +++++----
MD5 | 41 +++++++++--------
NAMESPACE | 25 ++++++++--
R/SoilTaxonomyDendrogram.R | 6 +-
R/aspect.plot.R | 19 ++++---
R/component.adj.matrix.R | 26 ++++++----
R/diagnosticPropertyPlot.R | 16 +++++-
R/dueling.dendrograms.R | 12 ++++
R/hillslope.probability.R | 2
R/plotAvailWater.R |only
R/plotSoilRelationGraph.R | 101 +++++++++++++++++++++++++++++++++++-------
R/polygonAdjacency.R |only
R/transect-functions.R |only
data/CDEC.snow.courses.rda |binary
data/amador.rda |binary
man/CDECquery.Rd | 74 ++++++++++++++++++++++++++++--
man/SoilTaxonomyDendrogram.Rd | 6 ++
man/aspect.plot.Rd | 5 +-
man/component.adj.matrix.Rd | 3 -
man/diagnosticPropertyPlot.Rd | 2
man/dist.along.grad.Rd |only
man/plotAvailWater.Rd |only
man/plotSoilRelationGraph.Rd | 28 +++++++++++
man/plotTransect.Rd |only
man/polygonAdjacency.Rd |only
25 files changed, 307 insertions(+), 83 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Diff between OUwie versions 1.43 dated 2014-07-26 and 1.44 dated 2015-02-19
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 10 +-
MD5 | 23 +++---
R/OUwie.R | 153 ++++++++++++++++++++++++++++++++++--------
R/OUwie.boot.R | 4 -
R/OUwie.fixed.R | 1
R/OUwie.joint.R | 190 ++++++++++++++++++++++++++++-------------------------
R/OUwie.sim.R | 8 +-
R/OUwie.slice.R | 17 ++--
R/expect.trendy.R |only
man/OUwie.Rd | 8 --
man/OUwie.boot.Rd | 4 -
man/OUwie.joint.Rd | 7 -
man/OUwie.slice.Rd | 6 -
13 files changed, 267 insertions(+), 164 deletions(-)
Title: Earth Mover's Distance for Differential Analysis of Genomics
Data
Diff between EMDomics versions 0.99.0 dated 2014-11-15 and 0.99.1 dated 2015-02-19
Description: The EMDomics algorithm is used to perform a supervised two-class
analysis to measure the magnitude and statistical significance of observed
continuous genomics data between two groups. Usually the data will be gene
expression values from array-based or sequence-based experiments, but data
from other types of experiments can also be analyzed (e.g. copy number
variation). Traditional methods like Significance Analysis of Microarrays
(SAM) and Linear Models for Microarray Data (LIMMA) use significance tests
based on summary statistics (mean and standard deviation) of the two
distributions. This approach lacks power to identify expression differences
between groups that show high levels of intra-group heterogeneity. The Earth
Mover's Distance (EMD) algorithm instead computes the "work" needed to
transform one distribution into the other, thus providing a metric of the
overall difference in shape between two distributions. Permutation of sample
labels is used to generate q-values for the observed EMD scores.
Author: Daniel Schmolze [aut, cre],
Andrew Beck [aut],
Sheida Nabavi [aut]
Maintainer: Daniel Schmolze
DESCRIPTION | 8 -
MD5 | 28 +--
NAMESPACE | 2
NEWS | 6
R/main.R | 4
build/vignette.rds |binary
inst/doc/EMDomics.R | 128 ++++++++---------
inst/doc/EMDomics.html | 346 +++++++++++++++++++++++-----------------------
man/EMDomics.Rd | 3
man/calculate_emd.Rd | 3
man/calculate_emd_gene.Rd | 3
man/emdomics-package.Rd | 3
man/plot_density.Rd | 3
man/plot_emdnull.Rd | 3
man/plot_perms.Rd | 3
15 files changed, 278 insertions(+), 265 deletions(-)
Title: Error Grid Analysis
Diff between ega versions 1.0.0 dated 2014-11-13 and 1.0.1 dated 2015-02-19
Description: Functions for assigning Clarke or Parkes (Consensus) error grid
zones to blood glucose values, and for plotting both types of error grids.
Author: Daniel Schmolze [aut, cre]
Maintainer: Daniel Schmolze
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
NAMESPACE | 2 +-
NEWS |only
R/ega.R | 18 +++++++++++-------
R/plots.R | 11 ++++++-----
inst/doc/ega.html | 14 +++++++-------
man/ega-package.Rd | 3 ++-
man/getClarkeZones.Rd | 3 ++-
man/getParkesZones.Rd | 3 ++-
man/glucose_data.Rd | 3 ++-
man/plotClarkeGrid.Rd | 3 ++-
man/plotParkesGrid.Rd | 3 ++-
13 files changed, 52 insertions(+), 40 deletions(-)
More information about disparityfilter at CRAN
Permanent link
Title: Geographic Display of Survey Data Statistics
Diff between mapStats versions 1.17 dated 2014-04-14 and 2.3 dated 2015-02-19
Description: Automated calculation and visualization of survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman
DESCRIPTION | 15 -
INDEX | 4
MD5 | 22 +-
NAMESPACE | 3
R/calcQuantiles.R | 113 --------------
R/calcStats.R | 219 +++++++++++++++++----------
R/mapStats.R | 78 +++------
R/plotStats.R | 374 +++++++++++++++++++++++++++++++++--------------
demo/map_examples.R | 184 +++++++++++++----------
man/mapStats-internal.Rd | 30 ++-
man/mapStats-package.Rd | 15 -
man/mapStats.Rd | 139 +++++++----------
12 files changed, 646 insertions(+), 550 deletions(-)
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Diff between FRESA.CAD versions 1.0 dated 2014-09-11 and 2.0 dated 2015-02-19
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena
FRESA.CAD-1.0/FRESA.CAD/R/BootVarNeRIElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/R/boostrapVarElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/data/CancerVarNames.rda |only
FRESA.CAD-1.0/FRESA.CAD/man/bootVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/DESCRIPTION | 21
FRESA.CAD-2.0/FRESA.CAD/MD5 | 154 -
FRESA.CAD-2.0/FRESA.CAD/NAMESPACE | 11
FRESA.CAD-2.0/FRESA.CAD/NEWS |only
FRESA.CAD-2.0/FRESA.CAD/R/FRESA.Model.R | 494 ++--
FRESA.CAD-2.0/FRESA.CAD/R/NeRIBasedFRESA.Model.R | 377 +--
FRESA.CAD-2.0/FRESA.CAD/R/ReclassificationFRESA.Model.R | 617 +----
FRESA.CAD-2.0/FRESA.CAD/R/backVarElimination.r | 250 +-
FRESA.CAD-2.0/FRESA.CAD/R/backVarNeRIElimination.r | 32
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidation.R | 545 +----
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidationNeRI.R | 255 --
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarElimination.r | 284 +-
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarNeRIElimination.r |only
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationFeatureSelection.R | 1032 ++++------
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationNeRIFeatureSelection.R | 210 +-
FRESA.CAD-2.0/FRESA.CAD/R/featureAdjustment.R | 61
FRESA.CAD-2.0/FRESA.CAD/R/getKNNpredictionFromFormula.r | 22
FRESA.CAD-2.0/FRESA.CAD/R/getVarNeRI.R | 35
FRESA.CAD-2.0/FRESA.CAD/R/getVarReclassification.R | 39
FRESA.CAD-2.0/FRESA.CAD/R/heatMaps.R | 86
FRESA.CAD-2.0/FRESA.CAD/R/improvedResiduals.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/listTopCorrelatedVariables.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/medianPredict.r | 44
FRESA.CAD-2.0/FRESA.CAD/R/modelFitting.R | 96
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidation.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidationNeRI.R |only
FRESA.CAD-2.0/FRESA.CAD/R/plotModels.ROC.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/predictForFresa.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/rankInverseNormalDataFrame.R | 91
FRESA.CAD-2.0/FRESA.CAD/R/reportEquivalentVariables.R | 12
FRESA.CAD-2.0/FRESA.CAD/R/residualtForNeRIs.R | 33
FRESA.CAD-2.0/FRESA.CAD/R/summary.bootstrapValidation.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/summaryReport.r | 2
FRESA.CAD-2.0/FRESA.CAD/R/timeSerieAnalysis.R | 34
FRESA.CAD-2.0/FRESA.CAD/R/uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/univariateRankVariables.R | 731 -------
FRESA.CAD-2.0/FRESA.CAD/R/update.uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/updateModel.R | 512 ++--
FRESA.CAD-2.0/FRESA.CAD/R/updateNeRImodel.R | 128 -
FRESA.CAD-2.0/FRESA.CAD/data/cancerVarNames.rda |only
FRESA.CAD-2.0/FRESA.CAD/man/CancerVarNames.Rd | 44
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.CAD-package.Rd | 264 +-
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.Model.Rd | 396 +--
FRESA.CAD-2.0/FRESA.CAD/man/NeRIBasedFRESA.Model.Rd | 272 +-
FRESA.CAD-2.0/FRESA.CAD/man/ReclassificationFRESA.Model.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/backVarElimination.Rd | 181 +
FRESA.CAD-2.0/FRESA.CAD/man/backVarNeRIElimination.Rd | 187 +
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidation.Rd | 292 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidationNeRI.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarElimination.Rd | 226 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationFeatureSelection.Rd | 447 ++--
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationNeRIFeatureSelection.Rd | 433 ++--
FRESA.CAD-2.0/FRESA.CAD/man/featureAdjustment.Rd | 146 -
FRESA.CAD-2.0/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 145 -
FRESA.CAD-2.0/FRESA.CAD/man/getVarNeRI.Rd | 184 +
FRESA.CAD-2.0/FRESA.CAD/man/getVarReclassification.Rd | 176 -
FRESA.CAD-2.0/FRESA.CAD/man/heatMaps.Rd | 189 +
FRESA.CAD-2.0/FRESA.CAD/man/improvedResiduals.Rd | 177 +
FRESA.CAD-2.0/FRESA.CAD/man/listTopCorrelatedVariables.Rd | 128 -
FRESA.CAD-2.0/FRESA.CAD/man/medianPredict.Rd | 186 +
FRESA.CAD-2.0/FRESA.CAD/man/modelFitting.Rd | 120 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidation.Rd | 121 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidationNeRI.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/plotModels.ROC.Rd | 165 -
FRESA.CAD-2.0/FRESA.CAD/man/predictForFresa.Rd | 118 -
FRESA.CAD-2.0/FRESA.CAD/man/rankInverseNormalDataFrame.Rd | 111 -
FRESA.CAD-2.0/FRESA.CAD/man/reportEquivalentVariables.Rd | 159 -
FRESA.CAD-2.0/FRESA.CAD/man/residualForNeRIs.Rd | 123 -
FRESA.CAD-2.0/FRESA.CAD/man/summary.bootstrapValidation.Rd | 129 -
FRESA.CAD-2.0/FRESA.CAD/man/summaryReport.Rd | 162 -
FRESA.CAD-2.0/FRESA.CAD/man/timeSeriesAnalysis.Rd | 173 -
FRESA.CAD-2.0/FRESA.CAD/man/uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/univariateRankVariables.Rd | 461 ++--
FRESA.CAD-2.0/FRESA.CAD/man/update.uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/updateModel.Rd | 214 +-
FRESA.CAD-2.0/FRESA.CAD/man/updateNeRImodel.Rd | 236 +-
FRESA.CAD-2.0/FRESA.CAD/src |only
82 files changed, 6463 insertions(+), 6714 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Diff between EcoGenetics versions 1.0 dated 2015-01-30 and 1.1.0 dated 2015-02-19
Description: Analysis of phenotypic, genotypic and environmental data
with an object of class "ecogen", designed to make easy the
integration of the available information from multiple sources.
Also including geostatistical tools and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser
EcoGenetics-1.0/EcoGenetics/R/auxiliar.R |only
EcoGenetics-1.0/EcoGenetics/R/coordinates.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.sortalleles.R |only
EcoGenetics-1.0/EcoGenetics/R/environment.R |only
EcoGenetics-1.0/EcoGenetics/R/genotype.R |only
EcoGenetics-1.0/EcoGenetics/R/phenotype.R |only
EcoGenetics-1.0/EcoGenetics/R/structure.R |only
EcoGenetics-1.0/EcoGenetics/R/tab.R |only
EcoGenetics-1.0/EcoGenetics/man/auxiliar.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.lmtree-summary.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.sortalleles.Rd |only
EcoGenetics-1.1.0/EcoGenetics/DESCRIPTION | 46
EcoGenetics-1.1.0/EcoGenetics/MD5 | 158 +-
EcoGenetics-1.1.0/EcoGenetics/NAMESPACE | 23
EcoGenetics-1.1.0/EcoGenetics/NEWS |only
EcoGenetics-1.1.0/EcoGenetics/R/ZZZ.R | 2
EcoGenetics-1.1.0/EcoGenetics/R/eco.2columns.R | 109 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2geneland.R | 99 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2genepop.R | 186 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.2gstudio.R | 55
EcoGenetics-1.1.0/EcoGenetics/R/eco.2hierfstat.R | 89 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.R | 362 ++---
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.post.R | 300 +---
EcoGenetics-1.1.0/EcoGenetics/R/eco.alfreq.R | 104 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.append.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.association.R | 326 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.autocor.R | 629 ++++----
EcoGenetics-1.1.0/EcoGenetics/R/eco.boothet.R | 721 ++++------
EcoGenetics-1.1.0/EcoGenetics/R/eco.cbind.R | 232 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.char2num.R | 175 --
EcoGenetics-1.1.0/EcoGenetics/R/eco.clear.R | 32
EcoGenetics-1.1.0/EcoGenetics/R/eco.cormantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.forestplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.geary.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.getisord.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.joincount.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.laglistw.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.lmtree.R | 235 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.localmoran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.mantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.merge.R | 254 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.moran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.order.R | 191 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.pairtest.R | 30
EcoGenetics-1.1.0/EcoGenetics/R/eco.post.geneland.R | 113 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.rankplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.rarefact.R | 315 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.rbind.R | 93 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.remove.R | 42
EcoGenetics-1.1.0/EcoGenetics/R/eco.rescale.R | 21
EcoGenetics-1.1.0/EcoGenetics/R/eco.sort.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.subset.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.theilsen.R | 203 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.variogram.R | 119 -
EcoGenetics-1.1.0/EcoGenetics/R/ecogen.definition.R | 667 +++------
EcoGenetics-1.1.0/EcoGenetics/R/latlon2distm.R |only
EcoGenetics-1.1.0/EcoGenetics/R/other.classes.R | 577 ++++----
EcoGenetics-1.1.0/EcoGenetics/man/EcoGenetics-package.Rd | 152 +-
EcoGenetics-1.1.0/EcoGenetics/man/RelDist-methods.Rd | 51
EcoGenetics-1.1.0/EcoGenetics/man/eco.2columns.Rd | 8
EcoGenetics-1.1.0/EcoGenetics/man/eco.2geneland.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.2genepop.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2gstudio.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2hierfstat.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.post.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.alfreq.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.append.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.association.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.autocor.Rd | 110 -
EcoGenetics-1.1.0/EcoGenetics/man/eco.boothet.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.char2num.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.clear.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cormantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.geary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.getisord.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.joincount.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.laglistw.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.mctree-summary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.localmoran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.mantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.merge.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.moran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.order.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.pairtest.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.rarefact.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.rbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.remove.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.rescale.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.sort.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.subset.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.theilsen.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.variogram.Rd | 35
EcoGenetics-1.1.0/EcoGenetics/man/forestplot-methods.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/latlon2distm.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/rankplot-methods.Rd |only
99 files changed, 3261 insertions(+), 3737 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-25 2.55
2009-11-13 2.5
2009-09-23 2.4
2009-07-18 2.3
2009-06-26 2.1
2009-05-17 1.0
Title: Interact with Simile Models
Diff between Simile versions 1.3.2 dated 2015-02-14 and 1.3.3 dated 2015-02-19
Description: Allows a Simile model saved as a compiled binary to be
loaded, parameterized, executed and interrogated. This version works
with Simile v5.97 on.
Author: Simulistics Ltd
Maintainer: Jasper Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
exec/client5d.tcl | 20 +++++++++++++++-----
man/Simile-package.Rd | 7 +++++--
4 files changed, 27 insertions(+), 14 deletions(-)
Title: Data Augmentation and Multiple Imputation for Interval Censored
Data
Diff between MIICD versions 1.1 dated 2014-04-24 and 2.0 dated 2015-02-19
Description: Implements data augmentation schemes with multiple imputation steps for proportional hazards regression with interval censored data or proportional subdistribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. MIICD functions call Surv, survfit and coxph from survival package, FGR from riskRegression package, and mvrnorm from the MASS package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord
MIICD-1.1/MIICD/R/get.est.cr.cox.R |only
MIICD-1.1/MIICD/data/bcos.rda |only
MIICD-1.1/MIICD/man/ANDA.coxph.Rd |only
MIICD-1.1/MIICD/man/ANDA.crreg.Rd |only
MIICD-1.1/MIICD/man/PMDA.coxph.Rd |only
MIICD-1.1/MIICD/man/PMDA.crreg.Rd |only
MIICD-1.1/MIICD/man/get.est.FG.Rd |only
MIICD-1.1/MIICD/man/get.est.Rd |only
MIICD-1.1/MIICD/man/get.est.cr.cox.Rd |only
MIICD-1.1/MIICD/man/get.set.Rd |only
MIICD-1.1/MIICD/man/preproc.coxph.Rd |only
MIICD-1.1/MIICD/man/preproc.crreg.Rd |only
MIICD-2.0/MIICD/DESCRIPTION | 21 ++-
MIICD-2.0/MIICD/MD5 | 70 +++++++-----
MIICD-2.0/MIICD/NAMESPACE | 24 +++-
MIICD-2.0/MIICD/R/ANDA.coxph.R | 182 ++++++++++++++++----------------
MIICD-2.0/MIICD/R/ANDA.crreg.R | 164 ++++++++++++++--------------
MIICD-2.0/MIICD/R/DA.ci.R |only
MIICD-2.0/MIICD/R/DA.surv.R |only
MIICD-2.0/MIICD/R/ICCRD.R |only
MIICD-2.0/MIICD/R/MI.ci.R |only
MIICD-2.0/MIICD/R/MI.surv.R |only
MIICD-2.0/MIICD/R/MIICD.coxph.R | 138 ++++++++++++++++++++----
MIICD-2.0/MIICD/R/MIICD.crreg.R | 154 +++++++++++++++++++++------
MIICD-2.0/MIICD/R/PMDA.coxph.R | 143 ++++++++++++++-----------
MIICD-2.0/MIICD/R/PMDA.crreg.R | 145 ++++++++++++++-----------
MIICD-2.0/MIICD/R/bcos.R |only
MIICD-2.0/MIICD/R/get.est.FG.R | 26 +---
MIICD-2.0/MIICD/R/get.est.R | 12 --
MIICD-2.0/MIICD/R/get.set.R | 11 +
MIICD-2.0/MIICD/R/get_est_mi.R |only
MIICD-2.0/MIICD/R/get_est_mi_surv.R |only
MIICD-2.0/MIICD/R/get_values_at_time.R |only
MIICD-2.0/MIICD/R/get_z.R |only
MIICD-2.0/MIICD/R/post_point_est_CI.R |only
MIICD-2.0/MIICD/R/preproc.coxph.R | 10 -
MIICD-2.0/MIICD/R/preproc.crreg.R | 12 --
MIICD-2.0/MIICD/data/BCOS.rda |only
MIICD-2.0/MIICD/data/ICCRD.rda |only
MIICD-2.0/MIICD/man/DA.ci.Rd |only
MIICD-2.0/MIICD/man/DA.surv.Rd |only
MIICD-2.0/MIICD/man/ICCRD.Rd |only
MIICD-2.0/MIICD/man/MI.ci.Rd |only
MIICD-2.0/MIICD/man/MI.surv.Rd |only
MIICD-2.0/MIICD/man/MIICD-package.Rd | 52 +++++----
MIICD-2.0/MIICD/man/MIICD.coxph.Rd | 104 ++++++++++--------
MIICD-2.0/MIICD/man/MIICD.crreg.Rd | 127 ++++++++++++++--------
MIICD-2.0/MIICD/man/bcos.Rd | 39 +++---
MIICD-2.0/MIICD/man/plot.DA_ci.Rd |only
MIICD-2.0/MIICD/man/plot.DA_surv.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_coxph.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_crreg.Rd |only
MIICD-2.0/MIICD/man/plot.MI_ci.Rd |only
MIICD-2.0/MIICD/man/plot.MI_surv.Rd |only
54 files changed, 867 insertions(+), 567 deletions(-)
Title: Dynamic Generation of Scientific Reports
Diff between R.rsp versions 0.19.0 dated 2014-06-08 and 0.20.0 dated 2015-02-19
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.rsp-0.19.0/R.rsp/R/captureViaRaw.R |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.html |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.pdf |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.tex.rsp |only
R.rsp-0.19.0/R.rsp/man/getAttributes.RspObject.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspDocument.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspProduct.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspString.Rd |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/DESCRIPTION | 19
R.rsp-0.20.0/R.rsp/MD5 | 257 ++++---
R.rsp-0.20.0/R.rsp/NAMESPACE | 241 ++++++
R.rsp-0.20.0/R.rsp/NEWS | 85 ++
R.rsp-0.20.0/R.rsp/R/006.fixVarArgs.R | 7
R.rsp-0.20.0/R.rsp/R/999.NonDocumentedObjects.R | 1
R.rsp-0.20.0/R.rsp/R/999.RRspPackage.R | 6
R.rsp-0.20.0/R.rsp/R/999.package.R | 1
R.rsp-0.20.0/R.rsp/R/FileRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemon.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemonRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/RspDirective,COPY-PASTE.R |only
R.rsp-0.20.0/R.rsp/R/RspDirective,IF-THEN-ELSE.R | 25
R.rsp-0.20.0/R.rsp/R/RspDirective.R | 106 ++-
R.rsp-0.20.0/R.rsp/R/RspDocument.R | 346 ++++++----
R.rsp-0.20.0/R.rsp/R/RspException.R | 4
R.rsp-0.20.0/R.rsp/R/RspFileProduct.R | 40 +
R.rsp-0.20.0/R.rsp/R/RspObject.R | 95 --
R.rsp-0.20.0/R.rsp/R/RspParser.R | 13
R.rsp-0.20.0/R.rsp/R/RspProduct.R | 61 -
R.rsp-0.20.0/R.rsp/R/RspRSourceCode.R | 2
R.rsp-0.20.0/R.rsp/R/RspRSourceCodeFactory.R | 8
R.rsp-0.20.0/R.rsp/R/RspResponse.R | 2
R.rsp-0.20.0/R.rsp/R/RspString.R | 58 -
R.rsp-0.20.0/R.rsp/R/RspVoid.R |only
R.rsp-0.20.0/R.rsp/R/attributes.R |only
R.rsp-0.20.0/R.rsp/R/buildNonSweaveVignette.R | 2
R.rsp-0.20.0/R.rsp/R/compileAsciiDocNoweb.R | 2
R.rsp-0.20.0/R.rsp/R/compileKnitr.R | 2
R.rsp-0.20.0/R.rsp/R/compileLaTeX.R | 20
R.rsp-0.20.0/R.rsp/R/compileMarkdown.R | 37 -
R.rsp-0.20.0/R.rsp/R/epsDev.DEPRECATED.R | 36 -
R.rsp-0.20.0/R.rsp/R/indexOfNonQuoted.R | 12
R.rsp-0.20.0/R.rsp/R/parseInternetMediaType.R | 2
R.rsp-0.20.0/R.rsp/R/parseRVignetteMetadata.R | 53 -
R.rsp-0.20.0/R.rsp/R/rcat.R | 33
R.rsp-0.20.0/R.rsp/R/rfile.R | 10
R.rsp-0.20.0/R.rsp/R/rsptex.R | 2
R.rsp-0.20.0/R.rsp/R/translateRsp.R | 5
R.rsp-0.20.0/R.rsp/R/translateRspV1.R | 6
R.rsp-0.20.0/R.rsp/R/xweavetangle.R | 193 ++---
R.rsp-0.20.0/R.rsp/R/zzz.CmdArgsFunctions.R |only
R.rsp-0.20.0/R.rsp/R/zzz.R | 23
R.rsp-0.20.0/R.rsp/build/vignette.rds |binary
R.rsp-0.20.0/R.rsp/exec |only
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.html |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 35 -
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
R.rsp-0.20.0/R.rsp/inst/doc/templates/,install_extras | 2
R.rsp-0.20.0/R.rsp/inst/doc/templates/Makefile | 7
R.rsp-0.20.0/R.rsp/inst/doc/templates/enginesMap.R | 2
R.rsp-0.20.0/R.rsp/inst/rsp/src/simpleFooter.html.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.asciidoc.Rnw | 1
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.knitr.Rnw.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_encodings |only
R.rsp-0.20.0/R.rsp/inst/rsp_examples/LoremIpsum.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis.rsp | 3
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.tex.rsp | 7
R.rsp-0.20.0/R.rsp/inst/rsp_tests/R-vignette.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/cutnpaste.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R | 3
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt.rsp | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/trimming-4.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/tcl/r-httpd.tcl | 4
R.rsp-0.20.0/R.rsp/man/Non-documented_objects.Rd | 1
R.rsp-0.20.0/R.rsp/man/R.rsp-package.Rd | 7
R.rsp-0.20.0/R.rsp/man/RRspPackage.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCode.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCodeChunk.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspComment.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspConstruct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspCutDirective.Rd |only
R.rsp-0.20.0/R.rsp/man/RspDirective.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspDocument.Rd | 5
R.rsp-0.20.0/R.rsp/man/RspErrorDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspEvalDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspException.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspFileProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspIfDirective.Rd | 48 -
R.rsp-0.20.0/R.rsp/man/RspIncludeDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspMetaDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspObject.Rd | 7
R.rsp-0.20.0/R.rsp/man/RspPageDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspRSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspShSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspString.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspStringProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspText.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnknownDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVariableDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVoid.Rd |only
R.rsp-0.20.0/R.rsp/man/buildNonSweaveTexToPdf.Rd | 2
R.rsp-0.20.0/R.rsp/man/compileLaTeX.Rd | 11
R.rsp-0.20.0/R.rsp/man/compileMarkdown.Rd | 5
R.rsp-0.20.0/R.rsp/man/getAttributes.default.Rd |only
R.rsp-0.20.0/R.rsp/man/preprocess.RspDocument.Rd | 11
R.rsp-0.20.0/R.rsp/man/rargs.Rd | 2
R.rsp-0.20.0/R.rsp/man/rfile.Rd | 6
R.rsp-0.20.0/R.rsp/tests/000.session_information.R |only
R.rsp-0.20.0/R.rsp/tests/RspConstruct.R |only
R.rsp-0.20.0/R.rsp/tests/RspProduct.R |only
R.rsp-0.20.0/R.rsp/tests/RspString.R |only
R.rsp-0.20.0/R.rsp/tests/capabilities.R | 6
R.rsp-0.20.0/R.rsp/tests/deparse.R | 7
R.rsp-0.20.0/R.rsp/tests/rclean.R |only
R.rsp-0.20.0/R.rsp/tests/rcompile.R | 2
R.rsp-0.20.0/R.rsp/tests/rscript.R | 34
R.rsp-0.20.0/R.rsp/tests/wstring.R |only
R.rsp-0.20.0/R.rsp/vignettes/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/vignettes/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
146 files changed, 1629 insertions(+), 983 deletions(-)
Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.0 dated 2015-02-07 and 1.1 dated 2015-02-19
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 1
DESCRIPTION | 8
MD5 | 15
NAMESPACE | 2
R/power.R | 851 +++++++++++++++++++++++++++------------------------
inst/CITATION | 16
man/power.rr.plot.Rd |only
man/power.rr.test.Rd | 228 ++++++-------
man/rr-package.Rd | 6
9 files changed, 605 insertions(+), 522 deletions(-)
Title: Floating Grid Permutation Technique
Diff between fgpt versions 2.2 dated 2015-02-18 and 2.3 dated 2015-02-19
Description: A permutation technique to explore and control for spatial autocorrelation. This package contains low level functions for performing permutations and calculating statistics as well as higher level functions. Higher level functions are an easy to use function for performing spatially restricted permutation tests and summarize and plot results.
Author: Reinder Radersma & Ben Sheldon
Maintainer: Reinder Radersma
DESCRIPTION | 12
MD5 | 22 -
inst/doc/intro-fgpt.R | 3
inst/doc/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
inst/doc/intro-fgpt.pdf |binary
man/Gpulex.Rd | 2
man/Pmajor.Rd | 2
man/fgeasy.Rd | 2
man/fgperm.Rd | 2
man/fgpt-package.Rd | 2
man/fgstat.Rd | 2
vignettes/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
12 files changed, 1030 insertions(+), 1031 deletions(-)
Title: Functions for the Book "An Introduction to the Bootstrap"
Diff between bootstrap versions 2014.4 dated 2014-04-27 and 2015.2 dated 2015-02-19
Description: Software (bootstrap, cross-validation, jackknife) and data
for the book "An Introduction to the Bootstrap" by B. Efron and
R. Tibshirani, 1993, Chapman and Hall.
_____________________________________________________________
This package is primarily provided for projects already based
on it, and for support of the book. New projects should
preferentially use the recommended package "boot".
Author: S original, from StatLib, by Rob Tibshirani. R port by
Friedrich Leisch.
Maintainer: Scott Kostyshak
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
NEWS | 22 ++++++++++++++++++----
R/bcanon.R | 11 +++++++++--
man/bcanon.Rd | 2 +-
man/scor.Rd | 2 +-
tests |only
7 files changed, 39 insertions(+), 17 deletions(-)